syedzayyan/paper_mill_benchmark huggingface dataset:
Implementing effective community-based surveillance in research studies of maternal, newborn and infant outcomes in low resource settings.

Globally adopted health and development milestones have not only encouraged improvements in the health and wellbeing of women and infants worldwide, but also a better understanding of the epidemiology of key outcomes and the development of effective interventions in these vulnerable groups.Monitoring of maternal and child health outcomes for milestone tracking requires the collection of good quality data over the long term, which can be particularly challenging in poorly-resourced settings.Despite the wealth of general advice on conducting field trials, there is a lack of specific guidance on designing and implementing studies on mothers and infants.Additional considerations are required when establishing surveillance systems to capture real-time information at scale on pregnancies, pregnancy outcomes, and maternal and infant health outcomes.Main body based on two decades of collaborative research experience between the kintampo health research centre in ghana and the london school of hygiene and tropical medicine, we propose a checklist of key items to consider when designing and implementing systems for pregnancy surveillance and the identification and classification of maternal and infant outcomes in research studies.These are summarised under four key headings: understanding your population; planning data collection cycles; enhancing routine surveillance with additional data collection methods; and designing data collection and management systems that are adaptable in real-time.Conclusion high-quality population-based research studies in low resource communities are essential to ensure continued improvement in health metrics and a reduction in inequalities in maternal and infant outcomes.We hope that the lessons learnt described in this paper will help researchers when planning and implementing their studies.

Journal: Emerging themes in epidemiology (2022)
Publication types: Journal Article
The Effect of Dysglycaemia on Changes in Pulmonary and Aerobic Function in Cystic Fibrosis.

Cross-sectional studies have reported lower pulmonary and aerobic function during exercise in people with cystic fibrosis-related diabetes (cfrd) compared to non-cfrd counterparts.However, this association has yet to be longitudinally investigated.Therefore, this study examines these differences over time between people with cystic fibrosis (cf) of differing glycaemic status.Annual review data, including cardiopulmonary exercise tests and pulmonary function tests, were retrospectively analysed at baseline (t0,n= 82) and at a one-year follow-up (t1,n= 54).Data was analysed in three groups: normal glucose tolerance (ngt), impaired glucose tolerance (igt), and cfrd.Further analyses were undertaken, with a dichotomous split of ngt and a combined igt/cfrd group.At baseline, a significant reduction in the majority of variables, including forced expiratory volume in one second (fev1) and maximal oxygen uptake (vo2max), was observed in the cfrd (n= 19) group compared to ngt (n= 58).At follow-up, no significant differences were observed, and no interaction effect between cfrd status and time was identified.Fev1and vo2maxpresented with varying directions and magnitudes of change within patients.In summary, patients with cfrd have a reduced aerobic and pulmonary function compared to non-cfrd counterparts, although such changes disappeared at follow up.Varying responses for fev1and vo2maxhighlight the need to consider both variables as independent markers of function in cf.

Journal: Frontiers in physiology (2022)
Publication types: Journal Article
Feasibility of a 3D Printed Patient-Specific Model System to Determine Hemodynamic Energy Delivery During Extracorporeal Circulation.

Although many have studied the effects of pulsatile flow on extracorporeal circulation, its advantages remain controversial.One reason for this situation is that in most studies, pulsatility was evaluated using an in vitro model system.The most serious disadvantage of such model systems is that they lack consideration of anatomical variations due to the use of a straight tubing line to mimic the aorta.In the current study, the authors constructed and tested the feasibility of a three-dimensional (3d) printed, patient-specific, silicone aortic model to determine whether aortic cannula tip positional changes affect energy equivalent pressure (eep) and surplus hemodynamic energy (she) in carotid arteries.Donovan model systems were connected to a pulsatile pump (korea hybrid ventricular assist device [kh-vad]; korea artificial organ center, seoul, korea) and a 3d printed silicone model of the ascending aorta.The kh-vad mimicked the heart, and another pulsatile pump (twin-pulse life support [t-pls]; newheartbio co., seoul, korea) was connected to an aortic cannula, which was inserted at three different tip positions.Using this 3d printed silicone model of the ascending aorta, it was found that eep and she of both right and left carotid arteries were significantly affected by aortic cannula tip position.The authors suggest that the described 3d printed, patient-specific, aorta model provides a feasible option to measure hemodynamic energy accurately given the considerable anatomical differences of model circuits.

Journal: ASAIO journal (American Society for Artificial Internal Organs : 1992) (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Higher risk of renal disease in chronic hepatitis C patients: Antiviral therapy survival benefit in patients on hemodialysis.

& aims several studies have shown that chronic hepatitis c (chc) infection has a negative impact on kidney function, as well as survival, in patients with chronic kidney disease (ckd) or on hemodialysis.The aim of this nationwide registry study was to describe renal disease in swedish patients with chc.Methods in the present study, patients were identified for chc (b18.2) and ckd (n18) according to the international classification of diseases (icd)-10 in the nationwide swedish inpatient care day surgery (1997-2013) and non-primary outpatient care (2001-2013) patient registries.Hemodialysis was defined using the procedure code in the non-primary outpatient care.For each patient, up to five non-chc diagnosed age/sex/place of residency-matched comparators were drawn from the general population at the time of diagnosis.Follow-up started at the date of chc diagnosis and patients accrued person-time until, whichever came first, death, emigration or december 31st, 2013.Results between 2001 and 2013, 42,522 patients received a chc diagnosis.Of these patients, 2.5% (1,077/45,222) were diagnosed with ckd during 280,123 person-years, compared with 0.7% (1,454/202,694) in the matched general population comparators (1,504,765 person-years), resulting in a standardized incidence ratio (sir) of 4.0.There was a 3.3-7.0-fold risk of patients with chc requiring hemodialysis.Overall, 17% of patients with chc receiving hemodialysis were treated for chc; 24% in the treated cohort died compared with 56% of the untreated cohort (p <0.0001), with antiviral treatment improving survival with an odds ratio of 3.901 (p = 0.001).Conclusions the results from this nationwide registry study showed that patients with chc are at a higher risk of developing ckd.Furthermore, hepatitis c treatment seemed to improve survival for patients with chc on hemodialysis compared with untreated patients.Lay summary hepatitis c is an infectious disease that mainly infects the liver, but has also been shown to have negative effects on other organs.This nationwide study demonstrates an increased risk of hepatitis c patients developing reduced kidney function and the need for dialysis.The study also showed improved survival in dialysis patients who received antiviral treatment.

Journal: Journal of hepatology (2018)
Publication types: Journal Article
Multi-headed loop chimera states in coupled oscillators.

In this paper, we introduce a novel type of chimera state, characterized by the geometrical distortion of the coherent ring topology of coupled oscillators.The multi-headed loop chimeras are examined for a simple network of locally coupled pendulum clocks, suspended on the vertical platform.We determine the regions of the occurrence of the observed patterns, their structure, and possible co-existence.The representative examples of behaviors are shown, exhibiting the variety of configurations that can be observed.The statistical analysis of the solutions indicates the geometrical regions of the system with the highest probability of the chimeras' occurrence.We investigate the mechanism of the creation of the observed states, showing that the manipulation of the initial positions of chosen pendula may induce the desired patterns.Apart from the study of the isolated network, we also discuss the scenario of the movable platform, showing a possible influence of the global coupling structure on the stability of the observed states.The stability of loop chimeras is examined for varying both the amplitude and the frequency of the oscillations of the platform.We indicate the excitation parameters for which the solutions can survive as well as be destroyed.The bifurcation analysis included in the paper allows us to discuss the transitions between possible behaviors.The appearance of multi-headed loop chimeras is generalized into large networks of oscillators, showing the universal character of the observed patterns.One should expect to observe similar results also in other types of coupled oscillators, especially the mechanical ones.

Journal: Chaos (Woodbury, N.Y.) (2021)
Publication types: Journal Article
An Investigation of Stability and Species and Strain-Level Specificity in Bacterial Volatilomes.

Microbial volatilomics is a rapidly growing field of study and has shown great potential for applications in food, farming, and clinical sectors in the future.Due to the varying experimental methods and growth conditions employed in microbial volatilomic studies as well as strain-dependent volatilomic differences, there is limited knowledge regarding the stability of microbial volatilomes.Consequently, cross-study comparisons and validation of results and data can be challenging.In this study, we investigated the stability of the volatilomes of multiple strains of staphylococcus aureus, pseudomonas aeruginosaand escherichia coliacross three frequently used nutrient-rich growth media.Volatilomic stability was assessed based on media-, time- and strain-dependent variation across the examined bacterial volatilomes.Strain-level specificity of the observed volatilomes of e.Coliand p.Aeruginosastrains was further investigated by comparing the emission of selected compounds at varying stages of cell growth.Headspace solid phase microextraction (hs-spme) sampling coupled with gas chromatography mass spectrometry (gc-ms) was used to analyze the volatilome of each strain.The whole volatilomes of the examined strains demonstrate a high degree of stability across the three examined growth media.At the compound-level, media dependent differences were observed particularly when comparing the volatilomes obtained in glucose-containing brain heart infusion (bhi) and tryptone soy broth (tsb) growth media with the volatilomes obtained in glucose-free lysogeny broth (lb) media.These glucose-dependent volatilomic differences were primarily seen in the emission of primary metabolites such as alcohols, ketones, and acids.Strain-level differences in the emission of specific compounds in e.Coliand p.Aeruginosasamples were also observed across the media.These strain-level volatilomic differences were also observed across varying phases of growth of each strain, therefore confirming that these strains had varying core and accessory volatilomes.Our results demonstrate that, at the species-level, the examined bacteria have a core volatilome that exhibits a high-degree of stability across frequently-used growth media.Media-dependent differences in microbial volatilomes offer valuable insights into identifying the cellular origin of individual metabolites.The observed differences in the core and accessory volatilomes of the examined strains illustrate the complexity of microbial volatilomics as a study while also highlighting the need for more strain-level investigations to ultimately elucidate the whole volatilomic capabilities of microbial species in the future.

Journal: Frontiers in microbiology (2021)
Publication types: Journal Article
Metformin functionalized dendritic fibrous nanosilica (KCC-1-nPr-Met) as an innovative and green nanocatalyst for the efficient synthesis of tetrahydro-4H-chromene derivatives.

An innovative nanocatalyst (kcc-1-n pr-met) has been prepared from the covalent attachment of metformin on the channels and the pores of n-propyl amine functionalized dendritic fibrous nanosilica (dfns) and used towards efficient, green, and high yield synthesis of tetrahydro-4h-chromenes derivatives by one-pot three-component reaction of aromatic aldehydes, malononitrile, and dimedone in h2o-et oh at room temperature.The designed nanocatalyst has been characterized by energy dispersive x-ray spectroscopy (eds), fourier transform infrared spectroscopy (ft-ir), and adsorption/desorption analysis (bet) techniques.Also, field emission scanning electron microscopy (fe-sem) was used to study the morphology of prepared nanocatalyst.The engineered nanocatalyst with uniform fibrous spheres has dendritic structure, high pore volume (0.35 cm3/g), and great surface area (178 m2/g).Hence, the specific dendritic structure of the prepared nanocatalyst not only improve the diffusion ability of the reactants and products, but also, increase the availability of dynamic sites in the pores and channels of the catalyst.According to the obtained results, a unique strategy was proposed towards the synthesis of important biologically active scaffolds in the presence of nontoxic and environmental friendly nanocatalyst and media.Milder reaction conditions (room temperature), shorter reaction times (5-30 minutes), excellent yields (92%-98%) of the products with higher purity, very simple workup procedure, and using of et oh: h2o as a green solvent are the advantages of the presented work.

Journal: Journal of molecular recognition : JMR (2022)
Publication types: Journal Article
Active equine parvovirus-hepatitis infection is most frequently detected in Austrian horses of advanced age.

Equine parvovirus-hepatitis (eq pv-h) research is in its infancy.Information regarding prevalence, geographical distribution, genetic diversity, pathogenesis and risk factors enhances understanding of this potentially fatal infection.Objectives determining the prevalence of eq pv-h in austrian equids.Investigating factors increasing probability of infection, liver-associated biochemistry parameters, concurrent equine hepacivirus (eq hv) infection and phylogenetic analysis of austrian eq pv-h variants.Study design cross-sectional study.Methods sera from 259 horses and 13 donkeys in austria were analysed for anti-eq pv-h vp1-specific antibodies by luciferase immunoprecipitation system (lips) and eq pv-h dna by nested polymerase chain reaction (pcr).Associations between infection status, sex and age were described.Glutamate dehydrogenase (gldh), gamma-glutamyl transferase (ggt), bile acids and albumin concentrations were compared between horses with active infection and pcr-negative horses.Pcr targeting partial eq pv-h ns1 was performed and phylogenetic analysis of austrian eq pv-h variants was conducted.Complete coding sequences (cds) of four austrian variants were determined by next-generation sequencing (ngs) and compared with published sequences.Results horses' eq pv-h seroprevalence was 30.1% and dna prevalence was 8.9%.One horse was co-infected with eq hv.Significantly, higher probability of active eq pv-h infection was identified in 16- to 31-year-old horses, compared with 1- to 8-year-old horses (p = 0.002; or = 8.19; 95% ci = 1.79 to 37.50) and 9- to 15-year-old horses (p = 0.03; or = 2.96; 95% ci = 1.08 to 8.17).Liver-associated plasma parameters were not significantly different between horses with active infection and controls.Austrian eq pv-h variants revealed high similarity to sequences worldwide.No evidence of eq pv-h was detected in donkeys.Main limitations equids' inclusion depended upon owner consent.There was only one sampling point per animal and the sample of donkeys was small.Conclusions eq pv-h antibodies and dna are frequently detected in austrian horses, without associated hepatitis in horses with active infection.The risk of active eq pv-h infection increases with increasing age.Phylogenetic evidence supports close relation of eq pv-h variants globally, including austrian variants.

Journal: Equine veterinary journal (2022)
Publication types: Journal Article
Case Report: Therapeutic and immunomodulatory effects of plasmapheresis in long-haul COVID.

Many patients with covid-19 experience a range of debilitating symptoms months after being infected, a syndrome termed long-haul covid.A 68-year-old male presented with lung opacity, fatigue, physical and cognitive weaknesses, loss of smell and lymphocytopenia.After rounds of therapeutic plasma exchange (tpe), the patient returned to normal activities and work.Mechanistically in the patient's peripheral blood mononuclear cells (pbmcs), markers of inflammatory macrophages diminished and markers of lymphocytes, including natural killer (nk) cells and cytotoxic cd8 t-cells, increased.Circulating inflammatory proteins diminished, while positive regulators of tissue repair increased.This case study suggests that tpe has the capacity to treat long-haul covid.

Journal: F1000Research (2021)
Publication types: Case Reports;Journal Article
Changes in metamorphopsia following intravitreal aflibercept injection for diabetic macular edema.

The aim of the present study was to investigate changes in metamorphopsia in patients with diabetic macular edema (dme) following intravitreal aflibercept injection (iva) with the treat and extend (tae) regimen for a year.We performed a post hoc analysis of a multicenter, open-label, single-arm, prospective study.The study included 20 patients with dme.All eyes received 3 monthly loading injections of 2 mg aflibercept, followed by a tae regimen.Every visit, the severity of metamorphopsia and the best-corrected visual acuity (bcva) were evaluated, and optical coherence tomography (oct) images were obtained.The severity of metamorphopsia was measured using m-charts.The metamorphopsia scores before treatment and at 1, 2, 3, 6 and 12 months following treatment were 0.25 ± 0.23, 0.21 ± 0.15, 0.19 ± 0.23, 0.14 ± 0.16, 0.17 ± 0.20 and 0.10 ± 0.17, respectively, with significant improvement from before treatment to 3 and 12 months following treatment (p < 0.05 and p < 0.005, respectively).At the time of macular edema resolution, the presence of an epiretinal membrane (erm) was associated with the metamorphopsia score (p < 0.05).In conclusion, the metamorphopsia score in patients with dme improved following iva with the tae regimen for one year.The presence of erm was associated with the metamorphopsia score.

Journal: Scientific reports (2022)
Publication types: Journal Article;Multicenter Study;Research Support, Non-U.S. Gov't
Tropical rainforest species have larger increases in temperature optima with warming than warm-temperate rainforest trees.

While trees can acclimate to warming, there is concern that tropical rainforest species may be less able to acclimate because they have adapted to a relatively stable thermal environment.Here we tested whether the physiological adjustments to warming differed among australian tropical, subtropical and warm-temperate rainforest trees.Photosynthesis and respiration temperature responses were quantified in six australian rainforest seedlings of tropical, subtropical and warm-temperate climates grown across four growth temperatures in a glasshouse.Temperature-response models were fitted to identify mechanisms underpinning the response to warming.Tropical and subtropical species had higher temperature optima for photosynthesis (topt a) than temperate species.There was acclimation of topt ato warmer growth temperatures.The rate of acclimation (0.35-0.78°c °c-1) was higher in tropical and subtropical than in warm-temperate trees and attributed to differences in underlying biochemical parameters, particularly increased temperature optima of vcmax25and jmax25.The temperature sensitivity of respiration (q10) was 24% lower in tropical and subtropical compared with warm-temperate species.Overall, tropical and subtropical species had a similar capacity to acclimate to changes in growth temperature as warm-temperate species, despite being grown at higher temperatures.Quantifying the physiological acclimation in rainforests can improve accuracy of future climate predictions and assess their potential vulnerability to warming.

Journal: The New phytologist (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Relation between Plasma Trough Concentration of Pazopanib and Progression-Free Survival in Metastatic Soft Tissue Sarcoma Patients.

Pazopanib (paz) is an oral angiogenesis inhibitor approved to treat soft tissue sarcoma (sts) but associated with a large interpatient pharmacokinetic (pk) variability and narrow therapeutic index.We aimed to define the specific threshold of paz trough concentration (cmin) associated with better progression-free survival (pfs) in sts patients.Methods: in this observational study, paz cmin was monitored over the treatment course.For the primary endpoint, the 3-month pfs in sts was analyzed with logistic regression.Second, we performed exposure−overall survival (os) (cox model plus kaplan−meier analysis/log-rank test) and exposure−toxicity analyses.Results: ninety-five sts patients were eligible for pharmacokinetic/pharmacodynamic (pk/pd) assessment.In the multivariable analysis, paz cmin < 27 mg/l was independently associated with a risk of progression at 3 months (odds ratio (or) 4.21, 95% confidence interval (ci) (1.47−12.12), p = 0.008).A higher average of paz cmin over the first 3 months was associated with a higher risk of grade 3−4 toxicities according to the nci-ctcae version 5.0 (or 1.07 per 1 mg/l increase, ci95 (1.02−1.13), p = 0.007).Conclusion: paz cmin ≥ 27 mg/l was independently associated with improved 3-month pfs in sts patients.Pharmacokinetically-guided dosing could be helpful to optimize the clinical management of sts patients in daily clinical practice.

Journal: Pharmaceutics (2022)
Publication types: Journal Article