Hello everybody following this MFPS talk, my name is Christine Tasson and I would like to thank the organizer of MFPS for organizing this conference, this online conference and for the invitation. So today I will present a joint work with Martina Island which is on the linear non-linear substitution monad and if you are interested in knowing more on this work you can have a look at our archive paper. We get interested in this subject by discussing on what is model, what is the axiomatization of differential lambda calculus. So I will start by presenting this work that was introduced by Erard and Rény. When they were looking at semantics of linear logic they observed that in some models made of topological vector spaces and smooth functions there is a differentiation operator and if there is a differentiation operator in the semantics there might be a differentiation operator in the same syntax that behaves well and the question is what is its signification, what is its meaning. So the differential lambda calculus is an extension of the standard lambda calculus with a differentiation operator that is a kind of linear application and that corresponds to the derivation in standard mathematics. If we have a look at reduction beta reduction is for the usual abstraction so for instance if we have an abstraction applied to term n the beta reduction will replace every occurrence of x by n and there is no more binding by x at the end of the reduction. Now if we look at the differential application the reduction is a little bit different because we will read the idea is to replace only one exactly one occurrence of x in term m n by n. Okay so here if I want to replace only one occurrence of x in n I have to choose one and to replace it by n and I keep the other occurrences of x and the binding of this variable because I can make different choices for substituting one variable I have to add some additive structure to my calculus to be able to superpose the different choices non-deterministically different choices of variables that I replace. So this has to be compared to the linear approximation of a non-linear function. Now on we were interested in understanding what is the axiomatization of the differential lambda calculus and there are some categorical axiomatization. So we start from a model of lambda calculus which is a Cartesian closed category. We add some additive structure to interpret this non-deterministic choice and then we add a differential operator. The role of the differential operator is to take a morphism from a to b and to compute new morphism from a cross a to b which is mimicking the differential operator but here you know that there is a variable x which is non-linear and another one u which is linear and we have to ensure that it is the same for this differential operator but we have no tool to say that this variable a this type a is linear so one way to do that is to say that the differential operator applied to f commutes on the left hand side with the the additive structure but I think that it is not necessary to to use the additive structure to ensure linearity. So if we want to speak of linear variables and non-linear variables we can go back to linear logic in which the idea is to annotate non-linear types with a shriek. Then in linear logic you have two kinds of types the one that are annotated which are non-linear and the one that are not annotated which are linear. So now a differential category is a model of linear logic that is a symmetric monoidal closed category together with a co-algebra modality that gives rise to a co-commutative common rate and we have to ask for an additive structure for interpreting the non-deterministic choice and we have to add a so a deriving a transformation that will transform a morphism from a to b that is understood in linear logic as a morphism a linear morphism from shriek a to b into a morphism from linear a turns shriek a that is non-linear a to b by pre-composing by this derivation transformation. Okay that's the problem here is that when we add this shriek it can appear everywhere because it is a common ad on our basic categories. So we could have morphism from bong a turns bong b turns bong c turns d to bong a. So here we don't we are not able to recognize what are the linear variables and the non-linear ones because there are shriek at different places and here what is the meaning of non-linear variables at the result of the morphism. So to to avoid this problem we can use a different approach in which the shriek is hidden and for this we can use the term calculus for inter-synistic linear logic which was introduced in the 20s and in the sorry in the 20th century. And here I used the dual inter-synistic linear logic presentation that judgments are made of two different contexts one for the linear types and one for the non-linear types and a term can have any type. So there are three types of rules the first the first group of rule is standard for multiplicative linear logic if we just get rid of delta which is which stands for the non-linear context then we just have a multiplicative linear logic. So what do those do these rules say? The first one is an axiom if I have a linear variable then I can just get a linear term a term type. I have an abstraction that takes a linear variable here and transform it to an abstraction of type A linear B and I have a linear application which will concatenate the the context. Okay now for the non-linear group if we get rid of gamma here of the non-linear of the linear part sorry then it is just simply typed lambda calculus. Okay and what does it say? It says that from a non-linear type I can deduce a linear type and if I have a non-linear variable then I can just compute an abstraction and I have the standard application. Notice that here there is this delta here and delta here are contracted. So this axiom here because of the presence of delta means that we have weakening and this application here because delta is contracted means that we have contraction. Notice also that here I first term to have a non-linear variable it is to avoid repeating linear variables and now I have a last rule which is a linear non-linear rule and which says that if I know how to type a term t with a linear variable x that means that t has only one exactly one occurrence of x in it. Okay so if I know how to type t with this linear variable then I can fit it with a non-linear variable because x appears only once in t and it's not a problem for non-linear variables to appear zero times once or many times. So here we have a version of linear logic without the shriek and we want to inspire our axiomatization from this presentation and to do that we have to we have to move from categorical axiomatization to multi-categorical axiomatization. So let's have a look at on what is a categorical axiomatization in a category x which is equipped with the right structure either symmetric monoidal closed category or Cartesian closed category types are interpreted as objects and terms are interpreted as morphisms but to have a morphism which takes into account the context I have to turn the context which is a sequence of type into an object of the category that is why I need to have constructions constructions such that tons of product or Cartesian products so in multiplicative linear logic a proof or term will be interpreted as a morphism from the tons of product of the types to C and in lambda calculus it will be interpreted as a morphism from the Cartesian product to C. What we want to do is to replace this tons of product and Cartesian product with a multi-category which defines the interpretation of terms as multi-morphisms so I don't have to turn this context into an object of my category so in a multi-category types are interpreted as objects in the category and terms are interpreted as multi-morphisms and it is a structure of the multi-category which will tell me what is the structure of the context so in a symmetric multi-category I will interpret a multiplicative linear logic proof and in a Cartesian multi-category I will interpret lambda calculus there. But in order to express how to describe the context Cartesian context with weakening and contraction or symmetric monoidal context with just the exchange I have to to describe multi-categories with a fancy presentation using distributors combined with a monad that describes the context. So to to be able to describe these multi-categories I have to introduce some some constructions which are distributors, classi by category and monads and two monads and I start from the well-known category of sets and relations because the category the two categories the back category of distributors which I call proof is a generation of real indeed a relation can be seen as a function from y cross x to 2 with the standard composition and a profanctor is is distributors from y up cross x to sets so I have replaced two by sets and the composition is a generalization when I would where I replace the existential quantifier sorry by this co-end and the wedge here by this Cartesian product. Okay so now a relation can a relation can also be seen as a function from x to the subsets of y so it is living in the classi category of the power set monad what I am saying there is that the real category can be in that identified with the classi category over the power set monad. Similarly a distributor can be seen as regarded as a function from x to a pre-shift of y where pre-shift is the pre-shift pseudomonad of on-cats and the by category proof is it can be seen as the classi by category induced by the this pre-shift pseudomonad on-cats. Okay so now I need something I need a tool to describe the context and for that I use monad so if I come back to the real setting I can see that the commutative monad which is generating finite multisets extends from set to rail. It is a monad on set and I can see it extend it to rail because there is a distributive law of the power set monad over the commutative monad in monad. Similarly a two monad t on-cats can be extended to proof to proof if there is a pseudos distributive law of the pre-shift pseudomonad over t and that is what we are using for describing multi-categories with special two monads for describing the context so we will use the two monad l which is acting on cats and which takes a category and computes the three symmetric monad l category and the monad n which is also two monad on-cats and which generates the three category with product. Okay so these two two monads are describing the context for multiplicative analogic m lambda calculus so a multi-category can be seen as a distributor in the class B category of the monad that we have extended to distributors so we can see m as a distributor from x to tx that is a distributor from tx up cross x to sets but we want to describe to interpret axioms and composition so we need to have a monadic structure on m that is an identity and a multi-composition so now if I come back to the axiomatization with a multi-category but now presented with distributors if I have this multi-category types are now interpreted as objects in x and terms are interpreted as elements of m but taken into account the context so let's have a look at the multiplicative linear logic interpretation so I choose for the two monad the the substitution two monad l which is generating the three symmetric monoidal category of x and I interpret a term with which is type in a linear context as a morphism a multimorphism with this type and in lambda calculus I choose m which is generating the three category with product over x and I interpret the term into my Cartesian multi-category which is multimorphism taking into account the type the non-linear types of my term t okay so now I know how to describe what is the axiomatization multiplicative linear logic and of lambda calculus but what I really want is to have the interpretation of a mixed linear non-linear calculus so I need to describe what is the correct substitution two monad t for mixed linear non-linear calculus and what are the three categories that are generated that that are the t-algebra so how can I mix the interpreted term with a mixed linear context and non-linear context so I know I have an idea of how to do that concretely because I know how to describe concretely concretely what are the objects of l of x there are sequences and morphisms are just bijections and sequence of morphisms and I know also how to describe n of x which is the three category with product over x and the objects are sequences okay but the morphisms are different they're made of functions and sequences of morphisms now I have an idea of what should be q which is the mixed linear non-linear substitution monad the objects are mixed sequences just has the context where we were looking at and the morphisms combine functions bijections and sequences of morphisms okay so the question now is how to construct q from l and m and for doing that I need to introduce or to study co-lax co-limits on a two category so what on our feed is that imagine we have a map in a two category which I call lambda and I can consider the co-lax co-limit which is a cocoon of this type so I have two maps to see and I have this two cell alpha this co-lax co-limits has two universal aspects one for the one cell and one for the two cells let's have a look on the one cell aspect the universal properties say that if I have another cocoon d with this structure f g and the two cell phi over lambda then I can factorize it so a morphism from c to d and if I take alpha followed by this unique morphism I get this cocoon okay and I have also two two cell aspects which say that if I have two co-cons which are correspond in correspondence then I have a correspondence between the two induced map from c to d okay now I have described this construction I can apply it to the map lambda from l to m remember l is the three symmetric monoidal two monads and n is the three category with product two monads and every category of product is a symmetric monoidal category and I can just compute the three category with product on a symmetric monoidal category that is why I have a map of monads between l and m so I can construct these co-lax co-limits in the two category of symmetric monoidal category because we want that our monad is a substitution monad for context has to to be symmetric monoidal in particular so let's have a look at these co-lax co-limits so I have this map lambda from lx to nx and I compute the the co-limit which is qx together with k l and alpha let's have a look at the concrete description of all these ingredients so we know that qx is made of sequences with two kinds of variables the linear ones on the left hand side and the non-linear ones on the right hand side lambda is taking a linear context so a sequence of linear types to a sequence of non-linear types living in mx k is taken linear types into a sequence of linear and non-linear types so we will put the linear types on the left hand side l is taking non-linear types and we put them into mixed linear non-linear context by putting them on the right hand side now we have these two two cell alpha so that there is typo here it's a morphism which takes a sequence in q it alpha is actually a morphism in in qx which takes sequence with only non-linear types and produce a sequence with the same types but by seeing them linearly so this morphism corresponds to this rule which is which can be deduced from the linear non-linear rule and which say well if i know how to type t with exactly x1 xl exactly one occurrence of x1 and xl then i can type t with non-linear variables even if i use them exactly once okay so now from the deconstruction and using one cell universality and two cell universality i can compute the properties of q of qx so first of all it is a symmetric monoidal category indeed i have computed my my conimit into the two category of symmetric monoidal category so the result is a symmetric monoidal category secondly it is nearly a Cartesian category what do i mean by this is that i can split it through the free category with product sorry here it should be with product so what is f doing it takes a linear non-linear context it puts everything in a non-linear context and then back to qx every types have been made in the non-linear side okay so intuitively f is taking mixed linear and non-linear things and it puts tricks everywhere behind it because it looks it looks at it at every types as a non-linear one and indeed f is a is a common add that is strictly monoidal and which is strictly idempotent so that means that we have a cell which is really important which is beta and which which is morphism in qx from a context with only non-linear variables to a context with both linear variables and non-linear variables again it is an instance of the linear non-linear rule which allows me to move linear variables into a non-linear side of the context okay so now what do i have i have computed a mixed non-linear context on each category x and i have described the structure of qx and from the universality of the co-limits i can prove that q is a two monodome cat and moreover i can describe what are the q-algebra uh what are the q-algebra what are the three uh well sorry what are what are the q-algebra so a q-algebra is a symmetric monoidal category with nearly Cartesian structure meaning that i can split so the Cartesian category and i have some currencies of course so this serum is a nice presentation of a more theoretical one which appears which appears in our paper but which is needed if we want to prove smoothly that q is a two monad and that its q-algebra have this structure okay so we are nearly done uh not really okay what we want to do is to model linear non-linear calculus so we are looking for a multi-category axiomatization that means that we need a q two monad q for describing the context so what we have done is that we have defined the two monad q on cats which describes the linear non-linear context and we have described its q-algebra but what we need to do now is to describe uh to describe what is a q multi-category going and to do that we need to extend q to a pseudo monad on the by category of distributors so how can we do that instead of extended directly q to a pseudo monad which is quite hard we use the equivalence presentation so distributive laws pseudo distributive laws and it is equivalent to prove that the pseudo the pseudo monad of pre-shifts if to pseudo q-algebras but the problem is when we apply the the pre-shift pseudo monad on l-algebra what we get is a pseudo l-algebra so l-algebra is symmetric strict monoidal category and what we get is just symmetric monoidal category and there is no way to have a coordinate here because in the universal property we need to have a unique map and it is not compatible with this weak city so how can we do that so we our idea is to start from our characterization of q-algebras and to deduce a pseudo version of of the q-algebras to see what are pseudo q-algebras and now we need to recover our faculty to to compute co-limits because our proof is based on this universality and on the co-limits so if we want to use the proof techniques that that we have developed we we need to to have a way to to to go back to a strict world and for that we can do power replacements that amounts to strictify the the the pseudo algebras in a world where we can compute co-limits but it's ongoing work and when we will have done that we will be back to describe what is the axiomatization of first mixed linear non-linear calculus and for that we'll need a closed structure that is to make two interpret abstract abstractions and we will follow the work of fiori plonkin and jury and the description of lambda calculus in the address and so the an orthogonal issue is the differential operator because we we don't really need the closed structure today to speak of differentiation so if we want to speak of the differentiation we need a derivation operator so remember in the differential linear logic that is the categorical axiomatization we have an operation transformation that goes from a and so uh trick a to trick linearity to trick a and what we want to have is to to include this derivation transformation transformation into our q multi-category context so a linear non-linear multi-map of type gamma non-linear b to c will have to be transformed by the derivation operator into a linear non-linear map with one occurrence of b which is linear and one occurrence of b which is non-linear and then the last ingredient would be to describe how this derivation operator acts with substitution and this is the channel which will induce an additive structure but what we believe is that we have a more primitive description of we will have a more primitive description of what it happens and a nice nice way to describe the linearity without referring the additive structure so I want to say thank you to to the to have a listen to the end of this talk and if you have questions or if you want to know more you can either ask them on the on slack or go to our archive paper thank you very much


Good morning, happy Wednesday. We're gonna get started. Our first presentation this morning is Dr. Lydia Sauer. She's gonna give us a presentation on clinical advances in fluorescence, lifetime imaging, and ophthalmology. Let's welcome her. Thank you very much. I'm really excited to be here. And thank you for the introduction. Does it work now? Perfect. These are my financial disclosures. And since it's very early in the morning, I would like to start with this picture that I took a couple years ago. And when we look at it, we see what's going on. We see it's a gecko that's just hanging out there enjoying its day. But do we really see all the information that we could possibly see? Or does this give us a much more detailed view of the picture? In the same way, we are very used to looking at these images in ophthalmology. This is a typical fundus autofluorescence intensity image. But when we look at flio images, suddenly we get a much more detailed view. And I'm gonna go a little bit further. This is a healthy eye. But I would like to look at some diseases. So here we see an eye with drusen due to macular degeneration. And we are very familiar with these pictures. But when we look at the flio, we suddenly get a completely different view of this picture. Or I have one more example. This eye almost looks healthy when we look at it. It's very difficult to delineate any pathology in this eye. But when we then take the flio and look at it, suddenly we clearly see something that we didn't see before. So this is what my talk is going to be about. It's about flio. Flio is a novel imaging technology that was developed in Jena and then produced by Heidelberg Engineering. The devices look very similar to the regular Spectralis OCT. But there's a lot more going on in the device. And it actually provides us a very high contrast picture of the back of the eye. And we can really delineate different information about fluorophores within their environment. And when we think of fluorescence, I'm just going to go back to the basics for a very brief moment. We can think of three dimensions in fluorescence. The first would be the spectral dimension. So when we think of the chemical view of things, the emission spectrum and the absorption spectrum and the emission spectrum are different in the fact that the emission spectrum is shifted towards longer wavelengths, which we see right here. When we come from an ophthalmological background, we always think of the brightness dimension first because that's what we're most used to, to the fundus outer fluorescence intensity images that just show us how bright do the fluorophores come back? And what I would like to focus on today is really the third dimension, the lifetime dimension, which essentially tells us how long do the fluorophores glow? So how long does it take for the fluorescence to fade away? And for that, there's a very nice little presentation that Chantal, a good friend of mine made, and I would like to show this to just highlight it a little bit more. So when we think of fluorescence, we count the fluorophores that are coming back. Doesn't really matter when they're coming back, some come back early, some later, but really what we're looking at is how bright are they? And this is our typical outer fluorescence image. When we look at flio, we give these times a color. So the fluorophores that come back first, we put in red color and say this is a short lifetime because they're coming back much faster. And then as time passes, we shift to longer lifetimes and the lifetimes turn to blue color. And this essentially transforms the outer fluorescence intensity image to the lifetime image. And we think that we get more information because in intensity imaging, it's dark at the phobia and dark at the optic nerve, whereas in flio images, we can clearly see differences between these areas. How it works is we have a 473-nanometer laser. It's a pulse laser that we send into the eye together with an IR laser for eye tracking. And then we collect the fluorescence that is coming back, but we actually split it up according to the wavelength of the fluorophores into two spectral channels. So a short spectral channel from 498 to 560 nanometers and then a long spectral channel from 560 to 720 nanometers. And this essentially gives us with one two-minute measurement these four images. So two outer fluorescence intensity and two outer fluorescence lifetime images. And when we think of healthy eyes, we always see the same pattern in these eyes. We see that they're long lifetimes at the optic nerve, which are depicted in blue and I actually added those curves to it. What you can see is the curve is much less steep. So it takes much longer until the fluorescence comes back. The intermediate lifetimes that are depicted kind of an orange-ish-greenish color that can be found all across the fundus are caused by the retina pigment epithelium and the lipofustin. And the short lifetimes in the center of the phobia are caused by macular pigment and the decay of the fluorescence is really steep. So going from this healthy eye and looking at the variety of different diseases that we can look at in ophthalmology, we clearly see that there are a lot of patterns that we can map out with flio that really look different from another. And I would like to go through a few of these diseases today just to point out really the highlights of what we think is where flio is really beneficial. And the first thing that I'm gonna start with is the whole question about macular pigment and how can we see that it's really macular pigment that we're imaging want to start with albinism because patients with albinism do not have any macular pigment and they also do not have a formal depression. And when we think of, or when we look at the flio images, we see that the short lifetimes in the center are just missing. So we cannot see them because they're absent. And we did some more studies looking at macular pigment, for example, in macular holes, in mactail, in other diseases, and we really were able to find out that the macular pigment is really causing these short lifetimes in the center. And the first disease that, or the second disease that I'm going to hit on is macular degeneration. It's a very common disease that we see in retina clinic all the time. And as I showed in the beginning, we really see this ring of blue that is a shift towards long lifetimes around the phobia. And we do not see any indication of this in the outer fluorescence intensity image. We see this ring in all patients with AMD, which is pretty striking. And we also did some statistics on it. We kind of produced a grid onto the back of the eye and looked at the area of that pattern, which is basically this ring right here. And we compared the lifetimes, not just between AMD eyes and healthy eyes, but also between AMD eyes of different stages, because we think that pattern actually progresses as the disease progresses. And we were able to find a significant difference for this pattern, whereas there was no significant difference in the phobia. And that really indicates that something must be going on in this area right here where we see that pattern. And it could be a deposition of something, for example, some bisrhodenoids or sub-RP deposits, but it could also be a metabolic change that we see. Because when we actually looked at our healthy group, and this is kind of interesting, that about 30% of our healthy subjects that were age-matched already showed a trace of that pattern. And we think that these patients were, a lot of them were of risk to develop macular degeneration. And we think that with FLIO, we might be able to see the first changes of this in the eye even years before macular degeneration is developing. So we're trying to do more analysis on this to really understand it, and especially follow-up measurements. And we also looked at neurovascular AMD. We found the same pattern, but what we saw is that sometimes in neurovascular AMD, the pattern is a little disturbed, especially when we have pigment epithelial detachments that are quite large. And we did a study just kind of looking at different PEDs. And we found that hemorrhagic PEDs at the shortest lifetimes, indicating that it might be blood that we see that has short lifetimes. And for that to kind of prove it, or kind of give another argument for it, we had this very interesting patient that presented with a fibrovascular AMD and came up, came to the office two weeks later with a new hemorrhagic PED. And what is really striking is how the wet, oops, sorry about that, how the wet in the center really increases. And we actually took his blood and did an ex vivo measurement of the blood, which you can see right here. And if we put the colors exactly to the flio image in vivo, you see that the blood is just completely wet. But if we increase the contrast a little bit, we can see that especially the erythrocyte sediments have the shortest lifetimes, which just helps us understand these pictures a bit more. And another disease that we are really excited about is macular telangulctasia type two, or in short, mactel. It's an inherited retinal disease that was initially believed to be pretty rare, but we keep finding more and more patients with this disease. And it was initially believed that it kind of starts between 40 and 60, but we keep finding younger patients that also have mactel. And it's fairly difficult to diagnose it with some imaging modalities, just by looking at the funders, because it can present similar to a lot of other diseases, especially AMD. So many patients have been misdiagnosed with AMD. And it's really valuable to have a tool that really lines out that this is mactel. So in patients with mactel, we see this prolongation of lifetimes at the temporal site of the fovea in all of the patients. It can sometimes present also as a wing. And when we compare different imaging modalities, we can really see that we can see mactel much better in flio than in a lot of the other ones, especially in early stages. The only other modality that shows mactel quite as well would be fluorescein angiography, but that again is invasive, whereas flio is a non-invasive two-minute picture, basically. So it really has an advantage here. And I would like to go a little bit further and present a very interesting family, because here in this family, the coven was diagnosed with mactel at age 21. And he is severely affected with the visual acuity of 2100. And what was interesting in this family is that they were diagnosed with chakumari tooth. And his father came in in his 50s, I believe, and he had early onset macular degeneration, is what it said. He also did not have any arms because he had burned them off in a barbecue accident. So it was all kind of very interesting to look at that family. And by looking at it a little bit further, we realized that also the coven has some peripheral neuropathy, which is the reason why the father lost his arms. So we investigated it a bit further and we were able to find a gene, HSAN is the gene mutation, but it's a neurological disease that causes peripheral neuropathy, but it's connected to the eye disease, to mactel. So we recruited a couple more patients and the patients with that mutation also have mactel. And going back to that family, the proven had two sisters. The middle sister was 26, the oldest was 28, and the middle sister actually had the mutation, but the oldest sister did not. Both of their clinical images looked completely normal, but the affected sister actually showed only inflio changes in the lifetimes, which you can see here in the wing, that is the way we can already see a trace of that mactel pattern, which could help us treat her much earlier. And we're really excited about this case, and this was recently published in the New England Journal of Medicine, as well as in Retina. So if you want to learn more about that, we're really happy about that. And we think that this really helps treating these, or approaching mactel a different way by understanding the causes behind it. So we go further and look at other family members trying to really map out which of the individuals could have early mactel changes, which wouldn't, and we found that very early mactel can present kind of in the superior area, and that some of the individuals, we just called flio positive, and others we called flio negative, and we will follow up on these to really see if we can detect mactel earlier. Here's another example of a family, the father had mactel, and two of the sons had flio positive findings, the other two had normal findings. So we'll follow up on these and see. Now of course we're wondering what is causing these long lifetimes. In HSN, we think it's a sphingolipid disturbance in the sphingolipid metabolism, and we think there could be toxic dysoxys sphingolipids that accumulate in the eye, and when we look at other patients, we see these crystals in the eye, and they really map out to the areas of long lifetimes. We try to look at progression, these are studies that are just ongoing, but really going back to the accumulation of things in the eye, this is another patient that presented in Dr. Hartnett's clinic, and it's a 14-year-old male that had a cherry red spot, and complete normal vision, it was a normal health examination where they found a cherry red spot, referred the patient to Dr. Hartnett, and we clearly see in flio that there are very much prolonged lifetimes, especially in the short spectral channel, which is kind of similar to what we see in mactel, and looking at his family a little bit further, we actually saw that his father has mactel. So is this a coincidence that a rare disease such as mactel correlates with this other disease, which we later found out was cyanlidosis? We're still investigating that. All right, I have a few more very short diseases that I'm gonna hit on. The first one is Stagard's disease. What we see in this disease is it's a retinal dystrophy that kind of presents with flecks, and I want to draw your attention really to this spot. If we look at the baseline imaging, it's red color, so short lifetimes. If we look at the follow-up, it shifts to blue. When we look at the outer fluorescence image, there's no trace of that flag in the baseline measurement, but it is there in the follow-up. So we can see how the structure progresses, but then also the patient reported a new scotoma right at this spot, and we can already see changes in the flio much earlier, so we think that with flio we can not only predict progression of structural things, but also of function. We also look at retinitis pigmentosa, investigate the wings that we see in outer fluorescence. We see them very pronounced in flio and some patients, and we're currently doing follow-up measurements. Carl Anderson has been really invested in that, and we think that at least from the first analysis, we think that the patients with the strong wings in flio are more likely to progress, but these studies are still ongoing. We also looked at plaquenol toxicity, plaquenol is an anti-inflammatory drug that is used for lupus and rheumatoid arthritis, and the problem is that it can cause irreversible eye problems, and we really try to find out, not only if we can see these damages, but also if we can see them early. So for example, this patient presented in the clinic, she was on plaquenol for 20 years and had a complete normal imaging, but had some reduced contrast sensitivity, some visual disturbances. She was taken off the drug, and the only thing where we really saw a difference was really in the flio, and we see that in some of the other patients that are on the drug as well. And skip this one. We look at more diseases. We have a lot more ongoing studies right now, and there's a lot more literature, if you would like to read up on that. But in the end, it's a new dimension of autofluorescence imaging. It's non-invasive and fast, and we basically see these really stable patterns in healthy eyes that change in early stages of diseases, and that then show us characteristic patterns in eyes with diseases. We think it's helpful to differentiate between the individual diseases. We think it's a suitable measurement method to follow up, especially on therapeutic or monitoring, and it's a possible tool for early diagnosis. And in the end, we're just beginning to fully understand the potential of this method. With that, I would like to thank you for your attention and thank all the collaborators, especially Dr. Weinstein, my mentor here, as well as Dr. Hammer from Jena and everybody else who's contributed to this. Thank you very much.


So what's next for American Fact Finder? American Fact Finder, I think most people have had issues with it. So I think this is perhaps good news for most people that it's going to just be going away entirely. So I'm going to talk today about the overview of what all is happening and the timeline for that migration to the new platform. The content that is included in the preview version as you're calling the data test and the limitations, some of the limitations that it has. I'll show you the new interface and explain how the Census Bureau is asking for feedback in terms of the questions they would like you to answer and the address to send it to. And then at the end I'll do some example searches. The content today is based on a webinar the Census Bureau did back in December and also on my own testing. I would say that my own testing is not nearly comprehensive and in the webinar the Census Bureau actually restrained from doing any example searches because they didn't want to prejudice people's experience with it.  There is a link at the end of my presentation to that Census Bureau webinar. So if you want to see it from the horses mouth you will see that I copied a lot of information from their content. They also said that there would be another webinar in March but that did not materialize. So this is the most current information that seems to be publicly available. I aim to have a 30-minute presentation. So we should have plenty of time for sample searches, questions. Go ahead and chat in questions as they come up for you. Because I'm in presenter mode I won't see the chat but Linda will prompt me when there are questions. Also use the chat to send any searches you would like to see do. There are some slides about the specific pieces of data that are included in the preview. So there might be some searches that I can't actually do that won't actually work in this version. But go ahead and send in any examples that you would like to see and we can at least try them. All right, so all of the Census Bureau's data products are intended to move into this new interface. And it really is time for a new interface. All of the Census Bureau's tools really have at least a few years of exposure. The most recent one, the API debuted in 2012. And so it's really time for a reworking of this. The unit within the Census Bureau that's leading the development is SEDCI as they're pronouncing the acronym. The Center for Enterprise Extermination Services. I think it's easy to forget how many tools the Census Bureau makes available. Right now there are 37 tools in all. So this is really a huge effort to get all of this in. And so as you can imagine, it's a multi-year effort. So this is directly from the Census Bureau's presentation. I think it requires a bit of explanation to understand what this all means. They do nicely have this legend at the bottom. But I think the thing that's probably easiest to miss is there are these red. So these red platforms are intended to represent the technology platform on which each tool is built. And as you see where we start out, each tool has its own platform. So this is really kind of a massive, not only time sink, but just resource sink in terms of having to maintain all these different platforms. Each one has its own funding. Each one had its own developments. So efficiency is a big reason for this transfer. So as you can see, here we are in actually stage two, labeled Begin Capability Transitions. All of last year was spent on creating this preview environment at data.census.gov, which is sort of the test environment for how all of this is going to work. Once they had the platform stable, then this year they began moving American FactFinder into this platform. And part of what that involves is loading the data into data.census.gov, and then encouraging people to test it and see where they run into problems. The other tools are beginning to be moved in. So you see Data Share It here and Quick Finder, Quick Fax. Both of those are on the move. Their platforms are going away, and their data are advancing into data.census.gov. It's not all there yet. When I looked at Quick Fax this week, it looked to me like it's still using the original interface. I haven't been historically a big user of Quick Fax, so it might be mistaken about that. If any of you use that a good bit, you may see differences there. But it did look to me like if you select Quick Fax in the data.census.gov interface, it sort of exits out to a Quick Fax interface. So one thing that's important to remember here is that this is a projected timeframe, and these dates could easily change. I would even say you should pretty much expect them to change. So then over time, you see that once we get to stage three, all of those legacy platforms will have gone away, and all of these tools will have moved into the new platform. Some of them will still probably have legacy development, maintenance, and funding aspects, so they're not completely within data.census.gov, but they're moving in that direction. This was something that I didn't clue into for a while. It's not actually going to continue to be called data.census.gov. It's actually going to become the Census Bureau's homepage, just census.gov. So that should happen in the next two years. I think I also forgot to point out data ferret moving in is again why we didn't do that August webinar on data ferret. So there you are. So then finally by 2022, stage four, they're hoping to finally be in full production mode, everything operating on the same platform, and all of those legacy things going away, not just the platforms, but the development, maintenance, and funding aspects as well. And there was one more question just to clarify the name of the tool, or is it just searching Census.gov? Yeah, so the preview version, they're calling data.census.gov, and they're expecting sometime in the next couple of years for that to change just to Census.gov to be the Census Bureau's main homepage. A couple of things that came up as questions in the Census Bureau's webinar, microdata. People were asking if microdata would be available in the tool, and they were saying that it is on the table, but that's further down the road. So it may be that when I talked to the head of the data ferret office, probably this was a couple of months ago now, he thought that within six months data ferret would be in this tool. But it sounded to me from the webinar like they might not be expecting it in the next six months. They might be expecting it like next year sometime. So all of the timeline is pretty much fluid. Somebody asked about access to historical data. I know that with academic researchers in particular, people really want access to all of the years of the Census. My answer to that has always been that's not the Census Bureau's prime objective. Their mission is to collect new data. And so I really don't expect that they're ever going to make all of the historical data available. But they know that people want it, and so I would expect that there would be some historical data available in the final product. It might just be further down the road in terms of once they've tested out the interface ways to do that, that they would get more of the historical data in there. Someone asked about the ability to add their own data so that they could combine it with Census data. And the Census Bureau presenter talked about the fact that it is possible with Census Business Builder and on that now for people to upload their own shapefiles to combine with the data that the Census Bureau presents in those tools. They know that people want other kinds of uploading of their own data to be possible, but that is to be determined. They haven't really gotten to that point yet. They kind of have to deal with their own data first. I'm not going to talk very much today about the technical back end of this. It's both my perception that that is sort of not the main interest of most of the people on this kind of webinar, but also it's not my expertise at all. So all I will say is that they mentioned in the webinar that the new platform is based on their API. And the result of that is that it both makes it easier for the Census Bureau to provide service and deliver data, but it also makes it easier for users because the current American Fact Finder display requires table formatting in order to display the data. And that locks down the data in very specific ways so that it's difficult to export it from the system and use it then. And with the new system being based on the API, they're no longer going to be tied to that kind of table formatting. So the public will have the same access that developers inside the Census Bureau have. So that's good news. Okay, so what's in the test system? You will see that out of 11 elements here, six of them are related to American Community Survey data. So that's really where they're focusing the development in terms of the American Fact Finder is, I would say, primarily used to access the American Community Survey.  They do have this nice big warning on the bottom. Everything in here is test data and should only be used for purposes of evaluating functionality as you have them. You will see in the next couple of slides some of those limitations and why the data should only be used for evaluating the platform. So as we go on, here are known limitations. First of all, there's no tract level access in this interface yet. They are developing that and some of their tools have mapping capabilities. So as they develop the geospatial tools, then they will also make the tract level geographies available. Again, data fair at cross-tabbing and further down the road. And someone asked in the Census Bureau webinar about whether it would be possible to directly access the Census Bureau data for services like ArcGIS online. The Census Bureau isn't paying attention to that right now, but they know that people want it so it may come later on. And then there are these known limitations. I'll particularly point out pseudo geographies. They actually have false geographies in there just to test the interface. And as you saw from the data content, it's very limited data sets that are available there. So there are going to be lots of queries that people try to do that they're not going to get any answer for because that's not what the system is intended to do. For now, until we hear otherwise, American FactFinder is still available and will still be available until they completely transition it over. And there will be lots of warning about that. So as we turn to look at the new interface itself, think about how you search. Think about how you like to search for things. We're not talking about really American FactFinder at this point because in those cases you don't have all these options in American FactFinder. But essentially what's driving the development of this new platform is lots and lots and lots of new users who've never had experience with the Census Bureau before coming in and finding it difficult to search for what they want. And so they've developed this interface specifically in the answer to those questions. The Census Bureau pretty much drives all of their development based on where they're getting the majority of their questions. And so given that new users are where they're getting the most of their questions, that's what's driving this interface. I recommend you think consciously about how you like to search and try that, try the way you regularly would search, but also try to mix it up. Try other ways of searching if you want to get a feel for how your users might approach this. This webinar series, the Help webinar series is oriented towards librarians, so I do assume that everybody here pretty much is a librarian. I really like using library patron searches, actual things that people have asked for as examples to try to do better searches and understand where people might run into problems. So this is it. This is the interface. And this is what you're going to see when you come to both the preview, data.census.gov, but then eventually, just as the Census Bureau's website, this is what it's going to look like. So it really is, as some people have described it, an approach to looking like Google. They want it to be super simple. There is an advanced search here, but it's kind of hidden. If you click on the search box, you get this option for the advanced search. And then when you click on that, you get to a screen that looks like this. To zoom it in a little bit, you see that at the top is this sort of exposed Boolean search option screen. So people can choose. They want all of these words, this exact word or phrase, at least one of these words, that kind of thing. And then down below that, you get sort of an access to the hierarchies of the Census Bureau. So if people want to look at geographies over years or particular surveys or particular industries, this is where you would access that. So my feeling in having used this a little bit, I will still say a little bit, even though I've been playing around with it for a few months, is that I think this is going to be challenging for new users. The Census Bureau has really focused on making access easier. You don't have to know as much to just throw in a search and find something, but new users are still going to have a great deal of difficulty evaluating what they find. And depending on how they do the search, they might not find something and not realize that something was available, that if they had just used different terms, they would have found more. They're also not going to be able to differentiate very easily between different kinds of information. So if they were looking at search results for sex age and they got a table from the American Community Survey and another table from the Decennial Census, they're not going to understand the difference between 100% data in the Census and calculated estimates from the American Community Survey. This question was asked in the Census Bureau webinar and the presenters answered, well, they're going to be able to tell the difference between those two because the estimates are going to have margins of error and the 100% data aren't. And the sources are going to tell them where the data comes from. And my reaction to that is, well, that's not enough information to really explain to them what the difference is. So I know because this question was asked in the webinar and because I have already sent feedback to them about this issue that they're going to get a lot of feedback. But as I say, the development of their tools is always based on where they get the most questions or where they get the most pushback about something. So I really encourage all of you to submit feedback about that kind of issue where you see ways that the Census Bureau could make it better. So we'll talk about that a little bit more. Another place where new users would have trouble, I actually did search, this is one of the examples for this webinar, a search for race income. And you don't find any tables for that because all of those tables that cross-tabulate race and income actually are for the single race alone categories. So they don't actually have the word race in the table title. So you have to search white income, black income, Native American income in order to find those tables. And then because the hierarchical lists are buried in the advanced search, I think it's going to be very hard for new users to find those. And so they're not going to automatically be exposed to complete lists of geographies or complete lists of topics. And that's going to make it very hard to explore and really discover some of the unusual tables that are actually available. So feedback now is critical because they're doing the development now. The Census Bureau does have a good record of doing development on a continual basis. Just as an example, this Center for Enterprise Dissemination Services and Consumer Innovation, SESI, has been around for quite a while. It's been operating for at least seven years, and I think longer than that, in trying to find a platform that would really work as not an alternative, but a replacement for American Factfinder. So these are the questions that the Census Bureau would like you to answer when you send them feedback. What was it that you actually searched for? What terms did you use? How did you construct it? Did you use and in the middle? Did you use quotation marks? And then what did you find? Was it what you expected to find? Did the search meet your expectation? And if not, how could they improve it? You can send lots of feedback. I would say a ton of feedback, maybe fewer than 10 emails so far, but I'm expecting to send more. One thing you need to be aware of, though, this is not something that you're going to get an answer from. If you actually have a question, then you need to contact the Census Bureau directly to actually get an answer, but they will take all kinds of feedback, whatever comments and suggestions you have. And again, please do send reports or requests, even if you know someone else has already reported or requested something, because they base their work on the number of requests they get about something, the number of questions they get about something. So the more you send, the more likely it is that they will respond to that. I have also pointed out navigation issues. I found it really difficult to find the links for the technical documentation. They are there when you get down to a specific table, but I felt like they were really hard to see and that not many people were going to find them, even if they were looking for them. I think it's hard to find them. The system does the thing where you do a search and it immediately presents you with a highlighted table, a kind of featured table. And the things that they suggest in my experience almost never super relevant to the thing that you actually searched. So I had sent them feedback about the relevance being an issue there. And then featured requests or suggestions. I found that when I searched for a town, it does give me a list of suggested other towns. So I found out that there's a Chapel Hill, Tennessee. I did not know that, but I didn't want Chapel Hill, Tennessee, but that's what it was giving me. And so I clicked on Chapel Hill, North Carolina to switch to that, but even though it's hyperlink, it doesn't return search results when I click on the link. All it does is repopulate the search box with the new geography. I didn't find that very helpful. And then finally, I think I already told you that example about adding race metadata for all the tables so that if you search for race income, you actually find something instead of having to search for white income or black income. Okay, so we're up to the test searches. Michelle, I had a couple of questions you want to wait. Great, yeah, go ahead. One is, is there a date by which we should send feedback? Nope, keep sending it. And then, but agencies looking to preserve historical data collections that might drop off the census site? If you could talk about that maybe. There's actually a lot of places to access historical data. So the first search that I'm going to do is just for race and income, so you can see this. So one of the things that I have reported and complained about is that this is really slow. I am expecting that that is partly because it is a test system, but given that the test system has less data in it than the real system will, I'm a little concerned about this. All right, so this is the results that I get in Chrome. That's actually another point for just your information. When the Census Bureau does development in the past, they have been extremely limited in the number of browsers that they are allowed to do development for. For a very long time, the Census Bureau was only allowed to do development for Internet Explorer. And this extended past 2010. I mean, this is not an old-time thing. This is really pretty recent. So I'm hoping that with the new platform, that kind of restriction will be done away with altogether. So it working in Chrome gives me hope. So you see here I did search for race and income, and I got a race table, which is good, is only about race, not about income. But I think that this UALL Tables link down here is pretty hard to see. It's pretty obvious that you could view the full table here, but if you want more tables, you really have to look for that link. It's also pretty settled to me that you can choose between tables, maps, and web pages here. But the Census Bureau is really expecting that this is going to replace their website. And so it's not just the data that are in here. It's also the maps and web pages. So eventually, when you search for American Housing Survey, you'll be able to get to both the web pages and the tables for that as well. That's not even on the chart in terms of, you know, the timeline chart in terms of when specifically that survey will get transferred over. But that's the intention long term. So if we go to view all tables, now you can see that particular table. You can filter the results if you want to add other terms. As I say, you're just not going to get to race and income tables because the income tables don't have race in their title. But you can browse down through all the other tables that are available. There's another question. I have a question. When will the Census tools be disabled? Is there a protected timeline? There is no specific date type of that. The timeline chart that I showed earlier is the only indication so far of what they're aiming for. And like I say, the legacy tools are going to continue to be available until the new platform is absolutely ready to go. So you don't need to be worried about not being able to get to the old interfaces. I would imagine that there will be a lot of buzz around the legacy tools being taken away. And even before that, a lot of buzz around, hey, data.census.gov is ready to go. Generally, my memory, when they premiered the new American Fact Finder interface, I think that was in 2011, there was at least a six-month period when both interfaces were available so that you could take some time to explore the new one before you actually had to start using it. And I would expect the same thing here. But they haven't published any dates any more specifically than that close to timeline five that I showed. So then that means that the 2020 Census will still be available in the legacy tools. Yes, I would expect that it will be. Yeah. It's hard to say. The 2020 data won't be out until 2021. And by that time, they are expecting American Fact Finder to be completely available, completely transitioned over to the new platform. So they might well decide not to put 2020 data into the old interface. And I wouldn't be surprised if that's part of what's driving the development timeline. They would rather not put it two places. But it depends on how long it takes. If the new interface, if the new platform isn't ready, then they're just going to have to. It's not like they can avoid releasing the data. There's a legal requirement that the census data be released within one year of taking the census. So if I change to black and income, again, it gives me a race table. Okay, I'm going to go back again and change to the advanced search. I don't know if I said this already. I do encourage you to do searches in both the basic and the advanced interfaces, the same search, because you learn different things about the interface by doing in both. I have quite different feedback for the Census Bureau about the advanced search than I do about the basic search. So I think it's a useful exercise. Here we go. I'm putting, I do want all the words, but I want both of the words up there. You could add something here if you wanted to be more specific. You can also go to geography to your surveys or industries to add additional pieces. I found this bit of the interface to be a little confusing because you have this enter text filter. I thought that you had to search in order to add a geography and it doesn't work that way. If you search for North Carolina here, what you get is the congressional districts, and that's the only option that it offers you. Instead, you have to go through this hierarchy and wait. Eventually you will get a list of all of the states and not only the states, but also the District of Columbia and all of the territories so that you can select from those lower level geographies instead of having to search for them. Because like I say, when you search for North Carolina and you don't get an option to select just North Carolina, all you get is the congressional districts. Well, I'm not sure how well it's going to work for us to do any more searching. In my slides, I do have some other example searches listed, so you can look at those and try those searches on your own and see what happens. For instance, I searched for the word rice and I discovered to my surprise that there are actually a lot of communities in the United States called rice or that have rice in their name. But there's not very much economic data in this new system. I got better results searching for NAICS codes for specific things, for specific industries than I did in getting anything with words describing commodities. So that's one thing. I searched for Education North Carolina and I expected to get a variety of different tables.  But the only thing that I got was a single school enrollment table. So I think that again is about metadata that's attached to those tables. So those were the three examples that I had to show you. They are adding data to the system as they go along. So I would expect that more economic census data will show up in there as they get around to moving census business builder into the system. Those are probably just further down the road because that's not what we're focused on transitioning right now. Do folks have other questions? We could answer any questions that you have or I could turn to the question about historical census data access. I'm not seeing any private ones. So in terms of census data access, I will mention this commercial product even though it is subscription based. You have to pay for it. Some people may have seen social explorer before for a long time it was developed by a university. And so during that time it was freely available, but it has it then quickly moved into a subscriber model. And it's now owned by I believe Oxford University Press. So it's not cheap. I don't offhand know what we're paying for it. But we actually have a subscription through our statewide NCOs collaboration of all public educational, well educational covers abroad. It's pretty much true, but it's both school and institutions of higher education as well as public libraries that pay for it. Our price wouldn't be helpful to you anyway if you're looking to subscribe to this as an individual institution. Social Explorer has all of the census data going back to 1790. That's a little misleading. They don't like situations where the data get complicated. And so there are pieces of the census data that are not available here. But it's really easy to use and it combines the mapping interface along with the tables. And it makes it really easy to export images of the maps. So it's super easy to use with undergraduates and people who aren't very knowledgeable about data. The irony here is that it basically uses American FactFinders original interface as a way to dig into the data. So you first choose the survey that you're working with. And then if we're going to go with the most current American community survey data, you begin a report. You drill down to the specific geography that you want and then choose from list either just one or use shift or control to choose multiples. Add them to your selections and then proceed to tables. This first selection box you get is all of the tables. And Social Explorer presents its own version of the tables in a lot of cases where they do things like calculate percentages for you, which the Census Bureau sort of notoriously does not do. You can switch over to the Census Bureau tables if you prefer. What I find most helpful is to search by keyword because that list of all the tables is really long. And then this is a much smaller list still long because there are so many tables without income that you can choose whatever one you are particularly interested in. I believe, yeah, it keeps the original labels for the Census Bureau's version. So if you're used to seeing the base and compressed tables from the American Community Survey, those will be familiar to you. The ones that are marked just T are Social Explorers tables. And then you again have to add show results. So here's your table. If you want to export it, you can export it easily to Excel. It lets you choose whether you want to have percentages or aggregates or not. And then you can just download it. If you need to use it in a statistical software, you can use the data download and do tag the limited files for data or it will give you set up files for SAS or SDSS. So you can also choose to include the geographic identifiers if people are doing geospatial data. That becomes important. So it's pretty easy to use. Social Explorers has added and authorized data in recent years. If you go to the tables list, you can see the long list. Environmental summaries is new. U.S. religion data from the RCMS is there. Crime data from the Uniform Crime Reports. Health data, cancer data, those are generally county level. Not anything smaller than that. So that reminds me to tell you that the geographies are based on the particular data set. So you'll get quite different things if you're looking at U.S. cancer data versus the UK census or the American Community Survey. So there are differences there among the different data sets that are available. I remember correctly the dictionary links are what will get you to the technical documentation. I still almost never use their technical documentation for Census Bureau products. I will always go directly to the Census Bureau itself, but there is some technical documentation here. Another product that actually was the basis for Social Explorer is something called NHGIS. This is the National Historical GIS System from the Minnesota Population Center. The Minnesota Population Center operates on grant funding. And so they make all of these products available for free. They collect statistics about them so they do ask you to register before you use them. But they are substantially less intuitive than Social Explorer. So I would never send an undergrad to use this product just right off of that. I would always sit down with somebody and give them a careful introduction before setting them loose from this. Even doctoral students or faculty. I think those are the two major ones that I would recommend for historical data. NHGIS is the first geocoding of all of the Census boundaries historically. This also has the Census Data Facts 1790. It's not complete yet, but they are working steadily to add as much as they can get their hands on. So I would expect that eventually this will be a complete collection of all of the Census data. We're pretty much at time. If anybody has remaining questions, my contact information is on the last slide in my presentation. And then we'll put those up on the website, along with a link to the recording. So do feel free to contact me if you have questions or if you just want to get in touch about your use of Census data. I would welcome that. Great. Thank you very much, Michelle. This is great. A little scary. Definitely useful. Many of my co-workers. If there are any final questions, feel free to chat with us. We can't see you typing, so just go ahead and chat and get them in there. Thank you, everybody, for coming, though. And thank you again, Michelle. We'll definitely have you come back and reassure us later on. Sure. Happy to do it.