Miracle-dz/UniFAR-FTUs huggingface dataset:
Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium

Drug efflux systems play a major role in resistance to a wide range of noxious compounds in several Gram negative species. Here, we report the drug resistance and virulence phenotypes of Salmonella mutants defective in either resistance‐nodulation‐division (RND)‐type systems and/or in drug efflux systems belonging to the major facilitator (MFS), multidrug and toxic compound extrusion (MATE), and ATP‐binding cassette (ABC) superfamilies. We determined that nine potential drug transporters contribute to drug resistance of Salmonella and found that the Salmonella‐specific MdsABC system conferred resistance to a variety of toxic compounds. The RND‐type MdsAB system could function with either MdsC, which is encoded in the same operon, or TolC as the outer membrane component. Although the Salmonella EmrAB, MdfA and MdtK are 90% identical in their amino acid sequences to their Escherichia coli homologues, the drug specificity of Salmonella transporters was different from that reported for equivalent E. coli transporters. Deletion of the macAB genes attenuated Salmonella virulence and a strain lacking all drug efflux systems was avirulent when mice were inoculated by the oral route. The promoter region of the macAB drug efflux system genes harbours a binding site for the response regulator PhoP, which functions to repress macAB transcription. The PhoP/PhoQ two‐component system is a major regulator of Salmonella virulence, which underscores the connection between drug efflux systems and virulence.
All Optical Nanostructed Sensor Based on Metal-Dielectric-Metal Plasmonic Waveguide

Based on a two-dimensional plasmonic metal-dielectric-metal waveguide with a thin metallic layer and dual nanocavites inserted in the core, a novel nanostructured absorber is presented. A transfer matrix model for the proposed structure is established, and the optical spectra are investigated. Design results show that a narrow reflection spectrum occurs at position of the near-unity absorption, and is significantly influenced by the environment. It is able to generate a sensitivity as high as 1000 nm/RIU, which be used as an excellent sensing platform for chemical and biochemically relevant molecules.
Experimental studies on the treatment and pathological basis of combined radiation and burn injury.

OBJECTIVE To investigate therapeutics for and the pathological basis of combined radiation and burn injuries. METHODS Combined radiation and burn injuries on mice and rats were inflicted by gamma ray irradiation from a (60)Co source and thermal radiation from a 5 kW bromotungsten lamp. RESULTS The dysfunction of myocardium played an important role in the development of early stage shock. Transfusion of irradiated (in vitro, 20 Gy) or stored (4 degrees C, 7 days) blood after irradiation was done to promote the success of allo-transplantation of bone marrow. Decrease of IL-4 mRNA expression was the molecular basis of depression of intestinal mucosa immune and intervention of IL-4 showed an antagonistic effect on enterogenic infection. A new lipid component extracted from burn eschar was documented for the first time and its toxic effects were elucidated. The survival rate of alloskin grafts after removal of burn eschar from the recipient animals was obviously increased in combined injury due to reduction of immune rejection activity by the radiation effect. In contrast, in animal models with simple burn, the alloskin grafts were all rejected within ten days after the procedure. A successful therapeutic result (survival rate: 92% for 30 days and 67% for 100 days) was obtained by comprehensive management of treated animals, while the untreated control animals all died within 3 - 7 days after injury. CONCLUSION The pathogenesis of injury caused by simultaneous radiation and burn is extremely complicated and the treatment is very difficult. A comprehensive management program consisting of several therapeutic measures aimed at key links of the pathogenesis may achieve significantly improved results.
Towards GUI interfaces handling complex multidomain antenna sitting computations

In this paper we describe a new hybrid weak coupling of asymptotic GO/PO techniques and Boundary Element Methods (BEM) based on the FACTOPO Domain Decomposition Methodology (DDM). In that way the modular domain decomposition approach already assessed with exact techniques as BEM and FEM is conserved with the utilization of GO/PO techniques resulting in important reduction of CPU time during parametric studies. Furthermore a graphical user interface (GUI) has been developed in C++ and QT for controlling the computation steps of the multidomain scenario. The accuracy and efficiency of this technique is assessed by performing the computation of the antenna radiation in a multi-domain way cross compared with reference integral equation results.
[Forensic application of expressmarker 22 STR loci direct PCR amplification kit].

OBJECTIVE To explore the application value of Expressmarker 22 STR loci direct PCR amplification kit. METHODS One thousand nine hundred and forty-eight samples (including samples spotted on FTA cards, filter papers and case samples) were tested using Expressmarker 22 STR loci direct PCR amplification kit. At the same time, all were tested using Sinofiler kit, Identifiler kit and PowerPlex 16 kit respectively for comparison. The genotypes were compared at the same STR loci among these four kits to test the sensitivity and accuracy of Expressmarker 22 STR loci direct PCR amplification kit. RESULTS 97.79% samples were successfully typed using Expressmarker 22 STR loci direct PCR amplification kit. The genotype profiles of the same samples using Expressmarker 22 STR loci direct PCR amplification kit were consistent with Sinofiler kit, Identifiler kit and PowerPlex 16 kit at the same STR loci. CONCLUSION Expressmarker 22 STR loci direct PCR amplification kit can provide huge information and accurate results
Datapath and memory co-optimization for FPGA-based computation

With the large resource densities available on modern FPGAs it is often the available memory bandwidth that limits the parallelism (and therefore performance) that can be achieved. For this reason the focus of this thesis is the development of an integrated scheduling and memory optimisation methodology to allow high levels of parallelism to be exploited in FPGA based designs. A manual translation from C to hardware is first investigated as a case study, exposing a number of potential optimisation techniques that have not been exploited in existing work. An existing outer loop pipelining approach, originally developed for VLIW processors, is extended and adapted for application to FPGAs. The outer loop pipelining methodology is first developed to use a fixed memory subsystem design and then extended to automate the optimisation of the memory subsystem. This approach allocates arrays to physical memories and selects the set of data reuse structures to implement to match the available and required memory bandwidths as the pipelining search progresses. The final extension to this work is to include the partitioning of data from a single array across multiple physical memories, increasing the number of memory ports through which data my be accessed. The facility for loop unrolling is also added to increase the potential for parallelism and exploit the additional bandwidth that partitioning can provide. We describe our approach based on formal methodologies and present the results achieved when these methods are applied to a number of benchmarks. These results show the advantages of both extending pipelining to levels above the innermost loop and the co-optimisation of the datapath and memory subsystem.
Finite Arithmetics

The paper presents the current state of knowledge in the field of logical investigations of finite arithmetics. This is an attempt to summarize the ideas and results in this area. Some new results are presented - these are mainly generalizations of the earlier results related to properties of sl-theories and some nontrivial cases of FM-representability theorem.
A COMPARATIVE APPROACH TO UNDERSTANDING CAUSES AND CONSEQUENCES OF MOLLUSC–DIGENEAN SIZE RELATIONSHIPS: A CASE STUDY WITH ALLOCREADIID TREMATODES AND CYCLOCALYX CLAMS

Allocreadiid flukes often parasitize and castrate sphaeriid freshwater clams. The effects of parasitic castrators on host population life history can lead to earlier reproductive onset, changes in body size, or changes in the number of reproductive events per year. However, little is known about whether species- or clade-level traits are associated with parasite prevalence. In this study, we examine if phenotypic effects, e.g., size change, seen at the population level, sort to the species or clade level. To answer this question, we determined if different-sized host species in the ecologically important, widespread, and common sphaeriid subgenus Cyclocalyx have different prevalences of allocreadiid infection. After showing that large species are more than 12 times more likely to have patent infections than small species, we examined the evolution of size within Cyclocalyx lineages. Transitions from large size to small size or vice versa have occurred at least twice and probably many times during lineage diversification, perhaps relating to trade-offs between clutch size and parasite risk. Finally, based on existing data, we show that it is unlikely that age and body size are correlated; therefore, a simple age-exposure model is not a sufficient explanation for parasite prevalence in this clade.
Claudin‐7 down‐regulation is an important feature in oral squamous cell carcinoma

Lourenço S V, Coutinho‐Camillo C M, Buim M E C, de Carvalho A C, Lessa R C, Pereira C M, Vettore A L, Carvalho A L, Fregnani J H, Kowalski L P & Soares F A (2010) Histopathology57, 689–698 Claudin‐7 down‐regulation is an important feature in oral squamous cell carcinoma
Targeting the ubiquitin–proteasome system for cancer therapy

Introduction: The ubiquitin–proteasome system (UPS) degrades 80 – 90% of intracellular proteins. Cancer cells take advantage of the UPS for their increased growth and decreased apoptotic cell death. Thus, the components that make up the UPS represent a diverse group of potential anti-cancer targets. The success of the first-in-class proteasome inhibitor bortezomib not only proved that the proteasome is a feasible and valuable anti-cancer target, but also inspired researchers to extensively explore other potential targets of this pathway. Areas covered: This review provides a broad overview of the UPS and its role in supporting cancer development and progression, especially in aspects of p53 inactivation, p27 turnover and NF-κB activation. Also, efforts toward the development of small molecule inhibitors (SMIs) targeting different steps in this pathway for cancer treatment are reviewed and discussed. Expert opinion: Whereas some of the targets in the UPS, such as the 20S proteasome, Nedd8 activating enzyme and HDM2, have been well-established and validated, there remains a large pool of candidates waiting to be investigated. Development of SMIs targeting the UPS has been largely facilitated by state-of-the-art technologies such as high-throughput screening and computer-assisted drug design, both of which require a better understanding of the targets of interest.
A Socioecological Approach to Improving Mammography Rates in a Tribal Community

This article highlights the processes and intermediate outcomes of a pilot project to increase mammography rates of women in an American Indian tribe in New Mexico. Using a socioecological framework and principles of community-based participatory research, a community coalition was able to (a) bolster local infrastructure to increase access to mammography services; (b) build public health knowledge and skills among tribal health providers; (c) identify community-specific knowledge, attitudes, and beliefs related to breast cancer; (d) establish interdependent partnerships among community health programs and between the tribe and outside organizations; and (e) adopt local policy initiatives to bolster tribal cancer control. These findings demonstrate the value of targeting a combination of individual, community, and environmental factors, which affect community breast cancer screening rates and incorporating cultural strengths and resources into all facets of a tribal health promotion intervention.
Inhibition of Endocannabinoid-Metabolizing Enzymes in Peripheral Tissues Following Developmental Chlorpyrifos Exposure in Rats

Repeated developmental exposure to the organophosphate (OP) insecticide chlorpyrifos (CPF) inhibits brain fatty acid amide hydrolase (FAAH) activity at low levels, whereas at higher levels, it inhibits brain monoacylglycerol lipase (MAGL) activity. FAAH and MAGL hydrolyze the endocannabinoids anandamide (AEA) and 2-arachidonylglycerol (2-AG), respectively. Peripherally, AEA and 2-AG have physiological roles in the regulation of lipid metabolism and immune function, and altering the normal levels of these lipid mediators can negatively affect these processes. Exposure to CPF alters brain endocannabinoid hydrolysis activity, but it is unclear whether low-level exposure alters this activity in peripheral tissues important in metabolic and immune function. Therefore, rat pups were exposed orally from day 10 to 16 to 0.5, 0.75, or 1.0 mg/kg CPF or 0.02 mg/kg PF-04457845 (a specific FAAH inhibitor). At 12 hours postexposure, FAAH, MAGL, and cholinesterase (ChE) activities were determined. All treatments inhibited FAAH activity in brain, spleen, and liver. CPF inhibited ChE activity in spleen and liver (all dosages) and in brain (highest dosage only). CPF inhibited total 2-AG hydrolysis and MAGL-specific activity in brain and spleen (high dosage only). In liver, total 2-AG hydrolysis was inhibited by all treatments and could be attributed to inhibition of non–MAGL-mediated 2-AG hydrolysis, indicating involvement of other enzymes. MAGL-specific activity in liver was inhibited only by the high CPF dosage, whereas PF-04457845 slightly increased this activity. Overall, exposure to low levels of CPF and to PF-04457845 can alter endocannabinoid metabolism in peripheral tissues, thus potentially affecting physiological processes.
Heritability of SF-36 Among Middle-Age, Middle-Class, Male–Male Twins

Objective:We sought to examine the relative importance of genetic and environmental factors for the MOS SF-36; a widely used, valid, and reliable measure of health-related quality of life and to discuss incorporating genetic influences into health services research. Data Sources:Data are from a nationally distributed, nonclinical cohort of 2928 middle age, middle-class, male–male twin members of the Vietnam Era Twin Registry. Study Design:This was a secondary data analysis, classic twin heritability analysis. Data Collection:A telephone survey was used to collect information on alcohol-related problems and health services use, including the SF-36. Principal Findings:Variance component analyses indicated that additive genetic factors accounted for 17% to 33% of the variance for each of the 8 domains of the SF-36. Shared environment accounted for 0% to 12% of the variance for each domain, with the majority of variance for each domain accounted for by nonshared, or unique environment and error. Physical and mental health summary measures indicated that approximately one-third of the variance was accounted for by additive genetic factors and the remainder accounted for by nonshared environment and error. Clinical condition, history of alcohol dependence, had a small-but-significant influence for all domains. Including condition proved to be a better-fitting model. However, confidence intervals temper uniform statistical significance for genetic factors. Conclusions:This study assessed the heritability of the SF-36 in a nonclinical, community sample of middle age, middle-class all-male twins. The moderate genetic effects on SF-36 domain and summary measures are new findings and thus may affect interpretations of SF-36 as a measure of health-related quality of life. Ideally, trait-based measures should identify genetic sources of variation and thus help understand any bias of the true effects of SF-36. Still the majority of variance is accounted for by nonshared or unique environmental factors and error. By extension, increased understanding of the importance of genetic and environmental factors that influence either predictors or outcomes of interest will expand the level of scientific debate in health services research and improve predictability.
Mechanisms of StpA-mediated RNA remodeling

In bacteria, transcription, translation and gene regulation are highly coupled processes. The achievement of a certain functional structure at a distinct temporal and spatial position is therefore essential for RNA molecules. Proteins that facilitate this proper folding of RNA molecules are called RNA chaperones. Here a prominent example from E. coli is reviewed: the nucleoid associated protein StpA. Based on its various RNA remodeling functions, we propose a mechanistic model that explains how StpA promotes RNA folding. Through transient interactions via the RNA backbone, thereby shielding repelling charges in RNA, it pre-positions the RNA molecules for the successful formation of transition states from encounter complexes.
Release of U18 snoRNA from its host intron requires interaction of Nop1p with the Rnt1p endonuclease

An external stem, essential for the release of small nucleolar RNAs (snoRNAs) from their pre‐mRNAs, flanks the majority of yeast intron‐encoded snoRNAs. Even if this stem is not a canonical Rnt1p substrate, several experiments have indicated that the Rnt1p endonuclease is required for snoRNA processing. To identify the factors necessary for processing of intron‐encoded snoRNAs, we have raised in vitro extracts able to reproduce such activity. We found that snoRNP factors are associated with the snoRNA‐ coding region throughout all the processing steps, and that mutants unable to assemble snoRNPs have a processing‐deficient phenotype. Specific depletion of Nop1p completely prevents U18 snoRNA synthesis, but does not affect processing of a dicistronic snoRNA‐coding unit that has a canonical Rnt1p site. Correct cleavage of intron‐encoded U18 and snR38 snoRNAs can be reproduced in vitro by incubating together purified Nop1p and Rnt1p. Pull‐down experiments showed that the two proteins interact physically. These data indicate that cleavage of U18, snR38 and possibly other intron‐encoded snoRNAs is a regulated process, since the stem is cleaved by the Rnt1p endonuclease only when snoRNP assembly has occurred.
Early Patterns of Sofosbuvir Utilization by State Medicaid Programs.

To the Editor: The cure rates associated with sofosbuvir, a new treatment for hepatitis C virus (HCV), have been remarkable.1 However, the high cost of the drug has raised concerns,2 particularly in regard to socioeconomically disadvantaged populations with a high prevalence of HCV infection, such as Medicaid beneficiaries. Demand for new HCV drugs in Medicaid populations drove historic surges in spending on drugs in 2014, the first full year during which sofosbuvir was available since its approval by the Federal Drug Administration (FDA) in late 2013.3 Given its recent introduction to the market, little is known about state-level utilization and .
Carotid intima-media thickness , thrombin and atherosclersosis S 74 Leserbrief Letter

To the editors: Thrombin is believed to play a role in the pathogenesis and progression of atherosclerosis (1, 2). To elucidate this role the relationship between thrombin generation and carotid intimamedia thickness (CIMT), supposed to be a marker of atherosclerosis, was investigated by Bernhard et al. (2) in 163 consecutive healthy persons (mean age: 59.8 years). All patients underwent ultrasound examination for CIMT measurement, thrombin generation was measured by means of a calibrated automated thrombogram (CAT). The authors observed in adults younger than 45 years without clinically overt atherosclerotic disease a significant association between endogenous thrombin potential (ETP), a marker of the individual potential of thrombin generation and CIMT. Given the significant association between ETP and CIMT the authors concluded that ETP may serve as an index for subclinical atherosclerosis in subjects younger than 45 years. There are several critical points concerning the relationship between CIMT, thrombin and atherosclerosis.
Neural connectivity as an intermediate phenotype: Brain networks under genetic control

Recent evidence suggests that default mode connectivity characterizes neural states that account for a sizable proportion of brain activity and energy expenditure, and therefore represent a plausible neural intermediate phenotype. This implies the possibility of genetic control over systems‐level connectivity features. Imaging genetics is an approach to combine genetic assessment with multimodal neuroimaging to discover neural systems linked to genetic abnormalities or variation. In the present contribution, we report results obtained from applying this strategy to both structural connectivity and functional connectivity data. Using data for serotonergic (5‐HTTLPR, MAO‐A) and dopaminergic (DARPP‐32) genes as examples, we show that systems‐level connectivity networks under genetic control can be identified. Remarkable similarities are observed across modalities and scales of description. Features of connectivity often better account for behavioral effects of genetic variation than regional parameters of activation or structure. These data provide convergent evidence for genetic control in humans over connectivity systems, whose characterization has promise for identifying neural systems mediating genetic risk for complex human behavior and psychiatric disease. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
A sensor for nuisance sewer gas monitoring

Nuisance gases such as H2S are the main cause of unpleasant odor and also corrosion in the sewer pipes. Although there are treatment methods available, they are expensive to use and have negative side effects. Hotspot monitoring helps to apply the treatments to specific locations of the sewer, and hence minimize their side effects. Here we present a new sensor and supporting platform for nuisance sewer gas detection and monitoring. The sensor is fabricated using a highly-selective microfluidic gas channel coupled with a sensitive metal oxide semiconductor (MOS) sensor and a designed supporting platform consists of a custom syringe pump, automated sample delivery and vaporization chamber. To demonstrate the sensor sensitivity regarding detection of hydrogen sulfide (H2S) (i.e., one of the main components in the sewer gas mixtures), different concentrations of H2S in a liquid phase are identified using special feature extraction methods. This shows the sensor capability and potential in identifying and measuring the concentration of H2S and other nuisance gases in a mixture.