bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oufti: an integrated software package for high‐accuracy, high‐throughput quantitative microscopy analysis
Authors: Paintdakhi Ahmad , Parry Bradley , Campos Manuel , Irnov Irnov , Elf Johan , Surovtsev Ivan , Jacobs‐Wagner Christine 
Published: November 2015

SummaryWith the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re‐emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today's single‐cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand‐alone, open‐source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non‐diffraction‐limited fluorescence signals and is scalable for high‐throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis and post‐processing analysis, makes the software broadly accessible to users irrespective of their computational skills.
The α‐hydroxyketone LAI‐1 regulates motility, Lqs‐dependent phosphorylation signalling and gene expression of Legionella pneumophila
Authors: Schell Ursula , Simon Sylvia , Sahr Tobias , Hager Dominik , Albers Michael F. , Kessler Aline , Fahrnbauer Felix , Trauner Dirk , Hedberg Christian , Buchrieser Carmen , Hilbi Hubert 
Published: November 2015

SummaryThe causative agent of Legionnaires' disease, Legionella pneumophila, employs the autoinducer compound LAI‐1 (3‐hydroxypentadecane‐4‐one) for cell–cell communication. LAI‐1 is produced and detected by the Lqs (Legionella quorum sensing) system, comprising the autoinducer synthase LqsA, the sensor kinases LqsS and LqsT, as well as the response regulator LqsR. Lqs‐regulated processes include pathogen–host interactions, production of extracellular filaments and natural competence for DNA uptake. Here we show that synthetic LAI‐1 promotes the motility of L. pneumophila by signalling through LqsS/LqsT and LqsR. Upon addition of LAI‐1, autophosphorylation of LqsS/LqsT by [γ‐32P]‐ATP was inhibited in a dose‐dependent manner. In contrast, the Vibrio cholerae autoinducer CAI‐1 (3‐hydroxytridecane‐4‐one) promoted the phosphorylation of LqsS (but not LqsT). LAI‐1 did neither affect the stability of phospho‐LqsS or phospho‐LqsT, nor the dephosphorylation by LqsR. Transcriptome analysis of L. pneumophila treated with LAI‐1 revealed that the compound positively regulates a number of genes, including the non‐coding RNAs rsmY and rsmZ, and negatively regulates the RNA‐binding global regulator crsA. Accordingly, LAI‐1 controls the switch from the replicative to the transmissive growth phase of L. pneumophila. In summary, the findings indicate that LAI‐1 regulates motility and the biphasic life style of L. pneumophila through LqsS‐ and LqsT‐dependent phosphorylation signalling.
Ectomycorrhizal fungal mycelia turnover in a longleaf pine forest
Authors: Hendricks Joseph J. , Mitchell Robert J. , Kuehn Kevin A. , Pecot Stephen D. 
Published: November 2015

SummaryElucidation of the patterns and controls of carbon (C) flow and nitrogen (N) cycling in forests has been hindered by a poor understanding of ectomycorrhizal fungal mycelia (EFM) dynamics.In this study,EFMstanding biomass (based on soil ergosterol concentrations), production (based on ergosterol accrual in ingrowth cores), and turnover rate (the quotient of annual production and average standing biomass estimates) were assessed in a 25‐yr‐old longleaf pine (Pinus palustris) plantation where C flow was manipulated by foliar scorching and N fertilization for 5 yr before study initiation.In the controls,EFMstanding biomass was 30 ± 7 g m−2, production was 279 ± 63 g m−2 yr−1, and turnover rate was 10 ± 3 times yr−1. The scorched × fertilized treatment had significantly higherEFMstanding biomass (38 ± 8 g m−2), significantly lower production (205 ± 28 g m−2 yr−1), and a trend of decreased turnover rate (6 ± 1 times yr−1).TheEFMturnover estimates, which are among the first reported for natural systems, indicate thatEFMare a dynamic component of ecosystems, and that conventional assessments have probably underestimated the role ofEFMin C flow and nutrient cycling.
A systematic review of the implementation of recommended psychological interventions for schizophrenia: Rates, barriers, and improvement strategies
Authors: Ince Paul , Haddock Gillian , Tai Sara 
Published: November 2015

PurposeA systematic review of the literature exploring if the UK recommendations for psychological interventions for schizophrenia were being met was carried out. Rates of implementation for cognitive behavioural therapy (CBT) and family intervention (FI) were compared. The barriers against implementation and described strategies aimed at improving implementation were reviewed.MethodsA literature search of electronic bibliography databases (Psychinfo, Medline, Pubmed, AMED, CINHAL, and EMBASE), reference and citation lists, the Evaluation and Review of NICE Implementation (ERNIE) database, a manual search of Clinical Psychology Forum, governmental reports, charity, and service user group reports was conducted.ResultsTwenty‐six articles met the inclusion criteria, 11 provided data on implementation rates, 13 explored the barriers to implementation, and 10 gave information about improvement strategies. Rates of implementation varied from 4% to 100% for CBT and 0% to 53% for FI, and studies varied in the methodology used and quality of the articles. Previously reported barriers to implementation were found, with organisational barriers being most commonly followed by barriers met by staff members and service users. Implementation strategies discovered included training packages for CBT, FI, and psychosocial interventions as well as empirical evidence suggesting methods for engagement with service users.ConclusionsRates of implementation for CBT and FI are still below recommended levels with wide variation of rates found. This suggests inequalities in the provision of psychological interventions for schizophrenia are still present. Previously identified barriers to implementation were confirmed. Attempted implementation strategies have been met with modest success.Practitioner points

Inequalities in the provision of psychological therapies for schizophrenia persist.

Good quality cognitive behavioural therapy and FI training do not ensure implementation.

Collaboration at all levels of healthcare is needed for effective implementation.
The Political Economy of Social Insurance: Towards a Fiscal‐Centred Framework
Authors: Koreh Michal 
Published: November 2015

AbstractThis article draws attention to social insurance (SI) as a revenue raising institution, and explores the potential merits of drawing on new fiscal sociology for studying the development of SI systems. This is done by revisiting previous research conducted in Germany, the USA, Finland and Israel and by offering a new reading of their findings. The reviewed cases support two interlocking claims drawn from new fiscal sociology to the study of SI. The first is that state actors may perceive SI as an extraction instrument and employ it to advance fiscal and/or economic interests other than covering the costs of SI schemes. The second is that the design and management of contribution policies for such purposes may have substantial ramifications for the development of SI schemes. In addition, while current understandings tend to associate fiscal concerns with welfare state retrenchment, this article shows that they can also play a major role in driving welfare state expansion.
Disenchanted Swiss Parliament? Electoral Strategies and Coalition Formation
Authors: Traber Denise 
Published: November 2015

AbstractThe Swiss party system has changed considerably since the 1990s. With the increasing electoral success of the right‐wing populist Swiss People's Party (SVP), the simultaneous defeat of the center‐right and a relatively stable left, it has become more polarized. In what respect have these changes in the electoral arena affected legislative politics in parliament? This article studies the voting behavior of party groups in the Swiss lower house between 1996 and 2013 in six different policy fields. The findings point to a growing level of conflict in the Swiss parliament. Overall agreement among the government parties is reduced, especially at final voting stages of the parliamentary debate. Moreover, electoral politics have become more important for the parties' behavior in parliament: in policy areas that are at the center of their party program, the SP and the SVP are less willing to move away from their original policy stance, with the consequence of increasing isolation in parliamentary votes.
‘Next‐Generation’ Surveillance: An Epidemiologists’ Perspective on the Use of Molecular Information in Food Safety and Animal Health Decision‐Making
Authors: Muellner P. , Stärk K. D. C. , Dufour S. , Zadoks R. N. 
Published: November 2015

SummaryAdvances in the availability and affordability of molecular and genomic data are transforming human health care. Surveillance aimed at supporting and improving food safety and animal health is likely to undergo a similar transformation. We propose a definition of ‘molecular surveillance’ in this context and argue that molecular data are an adjunct to rather than a substitute for sound epidemiological study and surveillance design. Specific considerations with regard to sample collection are raised, as is the importance of the relation between the molecular clock speed of genetic markers and the spatiotemporal scale of the surveillance activity, which can be control‐ or strategy‐focused. Development of standards for study design and assessment of molecular surveillance system attributes is needed, together with development of an interdisciplinary skills base covering both molecular and epidemiological principles.
Evaluation of the Biofire FilmArray BioThreat-E Test (v2.5) for Rapid Identification of Ebola Virus Disease in Heat-Treated Blood Samples Obtained in Sierra Leone and the United Kingdom
Authors: Weller Simon A. , Bailey Daniel , Matthews Steven , Lumley Sarah , Sweed Angela , Ready Derren , Eltringham Gary , Richards Jade , Vipond Richard , Lukaszewski Roman , Payne Phillippa M. , Aarons Emma , Simpson Andrew J. , Hutley Emma J. , Brooks Tim 
Published: November 2015

ABSTRACT

Rapid Ebola virus (EBOV) detection is crucial for appropriate patient management and care. The performance of the FilmArray BioThreat-E test (v2.5) using whole-blood samples was evaluated in Sierra Leone and the United Kingdom and was compared with results generated by a real-time Ebola Zaire PCR reference method. Samples were tested in diagnostic laboratories upon availability, included successive samples from individual patients, and were heat treated to facilitate EBOV inactivation prior to PCR. The BioThreat-E test had a sensitivity of 84% (confidence interval [CI], 64% to 95%) and a specificity of 89% (CI, 73% to 97%) in Sierra Leone (
n
= 60; 44 patients) and a sensitivity of 75% (CI, 19% to 99%) and a specificity of 100% (CI, 97% to 100%) in the United Kingdom (
n
= 108; 70 patients) compared to the reference real-time PCR. Statistical analysis (Fisher's exact test) indicated there was no significant difference between the methods at the 99% confidence level in either country. In 9 discrepant results (5 real-time PCR positives and BioThreat-E test negatives and 4 real-time PCR negatives and BioThreat-E test positives), the majority (
n
= 8) were obtained from samples with an observed or probable low viral load. The FilmArray BioThreat-E test (v2.5) therefore provides an attractive option for laboratories (either in austere field settings or in countries with an advanced technological infrastructure) which do not routinely offer an EBOV diagnostic capability.
Induction of the Lytic Cycle Sensitizes Epstein-Barr Virus-Infected B Cells to NK Cell Killing That Is Counteracted by Virus-Mediated NK Cell Evasion Mechanisms in the Late Lytic Cycle
Authors: Williams Luke R. , Quinn Laura L. , Rowe Martin , Zuo Jianmin 
Published: November 2015

ABSTRACT

Epstein-Barr Virus (EBV) persists for the lifetime of the infected host despite eliciting strong immune responses. This persistence requires a fine balance between the host immune system and EBV immune evasion. Accumulating evidence suggests an important role for natural killer (NK) cells in this balance. NK cells can kill EBV-infected cells undergoing lytic replication
in vitro
, and studies in both humans and mice with reconstituted human immune systems have shown that NK cells can limit EBV replication and prevent infectious mononucleosis. We now show that NK cells, via NKG2D and DNAM-1 interactions, recognize and kill EBV-infected cells undergoing lytic replication and that expression of a single EBV lytic gene, BZLF1, is sufficient to trigger sensitization to NK cell killing. We also present evidence suggesting the possibility of the existence of an as-yet-unidentified DNAM-1 ligand which may be particularly important for killing lytically infected normal B cells. Furthermore, while cells entering the lytic cycle become sensitized to NK cell killing, we observed that cells in the late lytic cycle are highly resistant. We identified expression of the vBcl-2 protein, BHRF1, as one effective mechanism by which EBV mediates this protection. Thus, contrary to the view expressed in some reports, EBV has evolved the ability to evade NK cell responses.

IMPORTANCE
This report extends our understanding of the interaction between EBV and host innate responses. It provides the first evidence that the susceptibility to NK cell lysis of EBV-infected B cells undergoing lytic replication is dependent upon the phase of the lytic cycle. Induction of the lytic cycle is associated with acquired sensitization to NK cell killing, while progress through the late lytic cycle is associated with acquired resistance to killing. We provide mechanistic explanations for this novel observation, indicating important roles for the BZLF1 immediate early transactivator, the BHRF1 vBcl-2 homologue, and a novel ligand for the DNAM-1 NK cell receptor.
Diseases Transmitted by Less Common House Pets
Authors: Chomel Bruno B. 
Published: November 2015

ABSTRACT
Beside dogs and cats, the most common pets worldwide, an increasing number of pocket pets and exotic pets are making their way to more and more households, especially in North America and Europe. Although many of these animals make appropriate pets, they also can be a source of many zoonotic diseases, especially in young children and immunocompromised individuals. Some of these diseases can be life threatening, such as rabies, rat bite fever, and plague. Some others are quite common, because of the frequency of the pathogens harbored by these species, such as salmonellosis in reptiles and amphibians. Appropriate knowledge of the zoonotic agents carried by these “new” pet species is strongly recommended prior to acquiring pocket or exotic pets. Furthermore, adopting wildlife as pets is strongly discouraged, because it is always a risky action that can lead to major health issues.
Diseases Transmitted by Man’s Worst Friend: the Rat
Authors: Fox James G. 
Published: November 2015

ABSTRACT

Historically, the rat has been considered a scourge to mankind, for example, rats infected with the plague bacillus that caused the Black Death, which accounted for millions of deaths in Europe during the Middle Ages. At least three pandemics (in the 5th and 6th, 8th through 14th, and 19th through 21st centuries) of plague ravaged civilizations, and the disease undoubtedly plagued humankind prior to recorded history. Also, numerous other diseases are spread to humans by rats; thus, a quote from Hans Zinsser’s text
Rats, Lice, and History
, “Man and rat will always be pitted against each other as implacable enemies,” conveys the general revulsion that society holds for the wild rat.
A qualitative study of self-evaluation of junior doctor performance: is perceived ‘safeness’ a more useful metric than confidence and competence?
Authors: Roland Damian , Matheson David , Coats Timothy , Martin Graham 
Published: November 2015

ObjectivesThe terms confidence and competence have been poorly defined and are often misused by junior doctors. Given safe practice relies on healthcare professionals being aware of their own skill sets improving self-assessment of confidence and competence is important. The aim of this work was to explore junior doctors’ understanding of how they perceive their own performance in respect of managing feverish children in an emergency department.SettingA children's emergency department in a tertiary hospital in the East Midlands, UK.Participants22 Junior doctors volunteered to undertake focus groups via a meta-planning methodology over 2 years (14 participants in the first year and 8 in the second).ResultsAlthough doctors were aware of the difference between confidence and competence they were not able to distinguish between them in practical terms. The feeling of being ‘safe’ emerged as a term in which there was a shared understanding compared to reported confidence and competence.ConclusionsA perception of ‘safeness’ is a concept that may aid self-evaluation and we present a matrix that might be used by supervisors and educators to examine this and its relationship with confidence and competence.
The largest expected earthquake magnitudes in Central Asia: statistical inference from an earthquake catalogue with uncertain magnitudes
Authors: Zöller Gert , Ullah Shahid , Bindi Dino , Parolai Stefano , Mikhailova Natalya 
Published: November 2015

Abstract

The knowledge of the largest expected earthquake magnitude in a region is one of the key issues in probabilistic seismic hazard calculations and the estimation of worst-case scenarios. Earthquake catalogues are the most informative source of information for the inference of earthquake magnitudes. We analysed the earthquake catalogue for Central Asia with respect to the largest expected magnitudes
m
T
in a pre-defined time horizon
T
f
using a recently developed statistical methodology, extended by the explicit probabilistic consideration of magnitude errors. For this aim, we assumed broad error distributions for historical events, whereas the magnitudes of recently recorded instrumental earthquakes had smaller errors. The results indicate high probabilities for the occurrence of large events (M≥8), even in short time intervals of a few decades. The expected magnitudes relative to the assumed maximum possible magnitude are generally higher for intermediate-depth earthquakes (51–300 km) than for shallow events (0–50 km). For long future time horizons, for example, a few hundred years, earthquakes with M≥8.5 have to be taken into account, although, apart from the 1889 Chilik earthquake, it is probable that no such event occurred during the observation period of the catalogue.
Pleistocene glaciation in Mediterranean Slovenia
Authors: Ferk Mateja , Gabrovec Matej , Komac Blaž , Zorn Matija , Stepišnik Uroš 
Published: November 2015

Abstract
Geomorphological research on glacial features in Slovenia has a long tradition; the first studies were published in the late nineteenth century by Brückner. Evidence of glacial erosion and deposition is preserved in the Slovenian Alps and on the highest plateaus of the Dinaric Mountains, including traces of ice fields and ice caps with outlet glaciers on the edges and some valley glaciers. The prevailing bedrock in all the glaciated areas is limestone, forming complex glacio-karst morphological systems. Modern glacial reconstruction techniques have been applied in the last few years, focusing on the interpretation of palaeoglacial topography and local equilibrium-line altitudes. Both past and present studies, however, lack precise chronological frameworks for the glacial advances, which should be the main goal of future research on glaciation in Slovenia.
SIGWEB annual report
Authors: Harper Simon 
Published: November 2015

Welcome to my last report as Chair. It's been a pleasure but now it's time for others to take over. However, I'm happy to say that the SIG as exhibiting increasing impact and influence, increasing funds, and increasing member benefits.
While the conferences we run and the research we publish are increasingly relevant to the community (seen by increasing conference attendance and therefore revenue, and increasing digital library downloads, again increasing revenue) we can also see an increase in membership.
In reality this is a similar picture to last year. Funds are increasing, conferences are making money, we are giving away more to students, members with childcare/care needs, and those on low income. This year differs because Membership is rising slightly.
In short SIGWEB has successfully expanded its range of conference sponsorships, is working hard on membership and volunteer development and benefits, and is financially healthy with a solid leadership.
Serum levels of 25(OH)D are not associated with venous thromboembolism in the elderly population
Authors: Delluc Aurélien , Moineau Marie-Pierre , Tromeur Cécile , Gouillou Maelenn , Lacut Karine , Carré Jean-Luc , Gentric Armelle , Gal Grégoire Le , Andro Marion 
Published: November 2015

SummaryThe prevalence of both vitamin D deficiency and venous thromboembolism (VTE) is important in the elderly. Previous studies have provided evidence for a possible association between vitamin D status and the risk of VTE. Thus, we aimed to investigate the association between vitamin D levels and VTE in the population aged 75 and over included in the EDITH case-control study. The association between vitamin D status and VTE was analysed. We also analysed the monthly and seasonal variations of VTE and vitamin D. Between May 2000 and December 2009, 340 elderly patients (mean age 81.5 years, 32 % men) with unprovoked VTE and their controls were included. The univariate and multivariate analysis found no significant association between serum levels of vitamin D and the risk of unprovoked VTE. In the unadjusted analysis, a higher BMI was statistically associated with an increased risk of VTE (OR 1.09; 95 % CI 1.05–1.13) whereas a better walking capacity and living at home were associated with a decreased rate of VTE: OR 0.57; 95 % CI 0.36–0.90 and 0.40; 95 % CI 0.25–0.66, respectively. Although not significant, more VTE events occurred during winter (p=0.09). No seasonal variations of vitamin D levels were found (p=0.11). In conclusion, in contrast with previous reports our findings suggest that vitamin D is not associated with VTE in the elderly population.