bluuebunny/crossref_metadata_2025 huggingface dataset:
Early home-based pulmonary rehabilitation following acute exacerbation of COPD: A feasibility study using an action research approach
Authors: Wageck Bruna , Cox Narelle S , Bondarenko Janet , Corbett Monique , Nichols Amanda , Moore Rosemary , Holland Anne E
Published: August 2020

Objective:

Pulmonary rehabilitation (PR) improves function, reduces symptoms and decreases healthcare usage in people with chronic obstructive pulmonary disease (COPD) following an acute exacerbation (AECOPD). However, rehabilitation uptake rates are low. This study aimed to address barriers to uptake and completion of PR following AECOPD.

Methods:

An action research approach was used to reflect on study feasibility, and to plan and implement an improved protocol. Phase I tested the feasibility of home-based PR started early after AECOPD. Phase II used qualitative interviews to identified potential barriers to program uptake. Phase III re-tested the program with changes to recruitment and assessment strategies.

Results:

Phase I: From 97 screened patients, 26 were eligible and 10 (38%) started home-based PR. Eight participants undertook ≥70% of PR sessions, achieving clinically meaningful improvement in 6-minute walk distance (mean (SD) change 76 (60) m) and chronic respiratory disease questionnaire total score (15 (21) units). Phase II: Potential barriers to uptake of home-based PR included access issues, confidence to exercise, and lack of information about PR benefits. Phase III: From 77 screened patients, 23 were eligible and 5 (22%) started the program.

Discussion:

Home-based PR improved clinical outcomes, but program eligibility and uptake remain challenging. Efforts should be made to ensure PR program eligibility criteria are broad enough to accommodate patient needs, and new ways of engaging patients are needed to improve PR uptake after AECOPD.
Recommendations From Black Sexual Minority Men: Building Trust to Improve Engagement and Impact of HIV/STI Research
Authors: Grieb Suzanne M. , Jackman Kevon-Mark , Tilchin Carla , Clark Charles , Sawyer Simone ,   USHINE Community Advisory Board, Rives Sarah , Childs LaNisha , Jennings Jacky M.
Published: August 2020

As demonstrated by the consistently documented disproportionately high rates of HIV and STIs (sexually transmitted infections) among Black sexual minority men (BSMM), current efforts to develop responsive interventions to reduce HIV and other STIs within this population have not been sufficient. It is therefore critical that public health researchers reflect meaningfully on the ways in which they investigate HIV and STIs. Engagement with BSMM is crucial in addressing the disproportionately high rates of HIV and STIs experienced, and thus the goal of the current research was to identify community-developed strategies that may enhance community engagement in research with BSMM. Seven focus groups ( N = 38) were held with cisgender BSMM ages 18 to 45 years in Baltimore, Maryland to explore how to better engage this population and improve HIV and STI research. Data analysis of the text was conducted using an iterative, thematic constant comparison process informed by grounded theory. Four distinct themes related to trust-building within the broader community emerged: (1) authentic engagement with the community, (2) increased transparency of the research process, (3) capacity building of research staff from the community, and (4) a balance of research and action. Strategies for researchers to build community trust were identified that are related to, but slightly distinct from, common discussions in the community engaged research literature that are centered more specifically on trust-building within community–academic partnerships. Engagement with BSMM is crucial in addressing HIV and STI health disparities. It is critical that community engagement also be a priority to policy makers, research institutions, and funding institutions.
The Health Equity Framework: A Science- and Justice-Based Model for Public Health Researchers and Practitioners
Authors: Peterson Amy , Charles Vignetta , Yeung David , Coyle Karin
Published: August 2020

In this article, we describe a science- and justice-based framework for promoting health equity designed for researchers and practitioners working across public health and social science fields. We developed the health equity framework (HEF; etr.org/healthequityframework ) in two phases of iterative development. Building on existing models, the HEF illustrates how health outcomes are influenced by complex interactions between people and their environments. The framework centers on three foundational concepts: equity at the core of health outcomes; multiple, interacting spheres of influence; and a historical and life-course perspective. Health equity is defined as having the personal agency and fair access to resources and opportunities needed to achieve the best possible physical, emotional, and social well-being. By centering population outcomes, the HEF encourages researchers and practitioners to think beyond traditional approaches that focus on individual behaviors and choices to assess and identify their gaps in acknowledging and addressing factors from multiple spheres of influence. We identified four, interacting spheres of influence that represent both categories of risk and protective factors for health outcomes as well as opportunities for strategies and interventions that address those factors. The HEF highlights the explicit and implicit interactions of multilevel influences on health outcomes and emphasizes that health inequities are the result of cumulative experiences across the life span and generations. The HEF is a practical tool for leaders and professionals in public health research and practice to reflect on and support a shift toward addressing health inequities resulting from the interplay of structural, relational, individual, and physiological factors.
Decreased Preoperative Estimated Glomerular Filtration Rate Was Related With Poor Prognosis of NSCLC Patients
Authors: Jia Wenqiao , Wang Cong , Cheng Yufeng
Published: August 2020

(1) Background:

The coexistence of chronic kidney disease (CKD) and cancer is common due to the increased incidence of cancer in patients with CKD. Glomerular filtration rate is the optimal way to measure kidney function. To date, little is known about the role preoperative renal function plays in the prognosis of NSCLC patients.

(2) Methods:

The study enrolled 140 patients who had been newly diagnosed NSCLC and received potential radical surgery for treatment from 2009 January to 2012 December. The detailed characteristics were collected including gender, age, smoking and drinking habits, KPS score, hemoglobin levels, tumor size, pathology type, differentiation, pTNM stage and serum creatinine before surgery. Univariate and multivariate analyses of overall survival (OS) and disease-free survival (DFS) were performed using Kaplan-Meier method and Cox model.

(3) Results:

The univariate analysis identified that the pTNM stage ( p < 0.001), eGFR level ( p = 0.006), and adjuvant treatment ( p = 0.007) were prognostic factors for OS, while drinking habit ( p = 0.032), pTNM stage ( p = 0.002) and eGFR level ( p = 0.006) were the prognostic factors for DFS. Further multivariate analysis found that pTNM stage (HR = 2.091, 95% CI 1.424-3.071; p < 0.001) and eGFR level (HR = 1.890, 95% CI 1.424-3.071; p = 0.004) were independent factors associated with OS. The pTNM stage (HR = 1.735, CI 1.215-2.479; p = 0.002) and eGFR (HR = 1.793, CI 1.193-2.696; p = 0.005) were independent factors associated with DFS. Further subgroup analyses found that in female patients/ no smoking patients/ patients younger than 60 years, better eGFR level was significantly associated with better OS and DFS.

(4) Conclusions:

Decreased preoperative eGFR was associated with poor clinical outcome of NSCLC patients.
Experimental investigation on shear properties of warp-knitted brush fabrics
Authors: Chu Yao , Lin Haitao , Jamshaid Hafsa , Zhang Qi , Ma Pibo
Published: August 2020

Warp-knitted brush fabrics are composed of an outer surface formed by weaving the front and rear needle beds with spacer yarns interposed between them. Warp-knitted brush fabrics can be used as a non-slip cover for car seat cushions; the adhesion between non-slip fabric and car seat is related to the shear strength of warp-knitted brush fabrics. In this article, to study the factors affecting the shear force of warp-knitted brush fabrics, three different processing methods and four different stretching speed intervals were used to find the effects of stiffeners and action of different speed intervals on shear properties of fabrics. The experimental results show that the stiffener treatment can improve the shear resistance of the warp-knitted brush fabrics, and the effect of different speed intervals can affect the shear resistance of fabrics. These findings will have a guiding significance in the design and production of warp-knitted brush fabrics applied to fabrics such as car seat cushions, and the results can also help to study the shear properties of warp-knitted brush fabrics for wider applications.
A potential prognostic marker in primitive lung neuroendocrine tumor: A case report
Authors: Russo Luigi , Grilli Bruna , Minopoli Anita , Capozzi Monica , Tafuto Salvatore , Correra Marco , Trillò Giusy , Isgrò Maria Antonietta , Cavalcanti Ernesta
Published: August 2020

Background:

The diagnosis and monitoring of primitive lung neuroendocrine tumors (lung pNETs) are usually performed by the measurement of serum chromogranin A (CgA) and urinary 5-hydroxyindolacetic acid (5-HIAA) levels. However, imaging techniques are necessary due to the poor diagnostic efficiency of the laboratory tests.

Methods:

A total-body computed tomography and bone scintigraphy scans showed multiple hepatic and bone metastases of a 55-year-old man affected by well-differentiated lung pNETs without severe initial symptoms. After diagnosis, he started therapy and was monitored with serum, urinary markers, and imaging techniques.

Results:

During follow-up, the urinary 5-HIAA levels did not significantly increase, while serum CgA and urinary para-hydroxyphenylacetic acid (pHPAA) levels (urinary organic acid physiologically present in the urines of healthy subjects) showed significant increases related to worsening clinical condition.

Conclusions:

The early increase in urinary pHPAA levels—usually not dosed in pNET patient monitoring—could be a promising prognostic marker.
From Zero to a National Data Set in 2 Weeks: Reflections on a COVID-19 Collaborative Survey Project
Authors: Hargittai Eszter , Nguyen Minh Hao , Fuchs Jaelle , Gruber Jonathan , Marler Will , Hunsaker Amanda , Karaoglu Gökçe
Published: August 2020

In March 2020, like much of the rest of the world, we went into lockdown. A week into our new reality, we decided to do a survey study about how people were experiencing the COVID-19 pandemic. In this piece, we describe what motivated us to do the study, how we went about it, and what others can learn from our experiences.
Differences in clinical characteristics of early- and late-onset neonatal sepsis caused by Klebsiella pneumoniae
Authors: You Ting , Zhang Han , Guo Lu , Ling Ke-Ran , Hu Xiao-Yu , Li Lu-Quan
Published: August 2020

To identify differences in the clinical characteristics of early- and late-onset sepsis (EOS and LOS) caused by Klebsiella pneumoniae ( K. pneumoniae) and to describe the risk factors for multidrug-resistant K. pneumoniae (MDR-KP) infection. Infants with K. pneumoniae-induced sepsis who were admitted to a children’s Hospital between Jan 2000 and Dec 2019 were included. All infants were divided into EOS and LOS groups, as well as MDR-KP and non-MDR-KP groups. Demographics, clinical characteristics, and risk factors were compared between the two groups. One hundred eighty infants (66 with EOS and 114 with LOS) were further analyzed, accounting for 36.8% of sepsis cases caused by MDR-KP. The frequency of respiratory failure, bronchopulmonary dysplasia, and intraventricular hemorrhage were more common in the LOS group and a higher rate of acute respiratory distress syndrome was more common in infants in the EOS group ( P < 0.05). K. pneumoniae showed a low sensitivity to penicillin, beta-lactams and cephalosporins, and it showed a high sensitivity to levofloxacin, ciprofloxacin, and amikacin. Prematurity, low birth weight, longer antibiotic exposure time, long duration of peripheral catheter insertion, long mechanical ventilation time, and long parenteral nutrition time were associated with an increased rate of MDR-KP infection by univariate analysis ( P < 0.05). The regression analysis identified a long antibiotic exposure time (OR = 1.37, 95% CI: 1.01–1.89) and long parenteral nutrition time (OR = 1.39, 95% CI: 1.01–1.89) as independent risk factors for a MDR-KP infection, and a greater gestational age and birth weight were associated with a lower risk of MDR-KP infection (OR = 0.57, 95% CI: 0.40–0.79). LOS caused by K. pneumoniae may lead to a higher frequency of complications. The risk factors for MDR-KP infection were longer duration of antibiotic exposure and parenteral nutrition. A greater gestational age and larger birth weight may decrease the risk of MDR-KP infection.
Financial Strain and Psychological Distress: Do Strains in the Work-Family Interface Mediate the Effects?
Authors: Chai Lei , Schieman Scott , Bierman Alex
Published: August 2020

Analyzing three waves of the Canadian Work Stress and Health Study with cross-lagged models, we asked: (1) How do two distinct directions of strain in the work-family interface—work-to-family conflict and family-to-work conflict—mediate the relationship between financial strain and psychological distress? and (2) Is reverse causality a possibility in these dynamics? Our results indicate that work-to-family conflict at Wave 2 mediates the relationship between financial strain at Wave 1 and distress at Wave 3, but family-to-work conflict does not function as a mediator. Financial strain is therefore indirectly associated with subsequently higher levels of distress. In tests for reverse causality, we found little evidence that distress is associated with subsequently higher levels of financial strain—and neither work-to-family conflict nor family-to-work conflict at Wave 2 mediates that relationship. We interpret our findings within the conceptual and empirical ideas associated with stress proliferation, social causation, and social selection/drift.
“Shot to the Heart”: Case Report and Concise Review of Cardiac Gunshot Injury
Authors: Kawall Tiffany , Seecheran Rajeev Virender , Seecheran Valmiki Krishna , Persad Sangeeta Anjali , Jagdeo Cathy-Lee , Seecheran Naveen Anand
Published: August 2020

Penetrative cardiac injury can often result in life-threatening sequelae such as myocardial contusion or rupture, coronary vessel and valvular damage, pericardial effusion with tamponade, and arrhythmias of which gunshot injury is a chief culprit. We report a case of a suspected acute coronary syndrome after a cardiac gunshot injury that was conservatively managed.
The Oncology Family Forum: Collaborating With Families to Codesign Pediatric Oncology Services
Authors: Radford Claire , Slater Penelope J , Fielden Philippa
Published: August 2020

The Oncology Services Group at Queensland Children’s Hospital established an Oncology Family Forum in 2018 to enable codesign of service improvements. A total of 26 family members attended the first 4 Forums, with between 12 and 15 attendees at each. Attendees represented a range of diagnoses, were 85% female, 85% resided within 40 km of the tertiary center, and 26% were on-treatment. In a survey of attendees, 83% agreed that the Forum had improved families’ service experience and 92% supported the codesign partnership and the exploration of their suggestions. A small proportion (25%) of attendees disagreed that there was enough time to share, 17% disagreed that all their questions were answered, and 17% disagreed that the Forum represented views of regional families. Respondents identified collaboration, improving understanding and communication as positive aspects of the Forums. Forums will continue to be offered regularly, augmented by videoconferencing (particularly during the COVID-19 pandemic), written responses to family questions and special interest discussion groups. The new collaborations and programs that have been initiated, codesigned, and progressed through these Forums will continue to be the focus of service delivery and quality improvements.
Inequality, Familial Aggregation, and Risk Prediction of Caries in Siblings
Authors: Sengupta K. , Ersbøll A.K. , Christensen L.B. , Mortensen L.H. , Andersen I.
Published: August 2020

Introduction:

Social and family conditions are likely of great importance to dental health; however, limited evidence of familial aggregation of caries among adolescent siblings exists. Moreover, social and family-level factors have never been evaluated as isolated caries predictors at the individual level.

Objectives:

The objectives were to evaluate socioeconomic patterning of caries among siblings, assess sibling-specific aggregation of caries within families, and examine if such aggregation differed by parental socioeconomic position (SEP). We also evaluated the discriminant ability of sibling caries, SEP, and other social and familial factors in predicting caries in cosiblings.

Methods:

This nationwide register-based study included all 15-y-olds in Denmark in 2003 (index siblings) and their biological siblings born within ±3 y (cosiblings). Clinical and sociodemographic data for each subject were compiled from Danish national dental, social, and population registers. Caries was measured by the decayed, missing, and filled tooth surfaces (DMFS) index. Predictors included SEP (parental education, income, and occupational social class), gender, birth order, immigration status, and household type. Adjusted SEP-caries associations were estimated using negative binomial regression. Familial aggregation was evaluated using adjusted pairwise odds ratios from alternating logistic regressions. Caries prediction was based on classification and regression tree (CART) analyses.

Results:

The study included 23,847 sibling pairs (n = 47,694). Socioeconomic patterning of caries was similar among the index and cosiblings with significant graded SEP-caries associations. Significant sibling-specific aggregation of caries was observed; cosiblings of caries-affected index siblings had odds of having caries 3.9 times (95% confidence interval: 3.65–4.18) as high as that of cosiblings with caries-free index siblings. This sibling similarity was stronger in socioeconomically disadvantaged families (adjusted pairwise odds ratios: 3.08–5.47). CART revealed index sibling caries as the single most important caries predictor, with caries predicted in ≥84% of cosiblings of adolescents with ≥3 carious tooth surfaces.

Conclusions:

Caries in a sibling should prompt preventive family-based approaches targeting cosiblings.

Knowledge Transfer Statement:

This study revealed significant socioeconomic patterning of caries in adolescent siblings. Prediction modeling indicated that the single most important caries predictor among cosiblings was index sibling caries. Information on sibling caries level should be routinely combined with clinical evaluation to identify children at risk. Moreover, information on social and family conditions should be used to target prevention and health promotion at the school or municipal level. These approaches could possibly contribute to reducing the existing caries inequalities.
Light Trapping Induced High Short-Circuit Current Density in III-Nitride Nanorods/Si (111) Heterojunction Solar Cells
Authors: Chang Ching-Wen , Wadekar Paritosh V. , Huang Hui-Chun , Chen Quark Yung-Sung , Wu Yuh-Renn , Chen Ray T. , Tu Li-Wei
Published: August 2020

An effective-area photovoltaic efficiency of 1.27% in power conversion, excluding the grid metal contact area and under 1 sun, AM 1.5G conditions, has been obtained for the p-GaN/i-InGaN/n-GaN diode arrays epitaxially grown on (111)-Si. The short-circuit current density is 14.96 mA/cm2 and the open-circuit voltage is 0.28 V. Enhanced light trapping acquired via multiple reflections within the strain and defect free III-nitride nanorod array structures and the short-wavelength responses boosted by the wide bandgap III-nitride constituents are believed to contribute to the observed enhancements in device performance.
A fatal fecaloma
Authors: Logre Elsa , Degravi Lauriane , Plantefève Gaëtan , Contou Damien
Published: August 2020

Background

Fecal impaction may complicate chronic constipation. We report a fatal case of fecal impaction in a patient treated with long-term neuroleptic treatment.

Case presentation

A 70-year-old man with a history of severe chronic psychosis treated with olanzapine was admitted to the emergency department for acute abdominal pain and increased abdominal perimeter. Abdominal computed tomography revealed a severe fecal impaction with no sign of peritonitis or acute mesenteric ischemia. The patient eventually died from multi-organ failure 2 days after his admission to the intensive care unit.

Conclusions

Chronic constipation with fecal impaction is a well-known complication of long-term neuroleptic treatment. Severe forms may be life-threatening. Prevention with systematic administration of laxatives appears of paramount importance.
Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome
Authors: Druet Tom , Legarra Andres
Published: August 2020

Background

X-chromosomal loci present different inheritance patterns compared to autosomal loci and must be modeled accordingly. Sexual chromosomes are not systematically considered in whole-genome relationship matrices although rules based on genealogical or marker information have been derived. Loci on the X-chromosome could have a significant contribution to the additive genetic variance, in particular for some traits such as those related to reproduction. Thus, accounting for the X-chromosome relationship matrix might be informative to better understand the architecture of complex traits (e.g., by estimating the variance associated to this chromosome) and to improve their genomic prediction. For such applications, previous studies have shown the benefits of combining information from genotyped and ungenotyped individuals.

Results

In this paper, we start by presenting rules to compute a genomic relationship matrix (GRM) for the X-chromosome (GX) without making any assumption on dosage compensation, and based on coding of gene content with 0/1 for males and 0/1/2 for females. This coding adjusts naturally to previously derived pedigree-based relationships (S) for the X-chromosome. When needed, we propose to accommodate and estimate dosage compensation and genetic heterogeneity across sexes via multiple trait models. Using a Holstein dairy cattle dataset, including males and females, we then empirically illustrate that realized relationships (GX) matches expectations (S). However, GX presents high deviations from S. GX has also a lower dimensionality compared to the autosomal GRM. In particular, individuals are frequently identical along the entire chromosome. Finally, we confirm that the heritability of gene content for markers on the X-chromosome that are estimated by using S is 1, further demonstrating that S and GX can be combined. For the pseudo-autosomal region, we demonstrate that the expected relationships vary according to position because of the sex-gradient. We end by presenting the rules to construct the 'H matrix’ by combining both relationship matrices.

Conclusions

This work shows theoretically and empirically that a pedigree-based relationship matrix built with rules specifically developed for the X-chromosome (S) matches the realized GRM for the X-chromosome. Therefore, applications that combine expected relationships and genotypes for markers on the X-chromosome should use S and GX.
Response of the gut microbiota during the Clostridioides difficile infection in tree shrews mimics those in humans
Authors: Gu Wenpeng , Li Wenge , Wang Wenguang , Kuang Dexuan , Zhang Wenzhu , Lu Caixia , Li Na , Tong Pinfen , Han Yuanyuan , Sun Xiaomei , Lu Jinxing , Wu Yuan , Dai Jiejie
Published: August 2020

Background

Clostridioides difficile is a major cause of antibiotic associated diarrhea. Several animal models are used to study C. difficile infection (CDI). The tree shrew has recently been developed as a model of primate processes. C. difficile infection has not been examined in tree shrews. We infected tree shrews with hyper-virulent C. difficile strains and examined the alterations in gut microbiota using 16S rRNA gene sequencing.

Results

C. difficile colonized the gastrointestinal tract of tree shrew and caused diarrhea and weight loss. Histopathologic examination indicated structures and mucosal cell destruction in ileal and colonic tissues. The gut microbial community was highly diversity before infection and was dominated by Firmicutes, Fusobacteria, Bacteroidetes, and Proteobacteria. Antibiotic administration decreased the diversity of the gut microbiota and led to an outgrowth of Lactobacillus. The relative abundance of Proteobacteria, Gammaproteobacteria, Enterobacteriales, Lachnospiraceae, Enterobacteriaceae, Escherichia, Blautia, and Tyzzerella increased following C. difficile infection. These taxa could be biomarkers for C. difficile colonization.

Conclusions

In general, the disease symptoms, histopathology, and gut microbiota changes following C. difficile infection in tree shrews were similar to those observed in humans.
Case report: the first case of unilateral retinal pigment epithelium dysgenesis in China
Authors: Ding Yuhua , Yao Bangtao , Xie Keren , Ye Hui , Yu Yan
Published: August 2020

Background

Unilateral retinal pigment epithelium dysgenesis (URPED) is a rare condition and is characterized by a unilateral and solitary lesion in the peripapillary region. The lesion presents with central atrophy, peripheral fibrosis, and hyperplastic changes in the retinal pigment epithelium (RPE). Herein, we report the first case of URPED in a Chinese individual using multimodal imaging techniques such as en-face optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA).

Case presentation

A 10-year-old girl presented with 20/40 vision in her left eye. Presented as a solitary, unilateral, large and yellowish-white lesion, with fringe-like margins was observed in the posterior pole and lower middle periphery of the left eye continuous with the optic nerve, indicated URPED. Infrared fundal (IR) images showed that the fringe-like contour of the lesion was visible, with diffuse hyperreflective signals specifically in the fovea, while with peripheral dark spots, having a typical leopard-spot like appearance. Fundus autofluorescence (FAF) revealed a markedly scalloped lesion containing a hypoautofluorescence area mixed with an isoautofluorescence area. Spectral-domain optical coherence tomography (SD-OCT) revealed the outer segments of photoreceptors presented with an inhomogeneous signal in the fovea, with a weak local signal. The ellipsoid and interdigitation zones were thinner than normal, while the RPE/Bruch’s complex was not flat, with locally visible protrusions. En-face OCT image at the level of the RPE zone showed a mottled hyperreflective signal with peripheral hyporeflective spots, fringe-like margin lesions. OCTA of the avascular area of the fovea in the superficial, deep, and outer retinal layers appeared to be oval in shape, the choroid capillary layer revealed an increase in the density of the choroidal vasculature in the fovea.

Conclusions

This is the first report on URPED in China. Both en-face OCT and OCTA were essential in observing and studying the disease. Further investigation is required to better define the en-face OCT and OCTA features of URPED and clarify the disease characteristics and prognosis.
Using autoencoders as a weight initialization method on deep neural networks for disease detection
Authors: Ferreira Mafalda Falcão , Camacho Rui , Teixeira Luís F.
Published: August 2020

Background

As of today, cancer is still one of the most prevalent and high-mortality diseases, summing more than 9 million deaths in 2018. This has motivated researchers to study the application of machine learning-based solutions for cancer detection to accelerate its diagnosis and help its prevention. Among several approaches, one is to automatically classify tumor samples through their gene expression analysis.

Methods

In this work, we aim to distinguish five different types of cancer through RNA-Seq datasets: thyroid, skin, stomach, breast, and lung. To do so, we have adopted a previously described methodology, with which we compare the performance of 3 different autoencoders (AEs) used as a deep neural network weight initialization technique. Our experiments consist in assessing two different approaches when training the classification model — fixing the weights after pre-training the AEs, or allowing fine-tuning of the entire network — and two different strategies for embedding the AEs into the classification network, namely by only importing the encoding layers, or by inserting the complete AE. We then study how varying the number of layers in the first strategy, the AEs latent vector dimension, and the imputation technique in the data preprocessing step impacts the network’s overall classification performance. Finally, with the goal of assessing how well does this pipeline generalize, we apply the same methodology to two additional datasets that include features extracted from images of malaria thin blood smears, and breast masses cell nuclei. We also discard the possibility of overfitting by using held-out test sets in the images datasets.

Results

The methodology attained good overall results for both RNA-Seq and image extracted data. We outperformed the established baseline for all the considered datasets, achieving an average F1 score of 99.03, 89.95, and 98.84 and an MCC of 0.99, 0.84, and 0.98, for the RNA-Seq (when detecting thyroid cancer), the Malaria, and the Wisconsin Breast Cancer data, respectively.

Conclusions

We observed that the approach of fine-tuning the weights of the top layers imported from the AE reached higher results, for all the presented experiences, and all the considered datasets. We outperformed all the previous reported results when comparing to the established baselines.
Extreme mobility of the world’s largest flying mammals creates key challenges for management and conservation
Authors: Welbergen Justin A. , Meade Jessica , Field Hume E. , Edson Daniel , McMichael Lee , Shoo Luke P. , Praszczalek Jenny , Smith Craig , Martin John M.
Published: August 2020

Background

Effective conservation management of highly mobile species depends upon detailed knowledge of movements of individuals across their range; yet, data are rarely available at appropriate spatiotemporal scales. Flying-foxes (Pteropusspp.) are large bats that forage by night on floral resources and rest by day in arboreal roosts that may contain colonies of many thousands of individuals. They are the largest mammals capable of powered flight, and are highly mobile, which makes them key seed and pollen dispersers in forest ecosystems. However, their mobility also facilitates transmission of zoonotic diseases and brings them in conflict with humans, and so they require a precarious balancing of conservation and management concerns throughout their Old World range. Here, we analyze the Australia-wide movements of 201 satellite-tracked individuals, providing unprecedented detail on the inter-roost movements of three flying-fox species:Pteropus alecto,P.poliocephalus, andP.scapulatusacross jurisdictions over up to 5 years.

Results

Individuals were estimated to travel long distances annually among a network of 755 roosts (P.alecto, 1427–1887 km;P.poliocephalus, 2268–2564 km; andP.scapulatus, 3782–6073 km), but with little uniformity among their directions of travel. This indicates that flying-fox populations are composed of extremely mobile individuals that move nomadically and at species-specific rates. Individuals of all three species exhibited very low fidelity to roosts locally, resulting in very high estimated daily colony turnover rates (P.alecto, 11.9 ± 1.3%;P.poliocephalus, 17.5 ± 1.3%; andP.scapulatus, 36.4 ± 6.5%). This indicates that flying-fox roosts form nodes in a vast continental network of highly dynamic “staging posts” through which extremely mobile individuals travel far and wide across their species ranges.

Conclusions

The extreme inter-roost mobility reported here demonstrates the extent of the ecological linkages that nomadic flying-foxes provide across Australia’s contemporary fragmented landscape, with profound implications for the ecosystem services and zoonotic dynamics of flying-fox populations. In addition, the extreme mobility means that impacts from local management actions can readily reverberate across jurisdictions throughout the species ranges; therefore, local management actions need to be assessed with reference to actions elsewhere and hence require national coordination. These findings underscore the need for sound understanding of animal movement dynamics to support evidence-based, transboundary conservation and management policy, tailored to the unique movement ecologies of species.
Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling
Authors: Dawa Jeanette , Emukule Gideon O. , Barasa Edwine , Widdowson Marc Alain , Anzala Omu , van Leeuwen Edwin , Baguelin Marc , Chaves Sandra S. , Eggo Rosalind M.
Published: August 2020

Background

There is substantial burden of seasonal influenza in Kenya, which led the government to consider introducing a national influenza vaccination programme. Given the cost implications of a nationwide programme, local economic evaluation data are needed to inform policy on the design and benefits of influenza vaccination. We set out to estimate the cost-effectiveness of seasonal influenza vaccination in Kenya.

Methods

We fitted an age-stratified dynamic transmission model to active surveillance data from patients with influenza from 2010 to 2018. Using a societal perspective, we developed a decision tree cost-effectiveness model and estimated the incremental cost-effectiveness ratio (ICER) per disability-adjusted life year (DALY) averted for three vaccine target groups: children 6–23 months (strategy I), 2–5 years (strategy II) and 6–14 years (strategy III) with either the Southern Hemisphere influenza vaccine (Strategy A) or Northern Hemisphere vaccine (Strategy B) or both (Strategy C: twice yearly vaccination campaigns, or Strategy D: year-round vaccination campaigns). We assessed cost-effectiveness by calculating incremental net monetary benefits (INMB) using a willingness-to-pay (WTP) threshold of 1–51% of the annual gross domestic product per capita ($17–$872).

Results

The mean number of infections across all ages was 2–15 million per year. When vaccination was well timed to influenza activity, the annual mean ICER per DALY averted for vaccinating children 6–23 months ranged between $749 and $1385 for strategy IA, $442 and $1877 for strategy IB, $678 and $4106 for strategy IC and $1147 and $7933 for strategy ID. For children 2–5 years, it ranged between $945 and $1573 for strategy IIA, $563 and $1869 for strategy IIB, $662 and $4085 for strategy IIC, and $1169 and $7897 for strategy IID. For children 6–14 years, it ranged between $923 and $3116 for strategy IIIA, $1005 and $2223 for strategy IIIB, $883 and $4727 for strategy IIIC and $1467 and $6813 for strategy IIID. Overall, no vaccination strategy was cost-effective at the minimum ($17) and median ($445) WTP thresholds. Vaccinating children 6–23 months once a year had the highest mean INMB value at $872 (WTP threshold upper limit); however, this strategy had very low probability of the highest net benefit.

Conclusion

Vaccinating children 6–23 months once a year was the most favourable vaccination option; however, the strategy is unlikely to be cost-effective given the current WTP thresholds.
A robust 11-genes prognostic model can predict overall survival in bladder cancer patients based on five cohorts
Authors: Lin Jiaxing , Yang Jieping , Xu Xiao , Wang Yutao , Yu Meng , Zhu Yuyan
Published: August 2020

Background

Bladder cancer is the tenth most common cancer globally, but existing biomarkers and prognostic models are limited.

Method

In this study, we used four bladder cancer cohorts from The Cancer Genome Atlas and Gene Expression Omnibus databases to perform univariate Cox regression analysis to identify common prognostic genes. We used the least absolute shrinkage and selection operator regression to construct a prognostic Cox model. Kaplan–Meier analysis, receiver operating characteristic curve, and univariate/multivariate Cox analysis were used to evaluate the prognostic model. Finally, a co-expression network, CIBERSORT, and ESTIMATE algorithm were used to explore the mechanism related to the model.

Results

A total of 11 genes were identified from the four cohorts to construct the prognostic model, including eight risk genes (SERPINE2, PRR11, DSEL, DNM1, COMP, ELOVL4, RTKN, and MAPK12) and three protective genes (FABP6, C16orf74, and TNK1). The 11-genes model could stratify the risk of patients in all five cohorts, and the prognosis was worse in the group with a high-risk score. The area under the curve values of the five cohorts in the first year are all greater than 0.65. Furthermore, this model’s predictive ability is stronger than that of age, gender, grade, and T stage. Through the weighted co-expression network analysis, the gene module related to the model was found, and the key genes in this module were mainly enriched in the tumor microenvironment. B cell memory showed low infiltration in high-risk patients. Furthermore, in the case of low B cell memory infiltration and high-risk score, the prognosis of the patients was the worst.

Conclusion

The proposed 11-genes model is a promising biomarker for estimating overall survival in bladder cancer. This model can be used to stratify the risk of bladder cancer patients, which is beneficial to the realization of individualized treatment.
Risk factors for malaria infection prevalence and household vector density between mass distribution campaigns of long-lasting insecticidal nets in North-western Tanzania
Authors: Mosha Jacklin F. , Lukole Eliud , Charlwood J. Derek , Wright Alexandra , Rowland Mark , Bullock Olivia , Manjurano Alphaxard , Kisinza William , Mosha Franklin W. , Kleinschmidt Immo , Protopopoff Natacha
Published: August 2020

Background

Long-lasting insecticidal nets (LLINs) are the most widely deployed vector control intervention in sub-Saharan Africa to prevent malaria. Recent reports indicate selection of pyrethroid insecticide resistance is widespread in mosquito vectors. This paper explores risk factors associated with malaria infection prevalence and vector density between mass distribution campaigns, changes in net coverage, and loss of protection in an area of high pyrethroid resistance in Northwest Tanzania.

Methods

A cross sectional malaria survey of 3456 children was undertaken in 2014 in Muleba district, Kagera region west of Lake Victoria. Vector density was assessed using indoor light traps and outdoor tent traps. Anophelines were identified to species using PCR and tested for Plasmodium falciparum circumsporozoite protein. Logistic regression was used to identify household and environmental factors associated with malaria infection and regression binomial negative for vector density.

Results

LLIN use was 27.7%. Only 16.9% of households had sufficient nets to cover all sleeping places. Malaria infection was independently associated with access to LLINs (OR: 0.57; 95% CI 0.34–0.98). LLINs less than 2 years old were slightly more protective than older LLINs (53 vs 65% prevalence of infection); however, there was no evidence that LLINs in good condition (hole index < 65) were more protective than LLINs, which were more holed. Other risk factors for malaria infection were age, group, altitude and house construction quality. Independent risk factors for vector density were consistent with malaria outcomes and included altitude, wind, livestock, house quality, open eaves and LLIN usage. Indoor collections comprised 4.6% Anopheles funestus and 95.4% Anopheles gambiae of which 4.5% were Anopheles arabiensis and 93.5% were Anopheles gambiae sensu stricto.

Conclusion

Three years after the mass distribution campaign and despite top-ups, LLIN usage had declined considerably. While children living in households with access to LLINs were at lower risk of malaria, infection prevalence remained high even among users of LLINs in good condition. While effort should be made to maintain high coverage between campaigns, distribution of standard pyrethroid-only LLINs appears insufficient to prevent malaria transmission in this area of intense pyrethroid resistance.
A novel method of calculating stroke volume using point-of-care echocardiography
Authors: Aligholizadeh Ehson , Teeter William , Patel Rajan , Hu Peter , Fatima Syeda , Yang Shiming , Ramani Gautam , Safadi Sami , Olivieri Peter , Scalea Thomas , Murthi Sarah
Published: August 2020

Background

Point-of-care transthoracic echocardiography (POC-TTE) is essential in shock management, allowing for stroke volume (SV) and cardiac output (CO) estimation using left ventricular outflow tract diameter (LVOTD) and left ventricular velocity time integral (VTI). Since LVOTD is difficult to obtain and error-prone, the body surface area (BSA) or a modified BSA (mBSA) is sometimes used as a surrogate (LVOTDBSA, LVOTDmBSA). Currently, no models of LVOTD based on patient characteristics exist nor have BSA-based alternatives been validated.

Methods

Focused rapid echocardiographic evaluations (FREEs) performed in intensive care unit patients over a 3-year period were reviewed. The age, sex, height, and weight were recorded. Human expert measurement of LVOTD (LVOTDHEM) was performed. An epsilon-support vector regression was used to derive a computer model of the predicted LVOTD (LVOTDCM). Training, testing, and validation were completed. Pearson coefficient and Bland-Altman were used to assess correlation and agreement.

Results

Two hundred eighty-seven TTEs with ideal images of the LVOT were identified. LVOTDCM was the best method of SV measurement, with a correlation of 0.87. LVOTDmBSA and LVOTDBSA had correlations of 0.71 and 0.49 respectively. Root mean square error for LVOTDCM, LVOTDmBSA, and LVOTDBSA respectively were 13.3, 37.0, and 26.4. Bland-Altman for LVOTDCM demonstrated a bias of 5.2. LVOTDCM model was used in a separate validation set of 116 ideal images yielding a linear correlation of 0.83 between SVHEM and SVCM. Bland Altman analysis for SVCM had a bias of 2.3 with limits of agreement (LOAs) of − 24 and 29, a percent error (PE) of 34% and a root mean square error (RMSE) of 13.9.

Conclusions

A computer model may allow for SV and CO measurement when the LVOTD cannot be assessed. Further study is needed to assess the accuracy of the model in various patient populations and in comparison to the gold standard pulmonary artery catheter. The LVOTDCM is more accurate with less error compared to BSA-based methods, however there is still a percentage error of 33%. BSA should not be used as a surrogate measure of LVOTD. Once validated and improved this model may improve feasibility and allow hemodynamic monitoring via POC-TTE once it is validated.
Trends in the incidence of oral cancer in Saudi Arabia from 1994 to 2015
Authors: Alshehri Bandar M.
Published: August 2020

Background

Oral cancer is one of the most common non-communicable diseases worldwide. This paper presents an evaluation of the trends and geographical distributions of oral cancers in the Saudi Arabian population.

Methods

Data from Saudi Cancer Registry reports were used in this analysis, which assessed the period between 1994 and 2015. All cancer cases are recorded in these reports, as well as the age, gender, region and histological cancer sites for each patient. Age-standardised and age-specific incidence rates were calculated in these reports. For the purposes of this paper, only cancers of the lips, tongue and mouth were considered oral cancers.

Results

Between 1994 and 2015, the Saudi Cancer Registry identified 172,424 cancer cases in total. Of these, 3184 were oral cancer. The mean age-standardised rate of oral cancer for the study period was 2.9 per 100,000 people; for females, it was 1.5, and for males, it was 1.4. The incidence of oral cancer varied by region, with Jazan displaying the highest age-standardised rate and Hail displaying the lowest. A positive correlation was observed between oral cancer incidence and age.

Conclusion

The overall trend of the age-standardised rate for both sexes remained constant from 1994 to 2015. However, the oral cancer incidence in Saudi Arabia varies by region. Studying this variation in more detail will help to guide awareness programmes in the regions that are most in need.
SRSF1 regulates exosome microRNA enrichment in human cancer cells
Authors: Xu Yi-Fan , Xu Xiaohui , Gin Amy , Nshimiyimana Jean D. , Mooers Blaine H. M. , Caputi Massimo , Hannafon Bethany N. , Ding Wei-Qun
Published: August 2020

Background

Exosomes are extracellular vesicles containing a variety of biological molecules including microRNAs (miRNAs). We have recently demonstrated that certain miRNA species are selectively and highly enriched in pancreatic cancer exosomes with miR-1246 being the most abundant. Exosome miRNAs have been shown to mediate intercellular communication in the tumor microenvironment and promote cancer progression. Therefore, understanding how exosomes selectively enrich specific miRNAs to initiate exosome miRNA signaling in cancer cells is critical to advancing cancer exosome biology.

Results

The aim of this study was to identify RNA binding proteins responsible for selective enrichment of exosome miRNAs in cancer cells. A biotin-labeled miR-1246 probe was used to capture RNA binding proteins (RBPs) from PANC-1 cells. Among the RBPs identified through proteomic analysis, SRSF1, EIF3B and TIA1 were highly associated with the miR-1246 probe. RNA immunoprecipitation (RIP) and electrophoretic mobility shift assay (EMSA) confirmed the binding of SRSF1 to miR-1246. Lentivirus shRNA knockdown of SRSF1 in pancreatic cancer cells selectively reduced exosome miRNA enrichment whereas GFP-SRSF1 overexpression enhanced the enrichment as analyzed by next generation small RNA sequencing and qRT-PCR. miRNA sequence motif analysis identified a common motif shared by 36/45 of SRSF1-associated exosome miRNAs. EMSA confirmed that shared motif decoys inhibit the binding of SRSF1 to the miR-1246 sequence.

Conclusions

We conclude that SRSF1 mediates selective exosome miRNA enrichment in pancreatic cancer cells by binding to a commonly shared miRNA sequence motif.

Graphical abstract