bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectral features of biogenic calcium carbonates and implications for astrobiology
Authors: Berg B. L. , Ronholm J. , Applin D. M. , Mann P. , Izawa M. , Cloutis E. A. , Whyte L. G. 
Published: September 2014

AbstractThe ability to discriminate biogenic from abiogenic calcium carbonate (CaCO3) would be useful in the search for extant or extinct life, since CaCO3can be produced by both biotic and abiotic processes on Earth. Bioprecipitated CaCO3material was produced during the growth of heterotrophic microbial isolates on medium enriched with calcium acetate or calcium citrate. These biologically produced CaCO3, along with natural and synthetic non-biologically produced CaCO3samples, were analysed by reflectance spectroscopy (0.35–2.5 μm), Raman spectroscopy (532 and 785 nm), and laser-induced fluorescence spectroscopy (365 and 405 nm excitation). Optimal instruments for the discrimination of biogenic from abiogenic CaCO3were determined to be reflectance spectroscopy, and laser-induced fluorescence spectroscopy. Multiple absorption features in the visible light region occurred in reflectance spectra for most biogenic CaCO3samples, which are likely due to organic pigments. Multiple fluorescence peaks occurred in emission spectra (405 nm excitation) of biogenic CaCO3samples, which also are best attributed to the presence of organic compounds; however, further analyses must be performed in order to better determine the cause of these features to establish criteria for confirming the origin of a given CaCO3sample. Raman spectroscopy was not useful for discrimination since any potential Raman peaks in spectra of biogenic carbonates collected by both the 532 and 785 nm lasers were overwhelmed by fluorescence. However, this also suggests that biogenic carbonates may be identified by the presence of this organic-associated fluorescence. No reliable spectroscopic differences in terms of parameters such as positions or widths of carbonate-associated absorption bands were found between the biogenic and abiogenic carbonate samples. These results indicate that the presence or absence of organic matter intimately associated with carbonate minerals is the only potentially useful spectral discriminator for the techniques that were examined, and that multiple spectroscopic techniques are capable of detecting the presence of associated organic materials. However, the presence or absence of intimately associated organic matter is not, in itself, an indicator of biogenicity.
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network
Authors: Pougach Ksenia , Voet Arnout , Kondrashov Fyodor A. , Voordeckers Karin , Christiaens Joaquin F. , Baying Bianka , Benes Vladimir , Sakai Ryo , Aerts Jan , Zhu Bo , Van Dijck Patrick , Verstrepen Kevin J. 
Published: September 2014

AbstractThe emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concertedcisandtransmutations allows expansion of a regulatory network.
Cross‐bonding cable and box model based on pulse reflection measurement
Authors: de Regt Jos J. , Hoogendorp Gerben , Wagenaars Paul , Wouters Peter A.A.F. , Popov Marjan , van der Sluis Lou , Steennis E. Fred 
Published: September 2014

Transients from lightning strikes can enter underground cables at overhead line to power cable transitions. Possible overvoltages on these surges at cross‐bonding connections of the cable screens are of major concern. A model is developed for modelling overvoltages from transient signal propagation through a combined cross‐bonding cable and box. This model is applied to the first Dutch 400 kV cable connection. Such model incorporates model parameters whose values depend on design details of the cross‐bonding box. The values for these model parameters are extracted from the measured transmission and reflection signal on steep pulses injected into the actual cross‐bonding box configuration. The model combines transmission line description for the cross‐bonding cables with mainly inductive behaviour of the cross‐bonding box. The obtained results are verified by measurements. The model is applied to investigate overvoltages induced at the cross‐bonding cable and box on 1.2/50 µs impulse voltage injection representing a lightning impulse voltage applied to the core conductor of the cross‐bonding cable. Furthermore, the effectiveness of surge arresters to reduce overvoltages at the cross‐bonding cable screen is demonstrated by simulations with this model in PSCAD.
Alpha and gamma oscillations characterize feedback and feedforward processing in monkey visual cortex
Authors: van Kerkoerle Timo , Self Matthew W. , Dagnino Bruno , Gariel-Mathis Marie-Alice , Poort Jasper , van der Togt Chris , Roelfsema Pieter R. 
Published: September 2014

SignificanceOne of the main unresolved questions in cognitive neuroscience is how low-level and high-level areas of the visual cortex interact with each other during perception and cognition. We investigated whether cortical oscillations can be used to distinguish feedforward from feedback processing. We studied the propagation of α- and γ-oscillations through the cortical layers and between different visual cortical areas. We induced oscillations in different areas with microstimulation and influenced them using a pharmacological approach. The results of these experiments demonstrate that γ-oscillations propagate in the feedforward direction, whereas α-oscillations propagate in the feedback direction. We conclude that high- and low-frequency oscillations provide markers of feedforward and feedback processing, respectively.
Magnetic structure and interaction in (Sb, Co) co-doped ZnO thin films
Authors: Samanta K , Sardar M , Singh S P , Katiyar R S 
Published: September 2014

Abstract
The magnetic behaviour of (Co, Sb) co-doped ZnO thin films grown by pulsed laser deposition is investigated. The irreversibility (ZFC–FC bifurcation) in low field (H = 100 Oe) magnetization and small hysteresis below 300 K are similar in samples with or without Sb co-doping. Both the phenomena originate from the presence of blocked supermoments in the samples. Incorporation of Sb only increases the saturation magnetization and coercivity. The quantitative increase in moment due to Sb co-doping suggests a transfer of electrons from Co ions to Sb-related acceptor complexes. This is supported by a decrease in the number of electronic transitions from Co d electrons to the conduction band seen in optical transmission spectroscopy when Sb is added. The high field susceptibility data show the existence of supermoments with antiferromagnetic interaction between them. We find that the value of the effective antiferromagnetic molecular field constant decreases with increasing Co concentration, revealing that the supermoments are bound magnetic polarons around intrinsic donors, rather than coming from Co precipitates. True ferromagnetism (overlapping polarons) can emerge either with larger intrinsic donors, or with acceptors with shallower levels, than those created by Sb co-doping. Our results suggest that Sb-related acceptor states may be unstable towards accepting electrons from deep d levels of Co ions.
Risk assessment of cartilaginous fish populations
Authors: Cortés Enric , Brooks Elizabeth N. , Shertzer Kyle W. 
Published: September 2014

AbstractWe review three broad categories of risk assessment methodology used for cartilaginous fish: productivity-susceptibility analysis (PSA), demographic methods, and quantitative stock assessments. PSA is generally a semi-quantitative approach useful as an exploratory or triage tool that can be used to prioritize research, group species with similar vulnerability or risk, and provide qualitative management advice. Demographic methods are typically used in the conservation arena and provide quantitative population metrics that are used to quantify extinction risk and identify vulnerable life stages. Stock assessments provide quantitative estimates of population status and the associated risk of exceeding biological reference points, such as maximum sustainable yield. We then describe six types of uncertainty (process, observation, model, estimation, implementation, and institutional) that affect the risk assessment process, identify which of the three risk assessment methods can accommodate each type of uncertainty, and provide examples mostly for sharks drawn from our experience in the United States. We also review the spectrum of stock assessment methods used mainly for sharks in the United States, and present a case study where multiple methods were applied to the same species (dusky shark, Carcharinus obscurus) to illustrate differing degrees of model complexity and type of uncertainty considered. Finally, we address the common and problematic case of data-poor bycatch species. Our main recommendation for future work is to use Management Strategy Evaluation or similar simulation approaches to explore the effect of different sources of uncertainty, identify the most critical data to satisfy predetermined management objectives, and develop harvest control rules for cartilaginous fish. We also propose to assess the performance of data-poor and -rich methods through stepwise model construction.
Where has all the recruitment research gone, long time
passing?
Authors: Rice Jake , Browman Howard I. 
Published: September 2014

Abstract
For most of the past 100 years, research into recruitment processes—as pioneered by Johan Hjort—has been a consistent focus of research in fisheries science. This was reflected not only in the literature but in the organizational structures and research strategies of national and international fisheries research and management institutions. Over the past decade or so, we perceived that recruitment research is fading, if not into obscurity then at least into a more marginal place in fisheries and marine research. In this paper, we assess if our perception is real by quantifying trends in scientific publications and in the work activities within ICES during specific periods extending back to the 1920s. Our analysis documents a decline in research on recruitment processes. We put forward three possible hypotheses to explain this decline: 1. All the key research questions about recruitment have been answered; 2. The volume of research on recruitment processes has declined because the answers are no longer relevant; 3. Recruitment research has been co-opted by more trendy, possibly ephemeral, and research topics. There is little evidence to support the first two of these hypotheses and we consider the third to be the most plausible. Finally, we conclude that this new terminology/repackaging of recruitment research does not bring with it new and fresh thinking and, therefore, comes at a cost that should be carefully considered.
Other Respiratory Viruses Are Important Contributors to Adult Respiratory Hospitalizations and Mortality Even During Peak Weeks of the Influenza Season
Authors: Gilca Rodica , Amini Rachid , Douville-Fradet Monique , Charest Hugues , Dubuque Josée , Boulianne Nicole , Skowronski Danuta M. , De Serres Gaston 
Published: September 2014

Background.  During peak weeks of seasonal influenza epidemics, severe respiratory infections without laboratory confirmation are typically attributed to influenza.
Methods.  In this prospective study, specimens and demographic and clinical data were collected from adults admitted with respiratory symptoms to 4 hospitals during the 8–10 peak weeks of 2 influenza seasons. Specimens were systematically tested for influenza and 13 other respiratory viruses (ORVs) by using the Luminex RVP FAST assay.
Results.  At least 1 respiratory virus was ide.jpegied in 46% (21% influenza, 25% noninfluenza; 2% coinfection) of the 286 enrolled patients in 2011–2012 and in 62% (46% influenza, 16% noninfluenza; 3% coinfection) of the 396 enrolled patients in 2012–2013. Among patients aged ≥75 years, twice as many ORVs (32%) as influenza viruses (14%) were detected in 2011–2012. During both seasons, the most frequently detected ORVs were enteroviruses/rhinoviruses (7%), respiratory syncytial virus (6%), human metapneumovirus (5%), coronaviruses (4%), and parainfluenza viruses (2%). Disease severity was similar for influenza and ORVs during both seasons.
Conclusions.  Although ORV contribution relative to influenza varies by age and season, during the peak weeks of certain influenza seasons, ORVs may be a more frequent cause of elderly hospitalization than influenza.
MDTraj: a modern, open library for the analysis of molecular dynamics trajectories
Authors: McGibbon Robert T. , Beauchamp Kyle A. , Schwantes Christian R. , Wang Lee-Ping , Hernández Carlos X. , Herrigan Matthew P. , Lane Thomas J. , Swails Jason M. , Pande Vijay S. 
Published: September 2014

Summary:MDTraj is a modern, lightweight and efficient software package for analyzing molecular dynamics simulations. MDTraj reads trajectory data from a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including RMSD, DSSP secondary structure assignment and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between molecular dynamics data and the rapidly-growing collection of industry-standard statistical analysis and visualization tools in Python.Availability:Package downloads, detailed examples and full documentation are available athttp://mdtraj.org. The source code is distributed under the GNU Lesser General Public License athttps://github.com/simtk/mdtraj.
Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events
Authors: Frésard Laure , Leroux Sophie , Roux Pierre-François , Klopp Christophe , Fabre Stéphane , Esquerré Diane , Dehais Patrice , Djari Anis , Gourichon David , Lagarrigue Sandrine , Pitel Frédérique 
Published: September 2014

ABSTRACTRNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates.We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time.By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.
A genome‐wide association study reveals a QTL influencing caudal supernumerary teats in Holstein cattle
Authors: Joerg H. , Meili C. , Ruprecht O. , Bangerter E. , Burren A. , Bigler A. 
Published: September 2014

SummarySupernumerary teats represent a common abnormality of the bovine udder. A genome‐wide association study was performed based on the proportion of the occurrence of supernumerary teats in the daughters of 1097 Holstein bulls. The heritability of caudal supernumerary teats without mammary gland in this study was 0.604. The largest proportion of the heritability was attributable to BTA 20. The strongest evidence for association was with five SNPs on chromosome 20, referred to as a QTL. The mode of inheritance at this QTL was dominant. These findings reveal that the occurrence of caudal supernumerary teats without mammary gland in Holstein cattle is influenced by a QTL on chromosome 20 and a polygenic part. The data support the high potential of the SNPs in the QTL region as markers for breeding against caudal supernumerary teats.
The Targeting of Indoleamine 2,3 Dioxygenase ‐Mediated Immune Escape in Cancer
Authors: Iversen Trine Zeeberg , Andersen Mads Hald , Svane Inge Marie 
Published: September 2014

AbstractThe era of immunotherapies was unleashed in 2010 with the Food and Drug Administration (FDA) approval of the first therapeutic vaccine sipuleucel‐T as a standard treatment for metastatic prostate cancer. Next, the first immune‐activating anticytotoxic lymphocyte antigen‐4 (CTLA‐4) antibody ipilimumab exhibiting ‘immune checkpoint blockade’ was approved by FDA and European Medical Agency (EMA) for the treatment of patients with metastatic melanoma. New generations of immune checkpoint blockading antibodies targeting programmed cell death 1 (PD‐1) and its ligand (PD‐L1) are now under intense investigation in metastatic melanoma (MM) and non‐small‐cell lung cancer (NSCLC), and impressive clinical results are anticipated. Despite these successes, only a fraction of patients become clinical responders to therapy. Thus, to improve the selection of patients likely to respond, scrutinizing different immune parameters during treatment is essential. In the summary of this PhD thesis, we investigated changes in immune parameters and their possible correlation with clinical efficacy in patients with MM during treatments with the standard chemo‐ and immunotherapies, temozolomide (TMZ) and interferon‐α2b/interleukin‐2 (IFN‐α/IL‐2) immunotherapy. The overall aim was to assess changes in frequency and absolute counts of different immune cell subsets before and after treatment and correlate to clinical benefit. Furthermore, the thesis covers a finalized, clinical phase 1 study in patients with NSCLC testing a peptide vaccination with a HLA‐A2‐restricted epitope derived from indoleamine 2,3 dioxygenase (IDO). The overall aim in this trial was to evaluate safety and tolerability of IDO as an anticancer vaccine target in patients with NSCLC and to assess whether immunity correlated to clinical response.
p38 MAPK in cardioprotection – are we there yet?
Authors: Martin E D , Bassi R , Marber M S 
Published: September 2014

PKs transfer a phosphate from ATP to the side‐chain hydroxyl group of a serine, threonine or tyrosine residue of a substrate protein. This in turn can alter that protein's function; modulating fundamental cellular processes including, metabolism, transcription, growth, division, differentiation, motility and survival. PKs are subdivided into families based on homology. One such group are the stress‐activated kinases, which as the name suggests, are activated in response to cellular stresses such as toxins, cytokines, mechanical deformation and osmotic stress. Members include the p38 MAPK family, which is composed of α, β, γ and δ, isoforms which are encoded by separate genes. These kinases transduce extracellular signals and coordinate the cellular responses needed for adaptation and survival. However, in cardiovascular and other disease states, these same systems can trigger maladaptive responses that aggravate, rather than alleviate, the disease. This situation is analogous to adrenergic, angiotensin and aldosterone signalling in heart failure, where inhibition is beneficial despite the importance of these hormones to homeostasis. The question is whether similar benefits could accrue from p38 inhibition? In this review, we will discuss the structure and function of p38, the history of p38 inhibitors and their use in preclinical studies. Finally, we will summarize the results of recent cardiovascular clinical trials with p38 inhibitors.Linked ArticlesThis article is part of a themed section on Conditioning the Heart – Pathways to Translation. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue‐8
Peanut avoidance and peanut allergy diagnosis in siblings of peanut allergic children
Authors: Lavine E. , Clarke A. , Joseph L. , Shand G. , Alizadehfar R. , Asai Y. , Chan E. S. , Harada L. , Allen M. , Ben‐Shoshan M. 
Published: September 2014

SummaryBackgroundStudies suggest that siblings of children with peanut allergy (PNA) have a higher prevalence of PNA than the general population.ObjectivesThe Canadian Peanut Allergy Registry was used to assess the percentage of siblings of registered index PNA children who were 1) never exposed to peanut or 2) reportedly diagnosed with PNA by a physician without either a history of allergic reaction or a confirmatory testing. Sociodemographic and clinical factors that may be associated with either outcome were evaluated.MethodsParents completed a questionnaire on siblings' sociodemographic characteristics, exposure and reaction to peanut, confirmatory tests performed and whether PNA had been diagnosed.ResultsOf 932 Registry families, 748 families responded, representing 922 siblings. 13.6% of siblings had never been exposed to peanut, 70.4% (n = 88) of which were born after the index child. Almost 9% of siblings (80) were reported as PNA, but almost half of this group had no history of an allergic reaction to peanut, including five children who also had no testing to confirm PNA. Of these 5, 4 were born after PNA diagnosis in the index child. In a multivariate regression analysis for siblings at least 3 years old, those born after PNA diagnosis in the index child were more likely to have never been exposed to peanut. In a univariate analysis, siblings born after the diagnosis of PNA in the index child were more likely to be diagnosed with PNA without supportive history or confirmatory testing.Conclusions and Clinical RelevanceThese data estimate that more than 10% of siblings of PNA patients will avoid peanut and that siblings born after the diagnosis of PNA in an index child are more likely to have never been exposed. Educational programs and guidelines that caution against unnecessary avoidance are required.