Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater.

Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.

Corpora cavernosum abscess and corporoglanular fistula following penile shunts for ischemic priapism.

Ischemic priapism is a urologic emergency requiring urgent intervention to prevent tissue necrosis and preserve erectile function. Cases refractory to aspiration and intra-cavernosal sympathomimetic therapy requires timely surgical shunting. Corpus cavernosum abscess following penile shunts is an exceedingly rare complication, with as few as 2 previous reported cases. We report our experience and outcome in the case of a 50-year-old patient who developed a corpora cavernosum abscess and concurrent corporoglanular fistula, following penile shunt procedures for ischemic priapism.

Designing Digital COVID-19 Screening: Insights and Deliberations.

Due to the global COVID-19 pandemic, public health control and screening measures have been introduced at healthcare facilities, including those housing our most vulnerable populations. These warning measures situated at hospital entrances are presently labour-intensive, requiring additional staff to conduct manual temperature checks and risk-assessment questionnaires of every individual entering the premises. To make this process more efficient, we present eGate, a digital COVID-19 health-screening smart Internet of Things system deployed at multiple entry points around a children's hospital. This paper reports on design insights based on the experiences of concierge screening staff stationed alongside the eGate system. Our work contributes towards social-technical deliberations on how to improve design and deploy of digital health-screening systems in hospitals. It specifically outlines a series of design recommendations for future health screening interventions, key considerations relevant to digital screening control systems and their implementation, and the plausible effects on the staff who work alongside them.

Nurse, Give Me the News! Understanding Support for and Opposition to a COVID-19 Health Screening System.

Helping the sick and protecting the vulnerable has long been the credo of the health profession. In response to the coronavirus-disease-2019 (COVID-19 pandemic), hospitals and healthcare institutions have rapidly employed public health measures to mitigate patient and staff infection. This paper investigates staff and visitor responses to the COVID-19 eGate health screening system; a self-service technology (SST) which aims to protect health care workers and facilities from COVID-19. Our study evaluates the in situ deployment of the eGate, and employs a System Usability Scale (SUS) and questionnaire (n = 220) to understand staff and visitor's acceptance of the eGate. In detailing the themes relevant to those who advocate for the system and those who oppose it, we contribute towards a more detailed understanding of the use and non-use of health-screening SSTs. We conclude with a series of considerations for the design of future interactive screening systems within hospitals.

The Terrestrial Biosphere Model Farm.

Model Intercomparison Projects (MIPs) are fundamental to our understanding of how the land surface responds to changes in climate. However, MIPs are challenging to conduct, requiring the organization of multiple, decentralized modeling teams throughout the world running common protocols. We explored centralizing these models on a single supercomputing system. We ran nine offline terrestrial biosphere models through the Terrestrial Biosphere Model Farm: CABLE, CENTURY, HyLand, ISAM, JULES, LPJ-GUESS, ORCHIDEE, SiB-3, and SiB-CASA. All models were wrapped in a software framework driven with common forcing data, spin-up, and run protocols specified by the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) for years 1901-2100. We ran more than a dozen model experiments. We identify three major benefits and three major challenges. The benefits include: (a) processing multiple models through a MIP is relatively straightforward, (b) MIP protocols are run consistently across models, which may reduce some model output variability, and (c) unique multimodel experiments can provide novel output for analysis. The challenges are: (a) technological demand is large, particularly for data and output storage and transfer; (b) model versions lag those from the core model development teams; and (c) there is still a need for intellectual input from the core model development teams for insight into model results. A merger with the open-source, cloud-based Predictive Ecosystem Analyzer (PEcAn) ecoinformatics system may be a path forward to overcoming these challenges.

Advanced Functions Embedded in the Second Version of Database, Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2.

The Global Evaluation of SARS-CoV-2/hCoV-19 Sequences 2 (GESS v2 https://shiny.ph.iu.edu/GESS_v2/) is an updated version of GESS, which has offered a handy query platform to analyze single-nucleotide variants (SNVs) on millions of high coverages and high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) complete genomes provided by the Global Initiative on Sharing Avian Influenza Data (GISAID). Including the tools in the first version, the GESS v2 is embedded with new functions, which allow users to search SNVs, given the viral nucleotide or amino acid sequence. The GESS v2 helps users to identify SNVs or SARS-CoV-2 lineages enriched in countries of user's interest and show the migration path of a selected lineage on a world map during specific time periods chosen by the users. In addition, the GESS v2 can recognize the dynamic variations of newly emerging SNVs in each month to help users monitor SNVs, which will potentially become dominant soon. More importantly, multiple sets of analyzed results about SNVs can be downloaded directly from the GESS v2 by which users can conduct their own independent research. With these significant updates, the GESS v2 will continue to serve as a public open platform for researchers to explore SARS-CoV-2 evolutionary patterns from the perspectives of the prevalence and impact of SNVs.

Do interoception and attending to the upper limbs affect body ownership and body representation in the grasp illusion?

Passively grasping an unseen artificial finger induces ownership over this finger and an illusory coming together of one's index fingers: a grasp illusion. Here we determine how interoceptive ability and attending to the upper limbs influence this illusion. Participants passively grasped an unseen artificial finger with their left index finger and thumb for 3 min while their right index finger, located 12 cm below, was lightly clamped. Experiment 1 (n = 30) investigated whether the strength of the grasp illusion (perceived index finger spacing and perceived ownership) is related to a person's level of interoceptive accuracy (modified heartbeat counting task) and sensibility (Noticing subscale of the Multidimensional Assessment of Interoceptive Awareness). Experiment 2 (n = 30) investigated the effect of providing verbal or tactile cues to guide participants' attention to their upper limbs. On their own, neither interoceptive accuracy and sensibility or verbal and tactile cueing had an effect on the grasp illusion. However, verbal cueing increased the strength of the grasp illusion in individuals with lower interoceptive ability. Across the observed range of interoceptive accuracy and sensibility, verbal cueing decreased perceived index spacing by 5.6 cm [1.91 to 9.38] (mean [95%CI]), and perceived ownership by ∼3 points on a 7-point Likert scale (slope -0.93 [-1.72 to -0.15]). Thus, attending to the upper limbs via verbal cues increases the strength of the grasp illusion in a way that is inversely proportional to a person's level of interoceptive accuracy and sensibility.

Updated SARS-CoV-2 single nucleotide variants and mortality association.

By analyzing newly collected SARS-CoV-2 genomes and comparing them with our previous study about SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found that the SNV clustering had changed remarkably since June 2020. Apart from that the group of SNVs became dominant, which is represented by two nonsynonymous mutations A23403G (S:D614G) and C14408T (ORF1ab:P4715L), a few emerging groups of SNVs were recognized with sharply increased monthly incidence ratios of up to 70% in November 2020. Further investigation revealed sets of SNVs specific to patients' ages and/or gender, or strongly associated with mortality. Our logistic regression model explored features contributing to mortality status, including three critical SNVs, G25088T(S:V1176F), T27484C (ORF7a:L31L), and T25A (upstream of ORF1ab), ages above 40 years old, and the male gender. The protein structure analysis indicated that the emerging subgroups of nonsynonymous SNVs and the mortality-related ones were located on the protein surface area. The clashes in protein structure introduced by these mutations might in turn affect the viral pathogenesis through the alteration of protein conformation, leading to a difference in transmission and virulence. Particularly, we explored the fact that nonsynonymous SNVs tended to occur in intrinsic disordered regions of Spike and ORF1ab to significantly increase hydrophobicity, suggesting a potential role in the change of protein folding related to immune evasion.

Fine-Grained Mapping of Cortical Somatotopies in Chronic Complex Regional Pain Syndrome.

It has long been thought that severe chronic pain conditions, such as complex regional pain syndrome (CRPS), are not only associated with, but even maintained by a reorganization of the somatotopic representation of the affected limb in primary somatosensory cortex (S1). This notion has driven treatments that aim to restore S1 representations in CRPS patients, such as sensory discrimination training and mirror therapy. However, this notion is based on both indirect and incomplete evidence obtained with imaging methods with low spatial resolution. Here, we used fMRI to characterize the S1 representation of the affected and unaffected hand in humans (of either sex) with unilateral CRPS. The cortical area, location, and geometry of the S1 representation of the CRPS hand were largely comparable with those of both the unaffected hand and healthy controls. We found no differential relation between affected versus unaffected hand map measures and clinical measures (pain severity, upper limb disability, disease duration). Thus, if any map reorganization occurs, it does not appear to be directly related to pain and disease severity. These findings compel us to reconsider the cortical mechanisms underlying CRPS and the rationale for interventions that aim to "restore" somatotopic representations to treat pain.SIGNIFICANCE STATEMENT This study shows that the spatial map of the fingers in somatosensory cortex is largely preserved in chronic complex regional pain syndrome (CRPS). These findings challenge the treatment rationale for restoring somatotopic representations in complex regional pain syndrome patients.

Is a 10-minute surgical scrub necessary in urologic prosthetic surgery? A randomized study of the effect of a 5- vs 10-minute surgical scrub on bacterial colony counts in the genital skin.

AIMS: To determine the antiseptic efficacy on bacterial colony counts of a 5- vs 10-minute surgical site scrub in urologic surgery. METHODS: A prospective cohort study was conducted in 101 patients presenting for elective urological procedures. Patients were randomized to a 5- or 10-minute groin scrub with Betadine (povidone-iodine). Skin swabs were taken immediately after skin clipping and following routine painting with Betadine. A third swab was taken after the betadine skin scrub. Bacterial colony counts were reported as a number of colony-forming units (CFUs). The primary outcome measure was a quantitative comparison of CFUs in the two arms. RESULTS: Fifty-three patients were randomized to a 5-minute scrub and 48 to a 10-minute scrub. After Betadine painting, CFUs were present in 38% of patients in the 5-minute group (mean, 33.5 CFU) and in 27% of the 10-minute group (mean, 45.4 CFU). Following the surgical scrub, only 7.5% of the 5-minute group and 8.3% of the 10-minute group had a measurable CFU count of greater than or equal to 1, and colony counts were low in both groups (5- minute group: mean, 1.5 CFU; 10-minute group: mean, 2.0 CFU). There was no significant difference in CFUs following a 5- or 10-minute scrub (P = 0.28). CONCLUSIONS: The addition of a surgical skin scrub leads to a fourfold reduction in the skin CFU count compared with Betadine painting. However, there is no difference between the antibacterial effects of a 5- and 10-minute scrub. A 5-minute scrub may be sufficient in urologic prosthetic surgery.

A Novel Finger Illusion Reveals Reduced Weighting of Bimanual Hand Cortical Representations in People With Complex Regional Pain Syndrome.

Complex regional pain syndrome (CRPS) is associated with deficits in sensorimotor control. Herein we have used a novel finger illusion to investigate whether CRPS is associated with reduced weighting of bimanual hand representations. The illusion normally induces a compelling feeling that the hands are close together when in fact they are 12 cm apart. People with CRPS and age, gender, and dominant hand-matched controls tested the illusion in the midline then on either side of the midline. The illusion had 2 variants; the passive pincer-grip position, without contact (no grasp condition) and with contact (grasp condition) of the artificial finger. The primary outcome was the perceived vertical distance between the index fingers. Twenty people with CRPS and 20 controls participated (mean age 44.4 ± 11.7 years). During the no grasp condition, participants with CRPS perceived the vertical distance significantly closer to the actual 12 cm (mean 8.0 cm, 95% confidence interval 6.5-9.5 cm), than controls did (mean 6.4 cm, 95% confidence interval 5.5-7.2 cm]). That is, the illusion was weaker in people with CRPS than in controls during no grasp. There was no such difference during grasp; that is, both groups showed the predicted illusion response. There was no effect of hand placement relative to midline or relative to the opposite hand. We conclude that people with unilateral CRPS have lower weighting of bimanual hand representation than controls have, independent of hand location. However, adding additional cutaneous input returns those with CRPS to the expected performance. We suggest the results have clear clinical and research implications. PERSPECTIVE: An abnormal weighting of bilateral hand representation may reflect a vulnerability for chronic CRPS, an adaptation to the disease, and/or a potential therapeutic target. That addition of cutaneous input immediately normalizes the problem points to the possible role of bimanual tasks in prevention or rehabilitation.

Mapping Color to Meaning in Colormap Data Visualizations.

To interpret data visualizations, people must determine how visual features map onto concepts. For example, to interpret colormaps, people must determine how dimensions of color (e.g., lightness, hue) map onto quantities of a given measure (e.g., brain activity, correlation magnitude). This process is easier when the encoded mappings in the visualization match people's predictions of how visual features will map onto concepts, their inferred mappings. To harness this principle in visualization design, it is necessary to understand what factors determine people's inferred mappings. In this study, we investigated how inferred color-quantity mappings for colormap data visualizations were influenced by the background color. Prior literature presents seemingly conflicting accounts of how the background color affects inferred color-quantity mappings. The present results help resolve those conflicts, demonstrating that sometimes the background has an effect and sometimes it does not, depending on whether the colormap appears to vary in opacity. When there is no apparent variation in opacity, participants infer that darker colors map to larger quantities (dark-is-more bias). As apparent variation in opacity increases, participants become biased toward inferring that more opaque colors map to larger quantities (opaque-is-more bias). These biases work together on light backgrounds and conflict on dark backgrounds. Under such conflicts, the opaque-is-more bias can negate, or even supersede the dark-is-more bias. The results suggest that if a design goal is to produce colormaps that match people's inferred mappings and are robust to changes in background color, it is beneficial to use colormaps that will not appear to vary in opacity on any background color, and to encode larger quantities in darker colors.

Female Pelvic Medicine & Reconstructive Surgery (FPMRS) challenges on behalf of the collaborative research in pelvic surgery consortium (CoRPS): managing complicated cases series 2: management of urinary incontinence in a neurogenic patient.

Discussion and management of incontinence in a patient with spina bifida by four international experts followed by a literature review.

Biomarkers of Cellular Senescence and Skin Aging.

Cellular senescence is an irreversible growth arrest that occurs as a result of different damaging stimuli, including DNA damage, telomere shortening and dysfunction or oncogenic stress. Senescent cells exert a pleotropic effect on development, tissue aging and regeneration, inflammation, wound healing and tumor suppression. Strategies to remove senescent cells from aging tissues or preneoplastic lesions can delay tissue dysfunction and lead to increased healthspan. However, a significant hurdle in the aging field has been the identification of a universal biomarker that facilitates the unequivocal detection and quantification of senescent cell types in vitro and in vivo. Mammalian skin is the largest organ of the human body and consists of different cell types and compartments. Skin provides a physical barrier against harmful microbes, toxins, and protects us from ultraviolet radiation. Increasing evidence suggests that senescent cells accumulate in chronologically aged and photoaged skin; and may contribute to age-related skin changes and pathologies. Here, we highlight current biomarkers to detect senescent cells and review their utility in the context of skin aging. In particular, we discuss the efficacy of biomarkers to detect senescence within different skin compartments and cell types, and how they may contribute to myriad manifestations of skin aging and age-related skin pathologies.

Loss of lamin B1 is a biomarker to quantify cellular senescence in photoaged skin.

Skin ageing is an inevitable consequence of life and accelerated by exposure to ultraviolet (UV) rays. Senescence is an irreversible growth arrest and senescent cells accumulate in ageing tissues, at sites of age-related pathologies and in pre-neoplastic lesions. Conventionally, senescent cells have been detected by senescence associated-ß-galactosidase (SA-ß-gal) staining, a procedure that requires enzymatic activity, which is lost in fixed tissue samples. We previously demonstrated that loss of lamin B1 is a novel marker to identify senescent cells. Here, we demonstrate that loss of lamin B1 facilitates the detection and quantification of senescent cells upon UV-exposure in vitro and upon chronic UV-exposure and skin regeneration in vivo. Taken together, this marker enables the study of environmental conditions on tissue ageing and regeneration in vivo, serves as a diagnostic tool to distinguish senescent from proliferating cells in pre-neoplastic lesions, and facilitates investigating the role of senescent cells in various age-related pathologies.

Semi-Automatic Electronic Stent Register: a novel approach to preventing ureteric stents lost to follow up.

BACKGROUND: Ureteric stents are indispensable tools in modern urology; however, the risk of them not being followed-up once inserted poses medical and medico-legal risks. Stent registers are a common solution to mitigate this risk; however, manual registers are logistically challenging, especially for busy units. METHODS: Western Sydney Local Health District developed a novel Semi-Automatic Electronic Stent Register (SAESR) utilizing billing information to track stent insertions. To determine the utility of this system, an audit was conducted comparing the 6 months before the introduction of the register to the first 6 months of the register. RESULTS: In the first 6 months of the register, 457 stents were inserted. At the time of writing, two of these are severely delayed for removal, representing a rate of 0.4%. In the 6 months immediately preceding the introduction of the register, 497 stents were inserted, and six were either missed completely or severely delayed in their removal, representing a rate of 1.2%. A non-inferiority analysis found this to be no worse than the results achieved before the introduction of the register. CONCLUSION: The SAESR allowed us to improve upon our better than expected rate of stents lost to follow up or severely delayed. We demonstrated non-inferiority in the rate of lost or severely delayed stents, and a number of other advantages including savings in personnel costs. The semi-automatic register represents an effective way of reducing the risk associated with a common urological procedure. We believe that this methodology could be implemented elsewhere.

Pediatric Psoriasis Comorbidity Screening Guidelines.

Importance: Psoriasis is a complex inflammatory skin condition associated with serious medical comorbidities in adults, including obesity, hypertension, dyslipidemia, type 2 diabetes mellitus, psoriatic arthritis, nonalcoholic fatty liver disease, depression, anxiety, and decreased quality of life. Because psoriasis begins in childhood in almost one-third of patients, early identification of risk may be critical to minimizing effects on future health. Objective: To develop the first set of guidelines for comorbidity screening for patients with pediatric psoriasis based on current evidence. Evidence Review: A literature review was performed using PubMed from January 1999 through December 2015. Limiting the search to human studies published in English and removing reviews and editorials produced 153 relevant manuscripts. An expert panel in psoriasis, pediatric dermatology, pediatric rheumatology, pediatric gastroenterology, pediatric endocrinology, and adult and pediatric cardiology used the patient-centered Strength of Recommendation Taxonomy (SORT) method to evaluate and grade the quality of evidence. Findings: Because of the limited number of pediatric studies published on these topics, the strength of the panel's recommendations is classified as SORT level C expert consensus recommendations. The majority of recommendations coincide with those endorsed by the American Academy of Pediatrics for the general pediatric patient but with added attention to signs and symptoms of arthritis, depression, and anxiety. The panel also identified key areas for further investigation. Conclusions and Relevance: Patients with pediatric psoriasis should receive routine screening and identification of risk factors for associated comorbidities. These guidelines are relevant for all health care providers caring for patients with pediatric psoriasis, including primary care clinicians, dermatologists, and pediatric specialists. Because these are the first pediatric guidelines, re-review and refinement will be necessary as studies further detail, and possibly stratify, risk in affected children.

Nuclear envelope localization of LEMD2 is developmentally dynamic and lamin A/C dependent yet insufficient for heterochromatin tethering.

Peripheral heterochromatin in mammalian nuclei is tethered to the nuclear envelope by at least two mechanisms here referred to as the A- and B-tethers. The A-tether includes lamins A/C and additional unknown components presumably INM protein(s) interacting with both lamins A/C and chromatin. The B-tether includes the inner nuclear membrane (INM) protein Lamin B-receptor, which binds B-type lamins and chromatin. Generally, at least one of the tethers is always present in the nuclear envelope of mammalian cells. Deletion of both causes the loss of peripheral heterochromatin and consequently inversion of the entire nuclear architecture, with this occurring naturally in rod photoreceptors of nocturnal mammals. The tethers are differentially utilized during development, regulate gene expression in opposite manners, and play an important role during cell differentiation. Here we aimed to identify the unknown chromatin binding component(s) of the A-tether. We analyzed 10 mouse tissues by immunostaining with antibodies against 7 INM proteins and found that every cell type has specific, although differentially and developmentally regulated, sets of these proteins. In particular, we found that INM protein LEMD2 is concomitantly expressed with A-type lamins in various cell types but is lacking in inverted nuclei of rod cells. Truncation or deletion of Lmna resulted in the downregulation and mislocalization of LEMD2, suggesting that the two proteins interact and pointing at LEMD2 as a potential chromatin binding mediator of the A-tether. Using nuclei of mouse rods as an experimental model lacking peripheral heterochromatin, we expressed a LEMD2 transgene alone or in combination with lamin C in these cells and observed no restoration of peripheral heterochromatin in either case. We conclude that in contrary to the B-tether, the A-tether has a more intricate composition and consists of multiple components that presumably vary, at differing degrees of redundancy, between cell types and differentiation stages.