README.md

---
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- dense
- generated_from_trainer
- dataset_size:129971
- loss:MultipleNegativesRankingLoss
base_model: thenlper/gte-small
widget:
- source_sentence: >-
    Integrated health care for infectious diseases and non-communicable diseases
    in low-and middle-income countries
  sentences:
  - >-
    The purposes of this study were to create a new flow-chart of prehospital
    electrocardiography (ECG)-transmission, evaluate its predictive ability for
    ST-elevation myocardial infarction (STEMI) and shorten door-to-balloon time
    (DTBT). The new transmission flow-chart was created using symptoms from
    previous medical records of STEMI patients. A total of 4090 consecutive
    patients transferred emergently to our hospital were divided into two
    groups: those in ambulances with an ECG-transmission device with the new
    flow-chart (ECGT-FC) and those transferred without an ECG-transmission
    device (non-ECGT) groups. A STEMI group comprising walk-in patients during
    the same period was used as a control group. The predictive ability of STEMI
    and the effectiveness of shortening the DTBT by the new flow-chart of
    ECG-transmission was evaluated. In the ECGT-FC group, the prevalence of
    STEMI in the ECG-transmission by the new flow-chart were significantly
    higher than in the non-ECG-transmission patients (6.71% vs. 0.19%; p<0.001).
    The sensitivity and specificity of the new ECG-transmission flow-chart were
    83.3% and 88.1%, respectively. The median DTBT was significantly shortened
    (p=0.045) and the prevalence of DTBT<90min was significantly higher in the
    ECGT-FC group (p=0.018) than the other groups. The sensitivity and
    specificity of the new flow-chart for ECG-transmission were high. The new
    flow-chart combined with an ECG-transmission device could detect STEMI
    efficiently and shorten DTBT.
  - >-
    Multiple strains of the SARS-CoV-2 have arisen and jointly influence the
    trajectory of the coronavirus disease (COVID-19) pandemic. However, current
    models rarely account for this multi-strain dynamics and their different
    transmission rate and response to vaccines. We propose a new mathematical
    model that accounts for two virus variants and the deployment of a
    vaccination program. To demonstrate utility, we applied the model to
    determine the control reproduction number 
  - >-
    The co-occurrence of infectious diseases (ID) and non-communicable diseases
    (NCD) is widespread, presenting health service delivery challenges
    especially in low-and middle-income countries (LMICs). Integrated health
    care is a possible solution but may require a paradigm shift to be
    successfully implemented. This literature review identifies integrated care
    examples among selected ID and NCD dyads. We searched PubMed, PsycINFO,
    Cochrane Library, CINAHL, Web of Science, EMBASE, Global Health Database,
    and selected clinical trials registries. Eligible studies were published
    between 2010 and December 2022, available in English, and report health
    service delivery programs or policies for the selected disease dyads in
    LMICs. We identified 111 studies that met the inclusion criteria, including
    56 on tuberculosis and diabetes integration, 46 on health system adaptations
    to treat COVID-19 and cardiometabolic diseases, and 9 on COVID-19, diabetes,
    and tuberculosis screening. Prior to the COVID-19 pandemic, most studies on
    diabetes-tuberculosis integration focused on clinical service delivery
    screening. By far the most reported health system outcomes across all
    studies related to health service delivery (n = 72), and 19 addressed health
    workforce. Outcomes related to health information systems (n = 5),
    leadership and governance (n = 3), health financing (n = 2), and essential
    medicines (n = 4)) were sparse. Telemedicine service delivery was the most
    common adaptation described in studies on COVID-19 and either
    cardiometabolic diseases or diabetes and tuberculosis. ID-NCD integration is
    being explored by health systems to deal with increasingly complex health
    needs, including comorbidities. High excess mortality from COVID-19
    associated with NCD-related comorbidity prompted calls for more integrated
    ID-NCD surveillance and solutions. Evidence of clinical integration of
    health service delivery and workforce has grown-especially for HIV and
    NCDs-but other health system building blocks, particularly access to
    essential medicines, health financing, and leadership and governance, remain
    in disease silos.
- source_sentence: >-
    Foot-and-mouth disease virus 3C(pro) inhibits interferon-/ response and
    expression of IFN-stimulated genes
  sentences:
  - >-
    Repeated bottleneck passages of RNA viruses result in accumulation of
    mutations and fitness decrease. Here, we show that clones of foot-and-mouth
    disease virus (FMDV) subjected to bottleneck passages, in the form of
    plaque-to-plaque transfers in BHK-21 cells, increased the thermosensitivity
    of the viral clones. By constructing infectious FMDV clones, we have
    identified the amino acid substitution M54I in capsid protein VP1 as one of
    the lesions associated with thermosensitivity. M54I affects processing of
    precursor P1, as evidenced by decreased production of VP1 and accumulation
    of VP1 precursor proteins. The defect is enhanced at high temperatures.
    Residue M54 of VP1 is exposed on the virion surface, and it is close to the
    B-C loop where an antigenic site of FMDV is located. M54 is not in direct
    contact with the VP1-VP3 cleavage site, according to the three-dimensional
    structure of FMDV particles. Models to account for the effect of M54 in
    processing of the FMDV polyprotein are proposed. In addition to revealing a
    distance effect in polyprotein processing, these results underline the
    importance of pursuing at the biochemical level the biological defects that
    arise when viruses are subjected to multiple bottleneck events.
  - >-
    To improve the delivery of liposomes to tumors using P-selectin glycoprotein
    ligand 1 (PSGL1) mediated binding to selectin molecules, which are
    upregulated on tumorassociated endothelium.
  - >-
    Foot-and-mouth disease is a highly contagious viral illness of wild and
    domestic cloven-hoofed animals. The causative agent, foot-and-mouth disease
    virus (FMDV), replicates rapidly, efficiently disseminating within the
    infected host and being passed on to susceptible animals via direct contact
    or the aerosol route. To survive in the host, FMDV has evolved to block the
    host interferon (IFN) response. Previously, we and others demonstrated that
    the leader proteinase (L(pro)) of FMDV is an IFN antagonist. Here, we report
    that another FMDV-encoded proteinase, 3C(pro), also inhibits IFN-α/β
    response and the expression of IFN-stimulated genes. Acting in a proteasome-
    and caspase-independent manner, the 3C(pro) of FMDV proteolytically cleaved
    nuclear transcription factor kappa B (NF-κB) essential modulator (NEMO), a
    bridging adaptor protein essential for activating both NF-κB and
    interferon-regulatory factor signaling pathways. 3C(pro) specifically
    targeted NEMO at the Gln 383 residue, cleaving off the C-terminal zinc
    finger domain from the protein. This cleavage impaired the ability of NEMO
    to activate downstream IFN production and to act as a signaling adaptor of
    the RIG-I/MDA5 pathway. Mutations specifically disrupting the cysteine
    protease activity of 3C(pro) abrogated NEMO cleavage and the inhibition of
    IFN induction. Collectively, our data identify NEMO as a substrate for FMDV
    3C(pro) and reveal a novel mechanism evolved by a picornavirus to counteract
    innate immune signaling.
- source_sentence: Measuring flourishing among adolescent and adult populations
  sentences:
  - >-
    Flourishing is an evolving wellbeing construct and outcome of interest
    across the social and biological sciences. Despite some conceptual
    advancements, there remains limited consensus on how to measure flourishing,
    as well as how to distinguish it from closely related wellbeing constructs,
    such as thriving and life satisfaction. This paper aims to provide an
    overview and comparison of the diverse scales that have been developed to
    measure flourishing among adolescent and adult populations to provide
    recommendations for future studies seeking to use flourishing as an outcome
    in social and biological research.
  - >-
    Although well-being at work is important for occupational health,
    multi-dimensional workplace well-being measures do not exist for Japanese
    workers. The purpose of this study was to investigate the validity of the
    Japanese version of the Workplace PERMA-Profiler. Japanese workers completed
    online surveys at baseline (N = 310) and 1 month later (N = 100). The
    Workplace PERMA-Profiler was translated according to international
    guidelines. Job and life satisfaction, work engagement, psychological
    distress, work-related psychosocial factors, and work performance were
    measured as comparisons for convergent validity. Cronbach's alphas,
    Intra-class Correlation Coefficients (ICCs), and measurement errors were
    calculated for the reliability, and the validity of the measure was tested
    by correlational analyses and confirmatory factor analysis. A total of 310
    (baseline) and 86 (follow-up) workers responded and were included in the
    analyses. Cronbach's alphas and ICCs of the Japanese Workplace
    PERMA-Profiler ranged from 0.75 to 0.96. Confirmatory factor analysis
    indicated that the 5-factor model demonstrated a marginally acceptable fit
    (χ2 (80) = 351.30, CFI = 0.892, TLI = 0.858, RMSEA = 0.105, SRMR = 0.051).
    Overall well-being and the five PERMA domains had moderate-to-strong
    correlations with job satisfaction, psychological distress (inversely), and
    work-related factors. The Japanese version of the Workplace PERMA-Profiler
    demonstrated adequate reliability and validity. This measure could be useful
    to assess well-being at work, promote well-being research among Japanese
    workers, and address the problem of definition for well-being in further
    studies.
  - >-
    We experience countless pieces of new information each day, but remembering
    them later depends on firmly instilling memory storage in the brain.
    Numerous studies have implicated non-rapid eye movement (NREM) sleep in
    consolidating memories via interactions between hippocampus and cortex.
    However, the temporal dynamics of this hippocampal-cortical communication
    and the concomitant neural oscillations during memory reactivations remains
    unclear. To address this issue, the present study used the procedure of
    targeted memory reactivation (TMR) following learning of object-location
    associations to selectively reactivate memories during human NREM sleep.
    Cortical pattern reactivation and hippocampal-cortical coupling were
    measured with intracranial EEG recordings in patients with epilepsy. We
    found that TMR produced variable amounts of memory enhancement across a set
    of object-location associations. Successful TMR increased hippocampal
    ripples and cortical spindles, apparent during two discrete sweeps of
    reactivation. The first reactivation sweep was accompanied by increased
    hippocampal-cortical communication and hippocampal ripple events coupled to
    local cortical activity (cortical ripples and high-frequency broadband
    activity). In contrast, hippocampal-cortical coupling decreased during the
    second sweep, while increased cortical spindle activity indicated continued
    cortical processing to achieve long-term storage. Taken together, our
    findings show how dynamic patterns of item-level reactivation and
    hippocampal-cortical communication support memory enhancement during NREM
    sleep.
- source_sentence: >-
    Agrobacterium tumefaciens Hfq binds to sRNA AbcR1 and its target mRNA
    atu2422
  sentences:
  - >-
    Amyloid β (Aβ) assemblies exist not only in the central nervous system, but
    can circulate within the bloodstream to trigger and exacerbate peripheral,
    cerebrovascular, and neurodegenerative disorders. Eliminating excess
    peripheral Aβ fibrils, therefore, holds promise to improve the management of
    amyloid-related diseases. Here, we present nanoemulsion-mediated ultrasonic
    ablation of circulating Aβ fibrils to both destroy established plaques and
    prevent the re-growth of ablated fragments back into toxic species. This
    approach is made possible using a de novo designed peptide emulsifier that
    contains the self-associating sequence from the amyloid precursor protein.
    Emulsification of the peptide surfactant with fluorous nanodroplets produces
    contrast agents that rapidly adsorb Aβ assemblies and allows their
    ultrasound-controlled destruction via acoustic cavitation. Vessel-mimetic
    flow experiments demonstrate that nanoemulsion-assisted Aβ disruption can be
    achieved in circulation using clinical diagnostic ultrasound transducers.
    Additional cell-based assays confirm the ablated fragments are less toxic to
    neuronal and glial cells compared to mature fibrils, and can be rapidly
    phagocytosed by both peripheral and brain macrophages. These results
    highlight the potential of nanoemulsion contrast agents to deliver new
    imaging enabled strategies for non-invasive management of Aβ-related
    diseases using traditional diagnostic ultrasound modalities.
  - >-
    The Hfq protein mediates gene regulation by small RNAs (sRNAs) in about 50%
    of all bacteria. Depending on the species, phenotypic defects of an hfq
    mutant range from mild to severe. Here, we document that the purified Hfq
    protein of the plant pathogen and natural genetic engineer Agrobacterium
    tumefaciens binds to the previously described sRNA AbcR1 and its target mRNA
    atu2422, which codes for the substrate binding protein of an ABC transporter
    taking up proline and γ-aminobutyric acid (GABA). Several other ABC
    transporter components were overproduced in an hfq mutant compared to their
    levels in the parental strain, suggesting that Hfq plays a major role in
    controlling the uptake systems and metabolic versatility of A. tumefaciens.
    The hfq mutant showed delayed growth, altered cell morphology, and reduced
    motility. Although the DNA-transferring type IV secretion system was
    produced, tumor formation by the mutant strain was attenuated, demonstrating
    an important contribution of Hfq to plant transformation by A. tumefaciens.
  - >-
    Hfq is an RNA-binding protein that functions in post-transcriptional gene
    regulation by mediating interactions between mRNAs and small regulatory RNAs
    (sRNAs). Two proteins encoded by BAB1_1794 and BAB2_0612 are highly
    over-produced in a Brucella abortus hfq mutant compared with the parental
    strain, and recently, expression of orthologues of these proteins in
    Agrobacterium tumefaciens was shown to be regulated by two sRNAs, called
    AbcR1 and AbcR2. Orthologous sRNAs (likewise designated AbcR1 and AbcR2)
    have been identified in B. abortus 2308. In Brucella, abcR1 and abcR2 single
    mutants are not defective in their ability to survive in cultured murine
    macrophages, but an abcR1 abcR2 double mutant exhibits significant
    attenuation in macrophages. Additionally, the abcR1 abcR2 double mutant
    displays significant attenuation in a mouse model of chronic Brucella
    infection. Quantitative proteomics and microarray analyses revealed that the
    AbcR sRNAs predominantly regulate genes predicted to be involved in amino
    acid and polyamine transport and metabolism, and Northern blot analyses
    indicate that the AbcR sRNAs accelerate the degradation of the target mRNAs.
    In an Escherichia coli two-plasmid reporter system, overexpression of either
    AbcR1 or AbcR2 was sufficient for regulation of target mRNAs, indicating
    that the AbcR sRNAs from B. abortus 2308 perform redundant regulatory
    functions.
- source_sentence: >-
    Neural correlates of advice evaluation and integration in the judge-advisor
    paradigm
  sentences:
  - >-
    Considering advice from others is a pervasive element of human social life.
    We used the judge-advisor paradigm to investigate the neural correlates of
    advice evaluation and advice integration by means of functional magnetic
    resonance imaging. Our results demonstrate that evaluating advice recruits
    the "mentalizing network," brain regions activated when people think about
    others' mental states. Important activation differences exist, however,
    depending upon the perceived competence of the advisor. Consistently,
    additional analyses demonstrate that integrating others' advice, i.e., how
    much participants actually adjust their initial estimate, correlates with
    neural activity in the centromedial amygdala in the case of a competent and
    with activity in visual cortex in the case of an incompetent advisor. Taken
    together, our findings, therefore, demonstrate that advice evaluation and
    integration rely on dissociable neural mechanisms and that significant
    differences exist depending upon the advisor's reputation, which suggests
    different modes of processing advice depending upon the perceived competence
    of the advisor.
  - >-
    The role of antibodies in kidney transplant (KT) has evolved significantly
    over the past few decades. This role of antibodies in KT is multifaceted,
    encompassing both the challenges they pose in terms of antibody-mediated
    rejection (AMR) and the opportunities for improving transplant outcomes
    through better detection, prevention, and treatment strategies. As our
    understanding of the immunological mechanisms continues to evolve, so too
    will the approaches to managing and harnessing the power of antibodies in
    KT, ultimately leading to improved patient and graft survival. This
    narrative review explores the multifaceted roles of antibodies in KT,
    including their involvement in rejection mechanisms, advancements in
    desensitization protocols, AMR treatments, and their potential role in
    monitoring and improving graft survival.
  - >-
    Humans regulate intergroup conflict through parochial altruism; they
    self-sacrifice to contribute to in-group welfare and to aggress against
    competing out-groups. Parochial altruism has distinct survival functions,
    and the brain may have evolved to sustain and promote in-group cohesion and
    effectiveness and to ward off threatening out-groups. Here, we have linked
    oxytocin, a neuropeptide produced in the hypothalamus, to the regulation of
    intergroup conflict. In three experiments using double-blind
    placebo-controlled designs, male participants self-administered oxytocin or
    placebo and made decisions with financial consequences to themselves, their
    in-group, and a competing out-group. Results showed that oxytocin drives a
    "tend and defend" response in that it promoted in-group trust and
    cooperation, and defensive, but not offensive, aggression toward competing
    out-groups.
pipeline_tag: sentence-similarity
library_name: sentence-transformers
language:
- en
---

# SentenceTransformer based on thenlper/gte-small

This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [thenlper/gte-small](https://huggingface.co/thenlper/gte-small). It maps sentences & paragraphs to a 384-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:** [thenlper/gte-small](https://huggingface.co/thenlper/gte-small) <!-- at revision 17e1f347d17fe144873b1201da91788898c639cd -->
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 384 dimensions
- **Similarity Function:** Cosine Similarity
<!-- - **Training Dataset:** Unknown -->
<!-- - **Language:** Unknown -->
<!-- - **License:** Unknown -->

### Model Sources

- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)

### Full Model Architecture

```
SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False, 'architecture': 'BertModel'})
  (1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
  (2): Normalize()
)
```

## Usage

### Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

```bash
pip install -U sentence-transformers
```

Then you can load this model and run inference.
```python
from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
    'Neural correlates of advice evaluation and integration in the judge-advisor paradigm',
    'Considering advice from others is a pervasive element of human social life. We used the judge-advisor paradigm to investigate the neural correlates of advice evaluation and advice integration by means of functional magnetic resonance imaging. Our results demonstrate that evaluating advice recruits the "mentalizing network," brain regions activated when people think about others\' mental states. Important activation differences exist, however, depending upon the perceived competence of the advisor. Consistently, additional analyses demonstrate that integrating others\' advice, i.e., how much participants actually adjust their initial estimate, correlates with neural activity in the centromedial amygdala in the case of a competent and with activity in visual cortex in the case of an incompetent advisor. Taken together, our findings, therefore, demonstrate that advice evaluation and integration rely on dissociable neural mechanisms and that significant differences exist depending upon the advisor\'s reputation, which suggests different modes of processing advice depending upon the perceived competence of the advisor.',
    'Humans regulate intergroup conflict through parochial altruism; they self-sacrifice to contribute to in-group welfare and to aggress against competing out-groups. Parochial altruism has distinct survival functions, and the brain may have evolved to sustain and promote in-group cohesion and effectiveness and to ward off threatening out-groups. Here, we have linked oxytocin, a neuropeptide produced in the hypothalamus, to the regulation of intergroup conflict. In three experiments using double-blind placebo-controlled designs, male participants self-administered oxytocin or placebo and made decisions with financial consequences to themselves, their in-group, and a competing out-group. Results showed that oxytocin drives a "tend and defend" response in that it promoted in-group trust and cooperation, and defensive, but not offensive, aggression toward competing out-groups.',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 384]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities)
# tensor([[1.0000, 0.9575, 0.8147],
#         [0.9575, 1.0000, 0.8303],
#         [0.8147, 0.8303, 1.0000]])
```

<!--
### Direct Usage (Transformers)

<details><summary>Click to see the direct usage in Transformers</summary>

</details>
-->

<!--
### Downstream Usage (Sentence Transformers)

You can finetune this model on your own dataset.

<details><summary>Click to expand</summary>

</details>
-->

<!--
### Out-of-Scope Use

*List how the model may foreseeably be misused and address what users ought not to do with the model.*
-->

<!--
## Bias, Risks and Limitations

*What are the known or foreseeable issues stemming from this model? You could also flag here known failure cases or weaknesses of the model.*
-->

<!--
### Recommendations

*What are recommendations with respect to the foreseeable issues? For example, filtering explicit content.*
-->

## Training Details

### Training Dataset

#### Unnamed Dataset

* Size: 129,971 training samples
* Columns: <code>sentence_0</code>, <code>sentence_1</code>, and <code>sentence_2</code>
* Approximate statistics based on the first 1000 samples:
  |         | sentence_0                                                                        | sentence_1                                                                         | sentence_2                                                                           |
  |:--------|:----------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|
  | type    | string                                                                            | string                                                                             | string                                                                               |
  | details | <ul><li>min: 6 tokens</li><li>mean: 19.55 tokens</li><li>max: 56 tokens</li></ul> | <ul><li>min: 3 tokens</li><li>mean: 210.7 tokens</li><li>max: 512 tokens</li></ul> | <ul><li>min: 24 tokens</li><li>mean: 312.31 tokens</li><li>max: 512 tokens</li></ul> |
* Samples:
  | sentence_0                                                                          | sentence_1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | sentence_2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
  |:------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
  | <code>Microbiology and immunomics in male infertility</code>                        | <code>Up to 50% of infertility is caused by the male side. Varicocele, orchitis, prostatitis, oligospermia, asthenospermia, and azoospermia are common causes of impaired male reproductive function and male infertility. In recent years, more and more studies have shown that microorganisms play an increasingly important role in the occurrence of these diseases. This review will discuss the microbiological changes associated with male infertility from the perspective of etiology, and how microorganisms affect the normal function of the male reproductive system through immune mechanisms. Linking male infertility with microbiome and immunomics can help us recognize the immune response under different disease states, providing more targeted immune target therapy for these diseases, and even the possibility of combined immunotherapy and microbial therapy for male infertility.</code> | <code>There are currently no sensitive and specific assays for activin B that could be utilized to study human biological fluids. The aim of this project was to develop and validate a 'total' activin B ELISA for use with human biological fluids and establish concentrations of activin B in the circulation and fluids from the reproductive organs. The new ELISA was validated and then used to measure activin B levels in the circulation of healthy participants, IVF patients, pregnant women and in ovarian follicular fluid and seminal plasma. Healthy adult subjects (n = 143), subjects from an IVF clinic (n = 27) and pregnancy groups (n = 29) were sampled. The sensitivity of the assay was 0.019 ng/ml. Validation of the activin B ELISA showed good recovery (90.7 +/- 9.8%) and linearity in biological fluid and cell culture media and low cross-reactivity with related analytes (inhibin B = 0.077% and activin A = 0.0034%). There was a negative correlation between activin B concentration (r = -0.281, P < ...</code> |
  | <code>Biomarkers of heterogeneity in type 1 diabetes</code>                         | <code>The 'Biomarkers of heterogeneity in type 1 diabetes' study cohort was set up to identify genetic, physiological and psychosocial factors explaining the observed heterogeneity in disease progression and the development of complications in people with long-standing type 1 diabetes (T1D).</code>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | <code>In patients with type 1 diabetes, there has been concern about the effects of recurrent hypoglycaemia and chronic hyperglycaemia on cognitive function. Because other biomedical factors may also increase the risk of cognitive decline, this study examined whether macrovascular risk factors (hypertension, smoking, hypercholesterolaemia, obesity), sub-clinical macrovascular disease (carotid intima-media thickening, coronary calcification) and microvascular complications (retinopathy, nephropathy) were associated with decrements in cognitive function over an extended time period. Type 1 diabetes patients (n = 1,144) who had completed a comprehensive cognitive test battery at entry into the Diabetes Control and Complications Trial were re-assessed at a mean of 18.5 (range: 15-23) years later. Univariate and multivariable models examined the relationship between cognitive change and the presence of micro- and macrovascular complications and risk factors. Univariate modelling showed that smoki...</code> |
  | <code>Role of Molecular Profiling and Subgroups in Pediatric Medulloblastoma</code> | <code>As advances in the molecular and genetic profiling of pediatric medulloblastoma evolve, associations with prognosis and treatment are found (prognostic and predictive biomarkers) and research is directed at molecular therapies. Medulloblastoma typically affects young patients, where the implications of any treatment on the developing brain must be carefully considered. The aim of this article is to provide a clear comprehensible update on the role molecular profiling and subgroups in pediatric medulloblastoma as it is likely to contribute significantly toward prognostication. Knowledge of this classification is of particular interest because there are new molecular therapies targeting the Shh subgroup of medulloblastomas. </code>                                                                                                                                                | <code>The Wnt/beta-catenin pathway plays important roles during embryonic development and growth control. The B56 regulatory subunit of protein phosphatase 2A (PP2A) has been implicated as a regulator of this pathway. However, this has not been investigated by loss-of-function analyses. Here we report loss-of-function analysis of PP2A:B56epsilon during early Xenopus embryogenesis. We provide direct evidence that PP2A:B56epsilon is required for Wnt/beta-catenin signaling upstream of Dishevelled and downstream of the Wnt ligand. We show that maternal PP2A:B56epsilon function is required for dorsal development, and PP2A:B56epsilon function is required later for the expression of the Wnt target gene engrailed, for subsequent midbrain-hindbrain boundary formation, and for closure of the neural tube. These data demonstrate a positive role for PP2A:B56epsilon in the Wnt pathway.</code>                                                                                                                              |
* Loss: [<code>MultipleNegativesRankingLoss</code>](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
  ```json
  {
      "scale": 20.0,
      "similarity_fct": "cos_sim"
  }
  ```

### Training Hyperparameters
#### Non-Default Hyperparameters

- `per_device_train_batch_size`: 32
- `per_device_eval_batch_size`: 32
- `num_train_epochs`: 1
- `max_steps`: 20
- `multi_dataset_batch_sampler`: round_robin

#### All Hyperparameters
<details><summary>Click to expand</summary>

- `overwrite_output_dir`: False
- `do_predict`: False
- `eval_strategy`: no
- `prediction_loss_only`: True
- `per_device_train_batch_size`: 32
- `per_device_eval_batch_size`: 32
- `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`: 5e-05
- `weight_decay`: 0.0
- `adam_beta1`: 0.9
- `adam_beta2`: 0.999
- `adam_epsilon`: 1e-08
- `max_grad_norm`: 1
- `num_train_epochs`: 1
- `max_steps`: 20
- `lr_scheduler_type`: linear
- `lr_scheduler_kwargs`: {}
- `warmup_ratio`: 0.0
- `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
- `hub_revision`: None
- `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
- `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
- `liger_kernel_config`: None
- `eval_use_gather_object`: False
- `average_tokens_across_devices`: False
- `prompts`: None
- `batch_sampler`: batch_sampler
- `multi_dataset_batch_sampler`: round_robin
- `router_mapping`: {}
- `learning_rate_mapping`: {}

</details>

### Framework Versions
- Python: 3.10.14
- Sentence Transformers: 5.0.0
- Transformers: 4.53.2
- PyTorch: 2.6.0+cu124
- Accelerate: 1.6.0
- Datasets: 3.6.0
- Tokenizers: 0.21.1

## Citation

### BibTeX

#### Sentence Transformers
```bibtex
@inproceedings{reimers-2019-sentence-bert,
    title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
    author = "Reimers, Nils and Gurevych, Iryna",
    booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
    month = "11",
    year = "2019",
    publisher = "Association for Computational Linguistics",
    url = "https://arxiv.org/abs/1908.10084",
}
```

#### MultipleNegativesRankingLoss
```bibtex
@misc{henderson2017efficient,
    title={Efficient Natural Language Response Suggestion for Smart Reply},
    author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
    year={2017},
    eprint={1705.00652},
    archivePrefix={arXiv},
    primaryClass={cs.CL}
}
```

#### If our work was helpful consider citing us ☺️
```bibtext
@misc{sinha2025bicaeffectivebiomedicaldense,
      title={BiCA: Effective Biomedical Dense Retrieval with Citation-Aware Hard Negatives}, 
      author={Aarush Sinha and Pavan Kumar S and Roshan Balaji and Nirav Pravinbhai Bhatt},
      year={2025},
      eprint={2511.08029},
      archivePrefix={arXiv},
      primaryClass={cs.IR},
      url={https://arxiv.org/abs/2511.08029}, 
}
```

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