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Summary The vast amount of publicly available genomic data requires analysis and visualization tools. Here, we present figeno, an application for generating publication-quality FIgures for GENOmics. Figeno particularly focuses on multi-region views across genomic breakpoints and on long reads with base modifications. In addition, we support epigenomic data including ATAC-seq, ChIP-seq or HiC, as well as whole genome sequencing data with copy numbers and structural variants. Availability and implementation Figeno is available as a python package with both a command line and graphical user interface. It can be installed via PyPI and the source code is available at https://github.com/CompEpigen/figeno. [ABSTRACT FROM AUTHOR]

Based on high quality surgery and scientific data, scientists and surgeons are committed to protecting patients as well as healthcare staff and hereby provide this Guidance to address the special issues circumstances related to the exponential spread of the Coronavirus disease 2019 (COVID-19) during this pandemic. As a basis, the authors used the British Intercollegiate General Surgery Guidance as well as recommendations from the USA, Asia, and Italy. The aim is to take responsibility and to provide guidance for surgery during the COVID-19 crisis in a simplified way addressing the practice of surgery, healthcare staff and patient safety and care. It is the responsibility of scientists and the surgical team to specify what is needed for the protection of patients and the affiliated healthcare team. During crises, such as the COVID-19 pandemic, the responsibility and duty to provide the necessary resources such as filters, Personal Protective Equipment (PPE) consisting of gloves, fluid resistant (Type IIR) surgical face masks (FRSM), filtering face pieces, class 3 (FFP3 masks), face shields and gowns (plastic ponchos), is typically left up to the hospital administration and government. Various scientists and clinicians from disparate specialties provided a Pandemic Surgery Guidance for surgical procedures by distinct surgical disciplines such as numerous cancer surgery disciplines, cardiothoracic surgery, ENT, eye, dermatology, emergency, endocrine surgery, general surgery, gynecology, neurosurgery, orthopedics, pediatric surgery, reconstructive and plastic surgery, surgical critical care, transplantation surgery, trauma surgery and urology, performing different surgeries, as well as laparoscopy, thoracoscopy and endoscopy. Any suggestions and corrections from colleagues will be very welcome as we are all involved and locked in a rapidly evolving process on increasing COVID-19 knowledge.

Purpose: The local health department (in German: Gesundheitsamt) ordered a shutdown of a teaching hospital due to the severe acute respiratory syndrome coronavirus (SARS-CoV-2) outbreak – one index patient and five infected healthcare workers – and put it under quarantine. For the first time, all patients plus all employees of one German hospital (healthcare providers, physicians, and nurses) were tested to detect silent or asymptomatic carriers. Methods: A serial polymerase chain reaction (PCR) test for SARS-CoV-2 was performed three times (1) between April 3rd and 5th, 2020 [n = 1171], (2) between April 8th and 9th, 2020 [n = 953] and (3) between April 14th and 17th, 2020 [n = 983]. Results: The teaching hospital’s proven coronavirus disease 2019 (COVID-19) patient load on Friday, April 3rd, 2020, was 34 patients, of whom 11 were on ventilation in the intensive care unit (ICU), one in the intermediate care unit (IMC), and 22 in the infectious disease ward. Another 32 patients in a different infectious disease ward were suspected for COVID-19 with test results pending. COVID-19 silent carrier (asymptomatic) positivity rates based on the phases of testing were (1) n = 24 (2.1%), (2) n = 25 (2.6%) and n = 9 (0.9%). The cumulative infection rate for healthcare providers, physical therapists, physicians, and nurses was 1.8%, 4.5%, 4.8%, and 11.9% which were associated with the type and extent of COVID-19 patient contact (p

Background: Despite the ample interest in the measurement of substance abuse and dependence, obtaining biological samples from participants as a means to validate a scale is considered time and cost intensive and is, subsequently, largely overlooked. Objectives: To report the psychometric properties of the drug use disorder (DUD) questionnaire including oral fluid and blood sample screening indicators measuring the three most commonly used illicit substances--marijuana, cocaine, and extramedicinal painkillers. Subjects: Participants were a subset ("N" = 2,702) of the 2007 U.S. National Roadside Survey that was administered to daytime and nighttime weekend drivers in the 48 contiguous states to examine the prevalence of substance use and misuse. Measures: Participants completed demographic and substance use questions as well as the DUD--a 12-item measure assessing substance abuse and dependence. Participants could potentially have completed the DUD three times for each of the three substances. Subscales of abuse and dependence were created using Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition Text Revision [DSM-IV-TR]) criteria of these diagnoses. Results: The DUD displayed adequate internal consistency on both subscales of substance abuse and dependence (Cronbach's alpha ranging from 0.71 to 0.84 and 0.83 to 0.92, respectively). The DUD also demonstrated construct validity in comparison to biological markers of each substance. Conclusions: The DUD is a biologically validated instrument that is both easy to utilize and may have valuable implications as a research tool among both clinical and nonclinical populations. (Contains 5 tables.)

The authors examine the relationships between forgiveness, family cohesion, and alcohol. In Study 1 (N = 190), participants reported lower levels of trust and forgiveness for family members who misuse alcohol. In Study 2 (N = 141), the authors present a model demonstrating family cohesion and trait forgiveness related to state forgiveness of an alcohol-misusing family member. State forgiveness was related to trust in that family member and, subsequently, higher levels of perceived misuser drinking refusal efficacy. (Contains 1 figure and 1 table.)

Purpose: To measure the flexural strength and Weibull characteristics of aged and nonaged printed interim dental material fabricated with different layer thickness. Material and methods: Bars (25×2×2 mm) were additively fabricated by using a polymer printer (Asiga Max) and an interim resin (Nexdent C&B MFH). Specimens were fabricated with the same printing parameters and postprocessing procedures, but with 7 different layer thickness: 50 (control or 50‐G group), 10 (10‐G group), 25 (25‐G group), 75 (75‐G group), 100 (100‐G group), 125 (125‐G group), and 150 μm (150‐G group). Two subgroups were created: nonaged and aged subgroups (n = 10). A universal testing machine was selected to measure flexural strength. Two‐parameter Weibull distribution values were computed. Two‐way ANOVA and Tukey tests were selected for statistical evaluation of the data (α = 0.05). Results: Artificial aging methods (p < 0.001) were a significant predictor of the flexural strength computed. Aged specimens acquired less flexural strength than nonaged specimens. The Weibull distribution obtained the highest shape for nonaged 50‐G and 75‐G group specimens compared with those of other nonaged groups, while the Weibull distribution showed the highest shape for aged 125‐G specimens. Conclusions: The flexural strength of the additively fabricated interim material examined was not influenced by the layer thickness at which the specimens were fabricated; however, artificial aging techniques reduced its flexural strength. Aged specimens presented lower Weibull distribution values compared with nonaged specimens, except for the 125‐G specimens. [ABSTRACT FROM AUTHOR]

Dislocation networks have been demonstrated to substantially enhance functional properties. As-sintered samples are virtually devoid of dislocations, new innovative techniques for introducing sufficiently high dislocation densities into polycrystalline ceramics are needed. While dislocation-based plasticity at high temperatures has been demonstrated for a large range of ceramic single crystals, plasticity in polycrystals is much less understood. Here, we demonstrate plastic strains in excess of several % based on dislocation motion in polycrystalline SrTiO3 at ≈ 1100 °C with 3.9 µm grain size. Ultra-high voltage electron microscopy reveals an associated increase in dislocation density by three orders of magnitude. Achievable strain rates are comparable to creep-based mechanisms and much less sensitive to applied stress than observed for metals. A specialized testing protocol allows quantification of the deformability via stress exponent, activation volume and activation enthalpy giving additional quantification. In conjunction with TEM images, the mechanical data gives insight into the underlying mechanisms. [ABSTRACT FROM AUTHOR]

Dislocation networks have been demonstrated to substantially enhance functional properties. As-sintered samples are virtually devoid of dislocations, new innovative techniques for introducing sufficiently high dislocation densities into polycrystalline ceramics are needed. While dislocation-based plasticity at high temperatures has been demonstrated for a large range of ceramic single crystals, plasticity in polycrystals is much less understood. Here, we demonstrate plastic strains in excess of several % based on dislocation motion in polycrystalline SrTiO3 at ≈ 1100 °C with 3.9 µm grain size. Ultra-high voltage electron microscopy reveals an associated increase in dislocation density by three orders of magnitude. Achievable strain rates are comparable to creep-based mechanisms and much less sensitive to applied stress than observed for metals. A specialized testing protocol allows quantification of the deformability via stress exponent, activation volume and activation enthalpy giving additional quantification. In conjunction with TEM images, the mechanical data gives insight into the underlying mechanisms. [ABSTRACT FROM AUTHOR]