syedzayyan/paper_mill_benchmark huggingface dataset:
Functional and phylogenetic analysis of TetX variants to design a new classification system.

Recently, many tet x variants such as tet(x3~14) were reported to confer resistance to tigecycline which is a last-resort antibiotic used to treat infections caused by multidrug-resistant bacteria.In this study, we identified essential residues including 329, 339, 340, 350, and 351 in tet x variants that mediated the evolution of the tigecycline-inactive tet(x2) enzyme to the active forms of tet(x3) and tet(x4).Based on their amino acid sequences and functional features, we classified tet x variants into tet x-a class, tet x-b class and tet x-c class.We further found that tet x-a class variants originated from bacteroidetes, with some variants further evolving to tet x-c class and acquired by enterobacteriaceae.On the other hand, our data showed that some variants genes belonging to tet x-a class evolved directly to tet x-b class, which was further transmitted to acinetobacter spp.This new classification system may facilitate better clinical management of patients infected by tet x-producing strains.

Journal: Communications biology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Enhanced boundary scavenging of241Am on the continental margin of the East China sea.

The241am concentrations were determined by sector field high-resolution inductively coupled plasma mass spectrometry for settling particles and surface sediments collected on the continental margin in the east china sea to discuss the behavior of241am in the studied area.A large and regular increase was noted from 97 m depth to 592 m depth in241am concentrations in settling particles from the cylindrical sediment traps, whereas only a slight increase in239+240pu concentrations was evident.The gradual increase in241am/239+240pu activity ratios from the cylindrical trap settling particles also was observed.These results were attributed to241am being scavenged by settling particles at a more rapid scavenging rate than239+240pu.There was an obvious tendency for241am fluxes to increase linearly with depth with the highest fluxes at near-bottom, and these fluxes were due to large advective import to the near-bottom.There was a tendency for241am concentrations in surface sediments to increase almost linearly with depth, showing the same tendency as210pb concentrations, and this tendency indicated that the enhanced boundary scavenging of241am as well as210pb occurred in the east china sea continental slope region due to the greater abundance of reactive finer particles.The241am concentrations in settling particles from the time-series sediment trap ranged from 1.05 to 4.20 m bq g-1, showing large variation.The241am concentrations from the time-series trap varied inversely with the total mass fluxes, indicating that241am concentrations were diluted by particles when mass flux increased.The241am fluxes showed large time-series variations and these variations were primarily controlled by mass flux variation.It seems that the high total mass flux events are due to resuspension of the underlying surface sediments and episodic lateral transport of particles that flow down the continental slope in the east china sea.

Journal: Journal of environmental radioactivity (2022)
Publication types: Journal Article
Evaluation of binocular function among pre- and early-presbyopes with asthenopia.

Individuals approaching presbyopia may exhibit ocular symptoms as they contend with visual demands of near work, coupled with natural age-related changes in accommodation.Therefore, accommodation and vergence of 30- to 40-year-old, myopic, soft contact lens wearing subjects with symptoms of asthenopia and no history of using multifocal lenses were evaluated.Patients and methods in this prospective, observational study, 253 subjects with asthenopia were evaluated by 25 qualified practitioners, each at a different clinical site.Subjects were 30-40 years in age, had symptoms of soreness, eyestrain, tired eyes, or headaches with near work, regularly performed 2-3 consecutive hours of near work, and were undiagnosed with presbyopia.Amplitude of accommodation (ac) and near point convergence (npc) were measured with a royal air force binocular gauge.Triplicate push up and push down ac and npc measures were recorded, and average ac values were compared to those calculated using the hofstetter formula (hf).Results the average ac push up/push down value was significantly better than the hf prediction for this age range (8.04±3.09 vs 6.23±0.80 d), although 22.5% of subjects had mean ac below their hf value (5.36±0.99 d).The average npc push up/push down value was 12.0±4.69 cm.The mean binocular ac value using the push up measure was significantly better than the push down measure (8.5±3.4 vs 7.6±3.0 d).The mean npc value using the push up measure was significantly worse than the push down measure (13.0±5.0 vs 11.0±4.7 cm).The most frequent primary diagnosis was ill-sustained accommodation (54%), followed by accommodative insufficiency (18%), and accommodative infacility (12%).Conclusion based upon a standardized assessment of accommodation and vergence, ill-sustained accommodation was the most frequent diagnosis among this population.

Journal: Clinical optometry (2018)
Publication types: Journal Article
Use of GELSECTAN®in Patients with Irritable Bowel Syndrome (IBS): an Italian Experience.

Irritable bowel syndrome is a chronic functional gastrointestinal disorder characterized by recurrent chronic abdominal pain and impaired bowel habits, which affects daily activity and work productivity, and is associated with a significant healthcare economic burden as well as an impaired quality of life and psycho-affective profile.Management of patients is a great challenge for physicians; at the present, the therapeutic strategy aimed to treat the different symptoms, and no medical therapy is proven to modify the natural history of the disease.Gelsectan®(xyloglucan, pea protein and tannins, xylo-oligosaccharides) is a medical device with both protective and prebiotic actions on the intestinal mucosa, able to restore intestinal permeability and to improve gastrointestinal symptoms, controlling diarrhoea, abdominal pain and bloating in adult patients with irritable bowel syndrome.We report and discuss four cases of different patients with irritable bowel syndrome successfully managed with gelsectan in the real clinical practice.Literature data, as well as these case reports, show that this device is effective and safe in improving symptoms and bowel habits associated to irritable bowel syndrome; its efficacy and safety were confirmed for the long-term use too.Agents with film-forming protective properties, such as gelsectan, represent a new alternative therapeutic option for the management of patients with irritable bowel syndrome.

Journal: Patient preference and adherence (2021)
Publication types: Case Reports;Journal Article
Lipid profile and atherogenic indices in patients with stable chronic obstructive pulmonary disease.

And aims limited number of studies investigated lipid profile in chronic obstructive pulmonary disease (copd) with inconsistent results.This study aimed to investigate lipid parameters in sera of patients with stable copd and their associations with disease severity, smoking, comorbidities and therapy.Methods and results the study included 137 copd patients and 95 controls.Triglycerides (tg), total cholesterol (tc), high-density lipoprotein cholesterol (hdl-c) and low-density lipoprotein cholesterol (ldl-c) were assessed.Non-hdl-c (nhc), atherogenic coefficient (ac), tg/hdl-c, atherogenic index of plasma (aip), castelli's risk index i and ii (cri-i, cri-ii), and monocyte to hdl ratio (mhr) were calculated.Hdl-c and mhr were increased, while other lipid parameters and indices were decreased in copd patients compared to healthy individuals.Smoking did not influence lipid parameters.However, lipid profile was altered only in more severe disease stages.Ac, cri-i and cri-ii showed positive association with lung function parameters in copd patients, and negative with copd multicomponent indices (ado, bodcat, bodex, codex and dose).Combined model that included cri-ii, c-reactive protein, fibrinogen and white blood cells showed great diagnostic performances, and correctly classified 72% of study participants with an auc of 0.800 (0.742-0.849), p < 0.001.Bronchodilator monotherapy and statins have opposite impact on tc, ldl-c and nhc, while tg, tg/hdl-c and aip were increased in copd patients with cardiovascular diseases.Conclusion lipid disbalance is present in copd, and it seems to occur later as the disease progresses.Further studies are needed to illuminate the underlying mechanism of dyslipidaemia.

Journal: Nutrition, metabolism, and cardiovascular diseases : NMCD (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Endothelial failure and rejection in recipients of corneas from the same donor.

To determine whether patients who receive corneas from the same donor have similar risks of endothelial failure and rejection.Methods and analysis patients with fuchs endothelial dystrophy (fed) and pseudophakic bullous keratopathy (pbk) who received their first corneal transplant between 1999 and 2016 were analysed.Patients receiving corneas from donors who donated both corneas for the same indication were defined as 'paired'.Gray's test was used to compare the cumulative incidence of endothelial failure and rejection within 5 years post-transplant for 'paired' and 'unpaired' groups.Cox regression models were fitted to determine whether there was an association between recorded donor characteristics (endothelial cell density (ecd), age and sex and endothelial graft failure and rejection.Results 10 838 patients were analysed of whom 1536 (14%) were paired.The unpaired group comprised 1837 (69%) recipients of single corneal donors and 7465 (69%) donors who donated both corneas for another indication.Ecd was lower for unpaired single cornea donors (p 0.16 for ecd, p>0.32 for donor age, p>0.14 for sex match and p>0.17 for the donor effect).Conclusion the absence of a significant difference in graft outcome for corneal transplants for fed and pbk between paired and unpaired donors may reflect a homogeneous donor pool in the uk.

Journal: BMJ open ophthalmology (2022)
Publication types: Journal Article
Trajectory of livestock genomics in South Asia: A comprehensive review.

Livestock plays a central role in sustaining human livelihood in south asia.There are numerous and distinct livestock species in south asian countries.Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs.This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry.The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, qtl discovery, genome-wide association studies (gwas), and genomic selection.The review concludes with recommendations for south asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies.This paper aims to present a comprehensive analysis of the dichotomy in the south asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Journal: Gene (2022)
Publication types: Journal Article;Review
Defining the Role of Isoeugenol fromOcimum tenuiflorumagainst Diabetes Mellitus-Linked Alzheimer's Disease through Network Pharmacology and Computational Methods.

The present study involves the integrated network pharmacology and phytoinformatics-based investigation of phytocompounds from ocimum tenuiflorumagainst diabetes mellitus-linked alzheimer's disease.It aims to investigate the mechanism of the ocimum tenuiflorumphytocompounds in the amelioration of diabetes mellitus-linked alzheimer's disease through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, go analysis, molecular dynamics simulations, and binding free energy analyses.A total of 14 predicted genes of the 26 orally bioactive compounds were identified.Among these 14 genes, gapdh and akt1 were the most significant.The network analysis revealed the age-rage signaling pathway to be a prominent pathway linked to gapdh with 50.53% probability.Upon the molecular docking simulation with gapdh, isoeugenol was found to possess the most significant binding affinity (-6.0 kcal/mol).The molecular dynamics simulation and binding free energy calculation results also predicted that isoeugenol forms a stable protein-ligand complex with gapdh, where the phytocompound is predicted to chiefly use van der waal's binding energy (-159.277 kj/mol).On the basis of these results, it can be concluded that isoeugenol from ocimum tenuiflorumcould be taken for further in vitro and in vivo analysis, targeting gapdh inhibition for the amelioration of diabetes mellitus-linked alzheimer's disease.

Journal: Molecules (Basel, Switzerland) (2022)
Publication types: Journal Article
ERS International Congress 2021: highlights from the Respiratory Infections Assembly.

The european respiratory society international congress 2021 took place virtually for the second year running due to the coronavirus pandemic.The congress programme featured more than 400 sessions and 3000 abstract presentations, covering the entire field of respiratory science and medicine.In this article, early career members of the respiratory infections assembly summarise a selection of sessions across a broad range of topics, including presentations on bronchiectasis, non-tuberculosis mycobacteria, tuberculosis, cystic fibrosis and covid-19.

Journal: ERJ open research (2022)
Publication types: Journal Article;Review
The Underappreciated Placebo Effects and Responses in Randomized Controlled Trials on Neck Pain: A Systematic Review With Meta-analysis.

To quantify placebo effects and responses in randomized controlled trials (rcts) on neck pain and explore how they would influence the treatment of neck pain.Data sources we searched medline (pub med), embase (ovid), cinahl (ebsco), physiotherapy evidence database (pedro), and world health organization international clinical trials registry platform from the inception of august 15, 2021, to identify relevant rcts.Study selection and data extraction the abstracts and full texts of potential studies were independently screened, and data extraction was also independently performed by 2 researchers.Scales of the score measuring neck pain and the scores both at baseline and the endpoint were extracted.Data synthesis a total of 60 rcts were included.The mean improvement in the pain score after placebo treatment was 15.65 (mean difference [md]=-15.65, 95% confidence interval; ci [-19.19, -12.12]; p<.05), which we defined as the placebo response.In the active groups, it was 25.91 (md=-25.91, 95% ci [-29.15, -22.68]; p<.05), and in the no-treatment groups, it was 5.80 (md=-5.80, 95% ci [13.28, 1.69]; p=.13).Using the 3 mds from the 3 groups, the placebo effect was calculated to account for 38.0% of the pain score improvement in the active group.Conclusions the pain scores of patients with neck pain were reduced after treatment with placebos, but the magnitude of pain score reduction was not clinically significant enough.The 38.0% amount of pain score reduction in patients treated with active interventions was caused by placebo.Interventions with considerable clinically significance for neck pain were still required.

Journal: Archives of physical medicine and rehabilitation (2023)
Publication types: Meta-Analysis;Systematic Review;Journal Article;Review;Research Support, Non-U.S. Gov't
Optimal timing for lung metastasectomy in patients with colorectal cancer.

S the possibility of occult metastasis remains a concern when deciding on lung metastasectomy.This study aimed to evaluate the utility of our two-step determination, which required confirmation that no new metastases had occurred over 3 months before surgery.Methods patients who were referred for colorectal lung metastases between 2007 and 2015 were reviewed.Immediate wedge resection was performed for cases with a single peripheral metastasis, whereas surgical indications for others were determined by the two-step determination.Early increase was defined as the emergence of new metastases within 4 months after the diagnosis of lung metastases.Results among 369 patients included, 92 were unresectable upon initial diagnosis, and 74 with single peripheral metastasis underwent immediate wedge resection.Surgical indications for the remaining 203 patients were ascertained based on the two-step determination.Surgery was not indicated in 48 patients (24%) due to new metastases or a favourable response to chemotherapy, with a median waiting duration of 4.8 months.Those who did not receive surgery had a worse prognosis than those who did (5-year overall survival: 21% vs 69%, p < 0.001) and were comparable to the initially unresectable group (5-year overall survival: 23%).Thirty-eight patients with early increase had lower surgical resection rates and worse prognoses than those without.Multivariable analysis identified early increase as an independent prognostic factor (hazard ratio: 4.49, p < 0.001).Conclusions patients with colorectal lung metastasis who developed new metastasis during the waiting period exhibited poor prognosis, suggesting the utility of the two-step determination of surgical indications.

Journal: Interactive cardiovascular and thoracic surgery (2022)
Publication types: Journal Article
Comparative Pharmacokinetic of Curcuminoids Formulations with an Omega-3 Fatty Acids Monoglyceride Carrier: A Randomized Cross-Over Triple-Blind Study.

There is a growing interest for curcuminoids in the general population and the scientific research community.Curcuminoids, derived from turmeric spice, are lipophiles and therefore have a low solubility in water which hence have a low bioavailability in the human plasma.To circumvent this issue, a natural product developed by biodroga nutraceuticals combined curcuminoids with omega-3 fatty acids (om3) esterified in monoglycerides (mag).The objective was to perform a 24 h pharmacokinetics in humans receiving a single dose of curcuminoid formulated by three different means, and to compare their plasma curcuminoids concentration.Sixteen males and fifteen females tested three formulations: 400 mg of curcuminoids powder extract, 400 mg of curcuminoids in rice oil and 400 mg of curcuminoids with 1 g mag-om3.Blood samples were collected at 0, 1, 2, 3, 4, 5, 6, 8, 10 and 24 h post dose intake.Plasma samples were analyzed by ultra high-performance liquid chromatography with a triple quadrupole mass spectrometer (uplc-ms/ms).Twenty-four hours after a single dose intake, the total plasma curcuminoids area under the curve (auc) reached 166.8 ± 17.8 ng/m l*h, 134.0 ± 12.7 ng/m l*h and 163.1 ± 15.3 ng/m l*h when curcuminoids were provided with mag-om3, with rice oil or in powder, respectively.The cmaxof total curcuminoids reached between 11.9-17.7 ng/m l at around 4 h (tmax).One-hour post-dose, the curcuminoids plasma concentration was 40% higher in participants consuming the mag-om3 compared to the other formulations.Thus, in a young population, plasma curcuminoids 24 h pharmacokinetics and its increase shortly after the single dose intake were higher when provided with mag-om3 than rice oil.

Journal: Nutrients (2022)
Publication types: Randomized Controlled Trial;Journal Article
Phenyl Bis-Sulfonamide Keap1-Nrf2 Protein-Protein Interaction Inhibitors with an Alternative Binding Mode.

Inhibitors of kelch-like ech-associated protein 1 (keap1) increase the activity of the transcription factor nuclear factor erythroid 2-related factor 2 (nrf2) by stalling its ubiquitination and degradation.This enhances the expression of genes encoding proteins involved in drug detoxification, redox homeostasis, and mitochondrial function.Nrf2 activation offers a potential therapeutic approach for conditions including alzheimer's and parkinson's diseases, vascular inflammation, and chronic obstructive airway disease.Non-electrophilic keap1-nrf2 protein-protein interaction (ppi) inhibitors may have improved toxicity profiles and different pharmacological properties to cysteine-reactive electrophilic inhibitors.Here, we describe and characterize a series of phenyl bis-sulfonamide ppi inhibitors that bind to keap1 at submicromolar concentrations.Structural studies reveal that the compounds bind to keap1 in a distinct "peptidomimetic" conformation that resembles the keap1-nrf2 etge peptide complex.This is different to other small molecule keap1-nrf2 ppi inhibitors, including bicyclic aryl bis-sulfonamides, offering a starting point for new design approaches to keap1 inhibitors.

Journal: Journal of medicinal chemistry (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Tools for assessing the scalability of innovations in health: a systematic review.

The last decade has seen growing interest in scaling up of innovations to strengthen healthcare systems.However, the lack of appropriate methods for determining their potential for scale-up is an unfortunate global handicap.Thus, we aimed to review tools proposed for assessing the scalability of innovations in health.Methods we conducted a systematic review following the cosmin methodology.We included any empirical research which aimed to investigate the creation, validation or interpretability of a scalability assessment tool in health.We searched embase, medline, cinahl, web of science, psyc info, cochrane library and eric from their inception to 20 march 2019.We also searched relevant websites, screened the reference lists of relevant reports and consulted experts in the field.Two reviewers independently selected and extracted eligible reports and assessed the methodological quality of tools.We summarized data using a narrative approach involving thematic syntheses and descriptive statistics.Results we identified 31 reports describing 21 tools.Types of tools included criteria (47.6%), scales (33.3%) and checklists (19.0%).Most tools were published from 2010 onwards (90.5%), in open-access sources (85.7%) and funded by governmental or nongovernmental organizations (76.2%).All tools were in english; four were translated into french or spanish (19.0%).Tool creation involved single (23.8%) or multiple (19.0%) types of stakeholders, or stakeholder involvement was not reported (57.1%).No studies reported involving patients or the public, or reported the sex of tool creators.Tools were created for use in high-income countries (28.6%), low- or middle-income countries (19.0%), or both (9.5%), or for transferring innovations from low- or middle-income countries to high-income countries (4.8%).Healthcare levels included public or population health (47.6%), primary healthcare (33.3%) and home care (4.8%).Most tools provided limited information on content validity (85.7%), and none reported on other measurement properties.The methodological quality of tools was deemed inadequate (61.9%) or doubtful (38.1%).Conclusions we inventoried tools for assessing the scalability of innovations in health.Existing tools are as yet of limited utility for assessing scalability in health.More work needs to be done to establish key psychometric properties of these tools.Trial registration we registered this review with prospero (identifier: crd42019107095).

Journal: Health research policy and systems (2022)
Publication types: Journal Article;Review;Systematic Review