syedzayyan/paper_mill_benchmark huggingface dataset:
Assessment of the hepatocyte protective effects of gypenoside and its phosphorylated derivative against DHAV-1 infection on duck embryonic hepatocytes.

Duck viral hepatitis (dvh) is an acute disease of young ducklings with no effective veterinary drugs for treatment.Gynostemma pentaphyllum is a well-known traditional chinese medicine that plays an important role in the treatment of various diseases.Gypenoside (gp), one of the main ingredients of gynostemma pentaphyllum, was reported with good hepatoprotective effects.However, its low solubility limits its application in the clinics.To improve its solubility and bioactivity, a phosphorylated derivative of gypenoside (p gp) was prepared by the sodium trimetaphosphate-sodium tripolyphosphate (stmp-stpp) method.An infrared spectroscopy method was applied to analyse the structures of gp and p gp.Then, a methyl thiazolyl tetrazolium (mtt) colorimetric assay was applied to study the hepatocyte protective efficacy of these two drugs against duck hepatitis a virus type 1 (dhav-1) infection, and q pcr, tunel labelling and flow cytometry methods were used to study the relevant hepatocyte protective in vitro.Results the infrared spectroscopy detection results showed that the phosphorylation modification of gp was successful.The mtt colorimetric assay results showed that both gp and p gp possessed good hepatocyte protective efficacy in vitro, and p gp performed better than gp when the drug was added before or after virus inoculation.Furthermore, the q pcr results revealed that both drugs could effectively inhibit the adsorption (when adding gp and p gp pre-virus inoculation), replication and release of dhav-1, and the viral inhibition rate of p gp was greater than that of gp.The subsequent tunel labelling and flow cytometry assays showed that both gp and p gp could significantly inhibit duck embryo hepatocyte apoptosis induced by dhav-1, and the inhibition effect of p gp was much stronger than that of gp.Conclusions gp exerts good hepatocyte protective efficacy not only by inhibiting the proliferation of dhav-1 but also by inhibiting duck embryonic hepatocyte apoptosis induced by dhav-1, and phosphorylation modification significantly improves the antiviral and the anti-apoptotic effects of gp.Therefore, p gp has the potential to be developed into a novel drug against dhav-1 infection.

Journal: BMC veterinary research (2019)
Publication types: Journal Article
The DarTG toxin-antitoxin system provides phage defence by ADP-ribosylating viral DNA.

Toxin-antitoxin (ta) systems are broadly distributed, yet poorly conserved, genetic elements whose biological functions are unclear and controversial.Some ta systems may provide bacteria with immunity to infection by their ubiquitous viral predators, bacteriophages.To identify such ta systems, we searched bioinformatically for those frequently encoded near known phage defence genes in bacterial genomes.This search identified homologues of dar tg, a recently discovered family of ta systems whose biological functions and natural activating conditions were unclear.Representatives from two different subfamilies, dar tg1 and dar tg2, strongly protected e.Coli mg1655 against different phages.We demonstrate that for each system, infection with either rb69 or t5 phage, respectively, triggers release of the dar t toxin, a dna adp-ribosyltransferase, that then modifies viral dna and prevents replication, thereby blocking the production of mature virions.Further, we isolated phages that have evolved to overcome dar tg defence either through mutations to their dna polymerase or to an anti-dar t factor, gp61.2, encoded by many t-even phages.Collectively, our results indicate that phage defence may be a common function for ta systems and reveal the mechanism by which dar tg systems inhibit phage infection.

Journal: Nature microbiology (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Partial Reconstruction of Uterus Cervix in Rat by Decellularized Human Uterine Cervical Scaffold Combined with Adipose-Derived Stem Cells (ADSCs).

Surgical management for cervical malformation remains as the main therapeutic challenge for gynecologists.A theoretical alternative is to generate a bioengineered uterus cervix, which requires scaffold structure and appropriate cellular constituents.Here, human uterine cervical tissue was decellularized with detergents to produce an acellular scaffold that retained extracellular matrix (ecm), characterized through histochemical studies and dna assessments.Recellularized scaffold was then established by decellularized scaffold reseeding with adipose-derived stem cells (adscs) isolated from rats.We tested these bioengineering samples in a rat model of partial cervical defect and found that recellularized scaffold improved regeneration abilities of the uterine cervix, promoted better vascularization, and achieved positive pregnancy outcomes.These results suggest that decellularized human uterine cervical scaffold combined with adscs could be used for uterine cervical regeneration and provide insights into treatments for cervical malformation.

Journal: Journal of immunology research (2022)
Publication types: Journal Article
Vocabulary Repetition Following Multisensory Instruction Is Ineffective on L2 Sentence Comprehension: Evidence From the N400.

Putting the principles of multisensory teaching into practice, this study investigated the effect of audio-visual vocabulary repetition on l2 sentence comprehension.Forty participants were randomly assigned to experimental and control groups.A sensory-based model of instruction (i.e., emotioncy) was used to teach a list of unfamiliar vocabularies to the two groups.Following the instruction, the experimental group repeated the instructed words twice, while the control group received no vocabulary repetition.Afterward, their electrophysiological neural activities were recorded through electroencephalography while doing a sentence acceptability judgment task with 216 sentences under acceptable (correct) and unacceptable (pragmatically violated) conditions.A one-way analysis of variance (anova), a multivariate analysis of variance (manova), and a bayesian repeated-measures anova were used to compare the behavioral and neurocognitive responses [n400 as the main language-related event-related brain potential (erp) effect] of the two groups.The results showed no significant n400 amplitude difference in favor of any of the groups.The findings corroborated the ineffectiveness of two repetitions preceded by multisensory instruction on l2 sentence comprehension.

Journal: Frontiers in psychology (2022)
Publication types: Journal Article
AK003290 Protects Myocardial Cells Against Apoptosis and Promotes Cardiac Function Recovery Via miR-539-3p/ErbB4Axis in Ischemic-Reperfusion Injury.

Acute myocardial infarction is the leading cause of death and disability worldwide.Reperfusion is the main treatment method.However, ischemia-reperfusion (i/r) injury aggravates tissue and cell damage.In this study, we aim to find a strategy to reduce i/r injury and promote cardiac function recovery.The expression of ak003290 was downregulated in i/r injury bothin vitroandin vivo.Overexpression of ak003290 reduced infarction area, oxidative stress, cell apoptosis, and promoted cardiac function recovery.Ak003290 was observed to sponge mi r-539-3p.Moreover, the expression of mi r-539-3p was upregulated in i/r injury.Overexpression of mi r-539-3p reversed the beneficial role of ak003290 in i/r injury.The target gene of mi r-539-3p was proved to be erb b4, as identified by database prediction, dual-luciferase reporter assay, and pull-down assay.The expression of erb b4was negatively correlated with the expression of mi r-539-3p, but positively correlated with the expression of ak003290.Subsequently, the key downstream proteins were determined.Ak003290 promoted p-akt and bcl-2 expression and inhibited p-erk1/2, bax, cytoplasmic cyto-c, and c-caspase-3 expression.The application of erb b4si rna significantly reversed the effect of ak003290 on the expression of these proteins.These results suggest that erb b4is the key downstream gene, which regulates myocardial cell apoptosis by influencing the mi r-539-3p expression.To the best of knowledge, this study is the first to demonstrate that the ak003290/mi r-539-3p/erb b4axis regulates myocardial cell apoptosis.These findings provide a potential novel target for the treatment of myocardial i/r injury.

Journal: DNA and cell biology (2021)
Publication types: Journal Article
All body region injuries are not equal: Differences in pediatric discharge functional status based on Abbreviated Injury Scale (AIS) body regions and severity scores.

Functional outcomes have been proposed for assessing quality of pediatric trauma care.Outcomes assessments often rely on abbreviated injury scale (ais) severity scores to adjust for injury characteristics, but the relationship between ais severity and functional impairment is unknown.This study's primary aim was to quantify functional impairment associated with increasing ais severity scores within body regions.The secondary aim was to assess differences in impairment between body regions based on ais severity.Methods children with serious (ais≥ 3) isolated body region injuries enrolled in a multicenter prospective study were analyzed.The primary outcome was functional status at discharge measured using the functional status scale (fss).Discharge fss was compared (1) within each body region across increasing ais severity scores, and (2) between body regions for injuries with matching ais scores.Results the study included 266 children, with 16% having abnormal fss at discharge.Worse fss was associated with increasing ais severity only for spine injuries.Abnormal fss was observed in a greater proportion of head injury patients with a severely impaired initial glasgow coma scale (gcs) (gcs< 9) compared to those with a higher gcs score (43% versus 9%; p < 0.01).Patients with ais 3 extremity and severe head injuries had a higher proportion of abnormal fss at discharge than ais 3 abdomen or non-severe head injuries.Conclusions ais severity does not account for variability in discharge functional impairment within or between body regions.Benchmarking based on functional status assessment requires clinical factors in addition to ais severity for appropriate risk adjustment.Level of evidence 1 (prognostic and epidemiological).

Journal: Journal of pediatric surgery (2022)
Publication types: Journal Article;Multicenter Study
Overexpression of YOD1 Promotes the Migration of Human Oral Keratinocytes by Enhancing TGF-β3 Signaling.

To investigate the effects of yod1 overexpression on the proliferation and migration of human oral keratinocytes (hoks), and to clarify whether the mechanisms involve transforming growth factor-β (tgf-β) signaling.Methods hoks were transfected with the plasmid p egfp-n3-yod1 containing yod1.The m rna levels of yod1 and tgf-β were determined by q pcr.The protein expressions of yod1, tgf-β, smad2/3, smad4, and phospho-smad2/3 were determined by western blotting.Cell proliferation and migration were evaluated by cell counting kit-8 assay and wound healing assay, respectively.Results the m rna and protein levels of yod1 were higher in hoks transfected with yod1.Yod1 overexpression significantly enhanced the migration of hoks.The m rna and protein levels of tgf-β3 were increased by yod1 overexpression.Hoks transfected with yod1 exhibited increased phospho-smad2/3 levels.Conclusion yod1 overexpression enhances cell migration by promoting tgf-β3 signaling which may play an important role in lip and palate formation.Yod1 mutation may contribute to aberrant tgf-β3 signaling associated with decreased cell migration resulting in nsclp.

Journal: Biomedical and environmental sciences : BES (2018)
Publication types: Journal Article
Transcranial direct current stimulation treatment in chronic after-stroke dysphagia: A clinical case.

Transcranial direct current stimulation (t dcs) is a non-invasive neuromodulation technique that has shown positive effects in a variety of motor diseases including dysphagia.However, its clinical application and underlying microstructural effects are still being researched.We tested whether t dcs applied together with swallowing training could benefit a treatment-resistent patient with dysphagia after a stroke.Method the clinical case was a 64 year old male who suffered from a left medial cerebellum stroke lesion leading to severe dysphagia.The treatment consisted of a traditional swallowing rehabilitation treatment, which served as a baseline measure, followed by an intervention adding t dcs (anodal/left m1/16 sessions/20 min/1m a).The variables measured were (1) clinical symptoms of dysphagia, (2) quality of life and (3) microstructural changes with magnetic resonance imaging (mri) and diffusion tensor imaging (dti).Results results showed (1) a slight reduction of the clinical symptoms, (2) an improvement in the quality of life domains of communication, fatigue and sleep and (3) an enhancement of the connectivity and increase of the number of fibers of the injured left medium cerebellum peduncle.Conclusions these results support the use of t dcs as a coadjuvant neurorehabilitation tool in cases which are resistant to traditional motor rehabilitation.

Journal: Psicothema (2019)
Publication types: Case Reports;Journal Article
Host-derived bacillus spp. as probiotic additives for improved growth performance in broilers.

In recent years, the utilization of antibiotics in animal feed has been restricted, probiotics have been increasingly used to replace antibiotics in maintaining animal health.The aim of this study was to screen and evaluate probiotics with excellent probiotic potential from the gut of healthy goslings for clinical application.Thirteen strains of bacillus (named ah-g201 to ah-g2013), including 2 strains of bacillus subtilis (b.Subtilis), 6 strains of bacillus licheniformis (b.Licheniformis) and 5 strains of bacillus amyloliquefaciens (b.Amyloliquefaciens), were isolated and identified.Then, acid and bile salts tolerance tests were performed to screen probiotics strains that could survive under different environments.The effects of screened probiotics on the growth of pathogenic escherichia coli (e.Coli) and salmonella were assessed.Furthermore, we performed the drug resistance tests and safety tests in animals.The results showed that b.Subtilis ah-g201, b.Licheniformis ah-g202 and ah-g204 exhibited higher gastrointestinal resistance under in vitro conditions, and showed a moderate level of resistance to the tested antibiotics.Importantly, ah-g201 and ah-g202 showed 24 to 60% inhibition rate against pathogenic e.Coli and salmonella.Moreover, the safety analysis of ah-g201 and ah-g202 suggested that the 2 probiotics strains have no adverse effects on body weight gain and feed intake in the broilers, and in addition, they have significantly improved growth performance.Finally, we analyzed effects of b.Subtilis ah-g201and b.Licheniformis ah-g202 on growth performance, immune organ index and the feces microbes of broilers.The results showed that broilers fed with high doses (5 × 109cfu/m l, for single strain) of a mixture of ah-g201 and ah-g202 exhibited good growth performance, and exhibited the greatest gain in spleen weight and the highest lactic acid bacteria counts.These findings indicate that the combined addition of b.Subtilis ah-g201 and b.Licheniformis ah-g202 has the potential to replace antibiotics and to improve the growth performance of broilers.

Journal: Poultry science (2023)
Publication types: Journal Article
Novel dichloromethane-fermenting bacteria in the Peptococcaceae family.

Dichloromethane (dcm; ch2cl2) is a toxic groundwater pollutant that also has a detrimental effect on atmospheric ozone levels.As a dense non-aqueous phase liquid, dcm migrates vertically through groundwater to low redox zones, yet information on anaerobic microbial dcm transformation remains scarce due to a lack of cultured organisms.We report here the characterisation of dcmf, the dominant organism in an anaerobic enrichment culture (dfe) capable of fermenting dcm to the environmentally benign product acetate.Stable carbon isotope experiments demonstrated that the organism assimilated carbon from dcm and bicarbonate via the wood-ljungdahl pathway.Dcmf is the first anaerobic dcm-degrading population also shown to metabolise non-chlorinated substrates.It appears to be a methylotroph utilising the wood-ljungdahl pathway for metabolism of methyl groups from methanol, choline, and glycine betaine.The flux of these substrates from subsurface environments may either directly (dcm, methanol) or indirectly (choline, glycine betaine) affect the climate.Community profiling and cultivation of cohabiting taxa in culture dfe without dcmf suggest that dcmf is the sole organism in this culture responsible for substrate metabolism, while the cohabitants persist via necromass recycling.Genomic and physiological evidence support placement of dcmf in a novel genus within the peptococcaceae family, 'candidatus formimonas warabiya'.

Journal: The ISME journal (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Development of a mathematical model for propagation of ultrasonic waves in thick-walled cylinders in the presence of a thermal gradient - Case of axial scanning.

Investigation of variations in ultrasonic wave velocity and travel path in the presence of thermal gradient is essential for accurate ultrasonic testing of engineering components which are subjected to high temperatures.In this paper, a mathematical model is developed for calculation of the wave velocity and travel path in thick-walled hollow cylinders that are subjected to thermal gradients during axial scanning.The cylinder is assumed to be homogeneous, isotropic, and made from structural steel.The independent variables are incidence angle, cylinder outer radius, and temperature of the cylinder's inner surface.The results obtained from the theoretical model indicate that the wave velocity and travel path are highly sensitive to inner-surface temperature of the cylinder.Moreover, at incidence angles much lower than critical angles (especially at low temperatures), the wave velocity is almost independent of the incidence angle and the travel path is very close to a straight line.However, as the incidence angle approaches one of the critical angles, the wave travel path considerably deviates from a straight line.An experimental setup was designed and built in-house for measuring the longitudinal wave velocity in a steel hollow cylinder in the presence of a thermal gradient.The preliminary experimental results were found to be in good agreement with theoretical results.

Journal: Ultrasonics (2022)
Publication types: Journal Article
Bioresponsive polyplexes - chemically programmed for nucleic acid delivery.

Introduction the whole delivery process of nucleic acids is very challenging.Appropriate carrier systems are needed, which show extracellular stability and intracellular disassembly.Viruses have developed various strategies to meet these requirements, as they are optimized by biological evolution to transfer genetic information into host cells.Taking viruses as models, smart synthetic carriers can be designed, mimicking the efficient delivery process of viral infection.These 'synthetic viruses' are pre-programmed and respond to little differences in their microenvironment, caused by either exogenous or endogenous stimuli.Areas covered this review deals with polymer-based, bioresponsive nanosystems (polyplexes) for the delivery of nucleic acids.Strategies utilizing p h-responsiveness, redox-responsiveness as well as sensitivity towards enzymes will be described more in detail.Systems, which respond to other endogenous triggers (i.e.Reactive oxygen species, adenosine triphosphate, hypoxia), will be briefly illustrated.Moreover, some examples for combined bioresponsiveness will be presented.Expert opinion bioresponsive polyplexes are a smart way to facilitate programmed, timely delivery of nucleic acids to desired, specific sites.Nevertheless, further optimization is necessary to improve the still moderate transfection efficiency and specificity - also in regard to medical translation.For this purpose, precise carrier structures are desirable and stability issues of bioresponsive systems must be considered.

Journal: Expert opinion on drug delivery (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Comparative Metabolomic Studies of Siberian Wildrye (Elymus sibiricusL.): A New Look at the Mechanism of Plant Drought Resistance.

Drought is one of the most important factors affecting plant growth and production due to ongoing global climate change.elymus sibiricushas been widely applied for ecological restoration and reseeding of degraded grassland in the qinghai-tibetan plateau (qtp) because of its strong adaptability to barren, salted, and drought soils.To explore the mechanism of drought resistance in e.Sibiricus, drought-tolerant and drought-sensitive genotypes of e.Sibiricuswere used in metabolomic studies under simulated long-term and short-term drought stress.A total of 1091 metabolites were detected, among which, 27 dms were considered to be the key metabolites for drought resistance of e.Sibiricusin weighted gene co-expression network analysis (wgcna).Ten metabolites, including 3-amino-2-methylpropanoic acid, coniferin, r-aminobutyrate, and so on, and 12 metabolites, including l-proline, l-histidine, n-acetylglycine, and so on, showed differential accumulation patterns under short-term and long-term drought stress, respectively, and thus, could be used as biomarkers for drought-tolerant and drought-sensitive e.Sibiricus.In addition, different metabolic accumulation patterns and different drought response mechanisms were also found in drought-tolerant and drought-sensitive genotypes of e.Sibiricus.Finally, we constructed metabolic pathways and metabolic patterns for the two genotypes.This metabolomic study on the drought stress response of e.Sibiricuscan provide resources and a reference for the breeding of new drought-tolerant cultivars of e.Sibiricus.

Journal: International journal of molecular sciences (2022)
Publication types: Journal Article
Cathodoluminescence of Ultrathin Twisted Ge1-xSnxS van der Waals Nanoribbon Waveguides.

Ultrathin van der waals semiconductors have shown extraordinary optoelectronic and photonic properties.Propagating photonic modes make layered crystal waveguides attractive for photonic circuitry and for studying hybrid light-matter states.Accessing guided modes by conventional optics is challenging due to the limited spatial resolution and poor out-of-plane far-field coupling.Scanning near-field optical microscopy can overcome these issues and can characterize waveguide modes down to a resolution of tens of nanometers, albeit for planar samples or nanostructures with moderate height variations.Electron microscopy provides atomic-scale localization also for more complex geometries, and recent advances have extended the accessible excitations from interband transitions to phonons.Here, bottom-up synthesized layered semiconductor (ge1-x snx s) nanoribbons with an axial twist and deep subwavelength thickness are demonstrated as a platform for realizing waveguide modes, and cathodoluminescence spectroscopy is introduced as a tool to characterize them.Combined experiments and simulations show the excitation of guided modes by the electron beam and their efficient detection via photons emitted in the ribbon plane, which enables the measurement of key properties such as the evanescent field into the vacuum cladding with nanometer resolution.The results identify van der waals waveguides operating in the infrared and highlight an electron-microscopy-based approach for probing complex-shaped nanophotonic structures.

Journal: Advanced materials (Deerfield Beach, Fla.) (2021)
Publication types: Journal Article