bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why research ethics should add retrospective review
Authors: Dawson Angus , Lignou Sapfo , Siriwardhana Chesmal , O’Mathúna Dónal P. 
Published: October 2019

Abstract
Research ethics is an integral part of research, especially that involving human subjects. However, concerns have been expressed that research ethics has come to be seen as a procedural concern focused on a few well-established ethical issues that researchers need to address to obtain ethical approval to begin their research. While such prospective review of research is important, we argue that it is not sufficient to address all aspects of research ethics. We propose retrospective review as an important complement to prospective review. We offer two arguments to support our claim that prospective review is insufficient. First, as currently practiced, research ethics has become for some a ‘tick box’ exercise to get over the ‘hurdle’ of ethics approval. This fails to capture much of what is important in ethics and does not promote careful reflection on the ethical issues involved. Second, the current approach tends to be rules-based and we argue that research ethics should go beyond this to develop people’s capacity to be sensitive to the relevant moral features of their research, their ethical decision-making skills and their integrity. Retrospective review of a project’s ethical issues, and how they were addressed, could help to achieve those aims better. We believe that a broad range of stakeholders should be involved in such retrospective review, including representatives of ethics committees, participating communities and those involved in the research. All stakeholders could then learn from others’ perspectives and experiences. An open and transparent assessment of research could help to promote trust and understanding between stakeholders, as well as identifying areas of agreement and disagreement and how these can be built upon or addressed. Retrospective review also has the potential to promote critical reflection on ethics and help to develop ethical sensitivity and integrity within the research team. Demonstrating this would take empirical evidence and we suggest that any such initiatives should be accompanied by research into their effectiveness. Our article concludes with a discussion of some possible objections to our proposal, and an invitation to further debate and discussion.
Crystal structure of diamondback moth ryanodine receptor Repeat34 domain reveals insect-specific phosphorylation sites
Authors: Xu Tong , Yuchi Zhiguang 
Published: October 2019

AbstractBackgroundRyanodine receptor (RyR), a calcium-release channel located in the sarcoplasmic reticulum membrane of muscles, is the target of insecticides used against a wide range of agricultural pests. Mammalian RyRs have been shown to be under the regulatory control of several kinases and phosphatases, but little is known about the regulation of insect RyRs by phosphorylation.ResultsHere we present the crystal structures of wild-type and phospho-mimetic RyR Repeat34 domain containing PKA phosphorylation sites from diamondback moth (DBM), a major lepidopteran pest of cruciferous vegetables. The structure has unique features, not seen in mammalian RyRs, including an additional α-helix near the phosphorylation loop. Using tandem mass spectrometry, we identify several PKA sites clustering in the phosphorylation loop and the newly identified α-helix. Bioinformatics analysis shows that this α-helix is only present in Lepidoptera, suggesting an insect-specific regulation. Interestingly, the specific phosphorylation pattern is temperature-dependent. The thermal stability of the DBM Repeat34 domain is significantly lower than that of the analogous domain in the three mammalian RyR isoforms, indicating a more dynamic domain structure that can be partially unfolded to facilitate the temperature-dependent phosphorylation. Docking the structure into the cryo-electron microscopy model of full-length RyR reveals that the interface between the Repeat34 and neighboring HD1 domain is more conserved than that of the phosphorylation loop region that might be involved in the interaction with SPRY3 domain. We also identify an insect-specific glycerol-binding pocket that could be potentially targeted by novel insecticides to fight the current resistance crisis.ConclusionsThe crystal structures of the DBM Repeat34 domain reveals insect-specific temperature-dependent phosphorylation sites that may regulate insect ryanodine receptor function. It also reveals insect-specific structural features and a potential ligand-binding site that could be targeted in an effort to develop green pesticides with high species-specificity.
Glucosamine impedes transforming growth factor β1-mediated corneal fibroblast differentiation by targeting Krüppel-like factor 4
Authors: Chen Ying-Jen , Huang Shih-Ming , Tai Ming-Cheng , Chen Jiann-Torng , Liang Chang-Min 
Published: October 2019

AbstractBackgroundTransforming growth factor (TGF) family members play important roles in the regulation of corneal integrity, and the pathogenesis of corneal fibrosis. Currently, there are no effective agents targeting TGF-β signaling to diminish corneal fibrosis. Glucosamine (GlcN), which is widely used in the treatment of osteoarthritis, abrogates the morphologic effects of TGF-β2 on retinal pigmented epithelial cells in a mouse disease model. Here, we sought to determine whether GlcN would exert beneficial effects against TGF-β1-induced corneal fibrosis.MethodsIn human corneal fibroblasts (HCFs) treated with GlcN, the expression of Krüppel-like factor 4 (KLF4) and its downstream signaling effects were determined in the presence and absence of TGF-β1 using immunoblot analysis. We further explored GlcN inhibition of fibroblast-to-myofibroblast differentiation via KLF4 siRNA. The effect of cycloheximide on KLF4 protein levels with or without GlcN administration was assessed to determine whether GlcN affects the stability of the KLF4 protein.ResultsIn HCFs, GlcN induced the expression of KLF4, which regulated the maturation and maintenance of the ocular surface. GlcN partially suppressed the TGF-β1-induced expression of alpha-smooth muscle actin (α-SMA) and reduced the collagen contraction capacity in HCFs, suggesting a decrease in fibroblast-to-myofibroblast differentiation. This effect appeared to be mediated through suppression of Smad2 phosphorylation and ERK-dependent signaling. The levels of KLF4 mRNA were increased by GlcN and decreased by TGF-β1 and the TGF-β1-induced α-SMA mRNA expression was upregulated when the KLF4 gene was silenced. GlcN also appeared to stabilize the KLF4 protein, reducing its turnover in corneal fibroblasts.ConclusionThese findings shed light on a novel mechanism by which GlcN suppresses TGF-β1-induced fibroblast-to-myofibroblast differentiation through the upregulation of KLF4 expression. Current strategies for treating corneal fibrosis were not effective. Elevating KLF4 levels through the use of GlcN might provide an effective alternative to alleviate the development and progression of corneal fibrosis.
Renal resistive index: a new reversible tool for the early diagnosis and evaluation of organ perfusion in critically ill patients: a case report
Authors: Anile Antonio , Ferrario Silvia , Campanello Lorena , Orban Maria Antonietta , Castiglione Giacomo 
Published: October 2019

Abstract

Background
We reported a case of early detection of peripheral hypoperfusion trough the evaluation of a new index in intensive care: Renal Doppler Resistive Index (RRI).

Case presentation
We admitted a 76-year-old man who underwent ileostomy and hernioplasty because of an intestinal occlusion due to obstructive strangulated right inguinal hernia. The post-operative period was characterised by hemodynamic instability and he needed an invasive hemodynamic monitoring, administration of vasopressors and continuous renal replacement therapy (CRRT). Then, hemodynamic stability was obtained and vasopressors interrupted. RRI was lower than 0.7. In the eleventh post-operative day, despite stable macrocirculatory parameters, we found increased values of RRI. An abdomen ultrasound first and then a CT scan revealed the presence of bleeding from the previous ileostomy. Hence, the patient immediately underwent another surgical operation.

Conclusions
RRI modification appears to be more precocious than any other hemodynamic, microcirculatory and metabolic parameter routinely used. RRI has been widely used to assess renal function in critically ill patients; now, we presume that RRI could represent a common and useful tool to manage target therapy in critical condition.
Schmallenberg virus: a systematic international literature review (2011-2019) from an Irish perspective
Authors: Collins Áine B. , Doherty Michael L. , Barrett Damien J. , Mee John F. 
Published: October 2019

Abstract
In Autumn 2011, nonspecific clinical signs of pyrexia, diarrhoea, and drop in milk yield were observed in dairy cattle near the German town of Schmallenberg at the Dutch/German border. Targeted veterinary diagnostic investigations for classical endemic and emerging viruses could not identify a causal agent. Blood samples were collected from animals with clinical signs and subjected to metagenomic analysis; a novel orthobunyavirus was identified and named Schmallenberg virus (SBV). In late 2011/early 2012, an epidemic of abortions and congenital malformations in calves, lambs and goat kids, characterised by arthrogryposis and hydranencephaly were reported in continental Europe. Subsequently, SBV RNA was confirmed in both aborted and congenitally malformed foetuses and also in Culicoides species biting midges. It soon became evident that SBV was an arthropod-borne teratogenic virus affecting domestic ruminants. SBV rapidly achieved a pan-European distribution with most countries confirming SBV infection within a year or two of the initial emergence. The first Irish case of SBV was confirmed in the south of the country in late 2012 in a bovine foetus.
Since SBV was first identified in 2011, a considerable body of scientific research has been conducted internationally describing this novel emerging virus. The aim of this systematic review is to provide a comprehensive synopsis of the most up-to-date scientific literature regarding the origin of SBV and the spread of the Schmallenberg epidemic, in addition to describing the species affected, clinical signs, pathogenesis, transmission, risk factors, impact, diagnostics, surveillance methods and control measures. This review also highlights current knowledge gaps in the scientific literature regarding SBV, most notably the requirement for further research to determine if, and to what extent, SBV circulation occurred in Europe and internationally during 2017 and 2018. Moreover, recommendations are also made regarding future arbovirus surveillance in Europe, specifically the establishment of a European-wide sentinel herd surveillance program, which incorporates bovine serology and Culicoides entomology and virology studies, at national and international level to monitor for the emergence and re-emergence of arboviruses such as SBV, bluetongue virus and other novel Culicoides-borne arboviruses.
An integrative review on methodological considerations in mental health research – design, sampling, data collection procedure and quality assurance
Authors: Badu Eric , O’Brien Anthony Paul , Mitchell Rebecca 
Published: October 2019

Abstract

Background
Several typologies and guidelines are available to address the methodological and practical considerations required in mental health research. However, few studies have actually attempted to systematically identify and synthesise these considerations. This paper provides an integrative review that identifies and synthesises the available research evidence on mental health research methodological considerations.

Methods
A search of the published literature was conducted using EMBASE, Medline, PsycINFO, CINAHL, Web of Science, and Scopus. The search was limited to papers published in English for the timeframe 2000–2018. Using pre-defined inclusion and exclusion criteria, three reviewers independently screened the retrieved papers. A data extraction form was used to extract data from the included papers.

Results
Of 27 papers meeting the inclusion criteria, 13 focused on qualitative research, 8 mixed methods and 6 papers focused on quantitative methodology. A total of 14 papers targeted global mental health research, with 2 papers each describing studies in Germany, Sweden and China. The review identified several methodological considerations relating to study design, methods, data collection, and quality assurance. Methodological issues regarding the study design included assembling team members, familiarisation and sharing information on the topic, and seeking the contribution of team members. Methodological considerations to facilitate data collection involved adequate preparation prior to fieldwork, appropriateness and adequacy of the sampling and data collection approach, selection of consumers, the social or cultural context, practical and organisational skills; and ethical and sensitivity issues.

Conclusion
The evidence confirms that studies on methodological considerations in conducting mental health research largely focus on qualitative studies in a transcultural setting, as well as recommendations derived from multi-site surveys. Mental health research should adequately consider the methodological issues around study design, sampling, data collection procedures and quality assurance in order to maintain the quality of data collection.
Spatial distribution of Anopheles gambiae sensu lato larvae in the urban environment of Yaoundé, Cameroon
Authors: Djamouko-Djonkam Landre , Mounchili-Ndam Souleman , Kala-Chouakeu Nelly , Nana-Ndjangwo Stella Mariette , Kopya Edmond , Sonhafouo-Chiana Nadége , Talipouo Abdou , Ngadjeu Carmene Sandra , Doumbe-Belisse Patricia , Bamou Roland , Toto Jean Claude , Tchuinkam Timoléon , Wondji Charles Sinclair , Antonio-Nkondjio Christophe 
Published: October 2019

Abstract

Background
The rapid and unplanned urbanization of African cities is considered to increase the risk of urban malaria transmission. The present study objective was to assess factors influencing the spatio-temporal distribution of Anopheles gambiae s.l. larvae in the city of Yaoundé, Cameroon.

Methods
All water bodies were checked once every 2 months for the presence of mosquito larvae from March 2017 to May 2018 in 32 districts of Yaoundé. Physico-chemical characteristics including the size, depth, turbidity, pH, temperature, conductivity, sulfates, organophosphates, hydrogen peroxide (H2O2), conductivity, iron and calcium were recorded and analyzed according to anopheline larvae presence or absence. High resolution satellite images from landsat sentinel Enhanced Thematic Mapper were used for spatial mapping of both field and environmental variables. Bivariate and multivariate logistic regression models were used to identify variables closely associated with anopheline larvae distribution.

Results
A total of 18 696 aquatic habitats were checked and only 2942 sites (15.7%) contained anopheline larvae. A high number of sites with anopheline larvae (≥ 69%) presented late instar larvae (L3, L4 and pupae). Anopheline mosquito larvae were sampled from a variety of breeding sites including puddles (51.6%), tire prints (12.9%), wells (11.7%) and drains (11.3%). Bivariate logistic regression analyses associated anopheline larvae presence with the absence of predators, absence of algae, absence of vegetation and depth of less than 1 m. Conductivity, turbidity, organophosphates, H2O2 and temperature were significantly high in breeding sites with anopheline larvae than in breeding sites without these larvae (P <  0.1). Anopheline species collected included An. coluzzii (91.1%) and An. gambiae s.s. (8.9%). GIS mapping indicated a heterogeneous distribution of anopheline breeding habitats in the city of Yaoundé. Land cover analysis indicated high variability of the city of Yaoundé’s landscape.

Conclusions
The data confirms adaptation of An. gambiae s.l. to the urban domain in the city of Yaoundé and calls for urgent actions to improve malaria vector control.
The STEM Faculty Instructional Barriers and Identity Survey (FIBIS): development and exploratory results
Authors: Sturtevant Hannah , Wheeler Lindsay 
Published: October 2019

AbstractBackgroundAs institutions and science, technology, engineering, and mathematics (STEM) departments emphasize faculty use of evidence-based instructional practices (EBIPs), various barriers and faculty perceptions hinder that process. While a large body of literature exists in this area, no survey instrument has been developed to comprehensively and systematically capture all these factors. We developed and piloted a survey instrument, the Faculty Instructional Barriers and Identity Survey (FIBIS), to delineate university STEM faculty perceptions of barriers to using EBIPs and examine the composition and sources of faculty professional identity, use of and dissatisfaction with these practices.ResultsInitial pilot study results with a small, targeted sample (n= 69) shows how FIBIS can be used to understand factors that impact instructional practices. For our sample, we found that higher perceived departmental barriers and limited supports correlate with lower work identity. Even at a research university, we do not see a negative correlation between research and teaching identities; STEM faculty can have both, despite hypothesized tensions in the literature. We also found that sense of belonging and faculty community were descriptively higher for underrepresented minority than non-underrepresented minority faculty. As previous work has suggested, use of EBIPs varied by department. Finally, descriptive differences were seen in faculty barriers for those who were and were not satisfied with EBIPs. This suggests another layer to add to models of faculty decision-making regarding the use of EBIPs: dissatisfaction with implementing these practices once they are attempted. Further work is needed to confirm and understand these initial findings.ConclusionsMany of the exploratory findings from our pilot of FIBIS align with previous qualitative work, suggesting that FIBIS is a tool that can capture faculty identity, use of EBIPs, and barriers to instruction. While we do not intend to generalize our claims, the following suggestions for our institution may demonstrate how FIBIS can be used to try and reduce STEM faculty barriers to implementing EBIPs: (1) developing a strong teaching community (especially needed for persistence of faculty from underrepresented minorities), (2) helping faculty connect to the university as a whole, and (3) working with departments to better support implementation of EBIPs. The results presented and implications of these findings demonstrate the potential of FIBIS as a tool for examining factors that influence STEM faculty instructional practice. Future work includes further validating the FIBIS barriers component of the survey so that FIBIS can be used to identify and support change in institutions of higher education.
Path minimization in a tandem running Indian ant in the context of colony relocation
Authors: Mukhopadhyay Snigdha , Pathak Manish Kumar , Annagiri Sumana 
Published: October 2019

The phenomenon of minimizing the path length to a target site in order to increase transport efficiency is described as path optimization, and it has been observed in many mammals, birds and some invertebrates like honeybees and ants. It has been demonstrated that ants can optimize their foraging path through an emergent process, involving the trail pheromone concentration, without individual ants having to measure and compare distances.
In the current study, we investigated if ants that use only tandem running to recruit their nestmates can minimize their path while relocating their entire colony into a new nest. As colony relocation directly impacts the survival of the whole colony, it would be particularly important to optimize their path to the new nest. Using the ponerine ant Diacamma indicum, we conducted relocation experiments, in which ants had to choose between different defined paths and contrasted our findings with open arena experiments, as they navigate to their new nest. After following 4100 unique transports by 450 different transporters, we found that these ants minimize their path. Individual leaders, as well as colonies, choose the shorter path significantly more than the longer path, and they showed a significant preference for the shorter arm at multiple decision points on encountering a combination of paths. Thus, we concluded that tandem leaders are capable of path minimization based on the information they themselves collect. Further investigation into the proximate mechanisms by which they achieve this is required.
Abdominal visceral adipose tissue is associated with unsuspected pulmonary embolism on routine CT scans in patients with gastrointestinal cancer
Authors: Xiao Xiaojuan , Wang Yao , Gao Ying , Xie Qiuxia , Zhou Xuhui , Lin Ling , Dekkers Ilona A. , Lamb Hildo J. 
Published: October 2019

Objective:
Unsuspected pulmonary embolism (UPE) has been increasingly diagnosed as an incidental finding on CT scans for routine staging in cancer patients. Previous studies suggest that obesity is an independent risk factor for venous thromboembolism in patients with malignant tumors. In this study, we aimed to investigate the association between abdominal adipose tissue, especially visceral adipose tissue (VAT) and the occurrence of UPE in hospitalized patients with gastrointestinal cancer.

Methods:
Routine contrast-enhanced chest and abdominal CT scans of 1974 patients were retrospectively assessed for the presence of UPE, of which 58 patients were identified with UPE and 108 non-UPE patients were selected as the non-UPE control group based on several matching criteria. Abdominal adipose tissue was measured by volumes of VAT and subcutaneous adipose tissue (SAT) at the navel level.

Results:
VAT, SAT, indwelling venous catheters, surgery, chemotherapy, and bed rest or immobilization were associated with the occurrence of UPE. Higher VAT volumes were associated with increased risk of UPE (odds ratio: 1.96; 95% confidence interval: 1.25, 3.06; p = 0.003) adjusting body mass index (BMI), bed rest or immobilization, surgery, chemotherapy and smoking, while SAT was not associated with UPE adjusting the same confounders (p = 0.117). No statistical association was found between BMI and UPE (p = 0.102).

Conclusion:
Higher VAT rather than SAT is associated with an increased risk of unsuspected pulmonary embolism on routine CT scans in hospitalized gastrointestinal cancer patients.

Advances in knowledge:
Our findings indicate that VAT is a stronger risk factor for unsuspected pulmonary embolism than BMI and SAT in hospitalized patients with gastrointestinal cancer.