Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemokine Signaling Guides Axons within the Retina in Zebrafish

Chemokines are a large family of secreted proteins that play an important role in the migration of leukocytes during hematopoiesis and inflammation. Chemokines and their receptors are also widely distributed in the CNS. Although recent investigations are beginning to elucidate chemokine function within the CNS, relatively little is known about the CNS function of this important class of molecules. To better appreciate the CNS function of chemokines, the role of signaling by stromal cell-derived factor-1 (SDF-1) through its receptor, chemokine (CXC motif) receptor 4 (CXCR4), was analyzed in zebrafish embryos. The SDF-1/CXCR4 expression pattern suggested that SDF-1/CXCR4 signaling was important for guiding retinal ganglion cell axons within the retina to the optic stalk to exit the retina. Antisense knockdown of the ligand and/or receptor and a genetic CXCR4 mutation both induced retinal axons to follow aberrant pathways within the retina. Furthermore, retinal axons deviated from their normal pathway and extended to cells ectopically expressing SDF-1 within the retina. These data suggest that chemokine signaling is both necessary and sufficient for directing retinal growth cones within the retina.
Polyethylene glycol precipitation for recovery of pathogenic viruses, including hepatitis A virus and human rotavirus, from oyster, water, and sediment samples

Polyethylene glycol 6000 precipitation was found to be an effective concentration method that enhanced the chances for detecting human virus pathogens in environmental samples. Percent recoveries from eluates of fresh and estuarine waters with 8% polyethylene glycol 6000 averaged 86 for hepatitis A virus, 77 for human rotavirus Wa, 87 for simian rotavirus SA11, and 68 for poliovirus. Percent recoveries of 97, 40, 97 and 105, respectively, for the same viruses were obtained from oyster eluates by the same procedure. Percent recoveries of 97 for hepatitis A virus and 78 for human rotavirus Wa were obtained from sediment eluates containing 2 M NaNO3 with a final concentration of 15% polyethylene glycol 6000. The polyethylene glycol method was shown to be more effective than the organic flocculation method for recovery of hepatitis A virus and rotaviruses Wa and SA11, but not of poliovirus 1 in laboratory studies. In field trials, hepatitis A virus or rotavirus or both were recovered from 12 of 18 eluates by polyethylene glycol, compared with recovery from 9 of 18 eluates by organic flocculation from fresh and estuarine waters subject to pollution.
A Study of Biofilm and Non-Line-of-Sight Bio-Hydroxyapatite Coatings Using a Serratia sp.

This study describes biofilm formation as a non line-of-sight coating method on support materials such as polyurethane foam, porous glass, polypropylene (PP) and titanium alloy, using a Serratia sp. , which can manufacture extracellular nanoscale scaffolded hydroxyapatite (HA) crystals via enzymatic cleavage of glycerol 2-phosphate (G2P) in the presence of CaCl2. Various microscopies and non-invasive magnetic resonance imaging were used to visualize the biofilm coating on the support surface. A novel micromanipulation technique was used to estimate the adhesive strength of native and HA-mineralized biofilms. The biofilm with HA was up to forty times stronger than that without HA. A coating of nano-HA (> 80 m) onto a biofilm-Ti disc was achieved.
DEVELOPMENT OF POLYMER CONCRETE AS A HIGHWAY PATCHING MATERIAL

A study has been conducted on the preparation and properties of polymer-concrete using polystyrene and/or poly(methyl methacrylate) as the polymeric component in the concrete composites formed. Both thermal and catalyzed polymerization methods were used to transform monomer-polymer mixtures into the polymeric component of polymer-concrete. Catalyst promoters were used to develop room-temperature polymerization systems which developed full strength within two hours. The effect of aggregates (silica sand, brown sand, gravel and limestone) on the physical properties of polymer-concrete compositions was also studied. In general, it was found that systems involving methyl methacrylate produced the best properties. Combinations containing from 9 to 15% of the polymer were studied, all gave higher compression, tensile, flexural and bonding strength than the corresponding control samples prepared without polymer. Abrasion resistance, water absorption, acid resistance and freeze-thaw durability were greatly improved with the use of either polymer system.
Analyzing available routing engines for InfiniBand-based clusters with Dragonfly topology

Dragonfly topologies have gathered great interest as one of the most promising interconnection patterns for the networks at the core of HPC clusters. In this paper, we configure several simulated InfiniBand-based clusters with a Dragonfly topology, and we analyze the performance in these configurations of the routing engines included in the latest release of the InfiniBand Subnet Manager (OpenSM v3.3.19).
Effect of rhythmic auditory stimulation on gait kinematic parameters of patients with multiple sclerosis

Purpose: This study aimed to examine the effect of rhythmic auditory stimulation on gait kinematic parameters of patients with multiple sclerosis. Subjects and Methods: In this study, 18 subjects, comprising 4 males and 14 females with Multiple Sclerosis with expanded disability status scale of 3 to 6 were chosen. Subjects were selected by available and targeted sampling and were randomly divided into two experimental (n = 9) and control (n = 9) groups. Exercises were gait with rhythmic auditory stimulation by a metronome device, in addition to gait without stimulation for the experimental and control groups, respectively. Training was carried out for 3 weeks, with 30 min duration for each session 3 times a week. Stride length, stride time, double support time, cadence and gait speed were measured by motion analysis device. Results: There was a significant difference between stride length, stride time, double support time, cadence and gait speed in the experimental group, before and after the training. Furthermore, there was a significant difference between the experimental and control groups in the enhancement of stride length, stride time, cadence and gait speed in favor of the experimental group. While this difference was not significant for double support time. Conclusion: The results of this study showed that rhythmic auditory stimulation is an effective rehabilitation method to improve gait kinematic parameters in patients with multiple sclerosis.
Improving the sensitivity of MASCOT search results validation by combining new features with Bayesian nonparametric model

The probability‐based search engine MASCOT has been widely used to identify peptides and proteins in shotgun proteomic research. Most subsequent quality control methods filter out ambiguous assignments according to the ion score and thresholds provided by MASCOT. On the basis of target‐decoy database search strategy, we evaluated the performance of several filter methods on MASCOT search results and demonstrated that using filter boundaries on two‐dimensional feature spaces, the MASCOT ion score and its relative score can improve the sensitivity of the filter process. Furthermore, using a linear combination of several characteristics of the assigned peptides, including the MASCOT scores, 15 previously employed features, and some newly introduced features, we applied a Bayesian nonparametric model to MASCOT search results and validated more correctly identified peptides in control and complex data sets than those could be validated by empirical score thresholds.
Sequence diversity and virulence in Zea mays of Maize streak virus isolates.

Full genomic sequences were determined for 12 Maize streak virus (MSV) isolates obtained from Zea mays and wild grass species. These and 10 other publicly available full-length sequences were used to classify a total of 66 additional MSV isolates that had been characterized by PCR-restriction fragment length polymorphism and/or partial nucleotide sequence analysis. A description is given of the host and geographical distribution of the MSV strain and subtype groupings identified. The relationship between the genotypes of 21 fully sequenced virus isolates and their virulence in differentially MSV-resistant Z. mays genotypes was examined. Within the only MSV strain grouping that produced severe symptoms in maize, highly virulent and widely distributed genotypes were identified that are likely to pose the most serious threat to maize production in Africa. Evidence is presented that certain of the isolates investigated may be the products of either intra- or interspecific recombination.
Transcranial electrical stimulation (tES – tDCS; tRNS, tACS) methods

Weak transcranial direct current stimulation (tDCS) with a homogenous DC field at intensities of around 1 mA induces long-lasting changes in the brain. tDCS can be used to manipulate brain excitability via membrane polarisation: cathodal stimulation hyperpolarises, while anodal stimulation depolarises the resting membrane potential, whereby the induced after-effects depend on polarity, duration and intensity of the stimulation. A variety of other parameters influence tDCS effects; co-application of neuropharmacologically active drugs may most impressively prolong or even reverse stimulation effects. Transcranial alternating stimulation (tACS) and random noise stimulation (tRNS) are used to interfere with ongoing neuronal oscillations and also finally produce neuroplastic effects if applied with appropriate parameters.
Measuring Kinesin's First Step*

A variety of models have recently emerged to explain how the molecular motor kinesin is able to maintain processive movement for over 100 steps. Although these models differ in significant features, they all predict that kinesin's catalytic domains intermittently separate from each other as the motor takes 8-nm steps along the microtubule. Furthermore, at some point in this process, one molecule of ATP is hydrolyzed per step. However, exactly when hydrolysis and product release occur in relation to this forward step have not been established. Furthermore, the rate at which this separation occurs as well as the speed of motor stepping onto and release from the microtubule have not been measured. In the absence of this information, it is difficult to critically evaluate competing models of kinesin function. We have addressed this issue by developing spectroscopic probes whose fluorescence is sensitive to motor-motor separation or microtubule binding. The kinetics of these fluorescence changes allow us to directly measure how fast kinesin steps onto and releases from the microtubule and provide insight into how processive movement is maintained by this motor.
Protelis: practical aggregate programming

The notion of a computational field has been proposed as a unifying abstraction for developing distributed systems, focusing on the computations and coordination of aggregates of devices instead of individual behavior. Prior field-based languages, however, have suffered from a number of practical limitations that have posed barriers to adoption and use. We address these limitations by introduction of Protelis, a functional language based on computational fields and embedded in Java, thereby enabling the construction of widely reusable components of aggregate systems. We demonstrate the simplicity of Protelis integration and programming through two examples: simulation of a pervasive computing scenario in the Alchemist simulator [24], and coordinated management of a network of services.
Attention-Deficit/Hyperactivity Disorder

Several lines of research are revising our picture of attention-deficit/hyperactivity disorder (ADHD). I highlight four emerging themes. First, models from temperament and personality research have been fruitful in clarifying the basic pathways to ADHD and their relation to typical development. Second, many kinds of attention are normal in ADHD, but cognitive control and vigilance are not. These last two are among present candidates for clinical markers that may help identify causes of ADHD. Third, any one cognitive marker pertains to only a subset of the ADHD population; the syndrome’s heterogeneity increasingly is a focus of research. Fourth, along with energetic pursuit of genes related to ADHD, resurgent interest in environmental causes of ADHD is notable. New insights into environmental effects are illustrated by recent data concerning lead exposure and ADHD.
A Lie-Backlund approach to equivalence and flatness of nonlinear systems

A new system equivalence relation, using the framework of differential geometry of jets and prolongations of infinite order, is studied. In this setting, two systems are said to be equivalent if any variable of one system may be expressed as a function of the variables of the other system and of a finite number of their time derivatives. This is a Lie-Backlund isomorphism. The authors prove that, although the state dimension is not preserved, the number of input channels is kept fixed. They also prove that a Lie-Backlund isomorphism can be realized by an endogenous feedback. The differentially flat nonlinear systems introduced by the authors (1992) via differential algebraic techniques, are generalized and the new notion of orbitally flat systems is defined. They correspond to systems which are equivalent to a trivial one, with time preservation or not. The endogenous linearizing feedback is explicitly computed in the case of the VTOL aircraft to track given reference trajectories with stability.
The class-level mutants of MuJava

This paper presents results from empirical studies of object-oriented, class level mutation operators, using the automated analysis and testing tool MuJava. Class mutation operators modify OO programming language features such as inheritance, polymorphism, dynamic binding and encapsulation. This paper presents data from 866 classes in six open-source programs. Several new class-level mutation operators are defined in this paper and an analysis of the number of mutants generated is provided. Techniques for eliminating some equivalent mutants are described and data from an automated tool are provided. One important result is that class-level mutation operators yield far more equivalent mutants than traditional, statement-level, operators. Another is that there are far fewer class-level mutants than statement-level mutants. Together, these data suggest that mutation for inter-class testing can be practically affordable.
A randomized study of two cups for vacuum extraction

O'Neil designed a set of suction cups which, because of more efficient lateral pull and greater maneuverability, were claimed to be more efficient and perinatally safer than the Malmström model. These claims were checked by comparing the two instruments in a randomized controlled trial comprising 410 attempted elective extractions. The two instrument groups were comparable at entry and the operators had a similar degree of experience, the sole inter-group difference being the 0.5 cm larger diameter of the O'Neil cups. No significant differences were found between the two types of instrument as to failure rate, incidence of correct cup positioning, and capacity of eliciting internal rotation nor was there a significant divergence in neonatal safety. In a few cases the perineum was lacerated by the traction cord affixed to the O'Neil instrument. The results of this study indicate that the relative advantages and disadvantages of the two cup models are unremarkable.
Establishing the resting state default mode network derived from functional magnetic resonance imaging tasks as an endophenotype: A twins study

The resting state default mode network (DMN) has been shown to characterize a number of neurological and psychiatric disorders. Evidence suggests an underlying genetic basis for this network and hence could serve as potential endophenotype for these disorders. Heritability is a defining criterion for endophenotypes. The DMN is measured either using a resting‐state functional magnetic resonance imaging (fMRI) scan or by extracting resting state activity from task‐based fMRI. The current study is the first to evaluate heritability of this task‐derived resting activity. 250 healthy adult twins (79 monozygotic and 46 dizygotic same sex twin pairs) completed five cognitive and emotion processing fMRI tasks. Resting state DMN functional connectivity was derived from these five fMRI tasks. We validated this approach by comparing connectivity estimates from task‐derived resting activity for all five fMRI tasks, with those obtained using a dedicated task‐free resting state scan in an independent cohort of 27 healthy individuals. Structural equation modeling using the classic twin design was used to estimate the genetic and environmental contributions to variance for the resting‐state DMN functional connectivity. About 9–41% of the variance in functional connectivity between the DMN nodes was attributed to genetic contribution with the greatest heritability found for functional connectivity between the posterior cingulate and right inferior parietal nodes (P < 0.001). Our data provide new evidence that functional connectivity measures from the intrinsic DMN derived from task‐based fMRI datasets are under genetic control and have the potential to serve as endophenotypes for genetically predisposed psychiatric and neurological disorders. Hum Brain Mapp 35:3893–3902, 2014. © 2014 Wiley Periodicals, Inc.
Violent victimization of adult patients with severe mental illness: a systematic review

The aims of this paper are to review data on the prevalence and correlates of violent victimization of persons with severe mental illness, to critically evaluate the literature, and to explore possible approaches for future research. PubMed/MEDLINE and PsycINFO databases were searched using several terms related to severe mental illness in successive combinations with terms describing victimization. The searches identified 34 studies. Nine epidemiological studies indicate that patients with severe mental illness are more likely to be violently victimized than other community members. Young age, comorbid substance use, and homelessness are risk factors for victimization. Victimized patients are more likely to engage in violent behavior than other members of the community. Violent victimization of persons with severe mental illness has long-term adverse consequences for the course of their illness, and further impairs the quality of lives of patients and their families. Victimization of persons with severe mental illness is a serious medical and social problem. Prevention and management of victimization should become a part of routine clinical care for patients with severe mental illness.
Fermentation of calcium-fortified soya milk does not appear to enhance acute calcium absorption in osteopenic post-menopausal women

Ageing women may choose to drink soya milk to reduce menopausal symptoms. As fermentation enriches soya milk with isoflavone aglycones, its beneficial qualities may improve. To reduce osteoporotic risk, however, soya milk must be Ca enriched, and it is not known how fermentation affects Ca bioavailability. A randomised crossover pilot study was undertaken to compare the Ca absorption of fortified soya milk with that of fermented and fortified soya milk in twelve Australian osteopenic post-menopausal women. The fortified soya milk was inoculated with Lactobacillus acidophilus American Type Culture Collection (ATCC) 4962 and fermented for 24 h at 37°C. Ca absorption from soya milk samples was measured using a single isotope radiocalcium method. Participants had a mean age of 54·8 (sd 12·3) years, with mean BMI of 26·5 (sd 5·5) kg/m2 and subnormal to normal serum 25-hydroxyvitamin D (mean 62·5 (sd 19·1) nmol/l). Participants consumed 185 kBq of 45Ca in 44 mg of Ca carrier. The mean fractional Ca absorption (α) from soya milk and fermented soya milk was 0·64 (sd 0·23) and 0·71 (sd 0·29), respectively, a difference not of statistical significance (P = 0·122). Although fermentation of soya milk may provide other health benefits, fermentation had little effect on acute Ca absorption.
The design of an efficient swap mechanism for hybrid DRAM-NVM systems

Non-Volatile Memory (NVM) is becoming an attractive candidate to be the swap area in embedded systems for its near-DRAM speed, low energy consumption, high density, and byte-addressability. Swapping data from DRAM out to NVM, however, can cause large performance/energy penalty and deplete the lifetime of NVM. Traditional swap mechanisms may need to be re-studied. Even through there are several swap mechanisms proposed for the hybrid DRAM-NVM systems, most of them have limited performance without considering the data access features of applications. In this paper, we analyze the data accesses features of different applications. Then, a swap mechanism, called Refinery Swap, is proposed to improve the performance of the system, reduce energy consumption, and increase the lifetime of NVM simultaneously. Refinery Swap presented two algorithms to exploit the data access features of applications and the characteristics of different kinds of memory medias. The swap operations in the system and the writes upon NVM are reduced using Refinery Swap. Extensive experiments are conducted with standard benchmarks. The experimental results show that the lifetime of NVM for the system with Refinery Swap can be 83 times that of Linux Swap. The performance of the system with Refinery Swap can be 17 times that of DR.Swap, the state-of-the-art swap mechanism for hybrid memory embedded systems. Moreover, the energy consumption of the system achieves 17 times lower.
GlideScope video laryngoscope: a randomized clinical trial in 203 paediatric patients.

BACKGROUND The GlideScope intubating device has been reported to provide a comparable or superior laryngoscopic view compared with direct laryngoscopy in adults. This study compared the use of the GlideScope with direct laryngoscopy for the laryngoscopic view and intubation time in children. METHODS The laryngoscopic view in 203 children was scored using both the Macintosh laryngoscope and the GlideScope using Cormack and Lehane (C&L) grades. After scoring each laryngoscopic view with and without BURP, the patients were randomly allocated to two groups. The trachea was intubated using direct laryngoscopy (Group DL, n=100) or the GlideScope (Group GS, n=103). We compared C&L grades for the two views in the same patient, and also the time to intubate for each group. RESULTS The GlideScope improved the view without BURP in the patients with C&L grade 2 (16/26, P<0.01) and with C&L grades 3 and 4 (7/11, P<0.05). The view with BURP was also improved by the GlideScope in C&L grade 2 (4/9, P<0.05) and with C&L grades 3 and 4 (4/5, P=0.059). The mean time for tracheal intubation was 36.0 (17.9) s in the GS group and 23.8 (13.9) s in the DL group (P<0.001). CONCLUSIONS In children, the GlideScope provided a laryngoscopic view equal to or better than that of direct laryngoscopy but required a longer time for intubation.