Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting Wahlund effects together with amplification problems: Cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania

Population genetics is a convenient tool to study the population biology of non‐model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. We used new tools (correlation between the number of times a locus is found in significant linkage disequilibrium and its genetic diversity, correlations between Wright's FIS and FST, FIS and number of missing data, FIT and allele size and standard errors comparisons) for the first time on a real data set of tsetse flies, a vector of dangerous diseases to humans and domestic animals in sub‐Saharan Africa. With these new tools, and cleaning data from null allele, temporal heterogeneity and short allele dominance effects, we unveiled the coexistence of two highly divergent cryptic clades in the same sites. These results are in line with other studies suggesting that the biodiversity of many taxa still largely remain undescribed, in particular pathogenic agents and their vectors. Our results also advocate that including individuals from different cohorts tends to bias subdivision measures and that keeping loci with short allele dominance and/or too frequent missing data seriously jeopardize parameter's estimations. Finally, separated analyses of the two clades suggest very small tsetse densities and relatively large dispersal.
Permutation Matrix Encryption Based Ultralightweight Secure RFID Scheme in Internet of Vehicles

Radio frequency identification (RFID) is a kind of non-contact automatic identification technology. The Internet of Vehicles (IoV) is a derivative of the Internet of Things (IoT), and RFID technology has become one of the key technologies of IoV. Due to the open wireless communication environment in RFID system, the RFID system is easy to be exposed to various malicious attacks, which may result in privacy disclosure. The provision of privacy protection for users is a prerequisite for the wide acceptance of the IoV. In this paper, we discuss the privacy problem of the RFID system in the IoV and present a lightweight RFID authentication scheme based on permutation matrix encryption, which can resist some typical attacks and ensure the user’s personal privacy and location privacy. The fast certification speed of the scheme and the low cost of the tag is in line with the high-speed certification requirement in the Internet of vehicles. In this thesis, the specific application scenarios of the proposed RFID authentication scheme in the IoV is also discussed.
Household renovation before and during pregnancy in relation to preterm birth and low birthweight in China

From October 2010 to April 2012, we conducted a cross-sectional study of associations between household environments and childhood health among preschool children in eight Chinese cities. Here, we analyze associations of early household renovation with preterm birth (PTB), low birthweight (LBW), term low birthweight (Term-LBW), and small for gestational age (SGA). Parents responded to questions about household renovation and their children's gestational age and birthweight. In the multivariate logistic regression analyses, household renovation in the year before pregnancy was significantly associated with LBW (sample size: N = 25 813; adjusted odds ratio (OR) with 95% confidence intervals (CIs): 1.23, 1.01-1.50) and Term-LBW (N = 24 823; 1.29, 1.01-1.67). Household renovation during pregnancy was significantly associated with PTB (N = 25 202; 1.28, 1.01-1.69). These significant associations were also found in the two-level (city-child) logistic regression analyses and in the sensitivity analyses among 21 009 children with complete data in all studied variates. Stronger associations were found in certain subgroups. Our findings indicate that household renovation within one year before pregnancy might be a risk factor for LBW and Term-LBW, while household renovation during pregnancy could be a risk factor for PTB.
Economic evaluations of physiotherapy interventions for neurological disorders: a systematic review

Abstract Purpose: To identify the existing evidence evaluating the cost-effectiveness of physiotherapy treatments for people with neurological disorders. Methods: Multiple databases were searched from database inception until July 2018. Studies estimating the cost-effectiveness as incremental cost-effectiveness ratios, cost per quality-adjusted life year, cost per disability-adjusted life year and cost per other measurable results were included. Physiotherapy Evidence Database scale, and Consensus on Health Economic Criteria list were used for rating the quality of the evidence. Results: Ten studies involving 1462 participants were included. Aerobic training, progressive strength training, and a pragmatic physiotherapy program (combination of stretching, strength, and balance training) were reported as potentially cost-effective for older adults with vascular cognitive impairment, falls prevention in Parkinson’s disease and multiple sclerosis respectively. Physiotherapy as an adjuvant for pain control was also reported as cost-effective for reflex sympathetic dystrophy. One study testing extra physiotherapy-by-physiotherapy assistant in cerebral palsy and two studies testing extra therapy using a robotic arm and Wii therapy for hand rehabilitation in stroke were reported as not cost-effective. Conclusions: There are limited studies that have evaluated the cost-effectiveness of physiotherapy treatments in neurological disorders. Three studies that combined extra physiotherapy-by-physiotherapy assistant and novel interventions with conventional physiotherapy were found not cost-effective. Implications for Rehabilitation Progressive muscle strengthening exercise over a period of 6-month is reported to be cost-effective for falls prevention in people with Parkinson’s disease Aerobic training is reported as potentially cost-effective for older adults with vascular cognitive impairment Physiotherapy given as an adjuvant treatment is reported to be potentially cost-effective for reflex sympathetic dystrophy of less than 1-year duration One study reported physiotherapy involving static stretching, aerobic exercise, strengthening exercise, and balance training as cost-effective for people with multiple sclerosis Additional physiotherapy-by-physiotherapy assistant or family member for improving motor development in cerebral palsy and the use of novel physiotherapy techniques such as robotics or Wii plus conventional physiotherapy for improving arm function in stroke are found not cost-effective Group therapy for improving physical activity in mild Alzheimer’s disease is found not cost-effective.
Antigen-Specific TCR Signatures of Cytomegalovirus Infection

CMV is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T cell repertoire is complex, and it is not yet clear which T cells protect best against virus reactivation and disease. In this study, we present a highly resolved characterization of CMV-specific human CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their TCR β-chains (TCRβ). Our analysis included recently identified T cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B–restricted epitopes. In eight healthy virus carriers, we identified a total of 1052 CMV-specific TCRβ sequences. HLA-C–restricted, CMV-specific TCRβ clonotypes dominated the ex vivo T cell response and contributed the highest-frequency clonotype of the entire repertoire in two of eight donors. We analyzed sharing and similarity of CMV-specific TCRβ sequences and identified 63 public or related sequences belonging to 17 public TCRβ families. In our cohort, and in an independent cohort of 352 donors, the cumulative frequency of these public TCRβ family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCRβ signatures as a biomarker for an antiviral T cell response to identify patients in need of treatment and to guide future development of immunotherapy.
Are children with unrecognised psychiatric disorders being excluded from school? A secondary analysis of the British Child and Adolescent Mental Health Surveys 2004 and 2007

Abstract Background There is limited research that explores the association between exclusion from school and mental health, but it seems intuitively plausible that the recognition of mental difficulties by key teachers and parents would influence the likelihood of exclusion from school. Methods A secondary analysis of the British Child and Adolescent Mental Health survey 2004, (n = 7997) and the 2007 follow-up (n = 5326) was conducted. Recognition of difficulty was assessed via a derived variable that combined the first item of the Impact supplement of the Strengths and Difficulties Questionnaire which asked parents and teachers if they thought that the child has difficulties with emotions, behaviour and concentration, and the presence/absence of psychiatric disorder measured by the Development and Well-being Assessment. Results Adjusted logistic regression models demonstrated that children with recognised difficulties were more likely to be excluded [adjusted odds ratio (OR) 5.78, confidence interval 3.45–9.64, p < 0.001], but children with unrecognised difficulties [adjusted OR 3.58 (1.46–8.81) p < 0.005] or recognised subclinical difficulties [adjusted OR 3.42 (2.04–5.73) p < 0.001] were also more likely to be excluded than children with no difficulties. Children with conduct disorder and attention deficit hyperactivity disorder were most likely to be excluded compared with other types of disorder. Conclusion Exclusion from school may result from a failure to provide timely and effective support rather than a failure to recognise psychopathology.
Learning for Question Answering and Text Classification: Integrating Knowledge-Based and Statistical

It is a time consuming and difficult task for an individual, a group, or an organization to classify large collections of documents under a content-driven taxonomy. In this paper, we outline an approach for building a system which makes the classification process the responsibility of the author of the document, thus allowing the author to explain classifications and verify (or correct) automated techniques. We present our preliminary work on such a system, Q&A, which enables the distribution of the task of semantic classification and knowledge acquisition by semiautomaticMly learning taxonomic categorizations and document indices as it captures interactions between experts and questionasking users.
Ciprofloxacin and Clinafloxacin Antibodies for an Immunoassay of Quinolones: Quantitative Structure–Activity Analysis of Cross-Reactivities

A common problem in the immunodetection of structurally close compounds is understanding the regularities of immune recognition, and elucidating the basic structural elements that provide it. Correct identification of these elements would allow for select immunogens to obtain antibodies with either wide specificity to different representatives of a given chemical class (for class-specific immunoassays), or narrow specificity to a unique compound (mono-specific immunoassays). Fluoroquinolones (FQs; antibiotic contaminants of animal-derived foods) are of particular interest for such research. We studied the structural basis of immune recognition of FQs by antibodies against ciprofloxacin (CIP) and clinafloxacin (CLI) as the immunizing hapten. CIP and CLI possess the same cyclopropyl substituents at the N1 position, while their substituents at C7 and C8 are different. Anti-CIP antibodies were specific to 22 of 24 FQs, while anti-CLI antibodies were specific to 11 of 26 FQs. The molecular size was critical for the binding between the FQs and the anti-CIP antibody. The presence of the cyclopropyl ring at the N1 position was important for the recognition between fluoroquinolones and the anti-CLI antibody. The anti-CIP quantitative structure–activity relationship (QSAR) model was well-equipped to predict the test set (pred_R2 = 0.944). The statistical parameters of the anti-CLI model were also high (R2 = 0.885, q2 = 0.864). Thus, the obtained QSAR models yielded sufficient correlation coefficients, internal stability, and predictive ability. This work broadens our knowledge of the molecular mechanisms of FQs’ interaction with antibodies, and it will contribute to the further development of antibiotic immunoassays.
The utility of a point‐of‐care sural nerve conduction device for detection of diabetic polyneuropathy: A cross‐sectional study

Introduction: Rapid and accessible methods for diagnosing diabetic polyneuropathy (DPN) have been developed, but not validated, in large cohorts of people with diabetes. Methods: The performance of a point‐of‐care device (POCD) was studied in 168 patients with type 2 diabetes, estimating the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) compared with conventional sural nerve conduction studies (NCS). Results: A POCD amplitude limit of 6 µV increased the sensitivity (96%) and NPV (98%), but decreased the specificity (71%) and PPV (54%) compared with the 4‐µV limit, which had values of 78%, 92%, 89%, and 71%, respectively. POCD on both legs showed better performance than on 1 leg. POCD amplitudes and conduction velocities correlated significantly with conventional sural NCS, but POCD values were underestimated compared with NCS. Discussion: The POCD may be used as a suitable screening tool for detection of DPN. Patients with abnormal and borderline results should undergo conventional NCS. Muscle Nerve 59:187–193, 2019
3D Printed Modular Immunofiltration Columns for Frequency Mixing-Based Multiplex Magnetic Immunodetection

For performing point-of-care molecular diagnostics, magnetic immunoassays constitute a promising alternative to established enzyme-linked immunosorbent assays (ELISA) because they are fast, robust and sensitive. Simultaneous detection of multiple biomolecular targets from one body fluid sample is desired. The aim of this work is to show that multiplex magnetic immunodetection based on magnetic frequency mixing by means of modular immunofiltration columns prepared for different targets is feasible. By calculations of the magnetic response signal, the required spacing between the modules was determined. Immunofiltration columns were manufactured by 3D printing and antibody immobilization was performed in a batch approach. It was shown experimentally that two different target molecules in a sample solution could be individually detected in a single assaying step with magnetic measurements of the corresponding immobilization filters. The arrangement order of the filters and of a negative control did not influence the results. Thus, a simple and reliable approach to multi-target magnetic immunodetection was demonstrated.
Epidemiological and molecular investigation of norovirus and astrovirus infections in Rio Branco, Acre, Northern Brazil: A retrospective study

Norovirus (NoV) is a major cause of nonbacterial acute gastroenteritis (AGE) outbreaks worldwide, with infections reported in semiclosed environments, particularly in hospitals and nursing homes. Astrovirus (HAstV) is prevalent worldwide, especially in developing countries. We aimed to determine the prevalence, spatial distribution, and genetic diversity of NoV and HAstV in children under 5 years of age in Rio Branco city, Acre State, Amazon Region, Brazil. Stool samples from children with (n = 240) and without (n = 248) AGE were collected from January to December 2012 from seven neighborhoods. The overall NoV prevalence was 12.3% (60 of 488); representing 15.8% (38 of 240) of the symptomatic samples and 8.9% (22 of 248) of the controls. HAstVs infection was observed in 4.7% (23 of 488) of the samples tested, 6.2% (15 of 240) of AGE cases, and 2.4% (6 of 248) of the controls (plus two without information about feces consistency). Infections were found in all age groups with higher frequency in children less than two years of age, for both viruses. NoV was detected in all neighborhoods, with a higher concentration in the fourth (30%; 18 of 60). NoV nucleotide sequencing performed in 86.7% (52 of 60) of the positive samples showed the circulation of the strains GII.4 (57.7%; 30 of 52), GIIPe/GII.4 (19.2%; 10 of 52), GII.7, GII.Pg/GII.1, and GII.Pc (3.8%; 2 of 52 for each), GII.6 and GII.Pg (1.9%; 1 of 52 for each), and GI.3 (7.7%; 4 of 52). Three GII.4 variants were detected: Den Haag_2006b (n = 1), New Orleans_2009 (n = 1), and Sydney_2012 (n = 14). HAstV types HAstV‐1a (81.8%; 9 of 11) and HAstV‐2c (18.2%; 2 of 11) were observed in the 47.8% (11 of 23) of characterized samples. This is the first data obtained in Acre State regarding the prevalence of these viruses and provides epidemiological and molecular information for a better understanding of their role among children with and without AGE.
Exploration of young adults’ influences on, and consequences of, avoiding alcohol consumption

Abstract Background: There is a wealth of research on motives for alcohol consumption among young people. However, little is known about motives to avoid alcohol in this population. Objectives: The study purpose was to explore what influences young adults’ decisions to avoid alcohol and their motives to avoid alcohol. Methods: Face-to-face, semi-structured, one-on-one interviews were conducted in 2015 with young adults (n = 30, Mage = 21.13 years, SD = 2.05) living in Australia who did not consume alcohol regularly. Interviews were analyzed using thematic content analysis. Results: Thematic analysis resulted in seven themes: being in control; avoiding negative health consequences; taste; socialization influences; being left out; peer pressure; strategies to curb excessive alcohol consumption. Conclusions/Importance: Findings from the present study contribute to the literature in identifying coping strategies that participants adopted when faced with questions concerning their abstinence. The data provide evidence that, even in a minority, strong identities and beliefs appear to be a robust means to counteract pressure to conform to the social norm to consume alcohol. Findings may inform the (1) development of youth-centered interventions that target values and social norms to help build resistance to pressures to consume alcohol from peers and the wider community and (2) creation of opportunities and promotion of activities that are fun and alcohol free.
Alanine, proline and urea are major organic osmolytes in the snail Theodoxus fluviatilis under hyperosmotic stress

ABSTRACT Hyperosmotic stress may result in osmotic volume loss from the body to the environment in animals that cannot control the water permeability of their integument. Euryhaline animals (which have a wide tolerance range of environmental salinities) have generally evolved the ability to counteract cell volume shrinkage by accumulating inorganic and organic osmolytes within their cells to balance internal and external osmolalities. Molluscs use very different combinations of amino acids and amino acid derivatives to achieve this goal. Theodoxus fluviatilis is a neritid gastropod that is distributed not only in limnic habitats in Europe but also in brackish waters (e.g. along the shoreline of the Baltic Sea). Animals from brackish sites survive better in high salinities than animals from freshwater locations. The results of the present study indicate that these differences in salinity tolerance cannot be explained by differences in the general ability to accumulate amino acids as organic osmolytes. Although there may be differences in the metabolic pathways involved in osmolyte accumulation in foot muscle tissue, the two groups of animals accumulate amino acid mixtures equally well when stepwise acclimated to their respective maximum tolerable salinity for extended periods. Among these amino acids, alanine and proline, as well as the osmolyte urea, hold a special importance for cell volume preservation in T. fluviatilis under hyperosmotic stress. It is possible that the accumulation of various amino acids during hyperosmotic stress occurs via hydrolysis of storage proteins, while alanine and proline are probably newly synthesised under conditions of hyperosmotic stress in the animals. Summary: Although alanine and proline play a crucial role in osmoregulation under hyperosmotic stress in both freshwater and brackish water Theodoxus fluviatilis snails, they differ in their mechanisms of organic osmolyte accumulation and the importance of urea in the process of osmoregulation.
Quantum Characteristics of a Nanomechanical Resonator Coupled to a Superconducting LC Resonator in Quantum Computing Systems

The mechanical and quantum properties of a nanomechanical resonator can be improved by connecting it to a superconducting resonator in a way that the resonator exhibits new phenomena that are possibly available to novel quantum technologies. The quantum characteristics of a nanomechanical resonator coupled to a superconducting resonator have been investigated on the basis of rigorous quantum solutions of the combined system. The solutions of the Schrödinger equation for the coupled system have been derived using the unitary transformation approach. The analytic formula of the wave functions has been obtained by applying the adiabatic condition for time evolution of the coupling parameter. The behavior of the quantum wave functions has been analyzed for several different values of parameters. The probability densities depicted in the plane of the two resonator coordinates are distorted and rotated due to the coupling between the resonators. In addition, we have shown that there are squeezing effects in the wave packet along one of the two resonator coordinates or along both the two depending on the magnitude of several parameters, such as mass, inductance, and angular frequencies.