Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon regulatory factor-1 ( IRF-1 ) shapes both innate and CD 8 + T cell immune responses against West Nile virus infection

Interferon regulatory factor (IRF)-1 is an immunomodulatory transcription factor that functions downstream of pathogen recognition receptor signaling and has been implicated as a regulator of type I interferon (IFN)-ab expression and the immune response to virus infections. However, this role for IRF-1 remains controversial because altered type I IFN responses have not been systemically observed in IRF-1 mice. To evaluate the relationship of IRF-1 and immune regulation, we assessed West Nile virus (WNV) infectivity and the host response in IRF-1 cells and mice. IRF-1 mice were highly vulnerable to WNV infection with enhanced viral replication in peripheral tissues and rapid dissemination into the central nervous system. Ex vivo analysis revealed a cell-type specific antiviral role as IRF-1 macrophages supported enhanced WNV replication but infection was unaltered in IRF-1 fibroblasts. IRF-1 also had an independent and paradoxical effect on CD8 T cell expansion. Although markedly fewer CD8 T cells were observed in naı̈ve animals as described previously, remarkably, IRF-1 mice rapidly expanded their pool of WNV-specific cytolytic CD8 T cells. Adoptive transfer and in vitro proliferation experiments established both cell-intrinsic and cell-extrinsic effects of IRF-1 on the expansion of CD8 T cells. Thus, IRF-1 restricts WNV infection by modulating the expression of innate antiviral effector molecules while shaping the antigenspecific CD8 T cell response. Citation: Brien JD, Daffis S, Lazear HM, Cho H, Suthar MS, et al. (2011) Interferon Regulatory Factor-1 (IRF-1) Shapes Both Innate and CD8 T Cell Immune Responses against West Nile Virus Infection. PLoS Pathog 7(9): e1002230. doi:10.1371/journal.ppat. 1002230 Editor: Jean K. Lim, Mount Sinai School of Medicine, United States of America Received January 3, 2011; Accepted July 14, 2011; Published September 1, 2011 Copyright: 2011 Brien et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: NIH grants U54 AI081680 (Pacific Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases Research), U19 AI083019 (M.G. and M.S.D), and R01 AI074973 (M.G. and M.S.D.) supported this work. J.D. B. , H.M. L, and M.S. were supported by NIH Training grants (T32-AI07163-30, T32AI007172, and T32-AI0074-11, respectively). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: diamond@borcim.wustl. edu
Multi-Stage Programming for GPUs in Modern C++ using PACXX

Writing and optimizing programs for high performance on systems with GPUs remains a challenging task even for expert programmers. One promising optimization technique is to evaluate parts of the program upfront on the CPU and embed the computed results in the GPU code allowing for more aggressive compiler optimizations. This technique is known as multi-stage programming and has proven to allow for signiﬁcant performance beneﬁts. Unfortunately, to achieve such optimizations in current GPU programming models like OpenCL, programmers are forced to manipulate the GPU source code as plain strings, which is error-prone and type-unsafe. In this paper we describe PACXX - a GPU programming approach using modern C++ standards, with the convenient features like type deduction, lambda expressions, and algorithms from the standard template library (STL). Using PACXX, a GPU program is written as a single C++ program, rather than two distinct host and kernel programs. We extend PACXX with an easy-to-use and type-safe API for multi-stage programming avoiding the pitfalls of string manipulation. Using just-in-time compilation techniques, PACXX generates efﬁcient GPU code at runtime. Our evaluation shows that using PACXX allows for writing multi-stage code easier and safer than currently possible. Using two detailed application studies we show that multi-stage programming can signiﬁcantly outperform equivalent non-staged programs. Furthermore, we show that PACXX generates code with performance comparable to industrial-strength OpenCL compilers.
Control of dynamic gaits for a quadrupedal robot

Quadrupedal animals move through their environments with unmatched agility and grace. An important part of this is the ability to choose between different gaits in order to travel optimally at a certain speed or to robustly deal with unanticipated perturbations. In this paper, we present a control framework for a quadrupedal robot that is capable of locomoting using several gaits. We demonstrate the flexibility of the algorithm by performing experiments on StarlETH, a recently-developed quadrupedal robot. We implement controllers for a static walk, a walking trot, and a running trot, and show that smooth transitions between them can be performed. Using this control strategy, StarlETH is able to trot unassisted in 3D space with speeds of up to 0.7m/s, it can dynamically navigate over unperceived 5-cm high obstacles and it can recover from significant external pushes.
Human Resistin Is a Systemic Immune-Derived Proinflammatory Cytokine Targeting both Leukocytes and Adipocytes

The characteristics of human resistin (RETN) are unclear and controversial despite intensive adipose-focused research. Its transcriptional and functional similarity with the murine myeloid-specific and CCAAT/enhancer binding protein epsilon (Cebpe)-dependent gene, resistin-like gamma (Retnlg), is unexplored. We examined the human CEBPE-regulatory pathway by unbiased reference and custom gene expression assays. Real-time RT-PCR analysis demonstrated lack of both the transcriptional factor CEBPE and RETN expression in adipose and muscle cells. In contrast, primary myelocytic samples revealed a concerted CEBPE-RETN transcription that was significantly elevated in inflammatory synoviocytes relative to intact peripheral blood mononuclear cells (PBMC). Mouse Cebpe and Retnlg were predictably expressed in macrophages, whereas Retn was abundant in adipocytes. Quite the opposite, a low and inconsistent RETN transcription was seen in some human white adipose tissue (WAT) biopsies without any relationship to body mass index, insulin sensitivity, or fat depot. However, in these cases, RETN was co-detected with CEBPE and the leukocyte-specific marker, EMR1, indicating the presence of inflammatory cells and their possible resistin-mediated effect on adipocytes. Indeed, addition of human resistin to WAT in culture induced, like in PBMC, the inflammatory cytokines IL6, IL8 and TNF. Importantly, the expression of the adipose-specific markers CEBPA, FABP4 and SLC2A4 was unchanged, while the expected inhibitory effect was seen with TNF. Both cytokines increased the mRNA level of CCL2 and MMP3, which may further promote inflammation in WAT. Thus, the myeloid-restricted nature of CEBPE precludes the expression of RETN in human adipocytes which, however, are targeted by this innate immune-derived proinflammatory cytokine.
Optimization of regional R&D funding investment structure using grey system methods

For the operation mechanism of R&D input-output system is imprecision, it is hard to predict the structure optimization of R&D funding investment. This paper confirms contribution degree of scientific and technological output from R&D funding by grey correlation analysis, and establishes objective function. At last, we predict and optimize the R&D funding investment of Jiangsu Province in twelfth five-year, and the best allocation program is given, which verifies the feasibility and effectiveness of the method.
A Highly Specific Monoclonal Antibody for Botulinum Neurotoxin Type A-Cleaved SNAP25

Botulinum neurotoxin type-A (BoNT/A), as onabotulinumtoxinA, is approved globally for 11 major therapeutic and cosmetic indications. While the mechanism of action for BoNT/A at the presynaptic nerve terminal has been established, questions remain regarding intracellular trafficking patterns and overall fate of the toxin. Resolving these questions partly depends on the ability to detect BoNT/A’s location, distribution, and movement within a cell. Due to BoNT/A’s high potency and extremely low concentrations within neurons, an alternative approach has been employed. This involves utilizing specific antibodies against the BoNT/A-cleaved SNAP25 substrate (SNAP25197) to track the enzymatic activity of toxin within cells. Using our highly specific mouse monoclonal antibody (mAb) against SNAP25197, we generated human and murine recombinant versions (rMAb) using specific backbone immunoglobulins. In this study, we validated the specificity of our anti-SNAP25197 rMAbs in several different assays and performed side-by-side comparisons to commercially-available and in-house antibodies against SNAP25. Our rMAbs were highly specific for SNAP25197 in all assays and on several different BoNT/A-treated tissues, showing no cross-reactivity with full-length SNAP25. This was not the case with other reportedly SNAP25197-selective antibodies, which were selective in some, but not all assays. The rMAbs described herein represent effective new tools for detecting BoNT/A activity within cells.
Temozolomide in malignant gliomas of childhood: a United Kingdom Children's Cancer Study Group and French Society for Pediatric Oncology Intergroup Study.

PURPOSE To determine the response rate of the malignant gliomas of childhood to an oral, daily schedule of temozolomide. PATIENTS AND METHODS A multicenter, phase II evaluation of an oral, daily schedule of temozolomide (200 mg/m(2) on 5 consecutive days) was undertaken in children with relapsed or progressive, biopsy-proven, high-grade glioma (arm A) and progressive, diffuse, intrinsic brainstem glioma (arm B). Evidence of activity was defined by radiologic evidence of a sustained reduction in tumor size on serial magnetic resonance imaging scans. RESULTS Fifty-five patients were recruited (34 to arm A and 21 to arm B) and received 215 cycles of chemotherapy. Grade 3/4 thrombocytopenia was the most frequent toxic event (7% of cycles). Prolonged myelosuppression resulted in significant treatment delays and dose reductions (17% and 22% of cycles, respectively). Two toxic deaths were documented and were related to myelosuppression and sepsis in one patient and pneumonia in a second. The overall (best) response rate was 12% for arm A (95% confidence interval [CI], 3 to 28 in the study cohort, and 2 to 31 for eligible patients) and 5% and 6%, respectively, for arm B (95% CI, 0 to 26 in the study cohort, and 0 to 27 for eligible patients). Stabilization of disease was also documented and was most noteworthy for brainstem gliomas, where two patients achieved both radiologic static disease and discontinued steroid medication. CONCLUSION Despite moderate toxicity, objective response rates to temozolomide have been low, indicating that temozolomide has minimal activity in the high-grade gliomas of childhood.
Guidelines for the Reporting of Treatment Trials for Alcohol Use Disorders.

BACKGROUND The primary goals in conducting clinical trials of treatments for alcohol use disorders (AUDs) are to identify efficacious treatments and determine which treatments are most efficacious for which patients. Accurate reporting of study design features and results is imperative to enable readers of research reports to evaluate to what extent a study has achieved these goals. Guidance on quality of clinical trial reporting has evolved substantially over the past 2 decades, primarily through the publication and widespread adoption of the Consolidated Standards of Reporting Trials statement. However, there is room to improve the adoption of those standards in reporting the design and findings of treatment trials for AUD. METHODS This paper provides a narrative review of guidance on reporting quality in AUD treatment trials. RESULTS Despite improvements in the reporting of results of treatment trials for AUD over the past 2 decades, many published reports provide insufficient information on design or methods. CONCLUSIONS The reporting of alcohol treatment trial design, analysis, and results requires improvement in 4 primary areas: (i) trial registration, (ii) procedures for recruitment and retention, (iii) procedures for randomization and intervention design considerations, and (iv) statistical methods used to assess treatment efficacy. Improvements in these areas and the adoption of reporting standards by authors, reviewers, and editors are critical to an accurate assessment of the reliability and validity of treatment effects. Continued developments in this area are needed to move AUD treatment research forward via systematic reviews and meta-analyses that maximize the utility of completed studies.
The Formation of Immunogenic Major Histocompatibility Complex Class II–Peptide Ligands in Lysosomal Compartments of Dendritic Cells Is Regulated by Inflammatory Stimuli

During their final differentiation or maturation, dendritic cells (DCs) redistribute their major histocompatibility complex (MHC) class II products from intracellular compartments to the plasma membrane. Using cells arrested in the immature state, we now find that DCs also regulate the initial intracellular formation of immunogenic MHC class II–peptide complexes. Immature DCs internalize the protein antigen, hen egg lysozyme (HEL), into late endosomes and lysosomes rich in MHC class II molecules. There, despite extensive colocalization of HEL protein and MHC class II products, MHC class II–peptide complexes do not form unless the DCs are exposed to inflammatory mediators such as tumor necrosis factor α, CD40 ligand, or lipoplolysaccharide. The control of T cell receptor (TCR) ligand formation was observed using the C4H3 monoclonal antibody to detect MHC class II–HEL peptide complexes by flow cytometry and confocal microscopy, and with HEL-specific 3A9 transgenic T cells to detect downregulation of the TCR upon MHC–peptide encounter. Even the binding of preprocessed HEL peptide to MHC class II is blocked in immature DCs, including the formation of C4H3 epitope in MHC class II compartments, suggesting an arrest to antigen presentation at the peptide-loading step, rather than an enhanced degradation of MHC class II–peptide complexes at the cell surface, as described in previous work. Therefore, the capacity of late endosomes and lysosomes to produce MHC class II–peptide complexes can be strictly controlled during DC differentiation, helping to coordinate antigen acquisition and inflammatory stimuli with formation of TCR ligands. The increased ability of maturing DCs to load MHC class II molecules with antigenic cargo contributes to the >100-fold enhancement of the subsequent primary immune response observed when immature and mature DCs are compared as immune adjuvants in culture and in mice.
Selection of Heart-Biometric Templates for Fusion

The heart is potentially a highly secured biometric modality. Although many templates have been proposed to be extracted from heart-signal for biometric authentication, they have yet to reach a single digit equal error rate (EER) of false matches and false non-matches when applied on large across-session data sets, where gallery and probe data are taken from different sessions. However, since different templates possess different strengths, the fusion of them has a great potential to improve the authentication performance. We propose an efficient template selection algorithm to select a suitable subset of templates from a given set to obtain a minimal EER. The fusion of the subset of templates selected by this algorithm from a set of seven state-of-the-art templates has obtained a significant 5% reduction of EER in authentication in our experiments on a large database of finger-based ECG signals captured in two different sessions.
Metamemory in strategy selection: Evidence for a dissociation in familiarity-based judgments between semantics and item activation strength

Two experiments investigated the metamemorial factors which influence rapid strategy selections (retrieve or calculate) in double-digit mental arithmetic problems. Using the GameShow paradigm (L. M. Reder & F. E. Ritter, 1992; C. D. Schunn et al., 1997) participants first predicted (within 850 ms) which strategy they would use to solve a sum and then solved the sum. Results revealed that predicted strategy selections were accurate, and that selection of the retrieve strategy was positively related to problem familiarity (L. M. Reder & F. E. Ritter, 1992; C. D. Schunn, et al., 1997), but not to the answer’s familiarity (but see C. A. Lebiere & J. R. Anderson 1998; G. D. Logan, 2002). Furthermore, the semantic properties of a problem (e.g., whether both numbers are divisible by 5 or 10) appeared to dictate strategy selection. The evidence presented supports an account of strategy selection in which retrieve and calculate selections are determined by pre-retrieval indications of memorial strength derived from the familiarity of the problem (see also L. M. Reder & F. E. Ritter, 1992; C. D. Schunn et al., 1997) but also from semantic level representations of the problem’s properties.
Deadlocks and Safety Properties

As we saw in the note about Monitors and Semaphores [3], deadlockis a common phenomenon when dealing with concurrency. Actually, one of the most common errors in concurrent systems are deadlocks. Deadlock is the first to pic we deal with in this lecture. The second topic isafety properties . They are properties stating that “something bad never happens”. Mutual exclusion is an example of a safety pr operty (no undesired interleaving is going on) and so is absence of deadlock. Part of this note and some of the examples in this note are insp ired by [5]. The examples of models to be run in MWB in this note are present d with emphasis on readability and may thus not compile due to extra line breaks .
Evidence for Mediodorsal Thalamus and Prefrontal Cortex Interactions during Cognition in Macaques

It is proposed that mediodorsal thalamus contributes to cognition via interactions with prefrontal cortex. However, there is relatively little evidence detailing the interactions between mediodorsal thalamus and prefrontal cortex linked to cognition in primates. This study investigated these interactions during learning, memory, and decision-making tasks in rhesus monkeys using a disconnection lesion approach. Preoperatively, monkeys learned object-in-place scene discriminations embedded within colorful visual backgrounds. Unilateral neurotoxic lesions to magnocellular mediodorsal thalamus (MDmc) impaired the ability to learn new object-in-place scene discriminations. In contrast, unilateral ablations to ventrolateral and orbital prefrontal cortex (PFv+o) left learning intact. A second unilateral MDmc or PFv+o lesion in the contralateral hemisphere to the first operation, causing functional MDmc–PFv+o disconnection across hemispheres, further impaired learning object-in-place scene discriminations, although object discrimination learning remained intact. Adaptive decision-making after reward satiety devaluation was also reduced. These data highlight the functional importance of interactions between MDmc and PFv+o during learning object-in-place scene discriminations and adaptive decision-making but not object discrimination learning. Moreover, learning deficits observed after unilateral removal of MDmc but not PFv+o provide direct behavioral evidence of the MDmc role influencing more widespread regions of the frontal lobes in cognition.
Restricted freedom: negotiating same-sex identifications in the residential spaces of a South African university

International higher education research focused on students who claim same-sex identifications in university residential spaces has tended to prioritise the ‘gay as victim’ discourse, often leading to the pathologising of same-sex identification. While there is emerging research seeking to challenge this dimension of scholarship by offering a more nuanced and ‘queer’ approach to doing research, such research has tended to be thin, often exclusively focusing on Western contexts. This paper responds to this limitation by showcasing the experiences of Black South African same-sex-identifying students residing in student accommodation spaces in one South African university. Ten participants (five men and five women) were selected to participate in the study through snowball sampling. Each participant was interviewed twice using grounded conversations – an interview technique designed to address unequal power relations during the interviewing process. Findings highlight that the experiences of same-sex-identifying students at the university where this study took place are complex, involving the accommodation of homophobia and heteronormativity as well as resist-stancing. This is mainly due to the fact that the university residential space was heterosexualised. The paper, therefore, argues for a ‘queering’ of higher education scholarship given the deeply heterosexualised and misogynistic cultures that exist in such spaces.
Social class and re-employment: changes in health and perceived financial circumstances

pattern with those in the lowest levels of organizations having the highest levels of sickness absence, least job satisfaction and the highest reports of stress and psychological strain (Fletcher and Payne, 1980). The evidence that physical and mental health varies by social class amongst the unemployed is much less clear. Rundquist and Sletto (1936) did find that the middle class unemployed had better 'general adjustment' and 'morale'. Cohn (1978) found they had higher satisfaction with self, and Hepworth (1980) found they had fewer symptoms of minor psychiatric morbidity, as well as better levels of satisfaction with life in general. Little (1976) found that almost half of a sample of unemployed technical professionals in America thought that the loss of theirjob, 'might not have been such a bad break after all'. Fineman (1983) studied British managers/professional workers and found many of them did not report severe negative consequences of being unemployed. Kaufman (1982) on the other hand focuses on unemployment amongst technical and professional workers and concludes that, 'the weight of evidence favours the conclusion that the psychological effects of unemployment are likely to be more extreme for professionals than for other workers' (p. 24). Payne, Warr and Hartley (1984) measured the health and well-being of 399 men, half of whom were white collar/ professionals and the other half semi-skilled or unskilled workers. All had been unemployed for between 6 and 11 months and they found no difference on any of these sorts of variables, although the working class did report more financial worries, and troubles with boredom. Catalano and Dooley (1983) found a more complex pattern in that economic recession was found to be associated with a higher incidence of illness and injury for the middle classes, but not higher or lower class respondents; they argued that this resulted from higher rates of undesirable job and financial events amongst the middle class.