syedzayyan/paper_mill_benchmark huggingface dataset:
Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities.

Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense "packing" in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions.Current empirical support, however, is mixed.We tested these expectations using published data on arbuscular mycorrhizal (am) fungal community composition worldwide.We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance.However, contrary to expectations, dominance was pronounced in communities where more specialists were present and, conversely, richness was higher in communities with more generalists.Thus, resource competition and niche packing appear to be of limited importance in am fungal community assembly; rather, patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes.

Journal: Ecology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Genetic Characteristics of Porcine Hemagglutinating Encephalomyelitis Coronavirus: Identification of Naturally Occurring Mutations Between 1970 and 2015.

Porcine hemagglutinating encephalomyelitis virus (phev) is a betacoronaviruscharacterized by neurological symptoms and a worldwide prevalence.Although phev is one of the earliest discovered porcine coronaviruses, it remains poorly studied.The full-length genome of the earliest phev strain collected in 1970 in the united states (phev/67 n/us/1970) was determined in october 2020.Using this virus as a prototype, we comparatively analyzed all available phev full-length sequences during 1970-2015.In phylogenetic trees based on phev full-length or spike glycoprotein open reading frame genomic sequences, phev/67 n/us/1970 was sorted into a clade different from that of viruses isolated in the united states in 2015.Intriguingly, united states and belgium viruses isolated in 2015 and 2005, respectively, revealed multiple deletion mutation patterns compared to the strain phev/67 n/us/1970, leading to a truncated or a non-functional ns2a coding region.In addition, the genomic similarity analysis showed a hypervariability of the spike glycoprotein coding region, which can affect at least eight potential linear b cell epitopes located in the spike glycoprotein.This report indicates that phevs in the united states underwent a significant genetic drift, which might influence phev surveillance in other countries.

Journal: Frontiers in microbiology (2022)
Publication types: Journal Article
Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis.

Photosynthesis is the energetic basis for most life on earth, and in plants it operates inside double membrane-bound organelles called chloroplasts.The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes.Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (ups) was not expected, owing to the barrier presented by the double-membrane envelope.Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated and processed via the chlorad pathway: they are degraded by the 26sproteasome following cdc48-dependent retrotranslocation to the cytosol.This demonstrates that the reach of the ups extends to the interior of endosymbiotically derived chloroplasts, where it acts to regulate photosynthesis, arguably the most fundamental process of life.

Journal: Science advances (2022)
Publication types: Journal Article
SARS-CoV-2 viroporin encoded by ORF3a triggers the NLRP3 inflammatory pathway.

Heightened inflammatory response is a prominent feature of severe covid-19 disease.We report that the sars-co v-2 orf3a viroporin activates the nlrp3 inflammasome, the most promiscuous of known inflammasomes.Ectopically expressed orf3a triggers il-1β expression via nfκb, thus priming the inflammasome.Orf3a also activates the nlrp3 inflammasome but not nlrp1 or nlrc4, resulting in maturation of il-1β and cleavage/activation of gasdermin.Notably, orf3a activates the nlrp3 inflammasome via both asc-dependent and -independent modes.This inflammasome activation requires efflux of potassium ions and oligomerization between the kinase nek7 and nlrp3.Importantly, infection of epithelial cells with sars-co v-2 similarly activates the nlrp3 inflammasome.With the nlrp3 inhibitor mcc950 and select fda-approved oral drugs able to block orf3a-mediated inflammasome activation, as well as key orf3a amino acid residues needed for virus release and inflammasome activation conserved in the new variants of sars-co v-2 isolates across continents, orf3a and nlrp3 present prime targets for intervention.

Journal: Virology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Care for Dying Children and Their Families in the PICU: Promoting Clinician Education, Support, and Resilience.

S to describe the consequences of workplace stressors on healthcare clinicians in picu, and strategies for personal well-being, and professional effectiveness in providing high-quality end-of-life care.Data sources literature review, clinical experience, and expert opinion.Study selection a sampling of foundational and current evidence was accessed.Data synthesis narrative review and experiential reflection.Conclusions the well-being of healthcare clinicians in the picu influences the day-to-day quality and effectiveness of patient care, team functioning, and the retention of skilled individuals in the picu workforce.End-of-life care, including decision making, can be complicated.Both are major stressors for picu staff that can lead to adverse personal and professional consequences.Overresponsiveness to routine stressors may be seen in those with moral distress, and underresponsiveness may be seen in those with compassion fatigue or burnout.Ideally, all healthcare professionals in picu can rise to the day-to-day workplace challenges-responding in an adaptive, effective manner.Strategies to proactively increase resilience and well-being include self-awareness, self-care, situational awareness, and education to increase confidence and skills for providing end-of-life care.Reactive strategies include case conferences, prebriefings in ongoing preidentified situations, debriefings, and other postevent meetings.Nurturing a culture of practice that acknowledges the emotional impacts of pediatric critical care work and celebrates the shared experiences of families and clinicians to build resilient, effective, and professionally fulfilled healthcare professionals thus enabling the provision of high-quality end-of-life care for children and their families.

Journal: Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies (2018)
Publication types: Journal Article;Review
The Long Road to Farewell: The Needs of Families With Dying Children.

Families of dying children are profoundly impacted by numerous interactions with health-care providers before, during, and after their child's death.However, there is a dearth of research on these families' direct, qualitative experiences with health-care providers.This study presents findings from interviews with 18 family members, predominantly parents, regarding their experiences with health-care providers during a child's terminal illness, from diagnosis to death.The importance of compassion emerged as a salient theme, manifested in myriad ways, and connected to participants' perception of caregiverpresencein multiple domains.Families were likewise negatively affected by a wide variety of situations and behaviors that represented individual or institutionalabandonmentornonpresence, and thus compounded the experience of loss.Specifics and implications for practice are explored.

Journal: Omega (2019)
Publication types: Journal Article
Lisinopril-Induced Small Bowel Angioedema: An Unusual Cause of Severe Abdominal Pain.

Angiotensin-converting enzyme inhibitors (ace-i) are one of the most frequently prescribed classes of medications with the rare adverse effect of angioedema, and isolated small bowel angioedema is a small subset of these cases.Isolated angioedema of the small bowel is a rare adverse effect of this commonly prescribed medication, and it mimics, symptomatically and radiographically, several other illnesses and is often misdiagnosed.While ace-i are thought to be safe, the risk of angioedema is approximately 0.7%.Isolated small bowel angioedema is often not diagnosed in a timely manner, and misdiagnosis leads to significant morbidity in afflicted patients.Case report we present the case of a 63-year-old woman with angioedema of the small bowel causing abdominal pain, nausea, vomiting, and diarrhea.Computed tomography demonstrated small bowel edema and ascites.The patient had been taking lisinopril for 7 years prior to presentation and had previously been seen by multiple physicians for abdominal pain.A diagnosis of ace-i-induced small bowel angioedema was made and lisinopril therapy was immediately stopped.Her symptoms improved with cessation of lisinopril, and follow-up imaging showed resolution of the angioedema 3 months later.Conclusions the course of ace-i-induced angioedema is unpredictable and often overlooked as a cause of abdominal pain.It commonly presents soon after starting ace-i therapy, but can present years after therapy initiation, as in this case.Significant morbidity, including unnecessary exploratory laparotomy, is associated with misdiagnosis of ace-i-induced angioedema of the small bowel.Prompt recognition and cessation of the offending drug is crucial but often delayed.

Journal: The American journal of case reports (2022)
Publication types: Case Reports;Journal Article
A Novel Cell-based In vitro Assay for Antiviral Activity of Interferons α, β, and γ by qPCR of MxA Gene Expression.

Human mx a gene is related to the class of interferon (ifn)-stimulated genes (isgs) that plays a role in antiviral resistance.Objective implementation of standard curves obtained from designing a procedure for data processing in relative q pcr between mx a expression and interferon's antiviral activity (iu/ml).These standard curves can be used to detect the antiviral activity of any new compound rapidly and safely.Methods to detect the optimum incubation time for maximum mx a gene expression in human peripheral blood mononuclear cells (pbmc), the isolated human pbmcs (1x106 cells) were incubated with a concentration of 1000 iu/ml of each ifn at different time intervals; 2 h, 4 h, 6 h, and 24 h post-treatment.A standard curve was performed for each ifn (α, β, and γ) at different concentrations (250, 500, 750, 1000, 1500, and 2000 iu/ml).Results as observed at 4 h incubation time of 1000 iu/ml concentration, ifn-γ provided a higher expression of mx a compared to ifn-α and ifn-β.Correlation analyses between ifn-α and ifn-β, ifn-β and ifn-γ were non-significant.However, there was a significant correlation between ifn-α and ifn-γ (p 7.31 and > 3.33, respectively.Conclusions the relative expression of mx a is a biomarker for ifn-α, β, and γ, especially ifn-α.It has compiled and validated a standard curve-based protocol for pcr data processing.It shows that the standard curve is an easy alternative tool to assess antiviral activity.We revised all patents relating to the antiviral assays of the used interferons.

Journal: Recent patents on biotechnology (2021)
Publication types: Journal Article
An overview of basic molecular biology of SARS-CoV-2 and current COVID-19 prevention strategies.

Coronavirus disease 2019 (covid-19) manifests as extreme acute respiratory conditions caused by a novel beta coronavirus named severe acute respiratory syndrome coronavirus-2 (sars-co v-2) which is reported to be the seventh coronavirus to infect humans.Like other sars-co vs it has a large positive-stranded rna genome.But, specific furin site in the spike protein, mutation prone and phylogenetically mess open reading frame1ab (orf1ab) separates sars-co v-2 from other rna viruses.Since the outbreak (february-march 2020), researchers, scientists, and medical professionals are inspecting all possible facts and aspects including its replication, detection, and prevention strategies.This led to the prompt identification of its basic biology, genome characterization, structural and expression based functional information of proteins, and utilization of this information in optimizing strategies to prevent its spread.This review summarizes the recent updates on the basic molecular biology of sars-co v-2 and prevention strategies undertaken worldwide to tackle covid-19.This recent information can be implemented for the development and designing of therapeutics against sars-co v-2.

Journal: Gene reports (2021)
Publication types: Journal Article;Review
Transferrin Saturation/Hepcidin Ratio DiscriminatesTMPRSS6-Related Iron Refractory Iron Deficiency Anemia from Patients with Multi-Causal Iron Deficiency Anemia.

Pathogenic tmprss6variants impairing matriptase-2 function result in inappropriately high hepcidin levels relative to body iron status, leading to iron refractory iron deficiency anemia (irida).As diagnosing irida can be challenging due to its genotypical and phenotypical heterogeneity, we assessed the transferrin saturation (tsat)/hepcidin ratio to distinguish irida from multi-causal iron deficiency anemia (ida).We included 20 irida patients from a registry for rare inherited iron disorders and then enrolled 39 controls with ida due to other causes.Plasma hepcidin-25 levels were measured by standardized isotope dilution mass spectrometry.Ida controls had not received iron therapy in the last 3 months and c-reactive protein levels were <10.0 mg/l.Irida patients had significantly lower tsat/hepcidin ratios compared to ida controls, median 0.6%/n m (interquartile range, iqr, 0.4-1.1%/n m) and 16.7%/n m (iqr, 12.0-24.0%/n m), respectively.The area under the curve for the tsat/hepcidin ratio was 1.000 with 100% sensitivity and specificity (95% confidence intervals 84-100% and 91-100%, respectively) at an optimal cut-off point of 5.6%/n m.The tsat/hepcidin ratio shows excellent performance in discriminating irida from tmprss6-unrelated ida early in the diagnostic work-up of ida provided that recent iron therapy and moderate-to-severe inflammation are absent.These observations warrant further exploration in a broader ida population.

Journal: International journal of molecular sciences (2022)
Publication types: Comparative Study;Journal Article
The Contribution of the Hunger Hormone Leptin in the Aetiology of Postoperative Anorexia after Laparoscopic and Open Gastrectomy in Gastric Cancer Patients.

Laparoscopic surgery produces lesser postoperative inflammation with a smaller cytokine and leptin response, and might thus reduce postoperative anorexia compared with open surgery.The aim of the present study was to determine the role of serum leptin in postoperative anorexia after laparoscopic gastric cancer surgery.Methods fifty-four consecutive patients with adenocarcinoma of the stomach were operated on either with open or laparoscopic surgery.Correlations were determined between the serum levels of leptin, clinico-pathological characteristics, serum haemoglobin, and albumin.Results serum leptin levels on day seven were correlated significantly to gender (p= 0.004), body mass index (bmi) (p= 0.002), and tumour grade (p= 0.033).In the patients with c-reactive protein (crp) < 100 mg/l (n= 46) the leptin levels on day seven were significantly lower after the laparoscopic operation (p= 0.042) and in patients with lower bmi (p= 0.001).The linear regression model determined a significant correlation between the relative concentration of leptin on day seven and laparoscopic surgery (beta-0.688;p< 0.0001), gender, bmi, location of the tumour, t stage, n stage, perioperative therapy, tumour grade, perineural invasion, lauren histological type, and ulceration.In patients with crp levels below 100 mg/m l, the serum level of albumin on day seven after surgery was significantly higher in patients after laparoscopic surgery.Conclusion laparoscopic surgery produced significantly lower relative leptin concentrations on day seven, and higher serum albumin levels in the subgroup with crp levels below 100 mg/l at discharge.These results suggested that laparoscopic gastric cancer surgery might reduce postoperative leptin response, leading to a better nutritional status at discharge compared with open surgery.

Journal: Biomolecules (2021)
Publication types: Journal Article
Effect of the Metal within Regioisomeric Paddle-Wheel-Type Metal-Organic Frameworks.

The effect of metal on the degree of flexibility upon evacuation of metal-organic frameworks (mofs) has been revealed with positional control of the organic functionalities.Although co-, cu-, and zn-based dmofs (dmof = dabco mof, dabco = 1,4-diazabicyclo[2.2.2]octane) with ortho-ligands (2,3-nh2cl) have frameworks that are inflexible upon evacuation, mofs with para-ligands (2,5-nh2cl) showed different n2uptake amounts after evacuation by metal exchange.Considering that the structural analyses were not fully sufficiently different to explain the drastic changes in n2adsorption after evacuation, quantum chemical simulation was explored.A new index (η) was defined to quantify the regularity around the metal based on differences in the oxygen-metal-oxygen angles.Within 2,5-nh2cl, the η value becomes larger as the metal are varied from co to zn.A large η value means that the structures around the metal center are less ordered.These results can be used to explain flexibility changes upon evacuation by altering the metal cation in this regioisomeric system.

Journal: Chemistry (Weinheim an der Bergstrasse, Germany) (2019)
Publication types: Journal Article
Rapid clearance of tacrolimus blood concentration triggered by variant pharmacogenes.

What is known and objective tacrolimus (tac) is an immunosuppressant with large interpatient pharmacokinetic variability and a narrow therapeutic index.We report a case of acute cellular rejection (acr) type ib with insufficient tac blood concentrations (tac c0).Case summary acr developed on the eighth postoperative day of kidney transplantation.During this period, tac c0were insufficient.This referred pharmacogenetic assessment disclosed the patient as a cyp3a5 expresser and cyp3a4*1b carrier.According to the genotype, higher doses of tac, 15 mg twice daily, were administered and targeted tac c0were achieved.What is new and conclusion our case presents an association of tac rapid clearance and two alleles modifying greater cyp3a enzyme activity.

Journal: Journal of clinical pharmacy and therapeutics (2022)
Publication types: Case Reports;Journal Article
CSCO expert consensus on the diagnosis and treatment of breast cancer brain metastasis.

Breast cancer is one of the most common malignancies among women worldwide.According to the international agency for research on cancer, breast cancer affected more chinese women than any other cancer in 2020.The brain is an increasingly common metastatic sites of breast cancer.Although the risk of developing brain metastases (bms) is lower in breast cancer than in lung cancer and melanoma, due to its high prevalence, it is the second most common cause of bm among solid tumors, being second only to lung cancer.The incidence of breast cancer brain metastasis (bcbm) differs by molecular subtype.Half of patients with advanced human epidermal growth factor receptor-2 (her2)-positive and one-third of patients with triple-negative breast cancer (tnbc) develop bm.The clinical manifestations of leptomeningeal metastasis (lm) are often non-specific and may manifest as a variety of signs and symptoms, mainly including brain parenchyma involvement and meningeal irritation syndromes cranial nerve involvement, increased intracranial pressure, and progressive brain dysfunction.Therefore, the chinese society of clinical oncology (csco) breast cancer committee has developed this expert consensus on bm, in an effort to improve the overall prognosis of bcbm and promote the standardized diagnosis and treatment of this disease.During the development of this expert consensus, we carried out a comprehensive literature review and referred to some of the most authoritative guidelines in china and abroad.In this consensus, we will discuss clinical manifestations, imaging examinations, pathological diagnosis, treatments, prognosis, follow-up and monitoring.We hope this consensus will be of help to all the clinicians majored in breast cancer and other similar professions.

Journal: Translational breast cancer research : a journal focusing on translational research in breast cancer (2022)
Publication types: Journal Article;Review
Delivering hydrophilic peptide inhibitors of heat shock protein 70 into cancer cells.

Heat shock protein 70 (hsp70) plays a major role in protein folding and has emerged as an attractive target in a wide range of cancers.Here we used a polymer nanogel to deliver two hydrophilic peptide inhibitors that block the interaction between the c-terminus of hsp70 and heat shock organizing protein (hop).The nanogels are able to load ∼200 wt% of the peptide inhibitors from solution via simple agitation at p h 7, and release them after cell uptake.Delivery of hsp70 inhibitors to hct116 cancer cells produced a clear hsp70 inhibition phenotype: downregulation of client proteins glucocorticoid receptor (gr), immunophilins (fkbp51 and fkbp52), the protein kinase akt-1, as well as the co-chaperone chip, and they induce cancer cell death.These results showcase the advantages of using versatile nanogels for delivery of hydrophilic cargo such as peptides and demonstrate the viability of these peptide inhibitors for targeting the hsp70-hop interaction in a cellular system.

Journal: Bioorganic chemistry (2022)
Publication types: Journal Article