Miracle-dz/UniFAR-FTUs huggingface dataset:
Absolute quantification of Medicago truncatula sucrose synthase isoforms and N-metabolism enzymes in symbiotic root nodules and the detection of novel nodule phosphoproteins by mass spectrometry

Mass spectrometry (MS) has become increasingly important for tissue specific protein quantification at the isoform level, as well as for the analysis of protein post-translational regulation mechanisms and turnover rates. Thanks to the development of high accuracy mass spectrometers, peptide sequencing without prior knowledge of the amino acid sequence—de novo sequencing—can be performed. In this work, absolute quantification of a set of key enzymes involved in carbon and nitrogen metabolism in Medicago truncatula ‘Jemalong A17’ root nodules is presented. Among them, sucrose synthase (SuSy; EC 2.4.1.13), one of the central enzymes in sucrose cleavage in root nodules, has been further characterized and the relative phosphorylation state of the three most abundant isoforms has been quantified. De novo sequencing provided sequence information of a so far unidentified peptide, most probably belonging to SuSy2, the second most abundant isoform in M. truncatula root nodules. TiO2-phosphopeptide enrichment led to the identification of not only a phosphorylation site at Ser11 in SuSy1, but also of several novel phosphorylation sites present in other root nodule proteins such as alkaline invertase (AI; EC 3.2.1.26) and an RNA-binding protein.
The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

The draft genome and transcriptome sequences of the wild potato species S. commersonii demonstrate the usefulness of genome sequences from wild relatives for elucidating evolutionary mechanisms contributing to Solanum species diversity and understanding changes in response to cold. Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.
Impact of an Educational Program about Pregnancy Induced Hypertension for Maternity Nurses on their performance and Pregnancy Outcomes for Mothers and Neonates

Background: Pregnancy induced hypertension (PIH) is connected with unfriendly results on neonatal, maternal dismalness and mortality. it is a standout amongst the most widely recognized reasons of both maternal and neonatal dismalness, influencing around 5 – 10 % of pregnant ladies Objective: This study aimed to evaluate the effect of educational program about pregnancy induced hypertension on performance of maternity nurse's and Pregnancy outcomes for mother and neonates Methodology: The study design was quasi-experimental. This study was done in the inpatient (obstetric and gynecological division) at three legislative healing facilities situated in Port Said city. Questioner surveys were utilized to catch demographic information, obstetric history and maternal and fetal confusions. observation checklist for nurses performance. The subjects of the study includes 2groups as the followings: convenience sample of 30 nurses who work in Port Said Hospitals and all inpatient women diagnosed with PIH who attended during the period of the program conduction (20 women). Results: The outcomes uncovered that there was a change in the medical attendants' abilities in giving nursing consideration to a patient with pregnancy-induced hypertension patients. Additionally, a factually noteworthy change for both to the moms and newborn outcomes receiving educational program implementation. Conclusion: Educational program for nurses working in maternity unit showed great impact on their performance with mothers suffering from PIH. With the perspective of the impact of the educational program on maternal and fetal and newborn health conditions . It was particularly obvious in the lower of blood pressure, proteinuria, and prenatal and postnatal complications. Similarly, neonatal outcomes were statistically significant improvement in the mothers group receiving nursing care after nursing educational program implementation as regards newborn measurements, and prenatal and postnatal complications. Recommendations: Future research regarding study factors affecting women with PIH self care practices, further studies related to mothers health problems that have an impact on neonate health, their growth and development should be investigated.
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results.
Andean and Tibetan patterns of adaptation to high altitude

High‐altitude hypoxia, or decreased oxygen levels caused by low barometric pressure, challenges the ability of humans to live and reproduce. Despite these challenges, human populations have lived on the Andean Altiplano and the Tibetan Plateau for millennia and exhibit unique circulatory, respiratory, and hematological adaptations to life at high altitude. We and others have identified natural selection candidate genes and gene regions for these adaptations using dense genome scan data. One gene previously known to be important in cellular oxygen sensing, egl nine homolog 1 (EGLN1), shows evidence of positive selection in both Tibetans and Andeans. Interestingly, the pattern of variation for this gene differs between the two populations. Continued research among Tibetan populations has identified statistical associations between hemoglobin concentration and single nucleotide polymorphism (SNP) genotype at EGLN1 and a second gene, endothelial PAS domain protein 1 (EPAS1).
Predictive Density Construction and Accuracy Testing with Multiple Possibly Misspecified Diffusion Models

This paper develops tests for comparing the accuracy of predictive densities derived from (possibly misspecified) diffusion models. In particular, we first outline a simple simulation-based framework for constructing predictive densities for one-factor and stochastic volatility models. We then construct tests that are in the spirit of Diebold and Mariano (1995) and White (2000). In order to establish the asymptotic properties of our tests, we also develop a recursive variant of the nonparametric simulated maximum likelihood estimator of Fermanian and Salanie (2004). In an empirical illustration, the predictive densities from several models of the one-month federal funds rates are compared.
Weight Cycling Increases T-Cell Accumulation in Adipose Tissue and Impairs Systemic Glucose Tolerance

Obesity is one of the leading causes of morbidity in the U.S. Accumulation of proinflammatory immune cells in adipose tissue (AT) contributes to the development of obesity-associated disorders. Weight loss is the ideal method to counteract the negative consequences of obesity; however, losses are rarely maintained, leading to bouts of weight cycling. Fluctuations in weight have been associated with worsened metabolic and cardiovascular outcomes; yet, the mechanisms explaining this potential correlation are not known. For determination of whether weight cycling modulates AT immune cell populations, inflammation, and insulin resistance, mice were subjected to a diet-switch protocol designed to induce weight cycling. Weight-cycled mice displayed decreased systemic glucose tolerance and impaired AT insulin sensitivity when compared with mice that gained weight but did not cycle. AT macrophage number and polarization were not modulated by weight cycling. However, weight cycling did increase the number of CD4+ and CD8+ T cells in AT. Expression of multiple T helper 1–associated cytokines was also elevated subsequent to weight cycling. Additionally, CD8+ effector memory T cells were present in AT of both obese and weight-cycled mice. These studies indicate that an exaggerated adaptive immune response in AT may contribute to metabolic dysfunction during weight cycling.
The Organization of the Cytoskeleton During Meiosis in Eggplant (Solanum Melongena (L.)): Microtubules and F-Actin are Both Necessary for Coordinated Meiotic Division

Address for reprints Because two division planes form at right angles, male meiosis in higher plants provides striking examples of both division control and spatial programming. To investigate these processes we have stained microtubules and actin filaments during male meiosis in the eggplant. Our results indicate the following. (1) That microtubules and their nucleation sites are involved in the establishment of polarity; this is supported by our observation that the drug CIPC affects spindle polarity. (2) That actin microfilaments are involved in spindle formation and integrity, but not in the establishment of polarity: cytochalasin B and D affect the organization of the spindle microtubules, but not their polarized distribution. (3) That microtubules radiating from the daughter nuclei at the cell poles during interkinesis probably establish the future division plane by concentrating actin in that plane (cf. the proposed role of asters in positioning the contractile ring in animal cells). (4) That this concentration of F-actin in the division plane may be involved in preparing the cytoplasm for cytokinesis and in memorizing the division plane (much as the preprophase band observed in polarized tissues does). (5) That phragmoplast formation is a two-step process. No phragmoplast forms after metaphase I, but a four-way phragmoplast forms after metaphase II, indicating that mitosis and cytokinesis are not obligatorily coupled. These studies demonstrate that actin and microtubules are jointly involved in the spatial coordination of the division process.
Community-Based Research as a Mechanism to Reduce Environmental Health Disparities in American Indian and Alaska Native Communities

Racial and ethnic minority communities, including American Indian and Alaska Natives, have been disproportionately impacted by environmental pollution and contamination. This includes siting and location of point sources of pollution, legacies of contamination of drinking and recreational water, and mining, military and agricultural impacts. As a result, both quantity and quality of culturally important subsistence resources are diminished, contributing to poor nutrition and obesity, and overall reductions in quality of life and life expectancy. Climate change is adding to these impacts on Native American communities, variably causing drought, increased flooding and forced relocation affecting tribal water resources, traditional foods, forests and forest resources, and tribal health. This article will highlight several extramural research projects supported by the United States Environmental Protection Agency (USEPA) Science to Achieve Results (STAR) tribal environmental research grants as a mechanism to address the environmental health inequities and disparities faced by tribal communities. The tribal research portfolio has focused on addressing tribal environmental health risks through community based participatory research. Specifically, the STAR research program was developed under the premise that tribal populations may be at an increased risk for environmentally-induced diseases as a result of unique subsistence and traditional practices of the tribes and Alaska Native villages, community activities, occupations and customs, and/or environmental releases that significantly and disproportionately impact tribal lands. Through a series of case studies, this article will demonstrate how grantees—tribal community leaders and members and academic collaborators—have been addressing these complex environmental concerns by developing capacity, expertise and tools through community-engaged research.
Sarcoma Derived from Cultured Mesenchymal Stem Cells

To study the biodistribution of MSCs, we labeled adult murine C57BL/6 MSCs with firefly luciferase and DsRed2 fluorescent protein using nonviral Sleeping Beauty transposons and coinfused labeled MSCs with bone marrow into irradiated allogeneic recipients. Using in vivo whole‐body imaging, luciferase signals were shown to be increased between weeks 3 and 12. Unexpectedly, some mice with the highest luciferase signals died and all surviving mice developed foci of sarcoma in their lungs. Two mice also developed sarcomas in their extremities. Common cytogenetic abnormalities were identified in tumor cells isolated from different animals. Original MSC cultures not labeled with transposons, as well as independently isolated cultured MSCs, were found to be cytogenetically abnormal. Moreover, primary MSCs derived from the bone marrow of both BALB/c and C57BL/6 mice showed cytogenetic aberrations after several passages in vitro, showing that transformation was not a strain‐specific nor rare event. Clonal evolution was observed in vivo, suggesting that the critical transformation event(s) occurred before infusion. Mapping of the transposition insertion sites did not identify an obvious transposon‐related genetic abnormality, and p53 was not overexpressed. Infusion of MSC‐derived sarcoma cells resulted in malignant lesions in secondary recipients. This new sarcoma cell line, S1, is unique in having a cytogenetic profile similar to human sarcoma and contains bioluminescent and fluorescent genes, making it useful for investigations of cellular biodistribution and tumor response to therapy in vivo. More importantly, our study indicates that sarcoma can evolve from MSC cultures.
The Contingent Effects of Management Support and Task Interdependence On Successful IS Implementation: A Meta-Analysis

The literature reports inconsistent findings for the effect of management support on the successful implementation of information systems innovations. This study proposes a contingent model that begins to explain this variance in the extant research findings. Conducting a meta-analysis of the IS implementation literature, we show, as hypothesized, that task interdependence moderates the effect of management support on implementation success and that there is no main effect of management support on implementation success. The implications for theory and practice are discussed.
A Multivariate Investigation of Postpartum Mood Disturbance

The interrelationships of ‘blues' and later postpartum depression with a number of biochemical, medical, and psychosocial variables have been examined in 52 subjects. The two syndromes shared only an impressive association with a prior history of gynaecological problems. Puerperal ‘blues' was characterised in addition by associations with primiparity, tearfulness during pregnancy, and reduced plasma total tryptophan in the early Puerperium. Depressive symptomatology up to nine months postpartum was related to an excess of male births and to an altered pattern of decline of non-esterified fatty acids immediately postpartum. In each case, the ‘risk’ variables were statistically independent and combined linearly. Stepwise discriminant analysis successfully discriminated ‘blues' and depression from their respective non-cases. ‘Blues and postpartum depression were only weakly related and, apart from gynaecological history, each was associated with separate and independent causative factors.
Effects of therapy cushions on classroom behaviors of children with autism spectrum disorder.

OBJECTIVE We investigated the effects of therapy cushions on the in-seat and on-task behaviors of 2 kindergarten students with autism spectrum disorder during math activities. METHOD We used a single-subject A-B-A-B-C design across 2 male participants who used chairs during baseline phases (A) and cushions during intervention phases (B). We included a choice phase (C) to determine participant seating preferences. Social validity was addressed by assessing teacher and participant seating preferences. Data were graphed and visually analyzed for functionally relevant changes between phases. RESULTS No clinically relevant changes in the in-seat or on-task behaviors of either participant were observed with cushion use. CONCLUSION. Therapy cushions may not impose sufficient postural demands or provide adequate sensory input to produce behavioral changes. Continued research in this area is needed.
Investigation on dislocation-based mechanisms of void growth and coalescence in single crystal and nanotwinned nickels by molecular dynamics simulation

Abstract Molecular dynamics simulations were conducted to elucidate dislocation mechanisms of the void growth and coalescence in single crystal and nanotwinned nickels subjected to uniaxial tension. The simulation results reveal that twin boundary is capable of decreasing the critical stress, suppressing the emission of dislocations and reducing the overall stiffness of the crystal. A size-scale dependence of critical stress is definitely illustrated through stress–strain response, where the larger void size leads to the lower critical stress and strain. It is the successive emissions of leading partials and the subsequent trailing partials that cause the atoms on the void surfaces to escape from the void surfaces continually, and consequently the voids grow to be larger and larger with increasing strain. The voids in the nanotwinned nickel coalesce earlier than those in the single crystal nickel even though the initiation of dislocations in the former is later than that in the latter. Void fraction remains a constant during elastic deformation, while it presents a linear increase with increasing strain during plastic deformation. Evolution of void fraction during void growth and coalescence is independent on void size.
Energy balance approach to shear band propagation in shear-blade tests

Progressive and catastrophic failure in soils has been commonly associated with the phenomenon of the shear band propagation. This paper is an attempt to validate the energy balance approach to modeling of the propagation of a two-dimensional, circular shaped shear band. This shear band can be observed in a shear blade test, performed in the novel shear-blade apparatus. The simplified analytical solution obtained in this paper is based on the fracture mechanics energy balance and the limiting equilibrium approaches. FLAC has been chosen as a standard FD tool to explore and compare numerical with experimental and analytical approaches. Comparison of results from different approaches provides an insight into the complex domain of modeling shear band propagation in soils.
Improved Constraints on the Neutral Intergalactic Hydrogen Surrounding Quasars at Redshifts z > 6

We analyze the evolution of H II regions around the seven known SDSS quasars at z > 6. The comparison between the observed and model radii of the H II regions generated by these quasars individually suggests that the surrounding intergalactic hydrogen is significantly neutral. When all constraints are combined, the existing quasar sample implies a volume-averaged neutral fraction that is larger than 10% at z > 6. This limited sample permits a preliminary analysis of the correlations between the quasar parameters, the sizes of their H II regions, and the associated constraints on the neutral hydrogen fraction. We find no evidence in these correlations to contradict the interpretation that the red side of the Gunn-Peterson trough corresponds to the boundary between an H II region and a partially neutral IGM.
Comparing Support Vector Machines with Gaussian Kernels to Radial Basis Function Classi

The Support Vector (SV) machine is a novel type of learning machine, based on statistical learning theory, which contains polynomial classi ers, neural networks, and radial basis function (RBF) networks as special cases. In the RBF case, the SV algorithm automatically determines centers, weights and threshold such as to minimize an upper bound on the expected test error. The present study is devoted to an experimental comparison of these machines with a classical approach, where the centers are determined by k{means clustering and the weights are found using error backpropagation. We consider three machines, namely a classical RBF machine, an SV machine with Gaussian kernel, and a hybrid system with the centers determined by the SV method and the weights trained by error backpropagation. Our results show that on the US postal service database of handwritten digits, the SV machine achieves the highest test accuracy, followed by the hybrid approach. The SV approach is thus not only theoretically well{founded, but also superior in a practical application. Copyright c Massachusetts Institute of Technology, 1996 This report describes research done at the Center for Biological and Computational Learning, the Arti cial Intelligence Laboratory of the Massachusetts Institute of Technology, and at AT&T Bell Laboratories (now AT&T Research, and Lucent Technologies Bell Laboratories). Support for the Center is provided in part by a grant from the National Science Foundation under contract ASC{9217041. BS thanks the M.I. T. for hospitality during a three{week visit in March 1995, where this work was started. At the time of the study, BS, CB, and VV were with AT&TBell Laboratories, NJ; KS, FG, PN, and TP were with the Massachusetts Institute of Technology. KS is now with the Department of Information Systems and Computer Science at the National University of Singapore, Lower Kent Ridge Road, Singapore 0511; CB and PN are with Lucent Technologies, Bell Laboratories, NJ; VV is with AT&T Research, NJ. BS was supported by the Studienstiftung des deutschen Volkes; CB was supported by ARPA under ONR contract number N00014-94-C-0186. We thank A. Smola for useful discussions. Please direct correspondence to Bernhard Scholkopf, bs@mpik-tueb.mpg. de, Max{Planck{Institut f ur biologische Kybernetik, Spemannstr. 38, 72076 T ubingen, Germany. Figure 1: A simple 2{dimensional classi cation problem: nd a decision function separating balls from circles. The box, as in all following pictures, depicts the region [ 1; 1].