Miracle-dz/UniFAR-FTUs huggingface dataset:
Interleukin-10 −592C/A, −819C/T and −1082A/G Polymorphisms with Risk of Type 2 Diabetes Mellitus: A HuGE Review and Meta-analysis

Background Several studies have been conducted in recent years to evaluate the risk of type 2 diabetes mellitus (T2DM) and polymorphisms of interleukin (IL)-10. However, the results remain conflicting rather than conclusive. This meta-analysis aimed to summarize the current evidence from case-control studies that evaluated this association. Methods We carried out a search in Medline, EMBASE, and the Chinese National Knowledge Infrastructure (CNKI) database for relevant studies. Data were extracted using a standardized form and pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of the association. Results 10 studies were included in our meta-analysis and systemic review. Our meta-analysis indicated that IL-10 −1082A/G polymorphism was associated with the risk of T2DM (GA vs. AA: OR = 1.21, 95% CI = 1.03–1.14; GA/GG vs. AA: OR = 1.22, 95% CI = 1.05–1.41), whereas there was no association between IL-10 −592C/A (CC/CA vs. AA: OR = 1.07, 95% CI = 0.59–1.93) or -819C/T (CC/CT vs. TT: OR = 0.93, 95% CI = 0.49–1.75) polymorphism and T2DM risk was found in our study. Conclusions This meta-analysis provides strong evidence that IL-10 −1082A/G polymorphism associated with risk of T2DM. However, no association of the IL-10 −592C/A or −819C/T polymorphism with T2DM risk was found. Additional well-designed large studies were required for the validation of our results.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins

Background Avidin is a chicken egg-white protein with high affinity to vitamin H, also known as D-biotin. Many applications in life science research are based on this strong interaction. Avidin is a homotetrameric protein, which promotes its modification to symmetrical entities. Dual-chain avidin, a genetically engineered avidin form, has two circularly permuted chicken avidin monomers that are tandem-fused into one polypeptide chain. This form of avidin enables independent modification of the two domains, including the two biotin-binding pockets; however, decreased yields in protein production, compared to wt avidin, and complicated genetic manipulation of two highly similar DNA sequences in the tandem gene have limited the use of dual-chain avidin in biotechnological applications. Principal Findings To overcome challenges associated with the original dual-chain avidin, we developed chimeric dual-chain avidin, which is a tandem fusion of avidin and avidin-related protein 4 (AVR4), another member of the chicken avidin gene family. We observed an increase in protein production and better thermal stability, compared with the original dual-chain avidin. Additionally, PCR amplification of the hybrid gene was more efficient, thus enabling more convenient and straightforward modification of the dual-chain avidin. When studied closer, the generated chimeric dual-chain avidin showed biphasic biotin dissociation. Significance The improved dual-chain avidin introduced here increases its potential for future applications. This molecule offers a valuable base for developing bi-functional avidin tools for bioseparation, carrier proteins, and nanoscale adapters. Additionally, this strategy could be helpful when generating hetero-oligomers from other oligomeric proteins with high structural similarity.
Static Modeling of Linear Object Deformation Based on Differential Geometry

We describe the modeling of linear object deformation based on differential geometry and its applications to manipulative operations. A particle-based approach, the finite element method, and the Cosserat theory have been applied to the modeling of linear object deformation. In this paper, we establish an alternative modeling approach based on an extension of differential geometry. First, we extend differential geometry to describe linear object deformation including flexure, torsion, and extension. Secondly, we show computational results to demonstrate the feasibility of the proposed modeling technique, and we compare computational and experimental results to demonstrate the accuracy of the model. Next, we apply the proposed approach to the grasping of a deformable linear object. We propose a disturbance force margin to indicate the stability of the grasping and we describe the computation of the margin using the proposed approach. Finally, we apply the proposed approach to the deformation path planning of a linear object. We formulate the minimization of potential energy during a deformation path. We compute the optimal deformation path and a feasible deformation path, which are compared with an experimental result.
Choriodecidual Infection Downregulates Angiogenesis and Morphogenesis Pathways in Fetal Lungs from Macaca Nemestrina

Background Intrauterine exposure to amniotic fluid (AF) cytokines is thought to predispose to bronchopulmonary dysplasia (BPD). We evaluated the effects of GBS exposure on RNA expression in fetal lung tissue to determine early molecular pathways associated with fetal lung injury that may progress to BPD. Methods Ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118–125 days gestation (term = 172 days) received choriodecidual inoculation of either: 1) Group B Streptococcus (n = 5) or 2) saline (n = 5). Cesarean section and fetal necropsy was performed in the first week after GBS or saline inoculation regardless of labor. RNA was extracted from fetal lungs and profiled by microarray. Results were analyzed using single gene, Gene Set, and Ingenuity Pathway Analysis. Validation was by RT-PCR and immunohistochemistry. Results Despite uterine quiescence in most cases, fetal lung injury occurred in four GBS cases (intra-alveolar neutrophils, interstitial thickening) and one control (peri-mortem hemorrhage). Significant elevations of AF cytokines (TNF-α, IL-8, IL-1β, IL-6) were detected in GBS versus controls (p<0.05). Lung injury was not directly caused by GBS, because GBS was undetectable by culture and PCR in the AF and fetal lungs. A total of 335 genes were differentially expressed greater than 1.5 fold (p<0.05) with GBS exposure associated with a striking upregulation of genes in innate and adaptive immunity and downregulation of pathways for angiogenesis, morphogenesis, and cellular growth and development. Conclusions A transient choriodecidual infection may induce fetal lung injury with profound alterations in the genetic program of the fetal lung before signs of preterm labor. Our results provide a window for the first time into early molecular pathways disrupting fetal lung angiogenesis and morphogenesis before preterm labor occurs, which may set the stage for BPD. A strategy to prevent BPD should target the fetus in utero to attenuate alterations in the fetal lung genetic program.
"The price of anything is the life you exchange for it" : a study on voluntary simplicity within the United States

American consumption based lifestyles have a grave impact on the environment and personal wellbeing of Americans, creating unhealthy consumption patterns, unforeseen negative effects on individuals, and ultimately unsustainable lifestyles overall. Voluntary simplicity (VS), or individuals who resist consumerist tendencies seeking a higher quality of life through simplicity, is an answer to these concerns by promoting low consumption lifestyles, independence, and resilience among individuals and their lifestyles. This thesis considered VS within the specific cultural context of the United States, utilizing mixed methods in order to obtain an understanding of the cultural context of the United States, the VS movement, and both US and non US simplifiers. This research assessed how the VS movement interacts with modern America through the application of the lens of modernity to both America in general and then VS. This thesis then utilized surveys to obtain information on the ranked intrinsic and extrinsic motivations, as well as the extrinsic barriers that both compel and repel both potential American simplifiers and non-American simplifiers from making this type of lifestyle transition. These motivations are structured within self-determination theory and the spectrum of motivation that it offers. A comparison was then made between the motivation of US and non-US citizens in order to ascertain the unique characteristics of American simplifiers. The results of the research showed that American modernity is current characterized with emphasis on the individual over the collective, and wealth or success as being the defining metrics for success. The VS community departs from that project of modernity through emphasizing different metrics of success, seeking different concepts of individual identity instead of purchased identity, and restructuring consumerist behavior to prioritize utility consumption over status consumption. The surveys showed that autonomy and heath are prime motivators both intrinsically and extrinsically within both US and non US simplifiers. The comparison between US and non US simplifiers showed more of an emphasis on autonomy in the US citizens than the non US, and a lack of emphasis on the community building motivations within both groups. The thesis concluded with a discussion on the implications of these motivations, the lack of communal desire by simplifiers, assessing whether or not VS individuals are the agents of change needed within the US on sustainability, the sustainability implications of VS, and the methods in which VS lifestyles can be promoted, primarily through the promotion of extrinsic benefits and the removal of extrinsic barriers. (Less)
Neural network based single image super resolution

In this paper a novel learning based technique for single image super resolution (SR) is proposed. We model the relationship between available low resolution (LR) image and desired high resolution (HR) image as multi-scale markov random field (MSMRF). We re-formulate the SR problem in terms of learning the mapping between LR-MRF and HR-MRF, which is generally non-linear. Instead of learning MSMRF parameters we use artificial neural networks to learn the desired mapping. The results compare favorably to more complex stat-of-the art techniques for 2 × 2 and 3 × 3 SR problem. We solve the SR problem using optical zoom as a cue by the proposed algorithm as well. The results on experiments with real data are presented.
Mining Diverse Views from Related Articles

The world wide web allows for diverse articles to be available on a news event, product or any topic. It is not impossible to find a few hundred articles that discuss a specific topic thus making it difficult for a user to quickly process the information. Summarization condenses huge volume of information related to a topic but does not provide a delineation of the issues pertaining to it. We want to extract the diverse issues pertaining to a topic by mining views from a collection of articles related to it. A view is a set of sentences, related in content, that address an issue relevant to a topic. We present a framework for extraction and ranking of views and have conducted experiments to evaluate the framework.
Strong Gravitational Lensing and Galactic Bulges

The lensing probabilities of quasars with image separations greater than Δθ and flux density ratios less than qr are calculated by foreground dark matter halos in a flat, cosmological constant-dominated (Λ cold dark matter) universe. The mass density of the lenses is taken to be the Navarro-Frenk-White profile on all mass scales plus a central point mass for low-mass halos with M < Mc = 5 × 1013 h-1 M☉. We introduce a quantity Meff, which is a point mass ranging from 1 to 1000 times the mass M• of a supermassive black hole (SMBH) inhabiting the center of each galaxy, to describe the contributions of galactic central SMBHs and galactic bulges to lensing probabilities. The lensing cross section and thus the lensing probability are quite sensitive to the flux density ratio qr of multiple images in our calculations. It is shown that in order to reproduce the lensing survey results of the Jodrell-Bank VLA Astrometric Survey and the Cosmic Lens All-Sky Survey for qr < 10, about 20% of the bulge mass is needed as a point mass for each galaxy. Since there is still considerable uncertainty regarding the value of the spectrum normalization parameter σ8, we investigate the effect of varying this parameter within its entire observational range (from 0.7 to 1.1), and we find that low-σ8 values (≤0.7) are ruled out and that the best-fit value is σ8 ≃ 1.0.
Accelerating search tree based brute force motif discovery technique on a processor cluster

Determination of conserved regions that plays vital roles on regulation of transcription and translation processes is one of the most challenging problems in bioinformatics. However, with the increasing power of distributed computing systems, solving these types of combinatorial problems by utilizing parallelized brute force or exhaustive search algorithms recently has gained popularity. In this paper, we investigated the parallelized implementation of a search tree based brute force technique to find motifs with different lengths. Experimental studies showed that parallelization of the brute force techniques with less communication overhead is significantly increased the usability of them to analyze long nucleotide sequences.
A Domain-Independent Algorithm for Multi-Plan Adaptation and Merging in Least-Commitment Planners

Solving problems in many real-world domains requires integrating knowledge from several past experiences. This integration requires the dynamic retrieval of multiple experiences and the extraction of their relevant subparts. Our solution is the Multi-Plan Adaptor (MPA), a method for merging partial-order plans in the context of case-based least-commitment planning. MPA provides this ability by extracting an intermediate goal statement from a partial plan, clipping a stored plan to the intermediate goal statement, and then splicing the clipping into the original partial plan. MPA is implemented in the NICOLE multistrategy reasoning system, where it is paired with MOORE, an asynchronous, resource-bounded memory module. MooRE initially retrieves its current "best guess" but continues search, spontaneously returning a better retrieval as soon as it is found.
Intelligent control of overhead gantry cranes

Overhead gantry crane systems have been integral part of many heavy industrial applications needing material handling and transportation. This can easily be seen in emerging countries growing rapidly. Single force control input applied to crane moves it to a desired position but also triggers undesired swing on the payload which makes it an interesting control problem for this underactuated system. Given an application and a work environment constraint the response time to the position error vs. the maximum allowable amplitude of the payload swing may vary. An intelligent control methodology has been given such an overhead crane system with an optimization parameter compromising between response rate and swing amplitude. The proposed controller does not rely on the knowledge of the crane dynamics making the solution applicable changing operation conditions, so it is a universal controller. Robust adaptive properties are established via a neural network based multi-loop controller architecture. Customization to fit two specific application requirements has been illustrated in the simulations. Stability proofs are given in the sense of Lyapunov. Simulation examples are shown to illustrate the effectiveness of the proposed controller that does not rely on prior knowledge of system dynamics.
A priori error estimates of mixed finite element methods for nonlinear quadratic convex optimal control problem

In this paper, we study an a priori error analysis for the quadratic optimal control problems governed by nonlinear elliptic partial differential equations using mixed finite element methods. The state and the co-state are approximated by the lowest order Raviart-Thomas mixed finite element spaces and the control is approximated by piecewise constant functions. A priori error estimates for the mixed finite element approximation of nonlinear optimal control problems is obtained. Some numerical examples are presented to confirm our theoretical results.
The Battle between Rotavirus and Its Host for Control of the Interferon Signaling Pathway

Viral pathogens must overcome innate antiviral responses to replicate successfully in the host organism. Some of the mechanisms viruses use to interfere with antiviral responses in the infected cell include preventing detection of viral components, perturbing the function of transcription factors that initiate antiviral responses, and inhibiting downstream signal transduction. RNA viruses with small genomes and limited coding space often express multifunctional proteins that modulate several aspects of the normal host response to infection. One such virus, rotavirus, is an important pediatric pathogen that causes severe gastroenteritis, leading to ∼450,000 deaths globally each year. In this review, we discuss the nature of the innate antiviral responses triggered by rotavirus infection and the viral mechanisms for inhibiting these responses.
Dynamic Distributed Computing with Byzantine Failures

Byzantine failure tolerance (BFT) is one of the most fundamental problem in distributed computing and has been researched extensively. However, due to the famous impossible result of FLP, there is no perfect way to solve it. Modern BFT protocols are usually proposed with practical assumptions such as partially synchrony, encrypted messages. Yet, designing dynamic BFT system with large number of nodes remains challenge. In this write-up, we will explore and review the techniques in the core of modern BFT protocols, and discuss the recent new approach by combining clustering and random walk to obtain reliable and efficient dynamic BFT system.
Git Blame Who?: Stylistic Authorship Attribution of Small, Incomplete Source Code Fragments

Abstract Program authorship attribution has implications for the privacy of programmers who wish to contribute code anonymously. While previous work has shown that individually authored complete files can be attributed, these efforts have focused on such ideal data sets as contest submissions and student assignments. We explore the problem of authorship attribution “in the wild,” examining source code obtained from open-source version control systems, and investigate how contributions can be attributed to their authors, either on an individual or a per-account basis. In this work, we present a study of attribution of code collected from collaborative environments and identify factors which make attribution of code fragments more or less successful. For individual contributions, we show that previous methods (adapted to be applied to short code fragments) yield an accuracy of approximately 50% or 60%, depending on whether we average by sample or by author, at identifying the correct author out of a set of 104 programmers. By ensembling the classification probabilities of a sufficiently large set of samples belonging to the same author we achieve much higher accuracy for assigning the set of samples to the correct author from a known suspect set. Additionally, we propose the use of calibration curves to identify which samples are by unknown and previously unencountered authors.
Distributed Processing of Biosignal-Database for Emotion Recognition with Mahout

This paper investigates the use of distributed processing on the problem of emotion recognition from physiological sensors using a popular machine learning library on distributed mode. Specifically, we run a random forests classifier on the biosignal-data, which have been pre-processed to form exclusive groups in an unsupervised fashion, on a Cloudera cluster using Mahout. The use of distributed processing significantly reduces the time required for the offline training of the classifier, enabling processing of large physiological datasets through many iterations.
PROCESS-BASED MODELLING OF THE INFORMATION SYSTEMS RESISTANCE PHENOMENON

This article aims to propose a process-based modelling of the Information Systems resistance phenomenon. Accordingly, we wrote a literature review to categorize the main points set forth by the extant scientific texts relating to the process taxonomy: input, output, players, and the resistance phenomenon. Based on the modelling, this article provides theoretical implications in terms of improving the understanding of the phenomenon among academicians as well as practical and managerial suggestions related to its mitigation.
Musicship: didactic considerations of music activity in preschool

This article, which is based on my thesis research, aims to describe and analyse the didactics of music activity in early childhood education and, through empirical research, to test concepts that can capture and denote the figuration of music activity. The overall research question was “What characterizes music activity and its possible figuration in preschool practices? ” “Possible figuration” refers to an interwoven presentation, a didactics-based concept (‘musicship’) that describes the transformation of the significance of music activity within interwoven empirical and theoretical threads of references. The empirical material comprises of video observations and reflections with teachers conducted one day a week for eight months at three preschools. As a theoretical resource, various concepts were tested within the framework of didactic theory, music didactics, and the theory of musicking. The concept of musicship arose when conducting the research. It is being introduced and developed as a resource for both critical and creative reflection on music activity. It is constantly recreated via music-related processes, moving between the actual and the possible, and facilitating the analysis and understanding of music activity.
HerMES: Clusters of Dusty Galaxies Uncovered by Herschel and Planck

The potential for Planck to detect clusters of dusty, star-forming galaxies at z greater than 1 is tested by examining the Herschel-SPIRE images of Planck Early Release Compact Source Catalog (ERCSC) sources lying in fields observed by the HerMES survey. Of the 16 Planck sources that lie in the roughly 90 sq. deg. examined, we find that twelve are associated with single bright Herschel sources. The remaining four are associated with overdensities of Herschel sources, making them candidate clusters of dusty, starforming galaxies. We use complementary optical and NIR data for these clumps to test this idea, and find evidence for the presence of galaxy clusters in all four cases. We use photometric redshifts and red sequence galaxies to estimate the redshifts of these clusters, finding that they range from 0.8 to 2.3. These redshifts imply that the Herschel sources in these clusters, which contribute to the detected Planck flux, are forming stars very rapidly, with typical total cluster star formation rates greater than 1000Msun per yr. The high redshift clusters discovered in these observations are used to constrain the epoch of cluster galaxy formation, finding that the galaxies in our clusters are 1 to 1.5 Gy old at z about 1 to 2. Prospects for the discovery of further clusters of dusty galaxies are discussed, using not only all sky Planck surveys, but also deeper, smaller area, Herschel surveys.