Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases

We report very high gene targeting frequencies in Drosophila by direct embryo injection of mRNAs encoding specific zinc-finger nucleases (ZFNs). Both local mutagenesis via nonhomologous end joining (NHEJ) and targeted gene replacement via homologous recombination (HR) have been achieved in up to 10% of all targets at a given locus. In embryos that are wild type for DNA repair, the products are dominated by NHEJ mutations. In recipients deficient in the NHEJ component, DNA ligase IV, the majority of products arise by HR with a coinjected donor DNA, with no loss of overall efficiency in target modification. We describe the application of the ZFN injection procedure to mutagenesis by NHEJ of 2 new genes in Drosophila melanogaster: coil and pask. Pairs of novel ZFNs designed for targets within those genes led to the production of null mutations at each locus. The injection procedure is much more rapid than earlier approaches and makes possible the generation and recovery of targeted gene alterations at essentially any locus within 2 fly generations.
Robust and accurate features for detecting and diagnosing autism spectrum disorders

In this paper, we report experiments on the Interspeech 2013 Autism Challenge, which comprises of two subtasks - detecting children with ASD and classifying them into four subtypes. We apply our recently developed algorithm to extract speech features that overcomes certain weaknesses of other currently available algorithms [1, 2]. From the input speech signal, we estimate the parameters of a harmonic model of the voiced speech for each frame including the fundamental frequency (f 0). From the fundamental frequencies and the reconstructed noise-free signal, we compute other derived features such as Harmonic-to-Noise Ratio (HNR), shimmer, and jitter. In previous work, we found that these features detect voiced segments and speech more accurately than other algorithms and that they are useful in rating the severity of a subject's Parkinson's disease [3]. Here, we employ these features, along with standard features such as energy, cepstral, and spectral features. With these features, we detect ASD using a regression and identify the sub-type using a classifier. We find that our features improve the performance, measured in terms of unweighted average recall (UAR), of detecting autism spectrum disorder by 2.3% and classifying the disorder into four categories by 2.8% over the baseline results.
Aluminum exclusion and aluminum tolerance in woody plants

The aluminum (Al) cation Al3+ is highly rhizotoxic and is a major stress factor to plants on acid soils, which cover large areas of tropical and boreal regions. Many woody plant species are native to acid soils and are well adapted to high Al3+ conditions. In tropical regions, both woody Al accumulator and non-Al accumulator plants occur, whereas in boreal regions woody plants are non-Al accumulators. The mechanisms of these adaptations can be divided into those that facilitate the exclusion of Al3+ from root cells (exclusion mechanisms) and those that enable plants to tolerate Al3+ once it has entered the root and shoot symplast (internal tolerance mechanisms). The biochemical and molecular basis of these mechanisms have been intensively studied in several crop plants and the model plant Arabidopsis. In this review, we examine the current understanding of Al3+ exclusion and tolerance mechanisms from woody plants. In addition, we discuss the ecology of woody non-Al accumulator and Al accumulator plants, and present examples of Al3+ adaptations in woody plant populations. This paper complements previous reviews focusing on crop plants and provides insights into evolutionary processes operating in plant communities that are widespread on acid soils.
Environmental Conditions Influence Allometric Patterns in the Blow Fly, Chrysomya albiceps

Abstract The objective of this research was to study variations in allometry of body characters in females and males of two populations of blow flies, Chrysomya albiceps (Wiedemann) (Diptera: Calliphoridae), under different environmental conditions to establish patterns of morphological variation. Body size of both males and females in the experimental population was significantly higher than in the individuals of the natural population, indicating an important influence of food on body size. All genitalic and non-genitalic characters in males and females of the two populations showed a trend towards negative allometry rather than isometry. Allometric patterns were modified in both sexes and between populations. The data show generally larger allometric slopes in females than in males. We confirmed that the environmental conditions have an important effect on allometric patterns and body size.
Percutaneous coronary intervention of chronic total occlusion in a left anterior descending coronary artery using an ipsilateral intraseptal bridging collateral tracking technique

As one of the great breakthrough techniques in the percutaneous coronary intervention (PCI) for the chronic total occlusions of coronary arteries, the controlled antegrade and retrograde subintimal tracking, so called the “CART” technique, has been developed. We present a first case in whom CTO of the mid LAD coronary artery was well‐recanalized using the CART technique via the ipsilateral intraseptal bridging collaterals in the PCI. © 2010 Wiley‐Liss, Inc.
A spatial Poisson hurdle model for exploring geographic variation in emergency department visits

Summary. We develop a spatial Poisson hurdle model to explore geographic variation in emergency department (ED) visits while accounting for zero inflation. The model consists of two components: a Bernoulli component that models the probability of any ED use (i.e. at least one ED visit per year), and a truncated Poisson component that models the number of ED visits given use. Together, these components address both the abundance of 0s and the right‐skewed nature of the non‐zero counts. The model has a hierarchical structure that incorporates patient and area level covariates, as well as spatially correlated random effects for each areal unit. Because regions with high rates of ED use are likely to have high expected counts among users, we model the spatial random effects via a bivariate conditionally auto‐regressive prior, which introduces dependence between the components and provides spatial smoothing and sharing of information across neighbouring regions. Using a simulation study, we show that modelling the between‐component correlation reduces bias in parameter estimates. We adopt a Bayesian estimation approach, and the model can be fitted by using standard Bayesian software. We apply the model to a study of patient and neighbourhood factors influencing ED use in Durham County, North Carolina.
THE REDUCTION IN VITRO IN VISCOSITY OF MUCOPROTEIN SOLUTIONS BY A NEW MUCOLYTIC AGENT, N‐ACETYL‐L‐CYSTEINE

The accumulation of viscid mucus is a problem frequently encountered in chronic diseases of the respiratory tract such as chronic bronchitis, emphysema, tuberculosis, and cystic fibrosis. I t is well known that the high viscosity of these secretions is due primarily to their content of mucoprotein and deoxyribonucleic acids. However, in the absence of acute infection, the secretions may be essentially mucoid, and mucoprotein has been isolated from bronchial secretions in yields of about 60 per cent of the total nitrogen. ’ During the investigation to develop a niucolytic agent that would be useful in the treatment of pulmonary disease, i t was discovered that L-cysteine and many of its congeners markedly reduced the viscosity of solutions containing mucoproteins from various sources. Subsequent to this finding, reports appeared in the literature that DL-penicillamine reduced the viscosity of serum containing a high concentration of macroglobulins,2 and that the intrinsic viscosity of solutions of glutenin, the principal protein of wheat gluten, is reduced markedly by disulfide bond-cleaving agents3 However, in studies on ribonuclease4 and human serum a l b ~ m i n , ~ the intrinsic viscosity of protein reduced by treatment with sulfhydryl compounds was essentially the same as or higher than that of the oxidized form. I t seems evident that the effect on intrinsic viscosity resulting from the treatment of proteins with sulfhydryl or other disulfide bondcleaving agents may vary, depending on the native conformation of the protein and the degree to which disulfide bonds fix the spatial arrangement of the primary structure. The present study was conducted to obtain information concerning the mode and mechanism of action of sulfhydryl compounds in reducing the viscosity of mucoprotein solutions. In addition, since the majority of these experiments were performed with a partially purified mucoprotein preparation (MP-50) extracted from porcine gastric mucin, a partial chemical analysis of this material was obtained and is reported here. I t should he noted that N-acetyl-L-cysteine (XAC) was the sulfhydryl compound used most frequently in this investigation since it was chosen for clinical study on the basis of its good mucolytic activity, relatively slight taste and odor, highly soluble disulfide oxidation product and low order of toxicity.
Cultural Integration: Genetics, Archaeology and the impact of the Viking Diaspora on the Isle of Man

Over the last two decades many in the archaeological community have developed a degree of scepticism and suspicion towards using genetics to study the past. My project aims to dispel some of these concerns, highlighting the inferences about demographic and social history which can be made from genetic data gathered from modern populations. Centred around the BritishIrish Isles and in particular, the Isle of Man, this study investigates for the first time, differing demographic histories in the male and female gene-pools. The focus of this research is the 400 years of Norwegian rule in the Irish Sea region following the Viking visitations of 900CE, when the Isle of Man was an important centre in the politics of the Irish Sea kingdom. DNA samples were collected from male volunteers, followed by the extraction of high resolution mtDNA and Y chromosome data. Volunteers were enlisted on the basis of surnames taken from 16-century documentation to ensure deep historical roots on the Island. The high quality genetic data generated for the Isle of Man not only gave greater distinguishing power for looking at closely related populations, but also allowed separate male and female population histories to be explored. Approximate Bayesian Computation (ABC) modelling was used to explore the
GLUT2 Expression and Function in β-cells of GK rats with NIDDM: Dissociation Between Reductions in Glucose Transport and Glucose-Stimulated Insulin Secretion

GLUT2 underexpression has been reported in the +-cells of Zucker diabetic fatty rats and db/db mice, models of spontaneously occurring NIDDM with antecedent obesity. To determine whether the +-cells of a nonobese rodent model of NIDDM exhibit the same abnormalities in GLUT2, we studied Goto-Kakizaki rats. In these mildly diabetic animals glucose-stimulated insulin secretion was reduced at all ages examined from 8 to 48 wk. In normal control Wistar rats, immunostainable GLUT2 was present on all insulin-positive cells in the pancreatic islets. Only 85% of +-cells were GLUT2-positive in GK rats at 12 wk of age, and only 34% were positive at 48 wk of age. GLUT2 mRNA was 50% of normal in 12-wk-old GK rats. In the latter age-group, glucose-stimulated insulin secretion was only 28% of normal at a time when 85% of +-cells were GLUT2-positive and initial 3-O-methyl-D-glucose transport rate was 77% of the control value. We conclude that although GLUT2 is underexpressed, neither the magnitude of the underexpression of GLUT2 nor of the reduction in GLUT2 transport function in islets of GK rats is sufficient by itself to explain the profound reduction in glucose-stimulated insulin secretion.
What kind of /r/ is linking /r/? An analysis of the realization of /r/ in linking /r/ in RP on the basis of Polish phonetic books

The paper looks at the phenomenon of linking /r/ in RP and aims to find out what Polish phoneticians say the realization of linking /r/ in RP is on the basis of their books. During the inspection of the material it has transpired that it is not easy to find what the phonetic value of linking /r/ is. This is largely due to the inconsistencies among the scholars, some of whom say that it is the alveolar tap and some that it is the post-alveolar approximant that is the usual variant used for the linking context. The author concludes by recommending further research in this field.
Computational Thermostabilization of an Enzyme

Thermostabilizing an enzyme while maintaining its activity for industrial or biomedical applications can be difficult with traditional selection methods. We describe a rapid computational approach that identified three mutations within a model enzyme that produced a 10°C increase in apparent melting temperature Tm and a 30-fold increase in half-life at 50°C, with no reduction in catalytic efficiency. The effects of the mutations were synergistic, giving an increase in excess of the sum of their individual effects. The redesigned enzyme induced an increased, temperature-dependent bacterial growth rate under conditions that required its activity, thereby coupling molecular and metabolic engineering.
Pneumococcal meningitis in children: relationship of antibiotic resistance to clinical characteristics and outcomes

Background. The relationship of antibiotic susceptibility to clinical outcome in children with pneumococcal meningitis is uncertain. Previous studies have been limited by inclusion of relatively few patients infected with nonsusceptible pneumococci and inconsistent use of empiric vancomycin. Methods. Medical records of 86 children with culture-confirmed pneumococcal meningitis at a single institution from October, 1991, to October, 1999, were retrospectively reviewed, and differences in presentation and outcome based on antibiotic susceptibility of pneumococcal isolates were assessed. Results. Of 86 isolates 34 were nonsusceptible to penicillin (12 resistant). Of 60 isolates for which cefotaxime susceptibility data were available, 17 were nonsusceptible (12 resistant). Antibiotic susceptibility was not significantly associated with death, intensive care unit admission, mechanical ventilation, focal neurologic deficits, seizures, secondary fever, abnormal neuroimaging studies or hospital days. Children with penicillin-resistant isolates had significantly higher median blood leukocyte counts (24 100/&mgr;l vs. 15 700/&mgr;l, P = 0.03) and lower median CSF protein concentrations (85 mg/dl vs. 219 mg/dl, P = 0.04), were more likely to have a CSF glucose concentration of ≥50 mg/dl (7 of 11 vs. 15 of 68, P = 0.009) and had lower rates of sensorineural hearing loss (1 of 8 vs. 25 of 40, P = 0.02) than children with isolates that were not resistant to penicillin. Children with cefotaxime-nonsusceptible isolates had an increased median duration of primary fever compared with those with nonsusceptible strains (6 days vs. 3.5 days, P = 0.02). Conclusions. In children with pneumococcal meningitis, penicillin resistance was associated with a reduced risk of hearing loss, while cefotaxime resistance was associated with a longer duration of fever. Other outcome measures were not significantly influenced by the antibiotic susceptibility of pneumococcal isolates.
Differential dynamic control of cardiac and splanchnic sympathetic nerve activity by the arterial baroreflex

The arterial baroreflex is the primary negative feedback system involved in stabilizing arterial pressure from external disturbances. Determining the dynamic characteristics of the baroreflex is important for our understanding of the mechanisms involved in rapid restoration of arterial pressure. This study examined the differences in the dynamic baroreflex control of cardiac (CSNA) and splanchnic (SSNA) sympathetic nerve activity. The baroreceptor region of the right aortic depressor nerve was isolated from the systemic circulation to control baroreceptor region pressure (BRP) with a Gaussian white noise signal while simultaneously recording CSNA and SSNA in anesthetized Sprague-Dawley rats. SSNA was recorded from a postganglionic branch of the splanchnic sympathetic nerve and CSNA was recorded from a branch of the left stellate ganglion. Neural arc transfer functions from BRP to SSNA (HSSNA) and BRP to CSNA (HCSNA) displayed derivative characteristics. When dynamic gain below 0.03 Hz was normalized to unity, HSSNA had a higher gain at frequencies 0.1 and 1 Hz and increasing slope from 0.1 to 1 Hz relative to HCSNA. The peak decrease in the step response was higher for SSNA than CSNA. These data indicate differential dynamic baroreflex control of SSNA and CSNA. Rapid changes in baroreceptor pressure input would result in a larger response in SSNA compared with CSNA.
Performance of a seeder according to the displacement velocity and furrowing mechanism for fertilizer deposition

Agribusiness daily increases the demand for machinery with better efficiency, seeking to reduce operating costs and improve the quality of the sowing process. The objective of present study was to evaluate the quality of the longitudinal seed distribution and the operating performance of a seeder-fertilizer according to displacement velocity and furrowing mechanism for fertilizer deposition. The assay was conducted in the experimental area of the Department of Agricultural Engineering of the Federal University of Ceara. The experimental design was randomized blocks, in a 2 x 3 factorial, with four replicates with two furrowing mechanisms for fertilizer deposition (double disc and shank) and three displacement velocities (4.7, 6.3 and 8.2 km h-1). The results demonstrate that for the quality of seed distribution, the best performance was obtained with the use of the shank at velocity of 6.3 km h-1. The tractor-seeder set provided better operating performance using the disc, which promoted the lowest specific consumption at the velocity of 4.7 km h-1.
Interrupted Time Series Design: A Useful Approach for Studying Interventions Targeting Participation

ABSTRACT Comparative effectiveness research (CER) strives for evidence to inform clinical decisions for specific clients in typical health care settings. While the randomized controlled trial (RCT) is well-aligned with the objectives of CER, this design may not be feasible or applicable to all research questions, particularly those pertaining to clinical decision making and individually based change. It is important, therefore, to consider alternative approaches, especially when studying complex and subjective outcomes such as children's participation. We propose the use of interrupted time series (ITS) quasi-experimental design for its potential application in determining the effectiveness of participation-focused interventions. In this perspective, ITS design is described, ascertaining its advantages and limitations, and suggestions are provided to overcome challenges to implementation. Results of a case study using the ITS approach to evaluate changes in participation of an adolescent with physical disabilities are described. Finally, strategies to implement this design in practice are suggested.
Efficient Computation of k-Nearest Neighbour Graphs for Large High-Dimensional Data Sets on GPU Clusters

This paper presents an implementation of the brute-force exact k-Nearest Neighbor Graph (k-NNG) construction for ultra-large high-dimensional data cloud. The proposed method uses Graphics Processing Units (GPUs) and is scalable with multi-levels of parallelism (between nodes of a cluster, between different GPUs on a single node, and within a GPU). The method is applicable to homogeneous computing clusters with a varying number of nodes and GPUs per node. We achieve a 6-fold speedup in data processing as compared with an optimized method running on a cluster of CPUs and bring a hitherto impossible -NNG generation for a dataset of twenty million images with 15 k dimensionality into the realm of practical possibility.
A comparison of logic-based infrastructures for concern detection and extraction

In this paper we evaluate logic code analysis and transformation frameworks for their suitability as basic infrastructures for fast detection and extraction of (crosscutting) concerns. Using design patterns as example concerns, we identify desirable properties that an infrastructure should fulfill. We then report our initial results of evaluating candidate systems with respect to these properties. We show how high precision design pattern detectors can be easily formulated as predicates that are evaluated in mere seconds even on the sources of large software systems, such as the Eclipse IDE. Although details still remain to be analyzed further, our current results suggest that the pair JTransformer & CTC is a good candidate for a general infrastructure, combining very good querying performance, scalability and short turn-around times with a seamless integration of querying and transformation capabilities.
An Efficient Algorithm for Maximizing Range Sum Queries in a Road Network

Given a set of positive-weighted points and a query rectangle r (specified by a client) of given extents, the goal of a maximizing range sum (MaxRS) query is to find the optimal location of r such that the total weights of all the points covered by r are maximized. All existing methods for processing MaxRS queries assume the Euclidean distance metric. In many location-based applications, however, the motion of a client may be constrained by an underlying (spatial) road network; that is, the client cannot move freely in space. This paper addresses the problem of processing MaxRS queries in a road network. We propose the external-memory algorithm that is suited for a large road network database. In addition, in contrast to the existing methods, which retrieve only one optimal location, our proposed algorithm retrieves all the possible optimal locations. Through simulations, we evaluate the performance of the proposed algorithm.