Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between Phylogeny and Pathotype for the Bacterial Blight Pathogen of Rice

Several transposable elements were isolated from the genome of Xanthomonas oryzae pv. oryzae. These elements and an avirulence gene isolated from X. oryzae pv. oryzae were used as hybridization probes for a collection of X. oryzae pv. oryzae strains from the Philippines. Each of the sequences was present in multiple copies in all strains examined and showed distinct patterns of hybridizing bands. Phenograms were derived from the restriction fragment length polymorphism data obtained for each of the individual probes and for pooled data from multiple probes. The phenograms derived from the different probes differed in topology and, on the basis of bootstrap analysis, were not equally robust. For all of the probes, including the avirulence gene, some groups (even some haplotypes) consisted of multiple races. The strains were grouped into four major clusters on the basis of the two probes giving the highest bootstrap values. These groups were inferred to represent phylogenetic lineages. Three of the six races of X. oryzae pv. oryzae appeared in more than one of the lineages, and another was present in two sublineages. For three of the races, strains representing different phenetic groups were inoculated on rice cultivars carrying 10 resistance genes. Two new races were differentiated, corresponding to pathogen lineages identified by DNA typing. On the basis of DNA and pathotypic analyses, together with information on the spatial and temporal distribution of the pathogen types from this and other studies, a general picture of X. oryzae pv. oryzae evolution in the Philippines is presented.
Computational method for the real-time calculation of the full-body muscle load distribution

A method is described for minimising a quadratic function subject to equality and inequality constraints. This approach is applicable to solving the full-body muscle load distribution problem and calculating joint contact loads. It has been found that this approach can provide the solution on modest computing facilities and in significantly less time than using active set and interior point quadratic programming techniques. Hence the approach is suitable for providing real-time feedback to subjects undergoing biomechanical analysis of muscle, skeletal and joint loadings.
The Effects of Using Bank Auditors on Audit Quality and the Agency Cost of Bank Loans

SYNOPSIS: In this study, we examine the effect of a borrower having the same auditor as its main creditor bank on audit quality and the cost of the firm's bank loans. Japan is chosen as the context for this study because of its long-established bank-based system and the heavy reliance of Japanese companies on bank loans as a source of financing. The recent accounting scandals at Olympus Corporation and Toshiba Corporation highlight concerns about audit quality in Japan. Using a sample of Japanese listed companies, we provide evidence that the more a borrowing company depends on its main bank loans as a source of financing, the more likely the company is to choose the same auditor as its main bank. We also provide empirical evidence that, compared with companies that use different auditors, companies that use the same auditor as their main banks have higher audit quality, which reduces agency problems and results in a lower cost of bank loans. As bank loans are the most important source of external financi.
Comparison of composite measures of disease activity in an early seropositive rheumatoid arthritis cohort

Objective: To evaluate concordance and agreement of the original DAS44/ESR-4 item composite disease activity status measure with nine simpler derivatives when classifying patient responses by European League of Associations for Rheumatology (EULAR) criteria, using an early rheumatoid factor positive (RF+) rheumatoid arthritis (RA) patient cohort. Methods: Disease-modifying anti-rheumatic drug-naïve RF+ patients (n = 223; mean duration of symptoms, 6 months) were categorised as ACR none/20/50/70 responders. One-way analysis of variance and two-sample t tests were used to investigate the relationship between the ACR response groups and each composite measure. EULAR reached/change cut-point scores were calculated for each composite measure. EULAR (good/moderate/none) responses for each composite measure and the degree of agreement with the DAS44/ESR-4 item were calculated for 203 patients. Results: Patients were mostly female (78%) with moderate to high disease activity. A centile-based nomogram compared equivalent composite measure scores. Changes from baseline in the composite measures in patients with ACRnone were significantly less than those of ACR20/50/70 responders, and those for ACR50 were significantly different from those for ACR70. EULAR reached/change cut-point scores for our cohort were similar to published cut-points. When compared with the DAS44/ESR-4 item, EULAR (good/moderate/none) percentage agreements were 92 with the DAS44/ESR-3 item, 74 with the Clinical Disease Activity Index, and 80 with the DAS28/ESR-4 item, the DAS28/CRP-4 item and the Simplified Disease Activity Index. Conclusion: The relationships of nine different RA composite measures against the DAS44/ESR-4 item when applied to a cohort of seropositive patients with early RA are described. Each of these simplified status and response measures could be useful in assessing patients with RA, but the specific measure selected should be pre-specified and described for each study.
Triangulation Approaches to Accounting Research

Multiple theoretical perspectives or research methods permit a wider and richer understanding of accounting practice than methodologically a singular approach. This claim, by some accounting researchers, advocates the use of a variety of theories and research methods, namely ‘triangulation’, as a way of taking advantage of their complementariness and building a more holistic analysis. This chapter illustrates the various forms of triangulations that can be applied in accounting research. The message of this chapter is that whilst conventional ‘paradigms’ can usefully explain qualitative, case study research, they need to be located in analyses embracing subjective and institutional factors for an adequate understanding of their import. As well as being a plea for greater theoretical plurality, the chapter also suggests a variety of research methods which can be developed jointly within a single study.
Relative Contributions of Connexins 40 and 43 to Atrial Impulse Propagation in Synthetic Strands of Neonatal and Fetal Murine Cardiomyocytes

Atrial tissue expresses both connexin 40 (Cx40) and 43 (Cx43) proteins. To assess the relative roles of Cx40 and Cx43 in atrial electrical propagation, we synthesized cultured strands of atrial myocytes derived from mice with genetic deficiency in Cx40 or Cx43 expression and measured propagation velocity (PV) by high-resolution optical mapping of voltage-sensitive dye fluorescence. The amount of Cx40 and/or Cx43 in gap junctions was measured by immunohistochemistry and total or sarcolemmal Cx43 or Cx40 protein by immunoblotting. Progressive genetic reduction in Cx43 expression decreased PV from 34±6 cm/sec in Cx43+/+ to 30±8 cm/sec in Cx43+/− and 19±11 cm/sec in Cx43−/− cultures. Concomitantly, the cell area occupied by Cx40 immunosignal in gap junctions decreased from 2.0±1.6% in Cx43+/+ to 1.7±0.5% in Cx43+/− and 1.0±0.2% in Cx43−/− strands. In contrast, progressive genetic reduction in Cx40 expression increased PV from 30±2 cm/sec in Cx40+/+ to 40±7 cm/sec in Cx40+/− and 45±10 cm/sec in Cx40−/− cultures. Concomitantly, the cell area occupied by Cx43 immunosignal in gap junctions increased from 1.2±0.9% in Cx40+/+ to 2.8±1.4% in Cx40+/− and 3.1±0.6% in Cx40−/− cultures. In accordance with the immunostaining results, immunoblots of the Triton X-100–insoluble fraction revealed an increase of Cx43 in gap junctions in extracts from Cx40-ablated atria, whereas total cellular Cx43 remained unchanged. Our results suggest that the relative abundance of Cx43 and Cx40 is an important determinant of atrial impulse propagation in neonatal hearts, whereby dominance of Cx40 decreases and dominance of Cx43 increases local propagation velocity.
Cognitive Functioning and Cerebrospinal Fluid Concentrations of Neuropeptides for Patients with Good Neurological Outcomes after Aneurysmal Subarachnoid Hemorrhage

OBJECTIVEMany patients exhibit cognitive disturbances after aneurysmal subarachnoid hemorrhage (SAH). Structural and functional neuroimaging has failed to demonstrate any correlation with these complaints. This study was performed to investigate whether neuropeptide concentrations in cerebrospinal fluid could be related to cognitive disturbances after SAH. METHODSLumbar cerebrospinal fluid was obtained, 3 to 6 months after surgery, from 17 patients who experienced good outcomes after aneurysmal SAH. The samples were analyzed for various neuropeptides using radioimmunoassays, and the peptide concentrations were evaluated in relation to scores on standardized neuropsychological tests. RESULTSThe neuropsychological test results were normal for eight individuals, whereas the remaining nine patients exhibited various degrees of cognitive impairment. There was no correlation between the concentrations of arginine vasopressin or neuropeptide Y and test performance. However, significant correlations between cognitive impairment and elevated levels of &bgr;-endorphins (P = 0.02), corticotropin-releasing factor (P = 0.004), and delta sleep-inducing peptide (P = 0.045) were noted. CONCLUSIONPatients with cognitive impairments after aneurysmal SAH exhibited higher cerebrospinal fluid concentrations of endorphins, corticotropin-releasing factor, and delta sleep-inducing peptide than did those with normal capacity. This is probably attributable to diffuse derangement of transmitter release in the brain, resulting from the insult or ensuing complications, although a secondary increase in corticotropin-releasing factor concentrations caused by increased stress during the testing because of reduced cognitive capacity cannot be excluded.
Turnout and Education: Is Education Proxying for Pre-Adult Experiences Within the Family?

This study uses a discordant sibling-based design to assess the extent to which education is proxying for pre-adult experiences and predispositions rooted in the family. It draws on a unique data set that combines official voting records with Census data on siblings and their parents. The results show that the association between education and voting is considerably reduced when parental education, parental voting and unobserved characteristics that are shared by siblings within the same family are taken into account. This finding is confirmed by a variety of robustness checks. We end with a discussion of the benefits and limitations of sibling-based designs for testing causal hypotheses.
Inheritance of the shared epitope and long‐term outcomes of rheumatoid arthritis among community‐based Caucasian females

Multiple HLA‐DRB1 alleles encoding a shared epitope (SE) at amino acid positions 70–74 are associated with susceptibility and severity of rheumatoid arthritis (RA). We examined the relationship between the number and DRB1 genotype of SE alleles inherited and long‐term outcomes of 180 community‐based, Caucasian female RA patients followed annually for up to 12 years. Outcomes examined were physician assessment of RA course; annual measures of pain, function, and number of painful joint groups; history of joint surgery; and resource utilization. Models accounted for correlation among serial observations for the same patient and adjusted for patient age and disease stage. We examined two genetic models: a SE model in which patients were classified according to the number of SE copies inherited and a genotype model in which patients were categorized into one of six groups based on the inherited DRB1 genotype. We used likelihood ratio tests to compare these genetic models and to compare alternative model specifications. Our results demonstrate strong associations between inheritance of the SE and long‐term outcomes of community‐based Caucasian females with RA. However, the pattern of results is not consistent across the outcomes. An additive model of risk is apparent for history of joint surgery and RA hospitalization. In contrast, a near reversal of this pattern is apparent for function, joint pain, pain rating, and RA physician visits. Finally, although the genotype model did not appear to be a better predictive model for RA outcomes overall, it did reveal some striking heterogeneity of SE alleles that was masked by the more parsimonious SE model. For example, the odds ratio (OR) for joint surgery for patients with 2 SE copies (OR = 3.16) reflects an average of 2 very different ORs when patients are further categorized according to genotype groups 4 and 5 (OR = 1.3 and 11.9, respectively). Genet. Epidemiol. 15:61–72,1998. © 1998 Wiley‐Liss, Inc.
Prenatal Cocaine: Quantity of Exposure and Gender Moderation

ABSTRACT. Animal but few human studies have demonstrated gender-influenced differences in outcome related to prenatal cocaine exposure. Pregnant participants in a prospective pregnancy study were interviewed for drug use. Exposure was considered positive if history or laboratory tests were positive. An ordinal measure of exposure was also constructed. Six years later, the child and primary caretaker were tested to assess drug use in the home since birth and teacher-assessed child behavior. Data were complete for 473 children (204 cocaine exposed). Twenty-four of the exposed children (12%) were considered to have persistent pregnancy exposure based on positive urine screen at delivery. Boys with any prenatal cocaine exposure scored significantly higher (more problem behaviors) than nonexposed boys on the hyperactivity item. In contrast, no similar cocaine effect was observed for girls. When cocaine exposure was expressed as the three-level ordinal variable, boys, but not girls, with persistent exposure had more behavior problems (0.5 to 1.0 SD higher). Even after control for important covariates, boys with persistent exposure had more problems in central processing, motor skills, handling abstract concepts, and passivity to the environment. The magnitude of the relations reported in this research were moderate to large. In summary, both gender and the level of exposure had a significant behavioral effect on school-age behavior. In these analyses, the behavior of boys, but not girls, prenatally exposed to cocaine was significantly and negatively affected, and these findings remained after control for covariates, including prenatal alcohol or other illicit drug exposures and postnatal drug use in the home.
Optimal Design and Multicoils Quench Analysis of the EMPS Superconducting Magnet Employing Hybrid Genetic Algorithm

A 5-T low-temperature superconducting magnet was designed and will be fabricated for electro-magnetic property measurement system (EMPS) whose sample space is 50 mm in diameter. Since the sample space is twice larger than that of the conventional property measurement systems, it will be possible to measure the electro-magnetic properties of several samples at a time, therefore, measurement time could be reduced. With the genetic algorithm incorporated with the linear-programming, key design of the 5-T LTS EMPS magnet is introduced and followed by the detailed magnet specifications including field uniformity at 50-mm space, magnetic hoop stress, critical current margin, and dimensions. The linear-programming restricts the magnet space and structure to minimize the total volume of the wires. Meanwhile, the genetic algorithm calculates the layers, turns, and detailed dimensions of the magnet in the magnet space confined by the linear-programming. Furthermore, quench analysis on multicoils employing finite difference equations in liquid helium was carried out to verify the thermal stability of the LTS magnet. The quench simulation code calculates temperature profiles of the magnet considering heat transfer among the unit cells and joule heat of the magnet in three-dimensional space. The LTS magnet for 5-T EMPS will be fabricated according to the design results.
Muscle-tendon units localization and activation level analysis based on high-density surface EMG array and NMF algorithm

Objective. Some skeletal muscles can be subdivided into smaller segments called muscle-tendon units (MTUs). The purpose of this paper is to propose a framework to locate the active region of the corresponding MTUs within a single skeletal muscle and to analyze the activation level varieties of different MTUs during a dynamic motion task. Approach. Biceps brachii and gastrocnemius were selected as targeted muscles and three dynamic motion tasks were designed and studied. Eight healthy male subjects participated in the data collection experiments, and 128-channel surface electromyographic (sEMG) signals were collected with a high-density sEMG electrode grid (a grid consists of 8 rows and 16 columns). Then the sEMG envelopes matrix was factorized into a matrix of weighting vectors and a matrix of time-varying coefficients by nonnegative matrix factorization algorithm. Main results. The experimental results demonstrated that the weightings vectors, which represent invariant pattern of muscle activity across all channels, could be used to estimate the location of MTUs and the time-varying coefficients could be used to depict the variation of MTUs activation level during dynamic motion task. Significance. The proposed method provides one way to analyze in-depth the functional state of MTUs during dynamic tasks and thus can be employed on multiple noteworthy sEMG-based applications such as muscle force estimation, muscle fatigue research and the control of myoelectric prostheses.
Depression of glutamatergic and gabaergic synaptic responses in striatal spiny neurons by stimulation of presynaptic GABAB receptors

The influence of γ‐aminobutyric acidB (GABAB) receptor stimulation on the excitatory and inhibitory synaptic potentials and membrane properties of identified striatal spiny neurons was examined in a corticostriatal slice preparation. Stimulation of the subcortical white matter evoked a monosynaptic, excitatory postsynaptic potential (EPSP) and a polysynaptic, inhibitory postsynaptic potential (IPSP) in spiny neurons. The EPSP had two components: a large amplitude response which could be blocked by the kainate/quisqualate receptor antagonist, 6‐cyano‐7‐nitroquinoxaline‐2,3‐dione (CNQX, 10μM), and a small amplitue, long‐duration depolarization which could be blocked by the N‐methyl‐D‐aspartate receptor antagonist, d‐(‐)‐2‐amino‐5‐phosphonovaleric acid (APV, 100 μM). The IPSP was observed as a membrane depolarization when recorded from neurons at resting membrane potential. However, when neurons were injected with the Na+‐channel blocker, QX‐314, allowing cells to be depolarized above their spike thresholds, a prominent hyperpolarizing IPSP was readily observed which could be blocked by the GABAA antagonist, bicuculline (10‐50 μM). This bicuculline‐sensitive IPSP was responsible for the inhibition of EPSP amplitude and probability of spike discharge revealed using paired stimulation of the subcortical white matter. The amplitude of both the EPSP and the IPSP were depressed by the GABAB receptor agonist, p‐chlorophenyl‐GABA (baclofen, 0.5‐100 μM) in a concentration‐dependent manner. Baclofen also blocked paired stimulus inhibition of spike discharge. These effects of baclofen persisted in slices in which the cortex was removed and were reversed by the GABAB receptor antagonist, 3‐amino‐3‐hydroxy‐2‐(4‐chlorophenyl)‐propanesulphonic acid (saclofen, 100‐500 μM). In contrast to its profound influence on synaptic input, baclofen did not alter resting membrane potential, input resistance, membrane current‐voltage relationship, or spike threshold of the cells recorded, and therefore did not appear to exert direct postsynaptic effects on the striatal spiny neurons.
Folic acid 5 or 15 mg/d similarly reduces plasma homocysteine in patients with moderate–advanced chronic renal failure

Background: Hyperhomocysteinaemia is an independent risk factor for cardiovascular disease with a remarkable prevalence in patients with chronic renal failure (CRF). Low doses of folic acid (FA) with or without vitamin B6 and B12 has been shown to effectively reduce plasma homocysteine (Hcy). The aim of this study was to compare the short‐term effects of two different oral doses of FA (5 vs 15 mg/d) on plasma Hcy levels in subjects suffering from moderate–severe CRF.
Cost-effectiveness of diabetes case management for low-income populations.

OBJECTIVE To evaluate the cost-effectiveness of Project Dulce, a culturally specific diabetes case management and self-management training program, in four cohorts defined by insurance status. DATA SOURCES/STUDY SETTING Clinical and cost data on 3,893 persons with diabetes participating in Project Dulce were used as inputs into a diabetes simulation model. STUDY DESIGN The Center for Outcomes Research Diabetes Model, a published, peer-reviewed and validated simulation model of diabetes, was used to evaluate life expectancy, quality-adjusted life expectancy (QALY), cumulative incidence of complications and direct medical costs over patient lifetimes (40-year time horizon) from a third-party payer perspective. Cohort characteristics, treatment effects, and case management costs were derived using a difference in difference design comparing data from the Project Dulce program to a cohort of historical controls. Long-term costs were derived from published U.S. sources. Costs and clinical benefits were discounted at 3.0 percent per annum. Sensitivity analyses were performed. PRINCIPAL FINDINGS Incremental cost-effectiveness ratios of $10,141, $24,584, $44,941, and $69,587 per QALY gained were estimated for Project Dulce participants versus control in the uninsured, County Medical Services, Medi-Cal, and commercial insurance cohorts, respectively. CONCLUSIONS The Project Dulce diabetes case management program was associated with cost-effective improvements in quality-adjusted life expectancy and decreased incidence of diabetes-related complications over patient lifetimes. Diabetes case management may be particularly cost effective for low-income populations.
Risk factors for the occurrence of Escherichia coli virulence genes eae, stx1 and stx2 in wild bird populations

SUMMARY Shiga toxin-producing Escherichia coli (STEC) can cause serious disease in human beings. Ruminants are considered to be the main reservoir of human STEC infections. However, STEC have also been isolated from other domestic animals, wild mammals and birds. We describe a cross-sectional study of wild birds in northern England to determine the prevalence of E. coli-containing genes that encode Shiga toxins (stx1 and stx2) and intimin (eae), important virulence determinants of STEC associated with human disease. Multivariable logistic regression analysis identified unique risk factors for the occurrence of each virulence gene in wild bird populations. The results of our study indicate that while wild birds are unlikely to be direct sources of STEC infections, they do represent a potential reservoir of virulence genes. This, coupled with their ability to act as long-distance vectors of STEC, means that wild birds have the potential to influence the spread and evolution of STEC.