Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia

Flowering time (i.e., heading date in crops) is an important ecological trait that determines growing seasons and regional adaptability of plants to specific natural environments. Rice (Oryza sativa L.) is a short-day plant that originated in the tropics. Increasing evidence suggests that the northward expansion of cultivated rice was accompanied by human selection of the heading date under noninductive long-day (LD) conditions. We report here the molecular cloning and characterization of DTH2 (for Days to heading on chromosome 2), a minor-effect quantitative trait locus that promotes heading under LD conditions. We show that DTH2 encodes a CONSTANS-like protein that promotes heading by inducing the florigen genes Heading date 3a and RICE FLOWERING LOCUS T 1, and it acts independently of the known floral integrators Heading date 1 and Early heading date 1. Moreover, association analysis and transgenic experiments identified two functional nucleotide polymorphisms in DTH2 that correlated with early heading and increased reproductive fitness under natural LD conditions in northern Asia. Our combined population genetics and network analyses suggest that DTH2 likely represents a target of human selection for adaptation to LD conditions during rice domestication and/or improvement, demonstrating an important role of minor-effect quantitative trait loci in crop adaptation and breeding.
Serum Iron Status of Under-Five Children with Sickle Cell Anaemia in Lagos, Nigeria

Background. Iron status in patients with sickle cell anaemia is a matter of continuing investigation. Objective. This paper aims to determine the serum iron status of under-five, sickle cell anaemia patients. Methods. The study spanned from December 2009 to February 2010 at the Consultant Outpatient Clinics involving 97 HbSS subjects and 97 age- and sex-matched HbAA controls. Biochemical iron status was assayed in subjects and controls. Results. Age range of the children was seven months to five years, with a mean of 30.6 (±15.97) months. Irrespective of gender, mean serum iron values were higher in HbAA controls than their HbSS counterparts but the observed difference was not significant (P = 0.299 and 0.111, resp.). The mean total iron binding capacity values of males and females were also not significantly different for sickle cell anaemia subjects and controls (P > 0.05). Males and females with HbAA had significantly lower serum ferritin when compared with their HbSS counterparts. Irrespective of gender, mean transferrin saturation was lower in HbSS subjects but the difference was not statistically significant (P > 0.05). Conclusion. Children with sickle cell anaemia have higher serum ferritin than controls, implying relatively higher iron content in the reticuloendothelial cells.
Umbilical Cord Blood T Cells Respond against the Melan-A/MART-1 Tumor Antigen and Exhibit Reduced Alloreactivity as Compared with Adult Blood-Derived T Cells

Umbilical cord blood (UCB) is increasingly used as a source of hematopoietic progenitor cells to treat a variety of disorders. UCB transplant is associated with comparatively reduced incidence of graft-versus-host disease, robust graft versus leukemia effect, and relatively high incidence of opportunistic infections, three processes in which donor-derived T lymphocytes are known to be predominantly involved. To examine the differential functionality of UCB T cells, CD8+ T cells specific for the melanoma-associated HLA-A2–restricted Melan-A26–35 A27L peptide were isolated from HLA-A2+ and HLA-A2− UCB samples and HLA-A2+ and HLA-A2− adult peripheral blood using A2/Melan-A tetramers. In UCB samples, A2/Melan-A+ CD8+ T cells were detected at a frequency of 0.04%, were more frequent in HLA-A2+ UCB, and were polyclonal and mostly naive. Consistent with Ag-driven expansion, the frequency of A2/Melan-A+ CD8+ T cells was increased following stimulation with cognate peptide or polyclonal activation, they acquired cell-surface markers reflective of effector/memory differentiation, their TCR repertoire became oligoclonal, and they expressed cytolytic activity and produced IFN-γ. Although functional properties of A2/Melan-A+ CD8+ T cells derived from HLA-A2+ UCB resembled those of HLA-A2+ adult peripheral blood, they were more likely to reach terminal differentiation following polyclonal stimulation and produced less IFN-γ in response to cognate peptide. A2/Melan-A+ CD8+ T cells from HLA-A2− UCB were poorly cytolytic, produced little IFN-γ, and were predominantly monofunctional or nonfunctional. These properties of UCB-derived CD8+ T cells could contribute to the reduced incidence of graft-versus-host disease and heightened incidence of opportunistic infections observed following UCB transplant.
A rule-based language for web data management

There is a new trend to use Datalog-style rule-based languages to specify modern distributed applications, notably on the Web. We introduce here such a language for a distributed data model where peers exchange messages (i.e. logical facts) as well as rules. The model is formally defined and its interest for distributed data management is illustrated through a variety of examples. A contribution of our work is a study of the impact on expressiveness of "delegations" (the installation of rules by a peer in some other peer) and explicit timestamps. We also validate the semantics of our model by showing that under certain natural conditions, our semantics converges to the same semantics as the centralized system with the same rules. Indeed, we show this is even true when updates are considered.
Novel Lectin-Like Bacteriocins of Biocontrol Strain Pseudomonas fluorescens Pf-5

ABSTRACT Bacteriocin LlpA, produced by Pseudomonas sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol. 185:897-908, 2003). Biocontrol strain Pseudomonas fluorescens Pf-5 contains two llpA-like genes, named llpA1Pf-5 and llpA2Pf-5. Recombinant Escherichia coli cells expressing llpA1Pf-5 or llpA2Pf-5 acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpABW11M1 antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1Pf-5 and LlpA2Pf-5 are able to inhibit P. fluorescens strains, as well as the related mushroom pathogen Pseudomonas tolaasii. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.
Former Male Elite Athletes Have a Higher Prevalence of Osteoarthritis and Arthroplasty in the Hip and Knee Than Expected

Background: Intense exercise has been reported as one risk factor for hip and knee osteoarthritis (OA). Purpose: This study aimed to evaluate (1) whether this is true for both former impact and nonimpact athletes, (2) if the risk of a hip or knee arthroplasty due to OA is higher than expected, and (3) if joint deterioration is associated with knee injuries. Study Design: Cohort study; Level of evidence, 3. Methods: The prevalence of OA and arthroplasty in the hip and knee were registered in 709 former male elite athletes with a median age of 70 years (range, 50-93 years), retired from sports for a median 35 years (range, 1-63 years), and compared with 1368 matched controls. Odds ratios (ORs) are presented as means with 95% confidence intervals (95% CIs). Results: The risk of hip or knee OA was higher in former athletes (OR, 1.9; 95% CI, 1.5-2.3), as was arthroplasty based on OA in either of these joints (OR, 2.2; 95% CI, 1.6-3.1). The risk of hip OA was doubled (OR, 2.0; 95% CI, 1.5-2.8) and hip arthroplasty was 2.5 times higher (OR, 2.5; 95% CI, 1.6-3.7) in former athletes than in controls, predominantly driven by a higher risk in former impact athletes. Also, the risk of knee OA was higher (OR, 1.6; 95% CI, 1.3-2.1), as was knee arthroplasty (OR, 1.6; 95% CI, 0.9-2.7), driven by a higher risk in both former impact and nonimpact athletes. Knee OA in impact athletes was associated with knee injury. Conclusion: Hip and knee OA and hip and knee arthroplasty are more commonly found in former male elite athletes than expected. A previous knee injury is associated with knee OA in former impact athletes but not in nonimpact athletes.
Cellular Mechanisms of Social Attachment

Pharmacological studies in prairie voles have suggested that the neuropeptides oxytocin and vasopressin play important roles in behaviors associated with monogamy, including affiliation, paternal care, and pair bonding. Our laboratory has investigated the cellular and neuroendocrine mechanisms by which these peptides influence affiliative behavior and social attachment in prairie voles. Monogamous prairie voles have a higher density of oxytocin receptors in the nucleus accumbens than do nonmonogamous vole species; blockade of these receptors by site-specific injection of antagonist in the female prairie vole prevents partner preference formation. Prairie voles also have a higher density of vasopressin receptors in the ventral pallidal area, which is the major output of the nucleus accumbens, than montane voles. Both the nucleus accumbens and ventral pallidum are key relay nuclei in the brain circuits implicated in reward, such as the mesolimbic dopamine and opioid systems. Therefore, we hypothesize that oxytocin and vasopressin may be facilitating affiliation and social attachment in monogamous species by modulating these reward pathways.
A Provable Generalized Tensor Spectral Method for Uniform Hypergraph Partitioning

Matrix spectral methods play an important role in statistics and machine learning, and most often the word 'matrix' is dropped as, by default, one assumes that similarities or affinities are measured between two points, thereby resulting in similarity matrices. However, recent challenges in computer vision and text mining have necessitated the use of multi-way affinities in the learning methods, and this has led to a considerable interest in hypergraph partitioning methods in machine learning community. A plethora of "higher-order" algorithms have been proposed in the past decade, but their theoretical guarantees are not well-studied. In this paper, we develop a unified approach for partitioning uniform hypergraphs by means of a tensor trace optimization problem involving the affinity tensor, and a number of existing higher-order methods turn out to be special cases of the proposed formulation. We further propose an algorithm to solve the proposed trace optimization problem, and prove that it is consistent under a planted hypergraph model. We also provide experimental results to validate our theoretical findings.
[Low-dose chest CT with millimetric thin slices: myth or reality?].

PURPOSE To evaluate the diagnostic accuracy of millimetric thin slices low dose chest CT. MATERIALS AND METHODS Forty one patients underwent a chest CT thin slices (1 mm every 10 mm) exploration using both a 170 milliamperage and a low dose acquisition using 80 mA. The examination were read by 2 senior radiologists specialized in chest imaging without knowledge of acquisition parameters and in a random order. A statistical analysis of interobserver agreement was performed using Kappa analysis. Doses of both acquisition were estimated by compagning the dose length product calculated by the CT software and be using a simulation software. RESULTS Excellent interobserver and intermodalities agreements were found. A 53% decrease in dose was estimated with the low dose modality compare to the normal dose. CONCLUSION Low dose thin slice chest CT using 80 mA has a similar diagnosis accuracy as standard dose thin slice chest CT and delivers half dose of irradiation.
Paradoxical association between body mass index and in-hospital mortality in elderly patients with chronic obstructive pulmonary disease in Japan

Background and objective The prevalence and mortality of chronic obstructive pulmonary disease (COPD) in elderly patients are increasing worldwide. Low body mass index (BMI) is a well-known prognostic factor for COPD. However, the obesity paradox in elderly patients with COPD has not been well elucidated. We investigated the association between BMI and in-hospital mortality in elderly COPD patients. Methods Using the Diagnosis Procedure Combination database in Japan, we retrospectively collected data for elderly patients (>65 years) with COPD who were hospitalized between July 2010 and March 2013. We performed multivariable logistic regression analysis to compare all-cause in-hospital mortality between patients with BMI of <18.5 kg/m2 (underweight), 18.5–22.9 kg/m2 (low–normal weight), 23.0–24.9 kg/m2 (high–normal weight), 25.0–29.9 kg/m2 (overweight), and ≥30.0 kg/m2 (obesity) with adjustment for patient backgrounds. Results In all, 263,940 eligible patients were identified. In-hospital mortality was 14.3%, 7.3%, 4.9%, 4.3%, and 4.4%, respectively, in underweight, low–normal weight, high–normal weight, overweight, and obese patients. Underweight patients had a significantly higher mortality than low–normal weight patients (odds ratio [OR]: 1.55, 95% confidence interval [CI]: 1.48–1.63), whereas lower mortality was associated with high–normal weight (OR: 0.76, CI: 0.70–0.82), overweight (OR: 0.73, CI: 0.66–0.80), and obesity (OR: 0.67, CI: 0.52–0.86). Higher mortality was significantly associated with older age, male sex, more severe dyspnea, lower level of consciousness, and lower activities of daily living. Conclusion Overweight and obese patients had a lower mortality than low–normal weight patients, which supports the obesity paradox.
An Electronic Publication Dedicated to Early Stellar Evolution and Molecular Clouds Discovery of Large-scale Gravitational Infall in a Massive Protostellar Cluster Chaotic Star Formation and the Alignment of Stellar Rotation with Disc and Planetary Orbital Axes

We report Mopra (ATNF), Anglo-Australian Telescope, and Atacama Submillimeter Telescope Experiment observations of a molecular clump in Carina, BYF73 = G286.21+0.17, which give evidence of large-scale gravitational infall in the dense gas. From the millimetre and far-infrared data, the clump has mass ∼ 2×10 4 M ⊙ , luminosity ∼ 2–3×10 4 L ⊙ , and diameter ∼ 0.9 pc. From radiative transfer modelling, we derive a mass infall rate ∼ 3.4×10 −2 M ⊙ yr −1. If confirmed , this rate for gravitational infall in a molecular core or clump may be the highest yet seen. The near-infrared K-band imaging shows an adjacent compact HII region and IR cluster surrounded by a shell-like photodissociation region showing H 2 emission. At the molecular infall peak, the K imaging also reveals a deeply embedded group of stars with associated H 2 emission. The combination of these features is very unusual and we suggest they indicate the ongoing formation of a massive star cluster. We discuss the implications of these data for competing theories of massive star formation. We investigate the evolution of the relative angle between the stellar rotation axis and the circumstellar disc axis of a star that forms in a stellar cluster from the collapse of a turbulent molecular cloud. This is an inherently chaotic environment with variable accretion, both in terms of rate and the angular momentum of the material, and dynamical interactions between stars. We find that the final stellar rotation axis and disc spin axis can be strongly misaligned, but this occurs primarily when the disc is truncated by a dynamical encounter so that the final disc rotation axis 1
Energy Efficient Routing Scheme for Sensor Networks Using Connected Dominating Set

A power efficient scheduling scheme extending the life time of sensor nodes on wireless sensor networks has been proposed in this paper. This power efficient sleep scheduling algorithm is based on the connected dominating set approach. This approach first constructs a connected dominating set for parent selection and uses the conjugative sleep scheduler scheme for data aggregation. The re-calculation of connected dominating set when the node is in ON condition and in OFF conditions have been discussed. Finally, the performance of connected dominating set approach is compared with minimum spanning tree approach. By simulating the network with different node density, it is observed that, our proposed approach performs better than spanning tree topology. Whenever a sensor node fails or a new node is added to the network, the conjugative scheduling scheme evaluates the route maintenance. Remaining power levels of nodes have been examined in order to increase the network lifetime.
Glucocorticoids in Health and Disease with Special Reference to Glucocorticoid Receptor Signalling Pathways and Molecular Networking

Glucocorticoids have a diverse role in physiological and pathological conditions, making them a class of potent drugs in clinical use ranging from organ transplantation, arthritis, asthma, and chronic obstructive pulmonary diseases (COPD) to oncological problems. The use of glucocorticoids in clinical practices, however, is associated with many side effects and steroid resistance in certain diseases. Understanding the underlying mechanism of glucocorticoid action is an ultimate concern in overcoming these complications. Several studies have pointed the role of glucocorticoid receptor interaction with many other signalling pathways in these situations. Designing of drugs that could modulate these interactions, while maintaining glucocorticoid receptor molecular network in a homeostatic balance, is a challenge in glucocorticoids pharmacology. Some prospective molecules like theophylline and compound A, are reported to have such effect.
Genes Contributing to Genetic Variation of Muscling in Sheep

Selective breeding programs aiming to increase the productivity and profitability of the sheep meat industry use elite, progeny tested sires. The broad genetic traits of primary interest in the progeny of these sires include skeletal muscle yield, fat content, eating quality, and reproductive efficiency. Natural mutations in sheep that enhance muscling have been identified, while a number of genome scans have identified and confirmed quantitative trait loci (QTL) for skeletal muscle traits. The detailed phenotypic characteristics of sheep carrying these mutations or QTL affecting skeletal muscle show a number of common biological themes, particularly changes in developmental growth trajectories, alterations of whole animal morphology, and a shift toward fast twitch glycolytic fibers. The genetic, developmental, and biochemical mechanisms underpinning the actions of some of these genetic variants are described. This review critically assesses this research area, identifies gaps in knowledge, and highlights mechanistic linkages between genetic polymorphisms and skeletal muscle phenotypic changes. This knowledge may aid the discovery of new causal genetic variants and in some cases lead to the development of biochemical and immunological strategies aimed at enhancing skeletal muscle.
The importance of cross-lingual information for matching Wikipedia with the Cyc ontology

In this paper we try to answer the question how cross-lingual evidence may improve matching between different classification schemas. We concentrate specifically on the task of mapping between Wikipedia categories and Cyc terms as well as the classification of Wikipedia articles to the Cyc taxonomy and show how this process may be improved by consuming the evidence that is available in different editions of Wikipedia. The results show that the performance of the mapping procedure may be improved from 0.6 to 4.9 percentage points, depending on the number of external Wikipedia editions and the given task.
Generating Instruction Sets And Microarchitectures From Applications

The design of application-specific instruction set processor(ASIP) system includes at least three interdependent tasks: microarchitecture design, instruction set design, and instruction set mapping for the application. We present a method that unifies these three design problems with a single formulation: a modified scheduling/allocation problem with an integrated instruction formation process. Micro-operations (MOPs) representing the application are scheduled into time steps. Instructions are formed and hardware resources are allocated during the scheduling process. The assembly code for the given application is obtained automatically at the end of the scheduling process. This approach considers MOP parallelism, instruction field encoding, delay load/store/branch, conditional execution of MOPs and the retargetability to various architecture templates. Experiments are presented to show the power and limitation of our approach. Performance improvement over our previous work is significant.
Majorana fermions emerging from magnetic nanoparticles on a superconductor without spin-orbit coupling

There exists a variety of proposals to transform a conventional s-wave superconductor into a topological superconductor, supporting Majorana fermion mid-gap states. A necessary ingredient of these proposals is strong spin-orbit coupling. Here we propose an alternative system consisting of a one-dimensional chain of magnetic nanoparticles on a superconducting substrate. No spin-orbit coupling in the superconductor is needed. We calculate the topological quantum number of a chain of finite length, including the competing effects of disorder in the orientation of the magnetic moments and in the hopping energies, to identify the transition into the topologically nontrivial state (with Majorana fermions at the end points of the chain).
Wireless sensor networks testbed: ASNTbed

Wireless sensor networks (WSNs) have been used in different types of applications and deployed within various environments. Simulation tools are essential for studying WSNs, especially for exploring large-scale networks. However, WSN testbeds are still required for further testing before the real implementation. In this paper we propose an indoor testbed which is built on the ceiling board of the demonstration room. The purpose of this testbed is to evaluate various types of algorithms and protocols before using them in real world applications. This paper focuses on how to implement such testbed and what are the main challenges that we experienced while implementing the ASNTbed (Advanced Sensor Networks Testbed) and how to solve them. This paper can be considered as a guideline to help other researchers and developers to implement similar testbed.