Miracle-dz/UniFAR-FTUs huggingface dataset:
Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0-1

Pyrenophora teres f. teres, the causal agent of net form net blotch (NFNB) of barley, is a destructive pathogen in barley-growing regions throughout the world. Typical yield losses due to NFNB range from 10 to 40%; however, complete loss has been observed on highly susceptible barley lines where environmental conditions favor the pathogen. Currently, genomic resources for this economically important pathogen are limited to a fragmented draft genome assembly and annotation, with limited RNA support of the P. teres f. teres isolate 0-1. This research presents an updated 0-1 reference assembly facilitated by long-read sequencing and scaffolding with the assistance of genetic linkage maps. Additionally, genome annotation was mediated by RNAseq analysis using three infection time points and a pure culture sample, resulting in 11,541 high-confidence gene models. The 0-1 genome assembly and annotation presented here now contains the majority of the repetitive content of the genome. Analysis of the 0-1 genome revealed classic characteristics of a “two-speed” genome, being compartmentalized into GC-equilibrated and AT-rich compartments. The assembly of repetitive AT-rich regions will be important for future investigation of genes known as effectors, which often reside in close proximity to repetitive regions. These effectors are responsible for manipulation of the host defense during infection. This updated P. teres f. teres isolate 0-1 reference genome assembly and annotation provides a robust resource for the examination of the barley–P. teres f. teres host–pathogen coevolution.
Molecular Diversity of Rhizobia Occurring on Native Shrubby Legumes in Southeastern Australia

ABSTRACT The structure of rhizobial communities nodulating native shrubby legumes in open eucalypt forest of southeastern Australia was investigated by a molecular approach. Twenty-one genomic species were characterized by small-subunit ribosomal DNA PCR-restriction fragment length polymorphism and phylogenetic analyses, among 745 rhizobial strains isolated from nodules sampled on 32 different legume host species at 12 sites. Among these rhizobial genomic species, 16 belonged to the Bradyrhizobium subgroup, 2 to theRhizobium leguminosarum subgroup, and 3 to the Mesorhizobium subgroup. Only one genomic species corresponded to a known species (Rhizobium tropici). The distribution of the various genomic species was highly unbalanced among the 745 isolates, legume hosts, and sites.Bradyrhizobium species were by far the most abundant, andRhizobium tropici dominated among the Rhizobiumand Mesorhizobium isolates in the generally acid soils where nodules were collected. Although a statistically significant association occurred between the eight most common genomic species and the 32 hosts, there was sufficient overlap in distributions that no clear specificity between rhizobial genomic species and legume taxa was observed. However, for three legume species, some preference for particular genomic species was suggested. Similarly, no geographical partitioning was found.
The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids This work was supported by Lilly Research Laboratories. Published, JLR Papers in Press, December 15, 2008.

Phospholipids are subjected to remodeling through the Lands cycle to attain appropriate FA compositions. In recent years, at least two families of lysophospholipid acyltransferases have been identified. Acyl-CoA lysocardiolipin acyltransferase 1 (ALCAT1) was initially identified as a microsomal lysocardiolipin acyltransferase. However, the physiological relevance of how this enzyme is involved in cardiolipin remodeling has not been elucidated. We report in this study that ALCAT1 possesses acyltransferase activities toward lysophosphatidylinositol (LPI) and lysophosphatidylglycerol (LPG). Membrane preparations from human embryonic kidney 293 (HEK293) cells overexpressing human ALCAT1 demonstrated significant increases in LPI acyltransferase (LPIAT) and LPG acyltransferase (LPGAT) activities using a variety of fatty acyl-CoAs. The enzyme affinities toward LPI and LPG were determined through kinetic studies suggesting that the LPI binding affinity to ALCAT1 depends on fatty acyl-CoA. Reduced expression of ALCAT1 in Hela cells resulted in significant reductions of LPIAT and LPGAT activities, but not ALCAT activity. Through structural and functional studies, we have identified critical amino acids D168 and L169 within ALCAT1 that are potentially involved in lysophospholipid substrate binding. Our studies provide the molecular basis for future investigations of the physiological function of ALCAT1 and offer evidence of critical amino acids involved in substrate binding for the family of glycerolipid acyltransferases.
The Politics of the Globalization of Law : Getting from Rights to Justice

1. The Politics of the Globalization of Law Alison Brysk and Arturo Jimenez-Bacardi Part I: The Globalization of Law And Human Rights 2. Treaties, Constitutions, and Courts: The Critical Combination Wayne Sandholtz 3. The International Criminal Court: Globalizing peace or justice? Tony Smith and Antonio Gonzalez 4. Global diffusion and the role of courts in shaping the human right to vote Ludvig Beckman 5. From Pirates to Pinochet: universal jurisdiction for torture Mark Berlin 6. Courts, advocacy groups, and human rights in Europe Rachel Cichowski Part II: Hard cases: from rights to justice? 7. The Power and Limits of International Law: Challenging the Bush Administration's Extra-Legal Detention System Arturo Jimenez-Bacardi 8. States of emergency vs. courts in Latin America Claire Wright 9. Law, rights, and barriers in the Israel-Palestine conflict Gershon Shafir 10. Non-state actors as violators in Mexico: A hard case for global human rights Alejandro Anaya 11. Extraordinary laws and torture in India in an era of globalization Jinee Lookaneeta
Time optimal attitude control of 3D pendulum

3D pendulum is a rigid body supported at a fixed pivot with three rotational degrees of freedom. The objective is to maneuver the 3D pendulum from an initial attitude and angular rate to a desired attitude and angular rate in minimum time in presence of uniform gravity, subjected to constraints on the control input. We derive the necessary conditions for time optimality for a 3D pendulum by formulating a discrete-time optimal control problem using a Lie group variational integrator. The approach does not use local parameterizations (like Euler angles or quaternion) for attitude representation but necessary conditions for optimality are derived directly on the special orthogonal group. Further, discrete-time, time optimal attitude control satisfying the necessary conditions is computed using geometrically exact technique on special orthogonal group, such that it preserves the geometric properties of a rigid body.
Birth weight, adulthood BMI, and subsequent weight gain in relation to leptin levels in Swedish women.

OBJECTIVE Leptin seems to be involved in the regulation of energy balance, although little is known about the epidemiology of leptin with respect to prediction of weight gain and incidence of obesity-related diseases. The dual aim of this study is to document characteristics of leptin after long-term storage, and to describe its relation to body weight, from birth to old age, in an ongoing prospective study. RESEARCH METHODS AND PROCEDURES A population-based sample of Swedish women was first examined at the ages of 38 to 60 and re-examined 24 years later. This study used 1358 frozen serum samples that had been stored 29 years for analysis of leptin concentrations and their relation to body weight history. RESULTS Leptin values obtained from stored samples showed the same correlation with relative weight as that seen in a contemporary sample with similar demographic characteristics. Lower self-reported birth weight was associated with higher leptin levels in adulthood (p = 0.01), controlling for age and adult BMI. Prospective analyses revealed that high leptin in 38 to 46-year-olds predicted subsequent long-term weight gain (p = 0.003), although no significant associations were seen in women initially aged 50 or older. DISCUSSION It is feasible to use frozen serum for studying leptin in relation to obesity and related developments many years later. High leptin level was a risk factor for subsequent weight gain in 38- and 46-year-old women. Retrospective analyses involving birth weight suggest that leptin resistance in adulthood might have fetal origins.
Focal segmental sclerotic lesions of the glomerulus in transplanted kidneys assessed using computerized image analysis

Abstract: Mechanisms responsible for the development of focal segmental sclerotic lesions of the glomerulus (FSGS lesions) in transplanted kidneys were investigated by morphometric analysis. The mean glomerular area and the interstitial area were measured using computerized image analysis to compare implantation biopsies (so‐called 1‐h biopsies; 1Bx) with later biopsies (episode Bx; EBx) that had been taken for diagnostic purposes to identify the cause of deteriorating renal function. Groups of patients with (group A, n = 15) or without (group B, n = 10) FSGS lesions were compared. Twelve of 15 in group A and all in group B had lost graft function due to chronic allograft nephropathy. It was found that neither the mean glomerular area nor the interstitial area differed significantly between the two groups in either 1Bx or EBx. The interstitial area was significantly increased (P = 0.007) and the mean glomerular area tended to be increased (P = 0.085) in EBx compared with 1Bx in group A but not in group B. The serum creatinine level at the time of EBx in group A correlated with the interstitial area (P = 0.031) but not the mean glomerular area. However, there was no similar correlation in group B. In conclusion, factors for the development of FSGS lesions in transplanted kidneys may be the increase in interstitial area and possible glomerular hypertrophy following transplantation, rather than pre‐existing reduced renal mass of the donor kidneys.
Social justice and low carbon development

The shift to low carbon development implies winners and losers. This chapter explores some of the different dimensions and interpretations of equity and social justice in the context of climate change and development. It initially examines the dominant application of social justice through the lens of equity within global mitigation agreements. Using examples drawn from Ghana’s low carbon development planning processes, the chapter then demonstrates how greater attention is required to the consideration of social justice in decision making and implementation of low carbon development at national level.
Calculative and collaborative HRM practices, turnover and performance

Purpose The purpose of this paper is to study the human resource management (HRM)–performance linkage by exploring alternative relationships between different HRM practices, categorised as either calculative or collaborative, and employee turnover and organisational and financial outcomes, in Uruguayan multinational companies (MNCs) and domestic companies, to better understand the implications of the Latin American context in this relationship. Design/methodology/approach The study is performed at the firm level, using data from a representative sample of 274 firms, including both multinationals and locally owned firms in Uruguay, collected through the Cranet 2009 survey. The authors tested the hypotheses of the proposed model using structural equation modelling (SEM) and hierarchical multiple regression analysis. Findings Empirical results show that collaborative HRM practices are significantly related to lower employee turnover rates, whereas calculative HRM practices are significantly associated with higher organisational and financial outcomes. These findings show the importance of the Latin American context in the relationships between HRM practices and firms’ outcomes. Research limitations/implications The use of survey data with single respondents might produce reliability problems. Additionally, the data used are cross-sectional, making it difficult to determine causality. Practical implications Managers in MNCs and local firms in the context of developing economies and Latin American cultures must be aware that different types of HRM practices will influence different outputs and impacts on overall outcomes. Originality/value The paper examines the extent to which HRM practices have a significant relationship with firm performance. In addition, it identifies the differential effects of calculative and collaborative HRM practices on performance, using data from a Latin American contextual setting rarely examined, in order to determine similarities and differences from results obtained in US and European contexts.
The costs of falls in the community to the North East Ambulance Service

Background: This study set out to quantify the immediate costs to the North East Ambulance Service (NEAS) of attending to fallers. Methods: Data from the Newcastle, UK area were collated by NEAS to identify those aged over 65 who had fallen and required an assistance only call or were subsequently transported to an Accident and Emergency (A&E) department. The 2001 census data for the total population served by NEAS in Newcastle were obtained. Results: The total population of Newcastle over the age of 65 was 41 338. Over 7 months NEAS attended to 1504 falls in Newcastle (at £115 per call out, this equates to £172 960). The faller was transported to A&E on 1339 occasions, while 165 falls required assistance only (11% of total) (36 falls requiring NEAS assistance per 1000 Newcastle population aged over 65 in 7 months). The total time on site for ambulance crews attending to fallers was 377.1 h (15.7 days in 7 months or 2.25 days per month). As the cost of emergency ambulance time is £123/h, the total cost was £46 383.30. Therefore, in Newcastle, attending to fallers in the community costs NEAS £376 018 per year (£145.83 per fall or £9.10 per person over the age of 65 per year). Conclusion: NEAS attend to a significant number of older people who fall in the community. In Newcastle alone the cost of this service equates to over 2 days of emergency ambulance crew time per month. Studies are needed to determine whether responding to falls in the community differently would be cost effective.
Gene expression in response to glyphosate treatment in fleabane (Conyza bonariensis) - glyphosate death response and candidate resistance genes.

BACKGROUND This study takes a whole-transcriptome approach to assess gene expression changes in response to glyphosate treatment in glyphosate-resistant fleabane. We assessed gene expression changes in both susceptible and resistant lines so that the glyphosate death response could be quantified, and constitutively expressed candidate resistance genes identified. There are three copies of the glyphosate target site (5-enolpyruvylshikimate-3-phosphate; EPSPS) gene in Conyza and because Conyza bonariensis is allohexaploid, there is a baseline nine copies of the gene in any individual. RESULTS Many genes were differentially expressed in response to glyphosate treatment. Known resistance mutations are present in EPSPS2 but they are present in a glyphosate-susceptible line as well as resistant lines and therefore not sufficient to confer resistance. EPSPS1 is expressed four times more than EPSPS2, further reducing the overall contribution of these mutations. CONCLUSION We demonstrate that glyphosate resistance in C. bonariensis is not the result of EPSPS mutations or overexpression, but due to a non-target-site mechanism. A large number of genes are affected by glyphosate treatment. We present a list of candidate non-target-site-resistance (NTSR) genes in fleabane for future studies into these mechanisms. © 2017 Society of Chemical Industry.
Serum hepcidin is associated with parameters of glucose metabolism in women with gestational diabetes mellitus

Abstract Objectives: Hepcidin is considered a major regulator of iron metabolism. Despite previous studies showing elevated ferritin and hepcidin levels in type 2 diabetes mellitus (DM), no study has investigated hepcidin levels in pregnant women with gestational DM (GDM). Methods: A case-control study was conducted in 30 cases of GDM, 47 pregnant women with impaired glucose tolerance (IGT) and 72 pregnant women with normal glucose tolerance (control) between April 2009 and July 2011. Serum hepcidin and other iron metabolism parameters were analyzed in all groups. Results: Serum ferritin and serum iron were significantly elevated in the GDM group compared to controls (p = 0.014, p = 0.018, respectively) and to the IGT group (p = 0.021, p = 0.008, respectively). Hepcidin levels were elevated significantly in the diabetic patients compared to the IGT group (p = 0.011) and controls (p = 0.002). We found no correlation between hepcidin and other iron metabolism parameters (Hb, serum iron and ferritin), whereas positive correlations were found between hepcidin and parameters of glucose metabolism (fasting blood glucose, fasting insulin level and glucose value response to glucose challenge test). Conclusions: Serum hepcidin concentrations were increased in pregnant women with IGT and GDM and this was not related to inflammation parameters.
Dengue Disease Spectrum among Infants in the 2001 Dengue Epidemic in Chennai, Tamil Nadu, India

ABSTRACT An investigation in a referral pediatric hospital has indicated that during a recent dengue outbreak in Chennai, Tamil Nadu, India, dengue in infancy constituted 20% of total dengue virus infections with low mortality rates in this hospital. In developing countries, strengthening of dengue management capabilities at hospitals can prevent dengue-related deaths in infants.
Identification of Social Responsibility Factors within Mega Construction Projects

Mega construction projects create buildings and major infrastructure to respond to work and life requirements while playing a vital role in promoting any nation’s economy. However, the industry is often criticised for not balancing economic, environmental and social dimensions of their projects, with emphasis typically on one aspect to the detriment of the others. This has resulted in many negative impacts including environmental pollution, waste throughout the project lifecycle, low productivity, and avoidable accidents. The identification of comprehensive Social Responsibility (SR) indicators, which combine social, environmental and economic aspects, is urgently needed. This is particularly the case in the context of the Kingdom of Saudi Arabia (KSA), which often has mega public construction projects. The aim of this paper is to develop a set of wide-ranging SR indicators which encompass social, economic and environmental aspects unique to the KSA. A qualitative approach was applied to explore relevant indicators through a review of the existing literature, international standards and reports. A list of appropriate indicators was developed, and its comprehensiveness was corroborated by interviews with experts on mega construction projects working with SR concepts in the KSA. The findings present 39 indicators and their metrics, covering 10 economic, 12 environmental and 17 social aspects of SR mapped against their references. These indicators are a valuable reference for decisionmakers and academics in the KSA to understand factors related to SR in mega construction projects. The indicators are related to mega construction projects within the KSA and require validation in a real case scenario or within a different industry to demonstrate their generalisability.
An assessment of salmon farms and wild salmonids as sources of Lepeophtheirus salmonis (Krøyer) copepodids in the water column in Loch Torridon, Scotland.

Wild salmonids and farmed salmon can both be sources of Lepeophtheirus salmonis (Krøyer, 1838) larvae. Farmed salmon smolts free of L. salmonis infections are stocked in sea cages and may subsequently contract L. salmonis infections, probably from wild fish. The contribution of gravid L. salmonis at Atlantic salmon, Salmo salar L. , farms to populations of L. salmonis larvae in the water column has in the past been based on estimated parameters, such as louse fecundity. This present study augments these calculations by combining empirical data on densities of infective L. salmonis copepodids in the field with estimates of the number of gravid L. salmonis on farmed and wild salmonids in Loch Torridon. Data collected between 2002 and 2007 show a significant correlation between mean densities of L. salmonis copepodids recovered in the water column and the numbers of gravid L. salmonis at the local salmon farms. Generally, the farms with greatest numbers of salmon were observed to have stronger correlations with densities of copepodids in the water than the farms with fewer fish. The study suggests that louse management approaches, e.g. treatment trigger levels, need to take account of individual farm biomass, or numbers of fish. This study highlights the importance of control of L. salmonis on salmon farms for the co-existence of both wild salmonid populations and the aquaculture industry.
Restless legs syndrome‐associated MEIS1 risk variant influences iron homeostasis

Restless legs syndrome (RLS) is a frequent sleep disorder that is linked to disturbed iron homeostasis. Genetic studies identified MEIS1 as an RLS‐predisposing gene, where the RLS risk haplotype is associated with decreased MEIS1 mRNA and protein expression. We show here that RNA interference treatment of the MEIS1 worm orthologue increases ferritin expression in Caenorhabditis elegans and that the RLS‐associated haplotype leads to increased expression of ferritin and DMT1 in RLS brain tissues. Additionally, human cells cultured under iron‐deficient conditions show reduced MEIS1 expression. Our data establish a link between the RLS MEIS1 gene and iron metabolism. Ann Neurol 2011;
Dividend Policies and Business Groups: the Case of Croatia

Abstract There are two competing hypothesizes on whether firms that are part of a business group should pay higher or lower dividends. Under one hypothesis, that can have different theoretical assumptions, firms that are a part of a business group should pay higher dividends. In contrast, if the pecking order hypothesis holds, firms that operate within a business group should pay lower dividends. The purpose of this paper is to examine the effect of group affiliation of Croatian firms, which are listed on the Zagreb Stock Exchange, on their propensity to pay dividends. Two panel data models were used in line with recent literature and the results of the study show some evidence that the pecking order theory was followed by Croatian firms. From this result the conclusion is that Croatian firms are more likely to pay dividends if they are not part of a business group.