bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data
Authors: Zhang Zhe , Zhang Qianqian , Xiao Qian , Sun Hao , Gao Hongding , Yang Yumei , Chen Jiucheng , Li Zhengcao , Xue Ming , Ma Peipei , Yang Hongjie , Xu Ningying , Wang Qishan , Pan Yuchun 
Published: October 2018

SummaryInbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reduced‐representation sequencing method. After imputation and quality control, 60 850 high‐confidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH‐related variables were compared between imputed and non‐missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction‐related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.
Recent developments and highlights in mechanisms of allergic diseases: Microbiome
Authors: Lunjani Nonhlanhla , Satitsuksanoa Pattraporn , Lukasik Zuzanna , Sokolowska Milena , Eiwegger Thomas , O'Mahony Liam 
Published: October 2018

AbstractAll body surfaces are exposed to a wide variety of microbes, which significantly influence immune reactivity within the host. This review provides an update on some of the critical novel findings that have been published on the influence of the microbiome on atopic dermatitis, food allergy and asthma. Microbial dysbiosis has consistently been observed in the skin, gut and lungs of patients with atopic dermatitis, food allergy and asthma, respectively, and the role of specific microbes in allergic disorders is being intensively investigated. However, many of these discoveries have yet to be translated into routine clinical practice.
Diagonal Likelihood Ratio Test for Equality of Mean Vectors in High-Dimensional Data
Authors: Hu Zongliang , Tong Tiejun , Genton Marc G. 
Published: October 2018

Abstract
We propose a likelihood ratio test framework for testing normal mean vectors in high-dimensional data under two common scenarios: the one-sample test and the two-sample test with equal covariance matrices. We derive the test statistics under the assumption that the covariance matrices follow a diagonal matrix structure. In comparison with the diagonal Hotelling's tests, our proposed test statistics display some interesting characteristics. In particular, they are a summation of the log-transformed squared t-statistics rather than a direct summation of those components. More importantly, to derive the asymptotic normality of our test statistics under the null and local alternative hypotheses, we do not need the requirement that the covariance matrices follow a diagonal matrix structure. As a consequence, our proposed test methods are very flexible and readily applicable in practice. Simulation studies and a real data analysis are also carried out to demonstrate the advantages of our likelihood ratio test methods.
Conservation geopolitics
Authors: Hodgetts Timothy , Burnham Dawn , Dickman Amy , Macdonald Ewan A. , Macdonald David W. 
Published: October 2018

AbstractWe reviewed recent work concerning the impact of geopolitics on wildlife conservation (and vice versa) and identified future priorities in conservation geopolitics research. Geopolitics is understood as both an analytical focus on geopolitical practices (especially concerning the behavior) of countries with respect to territory and national security and a set of theories developed to explain and predict those behaviors. We developed a typology of core geopolitical practices of relevance to conservation: territorial practices of colonization and the management of migrations and borders, and security practices relating to military, economic, and environmental security. We identified research that considers how these practices affect conservation situations and outcomes, noting the recent emergence of conceptual developments such as “environmental geopolitics” and “geopolitical ecology” that draw on multiple fields within the social sciences to theorize the links between geopolitics and environmental management. We defined a "geopolitical perspective" as a focus on geopolitical practices combined with an explicit engagement with geopolitical theory and identified conservation situations where this perspective could contribute to analytical clarity. We suggest the most pressing questions in conservation research to which the geopolitical perspective might contribute are how political and economic differences between countries affect biodiversity outcomes, how geopolitical practices to address those differences facilitate or frustrate conservation efforts, how national borders and human and wildlife movements can be better managed for the benefit of both, and how the most effective conservation strategies can be best selected to suit existing (and future) geopolitical realities.
Novel immune signatures associated with dysplastic naevi and primary cutaneous melanoma in human skin
Authors: Yan Bernice Y. , Garcet Sandra , Gulati Nicholas , Kiecker Felix , Fuentes‐Duculan Judilyn , Gilleaudeau Patricia , Sullivan‐Whalen Mary , Shemer Avner , Mitsui Hiroshi , Krueger James G. 
Published: October 2018

AbstractDysplastic naevi (DN) are benign lesions with atypical features intermediate between that of common melanocytic naevi (CMN) and malignant melanoma (MM). Debate remains over whether DN represent progressive lesions from CMN. Through gene expression profiling and analysis of molecular gene signatures, our study revealed progressive increases in immune activation and regulation, along with pathways implicated in melanomagenesis, from CMN to DN to MM. Using criteria of 1.5‐fold change and false discovery rate ≤0.05, we found differential expression of 7186 probes (6370 unique genes) with the largest difference detected between DN and MM from the standpoint of genomic melanoma progression. Despite progressive increases in the T‐helper type 1 (Th1)‐inducing gene (IL‐12), RT‐PCR indicated impaired Th1 or cytotoxic T‐cell response (decreased IFN‐γ) in MM. Concordantly, our results indicated progressive increases in molecular markers associated with regulatory T cells, exhausted T cells and tolerogenic dendritic cells, including detection of increased expression of suppressor of cytokine signalling 3 (SOCS3) in dendritic cells associated with MM. All together, our findings suggest that the increased immunosuppressive microenvironment of melanoma may contribute to unhampered proliferation of neoplastic cells. In addition, the detection of increased markers associated with tolerogenic dendritic cells in MM suggests that targeting these suppressive immune cell types may represent an alternative avenue for future immunotherapy.
Should Ki67 immunohistochemistry be performed on all lesions in multifocal small intestinal neuroendocrine tumours?
Authors: Numbere Numbereye , Huber Aaron R , Shi Chanjuan , Cates Justin M M , Gonzalez Raul S 
Published: October 2018

AimsWell‐differentiated small intestinal neuroendocrine tumours (SI‐NETs) are often multifocal, and this has been suggested to impart worse disease‐free survival. Practice guidelines have not been established for World Health Organisation (WHO) grading of multiple primary lesions.Methods and resultsWe identified 68 patients with ileal/jejunal SI‐NET for a combined total of 207 primary lesions. Each case was evaluated for patient age and sex; size of all tumours; presence of lymph node metastases, mesenteric tumour deposits or distant metastases; and disease‐specific outcome. Ki67 staining was performed on all 207 primary lesions. The relationship between multifocality and clinicopathological factors was compared using Fisher's exact test. Outcome was tested using Cox proportional hazard regression. Forty‐two patients had unifocal disease, and 26 had multifocal disease (median five lesions, range = 2–32). Most tumours were WHO grade 1 (201 of 207, 97%). Of the five patients with grades 2/3 tumours, three patients had unifocal disease, one patient had two subcentimetre grade 2 lesions (including the largest) and eight subcentimetre grade 1 lesions, and one patient had one 1.6‐cm grade 3 lesion and one subcentimetre grade 1 lesion. There was a positive correlation between tumour size and Ki67 index (coefficient 0.28; 95% confidence interval 0.05–0.52, P = 0.017). There was no significant association between multifocality and nodal metastases, mesenteric tumour deposits, distant metastases or disease‐specific survival.ConclusionsIn patients with multifocal SI‐NET, unless a particular lesion has a high mitotic rate, only staining the largest lesion for Ki67 should serve to grade almost all cases accurately. Multifocality does not appear to significantly impact patient survival.
Toothbrush wear in relation to toothbrushing effectiveness
Authors: Van Leeuwen Martijn P. C. , Van der Weijden Fridus A. , Slot Dagmar Else , Rosema Martijn A. M. 
Published: October 2018

AbstractObjectiveTo investigate to what extent the degree of toothbrush wear of 3‐month‐old manual toothbrushes influence plaque scores.Material and methodsDuring a recently published study with a follow‐up of 1 year, all participants performed a similar basic home‐based oral hygiene regimen. Hence, they were instructed to brush for 2 minutes twice daily according to the Bass method technique and using a standard dentifrice containing sodium fluoride. Toothbrushes were turned in every 3‐month, and the degree of wear was scored. The mean plaque score data were additionally analysed and correlated with wear scores of the toothbrushes.ResultsFor analysis, for each of 172 individual participants, a set of three identical, 3‐month‐old used toothbrushes were available. Toothbrush wear varied widely between participants. However, per patient, the 3‐month wear status of the three evaluated toothbrushes was strongly correlated (rho = 0.8, P < 0.0001). Participants who returned toothbrushes with extreme wear had significantly higher plaque scores than those who returned toothbrushes with no visible or light wear (P = 0.01).ConclusionToothbrush wear per individual patient is fairly consistent. Toothbrushes with extreme wear were less effective than those with no or light wear. Therefore, bristle splaying appears to be a more appropriate measure of brush replacement time then the commonly used toothbrush age. Splaying of the outer tufts beyond the base of the toothbrush is a condition that indicates it is time to change the brush.
The handover room: a qualitative enquiry into the experience of morning clinical handover for acute medical teams
Authors: Donnelly Sinead , Dinesh Dorothy , Dew Kevin , Stubbe Maria 
Published: October 2018

AbstractBackgroundEffective clinical handover has always been integral to delivering safe, high‐quality care in medical wards.AimAs handover activity increases in importance we wanted to explore the experience of physicians and trainee doctors. There is little research on internal medicine handover with even less based on direct observational research.MethodsData collection over 4 months by two general medicine physicians included participant observation of 37 meetings and 52 audio‐recorded individual interviews. Inductive thematic analysis of the transcribed interviews proceeded iteratively in parallel with data collection.ResultsThere was an excellent response rate from 27 of 28 invited trainees and 25 of 26 invited physicians. Overall the experience was positive. Acute medicine handover is a complex human endeavour, occurring daily with an unpredictable workload and areas of tension. Themes were grouped as structural (leadership role, start time, sequence, checklist, handbacks and efficiency) and relational (sensitivity, collegiality, acknowledgement, performance anxiety, tension, responsibility and leadership style). The physician leader needs to be skilled to follow the agreed and evolving process as well as being prepared, authoritative, flexible, equitable, aware and sensitive to the needs of senior colleagues and trainees. There was a tension between efficiency and teaching opportunities.ConclusionThis paper adds to a contextually sensitive understanding of the social dynamics of handover in acute medicine. Addressing the structural aspects is important to provide the necessary consistency and efficiency in what is an extremely complex and time‐sensitive environment. As we continue to work on the evolution of the handover process in acute internal medicine, we must also attend to the relational aspects which are dynamic and central to its sustainability.
Acute pulmonary embolism: a concise review of diagnosis and management
Authors: Hepburn‐Brown Morgan , Darvall Jai , Hammerschlag Gary 
Published: October 2018

AbstractAn acute pulmonary embolism (aPE) is characterised by occlusion of one or more pulmonary arteries. Physiological disturbance may be minimal, but often cardiac output decreases as the right ventricle attempts to overcome increased afterload. Additionally, ventilation‐perfusion mismatches can develop in affected vascular beds, reducing systemic oxygenation. Incidence is reported at 50–75 per 100 000 in Australia and New Zealand, with 30‐day mortality rates ranging from 0.5% to over 20%. Incidence is likely to increase with the ageing population, increased survival of patients with comorbidities that are considered risk factors and improving sensitivity of imaging techniques. Use of clinical prediction scores, such as the Wells score, has assisted in clinical decision‐making and decreased unnecessary radiological investigations. However, imaging (i.e. computed tomography pulmonary angiography or ventilation‐perfusion scans) is still necessary for objective diagnosis. Anti‐coagulation remains the foundation of PE management. Haemodynamically unstable patients require thrombolysis unless absolutely contraindicated, while stable patients with right ventricular dysfunction or ischaemia should be aggressively anti‐coagulated. Stable patients with no right ventricular dysfunction can be discharged home early with anti‐coagulation and review. However, treatment should be case dependent with full consideration of the patient’s clinical state. Direct oral anti‐coagulants have become an alternative to vitamin K antagonists and are facilitating shorter hospital admissions. Additionally, duration of anti‐coagulation must be decided by considering any provoking factors, bleeding risk and comorbid state. Patients with truly unprovoked or idiopathic PE often require indefinite treatment, while in provoked cases it is typically 3 months with some patients requiring longer periods of 6–12 months.
Identification of Lynch syndrome risk variants in the Romanian population
Authors: Iordache Paul D. , Mates Dana , Gunnarsson Bjarni , Eggertsson Hannes P. , Sulem Patrick , Benonisdottir Stefania , Csiki Irma Eva , Rascu Stefan , Radavoi Daniel , Ursu Radu , Staicu Catalin , Calota Violeta , Voinoiu Angelica , Jinga Mariana , Rosoga Gabriel , Danau Razvan , Sima Sorin Cristian , Badescu Daniel , Suciu Nicoleta , Radoi Viorica , Mates Ioan Nicolae , Dobra Mihai , Nicolae Camelia , Kristjansdottir Sigrun , Jonasson Jon G. , Manolescu Andrei , Arnadottir Gudny , Jensson Brynjar , Jonasdottir Aslaug , Sigurdsson Asgeir , le Roux Louise , Johannsdottir Hrefna , Rafnar Thorunn , Halldorsson Bjarni V. , Jinga Viorel , Stefansson Kari 
Published: October 2018

AbstractTwo familial forms of colorectal cancer (CRC), Lynch syndrome (LS) and familial adenomatous polyposis (FAP), are caused by rare mutations in DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2) and the genes APC and MUTYH, respectively. No information is available on the presence of high‐risk CRC mutations in the Romanian population. We performed whole‐genome sequencing of 61 Romanian CRC cases with a family history of cancer and/or early onset of disease, focusing the analysis on candidate variants in the LS and FAP genes. The frequencies of all candidate variants were assessed in a cohort of 688 CRC cases and 4567 controls. Immunohistochemical (IHC) staining for MLH1, MSH2, MSH6, and PMS2 was performed on tumour tissue. We identified 11 candidate variants in 11 cases; six variants in MLH1, one in MSH6, one in PMS2, and three in APC. Combining information on the predicted impact of the variants on the proteins, IHC results and previous reports, we found three novel pathogenic variants (MLH1:p.Lys84ThrfsTer4, MLH1:p.Ala586CysfsTer7, PMS2:p.Arg211ThrfsTer38), and two novel variants that are unlikely to be pathogenic. Also, we confirmed three previously published pathogenic LS variants and suggest to reclassify a previously reported variant of uncertain significance to pathogenic (MLH1:c.1559‐1G>C).
In silico and in vitro analyses of the pathological relevance of the R258H mutation of hepatocyte nuclear factor 4α identified in maturity‐onset diabetes of the young type 1
Authors: Sugawara Kenji , Nomura Kazuhiro , Okada Yuko , Sugano Aki , Matsumoto Masaaki , Takarada Toru , Takeuchi Atsuko , Awano Hiroyuki , Hirota Yushi , Nishio Hisahide , Takaoka Yutaka , Ogawa Wataru 
Published: October 2018

AbstractMutations of the hepatocyte nuclear factor 4α (HNF4α) gene give rise to maturity‐onset diabetes of the young type 1. Although many such mutations have been identified in affected individuals, part of these mutations has been characterized with regard to their pathological relevance. We here identified a missense mutation (c.773G>A, p.R258H) of HNF4A in a mother and daughter with early‐onset diabetes and impaired insulin secretion. In silico simulation and in vitro luciferase reporter analyses showed that the mutation impairs the stability of self‐dimerization and the transactivation activity of HNF4α. Although arginine‐258 does not appear to participate directly in dimerization, its mutation alters the electrostatic surface potential of the dimer interface. Our results thus suggest that this mutation impairs the function of HNF4α and thereby contributes to the pathogenesis of maturity‐onset diabetes of the young type 1.
Feasibility of an 8‐item questionnaire for early diagnosis of inflammatory bowel disease in primary care
Authors: Chmiel Corinne , Vavricka Stephan R. , Hasler Susann , Rogler Gerhard , Zahnd Nadine , Schiesser Salomé , Tandjung Ryan , Scherz Nathalie , Rosemann Thomas , Senn Oliver 
Published: October 2018

AbstractAimsDiagnosis of inflammatory bowel disease (IBD) is often associated with a diagnostic delay. Although faecal calprotectin is a helpful screening tool, the widespread use in primary care (PC) may not be appropriate due to the low prevalence of IBD in this setting. To increase pretest probability for a positive calprotectin test, an 8‐item questionnaire (CalproQuest) was tested for its feasibility and acceptability in PC.MethodsPopulation: PC patients with unspecific gastrointestinal complaints for at least 2 weeks. The CalproQuest consists of four major and four minor questions specific for IBD. It is considered positive if greater than or equal to two major or one major and two minor criteria are positive. Primary outcome: feasibility of CalproQuest, secondary outcome: patient's acceptance of stool sampling.ResultsOf 95 patients with a complete CalproQuest 52 (54.7%) were positive, 39 (41.1%) fulfilled two major and 13 (13.7%) one major and greater than or equal to two minor criteria. Twenty‐seven general practitioners completed 83 (87.4%) questionnaires on feasibility which was assessed positive. Eighty‐two patients (86.3%) completed questionnaires on acceptance which was high.ConclusionThe CalproQuest is a feasible instrument for assessing IBD in PC. Further prospective studies concerning validity and cost effectiveness of a combined use with the calprotectin test in this setting are necessary.
Bonamia in Ostrea angasi: Diagnostic performance, field prevalence and intensity
Authors: Buss Jessica J. , Wiltshire Kathryn H. , Prowse Thomas A. A. , Harris James O. , Deveney Marty R. 
Published: October 2018

AbstractBonamia spp. parasites threaten flat oyster (Ostrea spp.) farming worldwide. Understanding test performance is important for designing surveillance and interpreting diagnostic results. Following a pilot survey which found low Bonamia sp. intensity in farmed Ostrea angasi, we tested further oysters (n = 100–150) from each of three farms for Bonamia sp. using heart smear, histology and qPCR. We used a Bayesian Latent Class Model to assess diagnostic sensitivity (DSe) and specificity (DSp) of these tests individually or in combination, and to assess prevalence. Histology was the best individual test (DSe 0.76, DSp 0.93) compared to quantitative polymerase chain reaction (qPCR) (DSe 0.69, DSp 0.93) and heart smear (DSe 0.61, DSp 0.60). Histology combined with qPCR and defining a positive from either test as an infected case maximized test performance (DSe 0.91, DSp 0.88). Prevalence was higher at two farms in a high‐density oyster growing region than at a farm cultivating oysters at lower density. Parasite intensities were lower than in New Zealand and European studies, and this is probably contributed to differences in the performance of test when compared to other studies. Understanding diagnostic test performance in different populations can support the development of improved Bonamia surveillance programs.
Are coronectomy studies being cited? A bibliometric study
Authors: Yeung Andy Wai Kan , Wong Natalie Sui Miu , Leung Yiu Yan 
Published: October 2018

AbstractAimThe aim of the present bibliometric study was to analyze the citations received by coronectomy papers and their references.MethodsData were extracted from the Web of Science online database. After excluding irrelevant papers, full record and cited references from 79 papers were downloaded and imported into VOSviewer and CRExplorer for bibliometric analyses.ResultsThe 79 papers on coronectomy collectively had 9.7 citations per paper. The h‐index of this collection of papers was 17. The top five major contributing countries were the UK (N = 20, 25.3%), the USA (N = 10, 12.7%), Italy (N = 9, 11.4%), China (N = 5, 6.3%), and Turkey (N = 5, 6.3%). The top two major contributing journals, Journal of Oral and Maxillofacial Surgery and British Journal of Oral and Maxillofacial Surgery, together accounted for more than half of the 79 papers (N = 43, 54.4%).ConclusionsPapers dealing with postoperative morbidity topics had high citation counts in general, such as dry socket (27.4 citations per paper), infection (24.6 citations per paper), and safety (35.5 citations per paper). Citation per paper correlated with publication count at the affiliation level, but not at the author, country, and journal levels.