Miracle-dz/UniFAR-FTUs huggingface dataset:
Infection of Human Endothelial Cells by Japanese Encephalitis Virus: Increased Expression and Release of Soluble HLA-E

Japanese encephalitis virus (JEV) is a single stranded RNA virus that infects the central nervous system leading to acute encephalitis in children. Alterations in brain endothelial cells have been shown to precede the entry of this flavivirus into the brain, but infection of endothelial cells by JEV and their consequences are still unclear. Productive JEV infection was established in human endothelial cells leading to IFN-β and TNF-α production. The MHC genes for HLA-A, -B, -C and HLA-E antigens were upregulated in human brain microvascular endothelial cells, the endothelial-like cell line, ECV 304 and human foreskin fibroblasts upon JEV infection. We also report the release/shedding of soluble HLA-E (sHLA-E) from JEV infected human endothelial cells for the first time. This shedding of sHLA-E was blocked by an inhibitor of matrix metalloproteinases (MMP). In addition, MMP-9, a known mediator of HLA solubilisation was upregulated by JEV. In contrast, human fibroblasts showed only upregulation of cell-surface HLA-E. Addition of UV inactivated JEV-infected cell culture supernatants stimulated shedding of sHLA-E from uninfected ECV cells indicating a role for soluble factors/cytokines in the shedding process. Antibody mediated neutralization of TNF-α as well as IFNAR receptor together not only resulted in inhibition of sHLA-E shedding from uninfected cells, it also inhibited HLA-E and MMP-9 gene expression in JEV-infected cells. Shedding of sHLA-E was also observed with purified TNF-α and IFN-β as well as the dsRNA analog, poly (I:C). Both IFN-β and TNF-α further potentiated the shedding when added together. The role of soluble MHC antigens in JEV infection is hitherto unknown and therefore needs further investigation.
Cortical Thickness and Subcortical Gray Matter Reductions in Neuropsychiatric Systemic Lupus Erythematosus

Within systemic lupus erythematosus (SLE) patients can be divided into groups with and without central nervous system involvement, the latter being subcategorized as neuropsychiatric systemic lupus erythematosus (NPSLE). While a number of research groups have investigated NPSLE, there remains a lack of consistent application of this diagnostic criteria within neuroimaging studies. Previous neuroimaging research suggests that SLE patients have reduced subcortical and regional gray matter volumes when compared to controls, and that these group differences may be driven by SLE patients with neuropsychiatric symptoms. The current study sought to compare measures of cortical thickness and subcortical structure volume between NPSLE, SLE, and healthy controls. We hypothesized that patients with NPSLE (N = 21) would have thinner cortex and reduced subcortical gray matter volumes when compared to SLE (N = 16) and control subjects (N = 21). All subjects underwent MRI examinations on a 1.5 Tesla Siemens Sonata scanner. Anatomical reconstruction and segmentation were performed using the FreeSurfer image analysis suite. Cortical and subcortical volumes were extracted from FreeSurfer and analyzed for group differences, controlling for age. The NPSLE group exhibited decreased cortical thickness in clusters of the left frontal and parietal lobes as well as in the right parietal and occipital lobes compared to control subjects. Compared to the SLE group, the NPSLE group exhibited comparable thinning in clusters of the frontal and temporal lobes. Controlling for age, we found that between group effects for subcortical gray matter structures were significant for the thalamus (F = 3.06, p = .04), caudate nucleus (F = 3.19, p = .03), and putamen (F = 4.82, p = .005). These results clarify previous imaging work identifying cortical atrophy in a mixed SLE and NPSLE group, and suggest that neuroanatomical abnormalities are specific to SLE patients diagnosed with neuropsychiatric symptoms. Future work should help elucidate the underlying mechanisms underlying the emerging neurobiological profile seen in NPSLE, as well as clarify the apparent lack of overlap between cortical thinning and functional activation results and other findings pointing to increased functional activation during cognitive tasks.
Translational regulation of GluR2 mRNAs in rat hippocampus by alternative 3′ untranslated regions

The glutamate receptor 2 (GluR2) subunit determines many of the functional properties of the α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionate subtype of glutamate receptor. The roles of untranslated regions (UTRs) in mRNA stability, transport, or translation are increasingly recognized. The 3′ end of the GluR2 transcripts are alternatively processed to form a short and long 3′UTR, giving rise to two pools of GluR2 mRNA of 4 and 6 kb in length, respectively, in the mammalian brain. However, the role of these alternative 3′UTRs in GluR2 expression has not been reported. We demonstrate that in the cytoplasm of rat hippocampus, native GluR2 mRNAs bearing the long 3′UTR are mostly retained in translationally dormant complexes of ribosome‐free messenger ribonucleoprotein (mRNP), whereas GluR2 transcripts bearing the short 3′UTR are predominantly associated with actively translating ribosomes. One day after pilocarpine‐induced status epilepticus (SE), the levels of both long and short GluR2 transcripts were markedly decreased in rat hippocampus. However, GluR2 mRNAs bearing the long 3′‐UTRs were shifted from untranslating mRNP complexes to ribosome‐containing complexes after SE, pointing to a selective translational derepression of GluR2 mRNA mediated by the long 3′UTR. In Xenopus oocytes, expression of firefly luciferase reporters bearing alternative GluR2 3′UTRs confirmed that the long 3′UTR is sufficient to suppress translation. The stability of reporter mRNAs in oocytes was not significantly influenced by alternative 5′ or 3′UTRs of GluR2 over the time period examined. Overall, our findings that the long 3′UTR of GluR2 mRNA alone is sufficient to suppress translation, and the evidence for seizure‐induced derepression of translation of GluR2 via the long 3′UTR strongly suggests that a regulatory signaling mechanism exists that differentially targets GluR2 transcripts with alternative 3′UTRs.
Optimizing TCP Receive Performance

The performance of receive side TCP processing has traditionally been dominated by the cost of the 'per-byte' operations, such as data copying and checksumming. We show that architectural trends in modern processors, in particular aggressive prefetching, have resulted in a fundamental shift in the relative overheads of per-byte and per-packet operations in TCP receive processing, making per-packet operations the dominant source of overhead. Motivated by this architectural trend, we present two optimizations, receive aggregation and acknowledgment offload, that improve the receive side TCP performance by reducing the number of packets that need to be processed by the TCP/IP stack. Our optimizations are similar in spirit to the use of TCP Segment Offload (TSO) for improving transmit side performance, but without need for hardware support. With these optimizations, we demonstrate performance improvements of 45-67% for receive processing in native Linux, and of 86% for receive processing in a Linux guest operating system running on Xen.
Contribution of autoallergy to the pathogenesis in the NOD mice

Abstract The immunoglobulin isotype IgE is commonly associated with allergy. However, its involvement in autoimmune disease in general, and Type 1 diabetes (T1D) in particular, is still not completely clarified, nonetheless IgE has been observed in patients with T1D. In this article, we aimed to elucidate the contribution of IgE in the pathogenesis of the disease in a spontaneous model for T1D, i.e. the NOD mouse. We observed increased levels of IgE in splenic, lymph node and peripheral blood B cells in the NOD mice compared to the control C57BL/6 (B6) mice. No correlation was found between the IgE levels on B cells and those in the sera of these mice, indicating a B cell intrinsic property mediating IgE capture in NOD. Functionally, the B cells from NOD were similar to B6 in rescuing the IgE-mediated immune response via the low affinity receptor CD23 in a transgenic adoptive transfer system. However, the involvement of IgE in diabetes development was clearly demonstrated, as treatment with anti-IgE antibodies delayed the incidence of the diabetes in the NOD mice compared to the PBS treated group. Pancreas sections from a 13-week-old NOD revealed the presence of tertiary lymphoid structures with T cells, B cells, germinal centers and IgE suggesting the presence of autoantigen specific IgE. Our study provides an insight to the commonly overlooked immunoglobulin IgE and its potential role in autoimmunity.
The Influence of City Size on Dietary Choices and Food Recommendation

Contextual features have been leveraged by recommender systems in many different domains. Traditional contextual features -- such as location and time -- have successfully been combined with collaborative filtering or content-based features. However, it is likely that there are other -- domain-specific -- features that may have even more impact. In this paper, we focus on the influence of city size on food preferences. Apart from location and time, our results show that city size can significantly boost the performance of food recommendation.
Analysis of speech characteristics of neurological diseases and their classification

The characteristics of speech and voice in neurological diseases, such as, Parkinson's disease (PD), cerebellar demyelination, senile disease and stroke, have a realistic potential to provide information for early detection of onset, progression, and severity of these diseases. There are no risks involved in capturing and analysis of voice signals as it is noninvasive by nature and in carefully controlled circumstances, it can provide a large amount of meaningful data. The data collected in the present work consist of 136 sustained vowel phonations (/ah/), among them 83 phonations are from patients suffering from different neurological diseases and 53 phonations from controlled subjects including both male and female subjects. A total of 16 features were extracted from the voice data and significant differences between the two group `means' were evaluated using student's t-test. Significant findings in measurements were found in all types of shimmers and jitters features, except in measures of pitch. Further, all the 16 features were used as input to the artificial neural network (ANN) for classification. Two types of ANN are used for classification, the multilayer perceptron (MLP) network and radial basis function (RBF) network. 112 phonations were used to train the network and 24 phonations for testing. The RBF network gave a better classification with 90.12% for training set and 87.5% for test set compared to MLP with 86.66% for training set and 83.33% for test set.
Intestinal post-ischemic reperfusion injury: studies with neonatal necrotizing enterocolitis.

In the feline intestine studies have implicated superoxide (O.-) and other oxygen derived free radicals as initiators of injury as measured by increased capillary permeability during the reperfusion period. Biochemical mechanisms of this free radical generation include: xanthine oxidase dependent O. - production, hydrogen peroxide (H2O2) formation by superoxide dismutase (SOD), hydroxyl radical (OH-) production via the Haber-Weiss reaction, and lipid radical formation from membrane peroxidation. Pathological consequences of these events include inflammatory neutrophil infiltration, damage to the collagen and mucosal basement membrane, increased capillary permeability, edema, cell degeneration and necrosis. Animal models of neonatal necrotizing enterocolitis (NNEC) indicate that intestinal injury occurs after the etiologic factors (hypothermia, hypoxia) are removed. In order to determine the role of active oxygen species in the pathogenesis of NNEC, weanling hamsters and neonatal piglets were cold stressed and activities of pro/antioxidant enzymes were determined, and histopathologic and ultrastructural studies were performed. Cold stressed weanling hamsters showed a 55.7% (P less than 0.05) decrease in xanthine dehydrogenase/xanthine oxidase activity ratio. Light microscopy revealed scattered colonic mucosal erosions and submucosal edema in 50% of cold stressed animals. Transmission electron microscopy demonstrated degeneration of colonic mucosal epithelial cells, enlarged intracellular spaces, cytoplasmic vacuolization, and nuclear membrane swelling. The colonic serosa was also edematous and infiltrated with bacteria. Large intestinal tissue from cold stressed neonatal piglets showed a significant increase (P less than 0.05) in Mn and Cu, Zn, SOD, CAT, GSH-Red, total GSH, and Glc6-PD at 0 and 12 hrs. post stress. (ABSTRACT TRUNCATED AT 250 WORDS)
Partners of Cancer Patients

Abstract Although the adjustment of cancer patients' partners has been studied more extensively in recent years than previously, three areas of research have not been integrated into the literature: (1) the impact of cancer on the partner across different stages of the illness trajectory, (2) gender differences in partner's reactions and adjustment, and (3) psychosocial interventions for partners. In Part I of their review, the authors discussed the partners' experiences, how the illness affected partners, and how partners adjusted to and coped with the patient's illness. Part II reviews the interventions that have been developed to help patients' partners and concludes with suggestions for providing interventions tailored specifically for different populations of partners.
The RR Interval Spectrum, the ECG Signal, and Aliasing

A reliable spectral analysis requires sampling rate at least twice as large as the frequency bound, otherwise the analysis will be unreliable and plagued with aliasing distortions. The RR samplings do not satisfy the above requirements and therefore their spectral analysis might be unreliable. In order to demonstrate the feasibility of aliasing in RR spectral analysis, we have done an experiment which have shown clearly how the aliasing was developed. In the experiments, one of us (A.G) had kept his high breathing rate constant with the aid of metronome for more than 5 minutes. The breathing rate was larger than one-half the heart rate. Very accurate results were obtained and the resulting aliasing well understood. To our best knowledge this is the first controlled experiment of this kind coducted on humans. We compared the RR spectral analysis with the spectrum of the ECG signals from which the RR intervals were extracted. In the significant for RR analysis frequencies (below one-half Hertz) significant differences were observed. In conclusion we recommend to study the spectral analysis of the ECG signal in the free of aliasing frequency range.
Modeling Swarm Robotic Systems: a Case Study in Collaborative Distributed Manipulation

In this paper, we present a time-discrete, incremental methodology for modeling, at the microscopic and macroscopic levels, the dynamics of distributed manipulation experiments using swarms of autonomous robots endowed with reactive controllers. The methodology is well suited for non-spatial metrics, as it does not take into account robot trajectories or the spatial distribution of objects in the environment. The strength of the methodology lies in the fact that it has been generated by considering incremental abstraction steps, fromreal robots to macroscopic models, each with well-defined mappings between successive implementation levels. Precise heuristic criteria based on geometrical considerations and systematic tests with one or two real robots prevent the introduction of free parameters in the calibration procedure of models. As a consequence, we are able to generate highly abstracted macroscopic models that can capture the dynamics of a swarm of robots at the behavioral level while still being closely anchored to the characteristics of the physical setup. Although this methodology has been and can be applied to other experiments in distributed manipulation (e.g. object aggregation and segregation, foraging), in this paper we focus on a strictly collaborative case study concerned with pulling sticks out of the ground, an action that requires the collaboration of two robots to be successful. Experiments were carried out with teams consisting of two to 600 individuals at different levels of implementation (real robots, embodied simulations, microscopic and macroscopic models). Results show that models can deliver both qualitatively and quantitatively correct predictions in time lapses that are at least four orders of magnitude smaller than those required by embodied simulations and that they represent a useful tool for generalizing the dynamics of these highly stochastic, asynchronous, nonlinear systems, often outperforming intuitive reasoning. Finally, in addition to discussing subtle numerical effects, small prediction discrepancies, and difficulties in generating the mapping between different abstractions levels, we conclude the paper by reviewing the intrinsic limitations of the current modeling methodology and by proposing a few suggestions for future work.
Stimulation of the Human RAD51 Nucleofilament Restricts HIV-1 Integration In Vitro and in Infected Cells

ABSTRACT Stable HIV-1 replication requires the DNA repair of the integration locus catalyzed by cellular factors. The human RAD51 (hRAD51) protein plays a major role in homologous recombination (HR) DNA repair and was previously shown to interact with HIV-1 integrase (IN) and inhibit its activity. Here we determined the molecular mechanism of inhibition of IN. Our standard in vitro integration assays performed under various conditions promoting or inhibiting hRAD51 activity demonstrated that the formation of an active hRAD51 nucleofilament is required for optimal inhibition involving an IN-DNA complex dissociation mechanism. Furthermore we show that this inhibition mechanism can be promoted in HIV-1-infected cells by chemical stimulation of the endogenous hRAD51 protein. This hRAD51 stimulation induced both an enhancement of the endogenous DNA repair process and the inhibition of the integration step. Elucidation of this molecular mechanism leading to the restriction of viral proliferation paves the way to a new concept of antiretroviral therapy based on the enhancement of endogenous hRAD51 recombination activity and highlights the functional interaction between HIV-1 IN and hRAD51.
Secondary Structure and Membrane Topology of the Full-Length Dengue Virus NS4B in Micelles.

Dengue virus nonstructural protein 4B (NS4B) is a membrane protein consisting of 248 residues with a crucial role in virus replication and interference with the host innate immunity. The dengue virus serotype 3 NS4B was reconstituted into lyso-myristoyl phosphatidylglycerol (LMPG) micelles. Backbone resonance assignment of NS4B was obtained using conventional solution NMR experiments. Further studies suggested that NS4B contained eleven helices and six of them form five potential transmembrane regions. This study provides atomic level information for an important drug target to control flavivirus infections.
Uncovering a Large Set of Genes That Affect Surface Motility in Salmonella enterica Serovar Typhimurium

ABSTRACT We describe a large set of genes affecting motility in Salmonella enterica serovar Typhimurium. Identified in microarray experiments as displaying flagellar gene expression patterns or controlled by known flagellar regulators, we show that null mutations in these genes primarily affect swarming motility. Three genes function in chemotaxis.
Negative Regulation of Neural Stem/Progenitor Cell Proliferation by the Pten Tumor Suppressor Gene in Vivo

The mechanisms controlling neural stem cell proliferation are poorly understood. Here we demonstrate that the PTEN tumor suppressor plays an important role in regulating neural stem/progenitor cells in vivo and in vitro. Mice lacking PTEN exhibited enlarged, histoarchitecturally abnormal brains, which resulted from increased cell proliferation, decreased cell death, and enlarged cell size. Neurosphere cultures revealed a greater proliferation capacity for tripotent Pten –/– central nervous system stem/progenitor cells, which can be attributed, at least in part, to a shortened cell cycle. However, cell fate commitments of the progenitors were largely undisturbed. Our results suggest that PTEN negatively regulates neural stem cell proliferation.
Family resilience: a developmental systems framework

Abstract This article presents a brief overview of a family resilience conceptual framework, grounded in a multi-level developmental systems orientation. A family systems perspective broadens attention to resources for individual resilience throughout the family network of relationships. The concept of family resilience refers to the family as a functional system, impacted by highly stressful events and social contexts, and in turn, facilitating the positive adaptation of all members and strengthening the family unit. A research-informed map of key processes in family resilience is outlined, highlighting the recursive and synergistic influences of transactional processes within families and with their social environment. Varied process elements may be more or less useful, depending on different adverse situations over time, with a major crisis, trauma, or loss; disruptive transitions; or chronic multi-stress conditions. This perspective is attuned to the diversity of family cultures and structures, their resources and constraints, salient socio-cultural and developmental influences, and the viability of varied pathways in resilience.
Transcriptional and Histological Analyses of the Thymic Developmental Process in the Fetal Pig

The humanized pig model, in which human cells or tissues can be functionally maintained in pigs, can be an invaluable tool for human medical research. Although the recent development of immunodeficient pigs has opened the door for the development of such a model, the efficient engraftment and differentiation of human cells may be difficult to achieve. The transplantation of human cells into fetal pigs, whose immune system is immature, will ameliorate this problem. Therefore, we examined the development of porcine fetal thymus, which is critical for the establishment of the immune system. We first analyzed the levels of mRNA expression of genes that are relevant to the function of thymic epithelial cells or thymocytes in whole thymi from 35 to 85 days of gestation (DG) and at 2 days postpartum (DP) by quantitative RT-PCR. In addition, immunohistochemical analyses of thymic epithelial cells from DG35 to DG55 and DP2 were performed. These analyses showed that the thymic cortex was formed as early as DG35, and thymic medulla gradually developed from DG45 to DG55. These findings suggested that, at least before DG45, the thymus do not differentiate to form fully functional T cells.