Miracle-dz/UniFAR-FTUs huggingface dataset:
Highlights on Novel Technologies for the Detection of Antibodies to Ro60, Ro52, and SS-B

Objective. We aimed to compare a chemiluminescent immunoassay (CIA, QUANTA Flash) on BIO-FLASH with a multiplex flow immunoassay (MFI) on BioPlex 2200 for the detection of antibodies to Ro60, Ro52, and SS-B. Methods. The study included 241 samples, from patients suffering from systemic autoimmune diseases (n = 108) as well as disease controls (n = 133). All samples were tested for anti-Ro52, anti-Ro60, and anti-SS-B (La) antibodies on QUANTA Flash (INOVA Diagnostics, San Diego, USA) and BioPlex 2200 (Bio-Rad Laboratories Inc., Hercules, USA). Discrepant samples were tested by two independent methods: BlueDot/ANA and QUANTRIX Microarray (both D-tek, Belgium). Results. The overall qualitative agreements were 95.4% (95% confidence interval, CI 92.0–97.7%) for anti-Ro52, 98.8% (95% CI 96.4–99.7%) for anti-Ro60, and 91.7% (95% CI 87.5–94.9%) for anti-SS-B antibodies. There were 34 discrepant samples among all assays (20 anti-SS-B, 11 anti-Ro52, 3 anti-Ro60). 30/33 of retested samples (by D-tek dot blot) agreed with the QUANTA Flash results. Similar findings were obtained with QUANTRIX Microarray kit. Conclusion. QUANTA Flash and BioPlex 2200 show good qualitative agreement. The clinical performances were similar for anti-Ro52 and anti-Ro60 autoantibodies while differences were observed for anti-SS-B (La) antibodies.
A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa

During sexual development, Neurospora crassa inactivates genes in duplicated DNA segments by a hypermutation process, repeat-induced point mutation (RIP). RIP introduces C:G to T:A transition mutations and creates targets for subsequent DNA methylation in vegetative tissue. The mechanism of RIP and its relationship to DNA methylation are not fully understood. Mutations in DIM-2, a DNA methyltransferase (DMT) responsible for all known cytosine methylation in Neurospora, does not prevent RIP. We used RIP to disrupt a second putative DMT gene in the Neurospora genome and tested mutants for defects in DNA methylation and RIP. No effect on DNA methylation was detected in the tissues that could be assayed, but the mutants showed recessive defects in RIP. Duplications of the am and mtr genes were completely stable in crosses homozygous for the mutated potential DMT gene, which we call rid (RIP defective). The same duplications were inactivated normally in heterozygous crosses. Disruption of the rid gene did not noticeably affect fertility, growth, or development. In contrast, crosses homozygous for a mutation in a related gene in Ascobolus immersus, masc1, reportedly fail to develop and heterozygous crosses reduce methylation induced premeiotically [Malagnac, F. , Wendel, B. , Goyon, C. , Faugeron, G. , Zickler, D. , et al. (1997) Cell 91, 281–290]. We isolated homologues of rid from Neurospora tetrasperma and Neurospora intermedia to identify conserved regions. Homologues possess all motifs characteristic of eukaryotic DMTs and have large distinctive C- and N-terminal domains.
Insensitivity of Chromosome I and the Cell Cycle to Blockage of Replication and Segregation of Vibrio cholerae Chromosome II

ABSTRACT Vibrio cholerae has two chromosomes (chrI and chrII) whose replication and segregation are under different genetic controls. The region covering the replication origin of chrI resembles that of the Escherichia coli chromosome, and both origins are under control of the highly conserved initiator, DnaA. The origin region of chrII resembles that of plasmids that have iterated initiator-binding sites (iterons) and is under control of the chrII-specific initiator, RctB. Both chrI and chrII encode chromosome-specific orthologs of plasmid partitioning proteins, ParA and ParB. Here, we have interfered with chrII replication, segregation, or both, using extra copies of sites that titrate RctB or ParB. Under these conditions, replication and segregation of chrI remain unaffected for at least 1 cell cycle. In this respect, chrI behaves similarly to the E. coli chromosome when plasmid maintenance is disturbed in the same cell. Apparently, no checkpoint exists to block cell division before the crippled chromosome is lost by a failure to replicate or to segregate. Whether blocking chrI replication can affect chrII replication remains to be tested. IMPORTANCE Chromosome replication, chromosome segregation, and cell division are the three main events of the cell cycle. They occur in an orderly fashion once per cell cycle. How the sequence of events is controlled is only beginning to be answered in bacteria. The finding of bacteria that possess more than one chromosome raises the important question: how are different chromosomes coordinated in their replication and segregation? It appears that in the evolution of the two-chromosome genome of V. cholerae, either the secondary chromosome adapted to the main chromosome to ensure its maintenance or it is maintained independently, as are bacterial plasmids. An understanding of chromosome coordination is expected to bear on the evolutionary process of chromosome acquisition and on the efficacy of possible strategies for selective elimination of a pathogen by targeting a specific chromosome. Chromosome replication, chromosome segregation, and cell division are the three main events of the cell cycle. They occur in an orderly fashion once per cell cycle. How the sequence of events is controlled is only beginning to be answered in bacteria. The finding of bacteria that possess more than one chromosome raises the important question: how are different chromosomes coordinated in their replication and segregation? It appears that in the evolution of the two-chromosome genome of V. cholerae, either the secondary chromosome adapted to the main chromosome to ensure its maintenance or it is maintained independently, as are bacterial plasmids. An understanding of chromosome coordination is expected to bear on the evolutionary process of chromosome acquisition and on the efficacy of possible strategies for selective elimination of a pathogen by targeting a specific chromosome.
The "fear factor" in critical care tele-pediatrics

How do emotions affect telemedicine adoption and usage for critical-care episodes? We report on early findings from a grounded theory approach in a multiple-case study of critical care telepediatrics (research in progress). Thus far our findings suggest that specialists believe that generalist clinicians at remote “spoke” hospitals are anxious and fearful when performing in a high stress crisis situation involving an acutely ill or gravely injured child, leading to tunneling of attention (overlooking important clinical details). The specialists at tertiary care “hub” hospitals feel they are able to keep an emotional distance from the situation and they also report feeling less anxious because they have had extensive training for these acute care situations. Both emotional distance and higher skill level seem to help the specialists to take in more clinically-relevant information and use this to guide the generalists. The generalists’ fear of negative evaluation by the specialists, or embarrassment in front of other clinicians, may have some impact on their decision to use tele-pediatrics, but does not seem to be a salient concern during critical care episodes. These findings suggest that emotions do play a role in telemedicine use and possibly also in other forms of technology-mediated interorganizational collaboration.
Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate

Reprogramming of cell identities during development frequently requires changes in the chromatin state that need to be restricted to the correct cell populations. Here we identify an auxin hormone-regulated chromatin state switch that directs reprogramming from transit amplifying to primordium founder cell fate in Arabidopsis inflorescences. Upon auxin sensing, the MONOPTEROS transcription factor recruits SWI/SNF chromatin remodeling ATPases to increase accessibility of the DNA for induction of key regulators of flower primordium initiation. In the absence of the hormonal cue, auxin sensitive Aux/IAA proteins bound to MONOPTEROS block recruitment of the SWI/SNF chromatin remodeling ATPases in addition to recruiting a co-repressor/histone deacetylase complex. This simple and elegant hormone-mediated chromatin state switch is ideally suited for iterative flower primordium initiation and orchestrates additional auxin-regulated cell fate transitions. Our findings establish a new paradigm for nuclear response to auxin. They also provide an explanation for how this small molecule can direct diverse plant responses. DOI: http://dx.doi. org/10.7554/eLife.09269. 001
Genetic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates in Hong Kong

Abstract Objectives To characterize 250 drug-resistant Mycobacterium tuberculosis (MTB) isolates in Hong Kong with respect to their drug susceptibility phenotypes to five common anti-tuberculosis drugs (ofloxacin, rifampicin, ethambutol, isoniazid and pyrazinamide) and the relationship between such phenotypes and the patterns of genetic mutations in the corresponding resistance genes (gyrA, rpoB, embB, katG, inhA, ahpC and pncA). Methods The MIC values of the aforementioned anti-tuberculosis drugs were determined for each of the 250 drug-resistant MTB clinical isolates by the absolute concentration method. Genetic mutations in the corresponding resistance genes in these MTB isolates were identified by PCR-single-stranded conformation polymorphism/multiplex PCR amplimer conformation analysis (SSCP/MPAC), followed by DNA sequencing of the purified PCR products. Results Resistance to four or five drugs was commonly observed in these MTB isolates; such phenotypes accounted for over 34% of the 250 isolates. The most frequently observed phenotypes were those involving both rifampicin and isoniazid, with or without additional resistance to the other drugs. A total of 102 novel mutations, which accounted for 80% of all mutation types detected in the 7 resistance genes, were recovered. Correlation between phenotypic and mutational data showed that genetic changes in the gyrA, rpoB and katG genes were more consistently associated with a significant resistance phenotype. Despite this, however, a considerable proportion of resistant MTB isolates were found to harbour no detectable mutations in the corresponding gene loci. Conclusions These findings expand the spectrum of potential resistance-related mutations in MTB clinical isolates and help consolidate the framework for the development of molecular methods for delineating the drug susceptibility profiles of MTB isolates in clinical laboratories.
Reversal of Focal "Misery‐Perfusion Syndrome" By Extra‐Intracranial Arterial Bypass in Hemodynamic Cerebral Ischemia: A Case Study with 15O Positron Emission Tomography

Tomogrephic images of cerebral blood flow (CBF) and oxygen extraction fraction (OEF) using the UO continuous inhalation technique, and positron emission tomography, were obtained from a patient with cerebral ischemia distal to an occluded left internal carotid artery. There was a focal mismatch between CBF and oxygen metabolism in the brain supplied by tbe middle cerebral artery where CBF was decreased and OEF increased ("misery-perfusion syndrome" as opposed to "luxury-perfusioa syndrome"). These abnormalities were most marked in tbe parieto-ocdpital watershed area. After left superficial temporal to middle cerebral artery anastomosis, the clinical attacks ceased and a repeat study did not demonstrate tbe prerious CBF and OEF abnormalities. This suggests that this pattern of abnormalities indicates potential liable tissue. The concept of "mlsery-perfuslon" may be of some importance In tbe patbophysiological mechanisms of hemodynamic cerebral ischemia and serve as a rational basis for rerascularization procedures. Stroke, Vol 12, No 4, 1981
Investor Interests and Government Accounting Disclosure

Analyses disclosure levels from annual reports and budgets from US municipalities, based on the expected incentives of municipal bond investors. Disclosure levels for both budgets and annual reports are variable, suggesting that the quality of disclosures may be based on key actor incentives. Results suggest that annual report disclosures (especially those found in the statistical section) are responsive to investor incentives, while little relation is found between investor needs and budget disclosure. This suggests that annual report information which is historically based is responsive primarily to investor needs.
The Accountability of School Governing Bodies

The notion of accountability has been central to the reforms which have been introduced in education since the Education Reform Act of 1988. As a case in point, key responsibilities have been devolved from local education authorities to school governing bodies. While these bodies are now accountable for many aspects of education, it is not clear how they work in practice. The aim of this paper is to identify the nature of accountability of school governing bodies. The research it reports on involved interviews with a range of governors to determine both how they perceive themselves to be accountable and how such accountability operates in reality. From all this conclusions are drawn on the nature and effectiveness of governing body accountability.
Can Values be Manipulated Arbitrarily?

Earlier research has indicated that value changes initiated through self-confrontation procedures are apparently unidirectional-that is, occur only in a direction that serves positive self-conceptions. However, to rule out the possibility that the previous findings may be the result of statistical regression, the present study replicated this earlier research and controlled for this possible artifact. Results indicated that the experimental treatment led to significant increases in equality 3 to 5 weeks later only among respondents whose values were inconsistent with their self-conceptions. The results thus provide further support for Rokeach's (1973) theory of cognitive organization and change and suggest that it is unlikely self-confrontation can be used to manipulate values in whatever direction is arbitrarily decided upon by an experimenter.
The Efficiency of Islamic Banking Industry: A Non-Parametric Analysis with Non-Discretionary Input Variable

This paper investigates the performance of Malaysian Islamic banking sector during the period of 2001-2005. Several efficiency estimates of individual banks are evaluated using non-parametric Data Envelopment Analysis (DEA). Two different approaches have been employed to differentiate how efficiency scores vary with changes in inputs and outputs. To examine the impact of risk factor on Islamic bank efficiency, we have incorporated problem loans as a nondiscretionary input variable in our analysis. The findings suggest that during the period of study, scale inefficiency dominates pure technical inefficiency in the Malaysian Islamic banking sector. We found that foreign banks have exhibited higher technical efficiency compared to their domestic peers. The inclusion of risk factors has mixed impact on Malaysian Islamic banks’ efficiency. The results seems to suggest that while potential economies of scale may be overestimated when risk factors are excluded, pure technical efficiency estimates on the other hand, tend to be much more sensitive to the exclusion of risk factors. The empirical results from the Spearman and Pearson tests reinforce these findings.
A Procedure for Studying the Cognitive Processes Used during Problem Solving

The cognitive processes used by children during problem solving have received considerable attention in recent years. The identification of the processes used by both successful and unsuccessful problem solvers has been hampered by the difficulties involved in making accurate observations of mental processes which may or may not have physical manifestations during problem solving. In addition, problem solvers themselves often are unaware of many of the thought processes they use while attempting to solve problems. The most popularly used methods for studying problem solving processes are not sufficiently reliable or valid. This study explored the potential effectiveness of a new procedure for identifying and studying certain of the cognitive processes used during problem solving. In addition, the procedure was used to categorize the types of conceptual thinking problem solvers employ, to study the use of trial and error behavior, and to investigate problem solvers’ abilities to coordinate multiple bits of.
Human mobility, social ties, and link prediction

Our understanding of how individual mobility patterns shape and impact the social network is limited, but is essential for a deeper understanding of network dynamics and evolution. This question is largely unexplored, partly due to the difficulty in obtaining large-scale society-wide data that simultaneously capture the dynamical information on individual movements and social interactions. Here we address this challenge for the first time by tracking the trajectories and communication records of 6 Million mobile phone users. We find that the similarity between two individuals' movements strongly correlates with their proximity in the social network. We further investigate how the predictive power hidden in such correlations can be exploited to address a challenging problem: which new links will develop in a social network. We show that mobility measures alone yield surprising predictive power, comparable to traditional network-based measures. Furthermore, the prediction accuracy can be significantly improved by learning a supervised classifier based on combined mobility and network measures. We believe our findings on the interplay of mobility patterns and social ties offer new perspectives on not only link prediction but also network dynamics.
Potential Predictors for Serofast State after Treatment among HIV-Negative Persons with Syphilis in China: A Systematic Review and Meta-Analysis

Background: Several studies have been conducted in China in order to investigate the potential predictors of serofast state after treatment among syphilitic patients. However, there is a remarkable diversity among the results. This meta-analysis was conducted to assess potential predictors of serofast among syphilitic patients in China. Methods: International and national electronic databases were searched up to September 2013. Reference lists of retrieved articles were also reviewed. Cohort or case-control studies addressing risk factors of serofast among syphilitic patients were included in this study. Results: We assessed 27 separate studies involving overall 6682 HIV-negative participants with syphilis of which 1962 remained in the serofast state. The serofast was positively associated with older age(Ptrend=0.001), female(summary risk ratio[sRR]=1.50, 95%CI:1.34–;1.68), latent syphilis(sRRlatent vs primary=3.17, 95%CI: 2.66–;3.77; sRRlatent vs secondary=2.00, 95%CI: 1.48–;2.69) as well as non-penicillin treatment(sRR =2.99, 95%CI:2.45–;3.67), but negatively associated with higher baseline titers(sRR>1:32 vs ≤1:32=0.63, 95%CI: 0.54–;0.75). Compared with healthy group and serological cure group, respectively, the levels of CD4 (+), IL-2, and IL-6 among serofast patients were decreased (standardized mean difference[SMD]<0, P<0.05), but the levels of CD8(+) and IL-10 were increased(SMD>0, P<0.05). Some studies also hinted the serofast was associated with subtypes i of treponema pallidum(TP) repeat gene (RR i vs d=4.67,95%CI: 1.31–;16.69) and TP occult infection. Conclusion: The age, gender, stage of infection, baseline titers, treatment drug, cellular immune suppression and disorders, TP occult infection and subtypes i of TP repeat gene should be considered as important predictors of serofast. However, until now the definition and mechanism of serofast has still been not clear.
Anthelmintic Effect of Biocompatible Zinc Oxide Nanoparticles (ZnO NPs) on Gigantocotyle explanatum, a Neglected Parasite of Indian Water Buffalo

Helminth parasites of veterinary importance cause huge revenue losses to agrarian economy worldwide. With the emergence of drug resistance against the current formulations, there is a need to focus on the alternative approaches in order to control this menace. In the present study, biocompatible zinc oxide nanoparticles (ZnO NPs) were used to see their in vitro effect on the biliary amphistomes, Gigantocotyle explanatum, infecting Bubalus bubalis because these nanoparticles are involved in generation of free radicals that induce oxidative stress, resulting in disruption of cellular machinery. The ZnO NPs were synthesized by using egg albumin as a biotemplate and subsequently characterized by Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), X-ray Diffraction and Spectrophotometrical, which showed that ZnO NPs were highly purified wurtzite type polycrystals, with a mean size of 16.7 nm. When the parasites were treated with lower concentrations (0.004% and 0.008%) of the ZnO NPs, the worms mounted a protective response by stimulating the antioxidant system but the treatment of G. explanatum with 0.012% ZnO NPs produced significant inhibition of the antioxidant enzymes like superoxide dismutase (SOD) (p< 0.05) and glutathione S- transferase (GST) (p<0.01), while the level of malondialdehyde (MDA), a lipid peroxidation marker, was significantly (p< 0.01) elevated. SEM and histopathology revealed pronounced tegumental damage showing the disruption of surface papillae and the annulations, particularly in the posterior region near acetabulum. The under expression of a number of polypeptides, loss of worm motility in a time dependent manner, further reflect strong anthelmintic potential of ZnO NPs. It can be concluded that the anthelmintic effect might be due to the production of reactive oxygen species that target a variety of macromolecules such as nucleic acid, protein and lipids which are involved in different cellular processes.
Improving Parsing and PP Attachment Performance with Sense Information

To date, parsers have made limited use of semantic information, but there is evidence to suggest that semantic features can enhance parse disambiguation. This paper shows that semantic classes help to obtain significant improvement in both parsing and PP attachment tasks. We devise a gold-standard sense- and parse tree-annotated dataset based on the intersection of the Penn Treebank and SemCor, and experiment with different approaches to both semantic representation and disambiguation. For the Bikel parser, we achieved a maximal error reduction rate over the baseline parser of 6.9% and 20.5%, for parsing and PP-attachment respectively, using an unsupervised WSD strategy. This demonstrates that word sense information can indeed enhance the performance of syntactic disambiguation.