bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk insurance cost estimation using the example of a transport company energy saving project
Authors: Minnullina Anna , Minnullin Ruslan , Frolova Olya , Kosyakova Inessa
Published: October 2020

The main activity of energy service companies is possible with a flexible risk management system, which should be based on the implementation of certain principles. In this article, the authors propose their own set of principles, among which insurance occupies an important place. By property insuring, in case of its complete destruction, compensation can be obtained that allows to fully recover the costs incurred when purchasing energy-saving equipment. So, in the article, a business case is given for equipment insurance for a transport company based on scenario modeling.
Combined approach to forecasting the financial condition of a transport company based on cost optimization
Authors: Pirogova Oksana , Kuznetsova Svetlana , Khareva Victoria
Published: October 2020

The financial strategy of the company is one of the most important functional strategies that ensures the formation, efficient distribution and use of financial resources. Analysis and optimization of expenses, as a tool for implementing a financial strategy, allows you to reduce the cost of sales (services) and increase profit margins and, accordingly, increase the amount of financial resources for the development of the company. The article discusses the impact of cost optimization on the financial strategy of the organization and forecasting the main indicators of its activity using the example of the North-West Suburban Passenger Company (hereinafter referred to as JSC “SZPPK”), which carries out passenger rail transportation on the territory of St. Petersburg, in Leningrad, Novgorod, Pskov, Murmansk regions, as well as in the Republic of Karelia. To forecast the main indicators of the company’s activities, such as revenue, cost of sales (services), net profit, and the passenger turnover indicator was used in the article as a factor determining these indicators.
Algorithmic support for the dynamic functioning of transport systems in the region
Authors: Burlov V , Lepeshkin O , Lepeshkin M
Published: October 2020

The article deals with the development of algorithmic support for the implementation of the process of functioning of transport systems in the region with a dynamic change in the conditions of functioning of regional management of transport systems as a result of untimely decision-making. In managing the functioning of transport systems in the region, systematic and integrated approaches are not fully used in the formation of a set of management decisions aimed at ensuring the safety of transport systems, namely, there are no models that would establish a one-to-one correspondence between the situation (generating potential threats), information and analytical activities (identifying potential threats) and the system for ensuring the safety of transport systems, designed to develop an adequate management decision and its development. The proposed algorithmic software allows us to overcome these disadvantages in the managing the functioning of transport systems in the region.
COVID-19 as a trigger for global transport infrastructure digitalization
Authors: Medyakova E M , Kislitskaya N A , Kudinova S G , Gerba V A
Published: October 2020

The global transport infrastructure has evolved in recent years, gradually incorporating digital innovations into traditional processes and services. However, everywhere the process of digitalization was hindered by the priority and low cost of classic forms of transport services, the absence of strict requirements for compliance with the conditions of contactless movement of products and prevention of the spread of infections. According to the authors, the vector for total digitalization was taken after the spread of the SARS-CoV-2 virus. The authors analyzed the implementation of digital tools until 2019, assessing the degree of implementation and coverage of digital innovations in the global transport industry. Having studied the transport system of Russia, as one of the world’s largest systems, in the context of the COVID-19 pandemic, the authors showed how the structure of cargo turnover by the mode of transport has changed and which industries have suffered the most damage. Having calculated the forecast of digitalization growth and the dynamics of the share of digitized processes in the global transport infrastructure, the authors have come to the conclusions about the acceleration of the accumulated potential of digitalization of the transport sector in the context of the COVID-19 pandemic.
Energy consumption and energy intensity of the Russian GDP, taking into account the development of the transport network
Authors: Anisimova V Y , Podbornova E S , Tukavkin N M
Published: October 2020

The article studies energy consumption and energy intensity of gross domestic product (GDP) in the Russian Federation. Primary energy consumption and the structure of fuel and energy resources consumption in the Russian Federation during 2015-2019 were studied, the analysis of the achievement of target energy intensity of the Russian GDP was carried out, the dynamics of curtailment on demand for fuel and energy resources based on the use of technology was studied. The authors’ definition of energy efficiency, a strategy for the development of energy efficiency, an information system for the optimization and improvement of energy efficiency are presented as a scientific novelty in this paper. The authors substantiated that the informatization of the energy and production structure of an enterprise is one of the issues in the area of energy preservation and energy efficiency development.
Intensive development of the transport network and protection of the agricultural land
Authors: Bondarev B , Nosov S , Cherkashin K
Published: October 2020

Productive land, which primarily includes agricultural land, in any country in the globe, always had special status since they are the basis of the country’s food security. The tasks of identifying, recording and preserving land from misuse, depletion, and degradation are in priority when pursuing a state land policy. Recently, these issues have become particularly important due to the high rates of land depletion and degradation, urbanization, industrial and mining development. The most fertile land in Russia classified as the most valuable agricultural land. After analyzing the situation with the definition, recording, and protection of such land in the Russian Federation, the authors concluded that the country does not have clear, objective criteria and methodological approaches for identifying the most valuable land, as well as mechanisms for their protection. This paper provides the basic principles, methodological approaches and the results of the work on the identification and allocation of the most valuable land in agriculture and transport sector of Siberia. Land of 1-5 classes one way or another should be protected from unreasonable withdrawal from agricultural use, land of 6-8 classes may be provided for the development of transport.
Assessment of land plots for the needs of regional transportation network development
Authors: Meller N V , Nekrasova I Yu
Published: October 2020

This article highlights some issues related to the assessment of land plots for state and municipal needs, taking into account transport costs in the city of Tyumen, in terms of assessing the losses of the owner. It is timely and relevant tostudy the applied aspect of assessing the market value of a land plot in order to justify a compensation payment when withdrawing a land allotment for public needs. The significance of the work lies in obtaining and using results, formulated conclusions and proposals in the practice of calculating the compensation payment.
Development of the transport system in line with a systematic approach: legal opinion
Authors: Miroshnik S , Vlasova T , Duel V
Published: October 2020

The relevance of the research topic is caused by the role and importance of transport in human life. The development of integration processes leads to the need to create in the near future a unified transport model of a planetary scale, managed at a fundamentally new level reflecting the digital nature of modern public relations. The object of the study is the social relations that arise in the process of functioning of automobile transport, although many conclusions are fully applicable to the problems of developing a unified transport model that covers all types of vehicles. The purpose of scientific research is to prove that the successful development of the transport model and transport as its component element is possible only from the position of a systematic approach. During the study, dialectical and materialistic, systemic, logical methods were used, as well as methods of interpreting law and forecasting. It is concluded that the reform of the transport model should be carried out through the prism of the meaning of human life. The regulation of relations in society is carried out through a variety of rules of behavior, among which technical norms have gained particular importance in recent years. Life, health, and fate of man depend on their observance or non-observance. Therefore, the development of transport is unthinkable without improving technical standards. The main regulator of behavior is law, the specification of which is faced with many difficulties. Legal support of the transport model is an essential component of its successful functioning. The modern transport model is classified as inorganic. Its transformation from the perspective of a systematic approach, taking into account the need to improve the person himself, social and technical norms, objects, primarily transport and technology, will allow moving to a qualitatively new level - to become organic. Considering the ratio of the transport model and the person, it should be borne in mind that, on the one hand, a person acts as its creator, and on the other - an indispensable element. Therefore, the transformation of transport and the transport model in general into an organic whole is possible only when the person himself, his competence changes.
Semi-permeability of graphene nanodrums in sucrose solution
Authors: Dolleman Robin J , Katan Allard J , van der Zant Herre S J , Steeneken Peter G
Published: October 2020

Semi-permeable membranes are important elements in water purification and energy generation applications, for which the atomic thickness and strength of graphene can enhance efficiency and permeation rate while maintaining good selectivity. Here, we show that an osmotic pressure difference forms across a suspended graphene membrane as a response to a sucrose concentration difference, providing evidence for its semi-permeability. This osmotic pressure difference is detected via the deflection of the graphene membrane that is measured by atomic force microscopy. Using this technique, the time dependence of this deflection allows us to measure the water permeation rate of a single 3.4 µm diameter graphene membrane. Its value is close to the expected value of a single nanopore in graphene. The method thus allows one to experimentally study the semi-permeability of graphene membranes at the microscale when the leakage rate is minuscule. It can therefore find use in the development of graphene membranes for filtration, and can enable sensors that measure the concentration and composition of solutions.
Recent progress and strategies in photodetectors based on 2D inorganic/organic heterostructures
Authors: Li Hongwei , Dong Zhuo , Zhang Yan , Li Liqiang , Wang Zhongchang , Wang Cong , Zhang Kai , Zhang Han
Published: October 2020

Two-dimensional (2D) inorganic/organic heterostructures have attracted great attention in the field of optoelectronics due to their unique properties. Comparing with purity organic semiconductors or 2D inorganic heterostructures, the 2D inorganic/organic heterostructure overwhelms the current limitations of photodetectors and provides more opportunities for the optoelectronic field. However, no in-depth reviews on the important progresses, challenges, and optimizing strategies of performance of photodetectors based on 2D inorganic/organic heterostructures are found in literatures to date. Herein, this report firstly introduces unique features of 2D inorganic/organic heterostructures. Then, we sum up the main growing methods according to the technological principle, and the main properties of photodetectors, and summarize the progresses of photodetectors of 2D inorganic-organic heterostructures based on different physical mechanisms (mainly as photovoltaic effect and photoconductive effect). More importantly, this report presents some design strategies for optimizing photodetector performance of 2D inorganic-organic heterostructures, especially introducing 2D organic ultrathin film design strategy. Furthermore, future challenges and opportunities of 2D inorganic-organic heterostructures are highlighted.
Nonmuscle myosin-2 contractility-dependent actin turnover limits the length of epithelial microvilli
Authors: Chinowsky Colbie R. , Pinette Julia A. , Meenderink Leslie M. , Lau Ken S. , Tyska Matthew J.
Published: October 2020

Microvilli are critical for cellular homeostasis, enabling functions such as solute uptake and host defense. Here we report that nonmuscle myosin-2c localizes to the base of epithelial microvilli, where it controls protrusion length by regulating actin turnover. These findings offer insights that will likely apply to diverse epithelia.
Associations of Depressive Symptoms With All-Cause and Cause-Specific Mortality by Race in a Population of Low Socioeconomic Status: A Report From the Southern Community Cohort Study
Authors: Cui Yong , Zheng Wei , Steinwandel Mark , Cai Hui , Sanderson Maureen , Blot William , Shu Xiao-Ou
Published: October 2020

Depression is a leading cause of disability in the United States, but its impact on mortality rates among racially diverse populations of low socioeconomic status is largely unknown. Using data from the Southern Community Cohort Study, 2002–2015, we prospectively evaluated the associations of depressive symptoms with all-cause and cause-specific mortality in 67,781 Black (72.3%) and White (27.7%) adults, a population predominantly with a low socioeconomic status. Baseline depressive symptoms were assessed using the 10-item Center for Epidemiological Studies Depression Scale. The median follow-up time was 10.0 years. Multivariate Cox regression was used to estimate hazard ratios and 95% confidence intervals for death in association with depressive symptoms. Mild, moderate, and severe depressive symptoms were associated with increased all-cause (hazard ratio (HR) = 1.12, 95% confidence interval (CI): 1.03, 1.22; HR = 1.17, 95% CI: 1.06, 1.29; HR = 1.15, 95% CI: 1.03, 1.28, respectively) and cardiovascular disease–associated death (HR = 1.23, 95% CI: 1.05, 1.44; HR = 1.18, 95% CI: 0.98, 1.42; HR = 1.43, 95% CI: 1.17, 1.75, respectively) in Whites but not in Blacks (P for interaction < 0.001, for both). Mild, moderate, or severe depressive symptoms were associated with increased rates of external-cause mortality in both races (HR = 1.24, 95% CI: 1.05, 1.46; HR = 1.31, 95% CI: 1.06, 1.61; HR = 1.42, 95% CI: 1.11, 1.81, respectively; for all study subjects, P for interaction = 0.48). No association was observed for cancer-associated deaths. Our study showed that the association between depression and death differed by race and cause of death in individuals with a low socioeconomic status.
Renin–Angiotensin–Aldosterone System Inhibitors and COVID-19 Infection or Hospitalization: A Cohort Study
Authors: Dublin Sascha , Walker Rod L , Floyd James S , Shortreed Susan M , Fuller Sharon , Albertson-Junkans Ladia , Harrington Laura B , Greenwood-Hickman Mikael Anne , Green Beverly B , Psaty Bruce M
Published: October 2020

Background

Angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) may increase the risk of coronavirus disease 2019 (COVID-19) infection or affect disease severity. Prior studies have not examined risks by medication dose.

Methods

This retrospective cohort study included people aged ≥18 years enrolled in a US integrated healthcare system for at least 4 months as of 2/29/2020. Current ACEI and ARB use was identified from pharmacy data, and the estimated daily dose was calculated and standardized across medications. COVID-19 infections and hospitalizations were identified through 6/14/2020 from laboratory and hospitalization data. We used logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for race/ethnicity, obesity, and other covariates.

Results

Among 322,044 individuals, 826 developed COVID-19 infection. Among people using ACEI/ARBs, 204/56,105 developed COVID-19 (3.6 per 1,000 individuals) compared with 622/265,939 without ACEI/ARB use (2.3 per 1,000), yielding an adjusted OR of 0.91 (95% CI 0.74–1.12). For use of <1 defined daily dose (DDD) vs. nonuse, the adjusted OR for infection was 0.92 (95% CI 0.66–1.28); for 1 to <2 DDDs, 0.89 (95% CI 0.66–1.19); and for ≥2 DDDs, 0.92 (95% CI 0.72–1.18). The OR was similar for ACEIs and ARBs and in subgroups by age and sex. 26% of people with COVID-19 infection were hospitalized; the adjusted OR for hospitalization in relation to ACEI/ARB use was 0.98 (95% CI 0.63–1.54), and there was no association with dose.

Conclusions

These findings support current recommendations that individuals on these medications continue their use.
Significance of root hairs for plant performance under contrasting field conditions and water deficit
Authors: Marin M , Feeney D S , Brown L K , Naveed M , Ruiz S , Koebernick N , Bengough A G , Hallett P D , Roose T , Puértolas J , Dodd I C , George T S
Published: October 2020

Background and Aims

Previous laboratory studies have suggested selection for root hair traits in future crop breeding to improve resource use efficiency and stress tolerance. However, data on the interplay between root hairs and open-field systems, under contrasting soils and climate conditions, are limited. As such, this study aims to experimentally elucidate some of the impacts that root hairs have on plant performance on a field scale.

Methods

A field experiment was set up in Scotland for two consecutive years, under contrasting climate conditions and different soil textures (i.e. clay loam vs. sandy loam). Five barley (Hordeum vulgare) genotypes exhibiting variation in root hair length and density were used in the study. Root hair length, density and rhizosheath weight were measured at several growth stages, as well as shoot biomass, plant water status, shoot phosphorus (P) accumulation and grain yield.

Key Results

Measurements of root hair density, length and its correlation with rhizosheath weight highlighted trait robustness in the field under variable environmental conditions, although significant variations were found between soil textures as the growing season progressed. Root hairs did not confer a notable advantage to barley under optimal conditions, but under soil water deficit root hairs enhanced plant water status and stress tolerance resulting in a less negative leaf water potential and lower leaf abscisic acid concentration, while promoting shoot P accumulation. Furthermore, the presence of root hairs did not decrease yield under optimal conditions, while root hairs enhanced yield stability under drought.

Conclusions

Selecting for beneficial root hair traits can enhance yield stability without diminishing yield potential, overcoming the breeder’s dilemma of trying to simultaneously enhance both productivity and resilience. Therefore, the maintenance or enhancement of root hairs can represent a key trait for breeding the next generation of crops for improved drought tolerance in relation to climate change.
A Teleneuropsychology Consultation Service Model for Children with Neurodevelopmental and Acquired Disorders Residing in Rural State Regions
Authors: Sherwood Andrea R , MacDonald Beatriz
Published: October 2020

Objective

Accessing neuropsychological services, which are often centralized in urban regions, poses unique challenges to children and families in rural regions. In 2017, urban neuropsychologists and a pediatrician practicing in a rural region of New Mexico started to develop a teleneuropsychology (TeleNP) consultation service model to efficiently triage and determine a clinical course of action. This pilot project, aimed at expanding clinical access to specialized pediatric services in rural areas, evolved over the course of 2 years prior to the coronavirus disease 2019 pandemic.

Method

Providers earned the trust of the local community, gained understanding of pertinent sociocultural factors, and acquired knowledge of the clinical and educational concerns for the children residing in the rural community. The application of a culturally informed approach that highlights the importance of community participation and collaboration steered the decision to implement a TeleNP consultation model. By widening access to neuropsychology, this service helped to determine whether neuropsychological testing procedures were medically indicated.

Results

We summarize the distinct processes that needed to occur at each location to support the implementation of telemedicine. We propose a clinical service decision tree with specific criteria to help guide providers on how to triage cases in order to increase access to specialized healthcare.

Conclusion

The success of implementing a TeleNP consultation service hinges upon ongoing care coordination between providers, clerical staff, patients, and families with clear goals and expectations, maintenance of legal and ethical standards, and development of specific administrative and clinical processes supporting the use of TeleNP.
Can Outpatient Plastic Surgery Be Done Safely During a COVID-19 Surge? Results of a July 2020 Los Angeles Survey and Literature Review
Authors: Teitelbaum Steven , Diaz John , Singer Robert
Published: October 2020

Background

A moratorium was placed on nonurgent surgery throughout much of the United States in mid-March 2020 due to surging numbers of COVID-19 cases. Several months later, and with new safety precautions in place, elective surgery gradually resumed. However, no data exist on the safety of plastic surgery during the pandemic.

Objectives

This aim of this survey was to assess the safety of plastic surgery during the pandemic by quantifying: (1) the preoperative prevalence of SARS-CoV-2; (2) the risk of postoperative COVID-19; (3) outcomes and precious resource utilization for such cases; and (4) the risks to office staff.

Methods

Los Angeles plastic surgeons certified by the American Board of Plastic Surgery (ABPS) were sent an online survey in July 2020, during a local COVID-19 surge, querying about the number of procedures performed in the 8- to 10-week period since reopening, testing policies, surgical complications, and cases among staff.

Results

In total, 112 surgeons reported 5633 surgeries since resuming elective surgery. Of these, 103 (91.96%) surgeons obtained a preoperative SARS-CoV-2 polymerase chain reaction (PCR) test for every patient. The preoperative PCR test was positive in 41/5881 (0.69%). Positive tests within 2 weeks postoperation occurred in 7/5380 (0.13%) of surgical patients, 3/8506 (0.04%) of injection patients, and 6/2519 (0.24%) of energy therapy patients. Nine offices reported at least 1 staff member who developed COVID-19. All cases were mild, with no hospitalizations or deaths.

Conclusions

These data demonstrate that plastic surgery can be performed safely during a COVID-19 surge by ABPS diplomates. This has profound impact for patients, plastic surgeons, and health policy regulators.
Bright fluorescent nucleic acid detection with CRISPR-Cas12a and poly(thymine) templated copper nanoparticles
Authors: Bogers Janna F M , Berghuis Nicole F , Busker Ruud W , van Booma Angelo , Paauw Armand , van Leeuwen Hans C
Published: October 2020

Fluorescence-based diagnostic tools are attractive and versatile tests with multiple advantages: ease of use, sensitivity and rapid results. The advent of CRISPR-Cas technology has created new avenues for the development of diagnostic testing tools. In this study, by effectively combining the specific functions of two enzymes, CRISPR-Cas12a and terminal deoxynucleotidyl transferase (TdT), we developed a DNA detection assay that generates copper nanoparticles (CuNPs) that are easily visible to the naked eye under UV-light; we named this detection assay Cas12a Activated Nuclease poly-T Reporter Illuminating Particles (CANTRIP). Upon specific target DNA recognition by Cas12a, single-stranded DNA (ssDNA) reporter oligos with blocked 3′-ends are cut into smaller ssDNA fragments, thereby generating neo 3′-hydroxyl moieties. TdT subsequently elongates these newly formed ssDNA fragments, incorporating only dTTP nucleotides, and these poly(thymine)-tails subsequently function as scaffolds for the formation of CuNPs. These CuNPs produce a bright fluorescent signal upon UV excitation, and thus, this bright orange signal indicates the presence of target DNA, which in this proof-of-concept study consisted of anthrax lethal factor plasmid DNA. CANTRIP, which combines two detection platforms consisting of CRISPR-Cas12a and fluorescent CuNPs into a single reaction, appears to be a robust, low-cost and simple diagnostic tool.
Convalescent Plasma for Patients With Severe Coronavirus Disease 2019 (COVID-19): A Matched Cohort Study
Authors: Rogers Ralph , Shehadeh Fadi , Mylona Evangelia K , Rich Josiah , Neill Marguerite , Touzard-Romo Francine , Geffert Sara , Larkin Jerome , Bailey Jeffrey A , Lu Shaolei , Sweeney Joseph , Mylonakis Eleftherios
Published: October 2020

Background

The efficacy of convalescent plasma (CP) for the treatment of coronavirus disease 2019 (COVID-19) remains unclear.

Methods

In a matched cohort analysis of hospitalized patients with severe COVID-19, the impact of CP treatment on in-hospital mortality was evaluated using univariate and multivariate Cox proportional-hazards models, and the impact of CP treatment on time to hospital discharge was assessed using a stratified log-rank analysis.

Results

In total, 64 patients who received CP a median of 7 days after symptom onset were compared to a matched control group of 177 patients. The incidence of in-hospital mortality was 12.5% and 15.8% in the CP and control groups, respectively (P = .52). There was no significant difference in the risk of in-hospital mortality between the 2 groups (adjusted hazard ratio [aHR] 0.93, 95% confidence interval [CI] .39–2.20). The overall rate of hospital discharge was not significantly different between the 2 groups (rate ratio [RR] 1.28, 95% CI .91–1.81), although there was a significantly increased rate of hospital discharge among patients 65-years-old or greater who received CP (RR 1.86, 95% CI 1.03–3.36). There was a greater than expected frequency of transfusion reactions in the CP group (2.8% reaction rate observed per unit transfused).

Conclusions

We did not demonstrate a significant difference in risk of mortality or rate of hospital discharge between the CP and control groups. There was a signal for improved outcomes among the elderly, and further adequately powered randomized studies should target this subgroup when assessing the efficacy of CP treatment.
Associations of Plasma Folate and Vitamin B6 With Blood DNA Methylation Age: An Analysis of One-Carbon Metabolites in the VA Normative Aging Study
Authors: Nwanaji-Enwerem Jamaji C , Colicino Elena , Gao Xu , Wang Cuicui , Vokonas Pantel , Boyer Edward W , Baccarelli Andrea A , Schwartz Joel
Published: October 2020

One-carbon metabolism is an important contributor to aging-related diseases; nevertheless, relationships of one-carbon metabolites with novel DNA methylation-based measures of biological aging remain poorly characterized. We examined relationships of one-carbon metabolites with 3 DNA methylation-based measures of biological aging: DNAmAge, GrimAge, and PhenoAge. We measured plasma levels of 4 common one-carbon metabolites (vitamin B6, vitamin B12, folate, and homocysteine) in 715 VA Normative Aging Study participants with at least 1 visit between 1999 and 2008 (observations = 1153). DNA methylation age metrics were calculated using the HumanMethylation450 BeadChip. We utilized Bayesian Kernel Machine Regression models adjusted for chronological age, lifestyle factors, age-related diseases, and study visits to determine metabolites important to the aging outcomes. Bayesian Kernel Machine Regression models allowed for the estimation of the relationships of single metabolites and the cumulative metabolite mixture with methylation age. Log vitamin B6 was selected as important to PhenoAge (β = −1.62 years, 95% CI: −2.28, −0.96). Log folate was selected as important to GrimAge (β = 0.75 years, 95% CI: 0.41, 1.09) and PhenoAge (β = 1.62 years, 95% CI: 0.95, 2.29). Compared to a model where each metabolite in the mixture is set to its 50th percentile, the log cumulative mixture with each metabolite at its 30th (β = −0.13 years, 95% CI: −0.26, −0.005) and 40th percentile (β = −0.06 years, 95% CI: −0.11, −0.005) was associated with decreased GrimAge. Our results provide novel characterizations of the relationships between one-carbon metabolites and DNA methylation age in a human population study. Further research is required to confirm these findings and establish their generalizability.
TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data
Authors: Bolognini Davide , Magi Alberto , Benes Vladimir , Korbel Jan O , Rausch Tobias
Published: October 2020

Background

Tandem repeat sequences are widespread in the human genome, and their expansions cause multiple repeat-mediated disorders. Genome-wide discovery approaches are needed to fully elucidate their roles in health and disease, but resolving tandem repeat variation accurately remains a challenging task. While traditional mapping-based approaches using short-read data have severe limitations in the size and type of tandem repeats they can resolve, recent third-generation sequencing technologies exhibit substantially higher sequencing error rates, which complicates repeat resolution.

Results

We developed TRiCoLOR, a freely available tool for tandem repeat profiling using error-prone long reads from third-generation sequencing technologies. The method can identify repetitive regions in sequencing data without a prior knowledge of their motifs or locations and resolve repeat multiplicity and period size in a haplotype-specific manner. The tool includes methods to interactively visualize the identified repeats and to trace their Mendelian consistency in pedigrees.

Conclusions

TRiCoLOR demonstrates excellent performance and improved sensitivity and specificity compared with alternative tools on synthetic data. For real human whole-genome sequencing data, TRiCoLOR achieves high validation rates, suggesting its suitability to identify tandem repeat variation in personal genomes.
IL-1α released from oral epithelial cells upon candidalysin exposure initiates an early innate epithelial response
Authors: Hanaoka Mariko , Domae Eisuke
Published: October 2020

Candida albicans is a commensal fungus that predominantly resides on mucosal surfaces and can cause lethal systemic infection when the host defense is compromised. Candidalysin is a cytolytic peptide toxin produced by C. albicans hyphae that is essential for mucosal tissue damage and is believed to contribute to the establishment of systemic infection and mortality. Candidalysin is also required for the epithelial innate response in which proinflammatory cytokines and chemokines are produced and neutrophil recruitment is initiated. It was recently reported that epidermal growth factor receptor (EGFR) was essential for the candidalysin-triggered epithelial response. The present study identified IL-1α as another component of candidalysin-mediated initial epithelial activation. We found that human oral epithelial cells released IL-1α rapidly after candidalysin exposure. Blockade of IL-1α/IL-1 receptor (IL-1R) signaling in candidalysin-exposed cells resulted in decreased phosphorylation of IκBα, decreased induction of IκBζ and decreased production of granulocyte-macrophage colony-stimulating factor and IL-8. Expression of c-Fos, which is induced downstream of EGFR signaling in candidalysin-treated cells, is less affected by IL-1R blockade. Inversely, blockade of EGFR signaling does not affect candidalysin-mediated phosphorylation of IκBα and induction of IκBζ, suggesting that independent signaling pathways contribute to the induction of NF-κB and c-Fos downstream of the candidalysin pore formation site. Consistently, antibody inhibition of both EGFR and IL-1R enhanced the suppressive effect of cytokine production in candidalysin-treated cells. Thus, we identified the immediate release of IL-1α and its synergistic role with EGFR ligands on the initial activation of oral epithelial cells in response to candidalysin.
Stability in Personality After Physical Trauma
Authors: Gauffin Emelie , Willebrand Mimmie , Ekselius Lisa , Öster Caisa
Published: October 2020

Personality trait stability may be influenced by several factors, there among different life events such as psychological trauma. However, little is known regarding trait stability after physical trauma. Therefore, our primary aim was to assess the extent of stability in personality in burn patients during the first year after injury. Eighty-four burn patients, admitted to a national burn center, were assessed with the Swedish universities Scales of Personality during acute care and 12 months postburn. Personality domain scores remained stable between acute care and 12 months postburn. On the trait level, the only change was seen in personality trait Stress Susceptibility, where burn patients’ scores were lower compared with norm scores during acute care but then increased, and normalized, at 12 months postburn. To conclude, personality scores remained relatively stable during the first year after burn trauma.
Too Hot to Handle? Full-Thickness Burn Injury in a Child Caused by Cyanoacrylate Glue and Cotton—A Case Report and Experimental Study
Authors: Jacques Madeleine , Tran Sonia , Bertinetti Monique , Holland Andrew J A
Published: October 2020

Domestic superglue (cyanoacrylate) in the hands of children can have devastating consequences, especially when cotton clothing is involved. When cotton comes into contact with cyanoacrylate, an intense exothermic reaction occurs, creating temperatures high enough to cause significant thermal injury. A literature review found 16 such cases of burns documented (2 adult and 14 pediatric). This article presents a case report of a 4-year-old child sustaining a full-thickness burn injury to her leg requiring skin grafting when superglue was spilt onto cotton pants. She was sitting near a fan heater at the time. An experiment was conducted to replicate the exothermic reaction between superglue and cotton and to determine if the addition of radiant heat would have any significant effect. The maximum temperature reached with one 3-g tube of superglue onto cotton pyjamas was 91°C (196°F) and occurred approximately 90 seconds postapplication. It took more than 3 minutes for the temperature to cool below 40°C (104°F). The addition of radiant heat from a fan heater placed 60 cm from the clothing found that the temperature peak was similarly reached and cooled, but the temperature did not reduce below 52°C (126°F) for over 20 minutes, proving that potential harm may be amplified if first aid is not appropriately sought. Product labeling and the knowledge of potential harm from such mechanism of injury remain inadequate. It is hoped that the reporting of this case contributes to an increase in public education and awareness of such dangers and may contribute to preventing avoidable future incidences.
Sources of Medical Information for Oncology Physicians During the COVID-19 Pandemic: Results From a National Cross-Sectional Survey
Authors: Parsons Helen M , Vogel Rachel I , Blaes Anne H , Lou Emil , Beckwith Heather , Yuan Jianling , Ching Hui Jane Yuet
Published: October 2020

Because the coronavirus disease 2019 (COVID-19) has completely transformed the accepted norms and approaches to cancer care delivery in the United States, we sought to understand the sources of medical information that oncology physicians seek and trust. We recruited 486 oncology physicians to an anonymous cross-sectional online survey through social media from March 27, 2020, to April 10, 2020, with 79.2% reporting their sources of medical information during the COVID-19 pandemic. We found a diverse array of reported sources for COVID-19 information that most commonly included professional societies (90.7%), hospital or institutional communications (88.6%), and the Centers for Disease Control and Prevention (69.9%); however, trust in these sources of information varied widely, with professional societies being the most trusted source. These results highlight the important role that professional societies, hospitals, and the Centers for Disease Control and Prevention play in ensuring dissemination of consistent, high-quality practice recommendations for oncology physicians.
Supporting Exiles: The Role of Academics for Chile
Authors: Angell Alan
Published: October 2020

This article examines the response to the 1973 coup in Chile. The response was remarkable both in its intensity and duration and in the number of countries which condemned the coup and made efforts to give assistance to those forced into exile. In Britain, the academic community quickly organized to make a sustained effort to give support to those members of Chilean universities who were the victims of the coup. This led to the formation of Academics for Chile, which, thanks to World University Service, led to grants being made to some 900 academics and students from Chile. The development of Latin American studies in several universities in the UK meant that the academic community was well-informed about developments in that country and had close contacts with Chilean academics. Support was widespread amongst universities in the UK and, came not just from the left, but from those who wished to defend academic freedom and democracy.
Suppression of H2-cooling in protogalaxies aided by trapped Lyα cooling radiation
Authors: Wolcott-Green Jemma , Haiman Zoltán , Bryan Greg L
Published: October 2020

We study the thermal evolution of UV-irradiated atomic cooling haloes using high-resolution three-dimensional hydrodynamic simulations. We consider the effect of H− photodetachment by Lyα cooling radiation trapped in the optically-thick cores of three such haloes, a process that has not been included in previous simulations. Because H− is a precursor of molecular hydrogen, its destruction can diminish the H2 abundance and cooling. We find that the critical UV flux for suppressing H2-cooling is decreased by ∼15–50 per cent in our fiducial models. Previous one-zone modelling found a larger effect, with Jcrit reduced by a factor of a few; we show that adopting a constant halo mass to determine the trapped Lyα energy density, as is done in the one-zone models, yields a larger reduction in Jcrit, consistent with their findings. Our results nevertheless suggest that Lyα radiation may have an important effect on the thermal evolution of UV-irradiated haloes, and therefore on the potential for massive black hole formation.
Subaru/HSC deep optical imaging of infrared sources in the AKARI North Ecliptic Pole-Wide field
Authors: Oi Nagisa , Goto Tomotsugu , Matsuhara Hideo , Utsumi Yousuke , Momose Rieko , Toba Yoshoki , Malkan Matthew , Takagi Toshinobu , Huang Ting-Chi , Kim Seong Jin , Ohyama Youichi
Published: October 2020

We present a five-broad-band (grizy) photometric catalogue of Subaru/Hyper Suprime-Cam (HSC) optical imaging observations at around the North Ecliptic Pole (NEP) where the AKARI infrared (IR) satellite conducted a large survey (NEP-Wide survey). The observations cover almost all the NEP-Wide survey field down to the depth of 28.1, 26.8, 26.3, 25.5, and 25.0 mag (5σ) at grizy, respectively. The five-band HSC catalogue contains about 2.6 million objects, and 70 959 AKARI NEP-Wide counterpart sources are identified in the catalogue. We added existing supplementary catalogues from the u band to the far-IR band, and estimated photo-z for the AKARI-HSC sources. We achieved σΔz/(1 + zs) = 0.06 and an outlier rate of 13.4 per cent at z = 0.2–1.5. Using the spectral energy distribution (SED) template fitting, we classified the AKARI-HSC galaxies into four categories, namely quiescent, star-forming, Type1 active galactic nucleus (AGN), and Type2 AGN, in each redshift bin. At z > 1, the mean SED of star-forming galaxies in mid-IR (3–10 μm) range is significantly different from that of spiral galaxies in the nearby Universe, indicating that many of star-forming galaxies at z > 1 contain a heat source capable of heating dust to temperatures that radiate thermal emission in the mid-IR range. Furthermore, we estimated the number fraction of AGNs (fAGN) in each bin of redshift and IR luminosity (LIR), and examined the dependence of redshift and LIR. In log(LIR/L⊙) = 11.0–14.0, the fAGN shows a significant increase with increasing redshift, regardless of the LIR bins. In contrast, the fAGN shows a slight increase against LIR at z < 1 and no increase with increasing LIR at z > 1.
Searching for shocks in high-mass starless clump candidates
Authors: Zhu Feng-Yao , Wang Jun-Zhi , Liu Tie , Kim Kee-Tae , Zhu Qing-Feng , Li Fei
Published: October 2020

In order to search for shocks in the very early stage of star formation, we performed single-point surveys of SiO J = 1–0, 2–1, and 3–2 lines and the H2CO 212−111 line towards a sample of 100 high-mass starless clump candidates (SCCs) by using the Korean VLBI Network (KVN) 21-m radio telescopes. The detection rates of the SiO J = 1–0, 2–1, 3–2 lines, and the H2CO line are $31.0$, $31.0$, $19.5,$ and $93.0{{\ \rm per\ cent}}$, respectively. Shocks seem to be common in this stage of massive star formation. The widths of the observed SiO lines [full width at zero power (FWZP)] range from 3.4 to 55.1 km s−1. A significant fraction ($\sim 29{{\ \rm per\ cent}}$) of the detected SiO spectra have broad line widths (FWZP > 20 km s−1), which are very likely associated with fast shocks driven by protostellar outflows. This result suggests that about one third of the SiO-detected SCCs are not really starless but protostellar. On the other hand, about 40 ${{\ \rm per\ cent}}$ of the detected SiO spectra show narrow line widths (FWZP < 10 km s−1) probably associated with low-velocity shocks which are not necessarily protostellar in origin. The estimated SiO column densities are mostly 0.31−4.32 × 1012 cm−2. Comparing the SiO column densities derived from SiO J = 1–0 and 2–1 lines, we suggest that the SiO molecules in the SCCs may be in the non-LTE condition. The SiO abundances to H2 are usually 0.20−10.92 × 10−10.
Spectral energy distributions of dust and PAHs based on the evolution of grain size distribution in galaxies
Authors: Hirashita Hiroyuki , Deng Weining , Murga Maria S
Published: October 2020

Based on a one-zone evolution model of grain size distribution in a galaxy, we calculate the evolution of infrared spectral energy distribution (SED), considering silicate, carbonaceous dust, and polycyclic aromatic hydrocarbons (PAHs). The dense gas fraction (ηdense) of the interstellar medium (ISM), the star formation time-scale (τSF), and the interstellar radiation field intensity normalized to the Milky Way value (U) are the main parameters. We find that the SED shape generally has weak mid-infrared (MIR) emission in the early phase of galaxy evolution because the dust abundance is dominated by large grains. At an intermediate stage (t ∼ 1 Gyr for τSF = 5 Gyr), the MIR emission grows rapidly because the abundance of small grains increases drastically by the accretion of gas-phase metals. We also compare our results with observational data of nearby and high-redshift (z ∼ 2) galaxies taken by Spitzer. We broadly reproduce the flux ratios in various bands as a function of metallicity. We find that small ηdense (i.e. the ISM dominated by the diffuse phase) is favoured to reproduce the 8 $\rm{\mu m}$ intensity dominated by PAHs for both the nearby and the z ∼ 2 samples. A long τSF raises the 8 $\rm{\mu m}$ emission to a level consistent with the nearby low-metallicity galaxies. The broad match between the theoretical calculations and the observations supports our understanding of the grain size distribution, but the importance of the diffuse ISM for the PAH emission implies the necessity of spatially resolved treatment for the ISM.
Resolving the Disc–Halo Degeneracy – II: NGC 6946
Authors: Aniyan S , Ponomareva A A , Freeman K C , Arnaboldi M , Gerhard O E , Coccato L , Kuijken K , Merrifield M
Published: October 2020

The mass-to-light ratio (M/L) is a key parameter in decomposing galactic rotation curves into contributions from the baryonic components and the dark halo of a galaxy. One direct observational method to determine the disc M/L is by calculating the surface mass density of the disc from the stellar vertical velocity dispersion and the scale height of the disc. Usually, the scale height is obtained from near-IR studies of edge-on galaxies and pertains to the older, kinematically hotter stars in the disc, while the vertical velocity dispersion of stars is measured in the optical band and refers to stars of all ages (up to ∼10 Gyr) and velocity dispersions. This mismatch between the scale height and the velocity dispersion can lead to underestimates of the disc surface density and a misleading conclusion of the submaximality of galaxy discs. In this paper, we present the study of the stellar velocity dispersion of the disc galaxy NGC 6946 using integrated star light and individual planetary nebulae as dynamical tracers. We demonstrate the presence of two kinematically distinct populations of tracers that contribute to the total stellar velocity dispersion. Thus, we are able to use the dispersion and the scale height of the same dynamical population to derive the surface mass density of the disc over a radial extent. We find the disc of NGC 6946 to be closer to maximal with the baryonic component contributing most of the radial gravitational field in the inner parts of the galaxy (Vmax(bar) = 0.76(±0.14)Vmax).
Simulations of the Milky Way’s central molecular zone – I. Gas dynamics
Authors: Tress Robin G , Sormani Mattia C , Glover Simon C O , Klessen Ralf S , Battersby Cara D , Clark Paul C , Hatchfield H Perry , Smith Rowan J
Published: October 2020

We use hydrodynamical simulations to study the Milky Way’s central molecular zone (CMZ). The simulations include a non-equilibrium chemical network, the gas self-gravity, star formation, and supernova feedback. We resolve the structure of the interstellar medium at sub-parsec resolution while also capturing the interaction between the CMZ and the bar-driven large-scale flow out to $R\sim 5\, {\rm kpc}$. Our main findings are as follows: (1) The distinction between inner (R ≲ 120 pc) and outer (120 ≲ R ≲ 450 pc) CMZ that is sometimes proposed in the literature is unnecessary. Instead, the CMZ is best described as single structure, namely a star-forming ring with outer radius R ≃ 200 pc which includes the 1.3° complex and which is directly interacting with the dust lanes that mediate the bar-driven inflow. (2) This accretion can induce a significant tilt of the CMZ out of the plane. A tilted CMZ might provide an alternative explanation to the ∞-shaped structure identified in Herschel data by Molinari et al. (3) The bar in our simulation efficiently drives an inflow from the Galactic disc (R ≃ 3 kpc) down to the CMZ (R ≃ 200 pc) of the order of $1\rm \, M_\odot \, yr^{-1}$, consistent with observational determinations. (4) Supernova feedback can drive an inflow from the CMZ inwards towards the circumnuclear disc of the order of ${\sim}0.03\, \rm M_\odot \, yr^{-1}$. (5) We give a new interpretation for the 3D placement of the 20 and 50 km s−1 clouds, according to which they are close (R ≲ 30 pc) to the Galactic Centre, but are also connected to the larger scale streams at R ≳ 100 pc.