bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct niche partitioning of marine and freshwater microbes during colonisation
Authors: Dann Lisa M , Clanahan Michelle , Paterson James S , Mitchell James G 
Published: July 2019

ABSTRACTBacteria are ubiquitous on the Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses and chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain, but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting that successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show that microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology, and disease development by setting the initial conditions that determine the winners as a community develops.
Protein and carbohydrate intakes alter gut microbial community structure in crickets: a Geometric Framework approach
Authors: Ng Soon Hwee , Stat Michael , Bunce Michael , Simpson Stephen J , Simmons Leigh W 
Published: July 2019

ABSTRACTProteins and carbohydrates have profound impacts on the ecology of gut microbiota, but disentangling the single and interactive effects of different dietary constituents is challenging. Here, we used a multidimensional approach, the Geometric Framework, to study the interactions between nutrition and bacterial abundances with respect to protein and carbohydrate intakes in field cricket, Teleogryllus oceanicus. Our study revealed that species richness decreased as crickets consumed more macronutrients, and species evenness peaked at high intake of protein-rich diets. Sex and protein:carbohydrate (P:C) ratios in diets were the primary factors influencing the gut bacterial community, but most of the microbial operational taxonomic units (OTUs) that were significantly different between males and females were present in low abundance. In contrast, protein intake had a greater influence than carbohydrate consumption on the relative abundances of the core bacterial taxa, as an increase in dietary protein availability could remove the growth constraint imposed by limited nitrogen. Taken together, the use of the Geometric Framework provides a deeper insight into how nutritional intakes influence the relative abundances of gut microbes, and could be a useful tool to integrate the study of gut microbiome and fitness traits in a host.
Consider the Oyster Seller: Street Hawkers and Gendered Stereotypes in Early Modern London
Authors: Taverner Charlie 
Published: July 2019

Abstract
Oyster sellers were ubiquitous on London’s streets and as characters in high and low culture. This article contrasts the varied, sophisticated working life of mostly female hawkers with their sexualized representation in the multimedia genre of Cries. It connects these divergent stories to bigger narratives of socio-economic change in London, gender relations, and changing ways of imagining the emergent metropolis. While previous work focused on hawkers’ marginality and read the Cries uncritically, this article shows how humble food sellers kept the city fed, became symbolic of cultural change, and may have been affected by their representations.
Chemical Responses to the Biotic and Abiotic Environment by Early Diverging Metazoans Revealed in the Post-Genomic Age
Authors: Okamura Beth , Long Paul F , Mydlarz Laura D 
Published: July 2019

Abstract
For many years methodological constraints limited insights on the molecular biology of non-model organisms. However, the development of various sequencing platforms has led to an explosion of transcriptomic and genomic data on non-model systems. As a consequence the molecular drivers of organismal phenotypes are becoming clearer and the chemicals that animals use to detect and respond to their environments are increasingly being revealed—this latter area inspired our symposium theme. The papers in this volume broadly address this theme by their more specific focus in one of the following general areas: 1) sensory biology and the molecular basis of perception, 2) chemicals deployed to deal with the biotic and abiotic environment, and 3) chemical interactions along the parasite–mutualist continuum. Here we outline and synthesize the content of these papers—an exercise which demonstrates that sophisticated gene repertoires enable early diverging metazoans to encode many of the signaling, sensory, defensive, and offensive capacities typically associated with animals that have complex nervous systems. We then consider opportunities and associated challenges that may delay progress in comparative functional biochemistry, a reinvigorated field that can be expected to rapidly expand with new ’omics data. Future knowledge of chemical adaptations should afford new perspectives on the comparative evolution of chemical mediators.
Predictive analytics in health care: how can we know it works?
Authors: Van Calster Ben , Wynants Laure , Timmerman Dirk , Steyerberg Ewout W , Collins Gary S 
Published: July 2019

Abstract
There is increasing awareness that the methodology and findings of research should be transparent. This includes studies using artificial intelligence to develop predictive algorithms that make individualized diagnostic or prognostic risk predictions. We argue that it is paramount to make the algorithm behind any prediction publicly available. This allows independent external validation, assessment of performance heterogeneity across settings and over time, and algorithm refinement or updating. Online calculators and apps may aid uptake if accompanied with sufficient information. For algorithms based on “black box” machine learning methods, software for algorithm implementation is a must. Hiding algorithms for commercial exploitation is unethical, because there is no possibility to assess whether algorithms work as advertised or to monitor when and how algorithms are updated. Journals and funders should demand maximal transparency for publications on predictive algorithms, and clinical guidelines should only recommend publicly available algorithms.
Examining Refugee Integration: Perspective of Community Members
Authors: Weng Suzie S , Choi Shinwoo 
Published: July 2019

Abstract
The recent anti-immigrant sentiment portrayed through elections, policies, current events and media in the United States should be a concern for localities with regard to the wellbeing of refugees. This exploratory study was in response to the current climate in an attempt to capture how locals perceive refugees and what possible interventions locals believe are occurring to integrate refugees in the community. Semi-structured one-on-one interviews were conducted with 26 members of the community who currently live in the same location as their place of birth. Themes found include participant concerns, sympathy for refugees and community strategies for refugee integration. This study contributes to a more complex depiction of how some community members may perceive refugees in the current national climate of xenophobia, racism and/or nativism. Existing interventions identified by community members in this study indicate what may be working at the local level.
Data-driven estimates of global nitrous oxide emissions from croplands
Authors: Wang Qihui , Zhou Feng , Shang Ziyin , Ciais Philippe , Winiwarter Wilfried , Jackson Robert B , Tubiello Francesco N , Janssens-Maenhout Greet , Tian Hanqin , Cui Xiaoqing , Canadell Josep G , Piao Shilong , Tao Shu 
Published: July 2019

AbstractCroplands are the single largest anthropogenic source of nitrous oxide (N2O) globally, yet their estimates remain difficult to verify when using Tier 1 and 3 methods of the Intergovernmental Panel on Climate Change (IPCC). Here, we re-evaluate global cropland-N2O emissions in 1961–2014, using N-rate-dependent emission factors (EFs) upscaled from 1206 field observations in 180 global distributed sites and high-resolution N inputs disaggregated from sub-national surveys covering 15593 administrative units. Our results confirm IPCC Tier 1 default EFs for upland crops in 1990–2014, but give a ∼15% lower EF in 1961–1989 and a ∼67% larger EF for paddy rice over the full period. Associated emissions (0.82 ± 0.34 Tg N yr–1) are probably one-quarter lower than IPCC Tier 1 global inventories but close to Tier 3 estimates. The use of survey-based gridded N-input data contributes 58% of this emission reduction, the rest being explained by the use of observation-based non-linear EFs. We conclude that upscaling N2O emissions from site-level observations to global croplands provides a new benchmark for constraining IPCC Tier 1 and 3 methods. The detailed spatial distribution of emission data is expected to inform advancement towards more realistic and effective mitigation pathways.
Evaluation of Safety and Effectiveness of Elvitegravir/Cobicistat/Emtricitabine/Tenofovir Alafenamide Switch Followed by Ledipasvir/Sofosbuvir HCV Therapy in HIV–HCV Coinfection
Authors: Doyle Mary-Anne , Lee Terry , Singer Joel , Crawley Angela , Klein Marina , Cooper Curtis 
Published: July 2019

AbstractBackgroundWe conducted a pilot study assessing the feasibility, efficacy, and safety of a simplified combination HIV antiretroviral and hepatitis C virus (HCV) antiviral regimen in HIV–HCV coinfection.MethodsParticipants on suppressive antiretrovirals and HCV genotype 1 infection were switched to single-tablet daily-dosed elvitegravir/cobicistat/emtricitabine/tenofovir alafenamide (E/C/F/TAF) and 1 month later initiated single-tablet-regimen daily-dosed ledipasvir-sofosbuvir for 12 weeks. E/C/F/TAF was continued during HCV treatment and for 12 weeks after.ResultsTwenty-six individuals were screened, 25 enrolled, and 23 completed all HIV and HCV treatment. Participants were predominantly male, with a mean age (SD) of 55 (7.5) years. The median transient elastography score (interquartile range [IQR]) was 5.9 (5.3 to 7.6) kPa, and the mean CD4 count (SD) was 579 (223) cells/µL. The median adherence to HCV medications, assessed by pill count, was 100% (95% confidence interval [CI], 100%–100%), and HIV ranged from 99% to 100% (100%; 95% CI, 90%–100%) over the 7-month study duration. HIV undetectability was maintained in all but 1 participant enrolled with unsuspected multiclass resistance. Treatment was well tolerated, with no study medication modification due to adverse events and no serious adverse event related to the study drug. All participants achieved sustained virological response. The mean CD4 count (SD) increased to 673 (361) cells/µL, and the fibrosis score (IQR) declined to 5.2 (4.4 to 7.4) kPa by week 12 after HCV treatment. There was no treatment effect on glucose metabolism. Cholesterol increased during and after treatment.ConclusionsProvision of this 2-tablet daily HIV–HCV regimen is feasible, well tolerated, and safe, avoids drug–drug interactions between HIV and HCV medications, maintains HIV suppression in the absence of drug resistance, and is highly curative of HCV.
Experiences of South Asian patients in early inflammatory arthritis clinic: a qualitative interview study
Authors: Kumar Kanta , Reehal Joti , Stack Rebecca J , Adebajo Ade , Adams Jo 
Published: July 2019

Abstract

Objective
The aim was to explore how UK South Asian patients living with RA interact with health care professionals and experience receiving health information in an early inflammatory arthritis clinic.

Methods
A semi-structured interview schedule, designed in conjunction with a patient partner, was used for face-to-face interviews. South Asian participants with RA were recruited from Central Manchester University Hospitals National Health Service Foundation Trust. Data were recorded and transcribed by an independent company. Data were analysed using inductive thematic analysis.

Results
Fifteen participants were interviewed. Three predominant themes emerged around participants’ experiences and interaction with health care professionals in early inflammatory arthritis clinic. First, ‘the personal experiences of RA and cultural link to early inflammatory arthritis clinic’, where participants described the impact of RA as individuals and their altered roles within their cultural setting. Second, ‘experiences of interacting and receiving information in the early inflammatory arthritis clinic’, where participants described their limited engagement with health care professionals and the quality of information discussed in the clinic. Third, ‘views on future content for early inflammatory arthritis clinics’, where participants highlighted new innovative ideas to build on current practice.

Conclusion
We believe this to be the first study to generate insight into the experiences of South Asian patients of interacting with health care professionals while attending an early inflammatory arthritis clinic. Policy directives aimed at improving access to services and delivery of information for ethnic minority groups in early inflammatory arthritis clinics should include consideration of the different roles of cultures. Professionals should be cognizant of the factors that drive health inequalities and focus on improving service delivery.
The prospective association of objectively measured sleep and cerebral white matter microstructure in middle-aged and older persons
Authors: Kocevska Desana , Tiemeier Henning , Lysen Thom S , de Groot Marius , Muetzel Ryan L , Van Someren Eus J W , Ikram M Arfan , Vernooij Meike W , Luik Annemarie I 
Published: July 2019

AbstractStudy ObjectivesPoor sleep may destabilize axonal integrity and deteriorate cerebral white matter. In middle-aged and older adults sleep problems increase alongside structural brain changes, but the temporal relation between these processes is poorly understood. We studied longitudinal associations between sleep and cerebral white matter microstructure.MethodsOne thousand one persons (59.3 ± 7.9 years, 55% women) were followed across 5.8 years (3.9–10.8). Total sleep time (TST, hours), sleep efficiency (SE, percentage), sleep onset latency (SOL, minutes), and wake after sleep onset (WASO, minutes) were measured at baseline using a wrist-worn actigraph. White matter microstructure (global and tract-specific fractional anisotropy [FA] and mean diffusivity [MD]) was measured twice with diffusion tensor imaging (DTI).ResultsPoor sleep was associated with worse white matter microstructure up to 7 years later but did not predict trajectories of DTI over time. Longer TST was associated with higher global FA (β = 0.06, 95% CI: 0.01 to 0.12), but not with MD. Persons with higher SE had higher global FA (β = 0.01, 95% CI: 0.002 to 0.01) and lower MD (β = −0.01, 95% CI: −0.01 to −0.0004). Consistently, those with more WASO had lower global FA (β = −0.003, 95% CI: −0.005 to −0.001) and higher MD (β = 0.002, 95% CI: 0.0004 to 0.004). Global findings seemed to be driven by microstructural alterations in the cingulum, anterior forceps of corpus callosum, projection and association tracts.ConclusionsMiddle-aged and older persons with more WASO, lower SE and shorter TST have worse microstructure of cerebral white matter. Microstructural alterations are most pronounced projection and association tracts, in the cingulum, and in the anterior forceps of corpus callosum.
Acceleration of chemical shift encoding-based water fat MRI for liver proton density fat fraction and T2* mapping using compressed sensing
Authors: Lohöfer Fabian K. , Kaissis Georgios A. , Müller-Leisse Christina , Franz Daniela , Katemann Christoph , Hock Andreas , Peeters Johannes M. , Rummeny Ernst J. , Karampinos Dimitrios , Braren Rickmer F. 
Published: July 2019

AbstractObjectivesTo evaluate proton density fat fraction (PDFF) and T2* measurements of the liver with combined parallel imaging (sensitivity encoding, SENSE) and compressed sensing (CS) accelerated chemical shift encoding-based water-fat separation.MethodsSix-echo Dixon imaging was performed in the liver of 89 subjects. The first acquisition variant used acceleration based on SENSE with a total acceleration factor equal to 2.64 (acquisition labeled as SENSE). The second acquisition variant used acceleration based on a combination of CS with SENSE with a total acceleration factor equal to 4 (acquisition labeled as CS+SENSE). Acquisition times were compared between acquisitions and proton density fat fraction (PDFF) and T2*-values were measured and compared separately for each liver segment.ResultsTotal scan duration was 14.5 sec for the SENSE accelerated image acquisition and 9.3 sec for the CS+SENSE accelerated image acquisition. PDFF and T2* values did not differ significantly between the two acquisitions (paired Mann-Whitney and paired t-test P>0.05 in all cases). CS+SENSE accelerated acquisition showed reduced motion artifacts (1.1%) compared to SENSE acquisition (12.3%).ConclusionCS+SENSE accelerates liver PDFF and T2*mapping while retaining the same quantitative values as an acquisition using only SENSE and reduces motion artifacts.Strengths of this studyCompressed sensing allows accelerated imaging with reduction of motion artifacts without alteration of quantitative measurementsRobust results in fat and iron quantification in a heterogeneous patient cohortLimitations of this studyNo histopathological validation of the MR findings was performedThe study was not performed at different field strengths
Machine learning to predict early recurrence after oesophageal cancer surgery
Authors: Rahman Saqib A , Walker Robert C , Lloyd Megan A , Grace Ben L , van Boxel Gijs I , Kingma Feike , Ruurda Jelle P , van Hillegersberg Richard , Harris Scott , Parsons Simon , Mercer Stuart , Griffiths Ewen A , O’Neill J.Robert , Turkington Richard , Fitzgerald Rebecca C , Underwood Timothy J ,   On behalf of the OCCAMS Consortium, the full list of contributors is displayed in acknowledgements
Published: July 2019

ABSTRACTObjectiveTo develop a predictive model for early recurrence after surgery for oesophageal adenocarcinoma using a large multi-national cohort.Summary Background DataEarly cancer recurrence after oesophagectomy is a common problem with an incidence of 20-30% despite the widespread use of neoadjuvant treatment. Quantification of this risk is difficult and existing models perform poorly. Machine learning techniques potentially allow more accurate prognostication and have been applied in this study.MethodsConsecutive patients who underwent oesophagectomy for adenocarcinoma and had neoadjuvant treatment in 6 UK and 1 Dutch oesophago-gastric units were analysed. Using clinical characteristics and post-operative histopathology, models were generated using elastic net regression (ELR) and the machine learning methods random forest (RF) and XG boost (XGB). Finally, a combined (Ensemble) model of these was generated. The relative importance of factors to outcome was calculated as a percentage contribution to the model.ResultsIn total 812 patients were included. The recurrence rate at less than 1 year was 29.1%. All of the models demonstrated good discrimination. Internally validated AUCs were similar, with the Ensemble model performing best (ELR=0.785, RF=0.789, XGB=0.794, Ensemble=0.806). Performance was similar when using internal-external validation (validation across sites, Ensemble AUC=0.804). In the final model the most important variables were number of positive lymph nodes (25.7%) and vascular invasion (16.9%).ConclusionsThe derived model using machine learning approaches and an international dataset provided excellent performance in quantifying the risk of early recurrence after surgery and will be useful in prognostication for clinicians and patients.DRAFT VISUAL ABSTRACTIcons taken fromwww.flaticon.com, made by ‘Freepik’, ‘smashicons’, and ‘prettycons’. Reproduced under creative commons attribution licenseMINI-ABSTRACTEarly recurrence after surgery for adenocarcinoma of the oesophagus is common. We derived a risk prediction model using modern machine learning methods that accurately predicts risk of early recurrence using post-operative pathology
Physiological and pathophysiological homeostasis of astroglial channel proteins by Nedd4-2
Authors: Altas Bekir , Ju Anes , Solís Hugo Cruces , Karaca Samir , Winchenbach Jan , Kaplan Öyküm , Schwark Manuela , Wieser Georg L. , Chaugule Viduth K. , Majoul Irina , Hassan Mohamed A. , Goel Rashi , Wojcik Sonja M. , Pichler Andrea , Mitkovski Miso , de Hoz Livia , Urlaub Henning , Jahn Olaf , Saher Gesine , Rhee JeongSeop , Kawabe Hiroshi 
Published: July 2019

ABSTRACTNedd4-2 is an E3 ubiquitin ligase, missense mutation of which is related to familial epilepsy, indicating its critical role in regulating neuronal network activity. However, Nedd4-2 substrates involved in neuronal network function have yet to be identified. Using mouse lines lacking Nedd4-1 and Nedd4-2, we identified astrocytic channel proteins inwardly rectifying K+ channel 4.1 (Kir4.1) and Connexin43 as Nedd4-2 substrates. We found that the expression of Kir4.1 and Connexin43 is increased upon conditional deletion of Nedd4-2 in astrocytes, leading to an elevation of astrocytic membrane ion permeability and gap junction activity, with a consequent reduction of γ-oscillatory neuronal network activity. Interestingly, our biochemical data demonstrate that missense mutations found in familial epileptic patients produce gain-of-function of Nedd4-2 gene product. Our data reveal a process of coordinated astrocytic ion channel proteostasis that controls astrocyte function and astrocyte-dependent neuronal network activity, and elucidate a potential mechanism by which aberrant Nedd4-2 function leads to epilepsy.CONDENSED TITLEUbiquitination of Astrocytic Channels by Nedd4-2SUMMARYUbiquitination is a key regulatory machinery for protein expression. Our present work provides evidence that astrocytic ion channel proteostasis coordinated by an E3 ubiquitin ligase Nedd4-2 is of particular importance for the maintenance of neuronal network activity.