bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying High-Resolution Variant Classification to Cardiac Arrhythmogenic Gene Testing in a Demographically Diverse Cohort of Sudden Unexplained Deaths
Authors: Lin Ying , Williams Nori , Wang Dawei , Coetzee William , Zhou Bo , Eng Lucy S. , Um Sung Yon , Bao Ruijun , Devinsky Orrin , McDonald Thomas V. , Sampson Barbara A. , Tang Yingying 
Published: December 2017

Background—
Genetic variant interpretation contributes to testing yield differences reported for sudden unexplained death. Adapting a high-resolution variant interpretation framework, which considers disease prevalence, reduced penetrance, genetic heterogeneity, and allelic contribution to determine the maximum tolerated allele count in gnomAD, we report an evaluation of cardiac channelopathy and cardiomyopathy genes in a large, demographically diverse sudden unexplained death cohort that underwent thorough investigation in the United States’ largest medical examiner’s office.

Methods and Results—
The cohort has 296 decedents: 147 Blacks, 64 Hispanics, 49 Whites, 22 Asians, and 14 mixed ethnicities; 142 infants (1 to 11 months), 39 children (1 to 17 years), 74 young adults (18 to 34 years), and 41 adults (35 to 55 years). Eighty-nine cardiac disease genes were evaluated. Using a high-resolution variant interpretation workflow, we classified 17 variants as pathogenic or likely pathogenic (2 of which were incidental findings and excluded in testing yield analysis), 46 novel variants of uncertain significance, and 130 variants of uncertain significance. Nine pathogenic or likely pathogenic variants in ClinVar were reclassified to likely benign and excluded in testing yield analysis. The yields of positive cases by ethnicity and age were 21.4% in mixed ethnicities, 10.2% Whites, 4.5% Asians, 3.1% Hispanics, and 2% Blacks; 7.7% children, 7.3% in adults, 5.4% young adults, and 2.8% infants. The percentages of uncertain cases with variants of uncertain significance by ethnicity were 45.5% in Asians, 45.3% Hispanics, 44.20% Blacks, 36.7% Whites, and 14.3% in mixed ethnicities.

Conclusions—
High-resolution variant interpretation provides diagnostic accuracy and healthcare efficiency. Under-represented populations warrant greater inclusion in future studies.
The Court of Common Pleas of East Florida 1763-1783
Authors: Mirow M.C. 
Published: December 2017

Legal historians have surmised that court records of the British province of East Florida (1763-1783) have been either lost or destroyed. This assumption was based on the poor conditions for survival of documents in Florida and statements made in the secondary literature on the province. Nonetheless, a significant number of documents related to the courts of British East Florida exist in the National Archives (Kew). These materials reveal an active legal culture using English law in a wide range of courts including (1) the Court of Common Pleas; (2) the Court of Chancery; (3) the Court of General Sessions of the Peace, Oyer et Terminer, Assize and General Gaol Delivery; (4) Special Courts of Oyer et Terminer; (5) the Court of Vice-Admiralty; (6) the Court of Ordinary; (7) the General Court; and (8) a District Court. This article studies a portion of the documents related to the Court of Common Pleas to describe the nature of the court’s practice in civil litigation. It closely examines three cases for which sufficient extant pleadings permit the reconstruction of the general contours of recovery for breach of a sales contract through an action of trespass on the case, for contract enforcement through an action of covenant, and for recovery of a sum certain through an action of debt. The small window provided by these cases into the activities of this court reveals a heretofore unknown world of English common law in North America during and after the American Declaration of Independence. This new information supplements and challenges our established understanding of colonial law in North America in the revolutionary period and the use of law in the British Empire. This study illustrates the many opportunities these sources offer to legal historians of the period.
Market Orientation or Social Orientation?
Authors: Lu Weijing , Liu Chengcheng , Zhao Xiaoping 
Published: December 2017

AbstractThe current studies about the transformation of government-organized foundation (go-foundation) usually focus on “de-administration.” Basing on new institutionalism and resource dependence theory, the study adds substantive rationality to explaingo-foundation transformation in China, and chooses 4 typical cases in Lushan earthquake relief in 2013. The study finds that, thego-foundation goes towards two different directions during transformation: one is resource-oriented marketization and the other is value-oriented socialization. Different from enterprises, the influencing factors of foundation transformation not only include the institution system and resources but also inherent philanthropic value.
Middle Holocene Fisher-Hunter-Gatherers of Lake Turkana in Kenya and Their Cultural Connections with the North: The Pottery
Authors: Keding Birgit 
Published: December 2017

AbstractDuring the Early and Middle Holocene, large areas of today’s arid regions in North and East Africa were populated by fisher-hunter-gatherer communities who heavily relied on aquatic resources. In North Africa, Wavy Line pottery and harpoons are their most salient diagnostic features. Similar finds have also been made at sites in Kenya’s Lake Turkana region in East Africa but a clear classification of the pottery was previously not available. In order to elucidate the cultural connections between Lake Turkana’s first potters and North African groups, the pottery of the Koobi Fora region that was excavated by John Barthelme in the 1970/80s was re-assessed in detail. It was compared and contrasted – on a regional scale – with pottery from Lowasera and sites near Lothagam (Zu4, Zu6) and – on a supra-regional scale – with the pottery of the Central Nile Valley and eastern Sahara. The analyses reveal some significant points: Firstly, the early fisher pottery of Lake Turkana is clearly typologically affiliated with the Early Khartoum pottery and was thus part of the Wavy Line complex. Secondly, certain typological features of the Turkana assemblages, which include only a few Dotted Wavy Line patterns, tentatively hint to a date at least in the 7th millennium bp or earlier. Thirdly, the pottery features suggest that the East African fisher-hunter-gatherers adopted pottery from Northeast Africa.
Identification of a murine CD45−F4/80lo HSC-derived marrow endosteal cell associated with donor stem cell engraftment
Authors: Overholt Kathleen M. , Otsuru Satoru , Olson Timothy S. , Guess Adam J. , Velazquez Victoria M. , Desbourdes Laura , Dominici Massimo , Horwitz Edwin M. 
Published: December 2017

Key Points
Novel CD45–F4/80lo marrow cells are developmentally derived from hematopoietic progenitors and reside among the endosteal osteoblasts. In situ depletion of CD45 cells before marrow radioablation results in flattened osteoblasts and absent HSC engraftment.
Chest computed tomography-derived low fat-free mass index and mortality in COPD
Authors: McDonald Merry-Lynn N. , Diaz Alejandro A. , Rutten Erica , Lutz Sharon M. , Harmouche Rola , San Jose Estepar Raul , Kinney Greg , Hokanson John E. , Gower Barbara A. , Wouters Emiel F.M. , Rennard Stephen I. , Hersh Craig P. , Casaburi Richard , Dransfield Mark T. , Silverman Edwin K. , Washko George R. 
Published: December 2017

Low fat-free mass index (FFMI) is an independent risk factor for mortality in chronic obstructive pulmonary disease (COPD) not typically measured during routine care. In the present study, we aimed to derive fat-free mass from the pectoralis muscle area (FFMPMA) and assess whether low FFMIPMAis associated with all-cause mortality in COPD cases. We used data from two independent COPD cohorts, ECLIPSE and COPDGene.Two equal sized groups of COPD cases (n=759) from the ECLIPSE study were used to derive and validate an equation to calculate the FFMPMAmeasured using bioelectrical impedance from PMA. We then applied the equation in COPD cases (n=3121) from the COPDGene cohort, and assessed survival. Low FFMIPMAwas defined, using the Schols classification (FFMI <16 in men, FFMI <15 in women) and the fifth percentile normative values of FFMI from the UK Biobank.The final regression model included PMA, weight, sex and height, and had an adjusted R2of 0.92 with fat-free mass (FFM) as the outcome. In the test group, the correlation between FFMPMAand FFM remained high (Pearson correlation=0.97). In COPDGene, COPD cases with a low FFMIPMAhad an increased risk of death (HR 1.6, p<0.001).We demonstrated COPD cases with a low FFMIPMAhave an increased risk of death.
Efficient video collection association using geometry-aware Bag-of-Iconics representations
Authors: Wang Ke , Dunn Enrique , Rodriguez Mikel , Frahm Jan-Michael 
Published: December 2017

Abstract
Recent years have witnessed the dramatic evolution in visual data volume and processing capabilities. For example, technical advances have enabled 3D modeling from large-scale crowdsourced photo collections. Compared to static image datasets, exploration and exploitation of Internet video collections are still largely unsolved. To address this challenge, we first propose to represent video contents using a histogram representation of iconic imagery attained from relevant visual datasets. We then develop a data-driven framework for a fully unsupervised extraction of such representations. Our novel Bag-of-Iconics (BoI) representation efficiently analyzes individual videos within a large-scale video collection. We demonstrate our proposed BoI representation with two novel applications: (1) finding video sequences connecting adjacent landmarks and aligning reconstructed 3D models and (2) retrieving geometrically relevant clips from video collections. Results on crowdsourced datasets illustrate the efficiency and effectiveness of our proposed Bag-of-Iconics representation.
Investigating trehalose synthesis genes after cold acclimation in the Antarctic nematodePanagrolaimussp. DAW1
Authors: Seybold Anna C. , Wharton David A. , Thorne Michael A. S. , Marshall Craig J. 
Published: December 2017

Panagrolaimus sp. DAW1 is a freeze-tolerant Antarctic nematode which survives extensive intracellular ice formation. The molecular mechanisms of this extreme adaptation are still poorly understood. We recently showed that desiccation-enhanced RNAi-soaking can be used - in conjunction with qPCR - to screen for phenotypes associated with reduced expression of candidate genes in Panagrolaimus sp. DAW1. Here we present the use of this approach to investigate the role of trehalose synthesis genes in this remarkable organism.Previous studies have showed that acclimating Panagrolaimus sp. DAW1 at 5 °C before freezing or desiccation substantially enhances survival. In this study the expression of tps-2 and other genes associated with trehalose metabolism, as well as lea-1, hsp-70 and gpx-1 in cold-acclimated and non-acclimated nematodes was analyzed using qPCR. Pd-tps-2 and Pd-lea-1 were significantly up-regulated after cold-acclimation, indicating an inducible expression in the cold-adaptation of Panagrolaimus sp. DAW1. The role of trehalose synthesis genes in Panagrolaimus sp. DAW1 was further investigated by RNAi. Compared to the controls, Pd-tps-2a(RNAi)-treated and cold-acclimated nematodes showed a significant decrease in mRNA, but no change in trehalose content or freezing survival. The involvement of two other trehalose synthesis genes (tps-2b and gob-1) was also investigated.These findings provide the first functional genomic investigation of trehalose synthesis genes in the non-model organism Panagrolaimus sp. DAW1. The presence of several trehalose synthesis genes with different RNAi sensitivities suggests the existence of multiple backup systems in Panagrolaimus sp. DAW1, underlining the importance of this sugar in preparation for freezing.
Testing a key assumption in animal communication: between-individual variation in female visual systems alters perception of male signals
Authors: Ronald Kelly L. , Ensminger Amanda L. , Shawkey Matthew D. , Lucas Jeffrey R. , Fernández-Juricic Esteban 
Published: December 2017

ABSTRACTVariation in male signal production has been extensively studied because of its relevance to animal communication and sexual selection. Although we now know much about the mechanisms that can lead to variation between males in the properties of their signals, there is still a general assumption that there is little variation in terms of how females process these male signals. Variation between females in signal processing may lead to variation between females in how they rank individual males, meaning that one single signal may not be universally attractive to all females. We tested this assumption in a group of female wild-caught brown-headed cowbirds (Molothrus ater), a species that uses a male visual signal (e.g. a wingspread display) to make its mate-choice decisions. We found that females varied in two key parameters of their visual sensory systems related to chromatic and achromatic vision: cone densities (both total and proportions) and cone oil droplet absorbance. Using visual chromatic and achromatic contrast modeling, we then found that this between-individual variation in visual physiology leads to significant between-individual differences in how females perceive chromatic and achromatic male signals. These differences may lead to variation in female preferences for male visual signals, which would provide a potential mechanism for explaining individual differences in mate-choice behavior.
First de novo draft genome sequence of Oryza coarctata, the only halophytic species in the genus Oryza
Authors: Mondal Tapan Kumar , Rawal Hukam Chand , Gaikwad Kishor , Sharma Tilak Raj , Singh Nagendra Kumar 
Published: December 2017

Oryza coarctata plant, collected from Sundarban delta of West Bengal, India, has been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. We report for the first time the draft genome with the coverage of 85.71 % and deposited the raw data in NCBI SRA, with BioProject ID PRJNA396417.
Estimating the number of cases of podoconiosis in Ethiopia using geostatistical methods
Authors: Deribe Kebede , Cano Jorge , Giorgi Emanuele , Pigott David M. , Golding Nick , Pullan Rachel L. , Noor Abdisalan M. , Cromwell Elizabeth A. , Osgood‐Zimmerman Aaron , Enquselassie Fikre , Hailu Asrat , Murray Christopher J. L. , Newport Melanie J. , Brooker Simon J. , Hay Simon I. , Davey Gail 
Published: December 2017

Background: In 2011, the World Health Organization recognized podoconiosis as one of the neglected tropical diseases. Nonetheless, the magnitude of podoconiosis and the geographical distribution of the disease is poorly understood. Based on a nationwide mapping survey and geostatistical modelling, we predict the prevalence of podoconiosis and estimate the number of cases across Ethiopia. Methods: We used nationwide data collected in Ethiopia between 2008 and 2013. Data were available for 141,238 individuals from 1,442 communities in 775 districts from all nine regional states and two city administrations. We developed a geostatistical model of podoconiosis prevalence among adults (individuals aged 15 years or above), by combining environmental factors. The number of people with podoconiosis was then estimated using a gridded map of adult population density for 2015. Results: Podoconiosis is endemic in 345 districts in Ethiopia: 144 in Oromia, 128 in Southern Nations, Nationalities and People’s [SNNP], 64 in Amhara, 4 in Benishangul Gumuz, 4 in Tigray and 1 in Somali Regional State. Nationally, our estimates suggest that 1,537,963 adults (95% confidence intervals, 290,923-4,577,031 adults) were living with podoconiosis in 2015. Three regions (SNNP, Oromia and Amhara) contributed 99% of the cases. The highest proportion of individuals with podoconiosis resided in the SNNP (39%), while 32% and 29% of people with podoconiosis resided in Oromia and Amhara Regional States, respectively. Tigray and Benishangul Gumuz Regional States bore lower burdens, and in the remaining regions, podoconiosis was almost non-existent. Conclusions: The estimates of podoconiosis cases presented here based upon the combination of currently available epidemiological data and a robust modelling approach clearly show that podoconiosis is highly endemic in Ethiopia. Given the presence of low cost prevention, and morbidity management and disability prevention services, it is our collective responsibility to scale-up interventions rapidly.
Narrative der ‚guten Ernährung‘: Ernährungsidentitäten und die Aneignung öffentlicher Nachhaltigkeitsdiskurse durch Konsument*innen
Authors: Krüger Timmo , Strüver Anke 
Published: December 2017

ZusammenfassungIm Bereich der Ernährung sind es ganz alltägliche und allgemein akzeptierte Produktions- und Konsumpraktiken, die zu Nachhaltigkeitsproblemen führen. Als Lösung gilt in öffentlichen Nachhaltigkeitsdiskursen die Kombination aus ‚grünem Wachstum‘ und verantwortungsbewussten Konsument*innen. Die individuelle Aneignung dieser Diskurse steht im Zentrum dieses Aufsatzes. Auf Basis welcher Deutungsmuster, Werte und räumlichen Beziehungen werden Ernährungsidentitäten, Verantwortungszuweisungen und alltägliche Ernährungspraktiken naturalisiert und aufrecht erhalten bzw. kritisiert und verändert? Zur Beantwortung dieser Frage wird auf qualitative Interviews mit Konsument*innen zurückgegriffen, in denen sich eine komplexe und ambivalente Form der Aneignung öffentlicher Nachhaltigkeitsdiskurse zeigt. Einerseits werden dominante Muster der öffentlichen Nachhaltigkeitsdiskurse (re-)produziert. Andererseits wird dem Optimismus bezüglich des Gestaltungspotenzials von verantwortungsbewussten Konsument*innen eine Absage erteilt. Weiterhin werden Widrigkeiten beklagt, die einer als gelungen empfundenen Ernährungspraxis entgegenstehen. Die Umgangsweisen mit dem alltäglichen Scheitern bei der Umsetzung eigener Ansprüche sind sehr divers und reichen von Versuchen des ‚Wachrüttelns‘ anderer Konsument*innen über die Kompensation durch außeralltägliche Events, in denen die Idealvorstellungen einer guten Ernährung gelebt werden können, bis hin zum fatalistischen Einfügen in den Zwang der Verhältnisse. Darüber hinaus wird in gegenhegemonialen Narrativen die Kontingenz machtvoller Strukturen in Erinnerung gerufen, die immer auch auf Widerstand stoßen und somit stets verhandel- und veränderbar bleiben.
Histone Demethylase Activity of Utx Is Essential for Viability and Regulation of HOX Gene Expression in Drosophila
Authors: Copur Ömer , Müller Jürg 
Published: December 2017

Abstract
The trimethylation of histone H3 at lysine 27 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2) is essential for the repression of Polycomb target genes. However, the role of enzymatic demethylation of H3K27me3 by the KDM6-family demethylases Utx, Uty, and JmjD3 is less clear. Studies in both mice and worms led to the proposal that KDM6 proteins, but not their H3K27me3 demethylase activity, is critical for normal development. Here, we investigated the requirement of the demethylase activity of the single KDM6 family member Utx in Drosophila. We generated Drosophila expressing a full-length but catalytically inactive Utx protein and found that these mutants show the same phenotypes as animals lacking the Utx protein. Specifically, animals lacking maternally deposited active Utx demethylase in the early embryo show stochastic loss of HOX gene expression that appears to be propagated in a clonal fashion. This suggests that Utx demethylase activity is critical for the removal of ectopic H3K27 trimethylation from active HOX genes during the onset of zygotic gene transcription, and thereby prevents the inappropriate installment of long-term repression by Polycomb. Conversely, maternally deposited catalytically active Utx protein suffices to permit animals that lack zygotic expression of enzymatically active Utx to develop into morphologically normal adults, which eclose from the pupal case but die shortly thereafter. Utx demethylase activity is therefore also essential to sustain viability in adult flies. Together, these analyses identify the earliest embryonic stages and the adult stage as two phases during the Drosophila life cycle that critically require H3K27me3 demethylase activity.
The Missing Siblings of Infants Born Preterm
Authors: Alenius Suvi , Kajantie Eero , Sund Reijo , Näsänen-Gilmore Pieta , Vääräsmäki Marja , Gissler Mika , Hovi Petteri 
Published: December 2017

BACKGROUND:
Parents of very or extremely low birth weight infants have fewer subsequent children after preterm birth. Whether this applies to parents of less preterm infants is unknown.

METHODS:
In this nationwide cohort study, we identified all 230 308 traceable (&gt;99%) singletons (9983 preterm, 4.3%) live born in Finland between January 1, 1987, and September 30, 1990, and their parents. Quantitative contribution of gestational age of child to the birth of parental subsequent children was assessed by multivariate Cox regression models, stratifying by the number of previous children. The impact of gestational age on sibling count was estimated at individual and population level.

RESULTS:
Mothers of extremely preterm (23–27 completed weeks) infants were, compared with mothers of term infants (39–41 weeks), less likely to have a subsequent live-born child (adjusted hazard ratio [HR]: 0.74; 95% confidence interval: 0.63–0.86). Corresponding HRs and confidence intervals were as follows: 28 to 31 weeks: 0.72 (0.65–0.80), 32 to 33 weeks: 0.82 (0.74–0.90), and 34 to 36 weeks: 0.90 (0.87–0.93). These HRs were consistent with those of fathers and couples. The cohort included 8002 firstborn preterm children, of whom 356 (4.4%) died in infancy. The 8002 children had a total of 13 826 subsequent siblings (1138 less than expected); per 1000 preterm births, this translates to the death of 44 preterm infants and 142 missing subsequent siblings.

CONCLUSIONS:
Families with a preterm singleton child have fewer subsequent children. In a high-income country, the main population effect of preterm birth is caused by these “missing siblings,” whose number exceeds the number of those preterm infants who die.
Do reconhecimento recíproco à sociedade efetivamente social: considerações sobre a obra recente de Axel Honneth
Authors: De Souza Luiz Gustavo Da Cunha 
Published: December 2017

Este artigo apresenta uma discussão sobre a obra recente de Axel Honneth. Começando por uma exposição de seu projeto teórico mais amplo, descrito em O direito da liberdade (2011) como uma teoria da justiça sociologicamente ancorada, o artigo demonstra como Honneth se move da ideia de uma luta por reconhecimento em direção à ideia de intersubjetividade institucional. Este movimento, porém, é acompanhado por críticas que vêm nesta passagem o abandono das ambições críticas de seu modelo e um compromisso reformista com a ordem capitalista de mercado. A fim de responder a estas objeções, Honneth propõe uma reatualização da ideia do socialismo (2015) a partir da noção de liberdade social, concluindo com uma distinção entre duas formas de luta por reconhecimento, uma interna e outra externa – e defendendo as vantagens da primeira.