Miracle-dz/UniFAR-FTUs huggingface dataset:
Systemic Inflammation, Coagulation, and Clinical Risk in the START Trial

Abstract Background The Strategic Timing of AntiRetroviral Treatment (START) trial demonstrated that immediate (at CD4+ >500 cells/µL) vs deferred (to CD4+ <350 cells/µL or AIDS) antiretroviral therapy (ART) initiation reduced risk for AIDS and serious non-AIDS (SNA). We investigated associations of inflammation, coagulation, and vascular injury biomarkers with AIDS, SNA or death, and the effect of immediate ART initiation. Methods Biomarkers were measured from stored plasma prior to randomization and at month 8. Associations of baseline biomarkers with event risk were estimated with Cox regression, pooled across groups, adjusted for age, gender, and treatment group, and stratified by region. Mean changes over 8 months were estimated and compared between the immediate and deferred ART arms using analysis of covariance models, adjusted for levels at entry. Results Baseline biomarker levels were available for 4299 START participants (92%). Mean follow-up was 3.2 years. Higher levels of IL-6 and D-dimer were the only biomarkers associated with risk for AIDS, SNA or death, as well as the individual components of SNA and AIDS events (HRs ranged 1.37–1.41 per 2-fold higher level), even after adjustment for baseline CD4+ count, HIV RNA level, and other biomarkers. At month 8, biomarker levels were lower in the immediate arm by 12%–21%. Conclusions These data, combined with evidence from prior biomarker studies, demonstrate that IL-6 and D-dimer consistently predict clinical risk across a broad spectrum of CD4 counts for those both ART-naïve and treated. Research is needed to identify disease-modifying treatments that target inflammation beyond the effects of ART.
Chlamydia trachomatis serovar differentiation by direct sequence analysis of the variable segment 4 region of the major outer membrane protein gene

The polymerase chain reaction method was used to amplify DNA from the fourth variable segment of the gene encoding the major outer membrane protein of Chlamydia trachomatis. Direct sequencing of the amplified DNA from prototype strains confirmed previously identified nucleotide sequence differences that were specific for each serovar. This analysis revealed differences in the DNA sequences of prototype strains C/UW-1 and G/IOL-238 from those of prototype strains C/TW-3 and G/UW-57, sequenced previously. This method was also used to determine the serovar types of C. trachomatis in 125 urogenital specimens from infected patients. The most common serovars were E (38%), F (17%), and G and D (14% each). Serovar D was found significantly more often in specimens from men than in specimens from women (P = 0.004). Conversely, serovar G was found significantly more often in specimens from women than in specimens from men (P = 0.026). Only two serovar G isolates gave sequences identical to that of the prototype strain G/IOL-238, suggesting that this strain may be a serovar variant. Three isolates (D+, G-, and J') gave sequences which have not been reported previously. One isolate had the same sequence as the D- serovar variant. Sequence analysis of amplified DNA reveals subtle differences between C. trachomatis strains and provides a very sensitive method for molecular epidemiological analysis.
Transcriptional Profiling Reveals a Possible Role for the Timing of the Inflammatory Response in Determining Susceptibility to a Viral Infection

ABSTRACT Using a novel cDNA microarray prepared from sources of actively responding immune system cells, we have investigated the changes in gene expression in the target tissue during the early stages of infection of neonatal chickens with infectious bursal disease virus. Infections of two lines of chickens previously documented as genetically resistant and sensitive to infection were compared in order to ascertain early differences in the response to infection that might provide clues to the mechanism of differential genetic resistance. In addition to major changes that could be explained by previously described changes in infected tissue, some differences in gene expression on infection, and differences between the two chicken lines, were observed that led to a model for resistance in which a more rapid inflammatory response and more-extensive p53-related induction of apoptosis in the target B cells might limit viral replication and consequent pathology. Ironically, the effect in the asymptomatic neonatal infection is that more-severe B-cell depletion is seen in the more genetically resistant chicken. Changes of expression of many chicken genes of unknown function, indicating possible roles in the response to infection, may aid in the functional annotation of these genes.
Maximum Field Inside a Reverberation Chamber Modeled by the Generalized Extreme Value Distribution

Classically, the statistical model of the maximum field inside a reverberation chamber (RC) is derived from the field magnitude model that is only known for the overmoded RC. We propose in this paper to model the maximum field by the generalized extreme value (GEV) distribution, as an application of the Fisher-Tippett theorem that formulates the asymptotic distributions of sample maximum. As the knowledge of the parent distribution (field magnitude) is not required, the GEV distribution is suitable for both overmoded and undermoded regimes (few modes excited). A Monte Carlo simulation illustrates the use of the GEV distribution for the overmoded RC. Modal FEM analysis of the RC extends the application to the undermoded regime. Special attention is brought to the issue of GEV parameter estimation: The so-called L-moments technique is advantageously employed to estimate the parameters from the small data sample. Dispersion of the estimated parameters is approximated and reduced by averaging uncorrelated values obtained from a narrow frequency band
Cycling pattern and read/bake conditions dependence of random telegraph noise in decananometer NAND flash arrays

We conduct a thorough investigation of random telegraph noise (RTN) dependence on program/erase and read/bake conditions in state-of-the-art 1X and 2X Flash NAND technologies. We demonstrate that RTN depends only on the cycle number and not on the program level or cycling pattern. Moreover, if the cumulative distribution of RTN is considered, a negligible temperature dependence appears, in apparent contrast with thermal activation of single-trap time constants. RTN appears also to be independent of the read and bake temperature, although a slight asymmetry in the distribution tails is induced by charge detrapping. A Monte Carlo model is also presented to account for the experimental observations.
Antioxidant treatments do not improve force recovery after fatiguing stimulation of mouse skeletal muscle fibres

The contractile performance of skeletal muscle declines during intense activities, i.e. fatigue develops. Fatigued muscle can enter a state of prolonged low-frequency force depression (PLFFD). PLFFD can be due to decreased tetanic free cytosolic [Ca 2+ ] ([Ca 2+ ]i) and/or decreased myofibrillar Ca 2+ sensitivity. Increases in reactive oxygen and nitrogen species (ROS/RNS) may contribute to fatigue-induced force reductions. We studied whether pharmacological ROS/RNS inhibition delays fatigue and/or counteracts the development of PLFFD. Mechanically isolated mouse fast-twitch fibres were fatigued by sixty 150 ms, 70 Hz tetani given every 1 s. Experiments were performed in standard Tyrode solution (control) or in the presence of: NADPH oxidase (NOX) 2 inhibitor (gp91ds-tat); NOX4 inhibitor (GKT137831); mitochondria-targeted antioxidant (SS-31); nitric oxide synthase (NOS)
Quantitative measurement of airborne cockroach allergen in New York City apartments.

UNLABELLED We designed and tested a sampling and analysis system for quantitative measurement of airborne cockroach allergen with sufficient sensitivity for residential exposure assessment. Integrated 1-week airborne particle samples were collected at 10-15 LPM in 19 New York City apartments in which an asthmatic child who was allergic to cockroach allergen resided. Four simultaneous air samples were collected in each home: at heights of 0.3 and 1 m in the child's bedroom and in the kitchen. Extracts of air samples were analyzed by ELISA for the cockroach allergen Bla g2, modified by amplifying the colorimetric signal generated via use of AMPLI-Q detection system (DAKO Corporation, Carpinteria, CA, USA). Settled dust samples were quantified by conventional ELISA. Of the homes where cockroach allergen was detected in settled dust, Bla g2 also was detected in 87% and 93% of air samples in the bedroom and kitchen, respectively. Airborne Bla g2 levels were highly correlated within and between the bedroom and kitchen locations (P < 0.001). Expressed as picogram per cubic meter, the room average geometric mean for Bla g2 concentrations was 1.9 pg/m³ (95% CI 0.63, 4.57) and 3.8 pg/m³ (95% CI 1.35, 9.25) in bedrooms and kitchens, respectively. This method offers an attractive supplement to settled dust sampling for cockroach allergen exposure health studies. PRACTICAL IMPLICATIONS Until now, cockroach allergen exposures have usually been assessed by collection and analysis of settled dust, on the assumption that airborne cockroach allergen cannot be reliably measured. In this study, a sensitive and quantitative method for measuring indoor airborne exposures to cockroach allergens involving a 7-day integrated total suspended particulate (TSP) sample collected at approximately 10-15 l/min was developed. Investigators are now empowered with an alternative exposure assessment method to supplement their studies and the understanding of allergen aerodynamics in the homes of children with asthma. We report airborne cockroach allergen in apartments, suggesting an ongoing burden of inhalation exposure.
Statistical analysis of the DCT coefficients and their quantization error

A detailed probabilistic analysis of the DCT coefficients and the error incurred during the quantization and reconstruction of natural images is presented. The distribution of both the DCT coefficients and their quantization error were modeled with the generalised Gaussian function (GGF) which includes the Gaussian and Laplacian PDF as special cases. The /spl chi//sup 2/ and Kolmogorov-Smirnov goodness-of-fit tests were used to determine the free parameter of the GGF that yields the best fit to experimental data. This analysis has yielded several new results regarding the distribution of the coefficients, their differences and their quantization error. The results of this analysis can improve the design of practical DCT based compression systems.
I Knew I Would Be Safer. Experiences of Kenyan HIV Serodiscordant Couples Soon After Pre-Exposure Prophylaxis (PrEP) Initiation.

Pre-exposure prophylaxis (PrEP) for HIV-uninfected persons is highly efficacious for HIV prevention. Understanding how people at risk for HIV will use PrEP is important to inform PrEP scale-up and implementation. We used qualitative methods to gather insights into couples' early experiences with PrEP use within the Partners Demonstration Project, an open-label implementation study evaluating integrated delivery of PrEP and antiretroviral therapy (ART). PrEP is offered to HIV uninfected partners until the HIV-infected partner initiates and sustains ART use (i.e., PrEP as a "bridge" to ART initiation and viral suppression). From August 2013 to March 2014 we conducted 20 in-depth dyadic interviews (n = 40) with heterosexual HIV serodiscordant couples participating at the Thika, Kenya study site, exploring how couples make decisions about using PrEP for HIV prevention. We developed and applied deductive and inductive codes to identify key themes related to experiences of PrEP initiation and use of time-limited PrEP. Couples reported that PrEP offered them an additional strategy to reduce the risk of HIV transmission, meet their fertility desires, and cope with HIV serodiscordance. Remaining HIV negative at follow-up visits reinforced couples' decisions and motivated continued adherence to PrEP. In addition, confidence in their provider's advice and client-friendly services were critical to their decisions to initiate and continue use of PrEP. Strategies for wide-scale PrEP delivery for HIV serodiscordant couples in low resource settings may include building capacity of health providers to counsel on PrEP adoption while addressing couples' concerns and barriers to adoption and continued use.
Simple method for detecting fluconazole-resistant yeasts with chromogenic agar

A method for detecting fluconazole-resistant yeasts was developed that uses chromogenic agar containing fluconazole. Yeasts were plated on media with fluconazole at 0, 8, and 16 micrograms/ml. On media without fluconazole, normal growth of susceptible yeasts (defined as those having a fluconazole MIC of < 8 micrograms/ml) was detected, while fluconazole-containing media suppressed susceptible strains and normal colonies of resistant yeasts (fluconazole MICs of > or = 8 micrograms/ml) were detected. This method was used to screen for resistance in oropharyngeal candidiasis. Isolates having fluconazole MICs of > or = 8 micrograms/ml and < 8 micrograms/ml were correctly predicted in 43 of 45 cultures and 115 of 116 cultures, respectively. This screening method appears to be rapid and sensitive for detection of fluconazole-resistant yeasts.
Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Mouse Feces

ABSTRACT Mouse models are widely used for studying gastrointestinal (GI) tract-related diseases. It is necessary and important to develop a new set of primers to monitor the mouse gut microbiota. In this study, 16S rRNA gene-targeted group-specific primers for Firmicutes, Actinobacteria, Bacteroidetes, Deferribacteres, “Candidatus Saccharibacteria,” Verrucomicrobia, Tenericutes, and Proteobacteria were designed and validated for quantification of the predominant bacterial species in mouse feces by real-time PCR. After confirmation of their accuracy and specificity by high-throughput sequencing technologies, these primers were applied to quantify the changes in the fecal samples from a trinitrobenzene sulfonic acid-induced colitis mouse model. Our results showed that this approach efficiently predicted the occurrence of colitis, such as spontaneous chronic inflammatory bowel disease in transgenic mice. The set of primers developed in this study provides a simple and affordable method to monitor changes in the intestinal microbiota at the phylum level.
Computation of AC wet flashover voltage of ceramic and composite insulators

This paper presents a theoretical method for calculating the flashover voltage of ceramic and composite insulators under wet conditions. The insulator surface is assumed to be clean. A 3-dimensional computer package (Coulomb) was used to calculate the electric field of wet surfaces. The surface wettability has been varied from hydrophobic to hydrophilic using the Swedish transmission research institute (STRI) method of classification. The calculated results are in good agreement with published data.
Endoplasmic reticulum retention of KCNQ2 potassium channel mutants following temperature elevation.

BACKGROUND KCNQ2 plays a key role in the regulation of neuronal excitability. The R214W and Y284C mutants of KCNQ2 channels, which are associated with BFNC, can decrease channel function to cause neuronal hyperexcitability and promote seizures. Previous studies revealed that elevated temperature caused up-regulation of KCNQ2 expression. OBJECTIVE The present study sought to investigate the impact of temperature elevation on neuronal KCNQ2 ion channel mutants. METHODS Protein expression of wt KCNQ2 and the R214W, Y284C and truncated selective filter mutants at different temperatures was detected by live-cell confocal fluorescence microscopy and by Western blotting. Whole-cell patch clamp was performed to record the effect of temperature on the electrophysiological activity of KCNQ2 channels. RESULTS Temperature elevation caused an unexpected increase in voltage-dependent KCNQ2 channel activation but also increased the endoplasmic reticulum (ER) retention of KCNQ2 protein, and the ER retention was greater for mutants associated with BFNC than for wt KCNQ2. Temperature elevation did not increase the fluorescence intensity of cells transfected with a truncated selective filter mutant. CONCLUSIONS The direct effect of heat on KCNQ2 channels may be involved in excitability regulation of neurons, and the P-loop region is critical for temperature-dependent modulation of the expression and trafficking of KCNQ2 channels.
Synthetic octacalcium phosphate‐enhanced reparative dentine formation via induction of odontoblast differentiation

Synthetic octacalcium phosphate (OCP) has been suggested to be a useful biomaterial for the regeneration of hard tissues, including bone. However, it remains unknown whether OCP induces dentine formation by dental pulp. We investigated biomineralization of dental pulp exposed to synthetic OCP in vitro and in vivo. When dental pulp was exposed directly to OCP, rapid formation of reparative dentine (RD) was induced and expression of dentine sialoprotein synthesis was observed in dental pulp adjacent to newly synthesized RD. OCP inhibited the proliferation of rat pulp cells and also promoted their odontoblastic differentiation in vitro, as alkaline phosphatase activity, mineralization of pulp cells and the expression level of dentine sialophosphoprotein were enhanced. Direct contact between OCP and pulp cells is required for OCP to exhibit its effects in vitro. The expression level of Runx2, a transcription factor whose downregulation is closely related to odontoblast differentiation, was downregulated in pulp cells cultured with OCP. Structural changes of OCP during culture were determined by Fourier transform infrared spectroscopy. OCP tended to be converted to carbonate hydroxyapatite after incubation with or without pulp cells, which may be analogous to biological apatite crystals. Taken together, our data suggest that synthetic OCP supports RD formation by dental pulp and downregulation of Runx2 may be involved in that stimulatory activity. Furthermore, OCP–apatite conversion is involved in this stimulatory capacity of OCP. Copyright © 2013 John Wiley & Sons, Ltd.
Cloning of genes from members of the family Enterobacteriaceae with mini-Mu bacteriophage containing plasmid replicons

An in vivo cloning system that uses derivatives of the Escherichia coli bacteriophage Mu with plasmid replicons has been extended to five different species of the family Enterobacteriaceae. Mu and these mini-Mu replicon elements were introduced into strains of E. coli, Shigella flexneri, Salmonella typhimurium, Citrobacter freundii, and Proteus mirabilis by infection, by transformation, or by conjugation with newly constructed broad-host-range plasmids containing insertions of these elements. Lysates from these cells, lysogenic for Mu and mini-Mu elements, were used to infect sensitive recipient strains of E. coli, S. typhimurium, and C. freundii. Drug-resistant transductants had mini-Mu replicon elements with inserts of different DNA sequences. All of the lysogens made could be induced to yield high phage titers, including those coming from strains that were resistant to Mu and Mu derivatives. Clones of 10 particular genes were isolated by their ability to complement specific mutations in the recipient strains, even in the presence of the E. coli K-12 restriction system. Some of the mini-Mu replicon elements used contained lac gene fusing segments and resulted in fusions of the lac operon to control regions in the cloned sequences.
Characterizing doxorubicin‐induced apoptosis in HepG2 cells using an integrated microfluidic device

Apoptosis has now established its importance in numerous areas of biology and is recently receiving great attention as an important topic related to the development of diseases. In this work, an integrated microfluidic device was developed to characterize doxorubicin‐induced apoptosis in human hepatocellular carcinoma (HepG2) cells. A continuous concentration gradient of stimulator (doxorubicin) was generated in the upstream network and used to perfuse downstream cultured HepG2 cells. The appropriate fluorescent dyes were introduced into cells from the inlets connected to the cell culture chambers, allowing one to distinguish apoptotic cells from nonapoptotic or necrotic cells. The resultant fluorescence of cellular population was monitored and quantified with single‐cell resolution to infer the apoptosis process being studied. The feasibility of studying apoptosis was demonstrated by measuring several apoptotic events, including morphological alterations, plasma membrane phosphatidylserine externalization, and mitochondrial membrane potential collapse. This microfluidic device, integrating the cell culture, stimulation, staining, and washing steps into a single device, can simultaneously generate a number of experimental conditions and investigate multiple parameters relating stimulation to apoptosis. It offers a unique platform to characterize various cellular responses in a high‐throughput fashion, which is otherwise impossible with conventional methods.
Antimicrobial factors in the cervical mucus plug.

OBJECTIVE The cervical mucus plug is positioned between the microbe-rich vagina and the normally sterile uterine cavity, which suggests a host defense function, but few relevant data are available. We analyzed the composition and antimicrobial activity of cervical mucus plugs. STUDY DESIGN Cervical mucus plugs were collected from healthy women at delivery. Groups of plugs were randomly selected for electrolyte analysis, antimicrobial activity assays against group B Streptococcus, Escherichia coli, Candida albicans, and assays of known antimicrobial polypeptides. RESULTS Both intact cervical mucus plugs and their aqueous extracts exhibited antimicrobial activity against aerobic microbes, in the order of potency: group B Streptococcus > E coli > C albicans. Semiquantitative Western blotting of extracts showed that secretory leukoprotease inhibitor, lysozyme, lactoferrin, and neutrophil defensins were present at concentrations that were sufficient for antimicrobial activity. CONCLUSION The cervical mucus plug is not only a mechanical but also a chemical barrier to infection that ascends from the vagina.
Effect of Feeding Schedule on Tympanic Temperature of Steer Calves During Winter

Angus steer calves (n=135) were used in a 55d feedlot growing study to investigate the effects of feeding schedule on tympanic temperature response when limit feeding. Steers were fed a high moisture ear corn diet (58 Mcal/cwt NEg) at 0900h (AM), 1500h (PM) or 50% at 0900h and 50% at 1500h (SPLIT) to allow for 2.50lb ADG. Climatic data were collected at 30 min intervals throughout the study via an on site automated weather station. Tympanic temperatures (TT) were collected every 30 min (5 steers/trt) for 5d (d44 to d48). Mean ambient temperature during the 5d TT collection period was -6.5F (-23.1 to 9.1F). After 55d, BW (802, 808 and 802lb), ADG (2.56, 2.67 and 2.52lb) and feed efficiency (5.73, 5.52 and 5.87) did not differ (P>.10) between AM, PM and SPLIT respectively, but followed rankings of previous research. Diurnal TT patterns were assessed by separating the day into three periods based on mean hourly wind chills (44.2, 17.8 and 7.5F) for Period 1 (0800 to 1600h), Period 2 (1630 to 2100h) and Period 3 (2130 to 0730h) respectively. Peak TT occurred during Period 2 for AM (102.4F) and Period 3 for PM (103.2F). SPLIT fed steers exhibited TT peaks of 103.9F or greater in each period. These data indicate that by adjusting feeding schedule it is possible to alter the time at which peak TT may occur, so that peak TT coincides with colder periods of the day. Elevated TT across all periods for SPLIT suggests that these steers may have increased metabolic rate to maintain normal TT during extreme cold. Additional research is needed to explain the changes in TT and how feeding times may impact energy partitioning.