syedzayyan/paper_mill_benchmark huggingface dataset:
Faucet: streaming de novo assembly graph construction.

Motivation we present faucet, a two-pass streaming algorithm for assembly graph construction.Faucet builds an assembly graph incrementally as each read is processed.Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded.We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased.Results faucet pairs the de bruijn graph obtained from the reads with additional meta-data derived from them.We show these metadata-coverage counts collected at junction k-mers and connections bridging between junction pairs-contain most salient information needed for assembly, and demonstrate they enable cleaning of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy.We compared fauceted resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers.Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers meta spades and megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency-namely, minia and light assembler.However, on metagenomes tested, faucet,o outputs had 14-110% higher mean nga50 lengths compared with minia, and 2- to 11-fold higher mean nga50 lengths compared with light assembler, the only other streaming assembler available.Availability and implementation faucet is available at contact rshamir@tau.ac.il or eranhalperin@gmail.com.Supplementary information supplementary data are available at bioinformatics online.

Journal: Bioinformatics (Oxford, England) (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Simultaneous visual diagnosis of acute hepatopancreatic necrosis disease and Enterocytozoon hepatopenaei infection in shrimp with duplex recombinase polymerase amplification.

Shrimp is a globally popular seafood.Shrimp farming has been challenged by various infectious diseases that lead to significant economic losses.The prevention of two important shrimp infectious diseases, the acute hepatopancreatic necrosis disease (ahpnd) and the enterocytozoon hepatopenaei (ehp) infection, is highly dependent on early and accurate diagnostic.On-site monitoring of the two diseases in shrimp farming facilities demands point-of-care-testing (poct) type of diagnostic assays.This study established a duplex recombinase polymerase amplification (rpa) and lateral flow dipstick (lfd) combined assay that could simultaneously diagnose the two diseases.The optimized rpa-lfd assay could finish the diagnostic in 35 min with good specificity, and the sensitivity reached 101and 102gene copies per reaction for ehp and ahpnd, respectively, which were at the same level as the currently available molecular diagnostic assays.Test results of clinical samples showed 100% agreement of this assay with the industrial standard nested polymerase chain reaction (pcr) assays, and samples with both diseases were simultaneously identified.Because of the isothermal 37°c amplification and the visual reading of the signal on dipsticks, the dependence on equipment is minimal.This duplex rpa-lfd assay is well suited for simultaneous poct diagnostic of the two important shrimp infectious diseases.Moreover, the principle can be applied to multiplex poct diagnostic of other infectious diseases in aquaculture.

Journal: Journal of fish diseases (2021)
Publication types: Journal Article
Prevalence and Related Factors of White Coat Hypertension and Masked Hypertension in Shunde District, Southern China.

White coat hypertension (wch) and masked hypertension (mh) can increase the risk of target organ damage.Home blood pressure monitoring is an important method for detecting wch and mh.However, the prevalence and related factors of wch and mh in china have been rarely reported.objective:to explore the prevalence and related factors associated with white coat hypertension (wch) and masked hypertension (mh) in shunde district, southern china.methods:this study recruited subjects from the physical examination center in shunde hospital, southern medical university.Office blood pressure and home blood pressure values were collected using the home blood pressure monitor with telemedicine device and office blood pressure monitor, and the prevalence of wch and mh was calculated by the values.Multivariate logistic regression was used to explore the related factors for wch and mh.results:four-hundred and sixty-one participants (61% male), with an average age of 49 years, were included.The prevalence of wch and mh was 5.1 and 15.2%, respectively.Multivariate logistic regression analysis showed that smoking (or = 4.71, 95% ci = 1.05-21.15) and family history of coronary heart disease (or = 4.51, 95% ci = 1.08-18.93) were associated with higher odds of wch.The associated factors for higher odds of mh were smoking (or = 2.83, 95% ci = 1.11-7.23), family history of hypertension (or = 2.17, 95% ci = 1.11-4.26) and family history of coronary heart disease (or = 2.82, 95% ci = 1.07-7.45).conclusion:wch and mh are highly prevalent in the physical examination center in shunde hospital, southern medical university.We found smoking and family history of coronary heart disease were related factors for wch, and smoking, family history of hypertension and coronary heart disease were associated with the odds of mh.Home blood pressure monitoring with a telemedicine device should be recommended to identity abnormal bp phenotype.

Journal: Frontiers in physiology (2022)
Publication types: Journal Article
Personal PM2.5Elemental Components, Decline of Lung Function, and the Role of DNA Methylation on Inflammation-Related Genes in Older Adults: Results and Implications of the BAPE Study.

Epidemiological evidence of the effects of pm2.5elements on lung function and dna methylation is limited.We conducted a longitudinal panel study of 76 healthy older adults aged 60-69 years in jinan, china, from september 2018 to january 2019.We periodically measured individual 72 h pm2.5and element concentrations, lung function, and dna methylation levels of eight inflammation-related genes.We used linear mixed-effect models to investigate the effects of exposure to personal pm2.5elements on the lung function and dna methylation.Mediation analysis was used to investigate the underlying effect mechanism.Negative changes in the ratio of forced expiratory volume in 1 s to forced vital capacity, ranging from -1.23% [95% confidence interval (ci): -2.11%, -0.35%] to -0.77% (95% ci: -1.49%, -0.04%), were significantly associated with interquartile range (iqr) increases in personal pm2.5at different lag periods (7-12, 13-24, 25-48, 0-24, 0-48, and 0-72 h).Arsenic (as), nickel, rubidium (rb), selenium, and vanadium were significantly associated with at least three lung function parameters, and iqr increases in these elements led to 0.12-5.66% reductions in these parameters.Pm2.5elements were significantly associated with dna methylation levels.Dna methylation mediated 7.28-13.02% of the as- and rb-related reduced lung function.The findings indicate that exposure to elements in personal pm2.5contributes to reduced lung function through dna methylation.

Journal: Environmental science & technology (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Q fever in Bulgaria: Laboratory and epidemiological findings on human cases and outbreaks, 2011 to 2017.

Q fever is a zoonosis, included in category b of particularly dangerous infectious agents and as such merits careful surveillance and regular updating of the information about its distribution.aim this observational retrospective study aimed to provide an overview of q fever incidence in bulgaria in the period 2011 to 2017.methods aggregated surveillance data from bulgaria's mandatory surveillance system, laboratory data on individual samples received at the national reference laboratory rickettsiae and cell cultures and outbreak reports sent by the regional health authorities to the national centre of infectious and parasitic diseases, were used in this analysis.Cases were described by year, region, age group and most commonly identified risk behaviours.results a total of 139 confirmed cases were reported in the study period (average annual incidence: 0.27 cases/100,000 inhabitants).No seasonality or trend in reported cases was observed.Cases were mostly sporadic, with two small outbreaks in 2017.Identified risk behaviours among cases were occupational exposure and consumption of milk and dairy products, although exposure data were incomplete.The male/female ratio was 1.4.The identification and resolution of the two rural outbreaks in 2017 with a total of 18 cases involved good practices: active case finding and collaboration between public health and veterinary authorities.conclusion between 2011 and 2017, bulgaria retained low q fever incidence, mostly sporadic cases and two small outbreaks.Occupational exposure and consumption of milk and dairy products were the most often reported likely exposures among cases.The outbreak investigations demonstrate the application of good control practices.

Journal: Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin (2019)
Publication types: Journal Article;Observational Study
Pharmacological Regulation in the USA and Pharmacokinetics Parameters of Firocoxib, a Highly Selective Cox-2, by Pain Management in Horses.

The objective of the study was to conduct a review of the pharmacological regulation and pharmacokinetic parameters of firocoxib when administered orally or intravenously in horses.A search for literature was done in scopus and pub med for studies that had to evaluate the pharmacological regulation as well as the pharmacokinetic parameters of firocoxib when administered in horses.The nonsteroidal anti-inflammatory drugs have analgesic, anti-inflammatory, antipyretics, and antiendotoxic effects.The newly developed is selective to cox2 characterized by less adverse effects in veterinary patients when administered at the recommended doses and do not exceed the established prescribed time.Firocoxib is authorized by the food and drug administration for the treatment of pain in horses, whereas for humans, there is still no approval.Controversy has arisen because the administration of the same pharmaceutical presentation in horses and dogs has pharmacokinetic differences between animal species.However, special attention must be paid to pharmacokinetic differences between species like in horses and dogs.In the case of the horse, the dosage is 0.1 mg/kg in single dose or up to 14 days in oral paste formulation and can keep maintained on the same concentration for a period of 7-14 days in oral tablet formulation.Thorough knowledge of pharmacological regulations and pharmacokinetic parameters, it allows the posology and effective application of firocoxib in pathologies associated with chronic pain, avoiding the indiscriminate use by owners and in some cases veterinarians, thus reducing the negative impacts on horse's health.

Journal: Journal of equine veterinary science (2019)
Publication types: Journal Article;Review
Computerized cognitive training in people with depression: a protocol for a systematic review and meta-analysis.

People with depression often present with concurrent cognitive impairment.Computerized cognitive training (cct) is a safe and efficacious strategy to maintain or enhance cognitive performance in a range of clinical populations.However, its efficacy in people with depression and how it varies across populations and design factors are currently unclear.Methods we searched medline, embase, and psyc info from inception to 13 july 2021 for randomised controlled trials examining the efficacy of cct vs any control condition on cognitive, mood, psychiatric symptoms, psychosocial, and daily functioning in adults with depression.Eligible samples include studies specifically targeting people with major depressive disorder as well as those with other diagnoses where at least 50% of the sample meets the clinical criteria for depression, with the exception of major psychiatric disorders or dementia.The primary outcome is change in the overall cognitive performance.Multivariate analyses will be used to examine the effect sizes on each outcome category as well as possible effect modifiers and correlations between categories.The risk of bias will be assessed using the cochrane risk of bias tool version 2.Discussion to the best of our knowledge, this will be the first systematic review and meta-analysis of narrowly defined cct across clinical populations with depression.We aim to investigate not only whether cct is efficacious for cognition, but also how such effects vary across design factors, what other clinically relevant outcomes might respond to cct, and the extent to which they differ across populations.Systematic review registration prospero crd42020204209.

Journal: Systematic reviews (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Delirium in patients with hip fracture is associated with increased heart rate variability.

Heart rate variability (hrv) is a method to assess the autonomic nervous system and reflects possibly central brain states.Hrv has previously not been examined in patients with hip fracture and delirium.Aims to explore hrv parameters in hip fracture patients with and without delirium.Methods patients admitted to oslo university hospital with hip fracture and sinus rhythm in electrocardiogram (ecg) were included.Delirium was diagnosed using the confusion assessment method.Hrv was assessed preoperatively after a relaxing period of five minutes, by measuring an ecg signal over 5 min.Parameters in time domain (the standard deviation of the qrs distances-sdnn) and frequency domain (total power (tp), low frequency (lf), high frequency (hf) and lf/hf ratio) were calculated.Results seventy-five patients were included in the study, and 21 of them had subsyndromal delirium and were excluded from the analysis.Fifty-four patients with a mean age of 83.5 years (sd 8.6, 78% females) were included.Twenty-six patients (48%) had preoperative delirium, 11 (20%) developed delirium postoperatively, whereas 17 (31%) never developed delirium.Sdnn, tp and hf values were significantly higher in patients with delirium compared to patients without delirium, and lf and lf/hf were lower.Patients developing postoperative delirium had decreased lf and increased hf before symptom onset.Discussion increased sdnn, tp and hf and decreased lf values might reflect an abnormal stress response in delirium.Conclusion hrv measurements in patients with hip fractures provide additional information beyond heart rate and might be used to identify relevant pathophysiological factors in delirium.

Journal: Aging clinical and experimental research (2020)
Publication types: Journal Article
Simultaneous Detection of 2 Types of Malignancies in a Pediatric Patient on FDG PET/CT Led to Diagnosis of Li-Fraumeni Syndrome.

A 17-month-old girl underwent fdg pet/ct to evaluate a right adrenal lesion, which showed abnormal 18 f-fdg avidity.In addition, an unexpected lesion with mild 18 f-fdg uptake was noted in the right anterior thoracic wall.Pathology demonstrated adrenocortical carcinoma in the right adrenal and rhabdosarcoma in both the left forearm and right anterior thoracic wall.Gene analysis confirmed the diagnosis of li-fraumeni syndrome.The present case emphasized fdg pet/ct value of showing simultaneously multiple lesions in li-fraumeni syndrome, especially in the early stage without the gene analysis result.

Journal: Clinical nuclear medicine (2022)
Publication types: Case Reports;Journal Article
[18F]2-Fluoro-2-deoxy-sorbitol PET Imaging for Quantitative Monitoring of Enhanced Blood-Brain Barrier Permeability Induced by Focused Ultrasound.

Focused ultrasound in combination with microbubbles (fus) provides an effective means to locally enhance the delivery of therapeutics to the brain.Translational and quantitative imaging techniques are needed to noninvasively monitor and optimize the impact of fus on blood-brain barrier (bbb) permeability in vivo.Positron-emission tomography (pet) imaging using [18f]2-fluoro-2-deoxy-sorbitol ([18f]fds) was evaluated as a small-molecule (paracellular) marker of blood-brain barrier (bbb) integrity.[18f]fds was straightforwardly produced from chemical reduction of commercial [18f]2-deoxy-2-fluoro-d-glucose.[18f]fds and the invasive bbb integrity marker evan's blue (eb) were i.v.Injected in mice after an optimized fus protocol designed to generate controlled hemispheric bbb disruption.Quantitative determination of the impact of fus on the bbb permeability was determined using kinetic modeling.A 2.2 ± 0.5-fold higher pet signal (n= 5;p< 0.01) was obtained in the sonicated hemisphere and colocalized with eb staining observed post mortem.Fus significantly increased the blood-to-brain distribution of [18f]fds by 2.4 ± 0.8-fold (vt;p< 0.01).Low variability (=10.1%) of vtvalues in the sonicated hemisphere suggests reproducibility of the estimation of bbb permeability and fus method.[18f]fds pet provides a readily available, sensitive and reproducible marker of bbb permeability to noninvasively monitor the extent of bbb disruption induced by fus in vivo.

Journal: Pharmaceutics (2021)
Publication types: Journal Article
Metabolic and Toxic Myelopathies.

Metabolic and toxic causes of myelopathy form a heterogeneous group of disorders.In this review, we discuss the causes of metabolic and toxic myelopathies with respect to clinical presentation, pathophysiology, diagnostic testing, treatment, and prognosis.This review is organized by temporal course (hyperacute, acute, subacute, and chronic) and etiology (e.g., nutritional deficiency, toxic exposure).Broadly, the myelopathies associated with dietary toxins (neurolathyrism, konzo) and decompression sickness present suddenly (hyperacute).The myelopathies associated with heroin use and electrical injury present over hours to days (acutely).Most nutritional deficiencies (cobalamin, folate, copper) and toxic substances (nitrous oxide, zinc, organophosphates, clioquinol) cause a myelopathy of subacute onset.Vitamin e deficiency and hepatic myelopathy cause a chronic myelopathy.Radiation- and intrathecal chemotherapy-induced myelopathy can cause a transient and/or a progressive syndrome.For many metabolic and toxic causes of myelopathy, clinical deficits may stabilize or improve with rapid identification and treatment.Familiarity with these disorders is therefore essential.

Journal: Seminars in neurology (2021)
Publication types: Journal Article;Review
Corticospinal excitability and motor representation after long-term resistance training.

It is poorly understood how the central nervous system adapts to resistance training, especially after years of exposure.We compared corticospinal excitability and motor representation assessed with transcranial magnetic stimulation (tms) between long-term resistance trained (lrt, ≥3 years) versus untrained (unt) males (n = 15/group).Motor-evoked potentials (meps) were obtained from the biceps brachii during isometric elbow flexion.Stimulus-response curves were created at the hotspot during 10% maximum voluntary torque (mvt) contractions.Maximum peak-to-peak mep amplitude (mepmax) was acquired with 100% stimulator output intensity, whilst 25%-100% mvt was produced.Maps were created during 10% mvt contractions, with an individualised tms intensity eliciting 20% mepmax at the hotspot.Lrt had a 48% lower stimulus-response curve slope than unt (p < .05).Lrt also had a 66% larger absolute map size, although tms intensity used for mapping was greater in lrt versus unt (48% vs.26% above active motor threshold) to achieve a target 20% mepmax at the hotspot, due to the lower slope of lrt.Map size was strongly correlated with the tms intensity used for mapping (r = 0.776, p < .001).Once map size was normalised to tms intensity, there was no difference between the groups (p = .683).We conclude that lrt had a lower stimulus-response curve slope/excitability, suggesting higher neural efficiency.Tms map size was overwhelmingly determined by tms intensity, even when the mep response at the hotspot was matched among individuals, likely due to larger current spread with higher intensities.Motor representation appears similar between lrt and unt given no difference in the normalised map size.

Journal: The European journal of neuroscience (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Acute coronary syndrome because of a scorpion sting in a patient with chronic coronary syndrome: A case report and review of the literature.

The occurrence of acute coronary syndrome (acs) following a scorpion sting has been very rarely reported in literature, and most of the cases presented had a normal coronary angiogram.The possible pathogenetic mechanisms include imbalance in blood pressure and coronary spasm caused by a combination of sympathetic excitation with subsequent thrombosis of coronary vessels developed after the release of vasoactive, inflammatory, and thrombogenic substances contained in the scorpion venom.In this report, we present a case of a scorpion sting complicated by acs, called kounis syndrome (ks).His coronary angiogram revealed the presence of significant stenosis of the left anterior descending artery.He was treated successfully with percutaneous transluminal coronary angioplasty, antivenom serum, and supportive therapy.

Journal: Turk Kardiyoloji Dernegi arsivi : Turk Kardiyoloji Derneginin yayin organidir (2021)
Publication types: Case Reports;Journal Article;Review
Long-term washover fan accretion on a transgressive barrier island challenges the assumption that paleotempestites represent individual tropical cyclones.

Barrier island overwash occurs when the elevation of wave runup exceeds the dune crest and induces landward transport of sediment across a barrier island and deposition of a washover deposit.Washover deposition is generally attributed to major storms, is important for the maintenance of barrier island resilience to sea-level rise and is used to extend hurricane records beyond historical accounts by reconstructing the frequency and extent of washover deposits preserved in the sedimentary record.Here, we present a high-fidelity 3-year record of washover evolution and overwash at a transgressive barrier island site.During the first year after establishment, washover volume and area increased 1595% and 197%, respectively, from at least monthly overwash.Most of the washover accretion resulted from the site morphology having a low resistance to overwash, as opposed to being directly impacted by major storms.Washover deposits can accrete landward over multi-year time scales in the absence of large storms; therefore, paleotempestites can be more complex than single event beds.

Journal: Scientific reports (2020)
Publication types: Journal Article;Research Support, U.S. Gov't, Non-P.H.S.