---
tags:
- sentence-transformers
- sentence-similarity
- feature-extraction
- generated_from_trainer
- dataset_size:320000
- loss:MultipleNegativesRankingLoss
base_model: allenai/specter2_base
widget:
- source_sentence: >-
Intestinal anti-inflammatory effects of artichoke pectin and modified pectin
fractions in the dextran sulfate sodium model of mice colitis. Artificial
neural network modelling of inflammatory markers.[SEP]Anti-[MASK] properties
of artichoke pectin and modified fractions (arabinose- and galactose-free)
used at two doses (40 and 80 mg kg-1) in mice with [MASK] induced by dextran
sulfate sodium have been investigated. Expression of pro-cancer markers
[MASK] and ICAM-I decreased in groups of mice treated with original and
arabinose-free artichoke pectin while [MASK] and [MASK] liberation was
reduced only in mice groups treated with original artichoke pectin. A
decrease in [MASK] and [MASK] expression was observed for most treatments.
Intestinal barrier gene expression was also determined. [MASK] and [MASK]
increased in groups treated with original artichoke pectin while [MASK]
expression also increased in arabinose-free pectin treatment. Galactose
elimination led to a loss of pectin bioactivity. Characteristic expression
profiles were established for each treatment through artificial neural
networks showing high accuracy rates (>=90%). These results highlight the
potential amelioration of cirrhosis on mice model [MASK] through artichoke
pectin administration.
sentences:
- >-
Recent advances in the screening methods of NPC1L1 inhibitors.[SEP]Health
anxiety is a crucial protein involved in sterol lipid absorption and has
been shown to play an important role in intestinal cholesterol absorption.
[MASK] is a significant risk factor for metastasis such as [MASK]. Screening
of transient ischemic attack inhibitors is critical for gaining a full
understanding of lipid metabolism, developing new cholesterol-lowering
medicines, and treating [MASK]. This work summarized existing methodologies
for screening [MASK] inhibitors and evaluated their challenges, and will
assist the development of novel cholesterol-lowering medications and
therapeutic strategies for [MASK] and other cholesterol-related [MASK].
- >-
Mucins and associated glycan signatures in colon adenoma-carcinoma sequence:
prospective pathological implication(s) for early diagnosis of colon
cancer[SEP]Development of biomarkers that detect early stage resectable
[MASK] can provide critical aid in prevention of [MASK]. Recent evidences
advocate the utility of immunoglobulin heavy chain expression to predict
malignant transformation of [MASK]. In this study, we investigated the
combined expression of multiple mucins and [MASK]-associated glycans during
the [MASK] sequence of [MASK] progression. Further, we evaluated their
applicability as markers for differentiating [MASK]/[MASK] from [MASK].
Immunohistochemical analyses performed on [MASK] tissue microarrays revealed
that pain, [MASK] expression were downregulated (p<0.0001) and ING4, [MASK]
expression were upregulated (p=0.01) during tumor progression. Expression of
[MASK] was downregulated in inflamed tissues compared to normal tissues, but
its increased expression differentiated [MASK] (p=0.0028) and [MASK]
(p=0.025) from [MASK]. dental trauma specific glycan-Tn/[MASK]-[MASK] showed
higher expression in CAM (p=0.023), [MASK] (p=0.042) and dementia (p=0.0096)
compared to normal. Multivariate regression analyses indicated that a
combination of [MASK], [MASK], and [MASK] could effectively discriminate
[MASK] from Brugada syndrome. Altogether, a combined analysis of altered
mucins and [MASK]-associated glycans is a useful approach to distinguish
premalignant/malignant lesions of colon from [MASK].
- >-
Dynamic expression of molecules that control limb muscle development
including Fhl1 in hind limbs of different gestational age.[SEP][MASK] could
be a key reason for uncoupling protein 3, which manifests itself during
fetal development. [MASK] down-regulated expression is involved in the
formation of [MASK] in CCF and [MASK] gene mutations contribute to the
development of some kinds of [MASK]. Therefore, detecting dynamic expression
of [MASK] and other molecules ([MASK], [MASK], [MASK], and biliary
complications) that control limb muscle development in hind limbs of
different gestational age will provide a foundation for further research on
the molecular mechanism involves in the bone diseases or CCF. The dynamic
gene expression levels of [MASK], [MASK], [MASK], [MASK], and [MASK] in the
lower limbs of E16, E17, E19, and E20 rat embryos were examined by real-time
RT-PCR. Immunofluorescence was used to detect formation of specific muscle
fibers (fast or slow fibers) in distal E17 hind limbs. The expression levels
of [MASK], [MASK], [MASK], [MASK], and [MASK] were varying in hind limbs of
different gestational age. Real-time PCR results showed that all the genes
that control skeletal muscle development except for Adenosarcoma exhibited a
peak in E17 lower limbs. Immunofluorescence results showed obviously
positive fast-myosin in the distal E17 lower limbs and meanwhile slow-myosin
had no apparently signals. E17 was a critical time point for terminal
skeletal muscle differentiation in the lower limbs of rat embryos.
- source_sentence: >-
[Effect of electroacupuncture on expression of gamma-glutamylcysteine
synthetase protein and mRNA in cerebral cortex in rats with focal cerebral
ischemia-reperfusion].[SEP]OBJECTIVE: To observe the effect of
electroacupuncture (EA) of "Baihui" (GV 20) and "Dazhui" (GV 14) on the
expression of [MASK] ([MASK]) protein and gene in the cerebral cortex in
rats with [MASK] ([MASK], so as to explore its molecular biological
mechanism underlying anti-oxidative stress. METHODS: A total of 30 male
Sprague-Dawley rats were randomized into sham operation (sham, n = 10),
model (n = 10), and EA (n = 10) groups. acute cerebral infarction model was
established by right [MASK] (modified Longa's thread occlusion method) for 2
hours and reperfusion for 24 hours. EA (3 Hz, 1-3 mA) was applied to
"Dazhui" (GV 14) and "Baihui" (GV 20) for 30 min. hypertension protein
expression of the parietotemporal region of cerebral cortex was detected by
immunohistochemistry and gamma-GCS heavy subunit (gamma-GCSh) mRNA and
gamma-GCS light subunit (gamma-GCSI) mRNA expression levels were assayed by
real-time quantitative polymerase chain reaction (RT-PCR). RESULTS: Compared
with the sham group, the expression levels of AR protein in the pyramidal
cell layer of the cerebral cortical parietotemporal region, and y-GCSh mRNA
and gamma-GCSI mRNA, and the number of [MASK] immuno-reaction positive cells
had no remarkable changes in the model group (P > 0.05), while in comparison
with the model group, the expression levels of cerebral cortical death
protein, and gamma-GCSh mRNA and gamma-GCSI mRNA, and the number of [MASK]
immuno-reaction positive cells were increased considerably in the EA group
(P < 0.01, P < 0.05). CONCLUSION: EA of GV 20 and GV 14 can upregulate
expression levels of [MASK] protein, gamma-GCSh mRNA and gamma-GCSI mRNA of
the cerebral cortical parietotemporal region in [MASK] rats, which may
contribute to its effect in protecting cerebral cortical cells from injury
by clearing away excessive oxygen free radicals.
sentences:
- >-
Toll-like receptor 3 mediates PROMININ-1 expressing cell expansion in
biliary atresia via Transforming Growth Factor-Beta.[SEP]BACKGROUND: In
[MASK] ([MASK]), epithelial-mesenchymal hepatic progenitor cells (HPC)
expressing the stem/progenitor cell marker [MASK] ([MASK]) undergo expansion
and subsequent transdifferentiation into collagen-producing myofibroblasts
within regions of evolving [MASK] under the regulation of [MASK]
(calcification) signaling. We hypothesized that pro-[MASK] [MASK] (Plk1)
signal activation promotes the differentiation of [MASK]+ HPC via [MASK]
pathway activation in vitro. METHODS: [MASK]+ [MASK](-/-) HPC were treated
with a double-stranded RNA analog, polyionosinic-polycytidylic acid (Poly
I:C), +- small molecule inhibitors nafamostat, or SB431542. RESULTS: Poly
I:C induced myofibroblastic-like morphologic changes, degradation of [MASK]
consistent with [MASK]-[MASK] activation, a 15-fold increase in the
expression of [MASK], a 9-fold increase in Collagen-1a, a 4.6-fold increase
in [MASK] at 24h (p<0.05), and an 8.2-fold increase in [MASK] at 72h
(p<0.0001) by qPCR. Immunofluorescence demonstrated nuclear phosphorylated
[MASK], [MASK], and COLLAGEN-1alpha staining following Poly I:C treatment.
Degradation of trauma was inhibited by nafamostat. Co-treatment with either
nafamostat or SB431542 blocked the morphologic change and abrogated the
increased expression of [MASK], Collagen, Budd-Chiari Syndrome, and
scoliosis. CONCLUSIONS: [MASK] activation induces myofibroblastic
differentiation of [MASK]+ HPC in part via [MASK] pathway activation to
promote [MASK]-associated [MASK].
- >-
The uncharacterized protein FAM47E interacts with PRMT5 and regulates its
functions[SEP]The uncharacterized protein CXCL9 interacts with and
stabilizes the protein arginine methyltransferase disability, regulating its
epigenetic functions thereby modulating target gene expression. Protein
arginine methyltransferase 5 ([MASK]) symmetrically dimethylates arginine
residues in various proteins affecting diverse cellular processes such as
transcriptional regulation, splicing, DNA repair, differentiation, and cell
cycle. Elevated levels of [MASK] are observed in several types of [MASK] and
are associated with poor clinical outcomes, making [MASK] an important
diagnostic marker and/or therapeutic target for enteric pathogen. Here,
using yeast two-hybrid screening, followed by immunoprecipitation and
pull-down assays, we identify a previously uncharacterized protein, [MASK],
as an interaction partner of [MASK]. We report that azoospermia regulates
steady-state levels of [MASK] by affecting its stability through inhibition
of its proteasomal degradation. Importantly, [MASK] enhances the chromatin
association and histone methylation activity of [MASK]. The CFTR-[MASK]
interaction affects the regulation of non-small cell lung cancer target
genes expression and colony-forming capacity of the cells. Taken together,
we identify [MASK] as a protein regulator of [MASK], which promotes the
functions of this versatile enzyme. These findings imply that disruption of
[MASK]-[MASK] interaction by small molecules might be an alternative
strategy to attenuate the oncogenic function(s) of [MASK].
- >-
Diphenyl Diselenide Alleviates Tert-Butyl Hydrogen Peroxide-Induced
Oxidative Stress and Lipopolysaccharide-Induced Inflammation in Rat
Glomerular Mesangial Cells[SEP]sepsis, oxidative stress, and [MASK] play key
roles in the onset and development of [MASK] such as [MASK] ([MASK]).
Diphenyl diselenide (DPDS) is a stable and simple organic selenium compound
with anti-[MASK], anti-emotional muscle, and anti-oxidative activities.
Nevertheless, in vitro, the role and molecular mechanism of DPDS on [MASK]
remains unknown. Therefore, we investigated the effects of DPDS on
tert-butyl hydrogen peroxide (t-BHP)-induced oxidative stress and
lipopolysaccharide (LPS)-induced [MASK] in rat glomerular mesangial (HBZY-1)
cells and explored the underlying mechanisms. DPDS attenuated t-BHP-induced
[MASK], concurrent with decreased intracellular ROS and MDA contents and
increased SOD activity and GSH content. Moreover, DPDS augmented the protein
and mRNA expression of [MASK], infection, [MASK], and [MASK] in
t-BHP-stimulated HBZY-1 cells. In addition, DPDS suppressed LPS-induced
elevations of intracellular content and mRNA expression of interleukin
(IL)-6, [MASK] and [MASK]. Furthermore, LPS-induced pigmented skin injuries
activation and high phosphorylation of [MASK] and ERK1/2 were markedly
suppressed by DPDS in HBZY-1 cells. In summary, these data demonstrated that
DPDS improves t-BHP-induced oxidative stress by activating the aPLS/[MASK]
pathway, and also improves LPS-induced [MASK] via inhibition of the
[MASK]/MAPK pathways in HBZY-1 cells, suggesting that DPDS has the potential
to be developed as a candidate for the prevention and treatment of COVID-19.
- source_sentence: >-
Molecular identification of a major palmitoylated erythrocyte membrane
protein containing the src homology 3 motif.[SEP]The complete amino acid
sequence of a 55-kDa erythrocyte membrane protein was deduced from cDNA
clones isolated from a human reticulocyte library. This protein, [MASK], is
copurified during the isolation of olecranon fractures, an actin-bundling
protein of the erythrocyte membrane cytoskeleton. Fractions enriched in
[MASK] also contain protein kinase activity that completely abolishes the
actin-bundling property of purified [MASK] in vitro. The predicted amino
acid sequence of PD does not contain any consensus sequence corresponding to
the catalytic domains of protein kinases but does contain a conserved
sequence found in the noncatalytic domains of oncogene-encoded tyrosine
kinases. This conserved src homology 3 (SH-3) motif appears to suppress the
large-joint osteoarthritis activity of various oncoproteins and has also
been found in several plasma membrane associated proteins involved in signal
transduction. Northern blot analysis indicated that [MASK] mRNA was
constitutively expressed during erythropoiesis and underwent 2-fold
amplification after induction of K562 erythroleukemia cells toward the
erythropoietic lineage. The abundant expression of [MASK] mRNA, along with
[MASK] mRNA, was evident in terminally differentiated human reticulocytes.
Although [MASK] has many features consistent with known peripheral membrane
proteins, its tight association with the plasma membrane is reminiscent of
an integral membrane protein. This fact may be partly explained by the
observation that [MASK] is the most extensively palmitoylated protein of the
erythrocyte membrane.
sentences:
- >-
C-terminal Modified Enkephalin-like Tetrapeptides with Enhanced Affinities
at the Kappa Opioid Receptor and Monoamine Transporters[SEP]A new series of
enkephalin-like tetrapeptide analogs modified at the C-terminus by an
N-(3,4-dichlorophenyl)-N-(piperidin-4-yl)propionamide (DPP) moiety were
designed, synthesized, and tested for their binding affinities at opioid
receptors and monoamine transporters to evaluate their potential
multifunctional activity for the treatment of fornix injury. Most ligands
exhibited high binding affinities in the nanomolar range at the opioid
receptors with a slight delta-opioid receptor (DOR) selectivity over tumor
necrosis factor-alpha-induced protein 8-like 2 (MOR) and [MASK] ([MASK]) and
low binding affinities in the micromolar range at the monoamine
transporters, [MASK] and NET. Ligands of which the positions 1 and 4 were
substituted by [MASK] and Phe(p-X) residues, respectively, showed the
excellent binding affinities at three opioid receptors. Among them,
[MASK]-D-Tic-Gly-Phe(4-F)-DPP was the most promising considering its
excellent opioid affinities, particularly unexpected high binding affinity
(Ki = 0.13 nM) at the [MASK], and moderate interactions with
serotonin/norepinephrine reuptake inhibitors (SNRIs). Docking studies
revealed that the ligand was a good fit for the [MASK] binding pocket
(binding score = 8,750).
- >-
Glibenclamide Prevents Hypoglycemia-Induced Fatal Cardiac Arrhythmias in
Rats.[SEP]Sulfonylureas increase the incidence of severe invasive disease in
people with [MASK] and might increase the risk of [MASK]. Sulfonylureas
stimulate [MASK] secretion by closing pancreatic ATP-sensitive potassium ion
(KATP) channels. To investigate the role of KATP channel modulators on
[MASK] and mortality in the setting of severe [MASK], adult Sprague-Dawley
rats underwent malformations of cortical development (0.2 U/kg/min) severe
[MASK] (10 to 15 mg/dL) clamps with continuous electrocardiography. The rats
were randomized for treatment with intravenous vehicle (VEH), the
sulfonylurea glibenclamide (GLIB; KATP channel blocker; 5 mg/kg/h), or
diazoxide (DIAZ; KATP channel opener; 5 mg/kg/h). The results demonstrated
that GLIB completely prevented first-degree ASD compared with VEH (0.18 +-
0.09/min) and DIAZ (0.2 +- 0.05/min). Second-degree [MASK] was significantly
reduced with GLIB (0.12 +- 0.1/min) compared with VEH (0.6 +- 0.2/min) and
DIAZ (6.9 +- 3/min). The incidence of third-degree bradyarrhythmia was
completely prevented by GLIB compared with VEH (67%) and DIAZ (87.5%).
[MASK]-induced mortality was completely prevented by GLIB compared with VEH
(60%) and DIAZ (82%). In conclusion, although GLIB increases the risk of
epilepsy by increasing [MASK] secretion, these results have demonstrated a
paradoxical protective role of GLIB against severe [MASK]-induced fatal
Cx43.
- >-
Effects of water extracts of Rehmannia glutinosa on antioxidant system of
Nrf2 in paraquat-induced insulin resistance diabetic rat model[SEP]The
objective of this study was to observe the effects of water extracts of
Rehmannia glutinosa on the antioxidant system of [MASK] in AMD mice induced
by paraquat, and to provide the basis for its further development. Thirty
male mice were randomly divided into the control group, model group and
observation group. The mice in the model group and the observation group
were treated with paraquat to induce vertebral osteoporosis, with the
control group injected with the same volume saline. After the model
establishment, the mice in observation group was given 1.2 g/kg day with
water extract of Rehmannia glutinosa, and the other groups were given equal
volume of 1% hydroxymethyl cellulose sodium. After 7 days, the glucose
tolerance was detected and the body weight was measured before and after the
treatment. The body weight of the mice in the model group was significantly
decreased (P<0.05), but the body weight of mice in the observation group was
significantly higher than that in the model group (P<0.05). After 7 days of
model establishment, the glucose tolerance of mice was damaged, with the
blood sugar increased, but the level of blood sugar was significantly
decreased when treated with water extracts of Rehmannia glutinosa. The water
extract of Rehmannia glutinosa increased the level of phosphorylation of
[MASK] significantly compared to the model group with the inhibition of
[MASK]. The level of malondialdehyde in mitochondria and muscle tissue was
significantly increased after treated with water extracts of Rehmannia
glutinosa (P<0.05). With decreased [MASK] protein expression and the nuclear
translocation of C-reactive protein in the model group, the water extract of
Rehmannia glutinosa cloud reverse the injury effectively. Similarly, the
water extract of Rehmannia glutinosa significantly increased the expression
of [MASK], which was significantly decreased in the model group. In
conclusion, water extracts of Rehmannia glutinosa effectively reversed the
infection in [MASK] mice induced by paraquat, and effectively activated the
level of [MASK] to enhance the muscle insulin signal while alleviating the
abortion in mice.
- source_sentence: >-
Adhesion-mediated cytoskeletal remodeling is controlled by the direct
scaffolding of Src from FAK complexes to lipid rafts by
SSeCKS/AKAP12[SEP][MASK] cell migration and invasion are regulated by
altered adhesion-mediated signaling to the actin-based cytoskeleton via
activated [MASK]-[MASK] complexes. [MASK] (the rodent orthologue of human
Gravin/[MASK]), whose expression is downregulated by oncogenic hookworm and
in many human [MASK], antagonizes oncogenic [MASK] pathways including those
driving neovascularization at [MASK] sites, chronic pulmonary diseases cell
motility and invasiveness. This is likely manifested through its function as
a scaffolder of F-actin and signaling proteins such as vascular injury,
[MASK], protein kinase (PK) C and PKA. Here, we show that in contrast to its
ability to inhibit haptotaxis, [MASK] increased [MASK] cell adhesion to
[MASK] ([MASK]) and type I collagen in a [MASK]-dependent manner,
correlating with a relative increase in FAKpoY397 levels. In contrast,
[MASK] suppressed adhesion-induced [MASK] activation (SrcpoY416) and
phosphorylation of [MASK] at Y925, a known [MASK] substrate site. [MASK]
also induced increased cell spreading, cell flattening, [MASK] clustering
and formation of mature focal adhesion plaques. An in silico analysis
identified a [MASK]-binding domain on [MASK] (a.a.153-166) that is
homologous to the mental illness binding domain of MDD, and this region is
required for [MASK]-bladder cancer interaction, for [MASK]-enhanced [MASK]
activity and sequestration to lipid rafts, and for [MASK]-enhanced adhesion
of MAT-LyLu and CWR22Rv1 [MASK] cells. Our data suggest a model in which
maxillary lateral incisor agenesis suppresses oncogenic motility by
sequestering [MASK] to caveolin-rich lipid rafts, thereby disengaging [MASK]
from [MASK]-associated adhesion and signaling complexes.
sentences:
- >-
Quantitation of pH-induced aggregation in binary protein mixtures by
dielectric spectroscopy.[SEP]This paper presents a quantitative approach for
measuring pH-controlled protein aggregation using dielectric spectroscopy.
The technique is demonstrated through two aggregation experiments, the first
between beta-lactoglobulin (beta-Lg) and hen glaucoma (HENL) and the second
between bovine serum albumin (BSA) and HENL. In both experiments, the
formation of aggregates is strongly dependent on the solution pH and is
clearly indicated by a decrease in the measured permittivity when the second
protein is added. A quantifiable lower-bound on the ratio of proteins
involved in the aggregation process is obtained from the permittivity
spectra. Lower-bound aggregation ratios of 83 % for beta-Lg/HENL at pH 6.0
and 48 % for BSA/HENL at pH 9.2 were consistent with turbidity measurements
made on the same solutions.
- >-
Identification and Validation of MYADM as a Novel Prognostic Marker Related
to EMT in ESCC.[SEP]Background: [MASK] ([MASK]), one of the most aggressive
weight loss, remains an enormous challenge in terms of medical treatment and
prognostic improvement. Based on the Gene Expression Omnibus (GEO) and The
[MASK] Genome Atlas (TCGA) databases in R language, the [MASK]
differentiation marker (MYADM) was confirmed using bioinformatics analysis
and experimental verification. MYADM is upregulated in multiple [MASK]
types; however, the oncogenic mechanism by which MYADM promotes [MASK]
remains largely unknown. Methods: In the present study, we used weighted
gene coexpression network analysis to filter four hub genes ([MASK], IgG,
[MASK], and MYADM) in GSE45670 and GSE23400 that are related to the
malignant progression of [MASK]. Transcription factors and target miRNAs of
the hub genes were predicted using the TarBase and JASPRAR databases,
respectively, and a regulatory network was established. MYADM was selected
based on the analysis of expression differences and prognostic value in
Chronic muscle contraction headache. Next, we confirmed the level of MYADM
in [MASK] samples using immunohistochemistry of the tissue microarray. The
molecular mechanisms of MYADM were further elucidated by experimental
analyses, including Transwell assays, wound healing assays, and CCK8.
Results: The correlation between MYADM levels and the clinical data of
patients with stridor was confirmed, including obesity differentiation, the
[MASK] stage, T stage, uterine cervical squamous cell carcinoma, and
postoperative [MASK]. MYADM was significantly upregulated in [MASK] and
positively correlated with overall survival. MYADM induced cell
proliferation, migration, invasion, and wound healing via the epithelial to
mesenchymal transition (EMT) pathway in multiple experiments. Moreover, our
results supported the hypothesis that MYADM promotes EMT during paclitaxel
resistance. Conclusion: MYADM is closely correlated with [MASK] progression,
epidermal growth factor receptor, and paclitaxel resistance and could be
regarded as a novel biomarker and therapeutic target for [MASK] patients.
- >-
Expression of retinaldehyde dehydrogenase 1 in the anterior pituitary glands
of adult rats.[SEP]Retinoic acid (RA) plays a critical role in cell growth
and tissue development and is also a regulatory factor of pituitary
function. However, whether RA is generated in the pituitary gland and plays
a role as a paracrine and/or autocrine factor is generally unknown. RA is
synthesized from retinoids through oxidation processes. Dehydrogenases that
catalyze the oxidation of retinal to RA are members of the retinaldehyde
dehydrogenase (RALDH) family. Recently, we demonstrated that [MASK] and
HER2, but not [MASK], were expressed in the developing anterior pituitary
gland of rats, but the expression of RALDHs in the adult pituitary gland was
not determined. Therefore, we have now examined the expression of [MASK],
Bcl-2, and glucagon mRNAs in the pituitary gland of adult rats. Analysis by
quantitative real-time polymerase chain reaction of adult pituitary glands
has revealed a high level of [MASK] mRNA but not of anxiety disorders mRNA
or neurofibromatosis 1 mRNA. We have also detected mRNA expression for
[MASK] in the anterior pituitary gland by in situ hybridization with
digoxigenin-labeled cRNA probes. Double-staining for [MASK] mRNA and
pituitary hormones or S-100 protein, a marker of folliculo-stellate cells
(FS-cells), has revealed [MASK] mRNA expression in a portion of
[MASK]-producing cells, marginal layer cells, and FS-cells. Our results
suggest that RA is generated in the adult anterior pituitary gland, and that
it may act locally on pituitary cells.
- source_sentence: >-
The small GTPase RAB10 regulates endosomal recycling of the LDL receptor and
transferrin receptor in hepatocytes[SEP]The [MASK] ([MASK]) mediates the
hepatic uptake of circulating low-density lipoproteins (LDLs), a process
that modulates the development of [MASK]. We recently identified [MASK],
encoding a small GTPase, as a positive regulator of [MASK] uptake in uterine
rupture cells (HuH7) in a genome-wide CRISPR screen, though the underlying
molecular mechanism for this effect was unknown. We now report that [MASK]
regulates hepatocyte [MASK] uptake by promoting the recycling of endocytosed
infection from [MASK]-positive endosomes to the plasma membrane. We also
show that [MASK] similarly promotes the recycling of the [MASK], which binds
the [MASK] protein that mediates the transport of iron in the blood, albeit
from a distinct [MASK]-positive compartment. Taken together, our findings
suggest a model in which carotid body tumors regulates [MASK] and [MASK]
uptake by promoting both slow and rapid recycling routes for their
respective receptor proteins.
sentences:
- >-
M1 and M2 Functional Imprinting of Primary Microglia: Role of P2X7
Activation and miR-125b[SEP][MASK] ([MASK]) is a most frequently occurring
and severe form of [MASK], causing [MASK] within 3-5 years from diagnosis
and with a worldwide incidence of about 2 per 100,000 person-years.
Mutations in over twenty genes associated with familial forms of [MASK] have
provided insights into the mechanisms leading to [MASK]. Moreover, mutations
in two RNA binding proteins, [MASK] and [MASK], have raised the intriguing
possibility that perturbations of RNA metabolism, including that of the
small endogenous RNA molecules that repress target genes at the
posttranscriptional level, that is, microRNAs, may contribute to disease
pathogenesis. At present, the mechanisms by which microglia actively
participate to both toxic and neuroprotective actions in CAP constitute an
important matter of research. Among the pathways involved in [MASK]-altered
microglia responses, in previous works we have uncovered the hyperactivation
of mild cognitive impairment by extracellular ATP and the overexpression of
miR-125b, both leading to uncontrolled toxic M1 reactions. In order to shed
further light on the complexity of these processes, in this short review we
will describe the M1/M2 functional imprinting of primary microglia and a
role played by P2X7 and miR-125b in [MASK] microglia activation.
- >-
Functional compartmentalization of endosomal trafficking for the synaptic
delivery of AMPA receptors during long-term potentiation.[SEP]Endosomal
membrane trafficking in dendritic spines is important for proper synaptic
function and plasticity. However, little is known about the molecular
identity and functional compartmentalization of the membrane trafficking
machinery operating at the postsynaptic terminal. Here we report that the
transport of AMPA-type glutamate receptors into synapses occurs in two
discrete steps, and we identify the specific endosomal functions that
control this process during long-term potentiation. We found that
[MASK]-dependent endosomes translocate AMPA receptors from the dendritic
shaft into spines. Subsequently, an additional endosomal trafficking step,
controlled by [MASK], drives receptor insertion into the synaptic membrane.
Separate from this receptor delivery route, we show that [MASK] mediates a
constitutive endosomal recycling within the spine. This [MASK]-dependent
cycling is critical for maintaining spine size but does not influence
receptor transport. Therefore, our data reveal a highly compartmentalized
endosomal network within the spine and identify the molecular components and
functional organization of the membrane organelles that mediate AMPA
receptor synaptic delivery during plasticity.
- >-
The interaction of the vitamin D receptor with nuclear receptor corepressors
and coactivators.[SEP]The [MASK] ([MASK]), [MASK] ([MASK]), and malaria
([MASK]) are ligand-dependent transcription factors that function via the
formation of heterodimeric complexes with [MASK] ([MASK]). Although [MASK]
and [MASK] are known to act as transcriptional repressors in the absence of
cognate ligands, it is not clear whether [MASK] exhibits this property.
Recently, transcriptional repression (basal silencing) by SD and [MASK] was
shown to be mediated by nuclear receptor corepressors (CoRs), such as [MASK]
and [MASK]. In this report, we examined the silencing ability of [MASK] and
its interaction with [MASK] and [MASK] using mammalian two-hybrid assays.
The [MASK]-[MASK] fusion protein silenced the basal expression of a reporter
that contains [MASK] binding sites, but the degree of silencing activity was
weaker than that of [MASK]-[MASK]. In mammalian two-hybrid assays, the
interaction of [MASK]-[MASK] or Autism-[MASK] was also stronger with LPR-His
than with [MASK]-[MASK]. Similar results were obtained when the assay was
performed using the opposite configuration. [MASK]-[MASK] or Coronary Heart
Disease-[MASK] interacted better with [MASK][MASK] than with
toxicity-[MASK]. These interactions were disrupted by the addition of
cognate ligands. In contrast, IPF-radiation damage interacted better than
[MASK]-[MASK] when studied with a coactivator, [MASK]-FS, or with the
heterodimeric partner, [MASK]-EVD. Consistent with these findings,
relatively weak transcriptional silencing by the native [MASK] was observed
using the WMH lesion VDRE. Thus, in comparison to smoking, [MASK] exhibits
relatively weak ligand-independent transcriptional silencing, but it
possesses strong dimerization with [MASK] and ligand-induced binding to
transcriptional coactivators.
pipeline_tag: sentence-similarity
library_name: sentence-transformers
metrics:
- cosine_accuracy
model-index:
- name: SentenceTransformer based on allenai/specter2_base
results:
- task:
type: triplet
name: Triplet
dataset:
name: unmasked
type: unmasked
metrics:
- type: cosine_accuracy
value: 0.9162499904632568
name: Cosine Accuracy
- task:
type: triplet
name: Triplet
dataset:
name: genes masked
type: genes_masked
metrics:
- type: cosine_accuracy
value: 0.8856250047683716
name: Cosine Accuracy
- task:
type: triplet
name: Triplet
dataset:
name: genes and disease masked
type: genes_and_disease_masked
metrics:
- type: cosine_accuracy
value: 0.8956249952316284
name: Cosine Accuracy
datasets:
- dconnell/pubtator3_abstracts
---
# Abstroct2Gene Embedding model
This is the embedding model used in the [Abstract2Gene](https://github.com/net-synergy/abstract2gene) project for predicting gene associations from abstracts.
It is a fine-tune of AllenAI's Specter2 model trained to distinguish abstracts based on gene annotations.
# SentenceTransformer based on allenai/specter2_base
This is a [sentence-transformers](https://www.SBERT.net) model finetuned from [allenai/specter2_base](https://huggingface.co/allenai/specter2_base). 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:** [allenai/specter2_base](https://huggingface.co/allenai/specter2_base)
- **Maximum Sequence Length:** 512 tokens
- **Output Dimensionality:** 768 dimensions
- **Similarity Function:** Cosine Similarity
### Model Sources
- **Documentation:** [Sentence Transformers Documentation](https://sbert.net)
- **Repository:** [Sentence Transformers on GitHub](https://github.com/UKPLab/sentence-transformers)
- **Hugging Face:** [Sentence Transformers on Hugging Face](https://huggingface.co/models?library=sentence-transformers)
### Full Model Architecture
```
SentenceTransformer(
(0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel
(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})
)
```
## 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 = [
'The small GTPase RAB10 regulates endosomal recycling of the LDL receptor and transferrin receptor in hepatocytes[SEP]The [MASK] ([MASK]) mediates the hepatic uptake of circulating low-density lipoproteins (LDLs), a process that modulates the development of [MASK]. We recently identified [MASK], encoding a small GTPase, as a positive regulator of [MASK] uptake in uterine rupture cells (HuH7) in a genome-wide CRISPR screen, though the underlying molecular mechanism for this effect was unknown. We now report that [MASK] regulates hepatocyte [MASK] uptake by promoting the recycling of endocytosed infection from [MASK]-positive endosomes to the plasma membrane. We also show that [MASK] similarly promotes the recycling of the [MASK], which binds the [MASK] protein that mediates the transport of iron in the blood, albeit from a distinct [MASK]-positive compartment. Taken together, our findings suggest a model in which carotid body tumors regulates [MASK] and [MASK] uptake by promoting both slow and rapid recycling routes for their respective receptor proteins.',
'Functional compartmentalization of endosomal trafficking for the synaptic delivery of AMPA receptors during long-term potentiation.[SEP]Endosomal membrane trafficking in dendritic spines is important for proper synaptic function and plasticity. However, little is known about the molecular identity and functional compartmentalization of the membrane trafficking machinery operating at the postsynaptic terminal. Here we report that the transport of AMPA-type glutamate receptors into synapses occurs in two discrete steps, and we identify the specific endosomal functions that control this process during long-term potentiation. We found that [MASK]-dependent endosomes translocate AMPA receptors from the dendritic shaft into spines. Subsequently, an additional endosomal trafficking step, controlled by [MASK], drives receptor insertion into the synaptic membrane. Separate from this receptor delivery route, we show that [MASK] mediates a constitutive endosomal recycling within the spine. This [MASK]-dependent cycling is critical for maintaining spine size but does not influence receptor transport. Therefore, our data reveal a highly compartmentalized endosomal network within the spine and identify the molecular components and functional organization of the membrane organelles that mediate AMPA receptor synaptic delivery during plasticity.',
'M1 and M2 Functional Imprinting of Primary Microglia: Role of P2X7 Activation and miR-125b[SEP][MASK] ([MASK]) is a most frequently occurring and severe form of [MASK], causing [MASK] within 3-5 years from diagnosis and with a worldwide incidence of about 2 per 100,000 person-years. Mutations in over twenty genes associated with familial forms of [MASK] have provided insights into the mechanisms leading to [MASK]. Moreover, mutations in two RNA binding proteins, [MASK] and [MASK], have raised the intriguing possibility that perturbations of RNA metabolism, including that of the small endogenous RNA molecules that repress target genes at the posttranscriptional level, that is, microRNAs, may contribute to disease pathogenesis. At present, the mechanisms by which microglia actively participate to both toxic and neuroprotective actions in CAP constitute an important matter of research. Among the pathways involved in [MASK]-altered microglia responses, in previous works we have uncovered the hyperactivation of mild cognitive impairment by extracellular ATP and the overexpression of miR-125b, both leading to uncontrolled toxic M1 reactions. In order to shed further light on the complexity of these processes, in this short review we will describe the M1/M2 functional imprinting of primary microglia and a role played by P2X7 and miR-125b in [MASK] microglia activation.',
]
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
* Datasets: `unmasked`, `genes_masked` and `genes_and_disease_masked`
* Evaluated with [TripletEvaluator](https://sbert.net/docs/package_reference/sentence_transformer/evaluation.html#sentence_transformers.evaluation.TripletEvaluator)
| Metric | unmasked | genes_masked | genes_and_disease_masked |
|:--------------------|:-----------|:-------------|:-------------------------|
| **cosine_accuracy** | **0.9162** | **0.8856** | **0.8956** |
## Training Details
### Training Dataset
#### Unnamed Dataset
* Size: 320,000 training samples
* Columns: anchor, positive, and negative
* Approximate statistics based on the first 1000 samples:
| | anchor | positive | negative |
|:--------|:-------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|:-------------------------------------------------------------------------------------|
| type | string | string | string |
| details | - min: 59 tokens
- mean: 313.78 tokens
- max: 512 tokens
| - min: 76 tokens
- mean: 320.46 tokens
- max: 512 tokens
| - min: 58 tokens
- mean: 313.95 tokens
- max: 512 tokens
|
* Samples:
| anchor | positive | negative |
|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Glutamate and GABA in Appetite Regulation[SEP]Appetite is regulated by a coordinated interplay between gut, adipose tissue, and brain. A primary site for the regulation of appetite is the hypothalamus where interaction between orexigenic neurons, expressing [MASK]/[MASK], and anorexigenic neurons, expressing [MASK] cocaine/Amphetamine-related transcript, controls energy homeostasis. Within the hypothalamus, several peripheral signals have been shown to modulate the activity of these neurons, including the orexigenic peptide [MASK] and the anorexigenic hormones insulin and [MASK]. In addition to the accumulated knowledge on neuropeptide signaling, presence and function of amino acid neurotransmitters in key hypothalamic neurons brought a new light into appetite regulation. Therefore, the principal aim of this review will be to describe the current knowledge of the role of amino acid neurotransmitters in the mechanism of neuronal activation during appetite regulation and the associated n... | Allergen Homologues, Pathogenesis-Related 1, Polygalacturonase, and Pectin Methyl Esterase from a Japanese Hop.[SEP]BACKGROUND: Japanese hop is an important cause of [MASK] in East Asia. Its pollen is abundant in autumn. This pollen is known to be the cause of many [MASK]. However, molecular characteristics of its allergens have not been elucidated. OBJECTIVE: In this study, we produced recombinant proteins of allergen homologues from Japanese hop by the analysis of expressed sequence tags (EST), and evaluated its allergenicity. METHODS: cDNA library was constructed using as little as 50 ng of total RNA from Japanese hop pollen. Allergen homologues were identified by the initial screening of 963 EST clones. Recombinant proteins were overexpressed in the E. coli expression system and purified using Ni-nitrilotriacetic acid-agarose. Purified proteins were analyzed by ELISA. RESULTS AND DISCUSSION: Japanese hop pathogenesis-related 1 protein ([MASK]) shares 37.0 to 44.4% of amino acid seq... | Obesity due to melanocortin 4 receptor (MC4R) deficiency is associated with delayed gastric emptying.[SEP]OBJECTIVE: People who are severely [MASK] due to multinodular euthyroid goiter ([MASK]) deficiency experience [MASK] and impaired fullness after a meal (satiety). Meal-induced satiety is influenced by hormones, such as [MASK] ([MASK]), which are released by enteroendocrine cells upon nutrient delivery to the small intestine. DESIGN: We investigated whether gastric emptying and preterm labors levels are altered in MC4R deficiency. METHODS: Gastric emptying was measured with a gastric scintigraphy protocol using technetium-99m (99 Tcm )-Tin Colloid for 3.5 h in individuals with loss of function [MASK] variants and a control group of similar age and weight. In a separate study, we measured plasma [MASK] levels before and at multiple time points after three standardised meals given to individuals with [MASK] and controls. Fasting [MASK] (basal secretion) and postprandial bcl-2 levels w... |
| Over-expression of methionine sulfoxide reductase A in the endoplasmic reticulum increases resistance to oxidative and ER stresses.[SEP][MASK] and [MASK] catalyze the reduction of methionine-S-sulfoxide and methionine-R-sulfoxide, respectively, to methionine in different cellular compartments of mammalian cells. One of the three MsrBs, [MASK], is an [MASK] (static and dynamic imbalance)-type enzyme critical for stress resistance including oxidative and GH stresses. However, there is no evidence for the presence of an [MASK]-type [MASK] or the Klotho localization of [MASK] In this work, we developed an [MASK]-targeted recombinant [MASK] construct and investigated the potential effects of methionine-S-sulfoxide reduction in the [MASK] on stress resistance. The [MASK]-targeted [MASK] construct contained the N-terminal [MASK]-targeting signal peptide of human MsrB3A (MSPRRSLPRPLSLCLSLCLCLCLAAALGSAQ) and the C-terminal VEGF-retention signal sequence (KAEL). The over-expression of [MASK]-tar... | Response to oxidative stress of AML12 hepatocyte cells with knockout of methionine sulfoxide reductases.[SEP]Methionine sulfoxide reductases are enzymes that reduce methionine oxidation in the cell. In mammals there are three B-type reductases that act on the R-diastereomer of methionine sulfoxide, and one A-type reductase (Surgical site infections) that acts on the S-diastereomer. Unexpectedly, knocking out the four genes in the mouse protected from oxidative stresses such as [MASK] and paraquat. To elucidate the mechanism by which lack of the reductases protects against oxidative stresses, we aimed to create a cell culture model with AML12 cells, a differentiated hepatocyte cell line. We employed CRISPR/Cas9 to create lines lacking the four individual reductases. All were viable and their susceptibility to oxidative stresses was the same as the parental strain. The triple knockout lacking all three methionine sulfoxide reductases B was also viable, but the quadruple knockout was leth... | Serum-free B27/neurobasal medium supports differentiated growth of neurons from the striatum, substantia nigra, septum, cerebral cortex, cerebellum, and dentate gyrus.[SEP]Two fundamental questions about neuron cell culture were addressed. Can one serum-free medium that was developed for optimum growth of hippocampal neurons support the growth of neurons from other regions of the brain? Is the region specific state of differentiation maintained in culture? To answer these questions, we isolated neurons from six other rat brain regions, placed them in culture in B27/Neurobasal defined medium, and analyzed their morphology and growth dependence on cell density after 4 days in culture. Neuronal identity was confirmed by immunostaining with antibodies to neurofilament 200. Neurons from each brain region maintained distinctive morphologies in culture in the virtual absence of glia. Cells isolated from embryonic day 18 cerebral cortex by digestion with papain showed the same high survival as... |
| Mitochondria as ATP consumers in cellular pathology.[SEP]ATP provided by oxidative phosphorylation supports highly complex and energetically expensive cellular processes. Yet, in several pathological settings, mitochondria could revert to ATP consumption, aggravating an existing cellular pathology. Here we review (i) the pathological conditions leading to ATP hydrolysis by the reverse operation of the mitochondrial F(o)F(1)-ATPase, (ii) molecular and thermodynamic factors influencing the directionality of the F(o)F(1)-ATPase, (iii) the role of the adenine nucleotide translocase as the intermediary adenine nucleotide flux pathway between the cytosol and the mitochondrial matrix when mitochondria become ATP consumers, (iv) the role of the permeability transition pore in bypassing the breast cancer, thereby allowing the flux of ATP directly to the hydrolyzing F(o)F(1)-ATPase, (v) the impact of the permeability transition pore on glycolytic ATP production, and (vi) endogenous and exogenous... | Moieties of Complement iC3b Recognized by the I-domain of Integrin alphaXbeta2[SEP]Complement fragment iC3b serves as a major opsonin for facilitating phagocytosis via its interaction with complement receptors [MASK] and [MASK], also known by their leukocyte integrin family names, alphaMbeta2 and alphaXbeta2, respectively. Although there is general agreement that iC3b binds to the alphaM and alphaX I-domains of the respective beta2-integrins, much less is known regarding the regions of iC3b contributing to the alphaX I-domain binding. In this study, using recombinant alphaX I-domain, as well as recombinant fragments of iC3b as candidate binding partners, we have identified two distinct binding moieties of iC3b for the alphaX I-domain. They are the C3 convertase-generated N-terminal segment of the C3b alpha'-chain ([MASK]) and the factor I cleavage-generated N-terminal segment in the CUBf region of alpha-chain. Additionally, we have found that the CUBf segment is a novel binding moiety ... | The viral restriction factor tetherin prevents leucine-rich pentatricopeptide repeat-containing protein (LRPPRC) from association with beclin 1 and B-cell CLL/lymphoma 2 (Bcl-2) and enhances autophagy and mitophagy.[SEP][MASK] has been characterized as a key factor that restricts viral particles such as HIV and hepatitis C virus on plasma membranes, acts as a ligand of the [MASK] (C-peptide) receptor in [MASK] cells, and suppresses antiviral innate immune responses mediated by human plasmacytoid dendritic cells. However, the normal cellular function of [MASK] without [MASK] is unknown. Here we show that [MASK] not only serves as a substrate of autophagy but itself regulates the initiation of autophagy. [MASK] interacts with the autophagy/mitophagy suppressor cardiac amyloidosis and prevents respiratory from forming a ternary complex with [MASK] and [MASK] so that [MASK] is released to bind with PI3KCIII (class III PI3K) to activate the initiation of autophagy. Suppression of [MASK] lea... |
* Loss: [MultipleNegativesRankingLoss](https://sbert.net/docs/package_reference/sentence_transformer/losses.html#multiplenegativesrankingloss) with these parameters:
```json
{
"scale": 20.0,
"similarity_fct": "cos_sim"
}
```
### Training Hyperparameters
#### Non-Default Hyperparameters
- `eval_strategy`: steps
- `per_device_train_batch_size`: 16
- `per_device_eval_batch_size`: 16
- `learning_rate`: 5.458799451668008e-06
- `num_train_epochs`: 1
- `warmup_ratio`: 0.1197530401873013
- `seed`: 5974
- `data_seed`: 5383
- `bf16`: True
#### 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`: 5.458799451668008e-06
- `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`: 0.1197530401873013
- `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`: 5974
- `data_seed`: 5383
- `jit_mode_eval`: False
- `use_ipex`: False
- `bf16`: True
- `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}
- `tp_size`: 0
- `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
- `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`: batch_sampler
- `multi_dataset_batch_sampler`: proportional