Miracle-dz/UniFAR-FTUs huggingface dataset:
Formate hydrogen lyase mediates stationary-phase deacidification and increases survival during sugar fermentation in acetoin-producing enterobacteria

Two fermentation types exist in the Enterobacteriaceae family. Mixed-acid fermenters produce substantial amounts of lactate, formate, acetate, and succinate, resulting in lethal medium acidification. On the other hand, 2,3-butanediol fermenters switch to the production of the neutral compounds acetoin and 2,3-butanediol and even deacidify the environment after an initial acidification phase, thereby avoiding cell death. We equipped three mixed-acid fermenters (Salmonella Typhimurium, S. Enteritidis and Shigella flexneri) with the acetoin pathway from Serratia plymuthica to investigate the mechanisms of deacidification. Acetoin production caused attenuated acidification during exponential growth in all three bacteria, but stationary-phase deacidification was only observed in Escherichia coli and Salmonella, suggesting that it was not due to the consumption of protons accompanying acetoin production. To identify the mechanism, 34 transposon mutants of acetoin-producing E. coli that no longer deacidified the culture medium were isolated. The mutations mapped to 16 genes, all involved in formate metabolism. Formate is an end product of mixed-acid fermentation that can be converted to H2 and CO2 by the formate hydrogen lyase (FHL) complex, a reaction that consumes protons and thus can explain medium deacidification. When hycE, encoding the large subunit of hydrogenase 3 that is part of the FHL complex, was deleted in acetoin-producing E. coli, deacidification capacity was lost. Metabolite analysis in E. coli showed that introduction of the acetoin pathway reduced lactate and acetate production, but increased glucose consumption and formate and ethanol production. Analysis of a hycE mutant in S. plymuthica confirmed that medium deacidification in this organism is also mediated by FHL. These findings improve our understanding of the physiology and function of fermentation pathways in Enterobacteriaceae.
Flt-3 Ligand Reverses Late Allergic Response and Airway Hyper-Responsiveness in a Mouse Model of Allergic Inflammation1

Flt3 ligand (Flt3-L) is a growth factor for dendritic cells and induces type 1 T cell responses. We recently reported that Flt3-L prevented OVA-induced allergic airway inflammation and suppressed late allergic response and airway hyper-responsiveness (AHR). In the present study we examined whether Flt3-L reversed allergic airway inflammation in an established model of asthma. BALB/c mice were sensitized and challenged with OVA, and AHR to methacholine was established. Then mice with AHR were randomized and treated with PBS or 6 μg of Flt3-L i.p. for 10 days. Pulmonary functions and AHR to methacholine were examined after rechallenge with OVA. Treatment with Flt3-L of presensitized mice significantly suppressed (p < 0.001) the late allergic response, AHR, bronchoalveolar lavage fluid total cellularity, absolute eosinophil counts, and inflammation in the lung tissue. There was a significant decrease in proinflammatory cytokines (TNF-α, IL-4, and IL-5) in bronchoalveolar lavage fluid, with a significant increase in serum IL-12 and a decrease in serum IL-5 levels. There was no significant effect of Flt3-L treatment on serum IL-4 and serum total IgE levels. Sensitization with OVA significantly increased CD11b+CD11c+ cells in the lung, and this phenomenon was not significantly affected by Flt3-L treatment. These data suggest that Flt3-L can reverse allergic airway inflammation and associated changes in pulmonary functions in murine asthma model.
A Simple but Accurate Method for Evaluating Drug-Resistance in Infectious HCVcc System

Use of direct-acting antivirals sometimes causes viral drug resistance, resulting in inefficiency in treated patients in real-world practice. Therefore, how to rapidly and accurately evaluate drug resistance is an urgent problem to be solved for rational use and development of antivirals in the future. Here, we aim to develop a new method by which we can evaluate easily but effectively whether a drug will still be efficient in the future treatment in infectious hepatitis C virus cell culture system. HCV-infected Huh7.5 cells were treated with drugs and the culture supernatants were replaced with fresh culture media containing the same drugs at 24 hours. The supernatants were harvested at 48 hours and incubated with naïve Huh7.5 cells. Intracellular HCV RNAs or proteins in the newly infected cells were extracted and analyzed at 48 hours or longer. Results showed that after being treated with telaprevir mutant viruses were easily detected which were resistant to telaprevir, while after being treated with sofosbuvir drug-resistant viruses did not emerge. In conclusion, the new method is simple and quick but accurate to evaluate whether a drug will be still efficient in the forthcoming therapeutic regimen and whether drug resistance will occur after long-term treatment with drugs.
Similarities and Differences Matter: Considering the Influence of Gender on HIV Prevention Programs for Young Adults in an Urban HBCU

Human Immunodeficiency Virus/Acquired Immune Deficiency Syndrome (HIV/AIDS) disproportionately burdens African American youth and young adults. In studies conducted in Historically Black Colleges and Universities (HBCU) settings, African American youth generally perceive themselves as having a low risk of contracting HIV and sexually transmitted diseases (STDs) despite having higher rates of unprotected sexual encounters, multiple sex partners, and particularly low rates of HIV testing and awareness of HIV status. These findings position HBCUs in a pivotal role for theory-based research and practice to modify behaviors in order to decrease HIV acquisition risk. Get Students Mobilized and Retooled to Transform (SMART) is an interventional research project in an urban HBCU in a northeastern metropolitan area in the US. The project is designed to assess and then address irresponsible behavior among students on college campuses that leads to illicit drug use, excessive alcohol consumption and underage drinking, and risky sexual behaviors that increase the likelihood of acquiring HIV and STDs. As gender plays a critical role in interventions, this article explores gender similarities and differences to inform the planning and implementation of Get SMART and any subsequent projects that address substance and alcohol use and HIV in an HBCU setting. Survey research was conducted to find similar and different factors that may be valuable in implementing and tailoring evidence-based interventions in a predominantly African American campus setting. Survey results revealed that more young adult women consume alcohol and use marijuana than young adult men. Young adult men were also more likely to be tested for HIV when compared to young adult women.
Multi-target tracking control using Continuous Double Auction Parameter Selection

Multifunction sensor resource management can be formulated as a distributed parameter selection problem, whereby parameter selections are sought for each task which maximises the global performance of all tasks, subject to a resource constraint. This paper describes the application of the Continuous Double Auction Parameter Selection (CDAPS) algorithm to the sensor resource management problem, and demonstrates the algorithm on multi-target tracking control scenarios for a multi-function radar. CDAPS is shown to give a significant improvement in performance over conventional rule based methods. The continuous nature of CDAPS allows for the resource allocation to evolve over time instead of in fixed allocation frames, and the algorithm is computationally efficient as only partial participant preferences are computed.
Light‐induced c‐fos in melanopsin retinal ganglion cells of young and aged rodless/coneless (rd/rd cl) mice

Non‐rod, non‐cone ocular photoreceptors have been shown to mediate a range of irradiance detection tasks. The strongest candidates for these receptors are melanopsin‐positive retinal ganglion cells (RGCs). To provide a more complete understanding of these receptors in vivo, we have utilized a mouse that lacks rod and cone photoreceptors (rd/rd cl) and compared these animals to congenic wild‐types. Using real‐time polymerase chain reaction and immunohistochemistry, we address the following. (1) Is Fos expression within these RGCs driven by an input from the rods/cones or is it the product of the intrinsic photosensitivity of these neurons? We demonstrate that most Fos expression across the entire retina is due to the rods/cones, but in the absence of these photoreceptors, light will induce Fos within melanopsin RGCs. (2) Could the reported age‐related decline in circadian photosensitivity of rodents be linked to changes in the population of melanopsin RGCs? We show that old mice experience an ∼ 40% reduction in melanopsin RGCs. (3) Does the loss of inner retinal neurons affect the responses of melanopsin RGCs? Aged (∼ 700 days) rd/rd cl mice lose most of their inner retina but retain the retinal ganglion cell layer. In these mice, the proportion of melanopsin RGCs that express Fos in response to light is significantly reduced. Collectively, our data suggest that melanopsin RGCs form a heterogeneous population of neurons, and that most of the light‐induced c‐fos expression within these cells is associated with the endogenous photosensitivity of these neurons.
A longitudinal twin study of intelligence in the second year.

Data from 408 pairs of identical and same-sex fraternal twins assessed at home and in the laboratory at 14, 20, and 24 months are used to describe cognitive development in the second year and to identify genetic and environmental influences on phenotypic similarity. The primary dependent variables are the Bayley Mental Development Index and separate constructs (based on items from the Bayley and the Sequenced Inventory of Communication Development) to measure nonverbal ability, expressive language, and receptive language. These variables are supplemented with laboratory tests of word comprehension, visual attentiveness, and memory for locations. Various patterns of development emerge for separate constructs, for females versus males on each construct, and for individuals across constructs. These data suggest developmental transitions for many infants during the second year, but the timing of these transitions varies by measure. The dependent variables tend to be intercorrelated and are reasonably stable for individuals, with greater stability late in the second year, suggesting either increasing stability or more effective measurement. Expressive and receptive language scores are correlated and have comparable patterns of change within individuals, but there are also differences (e.g., receptive language accounts for the most variance in MDI at each age and across ages). There are genetic effects on MDI at each age and effects of shared environment at 20 and 24 months. Analyses of separate constructs reveal distinct patterns. Effects on nonverbal abilities are entirely genetic. Effects on language are primarily environmental, but genetic influence emerges for expressive language at 20 and 24 months and for receptive language at 14 months. Visual attentiveness tended to reveal effects comparable to the nonverbal construct, and word comprehension was related to the receptive composite. Scores on the memory for locations task were relatively uninformative. A Cholesky decomposition is used to identify influences that account for the same variance at each age (i.e., promote continuity) and that account for new variance at each assessment (i.e., promote change) and to explore overlap and distinctiveness among measures at each age.
Gaussian Processes for Natural Language Processing

Gaussian Processes (GPs) are a powerful modelling framework incorporating kernels and Bayesian inference, and are recognised as stateof-the-art for many machine learning tasks. Despite this, GPs have seen few applications in natural language processing (notwithstanding several recent papers by the authors). We argue that the GP framework offers many benefits over commonly used machine learning frameworks, such as linear models (logistic regression, least squares regression) and support vector machines. Moreover, GPs are extremely flexible and can be incorporated into larger graphical models, forming an important additional tool for probabilistic inference. Notably, GPs are one of the few models which support analytic Bayesian inference, avoiding the many approximation errors that plague approximate inference techniques in common use for Bayesian models (e.g. MCMC, variational Bayes). 1 GPs accurately model not just the underlying task, but also the uncertainty in the predictions, such that uncertainty can be propagated through pipelines of probabilistic components. Overall, GPs provide an elegant, flexible and simple means of probabilistic inference and are well overdue for consideration of the NLP community. This tutorial will focus primarily on regression and classification, both fundamental techniques of wide-spread use in the NLP community. Within NLP, linear models are near ubiquitous, because they provide good results for many tasks, support efficient inference (including dynamic programming in structured prediction) and support simple parameter interpretation. However, linear models are inherently limited in the types of relationships between variables they can model. Often
Does rumination mediate the relationship between emotion regulation ability and posttraumatic stress disorder?

Background and objectives Trauma-related rumination has been suggested to be involved in the maintenance of posttraumatic stress disorder (PTSD). This view has empirically been supported by extensive evidence using cross-sectional, prospective, and experimental designs. However, it is unclear why trauma survivors engage in rumination despite its negative consequences. The current study aimed to explore the hypothesis that low emotion regulation ability underlies trauma-related rumination. Methods Emotion regulation ability and trauma-related rumination were assessed in 93 road traffic accident survivors 2 weeks post-trauma. In addition, symptom levels of PTSD were assessed at 2 weeks as well as 1, 3, and 6 months follow-up. Results Emotion regulation ability was significantly related to trauma-related rumination as well as levels of PTSD symptoms. In addition, the association between low emotion regulation ability and PTSD was mediated by rumination. Conclusions The findings support the view that rumination is used as a dysfunctional emotion regulation strategy by trauma survivors.
Knowledge Refinement Effectiveness

Electronic knowledge repositories represent one of the fundamental tools for knowledge management (KM) initiatives. This research examines organizational and dyadic factors that determine the effectiveness of knowledge refinement, the process of evaluating, analyzing and optimizing the knowledge object to be stored in a repository. A survey study with a matched-triad design was conducted with 318 authors, validators and users of a global knowledge repository system. Results revealed that perceived procedural justice, expertise gap, communication frequency, and shared understanding significantly influenced the quality of refined knowledge, while perceived procedural justice also positively influenced the quality of initial knowledge contributions. These findings are discussed with respect to future research and managerial practices.
Probabilistic reachability and safe sets computation for discrete time stochastic hybrid systems

In this work probabilistic reachability for controlled discrete time stochastic hybrid systems is investigated. By a suitable formulation of the reachability problem within a stochastic optimal control framework, two complementary interpretations and their corresponding computational techniques are suggested. The results can be of interest for solving safety analysis and control design problems for stochastic hybrid systems, by the computation of maximal probabilistic safe sets and maximally safe policies. They can also be employed to solve regulation problems through the interpretation of the desired operating region for the system as a "safe set". The described methodology is applied to a simple temperature regulation problem
Analysis of Speed Performance In Soccer by a Playing Position and a Sports Level Using a Laser System

Abstract The purpose of this study was to determine the kinematic variables that identify the quality of velocity in soccer players at different competitive levels and playing positions. This study had two independent variables: 1) a competitive level (competitive and non-competitive players); and 2) a playing position, with four levels (central defenders, wide defenders/midfielders, central midfielders and forwards). Forty-two soccer players took part in a 30 m sprint-test, which was measured using a laser sensor-type 1 (LDM301-Jenoptik) at 2000 Hz. Absolute and relative times, average velocities and absolute and relative maximum velocities over 10 m sections were analyzed at 200 Hz with BioLaserSport®. There were no significant differences in average velocity between competitive and non-competitive players; however, the former reached a greater maximum velocity in the 10-20 m section. Average velocity in the 0-10 m section identified specificity among playing positions in competitive players. The forwards were the fastest followed by the central midfielders, the wide defenders/midfielders and the central defenders. No differences were found among the non-competitive players. Average velocity over the 0-10 meter section may be an important indicator when assigning a playing position for competitive players. These results support the use of more accurate systems, such as a laser system, to identify soccer players’ speed qualities (including maximum velocity) during short sprints.
Axonal regeneration from injured dorsal roots into the spinal cord of adult rats

Injury to the central processes of primary sensory neurons produces less profound changes in the expression of growth‐related molecules and less vigorous axonal regeneration than does injury to their peripheral processes. The left L4, L5, and L6 dorsal roots of deeply anaesthetized adult Sprague‐Dawley rats were severed and reanastomosed, and in some animals, the ipsilateral sciatic nerve was crushed to increase the expression of growth‐related molecules. After between 28 days and three months, the sciatic nerve of most animals was injected with transganglionic tracers and the animals were killed 2–3 days later. Other animals were perfused for electron microscopy. Very few regenerating axons entered the spinal cord of the rats without sciatic nerve injuries. Labelled axons, however, were always found in the spinal cord of rats with sciatic nerve injuries. They often entered the cord around blood vessels, ran rostrally within the superficial dorsal horn, and avoided the degenerating white matter. The animals with a conditioning sciatic nerve crush had many more myelinated axons around the dorsal root entry zone (DREZ) and on the surface of the cord. Thus, a conditioning lesion of their peripheral processes increased the ability of the central processes of myelinated A fibres to regenerate, including to sites (such as lamina II) they do not normally occupy. Astrocytes, oligodendrocytes, and meningeal fibroblasts in and around the DREZ may have inhibited regeneration in that region, but growth of the axons into the deep grey matter and degenerated dorsal column was also blocked. J. Comp. Neurol. 410:42–54, 1999. © 1999 Wiley‐Liss, Inc.
Evaluation of Micronutrient (Zinc, Magnesium, and Copper) Levels in Serum and Glycemic Status after Nonsurgical Periodontal Therapy in Type 2 Diabetic Patients with Chronic Periodontitis

Aims and Objectives: To find out the effect of nonsurgical periodontal therapy on serum zinc (Zn), magnesium (Mg), and copper (Cu) concentration and glycemic status in type 2 diabetes with chronic periodontitis (CP). Materials and Methods: One hundred and twenty patients were included in this study, which was further divided into three groups. Group 1 consisted of forty patients with CP, Group 2 consisted of forty patients of CP with controlled diabetes, and Group 3 consisted of forty patients of CP with uncontrolled diabetes. Periodontal parameters such as plaque index, gingival index, bleeding on probing, pocket depth, and clinical attachment levels (CALs) were evaluated. Blood samples were collected to assess the levels of fasting blood sugar, glycosylated hemoglobin, Zn, Mg, and Cu. All parameters were evaluated at baseline and 3 months after nonsurgical periodontal therapy. Results: The results showed statistically significant reduction in all the clinical parameters within the groups except for the CAL in group 1 patients (P = 0.05). The glycemic status also showed a statistically significant reduction after treatment (P < 0.001). The intragroup comparison was taken between the values of micronutrients, showed substantial increase in the levels of both Zn and Mg and decrease in the level of Cu after nonsurgical periodontal treatment (P < 0.001). Conclusion: Patients with diabetes and periodontitis had altered metabolism of Zn, Mg, and Cu contributing to the progression and complication of diabetes mellitus and periodontitis. Nonsurgical periodontal treatment improved the variation and concentration of plasma micronutrients and also the periodontal status and glycemic level.
Metagenomic Analyses of Viruses in Stool Samples from Children with Acute Flaccid Paralysis

ABSTRACT We analyzed viral nucleic acids in stool samples collected from 35 South Asian children with nonpolio acute flaccid paralysis (AFP). Sequence-independent reverse transcription and PCR amplification of capsid-protected, nuclease-resistant viral nucleic acids were followed by DNA sequencing and sequence similarity searches. Limited Sanger sequencing (35 to 240 subclones per sample) identified an average of 1.4 distinct eukaryotic viruses per sample, while pyrosequencing yielded 2.6 viruses per sample. In addition to bacteriophage and plant viruses, we detected known enteric viruses, including rotavirus, adenovirus, picobirnavirus, and human enterovirus species A (HEV-A) to HEV-C, as well as numerous other members of the Picornaviridae family, including parechovirus, Aichi virus, rhinovirus, and human cardiovirus. The viruses with the most divergent sequences relative to those of previously reported viruses included members of a novel Picornaviridae genus and four new viral species (members of the Dicistroviridae, Nodaviridae, and Circoviridae families and the Bocavirus genus). Samples from six healthy contacts of AFP patients were similarly analyzed and also contained numerous viruses, particularly HEV-C, including a potentially novel Enterovirus genotype. Determining the prevalences and pathogenicities of the novel genotypes, species, genera, and potential new viral families identified in this study in different demographic groups will require further studies with different demographic and patient groups, now facilitated by knowledge of these viral genomes.
Reduced Time-Expansion Graphs and Goal Decomposition for Solving Cooperative Path Finding Sub-Optimally

Solving cooperative path finding (CPF) by translating it to propositional satisfiability represents a viable option in highly constrained situations. The task in CPF is to relocate agents from their initial positions to given goals in a collision free manner. In this paper, we propose a reduced time expansion that is focused on makespan sub-optimal solving. The suggested reduced time expansion is especially beneficial in conjunction with a goal decomposition where agents are relocated one by one.