Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana

Despite the increasing number of genomic tools, identifying the genetics underlying adaptive complex traits remains challenging in the model species Arabidopsis thaliana. This is due, at least in part, to the lack of data on the geographical scale of adaptive phenotypic variation. The aims of this study were (i) to tease apart the historical roles of adaptive and nonselective processes in shaping phenological variation in A. thaliana in France and (ii) to gain insights into the spatial scale of adaptive variation by identifying the putative selective agents responsible for this selection. Forty‐nine natural stands from four climatically contrasted French regions were characterized (i) phenologically for six traits, (ii) genetically using 135 SNP markers and (iii) ecologically for 42 variables. Up to 63% of phenological variation could be explained by neutral genetic diversity. The remaining phenological variation displayed stronger associations with ecological variation within regions than among regions, suggesting the importance of local selective agents in shaping adaptive phenological variation. Although climatic conditions have often been suggested as the main selective agents acting on phenology in A. thaliana, both edaphic conditions and interspecific competition appear to be strong selective agents in some regions. In a first attempt to identify the genetics of phenological variation at different geographical scales, we phenotyped worldwide accessions and local polymorphic populations from the French RegMap in a genome‐wide association (GWA) mapping study. The genomic regions associated with phenological variation depended upon the geographical scale considered, stressing the need to account for the scale of adaptive phenotypic variation when choosing accession panels for GWAS.
Hypergraph Modelization of a Syntactically Annotated English Wikipedia Dump

Wikipedia, the well known internet encyclopedia, is nowadays a widely used source of information. To leverage its rich information, already parsed versions of Wikipedia have been proposed. We present an annotated dump of the English Wikipedia. This dump draws upon previously released Wikipedia parsed dumps. Still, we head in a different direction. In this parse we focus more into the syntactical characteristics of words: aside from the classical Part-of-Speech (PoS) tags and dependency parsing relations, we provide the full constituent parse branch for each word in a succinct way. Additionally, we propose a hypergraph network representation of the extracted linguistic information. The proposed modelization aims to take advantage of the information stocked within our parsed Wikipedia dump. We hope that by releasing these resources, researchers from the concerned communities will have a ready-to-experiment Wikipedia corpus to compare and distribute their work. We render public our parsed Wikipedia dump as well as the tool (and its source code) used to perform the parse. The hypergraph network and its related metadata is also distributed.
Effects of early intake of fruit or vegetables in relation to later asthma and allergic sensitization in school‐age children

Aim: To assess the associations between nutrition supplements in infancy and later asthma and allergy in school‐age children, and to explore the impact of environmental factors in early life. Methods: Five hundred and two children underwent clinical examination, skin prick test and a second parentally completed questionnaire within 2 y of a cross‐sectional questionnaire‐based study, including 4585 primary school children (6–16 y old) in 1994 from urban Oslo (37%), the mountainous area of Hallingdal (42%), and the industrial, coastal area of Odda (21%). The children were selected from the 1994 survey on the basis of reported diagnosed asthma (n=166), wheeze in the last 12 mo (n=155) and no asthma/no wheeze (n=181). Questions were related to nutrition and environmental exposure in early life. Possible associations between allergic sensitization or asthma at school age and exposures were estimated by logistic regression analysis, adjusting for potential confounders. Results: Daily intake of fresh fruit or vegetables, but not extra vitamins or cod liver oil supplements, in infancy decreased the risk of asthma (adjusted odds ratio (aOR) 0.57 (95% confidence interval (CI): 0.37–0.88). Early supplements of cod liver oil and extra vitamins were associated with increased allergic sensitization (aOR 1.78 (95% CI: 1.03–3.07) and 1.71 (95% CI: 1.01–2.88), respectively). A significantly higher prevalence of allergic sensitization was found in children living in Hallingdal compared to Odda, while the latter children, on the other hand, had the highest prevalence of house dust mite allergy ( p=0.001 vs Hallingdal and p=0.04 vs Oslo).
Genetic and antigenic characteristics of H4 subtype avian influenza viruses in Korea and their pathogenicity in quails, domestic ducks and mice.

In Korea, a nationwide surveillance programme was implemented in 2003 to identify highly pathogenic avian influenza viruses (AIVs). AIVs belonging to one of the most common haemagglutinin subtypes, H4, were isolated from two domestic ducks and 52 wild birds between 2004 and 2010. These H4 AIVs could be further classified into three neuraminidase subtypes: H4N6 (94.4%), H4N2 (3.7%) and H4N3 (1.9%). Phylogenetic analysis revealed that the H4 AIVs had a variety of genetic constellations, with at least nine different genotypes represented. The pathogenicity of these H4 viruses was assessed in quails, domestic ducks and mice. None of the H4 AIVs induced clinical signs in quails or domestic ducks. Viral shedding in quails was relatively high, and virus was recovered up to 5-7 days post-inoculation (p.i.) in oropharyngeal swabs, but the viruses replicated poorly in domestic ducks. Quails may act as an intermediate host in which AIVs are amplified and transmitted to other species. In mice, all of the AIVs were recovered efficiently at relatively high titres from the lungs up to 7 days p.i. , demonstrating the potential for AIVs to infect mice directly without prior adaptation. None of the AIVs induced clinical signs nor was any lethal to infected mice. However, there was significant loss of body weight in mice infected with viruses of duck origin. It is suggested that the active surveillance of influenza viruses needs to be enhanced in domestic poultry as well as in wild birds, and that it should include assessment of pathogenicity in animal models.
Sustained Expression of the Novel EBV-Induced Zinc Finger Gene, ZNFEB, Is Critical for the Transition of B Lymphocyte Activation to Oncogenic Growth Transformation1

EBV is a human tumor virus that infects and establishes latency in the majority of humans worldwide. In vitro, EBV growth transforms primary B lymphocytes into lymphoblastoid cell lines with high efficiency. We have used cDNA subtraction cloning to identify cellular target genes required for growth transformation and identified a new C2H2 (Krüppel-type) zinc finger gene, ZNFEB, that is trans-activated early following EBV infection. In this study, we characterize ZNFEB, including its intronless locus, and human and mouse protein variants. The gene is transiently expressed during normal lymphocyte activation, and its expression is sustained in EBV-positive but not EBV-negative B cell lines. There is limited expression in nonhemopoietic tissues. Its critical role in the growth transformation of B lineage cells is indicated by the abrogation of transformation with antisense strategies. ZNFEB maps to chromosome 18q12, a region with mutations in numerous, predominantly hemopoietic malignancies.
Minimal Metabolic Rate, What It Is, Its Usefulness, and Its Relationship to the Evolution of Endothermy: A Brief Synopsis

Minimal metabolic rate represents the minimal cost of living and appears to have the same relative composition of adenosine triphosphate processes in all organisms. Minimal metabolic rate is influenced by temperature and defines the standard metabolic rate (SMR) of animals. Animals that achieve SMR only for a given temperature are strictly ectothermic. Endotherms, on the other hand, are characterized by leakier membranes and an associated increase in cellular metabolism for a given temperature. The increase in cellular metabolism is coupled with an increase in heat production (i.e., obligatory thermogenesis) that, together with SMR, defines the basal metabolic rate of an endotherm. Consideration of minimal metabolic rate must take into account ecological and physiological processes, environmental influences, evolutionary arguments, and body size.
A change from nonsense to sense in the genetic code.

For the genetic information in a cistron to be translated into a polypeptide chain each coding unit in the nucleotide sequence must correspond to one of the twenty or so amino acids. If not every possible sequence corresponds to an amino acid, mutations that substitute one base for another could, in certain cases, cause the continuity of the information to be interrupted, and such "nonsense" mutations would block completion of the polypeptide chain. By virtue of a mutant with special properties, it is possible to identify nonsense mutations within the A cistron of the rII region of phage T4. In this paper the criterion for nonsense is applied to certain "ambivalent" rII mutants [1], i.e., ones whose phenotypes can be reversed by suppressor mutations in the bacterial host, Escherichia coli. The results show that an ambivalent mutation that behaves like nonsense in one bacterial host may nevertheless make sense in a second (suppressor containing) host. This suggests that a suppressor mutation in the bacterium can result in addition to the cell's dictionary of a new sensible coding unit, constituting a change in the genetic code of the bacterial cell.
A compound magnetic fi eld generating system for targeted killing of Staphylococcus aureus by magnetotactic bacteria in a micro fl uidic chip

A compound magnetic field generating system was built to kill Staphylococcus aureus (S. aureus) by magnetotactic bacteria (MTB) in a microfluidic chip in this paper. The system was consisted of coil pairs, a switch circuit, a control program and controllable electrical sources. It could produce a guiding magnetic field (gMF) of ± 1 mT along arbitrary direction in the horizontal plane, a rotating magnetic field (rMF) and a swing magnetic field (sMF, 2 Hz, 10 mT) by controlling the currents. The gMF was used to guide MTB swimming to the S. aureus pool in the microfluidic chip, and then the rMF enhanced the mixture of S. aureus and MTB cells, therefore beneficial to the attachments of them. Finally, the sMF was used to induce the death of S. aureus via MTB. The results showed that MTB could be navigated by the gMF and that 47.1% of S. aureus were killed when exposed to the sMF. It provides a new solution for the targeted treatment of infected diseases and even cancers.
Ionotropic glutamate-like receptor δ2 binds d-serine and glycine

The orphan glutamate-like receptor GluRδ2 is predominantly expressed in Purkinje cells of the central nervous system. The classification of GluRδ2 to the ionotropic glutamate receptor family is based on sequence similarities, because GluRδ2 does not form functional homomeric glutamate-gated ion channels in transfected cells. Studies in GluRδ2−/− knockout mice as well as in mice with naturally occurring mutations in the GluRδ2 gene have demonstrated an essential role of GluRδ2 in cerebellar long-term depression, motor learning, motor coordination, and synaptogenesis. However, the lack of a known agonist has hampered investigations on the function of GluRδ2. In this study, the ligand-binding core of GluRδ2 (GluRδ2–S1S2) was found to bind neutral amino acids such as d-serine and glycine, as demonstrated by isothermal titration calorimetry. Direct evidence for binding of d-serine and structural rearrangements in the binding cleft of GluRδ2–S1S2 is provided by x-ray structures of GluRδ2–S1S2 in its apo form and in complex with d-serine. Functionally, d-serine and glycine were shown to inactivate spontaneous ion-channel conductance in GluRδ2 containing the lurcher mutation (EC50 values, 182 and 507 μM, respectively). These data demonstrate that the GluRδ2 ligand-binding core is capable of binding ligands and that cleft closure of the ligand-binding core can induce conformational changes that alter ion permeation.
Experimental Study of On-Body Radio Channel Performance of a Compact Ultra Wideband Antenna

In this paper, on-body radio channel performance of a compact ultra wideband (UWB) antenna is investigated for body-centric wireless communications. Measurement campaigns were first done in the chamber and then repeated in an indoor environment for comparison. The path loss parameter for eight different on-body radio channels has been characterized and analyzed. In addition, the path loss was modeled as a function of distance for 34 different receiver locations for propagation along the front part of the body. Results and analysis show that, compared with anechoic chamber, a reduction of 16.34% path loss exponent is noticed in indoor environment. The antenna shows very good on-body radio channel performance and will be a suitable candidate for future efficient and reliable body-centric wireless communications.
The involvement of erythrocyte metabolism in organismal homeostasis in health and disease

Historically, study of erythrocyte homeostasis has focussed on the survival of erythrocytes in the blood bank and, especially in pathological circumstances, on the mechanisms leading to accelerated aging and removal from the circulation. Recent proteomic and metabolomic data suggest that erythrocyte metabolism involves more than ATP production and transport of oxygen and carbondioxide; is subject to regulation; and is likely to reflect organismal metabolism. Also, it has become clear that systemic diseases affect erythrocyte homeostasis. The perspectives emerging from these data include new possibilities to manipulate erythrocyte function and survival in vivo, and thereby organismal homeostasis.
Quiescent center formation in maize roots is associated with an auxin-regulated oxidizing environment

Embedded within the meristem of all Angiosperm roots is a population of slowly dividing cells designated the quiescent center (QC). In maize roots the QC can constitute upwards of 800-1200 cells, most of which spend an extended period of time (180-200 hours) in the G1 phase of the cell cycle. How the QC forms and is maintained is not known. Here we report that cells of the QC are characterized by their highly oxidized status. Glutathione and ascorbic acid occur predominately in the oxidized forms in the QC. This is contrasted with the status of these redox intermediates in adjacent, rapidly dividing cells in the root meristem, in which the reduced forms of these two species are favored. Using a redox sensitive fluorescent dye we were able to visualize an overall oxidizing environment in the QC, and we also made comparisons with the adjacent, rapidly dividing cells in the root meristem. Altering the distribution of auxin and the location of the auxin maximum in the root tip activates the QC, and cells leave G1 and enter mitosis. Commencement of relatively more rapid cell division in the QC is preceded by changes in the overall redox status of the QC, which becomes less oxidizing. We discuss how the position of the auxin maximum may influence the redox status of the QC and thereby modulate the cell cycle.
Biomarkers in Cardiomyopathies and Prediction of Sudden Cardiac Death.

BACKGROUND Cardiomyopathies are a major cause of heart diseases in all age groups leading to heart failure and arrhythmias. Additionally, they are an important cause of sudden cardiac death (SCD) in young people. Major advances have been made in the understanding of the complex and manifold underlying pathomechanisms and their correlating blood measured biomarkers. The aim of this review is to outline the role of such biomarkers in non-ischemic cardiomyopathies and their role in the prediction of SCD. METHODS A search in bibliographic databases was conducted. Most relevant references focusing on blood measured biomarkers in non-ischemic cardiomyopathies and biomarkers in SCD were reviewed regarding their role in pathophysiology and clinical practice. The references contain prospective and retrospective studies as well as meta-analyses. Current guidelines were analyzed concerning the implementation of biomarkers. RESULTS Most research on the role of biomarkers in cardiomyopathies is focused on myocardial stress (natriuretic peptides), injury (troponins), inflammation, and remodelling (fibrosis marker). Various studies suggest a potential application of biomarkers in diagnostics, prognosis and treatment response. Further approaches include microRNAs or multimarker approaches. Biomarkers to delineate patients being at risk for SCD have demonstrated predictive ability and could improve risk stratification strategies. CONCLUSION To improve the prognosis of cardiomyopathies an early onset of treatment is needed. This necessitates further research and a better integration of biomarkers in the diagnostic work-up of cardiomyopathies. Identification of patients being at risk for SCD is mandatory, however, reliable data of biomarkers are still lacking.
Externalities and Complementarities of HIV / AIDS Prevention Programs : Evidence from Secondary Schools in Malawi ∗

We study externalities and complementarities of three HIV/AIDS prevention interventions: HIV/AIDS education, easy access to male circumcision, and education support for girls. The study is based on a sample of 7,971 students in 33 secondary schools near Lilongwe, Malawi and we focus on the behavior within the existing 124 classes in these schools. In order to understand the potential externalities of the decision to get circumcised we randomize the fraction of students within classrooms who get offered this treatment (0%, 50% and 100%). We find evidence of peer effects given that untreated students in 50% Treatment classrooms were 3.8 percentage points (79%) more likely to get circumcised than students in No Treatment classrooms. We also provide evidence of important reinforcement effects in take-up when male circumcision is offered among close friends. Our research design to study the complementarities of these interventions is based on the randomized allocation of the different mix of interventions across classrooms. We find limited evidence of complementarities among the three interventions. (JEL: C93, I12) ∗We wish to thank Douglas Almond, Miguel Urquiola, Matthew Neidell, Prabhjot Singh as well as seminar participants at Columbia University, Georgetown University, and Cornell University. We also thank Jinho Kim, Taeksoo Kim, Hanyoun So, and all members of Project Malawi for their excellent fieldwork. We are grateful to Youngsim Baek and Susie Kim for their support and cooperation in the field. This project is supported by Korea International Cooperation Agency (KOICA) and Africa Future Foundation (AFF). All views expressed are ours, and all errors are our own. †bkim@kdischool.ac. kr, KDI School of Public Policy and Management, Sejong, Republic of Korea ‡hk788@cornell.edu, Department of Policy Analysis and Management, Cornell University, Ithaca, NY 14835. §cp2124@columbia.edu, School of International and Public Affairs, Columbia University, New York, NY, 10027.
QUANTIFICATION OF HEMODYNAMIC CHANGES INDUCED BY VIRTUAL PLACEMENT OF MULTIPLE STENTS ACROSS A WIDE‐NECKED BASILAR TRUNK ANEURYSM

OBJECTIVEThe porous intravascular stents that are currently available may not cause complete aneurysm thrombosis and may therefore fail to provide durable protection against aneurysm rupture when used as a sole treatment modality. The goal of this study was to quantify the effects of porous stents on aneurysm hemodynamics using computational fluid dynamics. METHODSThe geometry of a wide-necked saccular basilar trunk aneurysm was reconstructed from a patient's computed tomographic angiography images. Three commercial stents (Neuroform2; Boston Scientific/Target, San Leandro, CA; Wingspan; Boston Scientific, Fremont, CA; and Vision; Guidant Corp., Santa Clara, CA) were modeled. Various combinations of one to three stents were virtually conformed to fit into the vessel lumen and placed across the aneurysm orifice. An unstented aneurysm served as a control. Computational fluid dynamics analysis was performed to calculate the hemodynamic parameters considered important in aneurysm pathogenesis and thrombosis for each of the models. RESULTSThe complex flow pattern observed in the unstented aneurysm was suppressed by stenting. Stent placement lowered the wall shear stress in the aneurysm, and this effect was increased by additional stent deployment. Turnover time was moderately increased after single- and double-stent placement and markedly increased after three stents were placed. The influence of stent design on hemodynamic parameters was more significant in double-stented models than in other models. CONCLUSIONAneurysm hemodynamic parameters were significantly modified by placement of multiple stents. Because the associated modifications may be helpful as well as harmful in terms of rupture risk, use of this technique requires careful consideration.
A Survey on MapReduce Scheduling in Cloud Computing

A large-scale data processing is increasingly leveraging Map Reduce frameworks on Cloud computing platform. We aimed to study various job schedulers improved in Map Reduce, and identify research directions in this area. In this paper, the related techniques of Map Reduce and Hodoop are described briefly. Then a variety of Map Reduce schedulers are reviewed and classified, also the features of these schedulers are expressed.
Effects of composition and processing variables on the oxidative stability of protein-based and oil-in-water food emulsions

ABSTRACT Because many common foods are emulsions (mayonnaise, coffee creamers, salad dressing, etc.), a better understanding of lipid oxidation mechanisms in these systems is crucial for the formulation, production, and storage of the relevant consumer products. A research body has focused on the microstructural and oxidative stability of protein-stabilized oil-in-water emulsions that are structurally similar to innovative products that have been recently developed by the food industry (e.g., non-dairy creams, vegetable fat spreads, etc.) This review presents recent findings about the factors that determine the development of lipid oxidation in emulsions where proteins constitute the stabilizing interface. Emphasis is given to “endogenous” factors, such as those of compositional (e.g., protein/lipid phases, pH, presence of transition metals) or processing (e.g., temperature, droplet size) nature. Improved knowledge of the conditions that favor the oxidative protection of protein in emulsions can lead to their optimized use as food ingredients and thereby improve the organoleptic and nutritional value of the related products.