Miracle-dz/UniFAR-FTUs huggingface dataset:
Reverse transcriptase activity in chicken embryo fibroblast culture supernatants is associated with particles containing endogenous avian retrovirus EAV-0 RNA

We have recently shown that live attenuated virus vaccines produced on chicken-derived cells contain low levels of particle-associated reverse transcriptase (RT). In both virus and corresponding control harvests produced on chicken embryo fibroblasts, these activities were present at significantly higher concentrations than in the vaccines. In order to identify the putative retrovirus sequence responsible for this activity, a novel method for the selective PCR amplification of particle-associated retrovirus RNA that uses DNA primers complementary to the primer binding sites of the known exogenous retroviruses in combination with an anchor primer was applied. A product of the endogenous avian retrovirus family EAV-0, termed EAV-0(B1), was reproducibly generated with a tRNA(Trp)-derived primer from the RT peak fraction of a sucrose density gradient run with a harvest of a live attenuated measles vaccine. In contrast, no products were detected with primers derived from tRNA(Pro), tRNA(Lys)1,2 or tRNA(Lys)3. In the same fraction, genomic RNA of EAV-0(B1) was demonstrated by long PCR. Analysis of several sucrose density gradients from different harvests of various manufacturers demonstrated accumulation of, and colocalization with, RT activity for the EAV-0(B1) RNA but not for a chicken cellular mRNA. Synthesis of cDNA from EAV-0(B1) RNA was shown by endogenous RT reaction. Furthermore, complexes of naturally primed EAV-0(B1) RNA with RT were demonstrated. Taken together, these data strongly suggest that EAV-0 is able to produce virus-like particles with an active RT.
The mirror illusion: does proprioceptive drift go hand in hand with sense of agency?

Vection can be regarded as the illusion of “whole-body” position perception. In contrast, the mirror illusion is that of “body-part” position perception. When participants viewed their left hands in a mirror positioned along the midsaggital axis while moving both hands synchronously, they hardly noticed the spatial offset between the hand in the mirror and the obscured real right hand. This illusion encompasses two phenomena: proprioceptive drift and sense of agency. Proprioceptive drift represented a perceptual change in the position of the obscured hand relative to that of the hand in the mirror. Sense of agency referred to the participants' subjective sense of controlling body image as they would their own bodies. We examined the spatial offset between these two phenomena. Participants responded to a two-alternative forced choice (2AFC) question regarding the subjective position of their right hands and questionnaires regarding sense of agency at various positions of the right hand. We analyzed the 2AFC data using a support vector machine and compared its classification result and the questionnaire results. Our data analysis suggested that the two phenomena were observed in concentric space, but the estimated range of the proprioceptive drift was slightly narrower than the range of agency. Although this outcome can be attributed to differences in measurement or analysis, to our knowledge, this is the first report to suggest that proprioceptive drift and sense of agency are concentric and almost overlap.
Optimal management of urinary tract infections in older people

Urinary tract infections (UTI) occur frequently in older people. Unfortunately, UTI is commonly overdiagnosed and overtreated on the basis of nonspecific clinical signs and symptoms. The diagnosis of a UTI in the older patient requires the presence of new urinary symptoms, with or without systemic symptoms. Urinalysis is commonly used to diagnose infection in this population, however, the evidence for its use is limited. There is overwhelming evidence that asymptomatic bacteriuria should not be treated. Catheter associated urinary tract infection accounts for a significant amount of hospital-associated infection. Indwelling urinary catheters should be avoided where possible and alternatives sought. The use of narrow spectrum antimicrobial agents for urinary tract infection is advocated. Local guidelines are now widely used to reflect local resistance patterns and available agents. Guidelines need to be updated to reflect changes in antimicrobial prescribing and a move from broad to narrow spectrum antimicrobials.
Performance evaluation of time-based black hole attack detection in mobile ad hoc networks

Efficient and quick attack detection is critical in any networks, especially if the attack is harmful and can bring down the whole network within a short period of time. A black hole or packet drop attack is one example of a harmful attack in mobile ad hoc networks. In this study, we implement a series of time-based black hole attack detection of different time intervals and compare the results. We study the performances of the networks, the packet delivery ratio percentage, with detection interval time of 900, 450 and 300 seconds with a total of 900 seconds of simulation time. The results suggest that appropriate time interval is critical in providing reliable detection results in timely manner. In general, the 450 seconds detection interval time has provided more reliable results, with lower false positive percentage in comparison to those of the 300 seconds detection interval time. The best explanation to the high false positive rate in the shorter detection interval time is due to the insufficient time given to the packets to arrive to the destinations during the detection process. Meanwhile, implementing the attack detection only after 900 seconds may be considered too late and thus, may have a devastating impact to the networks.
The Human and Mouse SLC25A29 Mitochondrial Transporters Rescue the Deficient Ornithine Metabolism in Fibroblasts of Patients With the Hyperornithinemia-Hyperammonemia-Homocitrullinuria (HHH) Syndrome

The hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome is a disorder of the urea cycle (UCD) and ornithine degradation pathway caused by mutations in the mitochondrial ornithine transporter (ORNT1). Unlike other UCDs, HHH syndrome is characterized by a less severe and variable phenotype that we believe may, in part, be due to genes with redundant function to ORNT1, such as the previously characterized ORNT2 gene. We reasoned that SLC25A29, a member of the same subfamily of mitochondrial carrier proteins as ORNT1 and ORNT2, might also have overlapping function with ORNT1. Here, we report that both the human and mouse SLC25A29, previously identified as mitochondrial carnitine/acyl-carnitine transporter-like, when overexpressed transiently also rescues the impaired ornithine transport in cultured HHH fibroblasts. Moreover, we observed that, in the mouse, the Slc25a29 message is more significantly expressed in the CNS and cultured astrocytes when compared with the liver and kidney. These results suggest a potential physiologic role for the SLC25A29 transporter in the oxidation of fatty acids, ornithine degradation pathway, and possibly the urea cycle. Our results show that SLC25A29 is the third human mitochondrial ornithine transporter, designated as ORNT3, which may contribute to the milder and variable phenotype seen in patients with HHH syndrome.
Diagnostic accuracy of neuropsychological tests for classification of dementia

Although numerous studies have shown that each neuropsychological test is effective for diagnosing mild cognitive impairment (MCI) or Alzheimer’s disease (AD), studies comparing diagnostic accuracies of various neuropsychological tests are relatively rare and practical cutoff values are not available. The present study aimed to investigate the validity of neuropsychological tests and develop cutoff values for each in differentiating healthy control (HC), MCI and AD groups. A total of 84 HC, 187 with MCI and 195 with AD were evaluated by the selected seven neuropsychological tests using receiver operating characteristic (ROC) curve analysis. Logical Memory (LM) delayed recall (cutoff, 7) and Rey Auditory Verbal Learning Test (RAVLT) delayed recall (cutoff, 6) were effective for differentiating HC from MCI. To distinguish MCI and AD, Rey Osterrieth Complex Figure Test (ROCFT) 3 mindelayed recall (cutoff, 6) and LM immediate recall (cutoff, 4) were excellent. Delayed recall of verbal materials, as indexed by LM and RAVLT was sensitive for discriminating MCI from HC. Handling visual memory traces, as indexed by ROCFT and immediate verbal information by LM were sensitive for differentiating MCI and AD.
Random left censoring: a second look at bone lead concentration measurements

Bone lead concentrations measured in vivo by x-ray fluorescence (XRF) are subjected to left censoring due to limited precision of the technique at very low concentrations. In the analysis of bone lead measurements, inverse variance weighting (IVW) of measurements is commonly used to estimate the mean of a data set and its standard error. Student's t-test is used to compare the IVW means of two sets, testing the hypothesis that the two sets are from the same population. This analysis was undertaken to assess the adequacy of IVW in the analysis of bone lead measurements or to confirm the results of IVW using an independent approach. The rationale is provided for the use of methods of survival data analysis in the study of XRF bone lead measurements. The procedure is provided for bone lead data analysis using the Kaplan–Meier and Nelson–Aalen estimators. The methodology is also outlined for the rank tests that are used to determine whether two censored sets are from the same population. The methods are applied on six data sets acquired in epidemiological studies. The estimated parameters and test statistics were compared with the results of the IVW approach. It is concluded that the proposed methods of statistical analysis can provide valid inference about bone lead concentrations, but the computed parameters do not differ substantially from those derived by the more widely used method of IVW.
Protective activity of a novel resveratrol analogue, HS-1793, against DNA damage in 137Cs-irradiated CHO-K1 cells

Resveratrol has received considerable attention as a polyphenol with anti-oxidant, anti-carcinogenic, and anti-inflammatory effects. Radiation is an important component of therapy for a wide range of malignant conditions. However, it causes damage to normal cells and, hence, can result in adverse side effects. This study was conducted to examine whether HS-1793, a novel resveratrol analogue free from the restriction of metabolic instability and the high dose requirement of resveratrol, induces a protective effect against radiation-induced DNA damage. HS-1793 effectively scavenged free radicals and inhibited radiation-induced plasmid DNA strand breaks in an in vitro assay. HS-1793 significantly decreased reactive oxygen species and cellular DNA damage in 2 Gy-irradiated Chinese hamster ovary (CHO)-K1 cells. In addition, HS-1793 dose-dependently reduced the levels of phosphorylated H2AX in irradiated CHO-K1 cells. These results indicate that HS-1793 has chemical radioprotective activity. Glutathione levels and superoxide dismutase activity in irradiated CHO-K1 cells increased significantly following HS-1793 treatment. The enhanced biological anti-oxidant activity and chemical radioprotective activity of HS-1793 maintained survival of irradiated CHO-K1 cells in a clonogenic assay. Therefore, HS-1793 may be of value as a radioprotector to protect healthy tissue surrounding tumor cells during radiotherapy to obtain better tumor control with a higher dose.
Psychometric properties and reference values for the ImPACT neurocognitive test battery in a sample of elite youth ice hockey players.

This cross-sectional study aimed to determine psychometric properties and reference values for ImPACT in a sample of 704 elite ice hockey players aged 13-17. Baseline ImPACT tests were completed at the beginning of the 2011-2012 season. Players aged 16-17 had better visual motor processing speed, adjusted R(2) = . 0522, F(2, 45) = 10.79, β = 2.87, p < . 001, and impulse control, adjusted R = . 0185, F(2,45) = 7.46, β = -1.35, p = . 001, than younger players, and girls had greater total symptom ratings than boys (z = -3.47, p = .0005). There were no other sex- or age-related differences in neurocognitive performance, and no effect of previous concussion on ImPACT scores. Reference values with cut-off scores are presented.
Thermal Conductivity of Wet Fabrics

The thermal conductivity of wet fabrics parallel to warps (Kw; ) and normal to the fabric surface (Kv; ) were measured by a line heat source method. The results obtained when pl, the volume fraction of water in interfiber spaces, is between 0 and 1, are as follows:(1) The relation between Kv; and pl is approximately expressed by a quadratic curve, and that between Kw; and pl by a straight line. (2) The specific heat of wet fabrics calculated by the thermal properties of their components agrees well with the experimental values. (3) For 0<pl<1, the thermal conductivity of wet fabrics can be estimated from equations (2), (3), (4) and (5) except hairy fabrics of wool.
Primary chronic cold agglutinin disease: a population based clinical study of 86 patients.

BACKGROUND AND OBJECTIVES Our knowledge of primary chronic cold agglutinin disease (CAD) is incomplete. The aim of this study was to collect comprehensive and precise data the on epidemiology, clinical and pathological features, course, and therapy of CAD. DESIGN AND METHODS We performed a population-based retrospective follow-up study of as many as possible of all CAD patients in Norway. Eighty-six patients were studied. RESULTS The prevalence of primary CAD was 16 cases per million inhabitants. The incidence rate was 1 per million per year. The median age at onset was 67 years (range, 30-92) and the male to female ratio was 0.55. The median survival was 12.5 years from onset. Autoimmune diseases other than CAD were reported in 8% of patients, cold-induced circulatory symptoms in 91%, and exacerbation of hemolytic anemia during febrile illness in 74%. At least 51% had received red blood cell transfusions. The mean initial hemoglobin level was 9.2 g/dL (range, 4.5-15.6) and the median monoclonal immunoglobulin level 4.0 g/L (range, 0.0-47.3). Most laboratory findings did not change significantly during a median follow-up of 5 years. Monoclonal IgM was detected in 90%; IgG and IgA in 3.5% each; with kappa light chains in 94%. An abnormal kappa/lambda ratio in bone marrow was found in 90%, lymphoma in 76%, and lymphoplasmacytic lymphoma in 50%. Transformation to aggressive lymphoma occurred in 3.5% during 10 years. Rituximab therapy was the only treatment showing acceptable response rates (60%). INTERPRETATION AND CONCLUSIONS Primary CAD represents a spectrum of clonal lymphoproliferative bone marrow disorders, in most cases with morphological signs of lymphoma. Despite a favorable prognosis for survival, the disease is not indolent in terms of clinical manifestations.
Hormone Therapy and the Risk of Breast Cancer in BRCA1 Mutation Carriers

Background Hormone therapy (HT) is commonly given to women to alleviate the climacteric symptoms associated with menopause. There is concern that this treatment may increase the risk of breast cancer. The potential association of HT and breast cancer risk is of particular interest to women who carry a mutation in BRCA1 because they face a high lifetime risk of breast cancer and because many of these women take HT after undergoing prophylactic surgical oophorectomy at a young age. Methods We conducted a matched case–control study of 472 postmenopausal women with a BRCA1 mutation to examine whether or not the use of HT is associated with subsequent risk of breast cancer. Breast cancer case patients and control subjects were matched with respect to age, age at menopause, and type of menopause (surgical or natural). Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated with conditional logistic regression. Statistical tests were two-sided. Results In this group of BRCA1 mutation carriers, the adjusted OR for breast cancer associated with ever use of HT compared with never use was 0.58 (95% CI = 0.35 to 0.96; P = .03). In analyses by type of HT, an inverse association with breast cancer risk was observed with use of estrogen only (OR = 0.51, 95% CI = 0.27 to 0.98; P = .04); the association with use of estrogen plus progesterone was not statistically significant (OR = 0.66, 95% CI = 0.34 to 1.27; P = .21). Conclusion Among postmenopausal women with a BRCA1 mutation, HT use was not associated with increased risk of breast cancer; indeed, in this population, it was associated with a decreased risk.
Association between the herpes simplex virus major DNA-binding protein and alkaline nuclease

Herpes simplex virus encodes seven proteins which have been shown to be both necessary and sufficient for in vitro replication of origin-containing plasmids. We have shown previously that one of these proteins, the major DNA-binding protein mDBP, forms a complex with alkaline nuclease, which is not one of the seven essential proteins. In this study, we have employed immunological reagents and a series of deletion mutants to investigate this complex further. We have determined the regions of mDBP which are important in the formation of this complex, and we have shown that the intranuclear locations of alkaline nuclease and major DNA-binding protein overlap.
Chronic Intermittent Ethanol Regulates Hippocampal GABA(A) Receptor Delta Subunit Gene Expression

Chronic ethanol consumption causes structural and functional reorganization in the hippocampus and induces alterations in the gene expression of gamma-aminobutyric acid type A receptors (GABAARs). Distinct forced intermittent exposure models have been used previously to investigate changes in GABAAR expression, with contrasting results. Here, we used repeated cycles of a Chronic Intermittent Ethanol paradigm to examine the relationship between voluntary, dependence-associated ethanol consumption, and GABAAR gene expression in mouse hippocampus. Adult male C57BL/6J mice were exposed to four 16-h ethanol vapor (or air) cycles in inhalation chambers alternated with limited-access two-bottle choice between ethanol (15%) and water consumption. The mice exposed to ethanol vapor showed significant increases in ethanol consumption compared to their air-matched controls. GABAAR alpha4 and delta subunit gene expression were measured by qRT-PCR at different stages. There were significant changes in GABAAR delta subunit transcript levels at different time points in ethanol-vapor exposed mice, while the alpha4 subunit levels remained unchanged. Correlated concurrent blood ethanol concentrations suggested that GABAAR delta subunit mRNA levels fluctuate depending on ethanol intoxication, dependence, and withdrawal state. Using a vapor-based Chronic Intermittent Ethanol procedure with combined two-bottle choice consumption, we corroborated previous evidences showing that discontinuous ethanol exposure affects GABAAR delta subunit expression but we did not observe changes in alpha4 subunit. These findings indicate that hippocampal GABAAR delta subunit expression changes transiently over the course of a Chronic Intermittent Ethanol paradigm associated with voluntary intake, in response to ethanol-mediated disturbance of GABAergic neurotransmission.
Highlights Regarding Host Predisposing Factors to Recurrent Vulvovaginal Candidiasis: Chronic Stress and Reduced Antioxidant Capacity

We studied host factors that could predispose women to develop recurrent vulvovaginal candidiasis (RVVC), including glycemia, insulin resistance, chronic stress, antioxidant capacity, overall immune status, local inflammation and vaginal microbiota. The presence of yeasts in vaginal culture was screened in 277 women, with or without signs and symptoms of VVC and RVVC. The presence of an inflammatory process and microbiota were analyzed through vaginal bacterioscopy and cervical-vaginal cytology, respectively. Fasting-blood samples were collected by standard venipuncture for biochemical analyses. Flow cytometry was employed to obtain the T helper/T cytotoxic lymphocyte ratio, and insulin resistance was assessed by the HOMA index (HI). Yeasts were isolated from 71 (26%) women: 23 (32.4%) with a positive culture but without symptoms (COL), 22 (31%) in an acute episode (VVC), and 26 (36.6%) with RVVC. C. albicans was the main yeast isolated in all clinical profiles. The control group (negative culture) comprised 206 women. Diabetes mellitus and insulin resistance were more associated with the positive-culture groups (COL, VVC and RVVC) than with negative ones. The RVVC group showed lower mean levels of cortisol than the control group and lower antioxidant capacity than all other groups. The T Helper/T cytotoxic lymphocyte ratio was similar in all groups. The RVVC group showed a similar level of vaginal inflammation to the control group, and lower than in the COL and VVC groups. Only the CVV group showed a reduction in vaginal lactobacillus microbiota. Our data suggest that both chronic stress (decreased early-morning cortisol levels) and reduced antioxidant capacity can be host predisposing factors to RVVC.
Likelihood reinstates Archaeopteryx as a primitive bird

The widespread view that Archaeopteryx was a primitive (basal) bird has been recently challenged by a comprehensive phylogenetic analysis that placed Archaeopteryx with deinonychosaurian theropods. The new phylogeny suggested that typical bird flight (powered by the front limbs only) either evolved at least twice, or was lost/modified in some deinonychosaurs. However, this parsimony-based result was acknowledged to be weakly supported. Maximum-likelihood and related Bayesian methods applied to the same dataset yield a different and more orthodox result: Archaeopteryx is restored as a basal bird with bootstrap frequency of 73 per cent and posterior probability of 1. These results are consistent with a single origin of typical (forelimb-powered) bird flight. The Archaeopteryx–deinonychosaur clade retrieved by parsimony is supported by more characters (which are on average more homoplasious), whereas the Archaeopteryx–bird clade retrieved by likelihood-based methods is supported by fewer characters (but on average less homoplasious). Both positions for Archaeopteryx remain plausible, highlighting the hazy boundary between birds and advanced theropods. These results also suggest that likelihood-based methods (in addition to parsimony) can be useful in morphological phylogenetics.
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE—an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM—a collection of familial TFBS models and JASPAR phyloFACTS—a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at .