syedzayyan/paper_mill_benchmark huggingface dataset:
A novel denitrifying phosphorus removal and partial nitriﬁcation, anammox (DPR-PNA) process for advanced nutrients removal from high-strength wastewater.

This study developed a novel dpr-pna (denitrifying phosphorus removal, partial nitrification and anammox) process for sustaining high-strength wastewater treatment in a modified continuous flow reactor without external carbon source.After 259-days operation, a synchronous highly-efficient total inorganic nitrogen, po43--p and codcrremoval efficiencies of 88.5%, 89.5% and 90.1% were obtained, respectively even influent nitrogen loading rate up to 3.2 kg m-3d-1.Batch tests revealed that denitrifying phosphorus accumulating organisms (dpaos) using no3--n as electron acceptors significantly enriched (74% in total paos), which emerged remarkable positive impacts on deep-level nutrient removal as the key limiting factor.Furthermore, the no2--n inhibitory threshold value (∼20.0 mg l-1) for dpaos was identified, which demonstrated as an inhibitory component in excessive recycling nox--n.From the molecular biology perspective, dechloromonas-dpaos group (18.59%) dominated the excellent dephosphatation performance, while nitrosomonas-aob (ammonia oxidizing bacteria) group (16.26%) and candidatus_brocadia-an aob (anammox bacteria) group (15.12%) were responsible for the desirable nitrogen loss process.Overall, the present work highlighted the novel dpr-pna process for nutrients removal is a promising alternation for wastewater of high nitrogen but low carbon.

Journal: Chemosphere (2021)
Publication types: Journal Article
Tracking Social Media Discourse About the COVID-19 Pandemic: Development of a Public Coronavirus Twitter Data Set.

At the time of this writing, the coronavirus disease (covid-19) pandemic outbreak has already put tremendous strain on many countries' citizens, resources, and economies around the world.Social distancing measures, travel bans, self-quarantines, and business closures are changing the very fabric of societies worldwide.With people forced out of public spaces, much of the conversation about these phenomena now occurs online on social media platforms like twitter.Objective in this paper, we describe a multilingual covid-19 twitter data set that we are making available to the research community via our covid-19-tweet ids git hub repository.Methods we started this ongoing data collection on january 28, 2020, leveraging twitter's streaming application programming interface (api) and tweepy to follow certain keywords and accounts that were trending at the time data collection began.We used twitter's search api to query for past tweets, resulting in the earliest tweets in our collection dating back to january 21, 2020.Results since the inception of our collection, we have actively maintained and updated our git hub repository on a weekly basis.We have published over 123 million tweets, with over 60% of the tweets in english.This paper also presents basic statistics that show that twitter activity responds and reacts to covid-19-related events.Conclusions it is our hope that our contribution will enable the study of online conversation dynamics in the context of a planetary-scale epidemic outbreak of unprecedented proportions and implications.This data set could also help track covid-19-related misinformation and unverified rumors or enable the understanding of fear and panic-and undoubtedly more.

Journal: JMIR public health and surveillance (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Lateral Flow Assays in Infectious Disease Diagnosis.

Lateral flow immunoassays are widely used as diagnostic tests in many applications in human and other diagnostic areas.Assays for human applications have been commercially available since the 1980s and initially were primarily used to identify pregnancy by measuring human chorionic gonadotropin in urine and serum/plasma.Content the first infectious disease lateral flow assays were commercialized in the late 1980s identifying the presence of group a streptococcus pyogenes collected with throat swabs; innumerable other applications followed in the intervening decades.The severe acute respiratory syndrome-coronavirus 2 (sars-co v-2) pandemic has brought a vast number of new assays for which emergency use authorization (eua) has been requested in the usa.These assays have been designed for detection of the antibody response to an infection and viral antigens in respiratory samples.In view of the onslaught of new tests, this review will focus on the use of rapid lateral flow immunoassays for infectious diseases.Principles of lateral flow assays and approaches to the production of high-sensitivity point-of-care assays are presented.Market trends, customer requirements, and future directions of lateral flow assay technology and its applications in the infectious disease diagnostic space are discussed.Summary lateral flow immunoassays play an important role in infectious disease diagnostics.Advancements in technology have led to improved performance of these assays and acceptance by professional users.With the advent of the sars-co v-2 pandemic, the market has reached new levels requiring hundreds of millions of tests per year for professional and even home use.

Journal: Clinical chemistry (2021)
Publication types: Journal Article;Review
All in the mind? Estimating the effect of mental health on health behaviours.

Health behaviours and mental illness have been found to be strongly correlated, both across and within individuals.However, establishing the precise nature of this link, particularly in terms of causality and its direction, remains a challenge.Much of the relevant existing research follow an experimental design and focus on measuring how changes in health behaviours affect mental health.Objective the study examines changes in mental health and health behaviours within individuals across time and evaluates the evidence for a causal pathway from psychological distress to risky health behaviours.Method using a population representative longitudinal survey providing data from australian households, this study employs a fixed-effects panel model framework to account for unobserved time-invariant individual heterogeneity.An instrumental variable estimation strategy is employed to specifically evaluate the evidence of a causal pathway from psychological distress to risky health behaviours.Results the results confirm strong within-individual associations between psychological distress and health behaviours.Further evidence supports a causal relationship from psychological distress to health behaviours, though only for men and lifestyle habits.The case for a direct causal pathway is less straightforward when considering dietary habits, and potentially also for women.This lack of clarity suggests at least some of the observed within-individual associations reflect causal effects of psychological distress on risky health behaviours.Conclusions given the substantial burden of disease associated with unhealthy behaviours, further research examining potential causal pathways from mental health to health behaviours should be a priority, as there is the potential to reduce health burden through mental health improvements.

Journal: Social science & medicine (1982) (2019)
Publication types: Journal Article
Deep anterior lamellar keratoplasty for keratoconus: Elements for success.

Advanced keratoconus may require keratoplasty when the patient can no longer achieve functional vision with glasses and contact lenses.Deep anterior lamellar keratoplasty (dalk) has become the surgical treatment of choice due to its undisputed advantages over penetrating keratoplasty including the reduced risk of intraoperative complications, the absence of endothelial immune rejection, and the longer graft survival.Albeit "big-bubble" dalk still represents the most popular surgical method, several modifications have been developed over the years.This allowed standardization of the technique, with improved success rates and clinical outcomes.This review presents an overview on the literature on dalk surgery for keratoconus.We discuss state-of-the art surgical techniques, current evidence on the clinical outcomes and complications as well as possible future directions.

Journal: Saudi journal of ophthalmology : official journal of the Saudi Ophthalmological Society (2022)
Publication types: Journal Article
Neurologic and cognitive sequelae after SARS-CoV2 infection: Different impairment for ICU patients.

The exact incidence of neurological and cognitive sequelae of covid-19 in the long term is yet unknown.The aim of this research is to investigate the type of neurological and cognitive impairment in covid-19 cases of different severity.Two hundred fifteen patients, who had developed covid-19, were examined 4 months after the diagnosis by means of neurological exam and extensive cognitive evaluation, investigating general cognition, memory, verbal fluency, visuospatial abilities and executive functions.Fifty-two of them were treated in intensive care unit (icu patients), whereas 163 were not hospitalized (non-icu patients).Neurological deficits were found in 2/163 (1.2%) of non-icu and in 7/52 (13.5%) of the icu cases, all involving the peripheral nervous system.Icu patients performed significantly worse in all the neuropsychological tests and showed a worse age- and education-corrected cognitive impairment: cognitive impairment index (cii) was higher in icu than in non-icu patients (median icu 3 vs 2, p = .001).Cii significantly correlated with age in both groups, was unrelated to length of follow- up, diabetes and hypertension and - only for icu patients- to pa o2/fi o2at icu admission.Obtained results support the greater susceptibility of covid-19 patients, treated in icu, to develop neurological deficits and cognitive impairment at a four-month follow up, as compared to cases with mild/moderate symptoms.

Journal: Journal of the neurological sciences (2022)
Publication types: Journal Article
Characterisation of the Hippo signalling pathway during bovine preimplantation embryo development.

Blastocyst formation is an important milestone during preimplantation embryo development.During murine preimplantation embryogenesis, the hippo signalling pathway is known to play a significant role in lineage segregation and henceforth the formation of blastocysts.However, the role of this cell signalling pathway during bovine embryogenesis remains unknown.Thus, the aim of the present study was to characterise the hippo signalling pathway during bovine preimplantation embryo development.M rna transcripts of hippo signalling pathway constituents (i.e.Crumbs cell polarity complex component 3 (crb3), mammalian sterile 20-like 1 (mst1), mammalian sterile 20-like 2 (mst2), yes associated protein 1 (yap1), transcriptional coactivator with pdz-binding motif (taz)) were observed during all stages of bovine preimplantation embryo development.To evaluate the localisation of hippo pathway components, bovine embryos at timed stages of development were stained using specific antibodies and observed under a laser confocal microscope.Although mst1/2 proteins were in the cytoplasm during various stages of bovine embryonic development, taz and phosphorylated (p-) yap were detected in the nucleus during the blastocyst stages.Localisation of taz and p-yap proteins was distinct in the bovine compared with mouse model, suggesting that the hippo signalling pathway is regulated differently in early bovine embryos.

Journal: Reproduction, fertility, and development (2020)
Publication types: Journal Article
Synthesis of polymerizable quaternary thiazole salts and their application as antibacterial agents for dental resin.

For the purpose of endowing dental resin with antibacterial activity without impairing physicochemical properties, polymerizable quaternarized thiazole salts (qamemt-x) with different alkyl chain length (12, 14, and 16) were synthesized and characterized by ft-ir and1h-nmr spectra.After adding 5 wt% of qamemt-x into bis-gma/tegdma (50/50, wt./wt.) dental resin, double bond conversion (dc), volumetric shrinkage (vs), flexural strength (fs) and modulus (fm), water sorption (ws) and solubility (sl), and antibacterial activity against streptococcus mutans (s.Mutans) of obtained resin systems were investigated.The results showed that 5 wt% of qamemt-x had no influence on dc, fs, fm, ws, and sl (α > 0.05), while could reduce vs of dental resin (α < 0.05).Cured resins with 5 wt% of qamemt-x all showed antibacterial activity against s.Mutans, and qamemt-16 could endow cured resin with the strongest antibacterial activity which showed an antibacterial efficiency of more than 99%.

Journal: Journal of the mechanical behavior of biomedical materials (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Annular closure device breakage due to recurrent lumbar disc herniation: a case report.

Detailed surgical management, magnetic resonance imaging (mri), and computer tomography (ct) images of a broken annular closure device (acd) have not been reported yet.In this case, a 28-year-old male presented with a new onset of radiculopathy three years after lumbar discectomy and placement of an acd.The ct-myelography and mri revealed a recurrent disc herniation (rdh) and dislocation of a broken acd.Acd removal was performed and confirmed breakage due to rdh with scarring around the rdh and displaced acd.Implant-associated complications and management should be reported in detail in order to enhance knowledge on device-related complications.

Journal: Acta neurochirurgica (2021)
Publication types: Case Reports;Journal Article
Phytochemical Fingerprinting and In Vitro Bioassays of the Ethnomedicinal FernTectaria coadunata(J. Smith) C. Christensen from Central Nepal.

Tectaria coadunata, an ethnomedicinal fern used in nepal to treat a large number of diseases, has been poorly studied with regard to its phytochemical composition and possible bioactivity.This study was performed with the aim of supporting traditional medicine as a new source of bioactive constituents.Phytochemical compositions of methanol extracts were determined by nuclear magnetic resonance (nmr), liquid chromatography-diode array detector-mass spectrophotometry (lc-dad-ms), and liquid chromatography-fluorescence-mass spectrometry.Quali-quantitative data revealed large amount of procyanidins, mainly of the a-type, as well as eriodictyol-7-o-glucuronide and luteolin-7-o-glucoronide as main constituents.The antioxidant, cytotoxic, and inhibitory activity of five enzymes that are implicated in human diseases was evaluated for the extract and fractions.High free-radical scavenging activity in 2,2-diphenyl-1-picrylhydrazyl (dpph) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (abts) assays and inhibitory activities against cholinesterases and tyrosinase were observed.Furthermore, a moderate cytotoxic effect was observed on the 2008 and bx pc3 cell lines.Overall results showed potential usefulness of this fern as a source of phytochemicals for pharmaceutical uses.

Journal: Molecules (Basel, Switzerland) (2019)
Publication types: Journal Article
Development and validation of self-monitoring auto-updating prognostic models of survival for hospitalized COVID-19 patients.

Clinical prognostic models can assist patient care decisions.However, their performance can drift over time and location, necessitating model monitoring and updating.Despite rapid and significant changes during the pandemic, prognostic models for covid-19 patients do not currently account for these drifts.We develop a framework for continuously monitoring and updating prognostic models and apply it to predict 28-day survival in covid-19 patients.We use demographic, laboratory, and clinical data from electronic health records of 34912 hospitalized covid-19 patients from march 2020 until may 2022 and compare three modeling methods.Model calibration performance drift is immediately detected with minor fluctuations in discrimination.The overall calibration on the prospective validation cohort is significantly improved when comparing the dynamically updated models against their static counterparts.Our findings suggest that, using this framework, models remain accurate and well-calibrated across various waves, variants, race and sex and yield positive net-benefits.

Journal: Nature communications (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Monocyte/Macrophage Heterogeneity during Skin Wound Healing in Mice.

Monocytes (mos)/macrophages (mφs) orchestrate biological processes critical for efficient skin wound healing.However, current understanding of skin wound mo/mφ heterogeneity is limited by traditional experimental approaches such as flow cytometry and immunohistochemistry.Therefore, we sought to more fully explore mo/mφ heterogeneity and associated state transitions during the course of excisional skin wound healing in mice using single-cell rna sequencing.The live cd45+cd11b+ly6g- cells were isolated from skin wounds of c57bl/6 mice on days 3, 6, and 10 postinjury and captured using the 10x genomics chromium platform.A total of 2813 high-quality cells were embedded into a uniform manifold approximation and projection space, and eight clusters of distinctive cell populations were identified.Cluster dissimilarity and differentially expressed gene analysis categorized those clusters into three groups: early-stage/proinflammatory, late-stage/prohealing, and ag-presenting phenotypes.Signature gene and gene ontology analysis of each cluster provided clues about the different functions of the mo/mφ subsets, including inflammation, chemotaxis, biosynthesis, angiogenesis, proliferation, and cell death.Quantitative pcr assays validated characteristics of early- versus late-stage mos/mφs inferred from our single-cell rna sequencing dataset.Additionally, cell trajectory analysis by pseudotime and rna velocity and adoptive transfer experiments indicated state transitions between early- and late-state mos/mφs as healing progressed.Finally, we show that the chemokine ccl7, which was a signature gene for early-stage mos/mφs, preferentially induced the accumulation of proinflammatory ly6c+f4/80lo/- mos/mφs in mouse skin wounds.In summary, our data demonstrate the complexity of mo/mφ phenotypes, their dynamic behavior, and diverse functions during normal skin wound healing.

Journal: Journal of immunology (Baltimore, Md. : 1950) (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Minimally Invasive Surgery Approach is Not Associated With Differences in Long-Term Bowel Function Patient-Reported Outcomes After Elective Sigmoid Colectomy.

Postoperative bowel function is a common concern for patients undergoing a sigmoidectomy.We have previously demonstrated that patients with symptomatic bowel function preoperatively have substantial improvement at long-term follow-up.However, the effect of the operative approach on patient-reported bowel function is largely unknown.We aimed to evaluate the differences in long-term patient-reported bowel function after robotic or laparoscopic sigmoid colectomies for benign and malignant disease.Materials and methods a retrospective analysis of a prospectively collected institutional database from july 2015 to july 2020.Patients included underwent a sigmoid colectomy for benign or malignant disease and completed the colorectal functional outcome (corefo) questionnaire at preoperative presentation, postoperatively, and long-term follow-up.Differences between preoperative and postoperative scores, as well as differences between the robotic and laparoscopic cohorts, were compared using paired t-tests.Results a total of 169 patients met inclusion criteria with a median age of 61 y, and 55% of the patients underwent robotic sigmoid colectomy, with the most common diagnosis being diverticular disease (62%).There was no significant difference between the presentation, short-term, or long-term follow-up total corefo scores or subdomains based on the surgical technique.Patients that present asymptomatic remain asymptomatic, while those that are symptomatic demonstrate improvements for both the robotic and laparoscopic groups.Conclusions patient-reported long-term global bowel function does not appear to differ between patients who underwent elective robotic or laparoscopic sigmoid colectomy for benign or malignant disease.Patients that present asymptomatic remain asymptomatic, while those that are symptomatic demonstrate improvements, regardless of surgical technique.

Journal: The Journal of surgical research (2022)
Publication types: Journal Article
Extreme elevation of acute phase reactants and shock secondary to dabrafenib-trametinib.

The emerging role of braf and mek tyrosine-kinase inhibitors has shown new opportunities of treatment for patients with advanced melanoma and braf mutations.Its use is associated with some toxicities, as pyrexia, that clinicians may not be familiarized with.We present the case of a patient diagnosed with stage iv melanoma braf val600e mutated who was started on dabrafenib and trametinib and developed three severe episodes of fever, hypotension and acute phase reactants elevation during the first 3 months of therapy, in the absence of microbiological demonstration of infection.The episodes were initially managed as a septic shock with broad-spectrum antibiotics and vasoactive drugs, while treatment with dabrafenib and trametinib was withheld.After two subsequent dose reduction of dabrafenib, the patient did not experience new episodes of fever.

Journal: Melanoma research (2021)
Publication types: Case Reports;Journal Article
A Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19.

The ability to predict likely prognosis and infectiousness for patients with covid-19 would aid patient management decisions.Diagnosis is usually via real-time pcr, and it is unclear whether the semi-quantitative capability of this method, determining viral load through cycle threshold (ct) values, can be leveraged.Objectives we aim to review available knowledge on correlations between sars-cov-2 ct values and patient- or healthcare-related outcomes to determine whether ct values provide useful clinical information.Sources a pub med search was conducted on 1 june 2020 based on a search strategy of (ct value or viral load) and sars-co v-2.Data were extracted from studies reporting on the presence or absence of an association between ct values, or viral loads determined via ct value, and clinical outcomes.Content data from 18 studies were relevant for inclusion.One study reported on the correlation between ct values and mortality and one study reported on the correlation between ct values and progression to severe disease; both reported a significant association (p < 0.001 and p = 0.008, respectively).Fourteen studies reported on the correlation between ct value or viral loads determined via ct value and disease severity, and an association was observed in eight (57%) studies.Studies reporting on the correlation of viral load with biochemical and haematological markers showed an association with at least one marker, including increased lactate dehydrogenase (n = 4), decreased lymphocytes (n = 3) and increased high-sensitivity troponin i (n = 2).Two studies reporting on the correlation with infectivity showed that lower ct values were associated with higher viral culture positivity.Implications data suggest that lower ct values may be associated with worse outcomes and that ct values may be useful in predicting the clinical course and prognosis of patients with covid-19; however, further studies are warranted to confirm clinical value.

Journal: Infectious diseases and therapy (2020)
Publication types: Journal Article;Review