Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Genomic Loci Associated with the Photochemical Reflectance Index by Genome‐Wide Association Study in Soybean

The photochemical reflectance index (PRI) is determined from canopy spectral reflectance measurements and can provide important information about photosynthesis. The PRI can be used to assess the epoxidation state of xanthophyll pigments, which provides information on nonphotochemical quenching (NPQ) and the amount of energy used for photosynthesis. Genome‐wide association analyses were conducted to identify single‐nucleotide polymorphisms (SNPs) and genomic loci associated with PRI using data from a soybean [Glycine max (L.) Merr. ] diversity panel grown under field conditions over 2 yr. Based on a mixed linear model (MLM), 31 unique candidate SNPs that identify 15 putative loci on 11 chromosomes were identified. Several candidate genes known to be associated with NPQ, photosynthesis, and sugar transport processes were identified in the proximity of 10 putative loci. Violaxanthin de‐epoxidase, one of the identified genes, is directly involved in the xanthophyll cycle, which plays a major role in NPQ. This study is the first to identify genomic loci for PRI and illustrates the potential of canopy spectral reflectance measurements for high‐throughput phenotyping of a photosynthesis related trait. Significant SNPs, candidate genes, and genotypes contrasting for PRI identified in this study may prove useful for crop improvement efforts.
Treatment results among tuberculosis patients treated by private lung specialists involved in a public-private mix project in Vietnam.

SETTING Ho Chi Minh City, Vietnam. OBJECTIVES To determine treatment outcome among patients treated by private lung specialists in a public-private mix (PPM) project for improved TB control. METHODS Cohorts of patients treated by private lung specialists within the PPM project and in National Tuberculosis Programme (NTP) facilities were followed for up to 12 months. The quality of case management and treatment outcome was determined based on information in treatment cards. As a complement, questionnaire surveys of private providers (PPs) and patients and focus group discussions with PPs were conducted. RESULTS Among 400 patients treated by PPs, 36 different treatment regimens were used. Directly observed treatment was not used at all, and treatment evaluation with sputum smear microscopy and health education was inadequate. Overall treatment success was 60% and the default rate was 37%, which was considerably worse than in NTP facilities. CONCLUSION This PPM project, which used a combination of training, supervision, standardised referral and information system and financial incentives, did not achieve sufficiently good treatment outcome by PPs. Possible reasons for the poor outcome include absence of subsidisation of drug costs and lack of regulatory enforcement.
Inhibitory TCR Coreceptor PD-1 Is a Sensitive Indicator of Low-Level Replication of SIV and HIV-1

Ongoing antigenic stimulation appears to be an important prerequisite for the persistent expression of programmed death 1 (PD-1), an inhibitory TCR coreceptor of the CD28 family. Although recent publications have emphasized the utility of PD-1 as a marker for dysfunctional T cells in chronic viral infections, its dependence on antigenic stimulation potentially renders it a sensitive indicator of low-level viral replication. To explore the antigenic threshold for the maintenance of PD-1 expression on virus-specific T cells, we compared PD-1 expression on virus-specific and memory T cell populations in controlled and uncontrolled SIV and HIV-1 infection. In both controlled live attenuated SIV infection in rhesus macaques and HIV-1 infection in elite controllers, elevated levels of PD-1 expression were observed on SIV- and HIV-1–specific CD8+ T cells. However, in contrast to chronic wild-type SIV infection and uncontrolled HIV-1 infection, controlled SIV/HIV-1 infection did not result in increased expression of PD-1 on total memory T cells. PD-1 expression on SIV-specific CD8+ T cells rapidly decreased after the emergence of CTL escape in cognate epitopes, but was maintained in the setting of low or undetectable levels of plasma viremia in live attenuated SIV-infected macaques. After inoculation of naive macaques with a single-cycle SIV, PD-1 expression on SIV-specific CD8+ T cells initially increased, but was rapidly downregulated. These results demonstrate that PD-1 can serve as a sensitive indicator of persistent, low-level virus replication and that generalized PD-1 expression on T lymphocytes is a distinguishing characteristic of uncontrolled lentiviral infections.
AIDS: Calcification of the basal ganglia in infants and children

CT or postmortem examination demonstrated calcification of the basal ganglia in eight infants and children with acquired immune deficiency syndrome. Serial CT studies documented progression of both bilateral symmetric calcium densities and cerebral atrophy. Clinical features included progressive encephalopathy with dementia, and pyramidal tract signs. Postmortem examination of four children revealed variable degrees of calcific vasopathy of the basal ganglia, involving predominantly the putamen and globus pallidus.
VALIDATION AND USE OF AN INDIRECT ENZYME-LINKED IMMUNOSORBENT ASSAY FOR DETECTION OF ANTIBODIES TO WEST NILE VIRUS IN AMERICAN ALLIGATORS (ALLIGATOR MISSISSIPPIENSIS) IN FLORIDA

In October 2002, West Nile virus (WNV) was identified in farmed American alligators (Alligator mississippiensis) in Florida showing clinical signs and having microscopic lesions indicative of central nervous system disease. To perform seroepidemiologic studies, an indirect enzyme-linked immunosorbent assay (ELISA) was developed to determine exposure of captive and wild alligators to WNV. To validate the test, a group of WNV-seropositive and -seronegative alligators were identified at the affected farm using hemagglutination inhibition (HAI) and the plaque reduction neutralization test (PRNT). The indirect ELISA utilized a rabbit anti-alligator immunoglobulins polyclonal antibody as the secondary antibody, and inactivated WNV-infected Vero cells were used as the coating antigen. For all samples (n=58), the results of the ELISA were consistent with the HAI and PRNT findings. Plasma was collected from 669 free-ranging alligators from 21 sites across Florida in April and October 2003. Four samples collected in April and six in October were positive for WNV antibodies using HAI, PRNT, and the indirect ELISA. This indicated that wild alligators in Florida have been exposed to WNV. These findings can be used as a baseline for future surveys.
Board Characteristics, Compliance, and Firm Performance: Empirical Findings from Colombia

Abstract Using data from a single database of Colombian firms, we confirmed an endogenous relationship between specific board characteristics, compliance with corporate governance guidelines, and firm performance. A board comprising experts without conflicts of interest is more likely to control ethical behavior, implement audit committees, review compliance with accepted accounting standards, and approve and control the firm’s strategic planning, all of which will lead to an improvement in firm results, and engagement and retention of higher quality board members. Conclusions have strong implications for public policy and managerial practice.
Association of Enterohemorrhagic Escherichia coliHemolysin with Serotypes of Shiga-Like-Toxin-ProducingEscherichia coli of Human and Bovine Origins

ABSTRACT In this study we investigated whether the enterohemorrhagicEscherichia coli (EHEC) hemolysin gene ehxAcould be used as an indicator of pathogenicity in Shiga-like-toxin-producing Escherichia coli (SLTEC) isolates. The isolates in a collection of 770 SLTEC strains of human and bovine origins were assigned to group 1 (230 human and 138 bovine SLTEC isolates belonging to serotypes frequently implicated in human disease), group 2 (85 human and 183 bovine isolates belonging to serotypes less frequently implicated in disease), and group 3 (134 bovine isolates belonging to serotypes not implicated in disease). PCR amplification was used to examine all of the SLTEC isolates for the presence of ehxA and the virulence-associated geneseae, slt-I, and slt-II. The percentages of human isolates in groups 1 and 2 that were positive forehxA were 89 and 46%, respectively, and the percentages of bovine isolates in groups 1 to 3 that were positive forehxA were 89, 51, and 52%, respectively. The percentages of human isolates in groups 1 and 2 that were positive foreae were 92 and 27%, respectively, and the percentages of bovine isolates in groups 1 to 3 that were positive for eaewere 78, 15, and 19%, respectively. The frequencies of bothehxA and eae were significantly higher for group 1 isolates than for group 2 isolates. The presence of the ehxA gene was associated with serotype, as was the presence of the eae gene. Some serotypes, such as O117:H4, lacked both eae and ehxA and have been associated with severe disease, but only infrequently. Theslt-I genes were more frequent in group 1 isolates than in group 2 isolates, and the slt-II genes were more frequent in group 2 isolates than in group 1 isolates. In a second experiment we determined the occurrence of the ehxA andslt genes in E. coli isolated from bovine feces. Fecal samples from 175 animals were streaked onto washed sheep erythrocyte agar plates. Eight E. coli-like colonies representing all of the morphological types were transferred to MacConkey agar. A total of 1,080 E. coli isolates were examined, and the ehxA gene was detected in 12 independent strains, only 3 of which were positive for slt. We concluded that the ehxA gene was less correlated with virulence than the eae gene was and that EHEC hemolysin alone has limited value for screening bovine feces for pathogenic SLTEC because of presence of the ehxA gene in bovine isolates that are not SLTEC.
Role of phospholipase C in Dictyostelium: formation of inositol 1,4,5‐trisphosphate and normal development in cells lacking phospholipase C activity.

The micro‐organism Dictyostelium uses extracellular cAMP to induce chemotaxis and cell differentiation. Signals are transduced via surface receptors, which activate G proteins, to effector enzymes. The deduced protein sequence of Dictyostelium discoideum phosphatidylinositol‐specific phospholipase C (PLC) shows strong homology with the mammalian PLC‐delta isoforms. To study the role of PLC in Dictyostelium, a plc‐ mutant was constructed by disruption of the PLC gene. No basal or stimulated PLC activity could be measured during the whole developmental programme of the plc‐ cells. Loss of PLC activity did not result in a visible alteration of growth or development. Further analysis showed that developmental gene regulation, cAMP‐mediated chemotaxis and activation of guanylyl and adenylyl cyclase were normal. Although the cells lack PLC activity, inositol 1,4,5‐trisphosphate [Ins(1,4,5)P3] was present at only slightly lower concentrations compared with control cells. Mass analysis of inositol phosphates demonstrated the presence of a broad spectrum of inositol phosphates in Dictyostelium, which was unaltered in the plc‐ mutant. Cell labelling experiments with [3H]inositol indicated that [3H]Ins(1,4,5)P3 was formed in a different manner in the mutant than in control cells.
Explanation of the limited correlation between tumor CA 125 content and serum CA 125 antigen levels in patients with ovarian tumors

The concentration of the tumor marker CA 125 in tumor tissue, cyst fluid, ascites fluid, and serum from patients with epithelial ovarian tumors was quantitated. Immunohistologic studies showed that CA 125 was present in 90% of the nonmucinous epithelial ovarian tumors. Quantitative analysis of the fluid from 57 cysts revealed that CA 125 was present in concentrations of up to 2140,000 U/ml in samples from malignant nonmucinous epithelial ovarian lesions, and up to 116,000 U/ml in mucinous tumors, but also in concentrations of up to 371,000 U/ml in benign serous cystadenomas. In contrast, pre‐operative serum CA 125 levels were elevated in almost all of the patients with malignant ovarian tumors but not in most of those with benign ovarian tumors. These findings suggest that in benign ovarian tumors there is an effective barrier between the cyst fluid and the circulation that prevents the appearance of CA 125 in the serum, whereas in malignant tumors infiltrative growth leads to the release of antigen into the circulation. Furthermore, CA 125 values in ascites fluids were up to 130 times higher than the serum antigen levels, which indicates that the peritoneum serves as a barrier for high molecular weight tumor antigens. The current results show that tumor basement membranes and peritoneal barriers play a notable role in the transit of tumor antigens, one which must be taken into account in the monitoring of serum marker levels of cancer patients.
Constructing Transnational Solidarity: The Role of Campaign Governance

Our inductive study of two transnational labour solidarity efforts focuses on the role of campaign governance. Specifically, we study contrasting campaign strategies, tactics and coalition structures in campaigns by two global union federations, UNI Global Union and the IUF, contextualized in terms of how these campaigns unfolded in India. Our contribution consists of two arguments. The first is that a degree of internal consistency amongst different campaign elements is important for success, and the second is that a mode of articulation that allows for local concerns in affiliate countries to find voice in global campaigns is more likely to result in concrete gains at the local level.
Use of oral corticosteroids in the community and the prevention of secondary osteoporosis: a cross sectional study

Abstract Objective: To determine the prevalence of continuous use of oral steroids in the general population, the conditions for which they are prescribed, and the extent to which patients taking oral steroids are taking treatment to prevent osteoporosis. Design: A cross sectional study with a four year retrospective review of drug treatment. Setting: Eight large general practices in central and southern Nottinghamshire. Subjects: A population of 65 786 patients (52% women) registered with a general practitioner during 1995. Results: 303 patients (65% (197) women) aged 12-94 years were currently taking “continuous” (for at least three months) oral corticosteroid treatment. This figure represents 0.5% of the total population and 1.4% (245/17 114) of patients aged 55 years or more (1.7% (166/9601) of women). The usual steroid was prednisolone (97% (294/303)), the mean dose was 8.0 mg/day, and the median duration of oral steroid treatment determined in 149 patients was three years. The most common conditions for which continuous oral steroids were prescribed were rheumatoid arthritis (23% (70)), polymyalgia rheumatica (22% (66)), and asthma or chronic obstructive airways disease (19% (59)). Only 41 (14%) of the 303 patients taking oral steroids had received treatment for the prevention of osteoporosis over the past four years. Although 37 of the 41 patients were women, only 10% (18/181) of the women over 45 years taking continuous oral corticosteroids were currently taking hormone replacement therapy. Conclusions: If our figures are typical then they suggest that over 250 000 people in the United Kingdom are taking continuous oral steroids and that most of these are taking no prophylaxis against osteoporosis. Key messages The prevalence of use of oral corticosteroids in a community based population of 65 786 was 0.5%, rising to 1.7% in women aged >/=55 years The main indications for oral steroids were rheumatoid arthritis, polymyalgia, and asthma or chronic obstructive pulmonary disease Only 14% of patients taking oral steroids had received any treatment to prevent or treat osteoporosis These data suggest that over a quarter of a million people in the United Kingdom are currently taking oral corticosteroids and hence at risk of adverse effects
Intrinsic tryptophans of CRABPI as probes of structure and folding

The native state fluorescence and CD spectra of the predominantly β‐sheet cellular retinoic acid‐binding protein I (CRABPI) include contributions from its three tryptophan residues and are influenced by the positions of these residues in the three‐dimensional structure. Using a combination of spectroscopic approaches and single Trp‐mutants of CRABPI, we have deconvoluted these spectra and uncovered several features that have aided in our analysis of the development of structure in the folding pathway of CRABPI. The emission spectrum of native CRABPI is dominated by Trp 7. Trp 109 is fluorescence‐silent due to its interaction with the guanidino group of Arg 111. Although the far‐UV CD spectrum of CRABPI is largely determined by the protein's secondary structure, aromatic clustering around Trp 87 and the aromatic‐charge interaction between Arg 111 and Trp 109 give rise to a characteristic feature in the CD spectrum at 228 nm. The near‐UV CD bands of CRABPI arise largely from additive contributions of the three tryptophan residues. Trp 7 and Trp 87 give a negative CD band at 275 nm. The near‐UV CD band from Trp 109 is positive and shifted to longer wavelengths (to 302 nm) due to the charge‐aromatic interaction between Arg 111 and Trp 109. Our deconvolution of the equilibrium spectra have been used to interpret kinetic folding experiments monitored by stopped‐flow fluorescence. These dynamic experiments suggest the early evolution of a well‐populated, hydrophobically collapsed intermediate, which undergoes global rearrangement to form the fully folded structure. The results presented here suggest several additional strategies for dissecting the folding pathway of CRABPI.
Evaluating the Welfare of Index Insurance

Index insurance was conceived to be a product that would simplify the claim settlement process and make it more objective, reducing transaction costs and moral hazard. However, index insurance also exposes the insured to basis risk, which arises because there can be a mismatch between the index measurement and the actual losses of the insured. It is not easy to predict the direction in which basis risk is going to affect insurance demand, in contrast to the clear and strong predictions for standard indemnity insurance products. Index insurance can be theoretically conceptualized as a situation in which the individual faces compound risk, where one layer of risk corresponds to the potential individual’s loss and the other layer of risk is created by the potential mismatch between the index measurement and the actual loss. Experimental evidence shows that people exhibit preferences for compound risks that are different from preferences exhibited for their actuarially-equivalent counterparts. We study the potential link between index insurance demand and attitudes towards compound risks. We test the hypothesis that the compound risk nature of index insurance induced by basis risk negatively affects both the demand for the product and the welfare of individuals making take-up decisions. We study the impact of basis risk on insurance take-up and on expected welfare in a laboratory experiment with an insurance frame. We measure the expected welfare of index insurance to individuals while accounting for their risk preferences, and structurally decompose the sources of the welfare effects of index insurance. Our results show that the compound risk in index insurance decreases the welfare of index insurance choices made by individuals. The behavioral inability to process compound risks decreases welfare when there is a compound risk of loss, whereas loss probability, basis risk and premium only impact the welfare of insurance choices when the risk of loss is expressed in its reduced, non-compound form. We also see, again, that take-up is not a reliable indicator of welfare. Furthermore, the drivers of increased welfare from index insurance are not be the same drivers of increased take-up, so take-up is not even a useful proxy for guiding policy to improve welfare.
Association of the CTLA-4 1722TC polymorphism and systemic lupus erythematosus: a systematic review and meta analysis

Background: Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) is an important negative regulator of Tcell responses. The -1722TC polymorphism of the CTLA-4 gene may be associated with systemic lupus erythematosus (SLE) risk, but related results from previous studies have been inconsistent. We carried out a metaanalysis to assess this association more precisely. Methods: A systematic search through PubMed, Science Direct, and OVID, Iran doc, Iranmedex and SID (Scientific Information Database) databases was performed with the last search updated on December 30, 2011. The odds of ratio (OR) and its 95% confidence interval (95%CI) were used to assess the strength of the association. We evaluated both fixed and random effect models, depending on the presence of between-study heterogeneity. The analyses were conducted using STATA software, version 11.0. Results: A total of 9 independent studies on the CTLA-4 gene -1722TC polymorphism and SLE, including 1422 cases and 1417 controls were used in this meta-analysis. In the present meta-analysis, we found a significant association between -1722TC polymorphism and SLE risk in the overall analysis (TT versus TC/CC: OR=1.18, 95%CI 0.84-1.66, p= 0.32; TT/TC versus CC: OR = 2.06, 95%CI 1.07–3.99, p= 0.03; TT versus CC: OR = 2.32, 95%CI 1.62–3.32, p< 0.001; TC versus CC: OR = 1.99, 95%CI 1.42–2.78, p<0.001; TT versus TC: OR = 1.2, 95%CI 0.86–1.66,p= 0.28; T versus C: OR = 1.22, 95%CI 0.91–1.64,p= 0.16). In the subgroup analysis by ethnicity, -1722TC polymorphism was significantly associated with SLE risk in Asian population. Conclusion: This meta-analysis suggests a significant association between -1722TC polymorphism and SLE susceptibility. Large-scale and well-designed case-control studies are necessary to validate the risk identified in the present meta-analysis.
Liquidity Resilience in the UK Gilt Futures Market: Evidence from the Order Book

We analyse liquidity dynamics in the UK long gilt futures market. We use a novel order book dataset to assess liquidity resilience to sources of pressure such as policy operations or episodes of financial distress. Our results provide evidence in favour of resilience. We further show that this resilience does not come at the expense of a negative liquidity trend. These findings mitigate the potential trade-off faced by policy makers such as regulators in maintaining an adequate level of liquidity in the UK long gilt futures market.
A novel missense mutation in SCYL1BP1 produces geroderma osteodysplastica phenotype indistinguishable from that caused by nullimorphic mutations

Effect of aging on decreased skin elasticity and bone mass is well known. Geroderma osteodysplastica (GO) is a very rare autosomal recessive disorder that recapitulates these two phenotypes at a much younger age. Using homozygosity mapping and linkage analysis in four Saudi families we have identified two mutations in SCYL1BP1, consistent with the very recent report by Hennies et al. [Hennies et al. (2008); Nat Genet 40: 1410–1412]. Interestingly, the missense mutation identified in our study is associated with an identical phenotype to that seen with the other null mutations including the other mutation in this study. Our study, therefore, supplements the limited available data on SCYL1BP1 and further establishes deficiency of this recently described golgin as the only known cause of GO. © 2009 Wiley‐Liss, Inc.