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---
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:8000
- loss:MultipleNegativesRankingLoss
base_model: sentence-transformers/all-distilroberta-v1
widget:
- source_sentence: Is acute doxorubicin cardiotoxicity associated with p53-induced
inhibition of the mammalian target of rapamycin pathway?
sentences:
- Tyrosinase, the rate-limiting enzyme required for melanin production, has been
targeted to develop active brightening/lightening materials for skin products.
Unexpected depigmentation of the skin characterized with the diverse symptoms
was reported in some subjects who used a tyrosinase-competitive inhibiting quasi-drug,
rhododendrol. To investigate the mechanism underlying the depigmentation caused
by rhododendrol-containing cosmetics, this study was performed. The mechanism
above was examined using more than dozen of melanocytes derived from donors of
different ethnic backgrounds. The RNAi technology was utilized to confirm the
effect of tyrosinase to induce the cytotoxicity of rhododendrol and liquid chromatography-tandem
mass spectrometry was introduced to detect rhododendrol and its metabolites in
the presence of tyrosinase. Melanocyte damage was related to tyrosinase activity
at a certain threshold. Treatment with a tyrosinase-specific siRNA was shown to
dramatically rescue the rhododendrol-induced melanocyte impairment. Hydroxyl-rhododendrol
was detected only in melanocytes with higher tyrosinase activity. When an equivalent
amount of hydroxyl-rhododendrol was administered, cell viability was almost equally
suppressed even in melanocytes with lower tyrosinase activity.
- Doxorubicin is used to treat childhood and adult cancer. Doxorubicin treatment
is associated with both acute and chronic cardiotoxicity. The cardiotoxic effects
of doxorubicin are cumulative, which limits its chemotherapeutic dose. Free radical
generation and p53-dependent apoptosis are thought to contribute to doxorubicin-induced
cardiotoxicity. Adult transgenic (MHC-CB7) mice expressing cardiomyocyte-restricted
dominant-interfering p53 and their nontransgenic littermates were treated with
doxorubicin (20 mg/kg cumulative dose). Nontransgenic mice exhibited reduced left
ventricular systolic function (predoxorubicin fractional shortening [FS] 61+/-2%,
postdoxorubicin FS 45+/-2%, mean+/-SEM, P<0.008), reduced cardiac mass, and high
levels of cardiomyocyte apoptosis 7 days after the initiation of doxorubicin treatment.
In contrast, doxorubicin-treated MHC-CB7 mice exhibited normal left ventricular
systolic function (predoxorubicin FS 63+/-2%, postdoxorubicin FS 60+/-2%, P>0.008),
normal cardiac mass, and low levels of cardiomyocyte apoptosis. Western blot analyses
indicated that mTOR (mammalian target of rapamycin) signaling was inhibited in
doxorubicin-treated nontransgenic mice but not in doxorubicin-treated MHC-CB7
mice. Accordingly, transgenic mice with cardiomyocyte-restricted, constitutively
active mTOR expression (MHC-mTORca) were studied. Left ventricular systolic function
(predoxorubicin FS 64+/-2%, postdoxorubicin FS 60+/-3%, P>0.008) and cardiac mass
were normal in doxorubicin-treated MHC-mTORca mice, despite levels of cardiomyocyte
apoptosis similar to those seen in doxorubicin-treated nontransgenic mice.
- To examine the regulatory aspects of zinc-α2-glycoprotein (ZAG) association with
obesity-related insulin resistance. ZAG mRNA and protein were analyzed in subcutaneous
adipose tissue (AT) and circulation of lean, obese, prediabetic, and type 2 diabetic
men; both subcutaneous and visceral AT were explored in lean and extremely obese.
Clinical and ex vivo findings were corroborated by results of in vitro ZAG silencing
experiment. Subcutaneous AT ZAG was reduced in obesity, with a trend to further
decrease with prediabetes and type 2 diabetes. ZAG was 3.3-fold higher in subcutaneous
than in visceral AT of lean individuals. All differences were lost in extreme
obesity. Obesity-associated changes in AT were not paralleled by alterations of
circulating ZAG. Subcutaneous AT ZAG correlated with adiposity, adipocyte hypertrophy,
whole-body and AT insulin sensitivity, mitochondrial content, expression of GLUT4,
PGC1α, and adiponectin. Subcutaneous AT ZAG and adipocyte size were the only predictors
of insulin sensitivity, independent on age and BMI. Silencing ZAG resulted in
reduced adiponectin, IRS1, GLUT4, and PGC1α gene expression in primary human adipocytes.
- source_sentence: Is avoidance of polypharmacy and excessive blood pressure control
associated with improved renal function in older patients?
sentences:
- Elderly patients are particularly susceptible to polypharmacy. The present study
evaluated the renal effects of optimizing potentially nephrotoxic medications
in an older population. Retrospective study of patients' ≥ 60 years treated between
January of 2013 and February of 2015 in a Nephrology Clinic. The renal effect
of avoiding polypharmacy was studied. Sixty-one patients were studied. Median
age was 81 years (range 60-94). Twenty-five patients (41%) were male. NSAIDs alone
were stopped in seven patients (11.4%), a dose reduction in antihypertensives
was done in 11 patients (18%), one or more antihypertensives were discontinued
in 20 patients (32.7%) and discontinuation and dose reduction of multiple medications
was carried out in 23 patients (37.7%). The number of antihypertensives was reduced
from a median of 3 (range of 0-8) at baseline to a median of 2 (range 0-7), p
< 0.001 after intervention. After intervention, the glomerular filtration rate
(GFR) improved significantly, from a baseline of 32 ± 15.5 cc/min/1.73 m(2) to
39.5 ± 17 cc/min/1.73 m(2) at t1 (p < 0.001) and 44.5 ± 18.7 cc/min/1.73 m(2)
at t2 (p < 0.001 vs. baseline). In a multivariate model, after adjusting for ACEIs/ARBs
discontinuation/dose reduction, NSAIDs use and change in DBP, an increase in SBP
at time 1 remained significantly associated with increments in GFR on follow-up
(estimate = 0.20, p = 0.01).
- Endothelial dysfunction and hypertension is more common in individuals with diabetes
than in the general population. This study was aimed to investigate the underlying
mechanisms responsible for endothelial dysfunction of type 1 diabetic rats fed
with high-salt diet. Type 1 diabetes (DM) was induced by intraperitoneal injection
of streptozotocin (70 mg·kg(-1)). Normal or diabetic rats were randomly fed high-salt
food (HS, 8% NaCl) or standard food (CON) for 6 weeks. Both HS (143±10 mmHg) and
DM+HS (169±11 mmHg) groups displayed significantly higher systolic blood pressure
than those in the CON group (112±12 mmHg, P<0.01). DM+HS rats exhibited more pronounced
impairment of vasorelaxation to acetylcholine and insulin compared with either
DM or HS. Akt/endothelial nitric oxide synthase (eNOS) phosphorylation levels
and nitric oxide (NO) concentration in DM+HS were significantly lower than in
DM. The levels of caveolin-1 (cav-1) in DM+HS were significantly higher than that
in DM and HS. Co-immunoprecipitation results showed increased interaction between
cav-1 and eNOS in the DM+HS group. In the presence of cav-1 small interfering
RNA (siRNA), eNOS phosphorylations in human umbilical vein endothelial cells (HUVEC)
were significantly increased compared with control siRNA. Cav-1 was slightly but
not significantly lower in HUVEC cultured with high glucose and high-salt buffer
solution and pretreated with wortmannin or l-nitro-arginine methyl ester.
- 'Several studies have revealed a correlation between sialosyl Tn antigen (STN)
and certain clinicopathologic features of various cancers, and that STN is an
independent prognostic factor. However, the clinical significance of the expression
of STN in gastric cancer has not been reported. Thus, the purpose of this study
was to evaluate immunohistochemically the clinical significance of expression
of STN in gastric cancer. The expression of STN in surgically resected specimens
of human gastric cancer was evaluated immunohistochemically using a monoclonal
antibody (TKH-2), in 60 patients whose serum STN levels were measured and in 54
patients with advanced cancer who had been followed for more than 5 years after
gastrectomy. The correlations between the level of STN expression and clinicopathologic
factors were analyzed. The staining intensity was graded as follows: (-), less
than 5% of the cancer cells expressed STN; (+), 5-50%; (++), more than 50%. Sialosyl
TN antigen staining was detected mainly on the cell membrane, in the cytoplasm,
and in the luminal contents, and 57.2% of the 60 specimens expressed STN, whereas
the corresponding value for positive serum levels was 15%. A higher percentage
of advanced tumors expressed STN than did the early cases, but the difference
was not statistically significant. All cases with strong staining, the (++) cases,
were advanced cases either with lymph node metastases or with cancer invading
in or beyond the muscle layer proper. The expression of STN appeared to be related
to the clinical stage, the extent of cancer invasion, and the presence of lymph
node metastases. Sialosyl TN antigen was detected in the serum in less than 6%
of the patients whose tumors were (-) or (+) for STN expression, and in 86.7%
of the patients whose tumors expressed high levels of STN (++). The estimated
5-year survival in advanced cases (Stage III) was significantly better in those
with negative STN expression than in those with positive STN expression (P < 0.01).'
- source_sentence: Does platelet attachment stimulate endothelial cell regeneration
after arterial injury?
sentences:
- The efficacy of lansoprazole (LPZ) at inhibiting gastric acid secretion is influenced
by cytochrome P450 2C19 (CYP2C19) polymorphism. The purpose of the present study
was to investigate whether CYP2C19 polymorphism had an influence on the remission
of erosive reflux esophagitis (RE) during maintenance therapy with LPZ. Eighty-two
Japanese patients with initial healing of erosive RE by 8 weeks of LPZ therapy
were enrolled. As maintenance therapy, the patients were treated with LPZ (15
mg/day) for 6 months. The CYP2C19 genotype, Helicobacter pylori infection status,
and serum pepsinogen (PG) I/II ratio were assessed before treatment. The patients
were investigated for relapse by endoscopy at 6 months or when symptoms recurred.
The proportion of patients in remission after 6 months was 61.5%, 78.0%, and 100%
among homozygous extensive metabolizers (homo-EM), heterozygous EM (hetero-EM),
and poor metabolizers (PM), respectively. The percentage of PM patients who remained
in remission was significantly higher than that of homo-EM or hetero-EM.
- Arterial injury is associated with endothelial disruption and attachment of platelets
to an exposed subintimal layer. A variety of factors released by platelets may
affect the ability of endothelial cells bordering an injury to regenerate. In
this study an organ culture model of arterial injury was used to investigate the
relationship between attachment of platelets to a superficial arterial injury
and endothelial regeneration. A defined superficial endothelial injury was made
in whole vessel wall explants of rabbit thoracic aorta. Injured explants were
treated with either fresh whole platelets, the supernatant of platelets aggregated
by collagen, or basic fibroblast growth factor. Four days after injury and treatment,
the average distance of endothelial regeneration was determined. A dramatic increase
in the rate of endothelial cell regeneration was observed when injured vessels
were exposed to fresh whole platelets (p = 0.003). This increase in regeneration
was comparable to that observed with fibroblast growth factor. No increase in
the regenerative rate was found after exposure of explants to the supernatant
of aggregated platelets (p = 0.69).
- To introduce an elastomeric continuous infusion pump for pain control after outpatient
orbital implant surgery. Retrospective, noncomparative consecutive case series
of all patients undergoing enucleation, evisceration, or secondary orbital implantation
using the On-Q pain system between August 2004 and January 2006. Postoperative
pain score, need for narcotics, and adverse events were recorded. The On-Q catheter
is inserted intraoperatively through the lateral lower eyelid into the muscle
cone under direct visualization, prior to the orbital implant placement. The On-Q
system continually infuses anesthesia (bupivacaine) to the retrobulbar site for
5 days. Among 20 patients, mean postoperative period pain score, with On-Q in
place, was 1.3 (scale of 0 to 10). Nine patients (45%) did not need any adjunctive
oral narcotics. Two patients experienced postoperative nausea. One catheter connector
leaked, thereby decreasing delivery of retrobulbar anesthetic resulting a pain
level of 6, the highest level in the study. There were no postoperative infections.
No systemic toxic effects from bupivacaine were observed clinically.
- source_sentence: Do mid-regional proadrenomedullin levels predict recurrence of
atrial fibrillation after catheter ablation?
sentences:
- We evaluated the prognostic value of mid-regional proadrenomedullin (MR-proADM)
in atrial fibrillation (AF) patients undergoing radiofrequency ablation. Plasma
concentrations of MR-proADM were measured at baseline and after 12months in 87
AF patients in whom radiofrequency ablation was performed. The association between
MR-proADM and AF recurrence was tested by univariable and multivariable Cox models.
In all 87 patients radiofrequency ablation was successfully performed. Of the
total population 54% had paroxysmal AF. The mean left ventricular ejection fraction
was 54% (minimum 25%). After 12months of follow-up, 71% of the patients were free
of AF recurrence. At baseline, mean MR-proADM in the total population was 0.72nmol/l±0.22.
Patients with AF recurrence had significantly higher baseline MR-proADM (0.89nmol/l±0.29)
as compared with patients without AF recurrence (0.65nmol/l±0.14; p<0.001). After
12months, mean MR-proADM plasma concentration remained higher in patients with
AF recurrence (0.81nmol/l±0.22 as compared with patients free of AF 0.54nmol/l±0.20;
p<0.001). Receiver operating characteristic (ROC) curve analysis for MR-proADM
yields a specificity of 98% and a sensitivity of 64% with an optimal cut-off value
of 0.82nmol/l to predict recurrence of AF after catheter ablation. In the logistic
regression analysis only MR-proADM remained independently predictive for AF recurrence.
- There has been growing interest in the role that implicit processing of drug cues
can play in motivating drug use behavior. However, the extent to which drug cue
processing biases relate to the processing biases exhibited to other types of
evocative stimuli is largely unknown. The goal of the present study was to determine
how the implicit cognitive processing of smoking cues relates to the processing
of affective cues using a novel paradigm. Smokers (n = 50) and nonsmokers (n =
38) completed a picture-viewing task, in which participants were presented with
a series of smoking, pleasant, unpleasant, and neutral images while engaging in
a distractor task designed to direct controlled resources away from conscious
processing of image content. Electroencephalogram recordings were obtained throughout
the task for extraction of event-related potentials (ERPs). Smokers exhibited
differential processing of smoking cues across 3 different ERP indices compared
with nonsmokers. Comparable effects were found for pleasant cues on 2 of these
indices. Late cognitive processing of smoking and pleasant cues was associated
with nicotine dependence and cigarette use.
- To evaluate the role of toll-like receptors (TLR) 2 and 4 in host responses to
Aspergillus fumigatus by use of cultured telomerase-immortalized human corneal
epithelial cells (HCECs). HCECs were stimulated with inactive antigens from A.
fumigatus. The expression of TLR2 and TLR4, phosphorylation of Ikappa B-alpha
(pIkappa B-alpha), and release of interleukin (IL)-1beta and IL-6 was measured
with and without inhibitors to TLR2 and TLR4. Exposure of HCECs to A. fumigatus
antigens resulted in up-regulation of TLR2 and TLR4, activation of pIkappa B,
and release of IL-1beta and IL-6 in HCECs, effects that could be inhibited by
treatment with TLR2 and TLR4 antibodies.
- source_sentence: Are peripheral blood lymphocytes from patients with rheumatoid
arthritis differentially sensitive to apoptosis induced by anti-tumour necrosis
factor-alpha therapy?
sentences:
- The aim of this study was to investigate the prognostic effect of serum free light
chain (sFLC) response after 2 cycles of first-line chemotherapy (CT) in multiple
myeloma (MM) patients. The data of 78 newly diagnosed MM patients who had sFLC
levels at diagnosis and after 2 cycles of first-line CT were included in the study.
The prognostic effect of sFLCs were evaluated with normalization of sFLC κ/λ ratio
after 2 cycles of CT and involved/uninvolved (i/u) sFLCs. At the end of follow-up
the probability of overall survival (OS) was 95.7% versus 68.5% in patients with
and without normalized sFLC κ/λ ratio, respectively (P = .072). The probability
of OS with i/u sFLC assessment was 97.4% versus 55.8% with regard to i/u sFLC
≤ 10 and > 10, respectively (P = .001). In univariate and multivariate analysis
including sFLC ratio, age, sex, and International Staging System, i/u sFLC ratio
> 10 after 2 cycles of CT was identified as an independent risk factor for OS
(P = .015; hazard ratio [HR], 13.2; 95% confidence interval [CI], 1.668-104.65
vs. P = .011; HR, 15.17; 95% CI, 1.85-123.89).
- This study examined links between DNA methylation and birth weight centile (BWC),
and explored the impact of genetic variation. Using HumanMethylation450 arrays,
we examined candidate gene-associated CpGs in cord blood from newborns with low
(<15th centile), medium (40-60th centile) and high (>85th centile) BWC (n = 12).
Candidates were examined in an investigation cohort (n = 110) using pyrosequencing
and genotyping for putative methylation-associated polymorphisms performed using
standard PCR. Array analysis identified 314 candidate genes associated with BWC
extremes, four of which showed ≥ 4 BWC-linked CpGs. Of these, PM20D1 and MI886
suggested genetically determined methylation levels. However, methylation at three
CpGs in FGFR2 remained significantly associated with high BWC (p = 0.004-0.027).
- The efficacy of anti-tumour necrosis factor-alpha (TNF-alpha) therapies in rheumatoid
arthritis (RA) has been mainly attributed to TNF-alpha neutralisation. Other mechanism
as immune cell apoptosis, which is impaired in RA, may also be induced by anti-TNF-alpha
therapies. The aim of our study was to investigate whether TNF-alpha inhibitors
could induce apoptosis in vitro of the peripheral blood lymphocytes of RA patients.
Peripheral blood mononuclear cells (PBMC) isolated from 24 patients with RA and
18 healthy donors were incubated with anti-TNF-alpha agents, infliximab or etanercept,
in comparison with no agent and including an isotypic control, for 48 hours. Apoptosis
was detected and quantified by annexin V labelling of phosphatidylserine externalization
using cytofluorometric analysis and compared with PBMC production TNF-alpha in
vitro. In healthy donors, induced apoptosis was observed in 0.3% to 3.8% of lymphocytes
with both therapies. In RA patients the treatment induced lymphocyte apoptosis
in 17 of 24 patients with a percentage of annexin V-positive lymphocytes ranging
from 0.1% to 25%. Among these 17 RA patients, a significant in vitro lymphocyte
apoptosis (> 4%) was observed in 11 patients (46%) compared with healthy donors
(p < 0.01). The variability of the response to anti-TNF-alpha within the RA population
was not dependent on TNF-alpha synthesis or disease activity.
datasets:
- HariModelMaven/pumed-finetuning
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
- cosine_accuracy
model-index:
- name: SentenceTransformer based on sentence-transformers/all-distilroberta-v1
results:
- task:
type: triplet
name: Triplet
dataset:
name: ai pubmed validation
type: ai-pubmed-validation
metrics:
- type: cosine_accuracy
value: 1.0
name: Cosine Accuracy
---
# SentenceTransformer based on sentence-transformers/all-distilroberta-v1
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [sentence-transformers/all-distilroberta-v1](https://huggingface.co/sentence-transformers/all-distilroberta-v1) on the [pumed-finetuning](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning) dataset. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.
## Model Details
### Model Description
- **Model Type:** Sentence Transformer
- **Base model:** [sentence-transformers/all-distilroberta-v1](https://huggingface.co/sentence-transformers/all-distilroberta-v1) <!-- at revision 842eaed40bee4d61673a81c92d5689a8fed7a09f -->
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 768 dimensions
- **Similarity Function:** Cosine Similarity
- **Training Dataset:**
- [pumed-finetuning](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning)
<!-- - **Language:** Unknown -->
<!-- - **License:** Unknown -->
### Model Sources
- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)
### Full Model Architecture
```
SentenceTransformer(
(0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: RobertaModel
(1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
(2): Normalize()
)
```
## Usage
### Direct Usage (Sentence Transformers)
First install the Sentence Transformers library:
```bash
pip install -U sentence-transformers
```
Then you can load this model and run inference.
```python
from sentence_transformers import SentenceTransformer
# Download from the 🤗 Hub
model = SentenceTransformer("HariModelMaven/distilroberta-pubmed-embeddings")
# Run inference
sentences = [
'Are peripheral blood lymphocytes from patients with rheumatoid arthritis differentially sensitive to apoptosis induced by anti-tumour necrosis factor-alpha therapy?',
'The efficacy of anti-tumour necrosis factor-alpha (TNF-alpha) therapies in rheumatoid arthritis (RA) has been mainly attributed to TNF-alpha neutralisation. Other mechanism as immune cell apoptosis, which is impaired in RA, may also be induced by anti-TNF-alpha therapies. The aim of our study was to investigate whether TNF-alpha inhibitors could induce apoptosis in vitro of the peripheral blood lymphocytes of RA patients. Peripheral blood mononuclear cells (PBMC) isolated from 24 patients with RA and 18 healthy donors were incubated with anti-TNF-alpha agents, infliximab or etanercept, in comparison with no agent and including an isotypic control, for 48 hours. Apoptosis was detected and quantified by annexin V labelling of phosphatidylserine externalization using cytofluorometric analysis and compared with PBMC production TNF-alpha in vitro. In healthy donors, induced apoptosis was observed in 0.3% to 3.8% of lymphocytes with both therapies. In RA patients the treatment induced lymphocyte apoptosis in 17 of 24 patients with a percentage of annexin V-positive lymphocytes ranging from 0.1% to 25%. Among these 17 RA patients, a significant in vitro lymphocyte apoptosis (> 4%) was observed in 11 patients (46%) compared with healthy donors (p < 0.01). The variability of the response to anti-TNF-alpha within the RA population was not dependent on TNF-alpha synthesis or disease activity.',
'This study examined links between DNA methylation and birth weight centile (BWC), and explored the impact of genetic variation. Using HumanMethylation450 arrays, we examined candidate gene-associated CpGs in cord blood from newborns with low (<15th centile), medium (40-60th centile) and high (>85th centile) BWC (n = 12). Candidates were examined in an investigation cohort (n = 110) using pyrosequencing and genotyping for putative methylation-associated polymorphisms performed using standard PCR. Array analysis identified 314 candidate genes associated with BWC extremes, four of which showed ≥ 4 BWC-linked CpGs. Of these, PM20D1 and MI886 suggested genetically determined methylation levels. However, methylation at three CpGs in FGFR2 remained significantly associated with high BWC (p = 0.004-0.027).',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]
# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]
```
<!--
### Direct Usage (Transformers)
<details><summary>Click to see the direct usage in Transformers</summary>
</details>
-->
<!--
### Downstream Usage (Sentence Transformers)
You can finetune this model on your own dataset.
<details><summary>Click to expand</summary>
</details>
-->
<!--
### Out-of-Scope Use
*List how the model may foreseeably be misused and address what users ought not to do with the model.*
-->
## Evaluation
### Metrics
#### Triplet
* Dataset: `ai-pubmed-validation`
* Evaluated with [<code>TripletEvaluator</code>](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.TripletEvaluator)
| Metric | Value |
|:--------------------|:--------|
| **cosine_accuracy** | **1.0** |
<!--
## Bias, Risks and Limitations
*What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
-->
<!--
### Recommendations
*What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
-->
## Training Details
### Training Dataset
#### pumed-finetuning
* Dataset: [pumed-finetuning](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning) at [02cc2cc](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning/tree/02cc2cc18a0aad3651a3ee0164319a2281d4da6f)
* Size: 8,000 training samples
* Columns: <code>instruction</code>, <code>context</code>, and <code>context_neg</code>
* Approximate statistics based on the first 1000 samples:
| | instruction | context | context_neg |
|:--------|:-----------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|
| type | string | string | string |
| details | <ul><li>min: 11 tokens</li><li>mean: 26.36 tokens</li><li>max: 67 tokens</li></ul> | <ul><li>min: 31 tokens</li><li>mean: 320.03 tokens</li><li>max: 512 tokens</li></ul> | <ul><li>min: 82 tokens</li><li>mean: 321.22 tokens</li><li>max: 512 tokens</li></ul> |
* Samples:
| instruction | context | context_neg |
|:------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| <code>Do competency assessment of primary care physicians as part of a peer review program?</code> | <code>To design and test a program that assesses clinical competence as a second stage in a peer review process and to determine the program's reliability. A three-cohort study of Ontario primary care physicians. Reference physicians (n = 26) randomly drawn from the Hamilton, Ontario, area; volunteer, self-referred physicians (n = 20); and physicians referred by the licensing body (n = 37) as a result of a disciplinary hearing or peer review. Standardized patients, structured oral examinations, chart-stimulated recall, objective structured clinical examination, and multiple-choice examination. Test reliability was high, ranging from 0.73 to 0.91, and all tests discriminated among subgroups. Demographic variables relating to the final category were age, Canadian or foreign graduates, and whether or not participants were certified in family medicine.</code> | <code>Static stretch is frequently observed in the lung. Both static stretch and cyclic stretch can induce cell death and Na(+)/K(+)-ATPase trafficking, but stretch-induced alveolar epithelial cell (AEC) functions are much less responsive to static than to cyclic stretch. AEC remodeling under static stretch may be partly explained. The aim of this study was to explore the AEC remodeling and functional changes under static stretch conditions. We used A549 cells as a model of AEC type II cells. We assessed F-actin content and cell viability by fluorescence staining at various static-stretch magnitudes and time points. Specifically, we used scanning electron microscopy to explore the possible biological mechanisms used by A549 cells to 'escape' static-stretch-induced injury. Finally, we measured choline cytidylyltransferase-alpha (CCT alpha) mRNA and protein by real-time PCR and Western blot to evaluate cellular secretory function. The results showed that the magnitude of static stretch was the...</code> |
| <code>Is age an important determinant of the growth hormone response to sprint exercise in non-obese young men?</code> | <code>The factors that regulate the growth hormone (GH) response to physiological stimuli, such as exercise, are not fully understood. The aim of the present study is to determine whether age, body composition, measures of sprint performance or the metabolic response to a sprint are predictors of the GH response to sprint exercise in non-obese young men. Twenty-seven healthy, non-obese males aged 18-32 years performed an all-out 30-second sprint on a cycle ergometer. Univariate linear regression analysis was employed to evaluate age-, BMI-, performance- and metabolic-dependent changes from pre-exercise to peak GH and integrated GH for 60 min after the sprint. GH was elevated following the sprint (change in GH: 17.0 +/- 14.2 microg l(-1); integrated GH: 662 +/- 582 min microg l(-1)). Performance characteristics, the metabolic response to exercise and BMI were not significant predictors of the GH response to exercise. However, age emerged as a significant predictor of both integrated GH (beta ...</code> | <code>We have previously reported the crucial roles of oncogenic Kirsten rat sarcoma viral oncogene homolog (KRAS) in inhibiting apoptosis and disrupting cell polarity via the regulation of phosphodiesterase 4 (PDE4) expression in human colorectal cancer HCT116 cells in three-dimensional cultures (3DC). Herein we evaluated the effects of resveratrol, a PDE4 inhibitor, on the luminal cavity formation and the induction of apoptosis in HCT116 cells. Apoptosis was detected by immunofluorescence using confocal laser scanning microscopy with an antibody against cleaved caspase-3 in HCT116 cells treated with or without resveratrol in a two-dimensional culture (2DC) or 3DC. Resveratrol did not induce apoptosis of HCT116 cells in 2DC, whereas the number of apoptotic HCT116 cells increased after resveratrol treatment in 3DC, leading to formation of a luminal cavity.</code> |
| <code>Is terlipressin more effective in decreasing variceal pressure than portal pressure in cirrhotic patients?</code> | <code>Terlipressin decreases portal pressure. However, its effects on variceal pressure have been poorly investigated. This study investigated the variceal, splanchnic and systemic hemodynamic effects of terlipressin. Twenty cirrhotic patients with esophageal varices grade II-III, and portal pressure > or =12 mmHg were studied. Hepatic venous pressure gradient, variceal pressure and systemic hemodynamic parameters were obtained. After baseline measurements, in a double-blind administration, 14 patients received a 2mg/iv injection of terlipressin and six patients received placebo. The same measurements were repeated 60 min later. No demographic or biochemical differences were observed in basal condition between groups. Terlipressin produced significant decreases in intravariceal pressure from 20.9+4.9 to 16.3+/-4.7 mmHg (p<0.01, -21+/- 16%), variceal pressure gradient from 18.9+/-4.8 to 13.5+/-6.0 mmHg (p<0.01, -28+/-27%), estimated variceal wall tension from 78+/-29 to 59+/-31 mmHg x mm (p<0...</code> | <code>Based on the theories of brain reserve and cognitive reserve, we investigated whether larger maximal lifetime brain growth (MLBG) and/or greater lifetime intellectual enrichment protect against cognitive decline over time. Forty patients with multiple sclerosis (MS) underwent baseline and 4.5-year follow-up evaluations of cognitive efficiency (Symbol Digit Modalities Test, Paced Auditory Serial Addition Task) and memory (Selective Reminding Test, Spatial Recall Test). Baseline and follow-up MRIs quantified disease progression: percentage brain volume change (cerebral atrophy), percentage change in T2 lesion volume. MLBG (brain reserve) was estimated with intracranial volume; intellectual enrichment (cognitive reserve) was estimated with vocabulary. We performed repeated-measures analyses of covariance to investigate whether larger MLBG and/or greater intellectual enrichment moderate/attenuate cognitive decline over time, controlling for disease progression. Patients with MS declined in...</code> |
* Loss: [<code>MultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Evaluation Dataset
#### pumed-finetuning
* Dataset: [pumed-finetuning](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning) at [02cc2cc](https://huggingface.co/datasets/HariModelMaven/pumed-finetuning/tree/02cc2cc18a0aad3651a3ee0164319a2281d4da6f)
* Size: 1,000 evaluation samples
* Columns: <code>instruction</code>, <code>context</code>, and <code>context_neg</code>
* Approximate statistics based on the first 1000 samples:
| | instruction | context | context_neg |
|:--------|:-----------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------|
| type | string | string | string |
| details | <ul><li>min: 11 tokens</li><li>mean: 26.08 tokens</li><li>max: 52 tokens</li></ul> | <ul><li>min: 38 tokens</li><li>mean: 311.42 tokens</li><li>max: 512 tokens</li></ul> | <ul><li>min: 45 tokens</li><li>mean: 316.2 tokens</li><li>max: 512 tokens</li></ul> |
* Samples:
| instruction | context | context_neg |
|:----------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| <code>Are pre-transplant impedance measures of reflux associated with early allograft injury after lung transplantation?</code> | <code>Acid reflux has been associated with poorer outcomes after lung transplantation. Standard pre-transplant reflux assessment has not been universally adopted. Non-acid reflux may also induce a pulmonary inflammatory cascade, leading to acute and chronic rejection. Esophageal multichannel intraluminal impedance and pH testing (MII-pH) may be valuable in standard pre-transplant evaluation. We assessed the association between pre-transplant MII-pH measures and early allograft injury in lung transplant patients. This was a retrospective cohort study of lung transplant recipients who underwent pre-transplant MII-pH at a tertiary center from 2007 to 2012. Results from pre-transplant MII-pH, cardiopulmonary function testing, and results of biopsy specimen analysis of the transplanted lung were recorded. Time-to-event analyses were performed using Cox proportional hazards and Kaplan-Maier methods to assess the associations between MII-pH measures and development of acute rejection or lymphocytic...</code> | <code>The yeast cell cycle is largely controlled by the cyclin-dependent kinase (CDK) Cdc28. Recent evidence suggests that both CDK complex stability as well as function during mitosis is determined by precise regulation of Swe1, a CDK inhibitory kinase and cyclin binding partner. A model of mitotic progression has been provided by study of filamentous yeast. When facing nutrient-limited conditions, Ras2-mediated PKA and MAPK signaling cascades induce a switch from round to filamentous morphology resulting in delayed mitotic progression. To delineate how the dimorphic switch contributes to cell cycle regulation, temperature sensitive cdc28 mutants exhibiting constitutive filamentation were subjected to epistasis analyses with RAS2 signaling effectors. It was found that Swe1-mediated inhibitory tyrosine phosphorylation of Cdc28 during filamentous growth is in part mediated by Ras2 activation of PKA, but not Kss1-MAPK, signaling. This pathway is further influenced by Cks1, a conserved CDK-bind...</code> |
| <code>Is predictive accuracy of the TRISS survival statistic improved by a modification that includes admission pH?</code> | <code>To determine if pH measured at the time of hospital admission and corrected for PCO2 was an independent predictor of trauma survival. Phase 1 was a retrospective case-control analysis of 1708 patients, followed by multivariate multiple logistic regression analysis of a subset of 919 patients for whom the Revised Trauma Score (RTS), Injury Severity Score (ISS), and pH were available. Phase 2 was a prospective comparison of a mathematical model of survival derived in phase 1 (pH-TRISS) with the TRISS method in 508 of 1325 subsequently admitted trauma patients. Urban level 1 trauma center. All patients admitted with blunt or penetrating trauma during the study period. Survival vs mortality. In phase 1, factors significantly associated with mortality by t test and chi 2 analysis included the RTS, ISS< Glasgow Coma Scale, corrected pH (CpH), and sum of the head, chest, and abdominal components of the Abbreviated Injury Scale-85 (AIS85) (HCAISS) (for all, P < .0001). The TRISS statistic was ...</code> | <code>Ovarian cancer is the most lethal gynecologic malignancy, and there is an unmet clinical need to develop new therapies. Although showing promising anticancer activity, Niclosamide may not be used as a monotherapy. We seek to investigate whether inhibiting IGF signaling potentiates Niclosamide's anticancer efficacy in human ovarian cancer cells. Cell proliferation and migration are assessed. Cell cycle progression and apoptosis are analyzed by flow cytometry. Inhibition of IGF signaling is accomplished by adenovirus-mediated expression of siRNAs targeting IGF-1R. Cancer-associated pathways are assessed using pathway-specific reporters. Subcutaneous xenograft model is used to determine anticancer activity. We find that Niclosamide is highly effective on inhibiting cell proliferation, cell migration, and cell cycle progression, and inducing apoptosis in human ovarian cancer cells, possibly by targeting multiple signaling pathways involved in ELK1/SRF, AP-1, MYC/MAX and NFkB. Silencing IGF...</code> |
| <code>Does exposure to intermittent nociceptive stimulation under pentobarbital anesthesia disrupt spinal cord function in rats?</code> | <code>Spinal cord plasticity can be assessed in spinal rats using an instrumental learning paradigm in which subjects learn an instrumental response, hindlimb flexion, to minimize shock exposure. Prior exposure to uncontrollable intermittent stimulation blocks learning in spinal rats but has no effect if given before spinal transection, suggesting that supraspinal systems modulate nociceptive input to the spinal cord, rendering it less susceptible to the detrimental consequences of uncontrollable stimulation. The present study examines whether disrupting brain function with pentobarbital blocks descending inhibitory systems that normally modulate nociceptive input, making the spinal cord more sensitive to the adverse effect of uncontrollable intermittent stimulation. Male Sprague-Dawley rats received uncontrollable intermittent stimulation during pentobarbital anesthesia after (experiment 1) or before (experiment 2) spinal cord transection. They were then tested for instrumental learning at ...</code> | <code>Increased serum hepcidin has been reported in patients receiving chronic hemodialysis, and hypothesized to contribute to the alterations of iron metabolism of end-stage renal disease. However, no quantitative assessment is available to date; the clinical determinants are still under definition; and the role of genetic factors, namely HFE mutations, has not yet been evaluated. The aim of this study was to quantitatively assess serum hepcidin-25 in hemodialysis patients versus controls, and analyze the relationship between hepcidin, iron indices, HFE genotype, and erythropoietic parameters. Sixty-five hemodialysis patients and 57 healthy controls were considered. Hepcidin-25 was evaluated by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, HFE genotype by restriction analysis. Serum hepcidin-25 was higher in hemodialysis patients compared with controls. In patients, hepcidin-25 correlated positively with ferritin and C reactive protein, and negatively with s...</code> |
* Loss: [<code>MultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: steps
- `per_device_train_batch_size`: 16
- `per_device_eval_batch_size`: 16
- `learning_rate`: 2e-05
- `num_train_epochs`: 1
- `warmup_ratio`: 0.1
- `batch_sampler`: no_duplicates
#### All Hyperparameters
<details><summary>Click to expand</summary>
- `overwrite_output_dir`: False
- `do_predict`: False
- `eval_strategy`: steps
- `prediction_loss_only`: True
- `per_device_train_batch_size`: 16
- `per_device_eval_batch_size`: 16
- `per_gpu_train_batch_size`: None
- `per_gpu_eval_batch_size`: None
- `gradient_accumulation_steps`: 1
- `eval_accumulation_steps`: None
- `torch_empty_cache_steps`: None
- `learning_rate`: 2e-05
- `weight_decay`: 0.0
- `adam_beta1`: 0.9
- `adam_beta2`: 0.999
- `adam_epsilon`: 1e-08
- `max_grad_norm`: 1.0
- `num_train_epochs`: 1
- `max_steps`: -1
- `lr_scheduler_type`: linear
- `lr_scheduler_kwargs`: {}
- `warmup_ratio`: 0.1
- `warmup_steps`: 0
- `log_level`: passive
- `log_level_replica`: warning
- `log_on_each_node`: True
- `logging_nan_inf_filter`: True
- `save_safetensors`: True
- `save_on_each_node`: False
- `save_only_model`: False
- `restore_callback_states_from_checkpoint`: False
- `no_cuda`: False
- `use_cpu`: False
- `use_mps_device`: False
- `seed`: 42
- `data_seed`: None
- `jit_mode_eval`: False
- `use_ipex`: False
- `bf16`: False
- `fp16`: False
- `fp16_opt_level`: O1
- `half_precision_backend`: auto
- `bf16_full_eval`: False
- `fp16_full_eval`: False
- `tf32`: None
- `local_rank`: 0
- `ddp_backend`: None
- `tpu_num_cores`: None
- `tpu_metrics_debug`: False
- `debug`: []
- `dataloader_drop_last`: False
- `dataloader_num_workers`: 0
- `dataloader_prefetch_factor`: None
- `past_index`: -1
- `disable_tqdm`: False
- `remove_unused_columns`: True
- `label_names`: None
- `load_best_model_at_end`: False
- `ignore_data_skip`: False
- `fsdp`: []
- `fsdp_min_num_params`: 0
- `fsdp_config`: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
- `fsdp_transformer_layer_cls_to_wrap`: None
- `accelerator_config`: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
- `deepspeed`: None
- `label_smoothing_factor`: 0.0
- `optim`: adamw_torch
- `optim_args`: None
- `adafactor`: False
- `group_by_length`: False
- `length_column_name`: length
- `ddp_find_unused_parameters`: None
- `ddp_bucket_cap_mb`: None
- `ddp_broadcast_buffers`: False
- `dataloader_pin_memory`: True
- `dataloader_persistent_workers`: False
- `skip_memory_metrics`: True
- `use_legacy_prediction_loop`: False
- `push_to_hub`: False
- `resume_from_checkpoint`: None
- `hub_model_id`: None
- `hub_strategy`: every_save
- `hub_private_repo`: None
- `hub_always_push`: False
- `gradient_checkpointing`: False
- `gradient_checkpointing_kwargs`: None
- `include_inputs_for_metrics`: False
- `include_for_metrics`: []
- `eval_do_concat_batches`: True
- `fp16_backend`: auto
- `push_to_hub_model_id`: None
- `push_to_hub_organization`: None
- `mp_parameters`:
- `auto_find_batch_size`: False
- `full_determinism`: False
- `torchdynamo`: None
- `ray_scope`: last
- `ddp_timeout`: 1800
- `torch_compile`: False
- `torch_compile_backend`: None
- `torch_compile_mode`: None
- `dispatch_batches`: None
- `split_batches`: None
- `include_tokens_per_second`: False
- `include_num_input_tokens_seen`: False
- `neftune_noise_alpha`: None
- `optim_target_modules`: None
- `batch_eval_metrics`: False
- `eval_on_start`: False
- `use_liger_kernel`: False
- `eval_use_gather_object`: False
- `average_tokens_across_devices`: False
- `prompts`: None
- `batch_sampler`: no_duplicates
- `multi_dataset_batch_sampler`: proportional
</details>
### Training Logs
| Epoch | Step | Training Loss | Validation Loss | ai-pubmed-validation_cosine_accuracy |
|:-----:|:----:|:-------------:|:---------------:|:------------------------------------:|
| -1 | -1 | - | - | 1.0 |
| 0.2 | 100 | 0.0058 | 0.0046 | 1.0 |
| 0.4 | 200 | 0.0051 | 0.0035 | 1.0 |
| 0.6 | 300 | 0.0043 | 0.0031 | 1.0 |
| 0.8 | 400 | 0.0026 | 0.0034 | 1.0 |
| 1.0 | 500 | 0.0048 | 0.0034 | 1.0 |
### Framework Versions
- Python: 3.11.11
- Sentence Transformers: 3.4.1
- Transformers: 4.48.3
- PyTorch: 2.5.1+cu124
- Accelerate: 1.3.0
- Datasets: 3.3.2
- Tokenizers: 0.21.0
## Citation
### BibTeX
#### Sentence Transformers
```bibtex
@inproceedings{reimers-2019-sentence-bert,
title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
author = "Reimers, Nils and Gurevych, Iryna",
booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
month = "11",
year = "2019",
publisher = "Association for Computational Linguistics",
url = "https://arxiv.org/abs/1908.10084",
}
```
#### MultipleNegativesRankingLoss
```bibtex
@misc{henderson2017efficient,
title={Efficient Natural Language Response Suggestion for Smart Reply},
author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
year={2017},
eprint={1705.00652},
archivePrefix={arXiv},
primaryClass={cs.CL}
}
```
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