Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of anaerobic sulfite reduction by Salmonella typhimurium and purification of the anaerobically induced sulfite reductase

Mutants of Salmonella typhimurium that lack the biosynthetic sulfite reductase (cysI and cysJ mutants) retain the ability to reduce sulfite for growth under anaerobic conditions (E. L. Barrett and G. W. Chang, J. Gen. Microbiol., 115:513-516, 1979). Here we report studies of sulfite reduction by a cysI mutant of S. typhimurium and purification of the associated anaerobic sulfite reductase. Sulfite reduction for anaerobic growth did not require a reducing atmosphere but was prevented by an argon atmosphere contaminated with air (less than 0.33%). It was also prevented by the presence of 0.1 mM nitrate, which argues against a strictly biosynthetic role for anaerobic sulfite reduction. Anaerobic growth in liquid minimal medium, but not on agar, was found to require additions of trace amounts (10(-7)M) of cysteine. Spontaneous mutants that grew under the argon contaminated with air also lost the requirement for 10(-7)M cysteine for anaerobic growth in liquid. A role for sulfite reduction in anaerobic energy generation was contraindicated by the findings that sulfite reduction did not improve cell yields, and anaerobic sulfite reductase activity was greatest during the stationary phase of growth. Sulfite reductase was purified from the cytoplasmic fraction of the anaerobically grown cysI mutant and was purified 190-fold. The most effective donor in crude extracts was NADH. NADPH and methyl viologen were, respectively, 40 and 30% as effective as NADH. Oxygen reversibly inhibited the enzyme. Two high-molecular-weight proteins separated by gel filtration (Mr 360,000 and 490,000, respectively) were required for maximal activity with NADH. Indirect evidence, including in vitro complementation experiments with a cysG mutant extract, suggested that the 360,000-Mr component contains siroheme and is the terminal reductase. This component was further purified to near homogeneity and was found to consist of a single subunit of molecular weight 67,500. The anaerobic sulfite reductase showed some resemblance to the biosynthetic sulfite reductase, but apparently it has a unique, as yet unidentified function.
Making heads or tails of phospholipids in mitochondria

Mitochondria are dynamic organelles whose functional integrity requires a coordinated supply of proteins and phospholipids. Defined functions of specific phospholipids, like the mitochondrial signature lipid cardiolipin, are emerging in diverse processes, ranging from protein biogenesis and energy production to membrane fusion and apoptosis. The accumulation of phospholipids within mitochondria depends on interorganellar lipid transport between the endoplasmic reticulum (ER) and mitochondria as well as intramitochondrial lipid trafficking. The discovery of proteins that regulate mitochondrial membrane lipid composition and of a multiprotein complex tethering ER to mitochondrial membranes has unveiled novel mechanisms of mitochondrial membrane biogenesis.
A toolkit for measurement error correction, with a focus on nutritional epidemiology

Exposure measurement error is a problem in many epidemiological studies, including those using biomarkers and measures of dietary intake. Measurement error typically results in biased estimates of exposure‐disease associations, the severity and nature of the bias depending on the form of the error. To correct for the effects of measurement error, information additional to the main study data is required. Ideally, this is a validation sample in which the true exposure is observed. However, in many situations, it is not feasible to observe the true exposure, but there may be available one or more repeated exposure measurements, for example, blood pressure or dietary intake recorded at two time points. The aim of this paper is to provide a toolkit for measurement error correction using repeated measurements. We bring together methods covering classical measurement error and several departures from classical error: systematic, heteroscedastic and differential error. The correction methods considered are regression calibration, which is already widely used in the classical error setting, and moment reconstruction and multiple imputation, which are newer approaches with the ability to handle differential error. We emphasize practical application of the methods in nutritional epidemiology and other fields. We primarily consider continuous exposures in the exposure‐outcome model, but we also outline methods for use when continuous exposures are categorized. The methods are illustrated using the data from a study of the association between fibre intake and colorectal cancer, where fibre intake is measured using a diet diary and repeated measures are available for a subset. © 2014 The Authors. Statistics in Medicine Published by John Wiley & Sons, Ltd.
Lyapunov Theory for Zeno Stability

Zeno behavior is a dynamic phenomenon unique to hybrid systems in which an infinite number of discrete transitions occurs in a finite amount of time. This behavior commonly arises in mechanical systems undergoing impacts and optimal control problems, but its characterization for general hybrid systems is not completely understood. The goal of this paper is to develop a stability theory for Zeno hybrid systems that parallels classical Lyapunov theory; that is, we present Lyapunov-like sufficient conditions for Zeno behavior obtained by mapping solutions of complex hybrid systems to solutions of simpler Zeno hybrid systems defined on the first quadrant of the plane. These conditions are applied to Lagrangian hybrid systems, which model mechanical systems undergoing impacts, yielding simple sufficient conditions for Zeno behavior. Finally, the results are applied to robotic bipedal walking.
Multitalker Speech Separation With Utterance-Level Permutation Invariant Training of Deep Recurrent Neural Networks

In this paper, we propose the utterance-level permutation invariant training (uPIT) technique. uPIT is a practically applicable, end-to-end, deep-learning-based solution for speaker independent multitalker speech separation. Specifically, uPIT extends the recently proposed permutation invariant training (PIT) technique with an utterance-level cost function, hence eliminating the need for solving an additional permutation problem during inference, which is otherwise required by frame-level PIT. We achieve this using recurrent neural networks (RNNs) that, during training, minimize the utterance-level separation error, hence forcing separated frames belonging to the same speaker to be aligned to the same output stream. In practice, this allows RNNs, trained with uPIT, to separate multitalker mixed speech without any prior knowledge of signal duration, number of speakers, speaker identity, or gender. We evaluated uPIT on the WSJ0 and Danish two- and three-talker mixed-speech separation tasks and found that uPIT outperforms techniques based on nonnegative matrix factorization and computational auditory scene analysis, and compares favorably with deep clustering, and the deep attractor network. Furthermore, we found that models trained with uPIT generalize well to unseen speakers and languages. Finally, we found that a single model, trained with uPIT, can handle both two-speaker, and three-speaker speech mixtures.
A coordinated scheduling strategy in multi-cell OFDM systems

A novel coordinated scheduling algorithm for OFDM-based systems in multi-cell scenario is proposed in this paper. The studied algorithm based on the utility function is general for the downlink of networks. The algorithm coordinates the subcarrier assignment over the BS cluster. We first establish the framework for this inter-cell coordinated optimization problem through utility-based method. The goal of the scheduling algorithm is maximizing the aggregate utility of users. Then the globally optimal scheduling strategy is studied by solving the model. Subsequently, a sub-optimal strategy is proposed in practical for simplification. Finally, system level simulation is adopted in Mobile WiMAX system by comparing with existed strategies. The results show that better fairness among users in the network can be achieved by the coordinated scheduling strategy at the cost of a little degradation of average sector throughputs. Besides, the gain of the inter-cell strategy on cell-edge throughput increases with the number of users per sector.
Transmission of Vibrio cholerae Is Antagonized by Lytic Phage and Entry into the Aquatic Environment

Cholera outbreaks are proposed to propagate in explosive cycles powered by hyperinfectious Vibrio cholerae and quenched by lytic vibriophage. However, studies to elucidate how these factors affect transmission are lacking because the field experiments are almost intractable. One reason for this is that V. cholerae loses the ability to culture upon transfer to pond water. This phenotype is called the active but non-culturable state (ABNC; an alternative term is viable but non-culturable) because these cells maintain the capacity for metabolic activity. ABNC bacteria may serve as the environmental reservoir for outbreaks but rigorous animal studies to test this hypothesis have not been conducted. In this project, we wanted to determine the relevance of ABNC cells to transmission as well as the impact lytic phage have on V. cholerae as the bacteria enter the ABNC state. Rice-water stool that naturally harbored lytic phage or in vitro derived V. cholerae were incubated in a pond microcosm, and the culturability, infectious dose, and transcriptome were assayed over 24 h. The data show that the major contributors to infection are culturable V. cholerae and not ABNC cells. Phage did not affect colonization immediately after shedding from the patients because the phage titer was too low. However, V. cholerae failed to colonize the small intestine after 24 h of incubation in pond water—the point when the phage and ABNC cell titers were highest. The transcriptional analysis traced the transformation into the non-infectious ABNC state and supports models for the adaptation to nutrient poor aquatic environments. Phage had an undetectable impact on this adaptation. Taken together, the rise of ABNC cells and lytic phage blocked transmission. Thus, there is a fitness advantage if V. cholerae can make a rapid transfer to the next host before these negative selective pressures compound in the aquatic environment.
Linkage of IL-6 with neutrophil chemoattractant expression in virus-induced ocular inflammation.

PURPOSE Herpes simplex virus (HSV)-1 infection of the murine cornea is known to stimulate a vigorous interleukin (IL)-6 response, but whether this pleiotropic cytokine is an essential participant in corneal inflammation is unclear. This study was designed to compare the early inflammatory response in IL-6 gene-deficient mice to that in wild-type hosts. METHODS Gene knockout and wild-type mice (C57BL/6 background) were infected intracorneally with HSV-1 (strain RE) and observed through clinical examination and immunohistochemistry for the development of corneal opacity. Virus corneal titers were determined by standard plaque assay on Vero cells. Cytokine and chemokine levels in corneal lysates were measured with commercial ELISA kits. RESULTS Corneal opacity in IL-6(-/-) mice was substantially diminished in comparison with IL-6(+/+) hosts 24 to 48 hours after intracorneal viral infection, and corneal levels of (MIP)-2 and MIP-1alpha were significantly reduced. Local administration of IL-6 at the time of infection restored corneal opacity and chemokine levels to that of wild-type hosts. Antibody neutralization of endogenous IL-6 in IL-6(+/+) animals reduced corneal opacity scores and MIP-2 levels to that of IL-6(-/-) mice. Ex vivo studies with excised corneal buttons revealed that uninfected IL-6(-/-) corneas injected with IL-6 produced MIP-2 and MIP-1alpha at levels comparable to that seen in IL-6(+/+) hosts. CONCLUSIONS Collectively, these results suggest that IL-6 promotes corneal inflammation by acting in an autocrine-paracrine fashion to induce resident corneal cells to make MIP-2 and MIP-1alpha, which in turn recruit neutrophils to the virus infection site.
Organization and Dynamics of Plant Chromatin

Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq). DHSs are most frequently associated with various cis -regulatory DNA elements, including promoters, enhancers, and silencers in both animal and plant genomes. Genome-wide identification of DHSs provides an efficient method to interpret previously un-annotated regulatory DNA sequences. In this review, we provide an overview of the historical perspective of DHS research in eukaryotes. We summarize the main achievements of DHS research in model animal species and review the recent progress of DHS research in plants. We finally discuss possible future directions of using DHS as a tool in plant genomics research. © 2014 S. Karger AG, Basel Published online: June 6, 2014 Jiming Jiang Department of Horticulture University of Wisconsin-Madison Madison, WI 53706 (USA) E-Mail jjiang1 @ wisc.edu © 2014 S. Karger AG, Basel 1424–8581/14/1433–0018$39.50/0
When Is a Sprint a Sprint? A Review of the Analysis of Team-Sport Athlete Activity Profile

The external load of a team-sport athlete can be measured by tracking technologies, including global positioning systems (GPS), local positioning systems (LPS), and vision-based systems. These technologies allow for the calculation of displacement, velocity and acceleration during a match or training session. The accurate quantification of these variables is critical so that meaningful changes in team-sport athlete external load can be detected. High-velocity running, including sprinting, may be important for specific team-sport match activities, including evading an opponent or creating a shot on goal. Maximal accelerations are energetically demanding and frequently occur from a low velocity during team-sport matches. Despite extensive research, conjecture exists regarding the thresholds by which to classify the high velocity and acceleration activity of a team-sport athlete. There is currently no consensus on the definition of a sprint or acceleration effort, even within a single sport. The aim of this narrative review was to examine the varying velocity and acceleration thresholds reported in athlete activity profiling. The purposes of this review were therefore to (1) identify the various thresholds used to classify high-velocity or -intensity running plus accelerations; (2) examine the impact of individualized thresholds on reported team-sport activity profile; (3) evaluate the use of thresholds for court-based team-sports and; (4) discuss potential areas for future research. The presentation of velocity thresholds as a single value, with equivocal qualitative descriptors, is confusing when data lies between two thresholds. In Australian football, sprint efforts have been defined as activity >4.00 or >4.17 m·s−1. Acceleration thresholds differ across the literature, with >1.11, 2.78, 3.00, and 4.00 m·s−2 utilized across a number of sports. It is difficult to compare literature on field-based sports due to inconsistencies in velocity and acceleration thresholds, even within a single sport. Velocity and acceleration thresholds have been determined from physical capacity tests. Limited research exists on the classification of velocity and acceleration data by female team-sport athletes. Alternatively, data mining techniques may be used to report team-sport athlete external load, without the requirement of arbitrary or physiologically defined thresholds.
Spironolactone is an antagonist of NRG1‐ERBB4 signaling and schizophrenia‐relevant endophenotypes in mice

Enhanced NRG1‐ERBB4 signaling is a risk pathway in schizophrenia, and corresponding mouse models display several endophenotypes of the disease. Nonetheless, pathway‐directed treatment strategies with clinically applicable compounds have not been identified. Here, we applied a cell‐based assay using the split TEV technology to screen a library of clinically applicable compounds to identify modulators of NRG1‐ERBB4 signaling for repurposing. We recovered spironolactone, known as antagonist of corticosteroids, as an inhibitor of the ERBB4 receptor and tested it in pharmacological and biochemical assays to assess secondary compound actions. Transgenic mice overexpressing Nrg1 type III display cortical Erbb4 hyperphosphorylation, a condition observed in postmortem brains from schizophrenia patients. Spironolactone treatment reverted hyperphosphorylation of activated Erbb4 in these mice. In behavioral tests, spironolactone treatment of Nrg1 type III transgenic mice ameliorated schizophrenia‐relevant behavioral endophenotypes, such as reduced sensorimotor gating, hyperactivity, and impaired working memory. Moreover, spironolactone increases spontaneous inhibitory postsynaptic currents in cortical slices supporting an ERBB4‐mediated mode‐of‐action. Our findings suggest that spironolactone, a clinically safe drug, provides an opportunity for new treatment options for schizophrenia.
The Implications of Visualization Ability and Structure Preview Design for Web Information Search Tasks

This study investigates the effects of users' visualization ability and Web site structure display design on users' performance and memory organization in Web site information search tasks using a browsing strategy. A human-centered design-structure preview-was proposed in this study. Structure preview is a Web site navigation menu in which each menu item serves as a link to one Web page, similar to a menu design in Microsoft Windows 95 and Windows 98. An experiment was conducted in which 40 individuals participated. The experimental design was a 2-factor factorial design. Independent variables were visualization ability (low and high) and Web site design (conventional and structure preview). Twenty participants were identified as users with low visualization ability and 20 participants were identified as users with high visualization ability. Dependent variables were the number of identified items, the number of steps per item, and memory organization. Results indicated that both low- and high-visualization users' performance improved significantly (76.3% more identified items and 83.4% fewer steps per item for low-visualization users; 36.5% more identified items and 78.4% fewer steps per item for high-visualization users) when using the structure preview design than when using the conventional design. When using the conventional design, high-visualization users had significantly better performance (36.9% more identified items and 23.6% fewer steps per item) than low-visualization users. Also, the memory organization of all users (including both low- and high-visualization users) improved significantly (42.9%) when using the structure preview design compared with the conventional design.
Light fidelity (Li-Fi): towards all-optical networking

Motivated by the looming radio frequency (RF) spectrum crisis, this paper aims at demonstrating that optical wireless communication (OWC) has now reached a state where it can demonstrate that it is a viable and matured solution to this fundamental problem. In particular, for indoor communications where most mobile data traffic is consumed, light fidelity (Li-Fi) which is related to visible light communication (VLC) offers many key advantages, and effective solutions to the issues that have been posed in the last decade. This paper discusses all key component technologies required to realize optical cellular communication systems referred to here as optical attocell networks. Optical attocells are the next step in the progression towards ever smaller cells, a progression which is known to be the most significant contributor to the improvements in network spectral efficiencies in RF wireless networks.
Measuring change in undergraduate students' perceptions about aging using the Palmore Facts on Aging Quiz.

Measurements of the effects of receiving information about aging was carried out with a group of 61 undergraduate students enrolled in a class in human development from middle childhood through old age. A comparison group consisted on 61 undergraduate students in a child development class. The Palmore Facts on Aging Quiz (FAQ) was administered before and after a five-week period of instruction about the aging process. Students who received information about aging became more accurate in their perceptions of the process as compared to students in the child development class. The use of the FAQ in gerontological training and assessment is discussed.
Incidence, recurrence, and outcomes of herpes simplex virus eye disease in Olmsted County, Minnesota, 1976-2007: the effect of oral antiviral prophylaxis.

OBJECTIVES To provide an estimate of the incidence of herpes simplex virus (HSV) eye disease in a community-based cohort, and to investigate the effect of prophylactic oral antiviral therapy on HSV recurrences and outcomes. METHODS All Olmsted County, Minnesota, residents diagnosed with ocular HSV from 1976 through 2007 were retrospectively reviewed. The frequency of recurrences and adverse outcomes, such as vision loss or need for surgery, were compared between untreated patients and those treated prophylactically with oral antiviral medication. RESULTS Three hundred ninety-four patients with ocular HSV were identified, yielding an annual incidence of 11.8 per 100,000 people (95% confidence interval [CI], 10.6-13.0). No trends in incidence or adverse outcomes were identified during the 32-year period. Oral antiviral therapy was prescribed in 175 patients. Patients were 9.4 times more likely (95% CI, 5.0-17.9) to have a recurrence of epithelial keratitis, 8.4 times more likely (95% CI, 5.2-13.7) to have a recurrence of stromal keratitis, and 34.5 times more likely (95% CI, 10.8-111.1) to have a recurrence of blepharitis or conjunctivitis if not being treated prophylactically at the time of the recurrence. Twenty patients experienced adverse outcomes, and 17 (85%) were not being treated with oral antiviral medications immediately preceding the adverse event. CONCLUSIONS Oral antiviral prophylaxis was associated with a decreased risk of recurrence of epithelial keratitis, stromal keratitis, conjunctivitis, and blepharitis due to HSV. Patients with adverse outcomes due to ocular HSV were usually not being treated with oral antiviral prophylaxis.