syedzayyan/paper_mill_benchmark huggingface dataset:
SRY-Box 21 Antisense RNA 1 Knockdown Diminishes Amyloid Beta25-35-Induced Neuronal Damage by miR-132/PI3K/AKT Pathway.

Our study aimed to explore the function and mechanism of action of long noncoding rna (lnc rna) sry-box 21 antisense rna 1 (sox21-as1) in amyloid beta25-35(aβ25-35)-induced neuronal damage.To induce neuronal damage, neuronal cells and differentiated imr-32 neuroblastoma cells were challenged by aβ25-35.Sox21-as1 and mi r-132 quantities were detected by quantitative reverse transcription polymerase chain reaction.Cell damage was evaluated by detecting the changes of cell viability, apoptosis, and oxidative stress.Cell viability was measured using cell counting kit-8.Cell apoptosis was evaluated by flow cytometry and caspase-3 activity.The oxidative stress was analyzed by reactive oxygen species level.The expression of proteins associated with the phosphoinositide 3-kinase (pi3k)/protein kinase b (akt) pathway was examined by western blot.Sox21-as1 abundance was up-regulated in aβ25-35-challenged neuronal cells.Silencing of sox21-as1 attenuated aβ25-35-induced viability reduction and promotion of apoptosis and oxidative stress, suggesting that silencing of sox21-as1 repressed aβ25-35-induced neuronal damage.Mi r-132 quantity was reduced in aβ25-35-challenged neuronal cells, and negatively controlled by sox21-as1.Mi r-132 knockdown abolished the effect of sox21-as1 silencing on aβ25-35-induced neuronal damage, indicating that sox21-as1 controls aβ25-35-induced neuronal damage via regulating mi r-132.The pi3k/akt signaling was repressed in aβ25-35-challenged cells, but this effect was counteracted upon overexpression of mi r-132.In conclusion, sox21-as1 knockdown mitigated aβ25-35-dependent neuronal cell damage by promoting mi r-132/pi3k/akt pathway.

Journal: Neurochemical research (2021)
Publication types: Journal Article
Differentiable Network Pruning via Polarization of Probabilistic Channelwise Soft Masks.

Channel pruning has been demonstrated as a highly effective approach to compress large convolutional neural networks.Existing differentiable channel pruning methods usually use deterministic soft masks to scale the channelwise outputs and explore an appropriate threshold on the masks to remove unimportant channels, which sometimes causes unexpected damage to the network accuracy when there are no sweet spots that clearly separate important channels from redundant ones.In this article, we introduce a new differentiable channel pruning method based on polarization of probabilistic channelwise soft masks (ppsms).We use variational inference to approximate the posterior distributions of the masks and simultaneously exploit a polarization regularization to push the probabilistic masks towards either 0 or 1; thus, the channels with near-zero masks can be safely eliminated with little hurt on network accuracy.Our method significantly relieves the difficulty faced by the existing methods to find an appropriate threshold on the masks.The joint inference and polarization of probabilistic soft masks enable ppsm to yield better pruning results than the state of the arts.For instance, our method prunes 65.91% flops of res net50 on the image net dataset with only 0.7% model accuracy degradation.

Journal: Computational intelligence and neuroscience (2022)
Publication types: Journal Article
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse.

Replication origins, fragile sites, and r dna have been implicated as sources of chromosomal instability.However, the defining genomic features of replication origins and fragile sites are among the least understood elements of eukaryote genomes.Here, we map sites of replication initiation and breakage in primary cells at high resolution.We find that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(d a:d t) tracts flanking the initiation site.Paradoxically, long (>20 bp) (d a:d t) tracts are also preferential sites of polar replication fork stalling and collapse within early-replicating fragile sites (erfss) and late-replicating common fragile sites (cfss) and at the r dna replication fork barrier.Poly(d a:d t) sequences are fragile because long single-strand poly(d a) stretches at the replication fork are unprotected by the replication protein a (rpa).We propose that the evolutionary expansion of poly(d a:d t) tracts in eukaryotic genomes promotes replication initiation, but at the cost of chromosome fragility.

Journal: Cell (2018)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, N.I.H., Intramural;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.
Comparison of sequential organ failure assessment score and cardiac surgery score systems for mortality prediction after emergency acute aortic dissection surgery.

Acute type a aortic dissection (ataad) is one of the most mortal cardiovascular diseases and requires urgent diagnosis and surgery.The patient's clinical findings, complications, and patient's history are closely related to mortality rates.Cardiac surgery score (casus) is a scoring system which is calculated by considering the special pathophysiological conditions of patients undergoing cardiac surgery and predicts post-operative results with high accuracy.Methods following the ethical approval from institutional ethics committee (id: 2021/7/496), the data of consecutive 50 ataad patients who underwent emergent surgery in our hospital between january 1, 2019, and december 31, 2020, were evaluated.The sequential organ failure assessment and casus scores were calculated using the worst values of the daily laboratory and neurological status for both in admission to emergency department and during intensive care unit (icu) follow-up period.The average and the total values of these scores were recorded for pre-operative, post-operative 1st day, and for the categorical data were defined as frequency and percentage.We used the mann-whitney u test for the independent continuous data comparisons and pearson chi-square or fisher exact test for categorical data comparison whole icu period.Continuous data were presented as median and interquartile ranges (25-75th).Results the study comprised 50 patients, the rate of death was 34% (n=17).In total group, there were hypertension 72% (n=36), diabetes mellitus 24% (n=12), initial hemoglobin 12.5 g/d l (10.7-14.1, 25-75th), creatinine 1.09 mg/d l (0.85-1.33, 25-75th), and 72% (n=36) of these patients were male.The casusmean and sofamean scores were higher in the death-group when compared with the group who survived (12.9 [9.5-13.8, 25-75th], 3 [2-5, 25-75th]; 8 [6.1-9.2, 25-75th], 2.6 (2-4.5, 25-75th], p<0.001, respectively].Casusmean was independently associated with the 1-month mortality in model 1 (hr 1.25 [1.14-1.37] (p<0.001).Conclusion according to our results increase in casus mean was the main predictor of 1 month mortality.When casus mean exceeds 8.3 the patient should be followed up more carefully for major adverse events including death.

Journal: Ulusal travma ve acil cerrahi dergisi = Turkish journal of trauma & emergency surgery : TJTES (2022)
Publication types: Journal Article
Group 3 innate lymphoid cells require BATF to regulate gut homeostasis in mice.

Group 3 innate lymphoid cells (ilc3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues.The mechanisms that maintain lineage identity of intestinal ilc3s and ilc3-mediated orchestration of microbiota and mucosal t cell immunity are elusive.Here, we identified batf as a gatekeeper of ilc3 homeostasis in the gut.Depletion of batf in ilc3s resulted in excessive interferon-γ production, dysbiosis, aberrant t cell immune responses, and spontaneous inflammatory bowel disease (ibd), which was considerably ameliorated by the removal of adaptive immunity, interferon-γ blockade, or antibiotic treatment.Mechanistically, batf directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility, and inhibits their expression.Conversely, batf promotes chromatin accessibility of genes involved in mhcii antigen processing and presentation pathways, which in turn directly promotes the transition of precursor ilc3s to mhcii+ ilc3s.Collectively, our findings reveal that batf is a key transcription factor for maintaining ilc3 stability and coordinating ilc3-mediated control of intestinal homeostasis.

Journal: The Journal of experimental medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Anti-inflammatory sesquiterpenoids from the heartwood of Juniperus formosana Hayata.

Juniperus formosana hayata (j.Formosana) is a commom needlebush cultivar growing in china.Six new compounds (1-6), including four cadinene sesquiterpenoids (1-4), one abietane diterpenoid (5), and one β-naphthol derivative (6), along with 18 known compounds (7-24) were isolated and identified through phytochemical investigation on the heartwood of j.Formosana.The structures of these compounds were fully elucidated by their 1d and 2d nmr, hr-esi-ms, uv, and ir spectral data analyses.The absolute configurations of compounds 1, 3, and 5 were confirmed by experimental and calculated electronic circular dichroism (ecd) data.Moreover, x-ray crystallographic analysis was carried out to characterize the structure of compound 4.The inhibitory effects on the nitric oxide (no) production of all the isolated compounds were initially examined in raw264.7 macrophages induced by lipopolysaccharide (lps).The results showed that compounds 3 and 12 possessed significant inhibitory potency on no generation with ic50values of 3.41 μm and 6.15 μm among the new and known compounds, respectively.The expressions of il-1β, il-6, and tnf-α were measured in lps-stimulated raw264.7 cells to evaluate the anti-inflammatory effects of compounds 1-24.Compounds 1-6 and 9-12 exhibited potent anti-inflammatory effects.Additionally, the expressions of p38, erk, and iκbα proteins were further determined to explore the anti-inflammatory mechanism of the most potent compounds 3 and 12.Overall, our findings indicate the potential of j.Formosana for developing medicine candidates as the treatments of inflammation.

Journal: Fitoterapia (2022)
Publication types: Journal Article
Faecal microbiota transplantation-mediated jejunal microbiota changes halt high-fat diet-induced obesity in mice via retarding intestinal fat absorption.

Faecal microbiota transplantation (fmt) is considered as a promising technology to fight against obesity.Wild boar has leanermuscle and less fat in comparison to the domestic pig, which were thought to be related with microbiota.To investigate the function and mechanism of the wild boar microbiota on obesity, we first analysed the wild boar microbiota composition via 16s r dna sequencing, which showed that firmicutes and proteobacteria were the dominant bacteria.Then, we established a high-fat diet (hfd)-induced obesity model, and transfer low and high concentrations of wild boar faecal suspension in mice for 9 weeks.The results showed that fmt prevented hfd-induced obesity and lipid metabolism disorders, and altered the jejunal microbiota composition especially increasing the abundance of the lactobacillus and romboutsia, which were negatively correlated with obesity-related indicators.Moreover, we found that the anti-obesity effect of wild boar faecal suspension was associated with jejunal n6-methyladenosine (m6a) levels.Overall, these results suggest that fmt has a mitigating effect on hfd-induced obesity, which may be due to the impressive effects of fmt on the microbial composition and structure of the jejunum.These changes further alter intestinal lipid metabolism and m6a levels to achieve resistance to obesity.

Journal: Microbial biotechnology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Sweep imaging with Fourier transform as a tool with MRI for evaluating the effect of teriparatide on cortical bone formation in an ovariectomized rat model.

Teriparatide (tptd) is a drug for osteoporosis that promotes bone formation and improves bone quality.However, the effects of tptd on cortical bone are not well understood.Sweep imaging with fourier transform (swift) has been reported as a useful tool for evaluating bound water of cortical bone, but it has yet to be used to investigate the effects of tptd on cortical bone.This study aimed to evaluate the consequences of the effect of tptd on cortical bone formation using swift.Methods twelve-week-old female sprague-dawley rats (n = 36) were reared after ovariectomy to create a postmenopausal osteoporosis model.They were divided into two groups: the tptd and non-tptd groups.Rats were euthanized at 4, 12, and 24 weeks after initiating tptd treatment.Tibial bones were evaluated using magnetic resonance imaging (mri) and bone histomorphometry.In mri, proton density-weighted imaging (pdwi) and swift imaging were performed.The signal-to-noise ratio (snr) was calculated for each method.The same area evaluated by mri was then used to calculate the bone formation rate by bone histomorphometry.Measurements were compared using the mann-whitney u-test, and a p-value of < 0.05 was considered significant.Results pdwi-snr was not significantly different between the two groups at any time point (p = 0.589, 0.394, and 0.394 at 4, 12, and 24 weeks, respectively).Contrarily, swift-snr was significantly higher in the tptd group than in the non-tptd group at 4 weeks after initiating treatment, but it was not significantly different at 12 and 24 weeks (p = 0.009, 0.937, and 0.818 at 4, 12, and 24 weeks, respectively).The bone formation rate assessed by histomorphometry was significantly higher in the tptd group than in the non-tptd group at all timepoints (p < 0.05, all weeks).In particular, at 4 weeks, the bone formation rate was markedly higher in the tptd group than in the non-tptd group (p = 0.028, 1.98 ± 0.33 vs.0.09 ± 0.05 μm3/μm2/day).Conclusions swift could detect increased signals of bound water, reflecting the effect of tptd on the cortical bone.The signal detected by swift reflects a marked increase in the cortical bone formation rate.

Journal: BMC musculoskeletal disorders (2022)
Publication types: Journal Article
Multi-objective evaluation of freshly distilled brandy: Characterisation and distribution patterns of key odour-active compounds.

The characterisation and distribution patterns of key odour-active compounds in head, heart1, heart2, tail, and stillage cuts of freshly distilled brandy were investigated by gas chromatography-olfactometry-mass spectrometry coupled with aroma extract dilution analysis (aeda) and chemometrics analysis.Results from aeda showed that there were 50, 61, 48, 25, and 18 odour-active compounds in the head, heart1, heart2, tail, and stillage cuts, respectively.Besides, 19, 22, 11, 5, and 4 quantified compounds with odour activity values ≥ 1, respectively, were considered to be potential contributors to the aroma profile of different distillation cuts.Especially, the chemometrics analysis illustrated the heart1 fraction was characterized by 3-methylbutanol, ethyl hexanoate, 1-hexanol, ethyl octanoate, benzaldehyde, ethyl decanoate, and 2-phenylethyl acetate; (e)-hex-3-en-1-ol, (z)-hex-3-en-1-ol, and 2-phenylethyl acetate greatly contributed to the characteristics of the heart2 cut.Furthermore, different volatile compounds with a variety of boiling points and solubilities followed diverse distillation rules during the second distillation.Our findings may provide a rational basis for concentrating more pleasant aroma components contributing to brandy.

Journal: Food chemistry: X (2022)
Publication types: Journal Article
Pars Plana Vitrectomy with and without Supplemental Scleral Buckle for the Repair of Rhegmatogenous Retinal Detachment: A Meta-analysis.

Topic it is unclear whether there are differences in safety and efficacy between pars plana vitrectomy (ppv) alone and ppv with a supplemental scleral buckle (sb; ppv-sb) for the treatment of rhegmatogenous retinal detachment.Clinical relevance this meta-analysis aimed to compare the safety and efficacy of these surgical procedures.Methods in this meta-analysis, ovid medline, embase, and cochrane library were systematically searched (january 2000-june 2021).The primary outcome was the final best corrected visual acuity (bcva), whereas the secondary outcomes were reattachment rates and complications.The risk of bias was assessed using the cochrane risk-of-bias tool for randomized controlled trials (rcts) and the risk of bias in nonrandomized studies of interventions tool for nonrandomized studies.Results this study included 15 661 eyes from 38 studies (32 observational studies and 6 rcts).The median follow-up duration was 6 months.The final bcva was similar between ppv and ppv-sb (weighted mean difference [wmd], -0.03 logarithm of the minimum angle of resolution [-0.14 to 0.07]; p = 0.55).There was a significant difference in the single-operation success rate (sosr) (88.2% versus 86.3%; relative risk [rr], 0.97 [0.95-1.00]; p = 0.03), favoring ppv-sb; however, there was no significant difference in the final reattachment rate (rr, 1.00 [0.99-1.01]; p = 0.56).Pars plana vitrectomy required a significantly higher number of operations to achieve final anatomical reattachment (wmd, 0.13 [0.02-0.24]; p = 0.02).In terms of complications, ppv was significantly less likely to be associated with macular edema (rr, 0.47 [0.25-0.88]; p = 0.02) and epiretinal membrane formation (rr, 0.70 [0.52-0.94]; p = 0.02), but these differences were no longer significant in studies published after 2010 or in rcts.Significant proliferative vitreoretinopathy, lens status, and macular attachment status did not mediate differences in these effects.Conclusions there were no significant differences in the final visual acuity outcomes between ppv and ppv-sb.Pars plana vitrectomy with supplemental sb was associated with a greater sosr than standalone ppv, although the magnitude of the effect was small, with a high number needed to treat.The final reattachment rate was similar.In recent studies and in rcts, the risk of complications was similar between the procedures.

Journal: Ophthalmology. Retina (2022)
Publication types: Journal Article;Meta-Analysis;Review;Systematic Review
Safety and practicality of high dose inhaled nitric oxide in emergency department COVID-19 patients.

Inhaled nitric oxide (i no) is a selective pulmonary vasodilator and mild bronchodilator that has been shown to improve systemic oxygenation, but has rarely been administered in the emergency department (ed).In addition to its favorable pulmonary vascular effects, in-vitro studies report that no donors can inhibit replication of viruses, including sars coronavirus 2 (sars-co v-2).This study evaluated the administration of high-dose i no by mask in spontaneously breathing emergency department (ed) patients with respiratory symptoms attributed to coronavirus disease 2019 (covid-19).Methods we designed a randomized clinical trial to determine whether 30 min of high dose i no (250 ppm) could be safely and practically administered by emergency physicians in the ed to spontaneously-breathing patients with respiratory symptoms attributed to covid-19.Our secondary goal was to learn if i no could prevent the progression of mild covid-19 to a more severe state.Findings we enrolled 47 ed patients with acute respiratory symptoms most likely due to covid-19: 25 of 47 (53%) were randomized to the i no treatment group; 22 of 47 (46%) to the control group (supportive care only).All patients tolerated the administration of high-dose i no in the ed without significant complications or symptoms.Five patients receiving i no (16%) experienced asymptomatic methemoglobinemia (met hb) > 5%.Thirty-four of 47 (72%) subjects tested positive for sars-co v-2: 19 of 34 were randomized to the i no treatment group and 15 of 34 subjects to the control group.Seven of 19 (38%) i no patients returned to the ed, while 4 of 15 (27%) control patients did.One patient in each study arm was hospitalized: 5% in i no treatment and 7% in controls.One patient was intubated in the i no group.No patients in either group died.The differences between these groups were not significant.Conclusion a single dose of i no at 250 ppm was practical and not associated with any significant adverse effects when administered in the ed by emergency physicians.Local disease control led to early study closure and prevented complete testing of covid-19 safety and treatment outcomes measures.

Journal: The American journal of emergency medicine (2022)
Publication types: Journal Article;Randomized Controlled Trial
The clinical, molecular, and therapeutic features of patients with IL10/IL10R deficiency: a systematic review.

Interleukin10 (il10) and il10 receptor (il10r) deficiencies are monogenic inborn errors of immunity (iei) causing early-onset inflammatory bowel diseases (ibd).In this report, we systematically reviewed articles that included related keywords using pub med, web of science, and scopus databases.The articles were screened for eligibility criteria before data extraction.We assessed 286 patients (44.5% female) with il10 and/or il10r deficiencies who were predominantly from china (40.7%), italy (13.9%), and south korea (8.5%).The median age of onset was 1.0 (0.3-4.0) months with a median age of genetic diagnosis at 16.0 (7.4-81.0) months.Consanguinity was reported in all evaluable patients with il10 deficiency and in 38.2% of patients with il10r deficiency (22.9% of patients with il10ra, and 79.4% of patients with il10rb deficiency).The most prevalent mutations in il10ra were c.301c>t (p.r101w) and c.537g>a (p.t179t), those in il10rb were c.139a>g (p.k47e) and c.611g>a (p.w204x).Auto-inflammation and enteropathy were present in all cases.The first presentation of both groups was protracted diarrhea (45.7%), bloody diarrhea (17.8%), and colitis (15.5%).Patients with il10r deficiency had a high frequency of dermatologic manifestations (50.5%) and failure to thrive (60.5%), while il10-deficient patients lacked those complications.In the majority of patients, the basic immunologic parameters were in normal ranges.Of the entire publications, 30.7% underwent hemopoietic stem cell transplantation, 57.5% surgery, and 86.6% immunosuppressive treatment.The 10-year survival rate was higher in patients with il10 deficiency than in patients with il10r deficiency.In conclusion, il10/il10r deficiency predominantly presents with treatment-resistant, early-onset ibd within the first months of life.We detected no clear correlation between the phenotype of patients carrying the same variant.The high prevalence of distinct clinical manifestations reported in il10ra- and il10rb-deficient patients might be attributable to the interactions between the target tissue and cytokines other than il10 capable of binding to il10rb.These results gain translational significance by contributing to earlier diagnosis, adequate therapy, and avoiding delay in the diagnosis and unfavorable outcomes.

Journal: Clinical and experimental immunology (2022)
Publication types: Journal Article;Systematic Review;Research Support, Non-U.S. Gov't