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: >-
      Does inhibition of autophagy by 3-MA enhance the effect of 5-FU-induced
      apoptosis in colon cancer cells?
    sentences:
      - >-
        Insulin- and insulin growth factor-1 stimulated signaling through the
        insulin receptor substrate-1 (IRS-1) promotes hepatocellular
        proliferation and survival. IRS-1 over-expression in transgenic (Tg)
        mouse livers caused constitutive activation of Erk mitogen activated
        protein kinase (MAPK) and phosphatidylinositol-3 kinase (PI3K) resulting
        in significantly increased levels of DNA synthesis and larger hepatic
        masses relative to non-transgenic (non-Tg) littermates. However, the
        livers eventually ceased to grow but remained approximately 25% larger
        than non-Tg livers. We hypothesized that this growth homeostasis was
        achieved by parallel activation of pro-apoptosis pathways. Since
        Fas-mediated apoptosis is a common mechanism of hepatocyte destruction,
        we investigated the potential role of Fas receptor as a regulator of
        hepatic mass in IRS-1 transgenic mice. Significantly increased
        Fas-receptor levels were detected in the livers of IRS-1 Tg compared to
        non-Tg mice by Western blot analysis. Functional activation of
        Fas-receptor in IRS-1 Tg livers was demonstrated by increased
        hepatocellular apoptosis caused by intravenous injection of anti-Fas
        (Jo-2).
      - >-
        5-fluorouracil-(5-FU)-based adjuvant chemotherapy is widely used for the
        treatment of colorectal cancer. However, 5-FU resistance in the course
        of treatment has become more common. Therefore, new therapeutic
        strategies and/or new adjuvant drugs still need to be explored. Two
        colon-cancer-derived cell lines, colon26 and HT29, were used to
        investigate the effect of 5-FU, 3-methyladenine (3-MA, an autophagy
        inhibitor), or their combination on apoptotic cell death and autophagy.
        MTT assay, Hochest plus propidium iodide (PI) staining, and DNA
        fragmentation assay were used to observe apoptosis. Meanwhile,
        monodansylcadaverine (MDC) was used to detect autophagy. Finally,
        immunoblotting assay was used to explore the molecular change that
        occurred. We observed the apoptosis induced by 5-FU in colon cancer
        cells. Meanwhile, autophagy was also stimulated. The combination
        treatment of 3-MA and 5-FU significantly increased the apoptotic cell
        death. By isolating the subcellular fractions of mitochondria and
        cytosol, we observed that the release of cytochrome c was increased in
        combination-treated cells. Cytochrome c resulted in the activation of
        caspase-3, thus activating PARP. Moreover, the anti-apoptotic protein,
        Bcl-xL, was significantly downregulated by 3-MA.
      - >-
        To measure the serum highly sensitive C-reactive protein (hs-CRP) and
        adiponectin levels, assess insulin sensitivity index (SI) and acute
        insulin response (AIR) in normal control (NC) subjects, patients with
        impaired glucose tolerance (IGT) and newly diagnosed type 2 diabetes
        mellitus (DM), and further explore the possible correlation between
        hs-CRP and SI, AIR and adiponectin in IGT and newly diagnosed type 2 DM
        groups. Age and sex matched 28 normal subjects, 31 patients with IGT,
        and 31 patients with newly diagnosed type 2 DM were included in the
        study. SI and AIR were assessed by the reduced sample number of
        Bergman's minimal model method with intravenous glucose tolerance test
        in subjects of each group. Compared with NC group, serum hs-CRP was
        significantly increased in IGT and type 2 DM groups (p < 0.001),
        although there was no significant difference between the latter groups.
        Hs-CRP was negatively correlated with high density lipoprotein
        cholesterol (HDL-C), SI and adiponectin levels (p < 0.05 to p < 0.001),
        and positively correlated with systolic blood pressure (SBP), fasting
        plasma glucose (FPG), BMI, waist-to-hip ratio (WHR), postprandial 2h
        plasma glucose (2hPG), fasting serum insulin (FINS) and postprandial
        serum insulin (PSI) in IGT and newly diagnosed type 2 DM groups (p <
        0.05 to p < 0.001). In general multivariate regression, only adiponectin
        was the significantly independent determinant for serum hs-CRP
        (regression coefficient -1.380; 95% CI -2.062 to 0.698, p < 0.001);
        meanwhile, TG, SI, hs-CRP, FINS, 2hPG and WHR were significantly
        independent determinants for serum adiponectin concentration (p < 0.05
        to p < 0.001).
  - source_sentence: >-
      Is myostatin expression altered by insulin deficiency and replacement in
      streptozotocin-diabetic rat skeletal muscles?
    sentences:
      - >-
        Insulin is a major post-prandial muscle-anabolic hormone. A substantial
        loss of skeletal muscle mass occurs in insulin-deprived diabetes and is
        reversed by insulin treatment. Myostatin is a negative regulator of
        muscle mass upregulated in several chronic catabolic conditions. Whether
        myostatin expression is altered in insulin-deprived diabetes is unknown.
        In spite of opposite effects on muscle mass the potential role of basal
        circulating insulin in the regulation of myostatin expression is also
        undetermined. We measured (Northern Blot) myostatin transcript levels in
        muscle groups with different fiber composition in
        streptozotocin-diabetic male rats receiving one of the following
        treatments for eight weeks: (1) control (C); (2) diabetes without
        treatment (DM); (3) diabetes with once-daily slow-acting insulin
        treatment (INS). INS normalized plasma insulin and prevented weight
        reduction observed in DM. In fast-twitch gastrocnemius muscle myostatin
        transcript levels were unchanged (P>0.4) in both DM and INS compared to
        C. Myostatin transcripts were not measurable in any group in slow-twitch
        soleus muscle.
      - >-
        A 'cannot intubate-cannot ventilate' situation requires emergency
        insertion of an infraglottic surgical airway. We present a case of
        postoperative macroglossia requiring emergency insertion of an uncuffed
        percutaneous cricothyroidotomy tube. The supraglottic leak was
        eliminated by the insertion of a laryngeal mask airway with an occluded
        15-mm connector. A 49-yr-old man underwent clipping of a left posterior
        inferior cerebellar artery aneurysm and his tracheal tube was removed
        postoperatively. Two hours later, he became dyspneic and developed
        significant macroglossia. After application of topical anesthesia,
        direct laryngoscopy, oral fibreoptic bronchoscopy and laryngeal mask
        insertion were unsuccessful. The patient became progressively hypoxemic,
        pulseless electrical activity ensued, and cardiopulmonary resuscitation
        was initiated. An uncuffed percutaneous cricothyroidotomy tube was
        inserted. Oxygenation and hemodynamics were restored. As the
        cricothyroidotomy tube was uncuffed, there was a large supraglottic leak
        with manual ventilation. A laryngeal mask airway was inserted and the
        cuff was inflated. The 15-mm connector was occluded by a piece of tape.
        Subsequently, there was no further supraglottic leak with manual
        ventilation. He was taken to operating room and a surgical tracheotomy
        was performed.
      - >-
        Sepsis is an emergency condition with high mortality and morbidity rate.
        There are limited data on the association of cancer as a risk factor for
        mortality in sepsis patients in the emergency department (ED). This
        retrospective study was conducted at the ED, Faculty of Medicine,
        Ramathibodi Hospital, Bangkok, Thailand. The study period was between
        January 1st and December 31st, 2014. The inclusion criteria were as
        follows: adult patients over 15 years of age who presented at the ED
        with suspicion of sepsis, received treatment at the ED, and whose blood
        culture was found to be positive. Clinical data were recorded from
        medical records including the Mortality in Emergency Department Sepsis
        score (MEDS score). The primary outcome of this study was mortality at
        one month. Multivariate logistic regression analysis was used to
        identify independent factors associated with death. During the study
        period, there were 775 eligible patients. The two most common pathogens
        identified from blood cultures were Staphylococcus aureus (193 patients;
        24.9%) and Escherichia coli (158 patients; 20.4%). At one month after
        presenting at the ED, 110 patients (14.2%) had died. There were four
        significant factors for death, having cancer, being on an endotracheal
        tube, initial diagnosis of bacteremia, and high MED scores. Having
        cancer had an adjusted OR of 2.12 (95% CI of 1.29, 3.47).
  - source_sentence: >-
      Is elevated plasma aldosterone an independent risk factor for erectile
      dysfunction in men?
    sentences:
      - >-
        The aims of this study were to demonstrate the tumorigenicity of CD133+
        colon cancer cells in vitro, analyze the correlations between spheroid
        formation and clinicopathologic variables, and screen for overexpressed
        genes in CD133+ colon cancer stem cells. Moreover, the aim of this study
        was to establish a living tumor tissue bank using surgically resected
        specimens. Using LoVo cell line, we isolated CD133+ cells and performed
        clonogenic assay and animal experiment to test tumorigenicity of CD133+
        cells. Twenty-nine surgical samples were freshly collected from 27
        patients who received curative or palliative surgery, and the samples
        were mechanically and enzymatically dissociated into single cells. We
        confirmed the enhanced tumorigenicity of CD133+ cells isolated from LoVo
        cell line both in vitro and in vivo. Of these 29 samples, 8 (28%)
        contained >3% CD133+ cells. Sphere formation was significantly higher in
        samples from patients with lymphatic invasion than in those without
        lymphatic invasion [54.5% (6/11) vs. 12.5% (2/16); P=0.033] and in
        samples containing >3% of CD133+ cells than in those containing ≤3% of
        CD133+ cells [36.4% (4/11) vs. 0% (0/16); P=0.019].
      - "Erectile dysfunction (ED) and cardiovascular disease (CVD) share a great number of common risk factors. There is growing evidence that aldosterone, an independent CVD risk factor, is associated with ED. The purpose of this study was to determine the relationship between plasma aldosterone and erectile dysfunction. This study recruited 287 participants, ranging from 18 to 84\_years old; 217 were suffering from ED, diagnosed by the International Index of Erectile Function 5 (IIEF-5) scores. Based on IIEF-5 scores, patients were divided into one control group and three ED groups (mild ED; moderate ED; severe ED). The differences in principal characteristics, blood routine, sexual hormone, adrenal hormone, thyroid hormone, renal function, liver function and blood lipid were compared between ED and control groups. Our study demonstrated that the difference of mean plasma aldosterone levels between ED group and the control group was statistically significant (P\_<\_0.05). Stepwise logistic regression analysis of all the possible factors support the role of aldosterone as an independent risk factor for ED (OR 1.011; 95\_% CI 1.003-1.018; P\_=\_0.004). Similar statistical methods were applied to the comparison between moderate to severe ED group and control to mild ED group (OR 1.017; 95\_% CI 1.009-1.024; P\_<\_0.001). ROC curve and the area under the curve (0.718; 95\_% CI 0.643-0.794; P\_<\_0.001) were performed to assess the diagnostic effect and to compare the severity of risk with the known independent risk factors, such as age and cholesterol (0.704; 95\_% CI 0.631-0.778; P\_<\_0.001). When using a 374\_pg/mL cut-off value from Youden index, the OR of ED group versus controls is 3.106 (95\_% CI 1.458-6.617), while the OR of moderate to severe ED versus control and mild ED is 5.480 (95\_% CI 3.108-9.662)."
      - >-
        The objective of this study was to examine clinical outcomes and
        recanalization rates in a multicenter cohort of stroke patients
        receiving intravenous tissue plasminogen activator by site of occlusion
        localized with bedside transcranial Doppler. Angiographic studies with
        intraarterial thrombolysis suggest more proximal occlusions carry
        greater thrombus burden and benefit less from local therapy. Using
        validated transcranial Doppler criteria for specific arterial occlusion
        (Thrombolysis in Brain Ischemia flow grades), we compared the rate of
        dramatic recovery (National Institutes of Health Stroke Scale score < or
        =2 at 24 hours) and favorable outcomes at 3 months (modified Rankin
        Scale < or =1) for each occlusion site. We determined the likelihood of
        recanalization at various occlusion sites and its predictors. Then,
        stepwise logistic regression was used to determine predictors of
        complete recanalization. Three hundred thirty-five patients had a mean
        age 69+/-13 years and 48.5% were women (median baseline National
        Institutes of Health Stroke Scale score 16 [range, 3 to 32], mean time
        to transcranial Doppler 140+/-84 minutes, and mean time to intravenous
        tissue plasminogen activator 145+/-68 minutes). Distal middle cerebral
        artery occlusion had an OR of 2 for complete recanalization (50 of 113
        [44.2%], 95% CI: 1.1 to 3.1, P=0.005), proximal middle cerebral artery
        0.7 (49 of 163 [30%], 95% CI: 0.4 to 1.1, P=0.13), terminal internal
        carotid artery 0.1 (one of 17 [5.9%], 95% CI: 0.015 to 0.8, P=0.015),
        tandem cervical internal carotid artery/middle cerebral artery 0.7 (6 of
        22 [27%], 95% CI: 0.3 to 1.9, P=0.5), and basilar artery 0.96 (3 of 10
        [30%], 95% CI: 0.2 to 4, P=0.9). Prerecombinant tissue plasminogen
        activator National Institutes of Health Stroke Scale score, systolic
        blood pressure, glucose, and Thrombolysis in Brain Ischemia flow grade
        at the occlusion site were the negative independent predictors for
        complete recanalization in the final model. There were no associations
        among time to treatment, stroke mechanisms, or recanalization rate.
        Patients with no flow (Thrombolysis in Brain Ischemia 0) at the
        occlusion site had less probability of complete recanalization than
        patients with dampened flow (Thrombolysis in Brain Ischemia 3) (OR(adj):
        0.256, 95% CI: 0.11 to 0.595, P=0.002). Continuous transcranial Doppler
        monitoring (exposure to ultrasound) was a positive predictor for
        complete recanalization (OR(adj): 3.02, 95% CI: 1.396 to 6.514,
        P=0.005). National Institutes of Health Stroke Scale score < or =2 at 24
        hours was achieved in 66 of 305 patients (22%): distal middle cerebral
        artery 33% (35 of 107), tandem cervical internal carotid artery/middle
        cerebral artery 24% (5 of 21), proximal middle cerebral artery 16% (24
        of 155), basilar artery 25% (2 of 8), and none of the patients with
        terminal internal carotid artery had dramatic recovery (0%, n=14;
        P=0.003). Modified Rankin Scale score < or =1 was achieved in 90 of 260
        patients (35%): distal middle cerebral artery 52% (50 of 96), proximal
        middle cerebral artery 25% (33 of 131), tandem cervical internal carotid
        artery/middle cerebral artery 21% (3 of 14), terminal internal carotid
        artery 18% (2 of 11), and basilar artery 25% (2 of 8) (P<0.001).
        Patients with distal middle cerebral artery occlusion were twice as
        likely to have a good long-term outcome as patients with proximal middle
        cerebral artery (OR: 2.1, 95% CI: 1.1 to 4, P=0.025).
  - source_sentence: >-
      Is the Artificial Urinary Sphincter Superior to a Secondary Transobturator
      Male Sling in Cases of a Primary Sling Failure?
    sentences:
      - >-
        We compared continence outcomes in patients with post-prostatectomy
        stress urinary incontinence treated with a salvage artificial urinary
        sphincter vs a secondary transobturator sling. We retrospectively
        reviewed the records of patients undergoing salvage procedures after
        sling failure from 2006 to 2012. Postoperative success was defined as
        the use of 0 or 1 pad, a negative stress test and pad weight less than 8
        gm per day. We performed the Wilcoxon test and used a Cox regression
        model and Kaplan-Meier survival analysis. A total of 61 men presenting
        with sling failure were included in study, of whom 32 went directly to
        an artificial urinary sphincter and 29 received a secondary sling. Of
        the artificial urinary sphincter cohort 47% underwent prior external
        beam radiation therapy vs 17% of the secondary sling cohort (p = 0.01).
        Average preoperative 24 hour pad weight and pad number were higher in
        the artificial urinary sphincter cohort. Median followup in artificial
        urinary sphincter and secondary sling cases was 4.5 (IQR 4-12) and 4
        months (IQR 1-5), respectively. Overall treatment failure was seen in
        55% of patients (16 of 29) with a secondary sling vs 6% (2 of 32) with
        an artificial urinary sphincter (unadjusted HR 7, 95% CI 2-32 and
        adjusted HR 6, 95% CI 1-31).
      - >-
        Subcortical band heterotopia (SBH) is a cortical malformation formed
        when neocortical neurons prematurely stop their migration in the white
        matter, forming a heterotopic band below the normotopic cortex, and is
        generally associated with intractable epilepsy. Although it is clear
        that the band heterotopia and the overlying cortex both contribute to
        creating an abnormal circuit prone to generate epileptic discharges, it
        is less understood which part of this circuitry is the most critical.
        Here, we sought to identify the origin of epileptiform activity in a
        targeted genetic model of SBH in rats. Rats with SBH (Dcx-KD rats) were
        generated by knocking down the Dcx gene using shRNA vectors transfected
        into neocortical progenitors of rat embryos. Origin, spatial extent, and
        laminar profile of bicuculline-induced interictal-like activity on
        neocortical slices were analyzed by using extracellular recordings from
        60-channel microelectrode arrays. Susceptibility to
        pentylenetetrazole-induced seizures was assessed by electrocorticography
        in head-restrained nonanesthetized rats. We show that the band
        heterotopia does not constitute a primary origin for interictal-like
        epileptiform activity in vitro and is dispensable for generating induced
        seizures in vivo. Furthermore, we report that most interictal-like
        discharges originating in the overlying cortex secondarily propagate to
        the band heterotopia. Importantly, we found that in vivo suppression of
        neuronal excitability in SBH does not alter the higher propensity of
        Dcx-KD rats to display seizures.
      - >-
        Cardiac glycosides such as digoxin and their endogenous counterpart
        digoxin-like immunoreactive factor (DLIF) may possess anti-inflammatory
        properties. Pro-inflammatory cytokines from human peripheral blood
        mononuclear cells (PBMC) were measured by ELISA using specific
        antibodies. Immunocytochemistry was used to localize NF-K: B.
        Non-stimulated PBMC constitutively secreted minimum amounts of
        cytokines. LPS (1 mg/L) stimulation lead to steep increases in
        TNF-alpha, IL-6 and IL-8 concentrations with peak rises at 8 h. An 8 h
        delay was observed for IL-10. Increases in IL-10 were sustained for18 h
        period. Significant inhibition (P > 0.05) of TNF-alpha, IL-6 and IL-8 at
        non-toxic of digoxin concentration (< 100 nM) and DLIF (10 nM digoxin
        equivalent (de)) was observed whereas no such effect was seen for IL-10.
        Inhibition of the degradation of activated NF-K: B in the PBMC was
        observed with the indicated concentrations of digoxin, DLIF or
        Pyrrolidine dithiocarbamate (PDTC).
  - source_sentence: >-
      Do transport properties of pancreatic cancer describe gemcitabine delivery
      and response?
    sentences:
      - >-
        Hormone receptor-positive, pre-menopausal breast cancer patients can be
        treated by chemotherapy and/or ovarian suppression therapy. We reported
        our experience of gonadotropin-releasing hormone analogue plus tamoxifen
        (GnRHa+T) or adriamycin and cyclophosphamide (AC) followed by tamoxifen
        (AC-->T) in pre-menopausal women with hormone-response, node-negative
        breast cancer. We retrospectively reviewed the records of 587
        pre-menopausal women with hormone-responsive, node-negative breast
        cancer. Of these, 269 were treated with adriamycin and cyclophosphamide
        (AC) followed by tamoxifen (AC-->T), and 318 were treated with
        gonadotropin-releasing hormone analogue plus tamoxifen (GnRHa+T). Among
        them, 151 patients were treated by goserelin acetate 3.6 mg/kg and 125
        patients were treated by leuprorelin acetate 3.75 mg/kg every 28 days
        subcutaneously. At a median follow-up time of 30 months, eight patients
        had relapsed and three had died. DFS did not differ between the AC-->T
        and GnRHa+T groups. Of the three deaths, two were not related to breast
        cancer. The third patient, in the AC-->T group, died because of brain
        metastasis. GnRHa+T treatment had no effect on blood profile and did not
        cause the development of detrimental symptoms but decreased bone mineral
        density. The efficacy of leuprorelin was similar to that of goserelin.
      - >-
        Atopy and systemic onset juvenile idiopathic arthritis (SoJIA) are two
        potential outcomes of a dysregulated immune system. Although rare, SoJIA
        causes 60% of the morbidity of JIA patients which exhibit a wide
        heterogeneity of prognosis and treatment. Co-morbidities can complicate
        the responses to therapy. To study the influence of co-existing atopy on
        the prognosis of SoJIA. Patients diagnosed with SoJIA between Jan 2006
        and Sep 2010 were screened, enrolled in this prospective cohort study,
        and followed for 2 years. Management of SoJIA patients was assessed by
        ACR Pedi30/50/70 criteria, laboratory variables, and systemic feature
        score. At disease onset, 61 SoJIA patients (34 male and 27 female) were
        enrolled and were divided into SoJIA patients with atopy (n = 27) or
        those without atopy (n = 34). Atopic group at disease onset had
        significantly higher numbers of affected joints, ferritin levels and IgE
        serum levels than the non-atopic group. At 3 and 6 months, fewer SoJIA
        patients with atopy reached the ACR Pedi50 criteria (p < 0.02). During
        the 2 years of follow-up time, the number of infections and the number
        of flares were significantly higher in the SoJIA with atopy group
        (p < 0.01).
      - >-
        The therapeutic resistance of pancreatic ductal adenocarcinoma (PDAC) is
        partly ascribed to ineffective delivery of chemotherapy to cancer cells.
        We hypothesized that physical properties at vascular, extracellular, and
        cellular scales influence delivery of and response to gemcitabine-based
        therapy. We developed a method to measure mass transport properties
        during routine contrast-enhanced CT scans of individual human PDAC
        tumors. Additionally, we evaluated gemcitabine infusion during PDAC
        resection in 12 patients, measuring gemcitabine incorporation into tumor
        DNA and correlating its uptake with human equilibrative nucleoside
        transporter (hENT1) levels, stromal reaction, and CT-derived mass
        transport properties. We also studied associations between CT-derived
        transport properties and clinical outcomes in patients who received
        preoperative gemcitabine-based chemoradiotherapy for resectable PDAC.
        Transport modeling of 176 CT scans illustrated striking differences in
        transport properties between normal pancreas and tumor, with a wide
        array of enhancement profiles. Reflecting the interpatient differences
        in contrast enhancement, resected tumors exhibited dramatic differences
        in gemcitabine DNA incorporation, despite similar intravascular
        pharmacokinetics. Gemcitabine incorporation into tumor DNA was inversely
        related to CT-derived transport parameters and PDAC stromal score, after
        accounting for hENT1 levels. Moreover, stromal score directly correlated
        with CT-derived parameters. Among 110 patients who received preoperative
        gemcitabine-based chemoradiotherapy, CT-derived parameters correlated
        with pathological response and survival.
datasets:
  - subhrajit-mohanty/PubMedQA_instruction_fotmatted
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 pub_med_qa_instruction_fotmatted 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:
- pub_med_qa_instruction_fotmatted

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("sentence_transformers_model_id")
# Run inference
sentences = [
    'Do transport properties of pancreatic cancer describe gemcitabine delivery and response?',
    'The therapeutic resistance of pancreatic ductal adenocarcinoma (PDAC) is partly ascribed to ineffective delivery of chemotherapy to cancer cells. We hypothesized that physical properties at vascular, extracellular, and cellular scales influence delivery of and response to gemcitabine-based therapy. We developed a method to measure mass transport properties during routine contrast-enhanced CT scans of individual human PDAC tumors. Additionally, we evaluated gemcitabine infusion during PDAC resection in 12 patients, measuring gemcitabine incorporation into tumor DNA and correlating its uptake with human equilibrative nucleoside transporter (hENT1) levels, stromal reaction, and CT-derived mass transport properties. We also studied associations between CT-derived transport properties and clinical outcomes in patients who received preoperative gemcitabine-based chemoradiotherapy for resectable PDAC. Transport modeling of 176 CT scans illustrated striking differences in transport properties between normal pancreas and tumor, with a wide array of enhancement profiles. Reflecting the interpatient differences in contrast enhancement, resected tumors exhibited dramatic differences in gemcitabine DNA incorporation, despite similar intravascular pharmacokinetics. Gemcitabine incorporation into tumor DNA was inversely related to CT-derived transport parameters and PDAC stromal score, after accounting for hENT1 levels. Moreover, stromal score directly correlated with CT-derived parameters. Among 110 patients who received preoperative gemcitabine-based chemoradiotherapy, CT-derived parameters correlated with pathological response and survival.',
    'Atopy and systemic onset juvenile idiopathic arthritis (SoJIA) are two potential outcomes of a dysregulated immune system. Although rare, SoJIA causes 60% of the morbidity of JIA patients which exhibit a wide heterogeneity of prognosis and treatment. Co-morbidities can complicate the responses to therapy. To study the influence of co-existing atopy on the prognosis of SoJIA. Patients diagnosed with SoJIA between Jan 2006 and Sep 2010 were screened, enrolled in this prospective cohort study, and followed for 2 years. Management of SoJIA patients was assessed by ACR Pedi30/50/70 criteria, laboratory variables, and systemic feature score. At disease onset, 61 SoJIA patients (34 male and 27 female) were enrolled and were divided into SoJIA patients with atopy (n\u2009=\u200927) or those without atopy (n\u2009=\u200934). Atopic group at disease onset had significantly higher numbers of affected joints, ferritin levels and IgE serum levels than the non-atopic group. At 3 and 6 months, fewer SoJIA patients with atopy reached the ACR Pedi50 criteria (p\u2009<\u20090.02). During the 2 years of follow-up time, the number of infections and the number of flares were significantly higher in the SoJIA with atopy group (p\u2009<\u20090.01).',
]
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

pub_med_qa_instruction_fotmatted

Dataset: pub_med_qa_instruction_fotmatted at 66d9473
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: 12 tokens mean: 26.21 tokens max: 56 tokens	min: 20 tokens mean: 320.41 tokens max: 512 tokens	min: 24 tokens mean: 319.78 tokens max: 512 tokens

Samples:

instruction	context	context_neg
`Do adipose-derived mesenchymal stem cells ameliorate STZ-induced pancreas damage in type 1 diabetes?`	To investigate the possibility of adipose-derived mesenchymal stem cells (ADSC) in the treatment of type 1 diabetes (T1D). ADSC were isolated from the adipotic tissue of abdomen in Sprague-Dawley rats (4-6 week-old,female) and expanded in vitro. Cells were then identified by testing their phenotypes through flow cytometry. Balb/c mice (8 week-old, male) were divided into 3 groups: T1D group, ADSC group and control group. Streptozocin (50 mg/kg·d) were injected intraperitoneally into mice of T1D group and ADSC group for 5 consecutive days to establish the T1D model. In ADSC group, ADSC were injected intravenously on day 3 of STZ injection. In control group, only PBS was injected. Fasting blood glucose (FGB) level was examined once a week. At the end of the 4th week, animals were killed. The pathological changes of islet were showed by histochemistry through hematoxylin-eosin staining (HE staining). β cell insulin expression was detected by quantum dots immunofluorescence histochemistry....	We conducted this pooled analysis to assess the prognostic value of pretreatment Quality of Life (QOL) assessments on overall survival (OS) in advanced non-small cell lung cancer (NSCLC). Four hundred twenty patients with advanced NSCLC (stages IIIB with pleural effusion and IV) from six North Central Cancer Treatment Group trials were included in this study. QOL assessments included the single-item Uniscale (355 patients), Lung Cancer Symptom Scale (217 patients), and Functional Assessment of Cancer Therapy-Lung (197 patients). QOL scores were transformed to a 0 to 100 scale with higher scores representing better status and categorized using the sample median or clinically deficient score (CDS, 50). Cox proportional hazards models stratified by study were used to evaluate the prognostic importance of QOL on OS alone and in the presence of other prognostic factors such as performance status, age, gender, body mass index, and laboratory parameters. Pretreatment QOL access...
`Is prevalence of asthma and allergic diseases in Croatian children increasing : survey study?`	To estimate the prevalence of asthma, allergic rhinitis, and atopic dermatitis among school children in the region of Primorsko-goranska County in Croatia, and compare the results with data from other countries. The study was conducted during the 2001-2002 school year, in complete adherence to the Phase One protocol of the International Study of Asthma and Allergies in Childhood (ISAAC). The target population comprised two age groups (6-7 and 13-14 years) in the region of Primorsko-Goranska County in Croatia. Data were collected using standardized ISAAC written questionnaire and asthma video questionnaire. There were 1,634 participating children in the 6-7 age group (response rate 80.3%) and 2,194 participating children in the 13-14 age group (response rate 89.8%). Estimated 12-month prevalence rates of symptoms were: wheezing 9.7% and 8.4%, allergic rhinitis symptoms 16.9% and 17.5%, allergic rhinoconjunctivitis symptoms 5.6% and 6.7%, and atopic dermatitis symptoms 5.4% and 3.4%, for...	Leaks of the blood-brain barrier can be detected on postcontrast-enhanced T1-weighted MRIs. Although early disruptions of the blood-brain barrier appear to be an important risk factor for tissue plasminogen activator-related hemorrhages in rodents, little is known about their incidence and consequences in human stroke. This is a retrospective analysis of a prospectively collected stroke database over the past 6 years. In 52 patients, multimodal MRI (including diffusion-weighted, perfusion-weighted, and postcontrast-enhanced T1-weighted MRI to detect blood-brain barrier changes) had been performed immediately before systemic thrombolysis and in 48 patients within a median of 30 minutes (interquartile range: 30 to 60 minutes) after recombinant tissue plasminogen activator treatment. The incidence of symptomatic hemorrhage (SICH), defined as any parenchymal hemorrhage leading to deterioration in the patient's clinical condition, was related to several clinical and imaging variables, inclu...
`Does synovial fluid glycosaminoglycan concentration correlate with severity of chondropathy or predict progression of osteoarthritis in a canine cruciate deficiency model?`	Considerable interest exists today in biochemical or immunochemical tests for monitoring the progression of osteoarthritis (OA). It has been suggested that measurements made on synovial fluid (SF) will more accurately reflect the magnitude of cartilage destruction in an index joint than those performed on serum. However, we have shown that the synovitis that occurs in OA affects the rate of protein clearance from the joint. We tested the hypothesis that if adjusted for clearance rate, the SF concentration of cartilage proteoglycans (PG) estimates severity of chondropathy and predicts progression of cartilage damage more accurately than if clearance is not taken into account. Clearance of radioiodinated serum albumin (RISA), a surrogate for the clearance of PG, was measured in 19 adult dogs at baseline and again 16 weeks and 32 weeks after anterior cruciate ligament transection (ACLT). Severity of chondropathy was determined arthroscopically after 16 weeks of instability and at postmort...	Previous research has demonstrated that chronic cigarette smoking and major depressive disorder (MDD) are each associated with cognitive decrements. Further, these conditions co-occur commonly, though mechanisms in the comorbid condition are poorly understood. There may be distinct, additive, or overlapping factors underlying comorbid cigarette smoking and MDD. The present study investigated the impact of smoking and MDD on executive function and emotion processing. Participants (N=198) were grouped by diagnostic category (MDD and healthy controls, HC) and smoking status (ever-smokers, ES and never-smokers, NS). Participants completed the Facial Emotion Perception Test (FEPT), a measure of emotional processing, and the parametric Go/No-go task (PGNG), a measure of executive function. FEPT performance was analyzed using ANCOVA with accuracy and reaction time as separate dependent variables. Repeated measures MANCOVA was conducted for PGNG with performance measure and task level as depen...

Loss: MultipleNegativesRankingLoss with these parameters:

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

Evaluation Dataset

pub_med_qa_instruction_fotmatted

Dataset: pub_med_qa_instruction_fotmatted at 66d9473
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: 26.49 tokens max: 67 tokens	min: 70 tokens mean: 317.54 tokens max: 512 tokens	min: 45 tokens mean: 317.42 tokens max: 512 tokens

Samples:

instruction	context	context_neg
`Is serum 25-hydroxyvitamin D3 related to physical activity and ethnicity but not obesity in a multicultural workforce?`	Recent research suggests that body vitamin D levels are decreased in coronary heart disease and diabetes, but it is unclear which cardiovascular risk factors are related to vitamin D status. To examine the relation between vitamin D status and major cardiovascular risk factors. Serum 25-hydroxyvitamin D3, a marker of recent sun exposure and vitamin D status, was measured in 390 New Zealand residents (95 Pacific Islanders, 74 Maori and 221 others mostly of European descent), who were part of a larger cross-sectional survey of a workforce (n = 5677) aged 40-64 years. Serum 25-hydroxyvitamin D3 levels were significantly lower in Pacific Islanders (mean (SE) = 56 (3) nmol/L; p = 0.0001) and Maoris (68 (3) nmol/L; p = 0.036) compared with Europeans (75 (2) nmol/L) after adjusting for age, sex and time of year. Also adjusting for ethnic group, 25-hydroxyvitamin D3 was higher in people doing vigorous (aerobic) leisure physical activities (71 (2) nmol/L; p = 0.0066) and moderate (non-aerobic) ...	Previous follow-up studies indicate that increased visual cortical, ventral cingulate and subcortical responses of depressed individuals to sad facial stimuli, but not happy stimuli could represent reversible markers of disease severity. We hypothesized that greater responses in these areas to sad stimuli, but not happy stimuli, would predict better subsequent clinical outcome. We also explored areas that would predict a poor outcome. Twelve melancholically depressed individuals in the early stages of antidepressant treatment in a secondary care setting participated in two experiments comparing responses to varying intensities of sad and happy facial stimuli, respectively, using event related functional MRI. They repeated the experiments after a mean delay of 12 weeks of treatment. There was a variation in response to treatment. Greater right visual cortex and right subgenual cingulate (R-BA25) responses to sad stimuli, but not happy stimuli, in the early stages of treatment were assoc...
`Does image subtraction facilitate assessment of volume and density change in ground-glass opacities in chest CT?`	To study the impact of image subtraction of registered images on the detection of change in pulmonary ground-glass nodules identified on chest CT. A cohort of 33 individuals (25 men, 8 women; age range 51-75 years) with 37 focal ground-glass opacities (GGO) were recruited from a lung cancer screening trial. For every participant, 1 to 3 follow-up scans were available (total number of pairs, 84). Pairs of scans of the same nodule were registered nonrigidly and then subtracted to enhance differences in size and density. Four observers rated size and density change of the GGO between pairs of scans by visual comparison alone and with additional availability of a subtraction image and indicated their confidence. An independent experienced chest radiologist served as an arbiter having all reader data, clinical data, and follow-up examinations available. Nodule pairs for which the arbiter could not establish definite progression, regression, or stability were excluded from further evaluation...	Betaine serves as a methyl donor in a reaction converting homocysteine to methionine. It is commonly used for the treatment of hyperhomocysteinemia in humans, which indicates it may be associated with reduced risk of atherosclerosis. However, there have been few data regarding its vascular effect. To investigate the effect of betaine supplementation on atherosclerotic lesion in apolipoprotein (apo) E-deficient mice. Four groups of apoE-deficient mice were fed AIN-93G diets supplemented with 0, 1, 2, or 4 g betaine/100 g diet (no, 1, 2, and 4% betaine, respectively). Wild-type C57BL/6 J mice were fed AIN-93G diet (wild-type). Mice were sacrificed after 0, 7, or 14 weeks of the experimental diets. Atherosclerotic lesion area in the aortic sinus, levels of tumor necrosis factor (TNF)-alpha and monocyte chemoattractant protein (MCP)-1 in aorta and serum, serum lipids, and methylation status of TNF-alpha promoter in aorta were determined. Linear regression analysis showed that the higher do...
`Is overexpression of peptidyl-prolyl isomerase-like 1 associated with the growth of colon cancer cells?`	To discover novel therapeutic targets for colon cancers, we previously surveyed expression patterns among 23,000 genes in colon cancer tissues using a cDNA microarray. Among the genes that were up-regulated in the tumors, we selected for this study peptidyl-prolyl isomerase-like 1 (PPIL1) encoding PPIL1, a cyclophilin-related protein. Western blot analysis and immunohistochemical staining using PPIL1-specific antibody showed that PPIL1 protein was frequently overexpressed in colon cancer cells compared with noncancerous epithelial cells of the colon mucosa. Colony formation assay showed a growth-promoting effect of wild-type PPIL1 on NIH3T3 and HEK293 cells. Consistently, transfection of short-interfering RNA specific to PPIL1 into SNUC4 and SNUC5 cells effectively reduced expression of the gene and retarded growth of the colon cancer cells. We further identified two PPIL1-interacting proteins, SNW1/SKIP (SKI-binding protein) and stathmin. SNW1/SKIP is involved in the regulation of tra...	Protocols call for the start of hormonal therapy with levothyroxine after the declaration of brain death. As the hormonal perturbations occur during the process of brain death, the role of the early initiation of levothyroxine therapy (LT) to salvage organs is not well defined. The aim of this study was to evaluate the impact of early LT (before the declaration of brain death) on the number of solid organs procured per donor. We performed an 8-year retrospective analysis of all trauma patients who progressed to brain death. Patients who consented for organ donation, received LT, and donated solid organs were included. Patients were dichotomized into two groups: early LT group, patients who received LT before the declaration of brain death, and late LT group, those who received LT after brain death. The two groups were compared for differences in demographics, clinical characteristics, need for vasopressor, and number of solid organ donation. A total of 100 solid organ donors were ident...

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	0.0041	0.0031	1.0
0.4	200	0.0023	0.0032	1.0
0.6	300	0.0027	0.0033	1.0
0.8	400	0.007	0.0030	1.0
1.0	500	0.0024	0.0028	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}
}