bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiological and molecular analysis of a waterborne outbreak of norovirus GII.4
Authors: ZHOU X. , LI H. , SUN L. , MO Y. , CHEN S. , WU X. , LIANG J. , ZHENG H. , KE C. , VARMA J. K. , KLENA J. D. , CHEN Q. , ZOU L. , YANG X. 
Published: March 2012

SUMMARYContaminated water is one of the main sources of norovirus (NoV) gastroenteritis outbreaks globally. Waterborne NoV outbreaks are infrequently attributed to GII.4 NoV. In September 2009, a NoV outbreak affected a small school in Guangdong Province, China. Epidemiological investigations indicated that household use water, supplied by a well, was the probable source (relative risk 1·9). NoV nucleic acid material in concentrated well-water samples was detected using real-time RT–PCR. Nucleotide sequences of NoV extracted from diarrhoea and well-water specimens were identical and had the greatest sequence identity to corresponding sequences from the epidemic strain GII.4-2006b. Our report documents the first laboratory-confirmed waterborne outbreak caused by GII.4 NoV genotype in China. Our investigations indicate that well water, intended exclusively for household use but not for consumption, caused this outbreak. The results of this report serve as a reminder that private well water intended for household use should be tested for NoV.
SECURING THE ENGLISHMAN'S CASTLE: SITUATIONAL CRIME PREVENTION IN THE NINETEENTH CENTURY
Authors: Smith David L. 
Published: March 2012

In 1839, the Constabulary ForceCommission, created by Parliament to study the conditions of crime and policing beyond London and to make recommendations for jurisdictional reforms, published its findings in theFirst Constabulary Report. To illustrate for readers the necessity of establishing constabularies modeled after London's Metropolitan Police Force in counties and boroughs throughout England and Wales, Edwin Chadwick, utilitarian reformer and principal draftsman of theReport, interwove the Commission's recommendations with numerous testimonies from representatives of the so-called criminal classes that pervaded nineteenth-century society. These sometimes graphic confessions were calculated to shock as much as persuade, which made for popular reading, notwithstanding widespread political opposition to the Commission's proposals (Philips 69). Section twenty eight, for example, contains the account of “J– R–,” a nineteen-year-old ex-sailor from Manchester who had committed a series of petty larcenies before turning to more serious burglaries of homes and businesses, at which he became quite adept. This young-but-seasoned offender's confession included what were intended to be alarming revelations about the physical vulnerabilities of English houses. JR testified that he had “[f]ound none or very few difficulties in the way of committing crime. The readiness with which property was got . . . was an encouragement” (Lefevre, Rowan, and Chadwick 27). In recounting the details of his crimes (and citing anecdotal evidence from fellow thieves), he pointed out that most houses were entered easily with the use of skeleton keys or through cellar windows, and that householders and servants practiced few if any serious security precautions (27–28). JR concluded that he did “not know of any places or kinds of property so protected as to induce depredators to refrain from attacking them” but added, no doubt with pressure from the interviewer, that the “most important obstruction which could be placed in the way of depredations is a more efficient police” (29).
Armed groups and intra-state conflicts: the dawn of a new era?
Authors: Blin Arnaud 
Published: March 2012

AbstractHave the various profound changes that have affected the world, and particularly its geostrategic dimensions, since the end of the Cold War radically altered the nature of conflicts? Twenty years after the collapse of the Soviet Union and ten years after the destruction of the twin towers in New York, there is an apparent degree of continuity in the resilience of former centres of unresolved conflicts and of armed groups involved in them. Nonetheless, whereas most armed conflicts can today be classified as ‘intra-state’, the general context has changed to the extent that reference is now made to the phenomenon of ‘new wars’. Increasingly inacceptable economic and political imbalances along with globalization, environmental damage and its consequences or the emergence of large-scale conflicts triggered by organized crime are some of the perils already affecting the nature of today's conflicts or potentially defining those of the future. As the period dominated by jihadist groups with a universalist vocation possibly draws to an end, the current trend seems to be towards a new generation of guerrilla fighters who stand to benefit, in particular, from the erosion of the nation-state and from geopolitical convulsions arising from the post-colonial legacy as the starting point for intensely zealous and violent long-term ventures. The impact of globalization could cause a flare-up of some existing conflicts that are currently limited in scope while the international community struggles to redefine other rules and to adapt them to the new dialectic of war and peace.
A Quantitative Model for Human Olfactory Receptors
Authors: Hassan Sk. Sarif , Pal Choudhury Pabitra , Bose Aritra 
Published: March 2012

AbstractA wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model, a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006). It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using this proposed quantitative model, one can easily make probable justification or deterministic nullification whether a given sequence of nucleotides is a probable human OR homologue or not, without seeking any biological experiment. Of course a further biological experiment is essential to validate the probable human OR homologue.
Improving metabolite evaluation in integrated pathway analysis
Authors: Kaur Rasanpreet , Dutta Anwesha , Kutmon Martina , Iersel Martijn , Evelo Chris 
Published: March 2012

AbstractBiological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use system-wide measurements to gain insights into this mechanism, we have to integrate large scale data analysis with modeled or measured fluxomics data results. For this we will develop a BridgeDb database for reaction identifiers, develop a PathVisio plugin for visualization of modeling results and architect a flexible, standards-based visualization approach (e.g. using MIM and SBGN) that will enable visualization of any conforming model, including visualization of the model output (e.g. flux changes). The focus here is on visualization of the modeling results, which will be critical for understanding how simulated models correlate with experimental measurements On the same lines, we will also find a solution to the problem of annotating metabolites in all pathways. The approach here is to use known Gene Ontology annotations for associated genes. Firstly we will incorporate automatically inferred GO categories into all WikiPathways. Develop GO visualization plugin to show gene categories on pathways and further assign automatically inferred GO categories to all addressable metabolites in WikiPathways. The last step would be to develop basic metabolite ontology analysis tools both with python GUIs and as Bioconductor modules.
The Rapid Establishment, Dispersal, and Increased Abundance of Invasive American Shad in the Pacific Northwest
Authors: Hasselman Daniel J , Hinrichsen Richard A , Shields Barbara A , Ebbesmeyer Curtis C 
Published: March 2012

Abstract
American shad (Alosa sapidissima) were repeatedly introduced into two Pacific coastal rivers in the late 1800s. They rapidly established, dispersed, and expanded their range over 5,000 km of coastline from Mexico to Russia. American shad also increased dramatically in abundance and now comprise the largest spawning run of anadromous fish in the Columbia River (&gt;4 million fish annually). Despite constituting a remarkable biological invasion, invasive shad have not been the subject of much scientific investigation and remain relatively obscure in the Pacific Northwest. In this first of two complementary articles, we attempt to raise the profile of invasive American shad among fisheries professionals and generate scientific interest in this biological invasion. We provide an overview of the history of their introduction and discuss the mechanisms that may have contributed to the species ‘establishment, rapid dispersal along the Pacific coast, and its increased abundance in the Columbia River. In the second accompanying article we discuss the possible ecological consequences of the invasion in Pacific coastal ecosystems but also its inherent value to studies of ecology and evolution. These articles are designed to be read in succession.
RESUMEN
el sábalo americano fue introducido repetidamente en dos ríos costeros del Pacífico hacia finales de 1800. Las poblaciones se establecieron, dispersaron y expandieron rápidamente su rango geográfico a lo largo de 5,000 km de línea de costa, desde México hasta Rusia. El sábalo americano también incrementó considerablemente su abundancia y a la fecha produce la mayor corrida de desove de un pez anádromo en el Río Columbia (&gt; 4 millones de individuos por año). A pesar de que ésta constituye una invasión biológica sorprendente, el sábalo americano no ha sido objeto importante de investigación científica, por lo que la especie permanece relativamente oscura en el Pacífico Noroeste. En estos dos primeros artículos complementarios, se realiza un esfuerzo por elevar el perfil del sábalo americano entre los profesionales de las pesquerías y para generar un interés científico acerca de su invasión. Se brinda un panorama de la historia de su introducción y se discuten los mecanismos que pudieron haber contribuido al establecimiento de la especie, su rápida dispersión a lo largo de la costa del Pacífico y su aumento de abundancia en el Río Columbia. En el segundo artículo se discuten las posibles consecuencias de la invasión en los ecosistemas costeros del Pacífico, pero también su valor inherente para estudios de ecología y evolución. Estos artículos se diseñaron para leerse consecutivamente.
American Shad of the Pacific Coast: A Harmful Invasive Species or Benign Introduction?
Authors: Hasselman Daniel J , Hinrichsen Richard A , Shields Barbara A , Ebbesmeyer Curtis C 
Published: March 2012

Abstract
Research on the ecological effects of aquatic invasive species in North America has largely focused on the Laurentian Great Lakes, with less attention directed to their influence in coastal ecosystems. American shad (Alosa sapidissima) were introduced to the Pacific coast in the late 1800s, rapidly established, dispersed, and became prolific. Despite constituting a remarkable biological invasion, shad in their introduced range have not been the subject of much scientific investigation. The species persists in relative obscurity in the Pacific Northwest and remains ecological overlooked and evolutionarily underappreciated. In this second of two complementary articles, we consider the potential ecological effects of invasive American shad on Pacific coastal ecosystems and the possible consequences for the persistence of native salmonids. We also reflect on the intrinsic value that this invasion provides to studies of ecology and evolution and highlight several areas of research that require immediate investigation if we are to determine whether nonindigenous shad constitute a harmful invasive species or a benign introduction.
RESUMEN
las investigaciones sobre los efectos ecológicos de especies acuáticas invasivas en Norteamérica se ha concentrado principalmente en la región de los grandes lagos, y con menos énfasis en la influencia de dichas especies en ecosistemas costeros. El sábalo americano fue introducido en la costa del Pacífico hacia finales de 1800, donde rápidamente se estableció, dispersó y proliferó. Si bien ésta constituye una invasión biológica notable, el sábalo no ha sido objeto importante de investigación científica dentro de su rango de introducción. La especie persiste en relativo anonimato en el Pacífico, se mantiene ecológicamente desapercibida y evolutivamente poco valorada. En este segundo de dos artículos complementarios, se estudian los efectos potenciales del sábalo americano en los ecosistemas costeros del Pacífico, y las posibles consecuencias de la invasión en los salmónidos nativos a la región. También se discute el valor intrínseco que tiene esta invasión para estudios ecológicos y evolutivos, y se destacan diversas áreas de investigación que requieren de atención inmediata con el fin de determinar en qué medida el sábalo americano representa una invasión nociva o una introducción benéfica.
Comparison of three models of actigraph accelerometers during free living and controlled laboratory conditions
Authors: Lee Ka‐Yiu , Macfarlane Duncan J. , Cerin Ester 
Published: March 2012

AbstractThe aim of this study was to compare the outputs of three commonly used uniaxial Actigraph models (Actitrainer, 7164 and GT1M) under both free‐living and controlled laboratory conditions. Ten adults (mean age = 24.7±1.1 years) wore the three Actigraph models simultaneously during one of day free‐living and during a progressive exercise protocol on a treadmill at speeds between 1.5 and 5.5 miles per hour (mph). During free‐living the three Actigraph models produced comparable outputs in moderate, vigorous and moderate‐to‐vigorous physical activity (MVPA) with effect sizes typically <0.2, but lower comparability was seen in sedentary and light categories, as well as in total step counts (effect sizes often >0.30). In controlled conditions, acceptable comparability between the three models was seen at all treadmill speeds, the exception being walking at 1.5 mph (mean effect size = 0.48). It is concluded that care should be taken if different Actigraph models are to be used to measure and compare light physical activity, step counts and walking at very low speeds. However, using any of these three different Actigraph models to measure and compare levels of MVPA in free‐living adults seems appropriate.
The analysis of 168 randomised controlled trials to test data integrity
Authors: Carlisle J. B. 
Published: March 2012

SummaryThe purpose of this study was to use some statistical methods to assess if randomised controlled trials (RCTs) published by one particular author (Fujii) contained data of unusual consistency. I searched seven electronic databases, retrieving 168 RCTs published by this author between 1991 and July 2011. I extracted rates for categorical variables and means (SDs) for continuous variables, and compared these published distributions with distributions that would be expected by chance. The published distributions of 28/33 variables (85%) were inconsistent with the expected distributions, such that the likelihood of their occurring ranged from 1 in 25 to less than 1 in 1 000 000 000 000 000 000 000 000 000 000 000 (1 in 1033), equivalent to p values of 0.04 to < 1 × 10−33, respectively. In 141 human studies, 13/13 published continuous variable distributions were inconsistent with expected, their likelihoods being: weight < 1 in 1033; age < 1 in 1033; height < 1 in 1033; last menstrual period 1 in 4.5 × 1015; baseline blood pressure 1 in 4.2 × 105; gestational age 1 in 28; operation time < 1 in 1033; anaesthetic time < 1 in 1033; fentanyl dose 1 in 6.3 × 108; operative blood loss 1 in 5.6 × 109; propofol dose 1 in 7.7 × 107; paracetamol dose 1 in 4.4 × 102; uterus extrusion time 1 in 33. The published distributions of 7/11 categorical variables in these 141 studies were inconsistent with the expected, their likelihoods being: previous postoperative nausea and vomiting 1 in 2.5 × 106; motion sickness 1 in 1.0 × 104; male or female 1 in 140; antihypertensive drug 1 in 25; postoperative headache 1 in 7.1 × 1010; postoperative dizziness 1 in 1.6 × 106; postoperative drowsiness 1 in 3.8 × 104. Distributions for individual RCTs were inconsistent with the expected in 96/134 human studies by Fujii et al. that reported more than two continuous variables, their likelihood ranging from 1 in 22 to 1 in 140 000 000 000 (1 in 1.4 × 1011), compared with 12/139 RCTs by other authors. In 26 canine studies, the distributions of 8/9 continuous variables were inconsistent with the expected, their likelihoods being: right atrial pressure < 1 in 1033; diaphragmatic stimulation (100 Hz) < 1 in 1033; pulmonary artery occlusion pressure < 1 in 1033; diaphragmatic stimulation (20 Hz) < 1 in 1033; heart rate 1 in 6.3 × 1010; mean pulmonary artery pressure 1 in 2.2 × 1014; mean arterial pressure 1 in 6.3 × 107; cardiac output 1 in 110. Distributions were inconsistent with the expected in 21/24 individual canine studies that reported more than two continuous variables, their likelihood ranging from 1 in 345 to 1 in 51 000 000 000 000 (1 in 5.1 × 1013).
Copy number variation in the genomes of domestic animals
Authors: Clop A. , Vidal O. , Amills M. 
Published: March 2012

SummaryCopy number variation (CNV) might be one of the main contributors to phenotypic diversity and evolutionary adaptation in animals and plants, employing a wide variety of mechanisms, such as gene dosage and transcript structure alterations, to modulate organismal plasticity. In the past 4 years, considerable advances have been made in the characterization of the genomic architecture of CNV in domestic species. First, low‐resolution CNV maps were produced for cattle, goat, sheep, pig, dog, chicken, duck and turkey, showing that these structural polymorphisms comprise a significant part of these genomes. Furthermore, CNVs have been associated with several pigmentation (white coat in horse, pig and sheep) and morphological (late feathering and pea comb in chicken) traits, as well as with susceptibility to a wide array of diseases and developmental disorders, for example osteopetrosis, anhidrotic ectodermal dysplasia, copper toxicosis, intersexuality, cone degeneration, periodic fever and dermoid sinus, among others. In the future, development of high‐resolution tools for CNV detection and typing combined with the implementation of databases integrating CNV, QTL and gene expression data will be essential to identify and measure the impact of this source of structural variation on the many phenotypes that are relevant to animal breeders and veterinary practitioners.
Exclusion of candidate genes for coat colour phenotypes of the American mink (Neovison vison)
Authors: Anistoroaei R. , Markakis M. N. , Vissenberg K. , Christensen K. 
Published: March 2012

SummaryIn a previous project, we screened the American mink Bacterial Artificial Chromosome library, CHORI‐231, for genes potentially involved in various coat colour phenotypes in the American mink. Subsequently, we 454 sequenced the inserts containing these genes and developed microsatellite markers for each of these genes. Here, we describe a lack of association between three different ‘roan‐type' phenotypes represented by Cross, Stardust and Cinnamon in American mink and six different genes that we considered to be potentially linked to these phenotypes. Thus, c‐KIT (HUGO‐approved symbol KIT), ATOH‐1 (HUGO‐approved symbol ATOH1) and POMC were excluded as potential candidates for these three phenotypes. In addition, MITF and SLC24A5 were excluded for Cross and Cinnamon, and KITL (HUGO‐approved symbol KITLG) for Cross and Stardust. Although most of these genes have been implicated as the cause of similar phenotypes in other mammals, including horses, pigs, cows, dogs, cats, mice and humans, they do not appear to be responsible for comparable phenotypes found in American mink.
Genome‐wide analysis of cytogenetic aberrations in ETV6/RUNX1‐positive childhood acute lymphoblastic leukaemia
Authors: Borst Louise , Wesolowska Agata , Joshi Tejal , Borup Rehannah , Nielsen Finn C. , Andersen Mette K. , Jonsson Olafur G. , Wehner Peder S. , Wesenberg Finn , Frost Britt‐Marie , Gupta Ramneek , Schmiegelow Kjeld 
Published: March 2012

SummaryThe chromosomal translocation t(12;21) resulting in the ETV6/RUNX1 fusion gene is the most frequent structural cytogenetic abnormality among patients with childhood acute lymphoblastic leukaemia (ALL). We investigated 62 ETV6/RUNX1‐positive childhood ALL patients by single nucleotide polymorphism array to explore acquired copy number alterations (CNAs) at diagnosis. The mean number of CNAs was 2·82 (range 0–14). Concordance with available G‐band karyotyping and comparative genomic hybridization was 93%. Based on three major protein‐protein complexes disrupted by these CNAs, patients could be categorized into four distinct subgroups, defined by different underlying biological mechanisms relevant to the aetiology of childhood ALL. When recurrent CNAs were evaluated by an oncogenetic tree analysis classifying their sequential order, the most common genetic aberrations (deletions of 6q, 9p, 13q and X, and gains of 10 and 21) seemed independent of each other. Finally, we identified the most common regions with recurrent gains and losses, which comprise microRNA clusters with known oncogenic or tumour‐suppressive roles. The present study sheds further light on the genetic diversity of ETV6/RUNX1‐positive childhood ALL, which may be important for understanding poor responses among this otherwise highly curable subset of ALL and lead to novel targeted treatment strategies.
Engaging with children's and parents' perspectives on domestic violence
Authors: Stanley Nicky , Miller Pam , Richardson Foster Helen 
Published: March 2012

ABSTRACTThis paper reports research undertaken in two sites in England which captured the views of parents and young people who had experienced domestic violence. Survivors, perpetrators and young people described feelings of guilt and shame that acted as barriers to the disclosure of domestic violence. They identified a range of effects on children, which continued beyond separation.All three groups of participants valued professionals who listened to them and validated their accounts. Professionals who appeared ineffective in the face of domestic violence could reinforce children's and victims' own sense of powerlessness. Mothers wanted support with managing the effects of separation and assistance with contact arrangements. The research identifies the need for practitioners to engage with the emotional content of disclosure of domestic violence and to undertake this work in separate sessions with parents and with children so that differing accounts can be heard safely. Interventions that enable parents to engage with children's experiences of domestic violence appear valuable. Rather than taking separation as the end‐point of intervention, social work needs to take account of the dynamics of separation and contact in parents' relationships and consider how they interact with violence and abuse to impact on children and young people.