Miracle-dz/UniFAR-FTUs huggingface dataset:
Virus‐Specific CD8+ T Cells Cross‐Reactive to Donor‐Alloantigen Are Transiently Present in the Circulation of Kidney Transplant Recipients Infected With CMV and/or EBV

T cells play a dual role in transplantation: They mediate transplant rejection and are crucial for virus control. Memory T cells generated in response to pathogens can cross‐react to alloantigen, a phenomenon called heterologous immunity. Virus‐specific CD8+ T cells cross‐reacting to donor‐alloantigen might affect alloimmune responses and hamper tolerance induction following transplantation. Here, we longitudinally studied these cross‐reactive cells in peripheral blood of 25 kidney transplant recipients with a cytomegalovirus and/or Epstein‐Barr virus infection. Cross‐reactive T cells were identified by flow cytometry as virus‐specific T cells that proliferate in response to donor cells in a mixed‐lymphocyte reaction. In 13 of 25 patients, we found cross‐reactivity to donor cells for at least 1 viral epitope before (n = 7) and/or after transplantation (n = 8). Cross‐reactive T cells were transiently present in the circulation, and their precursor frequency did not increase following transplantation or viral infection. Cross‐reactive T cells expressed interferon‐γ and CD107a in response to both alloantigen and viral peptide and resembled virus‐specific T cells in phenotype and function. Their presence was not associated with impaired renal function, proteinuria, or rejection. In conclusion, virus‐specific T cells that cross‐react to donor‐alloantigen are transiently detectable in the circulation of kidney transplant recipients.
Personality, Attentional Biases towards Emotional Faces and Symptoms of Mental Disorders in an Adolescent Sample

Objective To investigate the role of personality factors and attentional biases towards emotional faces, in establishing concurrent and prospective risk for mental disorder diagnosis in adolescence. Method Data were obtained as part of the IMAGEN study, conducted across 8 European sites, with a community sample of 2257 adolescents. At 14 years, participants completed an emotional variant of the dot-probe task, as well two personality measures, namely the Substance Use Risk Profile Scale and the revised NEO Personality Inventory. At 14 and 16 years, participants and their parents were interviewed to determine symptoms of mental disorders. Results Personality traits were general and specific risk indicators for mental disorders at 14 years. Increased specificity was obtained when investigating the likelihood of mental disorders over a 2-year period, with the Substance Use Risk Profile Scale showing incremental validity over the NEO Personality Inventory. Attentional biases to emotional faces did not characterise or predict mental disorders examined in the current sample. Discussion Personality traits can indicate concurrent and prospective risk for mental disorders in a community youth sample, and identify at-risk youth beyond the impact of baseline symptoms. This study does not support the hypothesis that attentional biases mediate the relationship between personality and psychopathology in a community sample. Task and sample characteristics that contribute to differing results among studies are discussed.
Modeling correlated main‐chain motions in proteins for flexible molecular recognition

We describe a new method for modeling protein and ligand main‐chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large‐scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph‐theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the protein. The available conformations of the flexible regions are then explored with ROCK by random‐walk sampling of the rotatable bonds. ROCK explores correlated motions by only sampling dihedral angles that preserve the coupled bond networks in the protein and generates conformers with good stereochemistry, without using a computationally expensive potential function. A representative set of the conformational ensemble generated this way can be used as targets for docking with SLIDE, which handles the flexibility of protein and ligand side‐chains. The realism of this protein main‐chain conformational sampling is assessed by comparison with time‐resolved NMR studies of cyclophilin A motions. ROCK is also effective for modeling the flexibility of large cyclic and polycyclic ligands, as demonstrated for cyclosporin and zearalenol. The use of this combined approach to perform docking with main‐chain flexibility is illustrated for the cyclophilin A–cyclosporin complex and the estrogen receptor in complex with zearalenol, while addressing the question of how much flexibility is allowed without hindering molecular recognition. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Performance Comparison of Discrete Orthonormal S-Transform for the Reconstruction of Medical Images

This paper investigates the performance of the Discrete Orthonormal S-Transform (DOST) technique for the reconstruction of medical images. This technique is compared with the q-Recursive Zernike Moment (q-RZM) and Discrete Wavelet Transform (DWT) based on the performance measurement, namely Mean Square Error (MSE) and Peak Signal to Noise Ratio (PSNR) on medical images. The ultimate goal is to find the best technique that can extract the important feature of the medical image. Computer Tomography (CT) and Magnetic Resonance (MR) images are used to test the viability of the techniques to be used for image compression. The experiment is done using MATLAB tool. From the results, the DOST technique has high PSNR value and outperforms q-recursive Zernike Moments and Discrete Wavelet Transform Techniques.
Risk Perception and Experience: Hazard Personality Profiles and Individual Differences

The dominance of the “psychometric” paradigm and the consequent emphasis on personality profiles of hazards has resulted in little attention being given to individual variability in risk judgments. This study examines how far differences in experience of risk activities can explain individual variability in risk assessments. A questionnaire study (n= 172) was used to explore the relationships between experience and risk perceptions in relation to 16 risk activities. It was expected that these relationships would differ for voluntary and involuntary activities. Measures of experience included assessments of “impact” and “outcome” valence as well as “frequency. ” These three aspects of experience each related to risk assessment but their relationship depended on whether the risk experiences were voluntary or not. The results indicate the importance of developing more fine‐grained ways of indexing risk experience.
New Scaling Factors of 2-D Isotropic-Dispersion Finite Difference Time Domain (ID-FDTD) Algorithm for Lossy Media

We modify the 2D explicit isotropic-dispersion finite-difference time-domain (ID-FDTD) scheme originally proposed for lossless media , which can drastically improve the accuracy of the 2-D ID-FDTD scheme for lossy media. The proposed scheme adopts new scaling factors for material properties such as the permittivity, permeability and conductivity. The new scaling factors can generate nearly the exact phase velocity and attenuation factor of a lossy medium for a single frequency. For the validation of the proposed scheme, two scattering problems are considered.
Learning from Ancient Athens: Demarchy and Corporate Governance

The corporate governance literature increasingly recognizes that firms can benefit from protecting and thereby inducing firm-specific investments of various stakeholders. Such investments by shareholders, employees, suppliers, customers, and the local community strengthen the sustainable competitive advantage of the firm. However, the protection of multiple stakeholders’ interests poses substantial implementation problems. This paper explores a novel approach to such protection, based on the creative use of random selection procedures in appointing stakeholder representatives to the board. These procedures are the foundation of demarchy, a form of governance that was successfully used in ancient Athenian democracy. The paper presents advantages and disadvantages of demarchy, develops a corporate governance proposal that combines demarchy with representative voting, and addresses key issues concerning its implementation. It is suggested that the use of demarchy opens new avenues for stakeholder involvement in corporate governance.
Practice Patterns for the Use of Antibiotic Agents in Damage Control Laparotomy and Its Impact on Outcomes.

BACKGROUND The purpose of this study was to identify practice patterns associated with the use of antimicrobial agents with damage control laparotomy (DCL) and the relationship with post-operative intra-abdominal infection (IAI) rates. PATIENTS AND METHODS The study was a retrospective review of trauma patients undergoing laparotomy at a Level 1 trauma center in 2010. Patients undergoing DCL versus those primarily closed (PCL) were compared for antimicrobial use (ABX) and its correlation with IAI rates (p < 0.05). Deaths with length of stay <5 days were excluded. RESULTS A total of 121 patients were identified (28 DCL, 93 PCL). The DCL group was more severely injured (Injury Severity Score [ISS]: 31.4 ± 15 DCL vs. 18 ± 12.7 PCL, p < 0.001) with more small and large bowel injuries (SLBI), although not statistically significant (53.6% DCL vs. 35.5% PCL, p = 0.12). Practice patterns of ABX administration in terms of pre-operative (94.6% PCL vs. 69.2% DCL, p = 0.0012) and post-operative administration (PCL: 50.5% none, 21.5% one day, 28% long term >1 d; DCL: 21.4% none, 25.0% one day, 53.6% long term >1 day, p = 0.0130) were significant. Regression analyses demonstrated that neither ISS nor DCL was an independent predictor of infection, but pre-operative ABX was a negative predictor (odds ratio [OR] 0.20, 95% confidence interval [CI] 0.05-0.91, p = 0.037), while post-operative ABX (OR 6.7, 95%CI 1.33-33.8, p = 0.044) and SLBI (OR 3.45, CI 1.03-11.5, p = 0.02) were positive predictors of infection with an receiver operating characteristic of 0.81. CONCLUSION Significant variations exist in the use of ABX in DCL and PCL. These variations may lead to deleterious results from both lack of initial pre-operative coverage and prolonged ABX use. The decrease in infection rates with pre-operative ABX yet significant increase with continued post-operative use even in the presence of SLBI suggests the need for a more standardized approach. With the increase in DCL and the open abdomen, more research is needed to clearly establish ABX protocols in this patient population.
Incorporating Complementary Annotation to a CCGbank for Improving Derivations for Japanese

Wide-coverage resources for lexicalized grammars have been obtained by converting the existing treebanks into collections of derivations. Additional annotations to the source treebank can be used to improve these derivations. A treebank annotation called the NTT treebank was used for this paper to improve a CCGbank for Japanese. The source treebank of the CCGbank itself is created by automatically converting chunk-dependencies, but the CCGbank contains errors caused by noisier phrase structures and a lack of linguistic information, which is difficult to represent in chunk-dependency. The NTT treebank provides cleaner trees and functional and semantic information, e.g., coordinations and predicate-argument structures. The effect of the improvement process is empirically evaluated in terms of the changes in the dependency relations extracted from the resulting derivations.
Decreased bone mineral density in subjects carrying familial defective apolipoprotein B-100.

CONTEXT Although numerous epidemiologic studies have documented associations between osteoporosis and cardiovascular disease, the mechanisms underlying this association remain to be clarified. One hypothesis is that hyperlipidemia may be a common predisposing factor to both atherosclerotic heart disease and bone fragility. OBJECTIVE To evaluate this, we compared bone mineral density (BMD) between subjects with and without the R3500Q APOB mutation, the cause of familial defective apolipoprotein B-100, which has been previously shown to markedly increase low-density lipoprotein cholesterol (LDL-C). We hypothesized that R3500Q carriers would have lower BMD due to lifetime, elevated LDL-C. DESIGN This was a a cross-sectional study in the Old Order Amish (OOA) population. PARTICIPANTS The R3500Q APOB mutation is present at a high frequency (∼6% vs <0.5%) in the OOA population due to a founder effect. Therefore, we conducted analysis on 1097 Amish individuals of whom 125 were R3500Q carriers. MAIN OUTCOME MEASURE BMD was measured by dual-energy x-ray absorptiometry. RESULTS After adjusting for age, age(2), sex, body mass index, and family structure, carriers for the Q risk allele had significantly lower BMD than noncarriers at the femoral neck (P = .037), lumbar spine (P = .035) and whole body (P = .016). Adjusting for LDL-C attenuated the association between R3500Q genotype and BMD but did not completely explain the relationship. Subgroup analyses showed no significant interactions with sex, age, or presence of metabolic syndrome. CONCLUSION These results use the unique genetic architecture of the OOA population to provide a novel line of evidence supporting a causal role for elevated LDL-C in lowering BMD.
Hepatitis C Virus NS2 Coordinates Virus Particle Assembly through Physical Interactions with the E1-E2 Glycoprotein and NS3-NS4A Enzyme Complexes

ABSTRACT The hepatitis C virus (HCV) NS2 protein is essential for particle assembly, but its function in this process is unknown. We previously identified critical genetic interactions between NS2 and the viral E1-E2 glycoprotein and NS3-NS4A enzyme complexes. Based on these data, we hypothesized that interactions between these viral proteins are essential for HCV particle assembly. To identify interaction partners of NS2, we developed methods to site-specifically biotinylate NS2 in vivo and affinity capture NS2-containing protein complexes from virus-producing cells with streptavidin magnetic beads. By using these methods, we confirmed that NS2 physically interacts with E1, E2, and NS3 but did not stably interact with viral core or NS5A proteins. We further characterized these protein complexes by blue native polyacrylamide gel electrophoresis and identified ≈520-kDa and ≈680-kDa complexes containing E2, NS2, and NS3. The formation of NS2 protein complexes was dependent on coexpression of the viral p7 protein and enhanced by cotranslation of viral proteins as a polyprotein. Further characterization indicated that the glycoprotein complex interacts with NS2 via E2, and the pattern of N-linked glycosylation on E1 and E2 suggested that these interactions occur in the early secretory pathway. Importantly, several mutations that inhibited virus assembly were shown to inhibit NS2 protein complex formation, and NS2 was essential for mediating the interaction between E2 and NS3. These studies demonstrate that NS2 plays a central organizing role in HCV particle assembly by bringing together viral structural and nonstructural proteins.
Better Quality Sleep Promotes Daytime Physical Activity in Patients with Chronic Pain? A Multilevel Analysis of the Within-Person Relationship

Background Promoting physical activity is key to the management of chronic pain, but little is understood about the factors facilitating an individual’s engagement in physical activity on a day-to-day basis. This study examined the within-person effect of sleep on next day physical activity in patients with chronic pain and insomnia. Methods 119 chronic pain patients monitored their sleep and physical activity for a week in their usual sleeping and living environment. Physical activity was measured using actigraphy to provide a mean activity score each hour. Sleep was estimated with actigraphy and an electronic diary, providing an objective and subjective index of sleep efficiency (A-SE, SE) and a sleep quality rating (SQ). The individual and relative roles of these sleep parameters, as well as morning ratings of pain and mood, in predicting subsequent physical activity were examined in multilevel models that took into account variations in relationships at the ‘Day’ and ‘Participant’ levels. Results Of the 5 plausible predictors SQ was the only significant within-person predictor of subsequent physical activity, such that nights of higher sleep quality were followed by days of more physical activity, from noon to 11pm. The temporal association was not explained by potential confounders such as morning pain, mood or effects of the circadian rhythm. Conclusions In the absence of interventions, chronic pain patients spontaneously engaged in more physical activity following a better night of sleep. Improving nighttime sleep may well be a novel avenue for promoting daytime physical activity in patients with chronic pain.
Altered Transforming Growth Factor-Beta Signaling in a Murine Model of Thoracic Aortic Aneurysm

Objective: Thoracic aortic aneurysms (TAAs) develop by a multifactorial process involving maladaptive signaling pathways that alter the aortic vascular environment. Transforming growth factor-beta (TGF-β) has been implicated in regulating the structure and composition of the extracellular matrix by differential activation of various intracellular signaling pathways. However, whether and to what degree TGF-β signaling contributes to TAA development remains unclear. Accordingly, the hypothesis that alterations in TGF-β signaling occur during aneurysm formation was tested in a murine model of TAA. Methods: TAAs were surgically induced in mice (C57BL/6J) and aortas were analyzed at predetermined time points (1, 2, and 4 weeks post-TAA induction). Quantitative real-time PCR (QPCR) was performed to evaluate the expression of 84 relevant TGF-β superfamily genes, and the protein levels of key signaling intermediates were measured by immunoblotting. Results were compared to unoperated reference control mice. Results: QPCR revealed increased expression of TGF-β superfamily ligands (Gdf-2, -6, -7, Inhba), ligand inhibitors (Bmper, Chrd, Gsc), and transcriptional regulators (Dlx2, Evi1), among other genes (Cdkn2b, Igf1, IL-6). Protein levels of TGF-β receptorII, Smad2, Smad1/5/8, phospho-Smad1/5/8, and Smurf1 were increased from control values post-TAA induction. Both TGF-β receptorI and Smad4 were decreased from control values, while ALK-1 levels remained unchanged. Conclusions: These alterations in the TGF-β pathway suggest a mechanism by which primary signaling is switched from a TGF-βRI/Smad2-dependent response, to an ALK-1/Smad1/5/8 response, representing a significant change in signaling outcome, which may enhance matrix degradation.
The EM Algorithm in Multivariate Gaussian Mixture Models using Anderson Acceleration

Over the years analysts have used the EM algorithm to obtain maximum likelihood estimates from incomplete data for various models. The general algorithm admits several appealing properties such as strong global convergence; however, the rate of convergence is linear which in some cases may be unacceptably slow. This work is primarily concerned with applying Anderson acceleration to the EM algorithm for Gaussian mixture models (GMM) in hopes of alleviating slow convergence. As preamble we provide a review of maximum likelihood estimation and derive the EM algorithm in detail. The iterates that correspond to the GMM are then formulated and examples are provided. These examples show how faster convergence is experienced when the data are well separated, whereas much slower convergence is seen whenever the sample is poorly separated. The Anderson acceleration method is then presented, and its connection to the EM algorithm is discussed. The work is then concluded by applying Anderson acceleration to the EM algorithm which results in reducing the number of iterations required to obtain convergence.
End-of-life care pathways for improving outcomes in caring for the dying.

BACKGROUND In many clinical areas, integrated care pathways are utilised as structured multidisciplinary care plans which detail essential steps in caring for patients with specific clinical problems. Particularly, care pathways for the dying have been developed as a model to improve the end-of-life care of all patients. They aim to ensure that the most appropriate management occurs at the most appropriate time and that it is provided by the most appropriate health professional. Clinical pathways for end-of-life care management are used widely around the world and have been regarded as the gold standard. Therefore, there is a significant need for clinicians to be informed about the utilisation of end-of-life care pathways with a systematic review. OBJECTIVES To assess the effects of end-of-life care pathways, compared with usual care (no pathway) or with care guided by another end-of-life care pathway across all healthcare settings (e.g. hospitals, residential aged care facilities, community). SEARCH STRATEGY The Cochrane Register of controlled Trials (CENTRAL), the Pain, Palliative and Supportive Care Review group specialised register, MEDLINE, EMBASE, review articles and reference lists of relevant articles were searched. The search was carried out in September 2009. SELECTION CRITERIA All randomised controlled trials (RCTs), quasi-randomised trial or high quality controlled before and after studies comparing use versus non-use of an end-of-life care pathway in caring for the dying. DATA COLLECTION AND ANALYSIS Results of searches were reviewed against the pre-determined criteria for inclusion by two review authors. MAIN RESULTS The search identified 920 potentially relevant titles, but no studies met criteria for inclusion in the review. AUTHORS' CONCLUSIONS Without further available evidence, recommendations for the use of end-of-life pathways in caring for the dying cannot be made. RCTs or other well designed controlled studies are needed for evaluating the use of end-of-life care pathways in caring for dying people.