metadata

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
            name: Cosine Accuracy

SentenceTransformer based on sentence-transformers/all-distilroberta-v1

This is a sentence-transformers model finetuned from sentence-transformers/all-distilroberta-v1 on the 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
Maximum Sequence Length: 512 tokens
Output Dimensionality: 768 dimensions
Similarity Function: Cosine Similarity
Training Dataset:
- pumed-finetuning

Model Sources

Documentation: Sentence Transformers Documentation
Repository: Sentence Transformers on GitHub
Hugging Face: Sentence Transformers on Hugging Face

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:

pip install -U sentence-transformers

Then you can load this model and run inference.

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]

Evaluation

Metrics

Triplet

Dataset: ai-pubmed-validation
Evaluated with TripletEvaluator

Metric	Value
cosine_accuracy	1.0

Training Details

Training Dataset

pumed-finetuning

Dataset: pumed-finetuning at 02cc2cc
Size: 8,000 training samples
Columns: instruction, context, and context_neg

Approximate statistics based on the first 1000 samples:

	instruction	context	context_neg
type	string	string	string
details	min: 11 tokens mean: 26.36 tokens max: 67 tokens	min: 31 tokens mean: 320.03 tokens max: 512 tokens	min: 82 tokens mean: 321.22 tokens max: 512 tokens

Samples:

instruction	context	context_neg
`Do competency assessment of primary care physicians as part of a peer review program?`	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.	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...
`Is age an important determinant of the growth hormone response to sprint exercise in non-obese young men?`	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 ...	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.
`Is terlipressin more effective in decreasing variceal pressure than portal pressure in cirrhotic patients?`	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...	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...

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "scale": 20.0,
    "similarity_fct": "cos_sim"
}

Evaluation Dataset

pumed-finetuning

Dataset: pumed-finetuning at 02cc2cc
Size: 1,000 evaluation samples
Columns: instruction, context, and context_neg

Approximate statistics based on the first 1000 samples:

	instruction	context	context_neg
type	string	string	string
details	min: 11 tokens mean: 26.08 tokens max: 52 tokens	min: 38 tokens mean: 311.42 tokens max: 512 tokens	min: 45 tokens mean: 316.2 tokens max: 512 tokens

Samples:

instruction	context	context_neg
`Are pre-transplant impedance measures of reflux associated with early allograft injury after lung transplantation?`	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...	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...
`Is predictive accuracy of the TRISS survival statistic improved by a modification that includes admission pH?`	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 ...	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...
`Does exposure to intermittent nociceptive stimulation under pentobarbital anesthesia disrupt spinal cord function in rats?`	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 ...	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...

Loss: MultipleNegativesRankingLoss with these parameters:

{
    "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

Click to expand

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

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

@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

@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}
}