bluuebunny/crossref_metadata_2025_split huggingface dataset:
The coast-wide collapse in marine survival of west coast Chinook and steelhead: slow-moving catastrophe or deeper failure?
Authors: Welch David W. , Porter Aswea D. , Rechisky Erin L. 
Published: November 2018

AbstractAccelerating decreases in survival are evident for northern Hemisphere salmon populations. We collated smolt survival and smolt-to-adult (marine) survival data for all regions of the Pacific coast of North America excluding California to examine the forces shaping salmon returns. A total of 3,055 years of annual survival estimates were available for Chinook (Oncorhynchus tshawytscha) and steelhead (O. mykiss). This dataset provides a fundamentally different perspective on west coast salmon conservation problems from the previously accepted view. We found that marine survival collapsed over the past half century by a factor of at least 4-5 fold to similar low levels (~1%) for most regions of the west coast. The size of the decline is too large to be compensated by freshwater habitat remediation or cessation of harvest, and too large-scale to be attributable to specific anthropogenic impacts such as dams in the Columbia River or salmon farming in British Columbia. Within the Columbia River, both smolt survivals during downstream migration in freshwater and adult return rates (SARs) of Snake River populations, often singled out as exemplars of poor survival, appear unexceptional and are in fact higher than estimates reported from other regions of the west coast lacking dams. Formal Columbia River rebuilding targets of 2-6% SARs may therefore be unachievable if regions with nearly pristine freshwater conditions also fail to achieve these targets. Finally, we present case studies demonstrating that the historical response to evidence that the salmon problems are primarily ocean-related was to re-emphasize freshwater actions and to stop work on ocean issues. With ocean temperatures forecast to increase far further, the failure of management to identify the drivers of salmon collapse and respond appropriately suggest that the future of most west coast salmon populations is bleak.
Role of geography and climatic oscillations in governing into-India dispersal of freshwater snails of the family: Viviparidae
Authors: Sil Maitreya , Aravind N. A. , Karanth K. Praveen 
Published: November 2018

AbstractThe Indian subcontinent has experienced numerous paleogeological and paleoclimatic events during the Cenozoic which shaped the biotic assembly over time in the subcontinent. The role of these events in governing the biotic exchange between Southeast Asia and Indian subregion is underexplored. We aimed to uncover the effects the collision of the Indian and Asian plate, marine transgression in the Bengal basin as well as the paleoclimatic changes in the subcontinent and adjoining regions, on the dispersal of freshwater snail family Viviparidae from Southeast Asia (SEA) to Indian subregion. Extensive sampling was carried out throughout the Indian subcontinent to capture the current diversity of the targeted lineages. Three mitochondrial and two nuclear markers were sequenced from these samples and combined with published sequences to reconstruct a near complete global phylogeny of Viviparidae. Molecular dating and ancestral range estimation were undertaken to obtain the time frame for the dispersal events. Results from these analyses were contrasted with paleoclimate and paleogeology to better understand the biogeography of Indian viviparids. Results support at least two dispersal events into India from Southeast Asia. The earlier event is likely to have occurred during a warm and humid Eocene period before a permanent land connection was established between the two landmasses. While the more recent dispersal occurred post-suturing and overlapped with a time in late Tertiary to Quaternary when arid climate prevailed. However, we could not firmly establish how the marine transgressions influenced the dispersal events. Even though most biotic exchange between India and SEA are noted to be post-suturing, our results add to a growing body of work that suggests faunal exchange pre-suturing probably mediated by intermittent land connections.
Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes
Authors: Zhou Wenzhi , Zhao Shanshan , He Shutao , Ma Qiuxiang , Lu Xinlu , Hao Xiaomeng , Wang Hongxia , Yang Jun , Zhang Peng 
Published: November 2018

AbstractHigh amylose starch, a desired raw material in the starch industry, can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava plants with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. A significant decrease in BE transcripts was confirmed in these transgenic plants by quantitative real-time RT-PCR. The absence of BE1 protein in the BE1-RNAi plant lines (BE1i) and a dramatically lower level of BE2 protein in the BE2-RNAi plant lines (BE2i) were further confirmed by Western blot assays. All transgenic plant lines were grown up in the field, but with reduced biomass production of the above-ground parts and storage roots compared to wild type (WT). Considerably high amylose content in the storage roots of BE2i plant lines was achieved, though not in BE1i plant lines. Storage starch granules of BE1i and BE2i plants had similar morphology as WT, however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines, compared to that of WT starch. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis; silencing of cassava BE1 or BE2 caused various changes to starch physico-chemical properties and amylopectin structure. We also report that remarkably high amylose content in cassava starch has been first obtained in transgenic cassava by silencing of BE2 expression, thus showing a high potential for future industrial utilization.
DrugCombDB: a comprehensive database of drug combinations toward network medicine and combination therapy
Authors: Deng Lei , Zou Bo , Zhang Wenhao , Liu Hui 
Published: November 2018

AbstractDrug combinations have demonstrated high efficacy and low adverse side effects compared to single drug administrations in cancer therapies, and thus draw intensive attentions from researchers and pharmaceutical enterprises. Thanks to the fast development of high-throughput screening (HTS) methods, the amount of available drug combination datasets has tremendously increased. However, existing drug combination databases are lack of indications of the drug combinations and quantitative dose-responses. Therefore, there is an urgent need for a comprehensive database that is crucial to both experimental and computational screening of drug combinations. In this paper, we present DrugCombDB, a comprehensive database dedicated to integrating drug combinations from various data sources. Concretely, the data sources include 1) high-throughput screening assays of drug combinations, 2) external databases, and 3) manual curations from PubMed literature. In total, DrugCombDB includes 1,127,969 experimental data points with quantitative dose response and concentrations of drug combinations covering 561 unique drugs and 104 human cancer cell lines, and 1,875 FDA approved or literature-supported drug combinations. In particular, we adopted the zero interaction potency (ZIP) model [2] to compute the scores determining the synergy or antagonism of two drugs. To facilitate the downstream usage of our data resource, we prepared multiple datasets that are ready for building prediction models of classification and regression analysis. A website with user-friendly data visualization is provided to help users access the wealth of data. Users can input a drug of interest to retrieve associated drug combinations, together with the supporting evidence sources and drug targets. Our database is available at http://drugcombdb.denglab.org/.
The Pupillary Light Response Reflects Visual Working Memory Content
Authors: Hustá Cecília , Dalmaijer Edwin , Belopolsky Artem , Mathôt Sebastiaan 
Published: November 2018

AbstractRecent studies have shown that the pupillary light response (PLR) is modulated by higher cognitive functions, presumably through activity in visual sensory brain areas. Here we use the PLR to test the involvement of sensory areas in visual working memory (VWM). In two experiments, participants memorized either bright or dark stimuli. We found that pupils were smaller when a pre-stimulus cue indicated that a bright stimulus should be memorized; this reflects a covert shift of attention during encoding of items into VWM. Crucially, we obtained the same result with a post-stimulus cue, which shows that internal shifts of attention within VWM affect pupil size as well. Strikingly, pupil size reflected VWM content only briefly. This suggests that a shift of attention within VWM momentarily activates an “active” memory representation, but that this representation quickly transforms into a “hidden” state that does not rely on sensory areas.
Garcinia cambogia extract removes calcium oxalate kidney stones in both genetic and non-genetic Drosophila models of nephrolithiasis
Authors: Fan Qiuxia , Feng Xiaoming , Hong Xizhen , Gong Siqiao , Tian Jianwei , Hou Fanfan , Zhang Fujian 
Published: November 2018

ABSTRACTKidney stone formers with family history have a high rate of stone recurrence after kidney stone removal surgery and there is no effective medication available for treatment. Here, we show that Garcinia cambogia extract (GCE) efficiently removes calcium oxalate kidney stones from Malpighian tubules in both genetic and non-genetic Drosophila models of nephrolithiasis, and hydroxycitrate -a major component of GCE, directly dissolves calcium oxalate stones in Drosophila Malpighian tubules ex vivo. Our study discovers a potential novel therapeutic strategy for the clinical treatment of nephrolithiasis and suggests that clinical-grade Garcinia cambogia extract could be used to treat patients with nephrolithiasis in the future.
Impact of high phosphorous and sodium on productivity and stress tolerance of Arundo donax plants
Authors: Cocozza Claudia , Brilli Federico , Miozzi Laura , Pignattelli Sara , Rotunno Silvia , Brunetti Cecilia , Giordano Cristiana , Pollastri Susanna , Centritto Mauro , Accotto Gian Paolo , Tognetti Roberto , Loreto Francesco 
Published: November 2018

AbstractArundo donax L. is an invasive species recently employed for biomass production that emits large amounts of isoprene, a volatile compound having important defensive role. Here, the potential of A. donax to grow in degraded soils, characterized by poor fertility, eutrophication and/or salinization, has been evaluated at morphological, biochemical and transcriptional level. Our results highlight sensitivity of A. donax to P deficiency. Moreover, we show that A. donax response to salt stress (high sodium, Na+), which impaired plant performance causing detrimental effects on leaf cells ultrastructure, is characterized by enhanced biosynthesis of antioxidant carotenoids and sucrose. Differently from Na+, high phosphorous (P) supply did not hamper photosynthesis although it affected carbon metabolism through reduction of starch content and by lowering isoprene emission. In particular, we revealed on salt-stress leaves that high P enhanced the expression of genes involved in abiotic stress tolerance, but further increased diffusive limitations to photosynthesis and slowed-down sugar turnover without modifying isoprene emission. Therefore, despite limiting productivity, high P improved A. donax tolerance to salinity by favouring the accumulation of carbohydrates that protect cells and increase osmotic potential, and by stimulating the synthesis of antioxidants that improves photo-protection and avoids excessive accumulation of reactive oxygen species.HighlightsArundo donax is sensitive to elevated salinity. High phosphorous supply to salt-stressed A. donax enhances transcriptomic changesthat induce the onset of physiological mechanisms of stress tolerance but limits productivity.
Social determinants of health, the family, and children's personal hygiene: a comparative study
Authors: Ramos-Morcillo Antonio Jesús , Moreno-Martínez Francisco José , Hernández-Susarte Ana María , Ruzafa-Martínez María 
Published: November 2018

AbstractAimsTo examine differences in personal hygiene and in the perception of social rejection between children in reception centers and children living in a family setting.BackgroundLittle attention has been paid to the influence of the family as a unit on the personal hygiene behaviors of children.DesignCross-sectional study.MethodsChildren aged between 7-12 years were recruited from 2015 through 2017 from two centers in the Network of State Care Centers and from three schools selected from a rural, suburban and urban setting in the same region. A validated questionnaire on child personal hygiene habits was completed by 51 children in reception centers and 454 in normal families.ResultsData shows worse results for the majority personal hygiene habits studied in children in reception centers than in children living in families. Multiple logistic regressions showed lower frequency of body washing, hand washing after defecating, use of soap in hand washing, tooth brushing, and dentist visits during the previous year. Also, a significantly higher proportion of children in reception centers had experienced social rejection for being dirty and smelling bad in comparison to the children living in families.ConclusionsDeficient hygiene habits were observed in the offspring of families affected by the main features of social inequality, who were more likely to perceive social rejection for this reason and less likely to consider their family as the greatest influence on their personal hygiene practices. Promoting family practices designed to improve personal hygiene habits are needed specially in vulnerable families.
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas
Authors: Zhu Bin , Poeta Maria Luana , Costantini Manuela , Zhang Tongwu , Shi Jianxin , Sentinelli Steno , Zhao Wei , Pompeo Vincenzo , Cardelli Maurizio , Alexandrov Boian S. , Otlu Burcak , Hua Xing , Jones Kristine , Brodie Seth , Toro Jorge R. , Yeager Meredith , Wang Mingyi , Hicks Belynda , Alexandrov Ludmil B. , Brown Kevin M. , Wedge David C. , Chanock Stephen , Fazio Vito Michele , Gallucci Michele , Landi Maria Teresa 
Published: November 2018

ABSTRACTIntratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.
Increased prediction ability in Norway spruce trials using a marker x environment interaction and non-additive genomic selection model
Authors: Chen Zhi-Qiang , Baison John , Pan Jin , Westin Johan , Rosario García Gil María , Wu Harry X. 
Published: November 2018

AbstractA genomic selection (GS) study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in two Northern Swedish trials at two locations using exome capture as a genotyping platform. Non-additive effects including dominance and first-order epistatic interactions (including additive by additive, dominance by dominance, and additive by dominance) and marker-by-environment interaction (M×E) effects were dissected in genomic and phenotypic selection models. GS models partitioned additive and non-additive genetic variances more precisely compared with pedigree-based models. In addition, predictive ability (PA) in GS was substantially increased by including dominance and slightly increased by including M×E effects when these effects are significant. For velocity, response to GS (RGS) per year increased 91.3/43.7%, 86.9/82.9%, and 78.9/80.8% compared with response to phenotypic selection (RPS) per year when GS was based on 1) main marker effects (M), 2) M + M×E effects (A), and 3) A + dominance effects (AD) for site 1/site 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also may improve the genetic gain when they are significant. For tree height, Pilodyn, and modulus of elasticity (MOE), RGS per year improved up to 84.2%, 91.3%, and 92.6% compared with RPS per year, respectively.
Age-associated different transcriptome profiling in zebrafish and rat: insight into diversity of vertebrate aging
Authors: Kijima Yusuke , Wantong Wang , Igarashi Yoji , Yoshitake Kazutoshi , Asakawa Shuichi , Suzuki Yutaka , Watabe Shugo , Kinoshita Shigeharu 
Published: November 2018

AbstractBackgroundAging and death are inevitable for most species and are of intense interest for human beings. Most mammals, including humans, show obvious aging phenotypes, for example, loss of tissue plasticity and sarcopenia. In this regard, fish provide attractive models because of their unique aging characteristics. First, the lifespan of fish is highly varied and some long-lived fish can live for over 200 years. Second, some fish show anti-aging features and indeterminate growth throughout their life. Because these characteristics are not found in mammalian model organisms, exploring mechanisms of senescence in fish is expected to provide new insights into vertebrate aging. Therefore, we conducted transcriptome analysis for brain, gill, heart, liver and muscle from 2-month-, 7-month-, 16month- and 39-month-old zebrafish. In addition, we downloaded RNA-seq data for sequential age related gene expression in brain, heart, liver and muscle of rat (1). These RNA-seq data from two species were compared, and common and species-specific features of senescence were analyzed.ResultsScreening of differentially expressed genes (DEGs) in all zebrafish tissues examined revealed up-regulation of circadian genes and down-regulation ofhmgb3a. Comparative analysis of DEG profiles associated with aging between zebrafish and rat showed both conserved and clearly different aging phenomena. Furthermore, up-regulation of circadian genes with aging and down-regulation of collagen genes were observed in both species. On the other hand, in zebrafish, up-regulation of autophagy related genes in muscle andatf3in various tissues suggested fish-specific anti- aging characteristics. Consistent with our knowledge of mammalian aging, a tissue deterioration-related DEG profile was observed in rat. We also detected aging-associated down-regulation of muscle development and ATP metabolism-related genes in zebrafish gill. Correspondingly, hypoxia-related genes were systemically up-regulated in aged zebrafish, suggesting age-related hypoxia as a senescence modulator in fish.ConclusionsOur results indicate both common and different aging profiles between fish and mammals. Gene expression profiles specific to fish will provide new insight for future translational research.
Network dynamics of Broca’s area during word selection
Authors: Conner Christopher R , Kadipasaoglu Cihan M , Shouval Harel Z , Hickok Gregory , Tandon Nitin 
Published: November 2018

AbstractCurrent models of word-production in Broca’s area posit that sequential and staggered semantic, lexical, phonological and articulatory processes precede articulation. Using millisecond-resolution intra-cranial recordings, we evaluated spatiotemporal dynamics and high frequency functional interconnectivity between ventro-lateral prefrontal regions during single-word production. Through the systematic variation of retrieval, selection, and phonological loads, we identified specific activation profiles and functional coupling patterns between these regions that fit within current psycholinguistic theories of word production. However, network interactions underpinning these processes activate in parallel (not sequentially), while the processes themselves are indexed by specific changes in network state. We found evidence that suggests that pars orbitalis is coupled with pars triangularis during lexical retrieval, while lexical selection in Broca’s area is terminated via coupled activity with M1 at articulation onset. Taken together, this work reveals that speech production relies on very specific inter-regional couplings in rapid sequence in the language dominant hemisphere.
Lin28B is involved in curcumin-reversed paclitaxel chemoresistance and associated with poor prognosis in hepatocellular carcinoma
Authors: Tian Nan , Shangguan Wenbing , Zhou Zuolin , yao Yao , Fan Chunlei , Cai Lijun 
Published: November 2018

AbstractChemoresistance remains a big challenge in hepatocellular carcinoma (HCC) treatment. Several studies indicated that RNA-binding protein Lin28B serves an oncogenic role in HCC, but its activity in HCC chemotherapy has never been assessed. In this study, we found that overexpression of Lin28B significantly increased the paclitaxel chemoresistance in two different HCC cells lines while silencing Lin28B reduced the chemoresistance in paclitaxel-resistance HCC cells. Curcumin, a natural anti-cancer agent, increased the sensitivity of HCC cells to paclitaxel through inhibiting NF-κB stimulated Lin28B expression both in vitro and in vivo. Furthermore, by analyzing TCGA (The Cancer Genome Atlas) LIHC (liver hepatocellular carcinoma) and GSE14520 databases, we found that Lin28B was highly up-regulated in HCC tissue compared with that in normal tissue and associated with α-fetoprotein levels, and that patients with Lin28B higher expression had a significant shorter overall survival time than those with Lin28B lower expression. Our data reveal that Lin28B may serve as a predictive biomarker and a treatment target to reverse HCC chemotherapy resistance in future clinical practice.Summary statementupregulation of Lin28B not only confers poor prognosis in HCC patients but also increases chemoresistance in HCC cells. Thus, Lin28B may serve as a predictive biomarker for use to reverse chemoresistance in clinical practice.