bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of RNA Methylation Status From Gene Expression Data Using Classification and Regression Methods
Authors: Xue Hao , Wei Zhen , Chen Kunqi , Tang Yujiao , Wu Xiangyu , Su Jionglong , Meng Jia
Published: July 2020

RNA N6-methyladenosine (m6A) has emerged as an important epigenetic modification for its role in regulating the stability, structure, processing, and translation of RNA. Instability of m6A homeostasis may result in flaws in stem cell regulation, decrease in fertility, and risk of cancer. To this day, experimental detection and quantification of RNA m6A modification are still time-consuming and labor-intensive. There is only a limited number of epitranscriptome samples in existing databases, and a matched RNA methylation profile is not often available for a biological problem of interests. As gene expression data are usually readily available for most biological problems, it could be appealing if we can estimate the RNA methylation status from gene expression data using in silico methods. In this study, we explored the possibility of computational prediction of RNA methylation status from gene expression data using classification and regression methods based on mouse RNA methylation data collected from 73 experimental conditions. Elastic Net-regularized Logistic Regression (ENLR), Support Vector Machine (SVM), and Random Forests (RF) were constructed for classification. Both SVM and RF achieved the best performance with the mean area under the curve (AUC) = 0.84 across samples; SVM had a narrower AUC spread. Gene Site Enrichment Analysis was conducted on those sites selected by ENLR as predictors to access the biological significance of the model. Three functional annotation terms were found statistically significant: phosphoprotein, SRC Homology 3 (SH3) domain, and endoplasmic reticulum. All 3 terms were found to be closely related to m6A pathway. For regression analysis, Elastic Net was implemented, which yielded a mean Pearson correlation coefficient = 0.68 and a mean Spearman correlation coefficient = 0.64. Our exploratory study suggested that gene expression data could be used to construct predictors for m6A methylation status with adequate accuracy. Our work showed for the first time that RNA methylation status may be predicted from the matched gene expression data. This finding may facilitate RNA modification research in various biological contexts when a matched RNA methylation profile is not available, especially in the very early stage of the study.
Transnational Solidarity, Migration, and the Refugee Crisis: (In)Formal Organising and Political Environments in Greece, Germany, and Denmark
Authors: Kanellopoulos Kostas , Duru Deniz Neriman , Zschache Ulrike , Loukakis Angelos , Kousis Maria , Trenz Hans-Jörg
Published: July 2020

Over the last decade, the unprecedented influx of refugees and migrants into the European Union has posed a significant challenge to Europe, with solidarity being contested at two fronts: first, the question of solidarity with refugees in terms of meeting adequate measures of protection and satisfying their elementary needs; and second, the question of solidarity within the European Union in terms of sharing the costs and burden of hosting these refugees among the member states. One driving factor of these contestations is that the solidarity challenge in facing the ‘refugee crisis’ is taken up differently in transit countries in the South of Europe and destination countries in the North. Wishing to shed light on how national contexts impact transnational solidarity organising, we draw on a fresh set of cross-national evidence from a random sample of 277 transnational solidarity organisations (TSOs) in Greece, Germany, and Denmark. The aim is to illustrate the effects of political opportunities and threats during the 2007–2016 crises period on migration-related solidarity activities organised by TSOs. We will do so through tri-national comparisons tracing migration-related TSO patterns across time. The data used is produced in the context of the TRANSSOL project by a new methodological approach (action organisation analysis) based on hubs-retrieved organisational websites and their subsequent content analysis.
Study on the relationship between the CO2 concentration and pedestrian flow in a building evacuation passageway
Authors: Lei Wenjun , Rong Chuanliang , Tai Chuanmin , Li Angui
Published: July 2020

People ubiquitously produce CO2. The quantitative relationship between the CO2 concentration and pedestrian flow needs to be determined if the CO2 concentration is to be used to reflect pedestrian flow. Therefore, a field test was carried out to measure the CO2 concentration and pedestrian flow in an evacuation passageway of a densely populated building. The results show that the variation in the CO2 concentration always lags behind the variation in the pedestrian parameters. When pedestrians enter a building evacuation passageway over a long time span with high randomness, the quantitative relationships between the pedestrian density and CO2 concentration and between the pedestrian flow rate and CO2 concentration are not clear. When all the people in the building are required to leave at the same time, the relationships between the pedestrian density and CO2 concentration and between the pedestrian flow rate and CO2 concentration can be described quantitatively. The CO2 concentration can be taken as an early warning index to manage pedestrians in evacuation passageways of densely populated buildings. Two possible methods are provided to help provide early warnings in pedestrian management. These results are expected to provide new ideas for pedestrian statistics and pedestrian flow management in densely populated buildings.
GoCrystal: A gamified visual analytics tool for analysis and visualization of atomic configurations and thermodynamic energy models
Authors: Chung Haeyong , Nandhakumar Santhosh , Vasu Gopinath Polasani , Vickers Austin , Lee Eunseok
Published: July 2020

In this article, we present GoCrystal, a new visual analytics tool for analysis and visualization of atomic configurations and thermodynamic energy models. GoCrystal’s primary objective is to support the visual analytics tasks for finding and understanding favorable atomic patterns in a lattice using gamification. We believe the performance of visual analytics tasks can be improved by employing gamification features. Careful research was conducted in an effort to determine which gamification features would be more applicable for analyzing and exploring atomic configurations and their associated thermodynamic free energy. In addition, we conducted a user study to determine the effectiveness of GoCrystal and its gamification features in achieving this goal, comparing with a conventional visual analytics model without gamification as a control group. Finally, we report the results of the user study and demonstrate the impact that gamification features have on the performance and time necessary to understand atomic configurations.
Early myocardial injury biomarkers in diabetic hyperlipidemic rats: Impact of 10-dehydrogingerdione and vitamin D3
Authors: Elseweidy Mohamed M , Aly Sousou I , Hammad Sally K , Shershir Noura I
Published: July 2020

Hyperlipidemia represents a major risk factor for cardiovascular diseases leading to myocardial injury. The present study aimed to illustrate the myocardial injury induced in a diabetic hyperlipidemic rat model and the effect of vitamin D3, 10-DHGD intake either individually or in combination form. Male albino rats were selected for the study, received alloxan, hypercholesterolemic diet, and categorized into four groups. The first one (DHC), received hypercholesterolemic diet only and referred to as control. The remaining groups (2, 3, 4) received vitamin D3, 10-DHGD, and combination of both, respectively. Certain biomarkers that were selected for MI evaluation included blood glucose, lipogram pattern, Copeptin, C-reactive protein, myeloperoxidase, heart fatty acid-binding protein, and histopathological changes in myocardium and aorta. Vitamin D3 and 10-DHGD intake induced significant hypoglycemic, hypolipidemic effects, decreased inflammation, and MI biomarkers. Decreased myocardial vacuoles, foam cells, and intimal lesions were also observed compared to DHC. Their combination intake induced more marked reduction in all biomarkers and showed a histopathological pattern similar to normal features of myocardium and aorta. Our findings suggest the therapeutic roles of vitamin D3, 10-DHGD, and their combination against myocardial injury in diabetic hyperlipidemic rats.

Impact statement

Hyperlipidemia represents a major risk factor for cardiovascular diseases leading to myocardial injury (MI). The present study aimed to illustrate the pattern of myocardial injury induced in diabetic hyperlipidemic rat model and the effect of vitamin D3, 10-dehydrogingerdione (10-DHGD) intake either individually or in combination form.
Lateral Ulnar Collateral Ligament Reconstruction for Posterolateral Rotatory Instability of the Elbow: A Systematic Review
Authors: Fares Austin , Kusnezov Nicholas , Dunn John C.
Published: July 2020

Background: Posterolateral rotatory instability (PLRI) is a common form of recurrent elbow instability. The aim of this systematic review is to present the outcomes and complications of lateral ulnar collateral ligament (LUCL) reconstruction surgery for PLRI. Methods: A literature search of LUCL reconstructions was performed, identifying 99 potential papers; 11 of which met inclusion/exclusion criteria, accounting for 148 patients. Papers were included if they reviewed cases of PLRI from 1976 to 2016 with reported outcome measures. Data were pooled and analyzed focusing on patient demographics as well as subjective and objective patient outcomes and complications. Results: The average age of patients was 34 years with a mean follow-up time of 49.8 months. The most common mechanism of injury was a traumatic elbow dislocation (66%), followed by cubitus varus deformity (7%), and unknown mechanisms (7%). Overall, 90% of patients achieved elbow stability and 2.7% experienced a failed reconstruction that necessitated an additional surgery. Furthermore, 93% were satisfied with the outcome of the reconstruction, and 83% reported good to excellent outcomes with 11% reporting moderate to severe persistent pain. Nearly half (45%) of reconstructions were done using a palmaris longus tendon graft, 24% with a triceps tendon graft, and 7% with a synthetic graft. Conclusions: Outcomes following LUCL reconstruction for PLRI are excellent and revision rates are low. LUCL reconstruction is a safe and reliable procedure.

Level of Evidence: IV Therapeutic
Radiographic Outcomes and Complications of Delayed Fixation of Distal Radius Fractures
Authors: Lee Stella J. , Stenquist Derek S. , Collins Jamie E. , Mora Ariana N. , Teplitz Brett A. , Blazar Philip E. , Earp Brandon E.
Published: July 2020

Background:

Surgeons are sometimes presented with patients with distal radius fractures who present in a delayed fashion or lose reduction after several weeks of attempted closed management. There are limited studies on delayed surgical treatment of distal radius fractures to assist providers in decision-making.

Methods:

We conducted a matched cohort study to compare radiographic outcomes and complications for patients with a distal radius fracture treated with delayed (3-5 weeks) or early (0-2 weeks) surgical fixation. Patients ages 18+ who underwent open reduction and internal fixation of distal radius fractures by a volar approach at 2 Level I trauma centers between 2003 and 2015 were eligible. We measured radiographic outcomes and reviewed medical records to determine operative approach and complications.

Results:

There were 25 cases and 50 controls matched for age (18-87), sex, and AO fracture type. The delayed group had surgery at a mean of 24.8 days from injury and the early group at 5.6 days. There was no statistically significant difference between the delayed and early cohorts in radiographic parameters on injury x-rays, in improvement in radiographic parameters on first postoperative x-rays, or in maintenance of radiographic parameters at union.

Conclusion:

We did not find significant differences in radiographic outcomes or complication rates between patients with delayed versus early surgical treatment for distal radius fracture. Providers treating patients with late presentation or late displacement have the option of surgical fixation beyond the first few weeks after injury.

Level of Evidence:

III (Retrospective matched cohort study)
MRI Findings in Patients Undergoing Triangular Fibrocartilage Complex Repairs Versus Patients Without Ulnar-Sided Wrist Pain
Authors: Verhiel Svenna H. W. L. , Blackburn Julia , Ritt Marco J. P. F. , Simeone Frank J. , Chen Neal C.
Published: July 2020

Background: The clinical picture of ulnar-sided wrist pain is oftentimes confusing because various pathologies may be coexistent. In this study, we aimed: (1) to compare the prevalence of potential causes of ulnar-sided wrist pain on magnetic resonance imaging (MRI) in patients who underwent triangular fibrocartilage complex (TFCC) repair and control subjects: and (2) to evaluate whether inferior clinical results were associated with specific patient characteristics or other potential causes of ulnar-sided wrist pain. Methods: We included 67 patients who underwent a TFCC repair and 67 control subjects. The MRI scans were examined for sources of ulnar-sided wrist pain. After TFCC repair, 42 patients (63%) completed surveys, including Quick Disabilities of the Arm, Shoulder and Hand and pain scores. Bivariate analysis was performed to compare our groups and to identify factors associated with our outcomes. Results: We found significantly higher rates of distal radioulnar joint (DRUJ) arthritis ( P = .033), extensor carpi ulnaris (ECU) pathology ( P = .028), and ulnar styloid fractures ( P = .028) in patients with TFCC repairs. With increasing age, increasing pathology in the pisotriquetral joint ( P = .040), more ulnocarpal abutment ( P = .0081), and more degenerative tears ( P < .001) were seen in both groups. No demographic characteristics or MRI findings were significantly associated with our outcomes. Conclusions: We observed higher rates of DRUJ arthritis and ECU pathology in patients with TFCC tears undergoing repair compared with age- and sex-matched controls. This may be due to damage to the TFCC itself altering relationships of the DRUJ and the ECU subsheath, or it may reflect various pathologies that cause ulnar-sided wrist pain and drive patients toward surgery.
Transitions from avoidance: Reinforcing competing behaviours reduces generalised avoidance in new contexts
Authors: Bennett Marc P , Roche Bryan , Dymond Simon , Baeyens Frank , Vervliet Bram , Hermans Dirk
Published: July 2020

Generalised avoidance behaviours are a common diagnostic feature of anxiety-related disorders and a barrier to affecting changes in anxiety during therapy. However, strategies to mitigate generalised avoidance are under-investigated. Even less attention is given to reducing the category-based generalisation of avoidance. We therefore investigated the potential of an operant-based approach. Specifically, it was examined whether reinforcing competing (non-avoidance) behaviours to threat-predictive cues would interfere with the expression of generalised avoidance. Using a matching-to-sample task, artificial stimulus categories were established using physically dissimilar nonsense shapes. A member of one category (conditioned stimulus; CS1) was then associated with an aversive outcome in an Acquisition context, unless an avoidance response was made. Next, competing behaviours were reinforced in response to the CS1 in new contexts. Finally, we tested for the generalisation of avoidance to another member of the stimulus category (generalisation stimulus; GS1) in both a Novel context and the Acquisition context. The selective generalisation of avoidance to GS1 was observed, but only in the Acquisition context. In the Novel context, the generalisation of avoidance to GSs was significantly reduced. A comparison group (Experiment 2), which did not learn any competing behaviours, avoided GS1 in both contexts. These findings suggest that reinforcing competing behavioural responses to threat-predictive cues can lead to reductions in generalised avoidance. This study is among the first study to demonstrate sustained reductions in generalised avoidance resulting from operant-based protocols, and the clinical and research implications are discussed.
Porous carbons derived from zinc-based nitrogen heterocyclic complexes combined with KOH activation for use as supercapacitors
Authors: Ru Shuai , Ai Zhaoquan
Published: July 2020

2,2’-Bipyridine with strong coordination ability for metal ions was used to prepare N-doped porous carbon materials by a facile method of solution agitation and annealing, with KOH as the activated solvent. Applied to supercapacitors, these porous carbon materials exhibit high specific capacitance and outstanding rate performance, which are attributed to their larger specific surface area, richer pore structure, and N-doping after KOH activation, leading to fast electron transport and increased ion storage in the unique architecture.
Dysfunction of adaptive immunity is related to severity of COVID-19: a retrospective study
Authors: Xie Liang , Wu Qinhan , Lin Qunying , Liu Xuhui , Lin Weihua , Hao Shengyu , Hu Weiping , Xiang Guiling , Lu Hongzhou , Li Shanqun
Published: July 2020

Background:

In December of 2019, coronavirus disease 2019 (Covid-19) was reported in Wuhan, China, and has now rapidly swept around the world. Much research has been carried out since the outbreak, but few studies have focused on the dysfunction of the adaptive immunity.

Methods:

In this retrospective and multi-center study, 373 patients with laboratory-confirmed COVID-19 from Shanghai Public Health Clinical Center and Affiliated Hospital of Putian University were recruited. Demographic, clinical, radiological features, and laboratory data were recorded and analyzed at admission and at discharge. Results of immunological tests were followed up until the patients were discharged.

Results:

Of the 373 patients with COVID-19 pneumonia, 322 were in the non-severe group and 51 were in the severe group. Number of T cells, CD4+ and CD8+ T cells, and total lymphocytes declined remarkably upon admission and elevated when the patients were discharged. At admission, counts of total lymphocytes, T cells, CD4+ and CD8+ T cells, and levels of C3 and C4 in the severe group were lower than those in the non-severe group, whereas the neutrophil to lymphocyte ratio (NLR) was higher in the severe group. Counts of T cells, CD4+ and CD8+ T cells, and total lymphocytes were negatively correlated with lactate dehydrogenase and C-reactive protein.

Conclusion:

COVID-19 might target adaptive immunity and cause a decrease in lymphocytes, especially T cells and subsets. Physicians should pay close attention to the adaptive immunity of patients upon admission. Monitoring NLR, T lymphocytes, and subsets would help physicians with the proper diagnosis and treatment of COVID-19. The reviews of this paper are available via the supplemental material section.
Pulmonary and systemic hemodynamics are associated with myocardial injury in the acute respiratory distress syndrome
Authors: Metkus Thomas S , Mathai Stephen C , Leucker Thorsten , Hassoun Paul M , Tedford Ryan J , Korley Frederick K
Published: July 2020

Background

Whether right and left heart hemodynamics are associated with myocardial injury in the acute respiratory distress syndrome (ARDS) is not known.

Methods

We performed a retrospective cohort study of subjects who had right heart catheterization within the ALVEOLI trial and Fluid and Catheter Treatment Trial. Myocardial injury was assessed using a highly sensitive troponin assay (hsTn; Abbot ARCHITECT). Hemodynamic variables included right atrial pressure, pulmonary artery wedge pressure, cardiac index and stroke volume, pulmonary vascular resistance, pulmonary arterial compliance, and pulmonary effective arterial elastance. We performed linear, logistic, and Cox regression to determine the association of hemodynamic variables with myocardial injury and to determine if hemodynamics mediated the association between myocardial injury and death.

Results

Among 252 ARDS patients, median day 0 troponin was 65.4 (13.8–397.8) ng/L. Lower cardiac index (β −0.23 SE 0.10; P < 0.001) and stroke volume (β −0.26 SE 0.005; P < 0.001), higher pulmonary vascular resistance (β 0.22 SE 0.11; P < 0.001), lower pulmonary arterial compliance (β −0.24 SE 0.06; P < 0.001), and higher arterial elastance (β 0.27 SE 0.43; P < 0.001) were associated with greater myocardial injury in univariable and adjusted models. Changes in stroke volume, cardiac index, pulmonary arterial compliance, pulmonary vascular resistance, and arterial elastance were all associated with progressive myocardial injury over three days. hsTn levels were associated with mortality; however, the association was attenuated after adjustment for each of stroke volume, pulmonary vascular resistance, pulmonary arterial compliance, and arterial elastance.

Conclusion

Pulmonary vascular hemodynamics are associated with myocardial injury in ARDS, while filling pressures are not. Pulmonary vascular disease may represent a treatable contributor to myocardial injury in ARDS.
Radiological, histopathological findings, and clinical outcome of pulmonary artery sarcoma
Authors: Zhang Shuai , Zhang Yu , Liu Min , Tao Xincao , Xie Wanmu , Wan Jun , Zhai Zhenguo
Published: July 2020

Pulmonary artery sarcoma is a rare malignancy with poor prognosis. Lack of specific clinical manifestations, some patients are even confirmed postoperatively or at autopsy, that leads to the delay in treatment. Early diagnosis and radical surgical resection provide the possibility of prolonged survival. We retrospectively enrolled 13 patients diagnosed with pulmonary artery sarcoma at our hospital between 2015 and 2019. Their clinical, laboratory, radiological, and histopathological data were collected and analyzed. Published case series were also reviewed. Results show that, the median age of the patients was 53 years, with 6 (46.2%) males. The most common symptom is exertional dyspnea. Erythrocyte sedimentation rate and C‐reactive protein were increased in 76.9% and 69.2% of these patients, while D‐Dimer remained normal or elevated slightly. Metastasis was present at diagnosis in eight (61.5%) patients. Ten patients were diagnosed histologically: three were diagnosed after pulmonary endarterectomy, four by endobronchial ultrasound‐guided transbronchial needle aspiration, two by percutaneous lung biopsy, and one by endovascular aspiration biopsy. Four patients underwent surgery and one is waiting for surgery. Nine patients received chemotherapy; and three of them received targeted therapy with anlotinib after chemotherapy. Two patients received anti‐PD‐1 monoclonal antibody. One patient died during endobronchial ultrasound‐guided transbronchial needle aspiration. Two patients died 9 and 13 months after diagnosis, respectively; one refused invasive diagnostic procedures and died three months after clinical diagnosis. In conclusion, the most appropriate approach to get tissue specimen needs to be tailored to every pulmonary artery sarcoma patient. Pulmonary endarterectomy combined with chemotherapy and targeted therapy has prolonged their survival time.
Clinical trial design in phase 2 and 3 trials for pulmonary hypertension
Authors: Nikkho Sylvia , Fernandes Peter , White R. James , Deng Chunqin (CQ) , Farber Harrison W. , Corris Paul A
Published: July 2020

This article on clinical trial design incorporates the broad experience of members of the Pulmonary Vascular Research Institute’s (PVRI) Innovative Drug Development Initiative (IDDI) as an open debate platform for academia, the pharmaceutical industry and regulatory experts surrounding the future design of clinical trials in pulmonary hypertension. It is increasingly clear that the design of phase 2 and 3 trials in pulmonary hypertension will have to diversify from the traditional randomised double‐blind design, given the anticipated need to trial novel therapeutic approaches in the immediate future. This article reviews a wide range of differing approaches and places these into context within the field of pulmonary hypertension.
Women are invisible?! A literature survey on gender gap and financial training
Authors: Sholevar Maryam , Harris Laurence
Published: July 2020

Most of the existing definitions and measurements of financial literacy have been tailored for developed countries. Although financial literacy and financial behaviour are usually assessed at the household level, the gender dimension of household agents is less explored which may overshadow the women’s low level of financial literacy. This paper is a selective systematic review aiming to survey the existing literature on financial training where the focus is on two main issues, namely, financial training and gender disparity in financial literacy. Based on a thorough literature review, we identify research gaps in each of these dimensions. The identified gaps are then used to formulate two promising research ideas. Specifically, the promising research ideas seek to investigate the gender disparity and propose a novel method for financial training.
Epidemiological factors associated with health knowledge of three common eye diseases: A community-based pilot survey in Hong Kong
Authors: Wong Perseus WF , Lau Jordy KP , Choy Bonnie NK , Shih Kendrick C , Ng Alex LK , Chan Jonathan CH , Wong Ian YH
Published: July 2020

Objectives:

To assess the proportions of respondents in the general community having heard or awareness, and their knowledge level, of three common eye diseases: age-related macular degeneration, cataract, and glaucoma. We also attempted to assess for risk factors that may be associated with any variations, which will help identify the areas of inadequate knowledge and demographics of potential audiences for focused health education.

Methods:

We conducted a community-based pilot survey for the residents from a southern suburb of Hong Kong in early 2016, by inviting all aged 50 or above to complete a standardized questionnaire in the local community hall.

Results:

Most of the 222 respondents have heard, or awareness, of cataract (92.79% or 81.98%, respectively), followed by glaucoma (86.94% or 52.70%, respectively), and age-related macular degeneration (51.35% or 29.28%, respectively). The results of Cronbach’s alpha (α > 0.7) and Spearman’s correlation coefficient (p < 0.01) suggested that the internal consistency, convergent and discriminant validities of the questionnaire were acceptable for the study population. Compared to a previous Hong Kong survey in 2002, the proportions of having heard of the three eye diseases were greater, but the overall knowledge remained limited. From a maximum knowledge score of 29, the median scores for age-related macular degeneration, cataract, and glaucoma were 9, 13, and 14, respectively. Except for the treatment of cataract, the knowledge level in most areas was low. Sociodemographic factors and medical history, rather than behavioral factors, were more likely to be associated with having a higher knowledge level. Subjects with family or friends with a history of glaucoma or age-related macular degeneration were more aware and knowledgeable, but not for subjects who were current and past smokers or alcohol drinkers. For age-related macular degeneration, gender modified the effect between age and knowledge level, while age was a confounder of having medical history, and having heard or awareness, of the disease.

Conclusion:

Despite a larger proportion of the community having heard or awareness since 15 years ago, much effort remains for improving health knowledge of these three eye diseases in Hong Kong. We recommend targeting respondents with higher lifestyle risks, such as current and past smokers or alcohol drinkers, as a focused audience, and utilizing family members, relatives, or friends as another way of distributing health information.
Faculty Perceptions of Certifications in Health Education and Public Health: Implications for Professional Preparation
Authors: Blavos Alexis , Kerr Dianne , Hancher-Rauch Heidi , Brookins-Fisher Jodi , Thompson Amy
Published: July 2020

Leaders in the fields of public health and health education/health promotion have been advocating for required credentialing for almost two decades. Recently, some have questioned whether increasing the number of certified professionals could help better differentiate properly trained health educators and public health professionals from others seeking to fill jobs in this professional area. The purpose of this article is to determine how the CHES/MCHES (Certified Health Education Specialist/Master Certified Health Education Specialist) and CPH (Certified in Public Health) credentials are regarded and promoted within the field of health education/health promotion. A cross-sectional survey research design was employed to determine program directors’ ( N = 90) views of credentialing issues. The health belief model and the transtheoretical model were used to determine perceived barriers, benefits, and self-efficacy with regard to promoting credentialing and readiness to require the CHES or CPH exam as part of the undergraduate curriculum. Ninety undergraduate programs completed the survey with the majority reporting that they do not require credentialing of faculty and students as part of their program of study. More than 70% of respondents, however, indicated that they thought credentialing in the fields of public health and health education/health promotion is an important issue. Most program directors indicated there is value in having students credentialed in health education or public health, yet few programs required the CHES or CPH exam as part of their curriculum or exit assessment. There are opportunities to use credentialing both in assessing program curriculum alignment with competencies and student mastery of said competencies.
A comparison of the persistence, toxicity, and exposure to high-volume natural plant-derived and synthetic pesticides
Authors: Smith Carr J , Perfetti Thomas A
Published: July 2020

The immobility of plants exerted evolutionary selection pressures resulting in the production of thousands of chemical substances thought to function as pesticides against predation by insects and animals. More than 10,000 plant-derived compounds have been isolated with the existence of about 100,000 such compounds postulated. In 1990, Ames et al. reported that 99.99% by weight of the pesticides ingested in a normal human diet are derived from natural plant-based sources. This surprising result raised the question as to whether these natural plant pesticides were toxic to humans. These authors examined a relatively small subset of natural pesticides and determined that their tumorigenicity in rodent cancer bioassays was similar to synthetic pesticides. In this analysis, we used standard United States Environmental Protection Agency programs to estimate the toxicity (T.E.S.T. 4.2) and persistence (EPI Suite 4.1) of a series of high-volume synthetic and natural pesticides. On average, synthetic pesticides were more persistent in the environment than were natural pesticides. This result is consistent with cost, time, and logistical constraints under which farmers apply a limited number of applications of pesticides during a crop cycle. Synthetic and natural pesticides are predicted to possess toxicities including mutagenicity and developmental toxicity. Synthetic pesticides are less often mutagenic.
Physical and mental health impacts of COVID-19 on healthcare workers: a scoping review
Authors: Shaukat Natasha , Ali Daniyal Mansoor , Razzak Junaid
Published: July 2020

Background

Coronavirus disease (COVID-19) pandemic has spread to 198 countries, with approximately 2.4 million confirmed cases and 150,000 deaths globally as of April 18. Frontline healthcare workers (HCWs) face a substantially higher risk of infection and death due to excessive COVID-19 exposure. This review aimed at summarizing the evidence of the physical and mental health impacts of COVID-19 pandemic on health-care workers (HCWs).

Methods

We used the Arksey O’Malley framework to conduct a scoping review. A systematic literature search was conducted using two databases: PubMed and Google Scholar. We found 154 studies, and out of which 10 met our criteria. We collected information on the date of publication, first author’s country, the title of the article, study design, study population, intervention and outcome, and key findings, and divided all research articles into two domains: physical and mental health impact.

Results

We reviewed a total of 154 articles from PubMed (126) and Google Scholar (28), of which 58 were found to be duplicate articles and were excluded. Of the remaining 96 articles, 82 were excluded after screening for eligibility, and 4 articles did not have available full texts. Ten full-text articles were reviewed and included in this study.

Our findings identified the following risk factors for COVID-19-related health impact: working in a high-risk department, diagnosed family member, inadequate hand hygiene, suboptimal hand hygiene before and after contact with patients, improper PPE use, close contact with patients (≥ 12 times/day), long daily contact hours (≥ 15 h), and unprotected exposure. The most common symptoms identified amongst HCWs were fever (85%), cough (70%), and weakness (70%). Prolonged PPE usage led to cutaneous manifestations and skin damage (97%), with the nasal bridge (83%) most commonly affected site. HCWs experienced high levels of depression, anxiety, insomnia, and distress. Female HCWs and nurses were disproportionately affected.

Conclusion

The frontline healthcare workers are at risk of physical and mental consequences directly as the result of providing care to patients with COVID-19. Even though there are few intervention studies, early data suggest implementation strategies to reduce the chances of infections, shorter shift lengths, and mechanisms for mental health support could reduce the morbidity and mortality amongst HCWs.
Predicting DNA binding protein-drug interactions based on network similarity
Authors: Wang Wei , Lv Hehe , Zhao Yuan
Published: July 2020

Background

The study of DNA binding protein (DBP)-drug interactions can open a breakthrough for the treatment of genetic diseases and cancers. Currently, network-based methods are widely used for protein-drug interaction prediction, and many hidden relationships can be found through network analysis. We proposed a DCA (drug-cluster association) model for predicting DBP-drug interactions. The clusters are some similarities in the drug-binding site trimmers with their physicochemical properties. First, DBPs-drug binding sites are extracted from scPDB database. Second, each binding site is represented as a trimer which is obtained by sliding the window in the binding sites. Third, the trimers are clustered based on the physicochemical properties. Fourth, we build the network by generating the interaction matrix for representing the DCA network. Fifth, three link prediction methods are detected in the network. Finally, the common neighbor (CN) method is selected to predict drug-cluster associations in the DBP-drug network model.

Result

This network shows that drugs tend to bind to positively charged sites and the binding process is more likely to occur inside the DBPs. The results of the link prediction indicate that the CN method has better prediction performance than the PA and JA methods. The DBP-drug network prediction model is generated by using the CN method which predicted more accurately drug-trimer interactions and DBP-drug interactions. Such as, we found that Erythromycin (ERY) can establish an interaction relationship with HTH-type transcriptional repressor, which is fitted well with silico DBP-drug prediction.

Conclusion

The drug and protein bindings are local events. The binding of the drug-DBPs binding site represents this local binding event, which helps to understand the mechanism of DBP-drug interactions.
Clonal evolution driven by superdriver mutations
Authors: Grossmann Patrick , Cristea Simona , Beerenwinkel Niko
Published: July 2020

Background

Tumors are widely recognized to progress through clonal evolution by sequentially acquiring selectively advantageous genetic alterations that significantly contribute to tumorigenesis and thus are termned drivers. Some cancer drivers, such as TP53 point mutation or EGFR copy number gain, provide exceptional fitness gains, which, in time, can be sufficient to trigger the onset of cancer with little or no contribution from additional genetic alterations. These key alterations are called superdrivers.

Results

In this study, we employ a Wright-Fisher model to study the interplay between drivers and superdrivers in tumor progression. We demonstrate that the resulting evolutionary dynamics follow global clonal expansions of superdrivers with periodic clonal expansions of drivers. We find that the waiting time to the accumulation of a set of superdrivers and drivers in the tumor cell population can be approximated by the sum of the individual waiting times.

Conclusions

Our results suggest that superdriver dynamics dominate over driver dynamics in tumorigenesis. Furthermore, our model allows studying the interplay between superdriver and driver mutations both empirically and theoretically.
Effects of HTR1B 3′ region polymorphisms and functional regions on gene expression regulation
Authors: Xia Xi , Ding Mei , Xuan Jin-feng , Xing Jia-xin , Pang Hao , Yao Jun , Wu Xue , Wang Bao-jie
Published: July 2020

Background

The HTR1B gene encodes the 5-hydroxytryptamine (5-HT1B) receptor, which is involved in a variety of brain activities and mental disorders. The regulatory effects of non-coding regions on genomic DNA are one of many reasons for the cause of genetic-related diseases. Post-transcriptional regulation that depends on the function of 3′ regulatory regions plays a particularly important role. This study investigated the effects, on reporter gene expression, of several haplotypes of the HTR1B gene (rs6297, rs3827804, rs140792648, rs9361234, rs76194807, rs58138557, and rs13212041) and truncated fragments in order to analyze the function of the 3′ region of HTR1B.

Results

We found that the haplotype, A-G-Del-C-T-Ins-A, enhanced the expression level compared to the main haplotype; A-G-Del-C-G-Ins-A; G-G-Del-C-G-Ins-G decreased the expression level. Two alleles, rs76194807T and rs6297G, exhibited different relative luciferase intensities compared to their counterparts at each locus. We also found that + 2440 ~ + 2769 bp and + 1953 ~ + 2311 bp regions both had negative effects on gene expression.

Conclusions

The 3′ region of HTR1B has a regulatory effect on gene expression, which is likely closely associated with the interpretation of HTR1B-related disorders. In addition, the HTR1B 3′ region includes several effector binding sites that induce an inhibitory effect on gene expression.
Genomics of sex allocation in the parasitoid wasp Nasonia vitripennis
Authors: Pannebakker Bart A. , Cook Nicola , van den Heuvel Joost , van de Zande Louis , Shuker David M.
Published: July 2020

Background

Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the best studied organism in terms of sex allocation, and well known for its response to local mate competition.

Results

We performed a genome-wide association study (GWAS) for single foundress sex ratios using iso-female lines derived from the recently developed outbred N. vitripennis laboratory strain HVRx. The iso-female lines capture a sample of the genetic variation in HVRx and we present them as the first iteration of the Nasonia vitripennis Genome Reference Panel (NVGRP 1.0). This panel provides an assessment of the standing genetic variation for sex ratio in the study population. Using the NVGRP, we discovered a cluster of 18 linked SNPs, encompassing 9 annotated loci associated with sex ratio variation. Furthermore, we found evidence that sex ratio has a shared genetic basis with clutch size on three different chromosomes.

Conclusions

Our approach provides a thorough description of the quantitative genetic basis of sex ratio variation in Nasonia at the genome level and reveals a number of inter-related candidate loci underlying sex allocation regulation.
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome
Authors: Le Vuong , Quinn Thomas P. , Tran Truyen , Venkatesh Svetha
Published: July 2020

Background

Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure their relative abundance. In this paper, we propose a sparse neural encoder-decoder network to predict metabolite abundances from microbe abundances.

Results

Using paired data from a cohort of inflammatory bowel disease (IBD) patients, we show that our neural encoder-decoder model outperforms linear univariate and multivariate methods in terms of accuracy, sparsity, and stability. Importantly, we show that our neural encoder-decoder model is not simply a black box designed to maximize predictive accuracy. Rather, the network’s hidden layer (i.e., the latent space, comprised only of sparsely weighted microbe counts) actually captures key microbe-metabolite relationships that are themselves clinically meaningful. Although this hidden layer is learned without any knowledge of the patient’s diagnosis, we show that the learned latent features are structured in a way that predicts IBD and treatment status with high accuracy.

Conclusions

By imposing a non-negative weights constraint, the network becomes a directed graph where each downstream node is interpretable as the additive combination of the upstream nodes. Here, the middle layer comprises distinct microbe-metabolite axes that relate key microbial biomarkers with metabolite biomarkers. By pre-processing the microbiome and metabolome data using compositional data analysis methods, we ensure that our proposed multi-omics workflow will generalize to any pair of -omics data. To the best of our knowledge, this work is the first application of neural encoder-decoders for the interpretable integration of multi-omics biological data.
Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica
Authors: Chen Yangan , Klinkhamer Peter G. L. , Memelink Johan , Vrieling Klaas
Published: July 2020

Background

Collectively, plants produce a huge variety of secondary metabolites (SMs) which are involved in the adaptation of plants to biotic and abiotic stresses. The most characteristic feature of SMs is their striking inter- and intraspecific chemical diversity. Cytochrome P450 monooxygenases (CYPs) often play an important role in the biosynthesis of SMs and thus in the evolution of chemical diversity. Here we studied the diversity and evolution of CYPs of two Jacobaea species which contain a characteristic group of SMs namely the pyrrolizidine alkaloids (PAs).

Results

We retrieved CYPs from RNA-seq data of J. vulgaris and J. aquatica, resulting in 221 and 157 full-length CYP genes, respectively. The analyses of conserved motifs confirmed that Jacobaea CYP proteins share conserved motifs including the heme-binding signature, the PERF motif, the K-helix and the I-helix. KEGG annotation revealed that the CYPs assigned as being SM metabolic pathway genes were all from the CYP71 clan but no CYPs were assigned as being involved in alkaloid pathways. Phylogenetic analyses of full-length CYPs were conducted for the six largest CYP families of Jacobaea (CYP71, CYP76, CYP706, CYP82, CYP93 and CYP72) and were compared with CYPs of two other members of the Asteraceae, Helianthus annuus and Lactuca sativa, and with Arabidopsis thaliana. The phylogenetic trees showed strong lineage specific diversification of CYPs, implying that the evolution of CYPs has been very fast even within the Asteraceae family. Only in the closely related species J. vulgaris and J. aquatica, CYPs were found often in pairs, confirming a close relationship in the evolutionary history.

Conclusions

This study discovered 378 full-length CYPs in Jacobaea species, which can be used for future exploration of their functions, including possible involvement in PA biosynthesis and PA diversity.
The kinematics and strategies of recovery steps during lateral losses of balance in standing at different perturbation magnitudes in older adults with varying history of falls
Authors: Batcir Shani , Shani Guy , Shapiro Amir , Alexander Neil , Melzer Itshak
Published: July 2020

Background

Step-recovery responses are critical in preventing falls when balance is lost unexpectedly. We investigated the kinematics and strategies of balance recovery in older adults with a varying history of falls.

Methods

In a laboratory study, 51 non-fallers (NFs), 20 one-time fallers (OFs), and 12 recurrent-fallers (RFs) were exposed to random right/left unannounced underfoot perturbations in standing of increasing magnitude. The stepping strategies and kinematics across an increasing magnitude of perturbations and the single- and multiple-step threshold trials, i.e., the lowest perturbation magnitude to evoke single step and multiple steps, respectively, were analyzed. Fall efficacy (FES) and self-reported lower-extremity function were also assessed.

Results

OFs had significantly lower single- and multiple-step threshold levels than NFs; the recovery-step kinematics were similar. Surprisingly, RFs did not differ from NFs in either threshold. The kinematics in the single-step threshold trial in RFs, however, showed a significant delay in step initiation duration, longer step duration, and larger center of mass (CoM) displacement compared with NFs and OFs. In the multiple-step threshold trial, the RFs exhibited larger CoM displacements and longer time to fully recover from balance loss. Interestingly, in the single-stepping trials, 45% of the step-recovery strategies used by RFs were the loaded-leg strategy, about two times more than OFs and NFs (22.5 and 24.2%, respectively). During the multiple-stepping trials, 27.3% of the first-step recovery strategies used by RFs were the loaded-leg strategy about two times more than OFs and NFs (11.9 and 16.4%, respectively), the crossover stepping strategy was the dominated response in all 3 groups (about 50%). In addition, RFs reported a lower low-extremity function compared with NFs, and higher FES in the OFs.

Conclusions

RFs had impaired kinematics during both single-step and multiple-step recovery responses which was associated with greater leg dysfunction. OFs and NFs had similar recovery-step kinematics, but OFs were more likely to step at lower perturbation magnitudes suggesting a more “responsive” over-reactive step response related from their higher fear of falling and not due to impaired balance abilities. These data provide insight into how a varying history of falls might affect balance recovery to a lateral postural perturbation.

Trial registration

This study was registered prospectively on November 9th, 2011 at clinicaltrials.gov (NCT01439451).