Miracle-dz/UniFAR-FTUs huggingface dataset:
T-cell immunity to peptide epitopes of liver-stage antigen 1 in an area of Papua New Guinea in which malaria is holoendemic

Liver-stage antigen 1 (LSA1) is one of several pre-erythrocytic antigens considered for inclusion in a multiantigen, multistage subunit vaccine against falciparum malaria. We examined T-cell proliferation and cytokine responses to peptides corresponding to amino acids 84 to 107, 1813 to 1835, and 1888 to 1909 of LSA1 in asymptomatic adults living in an area of Papua New Guinea where malaria is holoendemic. Whereas T cells from North Americans never exposed to malaria did not respond to any of the peptides, those from 52 of 55 adults from the area where malaria is endemic had vigorous proliferation responses to one or more of the LSA1 peptides (mean stimulation indices of 6.8 to 7.2). Gamma interferon (IFN-gamma) production driven by LSA1 peptides ranged from 34 to more than 3,500 pg/2 x 10(6) cells, was derived primarily from CD8+ cells, and was dissociated from T-cell proliferation. The frequencies of IFN-gamma response to the amino acid 1819 to 1835 and 1888 to 1909 peptides were significantly greater than that to the amino acid 84 to 107 peptide (87 and 88% versus 33% of subjects; P < 0.0001). In contrast to proliferation and IFN-gamma, interleukin 4 (IL-4) and/or IL-5 responses to LSA1 peptides were detected in only 18% of the subjects. These data show that T-cell immunity to epitopes in the N- and C-terminal regions of LSA1 are common in persons living in this area of Papua New Guinea where malaria is endemic. The dominance of type 1 CD8 cell IFN-gamma responses is consistent with a role for this T-cell population in immunity to liver-stage Plasmodium falciparum in humans.
Emergence of Extensively Drug-Resistant ( XDR ) 1 Haemophilus parainfluenzae in Switzerland 2 3 4

Emergence of Extensively Drug-Resistant (XDR) 1 Haemophilus parainfluenzae in Switzerland 2 3 4 Regula Tinguely, Salome N. Seiffert, Hansjakob Furrer, Vincent Perreten, 5 Sara Droz, and Andrea Endimiani 1* 6 7 8 Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland; 9 Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; 10 Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; 11 Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, 12 Switzerland 13 14 15 Running title: XDR H. parainfluenzae 16 17
Comparison of 2 manual therapy and exercise protocols for cervical radiculopathy: a randomized clinical trial evaluating short-term effects.

STUDY DESIGN Participant- and assessor-blinded randomized clinical trial. OBJECTIVES To compare a rehabilitation program thought to increase the size of the intervertebral foramen (IVF) of the affected nerve root to a rehabilitation program that doesn't include any specific techniques thought to increase the size of the IVF in patients presenting with cervical radiculopathy (CR). BACKGROUND Clinical approaches for the treatment of CR commonly include exercises and manual therapy techniques thought to increase the size of the IVF, but evidence regarding the effectiveness of these specific manual therapy techniques is scarce. METHODS Thirty-six participants with CR were randomly assigned either to a group that received a manual therapy and exercise program aimed at increasing the size of the IVF of the affected nerve root (experimental group, n=18) or to a group that received a manual therapy and exercise program without the specific goal of increasing the size of the IVF of the affected level and side (comparison group, n=18). Primary (Neck Disability Index) and secondary (shortened version of the Disabilities of the Arm, Shoulder and Hand questionnaire [QuickDASH] and numeric pain-rating scale) outcomes were evaluated at baseline, at the end of the 4-week program (week 4), and 4 weeks later (week 8). A mixed-model, 2-way analysis of variance was used to analyze treatment effects. RESULTS No significant group-by-time interaction or group effect was observed for Neck Disability Index, QuickDASH, and numeric pain-rating scale scores (P≥.14) following the intervention. However, both groups showed statistically and clinically significant improvement from baseline to week 4 and to week 8 in Neck Disability Index, QuickDASH, and numeric pain-rating scale scores (P<.05). CONCLUSION Results suggest that manual therapy and exercises are effective in reducing pain and functional limitations related to CR. The addition of techniques thought to increase the size of the IVF of the affected nerve root yielded no significant additional benefits. Given the absence of a "no treatment" group, a spontaneous resolution of symptoms cannot be excluded. However, the magnitude of improvement makes spontaneous resolution unlikely. The trial was registered at ClinicalTrials.gov (NCT01500044). LEVEL OF EVIDENCE Therapy, level 1b-.
The properties of P-type copper (I) iodide (CuI) as a hole conductor for solid-state dye sensitized solar cells

This research demonstrated the effect of solution concentration of copper (I) iodide (CuI) to the thin films properties and photovoltaic performance. The CuI concentration was varied from 0.01M to 0.09M. The CuI solution was prepared by mixing the CuI powder with 50 ml of acetonitrile as a solvent. A novel method of mist atomization technique has been used for the deposition of CuI materials. For the thin film properties, the surface morphology and electrical properties of CuI thin films which was deposited on the glass substrates were investigated. The result shows the CuI thin film properties strongly depends on its precursor concentration. The nano size CuI particles were observed for all thin films. The electrical properties indicates the increased of conductivity until optimum point of 0.05M. The highest device efficiency obtained in this research is 1.05%. The pore filling issues and electrical conductivity of hole conductor were the main factors contributed to the overall performance of solar cells.
Inclusion-body hepatitis in broiler chickens.

SUMMARY Eighty-six outbreaks of inclusion-body hepatitis were identified in broiler chickens in Ontario. The disease occurred mainly in birds 5 weeks old, and mortality (ranging from 0.1 to 7%) was most common in the spring. Grossly, the common lesions were stellate or punctiform hemorrhagic areas in extremely fatty livers, enlarged pale kidneys, hemorrhagic lesions in the visceral fat and muscles, pale bone marrow, and an extremely small firm bursa of Fabricius. Histological examination of tissues revealed intranuclear inclusion bodies in the hepatocytes with massive necrosis of liver parenchyma, regression of the follicles and proliferation of interstitial connective tissue in the bursa, aplastic bone marrow with little hemopoietic tissue functioning, and a moderate to severe nephrosis involving the proximal and distal convoluted tubules. Bacteriological examination was negative. Electron-microscope examination of the livers revealed abnormal intranuclear structures; however, no distinct virus particles were seen. A virus was isolated and produced cytopathic changes in chick and'duck embryo cell cultures.
Diffusion tensor imaging of early relapsing-remitting multiple sclerosis with histogram analysis using automated segmentation and brain volume correction

Diffusion tensor magnetic resonance imaging (DTI) reveals measurable abnormalities in normal-appear ing brain tissue (NA BT) in established multiple sclerosis (MS). However, it is unclear how early this occurs. Recent studies have employed whole brain histogram analysis to improve sensitivity, but concern exists regarding reliability of tissue/cerebrospinal fluid segmentation and possible intersubject brain volume differences, which can introduce partial volume error. To address this, 28 early relapsing-remitting MS subjects [median disease duration 1.6 years; median Expanded Disability Status Scale (EDSS) score 1.5] and 20 controls were compared with whole brain histogram analysis using an automated segmentation algorithm to improve reproducibility. Brain parenchymal volumes (BPV) were estimated for each subject in the analysis. The mean, peak height and peak location were calculated for DTI parameters [fractional anisotropy (FA), mean diffusivity and volume ratio]. A n increased FA peak height in MS subject NA BT was observed (P =0.02) accounting for age, gender and BPV. Removing BPV revealed additional abnormalities in NABT. The main conclusions are i) FA peak height is increased in NA BT in early MS, ii) partial volume edge effects may contribute to apparent NA BT histogram abnormalities, and iii) correction for brain volume differences should reduce potential partial volume edge effects.
The Lyme Disease Spirochete Borrelia burgdorferi Utilizes Multiple Ligands, Including RNA, for Interferon Regulatory Factor 3-Dependent Induction of Type I Interferon-Responsive Genes

ABSTRACT We recently discovered a critical role for type I interferon (IFN) in the development of murine Lyme arthritis. Borrelia burgdorferi-mediated induction of IFN-responsive genes by bone marrow-derived macrophages (BMDMs) was dependent upon a functional type I IFN receptor but independent of Toll-like receptor 2 (TLR2), TLR4, TLR9, and the adapter molecule MyD88. We now demonstrate that induction of the IFN transcriptional profile in B. burgdorferi-stimulated BMDMs occurs independently of the adapter TRIF and of the cytoplasmic sensor NOD2. In contrast, B. burgdorferi-induced transcription of these genes was dependent upon a rapid STAT1 feedback amplification pathway. IFN profile gene transcription was IRF3 dependent but did not utilize B. burgdorferi-derived DNA or DNase-sensitive ligands. Instead, IFN-responsive gene expression could be induced by B. burgdorferi-derived RNA. Interferon regulatory factor 3 (IRF3)-dependent IFN profile gene transcription was also induced by sonicated bacteria, by the lipoprotein OspA, and by factors released into the BSKII medium during culture of B. burgdorferi. The IFN-stimulatory activity of B. burgdorferi culture supernatants was not destroyed by nuclease treatment. Nuclease digestion also had no effect on IFN profile induction mediated by sonicated B. burgdorferi. Thus, B. burgdorferi-derived RNA, OspA, and non-nucleic acid ligands present in both sonicated bacteria and B. burgdorferi culture medium contribute to type I IFN-responsive gene induction. These findings suggest that B. burgdorferi invasion of joint tissue and the resultant type I IFN induction associated with Lyme arthritis development may involve multiple triggering ligands.
Time course and determinants of leptin decline during weight loss in obese boys and girls.

OBJECTIVE To investigate whether changes in leptin concentrations during weight loss can be explained by gender, puberty, baseline adiposity and changes in adiposity, body composition, rate of weight loss, physical activity and insulin concentrations. DESIGN A longitudinal study with 9 repeated measures during a 12-week weight loss programme. SUBJECTS Fifty-three boys and 62 girls (7.9-15.2 years) with body mass index (BMI) standard deviation scores (SDS) of median 2.78 and 2.70, respectively. MEASUREMENTS Height, weight, fat mass percentage assessed by bioimpedance, Tanner stages, testicular size, physical activity scores, blood leptin (ng/ml) and insulin concentrations (pmol/l) were measured at baseline, and except for Tanner stage and testicular size, repeated regularly during the programme. RESULTS The weight loss was accompanied by a steep decline in leptin concentrations during the first 10-11 days, followed by a less steep decline until day 82. Leptin declined to 39% in boys and 51% in girls of the level that was expected given the relationship at baseline between leptin and BMI SDS, and the BMI SDS changes during weight loss. The biphasic leptin decline was independent of gender, puberty, baseline adiposity or concomitant changes in BMI SDS, fat mass percentage, rate of weight loss, physical activity scores or insulin concentrations. CONCLUSION The biphasic leptin decline, which exceeded the level expected, was independent of puberty, baseline adiposity and changes in adiposity, body composition, rate of weight loss, physical activity scores and insulin concentrations. The dissociation of the leptin-weight relationship during weight loss may contribute to the general leptin variability in obese subjects.
Oxidized Low Density Lipoprotein Induces Bone Morphogenetic Protein-2 in Coronary Artery Endothelial Cells via Toll-like Receptors 2 and 4*

Vascular calcification is a common complication in atherosclerosis. Bone morphogenetic protein-2 (BMP-2) plays an important role in atherosclerotic vascular calcification. The aim of this study was to determine the effect of oxidized low density lipoprotein (oxLDL) on BMP-2 protein expression in human coronary artery endothelial cells (CAECs), the roles of Toll-like receptor (TLR) 2 and TLR4 in oxLDL-induced BMP-2 expression, and the signaling pathways involved. Human CAECs were stimulated with oxLDL. The roles of TLR2 and TLR4 in oxLDL-induced BMP-2 expression were determined by pretreatment with neutralizing antibody, siRNA, and overexpression. Stimulation with oxLDL increased cellular BMP-2 protein levels in a dose-dependent manner (40–160 μg/ml). Pretreatment with neutralizing antibodies against TLR2 and TLR4 or silencing of these two receptors reduced oxLDL-induced BMP-2 expression. Overexpression of TLR2 and TLR4 enhanced the cellular BMP-2 response to oxLDL. Furthermore, oxLDL was co-localized with TLR2 and TLR4. BMP-2 expression was associated with activation of nuclear factor-κB (NF-κB), p38 mitogen-activated protein kinase (MAPK), and extracellular signal-regulated kinase (ERK)1/2. Inhibition of NF-κB and ERK1/2 reduced BMP-2 expression whereas inhibition of p38 MAPK had no effect. In conclusion, oxLDL induces BMP-2 expression through TLR2 and TLR4 in human CAECs. The NF-κB and ERK1/2 pathways are involved in the signaling mechanism. These findings underscore an important role for TLR2 and TLR4 in mediating the BMP-2 response to oxLDL in human CAECs and indicate that these two immunoreceptors contribute to the mechanisms underlying atherosclerotic vascular calcification.
Dynamic stiffness of spin valves

The dynamics of the magnetic order parameters of ferromagnet/paramagnet/ferromagnet spin valves and isolated ferromagnets may be very different. We investigate the role of the nonequilibrium spin-current exchange between the ferromagnets in the magnetization precession and switching. We find a (low-temperature) critical current bias for a uniform current-induced magnetization excitation in spin valves, which unifies and generalizes previous ideas of Slonczewski and Berger. In the absence of an applied bias, the effect of the spin transfer can be expressed as magnetic-configuration-dependent Gilbert damping.
Comparison of cerebellothalamic and pallidothalamic projections in the monkey (Macaca fuscata): A double anterograde labeling study

To address the question of segregated projections from the internal segment of the globus pallidus (GPi) and the cerebellar nuclei (Cb) to the thalamus in the monkey, we employed a double anterograde labeling strategy combining the anterograde transport of horseradish peroxidase conjugated to wheat germ agglutinin (WGA‐HRP) with biotinylated dextran amine (BDA) transport. The tissue was processed sequentially for WGA‐HRP, and then BDA immunohistochemistry using two different chromogens. Since the two labels were easily distinguishable on the same histological section, the interrelationship between the cerebellar and pallidal projection systems could be directly evaluated. We found that both the cerebellothalamic and pallidothalamic label consisted of dense plexuses of labeled fibers and swellings in a patch‐like configuration. The patches or foci of labeling were distributed either as dense single label or as interdigitating patches of double label. We found dense single label in the central portion of the ventral anterior nucleus pars principalis (VApc) and the ventral lateral nucleus pars oralis (VLo) following the GPi injections or in the central portion of the ventral posterior lateral nucleus pars oralis (VPLo) and nucleus X (X) following the cerebellar nuclei injections. Complementary interdigitating patches of WGA‐HRP and BDA labeling were found primarily in transitional border regions between thalamic nuclei. On occasion, we found overlap of both labels. We observed a gradient pattern in the density of the pallidothalamic and cerebellothalamic projections. The pallidothalamic territory included VApc, VLo, and the ventral lateral nucleus pars caudalis (VLc), with the density of these projections decreasing along an anterior to posterior gradient in the thalamus. Occasional patches of pallidal label were found in VPLo and nucleus X. Conversely, the density of cerebellothalamic projections increased along the same gradient, with the cerebellothalamic territory extending anteriorly beyond the cell‐sparse zones of VPLo, X, and VLc to include VLo and VApc also. These data suggest that although the cerebellar and pallidal projections primarily occupy separate thalamic territories, individual thalamic nuclei receive differentially weighted inputs from these sources. © 1996 Wiley‐Liss, Inc.
Cap-independent translation of poliovirus mRNA is conferred by sequence elements within the 5' noncoding region

Poliovirus polysomal RNA is naturally uncapped, and as such, its translation must bypass any 5' cap-dependent ribosome recognition event. To elucidate the manner by which poliovirus mRNA is translated, we have determined the translational efficiencies of a series of deletion mutants within the 5' noncoding region of the mRNA. We found striking differences in translatability among the altered mRNAs when assayed in mock-infected and poliovirus-infected HeLa cell extracts. The results identify a functional cis-acting element within the 5' noncoding region of the poliovirus mRNA which enables it to translate in a cap-independent fashion. The major determinant of this element maps between nucleotides 320 and 631 of the 5' end of the poliovirus mRNA. We also show that this region (320 to 631), when fused to a heterologous mRNA, can function in cis to render the mRNA cap independent in translation.
Control design of interval systems with multi incident model parameters

This paper presents a controller design methodology for linear dynamic systems with interval parameters. In order to overcome the conservatism of classical Interval Analysis methods applied to this class of uncertain systems, the paper proposes a solution for the problem of multi-incidences of model parameters when the controller design is based on interval Diophantine equations. The paper includes numerical examples which illustrate the proposed methodology.
Antiphagocytic effect of the capsule of Staphylococcus simulans

An encapsulated strain of Staphylococcus simulans was observed to be more resistant to phagocytosis by human granulocytes than was a nonencapsulated strain. Phagocytosis of the encapsulated strain was enhanced by antisera to S. simulans, but opsonic activity of antisera was removed by absorption with S. simulans capsular material. The encapsulated strain of S. simulans was also more invasive than the nonencapsulated S. simulans in vivo. More encapsulated than nonencapsulated S. simulans were found in heart blood when equal numbers of organisms were injected intraperitoneally into mice. Invasion of the bloodstreams of mice by encapsulated S. simulans was prevented by passive immunization (rabbit antiserum). Thus, the capsule of S. simulans inhibited phagocytosis in vitro and contributed to virulence in vivo.
Parallel sparse matrix solution for direct circuit simulation on a multiple FPGA system

SPICE, from the University of California, at Berkeley, is the de facto world standard for circuit simulation. SPICE is used to model the behaviour of electronic circuits prior to manufacturing to decrease defects and hence reduce costs. However, accurate SPICE simulations of today's sub micron circuits can often take days or weeks on conventional processors. In a nutshell, a SPICE simulation is an iterative process that consists of two phases per iteration, namely, model evaluation followed by a matrix solution. The model evaluation phase has been found to be easily parallelisable unlike the subsequent phase, which involves the solution of highly sparse and asymmetric matrices. In this thesis, we present an FPGA implementation of a sparse matrix solver hardware, geared towards matrices that arise in SPICE circuit simulations. As such, we demonstrate how we extract parallelism at different granularities to accelerate the solution process. Our approach combines static pivoting with symbolic analysis to compute an accurate task flow-graph which efficiently exploits parallelism at multiple granularities and sustains high floating-point data rates. We also present a quantitative comparison between the performance of our hardware prototype and state-of-the-art software package running on a general purpose PC equipped with a 2.67 GHz six-core 12 thread Intel Core Xeon X5650 microprocessor and 6 GB memory. We report average speedups of 9.65x, 11.83x, 17.21x against UMFPACK, KLU, and Kundert Sparse matrix packages respectively. We also detail our approach to adapt our sparse LU hardware prototype from a single-FPGA architecture to a multi-FPGA system to achieve higher acceleration ratios up to 38x for certain circuit matrices.
Transjugular intrahepatic portosystemic shunt in liver transplant recipients.

AIM To evaluate the efficacy of transjugular intrahepatic portosystemic shunts (TIPSs) after liver transplantation (LT). METHODS Between November 1996 and December 2005, 10 patients with severe recurrent hepatitis C virus infection (n = 4), ductopenic rejection (n = 5) or portal vein thrombosis (n = 1) were included in this analysis. Eleven TIPSs (one patient underwent two TIPS procedures) were placed for management of therapy-refractory ascites (n = 7), hydrothorax (n = 2) or bleeding from colonic varices (n = 1). The median time interval between LT and TIPS placement was 15 (4-158) mo. RESULTS TIPS placement was successful in all patients. The mean portosystemic pressure gradient was reduced from 12.5 to 8.7 mmHg. Complete and partial remission could be achieved in 43% and 29% of patients with ascites. Both patients with hydrothorax did not respond to TIPS. No recurrent bleeding was seen in the patient with colonic varices. Nine of 10 patients died during the study period. Only one of two patients, who underwent retransplantation after the TIPS procedure, survived. The median survival period after TIPS placement was 3.3 (range 0.4-20) mo. The majority of patients died from sepsis with multiorgan failure. CONCLUSION Indications for TIPS and technical performance in LT patients correspond to those in non-transplanted patients. At least partial control of therapy-refractory ascites and variceal bleeding could be achieved in most patients. Nevertheless, survival rates were disappointing, most probably because of the advanced stages of liver disease at the time of TIPS placement and the high risk of sepsis as a consequence of immunosuppression.