Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for Apoptosis Induction in Myofibroblasts during Palatal Mucoperiosteal Repair

Apoptosis is thought to be a requisite event for maintaining kinetic homeostasis within continually renewing tissues such as the oral mucosa and skin. However, no systematic study of the apoptotic process in fibroblasts in the oral mucosa following injury has been performed. In this study, we have assessed the expression of transforming growth factor-β1 (TGF-β1) and basic fibroblast growth factor (bFGF), which are among the most important modulators of wound repair, during wound healing following mucoperiosteal injury in the rat plate. In addition, we have investigated fibroblast differentiation and apoptosis by immunohistochemical analysis for a-smooth-muscle (a-SM) actin or DNA strand breaks, respectively, to clarify the mechanisms of the wound healing process. TGF-β1-positive cells were noted in the subepithelium from Day 2 to Day 14 after injury, by which time the wounds were completely re-epithelialized. Strong expression of bFGF was observed, mainly in macrophages and monocytes at the injured site, from Day 10 to Day 14 after injury. TGF-β1 and bFGFimmunostaining was significantly lower during the later phase of wound healing. In addition, the number of myofibroblasts expressing a-SM actin increased (peak at Day 14), and thereafter gradually decreased. In parallel, the apoptosis in myofibroblasts was prominent on Day 14. These results suggest that TGF-β1 and bFGF may be potential stimulators of apoptosis in myofibroblasts after re-epithelialization in the palatal wound healing process. The regulation of apoptotic phenomena during wound healing may be important in scar establishment and development of pathological scarring.
Increased GABAA‐Receptor α1‐Subunit Expression in Hippocampal Dentate Gyrus after Early‐life Status Epilepticus

Summary: Purpose: Previous studies in neonatal (postnatal day 10) and adult rats suggest that status epilepticus (SE) induces changes in the α1 subunit of the GABAA receptor (GABRA1) in dentate granule neurons (DGNs) that are age dependent and vary inversely with the likelihood of epilepsy development. In the present study, we examined GABRA1 expression after SE at postnatal day 20 (P20), an intermediate age when only a subset of SE‐exposed animals develop epilepsy.
Measuring the signal-to-noise ratio of a neuron

Significance Neurons represent both signal and noise in binary electrical discharges termed action potentials. Hence, the standard signal-to-noise ratio (SNR) definition of signal amplitude squared and divided by the noise variance does not apply. We show that the SNR estimates a ratio of expected prediction errors. Using point process generalized linear models, we extend the standard definition to one appropriate for single neurons. In analyses of four neural systems, we show that single neuron SNRs range from −29 dB to −3 dB and that spiking history is often a more informative predictor of spiking propensity than the signal or stimulus activating the neuron. By generalizing the standard SNR metric, we make explicit the well-known fact that individual neurons are highly noisy information transmitters. The signal-to-noise ratio (SNR), a commonly used measure of fidelity in physical systems, is defined as the ratio of the squared amplitude or variance of a signal relative to the variance of the noise. This definition is not appropriate for neural systems in which spiking activity is more accurately represented as point processes. We show that the SNR estimates a ratio of expected prediction errors and extend the standard definition to one appropriate for single neurons by representing neural spiking activity using point process generalized linear models (PP-GLM). We estimate the prediction errors using the residual deviances from the PP-GLM fits. Because the deviance is an approximate χ2 random variable, we compute a bias-corrected SNR estimate appropriate for single-neuron analysis and use the bootstrap to assess its uncertainty. In the analyses of four systems neuroscience experiments, we show that the SNRs are −10 dB to −3 dB for guinea pig auditory cortex neurons, −18 dB to −7 dB for rat thalamic neurons, −28 dB to −14 dB for monkey hippocampal neurons, and −29 dB to −20 dB for human subthalamic neurons. The new SNR definition makes explicit in the measure commonly used for physical systems the often-quoted observation that single neurons have low SNRs. The neuron’s spiking history is frequently a more informative covariate for predicting spiking propensity than the applied stimulus. Our new SNR definition extends to any GLM system in which the factors modulating the response can be expressed as separate components of a likelihood function.
Nuclear translocation of p42/p44 mitogen‐activated protein kinase is required for growth factor‐induced gene expression and cell cycle entry

Mitogen‐activated protein kinase (MAPK) modules, composed of three protein kinases activated by successive phosphorylation, are involved in the signal transduction of a wide range of extracellular agents. In mammalian cells, mitogenic stimulation triggers the translocation of p42/p44MAPK from the cytoplasm to the nucleus, whereas the other protein kinases of the module remain cytosolic. Since MAPK has been shown to phosphorylate and activate nuclear targets, such as the transcription factor Elk1, it has been proposed, but not yet demonstrated, that MAPK nuclear translocation could represent a critical step in signal transduction. In this study, we sequestered p42/p44MAPK in the cytoplasm by the expression of a catalytically inactive form of cytoplasmic MAP kinase phosphatase (MKP‐3/Pyst‐1). Sequestering MAPK in the cytoplasm did not alter its activation or its ability to phosphorylate cytoplasmic substrates of MAPK (p90RSK1 or an engineered cytoplasmic form of Elk1). In contrast, prevention of MAPK nuclear translocation strongly inhibited Elk1‐dependent gene transcription and the ability of cells to reinitiate DNA replication in response to growth factors. Thus the relocalization of MAPK to the nucleus appears to be an important regulatory step for mitogen‐induced gene expression and cell cycle re‐entry.
Validity of diabetes self-reports in the Women’s Health Initiative

ObjectiveThis study aims to determine the positive and negative predictive values of self-reported diabetes during the Women’s Health Initiative (WHI) clinical trials. MethodsAll WHI trial participants from four field centers who self-reported diabetes at baseline or during follow-up, as well as a random sample of women who did not self-report diabetes, were identified. Women were surveyed regarding diagnosis and treatment. Medical records were obtained and reviewed for documented treatment with antidiabetes medications or for physician diagnosis of diabetes supported by laboratory measurements of glucose. ResultsWe identified 1,275 eligible participants; 732 consented and provided survey data. Medical records were obtained for 715 women (prevalent diabetes, 207; incident diabetes, 325; no diabetes, 183). Records confirmed 91.8% (95% CI, 87.0-95.0) of self-reported prevalent diabetes cases and 82.2% (95% CI, 77.5-86.1) of incident diabetes cases. Among those who never self-reported diabetes, there was no medical record or laboratory evidence for diabetes in 94.5% (95% CI, 89.9-97.2). Women with higher body mass index were more likely to accurately self-report incident diabetes. In a subgroup of participants enrolled in fee-for-service Medicare, a claims algorithm correctly classified nearly all diabetes cases and noncases. ConclusionsAmong WHI clinical trial participants, there are high positive predictive values of self-reported prevalent diabetes (91.8%) and incident diabetes (82.2%) and a high negative predictive value (94.5%) when diabetes is not reported. For participants enrolled in fee-for-service Medicare, a claims algorithm has high positive and negative predictive values.
CD4, Viral Load Response, and Adherence Among Antiretroviral-Naive Breast-feeding Women Receiving Triple Antiretroviral Prophylaxis for Prevention of Mother-to-Child Transmission of HIV in Kisumu, Kenya

Background:Health benefits and survival of an exclusively breast-fed infant is dependent on the mother's health; thus, the need for antiretroviral (ARV) intervention for prevention of mother-to-child transmission (PMTCT). Achieving maternal health benefits from these regimens requires adherence to the treatments and close monitoring. We evaluated virologic, immunologic responses, and adherence among women receiving maternal triple ARV prophylaxis consisting of lamivudine/zidovudine and nevirapine or nelfinavir in the Kisumu Breastfeeding Study. Methods:We analyzed baseline demographic data, trends in CD4+ count, and viral load (VL) at enrollment (32–34 weeks gestation), delivery, 14 and 24 weeks postpartum among 434 women who remained in the study at 24 weeks postpartum. Adherence rates were determined using pill counts reinforced by self-report and drug calendar. We dichotomized adherence as ≥95% versus <95%. Results:Among the 434 women, 84% (n = 366) had adherence ≥95%. The proportion of women with undetectable VL (<400 copies/mL) increased from 6% at baseline to 79%, and that of those with CD4+ count <250 cells per microliter decreased from 23% (100) at baseline to 5% (22) at 24 weeks postpartum. In discrete-survival model, time to achieving VL suppression was associated with baseline VL <5.0 log copies per milliliter, parity ≥2, and use of nelfinavir- versus nevirapine-based ARV. Association between undetectable VL with duration of therapy (P < 0.0001) and adherence with suppression of VL (P = 0.001) was observed. Conclusions:High baseline VL and short exposure to ARVs for PMTCT are risk factors for failing to achieve undetectable VL. These findings support the new WHO guidelines for early initiation of ARV prophylaxis for PMTCT for maximal reduction of maternal VL.
Does access to credit improve household welfare? Evidence from Ethiopia using endogenous regime switching regression

Purpose - The purpose of this paper is to investigate how credit access affects the welfare of households and sheds light on how household characteristics influence the decision to take credit and the efficiency in credit use. Design/methodology/approach - This study uses data from the fourth round of the Ethiopian Rural Household Survey conducted in 2009, and examines factors that determine the decision to take credit and the effect of such decision on household welfare. The household welfare variable is measured by the food security indicator and total food expenditure. The study employs endogenous Regime Switching model to account for endogeneity in access to credit and self-selection bias in the decision to participate in credit. Findings - The result from the kernel distribution shows households with access to credit have more consumption expenditure than those without access to credit. The ordinary least square regression shows that access to credit increases total consumption by 12 percent without considering self-selection bias. Participation in non-farm activity increases the demand for credit by 17 percent. Land holding, household size, and participation in saving associations increase the probability of getting credit by 5, 11, and 20 percent, respectively. Access to credit appears to have a positive impact on food security in both actual and counterfactual cases for the current credit receivers. Originality/value - This study provides a thorough analysis of the impacts of access to credit on household welfare in Ethiopia. The study contributes to the debate on the link between access to credit and household welfare and provides valuable input for policy makers.
Complete DNA Sequence and Comparative Analysis of the 50-Kilobase Virulence Plasmid of Salmonella entericaSerovar Choleraesuis

ABSTRACT The complete nucleotide sequence of pKDSC50, a large virulence plasmid from Salmonella enterica serovar Choleraesuis strain RF-1, has been determined. We identified 48 of the open reading frames (ORFs) encoded by the 49,503-bp molecule. pKDSC50 encodes a known virulence-associated operon, the spv operon, which is composed of genes essential for systemic infection by nontyphoidalSalmonella. Analysis of the genetic organization of pKDSC50 suggests that the plasmid is composed of several virulence-associated genes, which include the spvRABCD genes, plasmid replication and maintenance genes, and one insertion sequence element. A second virulence-associated region including the pef(plasmid-encoded fimbria) operon and rck (resistance to complement killing) gene, which has been identified on the virulence plasmid of S. enterica serovar Typhimurium, was absent. Two different replicon regions, similar to the RepFIIA and RepFIB replicons, were found. Both showed high similarity to those of the pO157 plasmid of enterohemorrhagic Escherichia coliO157:H7 and the enteropathogenic E. coli (EPEC) adherence factor plasmid harbored by EPEC strain B171 (O111:NM), as well as the virulence plasmids of Salmonella serovars Typhimurium and Enteritidis. Comparative analysis of the nucleotide sequences of the 50-kb virulence plasmid of serovar Choleraesuis and the 94-kb virulence plasmid of serovar Typhimurium revealed that 47 out of 48 ORFs of the virulence plasmid of serovar Choleraesuis are highly homologous to the corresponding ORFs of the virulence plasmid of serovar Typhimurium, suggesting a common ancestry.
A new Compact Support Kernel of support vector machines

A new kernel based on the KCS (kernels with compact support) kernel family is proposed. The training time of the support vector machines of the new kernel is shorter than that of the common kernels. The support vector rate of the classifying machines also keeps in a low level. Compared with other classifying kernels, a great deal of experimental results indicates that the new kernel has a better classifying performance in VAD (voice active detection).
Sequence-specific and Shape-selective RNA Recognition by the Human RNA 5-Methylcytosine Methyltransferase NSun6*

Human NSun6 is an RNA methyltransferase that catalyzes the transfer of the methyl group from S-adenosyl-l-methionine (SAM) to C72 of tRNAThr and tRNACys. In the current study, we used mass spectrometry to demonstrate that human NSun6 indeed introduces 5-methylcytosine (m5C) into tRNA, as expected. To further reveal the tRNA recognition mechanism of human NSun6, we measured the methylation activity of human NSun6 and its kinetic parameters for different tRNA substrates and their mutants. We showed that human NSun6 requires a well folded, full-length tRNA as its substrate. In the acceptor region, the CCA terminus, the target site C72, the discriminator base U73, and the second and third base pairs (2:71 and 3:70) of the acceptor stem are all important RNA recognition elements for human NSun6. In addition, two specific base pairs (11:24 and 12:23) in the D-stem of the tRNA substrate are involved in interacting with human NSun6. Together, our findings suggest that human NSun6 relies on a delicate network for RNA recognition, which involves both the primary sequence and tertiary structure of tRNA substrates.
Clinical characteristics and prognosis of drug-associated acute respiratory distress syndrome compared with non-drug-associated acute respiratory distress syndrome: a single-centre retrospective study in Japan

Objectives To report the clinical features and prognosis of drug-associatedacute respiratory distress syndrome (ARDS). Design A retrospective analysis of data collected during a prospective cohort study. Setting Intensive care unit in a teaching hospital. Participants A total of 197 Japanese patients with ARDS diagnosed by the Berlin definition who were admitted to the Division of Respiratory Medicine from October 2004 to December 2015 were enrolled in the study and were classified as two groups according to their causes: a drug-associated ARDS group (n=27) and a non-drug-associated ARDS group (n=170). Primary outcome measure is 28-day mortality, and the secondaryoutcome measure is ventilator-free days. Results The Acute Physiology and Chronic Health Evaluation II scores were significantly lower in the drug-associated ARDS group than in the non-drug-associated ARDS group (median (IQR): 18.0 (16.5–21.0) vs 23.0 (18.0–26.0), p<0.001), and the arterial oxygen tension/fractional inspired oxygen ratio was higher (148.0 (114.1–177.5) vs 101.0 (71.5–134.0), p=0.003). In the drug-associated ARDS group, although high-resolution CT scores indicative of the extent of fibroproliferation (301.6 (244.1–339.8) vs 208.3 (183.4–271.6), p<0.001), serum lactate dehydrogenase levels (477 (365–585) vs 322 (246–434), p=0.003) and the McCabe scores (score 1/2/3, n (%): 20 (74)/4 (15)/3 (11)vs154 (91)/7 (4)/9 (5), p=0.04) were significantly higher, ventilator weaning was earlier (p<0.001) and 28-day mortality was better (p=0.043). After adjusting for potentially confounding covariates, drug-associated ARDS group was associated with lower 28-day mortality (adjusted HR (HR) 0.275; 95% CI 0.106 to 0.711; p=0.008). Conclusions Although more severe lung damage with fibroproliferation was observed in patients with drug-associated ARDS, ventilator weaning was earlier, and their prognosis was better than the others. Further well-designed prospective studies are needed.
Chronic binge ethanol consumption accelerates progression of simian immunodeficiency virus disease.

BACKGROUND While alcohol consumption is known to increase the incidence and severity of infections, the impact of alcohol consumption on human immunodeficiency virus (HIV) disease progression has been difficult to assess. Therefore, we examined the effect of ethanol on simian immunodeficiency virus (SIV) disease progression in a well-defined model utilizing rhesus macaques. METHODS Alcohol was administered for 5 hours via an indwelling intragastric catheter to achieve an alcohol concentration of 50 to 60 mM for 4 consecutive days per week for the duration of the study. Control animals received isocaloric sucrose. After 3 months, animals were inoculated intravenously with 10,000 times the ID(50) of SIV(DeltaB670) and followed to end-stage disease. RESULTS Plasma SIV ribonucleic acid (RNA) was higher in alcohol-consuming animals compared with sucrose-treated animals during the early asymptomatic stage of disease but not at later time points. This increase in viral set point was associated with more rapid progression to end-stage disease in macaques administered alcohol (median=374 days) compared with sucrose (median=900 days). The decline in blood CD4+ cells was similar in both groups of animals. CONCLUSIONS This study indicates that frequent episodes of alcohol intoxication in SIV+ macaques increase viral set point in association with more rapid development of end-stage disease.
Increasing body mass index z-score is continuously associated with complications of overweight in children, even in the healthy weight range.

CONTEXT Overweight/obesity in children is increasing. Incidence data for medical complications use arbitrary cutoff values for categories of overweight and obesity. Continuous relationships are seldom reported. OBJECTIVES The objective of this study is to report relationships of child body mass index (BMI) z-score as a continuous variable with the medical complications of overweight. DESIGN This study is a part of the larger, prospective cohort Growth and Development Study. SETTING Children were recruited from the community through randomly selected primary schools. Overweight children seeking treatment were recruited through tertiary centers. PARTICIPANTS Children aged 6-13 yr were community-recruited normal weight (n = 73), community-recruited overweight (n = 53), and overweight treatment-seeking (n = 51). Medical history, family history, and symptoms of complications of overweight were collected by interview, and physical examination was performed. Investigations included oral glucose tolerance tests, fasting lipids, and liver function tests. MAIN OUTCOME MEASURE Adjusted regression was used to model each complication of obesity with age- and sex-specific child BMI z-scores entered as a continuous dependent variable. RESULTS Adjusted logistic regression showed the proportion of children with musculoskeletal pain, obstructive sleep apnea symptoms, headaches, depression, anxiety, bullying, and acanthosis nigricans increased with child BMI z-score. Adjusted linear regression showed BMI z-score was significantly related to systolic and diastolic blood pressure, insulin during oral glucose tolerance test, total cholesterol, high-density lipoprotein, triglycerides, and alanine aminotransferase. CONCLUSION Child's BMI z-score is independently related to complications of overweight and obesity in a linear or curvilinear fashion. Children's risks of most complications increase across the entire range of BMI values and are not defined by thresholds.
Influence of various amounts of fumaric acid on performance and parameters of the acid–base balance of growing bulls fed with grass or maize silage

The aim of the present study was to determine the effects of the potential methane reducer fumaric acid on the fattening performance and acid–base balance of growing bulls fed two different silage types as roughage (maize and grass silage). A total of 62 fattening bulls (German Holstein breed, initial body weight: 266 ± 42 kg), randomly assigned to eight feeding groups, received four levels of fumaric acid (0, 100, 200 or 300 g/d) at each silage type. The daily feed and water intake and the live weight were measured over the whole testing period of 280 days. In blood samples, blood cells and blood gases as a parameter of acid–base status were analysed. Feed and faeces were collected to determine the apparent nutrient digestibility. Five animals from each group fed maize or grass silage, supplemented with 0 g or 300 g fumaric acid, were slaughtered at 580 kg body weight. After slaughter, rumen fluid pH was measured and dressing percentage was calculated. Neither the total feed intake (8.81 ± 0.07 kg/d) nor the daily weight gain (1277±24 g/d) was influenced significantly by treatments. Fumaric acid supplementation did not influence the erythrocyte count or the blood gas concentration. The silage type significantly influenced the apparent digestibility of the whole diet. The dressing percentage was slightly higher (p < 0.1) after fumaric acid supplementation. No signs of an incompatibility to fumaric acid on the animals were observed over the whole experimental period. However, it seems to be necessary to conduct more long-term studies with different silage types and addition of organic acids combined with direct measurements of methane.