bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional dynamics of Emiliania huxleyi virus‐host interactions across multiple spatial scales
Authors: Middleton Julia E. , Martínez Martínez Joaquín , Wilson William H. , Record Nicholas R. 
Published: February 2017

AbstractMarine viruses have an important role in the dynamics of phytoplankton blooms and have increasing representation in ocean ecosystem and biogeochemical models. There are multiple described functional forms available for incorporating viruses into ocean models, but most of them have not been validated against time series abundance data. We reviewed the functional forms currently used for lytic marine virus‐host dynamics and evaluated them against a compiled database of Emiliania huxleyi and E. huxleyi‐virus (EhV) abundances. The database includes data aggregated from three scales: laboratory, mesocosm, and field studies. Data‐model comparison supported some standard functional forms, for example a linear infection term, and did not support other standard functional forms, for example a linear viral decay term. This analysis also provided evidence of density dependence within virion populations and a possible mechanism for lower virus‐host ratios at high virion abundances. Some of the patterns were scale‐dependent, suggesting that processes studied at one scale might not translate to another scale. As marine virus model formulations diversify over time, there is the need for model inter‐comparison and evaluation.
Pelagic food web response to whole lake N fertilization
Authors: Deininger A. , Faithfull C. L. , Karlsson J. , Klaus M. , Bergström A.‐K. 
Published: February 2017

AbstractAnthropogenic activities are increasing inorganic nitrogen (N) loadings to unproductive boreal lakes. In many of these lakes phytoplankton are N limited, consequently N fertilization may affect ecosystem productivity and consumer resource use. Here, we conducted whole lake inorganic N fertilization experiments with six small N limited unproductive boreal lakes (three control and three N enriched) in an area receiving low N deposition with one reference and two impact years. Our aim was to assess the effects of N fertilization on pelagic biomass production and consumer resource use. We found that phytoplankton primary production (PP) and biomass, and the PP: bacterioplankton production ratio increased after fertilization. As expected, the relative contribution of phytoplankton derived resources (autochthony) that supported the crustacean zooplankton community increased. Yet, the response in the consumer community was modest with autochthony only increasing in one of the three major zooplankton groups and with no effect on zooplankton biomass. In conclusion, our findings imply that newly available phytoplankton energy derived from N fertilization was not efficiently transferred up to zooplankton, indicating a mismatch between producer energy supply and consumer energy use with potential accumulation of phytoplankton biomass as the result.
Chemical archives in fishes beyond otoliths: A review on the use of other body parts as chronological recorders of microchemical constituents for expanding interpretations of environmental, ecological, and life‐history changes
Authors: Tzadik Orian E. , Curtis Joseph S. , Granneman Jennifer E. , Kurth Benjamin N. , Pusack Timothy J. , Wallace Amy A. , Hollander David J. , Peebles Ernst B. , Stallings Christopher D. 
Published: February 2017

AbstractMicrochemical analyses of fish otoliths have revolutionized fisheries science. Molecules deposited within otoliths may originate from ambient water and diet, with molecular concentrations being subject to subsequent physiological alteration after exposure. Analyses of otolith microstructure and incorporation of inorganic elements have led to major advances in stock assessment and fisheries ecology. However, the use of otoliths for microchemical analyses has drawbacks. Specifically, otolith removal from live specimens requires specimen sacrifice, which may be forbidden in the case of protected species. In addition, otoliths rarely contain sufficient concentrations of organic matter to allow reconstruction of food‐web relationships via multiple stable isotopes, and otolith microstructure can be difficult to interpret in some species. Here, we review alternatives to otoliths that can provide microchemical analytes for life‐history studies in fishes. Our focus is to describe advantages and disadvantages to the use of each alternative structure, with particular attention paid to trace‐element analysis for inorganic matrices and stable‐isotope analysis for organic ones. In general, the chronological analysis of elemental and isotopic values within each structure depends on the inert nature (or lack of molecular turnover) of the tissue. Structures with high turnover rates or those that are metabolically active will not effectively record elemental or isotopic compositions over time. Here, we provide an assessment of the use of bony endoskeleton, fin spines, fin rays, scales, and eye lenses as alternatives or complements to fish otolith analysis.
A practical method for the determination of total selenium in environmental samples using isotope dilution‐hydride generation‐inductively coupled plasma‐mass spectrometry
Authors: Kleckner Amy E. , Kakouros Evangelos , Robin Stewart A. 
Published: February 2017

AbstractA safe, practical, and accurate method for the determination of selenium (Se) in range of environmental samples was developed. Small sample masses, 5–20 mg, were amended with 82Se enriched isotope for the isotope dilution (ID), preceding a multi‐step wet digestion with nitric acid (HNO3) and hydrogen peroxide (H2O2). Samples were incubated in an autoclave for 3 h at 20 psi and 126°C. Digestates were subsequently reduced with concentrated hydrochloric acid to Se(IV) the most favorable valence for hydride generation (HG). The solutions were then analyzed on an ICP‐MS equipped with Flow Injection system (FIAS‐400). Polyatomic, isobaric, and background interferences were removed through the use of HG and ID with an 82Se enriched isotope spike. Recoveries for certified reference materials were determined and averaged 96% for biological tissues (NRCC DOLT3, DOLT4, DORM2, TORT2, and TORT3, and NIST 2976) and 108% for estuarine sediment (NRCC PACS2) with an average coefficient of variation for replicate measurements of ∼ 3.5%. Limit of detection was 0.13 ng Se g−1 dry weight or 0.19 ng Se L−1. This method can be broadly applied to biological tissues, sediments, suspended particulates, and water samples with minimal modifications making this method highly useful for assessing the ecotoxicology of total Se in aquatic ecosystems.
Genetic analyses of isolated high‐grade pancreatic intraepithelial neoplasia (HG‐PanIN) reveal paucity of alterations in TP53 and SMAD4
Authors: Hosoda Waki , Chianchiano Peter , Griffin James F , Pittman Meredith E , Brosens Lodewijk AA , Noë Michaël , Yu Jun , Shindo Koji , Suenaga Masaya , Rezaee Neda , Yonescu Raluca , Ning Yi , Albores‐Saavedra Jorge , Yoshizawa Naohiko , Harada Kenichi , Yoshizawa Akihiko , Hanada Keiji , Yonehara Shuji , Shimizu Michio , Uehara Takeshi , Samra Jaswinder S , Gill Anthony J , Wolfgang Christopher L , Goggins Michael G , Hruban Ralph H , Wood Laura D 
Published: February 2017

AbstractHigh‐grade pancreatic intraepithelial neoplasia (HG‐PanIN) is the major precursor of pancreatic ductal adenocarcinoma (PDAC) and is an ideal target for early detection. To characterize pure HG‐PanIN, we analysed 23 isolated HG‐PanIN lesions occurring in the absence of PDAC. Whole‐exome sequencing of five of these HG‐PanIN lesions revealed a median of 33 somatic mutations per lesion, with a total of 318 mutated genes. Targeted next‐generation sequencing of 17 HG‐PanIN lesions identified KRAS mutations in 94% of the lesions. CDKN2A alterations occurred in six HG‐PanIN lesions, and RNF43 alterations in five. Mutations in TP53, GNAS, ARID1A, PIK3CA, and TGFBR2 were limited to one or two HG‐PanINs. No non‐synonymous mutations in SMAD4 were detected. Immunohistochemistry for p53 and SMAD4 proteins in 18 HG‐PanINs confirmed the paucity of alterations in these genes, with aberrant p53 labelling noted only in three lesions, two of which were found to be wild type in sequencing analyses. Sixteen adjacent LG‐PanIN lesions from ten patients were also sequenced using targeted sequencing. LG‐PanIN harboured KRAS mutations in 94% of the lesions; mutations in CDKN2A, TP53, and SMAD4 were not identified. These results suggest that inactivation of TP53 and SMAD4 are late genetic alterations, predominantly occurring in invasive PDAC. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Coarse‐grained models for frontal photopolymerization with evolving conversion profile
Authors: Purnama Aloisius R , Hennessy Matthew G , Vitale Alessandra , Cabral João T 
Published: February 2017

AbstractWe introduce a series of ‘minimal’ models to describe a common light‐driven directional solidification process, known as frontal photopolymerization (FPP), focusing on experimental observables: the solidification kinetics, light attenuation and spatiotemporal monomer‐to‐polymer conversion. Specifically, we focus on FPP propagation that yields conversion profiles that are not invariant with time, and which cannot be simply described by the presence of mass or heat diffusion. The models are assessed against experimental data for the photopolymerization of a model trimethacrylate system. We find that the simplest model, comprising a single equation of motion for the conversion fraction ϕ and a generalized Beer–Lambert law, can only describe the experimental data by assuming an unphysical variation in optical absorption. Introducing a ϕ‐dependent reaction constant Keff is found to require a time dependence, regardless of the functional form in ϕ. We conclude by introducing a ‘minimal’ chemical model, which is based on a simple three‐step reaction scheme involving the spatiotemporal evolution of the photoinitiator fraction, relative fraction of radicals and monomer conversion fraction, that is able to capture the experimental data with a small number of parameters and under reasonable FPP assumptions. Our framework provides important predictive ability for ubiquitous solidification and patterning processes, including three‐dimensional printing, via photopolymerization. © 2017 Society of Chemical Industry
Climatological and case analyses of lower‐stratospheric fronts over North America
Authors: Attard Hannah E. , Lang Andrea L. 
Published: February 2017

Recent case‐study analyses produced a conceptual model suggesting that lower‐stratospheric fronts, the lower‐stratospheric half of a tropopause jet–front system, develop preferentially in southwesterly flow in the presence of lower‐stratospheric geostrophic warm air advection and ascent within the jet core. This conceptual understanding is examined by performing climatological and case analyses of 185 objectively identified lower‐stratospheric fronts that occurred over North America during the winter seasons (December, January and February) of 2004–2012 in the 1.0°×1.0°NCEP/NCAR Global Forecast System analysis.The climatological analysis shows a preference for strong southwesterly flow lower‐stratospheric fronts to occur over the Intermountain West region and relatively weaker southwesterly flow lower‐stratospheric fronts to occur over eastern North America. The southwesterly flow lower‐stratospheric fronts were composited according to their geographical location and the analysis shows that the composite lower‐stratospheric and tropospheric structures in these two locations have statistical differences. The case‐study analyses of southwesterly flow lower‐stratospheric fronts in these two regions highlight different, geographically dependent, frontal evolutions. The strong lower‐stratospheric front identified in the Intermountain West region interacted with an orographic gravity wave and associated lower‐stratospheric ascent that rearranged the local thermal field. The lower‐stratospheric front in eastern North America developed parallel to a surface front and was associated with diabatically reduced static stability in the upper troposphere, geostrophic warm air advection, and enhanced ascent.
Microexons: discovery, regulation, and function
Authors: Ustianenko Dmytro , Weyn‐Vanhentenryck Sebastien M. , Zhang Chaolin 
Published: February 2017

The importance of RNA splicing in numerous cellular processes is well established. However, an underappreciated aspect is the ability of the spliceosome to recognize a set of very small (3–30 nucleotide, 1–10 amino acid) exons named microexons. Despite their small size, microexons and their regulation through alternative splicing have now been shown to play critical roles in protein and system function. Here we review the discovery of microexons over time and the mechanisms by which their splicing is regulated, including recent progress made through deep RNA sequencing. We also discuss the functional role of microexons in biology and disease. WIREs RNA 2017, 8:e1418. doi: 10.1002/wrna.1418This article is categorized under:

RNA Evolution and Genomics > Computational Analyses of RNA
RNA Processing > Splicing Regulation/Alternative Splicing
RNA in Disease and Development > RNA in Disease
Potential of wheat bran to promote indigenous microbial enhanced oil recovery
Authors: Zhan Yali , Wang Qinghong , Chen Chunmao , Kim Jung Bong , Zhang Hongdan , Yoza Brandon A , Li Qing X 
Published: February 2017

Abstract
Microbial enhanced oil recovery (MEOR) is an emerging oil extraction technology that utilizes microorganisms to facilitate recovery of crude oil in depleted petroleum reservoirs. In the present study, effects of wheat bran utilization were investigated on stimulation of indigenous MEOR. Biostimulation conditions were optimized with the response surface methodology. The co-application of wheat bran with KNO3 and NH4H2PO4 significantly promoted indigenous MEOR (IMEOR) and exhibited sequential aerobic (O-), facultative (An-) and anaerobic (A0-) metabolic stages. The surface tension of fermented broth decreased by approximately 35%, and the crude oil was highly emulsified. Microbial community structure varied largely among and in different IMEOR metabolic stages. Pseudomonas sp., Citrobacter sp., and uncultured Burkholderia sp. dominated the O-, An- and early A0-stages. Bacillus sp., Achromobacter sp., Rhizobiales sp., Alcaligenes sp. and Clostridium sp. dominated the later A0-stage. This study illustrated occurrences of microbial community succession driven by wheat bran stimulation and its industrial potential.
Effects of Toasting Time on Digestive Hydrolysis of Soluble and Insoluble 00‐Rapeseed Meal Proteins
Authors: Salazar‐Villanea Sergio , Bruininx Erik M. A. M. , Gruppen Harry , Carré Patrick , Quinsac Alain , van der Poel Antonius F. B. 
Published: February 2017

AbstractThermal damage to proteins can reduce their nutritional value. The effects of toasting time on the kinetics of hydrolysis, the resulting molecular weight distribution of 00‐rapeseed meal (RSM) and the soluble and insoluble protein fractions separated from the RSM were studied. Hydrolysis was performed with pancreatic proteases to represent in vitro protein digestibility. Increasing the toasting time of RSM linearly decreased the rate of protein hydrolysis of RSM and the insoluble protein fractions. The extent of hydrolysis was, on average, 44% higher for the insoluble compared with the soluble protein fraction. In contrast, the rate of protein hydrolysis of the soluble protein fraction was 3–9‐fold higher than that of the insoluble protein fraction. The rate of hydrolysis of the insoluble protein fraction linearly decreased by more than 60% when comparing the untoasted to the 120 min toasted RSM. Increasing the toasting time elicited the formation of Maillard reaction products (furosine, Nε‐carboxymethyl‐lysine and Nε‐carboxyethyl‐lysine) and disulfide bonds in the insoluble protein fraction, which is proposed to explain the reduction in the hydrolysis rate of this fraction. Overall, longer toasting times increased the size of the peptides resulting after hydrolysis of the RSM and the insoluble protein fraction. The hydrolysis kinetics of the soluble and insoluble protein fractions and the proportion of soluble:insoluble proteins in the RSM explain the reduction in the rate of protein hydrolysis observed in the RSM with increasing toasting time.
Assessment of Variation in Castor Genetic Resources for Oil Characteristics
Authors: Yadav Praduman , Anjani K. 
Published: February 2017

AbstractCastor (Ricinus communis L.) oil is used in production of wide range of industrial products because of the presence of nearly 85% of ricinoleic acid in it. Any increase in the ricinoleic acid level would be great benefit to industry. None of the existing castor cultivars possess ≥90% ricinoleic acid because donors with this level of ricinoleic acid are not available to develop high ricinoleic type cultivars. In order to search for high ricinoleic acid genotypes, the present investigation was under taken. Fatty acid and oil content were assayed in 392 castor genotypes comprising 335 Indian and 57 non‐Indian collections. Great variation was observed among the collections for oil content and fatty acid composition. Oil content ranged from 38.5 to 53.5% while ricinoleic acid was between 71.15 and 93.68%. Diversity analysis was done using K‐means clustering which clustered the entire collection into 30 diverse groups by minimizing the dissimilarity within each cluster while maximizing the dissimilarity between clusters. Finally, 15 accessions having high oil (52–54%), high ricinoleic acid (91.12–93.68%) and high monounsaturates (92.8–94.95%) levels were identified. These would be of great value as donors to develop high oil, high ricinoleic type castor cultivars.
How do men and women help? Validation of a multidimensional measure of prosocial behavior
Authors: Nielson Matthew G. , Padilla‐Walker Laura , Holmes Erin K. 
Published: February 2017

ABSTRACTThe current study sought to address gender differences in prosocial behavior by creating and validating a multidimensional measure of prosocial behavior that more fully captures the ways that men help others. The new measure is directed toward family, friend, and strangers, and has five factors: defending, emotional support, inclusion, physical helping, and sharing. In Study 1, CFA analyses performed on a sample of 463 emerging adults online (mean age 23.42) revealed good model fit and divergent validity for each of the five factors. Study 2 replicated the analyses on a sample of 453 urban adolescents in the Northwest (mean age 18.37). Results established that all factors had good model fit, construct validity, and convergent validity. The discussion focuses on implications of this measure for future prosocial research including an increased diversity in how people (particularly men) help others and developmental differences toward different targets of prosocial behavior.
A global weak solution of the Dirac-harmonic map flow
Authors: Zhu Miaomiao , Jost Jürgen , Liu Lei 
Published: February 2017

We show the existence of a global weak solution of the heat flow for Dirac-harmonic maps from compact Riemann surfaces with boundary when the energy of the initial map and the

L^{2}

-norm of the boundary values of the spinor are sufficiently small. Dirac-harmonic maps couple a second order harmonic map type system with a first-order Dirac type system. The heat flow that has been introduced in [9] and that we investigate here is novel insofar as we only make the second order part parabolic, but carry the first order part along the resulting flow as an elliptic constraint. Of course, since the equations are coupled, both parts then change along the flow.

The solution is unique and regular with the exception of at most finitely many singular times. We also discuss the behavior at the singularities of the flow.
As an application, we deduce some existence results for Dirac-harmonic maps. Since we may impose nontrivial boundary conditions also for the spinor part, in the limit, we shall obtain Dirac-harmonic maps with nontrivial spinor part.
Cerebrospinal fluid markers detect Alzheimer's disease in nonamnestic dementia
Authors: Oboudiyat Carly , Gefen Tamar , Varelas Eleni , Weintraub Sandra , Rogalski Emily , Bigio Eileen H. , Mesulam M.‐Marsel 
Published: February 2017

AbstractIntroductionThe accuracy of cerebrospinal fluid (CSF) biomarkers for detecting Alzheimer's disease (AD) pathology has not been fully validated in autopsied nonamnestic dementias.MethodsWe retrospectively evaluated CSF amyloid β 1–42, phosphorylated‐tau, and amyloid‐tau index as predictors of Alzheimer pathology in patients with primary progressive aphasia, frontotemporal dementia, and progressive supranuclear palsy.ResultsNineteen nonamnestic autopsied cases with relevant CSF values were included. At autopsy, nine had AD and 10 had non‐AD pathologies. All six patients whose combined CSF phosphorylated‐tau and amyloid β levels were “consistent with AD” had postmortem Alzheimer pathology. The two patients whose biomarker values were “not consistent with AD” had non‐AD pathologies. The CSF values of the remaining eight non‐AD cases were in conflicting or borderline ranges.DiscussionCSF biomarkers reliably identified Alzheimer pathology in nonamnestic dementias and may be useful as a screening measure for inclusion of nonamnestic cases into Alzheimer's trials.
Update on Didactic and Clinical Education in Fluency Disorders: 2013–2014
Authors: Yaruss J. Scott , Lee Jieun , Kikani Kaya B. , Leslie Paula , Herring Caryn , Ramachandar Sujini , Tichenor Seth , Quesal Robert W. , McNeil Malcolm R. 
Published: February 2017

Purpose
This study surveyed didactic and clinical education in fluency disorders at undergraduate and graduate institutions in the United States that provide education in speech-language pathology to determine whether a previously observed reduction in requirements has continued since prior surveys (Yaruss, 1999; Yaruss & Quesal, 2002).

Method
The study involved a detailed questionnaire that was sent to 282 communication science and disorders departments. Questions examined didactic and clinical education, as well as faculty knowledge about fluency disorders.

Results
Comparisons with prior surveys revealed several findings, including (a) on average, programs have increased academic coursework and incorporated more practical sessions and competency-based testing in the classroom; (b) the number of faculty who possess extensive clinical experience with fluency disorders has decreased; and (c) although an increase in clinical requirements in fluency disorders was detected, the number of programs providing minimal education about fluency disorders remains high.

Conclusion
Given an expanding scope of practice, many programs have continued to try to provide adequate education about fluency disorders. Still, direct clinical experiences are limited, and faculty expertise in this area has continued to decrease. To raise students' confidence and competence in fluency disorders, efforts beyond graduate work—or systemic changes in the profession—may be necessary.