Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable templates for specification reuse

Software reuse should not be limited to only code. Software reuse should be engineered as early as possible in the software development life cycle. The authors address specification reuse by defining templates of specifications and then instantiating them to yield specific specifications. From the perspective of software reuse in the large, reusable templates should be created as scalably as possible. Existing technologies for building reusable templates suffer the problems of scalability. Schemes (generic and parameterized modules) in TUG (Tree Unified with Grammar) facilitate specifiers to build scalable templates hierarchically without replication. Reuse is performed vertically and horizontally. Vertical reuse makes a lower level scheme inherit all features from its upper level scheme. Horizontal reuse makes a scheme reusable within the same level of abstraction. Parametric building and incremental building are two techniques for realizing the vertical and horizontal reuse. They present a scheme for a generalized inventory control system and demonstrate how a generalized inventory control scheme can be reused to model a library system. Finally, the capabilities, strengths, and weaknesses are discussed.
Diffusion in gels containing immobilized cells: A critical review

Eleven experimental investigation of diffusion in gels containing immobilized cells are reviewed. The experimental data, which quantitatively express the diffusion coefficient as a function of the cell concentration, are compared with a number of well‐known equations developed for mass transfer in heterogeneous media. Based on this comparison, a procedure for the theoretical prediction of effective diffusion coefficients in cell‐containing gels is recommended.
New technology for rapid molecular diagnosis of bloodstream infections

Technologies for the correct and timely diagnosis of bloodstream infections are urgently needed. Molecular diagnostic methods have yet to have a major impact on the diagnosis of bloodstream infections; however, new methods are being developed that are beginning to address key issues. In this article, we discuss the key needs and objectives of molecular diagnostics for bloodstream infections and review some of the currently available methods and how these techniques meet key needs. We then focus on a new method that combines nucleic acid amplification with mass spectrometry in a novel approach to molecular diagnosis of bloodstream infections.
Protective effects of schizandrin and schizandrin B towards cisplatin nephrotoxicity in vitro

Renal proximal tubular epithelial cells are the main targets of toxic drugs such as cisplatin (CisPt), an alkylating agent indicated for the treatment of solid organ tumors. Current techniques aiming at reducing nephrotoxicity in patients receiving CisPt are still not satisfactory as they can only partially prevent acute kidney injury. New nephroprotective strategies remain to be developed. In the present in vitro study, schizandrin (Schi) and schizandrin B (Schi B), major phytochemicals from Schisandra chinensis (Turcz.) Baill. fruits, were tested on HK‐2 cells along four processes that could help alleviate CisPt toxicity. Results indicated that: (i) both Schi and Schi B enhanced cell survival via reducing apoptosis rate; (ii) only Schi showed moderate effects towards modulation of regeneration capacities of healthy cells; (iii) both Schi and Schi B limited extracellular matrix deposition; and (iv) both compounds could help preventing dedifferentiation processes via the β‐catenin pathway. Schi and Schi B present promising activities for future development of protective agents against CisPt nephrotoxicity. Copyright © 2013 John Wiley & Sons, Ltd.
RNA Respiratory Viruses in Solid Organ Transplantation

1. The seasonality of respiratory viral infections among transplant recipients usually follows that of the general population (2,3). 2. The viruses all cause a range of disease, from mild congestion and rhinorrhea to more severe tracheobronchitis, bronchiolitis and pneumonia. No one virus is exclusively associated with one clinical syndrome (i.e. influenza-like illness, croup, etc.). As such, diagnostic strategies should initially be broad, attempting to screen for all recognized viruses (3,4) with particular emphasis on ones that might be amenable to therapy. 3. Transplant recipients often present with mild or atypical symptoms and fever may be absent. Lung transplant recipients, for example, may initially only have subjective symptoms of shortness of breath or subtle changes in pulmonary function testing without more typical symptoms (5). 4. Viral shedding is usually prolonged among transplant recipients. Prolonged shedding is seen even with the use of antivirals and therefore may contribute to the increased risk of resistant variant emergence (1,6). 5. Transplant recipients are at higher risk of infectious complications compared to immunocompetent hosts. Respiratory viral infections are a significant risk factor for subsequent development of fungal and bacterial pneumonia (1). 6. Respiratory viral infections appear to be a risk factor for both acute and chronic rejection with the greatest risk in lung transplant recipients (5,7–9) (II-2), although data on this topic in the literature are conflicting (10). The pathogenesis of the link between respiratory viral infections and rejection is not clearly understood. 7. All pediatric solid organ and lung transplant recipients appear to have the greatest risk of both respiratory viral infections and more severe courses and complications (1). 8. All are potential nosocomial pathogens that can be potentially spread by staff or visitor with mild upper respiratory illness.
Variable rate vector quantization scheme based on quadtree segmentation

Quadtree segmentation is a hierarchical spatial decomposition technique that partitions an image into variable-sized blocks based on a quadtree structure. Different coding strategies can be adopted to encode blocks of different perceptual significance. In this paper, an novel variable rate vector quantization scheme based on quadtree segmentation is proposed with which low-detailed blocks are adaptively encoded by the mean-subsampled vector quantization while high-detailed blocks by the traditional vector quantization scheme. The simulation results show that the proposed variable-block-sized vector quantization scheme achieves better subjective image quality with higher PSNR at low bit rates.
Solid-state studies and antioxidant properties of the γ-cyclodextrin·fisetin inclusion compound

Fisetin is a natural antioxidant with a wide range of nutraceutical properties, including antidiabetic, neuroprotecting, and suppression or prevention of tumors. The present work describes the preparation of a water-soluble, solid inclusion compound of fisetin with gamma-cyclodextrin (γ-CD), a cyclic oligosaccharide approved for human consumption. A detailed physicochemical analysis of the product is carried out using elemental analysis, powder X-ray diffraction (PXRD), Raman, infrared and 13C{1H} CP-MAS NMR spectroscopies, and thermal analysis (TGA) to verify fisetin inclusion and to present a hypothetical structural arrangement for the host–guest units. The antioxidant activity of the γ-CD·fisetin inclusion compound is evaluated by the DPPH assay.
Ventrolateral Striatal Medium Spiny Neurons Positively Regulate Food-Incentive, Goal-Directed Behavior Independently of D1 and D2 Selectivity

The ventral striatum is involved in motivated behavior. Akin to the dorsal striatum, the ventral striatum contains two parallel pathways: the striatomesencephalic pathway consisting of dopamine receptor Type 1-expressing medium spiny neurons (D1-MSNs) and the striatopallidal pathway consisting of D2-MSNs. These two genetically identified pathways are thought to encode opposing functions in motivated behavior. It has also been reported that D1/D2 genetic selectivity is not attributed to the anatomical discrimination of two pathways. We wanted to determine whether D1- and D2-MSNs in the ventral striatum functioned in an opposing manner as previous observations claimed, and whether D1/D2 selectivity corresponded to a functional segregation in motivated behavior of mice. To address this question, we focused on the lateral portion of ventral striatum as a region implicated in food-incentive, goal-directed behavior, and recorded D1 or D2-MSN activity by using a gene-encoded ratiometric Ca2+ indicator and by constructing a fiberphotometry system, and manipulated their activities via optogenetic inhibition during ongoing behaviors. We observed concurrent event-related compound Ca2+ elevations in ventrolateral D1- and D2-MSNs, especially at trial start cue-related and first lever press-related times. D1 or D2 selective optogenetic inhibition just after the trial start cue resulted in a reduction of goal-directed behavior, indicating a shared coding of motivated behavior by both populations at this time. Only D1-selective inhibition just after the first lever press resulted in the reduction of behavior, indicating D1-MSN-specific coding at that specific time. Our data did not support opposing encoding by both populations in food-incentive, goal-directed behavior. SIGNIFICANCE STATEMENT An opposing role of dopamine receptor Type 1 or Type 2-expressing medium spiny neurons (D1-MSNs or D2-MSNs) on striatum-mediated behaviors has been widely accepted. However, this idea has been questioned by recent reports. In the present study, we measured concurrent Ca2+ activity patterns of D1- and D2-MSNs in the ventrolateral striatum during food-incentive, goal-directed behavior in mice. According to Ca2+ activity patterns, we conducted timing-specific optogenetic inhibition of each type of MSN. We demonstrated that both D1- and D2-MSNs in the ventrolateral striatum commonly and positively encoded action initiation, whereas only D1-MSNs positively encoded sustained motivated behavior. These findings led us to reconsider the prevailing notion of a functional segregation of MSN activity in the ventral striatum.
Metabolic Imaging of Human Cognition: An fMRI/1H-MRS Study of Brain Lactate Response to Silent Word Generation

Proton magnetic resonance spectroscopy (1H-MRS) allows in vivo assessment of the metabolism related to human brain functions. Visual, auditory, tactile, and motor stimuli induce a temporary increase in the brain lactate level, which may act as a rapid source of energy for the activated neurons. The authors studied the metabolism of the frontal lobes during cognitive stimulation and measured local lactate levels with standard 1H-MRS, after localizing the activated area by functional MRI. Lactate levels were monitored while the subjects either silently listed numbers (baseline) or performed a silent word-generation task (stimulus-activation). The cognitive stimulus-activation produced a 50% increase in the brain lactate level in the left inferior frontal gyrus. The results show that metabolic imaging of neuronal activity related to cognition is possible using 1H-MRS.
Molecular analysis of the rRNA genes of Babesia spp and Ehrlichia canis detected in dogs from RibeirÃo Preto, Brazil

The partial DNA sequences of the 18S rRNA gene of Babesia canis and the 16S rRNA gene of Ehrlichia canis detected in dogs from Ribeirão Preto, Brazil, were compared to sequences from other strains deposited in GenBank. The E. canis strain circulating in Ribeirão Preto is identical to other strains previously detected in the region, whereas the subspecies Babesia canis vogeli is the main Babesia strain circulating in dogs from Ribeirão Preto.
Portable traveling support system using image processing for the visually impaired

We have previously proposed a portable navigation system for the visually impaired (see Nakamura, K. et al., IEICE Trans. of Japan, vol.J79, p.1610-18, 1996; Takuno, S. et al., IEICE Trans. of Japan, vol.J83, p.293-302, 2000). However, there are some places where this system is unable to provide proper guidance. Since the traveling direction of the traveler in this system is measured by a terrestrial magnetism sensor, there is a possibility that the wrong direction is measured, due to the distortion of the terrestrial magnetism by vehicles, etc. Road markings, e.g., pedestrian crossing, white line of the road, are reliable information to measure the correct direction. Furthermore, street landmarks, e.g., electric pole, traffic-control sign and post box, are also useful for a traveler to confirm his position. Therefore, we have now adequately applied image processing to our portable navigation system to make it more reliable.
An evaluation of intrathecal ziconotide for the treatment of chronic pain

Ziconotide, the synthetic form of cone snail peptide ϖ-conotoxin MVIIA, is a neurone-specific N-type calcium channel blocker with an analgesic and neuroprotective effect. Intrathecal ziconotide has been recommended for approval by the FDA for the management of chronic pain. Spinally administered ziconotide produces analgesia by blocking neurotransmitter release from primary nociceptive afferents and prevents the propagation of pain signals to the brain. It has an advantage over intrathecal morphine in that there is no development of tolerance after prolonged use. Systemic toxicity is considerably reduced by administration of smaller doses intrathecally and selective delivery to the site of action in the nervous system. Nevertheless, there are neurological adverse effects due to delay in clearance of ziconotide from the neural tissues. Overall, ziconotide has a favourable risk/benefit ratio with advantages over several currently available intrathecal therapies for pain.
Dabigatran, rivaroxaban, apixaban, argatroban and fondaparinux and their effects on coagulation POC and platelet function tests

Abstract Background: In recent years, several selectively acting anticoagulants, including the direct thrombin inhibitors (DTI; argatroban, dabigatran) and the factor Xa inhibitors (rivaroxaban, apixaban, fondaparinux), have been developed. With their clinical application increasing, it is of interest to evaluate their interference with classical haemostaseological point-of-care tests. Additionally, the effect of the investigated anticoagulants on platelet function tests will come increasingly more into focus for monitoring not only hereditary platelet dysfunction, but also antiplatelet therapy. Methods: Blood samples from healthy volunteers were spiked with therapeutic and supratherapeutic concentrations of the drugs listed above and investigated with regard to their effects on the following POCTs: activated clotting time (ACT), thromboelastometry with ROTEM®, PFA® and Multiplate®. Light-transmission aggregometry (LTA) was used for a platelet function assay. Results: At supratherapeutic concentrations, ACT and ROTEM® analysis were always influenced after administration of the drugs listed above (except fondaparinux in EXTEM-CT). Therapeutic concentrations showed differential effects on these assays. LTA measurements revealed a distinct decrease in α-thrombin-induced platelet aggregation for both DTIs (therapeutic and supratherapeutic concentrations), while argatroban reduced platelet function in supratherapeutic concentrations. None of the drugs seemed to have any influence on PFA® or Multiplate®. Conclusions: Selective thrombin and factor Xa inhibitors exhibit distinct effects on POCTs and platelet function tests. This must be considered in assessing assay results when taking medical decisions.
A new high gain non-isolated DC-DC boost converter for photovoltaic application

This paper introduces a new topology of the high gain non-isolated DC-DC boost converter with central point on its output. The proposed converter is derived from the quadratic single switch boost converter and the three level boost converter. The static gain of this converter is bigger than the one from the conventional boost converter and the maximum voltage on both switches is half of the output voltage. Qualitative and quantitative analysis of the operation stages, the main waveforms and the experimental results of a 520 W prototype are presented. The converter is aimed for modular photovoltaic application.
Herpes Simplex Virus 1 Serine/Threonine Kinase US3 Hyperphosphorylates IRF3 and Inhibits Beta Interferon Production

ABSTRACT Viral infection initiates a series of signaling cascades that lead to the transcription of interferons (IFNs), finally inducing interferon-stimulated genes (ISGs) to eliminate viruses. Viruses have evolved a variety of strategies to modulate host IFN-mediated immune responses. Herpes simplex virus 1 (HSV-1) US3, a Ser/Thr kinase conserved in alphaherpesviruses, was previously reported to counteract host innate immunity; however, the molecular mechanism is elusive. In this study, we report that US3 blocks IFN-β production by hyperphosphorylating IFN regulatory factor 3 (IRF3). Ectopic expression of US3 protein significantly inhibited Sendai virus (SeV)-mediated activation of IFN-β and IFN-stimulated response element (ISRE) promoters and the transcription of IFN-β, ISG54, and ISG56. US3 was also shown to block SeV-induced dimerization and nuclear translocation of IRF3. The kinase activity was indispensable for its inhibitory function, as kinase-dead (KD) US3 mutants K220M and D305A could not inhibit IFN-β production. Furthermore, US3 interacted with and hyperphosphorylated IRF3 at Ser175 to prevent IRF3 activation. Finally, the US3 KD mutant viruses were constructed and denoted K220M or D305A HSV-1, respectively. Cells and mice infected with both mutant viruses produced remarkably larger amounts of IFN-β than those infected with wild-type HSV-1. For the first time, these findings provide convincing evidence that US3 hyperphosphorylates IRF3, blocks the production of IFN-β, and subverts host innate immunity.
Is the Union Employment Suppression Effect Diminishing? Further Evidence from Canada

That unions suppress employment growth among their employers has been such a ubiquitous finding that it has been dubbed “the one constant” in industrial relations research (Addison and Belfield, 2004). However, all of the empirical findings on which this conclusion is based come from data collected in 1998 or earlier, and the Canadian findings (Long, 1993) date from more than twenty-five years ago. Noting this, Walsworth (2010a) utilized data from the Statistics Canada Workplace and Employee Survey (WES) covering the period 1999-2005 to investigate the more recent magnitude of the employment growth suppression effect in Canada. He found that, compared to Long’s (1993) findings, the union employment suppression effect has apparently diminished in Canada. However, we note that Walsworth’s (2010a) analysis is not comparable to that conducted by Long (1993) in several ways. For example, Walsworth (2010a) did not segment his analysis by establishment size, or by industrial sector. Moreover, Walsworth (2010a) attempted no analysis of the reasons behind a possible diminution in the union employment growth suppression effect, an omission that we address by examining employee earnings growth and the union wage premium as possible contributing factors. We analyze WES data collected during 2001-2006 and, like Long (1993), find important differences when segmenting our analysis according to establishment size, as the union employment suppression effect was evidenced in large manufacturing establishments, but not in smaller manufacturing establishments. However, unlike Long (1993), we also find important differences between the manufacturing sector and the service sector, where we find no union employment suppression effect among larger service establishments, and a significant positive union effect on employment growth among smaller service establishments—the first finding of a positive union employment growth effect in any context. Our analysis suggests that a declining union wage premium may have played a role in these results.
Sexing the Sciuridae: a simple and accurate set of molecular methods to determine sex in tree squirrels, ground squirrels and marmots

We determined the sequence of the male‐specific minor histocompatibility complex antigen (Smcy) from the Y chromosome of seven squirrel species (Sciuridae, Rodentia). Based on conserved regions inside the Smcy intron sequence, we designed PCR primers for sex determination in these species that can be co‐amplified with nuclear loci as controls. PCR co‐amplification yields two products for males and one for females that are easily visualized as bands by agarose gel electrophoresis. Our method provides simple and reliable sex determination across a wide range of squirrel species.
The heat shock protein 70 molecular chaperone network in the pancreatic endoplasmic reticulum − a quantitative approach

Traditionally, the canine pancreatic endoplasmic reticulum (ER) has been the workhorse for cell‐free studies on protein transport into the mammalian ER. These studies have revealed multiple roles for the major ER‐luminal heat shock protein (Hsp) 70, IgG heavy chain‐binding protein (BiP), at least one of which also involves the second ER‐luminal Hsp70, glucose‐regulated protein (Grp) 170. In addition, at least one of these BiP activities depends on Hsp40. Up to now, five Hsp40s and two nucleotide exchange factors, Sil1 and Grp170, have been identified in the ER of different mammalian cell types. Here we quantified the various proteins of this chaperone network in canine pancreatic rough microsomes. We also characterized the various purified proteins with respect to their affinities for BiP and their effect on the ATPase activity of BiP. The results identify Grp170 as the major nucleotide exchange factor for BiP, and the resident ER‐membrane proteins ER‐resident J‐domain protein 1 plus ER‐resident J‐domain protein 2/Sec63 as prime candidates for cochaperones of BiP in protein transport in the pancreatic ER. Thus, these data represent a comprehensive analysis of the BiP chaperone network that was recently linked to two human inherited diseases, polycystic liver disease and Marinesco–Sjögren syndrome.
UDP Encapsulation in Linux

UDP encapsulation encompasses the techniques and protocols to encapsulate and decapsulate networking packets of various protocols inside UDP. UDP encapsulation has become prevalent in data centers, and in fact nearly all the solutions for network virtualization currently being proposed in IETF are based on UDP encapsulation. In this paper we present much of the recent work done by the Linux networking community to make UDP encapsulation a first class citizen. This cumulative work has resulted in greatly improved performance, robustness, and scalability. We begin by describing the basic support and model for UDP encapsulation. Next, we look at performance enhancements in the areas of load balancing, checksum offload, and segmentation offload. Finally, we examine two generic methods of UDP encapsulation: Fooover-UDP and Generic UDP Encapsulation.