bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light and temperature effects on photosynthetic activity of Eucheuma denticulatum and Kappaphycus alvarezii (brown and green color morphotypes) from Sulawesi Utara, Indonesia
Authors: Borlongan Iris Ann G. , Gerung Grevo S. , Nishihara Gregory N. , Terada Ryuta 
Published: December 2016

SUMMARYKnowledge concerning the effects of several abiotic factors on the physiology of carrageenophytes is essential both in ecological and economic standpoints, to ensure their sufficient supply for the sustainability of seaweed‐based industries. This paper presents the photosynthetic characteristics of farmed carrageenophytes,
E

ucheuma denticulatum and
K

appaphycus alvarezii [brown (BRN) and green (GRN) color morphotypes] from Sulawesi Utara (Sulawesi Island), Indonesia, as determined by examining their photosynthetic response across different temperatures and irradiances using dissolved oxygen measurements and pulse‐amplitude modulated fluorometer. Net photosynthesis–irradiance (
P

–

E
) curves at 26°C revealed that net photosynthetic rates of the three seaweeds gradually increased until the estimated saturation irradiances (
E

k
) of 58 μmol photons m−
2 s−1 (49–68 μmol photons m−
2 s−1, 95% Bayesian prediction intervals; BPI) for
E

. denticulatum, and 158 and 143 μmol photons m−
2 s−1 (134–185 and 99–203 μmol photons m−
2 s−1, 95% BPI) for BRN and GRN K

. alvarezii, respectively; and that no photoinhibition was observed at the highest irradiance of 1000 μmol photons m−
2 s−1. All seaweed samples exhibited photosynthetic tolerance to high PAR as shown by their recovery in maximum quantum yields (Fv

/
Fm
) following chronic exposures; as well as tolerance over a broad range of temperature, which is from 19 to 33°C for
E

. denticulatum, 20–29°C for BRN K

. alvarezii, and 17–32°C for GRN K

. alvarezii. Temperature responses of these carrageenophytes indicated that they were well‐adapted to the annual seawater temperatures in the cultivation site; however, they are also likely close to threshold levels for thermal inhibition, given the decline in Fv

/
Fm
above 30°C.
Fluid–rock interactions during continuous diagenesis of sandstone reservoirs and their effects on reservoir porosity
Authors: Yang Leilei , Xu Tianfu , Liu Keyu , Peng Bo , Yu Zhichao , Xu Xiaomeng 
Published: December 2016

AbstractThe Cretaceous sandstone reservoir in the Kuche Depression, Tarim Basin, western China, was investigated with reference to its reservoir property evolution during diagenesis. Six general diagenetic stages were recognized through petrographic, mineralogical and geochemical analyses. Fluid–rock interaction experiments were conducted under these six continuous diagenetic conditions, that is with a simulation sequence of compaction → early diagenesis → organic acid incursion I → elevated temperature/pressure → organic acid incursion II → late diagenesis. Corresponding to these six experimental stages, a total of six models were constructed. Finally, an extended model of fluid–rock interaction during diagenesis at a geological timescale (from 30 Ma to present) was constructed after various parameters had been validated. Results demonstrate that the diagenetic stages from both the experimental and numerical simulations generally matched findings obtained from the petrographic and geochemical analyses: (i) With compaction becoming weakened, cementation by various minerals was gradually increased. (ii) Quartz overgrowth occurred because the contemporaneous sedimentary water was alkaline. (iii) Most minerals (for example, calcite and feldspar minerals) displayed dissolution owing to the first organic acid incursion, resulting in the visual porosity increasing to 29·26%. (iv) Increases in temperature and pressure caused a minor fluctuation of the porosity change. (v) The cement that formed during earlier stages largely dissolved with the second organic acid incursion. (vi) During the last stage, the reservoir fluid was diluted by sedimentary alkaline water and most minerals precipitated under an alkalic environment. The present porosity simulated is about 11·4%, comparable with the actually measured data. This study demonstrates that the combination of petrographic observations, laboratory experiments and numerical simulations can not only reconstruct the diagenetic process, but also provide a quantitative evaluation and prediction of reservoir petrophysical properties.
Experimental characterization of meso‐scale deformation mechanisms and the RVE size in plastically deformed carbon steel
Authors: Ravindran Suraj , Koohbor Behrad , Kidane Addis 
Published: December 2016

AbstractThe local deformation response of low carbon steel subjected to uniaxial tensile loading is investigated, and the local strain field at sub‐grain scale is obtained using high‐spatial‐resolution digital image correlation. The implemented digital image correlation method enables the observation and study of inhomogeneous deformation response at microstructural levels. Detailed local deformation mechanisms including mesoscopic slip bands are captured. Furthermore, the local information is used for the determination of representative volume element size in polycrystalline low carbon steel. To obtain the representative volume element size, we proposed and successfully implemented a strain variation method. Further, the influence of global strain on the local deformation mechanisms and representative volume element size is discussed. The challenges associated with the local strain measurement using digital image correlation are also discussed.
AraQTL – workbench and archive for systems genetics in Arabidopsis thaliana
Authors: Nijveen Harm , Ligterink Wilco , Keurentjes Joost J. B. , Loudet Olivier , Long Jiao , Sterken Mark G. , Prins Pjotr , Hilhorst Henk W. , de Ridder Dick , Kammenga Jan E. , Snoek Basten L. 
Published: December 2016

SummaryGenetical genomics studies uncover genome‐wide genetic interactions between genes and their transcriptional regulators. High‐throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross‐analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/AraQTL/), an easily accessible workbench and database for comparative analysis and meta‐analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re‐using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene‐by‐environment interactions by comparing eQTLs under different conditions.
Global identification of alternative splicing via comparative analysis of SMRT‐ and Illumina‐based RNA‐seq in strawberry
Authors: Li Yongping , Dai Cheng , Hu Chungen , Liu Zhongchi , Kang Chunying 
Published: December 2016

SummaryAlternative splicing (AS) is a key post‐transcriptional regulatory mechanism, yet little information is known about its roles in fruit crops. Here, AS was globally analyzed in the wild strawberry Fragaria vesca genome with RNA‐seq data derived from different stages of fruit development. The AS landscape was characterized and compared between the single‐molecule, real‐time (SMRT) and Illumina RNA‐seq platform. While SMRT has a lower sequencing depth, it identifies more genes undergoing AS (57.67% of detected multiexon genes) when it is compared with Illumina (33.48%), illustrating the efficacy of SMRT in AS identification. We investigated different modes of AS in the context of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that of alternative acceptor sites (AA) is significantly increased post‐fertilization when compared with pre‐fertilization. When all the identified transcripts were combined, a total of 66.43% detected multiexon genes in strawberry undergo AS, some of which lead to a gain or loss of conserved domains in the gene products. The work demonstrates that SMRT sequencing is highly powerful in AS discovery and provides a rich data resource for later functional studies of different isoforms. Further, shifting AS modes may contribute to rapid changes of gene expression during fruit set.
Plant invasiveness and target plant density: high densities of native Schima wallichii seedlings reduce negative effects of invasive Ageratina adenophora
Authors: Thapa L B , Kaewchumnong K , Sinkkonen A , Sridith K 
Published: December 2016

SummaryEconomically feasible strategies to cope with invasive species are urgently needed. Plant density can be increased to reduce competitive effects on target plants. This study indicates that increasing native plant density can be used to reduce the effect of invasive Ageratina adenophora. Seedlings of an indigenous tree species, Schima wallichii, were grown in pots containing uninvaded or invaded soil, with or without A. adenophora leaf litter on the soil surface. Schima wallichii seedlings were also grown at four densities under four levels of A. adenophora leaf litter. Root and shoot biomass and length were measured as response parameters in both bioassays. Schima wallichii growth was inhibited by A. adenophora leaf litter and invaded soil. High litter levels reduced S. wallichii root length and dry weight at low plant densities. The inhibition disappeared at high S. wallichii plant densities. As A. adenophora did not inhibit S. wallichii growth at high plant densities, adjustments of seedling density should be studied as a possible management strategy for invasion by A. adenophora and potentially by other exotic plant species. As density‐dependent growth inhibition is the key characteristic of chemical interference, we propose that phytotoxins contribute to A. adenophora invasion particularly at low densities of native seedlings.
The role of allogenic keratin‐derived dressing in wound healing in a mouse model
Authors: Konop Marek , Sulejczak Dorota , Czuwara Joanna , Kosson Piotr , Misicka Aleksandra , Lipkowski Andrzej W. , Rudnicka Lidia 
Published: December 2016

AbstractKeratin is an interesting protein needed for wound healing and tissue recovery. We have recently proposed a new, simple and inexpensive method to obtain fur and hair keratin‐derived biomaterials suitable for medical application. The aim of the study was to evaluate the role of the fur keratin‐derived protein (FKDP) dressing in the allogenic full‐thickness surgical skin wound model. The data obtained using scanning electron microscopy showed that employed processed biomaterial had higher surface porosity compared with control raw material. From the MTS test, it was found keratin biomaterial is not only toxic to the NIH/3T3 cell line (p < 0.05), but also enhances cell proliferation compared with the control. In vivo studies have shown keratin dressings are tissue biocompatible, accelerate wound closure and epithelialization to the statistically significant differences on day 5 (p < 0.05) in comparison to control wounds. Histological examination revealed, that in FKDP‐treated wounds the inflammatory response contained predominantly macrophages whilst their morphological untreated variants showed mixed cell infiltrates rich in neutrophils. Predominant macrophages based response creates more favorable environment for healing. In FKDP‐dressed wounds the number of microhemorrhages was also significantly decreased (p < 0.05) as compared with undressed wounds. Applied keratin dressing favors reconstruction of a more regular skin structure and assures better cosmetic effect in terms of scar formation and appearance. In conclusion, fur keratin‐derived protein dressings significantly accelerated wound healing in the mouse model. Further studies are needed to determine the molecular mechanisms involved in the multilayer wound healing process and to assess the possible use of these dressings for medical purposes.
One-year Stability of Objectively Measured Physical Activity in Young Brazilian Adults
Authors: Martins Rafaela Costa , Reichert Felipe Fossati , Bielemann Renata Moraes , Hallal Pedro C. 
Published: December 2016

Background:To evaluate the 1-year stability of objectively measured physical activity among young adults living in South Brazil, as well as assessing the influences of temperature, humidity and precipitation on physical activity.Methods:A longitudinal study was conducted over 12 consecutive months (October 2012 to September 2013). Sixteen participants (8 men) used GT3X+ accelerometers 1 week per month for the entire year. Climate variables were obtained from an official climate information provider.Results:Physical activity was remarkably stable over the year—the proportion of the day spent in moderate-to-vigorous intensity physical activity (MVPA) was around 5% in every month. Average temperature (ρ = –0.64; P = .007), humidity (ρ = –0.68; P = .004) and rain (ρ = –0.67; P = .004) were inversely correlated to MVPA in the Summer. Rain was also inversely correlated to MVPA in the Spring (ρ = –0.54; P = .03).Conclusions:Objectively measured physical activity was stable over a 1-year period. Climate variables consistently influenced physical activity practice in the Summer, but not in the other seasons.
Improvement in Physical Activity in Persons With Obstructive Sleep Apnea Treated With Continuous Positive Airway Pressure
Authors: Jean Raymonde E. , Duttuluri Manideep , Gibson Charlisa D. , Mir Sadaf , Fuhrmann Katherine , Eden Edward , Supariwala Azhar 
Published: December 2016

Background:Exercise improves sleep quality, yet people with untreated obstructive sleep apnea (OSA) may engage in less physical activity (PA) due to fatigue and daytime sleepiness. We examined changes in PA and sleep quality before and after treatment with continuous positive airway pressure (CPAP) in OSA patients.Methods:In this prospective longitudinal study, persons with a primary diagnosis of OSA were enrolled at a community-based hospital in New York City. At 3 time intervals pre- and post-CPAP (3–8 months), we measured sleep quality using validated questionnaires, perceived PA using the International Physical Activity Questionnaire (IPAQ), and actual PA using pedometer steps per day. We sought to investigate how CPAP use and changes in sleep quality impacted the number of steps taken, as recorded in pedometer steps.Results:In total, 62 patients were enrolled in the study from March 2012 to July 2014. In all, patients averaged 53 years of age, and 26 patients (42%) were female. Among all participants, 86% of persons had moderate to severe sleep apnea (AHI ≥15). Approximately 73% of participants were compliant with CPAP use. Poor sleep quality correlated with lower actual PA (P = .004) at baseline. At 3 and 7 months, there was significant improvement in sleep quality (Δ –2.63 ± 3.4 and Δ –3.5 ± 3.8; P < .001) and actual PA (Δ 840 ± 1313 and Δ 1431 ± 1419 steps/day, P < .001) compared with baseline. On multivariate analyses, participants with a higher waist circumference had a significantly greater increase in actual PA (P = .018).Conclusion:Treatment of OSA with CPAP had a progressive incremental improvement in sleep quality and actual PA.
Duncan and Son: changing professional boundaries in the geological and medical sciences in the nineteenth and twentieth centuries
Authors: Carter Tim , Spurgeon Anne 
Published: December 2016

Abstract
The concept of the professional changed markedly from the mid-nineteenth to the early twentieth century. The contrasting careers of Peter Martin Duncan, father, and Cecil Cooke Duncan, son, provide a vignette of these changes in two people who were both actively engaged in geological and medical activities. Peter Martin trained as a doctor and practised for some 20 years. He later became Professor of Geology at Kings College, London and both Secretary and President of the Geological Society. He was a prolific author of both learned articles and books on science for the general public. In his time it was acceptable to combine all these roles into a single career. Cecil trained as a chemist. His career was as the public analyst in Worcester at a time when these posts were becoming professionalized. He contributed to control of health risks in the county. To him geology and natural history were serious leisure pastimes rather than part of his professionally defined career. Father and son therefore show the move from the time when there were fluid disciplinary boundaries to one where a single professional discipline defined and bounded working life and other areas of study became a matter for non-working hours.
Mechanisms of Acquired Drug Resistance to the HDAC6 Selective Inhibitor Ricolinostat Reveals Rational Drug-Drug Combination with Ibrutinib
Authors: Amengual Jennifer E. , Prabhu Sathyen A. , Lombardo Maximilian , Zullo Kelly , Johannet Paul M. , Gonzalez Yulissa , Scotto Luigi , Serrano Xavier Jirau , Wei Ying , Duong Jimmy , Nandakumar Renu , Cremers Serge , Verma Akanksha , Elemento Olivier , O'Connor Owen A. 
Published: December 2016

Abstract
Purpose: Pan-class I/II histone deacetylase (HDAC) inhibitors are effective treatments for select lymphomas. Isoform-selective HDAC inhibitors are emerging as potentially more targeted agents. ACY-1215 (ricolinostat) is a first-in-class selective HDAC6 inhibitor. To better understand the discrete function of HDAC6 and its role in lymphoma, we developed a lymphoma cell line resistant to ACY-1215.
Experimental Design: The diffuse large B-cell lymphoma cell line OCI-Ly10 was exposed to increasing concentrations of ACY-1215 over an extended period of time, leading to the development of a resistant cell line. Gene expression profiling (GEP) was performed to investigate differentially expressed genes. Combination studies of ACY-1215 and ibrutinib were performed in cell lines, primary human lymphoma tissue, and a xenograft mouse model.
Results: Systematic incremental increases in drug exposure led to the development of distinct resistant cell lines with IC50 values 10- to 20-fold greater than that for parental lines. GEP revealed upregulation of MAPK10, HELIOS, HDAC9, and FYN, as well as downregulation of SH3BP5 and LCK. Gene-set enrichment analysis (GSEA) revealed modulation of the BTK pathway. Ibrutinib was found to be synergistic with ACY-1215 in cell lines as well as in 3 primary patient samples of lymphoma. In vivo confirmation of antitumor synergy was demonstrated with a xenograft of DLBCL.
Conclusions: The development of this ACY-1215–resistant cell line has provided valuable insights into the mechanistic role of HDAC6 in lymphoma and offered a novel method to identify rational synergistic drug combinations. Translation of these findings to the clinic is underway. Clin Cancer Res; 23(12); 3084–96. ©2016 AACR.
Targeting the ATR/CHK1 Axis with PARP Inhibition Results in Tumor Regression in BRCA-Mutant Ovarian Cancer Models
Authors: Kim Hyoung , George Erin , Ragland Ryan L. , Rafail Stavros , Zhang Rugang , Krepler Clemens , Morgan Mark A. , Herlyn Meenhard , Brown Eric J. , Simpkins Fiona 
Published: December 2016

Abstract
Purpose: PARP inhibition (PARPi) has modest clinical activity in recurrent BRCA-mutant (BRCAMUT) high-grade serous ovarian cancers (HGSOC). We hypothesized that PARPi increases dependence on ATR/CHK1 such that combination PARPi with ATR/CHK1 blockade results in increased cell death and tumor regression.
Experimental Design: Effects of PARPi (olaparib), CHK1 inhibition (CHK1i;MK8776), or ATR inhibition (ATRi;AZD6738) alone or in combination on survival, colony formation, cell cycle, genome instability, and apoptosis were evaluated in BRCA1/2MUT HGSOC cells. Tumor growth in vivo was evaluated using a BRCA2MUT patient-derived xenograft (PDX) model.
Results: PARPi monotherapy resulted in a decrease in BRCAMUT cell survival, colony formation and suppressed but did not eliminate tumor growth at the maximum tolerated dose (MTD) in a BRCA2MUT PDX. PARPi treatment increased pATR and pCHK1, indicating activation of the ATR–CHK1 fork protection pathway is relied upon for genome stability under PARPi. Indeed, combination of ATRi or CHK1i with PARPi synergistically decreased survival and colony formation compared with single-agent treatments in BRCAMUT cells. Notably, PARPi led to G2 phase accumulation, and the addition of ATRi or CHK1i released cells from G2 causing premature mitotic entry with increased chromosomal aberrations and apoptosis. Moreover, the combinations of PARPi with ATRi or CHK1i were synergistic in causing tumor suppression in a BRCA2MUT PDX with the PARPi–ATRi combination inducing tumor regression and in most cases, complete remission.
Conclusions: PARPi causes increased reliance on ATR/CHK1 for genome stability, and combination PARPi with ATR/CHK1i is more effective than PARPi alone in reducing tumor burden in BRCAMUT models. Clin Cancer Res; 23(12); 3097–108. ©2016 AACR.
Intelectuales de la Educación en la reconstrucción de la democracia en la Argentina
Authors: Isola Nicolás José 
Published: December 2016

No final da ditadura na Argentina, em 1983, a reconstituição dos espaços de produção de conhecimento em educação mereceu uma série de debates sobre a modernização interrompida e o futuro da educação nacional. Estava em disputa a intenção de consolidar consensos que fortalecessem o discurso e as capacidades educacionais do Estado. Ao analisar os documentos e intervenções intelectuais, discuto tanto as tensões quanto as possibilidades que se apresentam nos depoimentos dos acadêmicos da Educação na Argentina na luta para o fortalecimento de uma burocracia estatal especializada.As conclusões permitem considerar três tensões: (i) a debilidade técnico-burocrática e estatística do sistema educativo; (ii) a falta de coesão deste espaço profissional; e (iii) a dificuldade para estabelecer um programa científico moderno, com acesso a posições de poder no Estado