Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Allopurinol and Inosine Administration on Xanthine Oxidoreductase Gene Expression in Selected Tissues of Broiler Chickens

Uric acid is considered the most significant factor in amelioration of oxidative burden in birds. Uric acid is formed in the terminal reactions of purine degradation by the enzyme xanthine oxidoreductase (XOR). In this study, inosine, a purine precursor, was fed to 3 groups of 5 birds: Group 1 was fed 0 (control), Group 2, 0.6 mols inosine/kg feed (INO) and Group 3, INO treatment plus 50 mg allopurinol/kg BM (INOAL). Allopurinol is a known inhibitor of XOR and thereby reduces uric acid (UA). INOAL birds showed lower total liver XOR activity (p = 0.005) but kidney XOR activity was not affected. Both INO and INOAL treated birds had higher plasma and kidney UA concentrations than controls. Liver uric acid (LUA) was significantly reduced in INOAL birds when compared to other treatments. XOR gene expression was increased (p = 0.007) in the liver tissue of INOAL birds when compared to CON and INO birds. However, there were no significant changes in XOR gene expression in the kidney tissue. To our knowledge, this is the first report of XOR gene expression measured under these conditions. These results suggest that regulation of UA production is tissue dependent. The results also indicate a compensatory effect of allopurinol on XOR gene expression which can be linked to a decrease in antioxidant protection from UA.
Near-Optimal Joint Object Matching via Convex Relaxation

Joint matching over a collection of objects aims at aggregating information from a large collection of similar instances (e.g. images, graphs, shapes) to improve maps between pairs of them. Given multiple matches computed between a few object pairs in isolation, the goal is to recover an entire collection of maps that are (1) globally consistent, and (2) close to the provided maps --- and under certain conditions provably the ground-truth maps. Despite recent advances on this problem, the best-known recovery guarantees are limited to a small constant barrier --- none of the existing methods find theoretical support when more than $50\%$ of input correspondences are corrupted. Moreover, prior approaches focus mostly on fully similar objects, while it is practically more demanding to match instances that are only partially similar to each other. In this paper, we develop an algorithm to jointly match multiple objects that exhibit only partial similarities, given a few pairwise matches that are densely corrupted. Specifically, we propose to recover the ground-truth maps via a parameter-free convex program called MatchLift, following a spectral method that pre-estimates the total number of distinct elements to be matched. Encouragingly, MatchLift exhibits near-optimal error-correction ability, i.e. in the asymptotic regime it is guaranteed to work even when a dominant fraction $1-\Theta\left(\frac{\log^{2}n}{\sqrt{n}}\right)$ of the input maps behave like random outliers. Furthermore, MatchLift succeeds with minimal input complexity, namely, perfect matching can be achieved as soon as the provided maps form a connected map graph. We evaluate the proposed algorithm on various benchmark data sets including synthetic examples and real-world examples, all of which confirm the practical applicability of MatchLift.
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data

UNLABELLED MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. AVAILABILITY MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant
Reactive obstacle avoidance and trajectory optimization for nonholonomic systems: two problems, one solution

This paper proposes a novel approach for optimizing feasible trajectories for nonholonomic systems. The method is iterative and based on the perturbation of the input functions of the system along the trajectory. The input functions are perturbed in such a way that a criterion relative to the path is minimized. We briefly present two applications of the method : one in trajectory optimization for complex nonholonomic systems and one in reactive obstacle avoidance for multi-body wheeled mobile robots. In both cases, the criterion to optimize is related to the distance to obstacles. The method thus modifies the current trajectory in order to make it maximize the distance to obstacles, while keeping the kinematic constraints satisfied at any time
Improving Mask Learning Based Speech Enhancement System with Restoration Layers and Residual Connection

For single-channel speech enhancement, mask learning based approach through neural network has been shown to outperform the feature mapping approach, and to be effective as a pre-processor for automatic speech recognition. However, its assumption that the mixture and clean reference must have the correspondent scale doesn’t hold in data collected from real world, and thus leads to significant performance degradation on parallel recorded data. In this paper, we first extend the mask learning based speech enhancement by integrating two types of restoration layer to address the scale mismatch problem. We further propose a novel residual learning based speech enhancement model via adding different shortcut connections to a feature mapping network. We show such a structure can benefit from both the mask learning and the feature mapping. We evaluate the proposed speech enhancement models on CHiME 3 data. Without retraining the acoustic model, the best bidirection LSTM with residue connections yields 24.90% relative WER reduction on real data and 34.57% WER on simulated data.
Learning to Recognize Human Activities Using Soft Labels

Human activity recognition system is of great importance in robot-care scenarios. Typically, training such a system requires activity labels to be both completely and accurately annotated. In this paper, we go beyond such restriction and propose a learning method that allow labels to be incomplete and uncertain. We introduce the idea of soft labels which allows annotators to assign multiple, and weighted labels to data segments. This is very useful in many situations, e.g., when the labels are uncertain, when part of the labels are missing, or when multiple annotators assign inconsistent labels. We formulate the activity recognition task as a sequential labeling problem. Latent variables are embedded in the model in order to exploit sub-level semantics for better estimation. We propose a max-margin framework which incorporate soft labels for learning the model parameters. The model is evaluated on two challenging datasets. To simulate the uncertainty in data annotation, we randomly change the labels for transition segments. The results show significant improvement over the state-of-the-art approach.
Development of a tactile sensor based on biologically inspired edge encoding

Here we present a novel biologically inspired tactile sensor based on the structure of the human fingertip. Unlike previous biologically inspired sensors, it is based on new theories of the functional morphology of the fingertip skin features and the Meissner's Corpuscles mechanoreceptors pervading them, particularly in the encoding of tactile edge information. Through mimicking the layered macro-structure of fingertip skin the sensor is highly conformable and very sensitive, as well as a strong and practical gripping tool. The tactile sensor is composed of a thin flexible rubber skin with structural details emulating those of the glabrous epidermis. This encases a clear, highly compliant polymer melt blend with similar mechanical properties to the dermis and subcutaneous fat. A camera is used to track markers on the internal structural details of the rubber skin enabling remote, detailed, direct and sensitive detection of surface deflections. Initial results presented here show the design to be a very capable, highly sensitive sensor as well as a very practical, affordable and scalable robotic fingertip.
Patients With Chronic Pelvic Pain: Endometriosis or Interstitial Cystitis/Painful Bladder Syndrome?

Background: Endometriosis and interstitial cystitis/painful bladder syndrome share similar symptoms. Interstitial cystitis was once considered rare, but it is now recognized as more common than previously thought. This review examines evidence that patients presenting with symptoms typically attributed to endometriosis or with unresolved pelvic pain after treatment for endometriosis may, in fact, have interstitial cystitis, and suggests approaches for appropriate diagnosis. Methods: A MedLine search using “chronic pelvic pain,” “endometriosis,” “interstitial cystitis,” and “bladder origin pain” as key words was performed for the most recent English-language articles. Additional references were obtained through cross-referencing the bibliography cited in each publication. Discussion: The symptoms of endometriosis and inter-stitial cystitis frequently overlap, and these 2 conditions may even coexist in the same patient. In cases of unresolved endometriosis and persistent pelvic pain, patients may have interstitial cystitis. A variety of tools are available to aid in identifying interstitial cystitis. Conclusion: Gynecologists should be alert to the possible presence of interstitial cystitis in patients who present with chronic pelvic pain typical of endometriosis.
Temporal variation in temperature determines disease spread and maintenance in Paramecium microcosm populations

The environment is rarely constant and organisms are exposed to temporal and spatial variations that impact their life histories and inter-species interactions. It is important to understand how such variations affect epidemiological dynamics in host–parasite systems. We explored effects of temporal variation in temperature on experimental microcosm populations of the ciliate Paramecium caudatum and its bacterial parasite Holospora undulata. Infected and uninfected populations of two P. caudatum genotypes were created and four constant temperature treatments (26°C, 28°C, 30°C and 32°C) compared with four variable treatments with the same mean temperatures. Variable temperature treatments were achieved by alternating populations between permissive (23°C) and restrictive (35°C) conditions daily over 30 days. Variable conditions and high temperatures caused greater declines in Paramecium populations, greater fluctuations in population size and higher incidence of extinction. The additional effect of parasite infection was additive and enhanced the negative effects of the variable environment and higher temperatures by up to 50 per cent. The variable environment and high temperatures also caused a decrease in parasite prevalence (up to 40%) and an increase in extinction (absence of detection) (up to 30%). The host genotypes responded similarly to the different environmental stresses and their effect on parasite traits were generally in the same direction. This work provides, to our knowledge, the first experimental demonstration that epidemiological dynamics are influenced by environmental variation. We also emphasize the need to consider environmental variance, as well as means, when trying to understand, or predict population dynamics or range.
Polarization reversal in antiferroelectric liquid crystals

We studied the change in polarization direction during field reversal in binary mixtures possessing antiferroelectric phase. Due to the coupling of the electric field with the spontaneous polarization of each smectic layer, the transition from antiferroelectric to the ferroelectric phase was induced. This transition was accompanied by changes in optical properties. Both three-state and V-shaped switching was observed. After removing the field, the sample transformed back to the antiferroelectric state. We have found that in some cases, the kinetics of this transition was very slow its time constant ranged from minutes to days, depending on temperature. In the same mixtures, we observed a large thermal hysteresis of the phase transition between the ferroelectric and antiferroelectric phases. We argue that all three phenomena: V-shaped antiferroelectric interactions acting between smectic layers are of comparable strength. We compare our results with the existing models of V-shaped switching and propose a modification of the models.
Conditioning including antithymocyte globulin followed by unmanipulated HLA-mismatched/haploidentical blood and marrow transplantation can achieve comparable outcomes with HLA-identical sibling transplantation.

The outcomes of 293 patients with leukemia undergoing HLA-identical sibling (n = 158) or related HLA-mismatched (n = 135) hematopoietic cell transplantation (HCT) performed during the same time period were compared. Patients received BUCY2 in HLA-identical sibling HCT or BUCY2 + ATG in mismatched HCT as conditioning regimens, followed by unmanipulated marrow and/or peripheral blood (PB) transplantation. All patients achieved full engraftment. The cumulative incidences of grades II to IV acute graft-versus-host disease (aGVHD) in the matched and mismatched cohorts were 32% (CI, 25%-39%) versus 40% (CI, 32%-48%, P = .13), respectively, with the relative risk (RR) = 0.64 (95% CI, 0.43-0.94), P = . 02. The incidence of chronic GVHD did not differ significantly between the cohorts (P = .97). Two-year incidences of treatment-related mortality and relapse for matched versus mismatched were 14% (range, 9%-20%) versus 22% (range, 15%-29%) with P = . 10 and 13% (range, 8%-19%) versus 18% (range, 10%-27%) with P = . 40, respectively. Two-year adjusted leukemia-free survival (LFS) and overall survival were 71% (range, 63%-78%) versus 64% (range, 54%-73%) with P = . 27 and 72% (range, 64%-79%) versus 71% (range, 62%-77%) with P = . 72, respectively. Multivariate analyses showed that only advanced disease stage and a diagnosis of acute leukemia had increased risk of relapse, treatment failure, and overall mortality. In summary, HCT performed with related HLA-mismatched donors is a feasible approach with acceptable outcomes.
Molecular Characterization of blaNDM-1 in a Sequence Type 235 Pseudomonas aeruginosa Isolate from France

ABSTRACT An NDM-1 carbapenemase-producing Pseudomonas aeruginosa isolate was recovered from a patient hospitalized in France after a previous hospitalization in Serbia. Genetic studies revealed that the blaNDM-1 gene was surrounded by insertion sequence ISAba125 and a truncated bleomycin resistance gene. This blaNDM-1 region was a part of the variable region of a new complex class 1 integron bearing IS common region 1 (ISCR1). The presence of ISPa7 upstream of this integron suggests insertion in a chromosomally located Tn402-like structure.
Level by level: making flow- and context-sensitive pointer analysis scalable for millions of lines of code

We present a practical and scalable method for flow- and context-sensitive (FSCS) pointer analysis for C programs. Our method analyzes the pointers in a program level by level in terms of their points-to levels, allowing the points-to relations of the pointers at a particular level to be discovered based on the points-to relations of the pointers at this level and higher levels. This level-by-level strategy can enhance the scalability of the FSCS pointer analysis in two fundamental ways, by enabling (1) fast and accurate flow-sensitive analysis on full sparse SSA form using a flow-insensitive algorithm and (2) fast and accurate context-sensitive analysis using a full transfer function and a meet function for each procedure. Our level-by-level algorithm, LevPA, gives rises to (1) a precise and compact SSA representation for subsequent program analysis and optimization tasks and (2) a flow- and context-sensitive MAY/MUST mod (modification) set and read set for each procedure. Our preliminary results show that LevPA can analyze some programs with over a million lines of C code in minutes, faster than the state-of-the-art FSCS methods.
Impact of advanced maternal age on neonatal survival of twin small‐for‐gestational‐age subtypes

Aim: We examined the impact of advanced maternal age (>40 years old) on the survival of twin small‐for‐gestational‐age (SGA) infants, that is, infants who were smaller in size than was expected for the baby's sex, genetic heritage, and gestational age.
Prevention of selenite-induced cataractogenesis by rutin in Wistar rats

Purpose To investigate whether rutin retards selenite-induced cataractogenesis in Wistar rat pups. Methods On postpartum day ten, Group I rat pups received an intraperitoneal injection of saline. Group II and III rat pups received a subcutaneous injection of sodium selenite. Group III also received an intraperitoneal injection of rutin once daily on postpartum days 9–14. Both eyes of each pup were examined from day 16 up to postpartum day 30. After sacriﬁce, extricated pup lenses were analyzed for mean activities of catalase, superoxide dismutase, glutathione peroxidase, glutathione S-transferase, and glutathione reductase. In addition, the mean concentrations of reduced glutathione (GSH) and of malondialdehyde were analyzed in samples of lenses and hemolysate. Results There was dense lenticular opaciﬁcation in all of Group II, minimal opaciﬁcation in 33.3% of Group III, no opaciﬁcation in 66.7% of Group III, and no opaciﬁcation in Group I. Signiﬁcantly lower mean activities of lenticular antioxidant enzymes were noted in Group II, compared to Group I and III. Significantly lower mean concentrations of GSH and higher mean concentrations of malondialdehyde were noted in samples of hemolysate and lens from Group II, compared to the values in Group I and III. Conclusion Rutin prevents experimental selenite-induced cataractogenesis in rat pups, possibly by preventing depletion of antioxidant enzymes and of GSH, and by inhibiting lipid peroxidation.
A duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains.

INTRODUCTION: This study aimed to develop a duplex endpoint PCR assay for rapid detection and differentiation of Leptospira strains. METHODS: Primers were designed to target the rrs (LG1/LG2) and ligB (LP1/LP2) genes to confirm the presence of the Leptospira genus and the pathogenic species, respectively. RESULTS: The assay showed 100% specificity against 17 Leptospira strains with a limit of detection of 23.1pg/µl of leptospiral DNA and sensitivity of 103 leptospires/ml in both spiked urine and water. CONCLUSIONS: Our duplex endpoint PCR assay is suitable for rapid early detection of Leptospira with high sensitivity and specificity.
Irrationality measure and lower bounds for pi(x)

In this note we show how the irrationality measure of $\zeta(s) = \pi^2/6$ can be used to obtain explicit lower bounds for $\pi(x)$. We analyze the key ingredients of the proof of the finiteness of the irrationality measure, and show how to obtain good lower bounds for $\pi(x)$ from these arguments as well. While versions of some of the results here have been done by other authors, our arguments are more elementary and yield a lower bound of order $x/\log x$ as a natural boundary.
OPFKA: Secure and efficient Ordered-Physiological-Feature-based key agreement for wireless Body Area Networks

Body Area Networks (BANs) are expected to play a major role in patient health monitoring in the near future. Providing an efficient key agreement with the prosperities of plug-n-play and transparency to support secure inter-sensor communications is critical especially during the stages of network initialization and reconfiguration. In this paper, we present a novel key agreement scheme termed Ordered-Physiological-Feature-based Key Agreement (OPFKA), which allows two sensors belonging to the same BAN to agree on a symmetric cryptographic key generated from the overlapping physiological signal features, thus avoiding the pre-distribution of keying materials among the sensors embedded in the same human body. The secret features computed from the same physiological signal at different parts of the body by different sensors exhibit some overlap but they are not completely identical. To overcome this challenge, we detail a computationally efficient protocol to securely transfer the secret features of one sensor to another such that two sensors can easily identify the overlapping ones. This protocol possesses many nice features such as the resistance against brute force attacks. Experimental results indicate that OPFKA is secure, efficient, and feasible. Compared with the state-of-the-art PSKA protocol, OPFKA achieves a higher level of security at a lower computational overhead.
A Modular Software System for Planning and Cost Modeling of a Wide Area Network

on the software modular design, a program for constructing a minimum-cost WAN design is built. In addition, a case study is carried out for the design of a nationwide WAN. The research achievements are expected to be very useful for enterprise WAN designers due to the essential roles of computer networks in maintaining the competitiveness of today's organizations. Besides, the development of large-scale WANs planning and cost-modeling software are important issues for large enterprises that use WANs, for carrier service providers, and for Internet Service Providers (ISP).