Miracle-dz/UniFAR-FTUs huggingface dataset:
Costimulation of T Cell Activation by Integrin-associated Protein (CD47) Is an Adhesion-dependent, CD28-independent Signaling Pathway

The integrin-associated protein (IAP, CD47) is a 50-kD plasma membrane protein with a single extracellular immunoglobulin variable (IgV)-like domain, a multiply membrane-spanning segment, and alternatively spliced short cytoplasmic tails. On neutrophils, IAP has been shown to function in a signaling complex with β3 integrins. However, the function of IAP on T cells, which express little or no β3 integrin, is not yet defined. Here, we show that mAbs recognizing IAP can enhance proliferation of primary human T cells in the presence of low levels of antiCD3, but have no effect on T cell proliferation on their own. Together with suboptimal concentrations of anti-CD3, engagement of IAP also enhances IL-2 production in Jurkat cells, an apparently integrin-independent function of IAP. Nonetheless, costimulation by IAP ligation requires cell adhesion. IAP costimulation does not require CD28. Furthermore, anti-IAP, but not anti-CD28, synergizes with suboptimal anti-CD3 to enhance tyrosine phosphorylation of the CD3 ζ chain and the T cell–specific tyrosine kinase Zap70. Ligation of human IAP transfected into the hemoglobin-specific 3.L2 murine T cell hybridoma costimulates activation for IL-2 secretion both with anti-CD3 and with antigenic peptides on antigen-presenting cells (APCs). Moreover, ligation of IAP but not CD28 can convert antagonist peptides into agonists in 3.L2 cells. Using costimulation by IAP ligation as an assay to analyze the structure–function relationships in IAP signaling, we find that both the extracellular and multiply membrane-spanning domains of IAP are necessary for synergy with the antigen receptor, but the alternatively spliced cytoplasmic tails are not. These data demonstrate that IAP ligation initiates an adhesiondependent costimulatory pathway distinct from CD28. We hypothesize that anti-IAP generates the costimulatory signal because it modulates interactions of the IgV domain with other plasma membrane molecules; this in turn activates effector functions of the multiply membrane-spanning domain of IAP. This model may have general significance for how IAP functions in cell activation.
Fast back-projection for non-line of sight reconstruction

Recent works have demonstrated non-line of sight (NLOS) reconstruction by using the time-resolved signal from multiply scattered light. These works combine ultrafast imaging systems with computation, which back-projects the recorded space-time signal to build a probabilistic map of the hidden geometry. Unfortunately, this computation is slow, becoming a bottleneck as the imaging technology improves. In this work, we propose a new back-projection technique for NLOS reconstruction, which is up to a thousand times faster than previous work, with negligible quality loss.
Calculation of Standard Atomic Volumes for RNA Cores and Comparison with Proteins: RNA is packed more tightly than Protein

Molecular Biophysics andBiochemistry, Yale University260 Whitney Ave, P.O. Box208114, New Haven, CT 06520USATraditionally, for biomolecular packing calculations research has focusedon proteins. Besides proteins, RNA is the other large biomolecule that hastertiary structure interactions and complex packing. No one has yetquantitatively investigated RNA packing nor compared its packing to thatof proteins because, until recently, there were no large RNA structures.Here we address this question in detail, using Voronoi volume calculationson a set of high-resolution RNA crystal structures. We do a carefulparameterization, taking into account many factors such as atomic radii,crystal packing, structural complexity, solvent, and associated protein toobtainaself-consistent,universalsetofvolumesthatcanbeappliedtobothRNA and protein.Wereportthis set ofvolumes,which wecall the NucProtparameter set. Our measured values are consistent across the manydifferent RNA structures and packing environments. However, ourvolumes are only deﬁned on well-packed atoms, those with sufﬁcientpacking neighbors, that typically occur on the interior of RNA molecularand not the unbounded atoms on the surface. When common atom typesare compared between proteins and RNA, nine of 12 types show that RNAhas a smaller volume and packs more tightly than protein, suggesting thatclose-packing may be as important for the folding of RNAs as it forproteins. Moreover, calculated partial speciﬁc volumes show that RNAbases pack more densely than corresponding aromatic residues fromproteins. Finally, we ﬁnd that RNA bases have similar packing volumes toDNA bases, despite the absence of tertiary contacts in DNA. Programs,parameter sets and raw data are available online at http://geometry.molmovdb. org
Predictive Line Buffer: A Fast, Energy Efficient Cache Architecture

Two of the most important factors in the design of any processor are speed and energy consumption. Depending on the application, and the processor type, generally one of these two factors will be more important than the other. In this paper, we propose a new cache architecture. Our proposed architecture does not require any changes to the processor architecture, it only assume the existence of a BTB, and it adds few gates and multiplexers for the prediction mechanism. By using Simplescalar simulator, CACTI 3.2 power simulator, and SPEC2000, Mediabench, and Mibench, we tested our proposed architecture using a wide variety of the programs in these three benchmarks. Our results show that our proposed architecture consumes less energy, and have better memory access time, than many existing cache architecture
Duodenal ulcer prevalence: Experimental evidence for the possible role of dietary lipids

Background and Aims : Mapping the geographical distribution of duodenal ulcer in relation to staple diets, and experiments on animal peptic ulcer models suggested that the lipid fraction in certain foodstuffs had a protective effect which was most marked in the lipid obtained from Horse gram (Dolichos biflorus). Lipid obtained from stored polished rice or rice bran was ulcerogenic. Further animal experiments were designed to investigate the protective and healing effects of Horse gram lipid (HGL) against peptic ulceration.
CP-Census: A Novel Model for Dense Variational Scene Flow from RGB-D Data

We present a novel method for dense variational scene flow estimation based a multiscale Ternary Census Transform in combination with a patchwise Closest Points depth data term. On the one hand, the Ternary Census Transform in the intensity data term is capable of handling illumination changes, low texture and noise. On the other hand, the patchwise Closest Points search in the depth data term increases the robustness in low structured regions. Further, we utilize higher order regularization which is weighted and directed according to the input data by an anisotropic diffusion tensor. This allows to calculate a dense and accurate flow field which supports smooth as well as non-rigid movements while preserving flow boundaries. The numerical algorithm is solved based on a primal-dual formulation and is efficiently parallelized to run at high frame rates. In an extensive qualitative and quantitative evaluation we show that this novel method for scene flow calculation outperforms existing approaches. The method is applicable to any sensor delivering dense depth and intensity data such as Microsoft Kinect or Intel Gesture Camera.
AUTOMATED EXTRACTION OF 3D TREES FROM MOBILE LIDAR POINT CLOUDS

This paper presents an automated algorithm for extracting 3D trees directly from 3D mobile light detection and ranging (LiDAR) data. To reduce both computational and spatial complexities, ground points are first filtered out from a raw 3D point cloud via blockbased elevation filtering. Off-ground points are then grouped into clusters representing individual objects through Euclidean distance clustering and voxel-based normalized cut segmentation. Finally, a model-driven method is proposed to achieve the extraction of 3D trees based on a pairwise 3D shape descriptor. The proposed algorithm is tested using a set of mobile LiDAR point clouds acquired by a RIEGL VMX-450 system. The results demonstrate the feasibility and effectiveness of the proposed algorithm.
Combining Tree Structures, Flat Features and Patterns for Biomedical Relation Extraction

Kernel based methods dominate the current trend for various relation extraction tasks including protein-protein interaction (PPI) extraction. PPI information is critical in understanding biological processes. Despite considerable efforts, previously reported PPI extraction results show that none of the approaches already known in the literature is consistently better than other approaches when evaluated on different benchmark PPI corpora. In this paper, we propose a novel hybrid kernel that combines (automatically collected) dependency patterns, trigger words, negative cues, walk features and regular expression patterns along with tree kernel and shallow linguistic kernel. The proposed kernel outperforms the exiting state-of-the-art approaches on the BioInfer corpus, the largest PPI benchmark corpus available. On the other four smaller benchmark corpora, it performs either better or almost as good as the existing approaches. Moreover, empirical results show that the proposed hybrid kernel attains considerably higher precision than the existing approaches, which indicates its capability of learning more accurate models. This also demonstrates that the different types of information that we use are able to complement each other for relation extraction.
Deformation-tracking impedance control in interaction with uncertain environments

A deformation-tracking impedance control strategy is discussed for applications where a manipulator interacts with environments of unknown geometrical and mechanical properties, especially with stiffness comparable to a controlled robot stiffness. Based on force-tracking impedance controls, the deformation-tracking strategy allows the control of a desired deformation of the target environment, requiring the on-line estimation of the environment stiffness. An Extended Kalman Filter is used for the estimation of the environment because of measurement uncertainties and errors in compound interaction model. The tasks presented involve full body spatial interactions with a time-varying environment stiffness. The Extended Kalman Filter and the deformation-tracking impedance control are validated in simulation and with experiments. In particular, a cooperative assembly task is also performed with a human operator acting as varying environment, i.e. unpredictably changing the handling arm stiffness.
Network Protocol Designs: Fast Queuing Policies via Convex Relaxation

With the recent rise of mobile and multimedia applications, other considerations such as power consumption and/or Quality of Service (QoS) are becoming increasingly important factors in designing network protocols. As such, we present a new framework for designing robust network protocols under varying network conditions that attempts to integrate various given objectives while satisfying some pre-specified levels of Quality of Service. The proposed framework abstracts a network protocol as a queuing policy, and relies on convex relaxation methods and the theory of mixing time for finding the fast queuing policies that drive the distribution of packets in a queue to a given target stationary distribution. In addition, we show how to augment the basic proposed framework to obtain a queuing policy that produces ε-approximation to the target distribution with faster convergence time which is useful in fast-changing network conditions. Both theoretical and simulation results are presented to verify the effectiveness of the proposed framework.
Total laparoscopic hysterectomy versus da Vinci robotic hysterectomy: is using the robot beneficial?

Objective To compare the outcomes of total laparoscopic to robotic approach for hysterectomy and all indicated procedures after controlling for surgeon and other confounding factors. Methods Retrospective chart review of all consecutive cases of total laparoscopic and da Vinci robotic hysterectomies between August 2007 and July 2009 by two gynecologic oncology surgeons. Our primary outcome measure was operative procedure time. Secondary measures included complications, conversion to laparotomy, estimated blood loss and length of hospital stay. A mixed model with a random intercept was applied to control for surgeon and other confounders. Wilcoxon rank-sum, chi-square and Fisher's exact tests were used for the statistical analysis. Results The 124 patients included in the study consisted of 77 total laparoscopic hysterectomies and 47 robotic hysterectomies. Both groups had similar baseline characteristics, indications for surgery and additional procedures performed. The difference between the mean operative procedure time for the total laparoscopic hysterectomy group (111.4 minutes) and the robotic hysterectomy group (150.8 minutes) was statistically significant (p=0.0001) despite the fact that the specimens obtained in the total laparoscopic hysterectomy group were significantly larger (125 g vs. 94 g, p=0.002). The robotic hysterectomy group had statistically less estimated blood loss than the total laparoscopic hysterectomy group (131.5 mL vs. 207.7 mL, p=0.0105) however no patients required a blood transfusion in either group. Both groups had a comparable rate of conversion to laparotomy, intraoperative complications, and length of hospital stay. Conclusion Total laparoscopic hysterectomy can be performed safely and in less operative time compared to robotic hysterectomy when performed by trained surgeons.
Type 2 diabetes impairs splanchnic uptake of glucose but does not alter intestinal glucose absorption during enteral glucose feeding: additional evidence for a defect in hepatic glucokinase activity.

We have previously reported that splanchnic glucose uptake, hepatic glycogen synthesis, and hepatic glucokinase activity are decreased in people with type 2 diabetes during intravenous glucose infusion. To determine whether these defects are also present during more physiological enteral glucose administration, we studied 11 diabetic and 14 nondiabetic volunteers using a combined organ catheterization-tracer infusion technique. Glucose was infused into the duodenum at a rate of 22 micromol. kg(-1). min(-1) while supplemental glucose was given intravenously to clamp glucose at approximately 10 mmol/l in both groups. Endogenous hormone secretion was inhibited with somatostatin, and insulin was infused to maintain plasma concentrations at approximately 300 pmol/l (i.e., twofold higher than our previous experiments). Total body glucose disappearance, splanchnic, and leg glucose extractions were markedly lower (P < 0.01) in the diabetic subjects than in the nondiabetic subjects. UDP-glucose flux, a measure of glycogen synthesis, was approximately 35% lower (P < 0.02) in the diabetic subjects than in the nondiabetic subjects. This was entirely accounted for by a decrease (P < 0.01) in the contribution of extracellular glucose because the contribution of the indirect pathway to hepatic glycogen synthesis was similar between groups. Neither endogenous and splanchnic glucose productions nor rates of appearance of the intraduodenally infused glucose in the portal vein differed between groups. In summary, both muscle and splanchnic glucose uptake are impaired in type 2 diabetes during enteral glucose administration. The defect in splanchnic glucose uptake appears to be due to decreased uptake of extracellular glucose, implying decreased glucokinase activity. Thus, abnormal hepatic and muscle (but not gut) glucose metabolism are likely to contribute to postprandial hyperglycemia in people with type 2 diabetes.
Semantic Profiles to Model the "Web of Things"

With the decrease of hardware production costs, putting connection capabilities to appliances has become affordable. At the same time, the widespread adoption of the Web has gained on Internet users. At the convergence of these two facts the idea of a ``Web of Things" has emerged, unleashing the current Internet of Things solutions by exposing connected objects as Web resources. While quite promising - now appliances are able to interoperate whatever their hardware or Operating Systems, using Web protocols stack - this vision still needs practical mechanisms to allow applications or users to interact with connected objects. In this paper, we propose an approach supporting the use of a ``Web of Things" through the creation of ontological models describing connected objects in order to make them ``speak the same language". In addition, we present a framework that processes such semantic models to allow seamless integration and use of such connected objects within Web applications.
of the Autumn Conference , Korean Statistical Society-79-Analyzing Exon Structure with PCA and ICA of Short-Time Fourier Transform

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.
A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

ABSTRACT A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of ∼5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.
Cystic Fibrosis Gene Therapy in the UK and Elsewhere

Abstract The cystic fibrosis transmembrane conductance regulator (CFTR) gene was identified in 1989. This opened the door for the development of cystic fibrosis (CF) gene therapy, which has been actively pursued for the last 20 years. Although 26 clinical trials involving approximately 450 patients have been carried out, the vast majority of these trials were short and included small numbers of patients; they were not designed to assess clinical benefit, but to establish safety and proof-of-concept for gene transfer using molecular end points such as the detection of recombinant mRNA or correction of the ion transport defect. The only currently published trial designed and powered to assess clinical efficacy (defined as improvement in lung function) administered AAV2-CFTR to the lungs of patients with CF. The U.K. Cystic Fibrosis Gene Therapy Consortium completed, in the autumn of 2014, the first nonviral gene therapy trial designed to answer whether repeated nonviral gene transfer (12 doses over 12 months) can lead to clinical benefit. The demonstration that the molecular defect in CFTR can be corrected with small-molecule drugs, and the success of gene therapy in other monogenic diseases, is boosting interest in CF gene therapy. Developments are discussed here.
Twelve-Month Antiretroviral Therapy Suppresses Plasma and Genital Viral Loads but Fails to Alter Genital Levels of Cytokines, in a Cohort of HIV-Infected Rwandan Women

Background Genital viral load (GVL) is the main determinant of sexual transmission of human immune-deficiency virus (HIV). The effect of antiretroviral therapy (ART) on local cervico-vaginal immunological factors associated with GVL is poorly described. We aimed to identify the risk factors of detectable GVL, and the impact of ART on HIV genital shedding and its correlates in a cohort of HIV-infected women, attending HIV care in Kigali, Rwanda. Materials and Methods All participants were evaluated for GVL, plasma viral load (PVL), CD4 count, various sexually-transmitted infections (STIs) at baseline and at month 12. Genital concentration of 19 cytokines and mRNA expression of APOBEC3G and BST2, two host HIV restriction factors, were evaluated at baseline in all participants. Cytokine levels were re-assessed at month 12 only in participants eligible for ART at baseline. Risk factors of GVL ≥40copies/mL at baseline and month 12 were assessed using logistic regression. Effect of 12-month ART on various local and systemic immunological parameters was examined using a paired t-test and McNemar as appropriate. Results 96 of the 247 women enrolled in the study were eligible for ART. After 12 months of ART, PVL and GVL decreased to undetectable level in respectively 74 and 88% of treated participants. ART did not affect cytokine levels. HIV genital shedding occurred only when PVL was detectable. At baseline, GVL was independently associated with IL-1β after controlling for PVL, age and N. gonorrhea infection (95% CI 1.32-2.15) and at month 12 with MIP-1β (95% CI 0.96-21.32) after controlling for baseline GVL, PVL and month 12 IL-8. Conclusion Suppressive ART does not necessarily reduce genital level of immune activation. Minimizing all conditions favoring genital inflammation, including active detection and treatment of STIs, might reduce the risk of HIV transmission as supplement to the provision of potent ART.
A pattern based approach to defining translations between languages.

The 2U Consortium have recently submitted a proposal for the definition of the UML 2.0 infrastructure. This uses a innovative technique of rapidly “stamping out” the definition using a small number of patterns commonly found in software architecture. The contribution of this paper is to introduce the idea of reusability of mappings between languages and defining some of the reusable mapping templates. This paper also illustrates how these templates can be used to stamp out mapping between languages by stamping out a mapping between UML and Java.