Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncovering subdominant cytotoxic T-lymphocyte responses in lymphocytic choriomeningitis virus-infected BALB/c mice

The cytotoxic T-lymphocyte response against lymphocytic choriomeningitis virus (LCMV) in BALB/c mice is predominantly directed against a single, Ld-restricted epitope in the viral nucleoprotein (residues 118 to 126). To investigate whether any Kd/Dd-restricted responses were activated but did not expand during the primary response, we used a BALB/c mutant, BALB/c-H-2dm2, which does not express the Ld molecule. Splenocytes from LCMV-infected BALB/c mice were transferred into irradiated BALB/c-H-2dm2 mice and rechallenged with LCMV. Thus, they were exposed to an antigenic stimulus without the involvement of the immunodominant Ld-restricted epitope. In this adoptive transfer model, the donor splenocytes protected the recipient mice against chronic LCMV infection by mounting a potent Kd- and/or Dd-restricted secondary antiviral response. Analysis of a panel of Kd binding LCMV peptides revealed that residues 283 to 291 from the viral glycoprotein (GP(283-291)) comprise a major new epitope in the adoptive transfer model. Because the donor splenocytes were first activated during the primary infection in BALB/c mice, the GP(283-291) epitope is a subdominant epitope in BALB/c mice that becomes dominant after rechallenge in BALB/c-H-2dm2 mice. This study makes two points. First, it shows that subdominant CTL responses can be protective, and second, it provides a general experimental approach for uncovering subdominant CTL responses in vivo. This strategy can be used to identify subdominant T-cell responses in other systems.
Microcirculation and blood rheology abnormalities in chronic heart failure.

BACKGROUND Generalized restricted blood flow is hallmark of CHF of any etiology, but the extent of microcirculation restriction and the role of intrinsic blood properties in heart failure remains unknown. OBJECTIVE The aim of this study was to estimate the microvascular blood flow and hemorheological properties in chronic heart failure to test the hypothesis that CHF patients have altered peripheral blood flow which contributes to the tissue perfusion disturbances. METHODS Cutaneous microvascular blood flow was estimated by Laser Doppler and Optical Tissue Oximetry techniques. Whole blood and plasma viscosity were measured by capillary viscometer, red blood cell aggregation was evaluated by direct microscopic method, erythrocyte deformability was assessed as elongation index in flow microchamber. Hematocrit-to-viscosity ratio was used as index of oxygen transport efficacy. RESULTS Depression of the regulatory mechanisms of microvascular blood flow as well as decreased tissue perfusion indicated the restricted blood flow in microcirculatory network in CHF. Increased blood and plasma viscosity, enhanced red blood cell aggregation and decreased erythrocyte deformability were registered in CHF. CONCLUSIONS Complex impairment of peripheral blood flow in CHF including restricted microcirculation, attenuated regulatory mechanisms and impaired hemorheological properties caused the reduced oxygen utilization contributing to symptoms and advance of heart failure.
Demonstration of the Presence of the “Deleted” MIR122 Gene in HepG2 Cells

MicroRNA 122 (miR-122) is highly expressed in the liver where it influences diverse biological processes and pathways, including hepatitis C virus replication and metabolism of iron and cholesterol. It is processed from a long non-coding primary transcript (~7.5 kb) and the gene has two evolutionarily-conserved regions containing the pri-mir-122 promoter and pre-mir-122 hairpin region. Several groups reported that the widely-used hepatocytic cell line HepG2 had deficient expression of miR-122, previously ascribed to deletion of the pre-mir-122 stem-loop region. We aimed to characterise this deletion by direct sequencing of 6078 bp containing the pri-mir-122 promoter and pre-mir-122 stem-loop region in HepG2 and Huh-7, a control hepatocytic cell line reported to express miR-122, supported by sequence analysis of cloned genomic DNA. In contrast to previous findings, the entire sequence was present in both cell lines. Ten SNPs were heterozygous in HepG2 indicating that DNA was present in two copies. Three validation isolates of HepG2 were sequenced, showing identical genotype to the original in two, whereas the third was different. Investigation of promoter chromatin status by FAIRE showed that Huh-7 cells had 6.2 ± 0.19- and 2.7 ± 0.01- fold more accessible chromatin at the proximal (HNF4α-binding) and distal DR1 transcription factor sites, compared to HepG2 cells (p=0.03 and 0.001, respectively). This was substantiated by ENCODE genome annotations, which showed a DNAse I hypersensitive site in the pri-mir-122 promoter in Huh-7 that was absent in HepG2 cells. While the origin of the reported deletion is unclear, cell lines should be obtained from a reputable source and used at low passage number to avoid discrepant results. Deficiency of miR-122 expression in HepG2 cells may be related to a relative deficiency of accessible promoter chromatin in HepG2 versus Huh-7 cells.
Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome

Patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) often suffer from gastrointestinal symptoms and many are diagnosed with irritable bowel syndrome (IBS). Previous studies, including from our laboratory, have demonstrated that the ME/CFS gut bacterial composition is altered and less diverse when compared to healthy individuals. Patients have increased biomarkers of inflammation and leaky gut syndrome. To further investigate dysbiosis in the ME/CFS gut microbiome, we sought to characterize the eukaryotes present in the gut of 49 individuals with ME/CFS and 39 healthy controls. Using 18S rRNA sequencing, we have identified eukaryotes in stool samples of 17 healthy individuals and 17 ME/CFS patients. Our analysis demonstrates a small, nonsignificant decrease in eukaryotic diversity in ME/CFS patients compared to healthy individuals. In addition, ME/CFS patients show a nonsignificant increase in the ratio of fungal phyla Basidiomycota to Ascomycota, which is consistent with ongoing inflammation in ME/CFS. We did not identify specific eukaryotic taxa that are associated with ME/CFS disease status.
Truncated Unscented Kalman Filtering

We devise a filtering algorithm to approximate the first two moments of the posterior probability density function (PDF). The novelties of the algorithm are in the update step. If the likelihood has a bounded support, we can use a modified prior distribution that meets Bayes' rule exactly. Applying a Kalman filter (KF) to the modified prior distribution, referred to as truncated Kalman filter (TKF), can vastly improve the performance of the conventional Kalman filter, particularly when the measurements are informative relative to the prior. The application of the TKF to practical problems in which the measurement noise PDF has unbounded support is achieved by imposing several approximating assumptions which are valid only when the measurements are informative. This implies that we adaptively choose between an approximation to the KF or the TKF according to the information provided by the measurement. The resulting algorithm based on the unscented transformation is referred to as truncated unscented KF.
Efficient Filter Approximation Using the Earth Mover's Distance in Very Large Multimedia Databases with Feature Signatures

The Earth Mover's Distance, proposed in computer vision as a distance-based similarity model reflecting the human perceptual similarity, has been widely utilized in numerous domains for similarity search applicable on both feature histograms and signatures. While efficiency improvement methods towards the Earth Mover's Distance were frequently investigated on feature histograms, not much work is known to study this similarity model on feature signatures denoting object-specific feature representations. Given a very large multimedia database of features signatures, how can k-nearest-neighbor queries be processed efficiently by using the Earth Mover's Distance? In this paper, we propose an efficient filter approximation technique to lower bound the Earth Mover's Distance on feature signatures by restricting the number of earth flows locally. Extensive experiments on real world data indicate the high efficiency of the proposal, attaining order-of-magnitude query processing time cost reduction for high dimensional feature signatures.
Can Chinese Phonemes Improve Machine Transliteration?: A Comparative Study of English-to-Chinese Transliteration Models

Inspired by the success of English grapheme-to-phoneme research in speech synthesis, many researchers have proposed phoneme-based English-to-Chinese transliteration models. However, such approaches have severely suffered from the errors in Chinese phoneme-to-grapheme conversion. To address this issue, we propose a new English-to-Chinese transliteration model and make systematic comparisons with the conventional models. Our proposed model relies on the joint use of Chinese phonemes and their corresponding English graphemes and phonemes. Experiments showed that Chinese phonemes in our proposed model can contribute to the performance improvement in English-to-Chinese transliteration.
The effect of the physician J-1 visa waiver on rural Wisconsin.

CONTEXT One strategy to increase the number of physicians in rural and other underserved areas grants a waiver to foreign physicians in this country on a J-1 education visa allowing them to stay in the United States if they practice in designated underserved areas. PURPOSE The goal of this study is to evaluate the retention and acceptance of the J-1 Visa Waiver physicians in rural Wisconsin. METHODS Sites in Wisconsin at which physicians with a J-1 Visa Waiver practiced between 1996 and 2002 were identified. A 12-item survey that assessed the acceptance and retention of these physicians was sent to leaders of institutions that had participated in this program. Retention of J-1 Visa Waiver physicians was compared to other physicians recruited to rural Wisconsin practices by the Wisconsin Office of Rural Health during the same time period. FINDINGS While there was a general perception that the communities were well satisfied with the care provided and the physicians worked well with the medical community, there was a lower satisfaction with physician integration into the community-at-large. This was found to correlate with the poor retention rate of physicians with a J-1 Visa Waiver. Physicians participating in a placement program without J-1 Visa Waivers entering practice in rural communities had a significantly higher retention rate. CONCLUSIONS Physicians with J-1 Visa Waivers appear to provide good care and work well in health care environments while fulfilling the waiver requirements. To keep these physicians practicing in these communities, successful integration into the community is important.
Flow and Coral Morphology Control Coral Surface pH: Implications for the Effects of Ocean Acidification

The future impact of ocean acidification (OA) on corals is disputed in part because mathematical models used to predict these impacts do not seem to capture, or offer a framework to adequately explain, the substantial variability in acidification effects observed in empirical studies. The build-up of a diffusive boundary layer (DBL), wherein solute transport is controlled by diffusion, can lead to pronounced differences between the bulk seawater pH, and the actual pH experienced by the organism, a factor rarely considered in mathematical modelling of ocean acidification effects on corals. In the present study, we developed a simple diffusion-reaction-uptake model that was experimentally parameterized based on direct microsensor measurements of coral tissue pH and O2 within the DBL of a branching and a massive coral. The model accurately predicts tissue surface pH for different coral morphologies and under different flow velocities as a function of ambient pH. We show that, for all cases, tissue surface pH is elevated at lower flows, and thus thicker DBLs. The relative effects of OA on coral surface pH was controlled by flow and we show that under low flow velocities tissue surface pH under OA conditions (pHSWS = 7.8) can be equal to the pH under normal conditions (pHSWS = 8.2). We conclude that OA effects on corals in nature will be complex as the degree to which they are controlled by flow appears to be species specific.
Bearing failure in bolted composite joints: analytical tools development

This paper presents an analytical tool development for simulating the bearing failure and response of bolted composite joints. It is implemented into a general-purpose finite element code ABAQUS. The main damage mechanisms observed from the experiments are described as accumulated compressive damage, induced by shear and compression failures of fiber and matrix. The contact problem at the pin/hole boundary, progressive damage, finite deformation and nonlinear material behavior are taken into account when developing the analytical tool. A complex approach based on a nonlinear shear elasticity theory combined with a continuum damage mechanics approach can also be utilized to represent the nonlinear material behavior during loading. The damage accumulation criteria based on the hybrid failure criteria of Hashin and Yamada-Sun are adopted, and a degradation model for the damaged ply is proposed for the stress redistribution analysis. The computed results, including progressive damage and strength response of the joints, agreed well with the existing experimental data.
Obesity Promotes Alterations in Iron Recycling

Hepcidin is a key hormone that induces the degradation of ferroportin (FPN), a protein that exports iron from reticuloendothelial macrophages and enterocytes. The aim of the present study was to experimentally evaluate if the obesity induced by a high-fat diet (HFD) modifies the expression of FPN in macrophages and enterocytes, thus altering the iron bioavailability. In order to directly examine changes associated with iron metabolism in vivo, C57BL/6J mice were fed either a control or a HFD. Serum leptin levels were evaluated. The hepcidin, divalent metal transporter-1 (DMT1), FPN and ferritin genes were analyzed by real-time polymerase chain reaction. The amount of iron present in both the liver and spleen was determined by flame atomic absorption spectrometry. Ferroportin localization within reticuloendothelial macrophages was observed by immunofluorescence microscopy. Obese animals were found to exhibit increased hepcidin gene expression, while iron accumulated in the spleen and liver. They also exhibited changes in the sublocation of splenic cellular FPN and a reduction in the FPN expression in the liver and the spleen, while no changes were observed in enterocytes. Possible explanations for the increased hepcidin expression observed in HFD animals may include: increased leptin levels, the liver iron accumulation or endoplasmic reticulum (ER) stress. Together, the results indicated that obesity promotes changes in iron bioavailability, since it altered the iron recycling function.
Electrical Remodeling in Pressure-Overload Cardiac Hypertrophy: Role of Calcineurin

Background—Myocyte hypertrophy accompanies many forms of heart disease, but its contribution to electrical remodeling is unknown. Methods and Results—We studied mouse hearts subjected to pressure overload by surgical thoracic aortic banding. In unbanded control hearts, action potential duration (APD) was significantly longer in subendocardial myocytes compared with subepicardial myocytes. Hypertrophy-associated APD prolongation was significantly greater in subendocardial myocytes compared with subepicardial myocytes, indicating stress-induced amplification of repolarization dispersion. To investigate the underlying basis, we performed voltage-clamp recordings on dissociated myocytes. Under control unoperated conditions, subendocardial myocytes exhibited significantly less transient outward current (Ito) than did subepicardial cells. Hypertrophy was not associated with significant changes in Ito, sustained current, or inward rectifier current densities, but peak L-type Ca2+ current density (ICa,L) increased 26% (P <0.05). Recovery from ICa,L inactivation was accelerated in hypertrophied myocytes. Inhibition of calcineurin with cyclosporin A prevented increases in heart mass and myocyte size but was associated with an intermediate APD. The hypertrophy-associated increase in ICa,L and the accelerated recovery from inactivation were blocked by cyclosporin A. Conclusions—These data reveal regional variation in the electrophysiological response within the left ventricle by way of a mechanism involving upregulated Ca2+ current and calcineurin. Furthermore, these results reveal partial uncoupling of electrophysiological and structural remodeling in hypertrophy.
Estimating the Independent Effects of Multiple Pollutants in the Presence of Measurement Error: An Application of a Measurement-Error–Resistant Technique

Misclassification of exposure usually leads to biased estimates of exposure–response associations. This is particularly an issue in cases with multiple correlated exposures, where the direction of bias is uncertain. It is necessary to address this problem when considering associations with important public health implications such as the one between mortality and air pollution, because biased exposure effects can result in biased risk assessments. The National Morbidity and Mortality Air Pollution Study (NMMAPS) recently reported results from an assessment of multiple pollutants and daily mortality in 90 U.S. cities. That study assessed the independent associations of the selected pollutants with daily mortality in two-pollutant models. Excess mortality was associated with particulate matter of aerodynamic diameter ≤10 μm/m3 (PM10), but not with other pollutants, in these two pollutant models. The extent of bias due to measurement error in these reported results is unclear. Schwartz and Coull recently proposed a method that deals with multiple exposures and, under certain conditions, is resistant to measurement error. We applied this method to reanalyze the data from NMMAPS. For PM10, we found results similar to those reported previously from NMMAPS (0.24% increase in deaths per 10-μg/m3 increase in PM10). In addition, we report an important effect of carbon monoxide that had not been observed previously.
Prevalence of traumatic dental injuries in children who attended two dental clinics in Targu Mures between 2003 and 2011.

AIMS This retrospective study aimed to assess the prevalence of dental trauma in deciduous and permanent teeth among children and teenagers who attended two dental clinics in Targu Mures, Romania, between 2003 and 2011 and the correlation of their risk of dental trauma with factors, including gender, age, physical activities and extent of incisor overjet. METHODS The study population consisted of patients aged between 1 and 18 years who attended the Clinic of Paediatric Dentistry and Orthodontics and the Clinic of Oral and Maxillofacial Surgery, Targu Mures, in the period between January 2003 and August 2011. Their records were reviewed and the following factors, relevant to dental trauma, were recorded: gender, age, type of dentition, injury aetiology, lesion type and location, number of teeth affected, occlusion, and radiography. For patients who attended the orthodontics clinic, the degree of overjet was also determined. RESULTS The overall prevalence of dental trauma was 24.5%. The frequency of traumatic injuries to deciduous teeth was approximately equal for boys and girls, and the most for those between 1 and 2 years. In the permanent dentition, a dental trauma was more frequently found boys, and the most affected age group was between 11 and 12 years, for both boys and girls. The most common causes were falls, in deciduous teeth especially during learning to walk, and in permanent teeth particularly during cycling or other sporting mishaps. The most frequent type of trauma found in the deciduous dentition was lateral luxation and in the permanent teeth it was fracture with the involvement of enamel and dentine, but without the exposure of the dental pulp. A positive relationship was noted between the presence of overjet associated with lip incompetence and the frequency of dental trauma. CONCLUSIONS The prevalence of dental trauma in children and adolescents who attended the Clinic of Paediatric Dentistry and Orthodontics and the Clinic of Oral and Maxillofacial Surgery, Targu Mures, was broadly similar to that found in other studies. More epidemiologic studies are needed to gain a more comprehensive overview of the prevalence of dental trauma in Romania.
Effect of laser linewidth on phase-OTDR based distributed vibration sensing regime

The effect of fiber laser linewidth on the optical time-domain reflectometer based vibration distributed sensing regime is studied experimentally in this paper. Lasers with multi-longitudinal modes, 5 kHz and ~800 Hz linewidth single longitudinal mode are interrogated as light source successively. Experiments show that narrower linewidth laser results in higher repeatable and stable scattering spectrum. When the 800 Hz linewidth laser is modulated into 50 ns width pulses, the signal to noise ratio is ~ 6 dB and the spatial resolution is improved to 3 m, breaking the traditional theory limit.
Effects of weather on corticosterone responses in wild free-living passerine birds.

Harsh weather can have devastating effects on both the survival and the breeding success of wild animals. Corticosterone, released in response to the stress caused by harsh conditions, may trigger physiological and behavioral changes that help ameliorate these effects. We examined three species of Arctic-breeding passerine birds for correlations between circulating plasma corticosterone levels and weather conditions at the time of capture. Furthermore, because persistently poor weather conditions may be required to initiate a stress response, we also looked for a relationship between corticosterone levels and weather conditions over the 24 and 72 h preceding capture. None of the three species showed substantial effects of weather on unstressed corticosterone levels during the breeding season, although one species showed a significant relationship with stress-induced corticosterone levels. In two species, however, variations in weather during molt (an energetically costly period when birds replace their feathers) explained from 35 to 88% of the individual variation in corticosterone levels. In a third molting species, weather conditions in the preceding 24 and 72 h explained between 20 and 30% of the individual variation in corticosterone levels. It thus appears that adverse weather may be a potent stimulator of corticosterone release during molt, but not during the breeding season. Although extreme weather conditions (those experienced once every few years) can disrupt breeding, since none of the birds abandoned breeding we might conclude that the storms in this study were well within the ability of the birds to cope physiologically.