Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective medium for isolation and enumeration of Bifidobacterium spp

A new method was developed for the isolation and enumeration of Bifidobacterium spp. from natural aquatic environments. The method was based on the utilization of a new medium, Bifidobacterium iodoacetate medium 25, and resuscitation techniques were used to isolate injured bifidobacteria. The new medium was tested with a nonselective reference medium on sewage and sewage-polluted surface waters. Relatively little colonial growth of any other bacterial genera occurred; when such colonies did grow, Bifidobacterium could be easily differentiated by its colonial morphology or, after Gram staining, by its typical bifidobacterial morphology.
Nonpeptide tachykinin receptor antagonists. III. SB 235375, a low central nervous system-penetrant, potent and selective neurokinin-3 receptor antagonist, inhibits citric acid-induced cough and airways hyper-reactivity in guinea pigs.

In this report the in vitro and in vivo pharmacological and pharmacokinetic profile of (-)-(S)-N-(alpha-ethylbenzyl)-3-(carboxymethoxy)-2-phenylquinoline-4-carboxamide (SB 235375), a low central nervous system (CNS)-penetrant, human neurokinin-3 (NK-3) receptor (hNK-3R) antagonist, is described. SB 235375 inhibited (125)I-[MePhe(7)]-neurokinin B (NKB) binding to membranes of Chinese hamster ovary (CHO) cells expressing the hNK-3R (CHO-hNK-3R) with a K(i) = 2.2 nM and antagonized competitively NKB-induced Ca(2+) mobilization in human embryonic kidney (HEK) 293 cells expressing the hNK-3R (HEK 293-hNK-3R) with a K(b) = 12 nM. SB 235375 antagonized senktide (NK-3R)-induced contractions in rabbit isolated iris sphincter (pA(2) = 8.1) and guinea pig ileal circular smooth muscles (pA(2) = 8.3). SB 235375 was selective for the hNK-3R compared with hNK-1 (K(i) > 100,000 nM) and hNK-2 receptors (K(i) = 209 nM), and was without effect, at 1 microM, in 68 other receptor, enzyme, and ion channel assays. Intravenous SB 235375 produced a dose-related inhibition of miosis induced by i.v. senktide in the rabbit (ED(50) of 0.56 mg/kg). Intraperitoneal SB 235375 (10-30 mg/kg) inhibited citric acid-induced cough and airways hyper-reactivity in guinea pigs. In mice oral SB 235375 (3-30 mg/kg) was without significant effect on the behavioral responses induced by intracerebral ventricular administration of senktide. Pharmacokinetic evaluation in the mouse and rat revealed that oral SB 235375 was well absorbed systemically but did not effectively cross the blood-brain barrier. The preclinical profile of SB 235375, encompassing high affinity, selectivity, oral activity, and low CNS penetration, suggests that it is an appropriate tool compound to define the pathophysiological roles of the NK-3Rs in the peripheral nervous system.
Sulfatide Storage in Neurons Causes Hyperexcitability and Axonal Degeneration in a Mouse Model of Metachromatic Leukodystrophy

Metachromatic leukodystrophy is a lysosomal storage disorder caused by deficiency in the sulfolipid degrading enzyme arylsulfatase A (ASA). In the absence of a functional ASA gene, 3-O-sulfogalactosylceramide (sulfatide; SGalCer) and other sulfolipids accumulate. The storage is associated with progressive demyelination and various finally lethal neurological symptoms. Lipid storage, however, is not restricted to myelin-producing cells but also occurs in neurons. It is unclear whether neuronal storage contributes to symptoms of the patients. Therefore, we have generated transgenic ASA-deficient [ASA(−/−)] mice overexpressing the sulfatide synthesizing enzymes UDP-galactose:ceramide galactosyltransferase (CGT) and cerebroside sulfotransferase (CST) in neurons to provoke neuronal lipid storage. CGT-transgenic ASA(−/−) [CGT/ASA(−/−)] mice showed an accumulation of C18:0 fatty acid-containing SGalCer in the brain. Histochemically, an increase in sulfolipid storage could be detected in central and peripheral neurons of both CGT/ASA(−/−) and CST/ASA(−/−) mice compared with ASA(−/−) mice. CGT/ASA(−/−) mice developed severe neuromotor coordination deficits and weakness of hindlimbs and forelimbs. Light and electron microscopic analyses demonstrated nerve fiber degeneration in the spinal cord of CGT/ASA(−/−) mice. CGT/ASA(−/−) and, to a lesser extent, young ASA(−/−) mice exhibited cortical hyperexcitability, with recurrent spontaneous cortical EEG discharges lasting 5–15 s. These observations suggest that SGalCer accumulation in neurons contributes to disease phenotype.
Effects of Orientation of Carbon Nanotubes on CNT Bundle Based Silk Composite Using Finite Element Method

Carbon Nanotubes (CNTs) have exceptional mechanical properties. They are the stiffest and strongest material, yet discovered, because of their high length to diameter ratio. In this paper a Representative Volume Element (RVE) model of CNT-silk composite is made. Then the orientations of the CNTs in the composite are varied and the effects of this variation are observed. The change is mainly observed between the interfaces of CNT and silk. Also there is a change in Young’s Modulus. COMSOL Multiphysics 4.2a is used for building model and performing simulations.
Experiments Adapting an Open-Domain Question Answering System to the Geographical Domain Using Scope-Based Resources

This paper describes an approach to adapt an existing multilingual Open-Domain Question Answering (ODQA) system for factoid questions to a Restricted Domain, the Geographical Domain. The adaptation of this ODQA system involved the modification of some components of our system such as: Question Processing, Passage Retrieval and Answer Extraction. The new system uses external resources like GNS Gazetteer for Named Entity (NE) Classification and Wikipedia or Google in order to obtain relevant documents for this domain. The system focuses on a Geographical Scope: given a region, or country, and a language we can semi-automatically obtain multilingual geographical resources (e.g. gazetteers, trigger words, groups of place names, etc.) of this scope. The system has been trained and evaluated for Spanish in the scope of the Spanish Geography. The evaluation reveals that the use of scope-based Geographical resources is a good approach to deal with multilingual Geographical Domain Question Answering.
Vectorization of Reed Solomon Decoding and Mapping on the EVP

Reed Solomon (RS) codes are used in a variety of (wireless) communication systems. Although commonly implemented in dedicated hardware, this paper explores the mapping of high-throughput RS decoding on vector DSPs. The four modules of such a decoder, viz. syndrome computation, key equation solver, Chien search, and Forney pose different vectorization challenges. Their vectorizations are explained in detail, including optimizations specific for embedded vector processor (EVP). For RS (255,239), this solution is benchmarked vs published implementations, and scalability up to vector size 64 is explored. The best and the worst case throughput of our implementation is 8 times and 2 times higher respectively than other architectures.
Imprecise security: Quality and complexity tradeoffs for hardware information flow tracking

Secure hardware design is a challenging task that goes far beyond ensuring functional correctness. Important design properties such as non-interference cannot be verified on functional circuit models due to the lack of essential information (e.g., sensitivity level) for reasoning about security. Hardware information flow tracking (IFT) techniques associate data objects in the hardware design with sensitivity labels for modeling security-related behaviors. They allow the designer to test and verify security properties related to confidentiality, integrity, and logical side channels. However, precisely accounting for each bit of information flow at the hardware level can be expensive. In this work, we focus on the precision of the IFT logic. The key idea is to selectively introduce only one sided errors (false positives); these provide a conservative and safe information flow response while reducing the complexity of the security logic. We investigate the effect of logic synthesis on the quality and complexity of hardware IFT and reveal how different logic synthesis optimizations affect the amount of false positives and design overheads of IFT logic. We propose novel techniques to further simplify the IFT logic while adding no, or only a minimum number of, false positives. Additionally, we provide a solution to quantitatively introduce false positives in order to accelerate information flow security verification. Experimental results using IWLS benchmarks show that our method can reduce complexity of GLIFT by 14.47% while adding 0.20% of false positives on average. By quantitatively introducing false positives, we can achieve up to a 55.72% speedup in verification time.
Discretion in Executive Incentive Contracts

We examine the role of discretion in executive incentive contracts. We consider the costs and benefits of using subjective performance evaluation of executives relative to objective performance measures. We formulate hypotheses based on the theoretical work on discretionary compensation and test these hypotheses empirically using a proprietary dataset of executive bonus plans. We show that discretion is less important in determining CEO pay than the pay of other executives. We also find that discretion is relatively important in determining executive bonuses at larger and privately held firms and that more diversified firms are relatively less likely to compensate their business unit managers based on firm-wide performance. Finally, we consider (and largely dismiss) tax-related explanations for our results. * We are grateful to Towers Perrin for allowing access to their proprietary data on management bonus plans. We are also grateful for helpful comments from George Baker, Linda Cohen, Robert Gibbons, Ehud Kamar, Lawrence Katz, Edward Lazear, Jonathan Levin, Scott Schaefer, Belen Villalonga, and Jan Zabojnik.
Optimizing the use of the Hard Disk in MapReduce Frameworks for Multi-core Architectures *

MapReduce simplifies parallel programming, abstracting the responsibility of the programmer, such asing the responsibility of the programmer, such as synchronization and task management. The paradigm allows the programmer to write sequential code that is automatically parallelized. The MapReduce Frameworks developed for multi-core architectures provide large processing keys which consequently growth intermediate data structure, which in some environments causes the use of all the available main memory. Recently, with the development of MapReduce frameworks for multi-core architectures that distribute keys through the memory hierarchy, the problem of using the entire main memory, by the data generated was minimized. But in an environment where all threads access the same hard disk, certain situations may lead a competition between the threads, to take keys generated from main memory to the hard disk, thus creating a bottleneck. Based on the behavior of threads and the growth of intermediate data structure in multi-core environments, we present an improvement of access to the hard disk in MapReduce frameworks for multi-core architectures. The main objective is to ensure that distinct threads do not compete to take the keys processed, from the memory until
The mechanisms of calcium cycling and action potential dynamics in cardiac alternans.

RATIONALE Alternans is a risk factor for cardiac arrhythmia, including atrial fibrillation. At the cellular level alternans manifests as beat-to-beat alternations in contraction, action potential duration (APD), and magnitude of the Ca(2+) transient (CaT). Electromechanical and CaT alternans are highly correlated, however, it has remained controversial whether the primary cause of alternans is a disturbance of cellular Ca(2+) signaling or electrical membrane properties. OBJECTIVE To determine whether a primary failure of intracellular Ca(2+) regulation or disturbances in membrane potential and AP regulation are responsible for the occurrence of alternans in atrial myocytes. METHODS AND RESULTS Pacing-induced APD and CaT alternans were studied in single rabbit atrial and ventricular myocytes using combined [Ca(2+)]i and electrophysiological measurements. In current-clamp experiments, APD and CaT alternans strongly correlated in time and magnitude. CaT alternans was observed without alternation in L-type Ca(2+) current, however, elimination of intracellular Ca(2+) release abolished APD alternans, indicating that [Ca(2+)]i dynamics have a profound effect on the occurrence of CaT alternans. Trains of 2 distinctive voltage commands in form of APs recorded during large and small alternans CaTs were applied to voltage-clamped cells. CaT alternans was observed with and without alternation in the voltage command shape. During alternans AP-clamp large CaTs coincided with both long and short AP waveforms, indicating that CaT alternans develop irrespective of AP dynamics. CONCLUSIONS The primary mechanism underlying alternans in atrial cells, similarly to ventricular cells, resides in a disturbance of Ca(2+) signaling, whereas APD alternans are a secondary consequence, mediated by Ca(2+)-dependent AP modulation.
Analysis of fluctuations in ultra-small semiconductor devices

A technique for the analysis of fluctuations in ultra small semiconductor devices is presented. This technique is applied to the computation fluctuations of threshold voltages and terminal characteristics of MOSFET devices due to the random doping fluctuations and oxide roughness. It is based on the linearization of transport equations with respect to the fluctuating quantities. This approach completely avoids computations for many device realizations and, therefore, it is computationally much more efficient than Monte-Carlo techniques.
Development of image quality assurance measures of the ExacTrac localization system using commercially available image evaluation software and hardware for image‐guided radiotherapy

Quality assurance (QA) of the image quality for image‐guided localization systems is crucial to ensure accurate visualization and localization of target volumes. In this study, a methodology was developed to assess and evaluate the constancy of the high‐contrast spatial resolution, dose, energy, contrast, and geometrical accuracy of the BrainLAB ExacTrac system. An in‐house fixation device was constructed to hold the QCkV‐1 phantom firmly and reproducibly against the face of the flat panel detectors. Two image sets per detector were acquired using ExacTrac preset console settings over a period of three months. The image sets were analyzed in PIPSpro and the following metrics were recorded: high‐contrast spatial resolution (f30,f40,f50 (lp/mm)), noise, and contrast‐to‐noise ratio. Geometrical image accuracy was evaluated by assessing the length between to predetermined points of the QCkV‐1 phantom. Dose and kVp were recorded using the Unfors RaySafe Xi R/F Detector. The kVp and dose were evaluated for the following: Cranial Standard (CS) (80 kV,80 mA,80 ms), Thorax Standard (TS) (120 kV,160 mA,160 ms), Abdomen Standard (AS) (120 kV,160 mA,130 ms), and Pelvis Standard (PS) (120 kV,160 mA,160 ms). With regard to high‐contrast spatial resolution, the mean values of the f30 (lp/mm), f40 (lp/mm) and f50 (lp/mm) for the left detector were 1.39±0.04,1.24±0.05, and 1.09±0.04, respectively, while for the right detector they were 1.38±0.04,1.22±0.05, and 1.09±0.05, respectively. Mean CNRs for the left and right detectors were 148±3 and 143±4, respectively. For geometrical accuracy, both detectors had a measured image length of the QCkV‐1 of 57.9±0.5mm. The left detector showed dose measurements of 20.4±0. 2μGy(CS), 191.8±0.7μGy(TS), 154.2±0.7μGy(AS), and 192.2±0.6μGy(PS), while the right detector showed 20.3±0. 3μGy(CS), 189.7±0.8μGy(TS), 151.0±0.7μGy(AS), and 189.7±0.8μGy(PS), respectively. For X‐ray energy, the left detector (right X‐ray tube) had mean kVp readings of 81.6±0.5(CS), 122.5±0.5(TS), 122.0±0.8(AS), and 122.1±0.7(PS), and the right detector (left X‐ray tube) had 81.6±0.5(CS), 120.8±0.5(TS), 120.9±0.6(AS), and 121.3±0.7(PS). Run charts were created so that each parameter could be tracked over time and the constancy of the system could be monitored. A methodology was developed to assess the basic image quality parameters recommended by TG‐142 for the ExacTrac system. The ExacTrac system shows a consistent dose, kVp, high‐contrast spatial resolution, CNR, and geometrical accuracy for each detector over the evaluated timeframe. PACS number: 87.10. ‐e
Activated calcineurin ameliorates contraction‐induced injury to skeletal muscles of mdx dystrophic mice

Utrophin expression is regulated by calcineurin and up‐regulating utrophin can decrease the susceptibility of dystrophic skeletal muscle to contraction‐induced injury. We overexpressed the constitutively active calcineurin‐A α in skeletal muscle of mdx dystrophic mice (mdx CnA*) and examined the tibialis anterior muscle to determine whether the presence of activated calcineurin promotes resistance to muscle damage after lengthening contractions. Two stretches (10 s apart) of 40% strain relative to muscle fibre length were initiated from the plateau of a maximal isometric tetanic contraction. Muscle damage was assessed 1, 5 and 15 min later by the deficit in maximum isometric force and by quantifying the proportion of muscle fibres staining positive for intracytoplasmic albumin. The force deficit at all time points after the lengthening contractions was approximately 80% in mdx muscles and 30% in mdxCnA* muscles. The proportion of albumin‐positive fibres was significantly less in control and injured muscles from mdxCnA* mice than from mdx mice. Compared with mdx mice, mean fibre cross‐sectional area was 50% less in muscles from mdxCnA* mice. Furthermore, muscles from mdxCnA* mice exhibited a higher proportion of fibres expressing the slow(er) myosin heavy chain (MyHC) I and IIa isoforms, prolonged contraction and relaxation times, lower absolute and normalized maximum forces, and a clear leftward shift of the frequency–force relationship with greater force production at lower stimulation frequencies. These are structural and functional markers of a slower muscle phenotype. Taken together, our findings show that muscles from mdxCnA* mice have a smaller mean fibre cross‐sectional area, a greater sarcolemmal to cytoplasmic volume ratio, and an increase in utrophin expression, promoting an attenuated susceptibility to contraction‐induced injury. We conclude that increased calcineurin activity may confer functional benefits to dystrophic skeletal muscles.
β1 Integrin Cytoplasmic Domain Residues Selectively Modulate Fibronectin Matrix Assembly and Cell Spreading through Talin and Akt-1*

The integrin β1 cytoplasmic domain (tail) serves as a scaffold for numerous intracellular proteins. The mechanisms by which the tail coordinates these proteins to facilitate extracellular matrix assembly and cell spreading are not clear. This study demonstrates that the β1 cytoplasmic domain can regulate cell spreading on fibronectin and fibronectin matrix assembly through Akt- and talin-dependent mechanisms, respectively. To identify these mechanisms, we characterized GD25 cells expressing the β1 integrin cytoplasmic domain mutants W775A and R760A. Although cell spreading appears normal in R760A mutant-integrin cells compared with wild type, it is inhibited in W775A mutant cells. In contrast, both mutant cell lines show defective fibronectin matrix assembly. Inhibition of cell spreading, but not matrix assembly, in the W775A mutant cells is due to a specific defect in Akt-1 activation. In addition, we find that both W775A and R760A mutant integrins have reduced surface expression of the 9EG7 epitope that correlates with reduced recruitment of talin to β1 integrin cytoplasmic complexes. Down-regulation of talin with small interfering RNA or expression of green fluorescent protein-talin head domain inhibits matrix assembly in β1 wild-type cells, mimicking the defect seen with the W775A and R760A mutant cells. These results demonstrate distinct mechanisms by which integrins regulate cell spreading and matrix assembly through the β1 integrin cytoplasmic tail.
Oracle in-database hadoop: when mapreduce meets RDBMS

Big data is the tar sands of the data world: vast reserves of raw gritty data whose valuable information content can only be extracted at great cost. MapReduce is a popular parallel programming paradigm well suited to the programmatic extraction and analysis of information from these unstructured Big Data reserves. The Apache Hadoop implementation of MapReduce has become an important player in this market due to its ability to exploit large networks of inexpensive servers. The increasing importance of unstructured data has led to the interest in MapReduce and its Apache Hadoop implementation, which has led to the interest of data processing vendors in supporting this programming style. Oracle RDBMS has had support for the MapReduce paradigm for many years through the mechanism of user defined pipelined table functions and aggregation objects. However, such support has not been Hadoop source compatible. Native Hadoop programs needed to be rewritten before becoming usable in this framework. The ability to run Hadoop programs inside the Oracle database provides a versatile solution to database users, allowing them use programming skills they may already possess and to exploit the growing Hadoop eco-system. In this paper, we describe a prototype of Oracle In-Database Hadoop that supports the running of native Hadoop applications written in Java. This implementation executes Hadoop applications using the efficient parallel capabilities of the Oracle database and a subset of the Apache Hadoop infrastructure. This system's target audience includes both SQL and Hadoop users. We discuss the architecture and design, and in particular, demonstrate how MapReduce functionalities are seamlessly integrated within SQL queries. We also share our experience in building such a system within Oracle database and follow-on topics that we think are promising areas for exploration.
Improvement of surfactin production in Bacillus subtilis using synthetic wastewater by overexpression of specific extracellular signaling peptides, comX and phrC

Surfactin is a biological surfactant with numerous potential applications. In this study, Bacillus subtilis was engineered to improve surfactin production by the activation of two competence‐stimulating pheromones, ComX and competence and sporulation factor (CSF) to stimulate the transcription of srfA operon. Both signaling factors, encoded by comX and phrC, were successfully overexpressed and subsequently increased surfactin production. Surfactin produced by engineered strains showed functional groups similar to the commercially available surfactin analyzed via Fourier transform infrared spectroscopy (FTIR). Surfactin production in the B. subtilis (pHT43‐comXphrC) strain was 6.4‐fold greater than in the wild strain, with approximately 135.1 mg/L surfactin produced after 48 h cultivation. To reduce the production costs of surfactin, synthetic wastewater was used, from which the B. subtilis (pHT43‐comXphrC) strain produced approximately 140.2 mg/L surfactin. The results obtained demonstrated the production of surfactin from synthetic wastewater, which is beneficial in lowering the overall production costs. Biotechnol. Bioeng. 2012;109: 2349–2356. © 2012 Wiley Periodicals, Inc.
Mutual terminology extraction using a statistical framework

In this paper, we explore a statistical framework for mutual bilingual terminology extraction. We propose three probabilistic models to assess the proposition that automatic alignment can play an active role in bilingual terminology extraction and translate it into mutual bilingual terminology extraction. The results indicate that such models are valid and can show that mutual bilingual terminology extraction is indeed a viable approach.