bluuebunny/crossref_metadata_2025_split huggingface dataset:
How often do they do it? An in-depth analysis of the hybrid zone of two grass snake species (Natrix astreptophoraandNatrix helvetica)
Authors: Asztalos Marika , Schultze Nadine , Ihlow Flora , Geniez Philippe , Berroneau Matthieu , Delmas Claudine , Guiller Gaëtan , Legentilhomme Jérôme , Kindler Carolin , Fritz Uwe 
Published: September 2020

AbstractWe examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.
Neuropsychiatric symptoms in limbic-predominant age-related TDP-43 encephalopathy and Alzheimer’s disease
Authors: Liu Kathy Y , Reeves Suzanne , McAleese Kirsty E , Attems Johannes , Francis Paul , Thomas Alan , Howard Robert 
Published: September 2020

Abstract
There is clinical overlap between presentations of dementia due to limbic-predominant age-related TDP-43 encephalopathy (LATE) and Alzheimer’s disease. It has been suggested that the combination of Alzheimer’s disease neuropathological change (ADNC) and LATE neuropathological changes (LATE-NC) is associated with greater neuropsychiatric symptom burden, compared to either pathology alone. Longitudinal Neuropsychiatric Inventory and psychotropic medication prescription data from neuropathologically diagnosed pure ADNC (n = 78), pure LATE-NC (n = 14) and mixed ADNC/LATE-NC (n = 39) brain bank donors were analysed using analysis of variance and linear mixed effects regression models to examine the relationship between diagnostic group and neuropsychiatric symptom burden. Nearly all donors had dementia; three (two pure LATE-NC and one pure ADNC) donors had mild cognitive impairment and another two donors with LATE-NC did not have dementia. The mixed ADNC/LATE-NC group was older than the pure ADNC group, had a higher proportion of females compared to the pure ADNC and LATE-NC groups, and had more severe dementia versus the pure LATE-NC group. After adjustment for length of follow-up, cognitive and demographic factors, mixed ADNC/LATE-NC was associated with lower total Neuropsychiatric Inventory and agitation factor scores than pure ADNC, and lower frontal factor scores than pure LATE-NC. Our findings indicate that concomitant LATE pathology in Alzheimer’s disease is not associated with greater neuropsychiatric symptom burden. Future longitudinal studies are needed to further investigate whether mixed ADNC/LATE-NC may be protective against agitation and frontal symptoms in dementia caused by Alzheimer’s disease or LATE pathology.
Indelible stain: territorial stigmatization and the limits of resistance
Authors: Power Martin J , Haynes Amanda , Devereux Eoin 
Published: September 2020

AbstractThis article examines the impact of territorial stigma in Limerick, a peripheral Irish city, and whether such stigma can be successfully resisted. It begins by exploring the development of the concept of territorial stigma and its five key characteristics. We reflect on how stigmatization has impacted communities in this city. We then utilize Katz’s (2004) three dimensions of resistance—resistance (denoting an ‘oppositional consciousness’), resilience (denoting coping with life under territorial stigma) and reworking (denoting the recasting of the objects of stigmatization through alternative interpretations) to make sense of how stigmatized identities are being challenged/erased/masked in the context of a top-down ‘rebranding’ of Limerick City. Ultimately the article argues that the capacity of grassroots resistance alone to alter discourses, which although locally focused are intermeshed with much larger ideological conflicts, is questionable.
Severe Acute Respiratory Syndrome Coronavirus 2 Surveillance in Decedents in a Large, Urban Medical Examiner’s Office
Authors: Brouwer Andrew F , Myers Jeffrey L , Martin Emily T , Konopka Kristine E , Lauring Adam S , Eisenberg Marisa C , Lephart Paul R , Nguyen Teresa , Jaworski Andrea , Schmidt Carl J 
Published: September 2020

Abstract

Background
Given the challenges in implementing widespread testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is increasing interest in alternative surveillance strategies.

Methods
We tested nasopharyngeal swabs from 1094 decedents in the Wayne County Medical Examiner’s Office for SARS-CoV-2. All decedents were assessed using a coronavirus disease 2019 (COVID-19) checklist, and decedents flagged using the checklist (298) were preferentially tested. A random sample of decedents not flagged using the checklist were also tested (796). We statistically analyzed the characteristics of decedents (age, sex, race, and manner of death), differentiating between those flagged using the checklist and not and between those SARS-CoV-2–positive and not.

Results
A larger percentage of decedents overall were male (70% vs 48%) and black (55% vs 36%) compared with the catchment population. Seven-day average percent positivity among flagged decedents closely matched the trajectory of percent positivity in the catchment population, particularly during the peak of the outbreak (March and April 2020). After a lull in May to mid-June, new positive tests in late June coincided with increased case detection in the catchment. We found large racial disparities in test results; SARS-CoV-2–positive decedents were substantially more likely to be black than SARS-CoV-2–negative decedents (82% vs 51%). SARS-CoV-2–positive decedents were also more likely to be older and to have died of natural causes, including of COVID-19 disease.

Conclusions
Disease surveillance through medical examiners and coroners could supplement other forms of surveillance and serve as a possible early outbreak warning sign.
George Washington’s Recurrent Health Problems and Fatal Infection Re-examined
Authors: Mackowiak Philip A 
Published: September 2020

Abstract
George Washington’s medical history has been recounted so many times and with such consistency that it seems that nothing new remains to be said about the panoply of disorders that plagued him during his life. The same can be said for the particular one that carried him off at age 67. We know that he had small pox, dysentery, recurrent attacks of malaria, and a host of other infections during his long and spectacularly productive career. His teeth were a source of unrelenting distress despite his assiduous attention to dental hygiene; and terminally, he developed a rapidly progressive upper respiratory infection, which killed him in little more than a day and a half despite the best medical care available.
Under cover of the night: context-dependency of anthropogenic disturbance on stress levels of wild roe deer Capreolus capreolus
Authors: Carbillet Jeffrey , Rey Benjamin , Palme Rupert , Morellet Nicolas , Bonnot Nadège , Chaval Yannick , Cargnelutti Bruno , Hewison A J M , Gilot-Fromont Emmanuelle , Verheyden Hélène 
Published: September 2020

Abstract
Wildlife populations are increasingly exposed to human-induced modifications of their habitats. To cope with anthropogenic stressors, animals can adjust their behaviour—for example, by shifting their activity to more sheltered habitats, or becoming more nocturnal. However, whether use of spatial and temporal adjustments in behaviour may regulate the endocrine response is poorly documented. Here, we analyzed faecal cortisol metabolites (FCMs) of wild roe deer (Capreolus capreolus) living in a human-dominated agro-ecosystem. Using Global Positioning System monitoring of 116 individuals, we assessed their spatial behaviour and tested whether proximity to anthropogenic structures (linear distance to built-up areas) and the use of refuge habitats (woodland and hedges) influenced FCM levels. In accordance with our predictions, individuals ranging closer to anthropogenic structures during daytime had higher FCM levels, but this relationship was buffered as use of refuge habitat increased. In addition, this link between proximity to anthropogenic structures and FCM levels disappeared when we analyzed spatial behaviour at night. Finally, FCM levels were higher when the ambient temperature was lower, and during years of low resource availability. Our results demonstrate that the stress levels of large mammals may be strongly influenced by their proximity to anthropogenic activities, but that these effects may be buffered by behavioural adjustments in terms of space use and circadian rhythm. Whereas most studies have focused on the influence of environmental heterogeneity, our analysis highlights the need to also consider the fine-scale spatial response of individuals when studying the hormonal response of wild animals to human disturbance. We emphasize the potential to mitigate this hormonal stress response, and its potential negative consequences on population dynamics, through the preservation or restoration of patches of refuge habitat in close proximity to human infrastructure.
CitrusKB: a comprehensive knowledge base for transcriptome and interactome ofCitrusspp. infected byXanthomonas citrisubsp.citriat different infection stages
Authors: Ferrasa Adriano , Murata Mayara M , Cofre Teresa D C G , Cavallini Juliana S , Peron Gustavo , Julião Maria H M , Belasque José , Ferreira Henrique , Ferro Maria Inês T , Leite Rui P , Penha Helen A , Carvalho Flávia M S , Varani Alessandro M , Herai Roberto H , Ferro Jesus A 
Published: September 2020

AbstractCitrus canker type A is a serious disease caused by Xanthomonas citri subsp. citri (X. citri), which is responsible for severe losses to growers and to the citrus industry worldwide. To date, no canker-resistant citrus genotypes are available, and there is limited information regarding the molecular and genetic mechanisms involved in the early stages of the citrus canker development. Here, we present the CitrusKB knowledge base. This is the first in vivo interactome database for different citrus cultivars, and it was produced to provide a valuable resource of information on citrus and their interaction with the citrus canker bacterium X. citri. CitrusKB provides tools for a user-friendly web interface to let users search and analyse a large amount of information regarding eight citrus cultivars with distinct levels of susceptibility to the disease, with controls and infected plants at different stages of infection by the citrus canker bacterium X. citri. Currently, CitrusKB comprises a reference citrus genome and its transcriptome, expressed transcripts, pseudogenes and predicted genomic variations (SNPs and SSRs). The updating process will continue over time by the incorporation of novel annotations and analysis tools. We expect that CitrusKB may substantially contribute to the field of citrus genomics. CitrusKB is accessible at http://bioinfo.deinfo.uepg.br/citrus. Users can download all the generated raw sequences and generated datasets by this study from the CitrusKB website.
Siberian sturgeon multi-tissue reference transcriptome database
Authors: Klopp Christophe , Cabau Cédric , Greif Gonzalo , Lasalle André , Di Landro Santiago , Vizziano-Cantonnet Denise 
Published: September 2020

Abstract
Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies.
Results: We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets.
Availability: The database is publicly available at http://siberiansturgeontissuedb.sigenae.org
Supplementary information: Supplementary data are available at Database online.
A hybrid therapy for arrhythmogenic congestive cavity in a single ventricle
Authors: Izumi Gaku , Yokoshiki Hisashi , Tachibana Tsuyoshi , Takeda Atsuhito 
Published: September 2020

Abstract
We describe a 15-year-old girl who underwent intraoperative catheter ablation for the ventricular tachycardia associated with Ebstein’s anomaly with functional pulmonary atresia and a small right ventricle (RV) after Fontan surgery. The computed tomography showed the dilated right atrium and RV due to the failure of RV plication. The activation mapping revealed that the ventricular tachycardia showed a focal pattern originating from the atrialized RV (aRV). With careful preparations, the procedure of catheter ablation combined with the adjustment of Starnes fenestration and plication of RV/atrialized RV was very effective for this patient.
Outcome quality of Class II division 1 Herbst-multibracket appliance treatment: influence of pretreatment Class II severity and skeletal maturity
Authors: Bock Niko C , Jost Julia , Ruf Sabine 
Published: September 2020

Summary

Background
No reliable predictive factors for treatment (Tx) success and outcome quality in Class II:1 Tx have been identified yet.

Objective
To assess the influence of pre-Tx Class II severity and skeletal maturity on outcome quality after Herbst-multibracket appliance (MBA) Tx.

Subjects and methods
All Class II:1 patients who completed Herbst-MBA Tx between 1986 and 2014 at University of Giessen, Germany. Pre-Tx (T0), post-Tx (T1), and (if available) post-retention (≥24 months; T2) study casts were evaluated using the Peer Assessment Rating (PAR) index and the Ahlgren scale. Three occlusal severity (mild, moderate, and severe) and four skeletal maturity (pre-peak, peak, post-peak, and adult) subgroup categories were defined.

Results
Four hundred eight-five patients (age at T0: 14.4 ± 3.2 years) could be evaluated; post-retention (T3) data were available for 230 patients. For the total sample, the median PAR score was 32.4 ± 8.85 at T0, 8.0 ± 4.52 at T1, and 8.8 ± 5.11 at T2. Very low correlations between the subgroup categories (occlusal severity/skeletal maturity) and PAR-score reduction were detected both during Tx (r = 0.12/r = 0.05) and the total observation period (r = 0.17/r = 0.03). The overall outcome quality according to Ahlgren was: 17.0% excellent, 34.8% good, 43.8% acceptable, 2.2% unacceptable, and 2.2% not assessable. The association with the subgroup categories was: p = 0.019 (occlusal severity)/p = 0.820 (skeletal maturity).

Limitations
Retrospective study design with follow-up data was not available from all subjects and no data from untreated controls. Tx was performed by several physicians using different kind of MBAs.

Conclusion
Class II:1 Herbst-MBA Tx is an effective and successful Tx approach irrespective of pre-Tx skeletal maturity but dependent—to a certain extent—on Class II severity. Thus, when considering a Herbst appliance for Class II correction, neither of the two variables should considerably limit the indication.
Burden of infections on older patients presenting to general practice: a registry-based study
Authors: Struyf Thomas , Nuyts Shauni , Tournoy Jos , Vaes Bert , Verbakel Jan Y , Van den Bruel Ann 
Published: September 2020

Abstract

Background
Estimates on the incidence rates of infections are needed to assess the burden of disease in the community.

Objective
To assess incidence rates of potentially serious infections in patients aged 65 years and over presenting to Flemish general practice from 2000 to 2015, and to describe patient characteristics.

Methods
We performed a retrospective study, based on data provided by the Intego morbidity registry of the KU Leuven, which includes the electronic medical records of 111 general practitioners. Incidence rates were calculated taking person-time at risk into account, and longitudinal trends from 2000 to 2015 were analysed using autoregressive time-series analyses.

Results
On average, a person aged 65 years or older has an 8.0% risk of getting a potentially serious infection each year. Acute cystitis was the most often occurring potentially serious infection [39.8/1000 person-years; 95% confidence interval (CI): 39.4–40.2], followed by influenza like illness (ILI, 24.3/1000 person-years; 95% CI: 24.0–24.6) and pneumonia (9.7/1000 person-years; 95% CI: 9.5–9.9). The incidence rates of pneumonia were higher in older age groups and in men, whereas they were markedly lower for ILI at older ages, in both genders. From 2000 to 2015, overall incidence rates decreased significantly for ILI, while they increased in women for pneumonia, acute cystitis and pyelonephritis. Common chronic comorbidities were non-insulin dependent diabetes, chronic obstructive pulmonary disease, asthma, heart failure and chronic renal insufficiency.

Conclusions
Potentially serious infections are quite common in an older patient population presenting to primary care. They are accompanied by several chronic comorbidities, which may differ by infection type.
Metabolic alterations and vulnerabilities in hepatocellular carcinoma
Authors: Tenen Daniel G , Chai Li , Tan Justin L 
Published: September 2020

Abstract
Liver cancer is a serious disease. It is ranked as the cancer with the second highest number of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC), which arises from transformed hepatocytes, is the major subtype of liver cancer. It accounts for 85% of total liver-cancer cases. An important aspect of HCC that has been actively studied is its metabolism. With the liver as the primary site of numerous metabolic processes in the body, it has been shown that the metabolism of HCC cells is highly dysregulated compared to that of normal hepatocytes. It is therefore crucial to understand the metabolic alterations caused by HCC and the underlying mechanisms for these alterations. This deeper understanding will allow diagnostic and therapeutic advancements in the treatment of HCC. In this review, we will summarize the current literature in HCC metabolic alterations, induced vulnerabilities, and potential therapeutic interventions.
Older Adults’ Experience of the COVID-19 Pandemic: A Mixed-Methods Analysis of Stresses and Joys
Authors: Whitehead Brenda R , Torossian Emily 
Published: September 2020

AbstractBackground and ObjectivesThe coronavirus disease 2019 (COVID-19) pandemic is experienced differently across individuals, and older adults’ different life experiences lead to a variety of ways of coping. The present study explores older adults’ reports of what about the pandemic is stressful, and what brings joy and comfort in the midst of stress.Research Design and MethodsAn online survey asked 825 U.S. adults aged 60 and older to complete questionnaires assessing 3 psychological well-being indicators: perceived stress, negative affect, and positive affect. Participants also responded to open-ended questions about what was stressful and what brought joy or comfort at the time of the survey. A mixed-method approach first qualitatively analyzed the open-ended responses, content analysis identified themes most frequently reported, and quantitative analysis examined the associations between various stressors and joys and the psychological well-being indicators.ResultsQualitative analysis revealed 20 stress categories and 21 joy/comfort categories. The most commonly reported stressors were confinement/restrictions, concern for others, and isolation/loneliness; the most commonly reported sources of joy/comfort were family/friend relationships, digital social contact, and hobbies. Demographic comparisons revealed variations in experience. Independent t tests revealed stress from concern for others, the unknown future, and contracting the virus to be significantly associated with poorer psychological well-being; faith, exercise/self-care, and nature were associated with more positive psychological well-being.Discussion and ImplicationsResults are discussed in the context of stress and coping theory, highlighting the importance of understanding the unique stress experience of each individual for effective distress intervention.
Loss ofAnks6leads to YAP deficiency and liver abnormalities
Authors: Airik Merlin , Schüler Markus , McCourt Blake , Weiss Anna-Carina , Herdman Nathan , Lüdtke Timo H , Widmeier Eugen , Stolz Donna B , Nejak-Bowen Kari N , Yimlamai Dean , Wu Yijen L , Kispert Andreas , Airik Rannar , Hildebrandt Friedhelm 
Published: September 2020

AbstractANKS6 is a ciliary protein that localizes to the proximal compartment of the primary cilium, where it regulates signaling. Mutations in the ANKS6 gene cause multiorgan ciliopathies in humans, which include laterality defects of the visceral organs, renal cysts as part of nephronophthisis and congenital hepatic fibrosis (CHF) in the liver. Although CHF together with liver ductal plate malformations are common features of several human ciliopathy syndromes, including nephronophthisis-related ciliopathies, the mechanism by which mutations in ciliary genes lead to bile duct developmental abnormalities is not understood. Here, we generated a knockout mouse model of Anks6 and show that ANKS6 function is required for bile duct morphogenesis and cholangiocyte differentiation. The loss of Anks6 causes ciliary abnormalities, ductal plate remodeling defects and periportal fibrosis in the liver. Our expression studies and biochemical analyses show that biliary abnormalities in Anks6-deficient livers result from the dysregulation of YAP transcriptional activity in the bile duct-lining epithelial cells. Mechanistically, our studies suggest, that ANKS6 antagonizes Hippo signaling in the liver during bile duct development by binding to Hippo pathway effector proteins YAP1, TAZ and TEAD4 and promoting their transcriptional activity. Together, this study reveals a novel function for ANKS6 in regulating Hippo signaling during organogenesis and provides mechanistic insights into the regulatory network controlling bile duct differentiation and morphogenesis during liver development.