Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic Distances Between Trees

&NA; Most existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of the distances are the ability to include substitution model parameters and to handle trees with different taxon sets in a principled way. We demonstrate some of the properties of these new distance measures and compare them to existing distances, in particular by applying multidimensional scaling to data sets previously reported as containing phylogenetic islands. [Metric; probability distribution; multidimensional scaling; information geometry.
Full-text publication of abstracts presented at European Orthodontic Society congresses.

INTRODUCTION Empirical evidence has indicated that only a subsample of studies conducted reach full-text publication and this phenomenon has become known as publication bias. A form of publication bias is the selectively delayed full publication of conference abstracts. The objective of this article was to examine the publication status of oral abstracts and poster-presentation abstracts, included in the scientific program of the 82nd and 83rd European Orthodontic Society (EOS) congresses, held in 2006 and 2007, and to identify factors associated with full-length publication. METHODS A systematic search of PubMed and Google Scholar databases was performed in April 2013 using author names and keywords from the abstract title to locate abstract and full-article publications. Information regarding mode of presentation, type of affiliation, geographical origin, statistical results, and publication details were collected and analyzed using univariable and multivariable logistic regression. RESULTS Approximately 51 per cent of the EOS 2006 and 55 per cent of the EOS 2007 abstracts appeared in print more than 5 years post congress. A mean period of 1.32 years elapsed between conference and publication date. Mode of presentation (oral or poster), use of statistical analysis, and research subject area were significant predictors for publication success. LIMITATIONS Inherent discrepancies of abstract reporting, mainly related to presentation of preliminary results and incomplete description of methods, may be considered in analogous studies. CONCLUSIONS On average 52.2 per cent of the abstracts presented at the two EOS conferences reached full publication. Abstracts presented orally, including statistical analysis, were more likely to get published.
Folliculotropism Does Not Affect Overall Survival in Mycosis Fungoides: Results from a Single-Center Cohort and Meta-Analysis

Background: Folliculotropic mycosis fungoides (FMF) is a distinct subtype of mycosis fungoides (MF) with unique clinicopathological features. The medical literature suggests that FMF has a more aggressive course and worse survival than classic MF. Previous studies do not use standardized treatment, and no studies have reported an association between treatment response and overall survival (OS). Objective: To compare OS for MF, FMF, and Sézary syndrome (SS) patients. Methods: Data were collected retrospectively from 218 patients (171 MF, 15 SS, 32 FMF) treated in a single academic center between 1970 and 2016. Results: Negative predictors of OS were age (OR = 1.07), male sex (OR = 1.63), and stage IIB, III, and IV (OR = 4.10, 5.42, and 7.54, respectively, vs. stage IA). Lack of initial PUVA response was strongly associated with negative OS (OR = 3.08). Kaplan-Meier analysis of age-, sex-, and stage-matched MF and FMF patients found similar OS between the 2 groups. The 5-year OS was 91% for FMF and 74% for MF. Meta-analysis of current data and 2 published studies where survival of FMF patients was compared to MF did not reveal statistically significant differences between these 2 diseases. Conclusions: When patients were matched for age, sex, and disease stage, folliculotropism did not affect OS in MF.
A Bayesian multivariate joint frailty model for disease recurrences and survival

Motivated by a study for soft tissue sarcoma, this article considers the analysis of diseases recurrence and survival. A multivariate frailty hazard model is established for joint modeling of three correlated time‐to‐event outcomes: local disease recurrence, distant disease recurrence (metastasis), and death. The goals are to find out (i) the effects of treatments on local and distant disease recurrences, and death, (ii) the effects of local and distant disease recurrences on death, and (iii) the correlation between local and distant recurrences. By our approach, all these three important questions, which are commonly asked in similar medical research studies, can be answered by a single model. We put the proposed joint frailty model in a Bayesian framework and use a hybrid Monte Carlo algorithm for the computation of posterior distributions. This hybrid algorithm relies on the evaluation of the gradient of target log density and a guided walk progress, and it combines these two strategies to suppress random walk behavior. A further distinction is that the hybrid algorithm can update all the components of a multivariate state vector simultaneously. Simulation studies are conducted to assess the proposed joint frailty model and the computation algorithm. The motivating soft tissue sarcoma data set is analyzed for illustration purpose. Copyright © 2016 John Wiley & Sons, Ltd.
Human Chorionic Gonadotropin Test: Old Uncertainties, New Perspectives, and Value in 46,XY Disorders of Sex Development

The human chorionic gonadotropin (hCG) test represents a key step in assessing Leydig cell function in prepubertal males, but differences in terms of hCG doses, number of injections, and sequence of blood drawing are published in the literature, showing poor standardization. The few available data in healthy boys are summarized here. A recombinant hCG (rhCG) formulation might permit overcoming some controversies as well as avoid the potential biological risk related to the injection of extractive hormones. Studies in humans are scarce, but they indicate that 250 µg rhCG in a single dose may represent a useful scheme for the dynamic evaluation of Leydig cell function in children as well as in adults. The main indication for hCG testing in childhood is the investigation of 46,XY disorders of sex differentiation. The test must also be considered in order to investigate the presence of functional testicular tissue when gonadal peptide hormones cannot be measured.
Publication Bias in Pediatric Hematology and Oncology: Analysis of Abstracts Presented at the Annual Meeting of the American Society of Pediatric Hematology and Oncology

Publication bias (PB) is a threat to the validity of medical literature, and has not been studied in the field of pediatric hematology/oncology. We analyzed the abstracts presented at the 2005 American Society of Pediatric Hematology/Oncology annual meeting to assess for PB. Abstracts were categorized by type of research, number of centers, funding status, presentation format, sample size, statistical significance, and the direction of results. Publication status was determined by searching PubMed. Thirty nine abstracts (51%) were categorized as clinical studies, 67 (36%) as basic research, and 24 (13%) as others. One hundred and twenty three abstracts (67%) were considered to have positive results, 14 (8%) negative results, and 47 (25%) with neutral or not stated results. About 62% of the abstracts were published in peer-reviewed journals at a median time to publication of 19 months (IQR = 11–29 months). Abstracts with positive results were more likely to get published than others (combined negative and neutral results) (P = .002). Factors like sample size, number of centers, or statistical significance reporting did not affect the publication rate. Our data suggests the existence of PB in the field of pediatric hematology/oncology. Still, further analysis of other international meetings is needed to validate our findings.
Vocative Intonation Preferences are Sensitive to Politeness Factors

Although intonation has been traditionally associated with the expression of attitudes and intentions on the part of the speaker, little is known about whether sociopragmatic factors, such as power or social distance, or situational ones, like physical distance or insistence, can constrain the use and felicity of pitch contours. This article investigates the felicity conditions underlying the choice of three vocative pitch contours in Central Catalan by means of two experiments, namely a production experiment based on the Discourse Completion Task (320 vocative contours produced by 20 speakers), and an acceptability judgment task in which 72 listeners were asked to rate the appropriateness match between a set of vocative contours and a previous discourse context (3,456 responses). The results from the two experiments show that both situational and social politeness factors govern the choice of vocative intonation. Finally, the results are discussed in line with the traditional classification of politeness strategies defined by Brown and Levinson, in the sense that the three intonation contours can be linked to negative, positive, and bald on-record politeness strategies.
Loss of Syndecan-1 Induces a Pro-inflammatory Phenotype in Endothelial Cells with a Dysregulated Response to Atheroprotective Flow*

Background: The endothelial glycocalyx extends into the arterial lumen and experiences shear forces from blood flow. Results: The loss of syndecan-1 results in a pro-inflammatory phenotype in endothelial cells with an altered response to atheroprotective flow. Conclusion: Syndecan-1 plays an important role in maintaining healthy endothelial phenotype. Significance: Therapies that retain syndecan-1 on endothelial cells may have the potential to reduce the progression of vascular disease. Fluid shear stresses are potent regulators of vascular homeostasis and powerful determinants of vascular disease progression. The glycocalyx is a layer of glycoaminoglycans, proteoglycans, and glycoproteins that lines the luminal surface of arteries. The glycocalyx interacts directly with hemodynamic forces from blood flow and, consequently, is a prime candidate for the mechanosensing of fluidic shear stresses. Here, we investigated the role of the glycocalyx component syndecan-1 (sdc-1) in controlling the shear stress-induced signaling and flow-mediated phenotypic modulation in endothelial cells. We found that knock-out of sdc-1 abolished several key early signaling events of endothelial cells in response to shear stress including the phosphorylation of Akt, the formation of a spatial gradient in paxillin phosphorylation, and the activation of RhoA. After exposure to atheroprotective flow, we found that sdc-1 knock-out endothelial cells had a phenotypic shift to an inflammatory/pro-atherosclerotic phenotype in contrast to the atheroprotective phenotype of wild type cells. Consistent with these findings, we found increased leukocyte adhesion to sdc-1 knock-out endothelial cells in vitro that was reduced by re-expression of sdc-1. In vivo, we found increased leukocyte recruitment and vascular permeability/inflammation in sdc-1 knock-out mice. Taken together, our studies support a key role for sdc-1 in endothelial mechanosensing and regulation of endothelial phenotype.
Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA

Human astroviruses are a major cause of pediatric gastroenteritis, especially in immunocompromised children. We conducted a retrospective study to demonstrate that diverse astrovirus genotypes can co-circulate in pediatric oncology patients. A subset of cases is associated with long-term virus shedding (range 17–183 days).
Efficacy of Modified Atkins Ketogenic Diet in Chronic Cluster Headache: An Open-Label, Single-Arm, Clinical Trial

Introduction Drug-resistant cluster headache (CH) is still an open clinical challenge. Recently, our group observed the clinical efficacy of a ketogenic diet (KD), usually adopted to treat drug-resistant epilepsies, on migraine. Aim Here, we aim to detect the effect of KD in a group of drug-resistant chronic CH (CCH) patients. Materials and methods Eighteen drug-resistant CCH patients underwent a 12-week KD (Modified Atkins Diet, MAD), and the clinical response was evaluated in terms of response (≥50% attack reduction). Results Of the 18 CCH patients, 15 were considered responders to the diet (11 experienced a full resolution of headache, and 4 had a headache reduction of at least 50% in terms of mean monthly number of attacks during the diet). The mean monthly number of attacks for each patient at the baseline was 108.71 (SD = 81.71); at the end of the third month of diet, it was reduced to 31.44 (SD = 84.61). Conclusion We observed for the first time that a 3-month ketogenesis ameliorates clinical features of CCH. Clinical Trial Registration www.ClinicalTrials. gov, identifier NCT03244735.
Stress relaxation study of HAZ reheat cracking in Type 347 stainless steel

Four different compositions of Type 347 austenitic stainless steel were studied using Gleeble - based stress relaxation tests to evaluate susceptibility to weld HAZ reheat cracking. Coupons extracted from plate were ther mally cycled to reproduce the coarse-grained region of the HAZ known to be most prone to such cracking. These samples were then reheated to various PWHT temperatures, and a strain comparable to 70% of the strain to cause vielding at the temperature was applied. Force in the specimens was recorded for up to 3 h while this total strain was kept constant. Force vs. time curves for all samples exhibited an increase attributed to volumetric shrinkage upon precipitation of Nb-rich particles as confirmed by constant-stress tests. Formation of Nb-rich precipitates strengthens the alloy, and stress buildup due to volumetric shrinkage in the age-hardening matrix leads to cracking along grain boundaries when stress cannot relax fast enough by yielding or creep.
Signal Transducer and Activator of Transcription 3 Control of Human T and B Cell Responses

Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that is activated downstream of many key cytokine receptors expressed by lymphocytes. As such, it plays a critical role in regulating B cells as well as CD4+ and CD8+ T cells. Patients with clinically significant immunodeficiency and immune dysregulation resulting from loss-of-function or gain-of-function mutations in STAT3 have been described. These individuals provide insight into the critical role of this transcription factor in the regulation of immune responses and the balance between effective immune protection and autoimmunity.
Estimation and interpretation of heterogeneous vaccine efficacy against recurrent infections

Vaccine‐induced protection may not be homogeneous across individuals. It is possible that a vaccine gives complete protection for a portion of individuals, while the rest acquire only incomplete (leaky) protection of varying magnitude. If vaccine efficacy is estimated under wrong assumptions about such individual level heterogeneity, the resulting estimates may be difficult to interpret. For instance, population‐level predictions based on such estimates may be biased. We consider the problem of estimating heterogeneous vaccine efficacy against an infection that can be acquired multiple times (susceptible‐infected‐susceptible model). The estimation is based on a limited number of repeated measurements of the current status of each individual, a situation commonly encountered in practice. We investigate how the placement of consecutive samples affects the estimability and efficiency of vaccine efficacy parameters. The same sampling frequency may not be optimal for efficient estimation of all components of heterogeneous vaccine protection. However, we suggest practical guidelines allowing estimation of all components. For situations in which the estimability of individual components fails, we suggest to use summary measures of vaccine efficacy.
2.1 A 28GHz/37GHz/39GHz multiband linear Doherty power amplifier for 5G massive MIMO applications

Millimeter-wave fifth-generation (5G) systems will extensively leverage massive multiple-input multiple-output (MIMO) architectures to improve their link performance. These array systems will employ many power amplifiers (PAs) operating at moderate output power (Pout), e.g., 16 PAs each with +7dBm Pout [1]. The PA energy efficiency is of paramount importance in MIMO systems for improved battery life and thermal management. Due to spectrum-efficient modulations with high peak-to-average power ratios, both PA peak efficiency and power back-off (PBO) efficiency are critical. To achieve 5G Gb/s data-rates with complex modulations, envelope tracking PAs require high-speed/high-precision supply modulators, and outphasing PAs need high-speed baseband computation, both of which pose substantial challenges in practice. Although Doherty PAs support high data-rates, existing silicon mm-wave Doherty PAs exhibit very limited PBO efficiency enhancement, mainly due to inefficient Doherty power combiners and imperfect main/auxiliary PA cooperation [2,3].
Altered functional and anatomical connectivity in schizophrenia.

BACKGROUND Schizophrenia is characterized by a lack of integration between thought, emotion, and behavior. A disruption in the connectivity between brain processes may underlie this schism. Functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) were used to evaluate functional and anatomical brain connectivity in schizophrenia. METHODS In all, 29 chronic schizophrenia patients (11 females, age: mean=41.3, SD=9.28) and 29 controls (11 females, age: mean=41.1, SD=10.6) were recruited. Schizophrenia patients were assessed for severity of negative and positive symptoms and general cognitive abilities of attention/concentration and memory. Participants underwent a resting-fMRI scan and a DTI scan. For fMRI data, a hybrid independent components analysis was used to extract the group default mode network (DMN) and accompanying time-courses. Voxel-wise whole-brain multiple regressions with corresponding DMN time-courses was conducted for each subject. A t-test was conducted on resulting DMN correlation maps to look between-group differences. For DTI data, voxel-wise statistical analysis of the fractional anisotropy data was carried out to look for between-group differences. Voxel-wise correlations were conducted to investigate the relationship between brain connectivity and behavioral measures. RESULTS Results revealed altered functional and anatomical connectivity in medial frontal and anterior cingulate gyri of schizophrenia patients. In addition, frontal connectivity in schizophrenia patients was positively associated with symptoms as well as with general cognitive ability measures. DISCUSSION The present study shows convergent fMRI and DTI findings that are consistent with the disconnection hypothesis in schizophrenia, particularly in medial frontal regions, while adding some insight of the relationship between brain disconnectivity and behavior.
Prolonged norovirus infection after pancreas transplantation: a case report and review of chronic norovirus

Norovirus is a major cause of self‐limited gastroenteritis worldwide. Prevention and treatment are thwarted by rapid viral evolution, and thus supportive care remains the mainstay of therapy. Chronic infection in immunocompromised hosts is increasingly described. We report a case of norovirus infection lasting 2543 days in a pancreas transplant recipient. Serial fecal specimens were obtained, from which a map of genetic relatedness was derived. The clinical course was complicated by renal failure that progressed to end‐stage renal disease. Minimization of immunosuppression was associated with resolution of the infection. Subsequently, the patient experienced a suspected allograft rejection that did not compromise pancreas function. The patient later underwent living‐related renal transplantation without recurrence of enteritis.
Influence of displacement damage dose on dark current distributions of irradiated CMOS image sensors

Dark current increase distributions due to displacement damages are modeled using displacement damage dose concept. Several CMOS image sensors have been exposed to neutrons or protons and we have characterized their degradation in terms of dark current increase. We have been able to extract a set of two factors from the experimental dark current increase distributions. These factors are used to predict and build dark current increase distribution and leads to a better understanding of displacement damage effects on CMOS image sensors.
Improving medical device regulation: the United States and Europe in perspective.

CONTEXT Recent debates and events have brought into question the effectiveness of existing regulatory frameworks for medical devices in the United States and Europe to ensure their performance, safety, and quality. This article provides a comparative analysis of medical device regulation in the two jurisdictions, explores current reforms to improve the existing systems, and discusses additional actions that should be considered to fully meet this aim. Medical device regulation must be improved to safeguard public health and ensure that high-quality and effective technologies reach patients. METHODS We explored and analyzed medical device regulatory systems in the United States and Europe in accordance with the available gray and peer-reviewed literature and legislative documents. FINDINGS The two regulatory systems differ in their mandate and orientation, organization, pre- and postmarket evidence requirements, and transparency of process. Despite these differences, both jurisdictions face similar challenges for ensuring that only safe and effective devices reach the market, monitoring real-world use, and exchanging pertinent information on devices with key users such as clinicians and patients. To address these issues, reforms have recently been introduced or debated in the United States and Europe that are principally focused on strengthening regulatory processes, enhancing postmarket regulation through more robust surveillance systems, and improving the traceability and monitoring of devices. Some changes in premarket requirements for devices are being considered. CONCLUSIONS Although the current reforms address some of the outstanding challenges in device regulation, additional steps are needed to improve existing policy. We examine a number of actions to be considered, such as requiring high-quality evidence of benefit for medium- and high-risk devices; moving toward greater centralization and coordination of regulatory approval in Europe; creating links between device identifier systems and existing data collection tools, such as electronic health records; and fostering increased and more effective use of registries to ensure safe postmarket use of new and existing devices.