Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic quasispecies associated with the initiation of infection and disease in ponies experimentally infected with equine infectious anemia virus

Equine infectious anemia virus (EIAV) provides a uniquely dynamic system in which to study the mechanism and role of genomic variation in lentiviral persistence and pathogenesis. We have used a Shetland pony model of infection to investigate the association of specific long terminal repeat (LTR) and env gene genomic sequences with the initiation of infection and the onset of disease. We analyzed viral RNA isolated from a pathogenic stock of virus (EIAV PV) and from plasma taken during the first disease episode from two ponies infected with EIAV PV. Overall sequence variation within gp90 was low in EIAV PV and only slightly higher in plasma virus samples isolated from ponies during the first disease episode. However, a high proportion of mutations were localized to the principal neutralizing domain in EIAV PV and to the principal neutralizing domain and the gp90 hypervariable region in the two pony-derived samples. The rate of fixation of mutations was analyzed and determined to be approximately 4 x 10(-2) mutations per site per year. Sequence diversity within the U3 region of the LTR was extremely low, which suggested that the previously reported hypervariability of this region may be a consequence of selection for replication of EIAV in different host cells. The predominant EIAV PV env and LTR sequences were used to construct chimeric viruses so that the contribution of these sequences to viral pathogenicity could be examined. The chimeras replicated in cultured equine monocytes to the same extent as the parental nonpathogenic virus and did not cause disease in Shetland ponies by 120 days postinfection, suggesting that the EIAV genomic determinants of pathogenesis are complex.
A Survey on Commercial Starter Kits for Building Real Robots

Many starter kits are commercially available now to assist robots’ hobbyists in designing, building, and programming working robots. This paper serves as a critical survey paper that describes the available robotics kits. This survey addresses issues such as modularity, reusability of the building blocks, versatility, price, etc. The paper pretends to shed some light to researchers and hobbyist on the possibility of building real robots with low-cost market available starter kits.
Bounds on causal effects in randomized trials with noncompliance under monotonicity assumptions about covariates

In randomized trials with nonrandom noncompliance, the causal effects of a treatment among the entire population cannot be estimated in an unbiased manner. Therefore, several authors have considered the bounds on the causal effects. Here, we propose bounds by applying an idea of VanderWeele (Biometrics 2008; 64:702–706), who showed that the sign of the unmeasured confounding bias can be determined under monotonicity assumptions about covariates in the framework of observational studies. In randomized trials with noncompliance by switching the treatment, we show that the lower or upper bound on the expectation of the potential outcome becomes the expectation from the per‐protocol analysis under monotonicity assumptions similar to those of VanderWeele. In particular, the monotonicity assumptions can yield both the lower and the upper bounds on causal effects when the monotonic relationship between the covariates and the treatment actually received depends on the treatment assigned. The results are extended to cases of noncompliance by subjects not receiving any treatment. Although the monotonicity assumptions are not themselves identifiable, they are nonetheless reasonable in some situations. Copyright © 2009 John Wiley & Sons, Ltd.
Propulsion Forces as a Function of Intensity for Weightlifting and Vertical Jumping

Four Olympic-style weightlifters and six athletes from other sports volunteered to perform maximal and submaximal vertical jumps with countermovement and/or snatch lifts on a Kistler force plate to compare the kinetics of the two activities at different levels of effort. Parameters studied included maximum vertical ground reaction force generated during a snatch lift or jump for both maximal and submaximal efforts and force duration at magnitudes greater than 50, 80 and 90 percent of max during the propulsion phase of each activity. Results indicated that in both activities, as the level of performance (intensity) increased, maximal propulsion force magnitudes generally decreased, whereas the duration of force at higher percentages of maximum increased. Qualitative similarities in the temporal pattern of vertical ground reaction force for each activity were observed in both unweighting and propulsion phases. Use of a double knee bend lifting technique accounted for an unweighting phase during the snatch lifts. Data indicated that the athletes used adjustments in temporal pattern of propulsive force application, rather than an increase in the magnitude of force generated for maximal versus submaximal efforts in both activities. Athletes who require improved jumping ability may benefit from utilizing Olympic lifting movements as part of their strength training program due to the applied overload and the similarities found between the propulsive force patterns of each activity.
Phthalates and Perfluorooctanesulfonic Acid in Human Amniotic Fluid: Temporal Trends and Timing of Amniocentesis in Pregnancy

Background: Measures of prenatal environmental exposures are important, and amniotic fluid levels may directly reflect fetal exposures during hypothesized windows of vulnerability. Objectives: We aimed to detect various phthalate metabolites and perfluorooctanesulfonic acid (PFOS) in human amniotic fluid, to study temporal exposure trends, and to estimate potential associations with gestational week of amniocentesis and maternal age and parity at amniocentesis. Methods: We studied 300 randomly selected second-trimester amniotic fluid samples from a Danish pregnancy-screening biobank covering 1980 through 1996. We used only samples from male offspring pregnancies. We assayed the environmental pollutants by liquid chromatography/triple quadrupole mass spectrometry and analyzed data using generalized linear regression models. Results: We detected the di(2-ethylhexyl) phthalate (DEHP) metabolite mono(2-ethyl-5-carboxypentyl) phthalate (5cx-MEPP) at a median concentration of 0.27 ng/mL [interquartile range (IQR): 0.20–0.37 ng/mL], the diisononyl phthalate (DiNP) metabolite mono(4-methyl-7-carboxyheptyl) phthalate (7cx-MMeHP) at 0.07 ng/mL (IQR: 0.05–0.11 ng/mL), and PFOS at 1.1 ng/mL (IQR: 0.66–1.60 ng/mL). An increase of 1 calendar year was associated with 3.5% lower [95% confidence interval (CI): –4.8%, –2.1%] 5cx-MEPP levels and with 7.1% higher (95% CI: 5.3%, 9.0%) 7cx-MMeHP levels. For each later gestational week of amniocentesis, 5cx-MEPP was 9.9% higher (95% CI: 4.8%, 15.2%), 7cx-MMeHP was 8.6% higher (95: CI: 2.7%, 14.9%), and PFOS was 9.4% higher (95: CI: 3.3%, 15.9%). We observed no associations with maternal age or parity. Conclusions: Measured metabolite levels appeared to parallel decreasing DEHP exposure and increasing DiNP exposure during the study period. The environmental pollutant levels were positively associated with later gestational age at amniocentesis during pregnancy weeks 12–22.
A Comparison of the Lasso and Marginal Regression

The lasso is an important method for sparse, high-dimensional regression problems, with efficient algorithms available, a long history of practical success, and a large body of theoretical results supporting and explaining its performance. But even with the best available algorithms, finding the lasso solutions remains a computationally challenging task in cases where the number of covariates vastly exceeds the number of data points. Marginal regression, where each dependent variable is regressed separately on each covariate, offers a promising alternative in this case because the estimates can be computed roughly two orders faster than the lasso solutions. The question that remains is how the statistical performance of the method compares to that of the lasso in these cases. In this paper, we study the relative statistical performance of the lasso and marginal regression for sparse, high-dimensional regression problems. We consider the problem of learning which coefficients are non-zero. Our main results are as follows: (i) we compare the conditions under which the lasso and marginal regression guarantee exact recovery in the fixed design, noise free case; (ii) we establish conditions under which marginal regression provides exact recovery with high probability in the fixed design, noise free, random coefficients case; and (iii) we derive rates of convergence for both procedures, where performance is measured by the number of coefficients with incorrect sign, and characterize the regions in the parameter space recovery is and is not possible under this metric. In light of the computational advantages of marginal regression in very high dimensional problems, our theoretical and simulations results suggest that the procedure merits further study.
Legitimizing Black academic failure: deconstructing staff discourses on academic success, appearance and behaviour

The continued lower academic attainment of Black (especially Black Caribbean) pupils is now well established. Yet, to date there has been no single coherent national Government strategy that has successfully closed the gap in educational attainment between either Black and White pupils or between Black pupils and the national average. Academic and policy debates centring on the causes and potential ways of addressing this gap remain marred by controversy and disagreement. This paper is based on qualitative research, which explores how staff and pupils at an inner city secondary school in the south of England construct academic success. Focusing on one aspect of the findings, it reveals that staff subscribe to two forms of success: an inclusive, low D to G grade success and an exclusive, high A* to C grade success, each of which are seen as attainable only by certain types of pupils. The appearance and behaviour of Black pupils, particularly those engaged in what is termed ‘Black street culture’, are seen as directly at odds with the aims of the school and therefore minimize their likelihood of attaining success in exclusive terms.
Recent educational interventions for improvement of asthma medication adherence

Poor adherence to asthma medication treatment is a dilemma as it decreases the chance of achieving and maintaining a proper asthma control. Another dilemma is that there seems to be a small range of functional interventions that enhance adherence to long-term medication treatments. The aim was to review the last five years of published educational interventions for improving adherence to asthma medication. Through systematic database searches 20 articles were identified, which matched the inclusion criteria and described educational interventions to improve asthma self-management including adherence. The current review showed that addressing unintentional non-adherence in terms of incorrect inhaler technique by recurrent education improved the technique among many patients, but not among all. Phoning patients, as a means to remove medication beliefs as adherence barriers, seemed to be an effective educational strategy, shown as increased adherence. Involving patients in treatment decisions and individualising or tailoring educational support also seemed to have favourable effect on adherence. To conclude, addressing specific adherence barriers such as poor inhaler technique or medication beliefs could favour adherence. To change adherence behavior, the current review proposes that educational adherence support should be a collaborative effort between the patient and the health-care professional based on each individual patient's needs and patient factors, including elements such as personality traits.
Composite fermions and quantum Hall systems: Role of the Coulomb pseudopotential

Abstract The mean-field composite fermion (CF) picture successfully predicts angular momenta of multiplets forming the lowest-energy band in fractional auantum Hall (FQH) systems. This success cannot be attributed to a cancellation between Coulomb and Chern-Simons interactions beyond the mean field, because these interactions have totally different energy scales. Rather, it results from the behaviour of the Coulomb pseudopotential V(L) (pair energy as a function of pair angular momentum) in the lowest Landau level (LL). The class of short-range repulsive pseudopotentials is defined that lead to short-range Laughlin-like correlations in many-body systems and to which the CF model can be applied. These Laughlin correlations are described quantitatively using the formalism of fractional parentage. The discussion is illustrated with an analysis of the energy spectra obtained in numerical diagonalization of up to 11 electrons in the lowest and excited LLs. The qualitative difference in the behaviour of V(L)is shown to invalidate sometimes the mean-field CF picture when applied to higher LLs. For example, the v =(7/3)state is not a Laughlin v =⅓state in the first excited LL. The analysis of the involved pseudopotentials also explains the success or failure of the CF picture when applied to other systems of charged fermions with Coulomb repulsion, such as the Laughlin auasiparticles in the FQH hierarchy or charged excitons in an electron-hole plasma.
Fractional, Circular, and Defective Coloring of Series‐Parallel Graphs

In this note we consider colorings of series‐parallel graphs. Specifically, we provide bounds on their fractional and circular chromatic numbers and the defective version of these parameters. The main result is that the fractional chromatic number of any series‐parallel graph of odd girth k is exactly 2k/(k−1) .
A reliable, compact, and low-cost Michelson wavemeter for laser wavelength measurement

We describe the construction and operation of a simple, compact, and cost effective Michelson wavemeter with picometer accuracy. The low cost of the device means that it can form the basis of an undergraduate laboratory experiment, yet it is sufficiently reliable and accurate that it has become an important tool in our research laboratory, where it is regularly used to tune lasers to atomic transitions. The usefulness and accuracy of the wavemeter is demonstrated by tuning two separate extended cavity diode lasers to achieve two-step excitation of the Rb 52D state, observed by detecting 420 nm blue fluorescence from the 52D→62P→52S decay path.
Inter-individual Variability in Activity of the Major Drug Metabolizing Enzymes in Liver Homogenates of 20 Individuals.

BACKGROUND Inter-individual variability in hepatic drug metabolizing enzyme (DME) activity is a major contributor to heterogeneity in drug clearance and safety. Accurate data on expression levels and activities of DMEs is an important prerequisite for in vitro-in vivo extrapolation and in silico based predictions. Characterization and assessment of inter-correlations of the major DMEs cytochrome P450s (CYPs) and UDP-glucuronosyltransferases (UGTs) have been extensively documented, but simultaneous quantification including other major DMEs has been lacking. OBJECTIVE Assessment of inter-donor variability and inter-correlations of CYPs, UGTs, sulfotransferases (SULTs), glutathione S-transferases (GSTs), NAD(P)H:quinone oxidoreductase 1 (NQO1) and NRH: quinone oxidoreductase 2 (NQO2) in a set of 20 individual liver homogenates. METHOD The main drug metabolizing isoforms of CYP and UGT have been reaction phenotype in individual liver microsomes and NQO1, NQO2, GSTT1 and GSTT2 in corresponding cytosol. In addition, we assessed overall SULT activity in liver cytosol using acetaminophen and 7-hydroxycoumarin as non-selective substrates and cytosolic GST activity using the non-selective substrate 1-chloro-2,4-dinitrobenzene (CDNB). Expression of GST isoforms was also assessed. RESULTS AND CONCLUSION While hepatic NQO1 activity was highly variable, NQO2 activity was more conserved. In addition, we found that of the hepatic GST isoforms, the variation in GSTM3 levels, which is poorly studied, was highest. The majority of significant correlations were found amongst CYP and UGT enzyme activities. The dataset presented provides the absolute quantification of the largest number of hepatic DME activities so far and constitute an essential resource for in silico toxicokinetic and metabolic modelling studies.
Comparison of the Effect of Fluoride Varnish, Chlorhexidine Varnish and Casein Phosphopeptide- Amorphous Calcium Phosphate (CPP-ACP) Varnish on Salivary Streptococcus mutans Level: A Six Month Clinical Study.

INTRODUCTION Dental caries is the most widespread disease which has a multi factorial origin. Streptococcus mutans is considered to be the chief pathogen in its development. Different varnishes are available which can be used for the prevention of the carious process. AIM To compare the effect of fluoride varnish, chlorhexidine varnish and fluoride varnish containing Casein Phosphopeptide - Amorphous Calcium Phosphate (CPP-ACP) on salivary Streptococcusmutans count in children with mixed dentition over a period of six months. MATERIALS AND METHODS Seventy two children of age 6-12 years with mixed dentition were selected fulfilling inclusion and exclusion criteria and divided into three groups: Group I- Fluoride varnish group; Group II- Chlorhexidine varnish group; Group III- MI varnish (fluoride varnish containing CPP-ACP) group. After thorough oral prophylaxis and restorative treatment the varnishes were applied to the teeth once a week for four consecutive weeks in the respective groups. Salivary Streptococcus mutans count (CFU/ml of saliva) was estimated at baseline, 1 month, 3 months and 6 months after varnish application. Bonferroni post-hoc test and paired t-test for inter group and intra group comparison was used in the study. RESULTS A statistically significant reduction in salivary S. mutans colony count was seen with all three groups at all the different time intervals. Maximum reduction was noted in chlorhexidine varnish group at all the intervals after varnish application. CONCLUSION Prevention of dental caries plays a vital role in paediatric dental practice. The use of dental varnish has proved to be effective in reducing the dental caries. Chlorhexidine varnish was found to show maximum reduction in salivary S. mutans count for six month period, when compared to MI varnish and fluoride varnish. Thus, chlorhexidine varnish can be used as potent caries inhibiting agent and promote good oral health.
Inoperable adenocarcinoma of the oesophagogastric junction: a comparative clinical study of laser coagulation versus self-expanding metallic stents with special reference to cost analysis.

AIMS Neither clinical nor financial comparisons yet exist between self-expanding metallic stents (SEMS) and laser therapy, concentrating on the treatment of obstructive adenocarcinomas of the oesophagogastric junction. The aim of our study was to compare the relative lifetime costs and clinical results of the Nd:YAG laser to those of SEMS as alternative forms of primary palliation of dysphagia for adenocarcinoma near the oesophagogastric junction. METHODS Fifty-two patients with distal oesophageal or oesophagogastric adenocarcinomas underwent palliative treatment for dysphagia: 32 treated with laser therapy and 20 with SEMS in this retrospective study. The clinical outcome and real cumulative costs as physical units and in financial terms were analysed for these study groups. RESULTS Although patients palliated with SEMS underwent fewer procedures (1.9+/-1.6 vs 3.4+/-4.0, P=0.0048) and spent less time in endoscopic theatre (38+/-25min vs 118+/-152min, P=0.0048), they spent as many days in hospital (12.9 vs 15.1, P=0.370) and required as high overall costs for therapy (5360 EUR vs 5450 EUR, P=0.679) as those treated with laser therapy. In addition, they had higher morbidity rates (30 vs 6.3%, P=0.043), hospital mortality (20 vs 3.1%, P=0.066), and 30-day mortality (40 vs 3.1%, P=0.0011) than did patients with laser therapy, with no evidence of SEMS being the more effective treatment modality. CONCLUSIONS In patients with adenocarcinoma at the distal oesophagus or at the oesophagogastric junction, laser therapy palliates dysphagia effectively with lower morbidity and mortality rates and without increased costs or hospital stays than does use of self-expanding metallic stents.
Revision for prosthetic joint infection following hip arthroplasty

Objectives We used the National Joint Registry for England, Wales, Northern Ireland and the Isle of Man (NJR) to investigate the risk of revision due to prosthetic joint infection (PJI) for patients undergoing primary and revision hip arthroplasty, the changes in risk over time, and the overall burden created by PJI. Methods We analysed revision total hip arthroplasties (THAs) performed due to a diagnosis of PJI and the linked index procedures recorded in the NJR between 2003 and 2014. The cohort analysed consisted of 623 253 index primary hip arthroplasties, 63 222 index revision hip arthroplasties and 7585 revision THAs performed due to a diagnosis of PJI. The prevalence, cumulative incidence functions and the burden of PJI (total procedures) were calculated. Overall linear trends were investigated with log-linear regression. Results We demonstrated a prevalence of revision THA due to prosthetic joint infection of 0.4/100 procedures following primary and 1.6/100 procedures following revision hip arthroplasty. The prevalence of revision due to PJI in the three months following primary hip arthroplasty has risen 2.3-fold (95% confidence interval (CI) 1.3 to 4.1) between 2005 and 2013, and 3.0-fold (95% CI 1.1 to 8.5) following revision hip arthroplasty. Over 1000 procedures are performed annually as a consequence of hip PJI, an increase of 2.6-fold between 2005 and 2013. Conclusions Although the risk of revision due to PJI following hip arthroplasty is low, it is rising and, coupled with the established and further predicted increased incidence of both primary and revision hip arthroplasty, this represents a growing and substantial treatment burden. Cite this article: E. Lenguerrand, M. R. Whitehouse, A. D. Beswick, S. A. Jones, M. L. Porter, A. W. Blom. Revision for prosthetic joint infection following hip arthroplasty: Evidence from the National Joint Registry. Bone Joint Res 2017;6:391–398. DOI: 10.1302/2046-3758.66. BJR-2017-0003.R1.