Miracle-dz/UniFAR-FTUs huggingface dataset:
Structurally Designed Attenuated Subunit Vaccines for S. aureus LukS-PV and LukF-PV Confer Protection in a Mouse Bacteremia Model

Previous efforts towards S. aureus vaccine development have largely focused on cell surface antigens to induce opsonophagocytic killing aimed at providing sterile immunity, a concept successfully applied to other Gram-positive pathogens such as Streptococcus pneumoniae. However, these approaches have largely failed, possibly in part due to the remarkable diversity of the staphylococcal virulence factors such as secreted immunosuppressive and tissue destructive toxins. S. aureus produces several pore-forming toxins including the single subunit alpha hemolysin as well as bicomponent leukotoxins such as Panton-Valentine leukocidin (PVL), gamma hemolysins (Hlg), and LukED. Here we report the generation of highly attenuated mutants of PVL subunits LukS-PV and LukF-PV that were rationally designed, based on an octameric structural model of the toxin, to be deficient in oligomerization. The attenuated subunit vaccines were highly immunogenic and showed significant protection in a mouse model of S. aureus USA300 sepsis. Protection against sepsis was also demonstrated by passive transfer of rabbit immunoglobulin raised against LukS-PV. Antibodies to LukS-PV inhibited the homologous oligomerization of LukS-PV with LukF-PV as well heterologous oligomerization with HlgB. Importantly, immune sera from mice vaccinated with the LukS mutant not only inhibited the PMN lytic activity produced by the PVL-positive USA300 but also blocked PMN lysis induced by supernatants of PVL-negative strains suggesting a broad protective activity towards other bicomponent toxins. These findings strongly support the novel concept of an anti-virulence, toxin-based vaccine intended for prevention of clinical S. aureus invasive disease, rather than achieving sterile immunity. Such a multivalent vaccine may include attenuated leukotoxins, alpha hemolysin, and superantigens.
Active Learning from Oracle with Knowledge Blind Spot

Active learning traditionally assumes that an oracle is capable of providing labeling information for each query instance. This paper formulates a new research problem which allows an oracle admit that he/she is incapable of labeling some query instances or simply answer "I don't know the label. " We define a unified objectivefunction to ensure that each query instance submitted to the oracleis the one mostly needed for labeling and the oracle should also hasthe knowledge to label. Experiments based on different types of knowledge blind spot (KBS) models demonstrate the effectiveness of theproposed design.
Primorskyibacter sedentarius gen. nov., sp. nov., a novel member of the class Alphaproteobacteria from shallow marine sediments.

Two gram-negative, aerobic, non-pigmented, non-motile, rod-shaped bacteria, strains KMM 9015 and KMM 9018(T), were isolated from a sample of shallow sediment collected from the Sea of Japan. An analysis of the nearly complete 16S rRNA gene sequences showed that the isolates were very close to each other phylogenetically (99.9 % sequence similarity) and their close relatives were Marinovum algicola FF3(T) (95.8 and 95.9 %, respectively) and members of the genera Leisingera (95.7-95.1 and 95.8-95.2 %), Phaeobacter (95.0-94.2 and 95.1-94.2 %) and Thalassobius (96.3-94.8 and 96.2-94.7 %) of the class Alphaproteobacteria. In phylogenetic trees based on 16S rRNA gene sequences, strains KMM 9015 and KMM 9018(T) were positioned as a distinct phylogenetic line adjacent to Marinovum algicola. The major isoprenoid quinone was Q-10, the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown lipid and the major fatty acid was C(18 : 1)ω7c, followed by 11-methyl C(18 : 1)ω7c, in both strains. The DNA G+C contents of strains KMM 9015 and KMM 9018(T) were 60.2 and 61.9 mol%, respectively. Based on distinctive phenotypic characteristics and phylogenetic analysis, strains KMM 9015 and KMM 9018(T) represent a novel species in a novel genus, for which the name Primorskyibacter sedentarius gen. nov., sp. nov. is proposed. The type strain of Primorskyibacter sedentarius is strain KMM 9018(T) ( = NRIC 0784(T) = JCM 16874(T)).
Analogue Synaptic Noise - Implications And Learning Improvements

We analyse the effects of analogue noise on the synaptic arithmetic during multilayer perceptron training by expanding the cost function to include noise-mediated penalty terms. Predictions are made in the light of these calculations which suggest that fault tolerance, generalisation ability and learning trajectory should be improved by such noise-injection. Extensive simulation experiments on two distinct classification problems substantiate the claims. The results appear to be perfectly general for all training schemes where weights are adjusted incrementally, and have wide-ranging implications for all applications, particularly those involving "inaccurate" analogue neural VLSI.
Investigating the Cause of Poor Efficiency in Thermal Power Plant – A Six-Sigma based Case Study

: Nowadays, energy in any form has become an essential commodity all over the world. Being a developing country India is facing energy shortage problems. The Indian government is investing into various projects for efficient utilisation of available resources and to improve power plant efficiency. Research scholars and agencies are seeing the quality of thermal power plant is a possible area of improvement. This paper focuses on identifying the causes of capacity waste in a thermal power plant. For this Six-Sigma improvement project, DMAIC (Define-measure-analysis-improve-control) approach has been adopted. The study found low availability of equipment is the primary cause of capacity wastage in a thermal power plant. Various suggestions were provided to reduce equipment availability problem and consequently to improve the plant efficiency.
An EM-algorithm approach for the design of orthonormal bases adapted to sparse representations

In this paper, we consider the problem of dictionary learning for sparse representations. Several algorithms dealing with this problem can be found in the literature. One of them, introduced by Sezer et al. in optimizes a dictionary made up of the union of orthonormal bases. In this paper, we propose a probabilistic interpretation of Sezer's algorithm and suggest a novel optimization procedure based on the EM algorithm. Comparisons of the performance in terms of missed detection rate show a clear superiority of the proposed approach.
CALL FOR PAPERS Cardiovascular Responses to Environmental Stress Selective TNF- (cid:2) targeting with inﬂiximab attenuates impaired oxygen metabolism and contractile function induced by an acute exposure to air particulate matter

attenuates impaired oxygen metabolism contractile function an acute air particulate Inﬂammation plays a central role in the onset and progression of cardiovascular diseases associated with the exposure to air pollution particulate matter (PM). The aim of this work was to analyze the cardioprotective effect of selective TNF- (cid:2) targeting with a blocking anti-TNF- (cid:2) antibody (inﬂiximab) in an in vivo mice model of acute exposure to residual oil ﬂy ash (ROFA). Female Swiss mice received an intraperitoneal injection of inﬂiximab (10 mg/kg body wt) or saline solution, and were intranasally instilled with a ROFA suspension (1 mg/kg body wt). Control animals were instilled with saline solution and handled in parallel. After 3 h, heart O 2 consumption was assessed by high-resolution respirometry in left ventricle tissue cubes and isolated mitochondria, and ventricular contractile reserve and lusitropic reserve were evaluated according to the Langendorff technique. ROFA instillation induced a signiﬁcant decrease in tissue O 2 consumption and active mitochondrial respiration by 32 and 31%, respec-tively, compared with the control group. While ventricular contractile state and isovolumic relaxation were not altered in ROFA-exposed mice, impaired contractile reserve and lusitropic reserve were observed in this group. Inﬂiximab pretreatment signiﬁcantly attenuated the decrease in heart O 2 consumption and prevented the decrease in ventricular contractile and lusitropic reserve in ROFA-exposed mice. Moreover, inﬂiximab-pretreated ROFA-exposed mice showed conserved left ventricular developed pressure and cardiac O 2 consumption in response to a (cid:3) -adrenergic stimulus with isoproterenol. These results provides direct evidence linking systemic inﬂammation and altered cardiac function following an acute exposure to PM and contribute to the understanding of PM-associated cardiovascular morbidity and mortality. emphasizes the importance of environmental factors ROFA-exposed mice compared with ROFA-exposed mice that did not receive inﬂiximab ( P (cid:7) 0.05). No signiﬁcant differences were observed among control groups with or without inﬂiximab or in state 4 respiration rates between the different groups. These results suggest that increased circulating TNF- (cid:2) levels in ROFA-exposed mice lead to impaired mitochondrial function, which might, in turn, account for decreased cardiac tissue O 2 consumption in this group.
CCL: a portable and tunable collective communication library for scalable parallel computers

A collective communication library for parallel computers includes frequently used operations such as broadcast, reduce, scatter, gather, concatenate, synchronize, and shift. Such a library provides users with a convenient programming interface, efficient communication operations, and the advantage of portability. A library of this nature, the collective communication library (CCL), intended for the line of scalable parallel computer products by IBM, has been designed. CCL is part of the parallel application programming interface of the recently announced IBM 9076 Scalable POWERparallel System 1 (SP1). We examine several issues related to the functionality, correctness, and performance of a portable collective communication library while focusing on three novel aspects in the design and implementation of CCL: (i) the introduction of process groups, (ii) the definition of semantics that ensures correctness, and (iii) the design of new and tunable algorithms based on a realistic point-to-point communication model. <<ETX>>
Making Program Refactoring Safer

Developers rely on compilation, test suites, and tools to preserve observable behavior during refactoring. However, most refactoring tools don't implement all the preconditions that guarantee refactoring correctness because formally identifying them is cost-prohibitive. Therefore, these tools could perform nonbehavior-preserving transformations. The authors present a tool for improving safety during refactoring that automatically generates a test suite suited for detecting behavioral changes. They used this tool to evaluate seven real case study refactorings (from 3 to 100 KLOC).
Three‐dimensional structure of fungal proteinase K reveals similarity to bacterial subtilisin.

The three‐dimensional structure of the fungal serine protease proteinase K has been determined at 3.3 A resolution by single crystal X‐ray diffraction analysis. The enzyme crystallizes in the tetragonal space group P4(3)2(1)2 with cell constants a = b = 68.3 A, c = 108.5 A. The asymmetric unit consists of one monomer of 27 000 daltons mol. wt. , approximately 50% higher than the so far assumed value of 18 500 daltons. The main chain fold of proteinase K shows a high degree of tertiary homology with the corresponding bacterial subtilisin BPN’. Proteinase K is the second enzyme in this family of serine proteases to be studied by X‐ray diffraction, thus confirming the existence of two unrelated families of serine proteases in pro‐and eukaryotes.
Single Endemic Genotype of Measles Virus Continuously Circulating in China for at Least 16 Years

The incidence of measles in China from 1991 to 2008 was reviewed, and the nucleotide sequences from 1507 measles viruses (MeV) isolated during 1993 to 2008 were phylogenetically analyzed. The results showed that measles epidemics peaked approximately every 3 to 5 years with the range of measles cases detected between 56,850 and 140,048 per year. The Chinese MeV strains represented three genotypes; 1501 H1, 1 H2 and 5 A. Genotype H1 was the predominant genotype throughout China continuously circulating for at least 16 years. Genotype H1 sequences could be divided into two distinct clusters, H1a and H1b. A 4.2% average nucleotide divergence was found between the H1a and H1b clusters, and the nucleotide sequence and predicted amino acid homologies of H1a viruses were 92.3%–100% and 84.7%–100%, H1b were 97.1%–100% and 95.3%–100%, respectively. Viruses from both clusters were distributed throughout China with no apparent geographic restriction and multiple co-circulating lineages were present in many provinces. Cluster H1a and H1b viruses were co-circulating during 1993 to 2005, while no H1b viruses were detected after 2005 and the transmission of that cluster has presumably been interrupted. Analysis of the nucleotide and predicted amino acid changes in the N proteins of H1a and H1b viruses showed no evidence of selective pressure. This study investigated the genotype and cluster distribution of MeV in China over a 16-year period to establish a genetic baseline before MeV elimination in Western Pacific Region (WPR). Continuous and extensive MeV surveillance and the ability to quickly identify imported cases of measles will become more critical as measles elimination goals are achieved in China in the near future. This is the first report that a single endemic genotype of measles virus has been found to be continuously circulating in one country for at least 16 years.
Searching XML Documents by Keywords in Structured P2P Networks

In this paper we present a scheme for searching XML documents by keywords in DHT-based structured P2P networks. Our idea is to construct an inverted index for XML documents in an DHT-based P2P network. To this end, we discuss how to decompose XML documents and store the resulting fragments in a DHT-based P2P network. Given a query in terms of keywords, we have to be able to find respective XML fragments that subsume given keywords. We address this problem by finding SLCAs (smallest lowest common ancestors) for the keywords with the help of the DHT-based inverted index. We also discuss the technique to reduce number of message transmissions among peers by introducing Bloom filters. We show the feasibility of the proposed scheme by experimentations.
The effects of alcohol cue exposure on non-dependent drinkers' attentional bias for alcohol-related stimuli.

AIMS The effects of university students' habitual drinking practices and experimental alcohol cue exposure on their attentional bias for alcohol-related stimuli were assessed. METHODS Participants were exposed in vivo to either an alcoholic or non-alcoholic beverage immediately prior to completing a cognitively demanding emotional Stroop task that uses alcohol-related and control words as potential distractors. RESULTS Regression analyses indicated that, for participants who were low consumers of alcohol, neither level of habitual drinking, type of cue exposure, nor their interaction predicted attentional bias for the alcohol-related stimuli. For high consumers of alcohol who were exposed to the alcoholic beverage (but not those exposed to the non-alcoholic beverage), the amount of alcohol that participants habitually drank significantly predicted the degree of attentional bias. CONCLUSIONS The results indicate that, among non-dependent drinkers (unlike alcohol-dependent participants), alcohol-related attentional bias is not a generalized phenomenon, but occurs only under a specific set of circumstances.
Finding Disjoint Routes in Telecommunications Networks with Two Technologies

We consider networks in which a cost is associated with each arc or edge and a transition cost is associated with each node. This la st cost is related to the presence of two technologies on the network and is incurred only when a flow enters and leaves the corresponding node on arcs of different types. The problem we consider consists in finding two node disjoint paths with minimum total cost. We show that it is strongly NP-complete. Then we propose two heuristics, study their worst case behavior, provide a lower bounding procedure based on Lagrangean relaxation, and finally embed those elements in a branch and bound procedure.
Female gametophytic cell specification and seed development require the function of the putative Arabidopsis INCENP ortholog WYRD

In plants, gametes, along with accessory cells, are formed by the haploid gametophytes through a series of mitotic divisions, cell specification and differentiation events. How the cells in the female gametophyte of flowering plants differentiate into gametes (the egg and central cell) and accessory cells remains largely unknown. In a screen for mutations that affect egg cell differentiation in Arabidopsis, we identified the wyrd (wyr) mutant, which produces additional egg cells at the expense of the accessory synergids. WYR not only restricts gametic fate in the egg apparatus, but is also necessary for central cell differentiation. In addition, wyr mutants impair mitotic divisions in the male gametophyte and endosperm, and have a parental effect on embryo cytokinesis, consistent with a function of WYR in cell cycle regulation. WYR is upregulated in gametic cells and encodes a putative plant ortholog of the inner centromere protein (INCENP), which is implicated in the control of chromosome segregation and cytokinesis in yeast and animals. Our data reveal a novel developmental function of the conserved cell cycle-associated INCENP protein in plant reproduction, in particular in the regulation of egg and central cell fate and differentiation.
Implementation issues for Modified Dijkstra's and Floyd-Warshall algorithms in OpenFlow

This paper continues the idea of a gearbox-like routing algorithm selection in runtime presented at IEEE LANMAN 2011. Following the results obtained by simulations, the objectives were this time to have a real implementation of the the Modified Dijkstra's and Floyd-Warshall algorithms in OpenFlow. The testbed under Fedora Core consisted on four virtual switches Open vSwitch 1.3 and a software controller Beacon 1.0. 2. The individual performance evaluation of the two algorithms was done based on the end-to-end available transfer rate, using RTSP video flows over UDP without transfer rate obtrusion. The congestion was realized by generating UDP background traffic using iperf.
Unsupervised feature selection based on clustering

Feature selection plays an important part in improving the classification accuracy and the quality of clustering in many applications. Feature selection has been widely studied in supervised learning, but in unsupervised learning it is still relatively rare. In this paper, a novel definition of feature differentiation for identifying (determining) the relatively important features is presented, and a one-pass clustering-based feature selection approach is introduced. The new method with nearly linear time complexity selects the optimal subset according to the variation of the feature differentiation. Experimental results on UCI datasets show that our method, by removing the irrelevant or redundant features, can achieve promising classification and clustering results for most datasets. Compared with other traditional feature selection approaches the proposed algorithm has obtained similar or even better performance in terms of dimensionality reduction and classification accuracy.
Implementation of virtual control strategies for natural rehabilitation of arm with visual and force feedback

Robotic training following stroke is an emerging rehabilitation technique to facilitate neuromuscular plasticity for regaining functional movements. Most existing training robots follow a defined task-based trajectory in assistive or resistive mode. Whilst this approach may be effective in certain cases it does not allow training of arm or leg in a natural way as the motion is precisely guided by the robot or exoskeleton. The ideal training would be to allow arm/leg follow a trajectory naturally without any augmented support and bring it back when the limb is diverted significantly from the goal. This paper presents implementation of this approach in a virtual environment using a simple force feedback joystick. This will guide the arm within a tunnel of trajectory by providing assistance or resistance depending on location of the arm. The technique can be extended for 3-dimensoional arm movement which can help learn neural plasticity naturally.
The yeast transcriptome in aerobic and hypoxic conditions: effects of hap1, rox1, rox3 and srb10 deletions

The transcriptome of Saccharomyces cerevisiae was screened using the high‐density membrane hybridization method, under aerobic and hypoxic conditions, in wild‐type and mutant backgrounds obtained by the disruption of the genes encoding the regulatory proteins Hap1, Rox1 and the Srb10 and Rox3 subunits of RNA polymerase II holoenzyme. None of the mutations studied was able to fully overcome the wild‐type hypoxic response. Deletion of the hap1 gene changed the expression profiles of individual open reading frames (ORFs) under both aerobic and hypoxic conditions. Major changes associated with rox3 deletion were related to the hypoxic activation. Rox3 also caused a repressor effect (oxygen‐independent) on a subset of genes related to subtelomeric proteins. With regard to the effect brought about by the deletion of rox1 and srb10, correspondence cluster analysis revealed that the transcriptome profile in aerobic conditions is very similar in the wild‐type and both deletion strains. In contrast, however, differences were found during hypoxia between the subgroup formed by wild‐type and the Δrox1 deletant compared with the Δsrb10 deletant. An analysis of selected ORFs responding to hypoxia, in association with a dependence on the regulatory factors studied, made it possible to identify the clusters that are related to different regulatory circuits.
Elliptic Calogero-Moser system from two-dimensional current algebra

We show that elliptic Calogero-Moser system and its Lax operator found by Krichever can be obtained by Hamiltonian reduction from the integrable Hamiltonian system on the cotangent bundle to the central extension of the algebra of SL(N,C) currents.Elliptic deformation of Yang-Mills theory is presented.
Capacity of Zero-Outage Scheme Under Imprecise Channel State Information

The capacity of zero-outage scheme with imprecise channel state information at the transmitter side (CSIT) for frequency flat, single-input multiple-output (SIMO) channels is examined. It is shown that when CSIT is not precise, the receiver signal-to-noise-ratio fluctuates and the scheme suffers from communication outages. Exact analytical expressions characterizing the outage capacity, the additional power required to compensate the effect of noisy CSIT are given and the impact of noisy CSIT on the ergodic capacity is examined.