syedzayyan/paper_mill_benchmark huggingface dataset:
Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines.

Coronaviruses, members of the coronavirinae subfamily in the coronaviridae family, are enveloped and positive-stranded rna viruses that infect animals and humans, causing intestinal and respiratory infections.Coronavirus disease 2019 (covid-19) is caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (sars-co v-2).This disease appeared, for the first time (december 2019), in china and has spread quickly worldwide causing a large number of deaths.Considering the global threat, the world health organization (who) has declared, in march 2020, covid-19 as a pandemic.Many studies suggest the great effect of the existing vaccines to protect against symptomatic cases of death by the covid-19 virus.This paper, proposes to compare the main antigenic proteins sequences of the existing vaccines with spike (s) protein of the sars-co v-2 genome.Our choice of s protein is justified by the major role that plays it in the receptor recognition and membrane fusion process based on an intelligent system.Herein, we focus on finding a correlation between s protein and compulsory vaccines in the countries that have a less death number by covid-19 virus.In this work, we have used a combination of coding methods, signal processing, and bioinformatic techniques with the goal to localize the similar patterns between the s gene of the sars-cov-2 genome and 14 investigated vaccines.Results a total of 8 similar sequences which have a size more than 6 amino acids were identified.Further, these comparisons propose that these segments can be implicated in the immune response against covid-19, which may explain the wide variation by country in the severity of this viral threat.Conclusions our in silico study suggests a possible protective effect of poliovirus, hib, hepatitis b, pcv10, measles, mumps, and rubella (mmr) vaccines against covid-19.

Journal: Beni-Suef University journal of basic and applied sciences (2022)
Publication types: Journal Article
Types of Community Support Services and Self-Efficacy for Continuous Community Living among Individuals with Disabilities and Caregivers.

This study explored the impacts of five types of community support services (i.e., center-based care, home-based care, respite care, caregiver assistance, and financial subsidies) on self-efficacy for continuous community living among individuals with disabilities and caregivers.Design cross-sectional.Method the sample consisted of a group of individuals with disabilities (n= 948) and a group of caregivers (n= 522).A mixed anova was applied to explore the differences in the perceived importance of improvements to community support services between the groups.Logistic regression analyses were conducted to examine the perceived importance of improvements to types of community support services for self-efficacy for continuous community living.Results caregivers perceived higher levels of importance for improvements to community support services than individuals with disabilities.Both groups reported that financial subsidies were the most important area for improvement.The greater importance of improvements to financial subsidies reported by caregivers predicted greater odds for self-efficacy for continuous community living.The greater importance of improvements to center-based services reported by individuals with disabilities predicted greater odds for self-efficacy for continuous community living.Conclusions the findings suggested that financial subsidies for caregivers and center-based services for individuals with disabilities could improve self-efficacy for continuous community living.

Journal: International journal of environmental research and public health (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Late patency of reconstructed visceral arteries after open repair of thoracoabdominal aortic aneurysm.

In the era of rising endovascular treatment of thoracoabdominal aortic aneurysms (taaas), the analysis of visceral vessel (vv) patency after open surgical repair is crucial to provide a future benchmark between these different approaches.This study reports the late outcomes of a single-center experience with open taaa repair, focusing on the results of different techniques adopted for renal and splanchnic revascularization.Methods data were analyzed for 382 consecutive open taaa repairs performed between january 2009 and july 2015 (284 men; mean age, 66 ± 10 years).Follow-up of surviving patients was carried out by computed tomography angiography and office checkups at 3 and 12 months and yearly afterward.Kaplan-meier analysis was performed for overall survival, patency of reconstructed vvs (celiac trunk, superior mesenteric artery, right renal artery, left renal artery), and reinterventions on visceral arteries.Furthermore, vv long-term patency was analyzed in subgroups of patients according to the revascularization strategy (patch inclusion of all vessels, group 1; one-vessel separate reattachment and patch inclusion of the remaining vessels, group 2; separate reattachment of all vvs, group 3).Results in-hospital mortality and paraparesis/paraplegia occurred in 7.6% and 8.1% of patients, respectively.Among the 353 survivors, 338 complied with the follow-up protocol, and adequate computed tomography angiography images were available in 247 patients (952 vvs were analyzed).Overall follow-up survival was 94%, 91%, and 70% at 1 year, 2 years, and 5 years, respectively.At the same time points, vv patency was 99%, 98%, and 98% for celiac trunk; 100%, 100%, and 100% for superior mesenteric artery; 100%, 96%, and 96% for right renal artery; and 91%, 87%, and 82% for left renal artery (log-rank test, p < .0001).Estimates for reinterventions on vvs were 1.2%, 6.3%, and 17% at the same time points.Freedom from occlusion of any vv at 1 year and 3 years was 95% and 87% for group 1, 89% and 79% for group 2, and 92% and 92% for group 3, respectively (log-rank test, p = .13).Conclusions long-term patency of vvs after open taaa repair performed in high-volume centers is high, regardless of the technique employed for revascularization.The left renal artery appears to be most prone to occlusion over time.

Journal: Journal of vascular surgery (2018)
Publication types: Journal Article
Does a Moderately Warming Climate Compensate for the Negative Effects of UV-B Radiation on Amphibians at High Altitudes? A Test ofRana kukunorisLiving on the Qinghai-Tibetan Plateau.

Both the warming climate and ultraviolet-b radiation (uvbr) are considered to be notable environmental factors affecting amphibian population decline, with particular effects on tadpole development.However, the phenotypes of tadpoles living at high altitudes may be improved by moderately warming temperatures, reducing or eliminating the negative effects of oxidative damage caused by cool temperatures or strong uvbr at high altitudes.To verify this hypothesis,rana kukunoristadpoles, which live at high altitudes, were used to test the effect of the interaction of temperature and uvbr on their development and antioxidant systems in a fully factorial design.The tadpoles were exposed to uvbr and uvbr-free environments at 14 (cool temperature) and 22 °c (warm temperature), respectively.Uvbr and a warm temperature had opposite influences on several traits of the tadpoles, including their survival, developmental rate, individual size, preferred body temperature, thermal tolerance temperature, oxidative damage, and enzymatic and nonenzymatic antioxidant systems.The moderate temperature could compensate for or override the negative effects of uvbr by increasing the tadpoles' preferred body temperature and critical tolerance temperature, thus enhancing the locomotion ability and thermal sensitivity of their antioxidant systems.Furthermore, the dark skin coloration and aggregation behavior of r.Kukunoristadpoles may also be effective strategies for allowing them to resist uvbr and helping them to better adapt to a warming environment with stronger uvbr.Thus, it is possible that a moderate degree of warming may increase the capacity of living organisms to adapt to environmental changes and thus have positive effects on the development of tadpoles living at high altitudes.

Journal: Biology (2022)
Publication types: Journal Article
Complete genome characterization of the 2018 dengue outbreak in Hunan, an inland province in central South China.

In 2018, a small-scale dengue epidemic broke out in hunan province, an inland province in central south china, with 172 people infected.To verify the causative agent, complete genome information was obtained by pcr and sequencing based on the viral rnas extracted from patient serum samples.Mutation and evolutionary analysis were performed by mega7.0 software.The online softwares "predict protein" and "mfold" were used to predict the secondary structure of proteins and untranslated regions, respectively.Phylogenetic analysis showed that all five isolates in this study were denv type 2, which is most closely related to the zhejiang strain (2017-mh110588).Compared with the denv-2 standard strain, 773 nucleotide mutations occurred in the isolated strain, of which 666 were nonsense mutations.Of the 80 mutated amino acids, 22 occurred in the structural protein region (2 in c region, 8 in pr m/m region, 12 in e region), and 58 in the non-structural (ns) protein region (9 in ns1 region, 10 in ns2 region, 12 in ns3 region, 7 in ns4 region, 20 in ns5 region).The pr m/m region had the highest aa mutation rate, while ns4b was conservative.Three amino acid mutations (e: n390th s, and ns5: s676th n, k800th t) may important for the replication and virulence of the denv.Secondary structure prediction observed 28 changes in polynucleotide binding regions and 110 changes in protein binding sites of coding sequence.2 and 4 base substitutions resulted in 2 and 6 significant changes in the rna secondary structure of 5' utr and 3' utr, respectively.Two significant positive selection sites were observed in ns5.To our knowledge, this research is the first complete genome analysis of the epidemic strain of the 2018 dengue outbreak in hunan and will benefit further research for virus traceability and vaccine development.

Journal: Virus research (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Total joint prosthesis for ankylosis after multiples condylar traumas.

Temporomandibular joint (tmj) ankylosis is a disease commonly associated with facial trauma, especially in the condylar region.Described as a heterotopic bone growth that causes mouth opening limitation, it may occur in trauma cases misdiagnosed or mistreated.We present the case of a 37-year-old female, with decreased mouth opening after three traumas in the region of the right condyle by a motorcycle accident.We performed custom-made total joint replacement of the tmj to rehabilitate the patient post arthroplasty.Tmj concepts®protocol was followed to perform the patient's rehabilitation.She is being followed since then by a physical therapist to regain the pre-pathosis status of mouth opening, speech, and mastication function.

Journal: National journal of maxillofacial surgery (2020)
Publication types: Case Reports;Journal Article
Intraoperative microseizure detection using a high-density micro-electrocorticography electrode array.

One-third of epilepsy patients suffer from medication-resistant seizures.While surgery to remove epileptogenic tissue helps some patients, 30-70% of patients continue to experience seizures following resection.Surgical outcomes may be improved with more accurate localization of epileptogenic tissue.We have previously developed novel thin-film, subdural electrode arrays with hundreds of microelectrodes over a 100-1000 mm2area to enable high-resolution mapping of neural activity.Here, we used these high-density arrays to study microscale properties of human epileptiform activity.We performed intraoperative micro-electrocorticographic recordings in nine patients with epilepsy.In addition, we recorded from four patients with movement disorders undergoing deep brain stimulator implantation as non-epileptic controls.A board-certified epileptologist identified microseizures, which resembled electrographic seizures normally observed with clinical macroelectrodes.Recordings in epileptic patients had a significantly higher microseizure rate (2.01 events/min) than recordings in non-epileptic subjects (0.01 events/min; permutation test,p= 0.0068).Using spatial averaging to simulate recordings from larger electrode contacts, we found that the number of detected microseizures decreased rapidly with increasing contact diameter and decreasing contact density.In cases in which microseizures were spatially distributed across multiple channels, the approximate onset region was identified.Our results suggest that micro-electrocorticographic electrode arrays with a high density of contacts and large coverage are essential for capturing microseizures in epilepsy patients and may be beneficial for localizing epileptogenic tissue to plan surgery or target brain stimulation.

Journal: Brain communications (2022)
Publication types: Journal Article
Pd Single-Atom Sites on the Surface of PdAu Nanoparticles: A DFT-Based Topological Search for Suitable Compositions.

Structure of model bimetallic pd au nanoparticles is analyzed aiming to find pd:au ratios optimal for existence of pd1 single-atom surface sites inside outer au atomic shell.The analysis is performed using density-functional theory (dft) calculations and topological approach based on dft-parameterized topological energy expression.The number of the surface pd1 sites in the absence of adsorbates is calculated as a function of pd concentration inside the particles.At low pd contents none of the pd atoms emerge on the surface in the lowest-energy chemical orderings.However, surface pd1 sites become stable, when pd content inside a pd-au particle reaches ca.60%.Further pd content increase up to almost pure pd core is accompanied by increased concentration of surface pd atoms, mostly as pd1 sites, although larger pd ensembles as dimers and linear trimers are formed as well.Analysis of the chemical orderings inside pd au nanoparticles at different pd contents revealed that enrichment of the subsurface shell by pd with predominant occupation of its edge positions precedes emergence of pd surface species.

Journal: Nanomaterials (Basel, Switzerland) (2021)
Publication types: Journal Article
Effect of dehydroepiandrosterone on atherosclerosis in postmenopausal women.

In china, cardiovascular disease (cvd) has surpassed malignant tumours to become the disease with the highest mortality rate, and atherosclerosis (as) is an important pathological cause of cvd.Dehydroepiandrosterone (dhea) is the most abundant steroid hormone in circulating human blood and is a precursor of estrogen and androgen.Dhea is converted into a series of sex hormones in local peripheral tissues where its acts physiologically.Dhea also acts therapeutically, thereby avoiding the adverse systemic reactions to sex hormones.Dhea inhibits as, thus inhibiting the development of cvd, and it improves the prognosis for cvd.The incidence of cvd in postmenopausal women is substantially higher than that in premenopausal women, and that incidence is believed to be related to a decrease in ovarian function.The current review analyzes the mechanisms of postmenopausal women's susceptibility to as.They tend to have dyslipidemia, and their vascular smooth muscle cells (vsmcs) proliferate and migrate more.In addition, oxidative stress and the inflammatory response of endothelial cells (ecs) are more serious in postmenopausal women.This review also discusses how dhea combats as by countering these mechanisms, which include regulating the blood lipid status, protecting ecs (including coping with oxidative stress and inflammatory reactions of the vascular endothelium, inhibiting apoptosis of ecs, and inducing no production) and inhibiting the proliferation and migration of vsmcs.As a result, dhea has great value in preventing as and inhibiting its progression in postmenopausal women.

Journal: Bioscience trends (2022)
Publication types: Journal Article;Review
Directed Evolution of (R)-2-Hydroxyglutarate Dehydrogenase Improves 2-Oxoadipate Reduction by 2 Orders of Magnitude.

Pathway engineering is commonly employed to improve the production of various metabolites but may incur in bottlenecks due to the low catalytic activity of a particular reaction step.The reduction of 2-oxoadipate to (r)-2-hydroxyadipate is a key reaction in metabolic pathways that exploit 2-oxoadipate conversion via α-reduction to produce adipic acid, an industrially important platform chemical.Here, we engineered (r)-2-hydroxyglutarate dehydrogenase from acidaminococcus fermentans(hgdh) with the aim of improving 2-oxoadipate reduction.Using a combination of computational analysis, saturation mutagenesis, and random mutagenesis, three mutant variants with a 100-fold higher catalytic efficiency were obtained.As revealed by rational analysis of the mutations found in the variants, this improvement could be ascribed to a general synergistic effect where mutation a206v played a key role since it boosted the enzyme's activity by 4.8-fold.The hgdh variants with increased activity toward 2-oxoadipate generated within this study pave the way for the bio-based production of adipic acid.

Journal: ACS synthetic biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition.

Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood.This study used a field experimental facility settled in central germany to analyze the effects of ambient vs.Future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process.Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization.The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one.Using mi seq illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues.Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (ca2+, and p h) and future (c/n, n, p, k+, ca2+, p h, and moisture) climate conditions.Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate.Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates.Activities of microbial β-glucosidase and n-acetylglucosaminidase in wheat litter were increased over time.Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate.Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.

Journal: Microbial ecology (2022)
Publication types: Journal Article
CD19+IgD+CD27- Naïve B Cells as Predictors of Humoral Response to COVID 19 mRNA Vaccination in Immunocompromised Patients.

Immunocompromised patients are considered high-risk and prioritized for vaccination against covid-19.We aimed to analyze b-cell subsets in these patients to identify potential predictors of humoral vaccination response.Patients (n=120) suffering from hematologic malignancies or other causes of immunodeficiency and healthy controls (n=79) received a full vaccination series with an m rna vaccine.B-cell subsets were analyzed prior to vaccination.Two independent anti-sars-co v-2 immunoassays targeting the receptor-binding domain (rbd) or trimeric s protein (tsp) were performed three to four weeks after the second vaccination.Seroconversion occurred in 100% of healthy controls, in contrast to 67% (rbd) and 82% (tsp) of immunocompromised patients, while only 32% (rbd) and 22% (tsp) achieved antibody levels comparable to those of healthy controls.The number of circulating cd19+ig d+cd27-naïve b cells was strongly associated with antibody levels (ρ=0.761, p<0.001) and the only independent predictor for achieving antibody levels comparable to healthy controls (or 1.07 per 10-μl increase, 95%ci 1.02-1.12, p=0.009).Receiver operating characteristic analysis identified a cut-off at ≥61 naïve b cells per μl to discriminate between patients with and without an optimal antibody response.Consequently, measuring of naïve b cells in immunocompromised hematologic patients could be useful in predicting their humoral vaccination response.

Journal: Frontiers in immunology (2021)
Publication types: Clinical Trial, Phase IV;Journal Article;Research Support, Non-U.S. Gov't
The Anaerobic Fungi: Challenges and Opportunities for Industrial Lignocellulosic Biofuel Production.

Lignocellulose is a promising feedstock for biofuel production as a renewable, carbohydrate-rich and globally abundant source of biomass.However, challenges faced include environmental and/or financial costs associated with typical lignocellulose pretreatments needed to overcome the natural recalcitrance of the material before conversion to biofuel.Anaerobic fungi are a group of underexplored microorganisms belonging to the early diverging phylum neocallimastigomycota and are native to the intricately evolved digestive system of mammalian herbivores.Anaerobic fungi have promising potential for application in biofuel production processes due to the combination of their highly effective ability to hydrolyse lignocellulose and capability to convert this substrate to h2and ethanol.Furthermore, they can produce volatile fatty acid precursors for subsequent biological conversion to h2or ch4by other microorganisms.The complex biological characteristics of their natural habitat are described, and these features are contextualised towards the development of suitable industrial systems for in vitro growth.Moreover, progress towards achieving that goal is reviewed in terms of process and genetic engineering.In addition, emerging opportunities are presented for the use of anaerobic fungi for lignocellulose pretreatment; dark fermentation; bioethanol production; and the potential for integration with methanogenesis, microbial electrolysis cells and photofermentation.

Journal: Microorganisms (2021)
Publication types: Journal Article;Review