Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic relationships between Bacillus species and related genera inferred from 16s rDNA sequences

Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus) of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups.
Volumetric Testing Parallel to the Boundary Surface for a Nonconforming Discretization of the Electric-Field Integral Equation

The volumetric monopolar-RWG discretization of the electric-field integral equation (EFIE) imposes no continuity constraint across edges in the surface discretization around a closed conductor. The current is expanded with the monopolar-RWG set and the electric field is tested over a set of tetrahedral elements attached to the boundary surface. This scheme is facet-oriented and therefore, well suited for the scattering analysis of nonconformal meshes or composite objects. The observed accuracy, though, is only competitive with respect to the RWG-discretization for a restricted range of heights of the tetrahedral elements. In this communication, we introduce a novel implementation of the volumetric monopolar-RWG discretization of the EFIE with testing over a set of wedges. We show with RCS and near-field results that this scheme offers improved accuracy for a wider range of heights than the approach with tetrahedral testing. The application of the wedge testing to the even-surface odd-volumetric monopolar-RWG discretization of the EFIE, edge-oriented and therefore less versatile, shows similar accuracy as with tetrahedral testing, which is a sign of robustness.
Switzerland's gains from trade with Europe

In this paper I look at the size of Switzerland's gains from trade through the lens of the workhorse model of modern trade theory. The model finds that most of Switzerland's gains from trade originate from the EU and that realistic changes in the degree of trade integration with EU countries may have non-trivial - but at same time not excessively large - effects on Swiss percapita incomes. The model also suggests that further trade integration with third countries, such as China and India, tends to increase Swiss welfare, but is unlikely to be able to compensate for possible losses stemming from deteriorating trade relations with European countries.
Cholesterol-lowering therapy for the treatment of nonalcoholic fatty liver disease: an update

Purpose of review To review recent human trials assessing cholesterol-lowering agents in nonalcoholic fatty liver disease (NAFLD). Recent findings Four randomized controlled trials (RCTs) assessed statins in NAFLD. In the only RCT with post-treatment biopsy, simvastatin did not change liver histology. In the remaining RCTs, atorvastatin was well tolerated, significantly improved radiological/biochemical markers of steatosis and plasma lipids, with neutral effects on glucose metabolism; in the Greek Atorvastatin and Coronary Heart Disease Evaluation (GREACE) study, atorvastatin reduced incident cardiovascular disease compared with both untreated NAFLD patients and with statin-treated patients without NAFLD. Ezetimibe was evaluated in two uncontrolled trials and two RCTs, consistently improving liver histology and plasma lipids, whereas glucose metabolism was generally unaffected; however, HbA1c increased with ezetimibe in one RCT. Summary From the analysis of available trials, it emerges that cholesterol-lowering agents may considerably benefit NAFLD patients. Statins are well tolerated, and atorvastatin improved surrogate markers of liver disease, whereas their effect on liver histology is unknown. Furthermore, the GREACE study was the first trial to show clinical benefit from the use of a pharmacological agent in NAFLD. Ezetimibe improved liver histology. The benefit of combination therapy, as well as the safety on glucose metabolism, need further evaluation.
Human Capital and Shocks: Evidence on Education, Health and Nutrition

Human capital, including health and nutrition, has played a key role in the literature on poverty traps. Economic shocks that affect human capital during early life are thought to translate into permanently reduced levels of human capital and, thereby, push individuals into poverty. Three potential concerns in this literature are explored with empirical evidence drawn from primary longitudinal survey data collected before and after two major shocks in Indonesia: the 1998 financial crisis and the 2004 Indian Ocean tsunami. First, it is very hard to identify shocks that are unanticipated and uncorrelated with other factors that affect human capital outcomes. Second, and related, there is abundant evidence that individuals, families and communities invest in strategies that are designed to mitigate the impact of such shocks. The nature and effectiveness of the myriad array of these behaviors vary with the context in ways that are not straightforward to measure or model. Third, the impacts of shocks on human capital outcomes in the short and longer-term may differ precisely because of the behavioral changes of individuals and their families so that drawing inferences about the longer-term impacts based on negative impacts in the short term can be very misleading. The picture of remarkable resilience that emerges from investigating the impacts of major shocks on child health and human capital in Indonesia is nothing short of stunning.
Access to Microcredit and Women's Entrepreneurship: Evidence from Bangladesh

This paper intends to assess the impact of access to microcredit on women’s entrepreneurship in Bangladesh. The descriptive statistics and multivariate techniques have been used to achieve the objective of the paper. The study uses Household Income and Expenditure survey (HIES) 2010 dataset. The HIES 2010 survey covers 12,240 households from all districts in the country. Considering the endogeneity in the microcredit program participation of women, the study uses an instrumental variables technique (IV method) to assess the impact of access to microcredit on the entrepreneurial status of women. After adjustment for the endogeneity, the results from the multivariate analysis indicate that access to microcredit has a significant and positive impact on women’s entrepreneurship. It also has a significant and positive impact on men’s entrepreneurship and the marginal effects of access to microcredit are stronger on men’s entrepreneurship than on women’s entrepreneurship.
Introduction and Appendix to Behavioral Risk Management in the Financial Services Industry: The Role of Culture, Governance, and Financial Reporting

This volume, four years in the making, includes nine research papers that aim to identify and understand the key factors affecting governance and culture in the banking industry. The volume is divided into two complementary parts. Part I introduces the concept of culture and its importance to risk management and financial stability. The articles present a framework for diagnosing and changing culture, describe how corporate culture is shaped, explore the importance of effective risk management, and examine the roles of deferred cash compensation and bank cash holdings in promoting financial stability. Part II assesses critical areas of corporate governance: the role of boards of directors, the monitoring function of large outside shareholders, the importance of financial disclosure and transparency, and the relationship between banks’ disclosure practices and performance. The appendix to the volume provides an extensive list of additional questions for future research. These questions extend and augment the important research presented in the volume and should help advance the burgeoning study of the role of culture and governance in banking.
Streptozotocin-Induced Diabetes Mellitus in Pigs

We induced, as a precondition for a pancreas transplant, insulin-dependent diabetes mellitus in 67 Yorkshire Landrace pigs by administering streptozotocin. A dosage of 150 mg/kg body weight gave rise to a long-lasting diabetes mellitus that persisted with time (follow-up period: 26 weeks). Consecutive measurements of serum glucose and plasma insulin, before and up to 30 hours after administering streptozotocin, revealed triphasic behavior: initial hyperglycemia (1st to 3rd hour), pronounced hypoglycemia (12th to 18th hour), then hyperglycemia (22nd hour on). IVGTTs done 1 to 7 days after administering streptozotocin revealed a reduction of the K-value (glucose disappearance rate) from 0.3 (day 2) to 0.07 (day 4). Immunohistochemical studies revealed a complete loss of all beta-cells, concomitantly with a relative increase in glucagon- and somatostatin-positive cells. We also observed a complete loss of pp (pancreatic polypeptide)-positive cells. Diabetes induced by streptozotocin at 150 mg/kg body weight is complete and permanent; our mortality rate was 0%. Given the high morbidity rate after pancreatectomy, streptozotocin should be the method of choice for inducing diabetes mellitus in pigs.
Longitudinal cephalometric standards for Norwegians between the ages of 6 and 18 years.

The purpose of the present study was to develop normative cephalometric standards for Norwegians from 6 to 18 years of age. The subjects in the study included 39 females and 35 males, from the Nittedal growth material. All subjects were Caucasians, and none had undergone orthodontic therapy, all had clinically acceptable normal occlusions and no apparent facial disharmony. Twenty-six measurements were analysed according to the cephalometric analysis used at the University of Oslo Department of Orthodontics. The measurements of posterior facial height, skeletal and soft tissue profiles were also included Comparisons between the dentofacial parameters of females and males at each age were performed using Student's t-test. Significant differences between females and males were present particularly at ages 12 and 15 years of age. There was a significant mean increase in NL/NSL in both sexes from 6 to 15 years of age, but more in females. There was a significant mean decrease in ML/NSL from 6 to 18 years of age, and the angle was significantly smaller in males than in females. The anterior and posterior facial height increased in both sexes from 6 to 18 years of age. The largest increase was in males. Males showed slightly more proclined upper incisors at age 9, 12, and 15 years than females. S-N-A increased more in males than females with the largest increase between 9 and 15 years of age. S-N-B increased in both sexes from 6 to 18 years of age with the largest increase in males. (ABSTRACT TRUNCATED AT 250 WORDS)
Development of competence in Streptococcus pneumoniae: pheromone autoinduction and control of quorum sensing by the oligopeptide permease

Competence for genetic transformation in the human pathogen Streptococcus pneumoniae is a transient physiological property. A competence‐stimulating peptide, CSP, was recently identified as the processed product of the comC gene. As conflicting results have been reported regarding CSP autoinduction, we monitored the CSP‐induced expression of comCDE in derivatives of strain R6 using comC::lacZ fusions. Autoinduction was demonstrated in this genetic background. The kinetics of CSP‐induced transcription of comCDE and of a late competence‐induced (cin) operon were compared. While the comCDE mRNA level was highest 5 min after CSP addition then decreased, maximal cin expression required 10 min exposure to CSP. Transformation frequencies paralleled cin expression. After 20 min exposure to CSP, both mRNAs disappeared almost completely, providing evidence for an intrinsic mechanism for shutting off CSP signal transduction. Investigation of spontaneous competence development in mixed cultures indicated that transformation of wild‐type cells was delayed in the presence of CSP non‐producers, consistent with a direct role of CSP in quorum sensing. The effect of varying inoculum size on the timing of competence development was investigated. While competence developed in wild‐type cultures at a similar critical density, about OD550 = 0.15, a mutant lacking the three oligopeptide‐binding lipoproteins transformed at a 50‐fold reduced cell density. The latter effect was mimicked in a strain harbouring a duplication of comC. Altogether, these results suggest that CSP does not accumulate passively in pneumoccal cultures, but that comCDE basal expression can be modulated.
The influence of missing value imputation on detection of differentially expressed genes from microarray data

MOTIVATION Missing values are problematic for the analysis of microarray data. Imputation methods have been compared in terms of the similarity between imputed and true values in simulation experiments and not of their influence on the final analysis. The focus has been on missing at random, while entries are missing also not at random. RESULTS We investigate the influence of imputation on the detection of differentially expressed genes from cDNA microarray data. We apply ANOVA for microarrays and SAM and look to the differentially expressed genes that are lost because of imputation. We show that this new measure provides useful information that the traditional root mean squared error cannot capture. We also show that the type of missingness matters: imputing 5% missing not at random has the same effect as imputing 10-30% missing at random. We propose a new method for imputation (LinImp), fitting a simple linear model for each channel separately, and compare it with the widely used KNNimpute method. For 10% missing at random, KNNimpute leads to twice as many lost differentially expressed genes as LinImp. AVAILABILITY The R package for LinImp is available at http://folk.uio. no/idasch/imp.
Systemic Risks and Financial Fragility in a Small Open Economy

This book contributes to a better understanding of financial system fragility in Bosnia and Herzegovina and similar countries in several ways. It is found that both country and period specifics must be accounted for. Accordingly, each country should develop its own tailored measure of systemic risk, since some of the widely used set of indicators may distort the perception of risk. There are substantial gains in modelling the risks of banking and currency crises as a system. It is demonstrated that even in a country with a simple financial system and dominant banking sector a single model cannot explain the evolution of systemic risk over the cycle. The nature of the risk factors, their relations with the perceived level of fragility, as well as the relationship between the measures of systemic risk were found to differ in pre-shock from the post-shock periods. Finally, it is shown that even simple financial systems are inherently unstable, with destabilizing relationships between the risks of banking and currency crises and developments in the real economy.
Development of Contact Material Solutions for Low-Voltage Circuit Breaker Applications (2)

The focus of the experimental studies was in the influence of contact material composition, production parameters and the contact material - breaker interaction, as the performance of the breaker is a function of breaker design, contact material and especially their interaction. Therefore, typical material combinations used for low voltage protection devices were compared by means of their switching behavior and performance. Model-switch tests have been carried out to show this performance under stable and well defined boundary conditions. The chosen test parameters simulate device tests, excluding the influence of switching device kinematics and tolerances. Focus of the tests was to scrutinize the influence of the material composition on the erosion behavior and contact resistance for AgWC materials. Additionally a comparison on the performance of different silver refractory metals like AgW or AgMo at comparable vol.-% refractory metal was made. Furthermore, the impact of different graphite contents, manufacturing parameters and fiber orientation of AgC materials on weld break forces have been worked out. This experimental quantification of influences can be seen as a basis for contact material selection during protection device design.
Neuronal Food Reward Activity in Patients With Type 2 Diabetes With Improved Glycemic Control After Bariatric Surgery

OBJECTIVE Obesity and type 2 diabetes mellitus (T2DM) are associated with altered food-related neuronal functions. Besides weight loss, substantial improvement of glucose metabolism in patients with T2DM can be achieved by bariatric surgery. We aimed to target the neuronal and behavioral correlates of improved glycemic control after bariatric surgery. RESEARCH DESIGN AND METHODS Two patient groups with T2DM were recruited. The treatment group (n = 12) consisted of patients who had undergone Roux-en-Y gastric bypass (RYGB) surgery, and a control group consisted of patients who did not undergo surgery (n = 12). The groups were matched for age and current BMI. HbA1c was matched by using the presurgical HbA1c of the RYGB group and the current HbA1c of the nonsurgical group. Neuronal activation during a food reward task was measured using functional MRI (fMRI). Behavioral data were assessed through questionnaires. RESULTS RYGB improved HbA1c from 7.07 ± 0.50 to 5.70 ± 0.16% (P < 0.05) and BMI from 52.21 ± 1.90 to 35.71 ± 0.84 kg/m2 (P < 0.001). Behavioral results showed lower wanting and liking scores as well as lower eating behavior–related pathologies for the patients after RYGB than for similar obese subjects without surgery but with impaired glycemic control. The fMRI analysis showed higher activation for the nonsurgical group in areas associated with inhibition and reward as well as in the precuneus, a major connectivity hub in the brain. By contrast, patients after RYGB showed higher activation in the visual, motor, cognitive control, memory, and gustatory regions. CONCLUSIONS In obese patients with diabetes, RYGB normalizes glycemic control and leads to food reward–related brain activation patterns that are different from those of obese patients with less-well-controlled T2DM and without bariatric surgery. The differences in food reward processing might be one factor in determining the outcome of bariatric surgery in patients with T2DM.
Direct stenting of de novo coronary stenoses with tacrolimus-eluting versus carbon-coated carbostents. The randomized JUPITER II trial.

AIMS Drug-eluting stents are being increasingly used for the treatment of de novo coronary lesions. This trial compared the performance of tacrolimus-eluting stents (TES) with that of equivalent carbon-coated stents (CCS). METHODS AND RESULTS The JUPITER II trial enrolled 332 patients (mean age = 64 years, 75% men) with de novo coronary stenoses. Patients were randomly assigned to TES versus CCS and underwent repeat coronary angiography at 6 months. The primary study endpoint was in-stent and in-segment late lumen loss (LLL). The main secondary endpoints included binary restenosis, and rates of major adverse clinical events (MACE), including death, myocardial infarction, target lesion revascularisation and stent thrombosis at 1, 6, and 12 months of follow-up. The procedure was successful in 99.4% of patients in both groups. There was no procedural death, 1 cardiac death at 2 months, and 1 acute and 2 subacute CCS thromboses. Angiographic follow-ups were available in 94.4% and 95.1% of patients assigned to TES and CCS, respectively. The mean in-segment and in-stent LLL was 0.42+/-0.46 mm and 0.65+/-0.47 mm, respectively, in the TES, versus 0.48+/-0.52 mm and 0.66+/-0.53 mm, respectively, in the CCS group (ns). The 12-month cumulative MACE rate was 19.5% in the CCS versus 16.1% in the TES group (ns). CONCLUSIONS Both stents showed high safety, with no stent thrombosis in the TES group. No difference was observed in 6-month angiographic results and 12-month MACE rates between TES and CCS.
Sex preparation and diaphragm acceptability in sex work in Nairobi, Kenya.

BACKGROUND Women in sex work stand to benefit if the contraceptive diaphragm alone or combined with a microbicide proves to be an effective barrier method against HIV and sexually transmissible infection (STI). Currently, contraceptive diaphragm users are advised to leave the diaphragm in situ without concomitant use of other intravaginal substances for at least 6 h after intercourse. METHODS We conducted in-depth interviews on sexual behaviour including post-coital intravaginal practices with 36 women in sex work and 26 of their clients and held two focus-group discussions, each with 10 women. RESULTS The women described adapting several potentially harmful substances, such as cloth and soapy water, for post-coital vaginal use to ensure personal hygiene, disease prevention and client pleasure. Some wanted to clean themselves and remove the diaphragm early, fearing exposure to HIV infection for themselves and their subsequent clients. Clients indicated their desire for 'dry sex', vaginal cleanliness and reduced risk of infection through vaginal cleaning. CONCLUSIONS The diaphragm as a female-controlled barrier method for HIV/STI prevention may have limited acceptability among women in sex work if its effectiveness depends on a 6-h post-coital wait before removal, along with avoidance of concomitant use of intravaginal substances. In keeping with the beliefs of the the female sex workers and their needs and practices, alternative intravaginal substances and modes of insertion that will not disrupt vaginal flora, injure vaginal epithelium, damage the diaphragm or counteract potentially beneficial effects of microbicides are needed. The possibility of removing the diaphragm sooner than the recommended 6 h for contraception should be further studied.