Here I describe the novel R package SNPfiltR and demonstrate its functionalities as the backbone of a customizable, reproducible SNP filtering pipeline implemented exclusively via the widely adopted R programming language. SNPfiltR extends existing SNP filtering functionalities by automating the visualization of key parameters such as depth, quality, and missing data, then allowing users to set filters based on optimized thresholds, all within a single, cohesive working environment. All SNPfiltR functions require a vcfR object as input, which can be easily generated by reading a SNP dataset stored as a standard vcf file into an R working environment using the function read.vcfR() from the R package vcfR. Performance benchmarking reveals that for moderately sized SNP datasets (up to 50M genotypes with associated quality information), SNPfiltR performs filtering with comparable efficiency to current state of the art command-line-based programs. These benchmarking results indicate that for most reduced-representation genomic datasets, SNPfiltR is an ideal choice for investigating, visualizing, and filtering SNPs as part of a cohesive and easily documentable bioinformatic pipeline. The SNPfiltR package can be downloaded from CRAN with the command [install.packages(“SNPfiltR”)], and a development version is available from GitHub at: (github.com/DevonDeRaad/SNPfiltR). Additionally, thorough documentation for SNPfiltR, including multiple comprehensive vignettes, is available at the website: (devonderaad.github.io/SNPfiltR/).

Understanding the genetic changes associated with the evolution of biological diversity is of fundamental interest to molecular ecologists. The assessment of genetic variation at hundreds or thousands of unlinked genetic loci forms a sound basis to address questions ranging from micro- to macro-evolutionary timescales, and is now possible thanks to advances in sequencing technology. Major difficulties are associated with i) the lack of genomic resources for many taxa, especially from tropical biodiversity hotspots, ii) scaling the numbers of individuals analyzed and loci sequenced, and iii) building tools for reproducible bioinformatic analyses of such datasets. To address these challenges, we developed a set of target capture probes for phylogenomic studies of the highly diverse, pantropically distributed and economically significant rosewoods (Dalbergia spp.), explored the performance of an overlapping probe set for target capture across the legume family (Fabaceae), and built a general-purpose bioinformatics pipeline. Phylogenomic analyses of Dalbergia species from Madagascar yielded highly resolved and well supported hypotheses of evolutionary relationships. Population genomic analyses identified differences between closely related species and revealed the existence of a potentially new species, suggesting that the diversity of Malagasy Dalbergia species has been underestimated. Analyses at the family level corroborated previous findings by the recovery of monophyletic subfamilies and many well-known clades, as well as high levels of gene tree discordance, especially near the root of the family. The new genomic and bioinformatics resources will hopefully advance systematics and ecological genetics research in legumes, and promote conservation of the highly diverse and endangered Dalbergia rosewoods.

Automatic molecular design on computers is an emerging technology for the determination of optimal fuel molecules. We developed a computer-aided molecular design framework through a transformation rule-based molecular evolution method. The reaction rule was used as the elementary step to change the molecular structure. A molecule can achieve structural variation continuously using a series of reaction rules. The finding of the optimal molecule can be seen as the evolution of structure in the chemical space, which was guided by using a global optimization algorithm to select the best reaction routine. We showed that the optimized molecule is independent of the input initial structure, proving the robustness of the method. We then applied the method to design gasoline molecules for motor and aviation gasoline. The designed molecules can not only serve as competitive candidate components for high-quality gasoline, but also accelerate the synthesis rate of new molecules in the laboratory.

The dissociation conditions of hydrate in clayey silts are of great significance for its efficient production. In this work, the dissociation conditions of methane hydrate in clayey silt cores were experimentally measured by step-heating method. Various cores including quartz powder, montmorillonite and South China Sea sediments were used for investigation. The results showed that the dissociation temperatures of methane hydrate in clayey silt cores depressed compared to bulk hydrate. In comparison to grain size, salinity and lithology had a more significant influence on the equilibrium temperature depression. A water activity meter was used to measure the water activity in clayey silt cores. The influence of salt and minerals on water activity was investigated. By combining the measured water activity data with the Chen-Guo model, a novel water activity measurement method (WAM) for the hydrate dissociation conditions prediction was proposed. The predicted results are in good agreement with the experimental data.

Particle clusters in CFB risers were identified from the instantaneous solids holdup signals by a new sliding-window based signal processing method. By shifting the sliding time window and calculating the mean and the standard deviation within it, a non-linear threshold curve for identifying the clusters was derived instead of the conventional constant threshold. The optimal sliding window size was determined as Wb = 1024 data points based on the bisection method on the entire piece of signals. Using the proposed method, a more realistic characterization of the clusters in both the HDCFB and LDCFB was obtained by considering the bulk fluctuation of the gas-solids flow. The clusters in the HDCFB have higher solids holdup and lower velocity than that in the LDCFB. The HDCFB is also found to have a greater number of loose clusters for better gas-solids contacting and exchanges in the center of the riser.

Ocean pollution is a worldwide environmental challenge that could be partially tackled through microbial applications. To shed light on the diversity and applications of the bacterial communities that inhabit the sediments trapped in artificial containers, we analyzed residues (Polyethylene terephthalate (PET) bottles and aluminum cans) collected from the Mediterranean Sea by scanning electron microscopy and Next Generation Sequencing. Moreover, we set a collection of culturable bacteria from the plastisphere that were screened for their ability to use PET as a carbon source. Our results reveal that Proteobacteria are the predominant phylum in all the samples and that Rhodobacteraceae, Woeseia, Actinomarinales, or Vibrio are also abundant in these residues. Moreover, we identified marine isolates with enhanced growth in the presence of PET: Aquimarina intermedia, Citricoccus spp., and Micrococcus spp. Our results suggest that the marine environment is a source of biotechnologically promising bacterial isolates that may use PET or PET additives as carbon sources.

We consider the discrete Schr\”odinger operator $H=-\Delta+V$ with a sparse potential $V$ and find conditions guaranteeing either existence of wave operators for the pair $H$ and $H_0=-\Delta$, or presence of dense purely point spectrum of the operator $H$ on some interval $[\lambda_0,0]$ with $\lambda_0<0$.

This investigation is concerned with the 2D acoustic scattering problem of a plane wave propagating in a non-lossy, isotropic, homogeneous fluid host and soliciting a linear, isotropic, macroscopically-homogeneous, generally-lossy, flat-plane layer in which the mass density and wavespeed are different from those of the host. The focus is on the inverse problem of the retrieval of the layer mass density. The data is the transmitted pressure field, obtained by simulation (resolution of the forward problem) in exact, explicit form via the domain integral form of the Bergman wave equation. This solution is exact and more explicit in terms of the mass-density contrast (between the host and layer) than the classical solution obtained by separation of variables. A perturbation technique enables the solution (in its form obtained by the domain integral method) to be cast as a series of powers of the mass density contrast, the first three terms of which are employed as the trial models in the treatment of the inverse problem. The aptitude of these models to retrieve the mass density contrast is demonstrated both theoretically and numerically.

This article is concerned with the study of the unique solvability of inverse boundary value problem for integro-differential heat equation. To study the solvability of the inverse problem, we first reduce the considered problem to an auxiliary system with trivial data and prove its equivalence (in a certain sense) to the original problem. Then using the Banach fixed point principle, the existence and uniqueness of a solution to this system is shown.

Understanding the mechanisms and genes that enable animal populations to adapt to pathogens is important from an evolutionary, health and conservation perspective. Berthelot’s pipit (Anthus berthelotii) experiences extensive and consistent spatial heterogeneity in avian pox infection pressure across its range of island populations, thus providing an excellent system with which to examine how pathogen-mediated selection drives spatial variation in immunogenetic diversity. Here we test for evidence of genetic variation associated with avian pox at both an individual and population-level. At the individual level, we find no evidence that variation in MHC class I and TLR4 (both known to be important in recognising viral infection) was associated with pox infection within two separate populations. However, using genotype-environment association (Bayenv) in conjunction with genome-wide (ddRAD-seq) data, we detected strong associations between population-level avian pox prevalence and allele frequencies of single nucleotide polymorphisms (SNPs) at a number of sites across the genome. These sites were located within genes involved in cellular stress signalling and immune responses, many of which have previously been associated with responses to viral infection in humans and other animals. Consequently, our analyses provide evidence that pathogen-mediated selection has shaped genomic variation among relatively recently colonised island bird populations, and highlights the utility of genotype-environment associations for identifying candidate genes involved in adaption to local pathogen pressures.

Abstract

Background: Malnutrition (under and overnutrition) occurs in children with solid tumors and has been linked with adverse outcomes during and after treatment. Assessment of nutritional status (NS) can be challenging due to large tumor burdens, atypical growth patterns and different methods for assessing NS. Methods: Retrospective longitudinal study of children with solid tumors (n=61). Anthropometric data assessed [(diagnosis, after diagnosis (1.5, 3, 6 and 12 months, 5 years), end of treatment (EOT), initial cancer survivorship program (CSP) visit]. Registered dietitian nutritionist nutritional assessment (NA) during treatment and Intensity of Treatment Rating (ITR) documented. Results: At diagnosis, prevalence of undernutrition [(Z-score -1.0 to -2.99)] and overnutrition (Z-score ≥ +2.0) were 13.8% and 8.6%, respectively; weight status categories, 8.6%, 6.9%/13.8% were underweight, overweight/obese, respectively. Weight loss and decreased weight-for-age Z-score (WAZ) occurred in 31.9% and 74.5% patients, respectively, at 1.5 months. At EOT, compared to diagnosis, WAZ and height-for-age Z-score (HAZ) decreased and BMIZ increased. From EOT to CSP visit, overweight/obesity doubled, 7.7%/5.8% and 15.2/11.9%, respectively. Thirty-one percent of patients received a NA, occurring at lowest WAZ. Over 50% had ITR of level 3 or 4 and 88.9% had NA in level 4. Conclusions: Suboptimal NS continues at diagnosis, during treatment and survivorship. Normalized measures, accounting for expected growth, should be used instead of raw numbers. More than one nutrition indicator will identify atypical growth patterns and a proactive approach would help prevent malnutrition. Evidence based research is essential and collaboration necessary to meet the needs of this population.

Habitat fragmentation is known to affect biodiversity, but the impact on pollinators and their interactions with plants is still unclear in anthropized landscapes. Islands are open-air laboratories for ecological studies with simplified communities and interactions, suitable to disentangle how land-use alteration impacts pollination ecology and its ecosystem service. Here, we used Maldives islands as model systems to investigate how pollinator richness, their mutualistic interactions with plants, and pollination efficiency are shaped by the degree of green area fragmentation (i.e., gardens, parks and semi-natural green covered patches), by considering both community- and species-level responses. To do this, we surveyed pollinators from 11 islands showing a gradient of green area fragmentation. In order to characterize the interactions between plants and pollinators and obtain a novel and comprehensive view of the key ecological dynamics, a DNA metabarcoding approach was adopted to identify the pollen carried by pollinators. We found that green area fragmentation at intermediate levels played positive effects on pollinator richness. However, fragmentation decreased interaction network complexity. Intriguingly, body size mediated the effect of landscape alteration on plant-pollinator interactions, as only the largest bee species expanded the foraging breath in terms of transported pollen richness at increasing fragmentation. In parallel, the pollination efficiency increased with pollinator species richness in two sentinel plants. This study shows that moderate landscape fragmentation of green areas shapes the ecosystem service of pollination, where in spite of interactions being less complex and mediated by pollinator body size, pollinator biodiversity and potential plant reproduction are supported.

TitleDo we also need recommendations on management of hypertension rise?Mini commentary forWen T et al. Trends and Outcomes for Deliveries with Hypertensive Disorders of Pregnancy from 2000 to 2018: A Cross-Sectional Study (Manuscript ID BJOG-21-1382.R1)

A document by maryam zamani. Click on the document to view its contents.

Background: Many couples experience decreasing sexual satisfaction in postpartum period. Various sexual health counseling approaches have been designed for postpartum women to address their common sexual concerns and problems. Objective: This study aimed to investigate the effectiveness of Women's Postpartum Sexual Health Program (WPSHP) on women's sexual satisfaction in postpartum period. Materials and Methods: The study was a single blind randomized clinical trial on 75 postpartum women aged 18-35 yr with low sexual satisfaction who attended urban health-care centres in Mashhad, Iran in 2016. Data were collected using a demographic questionnaire, the Depression Anxiety Stress Scales-21, and the Larson Sexual Satisfaction Questionnaire. The intervention group received counselling based on the WPSHP, a four-session, group-and couples-based program. The control group just received postpartum routine care. Results: Both the intervention and control groups were homogeneous for demographic variables. According to the Mann-Whitney test, sexual satisfaction score in the intervention group was significantly higher than the control group 8 weeks after the intervention (p < 0.001). According to the Wilcoxon test, there was a significant difference in the mean score of sexual satisfaction before and after intervention in the intervention group (p < 0.001). Conclusion: WPSHP caused higher levels of sexual satisfaction. It is therefore recommended to use this program in women during the postpartum period to promote their sexual satisfaction. Production and Hosting by Knowledge E Maryam Zamani et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are

A document by Alexis karpouzos. Click on the document to view its contents.

A document by Alexis karpouzos. Click on the document to view its contents.

A 53 year old male with a history of vascular ring repair secondary to a right sided aortic arch with retroesophageal subclavian artery and ligamentum arteriosum to the descending thoracic aorta presented to our institution with a large aortic pseudoaneurysm of the distal aortic arch. Computed tomography demonstrated a right sided aortic arch with a 5.8 cm pseudoaneurysm arising from the distal arch in the area of his previously divided ligamentum. The patient underwent a successful two-stage repair including a left carotid to subclavian bypass followed by total arch replacement with frozen elephant trunk. He recovered well postoperatively and computed tomography showed complete repair of the pseudoaneurysm with patent bypass graft.

With the growing demand for rectangular and square hollow steel sections in the last few decades, the cold roll forming process has become a widely acknowledged hollow sections manufacturing method; however, residual stress generated during the roll forming process is one of the primary concerns on roll-formed products. In this regard, several researchers have conducted numerical and experimental investigations of residual stress distributions on roll-formed steel sections. However, most of the studies found in the literature have been confined to the measurement of residual surface stresses. On the other hand, experimental studies conducted on fatigue and load-carrying capacity of hollow structural steels have shown that there is indeed a simple relation between the through-thickness residual stress distributions and mechanical properties of structures. Thus, this paper employed a proper numerical modelling procedure using LS-DYNA’s finite element code to explore through-thickness residual stress distributions generated during the roll forming process of rectangular and square hollow steel sections from different material grades. Moreover, a small-scale parametric study was conducted to explore the effects of the partial heating roll forming method on through-the-thickness residual stress distributions to satisfy the growing demand for residual stress-free roll-formed products.

This Supplementary Information includes: Section S1- Fabrication method                                        Section S2- Actuation method                                          Section S3- Analysis of sixth-DOF torque                     Section S4- Experiments                                                     Figures S1-S31                                                                         Supporting Table                                                                   References                                                                                Other supplementary materials for this manuscript include the following:Supporting SI Videos S1-S10 Corresponding author(s) Email:   gzlum@ntu.edu.sg  

Abstract Successful, patient-led advocacy and research in Long Covid is contributing to change our understanding of SARS-CoV-2 infection, viral-onset diseases, and knowledge building in medicine and beyond. It is my hope that patient-centred expertise will be further incorporated within the biomedical community. This would contribute to critical changes in medical awareness of chronic diseases and patient care.

Magnetic miniature robots (MMRs) are mobile actuators that can exploit their size to non-invasively access highly confined, enclosed spaces. By leveraging on such unique abilities, MMRs have great prospects to transform robotics, biomedicine and materials science. As having high dexterity is critical for MMRs to enable their targeted applications, existing MMRs have developed numerous soft-bodied gaits to locomote in various environments. However, there exist two critical limitations that have severely restricted their dexterity: (i) MMRs capable of multimodal soft-bodied locomotion have only demonstrated five-degrees-of-freedom (five-DOF) motions because the sixth-DOF rotation about their net magnetic moment axis is uncontrollable; (ii) six-DOF MMRs have only realized one mode of soft-bodied, swimming locomotion. Here we propose a six-DOF MMR that can execute seven modes of soft-bodied locomotion and perform 3-dimensional pick-and-place operations. By optimizing its harmonic magnetization profile, our MMR can produce 1.41-63.9 folds larger sixth-DOF torque than existing MMRs with similar profiles, without compromising their traditional five-DOF actuation capabilities. The proposed MMR demonstrated unprecedented dexterity; it could jump through narrow slots to reach higher grounds; use precise orientation control to roll, two-anchor crawl and swim across tight openings with strict shape constraints; perform undulating crawling across three different planes in convoluted channels. Keywords: Magnetic materials; soft actuators; miniature robots; locomotion. Corresponding author(s) Email:   gzlum@ntu.edu.sg  

Subcutaneous implantable cardioverter defibrillators (S-ICDs) are currently indicated for patients who meet ICD implantation criteria for the prevention of sudden cardiac death (SCD). In December 2020, a unique cardiac implantable electronic device (CIED) situation arose as both the S-ICD generator and electrode were under a device advisory. We would recommend all future CIED implantation guidelines receive a caveat regarding checking current CIED advisories, in order to avoid future similar scenarios.