Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Throughput Profiling of Anti-Glycan Humoral Responses to SIV Vaccination and Challenge

Recent progress toward an HIV vaccine highlights both the potential of vaccines to end the AIDS pandemic and the need to boost efficacy by incorporating additional vaccine strategies. Although many aspects of the immune response can contribute to vaccine efficacy, the key factors have not been defined fully yet. A particular area that may yield new insights is anti-glycan immune responses, such as those against the glycan shield that HIV uses to evade the immune system. In this study, we used glycan microarray technology to evaluate anti-glycan antibody responses induced by SIV vaccination and infection in a non-human primate model of HIV infection. This comprehensive profiling of circulating anti-glycan antibodies found changes in anti-glycan antibody levels after both vaccination with the Ad5hr-SIV vaccine and SIV infection. Notably, SIV infection produced generalized declines in anti-glycan IgM antibodies in a number of animals. Additionally, some infected animals generated antibodies to the Tn antigen, which is a cryptic tumor-associated antigen exposed by premature termination of O-linked glycans; however, the Ad5hr-SIV vaccine did not induce anti-Tn IgG antibodies. Overall, this study demonstrates the potential contributions that glycan microarrays can make for HIV vaccine development.
Can CCL2 serum levels be used in risk stratification or to monitor treatment response in systemic sclerosis?

Objective: The chemokine CCL2 has been consistently found to be up-regulated in systemic sclerosis. To explore the potential value of serum CCL2 measurement in disease assessment, we have compared CCL2 levels with clinical phenotype and investigated effect of therapy on circulating CCL2. Methods: Serum samples from a well characterised cohort of 94 systemic sclerosis (SSc) patients, 16 patients with primary Raynaud phenomenon and 11 healthy controls were examined by ELISA. Our cohort of patients included 50 patients with limited cutaneous (lc)SSc (20 with lcSSc alone and 30 with pulmonary arterial hypertension-lcSSc), and 44 with diffuse cutaneous (dc)SSc, 30 of which had early-onset dcSSc. Results: Serum levels of CCL2 were increased in both major SSc subsets. In early stage dcSSc 18/30 (60%) cases demonstrated markedly elevated CCL2, and this was associated with anti-topoisomerase or anti-RNA polymerase I/III antibody reactivity, and with greater frequency of major organ-based complications. Elevation of CCL2 serum levels in the lcSSc subset was not associated with pulmonary arterial hypertension, although there was a trend for reduction following treatment with prostacyclin analogues or bosentan. Conclusion: These findings suggest that the CCL2/CCR2 axis is a potential therapeutic target in SSc, particularly in the early dcSSc subset. CCL2 measurement may be useful for risk stratification in early stage disease, but its value in disease monitoring is questionable.
Optimizing CPU cache performance for Pregel-like graph computation

In-memory graph computation systems have been used to support many important applications, such as PageRank on the web graph and social network analysis. In this paper, we study the CPU cache performance of graph computation. We have implemented a graph computation system, called GraphLite, in C/C++ based on the description of Pregel. We analyze the CPU cache behavior of the internal data structures and operations of graph computation. Then we exploit CPU cache prefetching techniques to improve the cache performance. Real machine experimental results show that our solution achieves 1.9-2.2x speedups compared to the baseline implementation.
Dietary modulation of the human gut microflora using prebiotics

The human colonic flora has both beneficial and pathogenic potentials with respect to host health. There is now much interest in manipulation of the microbiota composition in order to improve the potentially beneficial aspects. The prebiotic approach dictates that non-viable food components are specifically fermented in the colon by indigenous bacteria thought to be of positive value, e.g. bifidobacteria, lactobacilli. Any food ingredient that enters the large intestine is a candidate prebiotic. However, to be effective, selectivity of the fermentation is essential. Most current attention and success has been derived using non-digestible oligosaccharides. Types primarily being looked at include those which contain fructose, xylose, soya, galactose, glucose and mannose. In particular, fructose-containing oligosaccharides, which occur naturally in a variety of plants such as onion, asparagus, chicory, banana and artichoke, fulfil the prebiotic criteria. Various data have shown that fructo-oligosaccharides (FOS) are specifically fermented by bifidobacteria. During controlled feeding studies, ingestion of these prebiotics causes bifidobacteria to become numerically dominant in faeces. Recent studies have indicated that a FOS dose of 4g/d is prebiotic. To exploit this concept more fully, there is a need for assessments of (a) improved determination of the gut microbiota composition and activity; (b) the use of molecular methodologies to assess accurately prebiotic identities and develop efficient bacterial probing strategies; (c) the prebiotic potential of raw and processed foods; and (d) the health consequences of dietary modulation.
The Quest-V Separation Kernel for Mixed Criticality Systems

Multi- and many-core processors are becoming increasingly popular in embedded systems. Many of these processors now feature hardware virtualization capabilities, such as the ARM Cortex A15, and x86 processors with Intel VT-x or AMD-V support. Hardware virtualization offers opportunities to partition physical resources, including processor cores, memory and I/O devices amongst guest virtual machines. Mixed criticality systems and services can then co-exist on the same platform in separate virtual machines. However, traditional virtual machine systems are too expensive because of the costs of trapping into hypervisors to multiplex and manage machine physical resources on behalf of separate guests. For example, hypervisors are needed to schedule separate VMs on physical processor cores. In this paper, we discuss the design of the Quest-V separation kernel, that partitions services of different criticalities in separate virtual machines, or sandboxes. Each sandbox encapsulates a subset of machine physical resources that it manages without requiring intervention of a hypervisor. Moreover, a hypervisor is not needed for normal operation, except to bootstrap the system and establish communication channels between sandboxes.
Targeting regulatory T cells to improve vaccine immunogenicity in early life

Human newborns and infants are bombarded with multiple pathogens on leaving the sterile intra-uterine environment, and yet have suboptimal innate immunity and limited immunological memory, thus leading to increased susceptibility to infections in early life. They are thus the target age group for a host of vaccines against common bacterial and viral pathogens. They are also the target group for many vaccines in development, including those against tuberculosis (TB), malaria, and HIV infection. However, neonatal and infant responses too many vaccines are suboptimal, and in the case of the polysaccharide vaccines, it has been necessary to develop the alternative conjugated formulations in order to induce immunity in early life. Immunoregulatory factors are an intrinsic component of natural immunity necessary to dampen or control immune responses, with the caveat that they may also decrease immunity to infections or lead to chronic infection. This review explores the key immunoregulatory factors at play in early life, with a particular emphasis on regulatory T cells (Tregs). It goes on to explore the role that Tregs play in limiting vaccine immunogenicity, and describes animal and human studies in which Tregs have been depleted in order to enhance vaccine responses. A deeper understanding of the role that Tregs play in limiting or controlling vaccine-induced immunity would provide strategies to improve vaccine immunogenicity in this critical age group. New adjuvants and drugs are being developed that can transiently suppress Treg function, and their use as part of human vaccination strategies against infections is becoming a real prospect for the future.
LSU Digital Commons LSU Digital Commons A small-gain theorem for motone systems with multivalued input- A small-gain theorem for motone systems with multivalued input-state characteristics state characteristics

We provide a new global small-gain theorem for feedback interconnections of monotone input-output systems with multi-valued input-state characteristics. This extends a recent small-gain theorem of Angeli and Sontag for monotone systems with singleton-valued characteristics. We prove our theorem using Thieme’s convergence theory for asymptotically autonomous systems. An illustrative example is also provided.
Semantic disambiguation of taxonomies

Polysemy is one of the most difficult problems when dealing with natural language resources. Consequently, automated ontology learning from textual sources (such as web resources) is hampered by the inherent ambiguity of human language. In order to tackle this problem, this paper presents an automatic and unsupervised method for disambiguating taxonomies (the key component of a final ontology). It takes into consideration the amount of resources available in the Web as the base for inferring information distribution and semantics. It uses cooccurrence analysis and clustering techniques in order to group those taxonomical concepts that belong to the same “sense”. The final results are automatically evaluated against WordNet synsets.
Aligning Coevolving Artifacts Between Software Product Lines and Products

Software product lines (SPLs) play a pivotal role for developing a vast amount of related programs efficiently and with high quality. To this end, the SPL engineering process is separated into two levels: domain engineering (DE), which captures variability and development artifacts of the entire SPL, and application engineering (AE), which encompasses a variant-specific subset of the aforementioned artifacts. In the industrial practice of evolving an SPL, it is common that evolution is performed on both levels, which may affect the same artifacts (e.g., code, models) in different ways due to changes on the product line (DE) and the variant level (AE). As a result, conflicts may arise that have to be solved properly to guarantee correctness and validity of the affected artifacts. In this paper, we propose a methodology for resolving such conflicts to ensure correctness and consistency among artifacts while minimizing manual effort. Our method is comprehensive in two ways: First, we consider all kinds of artifacts (code and non-code) that may be subject to evolutionary changes in both DE and AE. Second, we also take into account that changing one particular artifact (e.g., a requirement) may require further changes to other artifacts of the same level. This way, our method reflects common industrial practices in SPL development and, thus, provides benefits for efficiently evolving real-world SPLs.
Relationship of the Aircraft Mix Index With Performance and Objective Workload Evaluation Research Measures and Controllers' Subjective Complexity Ratings

Abstract : Aircraft mix (i.e., the mix of aircraft with different performance characteristics in a sector) has been repeatedly cited as a complexity factor in en route air traffic control. However, scant attention has been directed to a statistical examination of this relationship. The present study is the third in a series of investigations designed to define, quantify, and assess the validity of aircraft mix as a contributor to traffic complexity. Eighteen 30-minute samples of System Analysis Recording data were collected from the Fort Worth and Atlanta en route centers. Performance and Objective Workload Evaluation Research (POWER) measures and the Aircraft Mix Index (Pfleiderer, 2003a) were computed in 6-minute intervals for each of the 36 samples. Principal Components Analysis of the combined data sets produced four components with eigenvalues >1 accounting for approximately 71% of the variance. The Aircraft Mix Index was most closely associated with Component 1, which was composed of variables generally associated with traffic complexity. These variables were used as predictors against a criterion of controllers' subjective "Complexity" ratings in multiple regression analyses of low- and high-altitude sector samples. The Aircraft Mix Index failed to contribute significantly to the explained variance in the both the low-altitude (R=.69; R2=.47) and high-altitude (R=.57; R2=.33) sector models. In the aggregate, the results suggest that although aircraft mix appears to be associated with traffic complexity, it may not be as influential as other complexity factors in the en route environment.
Parameter-dependent stability conditions for quasi-LPV Model Predictive Control

This paper extends earlier work on nonlinear predictive control based on a representation of the nonlinear plant as quasi-LPV model. Since the scheduling parameters depend on state variables and inputs, they can be predicted. An efficient predictive scheme with guaranteed stability is proposed that involves solving a sequence of SOCP problems at each sampling period. Compared with previously reported work, the conservatism of the approach is reduced by allowing matrix variables in the stability conditions to be parameter dependent. The efficiency of the proposed method is illustrated with its application in simulation to a model of an arm-driven inverted pendulum. A comparison with other state-of-the-art NMPC methods is made to highlight the benefits of the proposed approach both in terms of closed-loop performance and computation time.
Transient receptor potential vanilloid 1 as a therapeutic target in analgesia

Introduction: The selective excitatory action of capsaicin followed by long-term chemoanalgesia due to an action on the ‘capsaicin receptor' of C-polymodal nociceptors, cloned 15 years ago, opened up fascinating perspectives for a class of nociceptor blocking analgesics. Areas covered: The TRPV1/capsaicin receptor is an integrative, chemoceptive, noxious heat-gated cation channel also gated by several endogenous ligands and sensitized by phosphorylation through intracellular cascades triggered from receptors of bradykinin, prostanoids, NGF and interactions with TRPA1. In this review, types of sensory receptors and unique mechanisms for blocking nociceptor action, e.g., ‘pore dilation' intracellular acidosis and the long-term function-related mitochondrial swelling at the nerve terminals and sensory neurons are summarized. In humans the 8% capsaicin dermal patch is already in usage for nondiabetic neuropathic pain and two topical preparations of civamide have also been approved recently for cluster headache and osteoarthritis. Evidence for epidermal nerve terminal loss in humans after topical applications and misleading results on sensory neuron death evoked by TRPV1 agonism in animals are discussed. Expert opinion: The unique ‘multisteric' gating of TRPV1 channel which is opened and modulated in various conformational changes to natural stimuli differs from the operation of canonical ligand-gated channels and makes it suitable to initiate development of second generation of TRPV1 antagonists without on-target side effects of hyperthermia and risk of burn injury.
Novel in vitro gene transfer method for study of local modulators in vascular smooth muscle cells.

Although many in vitro gene transfer methods already exist, such as calcium phosphate precipitation, electroporation, or cationic liposomes, these methods cause significant cell injury and cell death. The study of the biology of endogenous autocrine-paracrine vasoactive systems such as the renin-angiotensin system in vascular cells is limited by the lack of a suitable gene transfer method with high efficiency of transfection and expression that will permit cell biology studies. Recently, the Sendai virus (hemagglutinating virus of Japan, HVJ)-liposome-mediated gene transfer method has been shown to be an efficient and nontoxic method of gene transfer. In this study, we characterized the efficiency and suitability of the HVJ method for vascular biology research. Using SV40 T-antigen complementary DNA (cDNA), we initially compared the efficiency of the HVJ method and lipofection for transfection of cultured vascular smooth muscle cells (VSMCs). We observed that after 35 minutes of incubation, the HVJ method exhibited a 10-fold higher efficiency of transfection than lipofection. We used this method to study vascular angiotensin converting enzyme (ACE) expression in cultured VSMCs and cultured rat carotid arteries in vitro. The HVJ method of transfection of human ACE cDNA into VSMCs and COS cells was significantly more efficient than lipofection. Using this method, we demonstrated that transfection of ACE cDNA resulted in increased DNA synthesis, which was inhibited by the specific angiotensin II receptor antagonist DuP 753 (10(-6) M). (ABSTRACT TRUNCATED AT 250 WORDS)
Undercurrents A Computer-Based Gameplay Tool to Support Tabletop Roleplaying

This paper introduces Undercurrents, a computer-based gameplay tool for providing additional communication and media streams during tabletop roleplaying sessions. Based upon a client-server architecture, the system is intended to unobtrusively support secret communication, timing of audio and visual presentations to game events, and real-time documentation of the game session. Potential end users have been involved in the development and the paper provides details on the full design process.
Star formation histories within the Antennae galaxies (Arp 244)

With the imagery from GALEX, HST, 2MASS, and Spitzer, and at the resolution of MIPS 24 � m (� 6 ′′ ), we study the variations of the broadband spectral energy distributions (SEDs) of star-forming regions within the nearest prototypal major merger — the Antennae galaxies. By including MIPS 24 � m dust emission into stellar population analysis, we reliably, albeit roughly, constrain the star formation histories of these 24 � m selected star-forming regions across the merging disks of the Antennae. Our population analysis is consistent with the star formation scenario that, most regions across the whole system are at a modest level of star formation with the exception of some localized intense starburst sites in the well-known overlap regions and the western-loop regions of northern galaxy NGC 4038. Compared with all the other regions, the young overlap regions currently ( 80% from both hot dust and atomic/molecular lines) is comparable with that of the two galactic nuclei.
Stable and dynamic microtubules coordinately determine and maintain Drosophila bristle shape

Within interphase cells, microtubules (MTs) are organized in a cell-specific manner to support cell shape and function. Here, we report that coordination between stable and dynamic MTs determines and maintains the highly elongated bristle cell shape. By following MT-decorating hooks and by tracking EB1 we identified two MT populations within bristles: a stable MT population polarized with their minus ends distal to the cell body, and a dynamic MT population that exhibits mixed polarity. Manipulating MT dynamics by Klp10A downregulation demonstrates that MTs can initiate new shaft extensions and thus possess the ability to determine growth direction. Actin filament bundling subsequently supports the newly formed shaft extensions. Analysis of ik2 mutant bristles, established by elongation defects in the Drosophila ikkε homolog, led to the observation that stable and dynamic MT orientation and polarized organization are important for proper bristle elongation. Thus, we demonstrate for the first time that coordination between stable and dynamic MT sets that are axially organized yet differently polarized drives cell elongation.
Platelet-derived endothelial cell growth factor expression and angiogenesis in cervical intraepithelial neoplasia and squamous cell carcinoma of the cervix.

Growth and metastatic spread of invasive carcinoma depends on angiogenesis, the formation of new blood vessels. Platelet-derived endothelial cell growth factor (PD-ECGF) is an angiogenic growth factor for a number of solid tumors, including lung, bladder, colorectal, and renal cell cancer. Cervical intraepithelial neoplasia (CIN) is the precursor to squamous cell cervical carcinoma (SCC). Mean vessel density (MVD) increases from normal cervical tissue, through low- and high-grade CIN to SCC. We evaluated PD-ECGF immunoreactivity and correlated its expression with MVD in normal, premalignant, and malignant cervical tissue. PD-ECGF expression was assessed visually within the epithelial tissues and scored on the extent and intensity of staining. MVD was calculated by counting the number of vessels positive for von Willebrand factor per unit area subtending normal or CIN epithelium or within tumor hotspots for SCC. Cytoplasmic and/or nuclear PD-ECGF immunoreactivity was seen in normal epithelium. PD-ECGF expression significantly increased with histologic grade from normal, through low- and high-grade CIN, to SCC (P < .02). A progressive significant increase in the microvessel density was also seen, ranging from a mean of 28 vessels for normal tissue to 57 for SCC (P < .0005). No correlation was found between PD-ECGF expression and MVD (P = .45). We conclude that PD-ECGF expression and MVD increase as the cervix transforms from a normal to a malignant phenotype. PD-ECGF is thymidine phosphorylase, a key enzyme in the activation of fluoropyrimidines, including 5-fluorouracil. Evaluation of PD-ECGF thymidine phosphorylase expression may be important in designing future chemotherapeutic trials in cervical cancer.
A low power UWB-LNA using active dual loop negative feedback in CMOS 0.13µm

A low noise amplifier for UWB and broadband applications is presented. The active dual loop negative feedback architecture dissevers the severe tradeoff existing between the input impedance, gain and noise figure, and produces a flat S11 across the entire band. The LNA is composed of a voltage amplifying negative feedback amplifier with a transconductance amplifier forming a shunt-shunt feedback around it, thereby tailoring the input impedance with respect to the gain settings of the first amplifier. The values of the resistive feedback elements have been chosen such that they fulfill the requirements of gain, input impedance, noise figure and linearity. The design has been carried out in TSMC 0.13um CMOS Technology. From circuit simulations, the average gain of the LNA across 2–7GHz is 13dB. The noise figure is below 4dB with a minimum of 2.9dB. S11 is below −15dB for the entire frequency band. The design employs a DC-current re-use scheme to reduce the power consumption. The LNA draws 5.6mA from a 1.2V supply.