Miracle-dz/UniFAR-FTUs huggingface dataset:
DIACYLGLYCEROL ACYLTRANSFERASE1 Contributes to Freezing Tolerance1[OPEN]

ACYL-COA:DIACYLGLYCEROL ACYLTRANSFERASE1 confers freezing tolerance, and its expression and activity could underlie adaptive variation in freezing tolerance in Boechera stricta, a wild relative of Arabidopsis thaliana. Freezing limits plant growth and crop productivity, and plant species in temperate zones have the capacity to develop freezing tolerance through complex modulation of gene expression affecting various aspects of metabolism and physiology. While many components of freezing tolerance have been identified in model species under controlled laboratory conditions, little is known about the mechanisms that impart freezing tolerance in natural populations of wild species. Here, we performed a quantitative trait locus (QTL) study of acclimated freezing tolerance in seedlings of Boechera stricta, a highly adapted relative of Arabidopsis (Arabidopsis thaliana) native to the Rocky Mountains. A single QTL was identified that contained the gene encoding ACYL-COENZYME A:DIACYLGLYCEROL ACYLTRANSFERASE1 (BstDGAT1), whose expression is highly cold responsive. The primary metabolic enzyme DGAT1 catalyzes the final step in assembly of triacylglycerol (TAG) by acyl transfer from acyl-CoA to diacylglycerol. Freezing tolerant plants showed higher DGAT1 expression during cold acclimation than more sensitive plants, and this resulted in increased accumulation of TAG in response to subsequent freezing. Levels of oligogalactolipids that are produced by SFR2 (SENSITIVE TO FREEZING2), an indispensable element of freezing tolerance in Arabidopsis, were also higher in freezing-tolerant plants. Furthermore, overexpression of AtDGAT1 led to increased freezing tolerance. We propose that DGAT1 confers freezing tolerance in plants by supporting SFR2-mediated remodeling of chloroplast membranes.
Inquiry‐based learning as a ‘whole‐curriculum approach’: the experiences of first‐year nursing students

Anglia Polytechnic University implemented inquiry-based learning (IBL) as a ‘whole-curriculum’ strategy for preregistration nursing education, primarily to avoid the possibility of educational dissonance within a mixed methodology approach. An evaluation strategy was put in place to provide stakeholders with information about process and outcomes. Set against the context of this wider evaluation, this report presents some of the findings of interviews with 15 student representatives as they completed their first year of the IBL programme. The key issues identified concerned adaptation to the IBL process and learning within small groups. This evaluation offers a unique insight into the student experience within an IBL curriculum. The evaluation has enabled the course team to make pertinent modifications to both the programme and student support mechanisms and may provide other educators with pointers for their own curriculum development and implementation.
MtNODULE ROOT1 and MtNODULE ROOT2 Are Essential for Indeterminate Nodule Identity1[OPEN]

The loss of function of MtNOOT1 and MtNOOT2 leads to the complete loss of nodule identity, prevents the symbiotic process, and results in the absence of nitrogen fixation in Medicago truncatula. Symbiotic interactions between legume plants and rhizobia result in the formation of nitrogen-fixing nodules, but the molecular actors and the mechanisms allowing for the maintenance of nodule identity are poorly understood. Medicago truncatula NODULE ROOT1 (MtNOOT1), Pisum sativum COCHLEATA1 (PsCOCH1), and Lotus japonicus NOOT-BOP-COCH-LIKE1 (LjNBCL1) are orthologs of Arabidopsis (Arabidopsis thaliana) AtBLADE-ON-PETIOLE1/2 and are members of the NBCL gene family, which has conserved roles in plant development and is essential for indeterminate and determinate nodule identity in legumes. The loss of function of MtNOOT1, PsCOCH1, and LjNBCL1 triggers a partial loss of nodule identity characterized by the development of ectopic roots arising from nodule vascular meristems. Here, we report the identification and characterization of a second gene involved in regulating indeterminate nodule identity in M. truncatula, MtNOOT2. MtNOOT2 is the paralog of MtNOOT1 and belongs to a second legume-specific NBCL subclade, the NBCL2 clade. MtNOOT2 expression was induced during early nodule formation, and it was expressed primarily in the nodule central meristem. Mtnoot2 mutants did not present any particular symbiotic phenotype; however, the loss of function of both MtNOOT1 and MtNOOT2 resulted in the complete loss of nodule identity and was accompanied by drastic changes in the expression of symbiotic, defense, and root apical meristem marker genes. Mtnoot1 noot2 double mutants developed only nonfixing root-like structures that were no longer able to host symbiotic rhizobia. This study provides original insights into the molecular basis underlying nodule identity in legumes forming indeterminate nodules.
Red blood cell metabolic responses to refrigerated storage, rejuvenation, and frozen storage

Storage of red blood cells (RBCs) under blood bank conditions promotes metabolic modulation within the RBC. This “metabolic storage lesion” may affect the quality and safety of the transfused RBCs. The aim of this study is to determine the metabolic changes in stored RBCs over 42 days of routine storage followed by a US Food and Drug Administration‐approved method of rejuvenation, freezing, and preparation for transfusion.
Follow-up of Adult Participants in Drug Education Courses

A follow-up study of former participants in drug education courses at the National Drug Education Center in Oklahoma was conducted using a mail questionnaire with 41 % return. Almost all respondents reported that the course had been helpful, and 62 % were working in drug education or treatment programs. From one-fourth to one-third of the respondents had decreased or stopped using caffeine, tobacco, and alcohol following the course. The courses were also effective in reordering the respondents’ perspectives of drug use and abuse. Sixty-eight percent expressed a desire for a follow-up course to up-date their knowledge or to acquire additional skills.
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

MOTIVATION In 2001 and 2002, we published two papers (Bioinformatics, 17, 282-283, Bioinformatics, 18, 77-82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST.
MIASTENIA GRAVIS: EMBARAZO E IMPACTO PERINATAL

SUMMARY A total of 19 pregnancies in 9 patients with myasthenia gravis are analyzed. Two exacerbations of myasthenia gravis were observed. One associated to the use of aminoglycosides to treat an acute pyelonephritis. A debut of myasthenia gravis occurred during the 24th week of gestation. There were three cases of neonatal myasthenia gravis that appeared in the same patient, two newborn died after 29 and 25 days respectively, in spite of treatment. One case of preterm childbirth was observed and six cases (35%) of intrauterine growth retardation.
Modeling immune system control of atherogenesis

MOTIVATION Atherosclerosis is a disease that is present in almost all humans, typically beginning in early adolescence. It is a human disease broadly investigated, that is amenable to quantitative analysis. Oxidized low-density lipoproteins (LDLs) and their autoantibodies are involved in the development of atherosclerosis in animal models, but their role in humans is still not clear. Computer models may represent a virtual environment to perform experiments not possible in human volunteers that can provide a useful instrument for monitoring both the evolution of atherosclerotic lesions and to quantify the efficacy of treatments, including vaccines, oriented to reduce the LDLs and their oxidized fraction. RESULTS We report the application of an agent-based model to model both the immune response to atherogenesis and the atheromatous plaque progression in a generic artery wall. The level of oxidized LDLs, the immune humoral response with production of autoantibodies, the macrophages activity and the formation of foam cells are in good agreement with available clinical data, including the formation of atheromatous plaques in patients affected by hypercholesterolemia. AVAILABILITY The model is available at http://www.immunogrid. eu/atherogenesis/
The NGATHA Distal Organ Development Genes Are Essential for Style Specification in Arabidopsis[W]

Floral organ identities are specified by a few transcription factors that act as master regulators. Subsequently, specification of organ axes programs the distribution of distinct tissue types within the organs that themselves develop unique identities. The C-class, AGAMOUS-clade MADS box genes are primary promoters of the gynoecium, which is divided into a distal style and a subtending ovary along the apical-basal axis. We show that members of a clade of B3 domain transcription factors, NGATHA1 (NGA1) to NGA4, are expressed distally in all lateral organs, and all four have a redundant and essential role in style development. Loss of all four genes results in gynoecia where style is replaced by valve-like projections and a reduction in style-specific SHATTERPROOF1 (SHP1) expression. In agreement, floral misexpression of NGA1 promotes ectopic style and SHP1 expression. STYLISH1, an auxin biosynthesis inducer, conditionally activated NGA genes, which in turn promoted distal expression of other STY genes in a putative positive feedback loop. Inhibited auxin transport or lack of YABBY1 gene activities resulted in a basally expanded style domain and broader expression of NGA genes. We speculate that early gynoecium factors delimit NGA gene response to an auxin-based signal, elicited by STY gene activity, to restrict the activation of style program to a late and distal carpel domain.
Model-based analysis of interferon-beta induced signaling pathway

MOTIVATION Interferon-beta induced JAK-STAT signaling pathways contribute to mucosal immune recognition and an anti-viral state. Though the main molecular mechanisms constituting these pathways are known, neither the detailed structure of the regulatory network, nor its dynamics has yet been investigated. The objective of this work is to build a mathematical model for the pathway that would serve two purposes: (1) to reproduce experimental results in simulation of both early and late response to Interferon-beta stimulation and (2) to explain experimental phenomena generating new hypotheses about regulatory mechanisms that cannot yet be tested experimentally. RESULTS Experimentally determined time dependent changes in the major components of this pathway were used to build a mathematical model describing pathway dynamics in the form of ordinary differential equations. The experimental results suggested existence of unknown negative control mechanisms that were tested numerically using the model. Together, experimental and numerical data show that the epithelial JAK-STAT pathway might be subjected to previously unknown dynamic negative control mechanisms: (1) activation of dormant phosphatases and (2) inhibition of nuclear import of IRF1.
Low doses of bisphenol a induce gene expression related to lipid synthesis and trigger triglyceride accumulation in adult mouse liver

Changes in lifestyle are suspected to have strongly influenced the current obesity epidemic. Based on recent experimental, clinical, and epidemiological work, it has been proposed that some food contaminants may exert damaging effects on endocrine and metabolic functions, thereby promoting obesity and associated metabolic diseases such as nonalcoholic fatty liver disease (NAFLD). In this work, we investigated the effect of one suspicious food contaminant, bisphenol A (BPA), in vivo. We used a transcriptomic approach in male CD1 mice exposed for 28 days to different doses of BPA (0, 5, 50, 500, and 5,000 μg/kg/day) through food contamination. Data analysis revealed a specific impact of low doses of BPA on the hepatic transcriptome, more particularly on genes involved in lipid synthesis. Strikingly, the effect of BPA on the expression of de novo lipogenesis followed a nonmonotonic dose‐response curve, with more important effects at lower doses than at the higher dose. In addition to lipogenic enzymes (Acc, Fasn, Scd1), the expression of transcription factors such as liver X Receptor, the sterol regulatory element binding protein‐1c, and the carbohydrate responsive element binding protein that govern the expression of lipogenic genes also followed a nonmonotonic dose‐response curve in response to BPA. Consistent with an increased fatty acid biosynthesis, determination of fat in the liver showed an accumulation of cholesteryl esters and of triglycerides. Conclusion: Our work suggests that exposure to low BPA doses may influence de novo fatty acid synthesis through increased expression of lipogenic genes, thereby contributing to hepatic steatosis. Exposure to such contaminants should be carefully examined in the etiology of metabolic diseases such as NAFLD and nonalcoholic steatohepatitis. (Hepatology 2012)
Piezocision-assisted canine distalization

An increasing number of adult patients are seeking orthodontic treatment to improve their smile or their masticatory function. One of the biggest challenges an adult orthodontic patient faces is the time spent wearing brackets because time and esthetics have become increasingly important in this time. Over the years, several surgical techniques have been developed to address this issue and reduce overall treatment time. Although very effective, these techniques have proven to be quite invasive. A new, minimally invasive surgical procedure [piezocision] is presented in this case report that combines microincisions and localized piezoelectric surgery to achieve similar results rapidly and with minimal trauma.
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data

MOTIVATION High-throughput protein interaction data, with ever-increasing volume, are becoming the foundation of many biological discoveries, and thus high-quality protein-protein interaction (PPI) maps are critical for a deeper understanding of cellular processes. However, the unreliability and paucity of current available PPI data are key obstacles to the subsequent quantitative studies. It is therefore highly desirable to develop an approach to deal with these issues from the computational perspective. Most previous works for assessing and predicting protein interactions either need supporting evidences from multiple information resources or are severely impacted by the sparseness of PPI networks. RESULTS We developed a robust manifold embedding technique for assessing the reliability of interactions and predicting new interactions, which purely utilizes the topological information of PPI networks and can work on a sparse input protein interactome without requiring additional information types. After transforming a given PPI network into a low-dimensional metric space using manifold embedding based on isometric feature mapping (ISOMAP), the problem of assessing and predicting protein interactions is recasted into the form of measuring similarity between points of its metric space. Then a reliability index, a likelihood indicating the interaction of two proteins, is assigned to each protein pair in the PPI networks based on the similarity between the points in the embedded space. Validation of the proposed method is performed with extensive experiments on densely connected and sparse PPI network of yeast, respectively. Results demonstrate that the interactions ranked top by our method have high-functional homogeneity and localization coherence, especially our method is very efficient for large sparse PPI network with which the traditional algorithms fail. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions in PPI networks. AVAILABILITY MATLAB code implementing the algorithm is available from the web site http://home.ustc. edu.cn/∼yzh33108/Manifold.htm.
Branched-chain amino acid supplemented diet during maternal food restriction prevents developmental hypertension in adult rat offspring

Maternal food restriction is known to cause developmental hypertension in offspring. We have previously shown that maternal high-protein diet can reverse fetal programming of hypertension and that branched-chain amino acid (BCAA) concentrations in maternal and fetal plasma were increased by maternal high-protein intake. Then, we hypothesized that isocaloric supplementation with BCAA to a maternal food restriction can reverse the adverse outcome. Pregnant rats were divided into four groups at 7.5 days postcoitum: normally nourished (NN) and 70% undernourished (UN) groups with and without BCAA supplementation (NN–standard diet (SD), NN–BCAA, UN–SD and UN–BCAA groups). Compared with pups in the NN groups, those in the UN–SD group had significantly increased systolic blood pressure (SBP) at 8 and 16 weeks of age (P < 0.05). However, the elevation of SBP was not observed in offspring in the UN–BCAA group. Offspring glomeruli number of the UN groups was significantly lower (P < 0.05) than that of the NN groups, independent of BCAA supplementation. Angiotensin II receptor type 2 (ATR2) mRNA and protein expression in the kidney was significantly augmented in the UN–BCAA group at 30 weeks of age. In conclusion, BCAA supplementation during maternal food restriction prevents developmental hypertension together with increased ATR2 expression in adult offspring kidney.
Snapshot of Pharmacy Faculty Quality of Work Life and Productivity

ABSTRACTWhile much has been written about various aspects of pharmacy faculty quality of work life and productivity, there have been very few empiric investigations into these related phenomena. The purpose of this study was to provide an initial examination into a broad range of quality of work life and related issues among pharmacy faculty and compare their perceptions across a number of individual and institutional characteristics. A self-administered, anonymous survey was e-mailed to pharmacy faculty with a valid e-mail address listed by the American Association of Colleges of Pharmacy in 2005. The survey elicited responses on various single and multi-item measures of productivity, quality of work life, and demographic variables. Responding faculty reported only modest levels of commitment, satisfaction, and support, with relatively high consensus among department colleagues on a number of teaching and research issues. Faculty indicated areas of teaching and research in which they currently have the l.
Central nervous system disease in pediatric acute myeloid leukemia: A report from the Children's Oncology Group

The prognostic impact of central nervous system (CNS) involvement in children with acute myeloid leukemia (AML) has varied in past trials, and controversy exists over the degree of involvement requiring intensified CNS therapy. Two recent Children's Oncology Group protocols, AAML03P1 and AAML0531, directed additional intrathecal (IT) therapy to patients with CNS2 (≤5 white blood cell [WBC] with blasts) or CNS3 (>5 WBC with blasts or CNS symptoms) disease at diagnosis.
Detection of C4d‐fixing HLA antibodies in serum – a glass half full and half empty

Research efforts dedicated to provide new diagnostic and therapeutic modalities via better understanding of antibody-mediated (humoral) immune responses dominate the current era of transplantation medicine. The implementation of sensitive solid-phase assays for detection of donor specific anti-HLA antibodies (DSA) in serum together with immunohistochemical detection of complement degradation product C4d in transplant biopsies were most remarkable developments [1,2]. Assays based on single-antigen beads (SAB) or the so called Luminex technology also became broadly accepted because of their high sensitivity [3]. However, the specificity issue of DSAs detected by SAB and their clinical relevance are amatter of continuous debate in the transplant community [4]. Complement-mediated mechanisms are considered as important effectors of HLA-DSA-related pathology in the allograft [5]. Complement binding IgG1 and IgG3 HLA-DSA isotypes initiate the classic complement pathway via binding to C1q. Activated C1q subsequently activates its natural substrate C4 and other down-stream components ultimately leading to target cell lysis and death [5]. Complement fixation in the tissue as detected by C4d, a split product of C4 became a routine diagnostic modality in transplant pathology worldwide [2]. Considering the important role of complement activation, a logical next step is to refine assays for detection of HLA antibodies in serum to better define which circulating HLA-DSA are capable to bind complement and are potentially detrimental. The development of assays for detection of C1q or C4d HLA-DSA binding capability in serum in combination with Luminex technology could enhance immunologic risk stratification [6,7]. B€ ohmig and associates were first to establish a flowcytometry-based assay which allows for solid-phase detection of HLA antibody-triggered complement (split) product deposition [8]. The assay was further refined bymeans of Luminex-based SAB technology for identification of complementfixing DSA [9]. Similar developments were attempted for C1q and results of first studies were reported [10].
Prospective evaluation of quality of life in children treated in UKALL 2003 for acute lymphoblastic leukaemia: A cohort study

Health‐related quality of life (HRQoL) from diagnosis until end of treatment for children with acute lymphoblastic leukaemia was investigated, examining effects of age, gender, risk‐stratified treatment regimen, and therapy intensity (one vs. two ‘delayed intensifications’ [DIs]).
Periconceptional undernutrition suppresses cortisol response to arginine vasopressin and corticotropin-releasing hormone challenge in adult sheep offspring

Poor maternal nutrition during pregnancy can result in increased disease risk in adult offspring. Many of these effects are proposed to be mediated via altered hypothalamo–pituitary–adrenal axis (HPAA) function, and are sex and age specific. Maternal undernutrition around the time of conception alters HPAA function in foetal and early postnatal life, but there are limited conflicting data about later effects. The aim of this study was to investigate the effect of moderate periconceptional undernutrition on HPAA function of offspring of both sexes longitudinally, from juvenile to adult life. Ewes were undernourished from 61 days before until 30 days after conception or fed ad libitum. HPAA function in offspring was assessed by arginine vasopressin plus corticotropin-releasing hormone challenge at 4, 10 and 18 months. Plasma cortisol response was lower in males than in females, and was not different between singles and twins. Periconceptional undernutrition suppressed offspring plasma cortisol but not adrenocorticotropic hormone responses. In males, this suppression was apparent by 4 months, and was more profound by 10 months, with no further change by 18 months. In females, suppression was first observed at 10 months and became more profound by 18 months. Maternal undernutrition limited to the periconceptional period has a prolonged, sex-dependent effect on adrenal function in the offspring.