syedzayyan/paper_mill_benchmark huggingface dataset:
Commentary to "Translational machine learning for child and adolescent psychiatry".

In this commentary on 'translational machine learning for child and adolescent psychiatry,' by dwyer and koutsouleris, we summarize some of the main points made by the authors, which highlight the importance of emerging applications of machine learning for psychiatric disorders in youth but also emphasize principles of good practice.We also offer complementary insights regarding large-scale training, harmonization, and the ability of these artificial intelligence models to adapt to new datasets, which is critical for their stability across imaging centers, and hence for their widespread clinical adoption.

Journal: Journal of child psychology and psychiatry, and allied disciplines (2022)
Publication types: Journal Article;Comment
Management of patients with monkeypox virus infection and contacts in the community and in healthcare settings: a French position paper.

Scope since april 2022, a large number of monkeypox (mpx) cases have emerged across the globe in regions that are known to be totally free of zoonotic reservoir.The high council for public health is a national institute commissioned to provide guidelines to the french ministry of health.The objective of these guidelines and recommendations is to inform the public, people at risk of severe mpx infection, infected patients and their families and contacts and healthcare workers in charge of infected patients.Methods a review of the literature from the medline database was carried out using the single keyword 'monkeypox', including recent and older articles from january 2000 to june 2022.There was no filter for the type of study, except english language.The titles and summaries of all the articles were read by the experts to select articles of interest.The high council for public health brought together specialists with expertise in the field to analyse the scientific literature and international recommendations.Recommendations were classified with clinical practice methodology using four levels (strong recommendation, recommendation, optional recommendation and no recommendation) without grading the level of evidence.To develop and methodologically validate the recommendations, the appraisal of guidelines for research and evaluation instrument (agree-ii)chart was partially used.Questions addressed by the guidelines and recommendations: (a) what are the therapeutic management measures for hospitalized patients with severe forms of mpx infection, and what are the preventive measures to protect healthcare professionals?(b) what are the isolation and prevention measures in the community for patients with mild or moderate severity mpx infection?(c) what are the preventive measures for contacts of an mpx-infected person?(d) who should be vaccinated?(e) what are the specific prevention measures for children and schools?

Journal: Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases (2022)
Publication types: Review;Journal Article
Associations of health-related quality of life with depression and stigma in MERS-CoV survivors during the recovery period.

We explored factors related to health-related quality of life (hrqol), including psychiatric symptoms and stigma related to middle east respiratory syndrome coronavirus (mers-co v) infection, among mers-co v survivors during the recovery period.sixty-three mers-cov survivors were recruited from five hospitals for a cohort study, one year after their infection in 2015.The subjects' demographic information and medical conditions associated with mers-co v were recorded.Hrqol was evaluated using the short form-8 health survey (sf-8).Depression, post-traumatic stress symptoms, chronic fatigue, and perceived stigma were assessed using several questionnaires the mean physical component summary (pcs) and mean mental component summary (mcs) of the sf-8 score were below 50 t (43.47 ± 9.60, 45.74 ± 10.18).Depression, chronic fatigue, posttraumatic stress symptoms and stigma were negatively correlated with the sf-8 pcs and mcs.Multivariate logistic regression analysis showed that the pcs was associated with stigma (or 8.66, 95% ci 1.96-38.23), whereas mcs was associated with depression (or 26.62, 95% ci 3.56-198.85).the estimated hrqol of mers-co v survivors during recovery was poor and appeared to be associated with depression and mers-related stigma.

Journal: Medicine (2022)
Publication types: Journal Article
Herpes zoster vaccine coverage in Australia before and after introduction of a national vaccination program.

In australia, a herpes zoster (hz) vaccination program targeting adults aged 70 years old with catch-up for those 71-79 years began in november 2016 but there is limited information on vaccine uptake and coverage achieved since commencement.Methods we used a national de-identified electronic primary care dataset, medicine insight, and extracted records from patients turning 50-90 years old during 2016-2018.Among patients considered regular attenders, with at least one visit per year in the two years prior, we estimated the crude and adjusted average monthly hz vaccine uptake in the target population (70-79 years old) for each year since program implementation as well as cumulative vaccine coverage until december 2018.Multivariate logistic regression was used to analyse characteristics associated with higher coverage.Results among 52,229, 55,034, and 57,316 regular attenders turning 70-79 years old in 2016, 2017 and 2018 respectively, the average monthly vaccine uptake rate was 5.5%, 3.3%, and 1.6% respectively.Up to 31st december 2018, the estimated cumulative vaccine coverage in regularly attending adults was 46.9% (25,791/55,034).It was substantially lower at 41.6% (27,040/65,010) using an alternate definition of a regular attender.Vaccine coverage differed by sex (women: 48.5% versus men: 45.1%, adjusted or = 1.1, 95% ci: 1.1-1.2); by jurisdiction (compared to new south wales: 43.7%, south australia: 55.6%, a or = 1.6, 95% ci (1.5-1.8); northern territory: 27.6%, a or = 0.6, (0.5-0.7)); by remoteness status (compared to major cities: 47.6%, remote/very remote areas: 38.2%, a or = 0.7, (0.6-0.8)); and by socioeconomic disadvantage (compared to most disadvantaged: 41.8%, most advantaged: 48.6%, a or = 1.6 (1.2-2.1)).Conclusions our estimates of hz vaccine coverage are substantially higher than the only other reports based on the australian immunisation register however they still suggest that uptake is suboptimal.The use of electronic medical records can complement other data for estimating vaccine coverage in australian adults.

Journal: Vaccine (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Cloning, SNP detection, and growth correlation analysis of the 5' flanking regions of two myosin heavy chain-7 genes in Mandarin fish (Siniperca chuatsi).

Myosin heavy chains (myhs) play important roles in muscle growth and contraction.In fish, myhs contribute to hyperplasia and hypertrophy of muscle fibers, which can continue into adult life and thus result in indeterminate growth in some species.We previously identified two myh genes, myh-7a and myh-7b, that are differentially expressed in mandarin fish (siniperca chuatsi) and appear to function in early growth.However, the regulatory role of their 5' flanking regions is unknown.To examine the effects of single nucleotide polymorphisms (snps) in these regions, we used genome walking to amplify their flanking sequences and analyzed the regulatory elements and binding sites.A single snp locus was found in the flanking sequence of each gene.These snp loci are located in the conserved glucocorticoid receptor binding region (myh-7a: g-614a; allele frequency: g:a = 94.9:5.1; gg (89.76) and ag (10.24) genotypes) and the lim homeobox domain transcription factor binding sequence (myh-7b: c-1933a; allele frequency: c:a = 54.8:45.2; aa (20.82), ac (48.81), and cc (30.37) genotypes).At the g-614a loci, the gg genotype exhibited more superior growth traits (total length, body length, body height, etc.) than the ag genotype, with the exception of caudal peduncle length.Alternatively, at the c-1933a loci, the ac and aa genotypes showed significant differences in all growth traits, except for head length, with ac exhibiting superior traits.The aa and cc genotypes showed significant differences in caudal peduncle length and height, while no differences were observed between the ac and cc genotypes.Thus, these snps in the 5' flanking regions of myh-7a and myh-7b are correlated with superior growth and can be used for selecting mandarin fish during breeding.

Journal: Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology (2019)
Publication types: Journal Article
Microbial Production of Human Milk Oligosaccharides.

Human milk oligosaccharides (hmos) are complex nonnutritive sugars present in human milk.These sugars possess prebiotic, immunomodulatory, and antagonistic properties towards pathogens and therefore are important for the health and well-being of newborn babies.Lower prevalence of breastfeeding around the globe, rising popularity of nutraceuticals, and low availability of hmos have inspired efforts to develop economically feasible and efficient industrial-scale production platforms for hmos.Recent progress in synthetic biology and metabolic engineering tools has enabled microbial systems to be a production system of hmos.In this regard, the model organism escherichia colihas emerged as the preferred production platform.Herein, we summarize the remarkable progress in the microbial production of hmos and discuss the challenges and future opportunities in unraveling the scope of production of complex hmos.We focus on the microbial production of five hmos that have been approved for their commercialization.

Journal: Molecules (Basel, Switzerland) (2023)
Publication types: Journal Article;Review
Glial cell-derived neurotrophic factor alleviates sepsis-induced neuromuscular dysfunction by decreasing the expression of γ- and α7-nicotinic acetylcholine receptors in an experimental rat model of neuromyopathy.

Sepsis-induced neuromuscular dysfunction results from up-regulation of the expression of γ- and α7-nicotinic acetylcholine receptors (n ach r).Although glial cell derived neurotrophic factor (gdnf) has been implicated in repairing and supporting neurons, little is known about the effects of gdnf on demyelination of nerves in sepsis.In this study, we tested the hypothesis that gdnf could alleviate sepsis-induced neuromuscular dysfunction by decreasing the expression of γ- and α7-n ach r in an experimental rat model of neuromyopathy.Rats were randomly divided into a sham group and a sepsis group.Levels of inflammatory factors, muscle function, and nicotinic acetylcholine receptors were tested in rats after cecal ligation and puncture (clp).At 24 h after clp, gdnf was injected around the sciatic nerve of sepsis rats, cytokines were detected by enzyme-linked immunosorbent assay (elisa), and immunofluorescence staining was used to detect the expression of n ach rs.Gdnf and its downstream effector (erk1/2 and gfr-α), neuregulin-1 (nrg-1) and γ- and α7-n ach r were measured using western blot analysis.The expression of gdnf reached a minimum at 24 h after clp.Compared with the sham group, the release of cytokines and the expression of γ- and α7-n ach r were significantly increased in the sepsis group.The administration of gdnf significantly alleviated sepsis-induced neuromuscular dysfunction, as well as reducing the expression of γ- and α7-n ach r.In addition, the expression of erk1/2, gfr-α, nrg-1 were significantly increased after gdnf treatment.Gdnf administration may improve patient outcomes by reducing the demyelination of nerves and the expression of γ- and α7-n ach r.

Journal: Biochemical and biophysical research communications (2018)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Repeated water avoidance stress induces visceral hypersensitivity: Role of interleukin-1, interleukin-6, and peripheral corticotropin-releasing factor.

And aim repeated water avoidance stress (was) induces visceral hypersensitivity.Additionally, it is also known to activate corticotropin-releasing factor (crf), mast cells, and pro-inflammatory cytokines systems, but their precise roles on visceral sensation have not been determined definitely.The aim of the study was to explore this issue.Methods abdominal muscle contractions induced by colonic balloon distention, that is, visceromotor response (vmr) was detected electrophysiologically in conscious rats.Was or sham stress as control for 1 h daily was loaded, and the threshold of vmr was determined before and at 24 h after the stress.Results repeated was for three consecutive days reduced the threshold of vmr, but sham stress did not induce any change.Astressin, a crf receptor antagonist (50 μg/kg) intraperitoneally (ip) at 10 min before each was session, prevented the visceral allodynia, but the antagonist (200 μg/kg) ip at 30 min and 15 h before measurement of the threshold after completing 3-day stress session did not modify the response.Ketotifen, a mast cell stabilizer (3 mg/kg), anakinra, an interleukin (il)-1 receptor antagonist (20 mg/kg) or il-6 antibody (16.6 μg/kg) ip for two times before the measurement abolished the response.Conclusions repeated was for three consecutive days induced visceral allodynia, which was mediated through mast cells, il-1, and il-6 pathways.Inhibition of peripheral crf signaling prevented but did not reverse this response, suggesting that peripheral crf may be an essential trigger but may not contribute to the maintenance of repeated was-induced visceral allodynia.

Journal: Journal of gastroenterology and hepatology (2017)
Publication types: Journal Article
Predictors of Engagement and Attendance of a Family-Based Prevention Program for Underage Drinking in Mexico.

Underage drinking represents a major global health problem.Given the crisis that underage drinking represents, tomando buenas decisiones, a family-based prevention program, was adapted and piloted in mexico based on the existing guiding good choices program.Although family-based interventions in the usa are promising for preventing underage drinking, little is known about how adapted versions of these interventions may work in low-middle income countries, such as in latin america.The present study examined whether baseline individual, familial, and cultural factors predict participants' engagement and attendance in an adapted program for preventing underage drinking in zacatecas, mexico.The study was conducted with a sample of 178 parents who participated in the adapted program and were employed at local private companies.Latent growth curve modeling was used to analyze (a) change in engagement, (b) predictors of engagement, and (c) predictors of attendance.Results indicated that perceived engagement evidenced a significant linear increase throughout the intervention.Participants' familism values, such as perceived family as referents and family support, at baseline predicted both initial levels of and change in engagement.Perceived familial obligation also predicted change in engagement.Attendance was negatively predicted by male gender, by perceived stress, and by perceived familial obligations among women only.Poor family management, and perceived familial obligations among men, positively predicted attendance.Our findings have important implications for the conceptualization of engagement and attendance in family-based preventive interventions for underage drinking among hispanics.Researchers interested in implementing interventions in latin america can use these findings to better comprehend how and for whom adapted family-based preventive interventions work.

Journal: Prevention science : the official journal of the Society for Prevention Research (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
Design and evaluation of a dynamic air cushion for pressure ulcers prevention.

Wheelchair users have a higher risk of developing pressure ulcers due to prolonged seated pressure.Pressure ulcers can be painful, may require surgical intervention, and even become life-threatening if infection occurs.To prevent pressure ulcers from forming the patient must either offload themselves or rely on a caregiver to move them allowing pressure redistribution over the seated area.In this work, we designed a dynamic air cushion to relieve pressure on loaded areas using sequences of inflation and deflation of the air cushion cells.The purpose of these sequences is to offload pressure from high-risk areas.To evaluate the effect of the alternating sequences on seated pressure and blood perfusion, we recorded interface pressure, skin blood flow, superficial tissue oxygen saturation, blood concentrations of oxygenated hemoglobin, and deoxygenated hemoglobin from twenty-one healthy volunteers who were asked to sit on the air cushion for static mode recording (3 min) and during the inflation/deflation sequences (up to 22 min).The alternating sequences consisted of ten combined inflation and deflation steps.Results showed that, after applying the alternating sequences, interface pressure reduced significantly (p=0.02) compared to the static mode.Moreover, the coefficient of variation of the seated pressure was higher (p<0.001) during the alternation sequence compared to the static mode.However, interface pressure under the right and left ischial tuberosities increased (p<0.001) during the alternation sequence compared to the static mode.In addition, during the alternating sequences, males had larger dispersion index values of both right and left ischial tuberosities pressure compared to females.Furthermore, the maximum value of oxygen saturation (p=0.04) and skin blood flow (p=0.001) increased during the pressure alternation sequences compared to the static mode.The study findings highlighted the positive effects of the designed dynamic air-cushion to relieve pressure on compressed areas and enhance blood perfusion similar to manual offloading approaches.The outcomes of this study are encouraging to evaluate the performance of the designed air cushion in studies involving wheelchair users.

Journal: Journal of tissue viability (2022)
Publication types: Journal Article
Biallelic Mutations in Ubiquitin-Specific Peptidase 53 (USP53) Causing Progressive Intrahepatic Cholestasis. Report of a Case With Review of Literature.

Whole-exome sequencing studies have recently identified novel genes implicated in normal- or low-ggt pediatric cholestasis including ubiquitin-specific peptidase 53 (usp53).We identified novel biallelic mutations in the usp53gene in a 7-month-old infant with pruritus and progressive intrahepatic cholestasis.His liver biopsy showed portal and perivenular fibrosis with bland bilirubinostasis.His parents were asymptomatic heterozygous for the same mutation.He is currently on vitamin supplements and cholestyramine and his family has also been counseled for liver transplantation.Our report confirms that patients with biallelic mutation in usp53develop cholestatic liver disease.

Journal: Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society (2022)
Publication types: Case Reports;Journal Article;Review
Deregulated cellular circuits driving immunoglobulins and complement consumption associate with the severity of COVID-19 patients.

Sars-co v-2 infection causes an abrupt response by the host immune system, which is largely responsible for the outcome of covid-19.We investigated whether the specific immune responses in the peripheral blood of 276 patients were associated with the severity and progression of covid-19.At admission, dramatic lymphopenia of t, b, and nk cells is associated with severity.Conversely, the proportion of b cells, plasmablasts, circulating follicular helper t cells (c tfh) and cd56-cd16+nk-cells increased.Regarding humoral immunity, levels of ig m, ig a, and ig g were unaffected, but when degrees of severity were considered, ig g was lower in severe patients.Compared to healthy donors, complement c3 and c4 protein levels were higher in mild and moderate, but not in severe patients, while the activation peptide of c5 (c5a) increased from the admission in every patient, regardless of their severity.Moreover, total ig g, the ig g1 and ig g3 isotypes, and c4 decreased from day 0 to day 10 in patients who were hospitalized for more than two weeks, but not in patients who were discharged earlier.Our study provides important clues to understand the immune response observed in covid-19 patients, associating severity with an imbalanced humoral response, and identifying new targets for therapeutic intervention.

Journal: European journal of immunology (2021)
Publication types: Journal Article
Protocol to Study Spatial Subgoal Learning Using Escape Behavior in Mice.

Rodent spatial navigation is a key model system for studying mammalian cognition and its neural mechanisms.Of particular interest is how animals memorize the structure of their environments and compute multi-step routes to a goal.Previous work on multi-step spatial reasoning has generally involved placing rodents at the start of a maze until they learn to navigate to a reward without making wrong turns.It thus remains poorly understood how animals rapidly learn about the structure of naturalistic open environments with goals and obstacles.Here we present an assay in which mice spontaneously memorize two-step routes in an environment with a shelter and an obstacle.We allow the mice to explore this environment for 20 min, and then we remove the obstacle.We then present auditory threat stimuli, causing the mouse to escape to the shelter.Finally, we record each escape route and measure whether it targets the shelter directly (a 'homing-vector' escape) or instead targets the location where the obstacle edge was formerly located (an 'edge-vector' escape).Since the obstacle is no longer there, these obstacle-edge-directed escape routes provide evidence that the mouse has memorized a subgoal location,i.e., a waypoint targeted in order to efficiently get to the shelter in the presence of an obstacle.By taking advantage of instinctive escape responses, this assay probes a multi-step spatial memory that is learned in a single session without pretraining.The subgoal learning phenomenon it generates can be useful not only for researchers working on navigation and instinctive behavior, but also for neuroscientists studying the neural basis of multi-step spatial reasoning.

Journal: Bio-protocol (2022)
Publication types: Journal Article