Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray-Based Identification of htrA, a Streptococcus pneumoniae Gene That Is Regulated by the CiaRH Two-Component System and Contributes to Nasopharyngeal Colonization

ABSTRACT Nasopharyngeal carriage is the reservoir from which most disease with Streptococcus pneumoniae arises. Survival as a commensal in this environment is likely to require a set of adaptations distinct from those needed to cause disease, some of which may be mediated by two-component signal transduction systems (TCSTS). We examined the contributions of nine pneumococcal TCSTS to the process of nasopharyngeal colonization by using an infant rat model. Whereas deletions in all but one of these systems have been associated previously with a high degree of attenuation in a murine model of pneumonia, only the CiaRH system was necessary for efficient carriage. Transcriptional analysis by using microarray hybridization identified a locus consisting of two adjacent genes, htrA and spoJ, that was specifically and strongly downregulated in a ΔciaRH-null mutant. A S. pneumoniae strain lacking the htrA gene encoding a putative serine protease, but not one lacking spoJ, showed decreased fitness in a competitive model of colonization, a finding consistent with this gene mediating a portion of the carriage deficit observed with the ΔciaRH strain.
Long-term effects of pre-pubertal fluoxetine on behaviour and monoaminergic stress response in stress-sensitive rats

Objective Although prescription rates of antidepressants for children and adolescents have increased, concerns have been raised regarding effects on neurodevelopment and long-term outcome. Using a genetic animal model of depression, this study investigated the long-term effects of pre-pubertal administration of fluoxetine (FLX) on depressive-like behaviour in early adulthood, as well as on central monoaminergic response to an acute stressor. We postulated that pre-pubertal FLX will have lasting effects on animal behaviour and monoaminergic stress responses in early adulthood. Methods Flinders sensitive line (FSL) rats received 10 mg/kg/day FLX subcutaneously from postnatal day 21 (PnD21) to PnD34 (pre-pubertal). Thereafter, following normal housing, rats were either subjected to locomotor testing and the forced swim test (FST) on PnD60 (early adulthood), or underwent surgery for microdialysis, followed on PnD60 by exposure to acute swim stress and measurement of stressor-induced changes in plasma corticosterone and pre-frontal cortical monoamine concentrations. Results Pre-pubertal FLX did not induce a late emergent effect on immobility in FSL rats on PnD60, whereas locomotor activity was significantly decreased. Acute swim stress on PnD60 significantly increased plasma corticosterone levels, and increased pre-frontal cortical norepinephrine (NE) and 5-hydroxyindole-3-acetic acid (5-HIAA) concentrations. Pre-pubertal FLX significantly blunted the pre-frontal cortical NE and 5-HIAA response following swim stress on PnD60. Baseline dopamine levels were significantly enhanced by pre-pubertal FLX, but no further changes were induced by swim stress. Conclusion Pre-pubertal FLX did not have lasting antidepressant-like behavioural effects in genetically susceptible, stress-sensitive FSL rats. However, such treatment reduced locomotor activity, abrogated noradrenergic and serotonergic stressor responses and elevated dopaminergic baseline levels in adulthood.
Distributed Power Optimization for Security-Aware Multi-Channel Full-Duplex Communications: A Variational Inequality Framework

In this paper, we consider the physical layer security issue for the multi-channel full-duplex (FD) communications in the presence of eavesdroppers. There co-exist multiple FD pairs, where the two users in each pair perform bi-directional transmissions. The secure communication is then challenged by the users’ self-interference, external interference from other pairs, and threats from the eavesdroppers. We investigate the problem from a distributed perspective and formulate the problem as a non-cooperative game, where each user optimizes their power allocation over the channels to maximize their own secrecy rate. Confirming the existence of the Nash equilibrium, we introduce an equivalent variational inequality (VI) formulation to derive the sufficient condition for the equilibrium to be unique. We then develop the iterative security-aware water-filling (ISWF) algorithm that can be implemented at each individual user in a distributed manner and prove that the condition for the unique equilibrium also claims the convergence of ISWF algorithm. Furthermore, we extend our formulation to the heterogeneous cases that there co-exist FD and half-duplex users with different security requirements in the networks, and demonstrate that they can all be covered as special cases under our formulated VI framework. Finally, we present simulation results to validate our theoretical findings.
Medium-Range Oscillatory Network and the 20-Hz Sensorimotor Induced Potential

Although synchronously oscillating neuronal assemblies have been the subject of many studies, a clear identification of the spatiotemporal characteristics of a medium-range oscillatory network is still lacking. Herein, we present a method for the extraction of a new waveform, namely the mean induced potential (IP), which allows the identification of the spatiotemporal characteristics of induced EEG responses. The IP calculation was applied to the 20-Hz component of the sensorimotor rhythm in order to obtain a 20-Hz sensorimotor induced potential (20-Hz SIP). The spatiotemporal characteristics of the 20-Hz bursts seen after median nerve stimulation and self-paced finger movements were extracted by means of current source density reconstruction and synchronization analysis. A cortical network including the controlateral primary motor cortex, the supplementary motor area, and the controlateral supramarginalis gyrus was found to generate the 20-Hz bursts, and the various activated areas were found to be highly synchronized. Our results demonstrate for the first time the existence of a medium-range cortical network in the human sensorimotor region whose constituents oscillate synchronously.
Indoor endotoxin and glucan in association with airway inflammation and systemic symptoms.

Indoor bioaerosols (i.e., bacteria, fungi, endotoxin, and beta-1,3-glucan) were determined in daycare centers, office buildings, and domestic environments in the Taipei area. In addition, we used a questionnaire survey to determine associations between indoor dampness, bioaerosols, and airway inflammation and systemic symptoms. We demonstrated that the median levels of indoor bacteria and fungi were the highest in daycare centers, followed by those in homes and office buildings. Similar patterns were observed for endotoxin and beta-1,3-glucan. The prevalences of airway inflammation and systemic symptoms were higher for females in office buildings than for employees in daycare centers; all symptoms were more prevalent in females than males. With respect to the relationship between bioaerosol exposure and airway inflammation and systemic symptoms, we found a strong association between beta-1,3-glucan and lethargy/fatigue.
Toward a general theoretical framework for judgment and decision-making

Over the past 30 years, behavioral and experimental economists and psychologists have made great strides in identifying phenomena that cannot be explained by the classical model of rational choice—anomalies in the discounting of future wealth, present bias, loss aversion, the endowment effect, and aversion to ambiguity, for example. In response to these findings, there has been an enormous amount of research by behavioral scientists aimed at modeling and understanding the nature of these biases1. However, these models, typically assuming situation-specific psychological processes, have shed limited light on the conditions for and boundaries of the different biases, substantially neglecting their relative importance and joint effect. Much less attention has been paid to the investigation of the links between different biases. As a consequence of this approach, it is not always clear which model should be used to predict behavior in a new setting, and maybe a more general theory is needed. We believe that the field of neuroeconomics, which has experienced a rapid growth over the past decade, can play an important role in bridging these gaps, contributing to the building of a general theoretical framework for judgment and decision-making behaviors.
Cost effectiveness of alternative strategies for incorporating bevacizumab into the primary treatment of ovarian cancer

The objective of this study was to evaluate the comparative effectiveness of strategies that incorporated bevacizumab into the primary platinum‐based treatment of ovarian cancer: 1) no bevacizumab; 2) concurrent and maintenance bevacizumab for all; 3) bevacizumab for suboptimally debulked stage III and stage IV disease (high‐risk cohort); and the evaluation of an alternative exploratory strategy of 4) directed bevacizumab therapy based on a predictive test for bevacizumab responsiveness.
Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes

Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated in metagenomic projects. In this work, we identify, validate and analyze the genes coding for RNase P RNA (P RNA) from all published metagenomic projects. P RNA is the RNA subunit of a ubiquitous endoribonuclease RNase P that consists of one RNA subunit and one or more protein subunits. The bacterial P RNAs are classified into two types, Type A and Type B, based on the constituents of the structure involved in precursor tRNA binding. Archaeal P RNAs are classified into Type A and Type M, whereas the Type A is ancestral and close to Type A bacterial P RNA. Bacterial and some archaeal P RNAs are catalytically active without protein subunits, capable of cleaving precursor tRNA transcripts to produce their mature 5′-termini. We have found 328 distinctive P RNAs (320 bacterial and 8 archaeal) from all published metagenomics sequences, which led us to expand by 60% the total number of this catalytic RNA from prokaryotes. Surprisingly, all newly identified P RNAs from metagenomics sequences are Type A, i.e. neither Type B bacterial nor Type M archaeal P RNAs are found. We experimentally validate the authenticity of an archaeal P RNA from Sargasso Sea. One of the distinctive features of some new P RNAs is that the P2 stem has kinked nucleotides in its 5′ strand. We find that the single nucleotide J2/3 joint region linking the P2 and P3 stem that was used to distinguish a bacterial P RNA from an archaeal one is no longer applicable, i.e. some archaeal P RNAs have only one nucleotide in the J2/3 joint. We also discuss the phylogenetic analysis based on covariance model of P RNA that offers a few advantages over the one based on 16S rRNA.
Comparing accessibility evaluation and usability evaluation in HagáQuê

Usability and accessibility are two attributes very important in software design nowadays and, in general, are evaluated separately. On one hand, usability evaluation methods alone can't answer whether software is accessible to all kind of users. On the other hand, an accessibility evaluation can say little about software usability. However, it seems that usability and accessibility evaluation methods have some points in common. The aim of this article is to compare and discuss the similarities and differences between the results of accessibility and usability evaluations in HagáQuê, a comic book editor software for pedagogical usage.
Discovery of a Novel, Monocationic, Small-Molecule Inhibitor of Scrapie Prion Accumulation in Cultured Sheep Microglia and Rov Cells

Prion diseases, including sheep scrapie, are neurodegenerative diseases with the fundamental pathogenesis involving conversion of normal cellular prion protein (PrPC) to disease-associated prion protein (PrPSc). Chemical inhibition of prion accumulation is widely investigated, often using rodent-adapted prion cell culture models. Using a PrPSc-specific ELISA we discovered a monocationic phenyl-furan-benzimidazole (DB772), which has previously demonstrated anti-pestiviral activity and represents a chemical category previously untested for anti-prion activity, that inhibited PrPSc accumulation and prion infectivity in primary sheep microglial cell cultures (PRNP 136VV/154RR/171QQ) and Rov9 cultures (VRQ-ovinized RK13 cells). We investigated potential mechanisms of this anti-prion activity by evaluating PrPC expression with quantitative RT-PCR and PrP ELISA, comparing the concentration-dependent anti-prion and anti-pestiviral effects of DB772, and determining the selectivity index. Results demonstrate at least an approximate two-log inhibition of PrPSc accumulation in the two cell systems and confirmed that the inhibition of PrPSc accumulation correlates with inhibition of prion infectivity. PRNP transcripts and total PrP protein concentrations within cell lysates were not decreased; thus, decreased PrPC expression is not the mechanism of PrPSc inhibition. PrPSc accumulation was multiple logs more resistant than pestivirus to DB772, suggesting that the anti-PrPSc activity was independent of anti-pestivirus activity. The anti-PrPSc selectivity index in cell culture was approximately 4.6 in microglia and 5.5 in Rov9 cells. The results describe a new chemical category that inhibits ovine PrPSc accumulation in primary sheep microglia and Rov9 cells, and can be used for future studies into the treatment and mechanism of prion diseases.
Oxygen Saturation in Postoperative Patients at Low Risk for Hypoxemia: Is Oxygen Therapy Needed?

To evaluate the use of oxygen therapy in the immediate postoperative period, 293 postsurgical patients who had not had thoracic, upper abdominal, or neurologic surgery were randomly assigned upon admission to the postanesthesia care unit (PACU) to receive:1) 4 L unhumidified O2 via nasal cannula, 2) 40% oxygen by face tent, 3) nurse-coached lung hyperinflations, or 4) no oxygen enhancing regimen. Oxygen saturation was measured on all patients at the time of arrival in the PACU, after 15 min, and after 30 min in the PACU. Only 11 patients in all groups (4%) had their O2 saturation decrease to less than 90% during this time. Ten of these had an initial O2 saturation of 92% or less. Significant differences in O2 saturation were found at 15 min and 30 min between Groups 1 and 2 which received O2 compared to Groups 3 and 4 which did not receive supplemental oxygen. The clinical significance of these differences is open to question. Complaints of dryness were most common in those receiving unhumidified oxygen by nasal cannula. Fourteen percent of patients receiving oxygen by face tent found it uncomfortable and complained of nausea. Supplemental oxygen is not essential in maintaining adequate oxygen saturation in these PACU patients when oxygen saturation levels are more than 92% upon admission to the PACU. (Anesth Analg 1995;80:368-72)
Dynamic feedback linearization based control synthesis of the turbocharged Diesel engine

In this paper, a nonlinear control technique based on the property of flatness is proposed to control the diesel engine air system. More precisely, to achieve tracking of suitable references (corresponding to low emissions) for the air-fuel ratio and the fraction of the recirculated exhaust gas. The simulated diesel engine is a six cylinders medium duty Caterpillar 3126 B equipped with a variable geometry turbocharger and an exhaust gas recirculation valve. The proposed controller is designed on the reduced third order mean value model and implemented by endogenous linearizing dynamic feedback on the full order model. The controller is assessed through simulations with a SIL architecture using dSpace simulator. It exhibits good control performance without zero dynamics and ensures global stability and tracking of flat output references.
Commentary: Gain in Body Fat Is Associated with Increased Striatal Response to Palatable Food Cues, whereas Body Fat Stability Is Associated with Decreased Striatal Response

Citation: Cerolini S, Pazzaglia M and Lombardo C (2017) Commentary: Gain in Body Fat Is Associated with Increased Striatal Response to Palatable Food Cues, whereas Body Fat Stability Is Associated with Decreased Striatal Response. Front. Hum. Neurosci. 11:65. doi: 10.3389/fnhum.2017. 00065 Commentary: Gain in Body Fat Is Associated with Increased Striatal Response to Palatable Food Cues, whereas Body Fat Stability Is Associated with Decreased Striatal Response
Health services research

The scientific focus of academic surgery has changed dramatically over the past decade. Historically, surgeon-scientists engaged almost exclusively in basic science research. With the rise of health services and outcomes research, more trainees and junior faculty are pursuing research in these disciplines. Despite the increasing popularity of this field, there are very few resources for young surgeons interested in learning about these disciplines as applied to surgery. We developed this book, and have revised our contents in this second edition, to help fill this gap. We start with a description of the main research areas in health services research followed by a look ahead into emerging areas of investigation. We then include several chapters that introduce the tools necessary to conduct this type of research. The final chapters provide practical advice on career development and program building for surgeon-scientists interested in pursuing this area of scholarly work. 1.1 What Is Health Services Research? We often get asked how health services research is different from traditional “clinical research”. Studying the end results of surgical care is clearly not new. As long as surgeons have been operating, we have been studying our patient’s outcomes. Although there is clearly overlap between traditional clinically-focused scientific
Biomarkers of Response to Akt Inhibitor MK-2206 in Breast Cancer

Purpose: We tested the hypothesis that allosteric Akt inhibitor MK-2206 inhibits tumor growth, and that PTEN/PIK3CA mutations confer MK-2206 sensitivity. Experimental Design: MK-2206 effects on cell signaling were assessed in vitro and in vivo. Its antitumor efficacy was assessed in vitro in a panel of cancer cell lines with differing PIK3CA and PTEN status. Its in vivo efficacy was tested as a single agent and in combination with paclitaxel. Results: MK-2206 inhibited Akt signaling and cell-cycle progression, and increased apoptosis in a dose-dependent manner in breast cancer cell lines. Cell lines with PTEN or PIK3CA mutations were significantly more sensitive to MK-2206; however, several lines with PTEN/PIK3CA mutations were MK-2206 resistant. siRNA knockdown of PTEN in breast cancer cells increased Akt phosphorylation concordant with increased MK-2206 sensitivity. Stable transfection of PIK3CA E545K or H1047R mutant plasmids into normal-like MCF10A breast cells enhanced MK-2206 sensitivity. Cell lines that were less sensitive to MK-2206 had lower ratios of Akt1/Akt2 and had less growth inhibition with Akt siRNA knockdown. In PTEN-mutant ZR75-1 breast cancer xenografts, MK-2206 treatment inhibited Akt signaling, cell proliferation, and tumor growth. In vitro, MK-2206 showed a synergistic interaction with paclitaxel in MK-2206–sensitive cell lines, and this combination had significantly greater antitumor efficacy than either agent alone in vivo. Conclusions: MK-2206 has antitumor activity alone and in combination with chemotherapy. This activity may be greater in tumors with PTEN loss or PIK3CA mutation, providing a strategy for patient enrichment in clinical trials. Clin Cancer Res; 18(20); 5816–28. ©2012 AACR.
Panax notoginseng Attenuates Experimental Colitis in the Azoxymethane/Dextran Sulfate Sodium Mouse Model

Patients suffering from inflammatory bowel disease are at a high risk of developing colorectal cancer. To assess the anticancer potential of botanicals, in this study, we evaluated the effects of Panax notoginseng on azoxymethane/dextran sulfate sodium (DSS)‐induced colitis. One week after A/J mice received azoxymethane, the animals received DSS for 8 days or were supplemented with P. notoginseng extract, at 30 or 90 mg/kg. DSS‐induced colitis was scored with the disease activity index. The severity of the inflammatory lesions was evaluated by a colon tissue histological assessment. The expression of inducible nitric oxide synthase and cyclooxygenase‐2 (COX‐2) were also explored. We observed that the effects of P. notoginseng on the reduction of colon inflammation, expressed in disease activity index score, were in a dose‐related manner (p < 0.01). P. notoginseng inhibited the reduction of the colon length and the loss of bodyweight in dose‐related manner (all p < 0.05). The histological assessment of the colitis and inflammatory‐related immunohistochemical data also supported the pharmacological observations. Our data suggest that P. notoginseng is a promising candidate in preventing and treating colitis and inflammation‐associated colon carcinogenesis. Copyright © 2013 John Wiley & Sons, Ltd.
Selectivity/Specificity Improvement Strategies in Surface-Enhanced Raman Spectroscopy Analysis

Surface-enhanced Raman spectroscopy (SERS) is a powerful technique for the discrimination, identification, and potential quantification of certain compounds/organisms. However, its real application is challenging due to the multiple interference from the complicated detection matrix. Therefore, selective/specific detection is crucial for the real application of SERS technique. We summarize in this review five selective/specific detection techniques (chemical reaction, antibody, aptamer, molecularly imprinted polymers and microfluidics), which can be applied for the rapid and reliable selective/specific detection when coupled with SERS technique.
Comprehensive Numerical Simulation of Filling and Solidification of Steel Ingots

In this paper, a complete three-dimensional numerical model of mold filling and solidification of steel ingots is presented. The risk of powder entrapment and defects formation during filling is analyzed in detail, demonstrating the importance of using a comprehensive geometry, with trumpet and runner, compared to conventional simplified models. By using a case study, it was shown that the simplified model significantly underestimates the defects sources, reducing the utility of simulations in supporting mold and process design. An experimental test was also performed on an instrumented mold and the measurements were compared to the calculation results. The good agreement between calculation and trial allowed validating the simulation.