Miracle-dz/UniFAR-FTUs huggingface dataset:
The SaeRS Two-Component System Controls Survival of Staphylococcus aureus in Human Blood through Regulation of Coagulase

The SaeRS two-component system plays important roles in regulation of key virulence factors and pathogenicity. In this study, however, we found that the deletion mutation of saeRS enhanced bacterial survival in human blood, whereas complementation of the mutant with SaeRS returned survival to wild-type levels. Moreover, these phenomena were observed in different MRSA genetic background isolates, including HA-MRSA WCUH29, CA-MRSA 923, and MW2. To elucidate which gene(s) regulated by SaeRS contribute to the effect, we conducted a series of complementation studies with selected known SaeRS target genes in trans. We found coagulase complementation abolished the enhanced survival of the SaeRS mutant in human blood. The coa and saeRS deletion mutants exhibited a similar survival phenotype in blood. Intriguingly, heterologous expression of coagulase decreased survival of S. epidermidis in human blood. Further, the addition of recombinant coagulase to blood significantly decreased the survival of S. aureus. Further, analysis revealed staphylococcal resistance to killing by hydrogen peroxide was partially dependent on the presence or absence of coagulase. Furthermore, complementation with coagulase, but not SaeRS, returned saeRS/coa double mutant survival in blood to wild-type levels. These data indicate SaeRS modulates bacterial survival in blood in coagulase-dependent manner. Our results provide new insights into the role of staphylococcal SaeRS and coagulase on bacterial survival in human blood.
Influence of Powder Size on Production Parameters and Properties of Syntactic Invar Foams Produced by Means of Metal Powder Injection Moulding

The sintering behavior and the mechanical properties of syntactic foams produced by means of metal‐powder injection moulding depend on the interaction of the metal matrix and the integrated hollow spheres. In order to investigate these mechanisms, Ni‐powder size was varied in the production of FeNi36‐syntactic foams with integrated hollow micro glass spheres. For mechanical characterization tensile tests and RFDA‐measurements were performed as the respective parameters were expected to react most sensitively upon variations of the foam structure.
The Reflective Cracking in Flexible Pavements

Abstract Reflective cracking is a major concern for engineers facing the problem of road maintenance and rehabilitation. The problem appears due to the presence of cracks in the old pavement layers that propagate into the pavement overlay layer when traffic load passes over the cracks and due to the temperature variation. The stress concentration in the overlay just above the existing cracks is responsible for the appearance and crack propagation throughout the overlay. The analysis of the reflective cracking phenomenon is usually made by numerical modeling simulating the presence of cracks in the existing pavement and the stress concentration in the crack tip is assessed to predict either the cracking propagation rate or the expected fatigue life of the overlay. Numerical modeling to study reflective cracking is made by simulating one crack in the existing pavement and the loading is usually applied considering the shear mode of crack opening. Sometimes the simulation considers the mode I of crack opening, mainly when temperature effects are predominant.
Optimized Hybrid Modulation Strategy for AC Bypass Transformerless Single-Phase Photovoltaic Inverters

The full-bridge inverter, widely used for single-phase photovoltaic grid-connected applications, presents a leakage current issue. Therefore, an AC bypass branch is introduced to overcome this challenge. Nevertheless, existing modulation strategies entail drawbacks that should be addressed. One is the zero-crossing distortion (ZCD) of the AC current caused by neglecting the AC filter inductor voltage. Another is that the system cannot deliver reactive power because the AC bypass branch switches at the power frequency. To address these problems, this work proposes an optimized hybrid modulation strategy. To reduce ZCD, the phase angle of the inverter output voltage reference is shifted, thereby compensating for the neglected leading angle. To generate the reactive power, the interval of the negative power output is calculated using the power factor. In addition, the freewheeling switch is kept on when power is flowing into the grid and commutates at a high frequency when power is fed back to the DC side. In this manner, the dead-time insertion in the high-frequency switching area is minimized. Finally, the performances of the proposed modulation strategy and traditional strategies are compared on a universal prototype inverter. Experimental results validate the theoretical analysis.
Experimental evaluation of Physically Unclonable Functions in 65 nm CMOS

We present a silicon characterization vehicle implementing six different constructions of intrinsic Physically Unclonable Functions (PUFs). The design contains four different memory-based PUFs, one of which is a novel buskeeper PUF, and two different delay-based PUFs. Test chips are fabricated in 65 nm Low Power (LP) technology, using a standard cell ASIC design flow for the memory-based PUFs and a full custom flow for the delay-based ones. This test vehicle enables a comprehensive experimental evaluation of individual PUF implementations as well as a comparative analysis across different PUF types for the same silicon technology. PUF responses are obtained from 192 device samples and the uniqueness and reliability of the implemented PUFs are evaluated. In addition, the effects of varying temperature and silicon device ageing on the PUF characteristics are extensively studied.
Trends and Developments in Bioinformatics in 2010: Prospects and Perspectives

Summary Objectives To survey major developments and trends in the field of Bioinformatics in 2010 and their relationships to those of previous years, with emphasis on long-term trends, on best practices, on quality of the science of informatics, and on quality of science as a function of informatics. Methods A critical review of articles in the literature of Bioinformatics over the past year. Results Our main results suggest that Bioinformatics continues to be a major catalyst for progress in Biology and Translational Medicine, as a consequence of new assaying technologies, most predominantly Next Generation Sequencing, which are changing the landscape of modern biological and medical research. These assays critically depend on bioinformatics and have led to quick growth of corresponding informatics methods development. Clinical-grade molecular signatures are proliferating at a rapid rate. However, a highly publicized incident at a prominent university showed that deficiencies in informatics methods can lead to catastrophic consequences for important scientific projects. Developing evidence-driven protocols and best practices is greatly needed given how serious are the implications for the quality of translational and basic science. Conclusions Several exciting new methods have appeared over the past 18 months, that open new roads for progress in bioinformatics methods and their impact in biomedicine. At the same time, the range of open problems of great significance is extensive, ensuring the vitality of the field for many years to come.
Imputation for transcription factor binding predictions based on deep learning

Understanding the cell-specific binding patterns of transcription factors (TFs) is fundamental to studying gene regulatory networks in biological systems, for which ChIP-seq not only provides valuable data but is also considered as the gold standard. Despite tremendous efforts from the scientific community to conduct TF ChIP-seq experiments, the available data represent only a limited percentage of ChIP-seq experiments, considering all possible combinations of TFs and cell lines. In this study, we demonstrate a method for accurately predicting cell-specific TF binding for TF-cell line combinations based on only a small fraction (4%) of the combinations using available ChIP-seq data. The proposed model, termed TFImpute, is based on a deep neural network with a multi-task learning setting to borrow information across transcription factors and cell lines. Compared with existing methods, TFImpute achieves comparable accuracy on TF-cell line combinations with ChIP-seq data; moreover, TFImpute achieves better accuracy on TF-cell line combinations without ChIP-seq data. This approach can predict cell line specific enhancer activities in K562 and HepG2 cell lines, as measured by massively parallel reporter assays, and predicts the impact of SNPs on TF binding.
Ascites analysis by a microfluidic chip allows tumor-cell profiling

Significance Serial molecular analyses of tumor cells during treatment- and biopsy-driven clinical trials are emerging norms for many cancers. Yet surgical and image-guided biopsies are expensive and invasive, explaining why alternative sources for tumor cells are being sought. In ovarian cancer (and other abdominopelvic cancers), abdominal fluid buildup (ascites) occurs frequently. We demonstrate that ascites tumor cells (ATCs) present a valuable source of tumor cells, rendering ascites another form of “liquid biopsy. ” We evaluated 85 ovarian cancer-related markers and developed a unique, low cost miniaturized microfluidic ATC chip for on-chip enrichment and molecular profiling using small amounts of ascites. This approach could expand the utility of ATCs within cytotoxic and/or molecularly targeted ovarian cancer therapeutic trials. Ascites tumor cells (ATCs) represent a potentially valuable source of cells for monitoring treatment of ovarian cancer as it would obviate the need for more invasive surgical biopsies. The ability to perform longitudinal testing of ascites in a point-of-care setting could significantly impact clinical trials, drug development, and clinical care. Here, we developed a microfluidic chip platform to enrich ATCs from highly heterogeneous peritoneal fluid and then perform molecular analyses on these cells. We evaluated 85 putative ovarian cancer protein markers and found that nearly two-thirds were either nonspecific for malignant disease or had low abundance. Using four of the most promising markers, we prospectively studied 47 patients (33 ovarian cancer and 14 control). We show that a marker set (ATCdx) can sensitively and specifically map ATC numbers and, through its reliable enrichment, facilitate additional treatment-response measurements related to proliferation, protein translation, or pathway inhibition.
The Influence of Physical Activity and Sedentary Behavior on Living to Age 85 Years Without Disease and Disability in Older Women

Background Whether physical activity (PA) and sedentary behavior influence the odds of women living to age 85 years without chronic disease or disability is not well described. Methods Participants of the Women's Health Initiative (n = 49,612) were categorized based on health status by age 85 years: (i) lived without developing major chronic disease or mobility disability ("healthy"); (ii) lived and developed mobility disability with or without disease; (iii) lived and developed major chronic disease, but not mobility disability; and (iv) died before their 85th birth year. Multinomial logistic regression models that adjusted for covariates such as age, race/ethnicity, and body size estimated associations of self-reported PA and sitting time on developing major disease or mobility disability or dying before age 85 relative to being healthy. Results Mean ± SD baseline age was 70.2 ± 3.6 years. Distributions were: 22% healthy, 23% had mobility disability, 26% had major disease, and 29% died. Relative to those with high total PA, the adjusted odds ratios (OR) (confidence intervals [CI]) for mobility disability was 1.6 (1.4-1.7), 1.2 (1.1-1.3), and 1.1 (1.0-1.2) for women with no, low, and moderate total PA, respectively (p-trend < .001). The corresponding covariate-adjusted OR (CI) for mortality was 1.7 (1.5-1.8), 1.2 (1.1-1.3), and 1.0 (1.0-1.1) (p-trend < .001). Total PA was not associated with developing chronic disease before age 85 years. Sitting ≥10 relative to <5 hours per day increased the odds of mobility disability (1.1, CI: 1.0-1.3) and mortality (1.2, CI: 1.0-1.3) prior to age 85 years (p < .001). Conclusions Increasing PA to recommended levels and reducing sitting time are modifiable behaviors that may improve healthy aging in older women.
Audience Activity Recommendation Using Stacked-LSTM Based Sequence Learning

Recommender systems are used to suggest products to audiences by employing a similarity metric. One of the problem of such systems is that it does not incorporate the context of time. As result, it is not possible to change recommendation as audiences' preferences changes over time. In this paper, we will be presenting a solution based on recurrent neural network to alleviate this problem and highlight a use case on how recurrent neural network model can help us build a real-time recommender system. We will also discuss regarding the comparative study on the performance of different types of recurrent neural network models for the recommendation task.
Betacellulin regulates schwann cell proliferation and myelin formation in the injured mouse peripheral nerve

When a nerve fiber is cut or crushed, the axon segment that is separated from the soma degenerates distal from the injury in a process termed Wallerian degeneration (WD). C57BL/6OlaHsd‐WldS (WldS) mutant mice exhibit significant delays in WD. This results in considerably delayed Schwann cell and macrophage responses and thus in impaired nerve regenerations. In our previous work, thousands of genes were screened by DNA microarrays and over 700 transcripts were found to be differentially expressed in the injured sciatic nerve of WldS compared with wild‐type (WT) mice. One of these transcripts, betacellulin (Btc), was selected for further analysis since it has yet to be characterized in the nervous system, despite being known as a ligand of the ErbB receptor family. We show that Btc mRNA is strongly upregulated in immature and dedifferentiated Sox2+ Schwann cells located in the sciatic nerve distal stump of WT mice, but not WldS mutants. Transgenic mice ubiquitously overexpressing Btc (Tg‐Btc) have increased numbers of Schmidt‐Lantermann incisures compared with WT mice, as revealed by Coherent anti‐Stokes Raman scattering (CARS). Tg‐Btc mice also have faster nerve conduction velocity. Finally, we found that deficiency in Btc reduces the proliferation of myelinating Schwann cells after sciatic nerve injury, while Btc overexpression induces Schwann cell proliferation and improves recovery of locomotor function. Taken together, these results suggest a novel regulatory role of Btc in axon‐Schwann cell interactions involved in myelin formation and nerve repair. GLIA 2017 GLIA 2017;65:657–669
A STUDY ON THE PROPERTIES OF SURFACE – ACTIVE FLUIDS USED IN BURNISHING AND SHOT PEENING PROCESSES

A method is presented for the study of surface-active properties of a fluids, in burnishing and shot peening processes used, which consists in comparing mean plastic strains of thin metal foil subjected to tensile tests in the examined fluid and in air. As a surface-active additive to the fluid (mineral oil), methyl polymethacrylate solution was used. It was found that the surfactant activity coefficient depended on the type of examined fluid as well as on the thickness of the foil being stretched. Results of analyses of the surface-active properties of a fluid can be compared only when metal foils of equal thickness made from one specific material are used. It can be supposed that the introduction of methyl polymethacrylate solution as an additive to the metalworking fluid will have a beneficial effect on the course and the results of burnishing and shot peening of metals.
Consumer Wearable Information and Health Self Management by Older Adults.

BACKGROUND The present study was undertaken to build an evidence base focusing on an ageing population who are using or have used consumer wearables to collect and manage information about their personal health status. The primary objective was to understand the health self-management requirements, frailty and age related changes, and the health information support provided by consumer wearable devices, specifically in the context of older adults living independently. METHOD The study aimed to recruit older adults to respond to an online questionnaire. Inclusion criteria for the selection of study participants were: Aged 55 or over, independent living, and currently using or having used a wearable device or devices for health self-management in the past year. The online survey questionnaire represented a cross-section of variables in three sections: (1) Use of wearables for health monitoring, (2) Demographics and (3) Health, physical condition and wellness. A subset of the questions was drawn from the Tilburg Frailty Indicator. RESULTS Summary findings from the completed questionnaires suggest the use of wearable health information supports aspects of health self-management activities among independent living seniors. Personal variations and user characteristics in the extent and consistency of the use of wearable information, and user experience in the process, was more difficult to extrapolate, for example, in health information sharing. CONCLUSION Responses to the survey do not indicate widespread use of information from consumer wearables for health self-management among older adults. However, among the respondents, more than half were willing to participate in a follow-up interview by a researcher on their wearable health information use. Further research will explore what they have to say about this information use in relation to frailty and age related changes, and about the way that such information may be integrated into health and aged care support systems.
ERBB4 confers metastatic capacity in Ewing sarcoma

Metastatic spread is the single‐most powerful predictor of poor outcome in Ewing sarcoma (ES). Therefore targeting pathways that drive metastasis has tremendous potential to reduce the burden of disease in ES. We previously showed that activation of the ERBB4 tyrosine kinase suppresses anoikis, or detachment‐induced cell death, and induces chemoresistance in ES cell lines in vitro. We now show that ERBB4 is transcriptionally overexpressed in ES cell lines derived from chemoresistant or metastatic ES tumours. ERBB4 activates the PI3K‐Akt cascade and focal adhesion kinase (FAK), and both pathways contribute to ERBB4‐mediated activation of the Rac1 GTPase in vitro and in vivo. ERBB4 augments tumour invasion and metastasis in vivo, and these effects are blocked by ERBB4 knockdown. ERBB4 expression correlates significantly with reduced disease‐free survival, and increased expression is observed in metastatic compared to primary patient‐matched ES biopsies. Our findings identify a novel ERBB4‐PI3K‐Akt‐FAK‐Rac1 pathway associated with aggressive disease in ES. These results predict that therapeutic targeting of ERBB4, alone or in combination with cytotoxic agents, may suppress the metastatic phenotype in ES.
GLP-1R Signaling Directly Activates Arcuate Nucleus Kisspeptin Action in Brain Slices but Does not Rescue Luteinizing Hormone Inhibition in Ovariectomized Mice During Negative Energy Balance

Abstract Kisspeptin (Kiss1) neurons in the hypothalamic arcuate nucleus (ARC) are key components of the hypothalamic-pituitary-gonadal axis, as they regulate the basal pulsatile release of gonadotropin releasing hormone (GnRH). ARC Kiss1 action is dependent on energy status, and unmasking metabolic factors responsible for modulating ARC Kiss1 neurons is of great importance. One possible factor is glucagon-like peptide 1 (GLP-1), an anorexigenic neuropeptide produced by brainstem preproglucagon neurons. Because GLP fiber projections and the GLP-1 receptor (GLP-1R) are abundant in the ARC, we hypothesized that GLP-1R signaling could modulate ARC Kiss1 action. Using ovariectomized mice, we found that GLP-producing fibers come in close apposition with ARC Kiss1 neurons; these neurons also contain Glp1r mRNA. Electrophysiological recordings revealed that liraglutide (a long-acting GLP-1R agonist) increased action potential firing and caused a direct membrane depolarization of ARC Kiss1 cells in brain slices. We determined that brainstem preproglucagon mRNA is decreased after a 48-h fast in mice, a negative energy state in which ARC Kiss1 expression and downstream GnRH/luteinizing hormone (LH) release are potently suppressed. However, activation of GLP-1R signaling in fasted mice with liraglutide was not sufficient to prevent LH inhibition. Furthermore, chronic central infusions of the GLP-1R antagonist, exendin(9–39), in ad libitum–fed mice did not alter ARC Kiss1 mRNA or plasma LH. As a whole, these data identify a novel interaction of the GLP-1 system with ARC Kiss1 neurons but indicate that CNS GLP-1R signaling alone is not critical for the maintenance of LH during fasting or normal feeding.
Evidence of Disturbed Sleep in Children With Eosinophilic Esophagitis and Persistent Epigastric Pain

Objective To determine whether the experience of persistent epigastric pain is associated with sleep disturbances in children with eosinophilic esophagitis (EoE). We hypothesized that children with EoE and persistent epigastric pain would (1) self-report greater current and worst pain severity, and (2) experience more disturbed sleep on objective and subjective measures in comparison with children with EoE but no persistent pain and healthy children. Methods Fifty children with EoE were recruited for this cross-sectional study, of which 24 (48%) reported experiencing persistent epigastric pain. The remaining 26 (52%) children with EoE denied experiencing persistent pain. An additional 25 healthy children without EoE or persistent pain were included. All children provided severity ratings of current pain and worst pain experienced over the past week. Children then completed 12 consecutive nights of ambulatory sleep monitoring via actigraphy in the home. Caregivers provided information regarding their child's sleep patterns and internalizing symptoms. Results Children with EoE and persistent pain reported significantly greater severity of current pain (p < .001) and worst pain over the past week (p < .001) compared with EoE without persistent pain and healthy children. Compared with the other groups, children with EoE and persistent pain also demonstrated greater actigraphic sleep disturbances, lower sleep efficiency (p = .004) and greater wake after sleep onset (p = .034). Conclusions This study provides novel evidence that a significant proportion of children with EoE experience persistent symptoms of epigastric pain. Persistent pain was associated with significant sleep disturbances in children with EoE.