bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL28B polymorphism and early anemia predict the rapid null response in genotype‐1 chronic hepatitis C with dual therapy
Authors: Teng Wei , Chang Tzu‐Ching , Huang Chien‐Hao , Jeng Wen‐Juei , Chen Wei‐Ting , Huang Chang‐Wen , Ho Yu‐Pin , Lin Chun‐Yen , Sheen I‐Shyan 
Published: February 2015

SummaryBackground and aimsRapid null response (rNR), defined as less than one log decline of Hepatitis C virus (HCV‐RNA) at Week 4 of treatment with pegylated interferon‐α and ribavirin (PegIFN/RBV), is highly correlated with treatment failure in patients with chronic hepatitis C (CHC), genotype‐1 (GT‐1). In this study, we investigate the possible predictors of rNR.MethodsWe retrospectively analyzed a cohort of 199 GT‐1 CHC naive patients who had been treated with a dual therapy of PegIFN/RBV. Clinical parameters and genotypes of rs12979860, the single nucleotide polymorphisms (SNPs) of interleukin‐28B (IL28B) were analyzed for their relationship with rNR.ResultsOf the patients analyzed, 41.7% did not exhibit a rapid virological response (RVR). Only 13.1% of patients who experienced a rNR showed an RVR. The treatment failure rate was 36.2%. High baseline viral load (OR: 5.74; p = 0.028), nonrapid virological response (non‐RVR; OR: 4.32; p = 0.004) and rNR (OR: 51.82; p < 0.001) were the predictors of treatment failure. In addition, both the non‐CC allele of rs12979860 (OR: 13.8; p < 0.001) and the Hb (hemoglobin) decline to < 3 g/dL within 4 weeks of treatment (no early anemia; OR: 4.6; p = 0.024) were predictors of rNR.ConclusionsrNR predicted treatment failure early in GT‐1 CHC patients treated with PegIFN/RBV. Non‐CC genotype of rs12979860 and no early anemia were significant predictors of rNR.
Web Resources for Stem Cell Research
Authors: Wei Ting , Peng Xing , Ye Lili , Wang Jiajia , Song Fuhai , Bai Zhouxian , Han Guangchun , Ji Fengmin , Lei Hongxing 
Published: February 2015

Abstract
In this short review, we have presented a brief overview on major web resources relevant to stem cell research. To facilitate more efficient use of these resources, we have provided a preliminary rating based on our own user experience of the overall quality for each resource. We plan to update the information on an annual basis.
Protein expression of BIRC5, TK1, and TOP2A in malignant peripheral nerve sheath tumours – A prognostic test after surgical resection
Authors: Kolberg Matthias , Høland Maren , Lind Guro E. , Ågesen Trude H. , Skotheim Rolf I. , Sundby Hall Kirsten , Mandahl Nils , Smeland Sigbjørn , Mertens Fredrik , Davidson Ben , Lothe Ragnhild A. 
Published: February 2015

No consensus treatment regime exists beyond surgery for malignant peripheral nerve sheath tumours (MPNST), and the purpose of the present study was to find new approaches to stratify patients with good and poor prognosis and to better guide therapeutic intervention for this aggressive soft tissue cancer.From a total of 67 MPNSTs from Scandinavian patients with and without neurofibromatosis type 1, 30 MPNSTs were investigated by genome‐wide RNA expression profiling and 63 MPNSTs by immunohistochemical (IHC) analysis, and selected genes were submitted to analyses of disease‐specific survival.The potential drug target genes survivin (BIRC5), thymidine kinase 1 (TK1), and topoisomerase 2‐alpha (TOP2A), all encoded on chromosome arm 17q, were up‐regulated in MPNST as compared to benign neurofibromas. Each of them was found to be independent prognostic markers on the gene expression level, as well as on the protein level. A prognostic profile was identified by combining the nuclear expression scores of the three proteins. For patients with completely resected tumours only 15% in the high risk group were alive after two years, as compared to 78% in the low risk group.In conclusion, we found a novel protein expression profile which identifies MPNST patients with inferior prognosis even after assumed curative surgery. The tested proteins are drug targets; therefore the expression profile may provide predictive information guiding the design of future clinical trials. Importantly, as the effect is seen on the protein level using IHC, the biomarker panel can be readily implemented in routine clinical testing.
From pit to electronic trading: Impact on price volatility of U.S. Treasury futures
Authors: Orlowski Lucjan T. 
Published: February 2015

AbstractThis paper investigates the dynamics of price volatility and trading volume of 10‐year U.S. Treasury note futures within the context of transition from pit to electronic trading. The analysis is conducted over four discernible phases of futures trading evolution: the pit‐only phase, the leap to electronic trading, and the electronic trading dominant phase, which is divided further into two periods, the before and after the financial crisis of 2007/2009. Generalized autoregressive conditional heteroskedasticity with in‐mean conditional variance and generalized error distribution parameterization (GARCH‐M‐GED) tests are conducted to examine the conditional volatility of total returns index as a function of trading volume. The empirical results show a consistently negative relationship between the trading volume and price volatility for all four analyzed phases. They also show decreasing leptokurtosis (except for the direct effects of the recent crisis), continuously high persistency in volatility, as well as a weakening impact of unexpected ARCH‐type shocks during the most recent analyzed period. Overall, the shift to electronic trading entails a substantial increase in trading volume, but not in price volatility of Treasury futures.
New aristonectine elasmosaurid plesiosaur specimens from the Early Maastrichtian of Angola and comments on paedomorphism in plesiosaurs
Authors: Araújo R. , Polcyn M.J. , Lindgren J. , Jacobs L.L. , Schulp A.S. , Mateus O. , Gonçalves A. Olímpio , Morais M.-L. 
Published: February 2015

AbstractNew elasmosaurid plesiosaur specimens are described from the Early Maastrichtian of Angola. Phylogenetic analyses reconstruct the Angolan taxon as an aristonectine elasmosaurid and the sister taxon of an unnamed form of similar age from New Zealand. Comparisons also indicate a close relationship with an unnamed form previously described from Patagonia. All of these specimens exhibit an ostensibly osteologically immature external morphology, but histological analysis of the Angolan material suggests an adult with paedomorphic traits. By extension, the similarity of the Angolan, New Zealand and Patagonian material indicates that these specimens represent a widespread paedomorphic yet unnamed taxon.
Peripheral eyes: Brazilians and India, 1947–61
Authors: Chakravarti Ananya 
Published: February 2015

AbstractThe post-Second World War era witnessed the need for new political forms to accommodate the aspirations for national identity of newly decolonized nations within the hegemonic structure of the Cold War. Although both Cold War historiography and postcolonial studies have analysed these phenomena, the place of Latin America in general and Brazil in particular remains fraught with conceptual difficulties, largely due to the very different (post)colonial experience of this region from the rest of the ‘Third World’. This article examines how three Brazilian intellectuals and diplomats observed India from its independence until the annexation of Portuguese India by the Indian Union in 1961. In exploring their peripheral gaze, it shows how Brazilian self-identification with the West, and particularly its complex relationship with the heritage of European colonialism, prevented a truly commensurable experience, despite a sense of commonality with India based on their peripheral position in the global political structure.
Potassium fertilization: paradox or K management dilemma?
Authors: Bar-Yosef B. , Magen H. , Johnston A.E. , Kirkby E.A. 
Published: February 2015

AbstractIn 2014, Khan et al. presented evidence that soil exchangeable K (Exch-K) increases over time without addition of potassium (K) to the soil despite the removal of K in crops on a soil rich in montmorillonite and illite. The authors term this behavior ‘The potassium paradox’. From their review of the literature, the authors also report a lack of crop response to potassium chloride (KCl) fertilization. Close evaluation of these findings reveals that their observations can be interpreted and predicted using current knowledge of K in soil chemistry and its uptake by plants, and there is no paradox in K behavior in the soil–plant system. There is also no evidence of a detrimental effect of KCl on crop yield or quality. Their conclusion that the widely used Exch-K soil test is inadequate for managing K fertilization is discussed and some possible modifications to improve its performance are included. We believe that measurement of Exch-K is an essential and valuable tool and its use should be continued, along with improvements in recommending K fertilizer application.
Further insights into why potassium fertility is a paradox
Authors: Khan S.A. , Mulvaney R.L. , Ellsworth T.R. 
Published: February 2015

AbstractFor many years, crop potassium (K) availability has been estimated by soil testing the plow layer for exchangeable K, in conjunction with potassium chloride fertilization widely promoted as an essential prerequisite for ensuring crop yield and quality. As rigorously documented in our paper, both components of chemical-based K management are seriously flawed by the lack of a scientific basis. Under the pretext of providing economic benefit for the producer and a healthy food supply for the public at large, the real purpose is to generate revenue for the fertilizer industry.
Prediction uncertainties in the Cape Cod reserving method
Authors: Saluz Annina 
Published: February 2015

AbstractThe Cape Cod (CC) method was designed by Bühlmann and Straub in order to overcome some shortcomings of the chain ladder (CL) method. Owing to its simplicity and because of the advantages over the CL method, the CC method has become a well-established method in practice. In this paper we consider a distribution-free stochastic model for the CC method. Within this model we give the parameter estimates and we derive estimates for the conditional mean square error of prediction for the CC method. In addition, we derive an estimate for the uncertainty in the claims development result.
Epigenetic and transcriptional determinants of the human breast
Authors: Gascard Philippe , Bilenky Misha , Sigaroudinia Mahvash , Zhao Jianxin , Li Luolan , Carles Annaick , Delaney Allen , Tam Angela , Kamoh Baljit , Cho Stephanie , Griffith Malachi , Chu Andy , Robertson Gordon , Cheung Dorothy , Li Irene , Heravi-Moussavi Alireza , Moksa Michelle , Mingay Matthew , Hussainkhel Angela , Davis Brad , Nagarajan Raman P. , Hong Chibo , Echipare Lorigail , O’Geen Henriette , Hangauer Matthew J. , Cheng Jeffrey B. , Neel Dana , Hu Donglei , McManus Michael T. , Moore Richard , Mungall Andrew , Ma Yussanne , Plettner Patrick , Ziv Elad , Wang Ting , Farnham Peggy J. , Jones Steven J.M. , Marra Marco A. , Tlsty Thea D. , Costello Joseph F. , Hirst Martin 
Published: February 2015

AbstractWhile significant effort has been dedicated to the characterization of epigenetic changes associated with prenatal differentiation, relatively little is known about the epigenetic changes that accompany post-natal differentiation where fully functional differentiated cell types with limited lifespans arise. Here we sought to address this gap by generating epigenomic and transcriptional profiles from primary human breast cell types isolated from disease-free human subjects. From these data we define a comprehensive human breast transcriptional network, including a set of myoepithelial- and luminal epithelial-specific intronic retention events. Intersection of epigenetic states with RNA expression from distinct breast epithelium lineages demonstrates that mCpG provides a stable record of exonic and intronic usage, whereas H3K36me3 is dynamic. We find a striking asymmetry in epigenomic reprogramming between luminal and myoepithelial cell types, with the genomes of luminal cells harbouring more than twice the number of hypomethylated enhancer elements compared with myoepithelial cells.
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs
Authors: Amin Viren , Harris R. Alan , Onuchic Vitor , Jackson Andrew R. , Charnecki Tim , Paithankar Sameer , Lakshmi Subramanian Sai , Riehle Kevin , Coarfa Cristian , Milosavljevic Aleksandar 
Published: February 2015

AbstractTissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.
Coding principles of the canonical cortical microcircuit in the avian brain
Authors: Calabrese Ana , Woolley Sarah M. N. 
Published: February 2015

Significance
A six-layered neocortex is a hallmark feature of the mammalian brain. Connections among layers and progressive changes in the neural coding properties of each layer define a microcircuit thought to perform the computations underlying complex behavior. Birds lack a six-layered cortex. Yet, they demonstrate complex cognition and behavior. Recent anatomical studies propose that adjacent regions of the avian pallium are homologs of neocortical layers. Here, we show that the avian auditory pallium exhibits the same information-processing principles that define the mammalian neocortical microcircuit. Results suggest that the cortical microcircuit evolved in a common ancestor of mammals and birds and provide a physiological explanation for neural processes that give rise to complex behavior in the absence of cortical lamination.
RING finger protein 121 facilitates the degradation and membrane localization of voltage-gated sodium channels
Authors: Ogino Kazutoyo , Low Sean E. , Yamada Kenta , Saint-Amant Louis , Zhou Weibin , Muto Akira , Asakawa Kazuhide , Nakai Junichi , Kawakami Koichi , Kuwada John Y. , Hirata Hiromi 
Published: February 2015

SignificanceVoltage-gated sodium channels (NaV) are known to form clusters at the membranes of excitable cells; however, what governs their transport is largely unknown. We found that the endoplasmic reticulum (ER) andcis-Golgi associated ubiquitin ligase really interesting new gene (RING) finger protein 121 (RNF121) mediates the degradation and membrane localization of NaV. This apparent quality control of NaVensures the transport of properly folded channels to the membranes of excitable cells. To our knowledge, this is the first pathologically relevant identification of a voltage-gated ion channel as a substrate for ER-associated protein degradation, whose degradation is governed by an ER- and Golgi-associated E3-ubiquitin ligase.
Evidence and implications of higher-order scaling in the environmental variation of animal population growth
Authors: Ferguson Jake M. , Ponciano José M. 
Published: February 2015

Significance
We show that the variation of plant and animal populations through time can provide basic insights into how populations interact with their environment, even when environmental covariates are unobserved. We contrasted the effects of two types of temporal variation on population dynamics showing that fluctuations in the strength of competition among individuals can change a well-known scaling relation between the population variance and population abundances. The scaling of the population variance is explored using a large database of time series, as well as two well-studied ungulate populations. Our results suggest that higher-order variance scaling may be present in many animal populations, both reducing the long-run population variance relative to the standard model and providing important information on how populations are regulated by their environment.
Parameter-free methods distinguish Wnt pathway models and guide design of experiments
Authors: MacLean Adam L. , Rosen Zvi , Byrne Helen M. , Harrington Heather A. 
Published: February 2015

Significance
The canonical Wnt/β-catenin signaling pathway is important for essential cellular functions and is implicated in many diseases. We introduce a new mathematical model that focuses on β-catenin degradation and protein shuttling between cellular compartments. We compare our model to others and show that all fit to time-dependent experimental data. To evade this parameter problem, we use algebraic methods and characterize model features that are independent of the choice of parameter values. We find that multiple responses to Wnt are feasible under certain conditions for the new model, but not for the others; moreover, we provide dependencies between species (variables) that inform future experiments and model discrimination. We also highlight the wide applicability of these tools across problems in systems biology.
Focus on the success of others leads to selfish behavior
Authors: van den Berg Pieter , Molleman Lucas , Weissing Franz J. 
Published: February 2015

Significance
We report on a two-step decision-making experiment. The first part shows that humans differ consistently in the way they learn from others. Some individuals are success-based learners, who try to identify successful peers and mimic their behavior. Others are frequency-based learners, who tend to adopt the most frequent behavior in their group. The second part reveals that these differences in social learning have important consequences for the outcome of social interactions. In situations where participants had to choose between a selfish option and an option benefitting their group, groups of frequency-based learners achieved considerably higher levels of cooperation than groups of success-based learners. This is the first clear experimental evidence that learning strategies are an important determinant of social behavior.
Hunger promotes acquisition of nonfood objects
Authors: Xu Alison Jing , Schwarz Norbert , Wyer Robert S. 
Published: February 2015

Significance
Hunger is assumed to motivate eating, which satisfies the caloric needs underlying the motivation. However, hunger’s influence extends beyond food consumption to the acquisition of nonfood items that cannot satisfy the underlying need (e.g., binder clips), suggesting that domain-specific motives can influence behavior in unrelated domains that are irrelevant to the motive. This is likely to occur when the domain-specific response includes concepts and behaviors that can also guide decisions in other domains.
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
Authors: Bowman Gregory R. , Bolin Eric R. , Hart Kathryn M. , Maguire Brendan C. , Marqusee Susan 
Published: February 2015

Significance
Rational drug design efforts typically focus on identifying inhibitors that bind to protein active sites. Pockets that are not present in crystallographic structures yet can exert allosteric (i.e., long-range) control over distant active sites present an exciting alternative. However, identifying these hidden allosteric sites is extremely challenging because one usually has to simultaneously find a small molecule that binds to and stabilizes the open conformation of the pocket. Here, we present a means of combining advances in computer modeling—using Markov state models to capture long timescale dynamics—with biophysical experiments to identify hidden allosteric sites without requiring the simultaneous discovery of drug-like compounds that bind them. Using this technology, we discover multiple hidden allosteric sites in a single protein.
Allosteric and hyperekplexic mutant phenotypes investigated on an α
1
glycine receptor transmembrane structure
Authors: Moraga-Cid Gustavo , Sauguet Ludovic , Huon Christèle , Malherbe Laurie , Girard-Blanc Christine , Petres Stéphane , Murail Samuel , Taly Antoine , Baaden Marc , Delarue Marc , Corringer Pierre-Jean 
Published: February 2015

Significance
Pentameric ligand-gated ion channels (pLGICs) mediate neuronal communication in the central nervous system. Upon the neurotransmitter binding, these receptors undergo a rapid conformational change to open an integral ion channel. Mutations impairing the function of pLGICs are known to cause hyperekplexic, myasthenic, and epileptic syndromes. Here, we studied how the local perturbations caused by single mutations result in an alteration of the protein function. Using a chimeric protein assembled by the transmembrane domain of the human glycine receptors fused to the extracellular domain of the bacterial pLGIC GLIC, we performed functional experiments in parallel with X-ray crystallography. On this basis, we propose a molecular mechanism for channel opening that accounts for the phenotypes of several mutants causing hyperekplexia.
Interplay among nucleosomal DNA, histone tails, and corepressor CoREST underlies LSD1-mediated H3 demethylation
Authors: Pilotto Simona , Speranzini Valentina , Tortorici Marcello , Durand Dominique , Fish Alexander , Valente Sergio , Forneris Federico , Mai Antonello , Sixma Titia K. , Vachette Patrice , Mattevi Andrea 
Published: February 2015

Significance
The correct and regulated readout of epigenetic marks on chromatin is essential to modulate gene expression in living cells. The regulation of chromatin accessibility is ensured by such epigenetic tags, which form a platform for the binding of specific enzymatic modules. A clear example of this mechanism is represented by the histone demethylase LSD1-CoREST, which removes methylation marks from lysine 4 of histone protein H3. We developed a crosslinking technology to capture this histone demethylase in contact with the nucleosome and used this methodology to explore the structural and biophysical properties of this complex. This is one of the very few successful attempts to visualize the molecular mechanism underlying the recognition of the nucleosomal substrate by a histone-modifying enzyme complex.
Essential functions of primate frontopolar cortex in cognition
Authors: Boschin Erica A. , Piekema Carinne , Buckley Mark J. 
Published: February 2015

Significance
The frontopolar cortex (FPC) is a large region occupying the anterior portion of the brain’s frontal lobe, and has been suggested to play a role in complex, higher order behavior. However, the specific contributions of this area toward this type of behavior are still unclear. Using an animal model, we show that localized lesions to the FPC of nonhuman primates selectively impair the ability of the animal to learn rapidly about novel objects and rules, although sparing its ability to draw upon previously established knowledge about objects and rules. These findings suggest that the FPC makes a crucial contribution to the exploration and rapid acquisition of novel behavioral options, which is, in turn, an essential aspect of complex, higher order behavior.