syedzayyan/paper_mill_benchmark huggingface dataset:
Removal of pharmaceuticals from nitrified urine.

In this study, granular activated carbon (gac) was examined for the removal of five of the most commonly detected pharmaceuticals (naproxen, carbamazepine, acetaminophen, ibuprofen and metronidazole) from a nitrified urine to make the urine-derived fertiliser nutrient safe for food crops.Batch experiments were conducted to investigate the adsorption kinetics that described the removal of micropollutants (equal concentrations of 0.2 m m) from the synthetic nitrified urine at different gac dosages (10-3000 mg/l).Artificial neural network modelling was also used to predict and simulate the removal of pharmaceuticals from nitrified urine.Langmuir and freundlich isotherm models described the equilibrium data, with the langmuir model providing slightly higher correlations.At the highest dose of 3000 mg/l gac, all the pharmaceuticals showed a removal rates of over 90% after 1 h of adsorption time and 99% removal rates after 6 h of adsorption time.This study concludes that gac is able to remove the targeted xenobiotics without affecting the concentration of n and p in the urine, suggesting that nitrified urine could be safely used as a nutrient product in future.

Journal: Chemosphere (2021)
Publication types: Journal Article
A retrospective comparative study of infection control rate and clinical outcome between open debridement using antibiotic-impregnated cement beads and a two-stage revision in acute periprosthetic knee joint infection.

The aim of this study was to determine whether the infection control rate of a modified debridement, antibiotics, and implant retention (dair) protocol (dair with antibiotic-impregnated cement beads) is comparable to that of 2-stage revision for acute periprosthetic joint infection (pji) after total knee arthroplasty (tka).We also aimed to determine whether this modified dair technique produced better clinical results than those obtained using 2-stage revision in terms of functional outcome, range of motion (rom), and patient satisfaction at 2 years after surgery.this retrospective comparative study included patients who underwent modified dair (7 patients, 9 knees) or 2-stage revision (8 patients, 9 knees) for acute pji of the knee joint.Infection control rate, functional outcome measured using western ontario and mc master universities arthritis index (womac) score, rom and patient satisfaction were compared between the two groups.there was no difference in infection control rates between the modified dair and 2-stage revision groups (78% vs 78%, respectively).In contrast, surgical outcome in the modified dair group was tended to be better than 2-stage revision group, but it did not reach statistical significance.Median maximal range of flexion was 103° in the modified dair group and it was 90° in the 2-stage group (p = .191).In addition, the median womac function score was 24 in the modified dair group and it was 30 in the 2-stage group (p = .076).Median patient satisfaction measured using visual analogue scale was 8 in the modified dair group and 5 in the 2-stage group (p = .069).the infection control rates of the modified dair protocol and 2-stage revision protocol were similar for the treatment of acute pji of the knee joint.However, the modified dair protocol could not provide substantially increased functional outcomes and patient satisfaction compared to 2-stage revision.Therefore, the modified dair technique should be considered to be of limited use in patients with high surgical morbidity.

Journal: Medicine (2020)
Publication types: Comparative Study;Journal Article;Observational Study
An outbreak of duck hepatitis A virus infection in nomadic ducklings.

During winter of the year 2020, a flock of 9 day‐old 5000 non‐descript ducklings was affected with huge daily mortality, dullness, depression and opisthotonus.Clinically, there was severe depression, spasmodic paddling and opisthotonus.On post‐mortem, liver was enlarged and pale with patchy ecchymoses.Presence of perihepatitis and pericardititis during post‐mortem examination of one duckling might be attributed to secondary bacterial infection.Upon completion of disease episode, there was 80 percent mortality in eight days and only less than 20 percent weak ducklings survived.Liver homogenate which was subjected for molecular confirmation through one‐step reverse transcriptase polymerase chain reaction (rt‐pcr) using primers for rna dependent rna polymerase (3d) gene yielded positivity for duck hepatitis a virus (dhav‐1).Histological observation of liver revealed hepatocyte degeneration and necrosis.It is clear that dhav‐1 which is epornitic in nature causes a major devastating disease endangering duck farming.

Journal: Veterinaria italiana (2022)
Publication types: Journal Article
Complete Genome Sequence of Morganella morganii CTX51T, Isolated from a Human Cecal Adenocarcinoma.

We report the complete genome sequence of morganella morganii ctx51t, a strain isolated from the resected tumor of a patient with cecal colorectal adenocarcinoma of the cecum.The genome comprises a circular chromosome of 4.19 mbp, with an overall gc content of 50.4% and one circular plasmid of 8.48 kbp.

Journal: Microbiology resource announcements (2022)
Publication types: Journal Article
Life satisfaction, resilience and coping mechanisms among medical students during COVID-19.

Life satisfaction influences well-being.Medical students often experience more stress as compared to their counterparts in other disciplines as they are required to meet the demands of both academic workload and clinical responsibilities.However, during the current pandemic, in addition to academic changes, inability to complete clinical placements, loss of peer interaction and social connectedness and, deployment to areas in times of crisis could exacerbate their stress.This would impact their ability to cope with stress and eventually influence their life satisfaction.Students approach these challenges in various ways, either positively, religiously, or by avoiding.This study aimed to explore the association between resilience, coping mechanisms and life satisfaction in medical students during the pandemic.Methods a cross-sectional web-based survey was conducted from undergraduate medical students from year 1 to year 5.Three instruments were used to measure life satisfaction, resilience, and coping, namely the brief resilience scale, the satisfaction with life scale and the cope inventory.Mean and standard deviation were calculated for all continuous variables.Robust linear regression model was used for analysis.Hierarchical (forward) stepwise model building technique was used for final model.Alpha cut off was kept at 0.05.Results a total of 351 students (out of 500 students) completed the questionnaires.A moderately negative, slightly linear correlation between life satisfaction and avoidant coping was reported.Life satisfaction showed moderately positive, slightly linear correlation with resilience score.Three variables stayed significant in the final model: resilience, avoidant coping, and religion coping.Conclusion life satisfaction can be improved among medical students by focusing on strategies which enhance resilience.Religion is identified as a significant coping strategy among medical students.Students coping mechanism can vary and more research is needed to assess which types of coping strategies could contribute positively to the quality of their personal and professional lives.

Journal: PloS one (2022)
Publication types: Journal Article
Intractable Coronary Spasm Requiring Percutaneous Coronary Intervention after Coronary Artery Bypass Grafting in a Patient with Moyamoya Disease.

Moyamoya disease (mmd) is characterized by progressive steno-occlusive lesions of the distal or proximal branch of the internal carotid arteries, and cerebrovascular symptoms are its major complications.Extracranial vascular involvement including the coronary artery has been reported, and some case reports have described variant angina or myocardial infarction.However, no report has yet described a case of myocardial infarction after coronary artery bypass grafting (cabg).Here, we present a patient with mmd who suffered cardiac arrest caused by myocardial infarction due to a coronary spasm after offpump cabg and who was discharged successfully after treatment with a veno-arterial extracorporeal membrane oxygenator and percutaneous coronary intervention.

Journal: Journal of chest surgery (2021)
Publication types: Case Reports;Journal Article
Specific neuronal subpopulations in the amygdala of macaque monkeys express high levels of nonphosphorylated neurofilaments.

Pyramidal neurons in the neocortex that express nonphosphorylated neurofilaments (npnfs) are especially vulnerable to degeneration in alzheimer's disease.Since the basolateral nuclear complex of the amygdala (bnc) and cortical nuclear complex of the amygdala (cnc) are cortex-like structures, containing both pyramidal (pns) and nonpyramidal neurons (npns), it is of interest to determine which cell types in the primate bnc and cnc are npnf+.We also studied npnf expression in the non-cortex-like nuclei of the amygdala (central and medial nuclei).Digitized images of sections through fetal, newborn, infant, and adult macaque brains stained for npnfs, obtained from the macaque brain resource (mac brain resource, mbr), were analyzed.The pattern of npnf immunoreactivity (npnf-ir) in the bnc, cnc, and medial nucleus was essentially identical in all four age groups, but there were some age-dependent differences in the central nucleus.All bnc and cnc nuclei contained a moderate density of npnf+ npns.Both the somata and the entire dendritic arborizations of these npns were stained.Pns with robust npnf-ir in their somata and proximal dendrites were only seen in the basal magnocellular nucleus, where it appeared that virtually every pn was npnf+.This pattern of npnf expression is distinct from that seen in the mammalian neocortex, where npnf+ neurons are almost entirely pns, but is very similar to that seen in a recent study of the rat bnc.These findings, in conjunction with the cortical data, suggest the possibility that npnf+ neuronal subpopulations in the bnc and cnc might be especially vulnerable in alzheimer's disease.

Journal: Brain research (2022)
Publication types: Journal Article;Research Support, N.I.H., Extramural
Many-Body Exciton and Intervalley Correlations in Heavily Electron-Doped WSe2Monolayers.

In monolayer transition-metal dichalcogenide semiconductors, many-body correlations can manifest in optical spectra when electron-hole pairs (excitons) are photoexcited into a 2d fermi sea of mobile carriers.At low carrier densities, the formation of charged excitons (x±) is well documented.However, in wse2monolayers, an additional absorption resonance, often called x-', emerges at high electron density.Its origin is not understood.Here, we investigate the x-' state via polarized absorption spectroscopy of gated wse2monolayers in magnetic fields to 60t.Field-induced filling and emptying of the lowest optically active landau level in the k' valley causes repeated quenching of the corresponding optical absorption.Surprisingly, these quenchings are accompanied by absorption changes to higher landau levels in both k' and kvalleys, which are unoccupied.These results cannot be reconciled within a single-particle picture, and demonstrate the many-body nature and intervalley correlations of the x-' quasiparticle state.

Journal: Nano letters (2022)
Publication types: Journal Article
DL-3-n-butylphthalide promotes hippocampal neurogenesis and reduces mossy fiber sprouting in chronic temporal lobe epilepsy rats.

A decrease in hippocampal neurogenesis is considered an important cause of cognitive impairment, while changes in mossy fiber sprouting are closely related to development of spontaneous recurrent seizures in chronic temporal lobe epilepsy (tle).Racemic l-3-n-butylphthalide (dl-nbp) can alleviate cognitive impairment in ischemic stroke and alzheimer's disease by promoting neurogenesis.Dl-nbp treatment can also improve cognitive function and reduce seizure incidence in chronic epileptic mice.However, the mechanisms of action of dl-nbp remain unclear.The aim of the present study was to examine the effects of dl-nbp on mossy fiber sprouting, hippocampal neurogenesis, spontaneous epileptic seizures, and cognitive functioning in the chronic phase of tle.Methods nissl staining was used to evaluate hippocampal injury, while immunofluorescent staining was used to analyze hippocampal neurogenesis.The duration of spontaneous seizures was measured by electroencephalography.The morris water maze was used to evaluate cognitive function.Timm staining was used to assess mossy fiber sprouting.Results tle animals showed reduced proliferation of newborn neurons, cognitive dysfunction, and spontaneous seizures.Treatment with dl-nbp after tle increased the proliferation and survival of newborn neurons in the dentate gyrus, reversed the neural loss in the hippocampus, alleviated cognitive impairments, and decreased mossy fiber sprouting and long-term spontaneous seizure activity.Conclusions we provided pathophysiological and morphological evidence that dl-nbp might be a useful therapeutic for the treatment of tle.

Journal: BMC neurology (2022)
Publication types: Journal Article
IL-1β enhances cell viability and decreases 5-FU sensitivity in novel colon cancer cell lines derived from African American patients.

In the u.s., african americans (aas) present with the highest incidence and mortality rates for colorectal cancer (crc).When compared to caucasian american (ca) patients, aas also have reduced response to the first line standard of care chemotherapeutic agent 5-fluorouracil (5-fu).Previously, we observed differential gene expression between the two populations, suggesting that colon tumors from aa patients display a decreased antitumor immune response and an increased expression of genes encoding proteins involved in inflammatory processes, such as interleukin-1β (il-1β).Here, we investigate the role of il-1β in modifying chemotherapeutic response and altering expression of proteins in novel aa and well-established ca colon cancer cell lines.Methods rna sequencing analysis was performed to detect expression of genes involved in inflammation in aa and ca colon cancer cells.The effects of il-1β on 5-fu response was evaluated by assessing cell viability (mts assay) and apoptosis (flow cytometry analysis) following treatment with 5-fu alone or in combination with the cytokine.Further, we used an il-1 receptor antagonist (il-1ra) to inhibit il-1β-induced effects on 5-fu sensitivity and nf-k b pathway activation.Results aa colon cancer cell lines present significant increase in expression of genes il1r2(373-fold change (fc),irak1 (3.24 fc),ikbkb, (5.33 fc)nf-kb ia(5.95 fc),myd88, (3.72 fc),irak3(161 fc),traf5(4.1 fc).A significant decrease in the response to 5-fu treatment, as well as a significant increase in phosphorylation of iκbα and secretion of il-8, was seen following il-1β treatment, in both aa and ca cell lines.Finally, treatment with il-1ra was able to reverse the effects induced by il-1β, by increasing the cells sensitivity to 5-fu.Il-1ra also inhibited phosphorylation of iκbα and il-8 secretion.Conclusions our results suggest a differential expression of inflammatory genes and proteins that might regulate the different response to il-1β between aa and ca colon cancer cell lines.Our data also demonstrates that il-1β is involved in modulating 5-fu response in both aa and ca colon cancer cell lines.Further investigation of these mechanisms might help elucidate the differences seen in incidence, mortality and response to therapy in aa colon cancer patients.

Journal: Frontiers in oncology (2022)
Publication types: Journal Article
Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants.

Although many laboratories worldwide have developed their sequencing capacities in response to the need for sars-co v-2 genome-based surveillance of variants, only a few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases.Hence, we aimed here to provide simple quality control criteria for sars-co v-2 sequencing to prevent erroneous interpretation of low-quality or contaminated data.We retrospectively investigated 647 sars-co v-2 genomes obtained over 10 tiled amplicons sequencing runs.We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis.Based on data distribution, critical values were established for 11 selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral rna quantity.Low-frequency variants (<70% of supporting reads) can result from pcr amplification errors, sample cross contaminations, or presence of distinct sars-co v2 genomes in the sample sequenced.The number and the prevalence of low-frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations.Overall, we propose 11 metrics with fixed cutoff values as a simple tool to evaluate the quality of sars-co v-2 genomes, among which are cycle thresholds, mean depth, proportion of genome covered at least 10×, and the number of low-frequency variants combined with mutation prevalence data.

Journal: Journal of clinical microbiology (2021)
Publication types: Journal Article
Graphene Oxide-Reinforced Alginate Hydrogel for Controlled Release of Local Anesthetics: Synthesis, Characterization, and Release Studies.

In pain relief, lidocaine has gained more attention as a local anesthetic.However, there are several side effects that limit the use of local anesthetics.Therefore, it is hypothesized that a hydrogel system with facile design can be used for prolonged release of lidocaine.In this study, we developed a formulation comprises of sodium alginate (sa) and graphene oxide (go) to prolong the release of lidocaine.The gelation was induced by physically crosslinking the alginate with ca2+ions.The formation of blank sa and go-reinforced sa hydrogels was investigated with different concentration of ca2+ions.The controlled release of lidocaine hydrochloride (lh) on both hydrogel systems was studied in pbs solution.The go-reinforced sa hydrogels exhibited more sustained release than sa hydrogels without go.In vitro biocompatibility test in l929 fibroblast cells confirmed the non-toxic property of hydrogels.Furthermore, to prove thein-situgelation and biodegradability of hydrogels the hydrogels were injected on mice model and confirmed the stable gel formation.The hydrogels implanted onto the subcutaneous tissue of hydrogels retained over one week.These results indicate that lh-loaded go-reinforced sa hydrogel can be a potential biomaterial for controlled release of local anesthetics.

Journal: Gels (Basel, Switzerland) (2022)
Publication types: Journal Article
Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-l-glutamic Acid-coated Layer-by-Layer Nanoparticles.

The oncogenic transcription factor stat3 is aberrantly activated in 70% of breast cancers, including nearly all triple-negative breast cancers (tnbcs).Because stat3 is difficult to target directly, we considered whether metabolic changes driven by activated stat3 could provide a therapeutic opportunity.We found that stat3 prominently modulated several lipid classes, with most profound effects on n-acyl taurine and arachidonic acid, both of which are involved in plasma membrane remodeling.To exploit these metabolic changes therapeutically, we screened a library of layer-by-layer (lb l) nanoparticles (nps) differing in the surface layer that modulates interactivity with the cell membrane.We found that poly-l-glutamic acid (ple)-coated nps bind to stat3-transformed breast cancer cells with 50% greater efficiency than to nontransformed cells, and the heightened ple-np binding to tnbc cells was attenuated by stat3 inhibition.This effect was also observed in densely packed three-dimensional breast cancer organoids.As stat3-transformed cells show greater resistance to cytotoxic agents, we evaluated whether enhanced targeted delivery via ple-nps would provide a therapeutic advantage.We found that cisplatin-loaded ple-nps induced apoptosis of stat3-driven cells at lower doses compared with both unencapsulated cisplatin and cisplatin-loaded nontargeted nps.In addition, because radiation is commonly used in breast cancer treatment, and may alter cellular lipid distribution, we analyzed its effect on ple-np-cell binding.Irradiation of cells enhanced the stat3-targeting properties of ple-nps in a dose-dependent manner, suggesting potential synergies between these therapeutic modalities.These findings suggest that cellular lipid changes driven by activated stat3 may be exploited therapeutically using unique lb l nps.

Journal: Molecular cancer therapeutics (2021)
Publication types: Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
Resting State Abnormalities of the Default Mode Network in Mild Cognitive Impairment: A Systematic Review and Meta-Analysis.

Large-scale brain networks such as the default mode network (dmn) are often disrupted in alzheimer's disease (ad).Numerous studies have examined dmn functional connectivity in those with mild cognitive impairment (mci), a presumed ad precursor, to discover a biomarker of ad risk.Prior reviews were qualitative or limited in scope or approach.Objective we aimed to systematically and quantitatively review dmn resting state f mri studies comparing mci and healthy comparison (hc) groups.Methods pub med was searched for relevant articles.Study characteristics were abstracted and the number of studies showing no group difference or hyper- versus hypo-connnectivity in mci was tallied.A voxel-wise (es-sdm) meta-analysis was conducted to identify regional group differences.Results qualitatively, our review of 57 mci versus hc comparisons suggests substantial inconsistency; 9 showed no group difference, 8 showed mci > hc and 22 showed hc > mci across the brain, and 18 showed regionally-mixed directions of effect.The meta-analysis of 31 studies revealed areas of significant hypo- and hyper-connectivity in mci, including hypoconnectivity in the posterior cingulate cortex/precuneus (z = -3.1, p < 0.0001).Very few individual studies, however, showed patterns resembling the meta-analytic results.Methodological differences did not appear to explain inconsistencies.Conclusions the pattern of altered resting dmn function or connectivity in mci is complex and variable across studies.To date, no index of dmn connectivity qualifies as a useful biomarker of mci or risk for ad.Refinements to mci diagnosis, including other biological markers, or longitudinal studies of progression to ad, might identify dmn alterations predictive of ad risk.

Journal: Journal of Alzheimer's disease : JAD (2019)
Publication types: Journal Article;Meta-Analysis;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't;Research Support, U.S. Gov't, Non-P.H.S.;Systematic Review