Miracle-dz/UniFAR-FTUs huggingface dataset:
Two gastroenteritis outbreaks caused by sapovirus in Shenzhen, China

Human sapoviruses (SaVs) are a common cause of the acute gastroenteritis epidemic worldwide, and SaV outbreaks and infections have become more frequent in recent years. Since the end of December, 2015 to December, 2016, 2 gastroenteritis outbreaks occurred in 2 kindergarten classes (outbreaks A and B) in the Baoan district, Shenzhen, China. Feces and swabs were collected for laboratory tests of causative agents, and no bacterial pathogens were detected. Both the outbreaks were positive for SaV with a detection rate of 75% of symptomatic cases (6/8) in outbreak A and 71% (10/14) in outbreak B. For outbreak B, 1 of 3 asymptomatic teachers was detected to be SaV positive. The genome of some of the strains in this study was obtained, and the strains from outbreak A were genotyped into GII.3, while those from outbreak B were genotyped into GI.2, according to the phylogenetic analysis of the polymerase and the capsid region. No recombination was identified in either the GII.3 or GI.2 strain. GI.2 strains experience chronological variation, and the GI.2 strain in this study belonged to the most recent variant, which was observed from 2008 to 2016. The variation mainly occurred in the P domain from 1990 to 2016. Meanwhile, GII.3 strains shared greater similarity (>98.2%) at the amino acid identities; from 1999 to 2015, only 5 of them were in the predicted P domain. Our results suggest that it is necessary to conduct routine SaV surveillance and molecular characterization to further understand the SaV epidemic.
Gene structure and expression of the MboI restriction--modification system.

The genes from Moraxella bovis encoding the MboI restriction--modification system were cloned and expressed in Escherichia coli. Three open reading frames were found in the sequence containing the genes. These genes, which we named mboA, mboB, and mboC, had the same orientation in the genome. Genes mboA and mboC encoded MboI methyltransferases (named M.MboA and M.MboC) with 294 and 273 amino acid residues, respectively. The mboB gene coded for MboI restriction endonuclease (R.MboI) with 280 amino acid residues. Recombinant E.coli-MBOI, which contained the whole MboI system, overproduced R.MboI. R.MboI activity from E.coli-MBOI was 480-fold that of M.bovis. The amino acid sequences deduced from these genes were compared with those of other restriction--modification systems. The protein sequences of the MboI system had 38-49% homology with those of the DpnII system.
Applying Network Theory to Epidemics: Control Measures for Mycoplasma pneumoniae Outbreaks

We introduce a novel mathematical approach to investigating the spread and control of communicable infections in closed communities. Mycoplasma pneumoniae is a major cause of bacterial pneumonia in the United States. Outbreaks of illness attributable to mycoplasma commonly occur in closed or semi-closed communities. These outbreaks are difficult to contain because of delays in outbreak detection, the long incubation period of the bacterium, and an incomplete understanding of the effectiveness of infection control strategies. Our model explicitly captures the patterns of interactions among patients and caregivers in an institution with multiple wards. Analysis of this contact network predicts that, despite the relatively low prevalence of mycoplasma pneumonia found among caregivers, the patterns of caregiver activity and the extent to which they are protected against infection may be fundamental to the control and prevention of mycoplasma outbreaks. In particular, the most effective interventions are those that reduce the diversity of interactions between caregivers and patients.
Gelsolin as a negative prognostic factor and effector of motility in erbB-2-positive epidermal growth factor receptor-positive breast cancers.

PURPOSE erbB-2 and epidermal growth factor receptor (EGFR) may mediate motility via signaling that enables changes in the actin cytoskeleton. A physical basis for this motility may depend on the coexpression of gelsolin, a M(r) 80,000 actin-binding protein. EXPERIMENTAL DESIGN The expression of erbB-2, EGFR, and gelsolin was analyzed in 790 archival invasive breast cancers. These data were compared with histological, clinical, and outcome data (median follow-up, 16.3 years). RESULTS Protein overexpression was observed in overlapping subsets of breast cancers (38% of cases were erbB-2+; 15% of cases were EGFR+; and 56% of cases were gelsolin+). Tumor gelsolin was associated with overexpression of erbB-2 and EGFR, as well as with an aggressive tumor phenotype. By univariate and multivariate analyses, tumor gelsolin alone was not a prognostic factor. Overexpression of all three factors significantly predicted poor clinical outcome by univariate and multivariate analyses. For example, in node-positive patients, coexpression of all three markers was associated with a 3-year disease-specific survival (as compared with erbB-2+, EGFR+, gelsolin- patients, who had a median survival of 6 years). CONCLUSIONS These data suggest that gelsolin coexpression may be an important additional prognostic factor in erbB-2+, EGFR+ breast cancer patients. We hypothesize that this is due to the role of gelsolin in mediating motility and invasion.
A novel optimization algorithm for Chien search of BCH Codes in NAND flash memory devices

As NAND flash memory chips become denser, they are more vulnerable to random errors caused by ageing, read or write interference, and erase operations. These errors compromise both the data integrity and lifetime of flash memory so that error correction codes (ECC) are employed by the flash controller to strengthen the fault tolerance. The BCH (Bose Chaudhuri Hochquenghem) code is a widely used ECC technique in flash-based storage devices due to its strong error correction capability and high performance. The third step of decoding a BCH code is the Chien search process, which locates the errors in the received codeword. To increase the decoding throughput, parallel Chien search algorithms are used, but existing algorithms occupy more than 60% area of the total decoding logic, increasing the hardware complexity and energy consumption. To reduce the hardware complexity and overhead, in this paper, we propose a plane optimization algorithm to reduce the redundant XOR gates used in the Chien search process. Our study based on intensive experiments shows that for a (2047,1926, 11) BCH code with the parallel factor of 32, the proposed optimization algorithm reduces the number of XOR gates used in the Chien search process by 79%, 46% and 13%, respectively, compared to the straightforward implementation, the GMA approach and the strength-reduced architecture.
A Differential Approach to Undefined Behavior Detection

This article studies undefined behavior arising in systems programming languages such as C/C++. Undefined behavior bugs lead to unpredictable and subtle systems behavior, and their effects can be further amplified by compiler optimizations. Undefined behavior bugs are present in many systems, including the Linux kernel and the Postgres database. The consequences range from incorrect functionality to missing security checks. This article proposes a formal and practical approach that finds undefined behavior bugs by finding “unstable code” in terms of optimizations that leverage undefined behavior. Using this approach, we introduce a new static checker called Stack that precisely identifies undefined behavior bugs. Applying Stack to widely used systems has uncovered 161 new bugs that have been confirmed and fixed by developers.
Translational Control of Cytochrome c by RNA-Binding Proteins TIA-1 and HuR

ABSTRACT Stresses affecting the endoplasmic reticulum (ER) globally modulate gene expression patterns by altering posttranscriptional processes such as translation. Here, we use tunicamycin (Tn) to investigate ER stress-triggered changes in the translation of cytochrome c, a pivotal regulator of apoptosis. We identified two RNA-binding proteins that associate with its ∼900-bp-long, adenine- and uridine-rich 3′ untranslated region (UTR): HuR, which displayed affinity for several regions of the cytochrome c 3′UTR, and T-cell-restricted intracellular antigen 1 (TIA-1), which preferentially bound the segment proximal to the coding region. HuR did not appear to influence the cytochrome c mRNA levels but instead promoted cytochrome c translation, as HuR silencing greatly diminished the levels of nascent cytochrome c protein. By contrast, TIA-1 functioned as a translational repressor of cytochrome c, with interventions to silence TIA-1 dramatically increasing cytochrome c translation. Following treatment with Tn, HuR binding to cytochrome c mRNA decreased, and both the presence of cytochrome c mRNA within actively translating polysomes and the rate of cytochrome c translation declined. Taken together, our data suggest that the translation rate of cytochrome c is determined by the opposing influences of HuR and TIA-1 upon the cytochrome c mRNA. Under unstressed conditions, cytochrome c mRNA is actively translated, but in response to ER stress agents, both HuR and TIA-1 contribute to lowering its biosynthesis rate. We propose that HuR and TIA-1 function coordinately to maintain precise levels of cytochrome c production under unstimulated conditions and to modify cytochrome c translation when damaged cells are faced with molecular decisions to follow a prosurvival or a prodeath path.
Neural network models for combining evidence from spectral and suprasegmental features for text-dependent speaker verification

This paper proposes a method using neural network models for combining evidence from spectral and suprasegmental features for text-dependent speaker verification. Spectral features are extracted using the Dynamic Time Warping (DTW) technique. While extracting the spectral features, the DTW algorithm is used only to obtain a matching score and the information present in the warping path is ignored. In this work a method is discussed to extract suprasegmental features such as pitch and duration using the information in the warping path. Although the suprasegmental features may not yield good performance, combining the evidence from suprasegmental and spectral features improves the performance of the speaker verification system significantly.
Differential Regulation of Nitric Oxide Synthase-2 and Arginase-1 by Type 1/Type 2 Cytokines In Vivo: Granulomatous Pathology Is Shaped by the Pattern of l-Arginine Metabolism1

Type 2 cytokines regulate fibrotic liver pathology in mice infected with Schistosoma mansoni. Switching the immune response to a type 1-dominant reaction has proven highly effective at reducing the pathologic response. Activation of NOS-2 is critical, because type 1-deviated/NO synthase 2 (NOS-2)-deficient mice completely fail to control their response. Here, we demonstrate the differential regulation of NOS-2 and arginase type 1 (Arg-1) by type 1/type 2 cytokines in vivo and for the first time show a critical role for arginase in the pathogenesis of schistosomiasis. Using cytokine-deficient mice and two granuloma models, we show that induction of Arg-1 is type 2 cytokine dependent. Schistosome eggs induce Arg-1, while Mycobacterium avium-infected mice develop a dominant NOS-2 response. IFN-γ suppresses Arg-1 activity, because type 1 polarized IL-4/IL-10-deficient, IL-4/IL-13-deficient, and egg/IL-12-sensitized animals fail to up-regulate Arg-1 following egg exposure. Notably, granuloma size decreases in these type-1-deviated/Arg-1-unresponsive mice, suggesting an important regulatory role for Arg-1 in schistosome egg-induced pathology. To test this hypothesis, we administered difluoromethylornithine to block ornithine-aminodecarboxylase, which uses the product of arginine metabolism, l-ornithine, to generate polyamines. Strikingly, granuloma size and hepatic fibrosis increased in the ornithine-aminodecarboxylase-inhibited mice. Furthermore, we show that type 2 cytokine-stimulated macrophages produce proline under strict arginase control. Together, these data reveal an important regulatory role for the arginase biosynthetic pathway in the regulation of inflammation and demonstrate that differential activation of Arg-1/NOS-2 is a critical determinant in the pathogenesis of granuloma formation.
Continuous Measurement of Autoregulation by Spontaneous Fluctuations in Cerebral Perfusion Pressure: Comparison of 3 Methods

Background and Purpose— Clinical application of continuous autoregulation monitoring would benefit from a comparison of curves generated by online monitoring with standard autoregulation curves in animal models. We characterized the accuracy of 3 continuous monitors of autoregulation in a piglet model of hypotension. Methods— Piglets 5 to10 days old with intracranial pressure (ICP) at naïve or elevated (20 mm Hg) levels had gradual arterial hypotension induced by a balloon catheter in the inferior vena cava. Elevated ICP was maintained by a continuous infusion of artificial cerebrospinal fluid. Three indices of autoregulation were simultaneously and continuously calculated. A moving, linear Pearson's coefficient between spontaneous slow waves of cerebral perfusion pressure and slow waves of laser-Doppler flux or cortical oxygenation rendered the laser-Doppler index and cerebral-oximetry index, respectively. Similar correlation between slow waves of arterial blood pressure and ICP rendered the pressure-reactivity index. The lower limit of autoregulation was determined directly for each animal by plotting laser-Doppler cortical red blood cell flux as a function of cerebral perfusion pressure. Receiver-operator characteristics were determined for the 3 indices. Results— The areas under the receiver-operator characteristics curves for discriminating the individual lower limit of autoregulation at low and high ICP were 0.89 and 0.85 for the laser-Doppler index, 0.89 and 0.84 for the cerebral-oximetry index, and 0.79 and 0.79 for the pressure-reactivity index. The pressure-reactivity index performed equally well at low and high ICPs. Conclusions— Continuous monitoring of autoregulation by spontaneous slow waves of cerebral perfusion pressure can accurately detect loss of autoregulation due to hypotension in piglets by all 3 modalities.
Detection of pan and zoom in soccer sequences based on H.264/AVC motion information

Unsupervised detection of pan and zoom in soccer sequences allows automatic classification of shots and match analysis. In this work we propose a pan and zoom (both in and out) detector specifically designed for low resolution soccer sequences. Our implementation is based on the analysis of the distribution of the motion vectors, already available in the encoded sequence, among a specific subset of reliable MBs, selected by means of inexpensive image preprocessing.
Effect of heat treatment on the electrical resistance of photoresist as related to radioisotopic thermoelectric generator aging

Photoresist is used in electrical contact definition and processing in radioisotopic thermoelectric generators. Inadequate removal of material during processing could lead to electrical shorting when exposed to the high temperature use environment. This effect has been simulated through studies of the electrical resistance of thin layers of photoresist (Kodak Metal Etch Resist) on glass (Corning 7052) with tungsten electrodes. Results show that both the photoresist and the glass contribute to the resistance. The glass resistance decreases with increasing temperature and becomes significant at high temperatures. Annealing studies on the photoresist show that the resistance of the photoresist decreases by over five orders of magnitude upon annealing to 500/sup 0/C, with a corresponding decrease in activation energy from 0.27 eV (350/sup 0/C anneal) to 0.10 eV (500/sup 0/C anneal). Time dependent decreases in resistance of the photoresist were also measured for up to 8 to 9 days during high temperature anneals. Some electrolytic transport of tungsten may occur through the photoresist at high temperatures. Results are compared with data on thermoelectric generators and show that photoresist could cause the electrical aging (voltage degradation) problem observed in some generators.
Formal analysis of the effectiveness and predictability of random testing

There has been a lot of work to shed light on whether random testing is actually a useful testing technique. Despite its simplicity, several successful real-world applications appear in the literature. Although it is not going to solve all possible testing problems, random testing is an essential tool in the hands of software testers. In this paper, we address general questions about random testing, such as how long random testing needs on average to achieve testing targets (e.g., coverage), how does it scale and how likely is it to yield similar results if we re-run random testing on the same testing problem. Due to its simplicity that makes the mathematical analysis of random testing tractable, we provide precise and rigorous answers to these questions. Our formal results can be applied to most types of software and testing criteria. Simulations are carried out to provide further support to our formal results. The obtained results are then used to assess the validity of empirical analyses reported in the literature. Results show that random testing is more effective and predictable than previously thought.
Designing of Energy aware Quality of Service ( QoS ) based routing protocol for Efficiency Improvement in Wireless Sensor Network ( WSN )

New advancements in Wireless Sensor Networks (WSN), lead to many novel routing protocols specifically designed by considering QoS and energy efficiency as the main objective, to maximize the whole network efficiency and lifetime. As the issue of Quality of Service (QoS) provisioning in WSN networks has been acquiring increasing importance, particularly in view of the domains of application of these networks i.e., defense operations, emergency rescue missions, Health and Multimedia traffic, where we have need of more accuracy and guarantee for timely data transfer, therefore, to fulfill the requirements of these real time applications associated with wireless sensor networks, it is required that more reliable and dependable energy aware QoS based routing protocol in WSN should be developed for the usage of sensor nodes efficiently. The objective of this research is to focus on challenges related to the architecture and operation of handling QoS routing traffic in sensor network and designing an energy-aware QoS based routing protocol for Wireless Sensor Network (WSN) which will stumble on least cost, transmission energy, error rate and other communication parameters to enhance the efficiency of WSN performance in Military, Health and Environmental applications. The tasks of the research project started with the deep Investigation of the problem requirement followed by Designing, Development, Simulation, Modeling and Finally comprehensive analysis of the simulation results. Two approaches, WSN Nodes with normal condition (Before any assumption) and WSN Nodes after Secondary Route & Gateway assumption a part, are used. Both approaches works fine and reduces the congestion of the network along with enhanced energy life, resulting the QoS of the network and increased energy efficiency in sufficient amount ABSTRACT Journal of Information & Communication Technology Vol. 4, No. 1, (Spring 2010) 19-37
Unified Analytical Solution for Cylindrical Cavity Expansion of Saturated Soil Based on Large Deformation and Non-Drainage

Soil around the cylindrical pore is divided into elastic and plastic regions. In the elastic region, the small deformation theory is applied while in the plastic region, the large deformation theory and unified strength criterion are applied. According to the stress equilibrium equation and the boundary condition of continuous stress and deformation, the theoretical solution to plastic region radius, limit expansion pore pressure excess pore pressure and excess pore water pressure of the cylindrical cavity expansion can be derived when considering large deformation and non-drainage problems. Compared to the theoretical results of Cao L.F. , the theoretical calculation results are closer to the field test results which show that the theory has a certain value in engineering application. Through calculations and analysis, it is also derived that expansion pore pressure increase is non-linear with the increase of b value, while the excess pore water pressure is just the opposite.
PyMVPA: A Unifying Approach to the Analysis of Neuroscientific Data

The Python programming language is steadily increasing in popularity as the language of choice for scientific computing. The ability of this scripting environment to access a huge code base in various languages, combined with its syntactical simplicity, make it the ideal tool for implementing and sharing ideas among scientists from numerous fields and with heterogeneous methodological backgrounds. The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefit from a Python-based framework. For many years, a large fraction of both research communities have addressed, almost independently, very high-dimensional problems with almost completely non-overlapping methods. However, a number of recently published studies that applied ML methods to neuroscience research questions attracted a lot of attention from researchers from both fields, as well as the general public, and showed that this approach can provide novel and fruitful insights into the functioning of the brain. In this article we show how PyMVPA, a specialized Python framework for machine learning based data analysis, can help to facilitate this inter-disciplinary technology transfer by providing a single interface to a wide array of machine learning libraries and neural data-processing methods. We demonstrate the general applicability and power of PyMVPA via analyses of a number of neural data modalities, including fMRI, EEG, MEG, and extracellular recordings.
Band Gap Properties of Two-Dimensional Photonic Crystal Structures with Rectangular Lattice

Abstract In this paper we proposed a new structure of two-dimensional photonic crystals with rectangular lattice. After deducing the primitive lattice vectors and first Brillouin zone of the structures, we studied the band gap properties of horizontal and vertical rectangular lattice structures and compared them with conventional square lattice structure. The most excellent characteristic of these structures is their joint band gap regions, which make them suitable for designing polarization-independent devices. The other advantage of these structures is having band gaps at higher normalized frequencies.
Target-Aware Lattice Rescoring for Dialect Recognition

We observed that human listeners distinguish one dialect from another by paying special attention to some particular phonetic and/or phonotactic patterns. Motivated by this observation, we propose a technique that emulates this process. We explore a target-aware lattice rescoring (TALR) process that revises the n -gram statistics in a lattice with target dialect information. We then derive n -gram statistics as the phonotactic features from the lattice and develop a system under the vector space modeling framework. The experiment results show that the proposed technique consistently improves dialect recognition performance on 30-second test utterances. We achieved equal error rates (EERs) of 4.57% and 13.28% with 3-gram statistics for Chinese and English dialect recognition in 2007 NIST Language Recognition Evaluation 30-second closed test sets.