bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differences in immunohistochemical biomarkers between intra‐ and extrahepatic cholangiocarcinoma: A systematic review and meta‐analysis
Authors: Wiggers Jimme K. , Ruys Anthony T. , Groot Koerkamp Bas , Beuers Ulrich , ten Kate Fiebo J. , van Gulik Thomas M 
Published: May 2014

AbstractBackground and AimCholangiocarcinomas of different locations differ in growth patterns, symptoms, treatment response, and survival. Still, they are regarded in many studies as a uniform malignancy. Because intra‐ (iCCA) and extrahepatic (eCCA) cholangiocarcinoma display such differences, we performed a systematic review and meta‐analysis to analyze differences in the immunohistochemical profile of these tumors.MethodsIn February 2014, we searched the two main medical literature databases MEDLINE and EMBASE. We extracted risk ratios and 95% confidence intervals from the identified studies and performed random‐effects model meta‐analyses in accordance with PRISMA and REMARK guidelines.ResultsA total of 54 cohort studies, including 4458 patients and studying 102 individual markers met the inclusion criteria. Of the 57 markers that were evaluated in more than 30 iCCA and eCCA patients, 18 showed a statistically significant difference in expression between iCCA and eCCA. Biomarkers expressed differently between iCCA and eCCA included potential targets of therapy: EGFR, c‐erbB‐2 and VEGF‐A. Several markers showed no statistical difference but large 95% confidence intervals, suggesting insufficient sample size.ConclusionsThis systematic review shows differences in marker expression between iCCA and eCCA. Consequently, patients with iCCA and eCCA may benefit from different treatment strategies.
Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate
Authors: Babaie Ghobad , Kouhi Habibi Mina , Massah Amir , Dizadji Akbar , Izadinejad Laleh , Simon Anne 
Published: May 2014

AbstractThe full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.
Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography
Authors: WANG Wei , LI Hong‐Lei , XIANG Xiao‐Guo , CHEN Zhi‐Duan 
Published: April 2014

AbstractPrevious studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ‐petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ‐petA, and ITS dataset, and the combined rbcL, trnL‐F, matK/trnK, psbJ‐petA, and ITS dataset. Based on the tree‐based comparisons, BLAST searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ‐petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia–Cyrtorhyncha, Kumlienia, and Peltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus‐level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.
Texture and Sensory Evaluation of Composite Wheat‐Oat Bread Prepared with Novel Two‐Phase Method Using Oat Yeast‐Fermented Leaven
Authors: Różyło Renata , Dziki Dariusz , Laskowski Janusz , Skonecki Stanisław , Łysiak Grzegorz , Kulig Ryszard , Różyło Krzysztof 
Published: April 2014

AbstractA novel method that uses bioprocessed oat flour (yeast‐fermented leaven) for the preparation of composite wheat‐oat (50:50%) bread was proposed. The objective of the study was to compare physical (loaf volume and specific weight, crumb texture, changes in texture during storage, crumb heterogeneity) and sensorial (aroma, flavor, texture, overall acceptability) properties of bread produced by this method with the properties of bread produced by the standard methods (straight‐dough and two‐phase). It was observed that, after fermentation, oat leaven compared with wheat leaven had a more concise consistency and that, during dough preparation, a greater addition of water was required. The bread produced in this way is characterized by a comparable volume to bread produced from wheat yeast‐fermented leaven, while crumb firmness and elasticity are significantly greater. Methods using yeast‐fermented leaven prepared from different types of flour should be tested for other composite wheat breads.Practical ApplicationsIn general, a straight dough‐baking method sometimes with process modifications is applied for the preparation of composite wheat‐oat bread, but there is still lack of information describing the potential of using oat yeast‐fermented leaven. Besides the importance of health (latest studies show that longer fermentation process can be used to increase the antioxidant activity of bread), the preparation of oat yeast‐fermented leaven significantly increases dough yield and enhances the success – ease of dough formation. In this method, to initiate the fermentation of the leaven, a small amount of yeast (1%) is required. Using oat yeast‐fermented leaven produces satisfactory baking results and also economic benefits and it can be used for organic bread. In addition, there is no need to change the bakery equipment that enables the rapid introduction of this method into practice.
Dickens in New Zealand
Authors: Wevers Lydia 
Published: May 2014

AbstractFour months after the first settlers of the New Zealand Company landed on a windswept beach in Wellington New Zealand in 1840, they founded the first Pickwick Club outside Great Britain. The expressed aim of the Club was to spread the ‘fame of the author’ in ‘this savage land’, but it is an interesting paradox that a novel which makes fun of British institutions should also be the inspiration to earnestly reproduce them in the shanty towns of empire. This paper examines the social history of the Pickwick Club of New Zealand and its relation to colonialism and Victorian cultural ambitions.
The combination of liver stiffness measurement and NAFLD fibrosis score improves the noninvasive diagnostic accuracy for severe liver fibrosis in patients with nonalcoholic fatty liver disease
Authors: Petta Salvatore , Vanni Ester , Bugianesi Elisabetta , Di Marco Vito , Cammà Calogero , Cabibi Daniela , Mezzabotta Lavinia , Craxì Antonio 
Published: May 2014

AbstractBackground & AimsThe accuracy of noninvasive tools for the diagnosis of severe fibrosis in patients with nonalcoholic fatty liver disease(NAFLD) in clinical practice is still limited. We aimed at assessing the diagnostic performance of combined noninvasive tools in two independent cohorts of Italian NAFLD patients.MethodsWe analysed data from 321 Italian patients(179 Sicilian‐training cohort, and 142 northern Italy‐validation cohort) with an histological diagnosis of NAFLD. Severe fibrosis was defined as fibrosis ≥ F3 according to Kleiner classification. The APRI, AST/ALT, BARD, FIB‐4, and NFS scores were calculated according to published algorithms. Liver stiffness measurement(LSM) was performed by FibroScan. Cut‐off points of LSM, NFS and FIB‐4 for rule‐in or rule‐out F3‐F4 fibrosis were calculated by the reported formulas.ResultsIn the Sicilian cohort AUCs of LSM, NFS, FIB‐4, LSM plus NFS, LSM plus FIB‐4, and NFS plus FIB‐4 were 0.857, 0.803, 0.790, 0.878, 0.888 and 0.807, respectively, while in the northern Italy cohort the corresponding AUCs were 0.848, 0.730, 0.703, 0.844, 0.850, and 0.733 respectively. In the training cohort, the combination of LSM plus NFS was the best performing strategy, providing false positive, false negative and uncertainty area rates of 0%,1.1% and 48% respectively. Similar results were obtained in the validation cohort with false positive, false negative and uncertainty area rates of 0%,7.3% and 40.8%.ConclusionsThe combination of LSM with NFS, two complementary, easy‐to‐perform, and widely available tools, is able to accurately diagnose or exclude the presence of severe liver fibrosis, also reducing of about 50–60% the number of needed diagnostic liver biopsies.
Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographical breaks in a Mediterranean endemic marine cave mysid
Authors: Rastorgueff Pierre‐Alexandre , Chevaldonné Pierre , Arslan Defne , Verna Caroline , Lejeusne Christophe 
Published: April 2014

AbstractThe marine cave‐dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea, which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographical regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographical breaks, some dating back to the Oligo‐Miocene. Whether looking at the intralineage or interlineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to southeastern Italy. Typical genetic breaks such as the Almeria‐Oran Front or the Siculo‐Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present‐day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo‐Miocene and maintained by present‐day coastal topography, water circulation and habitat fragmentation.
Endoplasmic reticulum localized PerA is required for cell wall integrity, azole drug resistance, and virulence in Aspergillus fumigatus
Authors: Chung Dawoon , Thammahong Arsa , Shepardson Kelly M. , Blosser Sara J. , Cramer Robert A. 
Published: April 2014

SummaryGPI‐anchoring is a universal and critical post‐translational protein modification in eukaryotes. In fungi, many cell wall proteins are GPI‐anchored, and disruption of GPI‐anchored proteins impairs cell wall integrity. After being synthesized and attached to target proteins, GPI anchors undergo modification on lipid moieties. In spite of its importance for GPI‐anchored protein functions, our current knowledge of GPI lipid remodelling in pathogenic fungi is limited. In this study, we characterized the role of a putative GPI lipid remodelling protein, designated PerA, in the human pathogenic fungus Aspergillus fumigatus. PerA localizes to the endoplasmic reticulum and loss of PerA leads to striking defects in cell wall integrity. A perA null mutant has decreased conidia production, increased susceptibility to triazole antifungal drugs, and is avirulent in a murine model of invasive pulmonary aspergillosis. Interestingly, loss of PerA increases exposure of β‐glucan and chitin content on the hyphal cell surface, but diminished TNF production by bone marrow‐derived macrophages relative to wild type. Given the structural specificity of fungal GPI‐anchors, which is different from humans, understanding GPI lipid remodelling and PerA function in A. fumigatus is a promising research direction to uncover a new fungal specific antifungal drug target.
Phosphatase activity of the histidine kinases ensures pathway specificity of the ChrSA and HrrSA two‐component systems in Corynebacterium glutamicum
Authors: Hentschel Eva , Mack Christina , Gätgens Cornelia , Bott Michael , Brocker Melanie , Frunzke Julia 
Published: April 2014

SummaryThe majority of bacterial genomes encode a high number of two‐component systems controlling gene expression in response to a variety of different stimuli. The Gram‐positive soil bacterium Corynebacterium glutamicum contains two homologous two‐component systems (TCS) involved in the haem‐dependent regulation of gene expression. Whereas the HrrSA system is crucial for utilization of haem as an alternative iron source, ChrSA is required to cope with high toxic haem levels. In this study, we analysed the interaction of HrrSA and ChrSA in C. glutamicum. Growth of TCS mutant strains, in vitro phosphorylation assays and promoter assays of PhrtBA and PhmuO fused to eyfp revealed cross‐talk between both systems. Our studies further indicated that both kinases exhibit a dual function as kinase and phosphatase. Mutation of the conserved glutamine residue in the putative phosphatase motif DxxxQ of HrrS and ChrS resulted in a significantly increased activity of their respective target promoters (PhmuO and PhrtBA respectively). Remarkably, phosphatase activity of both kinases was shown to be specific only for their cognate response regulators. Altogether our data suggest the phosphatase activity of HrrS and ChrS as key mechanism to ensure pathway specificity and insulation of these two homologous systems.
Pressure–volume curves: revisiting the impact of negative turgor during cell collapse by literature review and simulations of cell micromechanics
Authors: Ding Yiting , Zhang Yanxiang , Zheng Quan‐Shui , Tyree Melvin T. 
Published: May 2014

Summary

The Scholander–Hammel pressure chamber has been used in thousands of papers to measure osmotic pressure, πc, turgor pressure, Pt, and bulk modulus of elasticity, ε, of leaf cells by pressure–volume (PV) curve analysis. PV analysis has been questioned in the past.

In this paper we use micromechanical analysis of leaf cells to examine the impact on PV curve analysis of negative turgor in living cells (Pt).

Models predict negative Pt (−0.1 to −1.8 MPa) depending on leaf cell size and shape in agreement with experimental values reported by J. J. Oertli. Modeled PV curves have linear regions even when Pt is quite negative, contrary to the arguments of M.T. Tyree. Negative Pt is totally missed by PV curve analysis and results in large errors in derived πc and Pt but smaller errors in ε.

A survey of leaf cell sizes vs habitat (arid, temperate, and rainforest), suggests that the majority of published PV curves result in errors of 0.1–1.8 MPa in derived πc and Pt, whereby the error increases with decreasing cell size. We propose that small cell size in leaves is an ecological adaptation that permits plants to endure negative values of water potential with relatively little water loss.
An insight into the sensitivity of maize to photoperiod changes under controlled conditions
Authors: CHEN QIANG , ZHONG HAO , FAN XIAN‐WEI , LI YOU‐ZHI 
Published: April 2014

AbstractResponse of maize to photoperiods affects adaption of this crop to environments. We characterize the phenotypes of four temperate‐adapted maize foundation parents, Huangzao 4, Chang 7‐2, Ye 478 and Zheng 58, and two tropically adapted maize foundation parents, M9 and Shuang M9 throughout the growth stage under three constant photoperiod regimes in a daily cycle of 24 h at 28 °C, and analysed expression of 48 photoperiod response‐associated genes. Consequently, long photoperiod (LP) repressed development of the tassels of photoperiod‐sensitive maize lines at V9 stage, and caused subsequent failure in flowering; failure of photoperiod‐sensitive maize lines in flowering under LP was associated with lower expression of flowering‐related genes; photoperiod changes could make a marked impact on spatial layout of maize inflorescence. The larger oscillation amplitude of expression of photoperiod‐responsive genes occurred in LP‐sensitive maize lines. In conclusion, failure in development of tassels at V9 stage under LP is an early indicator for judging photoperiod sensitivity. The adaptation of temperate‐adapted maize lines to LP is due to the better coordination of expression among photoperiod‐sensing genes instead of the loss of the genes. High photoperiod sensitivity of maize is due to high expression of circadian rhythm‐responding genes improperly early in the light.
Magnesium availability regulates the development of root hairs in Arabidopsis thaliana (L.) Heynh
Authors: NIU YAOFANG , CHAI RUSHAN , LIU LIJUAN , JIN GULEI , LIU MIAO , TANG CAIXIAN , ZHANG YONGSONG 
Published: April 2014

AbstractRoot hairs are reported to be plastic in response to nutrient supply, but relatively little is known about their development in response to magnesium (Mg) availability. Here, we showed that development of root hairs of Arabidopsis decreased progressively with increasing Mg supply, which was related to the initiation of new trichoblast files and likelihood of trichoblasts to form hairs. Tip‐focused reactive oxygen species (ROS) and cytosolic Ca2+ concentrations [(Ca2+)c] during elongation of root hairs were enhanced under low Mg but decreased under high Mg. Under low Mg, application of diphenylene iodonium (DPI) or BAPTA [1,2‐bis(o‐aminophenoxy)ethane‐N,N,N′,N′‐tetraacetic acid] blocked the enhanced development of root hairs and the opposite was true when the plants under high Mg were treated with phenazine methosulphate (PMS), methyl viologen (MV) or CaCl2. Furthermore, Mg availability did not alter root hair growth in rhd2‐1 mutant that contains lower levels of ROS and cytosolic [Ca2+]c. Transcriptome data and qPCR results revealed a greater fraction of morphogenetic H‐genes, and cell wall organization genes were up‐regulated by low Mg but down‐regulated by high Mg. Our data suggest a profound effect of Mg supply on the development of root hairs in Arabidopsis, through the characterized Ca2+ and ROS signals that modulate the elongation of root hairs and the expression of root‐hair morphogenetic genes.
Frontal EEG asymmetry as predictor of physiological responses to aversive memories
Authors: Meyer Thomas , Quaedflieg Conny W. E. M. , Giesbrecht Timo , Meijer Ewout H. , Abiad Schahrasad , Smeets Tom 
Published: April 2014

AbstractEvidence suggests that asymmetry in frontal electrical activity predicts responses to aversive experiences, such that higher left‐sided activity might dampen responses to trauma reminders. We measured frontal asymmetry at rest and during viewing of a trauma film, and assessed startle responses to film‐reminder images. To explore potential moderators, we compared two films (Study 1; N = 64) and modulated reappraisal (Study 2; N = 72). As expected, left frontal activation during film viewing predicted dampened responses in individuals who viewed a staged road accident. However, this effect tended to be reversed when a genocide documentary was used. In Study 2, all participants viewed the genocide film. Left frontal activity at rest again predicted higher startle responses, while reappraisal did not moderate the effects. Thus, the type of trauma film plays a crucial role in the effects of frontal asymmetry, which warrants further critical investigation.
Beyond Confession? ‘Political Religion’ and Ideological Incorrectness in the Study of Nazism
Authors: Wennberg Rebecca 
Published: May 2014

AbstractHolocaust studies have seen the rise of ‘political religion’ as part of a ‘confessional turn’. To account for the fact that Nazism experienced widespread support from the German population, ‘ideology’ was replaced with the broader and culturally more inclusive term ‘religion’. This article examines the mechanisms behind the rise of ‘political religion’ as well as the factors behind its subsequent decline. It argues that ‘political religion’, despite its culturally inclusive label, persists in connoting dogma and indoctrination. In this respect, the concept resembles rather than differs from the abandoned term ‘ideology’. Finally, the article draws from research on the Nazi principle of transgression and presents this principle as a form of ‘ideological incorrectness’. The concept of ‘ideological incorrectness’ should be seen as a move beyond belief simply understood as confession and, thus, a move beyond the conceptual constraints of ‘political religion’.
Psychologisation and Critique in Modern‐day Western Culture
Authors: Madsen Ole Jacob 
Published: May 2014

AbstractThe paper reflects on the advancement of the psychologisation of Western society through the notion of «the therapeutic ethos» and discusses political and moral implications of its “triumph”. It is argued that the attempt to exorcise a “therapeutic Zeitgeist” showcases the problems of critique of contemporary culture. The Zeitgeist reveals itself as much in the tools of critique as the objective of critique. I therefore conclude that popular critical methods like discourse analysis have itself become a hegemonic discourse, which rarely equals its philosophical originator Michel Foucault's imaginative radical ambition.
Rhodococcus globerulus bacteremia in an allogeneic hematopoietic stem cell transplant recipient: report of the first transplant case and review of the literature
Authors: Ramanan P. , Deziel P.J. , Razonable R.R. 
Published: May 2014

AbstractRhodococcus species are environmental organisms that predominantly cause opportunistic infections in immunocompromised hosts. Rhodococcus equi is the most common species associated with human infections, but there are uncommon but increasing number of cases of infections caused by non‐equi Rhodococcus species. We report a case of Rhodococcus globerulus bacteremia in an allogeneic hematopoietic stem cell transplant recipient, who presented with subacute systemic illness accompanied by severe hepatitis. In the context of this case, we review the literature on Rhodococcus species infections in transplant recipients.