bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population status and trend of the Critically Endangered Montserrat Oriole
Authors: OPPEL STEFFEN , CASSINI ANDREW , FENTON CALVIN , DALEY JAMES , GRAY GERARD 
Published: September 2013

SummaryMany island endemics are of great conservation concern due to small range and population sizes. The Montserrat OrioleIcterus oberiis a forest passerine endemic to the Caribbean island of Montserrat, where recent volcanic activity has destroyed a large proportion of suitable forest habitat. From 1997 to 2000 the Montserrat Oriole population declined dramatically even in the remaining forest habitat, leading to its classification as ‘Critically Endangered’. We present trend estimates of the Montserrat Oriole population from 2000 to 2013, and estimate the world population size in 2012 based on repeat point counts and beta-binomial mixture models. Montserrat Orioles recovered between 2003 and 2005, and we found no evidence for a continuing population decline. However, there was large uncertainty around trend estimates, and the power to detect a shallow negative trend was very low. Based on the comparison of count data at 42 points, the Montserrat Oriole population in 2013 was less than half as large as in 1998. To improve future trend estimates a new monitoring design was introduced in 2011, and applied to all subpopulations of the species in 2012. The world population in 2012 was estimated to hold between 307 (95% credible interval 212–503) and 690 birds (476–1131) birds in the two forest fragments on Montserrat, depending on whether the sampling area around each point count was assumed to encompass 100 m or 150 m. Based on these estimates, the Montserrat Oriole currently does not meet the IUCN criteria for ‘Critically Endangered’, and we recommend a revision of the species’ conservation status.
Left hemitruncus with normal right-sided pressures in an adult
Authors: Nigam Arima , Trehan Vijay 
Published: September 2013

AbstractHemitruncus is a rare congenital heart disease. Anomalous origin of the left pulmonary artery is not only rare but also pathogenetically different from anomalous origin of the right pulmonary artery from the ascending aorta. In most cases in isolated hemitrucus pressures in the right ventricle and the normally originating pulmonary artery are systemic or suprasystemic. We present a rare case of anomalous origin of the left pulmonary artery from the ascending aorta diagnosed in an adult with normal pressures in the right ventricle and normally originating pulmonary artery. To the best of our knowledge, this unique haemodynamics has never been reported in the literature.
Differential Contributions of Executive and Episodic Memory Functions to Problem Solving in Younger and Older Adults
Authors: Vandermorris Susan , Sheldon Signy , Winocur Gordon , Moscovitch Morris 
Published: September 2013

AbstractThe relationship of higher order problem solving to basic neuropsychological processes likely depends on the type of problems to be solved. Well-defined problems (e.g., completing a series of errands) may rely primarily on executive functions. Conversely, ill-defined problems (e.g., navigating socially awkward situations) may, in addition, rely on medial temporal lobe (MTL) mediated episodic memory processes. Healthy young (N = 18; M = 19; SD = 1.3) and old (N = 18; M = 73; SD = 5.0) adults completed a battery of neuropsychological tests of executive and episodic memory function, and experimental tests of problem solving. Correlation analyses and age group comparisons demonstrated differential contributions of executive and autobiographical episodic memory function to well-defined and ill-defined problem solving and evidence for an episodic simulation mechanism underlying ill-defined problem solving efficacy. Findings are consistent with the emerging idea that MTL-mediated episodic simulation processes support the effective solution of ill-defined problems, over and above the contribution of frontally mediated executive functions. Implications for the development of intervention strategies that target preservation of functional independence in older adults are discussed. (JINS, 2013, 19, 1–10)
Social Science and Systemic Failure
Authors: Rutland Peter 
Published: September 2013

Invisible Hands, Russian Experience, and Social Science: Approaches to Understanding Systemic Failure. By Stefan Hedlund. New York: Cambridge University Press, 2011. 324p. $95.00, cloth, $35.99 paper.In recent decades the study of social phenomena has been characterized by the increasing specialization of academic subdisciplines. At the same time, social science has had great difficulty in accounting for instances of systemic failure that challenge the artificial typologies often promoted by specialized scholarship. Increasing theoretical sophistication thus arguably has come at the expense of grasping the particular and unique nature of historical events. In Invisible Hands, Russian Experience, and Social Science, Stefan Hedlund examines the postcommunist Russian encounter with capitalism and the global financial crisis as examples of unprecedented events that challenged social scientists' assumptions about the causes of human behavior and the functioning of social and political institutions. In this symposium a group of political scientists have been asked to critically assess the book's account and to comment more broadly on what systemic failure can tell us about social science theorizing.—Jeffrey C. Isaac, Editor
Social Science and Systemic Failure
Authors: Carnaghan Ellen 
Published: September 2013

Invisible Hands, Russian Experience, and Social Science: Approaches to Understanding Systemic Failure. By Stefan Hedlund. New York: Cambridge University Press, 2011. 324p. $95.00, cloth, $35.99 paper.In recent decades the study of social phenomena has been characterized by the increasing specialization of academic subdisciplines. At the same time, social science has had great difficulty in accounting for instances of systemic failure that challenge the artificial typologies often promoted by specialized scholarship. Increasing theoretical sophistication thus arguably has come at the expense of grasping the particular and unique nature of historical events. In Invisible Hands, Russian Experience, and Social Science, Stefan Hedlund examines the postcommunist Russian encounter with capitalism and the global financial crisis as examples of unprecedented events that challenged social scientists' assumptions about the causes of human behavior and the functioning of social and political institutions. In this symposium a group of political scientists have been asked to critically assess the book's account and to comment more broadly on what systemic failure can tell us about social science theorizing.—Jeffrey C. Isaac, Editor
Social Science and Systemic Failure
Authors: Hanson Stephen E. 
Published: September 2013

Invisible Hands, Russian Experience, and Social Science: Approaches to Understanding Systemic Failure. By Stefan Hedlund. New York: Cambridge University Press, 2011. 324p. $95.00, cloth, $35.99 paper.In recent decades the study of social phenomena has been characterized by the increasing specialization of academic subdisciplines. At the same time, social science has had great difficulty in accounting for instances of systemic failure that challenge the artificial typologies often promoted by specialized scholarship. Increasing theoretical sophistication thus arguably has come at the expense of grasping the particular and unique nature of historical events. In Invisible Hands, Russian Experience, and Social Science, Stefan Hedlund examines the postcommunist Russian encounter with capitalism and the global financial crisis as examples of unprecedented events that challenged social scientists' assumptions about the causes of human behavior and the functioning of social and political institutions. In this symposium a group of political scientists have been asked to critically assess the book's account and to comment more broadly on what systemic failure can tell us about social science theorizing.—Jeffrey C. Isaac, Editor
Diversity of individual mobility patterns and emergence of aggregated scaling laws
Authors: Yan Xiao-Yong , Han Xiao-Pu , Wang Bing-Hong , Zhou Tao 
Published: September 2013

AbstractUncovering human mobility patterns is of fundamental importance to the understanding of epidemic spreading, urban transportation and other socioeconomic dynamics embodying spatiality and human travel. According to the direct travel diaries of volunteers, we show the absence of scaling properties in the displacement distribution at the individual level,while the aggregated displacement distribution follows a power law with an exponential cutoff. Given the constraint on total travelling cost, this aggregated scaling law can be analytically predicted by the mixture nature of human travel under the principle of maximum entropy. A direct corollary of such theory is that the displacement distribution of a single mode of transportation should follow an exponential law, which also gets supportive evidences in known data. We thus conclude that the travelling cost shapes the displacement distribution at the aggregated level.
Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation
Authors: Chanda Soham , Marro Samuele , Wernig Marius , Südhof Thomas C. 
Published: September 2013

Significance
A major challenge in modeling human diseases is to replicate disease phenotypes in neurons that are differentiated from nonneuronal cells, such as pluripotent stem cells or fibroblasts. However, evidence that phenotypes observed with this approach replicate an endogenous disease phenotype is lacking. This study demonstrates that induced neuronal (iN) cells obtained by direct conversion of fibroblasts to neurons, when produced from a previously described mouse mutant in neuroligin-3 that is linked to autism, exhibited a phenotype similar to that observed in endogenous neurons. These data show that the mutation studied is highly penetrant phenotypically and also that iN cells can faithfully reproduce a phenotype observed in endogenous neurons, thus validating the use of iN cells for studying disease models.
Pattern search in BioPAX models
Authors: Babur Özgün , Aksoy Bülent Arman , Rodchenkov Igor , Sümer Selçuk Onur , Sander Chris , Demir Emek 
Published: September 2013

Abstract
Motivation: BioPAX is a standard language for representing complex cellular processes, including metabolic networks, signal transduction and gene regulation. Owing to the inherent complexity of a BioPAX model, searching for a specific type of subnetwork can be non-trivial and difficult.
Results: We developed an open source and extensible framework for defining and searching graph patterns in BioPAX models. We demonstrate its use with a sample pattern that captures directed signaling relations between proteins. We provide search results for the pattern obtained from the Pathway Commons database and compare these results with the current data in signaling databases SPIKE and SignaLink. Results show that a pattern search in public pathway data can identify a substantial amount of signaling relations that do not exist in signaling databases.
Availability: BioPAX-pattern software was developed in Java. Source code and documentation is freely available at http://code.google.com/p/biopax-pattern under Lesser GNU Public License.
Contact: patternsearch@cbio.mskcc.org
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Freesia sneak virus in Commercial Freesia hybrida Cultivars in Korea
Authors: Jeong M. I. , Choi Y. J. , Joa J. H. , Choi K. S. , Chung B. N. 
Published: September 2013

In order to investigate the virus infection rate of commercial freesia cultivars in early February 2013, 19 freesia cultivars showing necrotic purple speckles or streaks on leaves, purple streaks parallel to the midrib, and necrotic speckles on leaves were collected from three different regions (Suwon and Icheon in Gyeonggi Province and Jeonju in North Jeonla Province) and used for virus detection. Nucleic acid extracts were analyzed for detection of major freesia-infecting viruses including Freesia sneak virus (FreSV) by reverse transcription (RT)-PCR with specific primer pairs. The FreSV CP gene was amplified using primer pair FreSV-F (5′-TTAGATAGTGAATCCATAAGCTGC-3′) and FreSV-R (5′-ATGTCTGGAAAATACTCCGTCCAA-3′). The approximately 1.3-kb fragment of the FreSV amplified product was cloned and sequenced (GenBank Accession No. KC771891 to 98). The nucleotide sequences of CP gene of FreSV korean isolates showed 99.2 to 99.8% similarity to other FreSV isolates DQ885455, FJ807730, and GU071089, which are registered in GenBank. FreSV was detected from 71.7% of 138 plants tested while the infection rate of Freesia mosaic virus (FreMV) was 34.8%. Neither Bean yellow mosaic virus (BYMV) nor Tobacco rattle virus (TRV) were detected from any plants tested in this study. In certain cultivars, such as ‘Bluebau’ (II) and ‘Pretty women,’ most plants planted in the field showed purple streak symptoms on the leaves. In conclusion, FreSV was detected from some symptomatic freesia cultivars showing purple streak or speckles on leaves with or without necrotic spots and necrotic speckles on leaves. FreSV is currently widespread in Korea and some freesia plants were mixed infected with FreMV. FreSV has been occurring in the Netherlands for over 40 years (2). It is a plant virus in the family Ophioviridae and Ophiovirus genus. Once it occurs in freesia plantation fields, eradication is almost impossible because FreSV is transmitted by zoospores of Olpidium brassicae, which is a soilborne root-infecting fungus (3). Resting spores of O. brassicae can remain dormant in the soil and can be infective for 20 years (1). To produce virus-free freesia plants, growers should consider whether or not their fields are contaminated with O. brassicae carrying FreSV. To our knowledge, this is the first report of FreSV in freesia plants in Korea. References: (1) R. N. Campbell. Can. J. Bot. 63:2288, 1985. (2) Y. Koot et al. Tijdschrift over Plantenziekten 60:157, 1954. (3) H. J. M. van Dorst. Neth. J. Plant Pathol. 81:45, 1975.
The Great Indian Calorie Debate: Explaining Rising Undernourishment during India's Rapid Economic Growth
Authors: Smith Lisa C. 
Published: September 2013

SummaryThe prevalence of undernourishment in India – the percent of people consuming insufficient calories to meet their energy requirements – has been rising steadily since the mid‐1980s. Paradoxically, this period has been one of robust poverty reduction and rapid economic growth. The reasons for the apparent reductions in calorie consumption underlying increased undernourishment have been the subject of intense debate both within India and internationally. This paper critically reviews this debate, finding that is has taken place outside of the context of India's recent nutrition and epidemiological transitions, which appear to have brought with them increased, not decreased, food consumption. The debate has also taken place under the unchallenged assumption that the data on which the conflicting trends are based, collected as part of the country's Household Consumption and Expenditure Surveys (HCESs), are reliable. The paper provides supporting literature and empirical evidence that one key factor driving the measured calorie decline is incomplete collection of data on food consumed away from peoples’ homes, which is widespread and rapidly increasing. The India example shows that complete measurement of this food source in the HCESs of all countries is vital for accurate measurement of undernourishment and, indeed, poverty at national, regional and global levels.
Ecological Patterns of
nifH
Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool
Authors: Wang Qiong , Quensen John F. , Fish Jordan A. , Kwon Lee Tae , Sun Yanni , Tiedje James M. , Cole James R. 
Published: September 2013

ABSTRACT

Biological nitrogen fixation is an important component of sustainable soil fertility and a key component of the nitrogen cycle. We used targeted metagenomics to study the nitrogen fixation-capable terrestrial bacterial community by targeting the gene for nitrogenase reductase (
nifH
). We obtained 1.1 million
nifH
454 amplicon sequences from 222 soil samples collected from 4 National Ecological Observatory Network (NEON) sites in Alaska, Hawaii, Utah, and Florida. To accurately detect and correct frameshifts caused by indel sequencing errors, we developed FrameBot, a tool for frameshift correction and nearest-neighbor classification, and compared its accuracy to that of two other rapid frameshift correction tools. We found FrameBot was, in general, more accurate as long as a reference protein sequence with 80% or greater identity to a query was available, as was the case for virtually all
nifH
reads for the 4 NEON sites. Frameshifts were present in 12.7% of the reads. Those
nifH
sequences related to the
Proteobacteria
phylum were most abundant, followed by those for
Cyanobacteria
in the Alaska and Utah sites. Predominant genera with
nifH
sequences similar to reads included
Azospirillum
,
Bradyrhizobium
, and
Rhizobium
, the latter two without obvious plant hosts at the sites. Surprisingly, 80% of the sequences had greater than 95% amino acid identity to known
nifH
gene sequences. These samples were grouped by site and correlated with soil environmental factors, especially drainage, light intensity, mean annual temperature, and mean annual precipitation. FrameBot was tested successfully on three ecofunctional genes but should be applicable to any.

IMPORTANCE
High-throughput phylogenetic analysis of microbial communities using rRNA-targeted sequencing is now commonplace; however, such data often allow little inference with respect to either the presence or the diversity of genes involved in most important ecological processes. To study the gene pool for these processes, it is more straightforward to assess the genes directly responsible for the ecological function (ecofunctional genes). However, analyzing these genes involves technical challenges beyond those seen for rRNA. In particular, frameshift errors cause garbled downstream protein translations. Our FrameBot tool described here both corrects frameshift errors in query reads and determines their closest matching protein sequences in a set of reference sequences. We validated this new tool with sequences from defined communities and demonstrated the tool’s utility on
nifH
gene fragments sequenced from soils in well-characterized and major terrestrial ecosystem types.
Acupuncture Referrals in Rural Primary Healthcare: A Survey of General Practitioners in Rural and Regional New South Wales, Australia
Authors: Wardle Jonathan Lee , Sibbritt David , Adams Jon 
Published: September 2013

Background Acupuncture services form a significant part of the Australian healthcare setting, with national registration of acupuncture practitioners, public subsidies for acupuncture services and high use of acupuncture by the Australian public. Despite these circumstances, there has been little exploration of the interface between acupuncture providers and conventional primary healthcare practitioners in rural and regional Australia. Methods A 27-item questionnaire was sent by post in the second half of 2010 to all 1486 general practitioners (GPs) currently practising in rural and regional Divisions of General Practice in New South Wales, Australia to explore their practices and attitudes to a variety of complementary and alternative medicine (CAM) practices. Their responses on other therapies have been published previously; this report covers acupuncture. Results A total of 585 GPs completed the questionnaire; 49 were returned as ‘no longer at this address’, resulting in an adjusted response rate of 40.7%. Two-thirds of GPs (68.3%) referred patients to an acupuncturist at least a few times per year, while only 8.4% stated that they would not refer patients to an acupuncturist under any circumstances. GPs being older (OR=6.08), GPs being women (OR=2.94), GPs practising in a rural rather than remote area (OR=6.25), GPs having higher levels of self-reported knowledge of acupuncture (OR=5.54), the use of complementary medicine (CAM) by a GP for their personal health (OR=2.37), previous prescription of CAM to other patients (OR=2.99), lack of other treatment options (OR=4.31) and GPs using CAM practitioners as the major source of their CAM information (OR=3.05) were all predictive of increased referral to acupuncture among rural GPs. Conclusions There is a significant interface between acupuncture and Australian rural and regional general practice, with generally high levels of support for acupuncture.
The global burden of unsafe medical care: analytic modelling of observational studies
Authors: Jha Ashish K , Larizgoitia Itziar , Audera-Lopez Carmen , Prasopa-Plaizier Nittita , Waters Hugh , Bates David W 
Published: September 2013

ObjectiveTo contextualise the degree of harm that comes from unsafe medical care compared with individual health conditions using the global burden of disease (GBD), a metric to determine how much suffering is caused by individual diseases.DesignAnalytic modelling of observational studies investigating unsafe medical care in countries’ inpatient care settings, stratified by national income, to identify incidence of seven adverse events for GBD modelling. Observational studies were generated through a comprehensive search of over 16 000 articles written in English after 1976, of which over 4000 were appropriate for full text review.ResultsThe incidence, clinical outcomes, demographics and costs for each of the seven adverse events were collected from each publication when available. We used disability-adjusted life years (DALYs) lost as a standardised metric to measure morbidity and mortality due to specific adverse events. We estimate that there are 421 million hospitalisations in the world annually, and approximately 42.7 million adverse events. These adverse events result in 23 million DALYs lost per year. Approximately two-thirds of all adverse events, and the DALYs lost from them, occurred in low-income and middle-income countries.ConclusionsThis study provides early evidence that adverse events due to medical care represent a major source of morbidity and mortality globally. Though suffering related to the lack of access to care in many countries remains, these findings suggest the importance of critically evaluating the quality and safety of the care provided once a person accesses health services. While further refinements of the estimates are needed, these data should be a call to global health policymakers to make patient safety an international priority.
The Information Content of Option-Based Forecasts of Volatility: Evidence from the Italian Stock Market
Authors: Muzzioli Silvia 
Published: September 2013

The aim of this paper is to comprehensively compare option-based measures of volatility, with the ultimate plan of devising a new volatility index for the Italian stock market. The performance of the different implied volatility measures in forecasting future volatility is evaluated both in a statistical and in an economic setting. The properties of the implied volatility measures are also explored, by looking at both the contemporaneous relationship between implied volatility changes and market returns and the usefulness of the proposed index in forecasting future market returns. The results of the paper are of practical importance for both policy-makers and investors. The volatility index, based on corridor measures, could be used to forecast market volatility, for value at risk purposes, in order to determine trading strategies on the underlying index and as an early warning for future market conditions.