bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast On-Target Lysis (YOTL), a Procedure for Making Auxiliary Mass Spectrum Data Sets for Clinical Routine Identification of Yeasts
Authors: Bernhard Mareike , Weig Michael , Zautner Andreas E. , Groß Uwe , Bader Oliver 
Published: September 2014

ABSTRACT
Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based species identification has become a reliable and fast tool for use in clinical diagnostics, including in mycology. To identify yeasts in the MALDI Biotyper system, a multistep extraction protocol, which is also used to generate the reference spectra, is recommended. Sample preparation by on-target lysis (OTL) requires significantly less hands-on time and is therefore highly desirable, but it results in too-low MALDI Biotyper log score values to allow automated species identification. To overcome this problem, we developed a procedure for generating and validating an OTL spectrum data set for the most relevant and frequently occurring yeast species in clinical specimens. The performance was evaluated against a set of OTL spectra derived during clinical routine procedures and from a set of closely related yeasts. In the diagnostic setting, the OTL procedure significantly decreased the workload but allowed species identification with high specificity and sensitivity. False identifications were not observed. The use of in-house-generated OTL reference spectra can highly accelerate MALDI-TOF MS-based yeast species identification using the MALDI Biotyper.
Comparative Genome Analysis of Four Elephant Endotheliotropic Herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from Cases of Hemorrhagic Disease or Viremia
Authors: Zong Jian-Chao , Latimer Erin M. , Long Simon Y. , Richman Laura K. , Heaggans Sarah Y. , Hayward Gary S. 
Published: September 2014

ABSTRACT

The genomes of three types of novel endotheliotropic herpesviruses (elephant endotheliotropic herpesvirus 1A [EEHV1A], EEHV1B, and EEHV2) associated with lethal hemorrhagic disease in Asian elephants have been previously well characterized and assigned to a new
Proboscivirus
genus. Here we have generated 112 kb of DNA sequence data from segments of four more types of EEHV by direct targeted PCR from blood samples or necropsy tissue samples from six viremic elephants. Comparative phylogenetic analysis of nearly 30 protein-encoding genes of EEHV5 and EEHV6 show that they diverge uniformly by nearly 20% from their closest relatives, EEHV2 and EEHV1A, respectively, and are likely to have similar overall gene content and genome organization. In contrast, seven EEHV3 and EEHV4 genes analyzed differ from those of all other EEHVs by 37% and have a G+C content of 63% compared to just 42% for the others. Three strains of EEHV5 analyzed clustered into two partially chimeric subgroups EEHV5A and EEHV5B that diverge by 19% within three small noncontiguous segments totaling 6.2 kb. We conclude that all six EEHV types should be designated as independent species within a proposed new fourth
Deltaherpesvirinae
subfamily of mammalian herpesviruses. These virus types likely initially diverged close to 100 million years ago when the ancestors of modern elephants split from all other placental mammals and then evolved into two major branches with high- or low-G+C content about 35 million years ago. Later additional branching events subsequently generated three paired sister taxon lineages of which EEHV1 plus EEHV6, EEHV5 plus EEHV2, and EEHV4 plus EEHV3 may represent Asian and African elephant versions, respectively.

IMPORTANCE
One of the factors threatening the long-term survival of endangered Asian elephants in both wild range countries and in captive breeding populations in zoos is a highly lethal hemorrhagic herpesvirus disease that has killed at least 70 young Asian elephants worldwide. The genomes of the first three types of EEHVs (or probosciviruses) identified have been partially characterized in the preceding accompanying paper (
L. K. Richman, J.-C. Zong, E. M. Latimer, J. Lock, R. C. Fleischer, S. Y. Heaggans, and G. S. Hayward
, J. Virol. 88:13523–13546, 2014,
http://dx.doi.org/10.1128/JVI.01673-14
). Here we have used PCR DNA sequence analysis from multiple segments of DNA amplified directly from blood or necropsy tissue samples of six more selected cases of hemorrhagic disease to partially characterize four other types of EEHVs from either Asian or African elephants. We propose that all six types and two chimeric subtypes of EEHV belong to multiple lineages of both AT-rich and GC-rich branches within a new subfamily to be named the
Deltaherpesvirinae
, which evolved separately from all other mammalian herpesviruses about100 million years ago.
Expanded Regulatory T Cells in Chronically Friend Retrovirus-Infected Mice Suppress Immunity to a Murine Cytomegalovirus Superinfection
Authors: Duppach Janine , Francois Sandra , Joedicke Jara J. , Dittmer Ulf , Kraft Anke R. M. 
Published: September 2014

ABSTRACT

It is still unclear whether expanded and activated regulatory T cells (Tregs) in chronic viral infections can influence primary immune responses against superinfections with unrelated viruses. Expanded Tregs found in the spleens of chronically Friend virus (FV)-infected mice decreased murine cytomegalovirus (mCMV)-specific CD8
+
T cell responses during acute mCMV superinfection. This suppression of mCMV-specific T cell immunity was found only in organs with FV-induced Treg expansion. Surprisingly, acute mCMV infection itself did not expand or activate Tregs.
Structural Plasticity of the Coiled-Coil Domain of Rotavirus NSP4
Authors: Sastri Narayan P. , Viskovska Maria , Hyser Joseph M. , Tanner Mark R. , Horton Lori B. , Sankaran Banumathi , Prasad B. V. Venkataram , Estes Mary K. 
Published: September 2014

ABSTRACT

Rotavirus (RV) nonstructural protein 4 (NSP4) is a virulence factor that disrupts cellular Ca
2+
homeostasis and plays multiple roles regulating RV replication and the pathophysiology of RV-induced diarrhea. Although its native oligomeric state is unclear, crystallographic studies of the coiled-coil domain (CCD) of NSP4 from two different strains suggest that it functions as a tetramer or a pentamer. While the CCD of simian strain SA11 NSP4 forms a tetramer that binds Ca
2+
at its core, the CCD of human strain ST3 forms a pentamer lacking the bound Ca
2+
despite the residues (E120 and Q123) that coordinate Ca
2+
binding being conserved. In these previous studies, while the tetramer crystallized at neutral pH, the pentamer crystallized at low pH, suggesting that preference for a particular oligomeric state is pH dependent and that pH could influence Ca
2+
binding. Here, we sought to examine if the CCD of NSP4 from a single RV strain can exist in two oligomeric states regulated by Ca
2+
or pH. Biochemical, biophysical, and crystallographic studies show that while the CCD of SA11 NSP4 exhibits high-affinity binding to Ca
2+
at neutral pH and forms a tetramer, it does not bind Ca
2+
at low pH and forms a pentamer, and the transition from tetramer to pentamer is reversible with pH. Mutational analysis shows that Ca
2+
binding is necessary for the tetramer formation, as an E120A mutant forms a pentamer. We propose that the structural plasticity of NSP4 regulated by pH and Ca
2+
may form a basis for its pleiotropic functions during RV replication.

IMPORTANCE
The nonstructural protein NSP4 of rotavirus is a multifunctional protein that plays an important role in virus replication, morphogenesis, and pathogenesis. Previous crystallography studies of the coiled-coil domain (CCD) of NSP4 from two different rotavirus strains showed two distinct oligomeric states, a Ca
2+
-bound tetrameric state and a Ca
2+
-free pentameric state. Whether NSP4 CCD from the same strain can exist in different oligomeric states and what factors might regulate its oligomeric preferences are not known. This study used a combination of biochemical, biophysical, and crystallography techniques and found that the NSP4 CCD can undergo a reversible transition from a Ca
2+
-bound tetramer to a Ca
2+
-free pentamer in response to changes in pH. From these studies, we hypothesize that this remarkable structural adaptability of the CCD forms a basis for the pleiotropic functional properties of NSP4.
The INCENTIVE protocol: an evaluation of the organisation and delivery of NHS dental healthcare to patients—innovation in thecommissioning of primary dental care service delivery and organisation in the UK
Authors: Pavitt Sue H , Baxter Paul D , Brunton Paul A , Douglas Gail , Edlin Richard , Gibson Barry J , Godson Jenny , Hall Melanie , Porritt Jenny , Robinson Peter G , Vinall Karen , Hulme Claire 
Published: September 2014

IntroductionIn England, in 2006, new dental contracts devolved commissioning of dental services locally to Primary Care Trusts to meet the needs of their local population. The new national General Dental Services contracts (nGDS) were based on payment for Units of Dental Activity (UDAs) awarded in three treatment bands based on complexity of care. Recently, contract currency in UK dentistry is evolving from UDAs based on volume and case complexity towards ‘blended contracts’ that include incentives linked with key performance indicators such as quality and improved health outcome. Overall, evidence of the effectiveness of incentive-driven contracting of health providers is still emerging. The INCENTIVE Study aims to evaluate a blended contract model (incentive-driven) compared to traditional nGDS contracts on dental service delivery in practices in West Yorkshire, England.Methods and analysisThe INCENTIVE model uses a mixed methods approach to comprehensively evaluate a new incentive-driven model of NHS dental service delivery. The study includes 6 dental surgeries located across three newly commissioned dental practices (blended contract) and three existing traditional practices (nGDS contracts). The newly commissioned practices have been matched to traditional practices by deprivation index, age profile, ethnicity, size of practice and taking on new patients. The study consists of three interlinked work packages: a qualitative study to explore stakeholder perspectives of the new service delivery model; an effectiveness study to assess the INCENTIVE model in reducing the risk of and amount of dental disease and enhance oral health-related quality of life in patients; and an economic study to assess cost-effectiveness of the INCENTIVE model in relation to clinical status and oral health-related quality of life.Ethics and disseminationThe study has been approved by NRES Committee London, Bromley. The results of this study will be disseminated at national and international conferences and in international journals.
A cross-sectional study on informed choice in the mammography screening programme in Germany (InEMa): a study protocol
Authors: Berens Eva-Maria , Reder Maren , Kolip Petra , Spallek Jacob 
Published: September 2014

IntroductionBreast cancer is the most prevalent cancer among women. In Germany, women are invited to a population-based mammography screening programme for the first time at the age of 50. Since it is still discussed whether the benefits of mammography screening outweigh its harms, the concept of informed choice has gained importance. The objective of this cross-sectional study is to assess the proportion of informed choices in the mammography screening programme. A special focus is on the examination of the impact of Turkish migration background and educational level on informed choices.Methods and analysisThe proportion of informed choices is evaluated in a cross-sectional study with 3-month follow-up for behavioural implementation of the screening intention. A randomly selected sample of 17 000 women aged 50 years living in Westphalia-Lippe, a region in the Federal State of North-Rhine Westphalia, is invited to participate in this study. To reach adequate numbers of Turkish women, all possibly Turkish women in the sample are identified through a name algorithm and contacted. The sample is drawn from women registered in the study area for which the registration offices consented to supply data for the study (88% of all towns/cities in the study region). Women identified through the Turkish name algorithm received all materials in German and Turkish. The primary outcome is informed choice. Data are collected on informed choice components (knowledge, attitude, decision/implementation) as well as on its possible determinants (eg, health behaviour, perceived behavioural control, subjective norms, invitation status, migration background and other demographic variables). Data are collected before the screening appointment and at 3 months follow-up.Ethics and disseminationThe study was approved by the ethical committee of the Medical Faculty of Muenster University. Results will be published in a relevant scientific journal and communicated to respondents and relevant institutions.
Adhesion-Mediated Signalling in Cancer: Recent Advances and Mathematical Modelling
Authors: Crociani Olivia , Becchetti Andrea , Fanelli Duccio , Arcangeli Annarosa 
Published: September 2014

Cancer can be viewed as a "tissue", where neoplastic cells are immersed into a peculiar microenvironment (the "tumor microenvironment", TME) which modulates tumor cell behaviour during multistep tumorigenesis. Based on this concept, antineoplastic therapy should be tuned to target not only tumor cells but also the cellular constituents of the TME. Such necessity is well exemplified by considering tumor angiogenesis, a major aspect of cancer biology.Ion channels and transporters are increasingly recognized as relevant players in the tumor cell-TME cross-talk. For example, during tumor neo-angiogenesis, soluble factors as well as fixed components of the extracellular matrix (ECM) and membrane proteins determine signal exchange between the TME and the implicated cell types. The signalling network is coordinated by functional "hubs", which may be constituted by integrin receptors associated with other proteins to form macromolecular signalling platforms at the adhesive sites. These complexes often include ion channels.The K+channels encoded by the human ether-à-go-go related gene (Kv11.1, or hERG1) are frequently overexpressed in human cancers and regulate intracellular signalling by physically associating with integrin subunits and growth factor/chemokine receptors. In colorectal cancer (CRC) we recently identified a novel signalling pathway centered on hERG1 channels and integrins. This pathway involves the p53 protein, which is encoded by a tumor suppressor gene often mutated in human cancers. p53 controls angiogenesis, through a mechanism regulated by hERG1 K+channels. The central role played by hERG1 in CRC angiogenesis suggests that targeting hERG1 may be an effective therapeutic option in patients with advanced CRC.To better understand the above process, it is necessary to study the interlaced dynamics of the key microscopic actors by using dedicated mathematical models. We here review a simple model, of reductionist inspiration, that explores the intimate connections between apoptosis and hypoxia, passing through angiogenesis. We show that a dynamical switch takes place between the normoxia and cellular death conditions. When oxygen lacks, cells can cross the transition line and so gain their way towards the normoxia regime, by implementing point mutations that affect the p53 production and activation rate, with the involvement of K+ion homeostasis, in agreement with the experimental observations.
Modular Leech Trees of Order at Most 8
Authors: Leach David 
Published: September 2014

In 1975, John Leech asked when can the edges of a tree on n vertices be labeled with positive integers such that the sums along the paths are exactly the integers 1, 2, …, n2. He found five such trees, and no additional trees have been discovered since. In 2011 Leach and Walsh introduced the idea of labeling trees with elements of the group Zk where k=n2+1 and examined the cases for n≤6. In this paper we show that no modular Leech trees of order 7 exist, and we find all modular Leech trees of order 8.
Raising the Bar for Antineoplastic Agents: How to Choose Threshold Values for Superiority Trials in Advanced Solid Tumors
Authors: Sobrero Alberto F. , Pastorino Alessandro , Sargent Daniel J. , Bruzzi Paolo 
Published: September 2014

Abstract
Purpose: To establish the concept of minimum clinically meaningful outcome (mCMO) of treatment in advanced solid tumors, to establish its threshold and evaluate how many superiority trials of new antineoplastic agents pass this threshold.
Experimental Design: We chose overall survival as the primary indicator of patient benefit. Four conceptually different types of treatment effect can be identified in OS curves: HR, gains in median OS, proportional, and absolute increases at long-term OS. We postulated threshold levels for these four parameters defining the mCMO and set the bar at three different levels of required benefit: high, medium, and low. The postulated values were then studied by comparing our thresholds with the actual results of the pivotal superiority phase III trials on new drugs reporting on mature OS data.
Results: Forty-three trials on 35,419 patients in 12 cancer types on 23 novel agents met these criteria. Only two trials reached the postulated “high” thresholds for HR and median OS. The number of “positive trials” increased to eight and 15 when the bar was lowered to the “medium” and “low” levels, respectively. The same analysis was done for proportional and absolute increases in long-term OS. No trial satisfied the criteria for long-term benefit, whereas only two and nine trials satisfied both parameters for the “medium and low” required benefit levels, respectively.
Conclusions: All four OS-related parameters contribute to define the mCMO. If the bar for the mCMO is raised too much, positive trials are exceptional. Clin Cancer Res; 21(5); 1036–43. ©2014 AACR.
See related commentary by Schilsky, p. 947
Bile Acids Regulate Nuclear Receptor (Nur77) Expression and Intracellular Location to Control Proliferation and Apoptosis
Authors: Hu Ying , Chau Thinh , Liu Hui-Xin , Liao Degui , Keane Ryan , Nie Yuqiang , Yang Hui , Wan Yu-Jui Yvonne 
Published: September 2014

Abstract
Bile acids (BA) are endogenous agents capable of causing cancer throughout the gastrointestinal (GI) tract. To uncover the mechanism by which BAs exert carcinogenic effects, both human liver and colon cancer cells as well as mouse primary hepatocytes were treated with BAs and assayed for viability, genotoxic stress, and transcriptional response. BAs induced both Nur77 (NR4A1) and proinflammatory gene expression. The intracellular location of BA-induced Nur77 was time dependent; short-term (1–3 hours) exposure induced nuclear Nur77, whereas longer (1–2 days) exposure also increased cytosolic Nur77 expression and apoptosis. Inhibiting Nur77 nuclear export with leptomycin B decreased lithocholic acid (LCA)-induced apoptosis. Extended (7 days) treatment with BA generated resistance to BA with increased nuclear Nur77, viability, and mobility. While, knockdown of Nur77 in BA-resistant cells increased cellular susceptibility to LCA-induced apoptosis. Moreover, in vivo mouse xenograft experiments demonstrated that BA-resistant cells form larger tumors with elevated Nur77 expression compared with parental controls. DNA-binding and gene expression assays identified multiple survival genes (CDK4, CCND2, MAP4K5, STAT5A, and RBBP8) and a proapoptosis gene (BID) as Nur77 targets. Consistently, BA-induced upregulation of the aforementioned genes was abrogated by a lack of Nur77. Importantly, Nur77 was overexpressed in high percentage of human colon and liver cancer specimens, and the intracellular location of Nur77 correlated with elevated serum total BA levels in patients with colon cancer. These data show for the first time that BAs via Nur77 have a dual role in modulating cell survival and death.
Implications: These findings establish a direct link between Nur77 and the carcinogenic effect of BAs. Mol Cancer Res; 13(2); 281–92. ©2014 AACR.
Influence of dabigatran and rivaroxaban on routine coagulation assays
Authors: Bailleul Els , Chatelain Bernard , Demulder Anne , Devreese Katrien , Douxfils Jonathan , Jochmans Kristin , Mullier François , Wijns Walter , Soumali Mohamed Rida , Coucke Wim , Vernelen Kris , Walle Philippe Van de , Blerk Marjan Van 
Published: September 2014

SummaryThe Belgian national External Quality Assessment Scheme performed a nationwide survey using lyophilised plasma samples spiked with dabigatran or rivaroxaban to demonstrate to the Belgian clinical laboratories how these drugs affect their routine coagulation assays prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen and antithrombin. Virtually all Belgian laboratories performing routine coagulation testing (189/192) participated in the survey. Both, dabigatran and rivaroxaban significantly prolonged the PT and aPTT in a concentration- and reagent-dependent manner. PT reagents were more influenced by rivaroxaban than by dabigatran and aPTT reagents more influenced by dabigatran than by rivaroxaban. Among PT reagents, Neoplastin R® was the most sensitive to rivaroxaban and Innovin ® and Thromborel S® the least sensitive. Converting PT results to INR only increased the variability between reagents. Among aPTT reagents, Actin FSL® was the least sensitive to dabigatran while the other aPTT reagents showed slightly higher sensitivities. The presence of dabigatran led to falsely reduced fibrinogen concentrations when measured with a low thrombin concentration reagent. The presence of dabigatran caused an overestimation of the antithrombin level when measured with a thrombin-based activity assay and the presence of rivaroxaban an overestimation of the antithrombin level when measured with a FXa-based assay. Instrument-related differences were found for all tested parameters. In conclusion, this paper provides detailed information on the effect of dabigatran and rivaroxaban on routine coagulation assays as performed with a large number of reagent/instrument combinations.
Glycoprotein Ibα clustering induces macrophage-mediated platelet clearance in the liver
Authors: Ma Na , Zhao Lili , Lijuan Cao , Zhang Yiwen , Zhang Jie , Yu Ziqiang , Wang Zhaoyue , Xia Lijun , Ruan Changgeng , Yan Rong , Chen Mengxing , Dai Kesheng 
Published: September 2014

SummaryMany immune thrombocytopenia (ITP) patients, particularly patients with anti-glycoprotein (GP) Ib-IX autoantibodies, do not respond to the conventional treatments such as splenectomy. However, the underlying mechanism remains unclear. Here we found that anti-GPIbα N-terminus antibody AN51, but not other anti-GPIbα antibodies (AK2, HIP1, VM16d, or WM23), induced GPIbα clustering that led to integrin αIIbβ3-dependent platelet aggregation. After intravenous injection, AN51 dose-dependently induced thrombocytopenia in guinea pigs, and the platelets were mainly removed by macrophages in the liver. N-acetyl-D-glucosamine, previously shown to inhibit integrin αMβ2-mediated phagocytosis of refrigerated platelets, dose-dependently inhibited AN51-induced platelet clearance. Furthermore, AN51 but not VM16d, induced rapid platelet clearance in the liver of cynomolgus macaques. Five of 22 chronic ITP patients had anti-GPIbα autoantibodies, and the autoantibodies from four of the five patients competed with AN51 for binding to platelets. These data indicate that GPIbα clustering induced by anti-GPIbα N-terminus antibody causes integrin αIIbβ3-dependent platelet aggregation, phagocytosis, and rapid platelet clearance in the liver. Our findings reveal a novel Fc-independent mechanism underlying the pathogenesis of ITP, and suggest new therapeutic strategies for ITP patients with anti-GPIbα autoantibodies.