bluuebunny/crossref_metadata_2025_split huggingface dataset:
ClickPoints: an expandable toolbox for scientific image annotation and analysis
Authors: Gerum Richard C. , Richter Sebastian , Fabry Ben , Zitterbart Daniel P. 
Published: November 2016

Summary

Optical recordings are ubiquitous in current scientific research. As recording and storing images and videos have become simpler and cheaper over the past years, new and more efficient tools are needed to analyse the growing amount of data. While current scientific image analysis tools focus on medical 3D data sets, a tool for efficiently handling large‐scale 2D time‐series recordings is still missing.

We developed ClickPoints, an expandable, open‐source, Python‐based software to fill this gap. ClickPoints combines and streamlines the three main steps of image analysis – visualization, annotation and evaluation – in one program.

ClickPoints enables the user to (i) efficiently review large data sets of images and videos, (ii) annotate interesting findings and (iii) facilitate manual and automatic evaluations. ClickPoints is highly versatile, ranging from clicking and selecting objects with simple markers, drawing masks and computing trajectories, up to (iv) custom‐written Python add‐ons for adapting or extending the available features. These add‐ons (v) reduce development time by utilizing ClickPoints’ display, interface and storage solutions. In addition, ClickPoints provides an (vi) extensive data base application programming interface to facilitate efficient storage and retrieval of results.

ClickPoints is designed to simplify repetitive and labour‐intensive scientific tasks, especially when dealing with large image and video time‐series recordings. ClickPoints offers cross‐platform support for Windows and Linux and is released under the GPLv3 license. Download, documentation and numerous examples are available at http://clickpoints.readthedocs.io.
Noninvasive markers for staging fibrosis in chronic delta hepatitis
Authors: Takyar V. , Surana P. , Kleiner D. E. , Wilkins K. , Hoofnagle J. H. , Liang T. J. , Heller T. , Koh C. 
Published: November 2016

SummaryBackgroundSerum fibrosis markers are useful in staging chronic hepatitis B (HBV) and C (HCV) virus but have not been evaluated in chronic hepatitis D virus (HDV).AimTo evaluate the utility of serum fibrosis markers [fibrosis‐4 score (FIB‐4), aspartate aminotransferase (AST) to alanine aminotransferase (ALT) ratio, aspartate aminotransferase ratio (AAR), age‐platelet index (API), AST‐to‐platelet‐ratio‐index (APRI) and Hui score] in HDV infection.MethodsClinical and histologic laboratory data from HBV, HCV and HDV patients were evaluated and serum fibrosis markers were calculated. The ability of fibrosis markers to detect advanced fibrosis (Ishak ≥4) and cirrhosis (Ishak = 6) were evaluated and compared between viral infections.ResultsA total of 1003 subjects (HCV = 701, HBV = 240 and HDV = 62) with mean age of 46 ± 11 and 66% male were evaluated. HDV subjects had higher ALT and AST than HCV and lower platelets than both HBV and HCV. Histologically, HDV had the greatest percentage of Ishak ≥4 and necroinflammation. FIB‐4 performed best in detecting advanced fibrosis and cirrhosis in all viral cohorts. In HDV, area under the receiver operator curve (AUROC) 95% confidence intervals for detecting advanced fibrosis were: FIB‐4 = 0.70 (0.55–0.84), API = 0.69 (0.55–0.82), APRI = 0.68 (0.54–0.82), Hui score = 0.63 (0.49–0.78), AAR = 0.63 (0.48–0.77). The AUROC for detecting cirrhosis in HDV were: FIB‐4 = 0.83 (0.69–0.97), API = 0.80 (0.66–0.95), APRI = 0.75 (0.61–0.89), Hui score = 0.70 (0.49–0.91) and AAR = 0.70 (0.48–0.93). Adjustment of published cut‐offs led to marginal improvements in FIB4 for advanced fibrosis and of APRI for cirrhosis in HDV.ConclusionsSerum fibrosis markers have lower performance accuracy in chronic HDV infected patients compared to HBV and HCV patients. Other noninvasive fibrosis markers should be explored to assist in the management of these patients.
The Matrix Verb as a Source of Comprehension Difficulty in Object Relative Sentences
Authors: Staub Adrian , Dillon Brian , Clifton Charles 
Published: November 2016

AbstractTwo experiments used eyetracking during reading to examine the processing of the matrix verb following object and subject relative clauses. The experiments show that the processing of the matrix verb following an object relative is indeed slowed compared to the processing of the same verb following a subject relative. However, this difficulty is entirely eliminated if additional material intervenes between the object gap and the matrix verb. An explanation in terms of spillover processing is ruled out, suggesting that it is the gap‐matrix verb sequence that is itself responsible for the difficulty. We consider two accounts of this difficulty, one emphasizing the potential difficulty of rapidly switching between the sentential subject's thematic or syntactic role in the embedded clause and its role in the matrix clause, and one emphasizing the potential difficulty of performing two demanding memory retrievals in rapid succession. The present experiments also closely replicate the previous findings from eyetracking that the noun phrase and the verb within an object relative are both loci of processing difficulty, but that the former induces substantially greater difficulty.
Coping with the cold: minimum temperatures and thermal tolerances dominate the ecology of mountain ants
Authors: BISHOP TOM R. , ROBERTSON MARK P. , VAN RENSBURG BERNDT J. , PARR CATHERINE L. 
Published: November 2016

1. Ants (Hymenoptera: Formicidae) are often cited as highly thermophilic and this has led to a range of studies investigating their thermal tolerances. It is unknown, however, if the geographic distribution of ant thermal tolerance conforms to the two major macropyhsiological rules that have been found in other taxa: Janzen's and Brett's rules. In addition, there is a paucity of data on how the lower thermal tolerances of ants are able to influence behaviour.2. These two knowledge gaps were addressed here by sampling ants across a 1500 m elevational gradient in southern Africa and estimating the upper (CTmax) and lower (CTmin) thermal tolerances of 31 and 28 species, respectively. Ant abundances and soil temperatures were also recorded across the gradient over 6 years.3. It was found that the average CTmin of the ants declined with elevation along with environmental temperatures. It was also found that the correlation between abundance and local temperature depended on the ant species' CTmin. The activity of species with a low CTmin was not constrained by temperature, whereas those with a high CTmin were limited by low temperatures.4. For the first time, evidence is provided here that the thermal tolerances of ants are consistent with two major macrophysiological rules: Brett's rule and Janzen's rule. A mechanistic link between physiology, behaviour and the environment is also shown, which highlights that the ability of ants to deal with the cold may be a key, but often overlooked, factor allowing multiple ant species to succeed within an environment.
Prioritization of K–12 World Language Education in the United States: State Requirements for High School Graduation
Authors: O'Rourke Polly , Zhou Qian , Rottman Isaac 
Published: November 2016

AbstractIn view of the importance of increasing multilingualism in the United States, the current study examined state policy for high school graduation requirements in the 50 states and the District of Columbia as an index of the way in which the study of world language is positioned and prioritized in K–12 education. Only seven states require the study of a world language other than English as a prerequisite for high school graduation for all students. The majority of states do not include world languages as a requirement for high school graduation, but almost half include world language coursework as an option of fulfilling an elective graduation requirement. Overall, while there are some positive developments, principally the Seal of Biliteracy initiative, world language education is not prioritized in state‐level policies. Continued efforts, possibly at the federal level, are required to maintain and promote world language education in the United States
Balancing generality and specificity in ecological gradient analysis with species abundance distributions and individual size distributions
Authors: Yen Jian D. L. , Thomson James R. , Keith Jonathan M. , Paganin David M. , Fleishman Erica , Dobkin David S. , Bennett Joanne M. , Mac Nally Ralph 
Published: November 2016

AbstractAimData on ecological communities are often condensed into single‐valued diversity indices, which support comparisons among ecosystems but may discard important information. At the other extreme, some studies retain full data on the identities of all species present, which retains maximum information on community structure but occludes comparisons among ecosystems. We sought to determine whether the analysis of species abundance distributions and individual size distributions could support more detailed inferences than diversity indices while remaining sufficiently general to identify fundamental ecological responses in multiple ecosystems.LocationThe United States and south‐eastern Australia.MethodsWe analysed changes in species abundance distributions and individual size distributions along environmental gradients. We compared analyses of distributions with analyses of five diversity indices and with a distance‐based multivariate analysis of species composition. We used data from 1438 fish communities in the United States and from 840 bird communities in the western United States and south‐eastern Australia. These communities were sampled over 10–20 years and included 298 species of birds and 488 species of fishes.ResultsAnalyses of species abundance distributions and individual size distributions identified environmental associations that were not found in analyses of diversity indices, and revealed common associations with shrubs in bird communities on different continents and with temperature in communities of birds and fishes. Individual size distributions were associated more closely with environmental variables than were species abundance distributions.Main conclusionsOur novel identification of ecological associations suggests that analyses of community distributions might reveal fundamental ecological processes common to multiple ecosystems. Close associations between individual sizes and environmental variables suggest that a greater focus on size in ecological analyses might assist in the development of general models of ecological communities.
Global production networks and uneven development: Exploring geographies of devaluation, disinvestment, and exclusion
Authors: Werner Marion 
Published: November 2016

AbstractThis paper examines global production networks through the lens of uneven development. Although originally concerned with asymmetries in the global economy, in the 1990s, global production network studies shifted decidedly towards a focus upon realizing the mutual benefits of engagement between multinationals, their suppliers, and the regions where the latter were located. Recent trends in supply chain restructuring, thrown into sharp relief by the 2008 financial crisis, have spurred more attention to the downsides of participation in global production networks, framed as empirical outcomes. Here, I explore this literature through the lens of three inter‐related processes of uneven development: strategies to defer devaluation, regional disinvestment, and constitutive exclusion. Viewed from this perspective, the global production network can serve as a powerful heuristic device to grasp emerging forms of territorial and social unevenness in the global economy.
Transition from being OK to NOT OK with tooth loss among a selection of older people in Iran: a qualitative study
Authors: Dezhdar Shahin , Fereidoonpoor Najmeh , Mostaghni Ehsan , Jahanpour Faezeh , Ravanipour Maryam 
Published: November 2016

BackgroundSeveral studies have covered oral health and dental decay in old age, but these studies mostly applied standard quantitative tools and did not include consideration of older people's views on oral problems, partial edentulism in particular.ObjectiveTo explore people's perceptions in terms of the transition from being OK to NOT OK with tooth loss among a selection of older people in Iran.Materials and methodsA qualitative content analysis study was chosen for the research by interviewing 15 older people using open‐ended questions. Criteria for participation in the study were as follows: fitting the Kennedy class I or class I modification I category, having a minimum of four teeth but not more than 20 and being aged 60 years or more. The recorded interviews were then transcribed, and a coding process was applied based on a qualitative, conventional content analysis.ResultsThe four main themes that emerged were as follows: (i) gradual realisation of the need to deal with the problem; (ii) the search for information on dental health; (iii) the challenge of adaptation; and (iv) tendency towards dental rehabilitation.ConclusionThe turning point in the transition from being OK to NOT OK seemed to be associated with an edentulous crisis that had occurred from another problem such as stomach ache, distention, or nocturnal dyspnoea due to swallowing food that had not been properly chewed and had an affect on an elderly person's life, physically and mentally. It is important to recognise the concept of healthy eating in relation to edentulism.
Use of computed tomography abdomen and pelvis for investigation of febrile neutropenia in adult haematology patients
Authors: Lim H. Y. , Ashby M. , Williams B. , Grigg A. 
Published: November 2016

We retrospectively evaluated the use of computed tomography abdomen and pelvis (CTAP) in febrile neutropenic autologous stem cell transplant (ASCT) and acute myeloid leukaemia (AML) patients. CTAP was more common in ASCT patients (59%) compared with AML (31%;
P
< 0.001). Although abnormal findings were reported in 51%, only 10% resulted in therapy change (addition of anaerobic antibiotic/bowel rest), which would have otherwise been instituted based on clinical grounds. CTAP in these patients rarely provide useful information unsuspected clinically.
Anterior Cantilever Resin‐Bonded Fixed Dental Prostheses: A Review of the Literature
Authors: Mourshed Bilal , Samran Abdulaziz , Alfagih Amal , Samran Ahalm , Abdulrab Saleem , Kern Matthias 
Published: November 2016

AbstractPurposeThis review evaluated the survival rate of single retainer anterior resin‐bonded fixed dental prostheses (RBFDPs) to determine whether the choice of material affects their clinical outcome.Materials and MethodsAn electronic search of the English peer‐reviewed dental literature in PubMed was conducted to identify all publications reporting on cantilever RBFDPs until May 2016. Study information extraction and methodological quality assessments were accomplished by two reviewers independently. The searched keywords were as follows: “resin‐bonded, single retainer, all‐ceramic resin‐bonded fixed dental prostheses (RBFDPs), all‐ceramic RBFDPs, cantilever resin, RBFDPs, cantilever resin‐bonded bridge, two units cantilevered, two‐unit cantilevered, metal‐ceramic cantilever, and metal‐ceramic.” Furthermore, the ‘‘Related Articles’’ feature of PubMed was used to identify further references of interest within the primary search. The bibliographies of the obtained references were used to identify pertinent secondary references. Review articles were also used to identify relevant articles. After the application of exclusion criteria, the definitive list of articles was screened to extract the qualitative data, and the results were analyzed.ResultsOverall 2588 articles were dedicated at the first review phase; however, only 311 studies were left after the elimination of duplicates and unrelated studies. Seventeen studies passed the second review phase. Five studies were excluded because they were follow‐up studies of the same study cohort. Twelve studies were finally selected.ConclusionsThe use of cantilever RBFDPs showed promising results and high survival rates.
Verse Epitaphs and the Memorialisation of Women in Reformation England
Authors: Hyde Jenni 
Published: November 2016

AbstractDuring the late twentieth century, scholars became interested in the ways in which early modern England adapted to the Reformation and how change was represented in popular culture. In the last fifteen years, there has been a particular focus on how Protestantism affected the relationship between the living and the dead. In 2000, for example, Ralph Houlbrooke's studyDeath,Religion,and the Family in England,1480–1750identified a failure on the part of the post‐Reformation church to replace old funerary customs with new, yet two years later inBeliefs and the Dead in Reformation England, Peter Marshall argued persuasively that the Reformation engendered a ‘cultural transformation’ in the understanding of both death and the dead. By, Scott Newstok'sQuoting Death in Early Modern Englanddescribed a paradox in which a Protestant nation that scorned Catholic death rituals became engrossed in commemorating its own dead through poetic memorialisation.This article surveys 21st century historiographical debates in order to contextualise women's verse epitaphs during the sixteenth century. In particular, it looks to the broadside literature that was the epitome of cheap print as a means of reflecting popular religious attitudes. It shows how several verse epitaphs of prominent women in Tudor society, such as William Elderton'sA proper new balad in praise of my ladie marques(), highlight issues of continuity and change in religious beliefs surrounding the memorialisation of pious women and the role of the supernatural.Video abstract (click to view)https://www.youtube.com/watch?v=Oyzjk8AaCP8
Performing Shakespeare in Europe
Authors: Mancewicz Aneta 
Published: November 2016

AbstractThe history of performing Shakespeare in Europe and the establishment of European Shakespeare Studies have been closely connected with European culture and politics. The emergence of the European Shakespeare Research Association, ESRA, has coincided with the fall of Communism and the political transformations in Europe after 1989, as well as the growing professionalisation and internationalisation of Shakespeare criticism. In the twenty‐first century, European studies of Shakespeare continue to flourish, with vibrant research centres extending from Murcia in Spain to Zaporizhzhia in Ukraine, and with a dynamic European Shakespeare Festivals Network. At the heart of European Shakespeare Studies has been the examination of Shakespeare's reception in different national traditions across Europe. Performance criticism has played a crucial role in this process, given that theatre as a medium transcends linguistic barriers, while encouraging local traditions of translation and staging. Productions of Shakespeare have also provided a forum for articulating current political and social concerns, particularly in times of censorship, which has made them exceptionally appealing to scholars interested in national cultures and histories. This article outlines four aspects that represent Shakespeare's relationship with European performance: theatrical exchanges between England and the Continent as the beginning of the European Shakespeare tradition, translation as an integral part of stage practice, the significance of performance criticism in European Shakespeare Studies and the notion of a shared European theatre tradition. Their discussion combines elements of a historical narrative with a critical overview. The article concludes with new perspectives in the twenty‐first century Shakespeare productions, as the Eurozone debt crisis and immigration crisis pose new challenges and responsibilities for artists and academics.
Is gibbon ape leukaemia virus still a threat?
Authors: Brown Katherine , Tarlinton Rachael E. 
Published: November 2016

Abstract

In the late 1960s and early 1970s, an outbreak of lymphoma and leukaemia in gibbons (Hylobatidae), attributed to the retrovirus gibbon ape leukaemia virus (GALV), was widely reported in the literature. The virus was identified in captive gibbon colonies in Thailand, the USA and Bermuda.

The virus is a known cell culture contaminant and, in particular, research into HIV can be impeded by expression of GALV particles in HIV permissive cell lines.

In this review, we bring together published work, laboratory records from early GALV research, correspondence about the transportation of gibbons during the 1960s and 1970s, phylogenetic analyses, laboratory screening and zoological records for the first time, to discover more about the origin and transmission of GALV.

Based on this evidence, we suggest that GALV may have been transmitted to gibbons as an iatrogenic event and was never widespread. Instead, all infected gibbons were probably transported from the site of the original outbreak, housed with gibbons from this site or infected with material derived from gibbons from this site.

We also propose that GALV is not an ongoing pathogen of captive gibbons.
Characterizing alloparental care in the pilot whale (Globicephala melas) population that summers off Cape Breton, Nova Scotia, Canada
Authors: Augusto Joana F. , Frasier Timothy R. , Whitehead Hal 
Published: November 2016

AbstractAlloparental care happens when a calf is cared for by an adult that is not their parent. Although alloparental care is common in social mammals, its prevalence is difficult to assess in cetaceans, and has not been studied in Globicephala melas. A population off Cape Breton, Nova Scotia, has been studied from whale‐watching vessels since 1998, during July and August each year. From 2009 to 2011, we collected photo identifications of calves and the adults accompanying them. Alloparental care was considered to be occurring when a calf was identified with more than one companion. We found that 85.7% of calves in 2009, 80.6% of calves in 2010 and 63% of calves in 2011 had alloparents. Mothers were difficult to identify. Nevertheless, none of the other companions of calves were assigned to the same unit as the mother. Five carers were sexed, four of them males. There were no cases of within‐ or between‐year alloparental care reciprocity. It is possible that delayed reciprocity is happening on a larger time scale in this population, but the most likely explanation is that alloparental care is a byproduct of this species’ social structure, with a very small cost to the alloparent's fitness.
METHYLENE BLUE SENSITIVITY 1 (MBS1) is required for acclimation of Arabidopsis to singlet oxygen and acts downstream of β‐cyclocitral
Authors: Shumbe Leonard , D'Alessandro Stefano , Shao Ning , Chevalier Anne , Ksas Brigitte , Bock Ralph , Havaux Michel 
Published: November 2016

AbstractSinglet oxygen (1O2) signalling in plants is essential to trigger both acclimatory mechanisms and programmed cell death under high light stress. However, because of its chemical features, 1O2 requires mediators, and the players involved in this pathway are largely unknown. The β‐carotene oxidation product, β‐cyclocitral, is one such mediator. Produced in the chloroplast, β‐cyclocitral induces changes in nuclear gene expression leading to photoacclimation. Recently, the METHYLENE BLUE SENSITIVITY protein MBS has been identified as a key player in 1O2 signalling leading to tolerance to high light. Here, we provide evidence that MBS1 is essential for acclimation to 1O2 and cross‐talks with β‐cyclocitral to mediate transfer of the 1O2 signal to the nucleus, leading to photoacclimation. The presented results position MBS1 downstream of β‐cyclocitral in 1O2 signalling and suggest an additional role for MBS1 in the regulation of plant growth and development under chronic 1O2 production.