WGA-LP: a pipeline for whole genome assembly of contaminated reads.

SUMMARY: Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. AVAILABILITY AND IMPLEMENTATION: WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Diagnostic value of cutaneous manifestation of SARS-CoV-2 infection.

BACKGROUND: One of the challenging aspects of SARS-CoV-2 infection is its diverse multisystemic disease presentation. OBJECTIVES: To evaluate the diagnostic value of cutaneous manifestations of SARS-CoV-2 infection and investigate their duration and timing in relation to other COVID-19 symptoms. METHODS: We used data from 336 847 UK users of the COVID Symptom Study app to assess the diagnostic value of body rash or an acral rash in SARS-CoV-2 infection, and data from an independent online survey of 11 544 respondents to investigate skin-specific symptoms and collect their photographs. RESULTS: Using data from the app, we show significant association between skin rashes and a positive swab test result (odds ratio 1·67, 95% confidence interval 1·42-1·97). Strikingly, among the respondents of the independent online survey, we found that 17% of SARS-CoV-2-positive cases reported skin rashes as the first presentation, and 21% as the only clinical sign of COVID-19. Together with the British Association of Dermatologists, we have compiled a catalogue of images of the most common skin manifestations of COVID-19 from 400 individuals (https://covidskinsigns.com), which we have made publicly available to assist clinicians in recognition of this early clinical feature of COVID-19. CONCLUSIONS: Skin rashes cluster with other COVID-19 symptoms, are predictive of a positive swab test, and occur in a significant number of cases, either alone or before other classical symptoms. Recognizing rashes is important in identifying new and earlier cases of COVID-19.

Magnetic Force Sensing Using a Self-Assembled Nanowire.

We present a scanning magnetic force sensor based on an individual magnet-tipped GaAs nanowire (NW) grown by molecular beam epitaxy. Its magnetic tip consists of a final segment of single-crystal MnAs formed by sequential crystallization of the liquid Ga catalyst droplet. We characterize the mechanical and magnetic properties of such NWs by measuring their flexural mechanical response in an applied magnetic field. Comparison with numerical simulations allows the identification of their equilibrium magnetization configurations, which in some cases include magnetic vortices. To determine a NW's performance as a magnetic scanning probe, we measure its response to the field profile of a lithographically patterned current-carrying wire. The NWs' tiny tips and their high force sensitivity make them promising for imaging weak magnetic field patterns on the nanometer-scale, as required for mapping mesoscopic transport and spin textures or in nanometer-scale magnetic resonance.

Imaging Stray Magnetic Field of Individual Ferromagnetic Nanotubes.

We use a scanning nanometer-scale superconducting quantum interference device to map the stray magnetic field produced by individual ferromagnetic nanotubes (FNTs) as a function of applied magnetic field. The images are taken as each FNT is led through magnetic reversal and are compared with micromagnetic simulations, which correspond to specific magnetization configurations. In magnetic fields applied perpendicular to the FNT long axis, their magnetization appears to reverse through vortex states, that is, configurations with vortex end domains or in the case of a sufficiently short FNT with a single global vortex. Geometrical imperfections in the samples and the resulting distortion of idealized magnetization configurations influence the measured stray-field patterns.

Association between speech-language, general cognitive functioning and behaviour problems in individuals with Williams syndrome.

BACKGROUND: Williams syndrome (WS) phenotype is described as unique and intriguing. The aim of this study was to investigate the associations between speech-language abilities, general cognitive functioning and behavioural problems in individuals with WS, considering age effects and speech-language characteristics of WS sub-groups. METHODS: The study's participants were 26 individuals with WS and their parents. General cognitive functioning was assessed with the Wechsler Intelligence Scale. Peabody Picture Vocabulary Test, Token Test and the Cookie Theft Picture test were used as speech-language measures. Five speech-language characteristics were evaluated from a 30-min conversation (clichés, echolalia, perseverative speech, exaggerated prosody and monotone intonation). The Child Behaviour Checklist (CBCL 6-18) was used to assess behavioural problems. RESULTS: Higher single-word receptive vocabulary and narrative vocabulary were negatively associated with CBCL T-scores for Social Problems, Aggressive Behaviour and Total Problems. Speech rate was negatively associated with the CBCL Withdrawn/Depressed T-score. Monotone intonation was associated with shy behaviour, as well as exaggerated prosody with talkative behaviour. WS with perseverative speech and exaggerated prosody presented higher scores on Thought Problems. Echolalia was significantly associated with lower Verbal IQ. No significant association was found between IQ and behaviour problems. Age-associated effects were observed only for the Aggressive Behaviour scale. CONCLUSIONS: Associations reported in the present study may represent an insightful background for future predictive studies of speech-language, cognition and behaviour problems in WS.

Endovascular treatment of CCSVI in patients with multiple sclerosis: clinical outcome of 462 cases.

Although it is still debated whether chronic cerebro-spinal venous insufficiency (CCSVI) plays a role in multiple sclerosis (MS) development, many patients underwent endovascular treatment (ET) of CCSVI. The objective of the study is to evaluate the outcome and safety of ET in Italian MS patients. Italian MS centers that are part of the Italian MS Study Group were all invited to participate to this retrospective study. A structured questionnaire was used to collect detailed clinical data before and after the ET. Data from 462 patients were collected in 33 centers. ET consisted of balloon dilatation (93 % of cases) or stent application. The mean follow-up duration after ET was 31 weeks. Mean EDSS remained unchanged after ET (5.2 vs. 4.9), 144 relapses occurred in 98/462 cases (21 %), mainly in RR-MS patients. Fifteen severe adverse events were recorded in 3.2 % of cases. Given the risk of severe adverse events and the lack of objective beneficial effects, our findings confirm that at present ET should not be recommended to patients with MS.

Effect of Multiple Firings on the Microshear Bond Strength Between a Translucent Zirconia and a Resin Cement.

PURPOSE: This study investigated the microshear bond strength between a resin cement and a translucent zirconia subjected to multiple characterization firings. METHODS AND MATERIALS: 5Y-PSZ zirconia blocks (Katana UTML) were sliced, sintered (1550°C, 2 h), and randomly divided into six groups (n=10) according to the number of characterization firings (0, 1, 2, 3, 5, or 10) and aging (baseline or after thermocycling). Each characterization firing was performed at 750°C for 1 minute. The ceramic surfaces were all sandblasted with 50 µm Al2O3 and silanized. Then, cylinders of resin cement (0.96 mm diameter × 2 mm height) were bonded onto their surfaces. The baseline samples were immersed in distilled water for 24 hours before the microshear bond strength (µSBS) tests. The aged samples were tested after 5000 thermocycles in water (5°C-55°C). The failure modes were classified as adhesive, predominantly adhesive, or cohesive. Scanning electron microscope images of the failure modes and the ceramic surfaces after the firings were taken. The µSBS data were analyzed by two-way ANOVA and Tukey's test. RESULTS: The number of characterization firings and aging affected the bond strength. The highest bond strength values were observed from the 2-firing group at baseline. The µSBS results after 1, 2, or 3 characterization firings were similar at baseline and after aging. On the other hand, 0, 5, and 10 firings revealed the lowest bond strengths. The most frequent failures were adhesive and predominantly adhesive. Zirconia grains were not affected by the multiple firings. CONCLUSION: One to three characterization firings after sintering improve the bond strength of 5Y-PSZ to the resin cement when compared to none or several (five or ten) firing cycles.

On the nonlinear threshold versus distance in long-haul highly-dispersive coherent systems.

We show that the accumulation rate of nonlinearity in highly-dispersive long-haul coherent links can also be measured from the nonlinear threshold decrease rate, and provide simulations of such rates for both single- and cross-channel effects. We then show how the estimated rate can be used for the overall system design.

PDM-iRZ-QPSK vs. PS-QPSK at 100 Gbit/s over dispersion-managed links.

We compare by simulation the performance of 100 Gbit/s PDM-iRZ-QPSK and PS-QPSK transmission both in homogeneous and hybrid QPSK/OOK DM links. We detail the reasons of the overall performance investigating each nonlinear effect (SPM, XPM and XPolM) individually. Moreover, we compare the accuracy of the noise loading method with the more realistic use of noisy in-line amplifiers. Results shows that i) PDM-iRZ-QPSK and PS-QPSK have same reach in both homogeneous and hybrid setups, ii) correct simulations must include distributed ASE.

Modeling nonlinearity in coherent transmissions with dominant intrachannel-four-wave-mixing.

By extending a well-established time-domain perturbation approach to dual-polarization propagation, we provide an analytical framework to predict the nonlinear interference (NLI) variance, i.e., the variance induced by nonlinearity on the sampled field, and the nonlinear threshold (NLT) in coherent transmissions with dominant intrachannel-four-wave-mixing (IFWM). Such a framework applies to non dispersion managed (NDM) very long-haul coherent optical systems at nowadays typical baudrates of tens of Gigabaud, as well as to dispersion-managed (DM) systems at even higher baudrates, whenever IFWM is not removed by nonlinear equalization and is thus the dominant nonlinearity. The NLI variance formula has two fitting parameters which can be calibrated from simulations. From the NLI variance formula, analytical expressions of the NLT for both DM and NDM systems are derived and checked against recent NLT Monte-Carlo simulations.

Vaccination of mice with chitosan nanogel-associated recombinant NcPDI against challenge infection with Neospora caninum tachyzoites.

The effects of nanogel encapsulation of recombinant NcPDI (recNcPDI) following vaccination of mice by intranasal or intraperitoneal routes and challenge infection with Neospora caninum tachyzoites were investigated. Nanogels were chitosan based, with an alginate or alginate-mannose surface. None of the mice receiving recNcPDI intraperitoneal (i.p.) (without nanogels) survived, whereas intranasal (i.n.) application protected 9 of 10 mice from disease. Association of recNcPDI with nanogels improved survival of i.p. vaccinated mice, but nanogels without recNcPDI gave similar protection levels. When nanogels were inoculated via the i.n. route, 80% of the mice were protected. Association of recNcPDI with the alginate-coated nanogels protected all mice against disease. Quantification of the cerebral parasite burden showed a significant reduction of parasite numbers in most experimental groups vaccinated i.n., except those vaccinated with alginate-mannose nanogels with or without recNcPDI. For i.p. vaccinated groups, no significant differences in cerebral infection densities were measured, but there was a reduction in the groups vaccinated with recNcPDI associated with both types of nanogels. Analysis of the immune responses of infected mice indicated that association of recNcPDI with nanogels altered the patterns of cytokine mRNA expression profiles, but had no major impact on the antibody subtype responses. Nevertheless, this did not necessarily relate to the protection.

Oviductal fluid counterbalances the negative effect of high temperature on sperm in an ectotherm model.

Global warming is affecting biodiversity; however, the extent to which animal reproductive processes respond to predicted temperature increments remains largely unexplored. The thermal environment has a pronounced impact on metabolic rates of ectotherms; therefore, an interesting question to assess is whether temperature increase might affect specific reproductive mechanisms like sperm performance in ectotherms. Moreover, in many species, oviductal fluid (OF) is known to regulate and maintain sperm quality; however, the role of OF in relation to the effects of high temperature on sperm remains unclear. Our aim was to experimentally test the effect of increased temperature on sperm velocity, swimming path and percentage of motility in neutral conditions at ejaculation (without OF) and in female's reproductive tract fluid (with OF), in a social ectotherm lizard model, Tropidurus spinulosus, which has specific thermal requirements for reproduction. Our results suggest that a rising temperature associated with global warming (+4°C) affects negatively sperm dynamics and survival. However, OF ameliorated the harmful effects of high temperature. This is an important point, as this study is the first to have tested the role of OF in preserving sperm from a warmer pre-fertilization environment. These results contribute to our understanding of how thermal environment changes might affect post-copulatory reproductive mechanisms. This article has an associated First Person interview with the first author of the paper.

qPCR and qRT-PCR analysis: Regulatory points to consider when conducting biodistribution and vector shedding studies.

Gene and cell therapy fields have experienced remarkable growth during the past decade. Demands for preclinical and clinical safety assessments of these cell and gene therapy test articles (TAs) have effectively increased the necessity for regulated biodistribution, vector shedding, gene expression, and/or pharmacokinetics bioanalysis studies. Guidance documents issued from numerous international regulatory authorities recommend the use of quantitative polymerase chain reaction (qPCR) and/or quantitative reverse transcriptase PCR (qRT-PCR) assays due to their highly sensitive and robust target-specific detection. However, only preclinical biodistribution assay sensitivity is specified in these documents. Criteria such as accuracy, precision, and repeatability are not yet defined. This guidance void has resulted in several conflicting institutional interpretations of essential parameters necessary for the development and validation of robust assays to support safety assessments of gene and cell therapy TAs. There is an urgent need for an ongoing discussion among bioanalytical scientists in this field to generate a "best practice" consensus around preclinical and clinical qPCR/qRT-PCR assay design. With regard to this need, we offer critical points to consider when developing, validating, running sample analysis, and reporting qPCR/qRT-PCR assays.

Echocardiographic assessment of hemodynamic changes produced by two methods of inducing fluid deficit in dogs.

BACKGROUND: Hydration status is important to the cardiovascular system because of its effects on preload. Decreased preload can alter echocardiographic measurements of systolic and diastolic function, potentially confounding interpretation of results. HYPOTHESIS/OBJECTIVES: Mild fluid deficits are associated with measurable echocardiographic changes that are validated by physical and biochemical markers of decreased intravascular volume. ANIMALS: Twenty-five healthy staff/student-owned dogs with no evidence of cardiac or renal disease. METHODS: Prospective, interventional laboratory study. Dogs were randomly assigned to water deprivation (WD) alone for 8 hours (n = 13) or to furosemide treatment (FTx, 2.5mg/kg IV) followed by WD for 8 hours (n = 12). Echocardiograms, biochemical sampling, and physical parameters were measured at baseline, and after 4 and 8 hours. RESULTS: Both protocols induced fluid deficit as indicated by significant (P < .00001) decreases in weight at 4 hours (WD, 1.1%; FTx, 3.7%) and 8 hours (WD, 2.7%; FTx, 4.5%). Furosemide significantly decreased left ventricular end-diastolic volume (54.3 +/- 19.3-42.1 +/- 17.3 mL, P < .0001), cardiac index (4.2 +/- 1.1-2.9 +/- 0.9 L/min/M2, P < .0001), and mitral valve E wave velocity (0.79 +/- 0.2-0.66 +/- 0.2 m/s, P = .0004). These changes were accompanied by significant increases in blood urea nitrogen concentration (13.8 +/- 2.6-14.8 +/- 2.7 mg/dL, P = .04), vasopressin concentration (1.4 +/- 1.2-3.3 +/- 1.9 pg/mL, P = .045), and PCV (49.8 +/- 4.5-53.2 +/- 6.5%, P = .006). Effects of water deprivation alone were similar, but less pronounced. CONCLUSIONS AND CLINICAL IMPORTANCE: Mild fluid deficits have measurable hemodynamic effects in dogs. Hydration status should be considered when evaluating cardiac function by echocardiogram.

Oropharyngeal dysphagia and language delay in partial trisomy 9p: case report.

The phenotype of partial trisomy 9p includes global developmental delay, microcephaly, bulbous nose, downturned oral commissures, malformed ears, hypotonia, and severe cognitive and language disorders. We present a case report and a comparative review of clinical findings on this condition, focusing on speech-language development, cognitive abilities and swallowing evaluation. We suggest that oropharyngeal dysphagia should be further investigated, considering that pulmonary and nutritional disorders affect the survival and quality of life of the patient. As far as we know, this is the first study of a patient with partial trisomy 9p described with oropharyngeal dysphagia.

Gradenigo's syndrome in a four-year-old patient: a rare diagnosis in the modern antibiotic era.

OBJECTIVE: This study gives details of a rare case of petrous apicitis that presented as Gradenigo's syndrome and was managed surgically. METHOD: This study presents a case report and review of the literature. RESULTS: A four-year-old female was admitted for failure to thrive following recent sinusitis. Physical examination was positive for right sided facial pain, photophobia and right abducens nerve palsy. Subsequent magnetic resonance imaging revealed a 1.3 × 1.7 × 1.4 cm abscess encompassing the right Meckel's cave. A computed tomography scan showed petrous apicitis and otomastoiditis, confirming Gradenigo's syndrome. The patient was taken to the operating theatre for right intact canal wall mastoidectomy with myringotomy and tube placement. She was discharged on six weeks of ceftriaxone administered by a peripherally inserted central catheter line. At a two-week post-operative visit, she showed notable improvement in neuropathic symptoms. CONCLUSION: This study presents a rare case of petrous apicitis managed surgically without the need for a craniotomy or transcochlear procedure.

Sexual dichromatism and color diversity in the spiny lava lizard Tropidurus spinulosus using lizard visual modelling.

Colors are important vehicles for social signals in many taxa. In Squamata, previous studies have linked color characteristics and chromatic diversity to sexual selection and, particularly, species showing male-biased body size dimorphism also showed male-biased dichromatism and color diversity. Sexual dichromatism may occur in body regions used for conspecific communication and it may be expressed at wavelengths, such as ultraviolet, easily perceivable by conspecifics. We tested this prediction in a social lizard model, Tropidurus spinulosus, using spectrophotometry and visual modelling which enable colors to be interpreted as the individuals of the same taxon see them. Our results indicate that sexual dichromatism occurs in the ventral regions and the flanks, which are the body regions involved in sexual displays. Males show greater color diversity, having larger color volumes and more contrasting colors. These findings reinforce the idea that sexual selection towards males is coupled with the evolution of male-biased, diverse, coloration which could act as a signal in social reproductive contexts.

Arthrospira platensis harvesting with membranes: fouling phenomenon with limiting and critical flux.

The present work deals with the harvesting of Arthrospira platensis (Spirulina) from a diluted culture medium. This cyanobacterium was retained by the European Space Agency as food supply for long term manned spatial missions, and integrated in the MELiSSA project: an artificial microecosystem which supports life in space. Membranes techniques seem to be adapted to efficiency, reliability and safety constraints, even if a well-known limitation is the progressive fouling and permeation flux decrease. Among usual solid/liquid separation processes, Arthrospira harvesting is performed by tangential ultrafiltration (tubular inorganic membrane 50 kD Céram-Inside from Tami, Nyons, France). To ensure a reliable separation step with the best biomass quality, a good comprehension of the ultrafiltration progress and fouling phenomenon is needed, in particular, the link between operating parameters, permeation flux and cleanability. Comparative experiments were made between limiting and critical flux with different suspensions: fresh biomass, stressed biomass and a suspension of Arthrospira platensis enriched with exopolysaccharides.