Miracle-dz/UniFAR-FTUs huggingface dataset:
Strain Typing of Borrelia burgdorferi, Borrelia afzelii, and Borrelia garinii by Using Multiple-Locus Variable-Number Tandem Repeat Analysis

ABSTRACT Human Lyme borreliosis (LB) is the most prevalent arthropod-borne infection in temperate climate zones around the world and is caused by Borrelia spirochetes. We have identified 10 variable-number tandem repeat (VNTR) loci present within the genome of Borrelia burgdorferi and subsequently developed a multiple-locus VNTR analysis (MLVA) typing system for this disease agent. We report here the successful application of MLVA for strain discrimination among a group of 41 globally diverse Borrelia isolates including B. burgdorferi, B. afzelii, and B. garinii. PCR assays displayed diversity at these loci, with total allele numbers ranging from two to nine and Nei's diversity (D) values ranging from 0.10 to 0.87. The average D value was 0.53 across all VNTR loci. A clear correlation exists between the repeat copy number and the D value (r = 0.62) or the number of alleles (r = 0.93) observed across diverse strains. Cluster analysis by the unweighted pair-group method with arithmetic means resolved the 30 observed unique Borrelia genotypes into five distinct groups. B. burgdorferi, B. afzelii, and B. garinii clustered into distinct affiliations, consistent with current 16S rRNA phylogeny studies. Genetic similarity and diversity suggest that B. afzelii and B. garinii are close relatives and were perhaps recently derived from B. burgdorferi. MLVA provides both phylogenetic relationships and additional resolution to discriminate among strains of Borrelia species. This new level of strain identification and discrimination will allow more detailed epidemiological and phylogenetic analysis in future studies.
No change in calculated creatinine clearance after tenofovir initiation among Thai patients.

OBJECTIVES Thai patients have a lower average body weight than patients from western Europe or the USA. Tenofovir is largely prescribed at the standard dosage of 300 mg once daily: therefore, the per kilogram dose is higher in Thailand than in the USA. We asked the question whether this higher per kilogram dose was associated with more nephrotoxicity. METHODS Thai patients from the Staccato trial were treated with tenofovir/lamivudine combined with ritonavir-boosted saquinavir. Creatinine values were measured before the start of tenofovir and then every 12 weeks. Renal function was assessed using the Cockcroft-Gault formula and the MDRD formula. To compare CL(CR) before and after tenofovir, the t-paired or Wilcoxon signed rank tests were used. One-way analysis of variance and Spearman's correlation coefficient were used to study CL(CR) longitudinally. RESULTS CL(CR) remained stable after a median of 21 weeks on tenofovir (difference of +1.06 mL/min; 95% CI -2.7-4.8, P=0.58), even among patients with underlying diseases. The mean CL(CR) remained stable across time (P=0.17). CONCLUSIONS We did not find renal dysfunction on tenofovir among Thai patients included in the Staccato trial. Tenofovir could be safely prescribed at a standard dosage of 300 mg once daily in the Thai population.
Pre-breakdown mechanisms in dielectric liquids and predicting models

This paper presents a synthetic review of the state of knowledge relative to the pre-breakdown phenomena in dielectric liquids and especially the initiation and propagation of streamer/discharge and their characteristic parameters. The main influencing parameters namely the structure, stopping length, velocity and propagation modes of streamers, current, charge and associated emitted light are developed. These parameters include especially the chemical composition of the liquid (pure or containing specific additives); the applied voltage; the electrode arrangement; the temperature and the hydrostatic pressure. The mechanisms involving in the inception and propagation of streamers are discussed. Recent models enabling to predict the type of streamers that can be initiated and their characteristics when propagating within liquid, are also presented and discussed. It is shown through the experiments and modeling that the pre-breakdown phenomena in dielectric liquids are governed by both electronic and gaseous mechanisms even if one of them is dominant in one case and the second in another.
Transparency Teaching in the Virtual Classroom: Assessing the Opportunities and Challenges of Integrating Transparency Teaching Methods with Online Learning

Abstract The existing literature on transparency teaching in higher education reveals that the adoption of transparent-oriented assignments improves the learning outcomes for underserved students at the introductory level, and decreases the rate of attrition among the student population with the highest risk of dropping out. Concurrently, the continued demand for online education programs has resulted in the expansion of course and degree offerings, and a steady increase in online student enrollment nationwide. However, a number of recent studies find that while the goal of online education is to improve access to higher education, that historically underrepresented groups report lower course completion rates and poorer grade performance in online classes, when compared to underrepresented students enrolled in hybrid and in person courses. Utilizing a quasiexperimental design, this article evaluates the implementation of transparency teaching methods in the online classroom versus the in-person classroom to determine if student learning outcomes vary according to course modality, focusing specifically on outcomes among the underserved student population. The goal of this study is to establish that transparent teaching methods help mitigate the negative effects of the virtual classroom for underserved students.
The financial crisis in the eurozone: a balance-of-payments crisis with a single currency?

In a pegged exchange-rate system, a balance-of-payments crisis happens when there is serious mistrust of whether a debtor country holds sufficient international reserves to monetise a capital withdrawal at the ongoing exchange-rate parity. In the eurozone (EZ), doubts that banks and governments of peripheral countries could settle debts when they matured led to a massive capital outflow after the fall of Lehman Brothers and, especially, the first Greek sovereign-debt crisis. This has led some authors to hold that the situation in the EZ is a balance-of-payments (BoP) crisis. However, the European Central Bank (ECB) offset massive financial capital withdrawals with a huge inflow of reserves to the EZ periphery, making the international reserves constraint irrelevant. This invalidated the BoP view in other authorsâ€™ opinion, who pointed out bad bank behaviour and a poor initial institutional design as the alternative root cause for the current mess. This position is known as the monetary sovereign (MS) view. In this paper, we provide a brief overview of the debate between both sides, with Cesaratto, as a representative for the BoP view, and Lavoie, De Grauwe and Wray, for the MS view, and discuss whether a reconciliation between these two positions can be possible. We step into the discussion to offer two additional arguments in favour of the second view: (i) A currency union requires a single monetary policy, as opposed to a fixed exchange-rate regime; TARGET2 balances combined with refinancing operations are an essential ingredient of monetary policy implementation. (ii) The current situation is more easily understood as another episode of financial instability after banks have granted huge amounts of credit (which they refinanced abroad). The situation got even worse because governments supporting troubled banks in their respective jurisdictions lacked a lender of last resort.
Rare mutations in a domain crucial for V3‐loopstructure prevail in replicating HIV from long‐term non‐progressors

Objective: To evaluate the role of the selective forces exerted by the host on the HIV‐1 structures involved in viral entry. Design and methods: The V3 region of the env gene was analysed in cell‐free HIV‐1 RNA from 17 infected subjects: 11 long‐term non‐progressors (LTNP) and six symptomless, typical progressor patients. To evaluate the potential biological significance of one of the rare variants detected in the LTNP, it was reproduced by recombinant PCR into a HIV‐1 molecular clone. Results: The intrapatient divergence of the V3‐loop sequences averaged 8.62% in LTNP and 5.29% in progressors, although LTNP displayed lower divergence from the clade B consensus than progressors (16.65 and 19.76%, respectively). The analysis of non‐synonymous and synonymous substitutions indicated that selective pressure was exerted in this region in both LTNP and progressors. Individual peculiarities (unique and rare V3‐loop variants) emerged, however, in most sequences from LTNP, and variants bearing mutations in a domain crucial for the V3‐loop structure were more prevalent in LTNP (P = 0.0012). The pNL4–3‐derived mutant reproducing a V3‐loop variant detected in a LTNP was efficiently expressed upon transfection, but the mutant virus was nearly completely unable to infect CD4+ cell lines, activated primary peripheral blood lymphocytes, or monocyte‐derived macrophages, suggesting that a defect impaired the entry phase of the replication cycle. Conclusions: The results indicate that host factors impose selective constraints on the evolution of the HIV‐1 structures involved in viral entry. In LTNP, these factors are likely to force the virus into attenuated variants.
Predictors of Fat Mass Changes in Response to Aerobic Exercise Training in Women

Abstract Sawyer, BJ, Bhammar, DM, Angadi, SS, Ryan, DM, Ryder, JR, Sussman, EJ, Bertmann, FMW, and Gaesser, GA. Predictors of fat mass changes in response to aerobic exercise training in women. J Strength Cond Res 29(2): 297–304, 2015—Aerobic exercise training in women typically results in minimal fat loss, with considerable individual variability. We hypothesized that women with higher baseline body fat would lose more body fat in response to exercise training and that early fat loss would predict final fat loss. Eighty-one sedentary premenopausal women (age: 30.7 ± 7.8 years; height: 164.5 ± 7.4 cm; weight: 68.2 ± 16.4 kg; fat percent: 38.1 ± 8.8) underwent dual-energy x-ray absorptiometry before and after 12 weeks of supervised treadmill walking 3 days per week for 30 minutes at 70% of . Overall, women did not lose body weight or fat mass. However, considerable individual variability was observed for changes in body weight (−11.7 to +4.8 kg) and fat mass (−11.8 to +3.7 kg). Fifty-five women were classified as compensators and, as a group, gained fat mass (25.6 ± 11.1 kg to 26.1 ± 11.3 kg; p < 0.001). The strongest correlates of change in body fat at 12 weeks were change in body weight (r = 0.52) and fat mass (r = 0.48) at 4 weeks. Stepwise regression analysis that included change in body weight and body fat at 4 weeks and submaximal exercise energy expenditure yielded a prediction model that explained 37% of the variance in fat mass change (R 2 = 0.37, p < 0.001). Change in body weight and fat mass at 4 weeks were moderate predictors of fat loss and may potentially be useful for identification of individuals who achieve less than expected weight loss or experience unintended fat gain in response to exercise training.
The roles of a Programme and Project Management Office to support collaborative university–industry R&D

While the literature provides some advice on managing programmes and projects in general, the specific context of the university–industry collaboration is being scarcely reported, demanding a strong research effort to produce effective guidelines. Pursuing this effort, a Programme and Project Management Office (PgPMO) structure, specifically devoted to support collaborative university–industry R&D funded contracts, is proposed. This paper is focused on the set of key functions and responsibilities established for the overall PgPMO, as well as on the equivalent ones for the four proposed PgPMO roles: the PgPMO Officer, PgPMO Finance, PgPMO Communication and PgPMO Quality Assurance Management. Additionally, it discusses the implementation process of such structure, shedding light on the success factors for its implementation. The PgPMO described in this paper has been implemented in two case studies. The programme stakeholders of both case studies perceived that such PgPMO structure has contributed to achieve the success of the corresponding university–industry programmes.
Horses for Courses: Setting Tasks for Spotting Talent

We investigate a distortion in the labour market that is rampant in developing countries and occurs in the form of inaccurate estimation of the innate talents of employees. We characterise the optimal level of difficulty in a predictive task that an employer, who acts as the evaluator, must choose in order to have the least noise in the talent estimation process. Contrary to the standard noise minimization result, our model re affirms the staffing policy of throwing employees in the deep end. We also find that the evaluator will not benefit from knowing the result of the predictive task set from beforehand. JEL: D82, D83
Temporal lobe abnormalities in first-episode psychosis.

OBJECTIVE The nature and time course of temporal lobe abnormalities in psychotic illness remain controversial. Confounds include disease chronicity, gender, and handedness. The present study investigated temporal substructures in right-handed male patients experiencing their first episode of psychotic illness. METHOD Magnetic resonance imaging scans were obtained for 25 minimally treated patients experiencing their first psychotic episode and 16 healthy comparison subjects. Group differences in volumes of the hippocampus, amygdala, planum temporale, and Heschl's gyrus were tested. RESULTS The patients had smaller bilateral hippocampal and left planum temporale volumes than the comparison subjects. Paranoid and nonparanoid patients differed in left amygdala volume. CONCLUSIONS The authors conclude that bilateral hippocampal and left planum temporale abnormalities are present near the onset of psychosis.
Dealing with Attrition and Missing Data in Longitudinal Studies: A Critique

Longitudinal studies in teenage pregnancy, like any other topical issue, have been greatly affected by the problem of participant drop out and missing data. Although existing evidence indicate that data from longitudinal studies can provide useful insights regarding individual behaviours; the quality of the data and representativeness of the findings can adversely be compromised by attrition and missing data. Using literature review, this article criticises two papers on teenage pregnancy that have utilised longitudinal data by examining the effectiveness of the measures taken to correct for the attrition and missing data. The article concludes that procedural strategies used to eliminate or reduce attrition and missing data before and during data collection are more effective than employing statistical strategies to deal with the effects afterwards. If statistical procedures have to be used, it is important to first make distinctions of the missing data mechanisms since this has a bearing on whether certain strategies of handling missing data – such as list-wise deletion, pairwise deletion, mean imputation or multiple imputation –will result in biases or not.
Intersample fluctuations in phosphocreatine concentration determined by 31P‐magnetic resonance spectroscopy and parameter estimation of metabolic responses to exercise in humans

1 The ATP turnover rate during constant‐load exercise is often estimated from the initial rate of change of phosphocreatine concentration ([PCr]) using 31P‐magnetic resonance spectroscopy (MRS). However, the phase and amplitude characteristics of the sample‐to‐sample fluctuations can markedly influence this estimation (as well as that for the time constant (τ) of the [PCr] change) and confound its physiological interpretation especially for small amplitude responses. 2 This influence was investigated in six healthy males who performed repeated constant‐load quadriceps exercise of a moderate intensity in a whole‐body MRS system. A transmit‐ receive surface coil was placed under the right quadriceps, allowing determination of intramuscular [PCr]; pulmonary oxygen uptake (V̇O2) was simultaneously determined, breath‐by‐breath, using a mass spectrometer and a turbine volume measuring module. 3 The probability density functions (PDF) of [PCr] and V̇O2 fluctuations were determined for each test during the steady states of rest and exercise and the PDF was then fitted to a Gaussian function. The standard deviation of the [PCr] and V̇O2 fluctuations at rest and during exercise (sr and sw, respectively) and the peak centres of the distributions (xcr and xcw) were determined, as were the skewness (γ1) and kurtosis (γ2) coefficients. 4 There was no difference between sr and sw for [PCr] relative to the resting control baseline (sr= 1.554%Δ (s.d.= 0.44), sw= 1.514%Δ (s.d.= 0.35)) or the PDF peak centres (xcr=−0.013 %Δ (s.d.= 0.09), xcw−0.197 %Δ (s.d.= 0.18)). The standard deviation and peak centre of the ‘noise’ in V̇O2 also did not vary between rest and exercise (sr= 0.0427 l min−1 (s.d.= 0.0104), sw= 0.0640 l min−1 (s.d.= 0.0292); xcr=−0.0051 l min−1 (s.d.= 0.0069), xcw 0.0022 l min−1 (s.d.= 0.0034)). 5 Our results demonstrate that the intersample ‘noise’ associated with [PCr] determination by 31P‐MRS may be characterised as a stochastic Gaussian process that is uncorrelated with work rate, as previously described for V̇O2. This ‘noise’ can significantly affect the estimation of τ[PCr] and especially the initial rate of change of [PCr], i.e. the fluctuations can lead to variations in estimation of the initial rate of change of [PCr] of more than twofold, if the inherent ‘noise’ is not accounted for. This ‘error’ may be significantly reduced in such cases if the initial rate of change is estimated from the time constant and amplitude of the response.
Are politically connected firms less constrained in credit markets

Utilizing a panel of over 2,000 Vietnamese SMEs over a 10-year period, we analyse the importance of being politically connected on both access and cost-of-credit obtained from formal financial institutions. Controlling for unobserved time-invariant firm-level heterogeneity, productivity self-selection concerns, and access to alternative credit markets, we show that political connections decreases the likelihood of being credit-constrained by 4 percentage points. Moreover, politically connected firms accessing credit face lower cost-of-capital than non-connected SMEs not excluded from formal financial markets. However, the impact of political connections is most valuable during periods of financial distress, but less prevalent during business cycle upswings.
beta-catenin expression in pilomatrixomas. Relationship with beta-catenin gene mutations and comparison with beta-catenin expression in normal hair follicles.

BACKGROUND beta-catenin functions in signal transduction in the Wnt signalling pathway, which has recently been implicated in hair follicle (HF) morphogenesis. beta-catenin gene mutations affecting exon 3 have been reported in a high percentage of human pilomatrixomas. However, the expression pattern of beta-catenin in human HFs and pilomatrixomas has not been reported. OBJECTIVES To analyse immunohistochemically the expression pattern of beta-catenin in normal anagen HFs and in 40 human pilomatrixomas. METHODS In 11 of these tumours we also studied exon 3 beta-catenin gene mutations by polymerase chain reaction and direct sequencing. As these mutations have been related to a replication error (RER) phenotype in other tumour types, we explored whether or not this association also occurs in pilomatrixomas. RESULTS beta-catenin was expressed in the cell membranes of the outer and inner root sheaths and in matrix cells located at the base and periphery of the HF bulb. However, central matrix cells that differentiate into cortical cells, cortical and cuticular cells expressed beta-catenin in the nucleus, suggesting a role in signal transduction. In addition, some fibroblasts of the dermal papilla also showed nuclear expression of beta-catenin. All 40 analysed pilomatrixomas showed intense nuclear and cytoplasmic beta-catenin expression in proliferating matrix (basaloid) cells. In areas of maturation, transitional cells mainly showed cytoplasmic and membranous expression of beta-catenin, while only a few cells retained nuclear expression. Shadow or ghost cells did not show beta-catenin expression. Three of 11 tumours (26%) had beta-catenin mutations. All three had the same heterozygote mis-sense mutation: a G to T change affecting the first nucleotide at codon 32 (D32Y). None of the 11 tumours studied had a positive RER phenotype. CONCLUSIONS Present and previous studies suggest that the Wnt/beta-catenin/Tcf-Lef pathway is activated in normal matrix cells of the HF to induce differentiation to the hair shaft. Additionally, the beta-catenin mutation in matrix cells of the HF stabilizes beta-catenin protein, which translocates into the nucleus, where it activates of gene transcription together with lymphoid enhancer factor-1 producing pilomatrixoma. These mutations occur without an underlying defect in DNA mismatch repair.
Axonal transport kinetics and posttranslational modification of synapsin I in mouse retinal ganglion cells

Synapsin I is a neuron-specific phosphoprotein primarily localized at the presynaptic terminals, where it is thought to play an important role in the mechanisms involved in neurotransmitter release. Its interaction with cytoskeletal proteins and with small synaptic vesicles is regulated in vitro by phosphorylation by a calcium/calmodulin- dependent kinase. Here, we present the first evidence that, in the mouse retinal ganglion cells, synapsin I, moving along the axon with the slow component of axonal transport, is phosphorylated in vivo at both the head and tail regions. In addition, our data suggest that, after synapsin I has reached the nerve endings, the relative proportion of differently phosphorylated molecules of synapsin I changes, and that these changes lead to a decrease of the overall content of phosphorus. The more basic forms, here collectively referred to as beta-forms, become predominant at the terminals after 7 d postlabeling, when the bulk of transported synapsin I has entered the superior colliculus. Along the axon, phosphorylation could be functional in preventing synapsin I from forming, with actin, a dense meshwork that would restrict organelle movement. On the other hand, at the terminals, the dephosphorylation-phosphorylation of synapsin I may regulate the clustering of small synaptic vesicles and modulate neurotransmitter release by controlling the availability of small synaptic vesicles for exocytosis.