Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the novel mitochondrial genome replication factor MiRF172 in Trypanosoma brucei

ABSTRACT The unicellular parasite Trypanosoma brucei harbors one mitochondrial organelle with a singular genome called the kinetoplast DNA (kDNA). The kDNA consists of a network of concatenated minicircles and a few maxicircles that form the kDNA disc. More than 30 proteins involved in kDNA replication have been described. However, several mechanistic questions are only poorly understood. Here, we describe and characterize minicircle replication factor 172 (MiRF172), a novel mitochondrial genome replication factor that is essential for cell growth and kDNA maintenance. By performing super-resolution microscopy, we show that MiRF172 is localized to the kDNA disc, facing the region between the genome and the mitochondrial membranes. We demonstrate that depletion of MiRF172 leads to a loss of minicircles and maxicircles. Detailed analysis suggests that MiRF172 is involved in the reattachment of replicated minicircles to the kDNA disc. Furthermore, we provide evidence that the localization of the replication factor MiRF172 not only depends on the kDNA itself, but also on the mitochondrial genome segregation machinery, suggesting an interaction between the two essential entities. This article has an associated First Person interview with the first author of the paper. Highlighted Article: MiRF172 is a novel protein involved in the reattachment of replicated minicircles in Trypanosoma brucei; this protein requires the mitochondrial segregation machinery for correct localization.
Beam Pull Out Tests of NSM - FRP and Steel Bars in Concrete

This paper describes an experimental investigation regarding a relatively new strengthening method for flexural concrete members, known as NSM technology (near-surface mounting). The study included fourteen simply supported concrete beams, strengthened by plac- ing either steel or carbon FRP bars in grooves cut on the tension face of the member and bond- ing with epoxy paste; specimens were loaded in bending till the occurrence of failure by debonding. Nine of the specimens were fabricated to have the bar fully bonded in one half-span, whereas the bonded length in the other half span of the typical member was limited. The bonded length was a parameter of study in the investigation. NSM bars were fully bonded in the case of the remaining five specimens. An objective of this experimental research was to examine the bond strength of the NSM method using realistic stress field conditions (beam pullout tests rather than standard pullout) while at the same time obtaining test results for comparison with those of the direct pull out tests. From the experimental evidence it is concluded that flexural curvature, which occurs in the beam-type tests, has a significant effect on the mode of failure of the upgraded system and on the strength of the failure interface, with a magnitude that depends strongly on the mechanical properties and the surface pattern of the bar. With increasing height of the surface deformations of smooth bars, the failure mode gradually changes from pullout at the bar-epoxy interface, to failure at the epoxy-concrete interface which is also observed in standard pullout tests. In this case, bond strength obtained from the beam tests is in general greater than the respective value recorded from direct pull out tests. This increase is attributed to the additional friction generated on the bar and on the epoxy filler's lateral surface owing to curvature compatibility between the bar and the surrounding concrete in the bending beam.
Temporal Difference Networks for Video Action Recognition

Deep convolutional neural networks have been great success for image based recognition tasks. However, it is still unclear how to model the temporal evolution of videos effectively by deep networks. While recent deep models for videos show improvement by incorporating optical flow or aggregating high level appearance across frames, they focus on modeling either the long term temporal relations or short term motion. We propose Temporal Difference Networks (TDN) that model both long term relations and short term motion from videos. We leverage a simple but effective motion representation: difference of CNN features in our network and jointly modeling the motion at multiple scales in a single CNN. It achieves state-of-the-art performance on three different video classification benchmarks, showing the effectiveness of our approach to learn temporal relations in videos.
Acute exercise remodels mitochondrial membrane interactions in mouse skeletal muscle

A unique property of mitochondria in mammalian cells is their ability to physically interact and undergo dynamic events of fusion/fission that remodel their morphology and possibly their function. In cultured cells, metabolic perturbations similar to those incurred during exercise influence mitochondrial fusion and fission processes, but it is unknown whether exercise acutely alters mitochondrial morphology and/or membrane interactions in vivo. To study this question, we subjected mice to a 3-h voluntarily exercise intervention following their normal physical activity patterns, and quantified mitochondrial morphology and membrane interactions in the soleus using a quantitative electron microscopy approach. A single exercise bout effectively decreased blood glucose (P < 0.05) and intramyocellular lipid content (P < 0.01), indicating increased muscle metabolic demand. The number of mitochondria spanning Z-lines and proportion of electron-dense contact sites (EDCS) between adjacent mitochondrial membranes were increased immediately after exercise among both subsarcolemmal (+116%, P < 0.05) and intermyofibrillar mitochondria (+191%, P < 0.001), indicating increased physical interactions. Mitochondrial morphology, and abundance of the mitochondrial pro-fusion proteins Mfn2 and OPA1 were unchanged. Collectively, these results support the notion that mitochondrial membrane dynamics are actively remodelled in skeletal muscle, which may be regulated by contractile activity and the metabolic state. Future studies are required to understand the implications of mitochondrial dynamics in skeletal muscle physiology during exercise and inactivity.
Improved retention associated with community-based accompaniment for antiretroviral therapy delivery in rural Rwanda.

BACKGROUND Minimizing death and ensuring high retention and good adherence remain ongoing challenges for human immunodeficiency virus (HIV) treatment programs. We examined whether the addition of community-based accompaniment (characterized by daily home visits from a community health worker, directly observed treatment, nutritional support, transportation stipends, and other support as needed) to the Rwanda national model for antiretroviral therapy (ART) delivery would improve retention in care, viral load suppression, and change in CD4 count, relative to the national model alone. METHODS We conducted a prospective observational cohort study among 610 HIV-infected adults initiating ART in 1 of 2 programs in rural Rwanda. Psychosocial and clinical characteristics were recorded at ART initiation. Death, treatment retention, and plasma viral load were assessed at 1 year. CD4 count was evaluated at 6-month intervals. Multivariable regression models were used to adjust for baseline differences between the 2 populations. RESULTS Eighty-five percent and 79% of participants in the community-based and clinic-based programs, respectively, were retained with viral load suppression at 1 year. After adjusting for CD4 count, depression, physical health quality of life, and food insecurity, community-based accompaniment was protective against death or loss to follow-up during the first year of ART (hazard ratio, 0.17; 95% confidence interval [CI], .09-.35; P < .0001). In a second multivariable analysis, individuals receiving accompaniment were more likely to be retained with a suppressed viral load at 1 year (risk ratio: 1.15; 95% CI, 1.03-1.27; P = .01). CONCLUSIONS These findings indicate that community-based accompaniment is effective in improving retention, when added to a clinic-based program with fewer patient support mechanisms.
Effects Of Nurse Prescribing Of Medication: A Systematic Review

Background: Nurse prescribing is being implemented increasingly. This article reviews the literature on the effects of it. Methods: Eleven databases and 6 websites were searched. The quality of the studies was determined. Outcomes were classified by the effects on medication prescribed, on patients, on professionals and on the health care system. Results: Twenty-three studies were included. All but two studies had a high risk of bias. Nurses sometimes differ from physicians in the number of patients they prescribe or in the choice of type of medication. Clinical parameters were the same or better for treatment by nurses; perceived quality of care by nurses is similar or better. The effects on professionals or on the health care system could not be described. Conclusion: The effects of nurse prescribing seem positive, although the high risk of bias in the studies means they must be regarded with caution. (aut. ref.)
How do developers fix issues and pay back technical debt in the Apache ecosystem?

During software evolution technical debt (TD) follows a constant ebb and flow, being incurred and paid back, sometimes in the same day and sometimes ten years later. There have been several studies in the literature investigating how technical debt in source code accumulates during time and the consequences of this accumulation for software maintenance. However, to the best of our knowledge there are no large scale studies that focus on the types of issues that are fixed and the amount of TD that is paid back during software evolution. In this paper we present the results of a case study, in which we analyzed the evolution of fifty-seven Java open-source software projects by the Apache Software Foundation at the temporal granularity level of weekly snapshots. In particular, we focus on the amount of technical debt that is paid back and the types of issues that are fixed. The findings reveal that a small subset of all issue types is responsible for the largest percentage of TD repayment and thus, targeting particular violations the development team can achieve higher benefits.
Assessment Of Results Of Open Arthrolysis In Post Traumatic Stiff Elbows

Background: Surgical management of posttraumatic elbow stiffness has been reported with poor outcome following treatment. Elbow arthrolysis done in any age group and even very old cases yield good results. The goal of our study was to assess the outcome in improvement of the range of motion of the elbow after surgical release by a tailor-made approach to yield good result.Materials and Methods: A retrospective and prospective study was conducted between oct 2006 to oct 2008 at department of orthopaedic surgery, G.S. V.M. medical college Kanpur. This study includes 25 cases of elbow stiffness due to various types of injuries. All the cases were treated with elbow arthrolysis if there was no progress after adequate supervised conservative management except in unreduced dislocations. All the cases were followed up for a minimum period of 2 years. Overall outcome was rated with the functional scoring system by Mayo Clinic Performance Index and Krishnamoorthy et. al (1976). Results: Nineteen(76%) out of 25 patients had excellent results with a mean preoperative range of motion of 38.4°,and postoperative range of motion of 106.80° with net gain in range of motion of 68.40° (' t ' test value is 9.33, P < 0.01). One (4%) of the patient had elbow instability. In cases where release was performed from three months to six months had mean gain of 76.92°. Cases in which release was performed after six months had gain of 63.57°. The mean pre-operative Mayo Clinic Performance Index score was 66°±9.35° and mean post-operative score was 95.4°±13.38° with average gain of 29.4°. (t test value 9.005, p<.001). According to Krishnamoorthy et al functional scoring system (1976), 19 patients (76%) achieve good result and 5 cases (20%) had fair result and 1 case (4%) had poor result.Conclusions: In cases of posttraumatic elbow stiffness after a failed initial conservative treatment, early arthrolysis with sequential surgical soft tissue release yields good result than delayed surgery.
Preclinical Potency and Biodistribution Studies of an AAV 5 Vector Expressing Human Interferon-β (ART-I02) for Local Treatment of Patients with Rheumatoid Arthritis

Introduction Proof of concept for local gene therapy for the treatment of arthritis with immunomodulatory cytokine interferon beta (IFN-β) has shown promising results in animal models of rheumatoid arthritis (RA). For the treatment of RA patients, we engineered a recombinant adeno-associated serotype 5 vector (rAAV5) encoding human (h)IFN-β under control of a nuclear factor κB promoter (ART-I02). Methods The potency of ART-I02 in vitro as well as biodistribution in vivo in arthritic animals was evaluated to characterize the vector prior to clinical application. ART-I02 expression and bioactivity after transduction was evaluated in fibroblast-like synoviocytes (FLS) from different species. Biodistribution of the vector after local injection was assessed in a rat adjuvant arthritis model through qPCR analysis of vector DNA. In vivo imaging was used to investigate transgene expression and kinetics in a mouse collagen induced arthritis model. Results Transduction of RA FLS in vitro with ART-I02 resulted in high expression levels of bioactive hIFN-β. Transduction of FLS from rhesus monkeys, rodents and rabbits with ART-I02 showed high transgene expression, and hIFN-β proved bioactive in FLS from rhesus monkeys. Transgene expression and bioactivity in RA FLS were unaltered in the presence of methotrexate. In vivo, vector biodistribution analysis in rats after intra-articular injection of ART-I02 demonstrated that the majority of vector DNA remained in the joint (>93%). In vivo imaging in mice confirmed local expression of rAAV5 in the knee joint region and demonstrated rapid detectable and sustained expression up until 7 weeks. Conclusions These data show that hIFN-β produced by RA FLS transduced with ART-I02 is bioactive and that intra-articular delivery of rAAV5 drives expression of a therapeutic transgene in the joint, with only limited biodistribution of vector DNA to other tissues, supporting progress towards a phase 1 clinical trial for the local treatment of arthritis in patients with RA.
Serum vitamin B-12 in children presenting with vasovagal syncope.

BACKGROUND AND OBJECTIVES The present study aims to determine the serum vitamin B-12 in children presenting with vasovagal syncope. METHODS AND STUDY DESIGN This is a prospective review of 160 children presenting with vasovagal syncope. Subgroup analysis was done based on the results of head up tilt test. RESULTS Head up tilt test gave positive results in 80 children and yielded negative results in the remaining 80 children. The tilt test positive children had significantly lower thyroid stimulating hormone concentrations (p=0.06), total iron binding capacity (p=0.04) and serum vitamin B-12 (p=0.01). The prevalence of vitamin B-12 deficiency was significantly higher in the tilt positive group (80% vs 52.5%, p=0.001). Out of 80 children with positive tilt test, 8 children (10%) showed cardioinhibitory response, 22 children (27.5%) demonstrated a vasodepressor response, 24 children (30%) displayed mixed response and 26 children (32.5%) had the postural orthostatic tachycardia syndrome. Erythrocyte sedimentation rate was significantly lower in the mixed response group than in the vasodepressor group (6.2±0.8 mm/h vs 14.3±2.5 mm/h, p=0.001). Serum vitamin B-12 was significantly lower in the postural orthostatic tachycardia syndrome (POTS) group than in the vasodepressor group (240.8±38.2 pg/mL vs 392.7±27.1 pg/mL, p=0.001). The prevalence of vitamin B-12 deficiency was significantly higher in the POTS group than in the vasodepressor group (92.3% vs 45.5%, p=0.001). CONCLUSIONS Vitamin B-12 deficiency causes reduction in myelinization, deceleration in nerve conduction and elevation in serum concentrations of noradrenaline. These factors may contribute to the impairment of autonomic functions which are involved in the pathogenesis of vasovagal syncope.
EFFECT OF DIETARY OREGANO ESSENTIAL OIL AGAINST VIBRIO BACTERIA IN SHRIMPS

The effect of dietary oregano essential oils on the growth of Vibrio bacteria in shrimps was evaluated. Shrimps were fed: (i) food with oregano oil with a high level of thymol; (ii) food with oregano oil with a high level of carvacrol, and (iii) food without oregano oil (the control). The animals were infected by three species of Vibrio (vulnificus, parahaemolyticus and cholerae). The microbial counts of Vibrio species were significantly lower (p <0.05) in tissues from animals whose food was supplemented with oregano oil. We concluded that dietary supplementation of shrimps with oregano oil provides antimicrobial activity into the body of the penaeids.
ACritical Test of Temporal and Spatial Accuracy of the Tobii T 60 XL Eye Tracker

Infant eye tracking is becoming increasingly popular for its presumed precision relative to traditional looking time paradigms and potential to yield new insights into developmental processes. However, there is strong reason to suspect that the temporal and spatial resolution of popular eye tracking systems is not entirely accurate, potentially compromising any data from an infant eye tracking experiment. Moreover, ‘‘best practices’’ for infant eye tracking, such as knowing which software tool enhances experimental flexibility, remain to be determined. The present investigation was designed to evaluate the temporal and spatial accuracy of data from the Tobii T60XL eye tracker through the use of visual latency and spatial accuracy tasks involving adults and infants. Systematic delays and drifts were revealed in oculomotor response times, and the system’s spatial accuracy was observed to deviate somewhat in excess of the manufacturer’s estimates; the experimental flexibility of the system appears dependent on the chosen software.
Experimental study on flexural capacity of normal section of high strength reinforced reactive powder concrete beam

Six high-strength steel reactive powder concrete(RPC) charpy-third points were statically tested,and the influence of stress performance on the beams was analysed when different longitudinal reinforcement ratio,longitudinal reinforcement grade,diameter and longitudinal reinforcement bar diameter in different pressure were changed.The conclusions are as follows:plane crosss-section assumption is also available to apply to high strength reinforced RPC beams;reinforcement ratio is the main factor bearing capacity of reinforced RPC beams;with the reference of ordinary reinforced concrete normal section bearing capacity calculation,the formula of normal section bearing capacity for high strength reinforced RPC is derived;the relative RPC compression zone height for the boundary of high-strength steel beams is 0.62.
An In-Depth Analysis of Disassembly on Full-Scale x86/x64 Binaries

It is well-known that static disassembly is an unsolved problem, but how much of a problem is it in real software—for instance, for binary protection schemes? This work studies the accuracy of nine state-of-the-art disassemblers on 981 real-world compiler-generated binaries with a wide variety of properties. In contrast, prior work focuses on isolated corner cases; we show that this has led to a widespread and overly pessimistic view on the prevalence of complex constructs like inline data and overlapping code, leading reviewers and researchers to underestimate the potential of binary-based research. On the other hand, some constructs, such as function boundaries, are much harder to recover accurately than is reflected in the literature, which rarely discusses much needed error handling for these primitives. We study 30 papers recently published in six major security venues, and reveal a mismatch between expectations in the literature, and the actual capabilities of modern disassemblers. Our findings help improve future research by eliminating this mismatch.
Breeding evaluation of pepper lines obtained by in vitro anther culture

The comparative breeding evaluation was carried out with six advanced pepper lines (Capsicum annuum L.) with androgenic origin and their initial pepper variety Hebar during the period 2008 - 2010 in field conditions at Plovdiv, Bulgaria. The genotypes were characterized by total and standard yield, plant height and fruit traits: length, width, wall thickness and weight. The response of two lines (4 and 6) and control variety to the Verticillium wilt was also investigated on artificial infected background. According to the results of the experimental work standard and total yield in all androgenic lines were higher compared to the initial variety but significant differences were established only for lines 1, 2, 4 and 6. Line 6 was characterized with the highest standard yield (4009 kg/da) followed by line 2 (3829 kg/da). They exceeded variety Hebar with 42.26% and 35.89%, respectively. Line 2 formed the heaviest (61.31 g) and longer (11.24 cm) fruits than most studied genotypes. Anther-derived lines were also with a good uniformity by studied traits. In line 6 was registered lower index of infestation byVerticillium dahliae Kleb. than the control during the investigated period. These perspective lines will be included as valuable genetic resources for future pepper breeding programs for development of new varieties.
Localized Dictionaries Based Orientation Field Estimation for Latent Fingerprints

Dictionary based orientation field estimation approach has shown promising performance for latent fingerprints. In this paper, we seek to exploit stronger prior knowledge of fingerprints in order to further improve the performance. Realizing that ridge orientations at different locations of fingerprints have different characteristics, we propose a localized dictionaries-based orientation field estimation algorithm, in which noisy orientation patch at a location output by a local estimation approach is replaced by real orientation patch in the local dictionary at the same location. The precondition of applying localized dictionaries is that the pose of the latent fingerprint needs to be estimated. We propose a Hough transform-based fingerprint pose estimation algorithm, in which the predictions about fingerprint pose made by all orientation patches in the latent fingerprint are accumulated. Experimental results on challenging latent fingerprint datasets show the proposed method outperforms previous ones markedly.
Enter Sandbox: Android Sandbox Comparison

Expecting the shipment of 1 billion Android devices in 2017, cyber criminals have naturally extended their vicious activities towards Google's mobile operating system. With an estimated number of 700 new Android applications released every day, keeping control over malware is an increasingly challenging task. In recent years, a vast number of static and dynamic code analysis platforms for analyzing Android applications and making decision regarding their maliciousness have been introduced in academia and in the commercial world. These platforms differ heavily in terms of feature support and application properties being analyzed. In this paper, we give an overview of the state-of-the-art dynamic code analysis platforms for Android and evaluate their effectiveness with samples from known malware corpora as well as known Android bugs like Master Key. Our results indicate a low level of diversity in analysis platforms resulting from code reuse that leaves the evaluated systems vulnerable to evasion. Furthermore the Master Key bugs could be exploited by malware to hide malicious behavior from the sandboxes.