bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross-sectional evaluation of surface contamination with 9 antineoplastic drugs in 93 Canadian healthcare centers: 2019 results
Authors: Palamini Marie , Gagné Sébastien , Caron Nicolas , Bussières Jean-François
Published: March 2020

Introduction

The primary objective was to describe environmental contamination with National Institute for Occupational Safety and Health Group 1 hazardous drugs in oncology pharmacies and outpatient clinics in Canada in 2019, as part of an annual surveillance project.

Methods

In each participating center, 12 standardized sites (6 in the oncology pharmacy and 6 in outpatient clinic) were sampled. Each sample was prepared to allow quantification of six antineoplastic drugs (cyclophosphamide, ifosfamide, methotrexate, gemcitabine, 5-fluorouracil, and irinotecan) by ultra-performance liquid chromatography-tandem mass spectrometry. Samples were also tested for three additional antineoplastic drugs (docetaxel, paclitaxel, and vinorelbine) without quantification. The impact of certain characteristics of the sampling sites was evaluated with a Kolmogorov–Smirnov test for independent samples.

Results

Ninety-three Canadian centers participated in 2019, with a total of 1045 surfaces sampled. Cyclophosphamide was the drug most often found in the surface samples (32.4% of samples with positive result), followed by gemcitabine (20.3%). The front grille inside the biological safety cabinet (81.5% of samples positive for at least one antineoplastic drug) and the armrest of a treatment chair (75.8%) were the most frequently contaminated surfaces. Centers with more oncology inpatient and outpatient beds, those that prepared more antineoplastic drugs each year, and those that used more cyclophosphamide each year had higher concentrations of cyclophosphamide contamination on the surfaces tested ( p <  0.0001).

Conclusion

Traces of dangerous drugs were found in oncology pharmacies and oncology outpatient clinics in 93 Canadian hospitals in 2019. However, the quantities measured were very small. Every healthcare worker should consider these work areas to be contaminated and should wear appropriate protective equipment.
Determinants of Sexual Violence Against Married Women: Qualitative Evidence From Ghana
Authors: Apatinga Gervin A. , Tenkorang Eric Y
Published: March 2020

Some evidence suggests that in sub-Saharan Africa, sexual violence is commonplace among married women, yet this problem is underresearched. Using qualitative methods and applying Heise’s social-ecological model, this study examined the experiences of 15 Ghanaian women suffering sexual violence in their marriages. Results from the thematic analysis indicate several determinants of sexual violence. Whereas some participants identified macro-level and exosystem factors, including poverty, others pointed to micro-level and ontogenic factors, such as husbands’ substance abuse. The results corroborate the core idea of Heise’s framework, namely, that structural- and individual-level factors make women vulnerable to violence. The study concludes that Ghanaian legal and policy frameworks must be enforced and strengthened to address the etiology of sexual violence and abuse.
Home-Based Educational Programs for Management of Dyspnea: A Systematic Literature Review
Authors: Chorattas Aristides , Papastavrou Evridiki , Charalambous Andreas , Kouta Christiana
Published: March 2020

Dyspnea or breathlessness is a symptom of a plethora of diseases; despite that its management poses a challenge, it leads to frequent hospitalizations and a poor quality of life. In lung cancer, dyspnea may appear at any time of the disease but mainly during the end-of-life period. This article aims to explore the effectiveness of home-based educational programs for the management of dyspnea. This is a systematic review. The inclusion criteria were studies published between 2000 and 2018, and structured nurse-led home educational programs for the management of dyspnea due to cancer. The search via PUBMED, COCHRANE, EBSCO, and Google Scholar was worldwide for English- and Greek-language articles. The keywords included “education, program, intervention, patient, dyspnea, breathlessness, cancer, home, nurse.” The review was expanded to dyspnea being due to any chronic disease as it gave only one research article for lung cancer. The review identified seven research articles evaluating the effectiveness of various home-based educational programs for dyspnea management due to chronic obstructive pulmonary disease, heart failure, and lung cancer. They showed that a structured home-based educational program is of benefit for the patients by improving their dyspnea levels and their quality of life. There is the need to evaluate the benefits of home-based educational programs for cancer patients with dyspnea at home either as part of a symptom alone support program or as part of the general support given to cancer patients at home.
Friction and wear behavior of Al–Si alloy cylinder liner prepared by surface shaping treatments
Authors: Li Cheng-Di , Chen Xiao , Zhang Xiao-Wei , Xu Shun-Jian , Hu Yao , Jian Hui-Hua , Xu Jiu-Jun
Published: March 2020

In order to improve the friction and wear behavior of Al–Si alloy cylinder liner, the surfaces of cylinder liner samples were prepared by three kinds of surface shaping treatments (chemical etching shaping, mechanical honing shaping, and laser ablation shaping). All the three kinds of surface shaping treatments can expose the silicon particles on the surface of Al–Si alloy cylinder liner, which prevents the contact aluminum from the counterface (piston ring). The area between the two protruding silicon particles can be stored for enhanced lubrication and reduce friction. These shaping surfaces were different. The edges of the silicon particles are made sharp by the chemical etching shaping treatment. The edges of the silicon particles are round but with burr by the mechanical honing shaping treatment. The edges of silicon particles are round but without burr by the laser ablation shaping treatment. The friction coefficient and weight loss are lowest by the laser ablation shaping in three kinds of surface shaping treatments. There are two reasons. On the one hand, the edges of silicon particles are round but without burr, which reduce the stress concentration. On the other hand, the silicon particles combine well with aluminum, which reduce the probability of falling off.
Resilience, Relationality, and Older People: The Importance of Intergenerationality
Authors: Chappell Anne , Welsh Elaine
Published: March 2020

In this article, we examine the concept of resilience. Debates range from defining it as an individualised attribute to understanding it as a relational social process. Concerns about an ageing population alongside a growing interest in well-being have led to an increase in the use of the term ‘resilience’ in UK policy and political rhetoric. Developing strategies for ‘bouncing back’ from difficult circumstances has been at the heart of much discussion of resilience. Drawing on qualitative data from interviews and focus groups with older people in the UK, we explore their perspectives on resilience. We found that relationships, including intergenerational ones, are crucial to older people’s understandings of resilience. Our data showed that narratives from the past were used to sustain resilience in the present and that negotiation and exchange between generations, as well as intergenerational connections in the community, fostered resilience among our participants. We found that relationality was at the heart of older people’s perspectives on resilience and that the social process of resilience was acted out in their everyday interactions with others as well as through their memories of past interactions. This article argues that recognising the significance of these daily practices contributes to a more nuanced understanding of resilience.
Outsider Inspections of Closed Institutions: An Insider Ethnographic View of Institutional Display
Authors: Andow Caroline
Published: March 2020

This article questions the value of internal inspections of closed institutions by external agencies, drawing on my unanticipated experience of being deeply immersed as a researcher inside a Secure Children’s Home at the time of an inspection. I describe how an ethnographic approach enabled me to see a dramatic change in the staff–young people relations – from adversarial to cooperative – in the presence of outside inspectors. I make sense of this change through an original application, and novel extension, of Goffman’s theorising. I conceptualise the staff and young people as insiders of a ‘total institution’ working together to perform a misleadingly harmonious ‘institutional display’, motivated by a shared sense of institutional identity. I argue that although the potential for insider misrepresentation can be acknowledged, the extent of it cannot be known by outsiders. This finding is of significance for social policy as closed institutions accommodate vulnerable populations and cases of institutional abuses attest the need for external monitoring. This article calls for recognition of the inherent limitation of external face-to-face inspection processes, and research into new methods of assessment.
Optimal control of a novel cutter head driving system for tunnel boring machine
Authors: Sun Chenchen , Gong Guofang , Yang Huayong , Wang Shuai
Published: March 2020

The cutter head of a tunnel boring machine may be trapped in extremely adverse geological environments, which requires a large enough driving torque to get rid of the trapped condition. In this paper, a novel driving scheme is proposed to improve the driving performance of the tunnel boring machine cutter head without increasing the installation power. First, the hydro-viscous clutch is introduced to achieve the soft start of the cutter head by the flexible effect of viscous oil film. Then, the flywheel is employed as the energy storage element to provide sufficient torque during the hydro-viscous clutch engagement, which assists the cutter head to get rid of the trapped condition. Moreover, an optimal state feedback control law based on a linear quadratic regulator is designed by compromising system impact and hydro-viscous clutch friction loss to optimize the hydro-viscous clutch engagement process and achieve favorable driving performance of the cutter head. Finally, numerical simulations are conducted to validate the effectiveness of the proposed driving technology.
Home Meal Preparation: A Powerful Medical Intervention
Authors: Klein Laura , Parks Kimberly
Published: March 2020

One of the principles of culinary medicine is to help patients learn how to make nutritious eating simple and easy. In this column, you will learn tools for preparing and storing food; a key component to successful home cooking. While this article is intended to help clinicians learn about food preparation, it is also designed to be used as an educational tool for patients.
Limited Improvements in Health Behaviors Suggest Need to Review Approaches to Health Promotion: A Repeated, Cross-Sectional Study
Authors: Becker Craig M. , Sewell Kerry , Bian Hui , Lee Joseph G. L.
Published: March 2020

Purpose. To broadly assess changes in key health behaviors (physical activity, fruit and vegetable consumption, smoking, and alcohol consumption) and one outcome (body mass index) between 2001-2006 and 2011-2016. Design. Repeated cross-sectional study. Setting. The United States of America. Participants. Noninstitutionalized adults age 24 to 39 participating in the National Health and Nutrition Examination Survey. Analysis. We used 2-sample t tests and χ2 tests to compare differences in health behaviors between the 2 time periods. Results. Data revealed a downward trend in both moderate and vigorous physical activity (P = .00), and fruit and vegetable consumption decreased (P = .003). Cigarette smoking decreased (P = .04), and there was no substantive change in heavy drinking between the 2 time periods. Body mass index was higher in the later time period (P = .00). Conclusion. Despite sustained funding efforts, we found little evidence that health behaviors improved between the 2 time periods. Indeed, many health behaviors have remained the same or worsened over time. These findings suggest the need to reflect on the appropriateness of the health promotion approaches being used.
Eigenvalues make the difference – A network analysis of the Chinese Super League
Authors: Zhao Yangqing , Zhang Hui
Published: March 2020

To evaluate collective (macro) performance data in the Chinese Super League, social network analyses and graph theory were implemented in team sports performance analyses. For each team, we constructed a weighted and directed network in which nodes corresponded to players and arrows to passes. A total of 1200 matches during the 2014–2018 seasons were analysed. The results showed significant differences in general network measures among team competitive levels, match locations and match outcomes. Successful teams and home teams had significantly higher link, diameter, density and cluster coefficient values than did the unsuccessful teams or visiting teams; however, the winning teams had significantly lower density and cluster coefficient 2 values than did the losing teams. This study suggested that successful teams or teams with advantages (home, winner) have a high level of total passes and eigenvalues. This is the first report in which eigenvalues (the degree of a team’s distribution of the ball during the match) were able to capture changes in dynamics between different teams. There were positive correlations between all the network variables and the total shots and no correlations between all the network variables and goals.
Prognostic scoring system for metastatic spine tumors derived from hepatocellular carcinoma
Authors: Uei Hiroshi , Tokuhashi Yasuaki
Published: March 2020

Purpose:

The prognosis of hepatocellular carcinoma (HCC) has recently improved, and so clinicians have greater opportunity to treat HCC-derived spinal metastases. Therefore, predicting life expectancy is important for determining the optimal treatment strategy for such tumors. This study aimed to investigate the prognostic factors for HCC-derived metastatic spine tumors and to develop a scoring system for predicting life expectancy in such cases.

Methods:

The posttreatment survival time and factors that might influence it were investigated in 62 patients with HCC-derived metastatic spine tumors who were treated at our department (surgery: 27 patients and conservative treatment: 35 patients), and a prognostic scoring system for predicting life expectancy was developed by combining the factors that significantly influenced survival.

Results:

In the univariate analyses, sex, the patient’s general condition, the presence/absence of major internal organ metastasis, the total revised Tokuhashi score, the serum albumin level, Child-Pugh class, spinal surgery, and bone-modifying agent (BMA) treatment were found to influence the posttreatment survival time. These factors were subjected to multivariate analysis, and a novel scoring system for predicting life expectancy based on the patient’s general condition, the serum albumin level (or Child-Pugh class), and BMA treatment was developed. In the retrospective analysis, the concordance rate between the patients’ life expectancy and actual survival times was 90.3%.

Conclusion:

The patient’s general condition, the serum albumin level (or Child-Pugh class), and BMA treatment influenced the posttreatment survival times of patients with HCC-derived metastatic spine tumors. A prognostic scoring system based on these factors was proposed.
Reducing Medication Risks in Older Adult Drinkers
Authors: Zanjani Faika , Schoenberg Nancy , Martin Catherine , Clayton Richard
Published: March 2020

Objectives: Prevalent concomitant alcohol and medication use among older adults is placing this group at risk for adverse health events. Given limited existing interventions to address concomitant alcohol and medication risk (AMR), a brief educational intervention was demonstrated. The purpose of the current study was to examine change in AMR behaviors 3 months post-education among older adult drinkers. Methods: A convenience sample of 58 older adult drinkers (mean age = 72) was recruited and followed ( n = 40; 70% at follow-up), from four pharmacies in rural Virginia. Results: Findings indicated decreased alcohol consumption in high-risk drinkers. Conclusion: Future research should explore methods to sustain reduced AMR.
Sexual Abstinence in the United States: Cohort Trends in Abstaining from Sex While Never Married for U.S. Women Born 1938 to 1983
Authors: Wu Lawrence L. , Martin Steven P. , England Paula , Mark Nicholas D. E.
Published: March 2020

In this data visualization, the authors document trends in abstaining from sex while never married for U.S. women born 1938–1939 to 1982–1983. Using data from the six most recent National Surveys of Family Growth, the authors’ estimates suggest that for women born in the late 1930s and early 1940s, 48 percent to 58 percent reported abstaining from sex while never married. Abstinence then declined rapidly among women born in the late 1940s through the early 1960s, leveling off at between 9 percent and 12 percent for more recent birth cohorts. Thus, for U.S. women born between the mid-1960s and the early 1980s, roughly one in nine abstained from sex while never married.
An Update on the Complexity and Importance of Accurately Diagnosing Post-Traumatic Stress Disorder and Comorbid Traumatic Brain Injury
Authors: Rosen Valerie , Ayers Gayle
Published: March 2020

As awareness for diagnosing and screening patients for trauma has grown, more effective evidence-based treatments are available to treat post-traumatic stress disorder (PTSD). Despite these gains, several patients are non-responsive to care and research has shifted to determining barriers for cure or improvement. With the advent of modern warfare, the combination of intermittent explosive devices and more robust armor has resulted in service members surviving blasts that historically would have been lethal, resulting in a rise in traumatic brain injuries (TBIs). Post-traumatic stress disorder and TBI are often comorbid and can serve as the aforementioned barriers for cure or improvement for each other if one goes unrecognized. This mini-review will discuss the importance of diagnosing both entities, especially when they are comorbid, by examining how misdiagnosis may interfere with treatment outcomes. Several recent advances in methods to successfully distinguish between the two disorders will be reviewed.
Reliability and Variability Assessment of Femoral Artery Pseudoaneurysm Measurements Between Pre- and Postprocessed B-mode Ultrasound Images
Authors: Kaifi Reham , Almatrafi Mohammed , Alahmary Ferdos , Chen Andrew , Macsata Robyn , Sarani Babak , Zderic Vesna
Published: March 2020

Objective:

To assess the reliability and variability of femoral artery pseudoaneurysm (FAP) measurements between pre- and postprocessed sonograms acquired in a major medical center in Saudi Arabia as compared with results obtained from a major medical center in the United States.

Methods:

Retrospective image analysis was conducted on 23 FAP sonograms, which were evaluated by four observers. Observers measured FAP sac and neck from pre- and postprocessed images and remeasured again after 2 weeks, to avoid recall bias.

Results:

The use of image processing was more profound for the novice observers in measuring FAP neck width and length. The intraclass correlation coefficient (ICC) for FAP neck width improved after segmentation from 0.63 to 0.91; in contrast, the ICC improved from 0.91 to 0.97 for experts. The average ICCs for FAP neck length improved from 0.40 to 0.79 for novices and from 0.86 to 0.95 for experts. The largest variation of values, within observers, were for neck length obtained from the original images. The range varied from 0.16 to 0.37 cm and was reduced to 0.10 to 0.18 cm with segmented images.

Conclusion:

As demonstrated previously, sonographic image processing resulted in increased reliability and decreased variability for FAP measurements.
Redefinition of coquimbite, AlFe3+3(SO4)6(H2O)12⋅6H2O
Authors: Mauro Daniela , Biagioni Cristian , Pasero Marco , Skogby Henrik , Zaccarini Federica
Published: March 2020

Coquimbite, AlFe3+3(SO4)6(H2O)12⋅6H2O, was considered as a pure Fe3+hydrated sulfate. However, previous mineralogical studies pointed out the occurrence of essential Al, occupying a distinct site in the crystal structure of this mineral. Through the critical re-examination of the available literature and new crystal-chemical data collected on a specimen from the Monte Arsiccio mine, Apuan Alps, Tuscany, Italy, the chemical formula of coquimbite has been revised, taking into account the occurrence of Al. Coquimbite has a homeotypic relationship with paracoquimbite, Fe4(SO4)6(H2O)12⋅6H2O; both mineral species belong to the coquimbite group. On the contrary, aluminocoquimbite, Al2Fe2(SO4)6(H2O)12⋅6H2O, has a different topology and does not belong to that group.
Successful treatment of thrombocytopenia with daratumumab after allogeneic transplant: a case report and literature review
Authors: Migdady Yazan , Ediriwickrema Asiri , Jackson Ryan Patrick , Kadi Wendy , Gupta Ridhi , Socola Francisco , Arai Sally , Martin Beth A.
Published: March 2020

Key Points

A source of treatment refractoriness in immune cytopenias appears to be residual CD138/38-positive lymphocyte populations. A short course of daratumumab is a novel treatment of refractory thrombocytopenia after failure of standard treatment options.
Regional distribution of high-attenuation areas on chest computed tomography in the Multi-Ethnic Study of Atherosclerosis
Authors: Choi Bina , Kawut Steven M. , Raghu Ganesh , Hoffman Eric , Tracy Russell , Madahar Purnema , Bernstein Elana J. , Barr R. Graham , Lederer David J. , Podolanczuk Anna
Published: March 2020

High-attenuation areas (HAA) are a computed tomography-based quantitative measure of subclinical interstitial lung disease (ILD). We aimed to validate HAA in lung regions that are less subject to artefacts, such as extravascular lung water or dependent atelectasis. We examined the associations of HAA within six lung regions (basilar, non-basilar, peel, core, basilar peel, basilar core) with serum biomarkers of lung remodelling, forced vital capacity (FVC), visually-assessed interstitial lung abnormalities (ILA), and all-cause and ILD-specific mortality.

We performed cross-sectional and longitudinal analyses of participants in the Multi-Ethnic Study of Atherosclerosis, a prospective cohort of 6814 adults aged 45–84 years without known cardiovascular disease who underwent cardiac computed tomography.

Median regional HAA ranged from 3.8% in the peel to 4.8% in the basilar core. Doubling of regional HAA was associated with greater serum matrix metalloproteinase-7 (range 3.8% to 10.3%; p≤0.01), higher odds of ILA (OR 1.42 to 2.20; p≤0.03), and a higher risk of all-cause mortality (hazard ratio 1.20 to 1.47; p≤0.001). Doubling of regional HAA was associated with greater serum interleukin-6 (4.9% to 10.3%; p≤0.005) and higher risk of ILD-specific mortality (hazard ratio 3.30 to 3.98; p<0.001), except in the basilar core. Doubling of regional HAA was associated with lower FVC in the non-basilar, core and basilar core (113 mL to 186 mL; p<0.001).

Associations of HAA with lung remodelling biomarkers, ILA risk and all-cause mortality were consistent across all regions of the lung, including dependent areas where atelectasis may be present. These findings support the validity of HAA as a measure of pathologic subclinical ILD.
Caffeine in preterm infants: where are we in 2020?
Authors: Moschino Laura , Zivanovic Sanja , Hartley Caroline , Trevisanuto Daniele , Baraldi Eugenio , Roehr Charles Christoph
Published: March 2020

The incidence of preterm birth is increasing, leading to a growing population with potential long-term pulmonary complications. Apnoea of prematurity (AOP) is one of the major challenges when treating preterm infants; it can lead to respiratory failure and the need for mechanical ventilation. Ventilating preterm infants can be associated with severe negative pulmonary and extrapulmonary outcomes, such as bronchopulmonary dysplasia (BPD), severe neurological impairment and death. Therefore, international guidelines favour non-invasive respiratory support. Strategies to improve the success rate of non-invasive ventilation in preterm infants include pharmacological treatment of AOP. Among the different pharmacological options, caffeine citrate is the current drug of choice. Caffeine is effective in reducing AOP and mechanical ventilation and enhances extubation success; it decreases the risk of BPD; and is associated with improved cognitive outcome at 2 years of age, and pulmonary function up to 11 years of age. The commonly prescribed dose (20 mg·kg−1loading dose, 5–10 mg·kg−1per day maintenance dose) is considered safe and effective. However, to date there is no commonly agreed standardised protocol on the optimal dosing and timing of caffeine therapy. Furthermore, despite the wide pharmacological safety profile of caffeine, the role of therapeutic drug monitoring in caffeine-treated preterm infants is still debated. This state-of-the-art review summarises the current knowledge of caff­eine therapy in preterm infants and highlights some of the unresolved questions of AOP. We speculate that with increased understanding of caffeine and its metabolism, a more refined respiratory management of preterm infants is feasible, leading to an overall improvement in patient outcome.
Mass-Spring-Damping Theory Based Equivalent Mechanical Model for Cylindrical Lithium-ion Batteries under Mechanical Abuse
Authors: Wang Wenwei , Li Yiding , Lin Cheng , Yang Sheng
Published: March 2020

An equivalent mechanical model with the equivalent physical meaning of mass-spring-damping is proposed for cylindrical lithium-ion batteries through experiments and theory. The equivalent mechanical model of a cylindrical lithium-ion battery consists of a spring-damping parallel unit. Therefore, a spring-damping parallel unit connecting a damping unit in series is selected to construct the constitutive characteristics of the battery under mechanical abuse. Comparison results show that the equivalent mechanical model can more effectively describe the mechanical properties of the batteries than most cubic fitting models, of which the average relative error of the equivalent mechanical model under different states-of-charge is less than 6.75%. Combined with the proposed equivalent mechanical model, the failure process of the batteries was simulated and analyzed using LS-Dyna and HyperWorks. Under rigid rod tests, failure occurred at the core and bottom of the batteries; under hemispherical punch tests, failure occurred at the core and top, consistent with the experimental results. The average prediction error for the failure displacement under different abuse conditions is less than 4% in the simulations. The equivalent mechanical model requires only a few parameters and can be recognized easily. In the future, the model can be used in safety warning devices based on mechanical penetration.
Timing of the reproductive cycle of waved whelk, Buccinum undatum, on the U.S. Mid-Atlantic Bight
Authors: Borsetti Sarah , Munroe Daphne , Rudders David , Chang Jui-Han
Published: March 2020

Development of the unmanaged waved whelk (Buccinum undatum) fishery on the Mid-Atlantic continental shelf of the United States has initiated investigation into fisheries-related biological and population attributes of the species in this region. Maturation and reproduction timing vary by location for this species and are likely linked to bottom water temperature. This study examined the seasonal fluctuations in relevant body metrics and gonadosomatic index in relation to bottom temperature to assess the timing of the reproductive cycle of the B. undatum population in the southern-most extent of this species’ range in the Atlantic. To characterize variation over the maturation schedule, nine locations in the Mid-Atlantic Bight (MAB) were sampled five times between January 2017 and September 2017. Maturity was assessed macroscopically, with morphological methods, and via gonadosomatic indices. Male behavioral maturity estimates, based on a penis length to shell length index (PL50), were compared to estimates made using other methods for assessing maturity to test the efficacy of this commonly used ratio. Mature whelk were found in all months and peak reproductive activity was observed in spring and early summer. This timing suggests that ideal sampling to visually identify maturity to estimate size of maturity would be late winter or early spring. Unique oceanographic dynamics in the MAB, such as strong seasonal stratification results in large changes in annual bottom temperature which appears to be closely linked to the reproductive cycle in this region. Our data suggest that B. undatum in the MAB experience spawning and development at ~ 7–8 °C; temperatures warmer than Canadian populations and cooler than some UK conspecifics. To our knowledge, this is the first study to document the annual reproductive cycle of waved whelk in the United States.
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
Authors: Manchanda Nancy , Portwood John L. , Woodhouse Margaret R. , Seetharam Arun S. , Lawrence-Dill Carolyn J. , Andorf Carson M. , Hufford Matthew B.
Published: March 2020

Background

Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.

Results

Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.

Conclusions

The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury
Authors: Zhao Xin , Du Wuying , Zhang Manchao , Atiq Zainab O. , Xia Fen
Published: March 2020

Background

Chemotherapy-induced peripheral neuropathy is not only one of the most common causes of dose reduction or discontinuation of cancer treatment, but it can also permanently decrease the quality of life of cancer patients and survivors. Notably, Sirt2 protects many organs from various injuries, including diabetic peripheral neuropathy. As demonstrated previously by our laboratory and others, the overexpression of Sirt2 can improve cisplatin-induced neuropathy, although the mechanism is still unclear.

Results

In this study, the underlying mechanism by which Sirt2 protects neurons from cisplatin-induced injury was explored using the RNAseq technique in cultured rodent neurons. Sirt2 status was modified by genetic knockout (Sirt2/KO) and was then reconstituted in Sirt2/KO cells (Sirt2/Res). We observed 323 upregulated genes and 277 downregulated genes in Sirt2-expressing cells (Sirt2/Res) compared to Sirt2-deficient cells (Sirt2/KO). Pathway analysis suggested that Sirt2 may affect several pathways, such as MAPK, TNF, and cytokine–cytokine interaction. Furthermore, cisplatin-induced changes to the transcriptome are strongly associated with Sirt2 status. Cisplatin induced distinctive transcriptome changes for 227 genes in Sirt2-expressing cells and for 783 genes in Sirt2-deficient cells, while changes in only 138 of these genes were independent of Sirt2 status. Interestingly, changes in the p53 pathway, ECM–receptor interactions, and cytokine–cytokine receptor interactions were induced by cisplatin only in Sirt2-deficient cells.

Conclusions

This study demonstrated that Sirt2 regulates the transcriptome in cultured rodent neuronal cells. Furthermore, Sirt2-associated transcriptome regulation may be an important mechanism underlying the role of Sirt2 in organ protection, such as in cisplatin-induced neuronal injury. Sirt2 may be a potential target for the prevention and treatment of chemotherapy-induced neuropathy.
Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize
Authors: Li Yixuan , Wei Kaifa
Published: March 2020

Background

The cytochrome P450s (CYP450s) as the largest enzyme family of plant metabolism participate in various physiological processes, whereas no study has demonstrated interest in comprehensive comparison of the genes in wheat and maize. Genome-wide survey, characterization and comparison of wheat and maize CYP450 gene superfamily are useful for genetic manipulation of the Gramineae crops.

Results

In total, 1285 and 263 full-lengthCYP450s were identified in wheat and maize, respectively. According to standard nomenclature, wheatCYP450s (TaCYP450s) were categorized into 45 families, while maizeCYP450s (ZmCYP450s) into 43 families. A comprehensive analysis of wheat and maize CYP450s, involved in functional domains, conserved motifs, phylogeny, gene structures, chromosome locations and duplicated events was performed. The result showed that each family/subfamily in both species exhibited characteristic features, suggesting their phylogenetic relationship and the potential divergence in their functions. Functional divergence analysis at the amino acid level of representative clans CYP51, CYP74 and CYP97 in wheat, maize and rice identified some critical amino acid sites that are responsible for functional divergence of a gene family. Expression profiles ofTa-,ZmCYP450s were investigated using RNA-seq data, which contribute to infer the potential functions of the genes during development and stress responses. We found in both speciesCYP450s had preferential expression in specific tissues, and many tissue-specific genes were identified. Under water-deficit condition, 82 and 39 significantly differentially expressedCYP450s were respectively detected in wheat and maize. These genes may have some roles in protecting plants against drought damage. Thereinto, fourteenCYP450swere selected to validate their expression level through qRT-PCR. To further elucidating molecular mechanisms of CYP450 action, gene co-expression network was constructed. In total, 477TaCYP450s were distributed in 22 co-expression modules, and some co-expressed genes that likely take part in the same biochemical pathway were identified. For instance, the expression ofTaCYP74A98_4Dwas highly correlated withTaLOX9,TaLOX36,TaLOX39,TaLOX44andTaOPR8, and all of them may be involved in jasmonate (JA) biosynthesis.TaCYP73A201_3Ashowed coexpression withTaPAL1.25,TaCCoAOMT1.2,TaCOMT.1,TaCCR1.6andTaLAC5, which probably act in the wheat stem and/or root lignin synthesis pathway.

Conclusion

Our study first established systematic information about evolutionary relationship, expression pattern and function characterization ofCYP450s in wheat and maize.
Power difference in a χ2 test vs generalized linear mixed model in the presence of missing data – a simulation study
Authors: Miller Mary L. , Roe Denise J. , Hu Chengcheng , Bell Melanie L.
Published: March 2020

Background

Longitudinal randomized controlled trials (RCTs) often aim to test and measure the effect of treatment between arms at a single time point. A two-sample χ2 test is a common statistical approach when outcome data are binary. However, only complete outcomes are used in the analysis. Missing responses are common in longitudinal RCTs and by only analyzing complete data, power may be reduced and estimates could be biased. Generalized linear mixed models (GLMM) with a random intercept can be used to test and estimate the treatment effect, which may increase power and reduce bias.

Methods

We simulated longitudinal binary RCT data to compare the performance of a complete case χ2 test to a GLMM in terms of power, type I error, relative bias, and coverage under different missing data mechanisms (missing completely at random and missing at random). We considered how the baseline probability of the event, within subject correlation, and dropout rates under various missing mechanisms impacted each performance measure.

Results

When outcome data were missing completely at random, both χ2 and GLMM produced unbiased estimates; however, the GLMM returned an absolute power gain up to from 12.0% as compared to the χ2 test. When outcome data were missing at random, the GLMM yielded an absolute power gain up to 42.7% and estimates were unbiased or less biased compared to the χ2 test.

Conclusions

Investigators wishing to test for a treatment effect between treatment arms in longitudinal RCTs with binary outcome data in the presence of missing data should use a GLMM to gain power and produce minimally unbiased estimates instead of a complete case χ2 test.
Memory complaints and depressive symptoms over time: a construct-level replication analysis
Authors: Mogle Jacqueline , Hill Nikki L. , Bhargava Sakshi , Bell Tyler Reed , Bhang Iris
Published: March 2020

Background

Memory complaints and depressive symptoms are frequently associated in older adults and both serve as potential indicators of future cognitive decline. However, the temporal ordering of the development of these two symptoms remains unclear. The goal of the current study was to examine concurrent and temporal relationships between memory complaints and depressive symptoms in older adults.

Methods

Data were drawn from two longitudinal, nationally representative datasets and included cognitively intact older adults aged 65 and over. The datasets in the current study were from the National Health and Aging Trends Study (NHATS) and the Health and Retirement Study (HRS). Using an integrative analytic framework, we tested bidirectional temporal relationships between memory complaints (memory ratings and perceived memory decline) and depressive symptoms over 6 to 9 years of data in over 5000 older adults across these two samples.

Results

Across both datasets, perceived memory decline predicted future depressive symptoms whereas memory ratings did not. Additionally, results showed that at times when depressive symptoms tended to be higher, memory complaints were also higher, but depressive symptoms did not predict future memory complaints. One finding that was inconsistent across datasets was memory ratings predicting depressive symptoms. After accounting for covariates, this relationship was only significant in one dataset.

Conclusions

Cognitively intact older adults who report memory decline may be at risk for developing depressive symptoms in the future. Furthermore, our findings highlight the importance of using immediate replication of results across datasets to determine the generalizability of conclusions.
Supporting at-risk older adults transitioning from hospital to home: who benefits from an evidence-based patient-centered discharge planning intervention? Post-hoc analysis from a randomized trial
Authors: Provencher Véronique , Clemson Lindy , Wales Kylie , Cameron Ian D. , Gitlin Laura N. , Grenier Ariane , Lannin Natasha A.
Published: March 2020

Background

Subgroups of older patients experience difficulty performing activities of daily living (ADL) following hospital discharge, as well as unplanned hospital readmissions and emergency department (ED) presentations. We examine whether these subgroups of “at-risk” older patients benefit more than their counterparts from an evidence-based discharge planning intervention, on the following outcomes: (1) independence in ADL, (2) participation in life roles, (3) unplanned re-hospitalizations, and (4) ED presentations.

Trial design and methods

This study used data from a randomized control trial involving 400 hospitalized older patients with acute and medical conditions, recruited through 5 sites in Australia. Participants receive either HOME, a patient-centered discharge planning intervention led by an occupational therapist; or a structured in-hospital consultation. HOME uses a collaborative approach for goal setting and includes pre and post-discharge home visits as well as telephone follow-up. Characteristics associated with higher risks of adverse outcomes were recorded and at-risk subgroups were created (mild cognitive impairment, walking difficulty, comorbidity, living alone and no support from family). Independence in ADL and participation in life roles were assessed with validated questionnaires. The number of unplanned re-hospitalizations and ED presentations were extracted from medical files. Linear regression models were conducted to detect variation in response to the intervention at 3-months, according to patients’ characteristics.

Results

Analyses revealed significant interaction effects for intervention by cognitive status for unplanned re-hospitalization (p = 0.003) and ED presentations (p = 0.021) at 3 months. Within the at-risk subgroup of mild cognitively impaired, the HOME intervention significantly reduced unplanned hospitalizations (p = 0.027), but the effect did not reach significance in ED visits. While the effect of HOME differed according to support received from family for participation in life roles (p = 0.019), the participation observed in HOME patients with no support was not significantly improved.

Conclusions

Findings show that hospitalized older adults with mild cognitive impairment benefit from the HOME intervention, which involves preparation and post-discharge support in the environment, to reduce unplanned re-hospitalizations. Improved discharge outcomes in this at-risk subgroup following an occupational therapist-led intervention may enable best care delivery as patients transition from hospital to home.

Trial registration

The trial was registered before commencement (ACTRN12611000615987).
Comparison of 18F-sodium fluoride PET/CT, 18F-fluorocholine PET/CT and diffusion-weighted MRI for the detection of bone metastases in recurrent prostate cancer: a cost-effectiveness analysis in France
Authors: Gauthé Mathieu , Zarca Kevin , Aveline Cyrielle , Lecouvet Frédéric , Balogova Sona , Cussenot Olivier , Talbot Jean-Noël , Durand-Zaleski Isabelle
Published: March 2020

Background

The diagnostic performance of 18F-sodium fluoride positron emission tomography/computed tomography (PET/CT) (NaF), 18F-fluorocholine PET/CT (FCH) and diffusion-weighted whole-body magnetic resonance imaging (DW-MRI) in detecting bone metastases in prostate cancer (PCa) patients with first biochemical recurrence (BCR) has already been published, but their cost-effectiveness in this indication have never been compared.

Methods

We performed trial-based and model-based economic evaluations. In the trial, PCa patients with first BCR after previous definitive treatment were prospectively included. Imaging readings were performed both on-site by local specialists and centrally by experts. The economic evaluation extrapolated the diagnostic performances of the imaging techniques using a combination of a decision tree and Markov model based on the natural history of PCa. The health states were non-metastatic and metastatic BCR, non-metastatic and metastatic castration-resistant prostate cancer and death. The state-transition probabilities and utilities associated with each health state were derived from the literature. Real costs were extracted from the National Cost Study of hospital costs and the social health insurance cost schedule.

Results

There was no significant difference in diagnostic performance among the 3 imaging modalities in detecting bone metastases. FCH was the most cost-effective imaging modality above a threshold incremental cost-effectiveness ratio of 3000€/QALY when imaging was interpreted by local specialists and 9000€/QALY when imaging was interpreted by experts.

Conclusions

FCH had a better incremental effect on QALY, independent of imaging reading and should be preferred for detecting bone metastases in patients with biochemical recurrence of prostate cancer.

Trial registration

NCT01501630. Registered 29 December 2011.
Homozygous NOTCH3 p.R587C mutation in Chinese patients with CADASIL: a case report
Authors: He Ruojie , Li Huan , Sun Yiming , Chen Menglong , Wang Liang , Zhu Yuling , Zhang Cheng
Published: March 2020

Background

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an inherited small vessel disease caused by mutations in NOTCH3 gene with remarkable phenotypic heterogeneity. Cases of CADASIL associated with homozygous NOTCH3 mutations are rare and subsequently understudied. In this study, we investigate the genetic and phenotypic features within patients of CADASIL with homozygous NOTCH3 mutations.

Case presentation

We recruited two affected individuals with CADASIL from a mainland Chinese family. The proband (Patient 1), a 60-year-old male, presented with slow progressive gait instability, severe cognitive impairment, and emotional disorder for more than 2 years with a history of ischemic stroke and hypertension. His younger brother (Patient 2) presented with apparent gait difficulties, dysarthria as well as cognitive decline at 59 years old. Brain magnetic resonance imaging (MRI) showed diffused white matter lesions involving bilateral periventricular white matter, semioval center region, and anterior temporal lobes. Molecular genetic testing identified a homozygous variant, c.1759C > T (p.R587C), in NOTCH3 gene in both patients. Pathological analysis revealed granular osmiophilic material (GOM) deposits in small arterial walls of skin from the proband. The diagnosis of CADASIL was confirmed.

Conclusions

Our cases of CADASIL with homozygous mutation c.1759C > T (p.R587C) in NOTCH3 share similar manifestation to the patients with heterozygous same mutation reported previously. Other than genetic factors, vascular risk factors or environmental factors might contribute to the phenotypic variation of CADASIL.