Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence of Genes Associated with Enterotoxigenic and Enterohemorrhagic Escherichia coli in Agricultural Waste Lagoons

ABSTRACT The prevalence among all Escherichia coli bacteria of the LTIIa toxin gene and STII toxin gene, both associated with enterotoxigenic E. coli, and of three genes (stxI, stxII, and eaeA) associated with enterohemorrhagic E. coli was determined in farm waste disposal systems seasonally for 1 year. Single- and nested-PCR results for the number of E. coli isolates carrying each toxin gene trait were compared with a five-replicate most-probable-number (MPN) method. The STII and LTIIa toxin genes were present continuously at all farms and downstream waters that were tested. Nested-MPN-PCR manifested sensitivity increased over that of single-MPN-PCR by a factor of 32 for LTIIa, 10 for STII, and 2 for the stxI, stxII, and eaeA genes. The geometric mean prevalence of each toxin gene within the E. coli community in waste disposal site waters after nested MPN-PCR was 1:8.5 E. coli isolates (1:8.5 E. coli) for the LTIIa toxin gene and 1:4 E. coli for the STII toxin gene. The geometric mean prevalence for the simultaneous occurrence of toxin genes stxI, stxII, and eaeA, was 1:182 E. coli. These findings based on total population analysis suggest that prevalence rates for these genes are higher than previously reported in studies based on surveys of single isolates. With a population-based approach, the frequency of each toxin gene at the corresponding disposal sites and the endemic nature of diseases on farms can be easily assessed, allowing farmers and public health officials to evaluate the risk of infection to animals or humans.
Exercise‐Induced Changes in Plasma Composition Increase Erythrocyte Na+,K+‐ATPase, but not Na+–K+–2Cl− Cotransporter, Activity to Stimulate net and Unidirectional K+ Transport in Humans

We tested the hypothesis that exercise‐induced changes in plasma composition result in peak stimulation of erythrocyte unidirectional K+ (JK,in) and net K+ (JK,net) transport within the first 120 s. In experimental series 1 (7 men; 2 women), plasma [K+] was continuously measured in vitro (37 °C) after the addition of red blood cells (RBCs) obtained from rested subjects (resting RBCs) into an exercise‐simulated plasma (ESP; increased plasma osmolality, [K+], [H+], [lactate] and [adrenaline] (epinephrine)), and JK,net calculated. In experimental series 2 (7 men; 4 women), resting RBCs were incubated in true exercise plasma (TEP) obtained after two 30 s bouts of high intensity leg cycling exercise to determine JK,net and JK,in (via RBC 86Rb accumulation). JK,net of resting RBCs increased from 0.9 ± 28.7 in resting plasma to 285 ± 164 mmol (l RBCs)−1 h−1 in ESP and to 178 ± 60 mmol (l RBCs)−1 h−1 after 10 s in TEP. Both JK,net and JK,in peaked within 10 s of incubation and decreased rapidly during the initial 120 s. The use of inhibitors for the Na+,K+‐ATPase (ouabain) and the Na+‐K+‐2Cl− cotransporter (NKCC; bumetanide) indicated that rapid increases in JK,in and JK,net upon incubation of resting RBCs in TEP were due primarily to increased Na+,K+‐ATPase activity; the NKCC appeared to be involved only when the Na+,K+‐ATPase was blocked. It is concluded that RBCs rapidly increase JK,in and JK,net in response to exercise‐induced changes in plasma composition.
Correntropy-based robust joint sparse representation for hyperspectral image classification

In the joint sparse representation (JSR) model, a test pixel and its spatial neighbors are simultaneously approximated by a sparse linear combination of all training samples, and then the test pixel is classified based on the joint reconstruction residual of each class. Due to the least-squares representation of reconstruction residual, the JSR model is usually sensitive to outliers, such as background and noisy pixels. In order to eliminate the effect of noisy and outliers, we propose a robust correntropy-based JSR (CJSR) model for the hyperspectral image classification. It replaces the traditional square of the Euclidean distance to the correntropy-based metric in measuring the joint approximation error. To solve the correntropy-based joint sparsity model, a half-quadratic optimization technique is developed to convert the original non-convex and nonlinear optimization problem into an iteratively reweighted JSR problem. As a result, the optimization of our model can handle the noise in the spatial neighborhood of each test pixel. It can adaptively assign small weights to noisy pixels and put more emphasis on noise-free pixels. Experiments demonstrate the effectiveness of our model in comparison to the related state-of-the-art sparsity models.
Molecular characterization of environmental and clinical echovirus 6 isolates from Poland, 2006–2014

The aim of this study was to investigate the genetic variability of echovirus 6 (E6) isolates from environmental samples and clinical cases of aseptic meningitis from 2006 to 2014. The analysis of the VP1 region showed the extensive diversity (up to 18.8%) and revealed that E6 circulating in Poland belong to four groups. Environmental strains clustered in three groups excepting the 2012 outbreak group, which shows the sudden introduction of new epidemic variant with Asiatic origin. Data from the study established relationships of E6 from Poland with previously characterized strains and confirmed the importance of both clinical and environmental surveillance. J. Med. Virol. 89:936–940, 2017. © 2016 Wiley Periodicals, Inc.
The role of cathelicidin and defensins in pulmonary inflammatory diseases

Antimicrobial peptides (AMPs) protect the epithelia of mucosal organs like the respiratory or the gastrointestinal tract from invading microorganisms. As an integral part of the innate immune system they display antimicrobial activity against Gram- and Gram-negative bacteria as well as against fungi and enveloped and non-enveloped viruses. Besides their microbicidal effects they have important functions in the regulation of repair and inflammation. AMPs are sometimes referred to as ‘alarmins’ due to their ability to recruit, modulate and activate components of the immune system. In contrast, some AMPs suppress activation of the immune system. AMPs are also involved in tissue repair, cancer biology and angiogenesis. Based on their antimicrobial and immunomodulatoy functions, AMPs are probably involved in the pathogenesis of infectious and inflammatory diseases of the lung. Inborn or acquired deficiencies contribute to susceptibility to infection and colonisation. The potential pro-inflammatory role of AMPs contributes to the disease processes in inflammatory disorders such as asthma, chronic obstructive pulmonary disease, sepsis or pulmonary fibrosis. This review summarises the knowledge about the functions of AMPs in the pulmonary innate host defence system and their role in respiratory disease.
Analysis of the IgG Immune Response to Treponema phagedenis-Like Spirochetes in Individual Dairy Cattle with Papillomatous Digital Dermatitis

ABSTRACT Papillomatous digital dermatitis (PDD) is a major infectious disease of the foot skin in dairy cattle. Treponema phagedenis-like spirochetes have been consistently detected in PDD lesions, and antibodies against these organisms have been demonstrated in affected cattle. However, little is known about the dominant antigens recognized by the immune system of affected cattle. Here, we investigated the IgG immune response to T. phagedenis-like isolates by Western blotting with different sera using whole-cell lysates and extracted glycolipid from 18 and 8 isolates, respectively, including those from different cattle on the same or different farms, isolates from different lesions affecting a single cow, and different isolates from the same lesion affecting a single cow. The reactivity of sera in Western blot assays revealed different banding patterns or showed no bands, suggesting that considerable antigenic variations, including glycolipid, may exist among the isolates, even in those from single individuals. With use of a total of 151 serum samples collected from three groups of cattle, i.e., PDD-positive cows on PDD-positive farms (group A), PDD-negative cows on PDD-positive farms (group B), and cows on PDD-free farms (group C), the levels of IgG antibodies against four T. phagedenis-like isolates were measured by enzyme-linked immunosorbent assay (ELISA). The optical density in groups A and B was significantly higher than that in group C, even though the value varied among the antigens used. Therefore, combinations of multiple Treponema species should be used for serological analysis and the development of a suitable vaccine because of antigenic variations.
Pharmacological and Biochemical Analysis of Interactions between N‐Acetylcysteine and Some Antiepileptic Drugs on Experimental Seizures in Mice

SUMMARY Purpose: In view of a putative role of oxidative stress in the pathophysiology of seizures, this study addressed the interactions between N‐acetylcysteine (NAC), a potent antioxidant and two antiepileptic drugs sodium valproate (SVP) and phenytoin (PHT) on experimental seizures in mice. Methods: The interaction was studied at three fixed ratio combinations (i.e., 1:1, 1:3, and 3:1) in the mouse maximal electroshock (MES) test using isobolographic analysis. Markers of oxidative stress (reduced glutathione [GSH] and malondialdehyde [MDA]) were estimated in the cortex of mice pretreated with either of these drugs alone or their 3:1 ratio combinations at the experimentally determined ED50 values (ED50 exp values). The grip strength and spontaneous alternation behavior (SAB) were also assessed. In addition, serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and calcium levels were estimated. Results: We found an anticonvulsant action of NAC in the MES test. Further, the ED50 exp values for the combinations of PHT and NAC did not differ from the theoretically calculated ED50 values indicating additive effects. In case of SVP and NAC, however, the ED50 exp values were lower than the theoretically calculated ED50 values. The interaction of SVP with NAC at the fixed ratios of 1:3 and 3:1 was found to be synergistic. No significant changes were observed in the grip strength, SAB, cortical GSH and MDA levels, serum AST, ALT, ALP, or calcium levels. Conclusion: Our results thus hold promise for the use of NAC as an adjunct to PHT and SVP therapy.
Characterization of the replication of plasmids containing hr sequences in baculovirus-infected Spodoptera frugiperda cells.

The replication of a series of plasmids, each containing one or more of 6 homologous regions (hrs) from the Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) genome, was investigated in AcMNPV-infected Spodoptera frugiperda cells. Although a construct containing hr2 showed the most efficient replication, the sequences flanking the hr region appeared to influence the levels of replication. Plasmids with non-hr-containing AcMNPV inserts showed greatly reduced replication relative to hr-containing plasmids. A variety of features of hr-containing plasmid replication were characterized. These included the time course of plasmid replication and the influence of plasmid concentration and multiplicity of infection of the helper AcMNPV on replication efficiency. It was found that replicated plasmid DNA was detectable by 36 hr p.i. and plateaued by 60 hr p.i. Under our experimental conditions, plasmid levels of 0.5-2 micrograms/1.25 x 10(6) cells and multiplicities of infection of 0.1 to 10 produced optimal levels of plasmid replication. The transfection procedure was shown to delay viral DNA replication by about 12 hr. Experiments directed toward determining the form of the replicated hr-containing plasmid DNA were conducted using partial restriction enzyme digestion. The results indicated that the AcMNPV-replicated plasmids were composed of high molecular weight concatemers.
Important Histologic Outcome Predictors for Patients With Invasive Ductal Carcinoma of the Breast

The pathologic diagnosis is regarded as the final diagnosis of a disease, and pathologic examination based on tumor histology is very important for the accurate assessment of the biological characteristics of tumors. The purpose of this study was to investigate the histologic factors that accurately predict patient outcome among 1042 patients with invasive ductal carcinoma of the breast. Both well-known histologic factors and our proposed histologic factors were examined according to several tumor statuses using multivariate analysis. This study clearly demonstrated that type 4 invasive ductal carcinomas having fibrotic foci and atypical tumor-stromal fibroblasts within the fibrotic foci are significant outcome predictors for lymph node-negative and lymph node-positive, the pathologic UICC-TNM stage II and III, luminal A-subtype, luminal B-subtype, and equivocal HER2 subtype invasive ductal carcinoma patients. Lymph vessel tumor embolus grades 2 and 3 were significant outcome predictors for lymph node-positive, UICC pTNM stages II and III, luminal A-subtype, and triple-negative invasive ductal carcinoma patients (except lymph vessel tumor embolus grade 2 in luminal A-subtype patients). More than 5 mitotic figures in metastatic carcinoma to the lymph nodes was a significant outcome predictor for lymph node-positive, UICC pTNM stage II, and luminal A-subtype invasive ductal carcinoma patients. A fibrotic focus diameter >8 mm was a significant outcome predictor for UICC pTNM stages I and III invasive ductal carcinoma patients. These findings strongly suggest that these histologic factors are very useful for accurately predicting the outcomes of patients with invasive ductal carcinoma of the breast.
Major Proteome Variations Associated with Cherry Tomato Pericarp Development and Ripening[OA]

Tomato (Solanum lycopersicum) is a model plant for studying fleshy fruit development. Several genetic and molecular approaches have been developed to increase our knowledge about the physiological basis of fruit growth, but very few data are yet available at the proteomic level. The main stages of fruit development were first determined through the dynamics of fruit diameter and pericarp cell number. Then, total proteins were extracted from pericarp tissue at six relevant developmental stages and separated by two-dimensional gel electrophoresis. Protein patterns were markedly different between stages. Proteins showing major variations were monitored. We identified 90 of 1,791 well-resolved spots either by matrix-assisted laser-desorption ionization time-of-flight peptide mass fingerprinting or liquid chromatography-mass spectrometry sequencing and expressed sequence tag database searching. Clustered correlation analysis results pointed out groups of proteins with similar expression profiles during fruit development. In young fruit, spots linked to amino acid metabolism or protein synthesis were mainly expressed during the cell division stage and down-regulated later. Some spots linked to cell division processes could be identified. During the cell expansion phase, spots linked to photosynthesis and proteins linked to cell wall formation transiently increased. In contrast, the major part of the spots related to C compounds and carbohydrate metabolism or oxidative processes were up-regulated during fruit development, showing an increase in spot intensity during development and maximal abundance in mature fruit. This was also the case for spots linked to stress responses and fruit senescence. We discuss protein variations, taking into account their potential role during fruit growth and comparing our results with already known variations at mRNA and metabolite-profiling levels.
Issues and Updates in Emerging Neurologic Viral Infections

This review discusses the recent advances in the identification of viral pathogens and other etiologies responsible for cases of suspected viral encephalitis. The authors describe new molecular diagnostic strategies for identifying novel causes of viral encephalitis, including MassTag PCR, DNA microarrays, and high-throughput DNA pyrosequencing. They also highlight the increasing recognition of immune-mediated causes of encephalitis among those cases previously thought to be viral encephalitis of unknown etiology. Lastly, they review some of the most recent updates in the field of emerging neurologic viral infections impacting the United States, including the neurologic complications of H1N1 virus and the reemergence of dengue virus in the Florida Keys.
Correlation as a Heuristic for Accurate and Comprehensible Ant Colony Optimization Based Classifiers

The primary objective of this research is to propose and investigate a novel ant colony optimization-based classification rule discovery algorithm and its variants. The main feature of this algorithm is a new heuristic function based on the correlation between attributes of a dataset. Several aspects and parameters of the proposed algorithm are investigated by experimentation on a number of benchmark datasets. We study the performance of our proposed approach and compare it with several state-of-the art commonly used classification algorithms. Experimental results indicate that the proposed approach builds more accurate models than the compared algorithms. The high accuracy supplemented by the comprehensibility of the discovered rule sets is the main advantage of this method.
Avian Influenza Virus Subtypes Inside and Outside the Live Bird Markets, 1993–2000: A Spatial and Temporal Relationship

SUMMARY. Between 1993 and 2000, gallinaceous birds, waterfowl, and environmental specimens from the live bird markets (LBMs) of the northeastern United States and non-LBM premises were tested for the presence of avian influenza virus (AIV), pathogenic properties of AIV subtypes, especially of hemagglutinin (H) subtypes H5 and H7, and a possible association between LBM and non-LBM infections. Ten H subtypes of AIV were isolated from the LBM specimens: H1, H2, H3, H4, H5, H6, H7, H9, H10, and H11. During this period, the 10 subtypes also were isolated from birds in non-LBM premises. In the LBMs, subtypes H2, H3, H4, H6, H7, and H11 were present for 5–8 yr despite efforts to clean and disinfect the premises. The H5 or H7 subtypes present during the same year in both LBMs and non-LBMs within a state or in contiguous states were (subtype/year): H5N2/1993, 1999, and H7N2/1994–99. The AIV subtypes including the H5 and H7 that were evaluated for pathogenicity in chickens were low pathogenic. The deduced amino acid sequence at the H cleavage site of H5 and H7 subtypes was consistent with those of low pathogenic AIV. Although the H5N2 and H7N2 subtypes remained low pathogenic, they did undergo mutations and acquired an additional basic amino acid at the H cleavage site; however, the minimum number of basic amino acids in correct sequence (B-X-B-R, where B = basic amino acid, X = need not be basic amino acid, and R = arginine) required for high pathogenicity was lacking. A low pathogenic H5 or H7 subtype may become highly pathogenic by acquiring additional basic amino acids at the H cleavage site. The LBMs have been and will likely continue to be a source of AIV for commercial poultry.
Optimistic Coarse-Grained Cache Semantics for Data Marts

Data marts and caching are two closely related concepts in the domain of multi-dimensional data. Both store pre-computed data to provide fast response times for complex OLAP queries, and for both it must be guaranteed that every query can be completely processed. However, they differ extremely in their update behaviour which we utilise to build a specific data mart extended by cache semantics. In this paper, we introduce a novel cache exploitation concept for data marts - coarse-grained caching - in which the containedness check for a multi-dimensional query is done through the comparison of the expected and the actual cardinalities. Therefore, we subdivide the multi-dimensional data into coarse partitions, the so called cubletets, which allow to specify the completeness criteria for incoming queries. We show that during query processing, the completeness check is done with no additional costs
ON SWAPPING THE STATES OF TWO QUDITS

The SWAP gate has become an integral component of quantum circuit architecture where its primary role is given to permuting the states of two qubits. We consider the question of whether a two-qudit quantum circuit composed entirely from instances of the generalized controlled-NOT gate can be constructed to permute the states of two qudits. Arguing via the signature of a permutation, we demonstrate the impossibility of such circuits for dimensions d ≡ 3 (mod 4).
Neuregulin‐2 is developmentally regulated and targeted to dendrites of central neurons

Neuregulin‐1 (NRG‐1) regulates numerous aspects of neural development and synaptic plasticity; the functions of NRG‐2 and NRG‐3 are presently unknown. As a first step toward understanding how NRGs contribute to distinct aspects of neural development and function, we characterized their regional and subcellular expression patterns in developing brain. The expression of NRG‐1–3 mRNAs was compared postnatally (P0, P7, adult) by using in situ hybridization. NRG‐1 expression is highest at birth, whereas NRG‐2 mRNA levels increase with development; expression of both genes is restricted to distinct brain regions. In contrast, NRG‐3 transcripts are abundant in most brain regions throughout development. NRG‐2 antibodies were generated to analyze protein processing, expression, and subcellular distribution. As with NRG‐1, the transmembrane NRG‐2 proprotein is proteolytically processed in transfected HEK 293 cells and in neural tissues, and its ectodomain is exposed and accumulates on the neuron surface. Despite the structural similarities between NRG‐1 and NRG‐2, we unexpectedly found that NRG‐2 colocalizes with MAP2 in proximal primary dendrites of hippocampal neurons in culture and in vivo, although it is not detectable in axons or in axon terminals. These findings were confirmed with NRG‐2 ectodomain antisera and epitope‐tagged recombinant protein. In cerebellum, NRG‐2 colocalizes with calbindin in proximal dendrites and soma of Purkinje cells. In contrast, NRG‐1 is highly expressed in axons of dissociated hippocampal neurons, as well as in somas and dendrites. The distinct temporal, regional, and subcellular expression of NRG‐2 suggests its unique and nonredundant role in neural function. J. Comp. Neurol. 472:156–172, 2004. Published 2004 Wiley‐Liss, Inc.
Energy-Efficient MAC-Layer Error Recovery for Mobile Multimedia Applications in 3GPP2 BCMCS

Combining broadcast and mobile phone technologies, 3GPP2 has introduced the Broadcast and Multicast Services (BCMCS) architecture to deliver multimedia content over cdma2000 1xEV-DO wireless networks. In designing a mobile device to support multimedia broadcast services, it is important to reduce delay and energy consumption, while maintaining a tolerable level of data loss. We analyse the energy consumed by a mobile device receiving broadcast services, focusing on error recovery using the Reed-Solomon (RS) MAC-layer coding scheme. Our model is based on the energy consumed by each computational component of the RS decoder, which we determined by running the decoding process on a realistic ARM7TDMI testbed with experimentally justified cache sizes, and characterizing the energy consumption accurately with the SNU Energy Explorer. By varying the radio channel conditions, RS coding scheme and other system parameters, we determined energy-efficient cache configurations and operating ranges for each RS encoding scheme, corresponding to given levels of service quality in a video application. We have also found that significant energy can be saved by selecting a size of error control block that is appropriate to the target video quality and the channel conditions at the mobile