Miracle-dz/UniFAR-FTUs huggingface dataset:
The Type 4 Pili of Enterohemorrhagic Escherichia coli O157:H7 Are Multipurpose Structures with Pathogenic Attributes

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O157:H7 produces long bundles of polar type 4 pili (T4P) called HCP (for hemorrhagic coli pili) that form physical bridges between bacteria associating with human and animal epithelial cells. Here, we sought to further investigate whether HCP possessed other pathogenicity attributes associated with T4P production. Comparative studies performed with wild-type EHEC EDL933 and an isogenic hcpA mutant revealed that HCP play different roles in the biology of this organism. We found that in addition to promoting bacterial attachment to host cells, HCP mediate (i) invasion of epithelial cells, (ii) hemagglutination of rabbit erythrocytes, (iii) interbacterial connections conducive to biofilm formation, (iv) specific binding to host extracellular matrix proteins laminin and fibronectin but not collagen, and (v) twitching motility. Nonadherent laboratory E. coli strain HB101 complemented with hcpABC genes on plasmid pJX22, which specifies for HCP overproduction in EDL933, became hyperadherent and invasive and produced a thick biofilm, suggesting that the presence of HCP confers HB101(pJX22) new attributes otherwise not exhibited by HB101. Analogous to other bacteria in which T4P are involved in the pathogenesis of several infectious diseases, our data strongly suggest that HCP display multiple functions that may contribute to EHEC colonization of different hosts and to virulence, survival, and transmission of this food-borne pathogen.
Performing high efficiency source code static analysis with intelligent extensions

This paper presents an industry practice for highly efficient source code analysis to promote software quality. As a continuous work of previously reported source code analysis system, we researched and developed a few engineering-oriented intelligent extensions to implement more cost-effective extended code static analysis and engineering processes. These include an integrated empirical scan and filtering tool for highly accurate noise reduction, and a new code checking test tool to detect function call mismatch problems, which may lead to many severe software defects. We also extended the system with an automated defect filing and verification procedure. The results show that, for a huge code base of millions of lines, our intelligent extensions not only contribute to the completeness and effectiveness of static analysis, but also establish significant engineering productivity.
Geographic variation in rodent-flea relationships in the presence of black-tailed prairie dog colonies

ABSTRACT We characterized the relationship between fleas and their rodent hosts in the presence of prairie dog colonies and compared them to adjacent assemblages away from colonies. We evaluated the rodent-flea relationship by quantifying prevalence, probability of infestation, flea load, and intensity of fleas on rodents. As prairie dog burrows provide refugia for fleas, we hypothesized that prevalence, flea load, and intensity would be higher for rodents that are associated with blacktailed prairie dog colonies. Rodents were trapped at off- and on-colony grids, resulting in the collection of 4,509 fleas from 1,430 rodents in six study areas. The rodent community composition varied between these study areas. Flea species richness was not different between prairie dog colonies and the surrounding grasslands (p = 0.883) but was positively correlated with rodent species richness (p = 0.055). Prairie dog colonies did not increase the prevalence of fleas (p > 0.10). Flea loads on rodents did not vary between off- and on-colony grids at three of the study areas (p > 0.10). Based on the prevalence, infestation rates, and flea loads, we identified Peromyscus maniculatus, Onychomys leucogaster, and two Neotoma species as important rodent hosts for fleas and Aetheca wagneri, Orchopeus leucopus, Peromyscopsylla hesperomys, Pleochaetis exilis, and Thrassis fotus as the most important fleas associated with these rodents. Prairie dog colonies did not seem to facilitate transmission of fleas between rodent hosts, and the few rodent-flea associations exhibited significant differences between off- and on-colony grids.
The Ku Protein Complex Interacts with YY1, Is Up-Regulated in Human Heart Failure, and Represses α Myosin Heavy-Chain Gene Expression

ABSTRACT Human heart failure is accompanied by repression of genes such as α myosin heavy chain (αMyHC) and SERCA2A and the induction of fetal genes such as βMyHC and atrial natriuretic factor. It seems likely that changes in MyHC isoforms contribute to the poor contractility seen in heart failure, because small changes in isoform composition can have a major effect on the contractility of cardiac myocytes and the heart. Our laboratory has recently shown that YY1 protein levels are increased in human heart failure and that YY1 represses the activity of the human αMyHC promoter. We have now identified a region of the αMyHC promoter that binds a factor whose expression is increased sixfold in failing human hearts. Through peptide mass spectrometry, we identified this binding activity to be a heterodimer of Ku70 and Ku80. Expression of Ku represses the human αMyHC promoter in neonatal rat ventricular myocytes. Moreover, overexpression of Ku70/80 decreases αMyHC mRNA expression and increases skeletal α-actin. Interestingly, YY1 interacts with Ku70 and Ku80 in HeLa cells. Together, YY1, Ku70, and Ku80 repress the αMyHC promoter to an extent that is greater than that with YY1 or Ku70/80 alone. Our results suggest that Ku is an important factor in the repression of the human αMyHC promoter during heart failure.
Bulk RNA degradation by nitrogen starvation‐induced autophagy in yeast

Autophagy is a catabolic process conserved among eukaryotes. Under nutrient starvation, a portion of the cytoplasm is non‐selectively sequestered into autophagosomes. Consequently, ribosomes are delivered to the vacuole/lysosome for destruction, but the precise mechanism of autophagic RNA degradation and its physiological implications for cellular metabolism remain unknown. We characterized autophagy‐dependent RNA catabolism using a combination of metabolome and molecular biological analyses in yeast. RNA delivered to the vacuole was processed by Rny1, a T2‐type ribonuclease, generating 3′‐NMPs that were immediately converted to nucleosides by the vacuolar non‐specific phosphatase Pho8. In the cytoplasm, these nucleosides were broken down by the nucleosidases Pnp1 and Urh1. Most of the resultant bases were not re‐assimilated, but excreted from the cell. Bulk non‐selective autophagy causes drastic perturbation of metabolism, which must be minimized to maintain intracellular homeostasis.
Caveolin Interacts with the Angiotensin II Type 1 Receptor during Exocytic Transport but Not at the Plasma Membrane*

The mechanisms involved in angiotensin II type 1 receptor (AT1-R) trafficking and membrane localization are largely unknown. In this study, we examined the role of caveolin in these processes. Electron microscopy of plasma membrane sheets shows that the AT1-R is not concentrated in caveolae but is clustered in cholesterol-independent microdomains; upon activation, it partially redistributes to lipid rafts. Despite the lack of AT1-R in caveolae, AT1-R·caveolin complexes are readily detectable in cells co-expressing both proteins. This interaction requires an intact caveolin scaffolding domain because mutant caveolins that lack a functional caveolin scaffolding domain do not interact with AT1-R. Expression of an N-terminally truncated caveolin-3, CavDGV, that localizes to lipid bodies, or a point mutant, Cav3-P104L, that accumulates in the Golgi mislocalizes AT1-R to lipid bodies and Golgi, respectively. Mislocalization results in aberrant maturation and surface expression of AT1-R, effects that are not reversed by supplementing cells with cholesterol. Similarly mutation of aromatic residues in the caveolin-binding site abrogates AT1-R cell surface expression. In cells lacking caveolin-1 or caveolin-3, AT1-R does not traffic to the cell surface unless caveolin is ectopically expressed. This observation is recapitulated in caveolin-1 null mice that have a 55% reduction in renal AT1-R levels compared with controls. Taken together our results indicate that a direct interaction with caveolin is required to traffic the AT1-R through the exocytic pathway, but this does not result in AT1-R sequestration in caveolae. Caveolin therefore acts as a molecular chaperone rather than a plasma membrane scaffold for AT1-R.
HPSVM: Heterogeneous Parallel SVM with Factorization Based IPM Algorithm on CPU-GPU Cluster

Support vector machine (SVM) is a supervised method widely used in the statistical classification and regression analysis. SVM training can be solved via the interior point method (IPM) with the advantages of low storage, fast convergence and easy parallelization. However, it is still confronted with the challenges of training speed and memory use. In this paper, we propose a parallel primal-dual IPM algorithm based on the incomplete Cholesky factorization (ICF) for efficiently training large-scale SVMs, named HPSVM, on CPU-GPU cluster. Our approach is distinguished from earlier work in that it is specifically designed to take maximal advantage of the CPU-GPU collaborative computation with the dual buffers 3-stage pipeline mechanism, and efficiently handles large-scale training datasets. In HPSVM, the heterogeneous hierarchical memory is fully explored to alleviate the bottleneck for optimizing data transfer, and the programming paradigm is presented to build an efficient collaboration mechanism between CPU and GPU. Comprehensive experiments show that HPSVM is up to 11 times faster than the CPU version on real datasets.
Far-field limit of PFA for SAR moving target imaging

In this paper, a new derivation of the polar format algorithm (PFA) for spotlight synthetic aperture radar (SAR) imaging is presented, which is useful when investigating its response to the moving target. Our derivation starts with examining the mostly adopted implementation of the PFA, i.e., the separable 1-D range and azimuth resampling procedures for their roles in range cell migration (RCM) correction, respectively. It is shown that the former performs RCM pre-deformation, while the latter is substantially the combination of RCM linearization and the keystone transform (KT), i.e., a well-known technique for SAR imaging of moving targets. The new formulation approach is applied to analyze the moving target. The far-field limit of the PFA for moving target focusing is derived, which can be used to predict the target's impulse response function (IRF). The presented work might be helpful when considering a SAR system with the capability of ground moving target indication and imaging (GMTI&Im).
PERAN IKLIM ORGANISASI TERHADAP WORK ENGAGEMENT DENGAN OPTIMISME SEBAGAI MEDIATOR

Work engagement telah banyak diteliti termasuk didalamnya antesedennya yaitu job resources dan personal resources. Meskipun demikian sangat sedikit studi yang menunjukkan prediktor maupun hasil dari work engagement yang secara berkelanjutan. Terdapat enam komponen kehidupan kerja yang berpotensi sebagai jalan untuk mengonsepkan climate for engagement. Ketika diukur sebagai konstruk iklim (pada tingkat unit atau organisasi), enam komponen kehidupan kerja (beban kerja, kontrol, reward, komunitas, keadilan, dan nilai-nilai) dapat mempengaruhi persepsi karyawan terhadap tuntutan pekerjaan dan sumber daya kerja, yang pada gilirannya mempengaruhi work engagement. Sementara pada satu sisi optimisme menjadi lebih menonjol dan merupakan prediktor yang lebih baik terhadap work engagement di bawah kondisi kerja tertentu. Hasil analisis menunjukkan bahwa optimisme dapat menjadi mediator parsial atas pengaruh iklim organisasi terhadap work engagement
Routing and Data Aggregation toward a High Speed Sink in Wireless Sensor Networks

In this work, we study the impact of data aggregation in WSNs with mobile sink nodes that can move at higher speeds. In these cases, propagated queries cannot be answered by using the sink's position when the query was sent, since the sink node will probably be elsewhere. Therefore, conventional data aggregation schemes may not be appropriate due to this high speed. Thus, we propose and evaluate the performance of three new algorithms for data routing and aggregation in WSNs when the sink is moving at a high speed. These algorithms explore the sink movement to create a routing graph composed of the union paths that intersect the sink's trajectory. At each hop, the sink speed and current network delays are used as metric to guide in-network data aggregation. Our results clearly show significant energy savings and efficient data delivery achieved by the proposed algorithms in different scenarios.
Antecedents and implications of uncertainty in management

Purpose – The purpose of this paper is to explain the antecedents of environmental uncertainty in management using a historical framework. The goal of developing passion and compassion in management practice and research cannot be achieved unless a better understanding is developed of the main challenge facing researchers and practitioners – uncertainty.Design/methodology/approach – The antecedents of uncertainty in management are explored using a historical framework. This enables the generation of insights into the nature and use of uncertainty over the decades.Findings – The importance of environmental uncertainty is escalating. The paper's historical, philosophical and critical view helps scholars explain and interpret uncertainty within their own research and formulate new research questions.Originality/value – Understanding the epistemological assumptions underlying paradigms will better enable researchers and practitioners to face a future filled with uncertainty and equivocality.
Distance matrices as invariant features for classifying MoCap data

This work introduces a new representation for Motion Capture data (MoCap) that is invariant under rigid transformation and robust for classification and annotation of MoCap data. This representation relies on distance matrices that fully characterize the class of identical postures up to the body position or orientation. This high dimensional feature descriptor is tailored using PCA and incorporated into an action graph based classification scheme. Classification experiments on publicly available data show the accuracy and robustness of the proposed MoCap representation.
Continuous versus single drainage of milk from the bovine mammary gland during a 24 hour period

Five primiparous and five multiparous cows were used to determine if mammary cisternal storage of milk during a 24 h period of milk accumulation limited milk secretion. In addition, we investigated if there is a parity effect for the capacity of the mammary cisternal compartment to hold a 24 h accumulation of milk secretion, and studied the movement of milk from the alveolar compartment into the cisternal compartment. All cows were fitted with catheters in all teats in order to collect cisternal and alveolar milk fractions separately. For a 24 h period of milk accumulation, the milk was drained once (after 24 h) from one side of the udder (OD), and continuously from the other side of the udder (CD). There was no significant parity effect for cisternal, alveolar and total milk volumes at 24 h. Therefore, data from primi‐ and multiparous cows were pooled for subsequent analyses. Cisternal milk volume from CD glands was higher than that from OD glands (P < 0.01), indicating that cisternal storage of milk in the mammary gland may be limiting to milk secretion during 24 h milking intervals. Alveolar volumes did not differ between OD and CD, but, as a result of the higher cisternal milk volume, total milk volume was highest in the CD glands (P = 0.05). Movement of milk from the alveolar into the cisternal compartment was intermittent. Moreover, analyses of the slopes of individual milk accumulation profiles of the first 6 h of accumulation revealed that the cisternal compartment starts filling immediately following milking, although the rate of filling is relatively low until 7–8 h postmilking.
Social identity-based motivation modulates attention bias toward negative information: an event-related brain potential study

Research has demonstrated that people readily pay more attention to negative than to positive and/or neutral stimuli. However, evidence from recent studies indicated that such an attention bias to negative information is not obligatory but sensitive to various factors. Two experiments using intergroup evaluative tasks (Study 1: a gender-related groups evaluative task and Study 2: a minimal-related groups evaluative task) was conducted to determine whether motivation to strive for a positive social identity – a part of one's self-concept – drives attention toward affective stimuli. Using the P1 component of event-related brain potentials (ERPs) as a neural index of attention, we confirmed that attention bias toward negative stimuli is not mandatory but it can depend on a motivational focus on affective outcomes. Results showed that social identity-based motivation is likely to bias attention toward affectively incongruent information. Thereby, early onset processes – reflected by the P1 component – appeared susceptible to top-down attentional influences induced by the individual's motivation to strive for a positive social identity.
Discounting in Pigeons When the Choice is between Two Delayed Rewards: Implications for Species Comparisons

Studies of delay discounting typically have involved choices between smaller, immediate outcomes and larger, delayed outcomes. In a study of delay discounting in humans, Green et al. (2005) added a period of time prior to both outcomes, creating a delay common to both. They found that the subjective value of the more delayed reward was well described by a hyperboloid discounting function and that the degree to which that outcome was discounted decreased as the common delay increased. In two experiments, we examined the effect of adding a common delay on the discounting of food rewards in pigeons. In Experiment 1, an adjusting-amount procedure was used to establish discounting functions when the common delay was 0, 3, 5, and 10 s, and different stimuli signaled time to the smaller, sooner and larger, later rewards. In contrast to humans, the pigeons showed increases in the degree of discounting when a common delay was added. In Experiment 2, the delay common to both rewards and the delay unique to the larger, later reward were each specifically signaled. With this procedure, the degree of discounting decreased as the common delay increased, a result consistent with that obtained with humans (Green et al., 2005). These findings reveal fundamental similarities between pigeons’ and humans’ choice behavior, and provide strong interspecies support for the hypothesis that choice between delayed outcomes is based on comparison of their hyperbolically discounted present subjective values.
Tramadol for neuropathic pain.

BACKGROUND Peripheral neuropathic pains often include symptoms such as burning or shooting sensations, abnormal sensitivity to normally painless stimuli, or an increased sensitivity to normally painful stimuli. Neuropathic pain is a common symptom in many diseases of the peripheral nervous system. OBJECTIVES We aimed to review systematically the evidence from randomised controlled trials for the efficacy of tramadol in treating neuropathic pain. SEARCH STRATEGY We searched the Cochrane Neuromuscular Disease Group Trials Register (June 2005), MEDLINE (January 1966 to June 2005), EMBASE (January 1980 to June 2005), and LILACS (January 1982 to June 2005) for randomised and quasi-randomised controlled trials. We also searched bibliographies of published trials. SELECTION CRITERIA We included randomised and quasi-randomised controlled trials comparing tramadol with placebo, other pain relieving treatment, or no treatment in people of both sexes and all ages with neuropathic pain of all degrees of severity. DATA COLLECTION AND ANALYSIS Two authors extracted data and scored trial quality. We calculated relative risks and numbers needed to treat for effectiveness and adverse effects. MAIN RESULTS We identified six eligible trials, four comparing tramadol with placebo, one comparing tramadol with clomipramine, and one comparing tramadol with morphine. All four trials comparing tramadol with placebo showed a significant reduction in neuropathic pain with tramadol. Three of the trials which compared tramadol to placebo (total 269 participants) were combined in a meta-analysis. The number needed to treat with tramadol compared to placebo to reach at least 50% pain relief was 3.8 (95% confidence interval 2.8 to 6.3). There were insufficient data to draw conclusions about the effectiveness of tramadol compared to either clomipramine or morphine.Only one trial considered subcategories of neuropathic pain. It found a significant therapeutic effect of tramadol on paraesthesiae, allodynia, and touch evoked pain. Numbers needed to harm were calculated for side effects resulting in withdrawal from the placebo controlled trials. Three trials provided these data, and the combined number needed to harm was 8.3 (95% confidence interval 5.6 to 17). AUTHORS' CONCLUSIONS Tramadol is an effective treatment for neuropathic pain.
The relationship between procrastination, delay of gratification, and job satisfaction among high school teachers

The present study aimed at determining whether a significant relationship exists between procrastination, delay of gratification, and job satisfaction, with work-related stress as an intervening variable among high school teachers. The sample consisted of 150 high school teachers from Karachi, Pakistan. The analysis showed a negative correlation between procrastination and job satisfaction, and a positive correlation between delay of gratification and job satisfaction. Also, procrastination and delay of gratification were significant predictors of work-related stress, and work-related stress was also a significant predictor of job satisfaction. In conclusion, when the teachers are not procrastinating on their job and score high on delay of gratification they will be more satisfied with their job and feel less stressed.
Object categories detection with incorporated geometric context

In this paper, we study object categories detection with a variety of geometric contexts. Usually, object categories are always associated with certain context information. It can help to remove false positive detection. With geometric contextual features, a support vector machine is trained to re-evaluate the initial detection results. Moreover, for the case of that there are determined object categories in an image and the region where an object exists is known, we convert the problem of object categories detection into the one of classification of several object categories. The region can be classified as the one with maximal initial detection score. Alternatively, the detection score for every object category model can be the re-evaluated result of a SVM trained with initial detection score and related geometric context feature. The proposed methods are verified on the dataset of PASCAL VOC 2010. The experimental results demonstrate that accuracy of detection can be improved further with the help of geometric context.