Miracle-dz/UniFAR-FTUs huggingface dataset:
Meta-analysis of randomized controlled trials of bosentan for treatment of pulmonary arterial hypertension

Background/Aims We assessed the efficacy and safety of bosentan in patients with pulmonary arterial hypertension (PAH). Methods We surveyed randomized controlled trials (RCTs) of the efficacy and safety of bosentan in patients with PAH using MEDLINE, EMBASE, the Cochrane Controlled Trials Register, and manual searches. Meta-analysis of RCTs was performed to determine treatment efficacy and safety outcomes. Results are presented as odds ratios (ORs) or weighted mean differences (WMDs). Results Meta-analysis of seven RCTs including a total of 410 patients and 296 controls revealed that the 6-minute work distance was significantly higher in the bosentan group than in the placebo group (WMD, 46.19; 95% confidence interval [CI], 21.20 to 71.19; p = 2.9 × 10-5). Compared with the placebo, bosentan significantly reduced the mean pulmonary arterial pressure in patients with PAH (WMD, -6.026; 95% CI, -8.785 to -3.268, p = 1.8 × 10-6). The bosentan therapy group worsened less clinically than the placebo group (OR, 0.252; 95% CI, 0.140 to 0.454; p = 4.6 × 10-7). The incidence of serious adverse events did not differ between the bosentan and placebo groups (OR, 0.948; 95% CI, 0.556 to 1.614; p = 0.843). However, the results of the abnormal liver function test (LFT) were significantly higher in the bosentan group than in the placebo group (OR, 2.312; 95% CI, 1.020 to 5.241; p = 0.045). Conclusions This meta-analysis shows that bosentan can treat PAH effectively. However, bosentan increased the incidence of abnormal LFT results compared with the placebo.
Genetic Basis and Consequences of Niche Construction: Plasticity‐Induced Genetic Constraints on the Evolution of Seed Dispersal in Arabidopsis thaliana

Because seed dispersal influences the environment experienced by seeds, that environment can change as dispersal evolves. The evolutionary potential of dispersal can in turn change as dispersal evolves, if its expression of genetic variation depends on the postdispersal environment. We examined whether seed dispersion patterns have a detectable genetic basis (and therefore evolutionary potential) and determined whether that genetic basis changed depending on one postdispersal environmental factor: conspecific density. We grew replicates of 12 ecotypes of Arabidopsis thaliana at high and low density and measured seed dispersion patterns and maternal traits associated with dispersal under controlled conditions. We found density‐dependent ecotypic variation for maternal traits that influence dispersal. Significant genetic variation for postdispersal sibling density was detected only when plants were grown at high density, suggesting that if dispersal evolves to result in lower postdispersal densities, the expression of genetic variation for dispersal would be reduced. This dynamic could lead to a plasticity‐induced constraint on the evolution of dispersal. The ability of organisms to alter the environment they experience and the ability of that environment to evolve can alter evolutionary dynamics by augmenting or reducing evolutionary potential and thereby facilitating or constraining evolutionary responses to selection.
On-line Adaption of Class-specific Codebooks for Instance Tracking

In this work, we demonstrate that an off-line trained class-specific detector can be transformed into an instance-specific detector on-the-fly. To this end, we make use of a codebook-based detector [1] that is trained on an object class. Codebooks model the spatial distribution and appearance of object parts. When matching an image against a codebook, a certain set of codebook entries is activated to cast probabilistic votes for the object. For a given object hypothesis, one can collect the entries that voted for the object. In our case, these entries can be regarded as a signature for the target of interest. Since a change of pose and appearance can lead to an activation of very different codebook entries, we learn the statistics for the target and the background over time, i.e. we learn on-line the probability of each part in the codebook belonging to the target. By taking the target-specific statistics into account for voting, the target can be distinguished from other instances in the background yielding a higher detection confidence for the target, see Fig. 1. A class-specific codebook as in [1, 2, 3, 4, 5] is trained off-line to identify any instance of the class in any image. It models the probability of the patches belonging to the object class p ( c=1|L ) and the local spatial distribution of the patches with respect to the object center p ( x|c=1,L ) . For detection, patches are sampled from an image and matched against the codebook, i.e. each patch P(y) sampled from image location y ends at a leaf L(y). The probability for an instance of the class centered at the location x is then given by
An optimisation approach to improving the accuracy of the Hough transform: plane orientations from skew symmetry

Straight lines from a single perspective image are used to determine orientations of objects in an image scene using skew symmetry. The lines are detected using a Hough transform followed by an optimization algorithm in order to remove discretization errors in the line parameters. The use of these accurate line parameter estimates is demonstrated with some test images for which the plane orientations are known. It is shown that orientations from skew symmetry can be reliably determined. <<ETX>>
Mortality, Causes of Death and Associated Factors Relate to a Large HIV Population-Based Cohort

Introduction Antiretroviral therapy has led to a decrease in HIV-related mortality and to the emergence of non-AIDS defining diseases as competing causes of death. This study estimates the HIV mortality rate and their risk factors with regard to different causes in a large city from January 2001 to June 2013. Materials and Methods We followed-up 3137 newly diagnosed HIV non-AIDS cases. Causes of death were classified as HIV-related, non-HIV-related and external. We examined the effect of risk factors on survival using mortality rates, Kaplan-Meier plots and Cox models. Finally, we estimated survival for each main cause of death groups through Fine and Gray models. Mortality Results 182 deaths were found [14.0/1000 person-years of follow-up (py); 95% confidence interval (CI):12.0–16.1/1000 py], 81.3% of them had a known cause of death. Mortality rate by HIV-related causes and non-HIV-related causes was the same (4.9/1000 py; CI:3.7–6.1/1000 py), external was lower [1.7/1000 py; (1.0–2.4/1000 py)]. Survival Results Kaplan-Meier estimate showed worse survival in intravenous drug user (IDU) and heterosexuals than in men having sex with men (MSM). Factors associated with HIV-related causes of death include: IDU male (subHazard Ratio (sHR):3.2; CI:1.5–7.0) and <200 CD4 at diagnosis (sHR:2.7; CI:1.3–5.7) versus ≥500 CD4. Factors associated with non-HIV-related causes of death include: ageing (sHR:1.5; CI:1.4–1.7) and heterosexual female (sHR:2.8; CI:1.1–7.3) versus MSM. Factors associated with external causes of death were IDU male (sHR:28.7; CI:6.7–123.2) and heterosexual male (sHR:11.8; CI:2.5–56.4) versus MSM. Conclusion and Recommendation There are important differences in survival among transmission groups. Improved treatment is especially necessary in IDUs and heterosexual males.
The anti‐protozoal drug pentamidine blocks KIR2.x‐mediated inward rectifier current by entering the cytoplasmic pore region of the channel

Background and purpose: Pentamidine is a drug used in treatment of protozoal infections. Pentamidine treatment may cause sudden cardiac death by provoking cardiac arrhythmias associated with QTc prolongation and U‐wave alterations. This proarrhythmic effect was linked to inhibition of hERG trafficking, but not to acute block of ion channels contributing to the action potential. Because the U‐wave has been linked to the cardiac inward rectifier current (IK1), we examined the action and mechanism of pentamidine‐mediated IK1 block.
Aligning gene expression time series with time warping algorithms

UNLABELLED motivation: Increasingly, biological processes are being studied through time series of RNA expression data collected for large numbers of genes. Because common processes may unfold at varying rates in different experiments or individuals, methods are needed that will allow corresponding expression states in different time series to be mapped to one another. RESULTS We present implementations of time warping algorithms applicable to RNA and protein expression data and demonstrate their application to published yeast RNA expression time series. Programs executing two warping algorithms are described, a simple warping algorithm and an interpolative algorithm, along with programs that generate graphics that visually present alignment information. We show time warping to be superior to simple clustering at mapping corresponding time states. We document the impact of statistical measurement noise and sample size on the quality of time alignments, and present issues related to statistical assessment of alignment quality through alignment scores. We also discuss directions for algorithm improvement including development of multiple time series alignments and possible applications to causality searches and non-temporal processes ('concentration warping').
The Gibberellic Acid Stimulated-Like Gene Family in Maize and Its Role in Lateral Root Development1[C][W][OA]

In an approach to study lateral root development in monocots, genome-wide searches for homologs of the Gibberellic Acid Stimulated Transcript-like (GAST-like) gene family in rice (Oryza sativa) and maize (Zea mays) were carried out. Six novel GAST-like genes in rice and 10 members of the gene family in maize, which were designated ZmGSL (for Z. mays Gibberellic Acid Stimulated-Like), were identified. The ZmGSL family encodes small proteins of 75 to 128 amino acids, which are characterized by a conserved 59 to 64 amino acid C-terminal domain. Within this domain, 17 amino acids, including 12 cysteines, are perfectly conserved. The transcript of the ZmGSL1 gene is differentially spliced into the alternative variants ZmGSL1a and ZmGSL1b, the latter of which is translated into a premature protein that lacks the C-terminal domain. The presence of an additional N-terminal cleavable signal sequence in eight of the 10 ZmGSL proteins suggests that they are secreted into the extracellular matrix. In-depth root-specific gene expression analyses carried out in the wild type and the lateral root mutants lrt1 and rum1 suggest a role for ZmGSL genes in early lateral root development, which is likely regulated by gibberellic acid. Expression patterns of ZmGSL1a and ZmGSL1b propose antagonistic functions of these splice variants during early lateral root formation.
Deliberate self-harm behavior among Italian young adults: correlations with clinical and nonclinical dimensions of personality.

This study aims to explore rates of deliberate self-harm (DSH) behaviors and their psychological and psychopathological correlates within a sample of nonclinical young adults (N = 365; 63% women; M age = 23 ± 4.06). Participants completed the Deliberate Self-Harm Inventory and other self-report questionnaires assessing clinical (borderline personality, dissociative, and depersonalization traits) and nonclinical (body perception, behavioral inhibition and activation, cognitive emotional regulation, and the Big Five traits) dimensions of their personality. The rate of DSH in the present sample was 39%, comparable to that found in previous studies of young adults in other countries. Further, consistent with past research, DSH was found to be associated with clinical dimensions of personality pathology, including borderline personality and dissociative symptoms. Finally, results revealed an association between DSH and nonclinical dimensions of personality, including the behavioral activation dimension of fun-seeking, more negative body perception and lower body protection, the use of more nonadaptive cognitive strategies for regulating emotions, higher levels of openness to experience, and lower levels of emotional stability. This pattern of results is consistent with those found for other impulsive behaviors and impulse control disorders.
Cryptogenic Subtype Predicts Reduced Survival Among Cancer Patients With Ischemic Stroke

Background and Purpose— Cryptogenic stroke is common in patients with cancer. Autopsy studies suggest that many of these cases may be because of marantic endocarditis, which is closely linked to cancer activity. We, therefore, hypothesized that among patients with cancer and ischemic stroke, those with cryptogenic stroke would have shorter survival. Methods— We retrospectively analyzed all adult patients with active systemic cancer diagnosed with acute ischemic stroke at a tertiary care cancer center from 2005 through 2009. Two neurologists determined stroke mechanisms by consensus. Patients were diagnosed with cryptogenic stroke if no specific mechanism could be determined. The diagnosis of marantic endocarditis was restricted to patients with cardiac vegetations on echocardiography or autopsy and negative blood cultures. Patients were followed until July 31, 2012, for the primary outcome of death. Kaplan–Meier statistics and the log-rank test were used to compare survival between patients with cryptogenic stroke and patients with known stroke mechanisms. Multivariate Cox proportional hazard analysis evaluated the association between cryptogenic stroke and death after adjusting for potential confounders. Results— Among 263 patients with cancer and ischemic stroke, 133 (51%) were cryptogenic. Median survival in patients with cryptogenic stroke was 55 days (interquartile range, 21–240) versus 147 days (interquartile range, 33–735) in patients with known stroke mechanisms (P<0.01). Cryptogenic stroke was independently associated with death (hazard ratio, 1.64; 95% confidence interval, 1.25–2.14) after adjusting for age, systemic metastases, adenocarcinoma histology, and functional status. Conclusions— Cryptogenic stroke is independently associated with reduced survival in patients with active cancer and ischemic stroke.
A Study on Topic Control Method for Robot-Assisted Therapies ~ Dementia Evaluation Using Simple Conversation with Robots ~

This paper developed the topic control system for dementia evaluation using simple conversations with a conversation robot. In the proposed method, some keywords in the daily conversation, i.e. norms, were first extracted and destination topic for dementia evaluation was determined based on the relationships among them on the concept space. Evaluation experiments were conducted and the obtained results showed that the proposed method could lead the current topic to the destination topic for dementia evaluation. We also showed problems and further works of this study.
Distributed variational sparse Bayesian learning for sensor networks

In this work we present a distributed sparse Bayesian learning (dSBL) regression algorithm. It can be used for collaborative sparse estimation of spatial functions in wireless sensor networks (WSNs). The sensor measurements are modeled as a weighted superposition of basis functions. When kernels are used, the algorithm forms a distributed version of the relevance vector machine. The proposed method is based on a combination of variational inference and loopy belief propagation, where data is only communicated between neighboring nodes without the need for a fusion center. We show that for tree structured networks, under certain parameterization, dSBL coincides with centralized sparse Bayesian learning (cSBL). For general loopy networks, dSBL and cSBL are differend, yet simulations show much faster convergence over the variational inference iterations at similar sparsity and mean squared error performance. Furthermore, compared to other sparse distributed regression methods, our method does not require any cross-tuning of sparsity parameters.
Software model checking in practice: an industrial case study

We present an application of software model checking to the analysis of a large industrial software product: Lucent Technologies' CDMA call-processing library. This software is deployed on thousands of base stations in wireless networks world-wide, where it sets up and manages millions of calls to and from mobile devices everyday. Our analysis of this software was carried out using VeriSoft, a tool developed at Bell Laboratories that implements model-checking algorithms for systematically testing concurrent reactive software. VeriSoft has now been used for over a year for analyzing several releases and versions of the CDMA call-processing software. Although we started this work with a fairly robust version of the software, the application of model checking exposed several problems that had escaped traditional testing. Model checking also helped developers maintain a high degree of confidence in the library as it evolved through its many releases and versions. To our knowledge, software model checking has rarely been applied to software systems of this scale. In this paper, we describe our experience in applying this technology in an industrial environment.
Stable mRNP Formation and Export Require Cotranscriptional Recruitment of the mRNA Export Factors Yra1p and Sub2p by Hpr1p

ABSTRACT Yra1p/REF participates in mRNA export by recruiting the export receptor Mex67p to messenger ribonucleoprotein (mRNP) complexes. Yra1p also binds Sub2p, a DEAD box ATPase/RNA helicase implicated in splicing and required for mRNA export. We identified genetic and physical interactions between Yra1p, Sub2p, and Hpr1p, a protein involved in transcription elongation whose deletion leads to poly(A)+ RNA accumulation in the nucleus. By chromatin immunoprecipitation (ChIP) experiments, we show that Hpr1p, Sub2p, and Yra1p become associated with active genes during transcription elongation and that Hpr1p is required for the efficient recruitment of Sub2p and Yra1p. The data indicate that transcription and export are functionally linked and that mRNA export defects may be due in part to inefficient loading of essential mRNA export factors on the growing mRNP. We also identified functional interactions between Yra1p and the exosome components Rrp45p and Rrp6p. We show that yra1, sub2, and Δhpr1 mutants all present defects in mRNA accumulation and that deletion of RRP6 in yra1 mutants restores normal mRNA levels. The data support the hypothesis that an exosome-dependent surveillance mechanism targets improperly assembled mRNPs for degradation.
Blood–Brain Barrier Permeability Is Increased After Acute Adult Stroke But Not Neonatal Stroke in the Rat

The immaturity of the CNS at birth greatly affects injury after stroke but the contribution of the blood–brain barrier (BBB) to the differential response to stroke in adults and neonates is poorly understood. We asked whether the structure and function of the BBB is disrupted differently in neonatal and adult rats by transient middle cerebral artery occlusion. In adult rats, albumin leakage into injured regions was markedly increased during 2–24 h reperfusion but leakage remained low in the neonates. Functional assays employing intravascular tracers in the neonates showed that BBB permeability to both large (70 kDa dextran) and small (3 kDa dextran), gadolinium (III)-diethyltriaminepentaacetic acid tracers remained largely undisturbed 24 h after reperfusion. The profoundly different functional integrity of the BBB was associated with the largely nonoverlapping patterns of regulated genes in endothelial cells purified from injured and uninjured adult and neonatal brain at 24 h (endothelial transcriptome, 31,042 total probe sets). Within significantly regulated 1266 probe sets in injured adults and 361 probe sets in neonates, changes in the gene expression of the basal lamina components, adhesion molecules, the tight junction protein occludin, and matrix metalloproteinase-9 were among the key differences. The protein expression of collagen-IV, laminin, claudin-5, occludin, and zonula occludens protein 1 was also better preserved in neonatal rats. Neutrophil infiltration remained low in acutely injured neonates but neutralization of cytokine-induced neutrophil chemoattractant-1 in the systemic circulation enhanced neutrophil infiltration, BBB permeability, and injury. The markedly more integrant BBB in neonatal brain than in adult brain after acute stroke may have major implications for the treatment of neonatal stroke.
Registration of pre- and postoperative surface scans for pediatric neurosurgery

Abstract A software for automatic registration and differential visualization of pre- and postoperative surface scans for use in pediatric neurosurgery is developed and implemented. The core operations of the registration include an automatic head extraction, a rough registration by aligning the main axes, a depth map-based registration for robust determination and registration of feature points in the facial area, and a fine registration. A graphical user interface is implemented for the difference visualization and program control.
Neuronal LRP1 Regulates Glucose Metabolism and Insulin Signaling in the Brain

Alzheimer's disease (AD) is a neurological disorder characterized by profound memory loss and progressive dementia. Accumulating evidence suggests that Type 2 diabetes mellitus, a metabolic disorder characterized by insulin resistance and glucose intolerance, significantly increases the risk for developing AD. Whereas amyloid-β (Aβ) deposition and neurofibrillary tangles are major histological hallmarks of AD, impairment of cerebral glucose metabolism precedes these pathological changes during the early stage of AD and likely triggers or exacerbates AD pathology. However, the mechanisms linking disturbed insulin signaling/glucose metabolism and AD pathogenesis remain unclear. The low-density lipoprotein receptor-related protein 1 (LRP1), a major apolipoprotein E receptor, plays critical roles in lipoprotein metabolism, synaptic maintenance, and clearance of Aβ in the brain. Here, we demonstrate that LRP1 interacts with the insulin receptor β in the brain and regulates insulin signaling and glucose uptake. LRP1 deficiency in neurons leads to impaired insulin signaling as well as reduced levels of glucose transporters GLUT3 and GLUT4. Consequently, glucose uptake is reduced. By using an in vivo microdialysis technique sampling brain glucose concentration in freely moving mice, we further show that LRP1 deficiency in conditional knock-out mice resulted in glucose intolerance in the brain. We also found that hyperglycemia suppresses LRP1 expression, which further exacerbates insulin resistance, glucose intolerance, and AD pathology. As loss of LRP1 expression is seen in AD brains, our study provides novel insights into insulin resistance in AD. Our work also establishes new targets that can be explored for AD prevention or therapy.
Multiprocessor Hash-Based Join Algorithms

This paper extends earlier research on hash-join algorithms to a multiprocessor architecture. Implementations of a number of centralized join algorithms are described and measured. Evaluation of these algorithms served to verify earlier analylical results. In addition, they demonstrate that bit vector filtering provides dramatic improvement in the performance of all algorithms including the sort mergejoin algorithm. Multiprocessor configurations of the centralized Grace and Hybrid hash-join algorithms are also presented. Both algorithms arc shown to provide linear increases in throughput with corresponding increases in processor and disk resources.