Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of autoimmune hepatitis in primary biliary cirrhosis

Aim/Background: Primary biliary cirrhosis (PBC) is a chronic cholestatic liver disease of unknown aetiology. Up to 10% of patients with typical features of PBC will have additional features of autoimmune hepatitis (AIH). A subset, however, have no such features but go on to develop a ‘sequential’ AIH overlap syndrome.
Pre‐mRNA 3′‐end processing complex assembly and function

The 3′‐ends of almost all eukaryotic mRNAs are formed in a two‐step process, an endonucleolytic cleavage followed by polyadenylation (the addition of a poly‐adenosine or poly(A) tail). These reactions take place in the pre‐mRNA 3′ processing complex, a macromolecular machinery that consists of more than 20 proteins. A general framework for how the pre‐mRNA 3′ processing complex assembles and functions has emerged from extensive studies over the past several decades using biochemical, genetic, computational, and structural approaches. In this article, we review what we have learned about this important cellular machine and discuss the remaining questions and future challenges. WIREs RNA 2011 2 321–335 DOI: 10.1002/wrna.54
First order representations of time-varying linear systems

We construct a special type of first order representation of a linear time-varying system given by linear ordinary differential equations with rational or meromorphic coefficients. Under certain conditions, such a representation yields a classical state space model. We show that every system admits a partition of its variables into inputs and outputs such that a state representation can be obtained. All the problems addressed in this paper can be solved algorithmically using non-commutative computer algebra over the polynomial ring K[s], where K is the field of rational or meromorphic functions, and we have the commutator rule sk - ks = k' for k isin K, reflecting the product rule of differentiation
Affective and impulsive personality disorder traits in the relatives of patients with borderline personality disorder.

OBJECTIVE This study tested the hypothesis that the risk for affective and impulsive personality disorder traits commonly found in patients with borderline personality disorder would be greater in the first-degree relatives of probands with borderline personality disorder than in two comparison groups. METHOD Blind family history interviews were conducted with family informants to assess the extent to which first-degree relatives of 29 probands with borderline personality disorder, 22 probands with other personality disorders who met three or fewer of the criteria for borderline personality disorder, and 43 probands with schizophrenia fulfilled operationalized criteria for the two kinds of personality disorder traits and for other diagnostic categories. The crude proportions of adult relatives with each diagnosis, as well as the age-adjusted morbid risks, were assessed in the three groups of relatives. RESULTS The risks for affective and impulsive personality disorder traits were independently greater in the 129 relatives of the borderline probands than in the 105 relatives of the probands with other personality disorders and the 218 relatives of the schizophrenic probands. There was no similarly greater risk for any other psychiatric disorder assessed, including major affective disorder. In addition, the relatives of borderline probands with current or past major depressive disorder showed a greater risk for major affective disorders than the relatives of never-depressed probands with other personality disorders but not the relatives of never-depressed borderline probands. CONCLUSIONS These results suggest familial transmission of the hallmark borderline-related personality characteristics and raise the possibility that these familial traits may be partially independent.
Functional base of support decreases with age.

BACKGROUND Poor balance in older persons increases the risk of injurious falls during daily activities. Functional base of support (FBOS), the anterior-posterior proportion of foot length used in maximal sustained forward and backward leaning, tests controlled center of mass movement, a component of balance required in daily activities. The purpose of this study was to examine the relationship between FBOS and age and establish the reliability of this measure. METHODS Subjects were 113 community-dwelling men and women, ages 20 to 91. FBOS, measured on a force platform, is the difference between mean center of pressure location during sustained forward and backward leaning, divided by foot length. Forward lean (FL), backward lean (BL), and average sway distance during normal standing (STAND SWAY) and while leaning (FBOS SWAY) were also measured. RESULTS Mean FBOS was . 60 +/- . 07 in subjects under age 60, and . 42 +/- . 12 in subjects 60 and older. FBOS remained constant in younger subjects; beyond age 60, FBOS declined about 16% per decade and was more variable. FL and BL also declined with age, remaining 66% and 34% of FBOS, respectively. STAND SWAY and FBOS SWAY were significantly correlated with each other, but not with FBOS. CONCLUSIONS FBOS is a reliable measure and is decreased on average in older persons. This decrease is not related to increased sway while standing or leaning. FBOS is a simple force platform test that has potential as a measure of change in this dimension of balance and as a predictor of falls risk in older persons.
A geometric approach to improve spectrum efficiency for cognitive relay networks

Cognitive radio (CR) enables dynamic spectrum access (DSA). In CR networks (CRNs), unlicensed cognitive users (CUs) can share the radio spectrum with the licensed primary users (PUs) if the incurred signal-to-noise-and-interference ratio (SNIR) to the PUs is above a predetermined threshold. In this paper, we investigate the use of relaying to enhance the spectrum utilization of an idealized two-dimensional geometric network in Rayleigh fading channels. To do so, the CUs should be made transparent to the PUs while achieving acceptable reliability themselves. Based on these conditions, we first derive the geometric condition under which CUs could transmit over a single hop with the PUs being active. If the destination is beyond the reach of the source in a single hop, multihop relaying will be used for shorter-distance less-power transmission. Then, we propose and analyze two multihop routing strategies, termed nearest-neighbor routing (NNR) and farthest-neighbor routing (FNR). In multihop relaying, we also study the benefits of concurrency, in which more than one CUs are allowed to transmit at the same time to improve the end-to-end (e2e) channel utilization. Finally, we compare the e2e performance of CRNs with and without relaying.
Loopback recovery from double-link failures in optical mesh networks

Network survivability is a crucial requirement in high-speed optical networks. Typical approaches of providing survivability have considered the failure of a single component such as a link or a node. We motivate the need for considering double-link failures and present three loopback methods for handling such failures. In the first two methods, two edge-disjoint backup paths are computed for each link for rerouting traffic when a pair of links fails. These methods require the identification of the failed links before recovery can be completed. The third method requires the precomputation of a single backup path and does not require link identification before recovery. An algorithm that precomputes backup paths for links in order to tolerate double-link failures is then presented. Numerical results comparing the performance of our algorithm with other approaches suggest that it is possible to achieve almost 100% recovery from double-link failures with a moderate increase in backup capacity. A remarkable feature of our approach is that it is possible to trade off capacity for restorability by choosing a subset of double-link failures and designing backup paths using our algorithm for only those failure scenarios.
Learned rewrite rules versus learned search control rules to improveplan qualityMuhammad

Domain independent planners can produce better-quality plans through the use of domain-dependent knowledge , typically encoded as search control rules. The planning-by-rewriting approach has been proposed as an alternative technique for improving plan quality. We present a system called Sys-REWRITE that automatically learns plan rewriting rules and compare it with Sys-SEARCH-CONTROL, a system that automatically learns search control rules for partial order planners. Our results support the usefulness of planning by rewriting approach to eeciently generate high quality plans and demonstrate a way of automatically learning these rules from analyzing partial-order planning episodes. Our empirical comparison of the two systems suggests that while Sys-REWRITE can quickly learn to produce higher quality plans than Sys-SEARCH-CONTROL, Sys-SEARCH-CONTROL is more eecient than Sys-REWRITE.
Bringing Up the Dead: Revisiting the Study of Suicide in Light of the Youth Problem

The study of suicide developed in the nineteenth century with the aim of understanding the phenomenon of suicide. Recently, however, the goal of understanding suicide has largely been abandoned and replaced with approaches concerned with suicide prevention. The emergence of youth suicide within the past few decades demands a return to the project of understanding suicide to make sense of this contemporary change. Research on suicide reveals a division between psychological and sociological approaches, and only a few works have sought to theoretically link them. Prompted by the lack of reconciliation of psychology and sociology, this investigation aims to bridge the gap between these disciplines. This is accomplished through a survey of literature illuminating various perspectives on suicide and a reflection on two approaches to the study of youth suicide that empirically link the individual and collective dimensions of study. The exploration of the convergence between these approaches provides insight into problems pertaining to youths' identity development and into features of contemporary reality.
Header Enrichment or ISP Enrichment?: Emerging Privacy Threats in Mobile Networks

HTTP header enrichment allows mobile operators to annotate HTTP connections via the use of a wide range of request headers. Operators employ proxies to introduce such headers for operational purposes, and---as recently widely publicized---also to assist advertising programs in identifying the subscriber responsible for the originating traffic, with significant consequences for the user's privacy. In this paper, we use data collected by the Netalyzr network troubleshooting service over 16 months to identify and characterize HTTP header enrichment in modern mobile networks. We present a timeline of HTTP header usage for 299 mobile service providers from 112 countries, observing three main categories: (1) unique user and device identifiers (e.g., IMEI and IMSI), (2) headers related to advertising programs, and (3) headers associated with network operations.
iFORM: Incorporating Find Occurrence of Regulatory Motifs

Motivation Accurately identifying binding sites of transcription factors (TFs) is crucial to understand the mechanisms of transcriptional regulation and human disease. Results We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use tool for scanning DNA sequence with TF motifs described as position weight matrices (PWMs). iFORM achieves higher accuracy and sensitivity by integrating the results from five classical motif discovery programs based on Fisher’s combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and has demonstrated its utility to further understand individual roles of functional elements. Availability iFORM can be freely accessed athttps://github.com/wenjiegroup/iFORM. Contact shuwj@bmi.ac. cn and boxc@bmi.ac. cn
Controlling singular values with semidefinite programming

Controlling the singular values of n-dimensional matrices is often required in geometric algorithms in graphics and engineering. This paper introduces a convex framework for problems that involve singular values. Specifically, it enables the optimization of functionals and constraints expressed in terms of the extremal singular values of matrices. Towards this end, we introduce a family of convex sets of matrices whose singular values are bounded. These sets are formulated using Linear Matrix Inequalities (LMI), allowing optimization with standard convex Semidefinite Programming (SDP) solvers. We further show that these sets are optimal, in the sense that there exist no larger convex sets that bound singular values. A number of geometry processing problems are naturally described in terms of singular values. We employ the proposed framework to optimize and improve upon standard approaches. We experiment with this new framework in several applications: volumetric mesh deformations, extremal quasi-conformal mappings in three dimensions, non-rigid shape registration and averaging of rotations. We show that in all applications the proposed approach leads to algorithms that compare favorably to state-of-art algorithms.
Control and host-dependent activation of insect toxin expression in a root-associated biocontrol pseudomonad.

Pseudomonas fluorescens CHA0 is a root-associated biocontrol agent that suppresses soil-borne fungal diseases of crops. Remarkably, the pseudomonad is also endowed with systemic and oral activity against pest insects which depends on the production of the insecticidal Fit toxin. The toxin gene (fitD) is part of a virulence cassette encoding three regulators (FitF, FitG, FitH) and a type I secretion system (FitABC-E). Immunoassays with a toxin-specific antibody and transcriptional analyses involving fitG and fitH deletion and overexpression mutants identified LysR family regulator FitG and response regulator FitH as activator and repressor, respectively, of Fit toxin and transporter expression. To visualize and quantify toxin expression in single live cells by fluorescence microscopy, we developed reporters which in lieu of the native toxin protein express a fusion of the Fit toxin with red fluorescent mCherry. In a wild-type background, expression of the mCherry-tagged Fit toxin was activated at high levels in insect hosts, i.e. when needed, yet not on plant roots or in batch culture. By contrast, a derepressed fitH mutant expressed the toxin in all conditions. P. fluorescens hence can actively induce insect toxin production in response to the host environment, and FitH and FitG are key regulators in this mechanism.
Preparation of wafer level glass-embedded high-aspect-ratio passives using a glass reflow process

This paper presents an innovative, uncomplicated and inexpensive method based on a glass reflow process to fabricate glass-embedded passives for RF MEMS packaging. Experimental results show that various glass-embedded passives, including annular cylindrical and coaxial cylindrical conductive through-holes, plate and coaxial torus trench capacitors, square spiral, circular spiral and meander trench inductors, and filters, can be manufactured void-free with vertical and smooth sidewall and large signal pathways. This glass-embedded design implements passives with large thickness and provides much surface space for 3D MEMS integration. The HFSS simulation results show that a minor thickness increase contributes to a large increase in Q and a relatively small decrease in L. The best Q (38.9-83.9) and L (19.9-15 nH) were achieved by using square spiral inductors.
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger

Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). While exported by the Sec pathway, the ATs are further secreted across the outer membrane via their own C-terminal translocator forming a β-barrel, through which the rest of the protein, namely the passenger, can pass. In several ATs, an autochaperone domain (AC) present at the C-terminal region of the passenger and upstream of the translocator was demonstrated as strictly required for proper secretion and folding. However, considering it was functionally characterised and identified only in a handful of ATs, wariness recently fells on the commonality and conservation of this structural element in the T5aSS. To circumvent the issue of sequence divergence and taking advantage of the resolved three-dimensional structure of some ACs, identification of this domain was performed following structural alignment among all AT passengers experimentally resolved by crystallography before searching in a dataset of 1523 ATs. While demonstrating that the AC is indeed a conserved structure found in numerous ATs, phylogenetic analysis further revealed a distribution into deeply rooted branches, from which emerge 20 main clusters. Sequence analysis revealed that an AC could be identified in the large majority of SAATs (self-associating ATs) but not in any LEATs (lipase/esterase ATs) nor in some PATs (protease autotransporters) and PHATs (phosphatase/hydrolase ATs). Structural analysis indicated that an AC was present in passengers exhibiting single-stranded right-handed parallel β-helix, whatever the type of β-solenoid, but not with α-helical globular fold. From this investigation, the AC of type 1 appears as a prevalent and conserved structural element exclusively associated to β-helical AT passenger and should promote further studies about the protein secretion and folding via the T5aSS, especially toward α-helical AT passengers.
Cardiac dysfunction in the trastuzumab clinical trials experience.

PURPOSE This study sought to estimate cardiac dysfunction (CD) risk for patients receiving trastuzumab; to characterize observed CD by severity, treatment, and clinical outcome; to assess effects of baseline clinical risk factors on CD; and to assess effects of cumulative doses of anthracyclines and trastuzumab on CD. PATIENTS AND METHODS A retrospective review of records for patients enrolled onto any of seven phase II and III trastuzumab clinical trials was performed. Predefined criteria were used for the diagnosis, and the New York Heart Association functional classification system was used to document CD severity. Product-limit estimates were used to summarize the cumulative anthracycline and trastuzumab doses at the time of CD onset. RESULTS Patients treated with trastuzumab were found to be at an increased risk for CD. The incidence was greatest in patients receiving concomitant trastuzumab and anthracycline plus cyclophosphamide (27%). The risk was substantially lower in patients receiving paclitaxel and trastuzumab (13%) or trastuzumab alone (3% to 7%); however, most of these patients had received prior anthracycline therapy. CD was noted in 8% of patients receiving anthracycline plus cyclophosphamide and 1% receiving paclitaxel alone. Most trastuzumab-treated patients developing CD were symptomatic (75%), and most improved with standard treatment for congestive heart failure (79%). CONCLUSION Trastuzumab is associated with an increased risk of CD, which is greatest in patients receiving concurrent anthracyclines. In most patients with metastatic breast cancer, the risk of CD can be justified given the improvement in overall survival previously reported with trastuzumab.
Better Be Convincing or Better Be Stylish? a Theory Based Multi-Agent Simulation to Explain Minority Influence in Groups Via Arguments or Via Peripheral Cues

Very often in the history of mankind, social changes took place because a minority was successful in persuading the dominant majority of a new idea. Social psychology provides empirically well-founded theories of social influence that can explain the power of minorities at individual level. In this contribution, we present an agent-based computer simulation of one such theory, the Elaboration Likelihood Model (ELM). After introducing the theoretical background and our agent model, we present three simulation experiments that confirm past laboratory research but also go beyond its findings by adopting the method of computer simulation. First, we found that even a minority with low argument quality can be successful as long as it has positive peripheral cues. Second, our results suggest that a higher personal relevance of a topic for the majority led it to be more receptive to minority influence only when the minority showed neutral peripheral cues and very good arguments. Third, we found evidence that a neutral or only slightly biased majority is influenced more easily than a strongly biased one. To sum up, we consider these results to illustrate the notion that a well-presented, comprehensible and valid computer simulation provides a useful tool for theory development and application in an exploratory manner as long as it is well founded in terms of the model and theory.
An In Vitro Fermentation Study on the Effects of Gluten FriendlyTM Bread on Microbiota and Short Chain Fatty Acids of Fecal Samples from Healthy and Celiac Subjects

Recently, an innovative gluten detoxification method called Gluten FriendlyTM (GF) has been developed. It induces structural modifications, which abolish the antigenic capacity of gluten and reduce the in vitro immunogenicity of the most common epitopes involved in celiac disease, without compromising the nutritional and technological properties. This study investigated the in vitro effects of GF bread (GFB) on the fecal microbiota from healthy and celiac individuals by a three-stage continuous fermentative system, which simulates the colon (vessel 1, proximal colon; vessel 2, transverse colon; and vessel 3, distal colon), as well as on the production of short chain fatty acids (SCFA, acetate, propionate, butyrate). The system was fed with GFB and the changes in microbiota through fluorescence in situ hybridization and in SCFA content were assessed. GFB exerted beneficial modulations such as bifidogenic effects in each compartment of the model both with healthy- and celiac-derived samples, as well as growth in Clostridium clusters XIVa+b in celiac-derived samples. Furthermore, increased levels of acetic acid were found in vessel 1 inoculated with the fecal microbiota of healthy individuals, as well as acetic and propionic in vessel 1 and 2 with celiac-derived samples. In addition, the use of multivariate approaches showed that the supplementation of GFB could result in a different modulation of the fecal microbiota and SCFA, as a function of initial equilibrium.
Dying for palliative care

EDITOR,—In their prospective series of 119 patients admitted after a first seizure Ronald A Schoenenberger and Sabine M Heim found that no focal lesion would have been missed if computed tomography had been performed only in patients who either presented with a focal deficit or did not misuse alcohol and did not have a focal deficit.1 They conclude that although computed tomography of the brain remains necessary in most patients after a first seizure, it may …
Application of Kullback-Leibler Metric to Speech Recognition

Article discusses the application of Kullback-Leibler divergence to the recognition of speech signals and suggests three algorithms implementing this divergence criterion: correlation algorithm, spectral algorithm and filter algorithm. Discussion covers an approach to the problem of speech variability and is illustrated with the results of experimental modeling of speech signals. The article gives a number of recommendations on the choice of appropriate model parameters and provides a comparison to some other methods of speech recognition.