Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genotyping of Campylobacter jejuni by Amplified Fragment Length Polymorphism, Multilocus Sequence Typing, and Short Repeat Sequencing: Strain Diversity, Host Range, and Recombination

ABSTRACT Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic repeats (CRISPRs). MLST and AFLP analysis yielded more than 100 different profiles and patterns, respectively. These multiple-locus typing methods resulted in similar genetic clustering, indicating that both are useful in disclosing genetic relationships between Campylobacter jejuni isolates. Group separation analysis of the AFLP analysis and MLST data revealed an unexpected association between cattle and human strains, suggesting a common source of infection. Analysis of the polymorphic CRISPR region carrying short repeats allowed about two-thirds of the typeable strains to be distinguished, similar to AFLP analysis and MLST. The three methods proved to be equally powerful in identifying strains from outbreaks of human campylobacteriosis. Analysis of the MLST data showed that intra- and interspecies recombination occurs frequently and that the role of recombination in sequence variation is 50 times greater than that of mutation. Examination of strains cultured from cecum swabs revealed that individual chickens harbored multiple Campylobacter strain types and that some genotypes were found in more than one chicken. We conclude that typing of Campylobacter strains is useful for identification of outbreaks but is probably not useful for source tracing and global epidemiology because of carriage of strains of multiple types and an extremely high diversity of strains in animals.
Three essays on crop yield, crop insurance and climate change

The main subject of this dissertation includes the study of the impact of weather on crop yields and developing crop revenue insurance product. The dissertation limits its analysis to the state of Iowa because it's a critical corn production area in the United States. Chapter 2 introduced a dynamic linear model to measure weather-adjusted trends in Iowa corn yields. The weather factors consist of the amount of rainfall, temperature and a measurement of soil moisture. Results show a significant improved yield growth in the 1990s, controlling for the impact of weather. Results also indicate that the critical temperature varies across the state of Iowa. The critical temperature is higher in the areas of the state with higher soil quality and is most suitable to grow corn. Chapter 3 develops a long-term corn revenue insurance product that provides crop growers with yield or revenue protection for as long as five years into the future. The premium rates are calculated at both county and farm level. Chapter 4 estimates the impact of projected climate change on Iowa corn yield. The climate projection indicates a significant increase in the daily maximum temperature in July, whereas a significant increment trend is not found in the amount of rainfall during June to August. Controlling for the uncertainty in yield projection, results indicate that projected climate change will cause a statewide reduction of corn yield by 10% at the end of this century. Controlling for uncertainty in climate projection and allowing for uncertainty in yield projections, results show that projected climate change reduces Iowa corn yield by 9%.
Process Metrics Are Not Bad Predictors of Fault Proneness

The correct prediction of faulty modules or classes has a number of advantages such as improving the quality of software and assigning capable development resources to fix such faults. There have been different kinds of fault/defect prediction models proposed in literature, but a great majority of them makes use of static code metrics as independent variables for making predictions. Recently, process metrics have gained a considerable attention as alternative metrics to use for making trust-worthy predictions. The objective of this paper is to investigate different combinations of static code and process metrics for evaluating fault prediction performance. We have used publicly available data sets, along with a frequently used classifier, Naive Bayes, to run our experiments. We have, both statistically and visually, analyzed our experimental results. The statistical analysis showed evidence against any significant difference in fault prediction performances for a variety of different combinations of metrics. This reinforced earlier research results that process metrics are as good as predictors of fault proneness as static code metrics. Furthermore, the visual inspection of box plots revealed that the best set of metrics for fault prediction is a mix of both static code and process metrics. We also presented evidence in support of some process metrics being more discriminating than others and thus making them as good predictors to use.
Nonoverlapping roles of PD-1 and FoxP3 in maintaining immune tolerance in a novel autoimmune pancreatitis mouse model

Significance We investigated the effect of PD-1 (programmed-death 1), a negative immunoreceptor, on the function of transcription factor FoxP3+ Treg cells. When a moderately down-modulated transcription factor FoxP3 knock-in mouse, which did not show any autoimmunity, was made PD-1–deficient, the mouse developed severe pancreatitis and died soon after birth. PD-1 deficiency also induced instability of Treg cell status and increased so-called ex-Treg cells, which showed the helper effector activity with self-antigen recognition. PD-1–deficient T reg cells, however, did not compromise their function but rather increased their suppressive activity. Thus, PD-1 and Treg cells mutually influence and both are required for protection from autoimmunity. PD-1 (programmed-death 1), an immune-inhibitory receptor required for immune self-tolerance whose deficiency causes autoimmunity with variable severity and tissue specificity depending on other genetic factors, is expressed on activated T cells, including the transcription factor FoxP3+ Treg cells known to play critical roles in maintaining immune tolerance. However, whether PD-1 expression by the Treg cells is required for their immune regulatory function, especially in autoimmune settings, is still unclear. We found that mice with partial FoxP3 insufficiency developed early-onset lympho-proliferation and lethal autoimmune pancreatitis only when PD-1 is absent. The autoimmune phenotype was rescued by the transfer of FoxP3-sufficient T cells, regardless of whether they were derived from WT or PD-1–deficient mice, indicating that Treg cells dominantly protect against development of spontaneous autoimmunity without intrinsic expression of PD-1. The absence of PD-1 combined with partial FoxP3 insufficiency, however, led to generation of ex-FoxP3 T cells with proinflammatory properties and expansion of effector/memory T cells that contributed to the autoimmune destruction of target tissues. Altogether, the results suggest that PD-1 and FoxP3 work collaboratively in maintaining immune tolerance mostly through nonoverlapping pathways. Thus, PD-1 is modulating the activation threshold and maintaining the balance between regulatory and effector T cells, whereas FoxP3 is sufficient for dominant regulation through maintaining the integrity of the Treg function. We suggest that genetic or environmental factors that even moderately affect the expression of both PD-1 and FoxP3 can cause life-threatening autoimmune diseases by disrupting the T-cell homeostasis.
Nonlinear Effects of Government Debt on Private Consumption in OECD Countries

This paper investigates nonlinear effects of government debt on private consumption in 16 OECD countries. The estimated consumption function shows smooth regime switching depending on the debt-to-GDP ratio, and the threshold level of regime switching is found to be the ratio of 83.7 percent. The results reveal that a higher level of government debt crowds out private consumption to a greater extent, and that the degree of the crowding out effect has deteriorated since the global financial crisis.
Biophysical and biochemical basis of resistance to pod borer, Helicoverpa armigera (Hubner) in chickpea

Studies on the biophysical and biochemical basis of resistance to chickpea pod borer, Helicoverpa armigera (Hubner) was assessed under field condition at RARS campus, Vijayapur, Karnataka during rabi, 2015-16. Results revealed that at BGD 111-01 chickpea genotype showed resistance to the pod borer and recorded lower egg load on the crop (5.00 / mt row length) lower larval incidence (2.00 / mt row length) at reproductive stage and lower pod damage at harvest (6.60%) compared to Bidar bold genotype. Further, BGD 111-01 genotype had registered higher number trichome density on leaf surface, higher amount of phenol and lower amount of total sugar, reducing sugar, protein compared to Susceptible genotype (Bidar bold). Correlation study also indicated that negative correlation was found between per cent pod borer infestation with phenol content and was positively correlated with total sugar, reducing sugar, protein and total chlorophyll content.
FUNDING HIGHER EDUCATION I N T HE UK: T HE R OLE OF F EES A ND LOANS*

Higher education has undergone considerable expansion in recent decades in a number of OECD countries. Expansion has been especially dramatic in the UK where aggregate student numbers have doubled in 20 years. However, over the same period, funding per student has halved in real terms. In the UK as well as in other countries, most notably Australia, innovation to diversify the funding base has taken place. This has included a limited role for fee contributions. This paper makes the case for much greater reliance on fee contributions from students, accompanied by a greater availability of income contingent loans. Over the last 40 years of the twentieth century, the higher education (HE) marketplace in the UK changed profoundly, with the pace of change accelerating dramatically over the last decade. Major systemic changes include: • A threefold increase in the number of universities since the 1960s: partly as a consequence of new entry, with around 20 new universities created in the 1960s; and partly as a result of the abolition of the so-called ‘binary divide’ in the early 1990s, which resulted in over 40 former polytechnics gaining university status. There are now almost 100 universities in the UK. • A growth in consumers which outstripped the growth in providers. In the early 1960s there were just 400,000 (full-time and part-time) students at British higher education institutions; in the year 2000 there were over 2,000,000. • An irrevocable change in the balance between public and private funding: in the 1960s universities in the UK were almost entirely publicly funded, now direct public subventions account for on average around two thirds of total income. • Changes in the mechanisms for disbursing public funds, both to providers and consumers: for the former there has been a shift away from block grants to fund teaching and research, to earmarked funding which is partly formulaic, partly performance based; for students there has been a shift from income support transfers to student loans. • Despite a trend decline in public funding, a dramatic increase in regulation and compliance requirements, with formal performance appraisal of teaching and research now well embedded; in the case of the former, with periodic ‘Subject Reviews’ and in the latter quinquennial ‘Research Assessment Exercises’. The potential for such major systemic changes to impact on performance was recognised by the creation in the mid 1990s of the National Committee of Inquiry into
1 Body Size and Growth Rate Influence Emigration Timing of Oncorhynchus mykiss 1 2

18 Juvenile Oncorhynchus mykiss migrate extensively in freshwater during fall. We used 19 individual tagging to study the spatial origin, influences, and outcomes of fall migration on fish 20 that emigrated from summer rearing tributaries during fall (early-emigrants) and those that did 21 not (late-emigrants) in the South Fork John Day River, Oregon. Fall migration amplified body 22 size differences between early and late-emigrants. There were more early-emigrants from a 23 lower gradient stream than from a higher gradient stream. Early-emigration was positively 24 related to individual summer growth rate and fall body size. Oncorhynchus mykiss dispersed 25 downstream into higher order streams during fall. Early-emigrants shifted to an alternative 26 location and experienced significantly greater winter growth compared to late-emigrants that 27 remained in tributaries. Early-emigrants initiated smolt migration sooner the following spring 28 than late-emigrants. Early and late-emigration from the South Fork John Day was associated 29 with asynchronous emigrant-to-adult survival rates. 30
Implications of prosthesis funding structures on the use of prostheses: experiences of individuals with upper limb absence

Background: While sparsely researched, funding structures may play an important role in use of and satisfaction with prostheses and related health services. Objectives: The objectives of this study were to (1) quantify the direct costs of prosthesis wear, (2) explore variations in funding distribution, and (3) describe the role of affordability in prosthesis selection and wear. Study design: An anonymous, online cross-sectional descriptive survey was administered. Methods: Analyses were conducted of qualitative and quantitative data extracted from an international sample of 242 individuals with upper limb absence. Results: Access to prosthesis funding was variable and fluctuated with age, level of limb absence and country of care. Of individuals who gave details on prosthetic costs, 63% (n = 69) were fully reimbursed for their prosthetic expenses, while 37% (n=40) were financially disadvantaged by the cost of components (mean [SD] US$9,574 [$9,986]) and their ongoing maintenance (US$1,936 [$3,179]). Of the 71 non-wearers in this study, 48% considered cost an influential factor in their decision not to adopt prosthesis use. Conclusions: Prosthesis funding is neither homogeneous nor transparent and can be influential in both the selection and use of a prosthetic device. Clinical relevance Inequitable access to prosthesis funding is evident in industrialized nations and may lead to prosthesis abandonment and/or diminished quality of life for individuals with upper limb absences. Increased efforts are required to ensure equitable access to upper limb prosthetics and related services in line with individuals’ needs.
Risk Factors for Peripheral Vascular Disease in Hypertensive Subjects with Type 2 Diabetes Mellitus

Possible factors predisposing to peripheral vascular disease (PVD) in hypertensive subjects with Type 2 diabetes mellitus were studied. Details of age, sex, duration of diabetes, blood pressure, and smoking habit were recorded in 180 subjects of either White, West Indian Black or Asian ethnic origin. Glycosylated haemoglobin, fasting serum total cholesterol, total high density lipoprotein (HDL), HDL2, low density lipoprotein (LDL‐cholesterol), and triglycerides were measured in all subjects. Peripheral vascular disease was defined as an ankle/brachial systolic pressure < 1.0 as measured by the Doppler technique. Multivariate analysis was performed and the following factors were identified as being strongly associated with the presence of PVD with a statistical significance of p < 0.001; LDL‐cholesterol, total HDL‐cholesterol, age, male sex, diet or oral hypoglycaemic therapy, diastolic blood pressure, and of p < 0.003; systolic blood pressure. When blood pressure was excluded from the analysis the other factors retained their predictive value. We conclude that hypertension and dyslipidaemia are important risk factors for peripheral vascular disease in Type 2 diabetes mellitus.
The Impact of Low-Cost Economies on UK Import Prices

The share of UK imports from developing countries has increased sharply in recent years. Using measures of bilateral trade prices, this article suggests that increased sourcing from low-cost economies has put significant downward pressure on the relative price of UK goods imports. However, this effect may have dissipated over time as the prices of UK imports from low-cost economies have risen more rapidly than in the past and developing economies' increasing demand for raw materials has contributed to higher oil and commodities prices.
When Should Children with HIV Infection Be Started on Antiretroviral Therapy?

Background to the debate: The advent of highly active antiretroviral therapy (HAART) dramatically improved the prognosis for both adults and children infected with HIV who had access to treatment. However, the optimal timing for initiating treatment remains controversial, particularly in children. This debate lays out the case for deferred treatment against the case for early initiation of HAART in children.
IL‐8 inhibits cAMP‐stimulated alveolar epithelial fluid transport via a GRK2/PI3K‐dependent mechanism

Patients with acute lung injury (ALI) who retain maximal alveolar fluid clearance (AFC) have better clinical outcomes. Experimental and small clinical studies have shown that β2‐adrenergic receptor (β2AR) agonists enhance AFC via a cAMP‐dependent mechanism. However, two multicenter phase 3 clinical trials failed to show that β2AR agonists provide a survival advantage in patients with ALI. We hypothesized that IL‐8, an important mediator of ALI, directly antagonizes the alveolar epithelial response to β2AR agonists. Short‐circuit current and whole‐cell patch‐clamping experiments revealed that IL‐8 or its rat analog CINC‐1 decreases by 50% β2AR agonist‐stimulated vectorial Cl– and net fluid transport across rat and human alveolar epithelial type II cells via a reduction in the cystic fibrosis transmembrane conductance regulator activity and biosynthesis. This reduction was mediated by heterologous β2AR desensitization and down‐regulation (50%) via the G‐protein‐coupled receptor kinase 2 (GRK2)/PI3K signaling pathway. Inhibition of CINC‐1 restored β2AR agonist‐stimulated AFC in an experimental model of ALI in rats. Finally, consistent with the experimental results, high pulmonary edema fluid levels of IL‐8 (>4000 pg/ml) were associated with impaired AFC in patients with ALI. These results demonstrate a novel role for IL‐8 in inhibiting β2AR agonist‐stimulated alveolar epithelial fluid transport via GRK2/PI3K‐dependent mechanisms. —Roux, J., McNicholas, C. M. , Carles, M. , Goolaerts, A. , Houseman, B. T. , Dickinson, D. A. , Iles, K. E. , Ware, L. B. , Matthay, M. A. , Pittet, J.‐F. IL‐8 inhibits cAMP‐stimulated alveolar epithelial fluid transport via a GRK2/PI3K‐dependent mechanism. FASEB J. 27, 1095–1106 (2013). www.fasebj. org
Articular Cartilage Lesions of the Knee

From *Santa Monica Orthopaedic and Sports Medicine Group, Santa Monica, California; ‡University of Missouri at Kansas City and University of Kansas, Shawnee Mission, Kansas; §Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania; iDivision of Sports Medicine, Children’s Hospital, Boston, Massachusetts; Baylor Sports Medicine Group, Houston, Texas; Orthopaedische Universitaetsklinik, Freiburg, Germany; Brigham Orthopedic Association, Boston, Massachusetts; and Gothenburg Medical Center, Vastra Frolunda, Sweden
Induction of the LH Surge in Premenarchal Girls Confirms Early Maturation of the Hypothalamic–Pituitary–Ovarian Axis

Purpose: To determine whether premenarchal girls exhibit positive estradiol feedback similar to regularly cycling adult women when given exogenous estradiol. Methods: This was a prospective clinical cohort study at 2 institutions. Nine girls and 6 women received a 7-day course of transdermal estradiol designed to produce physiologic, mid-cycle circulating estradiol levels. Participants collected daily morning urine for luteinizing hormone (LH), estradiol metabolites (E1c), and progesterone metabolites (Pdg), corrected for creatinine. Main outcomes were percentage increase in LH from nadir to peak and the absolute value of peak LH between the 2 groups, using t testing and linear mixed-effects modeling. Results: All participants exhibited a positive feedback response to estradiol. Adult women had a 532.8% (95% confidence interval [CI]: 253.7-1119) increase in LH after estradiol exposure; premenarchal girls had a 497.9% increase (95% CI: 274.5-903.2; P = .86). The absolute value of the LH surge in women was 9.50 mLU/mgCr (95% CI: 2.59- 43 34.90) and in premenarchal girls was 2.57 mLU/mgCr (95% CI: 0.53-12.49; P = .15). Conclusions: Premenarchal girls can mount an LH surge proportionally similar to regularly cycling adults. This occurs earlier in puberty than previously believed, in contrast to current dogma that maturation of the hypothalamic–pituitary–ovarian axis occurs after menarche and is the rate-limiting step for the establishment of regular, ovulatory cycles. Failure to achieve regular cycles may instead be due to nutritional or ovarian factors. Young girls who fail to ovulate shortly after menarche may warrant further evaluation for endocrinopathies.
Survival of Some Medically Important Fungi on Hospital Fabrics and Plastics

ABSTRACT Tests of the survival of Candida spp. ,Aspergillus spp. , a Fusariumsp. , a Mucor sp. , and aPaecilomyces sp. on hospital fabrics and plastics indicated that viability was variable, with most fungi surviving at least 1 day but many living for weeks. These findings reinforce the need for appropriate disinfection and conscientious contact control precautions.
An evolutionary perspective of opportunism in high-technology alliance: the evidence from South Korean companies

Abstract Adopting an evolutionary perspective, we introduce an alternative approach to the opportunism in strategic alliance where the accumulated risks during alliance operation lead to opportunism in alliance. To examine this process, a total of 358 employees from South Korean firms in the high technology sector completed a survey on opportunism in strategic alliance, measuring each firm's perceived risks on the relational and operational issues in alliance and their antecedents and outcomes. Key results show that perceived risks on the relationship between alliance partners cause a passive type of opportunism, whereas perceived risks both on the relationship between alliance partners and on the achievement of alliance objectives cause an active type of opportunism. Specifically, cultural difference showed the largest influence on relational risks, whereas issues in equity involvement showed the largest influence on performance risk. Based on the findings, theoretical and practical implications on the opportunism management in strategic alliance are discussed.