Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Lipoteichoic Acid Glycosyltransferase Enzyme Reveals that GW-Domain-Containing Proteins Can Be Retained in the Cell Wall of Listeria monocytogenes in the Absence of Lipoteichoic Acid or Its Modifications

ABSTRACT Listeria monocytogenes is a foodborne Gram-positive bacterial pathogen, and many of its virulence factors are either secreted proteins or proteins covalently or noncovalently attached to the cell wall. Previous work has indicated that noncovalently attached proteins with GW (glycine-tryptophan) domains are retained in the cell wall by binding to the cell wall polymer lipoteichoic acid (LTA). LTA is a glycerol phosphate polymer, which is modified in L. monocytogenes with galactose and d-alanine residues. We identified Lmo0933 as the cytoplasmic glycosyltransferase required for the LTA glycosylation process and renamed the protein GtlA, for glycosyltransferase LTA A. Using L. monocytogenes mutants lacking galactose or d-alanine modifications or the complete LTA polymer, we show that GW domain proteins are retained within the cell wall, indicating that other cell wall polymers are involved in the retention of GW domain proteins. Further experiments revealed peptidoglycan as the binding receptor as a purified GW domain fusion protein can bind to L. monocytogenes cells lacking wall teichoic acid (WTA) as well as purified peptidoglycan derived from a wild-type or WTA-negative strain. With this, we not only identify the first enzyme involved in the LTA glycosylation process, but we also provide new insight into the binding mechanism of noncovalently attached cell wall proteins. IMPORTANCE Over the past 20 years, a large number of bacterial genome sequences have become available. Computational approaches are used for the genome annotation and identification of genes and encoded proteins. However, the function of many proteins is still unknown and often cannot be predicted bioinformatically. Here, we show that the previously uncharacterized Listeria monocytogenes gene lmo0933 likely codes for a glycosyltransferase required for the decoration of the cell wall polymer lipoteichoic acid (LTA) with galactose residues. Using L. monocytogenes mutants lacking LTA modifications or the complete polymer, we show that specific cell wall proteins, often associated with virulence, are retained within the cell wall, indicating that additional cell wall polymers are involved in their retention.
Bazooka is a permissive factor for the invasive behavior of discs large tumor cells in Drosophila ovarian follicular epithelia

Drosophila Bazooka and atypical protein kinase C are essential for epithelial polarity and adhesion. We show here that wild-type bazooka function is required during cell invasion of epithelial follicle cells mutant for the tumor suppressor discs large. Clonal studies indicate that follicle cell Bazooka acts as a permissive factor during cell invasion, possibly by stabilizing adhesion between the invading somatic cells and their substratum, the germline cells. Genetic epistasis experiments demonstrate that bazooka acts downstream of discs large in tumor cell invasion. In contrast, during the migration of border cells, Bazooka function is dispensable for cell invasion and motility, but rather is required cell-autonomously in mediating cell adhesion within the migrating border cell cluster. Taken together, these studies reveal Bazooka functions distinctly in different types of invasive behaviors of epithelial follicle cells, potentially by regulating adhesion between follicle cells or between follicle cells and their germline substratum.
The Baculovirus/Insect Cell System as an Alternative to Xenopus Oocytes

Two plant (Arabidopsis thaliana) K+ transport systems, KAT1 and AKT1, have been expressed in insect cells (Sf9 cell line) using recombinant baculoviruses. Microscopic observation after immunogold staining revealed that the expressed AKT1 and KAT1 polypeptides were mainly associated with internal membranes, but that a minute fraction was targeted to the cell membrane. KAT1 was known, from earlier electrophysiological characterization in Xenopus oocytes, to be an inwardly rectifying voltage-gated channel highly selective for K+, while similar experiments had failed to characterize AKT1. Insect cells expressing KAT1 displayed an exogenous inwardly rectifying K+ conductance reminiscent of that described previously in Xenopus oocytes expressing KAT1. Under similar conditions, cells expressing AKT1 showed a disturbed cell membrane electrical stability that precluded electrophysiological analysis. Use of a baculovirus transfer vector designed so as to decrease the expression level allowed the first electrophysiological characterization of AKT1. The baculovirus system can thus be used as an alternative method when expression in Xenopus oocytes is unsuccessful for electrophysiological characterization of the ion channel of interest. The plant AKT1 protein has been shown in this way to be an inwardly rectifying voltage-gated channel highly selective for K+ ions and sensitive to cGMP.
Self-reported oral parafunctions and pain intensity in temporomandibular disorder patients.

AIM To examine the relationship between different types of self-reported oral parafunctions and pain intensity in patients with temporomandibular disorders (TMD). METHODS Two cohorts of TMD pain patients, 1 comprising 303 patients and the other comprising 226 patients, completed a 12-item oral parafunctions questionnaire as well as the Research Diagnostic Criteria Axis II questionnaire, which includes a characteristic pain intensity score (CPI). Relationships between oral parafunctions and CPI were examined; age and gender were controlled for. The effects of phrasing of the oral parafunction questions were also examined. For 1 cohort, the questions were directed at the mere occurrence of the parafunctions; in the other, the questions addressed the perceived stressfulness of parafunctional behavior to the jaw. RESULTS A principal component analysis of the responses to the questionnaires led to 3 factors (scales) in both cohorts: (1) a BRUX scale for bruxism activities; (2) a BITE scale for biting activities (eg, chewing gum, nails); and (3) a SOFT scale for soft tissue activities (eg, tongue, lips). Statistical significance was reached for 2 of the 6 relationships studied (P < .05), but with a very low explained variance (approximately 3.5%). CONCLUSION No clinically relevant relationships were found between different types of self-reported oral parafunctions and TMD pain complaints.
Digoxin and Risk of Death in Adults With Atrial Fibrillation: The ATRIA-CVRN Study

Background—Digoxin remains commonly used for rate control in atrial fibrillation, but limited data exist supporting this practice and some studies have shown an association with adverse outcomes. We examined the independent association between digoxin and risks of death and hospitalization in adults with incident atrial fibrillation and no heart failure. Methods and Results—We performed a retrospective cohort study of 14 787 age, sex, and high-dimensional propensity score-matched adults with incident atrial fibrillation and no previous heart failure or digoxin use in the AnTicoagulation and Risk factors In Atrial fibrillation-Cardiovascular Research Network (ATRIA-CVRN) study within Kaiser Permanente Northern and Southern California. We examined the independent association between newly initiated digoxin and the risks of death and hospitalization using extended Cox regression. During a median 1.17 (interquartile range, 0.49–1.97) years of follow-up among matched patients with atrial fibrillation, incident digoxin use was associated with higher rates of death (8.3 versus 4.9 per 100 person-years; P<0.001) and hospitalization (60.1 versus 37.2 per 100 person-years; P<0.001). Incident digoxin use was independently associated with a 71% higher risk of death (hazard ratio, 1.71; 95% confidence interval, 1.52–1.93) and a 63% higher risk of hospitalization (hazard ratio, 1.63; 95% confidence interval, 1.56–1.71). Results were consistent in subgroups of age and sex and when using intent-to-treat or on-treatment analytic approaches. Conclusions—In adults with atrial fibrillation, digoxin use was independently associated with higher risks of death and hospitalization. Given other available rate control options, digoxin should be used with caution in the management of atrial fibrillation.
The Relationship between CD27 Negative and Positive B Cell Populations in Human Peripheral Blood

CD27 expression has been used to distinguish between memory and naive B cells in humans. However, low levels of mutated and isotype-switched CD27−IgD− cells are seen in healthy adults, and these are increased in some autoimmune diseases and in the elderly. Thus CD27 is not a universal marker of memory B cells in humans. Various hypotheses have been put forward as to the function of the CD27− memory population. Since we have previously found high-throughput IGHV repertoire analysis useful to distinguish “innate-like” memory B cells (CD27+IgD+), we have employed similar analyses to elucidate the relationship between CD27− and CD27+ memory B cells. IgM+IgD− memory cells in both the CD27+ and CD27− compartments share the unique characteristics of the “innate-like” IgM+IgD+CD27+ cells. The switched CD27+ and CD27− memory cells share a similar IGHV repertoire, having more in common with each other than with “innate-like” memory cells, although it is interesting that IgG2 and IgA2 subclasses of antibody in both switched memory populations have a more “innate-like” repertoire. Clonality analysis shows evidence of a close clonal relationship between the two populations in that both CD27− and CD27+ switched memory cells can be found in the same genealogical tree. The expression of CD27 does not appear to occur in a linear developmental fashion, since we see CD27− cells as precursors of CD27+ cells and vice versa. Despite the similarities, the CDR-H3 repertoire of the CD27− cells is significantly different from both the CD27+IgD+ and CD27+IgD− populations, indicating that perhaps the lack of CD27 might be related to binding properties of the Ig CDR-H3 region.
T'ain't What You Say, It's the Way That You Say It—Left Insula and Inferior Frontal Cortex Work in Interaction with Superior Temporal Regions to Control the Performance of Vocal Impersonations

Historically, the study of human identity perception has focused on faces, but the voice is also central to our expressions and experiences of identity [Belin, P., Fecteau, S. , & Bedard, C. Thinking the voice: Neural correlates of voice perception. Trends in Cognitive Sciences, 8, 129–135, 2004]. Our voices are highly flexible and dynamic; talkers speak differently, depending on their health, emotional state, and the social setting, as well as extrinsic factors such as background noise. However, to date, there have been no studies of the neural correlates of identity modulation in speech production. In the current fMRI experiment, we measured the neural activity supporting controlled voice change in adult participants performing spoken impressions. We reveal that deliberate modulation of vocal identity recruits the left anterior insula and inferior frontal gyrus, supporting the planning of novel articulations. Bilateral sites in posterior superior temporal/inferior parietal cortex and a region in right middle/anterior STS showed greater responses during the emulation of specific vocal identities than for impressions of generic accents. Using functional connectivity analyses, we describe roles for these three sites in their interactions with the brain regions supporting speech planning and production. Our findings mark a significant step toward understanding the neural control of vocal identity, with wider implications for the cognitive control of voluntary motor acts.
Driving Mechanisms for Combustion Instability

The processes affecting the nonlinear acoustic stability of a combustor are examined in an overview fashion. Emphasis is placed on liquid-propellant rocket motors but other systems are briefly mentioned and some broadly applied principles and observations are discussed. A nonlinear wave equation is developed for a two-phase mixture and the roles of various terms in the equations are discussed. A review is made of various combustion processes, their associated characteristic times, and the impacts on stability in certain cases. Many relevant scales for length and time are identified. Special issues for supercritical and transcritical combustion are discussed. Bistable operational domains are shown to be present in some systems, making nonlinear triggering of an instability a possibility. Relations between the natural frequency of oscillation for the combustion chamber and the characteristic combustion times are identified with regard to impact on the combustor stability. The amplitude of the limit cycle and the transient time for limit-cycle development are related to the mean-flow Mach number. The role of shock-wave dissipation in amplitude determination is described.
An evaluation of peer-led STD/HIV prevention work in a public sex environment

This paper describes an independent evaluation of a peer-led STD/HIV prevention intervention conducted by Gay Men Fighting AIDS (GMFA) in a public sex environment (PSE). A variety of quantitative and qualitative research methods were employed to collect data on the intervention process as well as its outcomes. The main aim of the intervention was the distribution of condoms and safer sex literature to PSE users. During a five-month period, over 100,000 condoms and 2,200 safer sex information packs were distributed by GMFA volunteers to the PSE users. Condom provision was identified as the most needed health promotion activity in PSEs in a survey of gay and bisexual men (n = 688) conducted by the evaluators. Data collected showed that condoms provided by GMFA, as well as from other sources, were being used in the PSE. The peer-led focus of the intervention was acceptable to the PSE users. In addition, high levels of commitment and input from the volunteers contributed considerable added value to the intervention. The evaluation found that GMFA was successful in reaching the target population and addressing their needs and demands.
Prediction and Validation of Disease Genes Using HeteSim Scores

Deciphering the gene disease association is an important goal in biomedical research. In this paper, we use a novel relevance measure, called HeteSim, to prioritize candidate disease genes. Two methods based on heterogeneous networks constructed using protein-protein interaction, gene-phenotype associations, and phenotype-phenotype similarity, are presented. In HeteSim_MultiPath (HSMP), HeteSim scores of different paths are combined with a constant that dampens the contributions of longer paths. In HeteSim_SVM (HSSVM), HeteSim scores are combined with a machine learning method. The 3-fold experiments show that our non-machine learning method HSMP performs better than the existing non-machine learning methods, our machine learning method HSSVM obtains similar accuracy with the best existing machine learning method CATAPULT. From the analysis of the top 10 predicted genes for different diseases, we found that HSSVM avoid the disadvantage of the existing machine learning based methods, which always predict similar genes for different diseases. The data sets and Matlab code for the two methods are freely available for download at http://lab.malab. cn/data/HeteSim/index.jsp.
Road2Vec: Measuring Traffic Interactions in Urban Road System from Massive Travel Routes

Good characterization of traffic interactions among urban roads can facilitate traffic-related applications, such as traffic control and short-term forecasting. Most studies measure the traffic interaction between two roads by their topological distance or the correlation between their traffic variables. However, the distance-based methods neglect the spatial heterogeneity of roads’ traffic interactions, while the correlation-based methods cannot capture the non-linear dependency between two roads’ traffic variables. In this paper, we propose a novel approach called Road2Vec to quantify the implicit traffic interactions among roads based on large-scale taxi operating route data using a Word2Vec model from the natural language processing (NLP) field. First, the analogy between transportation elements (i.e., road segment, travel route) and NLP terms (i.e., word, document) is established. Second, the real-valued vectors for road segments are trained from massive travel routes using the Word2Vec model. Third, the traffic interaction between any pair of roads is measured by the cosine similarity of their vectors. A case study on short-term traffic forecasting is conducted with artificial neural network (ANN) and support vector machine (SVM) algorithms to validate the advantages of the presented method. The results show that the forecasting achieves a higher accuracy with the support of the Road2Vec method than with the topological distance and traffic correlation based methods. We argue that the Road2Vec method can be effectively utilized for quantifying complex traffic interactions among roads and capturing underlying heterogeneous and non-linear properties.
Analysis of nanoindentation curves in the case of bulk amorphous polymers

Abstract Load versus displacement curves obtained from nanoindentation experiments on polymers are particularly difficult to analyze due to their complex mechanical and especially time-dependent behavior. The indentation curves obtained on two amorphous polymers (polycarbonate (PC) and polymethyl methacrylate (PMMA)) show an increase in the indentation depth during load hold time. A non-linear time-dependent model shows that this phenomenon could be decomposed in a first part due to a viscoelastic response and a second part assigned both to a viscoelastic and a viscoplastic response. If the first part is not achieved, the values of the elastic modulus computed using the Oliver and Pharr method are abnormally high. If it is achieved, the beginning of the unloading curve presents an abnormality that is linked to the increase in indentation depth during hold load time. Nevertheless, if the load hold time is high enough and if the contact stiffness is calculated from the initial slope of the power fit of the unloading curve, the values of the elastic modulus computed using the Oliver and Pharr method are close to those obtained by tensile tests.
Rainfall can explain adaptive phenotypic variation with high gene flow in the New Holland Honeyeater (Phylidonyris novaehollandiae)

Identifying environmentally driven changes in traits that serve an ecological function is essential for predicting evolutionary outcomes of climate change. We examined population genetic structure, sex-specific dispersal patterns, and morphology in relation to rainfall patterns across an island and three peninsulas in South Australia. The study system was the New Holland Honeyeater (Phylidonyris novaehollandiae), a nectarivorous passerine that is a key pollinator species. We predicted that rainfall-related mechanisms would be driving local adaptation of morphological traits, such that in areas of lower rainfall, where nectar is less available, more insectivorous traits – shorter, deeper bills, longer tarsi, and longer wings – would be favored. The study populations differed in phenotype across the Eyre, Yorke, and Fleurieu Peninsulas and Kangaroo Island despite high gene flow (single continuous population) and sex-biased dispersal (males were philopatric and females dispersed). We tested the role of rainfall in shaping the observed phenotypic differences, and found strong support for our predicted relationships: birds in areas of higher rainfall had higher condition indices, as well as longer bill-head length, deeper bills, and shorter tarsi. Bill depth in males in high-rainfall sites showed signals of stabilizing selection, suggesting local adaptation. In addition to these local indications of selection, a global pattern of directional selection toward larger size for bill-head length, bill-nostril length, and wing length was also observed. We suggest this pattern may reflect an adaptive response to the relatively dry conditions that South Australia has experienced over the last decade. We conclude that rainfall has shaped aspects of phenology in P. novaehollandiae, both locally, with different patterns of stabilizing and directional selection, and globally, with evidence of adaptive divergence at a landscape scale.
On the Monotonicity of the Generalized Marcum and Nuttall ${Q}$ -Functions

Monotonicity criteria are established for the generalized Marcum <i>Q</i> -function, <i>QM</i>(alpha,beta), the standard Nuttall <i>Q</i>-function, <i>QM</i>,<i>N</i>(alpha,beta) , and the normalized Nuttall <i>Q</i>-function, <i>QM</i>,<i>N</i>(alpha,beta), with respect to their real order indices <i>M</i>,<i>N</i>. Besides, closed-form expressions are derived for the computation of the standard and normalized Nuttall <i>Q</i>-functions for the case when <i>M</i>,<i>N</i> are odd multiples of 0.5 and <i>M</i> ges <i>N</i>. By exploiting these results, novel upper and lower bounds for <i>QM</i>,<i>N</i>(alpha,beta) and <i>QM</i>,<i>N</i>(alpha,beta) are proposed. Furthermore, specific tight upper and lower bounds for <i>QM</i>(alpha,beta), previously reported in the literature, are extended for real values of <i>M</i>. The offered theoretical results can be efficiently applied in the study of digital communications over fading channels, in the information-theoretic analysis of multiple-input multiple-output systems and in the description of stochastic processes in probability theory, among others.
The Resurgence of Growth in the Late 1990s: Is Information Technology the Story?

The performance of the U.S. economy over the past several years has been remarkable, including a rebound in labor productivity growth after nearly a quarter century of sluggish gains. To assess the role of information technology in the recent rebound, this paper re-examines the growth contribution of computers and related inputs with the same neoclassical framework that we have used in earlier work. ; Our results indicate that the contribution to productivity growth from the use of information technology - including computer hardware, software, and communication equipment - surged in the second half of the 1990s. In addition, technological advance in the production of computers appears to have contributed importantly to the speed-up in productivity growth. All in all, we estimate that the use of information technology and the production of computers accounted for about two-thirds of the 1 percentage point step-up in productivity growth between the first and second halves of the decade. Thus, to answer the question posed in the title of this paper, information technology largely is the story.