Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Epidemiology and Evolution of European Bat Lyssavirus 2

Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1) and European Bat Lyssavirus 2 (EBLV-2). Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986–1987) identified 263 cases (more than a fifth of all reported cases to date). Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97%) being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; Myotis daubentonii and Myotis dasycneme. The limited number of EBLV-2 cases in Europe prompted the establishment of a network of European reference laboratories to collate all available viruses and data. Despite the relatively low number of EBLV-2 cases, a large amount of anomalous data has been published in the scientific literature, which we have here reviewed and clarified. In this review, 29 EBLV-2 full genome sequences have been analysed to further our understanding of the diversity and molecular evolution of EBLV-2 in Europe. Analysis of the 29 complete EBLV-2 genome sequences clearly corroborated geographical relationships with all EBLV-2 sequences clustering at the country level irrespective of the gene studied. Further geographical clustering was also observed at a local level. There are high levels of homogeneity within the EBLV-2 species with nucleotide identities ranging from 95.5–100% and amino acid identities between 98.7% and 100%, despite the widespread distribution of the isolates both geographically and chronologically. The mean substitution rate for EBLV-2 across the five concatenated genes was 1.65 × 10−5, and evolutionary clock analysis confirms the slow evolution of EBLV-2 both between and within countries in Europe. This is further supported by the first detailed EBLV-2 intra-roost genomic analysis whereby a relatively high sequence homogeneity was found across the genomes of three EBLV-2 isolates obtained several years apart (2007, 2008, and 2014) from M. daubentonii at the same site (Stokesay Castle, Shropshire, UK).
Dental overjet, articulatory compensation and acoustics of speech

Purpose: Dentofacial abnormalities such as dental overjet (horizontal overlap of upper and lower incisors) have been linked, with mixed evidence at times, to misarticulations before and after corrective surgery in severe cases 1 . Many individuals, even in surgical populations, appear to successfully achieve typical-sounding productions by using compensatory adaptation of the speech articulators 2 . This may explain the seeming inconsistencies in the literature, especially in studies where the sample is not selected for occlusal or speech problems. However, previous research relating to malocclusion and speech has largely been based on perceptual judgments of misarticulation rather than objective acoustic measures. As such, this study seeks to investigate the association between degree of increased overjet (protrusion of upper incisors) in non-surgical populations and speech production using acoustic analysis. Methods: Native English speakers recorded 13 target words containing either the English fricatives /s, z, ? /, affricates /t? , d? /, or vowels /i, u, ? /. Measurements of dental overjet as well as language background information were collected. Each segment was analysed by spectral moments for fricatives and formant values for vowels, then related to the speaker’s degree of overjet. Results: Preliminary analysis suggests that acoustic values of certain fricatives correlate to amount of overjet, as do some vowel formants. Trained listeners note that intelligibility does not appear to be compromised perceptually. Conclusion: The results of this experiment add to the literature on the relationship between dental anomalies and articulation with quantitative acoustic measures, as well as on the role of articulatory compensation in the case of increased overjet. References 1 Ruscello, D.M. , Tekieli, M.E. , & Van Sickels, J.E. (1985). Speech production before and after orthognathic surgery: A review. Oral Surgery, Oral Medicine, Oral Pathology, 59 (1), 10-14. 2 Johnson, N.C. , & Sandy, J.R. (1999). Tooth position and speech – is there a relationship? The Angle Orthodontist , 69 (4), 306-310.
Laxative Use in the Setting of Positive Testing for Clostridium difficile Infection

diarrhea in long-term care facilities: what you get is not what you see. Infect Control Hosp Epidemiol 2008;29:760–763. 3. Guerrero DM, Nerandzic MM, Jury LA, Chang S, Jump RL, Donskey CJ. Clostridium difficile infection in a Department of Veterans Affairs long-term care facility. Infect Control Hosp Epidemiol 2011;32:513–515. 4. Mylotte JM, Russell S, Sackett B, Vallone M, Antalek M. Surveillance for Clostridium difficile infection in community nursing homes. J Am Geriatr Soc 2013;61:122–125. 5. Brown KA, Jones M, Daneman N, et al. Importation, antibiotics, and Clostridium difficile infection in veteran long-term care: a multilevel case-control study. Ann Intern Med 2016;164:787–794.
Role of forkhead box protein A3 in age-associated metabolic decline

Significance This paper reports that the transcription factor forkhead box protein A3 (Foxa3) is directly involved in the development of age-associated obesity and insulin resistance. Mice that lack the Foxa3 gene remodel their fat tissues, store less fat, and burn more energy as they age. These mice also live significantly longer. We show that Foxa3 suppresses a key metabolic cofactor, PGC1α, which is involved in the gene programs that turn on energy expenditure in adipose tissues. Overall, these findings suggest that Foxa3 contributes to the increased adiposity observed during aging, and that it can be a possible target for the treatment of metabolic disorders. Aging is associated with increased adiposity and diminished thermogenesis, but the critical transcription factors influencing these metabolic changes late in life are poorly understood. We recently demonstrated that the winged helix factor forkhead box protein A3 (Foxa3) regulates the expansion of visceral adipose tissue in high-fat diet regimens; however, whether Foxa3 also contributes to the increase in adiposity and the decrease in brown fat activity observed during the normal aging process is currently unknown. Here we report that during aging, levels of Foxa3 are significantly and selectively up-regulated in brown and inguinal white fat depots, and that midage Foxa3-null mice have increased white fat browning and thermogenic capacity, decreased adipose tissue expansion, improved insulin sensitivity, and increased longevity. Foxa3 gain-of-function and loss-of-function studies in inguinal adipose depots demonstrated a cell-autonomous function for Foxa3 in white fat tissue browning. Furthermore, our analysis revealed that the mechanisms of Foxa3 modulation of brown fat gene programs involve the suppression of peroxisome proliferator activated receptor γ coactivtor 1 α (PGC1α) levels through interference with cAMP responsive element binding protein 1-mediated transcriptional regulation of the PGC1α promoter. Overall, our data demonstrate a role for Foxa3 in energy expenditure and in age-associated metabolic disorders.
Streptococcal pharyngitis, rheumatic fever and rheumatic heart disease: Eight-year prospective surveillance in Rupnagar district of Punjab, India.

BACKGROUND Rheumatic fever (RF)/rheumatic heart disease (RHD) continue to be a neglected public health priority. We carried out a registry-based control project, prospective surveillance and sample surveys to estimate the burden of disease. METHODS We trained healthcare providers and established a surveillance system for the 1.1 million population of Rupnagar district in Punjab. In sample surveys conducted among schools, physicians examined the sampled children. Children with a cardiac murmur were investigated by echocardiography. Throat swabs were obtained from a sub-sample, and group A streptococci (GAS) were identified and emm typed by standard laboratory methods. We estimated the morbidity rates for RF/RHD from surveillance data and school surveys using a correction factor to account for under-registration of cases in the registry. RESULTS A total of 813 RF/RHD cases were registered from 2002 to 2009. Of the 203 RF and 610 RHD cases, respectively, 51.2% and 36.7% were males. In the age group of 5-14 years, RF was more common (80%) than RHD (27%). The prevalence of RF/RHD in 5-14-year-old students was 1.0/1000 (95% CI 0.8-1.3). The school survey indicated that about two-thirds of the RF/RHD cases were enrolled in the hospital-based registries. Based on the school survey, the prevalence of RF/RHD was estimated to be 143/100,000 population. In the registry, the annual incidence of acute RF was estimated to be at least 8.7/100 000 children in the age group of 5-14 years. The prevalence of GAS was 2% (13/656) in children with sore throat and 0.5% (14/2920) among those not having sore throat. Typing of 27 GAS revealed 16 emm types. We estimate that about 1000 episodes of GAS pharyngitis lead to one episode of acute RF. CONCLUSION RF/RHD continue to be a public health problem in Punjab, India.
Sim-to-Real Reinforcement Learning for Deformable Object Manipulation

We have seen much recent progress in rigid object manipulation, but interaction with deformable objects has notably lagged behind. Due to the large configuration space of deformable objects, solutions using traditional modelling approaches require significant engineering work. Perhaps then, bypassing the need for explicit modelling and instead learning the control in an end-to-end manner serves as a better approach? Despite the growing interest in the use of end-to-end robot learning approaches, only a small amount of work has focused on their applicability to deformable object manipulation. Moreover, due to the large amount of data needed to learn these end-to-end solutions, an emerging trend is to learn control policies in simulation and then transfer them over to the real world. To-date, no work has explored whether it is possible to learn and transfer deformable object policies. We believe that if sim-to-real methods are to be employed further, then it should be possible to learn to interact with a wide variety of objects, and not only rigid objects. In this work, we use a combination of state-of-the-art deep reinforcement learning algorithms to solve the problem of manipulating deformable objects (specifically cloth). We evaluate our approach on three tasks --- folding a towel up to a mark, folding a face towel diagonally, and draping a piece of cloth over a hanger. Our agents are fully trained in simulation with domain randomisation, and then successfully deployed in the real world without having seen any real deformable objects.
Firm Investment in Imperfect Capital Markets: A Structural Estimation

We set up a dynamic model of firm investment in which liquidity constraints enter explicity into the firm's maximization problem. The optimal policy rules are incorporated into a maximum likelihood procedure which estimates the structural parameters of the model. Investment is positively related to the firm's internal financial position when the firm is relatively poor. This relationship disappears for wealthy firms, which can reach their desired level of investment. Borrowing is an increasing function of financial position for poor firms. This relationship is reversed as a firm's financial position improves, and large firms hold little debt. Liquidity constrained firms may be unused credits lines and the capacity to invest further if they desire. However the fear that liquidity constraints will become binding in the future induces them to invest only when internal resources increase. We estimate the structural parameters of the model and use them to quantify the importance of liquidity constraints on firms' investment. We find that liquidity constraints matter significantly for the investment decisions of firms. If firms can finance investment by issuing fresh equity, rather than with internal funds or debt, average capital stock is almost 35% higher over a period of 20 years. Transitory shocks to internal funds have a sustained effect on the capital stock. This effect lasts for several periods and is more persistent for small firms than for large firms. A 10% negative shock to firm fundamentals reduces the capital stock of firms which face liquidity constraints by almost 8% over a period as opposed to only 3.5% for firms which do not face these constraints.
Heydrichia (?) poignantii, sp nov (Sporolithaceae, Sporolithales, Rhodophyta), a 100 million year old fossil coralline red alga from north-eastern Brazil, and a new Hauterivian record of Sporolithon from Switzerland

Fossil specimens of Heydrichia (? ) poignantii, sp. nov. (Sporolithaceae, Sporolithales, Rho- dophyta), representing the first confirmation of the genus in the fossil record, were discovered in thin sections of Albian limestones from the Riachuelo Formation, Sergipe Basin, and in thin sections of Al- bian - Cenomanian limestones from the Ponta do Mel Formation, Potiguar Basin in north-eastern Brazil. A detailed morphological-anatomical account of the species is provided, and its placement in Heydrichia is discussed in relation to current classification proposals. Comparisons with the four other known spe- cies of the genus, all non-fossil, show that H. poignantii is the only known species of Heydrichia in which thalli are encrusting to sparsely warty to horizontally layered with overlapping lamellate branches that commonly appear variously curved or arched, and in which thalli have sporangial complexes that become buried in the thallus. The evolutionary history of Heydrichia remains uncertain, but available data suggest that the genus may have diverged from the sporolithacean genus Sporolithon, known as early as Hauterivian times (c. 129.4-132.9 ± 1 Ma) from Spain (and newly reported here from Switzer- land), or it may have arisen from a graticulacean alga such as Graticula, dating from mid-Silurian times (c. 427-435 Ma). Current data also suggest that Heydrichia is more likely to have arrived in Brazil from Central Atlantic waters than from higher latitude South Atlantic waters. This implies that currently living species in southern Africa probably arose later from ancestors further equatorward in the South At- lantic, although confirming studies are needed. All non-fossil species of Heydrichia are known only from the southern hemisphere.
WIDER Working Paper 2014 / 037 Regional integration in Africa Challenges and prospects

The small, sparsely populated, fragmented, and often isolated economies across Africa make a compelling case for these economies to integrate regionally to, reap efficiency gains, exploit economies of scale, and reduce the thickness of borders. But lack of complementarities among partners and diminishing returns to the exploitation of resources has reduced supply response to market-integration-oriented regional policies. African Regional Economic Communities (RECs) have pursued the “linear model” of integration with a stepwise integration of goods, labor, and capital markets, as well as eventual monetary and fiscal integration. Estimates reported here reveal the shortcomings of the linear model of integration, as behind-the-border measures aiming to reduce trade costs were largely ignored across African RECs until recently. While this is probably due to the difficulty in gaining the confidence necessary to get collection action started, many behind-the-border measures could still have been undertaken unilaterally. DE MELO, Jaime, TSIKATA, Yvonne. Regional integration in Africa: Challenges and prospects. In: Monga, C. & Yifu Lin, J. The Oxford Handbook of Africa and Economics: Policies and Practices. Oxford : Oxford University Press, 2014. DOI : 10.1093/oxfordhb/9780199687107.013. 014
Cognitive predictors of physical activity behaviors among rural patients with type 2 diabetes: applicability of the Extended Theory of Reasoned Action (ETRA)

Background: This study aims to examine the cognitive-behavioral determinants of physical activity behaviors (PABs) of patients diagnosed with type 2 diabetes. Subjects and methods: In this cross-sectional study, census sampling was employed to enroll 120 rural patients with type 2 diabetes in the Chalderan County in 2015. To collect data, a valid and reliable instrument, based on the Extended Theory of Reasoned Action (ETRA) constructs, was used. Data were analyzed by SPSS 21 software using descriptive and inferential statistical methods. Results: Using the one-way ANOVA test, it was found that PABs had statistically significant correlation with all ETRA constructs except subjective norms (P=0.574). Knowledge (P=0.015), self-efficacy (P<0.001) and behavioral intention (P<0.001) had a significant association with PABs, respectively. Also, ETRA structures were able to reflect 41.0% of the behavioral changes. Among structures, knowledge (P=0.014), self-efficacy (P<0.001), and behavioral intention (P=0.020) were significant predictors of PABs (R2=0.414). Conclusions: Health care providers may consider the ETRA an appropriate framework to design educational interventions aimed at improving PABs among rural patients with type 2 diabetes.
Is Providing a "Study Hall" the Key to Flipped Classroom Effectiveness?

W e were excited to read the recent study by Graham et al regarding the effectiveness of the flipped classroom (FC) in acquiring and retaining knowledge in an internal medicine residency program. This was a well-constructed and well-executed study that demonstrated a significant increase in knowledge acquisition and a sustained effect after several months for residents in a FC compared with a traditional didactic format. These findings contrast with prior systematic review results that failed to show a learning benefit via the FC method in graduate medical education. A striking difference between this study and those included in the systematic review was the provision of protected study time to do the prework embedded within the process. Thus, this study does not compare a true FC model to a traditional lecture format, but rather the FC model plus protected study time versus traditional lecture format. This is a critical distinction as prior studies have shown poor compliance with prework, with rates of compliance ranging from only 25% to 69%, even when the prework requires only watching a 10-minute video. Consistent with this is Graham and colleagues’ finding that 66% of study participants thought this style of learning would not be feasible on an inpatient rotation, which many respondents (24%) attributed to a lack of protected study time. On a positive note, this study provides a possible solution to making the FC model effective in graduate medical education, namely structured learning time for prework. Importantly, this makes it impossible to distinguish the effects of the FC from the effects of dedicated study time. As the authors appropriately state, ‘‘. our results do not delineate whether the impact of the flipped classroom derived from the prework or the active learning experience. ’’ Future studies and systematic reviews should distinguish this methodological difference. We feel compelled to point out that, after residency, protected study time does not exist. Consequently, an important future question is whether providing protected study time across an entire curriculum would limit growth of residents’ ability to selfregulate their learning.
Trends of Major Cardiovascular Risk Factors in Iranian Population During Years 2001 - 2013: The Isfahan Cohort Study

Background: Trends of major cardiovascular risk factors are less investigated in Middle-Eastern countries. Objectives: This study aimed to assess the trend of major cardiovascular risk factors among Iranian individuals. Methods: This Longitudinal population-based study was performed by multistage random sampling on 6504 participants aged at least 35 years for 12 years initiating in 2001 until 2013 in three phases. Cardiovascular risk factors including systolic blood pressure (SBP), diastolic blood pressure (DBP), waist circumference (WC), waist to hip ratio (WHR), body mass index (BMI), fasting blood sugar (FBS) and lipid indices were measured for each subject in 2001, 2007 and 2013 and were analyzed using repeated measure analysis of variance using Bonferroni correction. Results: Mean value of SBP, DBP, BMI and FBS increased significantly in both genders during follow-up (SBP: 119.3 ± 18.7 to 128.4 ± 17.5 mmHg, P value < 0.001, DBP: 76.7 ± 11.8 to 82.8 ± 12.5 mmHg, P value < 0.001, BMI: 27.4 ± 4.4 to 28 ± 4.6 kg/m, P value < 0.001, FBS: 86.7 ± 29.6 to 106.5 ± 38 mg/dL, P value < 0.001). Lipid profiles including total cholesterol (TC), triglyceride (TG), lowdensity lipoprotein cholesterol (LDL-C) and TG/ high-density lipoprotein cholesterol (HDL-C) showed favorable downward patterns in population (TC: 219.5±51.3 to 200.1±40.9 mg/dL, P value < 0.001, TG: 200.2± 110.3 to 155.1±85 mg/dL, P value < 0.001, LDL-C: 132.6 ± 42.4 to 111.7 ± 27.8 mg/dL, P value < 0.001, TG/HDL-C: 4.5 ± 2.8 to 3.9 ± 2.8, P value < 0.001) with an exception of HDL-C showing less desirable results. In spite of controversial results in terms of WC and WHR changes relative to gender, total population changes of those variables were not significant. Conclusions: Although favorable patterns were observed in most lipid indices, other risk factors showed an inverse or insignificant trend. Several health-promoting strategies are required in order to improve lifestyle in a way that those raising cardiovascular risk factor trends would decline.