syedzayyan/paper_mill_benchmark huggingface dataset:
Effects of undernutrition on opportunistic infections among adults living with HIV on ART in Northwest Ethiopia: Using inverse-probability weighting.

Opportunistic infections (ois) are the leading causes of hospitalization, morbidity, and mortality (accounting for 94.1% of all deaths) in people living with human immunodeficiency virus (plhiv).Despite evidence suggested that undernutrition significantly increases the risk of ois in plhiv, to our knowledge, no study has examined the actual effects of undernutrition on ois in this population, particularly in low-income countries.Thus, this study examined the effects of undernutrition on ois in adults living with hiv receiving antiretroviral therapy (art).Methods we conducted a retrospective cohort study among 841adults living with hiv receiving art between june 2014 and june 2020 at debre markos comprehensive specialized hospital, northwest ethiopia.Study participants were selected using a simple random sampling technique.Data from participants' medical records were extracted using a project-specific data extraction checklist.The kaplan meier survival curve estimated the ois free survival time.The effects of undernutrition on time to develop ois was estimated using inverse-probability weighting.Finally, regression coefficients with 95% confidence intervals (95% cis) were reported, with a statistical significance of p < 0.05.Results of 841 study participants, 262 (31.2%) developed ois, and the overall incidence rate was 16.7 (95% ci: 14.8, 18.8) per 100 person-years.The inc widence of ois in undernourished participants (21/100 person-years, 95% ci: 17.8, 27.4) was higher than well-nourished participants (15.0/100 person-years, 95% ci: 12.9, 17.4).When everyone in the population of interest is well-nourished, average time to develop ois is estimated as 26.5 (coefficient: 26.5, 95% ci: 20.6, 32.4, p < 0.001) months.When everyone in the population of interest is undernourished, average time to develop ois is estimated as 17.7 (95% ci: 12.8, 22.6) months.However, when everyone is undernourished, average time to develop ois decreases by 8.8 (coefficient: -8.8, 95% ci: -16.6, -1.0, p = 0.026) months.Lastly, exposure to undernourishment (intervention) (ratio of average treatment effects to well-nourished potential outcome means in this study was a 32.5% reduction in ois among adults living with hiv on art.Conclusion we found that undernutrition significantly shortened time to develop ois in adults living with hiv.This implies that the occurrence of ois in this vulnerable population can be improved through different cost-effective nutritional interventions, such as routine nutritional assessments and education.

Journal: PloS one (2022)
Publication types: Journal Article
Detection of protein targets with a single binding epitope using DNA-templated photo-crosslinking and strand displacement.

Dna-based probes are powerful analytical tools for protein detection and analysis.Target-induced dna assembly is a widely used strategy to transduce target-ligand binding to detectable signals.However, most of the existing methods based on dna assembly require two or more binding sites on the target protein.Here we report a novel detection method suitable for protein targets with just a single binding site.This method is based on target-induced probe assembly, dna-templated photo-crosslinking, and dna-mediated toehold strand displacement to form a tri-probe complex that is specific for target protein.

Journal: Analytical biochemistry (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Acquired mild cognitive impairment in adults with Down syndrome: Age-related prevalence derived from single point assessment data normed by degree of intellectual disability.

Individuals with down syndrome (ds) are at significant risk for early onset alzheimer's disease (ad), likely due to the triplication of genes on chromosome 21 that facilitate ad neuropathology.To aid the effective early diagnosis of dementia in ds, we demonstrate the strategy of using single point assessment of cognitive performance with scoring normed for degree of intellectual disability to generate age related prevalence data for acquired mild cognitive impairment (amci).Methods four hundred and twelve adults with ds were assessed using the neuropsychological assessment of dementia in adults with intellectual disability.Normative data, banded by degree of intellectual disability, allowed identification of amci by atypical deviation from expected performance.Results amci was evident in approximately 20% of adults with ds aged 40 and under, 40% aged 41-50 and 45% aged 51 and over.Relative risk increased significantly in those aged 46 and over.Analysis of prevalence by 5-year age bands revealed two peaks for higher prevalence of amci.Conclusions psychometric data indicate single point assessment of amci is possible for the majority of adults with ds.Two peaks for age-related prevalence of amci suggest the risk for onset of ad conferred by trisomy of chromosome 21 is moderated by another factor, possibly apo e status.

Journal: International journal of geriatric psychiatry (2022)
Publication types: Journal Article
Cost Effectiveness of a Novel Attempt to Reduce Readmission after Ileostomy Creation.

And objectives dehydration is a common complication after ileostomy creation and is the most frequent reason for postoperative readmission to the hospital.We sought to determine the clinical and economic impact of an outpatient intervention to decrease readmissions for dehydration after ileostomy creation.Methods all new ileostomates from 09/2011 through 10/2012 at the university of florida were enrolled to receive an ileostomy education and management protocol and a daily telephone call for 3 weeks after discharge.Counseling and medication adjustments were provided, with a satisfaction survey at the end.Outcomes of these patients were compared to those in a historical control cohort.A cost analysis was conducted to calculate the savings to the hospital.Results thirty-eight patients were enrolled.All patients required telephone counseling, and the mean satisfaction score rating was 4.69, on a scale of 1 to 5.The readmission rate for dehydration within 30 days of discharge decreased significantly from 65% before intervention to 16% (5/32 patients) after intervention (p= .002).The length of readmission hospital stay decreased from a mean of 4.2 days before the introduction of the intervention to 3 days after.Cost analysis revealed that the actual total hospital cost of dehydration-specific readmission decreased from $88,858 to $25,037, a saving of $63,821.Conclusion a standardized ileostomy pathway with comprehensive patient education and outpatient telephone follow-up is cost effective, has a positive influence on patient satisfaction, and reduces dehydration-related readmission rates.

Journal: JSLS : Journal of the Society of Laparoendoscopic Surgeons (2017)
Publication types: Journal Article
Amorphous solid dispersions of cyclosporine A with improved bioavailability prepared via hot melt extrusion: Formulation, physicochemical characterization, and in vivo evaluation.

In this study, the amorphous solid dispersions of cyclosporine a (cs a-asds) were prepared by hot melt extrusion (hme) with pvp k12 as carrier to improve the oral bioavailability of cs a.The polymers were screened by solubilization and recrystallization inhibition experiments, then the cs a-asds were prepared with optimized technological parameters and characterized on thermodynamics and morphology.The results showed that cs a was dispersed among pvp k12 as amorphous form in cs a-asds, and the infrared spectrum testified that there was possible hydrogen bond interaction between cs a and pvp k12.The in vivo pharmacokinetics of cs a formulations in rats were analyzed via lc-ms.The auc of cs a-asd tablets increased by 7.3 times compared to cs a bulk powder and 3.1 times in contrast to cs a-pm tablets, respectively.The experiment proved that cs a-asd tablets significantly improved the dissolution and absorption of the drug.This study had a reference value for the bioavailability improvement of oral cs a preparations.

Journal: European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences (2022)
Publication types: Journal Article
Antibiotic Resistance of Lactobacillus spp. and Streptococcus thermophilus Isolated from Chinese Fermented Milk Products.

The aim of the present study was to investigate the phenotypic and genotypic antimicrobial resistance and the transferability of resistance markers in 87 lactic acid bacterial strains recovered from fermented milk products obtained from different areas of china.The isolates were identified as 21 lactobacillus bulgaricus, 8 lactobacillus casei, 6 lactobacillus rhamnosus, 3 lactobacillus paracasei, 2 lactobacillus acidophilus, and 47 streptococcus thermophilus strains.High levels of intrinsic resistance were revealed among the tested species.The following resistance genes were detected in strains isolated from fermented milk products: tet(m) in two l.Bulgaricus and two s.Thermophilus isolates, str a and str b in nine and seven s.Thermophilus isolates, respectively; sul1 in six l.Bulgaricus and seven s.Thermophilus isolates, sul2 in one s.Thermophilus isolate, aac(6')-aph(2′′) in two l.Bulgaricus isolates, and aph(3′′)-ii and aph(3′′)-iii in one s.Thermophilus and two l.Bulgaricus isolates, respectively.Transfer of the monitored antibiotic resistance genes was not observed in the filter mating assays of this study.To our knowledge, the str a, str b, sul1, sul2, and aph(3′′)-ii genes in s.Thermophilus, and the sul1 and aac(6')-aph(2′′) genes in l.Bulgaricus were identified for the first time.These results indicate the potential risks posed by lactic acid bacteria (lab) in fermented milk products in expanding the antibiotic resistance gene reservoir and transferring antibiotic resistance genes among bacteria.Further investigations are required to identify the potential sources of contamination and the dissemination routes of antibiotic resistance genes among lab in fermented milk products.

Journal: Foodborne pathogens and disease (2019)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Genotype-determined EGFR-RTK heterodimerization and its effects on drug resistance in lung Cancer treatment revealed by molecular dynamics simulations.

Epidermal growth factor receptor (egfr) and its signaling pathways play a vital role in pathogenesis of lung cancer.By disturbing egfr signaling, mutations of egfr may lead to progression of cancer or the emergence of resistance to egfr-targeted drugs.Results we investigated the correlation between egfr mutations and egfr-receptor tyrosine kinase (rtk) crosstalk in the signaling network, in order to uncover the drug resistance mechanism induced by egfr mutations.For several egfr wild type (wt) or mutated proteins, we measured the egfr-rtk interactions using several computational methods based on molecular dynamics (md) simulations, including geometrical characterization of the interfaces and conventional estimation of free energy of binding.Geometrical properties, namely the matching rate of atomic solid angles in the interfaces and center-of-mass distances between interacting atoms, were extracted relying on alpha shape modeling.For a couple of rtk partners (c-met, erb b2 and igf-1r), results have shown a looser egfr-rtk crosstalk for the drug-sensitive egfr mutant while a tighter crosstalk for the drug-resistant mutant.It guarantees the genotype-determined egfr-rtk crosstalk, and further proposes a potential drug resistance mechanism by amplified egfr-rtk crosstalk induced by egfr mutations.Conclusions this study will lead to a deeper understanding of egfr mutation-induced drug resistance mechanisms and promote the design of innovative drugs.

Journal: BMC molecular and cell biology (2021)
Publication types: Journal Article
Utility of Epstein-Barr Viral Load in Blood for Diagnosing and Predicting Prognosis of Lymphoma: A Comparison with Epstein-Barr Virus-Encoded RNA in Situ Hybridization.

Epstein-barr virus (ebv) is a ubiquitous pathogen that persists in a small portion of b cells after primary infection and is etiologically associated with multiple lymphoma subtypes.We evaluated the clinical utility of ebv real-time quantitative pcr in comparison with the widely used epstein-barr virus-encoded rna (eber) in situ hybridization (ish) method in 912 patients with four lymphoma subtypes: diffuse large b-cell lymphoma (dlbcl), extranodal natural killer/t-cell lymphoma (enktcl), peripheral t-cell lymphoma (ptcl), and hodgkin lymphoma.We also assessed the impact of ebv positivity determined from each method or a combination of both methods on mortality using kaplan-meier survival analysis and cox proportional hazard regression.Ebv real-time quantitative pcr identified more positive cases than eber-ish for all subtypes, except enktcl.Ebv dna-positive patients with enktcl and ptcl displayed poorer overall survival (os) than ebv dna-negative patients (p = 0.0016 and p = 0.0013, respectively).In addition, among those with eber-positive dlbcl and enktl and those with eber-negative ptcl, os was significantly worse for ebv dna-positive patients (p = 0.027, p = 0.0016, and p = 0.0018, respectively).Eber positivity was associated with worse os for dlbcl (p = 0.037), in reanalyses including only the 862 patients with unambiguous eber-ish results.Overall, ebv dna positivity is a more effective prognostic marker than eber-ish status for patients with certain lymphoma subtypes.

Journal: The Journal of molecular diagnostics : JMD (2022)
Publication types: Journal Article
Genetic polymorphisms of human hepatic OATPs: functional consequences and effect on drug pharmacokinetics.

1.Organic anion transporting polypeptides (oatps) belong to the superfamily of solute carriers (slc), which are important membrane transporters in animals and humans.Liver is an important organ for drug disposition.In human liver, three oatps, namely oatp1b1, 1b3 and 2b1, are expressed on the basolateral membrane of hepatocytes.2.Oatps have multiple substrate specificity, mediating transport of a wide range of endo- and exogenous substances such as bile salts, bilirubin, hormones and their conjugates, toxins and various drugs.Therefore, they are important for drug disposition in human body.In this review, we compiled a complete list of the substrates for human hepatic oatps.3.Oatp genes have single-nucleotide polymorphisms (snps), which could lead to the alteration of their function, and thus might result in the change of pharmacokinetic properties for their substrate drugs.In this review, we summarized the genetic polymorphisms of the three hepatic oatps and their effect onin vitrotransport function andin vivopharmacokinetics of substrate drugs.4.Finally, some concerns and perspectives on oatp polymorphism research are discussed.

Journal: Xenobiotica; the fate of foreign compounds in biological systems (2020)
Publication types: Journal Article
Occurrence and removal of bisphenol analogues in wastewater treatment plants and activated sludge bioreactor.

The occurrence and removal of ten bisphenol analogues (bps) in municipal wastewater treatment plants (wwtps) and laboratory scale activated sludge bioreactor (asbr) were studied.All targeted bps except for tetrachlorobisphenol a (tcbpa) were detected in the four wwtps (w1, w2, w3 and w4) in the ng/l and ng/g dry weight range in wastewater and activated sludge, respectively, indicating that in addition to bpa, the bpa substitutes were widely used in our daily life and industrial production.Discrepant results regarding the removal efficiencies of bps by different wastewater treatment processes were obtained.The removal rates were 55.6%, 24.4%, -10.1%, 71.4%, 38.9%, 58.0%, 39.1% and 6.4% in w1, 65.4%, 32.8%, 44.7, -13.5%, 20.1%, -29.6%, -25.1% and 99.4% in w2, 11.6%, 48.8%, 38.9%, 22.0%, 99.0%, -29.2%, -56.5% and 32.6% in w3, 33.9%, 30.5%, 17.4%, -47.6%, 62.9%, 83.0%, 4.4% and -4.3% in w4, for bpa, bpb, bpe, bpf, bps, bpz, bpaf and bpap, respectively.The removal of ten targeted bps in lab-scale continuous flow conventional asbr and the key factors were investigated.The simulated laboratory-scale asbr were highly effective in removing bpa, bpb, bpe, bpf, bpm and bps with removal efficiencies of >94.3%, while bpz, bpap, bpaf and tcbpa were recalcitrant to elimination in the stimulated bioreactor with removal efficiencies of 71.3 ± 13.7%, 55.1 ± 21.2%, 47.4 ± 9.5% and 45.3 ± 16.6%, respectively.Protonation, hydrophobicity and molecular features of bps were critical for their elimination in wastewater.

Journal: The Science of the total environment (2021)
Publication types: Journal Article
Diffuse Arterial Atherosclerosis Presenting With Acute Ischemic Gastritis.

Ischemic gastritis is a rare cause of gastrointestinal bleeding due to the rich blood supply of the stomach.A 66-year-old lady with a history of coronary artery disease and hyperlipidemia presented with acute abdominal pain, diarrhea, and recent coffee-ground emesis.She had diffuse abdominal tenderness on physical exam with mild leukocytosis.A ct scan of the abdomen showed new peripheral wedge-shaped hypoenhancing regions in the spleen and both kidneys, suggestive of embolic infarcts.Posterior pneumatosis of the stomach suggestive of gastric wall ischemia was detected, with associated portal venous gas.She was started on heparin anticoagulation, broad-spectrum antibiotics, and intravenous fluids and underwent an urgent upper endoscopy showing hemorrhagic mucosa and fibrinous debris.A transesophageal echocardiogram showed mild aortic atherosclerosis.A ct angiogram of the abdomen showed calcified plaques at the origins of the hepatic artery, celiac artery, and superior mesenteric artery with severe ostial narrowing.Symptoms resolved, and she was started on statin therapy, prophylactic anticoagulation with apixaban, and high-dose peptic ulcer prophylaxis with pantoprazole.This ischemic gastritis case with multiple embolic spleen and kidney lesions is likely a sequela of extensive atherosclerosis and suggests that extensive atherosclerosis should be considered as a rare cause of acute gastrointestinal bleeding.

Journal: Cureus (2022)
Publication types: Case Reports;Journal Article
Irregular erythrocyte antibodies among antenatal women and their neonatal outcome at a tertiary care hospital in Northern India.

Red blood cell alloimmunisation during the pregnancy is a significant cause for neonatal mortality and morbidity.This study was planned to determine the prevalence and specificity of irregular erythrocyte antibodies in antenatal mothers and their neonatal outcome.Methods in this observational study, blood grouping and red cell antibody screening of mothers were performed at first visit and after 28 weeks of gestation and positive cases were identified and followed up monthly till delivery by repeating antibody titre and middle cerebral artery-peak systolic velocity.After delivery of alloimmunised mothers, cord blood haemoglobin, bilirubin and direct antiglobulin tests (dat) were analysed and further outcome of neonate was recorded.Results among 652 registered antenatal cases, 18 multigravida women were found to be alloimmunised, accounting to prevalence of 2.8%.Most common alloantibody identified was anti d (>70%) followed by anti-lea, anti-c, anti-leb, anti-e and anti-jka.Only 47.7% rh d negative women received anti-d prophylaxis during previous pregnancies or whenever indicated.Dat was positive in 56.2% of neonates.Among nine dat positive neonates, two early neonatal deaths due to severe anaemia were observed following birth resuscitation.Four antenatal mothers required intrauterine transfusion in view of fetal anaemia while three neonates received double volume exchange transfusion and top up transfusions after birth.Conclusions this study emphasises importance of red cell antibody screening for all multigravida antenatal women at registration of pregnancy and additionally at 28 weeks or later in high-risk cases irrespective of rh d status.

Journal: Postgraduate medical journal (2021)
Publication types: Journal Article
Clinical Characteristics and Treatment for Dupilumab-Related Ocular Complications in Atopic Dermatitis Patients.

Ocular adverse events have been reported in association with dupilumab, a monoclonal antibody to treat allergic diseases including atopic dermatitis (ad).We describe clinical findings and treatment of dupilumab-related ocular complications.Patients and methods retrospective study of 19 dupilumab-treated ad patients seen for a new ocular complaint.Primary outcomes were specific ocular exam findings (conjunctival injection, corneal fluorescein staining, blepharitis, meibomian gland dysfunction (mgd)), treatments, and follow-up.Results nineteen dupilumab-treated ad patients were included.Median age was 47 years (range 18-73).Over half were women (11/19) and majority were caucasian (13/19).Symptom onset occurred at a mean of 99 days (range 23-520 days) from first dupilumab dose.The most common symptoms were redness (63%), tearing (47%), and pruritus (37%).Most common ocular findings were conjunctival injection (75%) and corneal staining (60%).Blepharitis was seen in about a third (30%), and 25% had mgd.Initially, 10% were observed without treatment, while 15% were treated with artificial tears alone.Other treatments included antihistamine drops (20%) and steroid drops alone (15%).In 40% of patients, a combination of steroids and various other topical eye drops were prescribed.Eighty-four percent (16/19) of patients were seen for follow-up.Steroid drops were required at follow-up in 3 out of 4 patients initially treated with antihistamines alone and in two-thirds of patients initially treated with artificial tears only.Mean follow-up period was 88 days (range 5-369).Dupilumab was discontinued in 31.5% (6/19) of patients; of those who discontinued, 3 restarted it later.Conclusion conjunctival injection was the most frequent dupilumab-related ocular symptom and most common exam finding followed by corneal staining.Most patients initially treated with antihistamine drops or artificial tears alone subsequently required steroid drops to control symptoms.Some patients who discontinued dupilumab restarted the medication after achieving adequate control of ocular symptoms.

Journal: Clinical ophthalmology (Auckland, N.Z.) (2022)
Publication types: Journal Article
Loss of primary cilia promotes inflammation and carcinogenesis.

Primary cilia (pc) are important signaling hubs, and we here explored their role in colonic pathology.In the colon, pc are mostly present on fibroblasts, and exposure of mice to either chemically induced colitis-associated colon carcinogenesis (cac) or dextran sodium sulfate (dss)-induced acute colitis decreases pc numbers.We generated conditional knockout mice with reduced numbers of pc on colonic fibroblasts.These mice show increased susceptibility to cac, as well as dss-induced colitis.Secretome and immunohistochemical analyses of dss-treated mice display an elevated production of the proinflammatory cytokine il-6 in pc-deficient colons.An inflammatory environment diminishes pc presence in primary fibroblast cultures, which is triggered by il-6 as identified by rna-seq analysis together with blocking experiments.These findings suggest an activation loop between il-6 production and pc loss.An analysis of pc presence on biopsies of patients with ulcerative colitis or colorectal cancer (crc) reveals decreased numbers of pc on colonic fibroblasts in pathological compared with surrounding normal tissue.Taken together, we provide evidence that a decrease in colonic pc numbers promotes colitis and crc.

Journal: EMBO reports (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't