Miracle-dz/UniFAR-FTUs huggingface dataset:
Epstein–Barr virus nuclear antigen-1 B-cell epitopes in multiple sclerosis twins

Background: Compared with quantitative observations, the search for qualitative changes that may characterize the immune response to Epstein–Barr virus (EBV) in multiple sclerosis (MS) has been less intense. Objective: To examine the B-cell epitopes of antibodies against the Epstein–Barr nuclear antigen-1 (EBNA-1) and their relevance for MS, through a study in disease-discordant identical twins. Methods: We evaluated the antibodies to all unique, maximally overlapping octapeptides of EBNA-1 in 12 pairs of monozygotic (MZ) twins (9 MS-discordant, 3 healthy), 3 non-twin patients and 2 healthy subjects. All except one of the patients were untreated. The EBV serology of these individuals had been assessed in advance using commercially available and in-house enzyme-linked immunosorbent assay (ELISA) kits, including assays for antibodies against select peptides of EBNA-1: EBNA-72 (GAGGGAGAGG) and EBNA-206 (EADYFEYHQEGGPDGE). Results: The glycine–alanine rich domain of EBNA-1 was immunodominant in all subjects. Compared with healthy individuals, and similarly to what has been described in infectious mononucleosis (IM) patients, affected co-twins and non-twin patients had a significantly increased response to another EBNA-1 epitope (aa. 401–411). Conclusion: In a study that controls for confounders, our data focus an EBNA-1 specificity that may be associated with MS pathogenesis.
Opposed-phase MRI for fat quantification in fat-water phantoms with 1H MR spectroscopy to resolve ambiguity of fat or water dominance.

OBJECTIVE The purpose of the study was to quantify the fat fraction in nine fat-water phantoms containing 0-80% fat using opposed-phase imaging with the qualitative guidance of 1H MR spectroscopy (MRS), which was used by observer 1 to visually assess the sizes of the water and fat peaks to apply two alternative mathematic formulas for the calculation of the fat fraction. In addition, the fat fraction was also quantified directly with 1H MRS as an independent method by two observers (observers 2 and 3). CONCLUSION The fat fraction calculated with opposed-phase imaging (FF(OPI)) and that calculated with 1H MRS (FF(MRS)) correlated well with the known fat fractions of the phantoms (FF(P)): r = 0.99 for FF(OPI); p < 0.0001 and r = 0.96-0.98 for FF(MRS); p < 0.001, for observers 2 and 3, respectively. Opposed-phase imaging should be combined with 1H MRS to ensure accurate quantification of the fat fraction.
Empathy in intergenerational emotion communication : Effects of actor age , affiliative context and perceiver ’ s age on empathic reactions to facial expressions

Positive interactions and social bonds between younger and older adults seem to be at risk as previous research suggests a lack of empathy to the elderly. This dissertation set out to investigate empathic reactions to emotional facial expressions of the elderly. There are a number of elements that might potentially be accountable for the reduction or absence of empathy by younger adults: This work focused on age-related changes of older faces, stereotype expectations and affiliative context as moderators of empathy and measured their effects on a cognitive and an affective dimension. A second goal was to assess empathic capabilities of the elderly themselves on the same dimensions. Three studies were conducted, and their results are reported in three individual research manuscripts. Study 1 focused on the effect of wrinkles and stereotypes on decoding accuracy and facial mimicry of emotional facial expressions. It revealed that wrinkles and stereotypes have an impact on decoding accuracy, however facial mimicry reactions to the emotion expressions of older adults were present regardless of those decoding biases. Study 2 focused on the affiliative context of interactions between younger and older adults, and suggested that the type of emotion display (happy vs. angry) as well as the observer’s relationship to the expresser (in-group vs. outgroup member) impacted on facial mimicry in real-life interactions. It revealed that mimicry of happy expressions of older adults was present during the two emotional events (happy and angry). However, mimicry of younger compared to older adults was stronger in the happy event, whereas no difference occurred in mimicry in the angry event. Study 3 investigated empathic capabilities of older compared to younger adults and found no differences in affective empathy, although decoding accuracy was reduced for some emotions in the older participant sample. Collectively, these results indicate that affective empathic responding via facial mimicry toward the elderly is essentially intact regardless of reduced decoding accuracy for older faces and affiliative context. They further indicate that older adults possess the same affective capabilities as younger adults. In sum, this work provides a more positive outlook for intergenerational interactions than previously suggested.
Normal M mode values in healthy Turkish children.

AIM Evaluation of cardiac structures requires a large study group for accurate data on normal values. The aim of the study was to obtain normal M mode echocardiographic values in a substantial sample of healthy term neonates and children to develop centile charts. MATERIALS AND METHODS Data were obtained over 2 years from a single center in Turkey, from 1200 healthy infants and children aged 1 day to 17 years. Using echocardiographic investigation, measurements were obtained of the following: left ventricular dimension at end diastole and end systole; thickness of interventricular septum and posterior wall of the left ventricle; aortic and pulmonary root diameter; and left atrial dimension. The influence of systematic errors as statistical noise in this large sample was decreased using third- degree polynomial curves. RESULTS Measurements are presented graphically as curved lines of centiles with respect to body weight for healthy term neonates and children. The values showed a good correlation with body weight and allowed the construction of percentile curves (5%, 25%, 50%, 75%, and 95%). Higher values were observed in boys during adolescence. CONCLUSION The presented charts and tables make it possible to judge the echocardiographic measurements of a particular patient as normal or abnormal.
Prospective surveillance for invasive fungal infections in hematopoietic stem cell transplant recipients, 2001-2006: overview of the Transplant-Associated Infection Surveillance Network (TRANSNET) Database.

BACKGROUND The incidence and epidemiology of invasive fungal infections (IFIs), a leading cause of death among hematopoeitic stem cell transplant (HSCT) recipients, are derived mainly from single-institution retrospective studies. METHODS The Transplant Associated Infections Surveillance Network, a network of 23 US transplant centers, prospectively enrolled HSCT recipients with proven and probable IFIs occurring between March 2001 and March 2006. We collected denominator data on all HSCTs preformed at each site and clinical, diagnostic, and outcome information for each IFI case. To estimate trends in IFI, we calculated the 12-month cumulative incidence among 9 sequential subcohorts. RESULTS We identified 983 IFIs among 875 HSCT recipients. The median age of the patients was 49 years; 60% were male. Invasive aspergillosis (43%), invasive candidiasis (28%), and zygomycosis (8%) were the most common IFIs. Fifty-nine percent and 61% of IFIs were recognized within 60 days of neutropenia and graft-versus-host disease, respectively. Median onset of candidiasis and aspergillosis after HSCT was 61 days and 99 days, respectively. Within a cohort of 16,200 HSCT recipients who received their first transplants between March 2001 and September 2005 and were followed up through March 2006, we identified 718 IFIs in 639 persons. Twelve-month cumulative incidences, based on the first IFI, were 7.7 cases per 100 transplants for matched unrelated allogeneic, 8.1 cases per 100 transplants for mismatched-related allogeneic, 5.8 cases per 100 transplants for matched-related allogeneic, and 1.2 cases per 100 transplants for autologous HSCT. CONCLUSIONS In this national prospective surveillance study of IFIs in HSCT recipients, the cumulative incidence was highest for aspergillosis, followed by candidiasis. Understanding the epidemiologic trends and burden of IFIs may lead to improved management strategies and study design.
Design of a Two Octave Gysel Power-Divider Using DGS and DMS

Manuscript Received 26-February-2013 and revised 23-June-2013 ISSN 2322-3936 Accepted on 2July-2013 Abstract— This paper proposes a two way L and S band Gysel power divider/combiner that uses line to ground resistors. Step by step methods to obtain a wide isolation and transmission bandwidth are presented. A design that uses five resistors is selected and optimized based on Quasi Newton method. Then the Defected Microstrip Structure (DMS) and Defected Ground Structure (DGS) is used to obtain better transmission and isolation in wider bandwidth. By resizing the structure to meet impedance matching, the two-way L and S band power divider is achieved. Also the optimization of the design is checked using circuit configuration. Finally, the theoretical results are validated by comparison with simulations of structure and experimental results. The simulations are found to be in good agreement with measurement results in the range of 0.7 to 4.3 GHz.
Implementation of the Xpert MTB/RIF assay for tuberculosis in Mongolia: a qualitative exploration of barriers and enablers

Objective The aim of our study was to identify barriers and enablers to implementation of the Xpert MTB/RIF test within Mongolia’s National Tuberculosis Program. Methods Twenty-foursemi-structured interviews were conducted between June and September 2015 with laboratory staff and tuberculosis physicians in Mongolia’s capital Ulaanbaatar and regional towns where Xpert MTB/RIF testing had been implemented. Interviews were recorded, transcribed, translated and analysed thematically using NVIVO qualitative analysis software. Results Eight laboratory staff (five from the National Tuberculosis Reference Laboratory in Ulaanbaatar and three from provincial laboratories) and sixteen tuberculosis physicians (five from the Mongolian National Center for Communicable Diseases in Ulaanbaatar, four from district tuberculosis clinics in Ulaanbaatar and seven from provincial tuberculosis clinics) were interviewed. Major barriers to Xpert MTB/RIF implementation identified were: lack of awareness of program guidelines; inadequate staffing arrangements; problems with cartridge supply management; lack of local repair options for the Xpert machines; lack of regular formal training; paper based system; delayed treatment initiation due to consensus meeting and poor sample quality. Enablers to Xpert MTB/RIF implementation included availability of guidelines in the local language; provision of extra laboratory staff, shift working arrangements and additional modules; capacity for troubleshooting internally; access to experts; opportunities for peer learning; common understanding of diagnostic algorithms and decentralised testing. Conclusion Our study identified a number of barriers and enablers to implementation of Xpert MTB/RIF in the Mongolian National Tuberculosis Program. Lessons learned from this study can help to facilitate implementation of Xpert MTB/RIF in other Mongolian locations as well as other low-and middle-income countries.
Fighting Sharka in Peach: Current Limitations and Future Perspectives

Sharka, caused by Plum Pox Virus (PPV), is by far the most important infectious disease of peach [P. persica (L.) Batsch] and other Prunus species. The progressive spread of the virus in many important growing areas throughout Europe poses serious issues to the economic sustainability of stone fruit crops, peach in particular. The adoption of internationally agreed-upon rules for diagnostic tests, strain-specific monitoring schemes and spatial–temporal modeling of virus spread, are all essential for a more effective sharka containment. The EU regulations on nursery activity should be modified based on the zone delimitation of PPV presence, limiting open-field production of propagation materials only to virus-free areas. Increasing the efficiency of preventive measures should be augmented by the short-term development of resistant cultivars. Putative sources of resistance/tolerance have been recently identified in peach germplasm, although the majority of novel resistant sources to PPV-M have been found in almond. However, the complexity of introgression from related-species imposes the search for alternative strategies. The use of genetic engineering, particularly RNA interference (RNAi)-based approaches, appears as one of the most promising perspectives to introduce a durable resistance to PPV in peach germplasm, notwithstanding the well-known difficulties of in vitro plant regeneration in this species. In this regard, rootstock transformation to induce RNAi-mediated systemic resistance would avoid the transformation of numerous commercial cultivars, and may alleviate consumer resistance to the use of GM plants.
Ischemia-Reperfusion Injury and Volatile Anesthetics

Ischemia-reperfusion injury (IRI) is induced as a result of reentry of the blood and oxygen to ischemic tissue. Antioxidant and some other drugs have protective effect on IRI. In many surgeries and clinical conditions IRI is counteract inevitable. Some anesthetic agents may have a protective role in this procedure. It is known that inhalational anesthetics possess protective effects against IRI. In this review the mechanism of preventive effects of volatile anesthetics and different ischemia-reperfusion models are discussed.
BayClone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data

In this paper, we present a novel feature allocation model to describe tumor heterogeneity (TH) using next-generation sequencing (NGS) data. Taking a Bayesian approach, we extend the Indian buffet process (IBP) to define a class of nonparametric models, the categorical IBP (cIBP). A cIBP takes categorical values to denote homozygous or heterozygous genotypes at each SNV. We define a subclone as a vector of these categorical values, each corresponding to an SNV. Instead of partitioning somatic mutations into non-overlapping clusters with similar cellular prevalences, we took a different approach using feature allocation. Importantly, we do not assume somatic mutations with similar cellular prevalence must be from the same subclone and allow overlapping mutations shared across subclones. We argue that this is closer to the underlying theory of phylogenetic clonal expansion, as somatic mutations occurred in parent subclones should be shared across the parent and child subclones. Bayesian inference yields posterior probabilities of the number, genotypes, and proportions of subclones in a tumor sample, thereby providing point estimates as well as variabilities of the estimates for each subclone. We report results on both simulated and real data. BayClone is available at http://health.bsd. uchicago.edu/yji/soft.html.
Effect of Hardness and Surface Roughness on Slip Resistance of Rubber

Slip resistance is now considered a primary property for footwear. Continuous attempts are being made to design the footwear with suitable materials to provide sufficient grip under the foot at workplaces, on pedestrian pathways, and in the home to reduce slip, trip, and fall accidents. In footwear, the type of sole used, along with the bottom profile, made with the correct design of cleats and drain channel, is greatly influencing slip resistance. In this study, the influence of shore hardness and surface roughness of rubber soling material on slip resistance under dry, wet, detergent, and oil-floor conditions were made at five different slip speeds. The instrument used for this entire study was dynamic slip-resistance test equipment (SATRA Model, STM 603). The overall friction coefficient is caused by the boundary lubrication effect, as the dilute fluids do not have a significant effect on hysteresis, but do affect the adhesion component. This trend of coefficient of friction (COF) is observed in all flooring conditions. Increasing the sliding speed decreases the COF for all four flooring conditions. In the dry flooring condition, the COF is ~1.0 for sole hardness between 65 and 75, and the COF is about 0.50 for shore hardness above 85. Rubber soles with a surface roughness of 221.19 root mean square (rms) (nm) registers a COF of 1.0, whereas soles having a surface roughness of 37.37 rms (nm) registers a COF of ~0.50. For rubber sole material with less hardness, reduction of the COF for dry and wet condition is ~7 %, for detergent contaminants, the reduction is about 30 %, and, for the oil-floor condition, the reduction is 88 %. There is a marked reduction in COF when tested with different sliding speeds; the difference for dry and wet tests is ~7 %–8 % when increasing the speed from 0.1 m/s to 0.5 m/s. But this difference is found to be 10 % for detergent solution and 28 % for oil.
Influence of Slenderness on Stress-Strain Behavior of Concrete-Filled FRP Tubes: Experimental Study

Concrete-filled fiber reinforced polymer (FRP) tubes (CFFTs) have received significant research attention over the last two decades, with recent experimental studies identifying significant benefits of CFFTs filled with high-strength concretes (HSC). However, many test parameters of high-strength CFFTs, such as specimen slenderness, remain experimentally limited. This paper presents an experimental investigation on the axial compressive behavior of 33 monotonically loaded circular normal-strength and high-strength CFFTs (NSCFFTs and HSCFFTs). The influence of specimen slenderness is investigated on test specimens with height-to-diameter ratios (H/D) of 1, 2, 3, and 5. The CFFT specimens were instrumented with numerous lateral strain gauges to examine the development of hoop strains along the specimen height and around specimen perimeter. The experimentally recorded stress-strain relationships are presented graphically and the ultimate axial stresses and strains, and FRP tube hoop strains at rupture are tabulated. The results indicate that specimens with a height-to-diameter ratio (H/D) of 1 outperform specimens with a H/D ratio of 2 to 5, with significantly increased strength and strain enhancements. The influence of slenderness on specimens with a H/D ratio between 2 and 5 was found to be significant in regards to axial strain enhancement, with a decrease observed as specimen slenderness increased. Conversely, the influence of slenderness on axial strength enhancement of specimens with a H/D ratio between 2 and 5 was found to be negligible. The strain results indicate that hoop rupture strains along the height of CFFTs become more uniform for specimens with higher amounts of confinement. On the other hand, the variation of hoop strains around the perimeter of CFFTs was not observed to be significantly influenced by slenderness, concrete strength or amount of confinement.
A Survey of Merger Remnants. II. The Emerging Kinematic and Photometric Correlations

This paper is the second in a series exploring the properties of 51 optically selected, single-nuclei merger remnants. Spectroscopic data have been obtained for a subsample of 38 mergers and combined with previously obtained infrared photometry to test whether mergers exhibit the same correlations as elliptical galaxies among parameters such as stellar luminosity and distribution, central stellar velocity dispersion (σ0), and metallicity. Paramount to the study is to test whether mergers lie on the fundamental plane. Measurements of σ0 have been made using the Ca triplet absorption line at 8500 Å for all 38 mergers in the subsample. Additional measurements of σ0 were made for two of the mergers in the subsample using the CO absorption line at 2.29 μm. The results indicate that mergers show a strong correlation among the parameters of the fundamental plane but fail to show a strong correlation between σ0 and metallicity (Mg2). In contrast to earlier studies, the σ0 values of the mergers are consistent with objects that lie somewhere between intermediate-mass and luminous giant elliptical galaxies. However, the discrepancies with earlier studies appear to correlate with whether the Ca triplet or CO absorption lines are used to derive σ0, with the latter almost always producing smaller values. Finally, the photometric and kinematic data are used to demonstrate for the first time that the central phase-space densities of mergers are equivalent to those in elliptical galaxies. This resolves a long-standing criticism of the merger hypothesis.
Expression of Herpes Simplex Virus ICP47 and Human Cytomegalovirus US11 Prevents Recognition of Transgene Products by CD8+ Cytotoxic T Lymphocytes

ABSTRACT The in vivo persistence of gene-modified cells may be limited by the development of a host immune response to vector-encoded proteins. Herpesviruses evade cytotoxic T-lymphocyte (CTL) recognition by expressing genes which interfere selectively with presentation of viral antigens by class I major histocompatibility complex (MHC) molecules. Here, we studied the use of retroviral vectors encoding herpes simplex virus ICP47, human cytomegalovirus (HCMV) US3, or HCMV US11 to decrease presentation of viral proteins and transgene products to CD8+ CTL. Human fibroblasts and T cells transduced to express the ICP47, US3, or US11 genes alone exhibited a decrease in cell surface class I MHC expression. The combination of ICP47 and US11 rendered fibroblasts negative for surface class I MHC and allowed a class I MHC-low population of T cells to be sorted by flow cytometry. Fibroblasts and T cells expressing both ICP47 and US11 were protected from CTL-mediated lysis and failed to stimulate specific memory T-cell responses to transgene products in vitro. Our findings suggest that expression of immunoregulatory viral gene products could be a potential strategy to prolong transgene expression in vivo.
Deep Neural Network Based Precursor microRNA Prediction on Eleven Species

MicroRNA (miRNA) are small non-coding RNAs that regulates the gene expression at the post-transcriptional level. Determining whether a sequence segment is miRNA is experimentally challenging. Also, experimental results are sensitive to the experimental environment. These limitations inspire the development of computational methods for predicting the miRNAs. We propose a deep learning based classification model, called DP-miRNA, for predicting precursor miRNA sequence that contains the miRNA sequence. The feature set based Restricted Boltzmann Machine method, which we call DP-miRNA, uses 58 features that are categorized into four groups: sequence features, folding measures, stem-loop features and statistical feature. We evaluate the performance of the DP-miRNA on eleven twelve data sets of varying species, including the human. The deep neural network based classification outperformed support vector machine, neural network, naive Baye's classifiers, k-nearest neighbors, random forests, and a hybrid system combining support vector machine and genetic algorithm.