Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete mitochondrial genome of Rasbora borapetensis (Cypriniformes: Cyprinidae: Rasbora)

Abstract The traditional polymerase chain reaction method was employed to obtain the complete mitochondrial genome of Rasbora borapetensis. The mitogenome was determined to be a 16,510 bp long circular molecule. It contained the typical complement of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. This is first report on the complete mitogenome sequence of R. borapetensis.
Degenerative diseases of the lumbar spine

Purpose: To compare a T2* weighted 2D spoiled gradient echo multiecho sequence (MEDIC) with magnetization transfer saturation pulse versus lumbar myelography and postmyelographic computed tomography (pCT). Material and Methods: 84 disk levels in 27 patients were examined. The vertebral bodies, intervertebral disks, neural foramina, cauda equina, ligamentum flavum, and narrowing of the spinal canal were investigated using an evaluation scale. In addition, the pCT and the MEDIC sequence were evaluated for assessing the narrowing of the neural foramina in a phantom study using a cadaver preparation of the lumbar spine. Results: A total of 28 disk herniations, 11 cases of osteophytes narrowing the spinal canal or the neural foramina, and 7 spinal canal stenoses were detected. The pCT was significantly better in visualizing the cauda equina. The MEDIC sequence was significantly superior in visualizing the extension of the ligamentum flavum. No statistical differences between either image modality were found concerning assessment of the narrowing of the neural foramina and the spinal canal, nor regarding evaluation of the vertebral disk and the vertebral body. Measurements of the phantom study showed that the MEDIC sequence did not overestimate narrowing of the neural foramina. Conclusions: The T2* MEDIC sequence has proved to be as accurate as pCT in evaluating osteophytes and narrowing of the neural foramina. In doubtful standard magnetic resonance imaging findings, this means that an additional axial T2* MEDIC sequence may be of value in reaching the same accuracy as pCT.
Comparative study of the active cadmium efflux systems operating at the plasma membrane and tonoplast of cucumber root cells

The strategies developed by plants to avoid the toxicity of cadmium (Cd) and other heavy metals involve active sequestration of metals into the apoplast and vacuoles. The protein systems excluding heavy metals from the cell cytosol localize to the plasma membrane and tonoplast and are energized either by ATP or by the electrochemical gradient generated by H+-ATPase or by V-ATPase and pyrophosphatase (PPase), respectively. In this work, a comparative study on the contribution of both the plasma membrane and tonoplast in the active detoxification of plant cells after treatment with Cd was performed. The studies using plants treated and untreated with Cd reveal that both, H+-coupled and MgATP-driven efflux of Cd across plasma membranes and tonoplast is markedly stimulated in the presence of Cd in the environment. Previous studies on plasma-membrane localized H+-coupled Cd efflux together with the present data demonstrating tonoplast H+/Cd2+ antiport activity suggest that H+-coupled secondary transport of Cd displays a lower affinity for Cd when compared with Cd primary pumps driven by MgATP. In addition, it is shown that MgATP-energized Cd efflux across both membranes is significantly enhanced by cysteine, dithiothreitol, and glutathione. These results suggest that Cd is excluded from the cytosol through an energy-dependent system as a free ion as well as a complexed form. Although both membranes contribute in the active exclusion of ionized and complexed Cd from the cytosol, the overall calculation of Cd accumulation in the everted plasma membranes and vacuolar vesicles suggests that the tonoplast and vacuole have a major function in Cd efflux from the cytosol in the roots of cucumber subjected to Cd stress.
Compiling for reconfigurable computing: A survey

Reconfigurable computing platforms offer the promise of substantially accelerating computations through the concurrent nature of hardware structures and the ability of these architectures for hardware customization. Effectively programming such reconfigurable architectures, however, is an extremely cumbersome and error-prone process, as it requires programmers to assume the role of hardware designers while mastering hardware description languages, thus limiting the acceptance and dissemination of this promising technology. To address this problem, researchers have developed numerous approaches at both the programming languages as well as the compilation levels, to offer high-level programming abstractions that would allow programmers to easily map applications to reconfigurable architectures. This survey describes the major research efforts on compilation techniques for reconfigurable computing architectures. The survey focuses on efforts that map computations written in imperative programming languages to reconfigurable architectures and identifies the main compilation and synthesis techniques used in this mapping.
The impact of outcome reporting bias in randomised controlled trials on a cohort of systematic reviews

Objective To examine the prevalence of outcome reporting bias—the selection for publication of a subset of the original recorded outcome variables on the basis of the results—and its impact on Cochrane reviews. Design A nine point classification system for missing outcome data in randomised trials was developed and applied to the trials assessed in a large, unselected cohort of Cochrane systematic reviews. Researchers who conducted the trials were contacted and the reason sought for the non-reporting of data. A sensitivity analysis was undertaken to assess the impact of outcome reporting bias on reviews that included a single meta-analysis of the review primary outcome. Results More than half (157/283 (55%)) the reviews did not include full data for the review primary outcome of interest from all eligible trials. The median amount of review outcome data missing for any reason was 10%, whereas 50% or more of the potential data were missing in 70 (25%) reviews. It was clear from the publications for 155 (6%) of the 2486 assessable trials that the researchers had measured and analysed the review primary outcome but did not report or only partially reported the results. For reports that did not mention the review primary outcome, our classification regarding the presence of outcome reporting bias was shown to have a sensitivity of 88% (95% CI 65% to 100%) and specificity of 80% (95% CI 69% to 90%) on the basis of responses from 62 trialists. A third of Cochrane reviews (96/283 (34%)) contained at least one trial with high suspicion of outcome reporting bias for the review primary outcome. In a sensitivity analysis undertaken for 81 reviews with a single meta-analysis of the primary outcome of interest, the treatment effect estimate was reduced by 20% or more in 19 (23%). Of the 42 meta-analyses with a statistically significant result only, eight (19%) became non-significant after adjustment for outcome reporting bias and 11 (26%) would have overestimated the treatment effect by 20% or more. Conclusions Outcome reporting bias is an under-recognised problem that affects the conclusions in a substantial proportion of Cochrane reviews. Individuals conducting systematic reviews need to address explicitly the issue of missing outcome data for their review to be considered a reliable source of evidence. Extra care is required during data extraction, reviewers should identify when a trial reports that an outcome was measured but no results were reported or events observed, and contact with trialists should be encouraged.
Comparison of HIV detection by virus isolation in lymphocyte cultures and molecular amplification of HIV DNA and RNA by PCR in offspring of seropositive mothers.

An early and accurate diagnosis of HIV infection is needed in the offspring of seropositive mothers. To this end, we have used two techniques for the direct detection of HIV in 12 newborns tested within 2 weeks after birth and 12 children. HIV isolation was carried out in lymphocyte cocultures and compared with detection of DNA and RNA sequences by molecular amplification using the polymerase chain reaction (PCR). In lymphocyte cocultures, HIV was isolated in 8 of 24 cases (33%), including 3 newborns, 3 symptomatic children, and 2 asymptomatic ones. HIV DNA was detected by PCR in twice as many cases, i.e., in 16/24 cases (66%), including 7/12 newborns, 4/4 symptomatic children, and 5/8 asymptomatic ones, 2 of whom became seronegative, HIV RNA was detected in 10 of 16 cases (60%) with detectable HIV DNA, including all of the cases who had a positive HIV isolation. Only children with clinical or biological signs of HIV infection were positive for HIV RNA. Furthermore, signs of HIV infection appeared within 6 months in three of the four newborns who were positive for HIV RNA at birth. These results indicate that HIV DNA detection by PCR is far more sensitive than HIV isolation in culture for the early diagnosis of HIV infection in offspring of seropositive mothers. HIV RNA detection appears to be a useful prognostic marker since it does correlate with disease progression and may serve as a clue for HIV replication in vivo.
On linearly constrained minimum variance beamforming

Beamforming is a widely used technique for source localization in signal processing and neuroimaging. A number of vector-beamformers have been introduced to localize neuronal activity by using magnetoencephalography (MEG) data in the literature. However, the existing theoretical analyses on these beamformers have been limited to simple cases, where no more than two sources are allowed in the associated model and the theoretical sensor covariance is also assumed known. The information about the effects of the MEG spatial and temporal dimensions on the consistency of vector-beamforming is incomplete. In the present study, we consider a class of vector-beamformers defined by thresholding the sensor covariance matrix, which include the standard vector-beamformer as a special case. A general asymptotic theory is developed for these vector-beamformers, which shows the extent of effects to which the MEG spatial and temporal dimensions on estimating the neuronal activity index. The performances of the proposed beamformers are assessed by simulation studies. Superior performances of the proposed beamformers are obtained when the signal-to-noise ratio is low. We apply the proposed procedure to real MEG data sets derived from five sessions of a human face-perception experiment, finding several highly active areas in the brain. A good agreement between these findings and the known neurophysiology of the MEG response to human face perception is shown.
Endoscopic Stenting for Biliary and Pancreatic Malignancies

Endoscopic treatment of pancreatobiliary malignancies has been recognized in the last decades as the treatment of choice in inoperable patients. Endoscopic armamentarium includes biliary stents (plastic and metallic) to bypass neoplastic strictures of the biliary tree, and pancreatic stents to palliate the obstructive pain caused by stenoses of the main pancreatic duct. A major issue is the long-term patency of plastic stents that will eventually clog on average after 3 to 4 months. Self-expandable metallic stents have longer patency, but they can also become occluded by tumor ingrowth or overgrowth; they are also much more expensive; their use is thus recommended in patients with longer life expectancy. Decompression of the dilated main pancreatic duct in pancreatic carcinoma may be effective in the relief of obstructive pain. Endoscopic palliation in pancreatic and biliary malignancies appears safe and effective; management of patient in referral centers, with an available team of gastroenterologists with endoscopic skills, surgeons, and radiologists is recommended.
Two SET domain containing genes link epigenetic changes and aging in Caenorhabditis elegans

Changes in epigenetic status and chromatin structure have been shown to associate with aging in many organisms. Here, we report an RNAi screen of putative histone methyltransferases and demethylases in wild‐type Caenorhabditis elegans using reproduction inhibitor. We identified six genes that when inactivated by RNAi, consistently extend lifespan. Five of these genes do not require germline proliferation to affect lifespan. We further characterized two of these genes, the highly homologous SET domain containing genes, set‐9 and set‐26. They share redundant functions in maintaining normal lifespan, while exhibiting differential tissue expression patterns. Furthermore, we found that set‐9 and set‐26 partially act through the Forkhead box O (FOXO) transcription factor, DAF‐16, to modulate lifespan. Interestingly, inactivation of somatic SET‐26 alone results in a robust lifespan extension and alters the levels of histone H3 protein and the repressive histone marks, H3K9me3 and H3K27me3, in an age‐dependent manner. We hypothesize that inactivation of SET‐26 triggers compensation mechanisms to restore repressive chromatin structure and hence affects chromatin stability to promote longevity.
The Effect of an Impulsive Personality on Overeating and Obesity: Current State of Affairs

The worldwide obesity epidemic brings with it health-related, psychological and social problems and consequently a dramatic increase in health costs. Something needs to be done to stop or even reverse this trend and psychological and environmental factors seem to be our best bet. One psychological factor with potential is impulsivity. Research in populations that typically overeat (the obese and Bulimia Nervosa patients), in populations that are typically impulsive (e.g. Attention Deficit Hyperactivity Disorder patients) and in healthy participants has indeed begun to indicate that impulsivity plays a role in the problem of overeating. However, more research including actual food intake and true experimental research is needed to conclude that impulsivity actually causes overeating in the short term and possibly overweight or even obesity in the long run.
Adverse Cardiovascular Effects with Acute Particulate Matter and Ozone Exposures: Interstrain Variation in Mice

Objectives Increased ambient particulate matter (PM) levels are associated with cardiovascular morbidity and mortality, as shown by numerous epidemiology studies. Few studies have investigated the role of copollutants, such as ozone, in this association. Furthermore, the mechanisms by which PM affects cardiac function remain uncertain. We hypothesized that PM and O3 induce adverse cardiovascular effects in mice and that these effects are strain dependent. Study design After implanting radiotelemeters to measure heart rate (HR) and HR variability (HRV) parameters, we exposed C57Bl/6J (B6), C3H/HeJ (HeJ), and C3H/HeOuJ (OuJ) inbred mouse strains to three different daily exposures of filtered air (FA), carbon black particles (CB), or O3 and CB sequentially [O3CB; for CB, 536 ± 24 μg/m3; for O3, 584 ± 35 ppb (mean ± SE)]. Results We observed significant changes in HR and HRV in all strains due to O3CB exposure, but not due to sequential FA and CB exposure (FACB). The data suggest that primarily acute HR and HRV effects occur during O3CB exposure, especially in HeJ and OuJ mice. For example, HeJ and OuJ mice demonstrated dramatic increases in HRV parameters associated with marked brady-cardia during O3CB exposure. In contrast, depressed HR responses occurred in B6 mice without detectable changes in HRV parameters. Conclusions These findings demonstrate that important interstrain differences exist with respect to PM- and O3-induced cardiac effects. This interstrain variation suggests that genetic factors may modulate HR regulation in response to and recuperation from acute copollutant exposures.
Mechanisms of noise-resistance in genetic oscillators

A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The integration of these “circuits” at the cellular level imposes strong constraints on their functioning and design. Here, we study a recently proposed model [Barkai, N. & Leibler, S. (2000) Nature (London), 403, 267–268] that incorporates just the essential elements found experimentally. We show that this type of oscillator is driven mainly by two elements: the concentration of a repressor protein and the dynamics of an activator protein forming an inactive complex with the repressor. Thus, the clock does not need to rely on mRNA dynamics to oscillate, which makes it especially resistant to fluctuations. Oscillations can be present even when the time average of the number of mRNA molecules goes below one. Under some conditions, this oscillator is not only resistant to but, paradoxically, also enhanced by the intrinsic biochemical noise.
Intercloud Architecture for interoperability and integration

This paper presents on-going research to develop the Intercloud Architecture Framework (ICAF) that addresses problems in multi-provider multi-domain heterogeneous cloud based infrastructure services and applications integration and interoperability. The paper refers to existing standards in Cloud Computing, in particular, recently published NIST Cloud Computing Reference Architecture (CCRA). The proposed ICAF defines four complementary components addressing Intercloud integration and interoperability: multilayer Cloud Services Model that combines commonly adopted cloud service models, such as IaaS, PaaS, SaaS, in one multilayer model with corresponding inter-layer interfaces; Intercloud Control and Management Plane that supports cloud based applications interaction; Intercloud Federation Framework, and Intercloud Operation Framework. The paper briefly describes the architectural framework for cloud based infrastructure services provisioned on-demand being developed in the framework of the GEYSERS project that is used as a basis for building multilayer cloud services integration framework that allows optimized provisioning of both computing, storage and networking resources. The proposed architecture is intended to provide an architectural model for developing Intercloud middleware and in this way will facilitate clouds interoperability and integration.
Outcome of open reduction for the neglected posterior dislocation of the elbow in a low-to-middle income country

Background Neglected posterior dislocation of the elbow is common in developing countries. We evaluated the clinical results of open reduction focusing on range of motion (ROM), stability and pain. Materials and Methods Sixteen patients were treated for neglected dislocation of the elbow between January 2008 and December 2012 at St. Luke’s Catholic Hospital and College of Nursing, Wolisso, Ethiopia. Mean time from injury was 2.8 months (range, 2–48 months). All patients underwent open reduction using Speed’s technique. Mean follow-up was 12 months (range, 12–36 months). Range of motion (ROM) was measured, stability was checked with the lateral pivot shift apprehension test. Results All patients improved their range of motion (ROM). Pain decreased. One patient developed instability during the rehabilitation programme; in the remaining patients pivot shift test was negative. Conclusion Open reduction is an effective method to restore joint stability, improve function of neglected posterior dislocation of the elbow.
Stacking-Based Visualization of Trajectory Attribute Data

Visualizing trajectory attribute data is challenging because it involves showing the trajectories in their spatio-temporal context as well as the attribute values associated with the individual points of trajectories. Previous work on trajectory visualization addresses selected aspects of this problem, but not all of them. We present a novel approach to visualizing trajectory attribute data. Our solution covers space, time, and attribute values. Based on an analysis of relevant visualization tasks, we designed the visualization solution around the principle of stacking trajectory bands. The core of our approach is a hybrid 2D/3D display. A 2D map serves as a reference for the spatial context, and the trajectories are visualized as stacked 3D trajectory bands along which attribute values are encoded by color. Time is integrated through appropriate ordering of bands and through a dynamic query mechanism that feeds temporally aggregated information to a circular time display. An additional 2D time graph shows temporal information in full detail by stacking 2D trajectory bands. Our solution is equipped with analytical and interactive mechanisms for selecting and ordering of trajectories, and adjusting the color mapping, as well as coordinated highlighting and dedicated 3D navigation. We demonstrate the usefulness of our novel visualization by three examples related to radiation surveillance, traffic analysis, and maritime navigation. User feedback obtained in a small experiment indicates that our hybrid 2D/3D solution can be operated quite well.
The incidence of vitreous loss and visual outcome in patients undergoing cataract surgery in a teaching hospital.

PURPOSE To determine the incidence of vitreous loss in patients undergoing cataract surgery and the visual outcome in a tertiary teaching hospital. METHODS Hospital records of 2095 consecutive patients undergoing cataract surgery between July 1999 and June 2000 were reviewed in this non-concurrent cohort study. Incidence and visual outcome of vitreous loss managed using standard vitrectomy techniques were assessed for different cataract surgical techniques (extracapsular, Blumenthal technique and phacoemulsification) as well as at different levels of surgical training. The outcome was compared with matched cases without vitreous loss (controls). RESULTS Vitreous loss occurred in 160 of 2095 eyes (7.63%; CI -7 to 9.3): 8.3% for ECCE, 8.1% for the Blumenthal technique and 5% with phacoemulsification. Vision > or = 6/18 was achieved in 85% of cases and 95% of controls. For experienced surgeons, 95% of the cases and controls had vision > or = 6/18. 5.8% of cases and 0.7% of controls had vision < 6/60. One patient in each group was blind following cataract surgery; both had operable cataracts in the fellow eye. CONCLUSIONS The vitreous loss rate in this tertiary teaching hospital is relatively high. This complication, managed with standard surgical techniques, is compatible with good visual outcome. In eyes with vitreous loss, the final visual acuity achieved by experienced surgeons was similar to that in uncomplicated cases.
A novel compact balun structure for multilayer MMICs

A novel compact MMIC balun and its design methodology has been developed, and turns out to combine the good balance of a MARCHAND-type balun with the compactness of a MMIC transmission line transformer. Analysis using accurate quasi-static as well as parallel independent full-wave simulation shows good performance. Application of this component is seen for example in microwave and RF frequency conversion and power amplifiers. A novel compact balun structure for multilayer MMICs M Engels and R H Jansen Aachen University of Technology (RWTH), Dept. of El. Engineering, ITHE, Kopernikusstr.16, D-52074 Aachen, Germany. Abstract A novel compact MMIC balun and its design methodology has been developed, and turns out to combine the good balance of a MARCHAND-type balun with the compactness of a MMIC transmission line transformer. Analysis using accurate quasi-static as well as parallel independent full-wave simulation shows good performance. Application of this component is seen for example in microwave and RF frequency conversion and power amplifiers.