Miracle-dz/UniFAR-FTUs huggingface dataset:
Bartender: a fast and accurate clustering algorithm to count barcode reads

Motivation Barcode sequencing (bar‐seq) is a high‐throughput, and cost effective method to assay large numbers of cell lineages or genotypes in complex cell pools. Because of its advantages, applications for bar‐seq are quickly growing—from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo‐barcodes, such as shRNAs or sgRNAs to simultaneously screen large numbers of cell perturbations. However, the computational pipelines for bar‐seq clustering are not well developed. Available methods often yield a high frequency of under‐clustering artifacts that result in spurious barcodes, or over‐clustering artifacts that group distinct barcodes together. Here, we developed Bartender, an accurate clustering algorithm to detect barcodes and their abundances from raw next‐generation sequencing data. Results In contrast with existing methods that cluster based on sequence similarity alone, Bartender uses a modified two‐sample proportion test that also considers cluster size. This modification results in higher accuracy and lower rates of under‐ and over‐clustering artifacts. Additionally, Bartender includes unique molecular identifier handling and a ‘multiple time point’ mode that matches barcode clusters between different clustering runs for seamless handling of time course data. Bartender is a set of simple‐to‐use command line tools that can be performed on a laptop at comparable run times to existing methods. Availability and implementation Bartender is available at no charge for non‐commercial use at https://github.com/LaoZZZZZ/bartender‐1.1. Contact sasha.levy@stonybrook.edu or song.wu@stonybrook.edu Supplementary information Supplementary data are available at Bioinformatics online.
Time Gain Needed for In-Ambulance Telemedicine: Cost-Utility Model

Background Stroke is a very time-sensitive pathology, and many new solutions target the optimization of prehospital stroke care to improve the stroke management process. In-ambulance telemedicine, defined by live bidirectional audio-video between a patient and a neurologist in a moving ambulance and the automated transfer of vital parameters, is a promising new approach to speed up and improve the quality of acute stroke care. Currently, no evidence exists on the cost effectiveness of in-ambulance telemedicine. Objective We aim to develop a first cost effectiveness model for in-ambulance telemedicine and use this model to estimate the time savings needed before in-ambulance telemedicine becomes cost effective. Methods Current standard stroke care is compared with current standard stroke care supplemented with in-ambulance telemedicine using a cost-utility model measuring costs and quality-adjusted life-years (QALYs) from a health care perspective. We combine a decision tree with a Markov model. Data from the UZ Brussel Stroke Registry (2282 stroke patients) and linked hospital claims data at individual level are combined with literature data to populate the model. A 2-way sensitivity analysis varying both implementation costs and time gain is performed to map the different cost-effective combinations and identify the time gain needed for cost effectiveness and dominance. For several modeled time gains, the cost-effectiveness acceptability curve is calculated and mapped in 1 figure. Results Under the base-case scenario (implementation cost of US $159,425) and taking a lifetime horizon into account, in-ambulance telemedicine is a cost-effective strategy compared to standard stroke care alone starting from a time gain of 6 minutes. After 12 minutes, in-ambulance telemedicine becomes dominant, and this results in a mean decrease of costs by US –$30 (95% CI –$32 to –$29) per patient with 0.00456 (95% CI 0.00448 to 0.00463) QALYs on average gained per patient. In over 82% of all probabilistic simulations, in-ambulance telemedicine remains under the cost-effectiveness threshold of US $47,747. Conclusions Our model suggests that in-ambulance telemedicine can be cost effective starting from a time gain of 6 minutes and becomes a dominant strategy after approximately 15 minutes. This indicates that in-ambulance telemedicine has the potential to become a cost-effective intervention assuming time gains in clinical implementations are realized in the future.
Developmental Osteology of the Parafrontal Bones of the Sphaerodactylidae

Well‐resolved phylogenetic hypotheses and ontogenetic data are often necessary for investigating the evolution of structural novelty. The Sphaerodactylidae comprises 12 genera of predominantly miniaturized geckos. The genera Aristelliger and Teratoscincus are exceptions, with taxa reaching snout‐to‐vent lengths far exceeding those of other sphaerodactylids. These two genera possess enigmatic, supraorbital ossifications—parafrontal bones—which are encountered nowhere else among squamates. At the time of their discovery, these structures were believed to be the result of evolutionary convergence. Although relationships between other sphaerodactylids remain unresolved, recent molecular and morphological data have supported a close relationship between Aristelliger and Teratoscincus. We investigated the ontogeny of parafrontal bones to better understand relationships between sphaerodactylid body size and the presence of parafrontals, and to evaluate whether ontogenetic data support the homology of parafrontals between Aristelliger and Teratoscincus. We hypothesize that the parafrontals of Aristelliger and Teratoscincus are homologous and that there is a threshold body size in sphaerodactylids below which parafrontals do not develop, thus explaining their absence from the miniaturized taxa. The presence of parafrontals was investigated in all sphaerodactylid genera using cleared‐and‐stained, radiographed, and skeletonized specimens. Total surface area of parafrontals was measured for seven species of Aristelliger and six species of Teratoscincus throughout their ontogeny. Histology was used to investigate the cellular composition of the parafrontals throughout their ontogeny. Our data suggest that parafrontals have evolved in parallel from a homologous, parafrontal precursor and that the onset of parafrontal development is not strictly dependent on a threshold body size. Anat Rec, 301:581–606, 2018. © 2017 Wiley Periodicals, Inc.
Altered functional connectivity of the subthalamus and the bed nucleus of the stria terminalis in obsessive-compulsive disorder

Background The assessment of inter-regional functional connectivity (FC) has allowed for the description of the putative mechanism of action of treatments such as deep brain stimulation (DBS) of the nucleus accumbens in patients with obsessive–compulsive disorder (OCD). Nevertheless, the possible FC alterations of other clinically-effective DBS targets have not been explored. Here we evaluated the FC patterns of the subthalamic nucleus (STN) and the bed nucleus of the stria terminalis (BNST) in patients with OCD, as well as their association with symptom severity. Methods Eighty-six patients with OCD and 104 healthy participants were recruited. A resting-state image was acquired for each participant and a seed-based analysis focused on our two regions of interest was performed using statistical parametric mapping software (SPM8). Between-group differences in FC patterns were assessed with two-sample t test models, while the association between symptom severity and FC patterns was assessed with multiple regression analyses. Results In comparison with controls, patients with OCD showed: (1) increased FC between the left STN and the right pre-motor cortex, (2) decreased FC between the right STN and the lenticular nuclei, and (3) increased FC between the left BNST and the right frontopolar cortex. Multiple regression analyses revealed a negative association between clinical severity and FC between the right STN and lenticular nucleus. Conclusions This study provides a neurobiological framework to understand the mechanism of action of DBS on the STN and the BNST, which seems to involve brain circuits related with motor response inhibition and anxiety control, respectively.
Influence of Gamma Irradiation and Nitrogen Fertilizer Levels on Gemmeiza-9 Wheat Cultivar Yield and its Attributes

The present study was conducted in an Extension field at Belbees district, Sharkia Governorate during two winter successive seasons, 2007-2008 and 2008-2009 to investigate the influence of four gamma –irradiation doses (0,10,20and30Gy) and 6 nitrogen fertilizer levels (0,25,50,75,100 and125KgN/fad,) , on yield and it's attributes of bread wheat cultivar Gemmeiza-9 The obtained results indicated that, wheat grains irradiated with low dose (10Gy) of Gamma radiation surpassed the other tow irradiation doses (20 and 30 Gy) and the control in each of plant height(cm), spike length (cm), Flag leaf area(cm 2 )at heading ,number of spikes /m 2 , number of spikelets /spike, number of grains / spikelet, grain weight/spike(g) , grain weight/spikelet (mg), 1000- grains weight(g), grain , straw and biological yields/fad. Each increment in nitrogen supply caused significant increase in each above mentioned yield and yield components studied.
Risk profiles for acute health events after incident atrial fibrillation in patients with end-stage renal disease on hemodialysis

Background Little is known about the cardiovascular risks of incident atrial fibrillation/flutter (AF) in patients with end-stage renal disease (ESRD) undergoing hemodialysis (HD). Methods We studied older US patients who newly initiated HD for ESRD (2006-11) and who had not previously been diagnosed with AF, stroke, myocardial infarction (MI) or hip fracture. We used Cox regression with AF as a time-varying covariate, adjusted for socio-demographic characteristics and comorbidities to estimate hazard ratios [HRs (95% confidence intervals)] for the events of ischemic stroke, MI and death. Hip fracture served as a negative control outcome. Results We identified 85 377 older patients (mean age: 76.5 years) who initiated HD; of these, 14.3% were subsequently diagnosed with AF (14.9% thereof as primary diagnosis) and 49.8% died during follow-up. Incident AF was associated with nine times higher adjusted mortality during the first 30 days [9.2 (8.8-9.6)], 5-fold higher mortality between 31 and 90 days [4.6 (4.3-4.8)] and double the mortality beyond 90 days from first AF diagnosis [2.2 (2.1-2.3)]. Incident AF was similarly associated with higher adjusted risk of ischemic stroke: 2.1 (1.6-2.7) during the first 30 days, 2.5 (2.0-3.0) between 31 and 90 days and 1.5 (1.3-1.7) beyond 90 days. Similar findings were obtained for MI. However, the risk of hip fracture was only marginally increased following AF diagnosis [≤30 days: 1.1 (0.7-1.6); 31-90 days: 1.4 (1.0-1.8); >90 days: 1.2 (1.1-1.4)]. All associations were attenuated and the association with hip fracture was null when incident AF was defined by a primary diagnosis code. Conclusions AF was strongly associated with increased risks of ischemic stroke, MI and death, with risks highest soon after AF diagnosis but extending beyond 90 days.
From genetics to response to injury: vascular smooth muscle cells in aneurysms and dissections of the ascending aorta

Vascular smooth muscle cells (vSMCs) play a crucial role in both the pathogenesis of Aneurysms and Dissections of the ascending thoracic aorta (TAAD) in humans and in the associated adaptive compensatory responses, since thrombosis and inflammatory processes are absent in the majority of cases. Aneurysms and dissections share numerous characteristics, including aetiologies and histopathological alterations: vSMC disappearance, medial areas of mucoid degeneration, and extracellular matrix (ECM) breakdown. Three aetiologies predominate in TAAD in humans: (i) genetic causes in heritable familial forms, (ii) an association with bicuspid aortic valves, and (iii) a sporadic degenerative form linked to the aortic aging process. Genetic forms include mutations in vSMC genes encoding for molecules of the ECM or the TGF-β pathways, or participating in vSMC tone. On the other hand, aneurysms and dissections, whatever their aetiologies, are characterized by an increase in wall permeability leading to transmural advection of plasma proteins which could interact with vSMCs and ECM components. In this context, blood-borne plasminogen appears to play an important role, because its outward convection through the wall is increased in TAAD, and it could be converted to active plasmin at the vSMC membrane. Active plasmin can induce vSMC disappearance, proteolysis of adhesive proteins, activation of MMPs and release of TGF-β from its ECM storage sites. Conversely, vSMCs could respond to aneurysmal biomechanical and proteolytic injury by an epigenetic phenotypic switch, including constitutional overexpression and nuclear translocation of Smad2 and an increase in antiprotease and ECM protein synthesis. In contrast, such an epigenetic phenomenon is not observed in dissections. In this context, dysfunction of proteins involved in vSMC tone are interesting to study, particularly in interaction with plasma protein transport through the wall and TGF-β activation, to establish the relationship between these dysfunctions and ECM proteolysis.
Enhancement bandwidth of triangular microstrip antenna using peripheral slit technique fed by coplanar waveguide for mobile communication

This paper proposed new design of triangular microstrip antenna using slit technique fed by coplanar waveguide to enhanced bandwidth for mobile communication purposes. Antenna designed using FR4 substrate with value (εr) = 4.3, substrate thickness (h) of 1.6 mm and loss tangent (tan δ) of 0.0265. From the simulation result shown return loss of −19.57 dB and VSWR 1.242 at work of frequency of 1800 MHz can be achieved by controlling the height of slit L1 and L2. Bandwidth of proposed antenna is 315 MHz which equal to an increase 61.53 % compared to the conventional triangular microstrip antenna and also the dimension of antenna can be reduced until 32.57 %.
Anti-Aging Medicine: Molecular Basis for Endothelial Cell-Targeted Strategies – A Mini-Review

Due to improvements in lifestyle and healthcare, the proportion of aged people is rising steadily, especially in developed countries. With aging, some physiological functions are altered and resemble those occurring in disease conditions such as hypertension, chronic coronary disease and diabetes. Thus, there is the urge to better understand molecular and cellular mechanisms underlying aging and aging-related diseases. In rodents and possibly primates, calorie restriction is an effective approach to extend lifespan by reducing free radical-induced damage. Increased production of oxygen-derived free radicals plays an important role in the process of aging. Reactive oxygen species are generated by different intracellular molecular pathways principally located in the cytoplasm and in the mitochondria. The mitochondrial protein p66Shc is considered a longevity assurance gene since its genetic deletion extends the lifespan of rodents and displays protective effects in several models of cardiovascular disease. Silent mating type information regulation 2 homolog 1 Saccharomyces cerevisiae (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylase that may also be involved in aging and diseases. SIRT1 also deacetylates a number of nonhistone target proteins, including p53, endothelial nitric oxide synthase and forkhead box protein. This review focuses on the latest scientific advances in understanding aging as well as delineates the possible therapeutic implications of p66Shc and SIRT1 in this process.
Common Mental Disorders in Primary Health Care Units

BACKGROUND: Considering the high worldwide prevalence of common mental disorders (CMDs), characterizing the association between CMD and quality of life (QoL) constitute a valuable measure to gauge patient’s functional impairment due to CMD symptoms. OBJECTIVE: To investigate factors associated with the incidence of CMD and its impact on the QoL in primary health care (PHC) patients. DESIGN: Cross-sectional study completed in a municipality in Brazil. Standardized tools included the Self-Reporting Questionnaire–20 to detect CMDs and the WHOQOL-brief to assess QoL, in addition to a sociodemographic and treatment-related questionnaire. RESULTS: A total of 41.4% of the patients met cutoff scores for a CMD, and the presence of a CMD was associated with female gender and marital status. Patients with CMDs had lower QoL scores than patients who were negative for a CMD. CONCLUSIONS: CMDs are highly prevalent in PHC settings and affect patients’ QoL. The high frequency of CMD in those that seek care through PHC necessitate incorporating mental health services into the range of available services.
Frontal Lobe Epilepsy Surgery in Childhood and Adolescence: Predictors of Long-Term Seizure Freedom, Overall Cognitive and Adaptive Functioning

BACKGROUND Although frontal lobe resections account for one-third of intralobar resections in pediatric epilepsy surgery, there is a dearth of information regarding long-term seizure freedom, overall cognitive and adaptive functioning. OBJECTIVE To identify outcome predictors and define the appropriate timing for surgery. METHODS We retrospectively analyzed the data of 75 consecutive patients aged 10.0 ± 4.9 yr at surgery that had an 8.1 yr mean follow-up. RESULTS Etiology comprised focal cortical dysplasia (FCD) in 71% and benign tumors in 16% cases. All patients but one had a magnetic resonance imaging-visible lesion. At last follow-up, 63% patients remained seizure-free and 37% had discontinued antiepileptic drugs. Presurgical predictors of seizure freedom were a shorter epilepsy duration, strictly regional epileptic discharges in electroencephalography (EEG), and an epileptogenic zone and/or lesion distant from eloquent cortex. Postsurgical predictors were the completeness of resection and the lack of early postoperative seizures or epileptic discharges in EEG. Higher presurgical overall cognitive and adaptive functioning was related to later epilepsy onset and to a sublobar epileptogenic zone and/or lesion. Following surgery, scores remained stable in the majority of patients. Postsurgical gains were determined by higher presurgical performance and tumors vs FCD. CONCLUSION Our findings highlight the favorable long-term outcomes following frontal lobe epilepsy surgery in childhood and adolescence and underline the importance of early surgical intervention in selected candidates. Early postsurgical relapses and epileptic discharges in EEG constitute key markers of treatment failure and should prompt timely reevaluation. Postsurgical overall cognitive and adaptive functioning is stable in most patients, whereas those with benign tumors have higher chances of improvement.
Magnetic resonance imaging studies in bipolar disorder and schizophrenia: meta-analysis.

BACKGROUND Several magnetic resonance imaging (MRI) studies have identified structural abnormalities in association with bipolar disorder. The literature is, however, heterogeneous and there is remaining uncertainty about which brain areas are pivotal to the pathogenesis of the condition. AIMS To identify, appraise and summarise volumetric MRI studies of brain regions comparing bipolar disorder with an unrelated control group and individuals with schizophrenia. METHOD A systematic review and random-effects meta-analysis was carried out to identify key areas of structural abnormality in bipolar disorder and whether the pattern of affected areas separated bipolar disorder from schizophrenia. Significant heterogeneity was explored using meta-regression. RESULTS Participants with bipolar disorder are characterised by whole brain and prefrontal lobe volume reductions, and also by increases in the volume of the globus pallidus and lateral ventricles. In comparison with schizophrenia, bipolar disorder is associated with smaller lateral ventricular volume and enlarged amygdala volume. Heterogeneity was widespread and could be partly explained by clinical variables and year of publication, but generally not by differences in image acquisition. CONCLUSIONS There appear to be robust changes in brain volume in bipolar disorder compared with healthy volunteers, although most changes do not seem to be diagnostically specific. Age and duration of illness appear to be key issues in determining the magnitude of observed effect sizes.
Development of a Global Respiratory Severity Score for Respiratory Syncytial Virus Infection in Infants

Background Respiratory syncytial virus (RSV) infection in infants has recognizable clinical signs and symptoms. However, quantification of disease severity is difficult, and published scores remain problematic. Thus, as part of a RSV pathogenesis study, we developed a global respiratory severity score (GRSS) as a research tool for evaluating infants with primary RSV infection. Methods Previously healthy infants <10 months of age with RSV infections representing the spectrum of disease severity were prospectively evaluated. Clinical signs and symptoms were collected at 3 time points from hospitalized infants and those seen in ambulatory settings. Data were also extracted from office, emergency department, and hospital records. An unbiased data-driven approach using factor analysis was used to develop a GRSS. Results A total of 139 infants (84 hospitalized and 55 nonhospitalized) were enrolled. Using hospitalization status as the output variable, 9 clinical variables were identified and weighted to produce a composite GRSS. The GRSS had an area under the receiver operator curve of 0.961. Construct validity was demonstrated via a significant correlation with length of stay (r = 0.586, P < .0001). Conclusions Using routine clinical variables, we developed a severity score for infants with RSV infection that should be useful as an end point for investigation of disease pathogenesis and as an outcome measure for therapeutic interventions.
Predictors of antimalarial self-medication in illegal gold miners in French Guiana: a pathway towards artemisinin resistance

Background Malaria is endemic in French Guiana (FG), South America. Despite the decrease in cases in the local population, illegal gold miners are very affected by malaria (22.3% of them carried Plasmodium spp.). Self-medication seems to be very common, but its modalities and associated factors have not been studied. The aim of this study was to evaluate parasite susceptibility to drugs and to document behaviours that could contribute to resistance selection in illegal gold miners. Methods This multicentric cross-sectional study was conducted in resting sites along the FG-Surinamese border. Participating gold miners working in FG completed a questionnaire and provided a blood sample. Results From January to June 2015, 421 illegal gold miners were included. Most were Brazilian (93.8%) and 70.5% were male. During the most recent malaria attack, 45.5% reported having been tested for malaria and 52.4% self-medicated, mainly with artemisinin derivatives (90%). Being in FG during the last malaria attack was the main factor associated with self-medication (adjusted OR = 22.1). This suggests that access to malaria diagnosis in FG is particularly difficult for Brazilian illegal gold miners. Treatment adherence was better for persons who reported being tested. None of the 32 samples with Plasmodium falciparum presented any mutation on the pfK13 gene, but one isolate showed a resistance profile to artemisinin derivatives in vitro. Conclusions The risk factors for the selection of resistance are well known and this study showed that they are present in FG with persons who self-medicated with poor adherence. Interventions should be implemented among this specific population to avoid the emergence of artemisinin resistance.