bluuebunny/crossref_metadata_2025_split huggingface dataset:
Female and male life tables for seven wild primate species
Authors: Bronikowski Anne M. , Cords Marina , Alberts Susan C. , Altmann Jeanne , Brockman Diane K. , Fedigan Linda M. , Pusey Anne , Stoinski Tara , Strier Karen B. , Morris William F. 
Published: March 2016

AbstractWe provide male and female census count data, age-specific survivorship, and female age-specific fertility estimates for populations of seven wild primates that have been continuously monitored for at least 29 years: sifaka (Propithecus verreauxi) in Madagascar; muriqui (Brachyteles hypoxanthus) in Brazil; capuchin (Cebus capucinus) in Costa Rica; baboon (Papio cynocephalus) and blue monkey (Cercopithecus mitis) in Kenya; chimpanzee (Pan troglodytes) in Tanzania; and gorilla (Gorilla beringei) in Rwanda. Using one-year age-class intervals, we computed point estimates of age-specific survival for both sexes. In all species, our survival estimates for the dispersing sex are affected by heavy censoring. We also calculated reproductive value, life expectancy, and mortality hazards for females. We used bootstrapping to place confidence intervals on life-table summary metrics (R0, the net reproductive rate;λ, the population growth rate; andG, the generation time). These data have high potential for reuse; they derive from continuous population monitoring of long-lived organisms and will be invaluable for addressing questions about comparative demography, primate conservation and human evolution.
Comparative transcriptome analysis among parental inbred and crosses reveals the role of dominance gene expression in heterosis in Drosophila melanogaster
Authors: Wu Xianwen , Li Rongni , Li Qianqian , Bao Haigang , Wu Changxin 
Published: March 2016

AbstractWe observed heteroses for body weight in Drosophila melanogaster after generating hybrids from three inbred lines. To better understand the mechanism for this phenomenon at the mRNA level, we compared the mRNA profiles of the parental and hybrid lines using high-throughput RNA-seq. A total of 5877 differentially expressed genes (DEGs) were found and about 92% of these exhibited parental expression level dominance. Genes in the dominance category were functionally characterized using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the gene classifications offered by the Gene Ontology (GO) Consortium. The analysis identified genes associated with crucial processes such as development and growth in all three crosses. Functional assignments involving aminoglycan metabolism, starch and sucrose metabolism, and galactose metabolism are significantly overrepresented amongst the 215 common dominance DEGs. We conclude that dominance DEGs are important in heteroses in Drosophila melanogaster and contribute specifically to body weight heterosis.
Significant impact of miRNA–target gene networks on genetics of human complex traits
Authors: Okada Yukinori , Muramatsu Tomoki , Suita Naomasa , Kanai Masahiro , Kawakami Eiryo , Iotchkova Valentina , Soranzo Nicole , Inazawa Johji , Tanaka Toshihiro 
Published: March 2016

AbstractThe impact of microRNA (miRNA) on the genetics of human complex traits, especially in the context of miRNA-target gene networks, has not been fully assessed. Here, we developed a novel analytical method, MIGWAS, to comprehensively evaluate enrichment of genome-wide association study (GWAS) signals in miRNA–target gene networks. We applied the method to the GWAS results of the 18 human complex traits from >1.75 million subjects and identified significant enrichment in rheumatoid arthritis (RA), kidney function and adult height (P < 0.05/18= 0.0028, most significant enrichment in RA with P = 1.7 × 10−4). Interestingly, these results were consistent with current literature-based knowledge of the traits on miRNA obtained through the NCBI PubMed database search (adjusted P = 0.024). Our method provided a list of miRNA and target gene pairs with excess genetic association signals, part of which included drug target genes. We identified a miRNA (miR-4728-5p) that downregulates PADI2, a novel RA risk gene considered as a promising therapeutic target (rs761426, adjusted P = 2.3 × 10−9). Our study indicated the significant impact of miRNA–target gene networks on the genetics of human complex traits and provided resources which should contribute to drug discovery and nucleic acid medicine.
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase
Authors: Nilsson Avlant , Nielsen Jens 
Published: March 2016

AbstractIntermediary metabolism provides living cells with free energy and precursor metabolites required for synthesizing proteins, lipids, RNA and other cellular constituents, and it is highly conserved among living species. Only a fraction of cellular protein can, however, be allocated to enzymes of intermediary metabolism and consequently metabolic trade-offs may take place. One such trade-off, aerobic fermentation, occurs in both yeast (the Crabtree effect) and cancer cells (the Warburg effect) and has been a scientific challenge for decades. Here we show, using flux balance analysis combined with in vitro measured enzyme specific activities, that fermentation is more catalytically efficient than respiration, i.e. it produces more ATP per protein mass. And that the switch to fermentation at high growth rates therefore is a consequence of a high ATP production rate, provided by a limited pool of enzymes. The catalytic efficiency is also higher for cells grown on glucose compared to galactose and ethanol, which may explain the observed differences in their growth rates. The enzyme F1F0-ATP synthase (Complex V) was found to have flux control over respiration in the model, and since it is evolutionary conserved, we expect the trade-off to occur in organisms from all kingdoms of life.
Identification of candidate diagnostic biomarkers for adolescent idiopathic scoliosis using UPLC/QTOF-MS analysis: a first report of lipid metabolism profiles
Authors: Sun Zhi-jian , Jia Hong-mei , Qiu Gui-xing , Zhou Chao , Guo Shigong , Zhang Jian-guo , Shen Jian-xiong , Zhao Yu , Zou Zhong-mei 
Published: March 2016

AbstractAdolescent idiopathic scoliosis (AIS) is a complex spine deformity, affecting approximately 1–3% adolescents. Earlier diagnosis could increase the likelihood of successful conservative treatment and hence reduce the need for surgical intervention. We conducted a serum metabonomic study to explore the potential biomarkers of AIS for early diagnosis. Serum metabolic profiles were firstly explored between 30 AIS patients and 31 healthy controls by ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Then, the candidate metabolites were validated in an independent cohort including 31 AIS patients and 44 controls. The results showed that metabolic profiles of AIS patients generally deviated from healthy controls in both the discovery set and replication set. Seven differential metabolites were identified as candidate diagnostic biomarkers, including PC(20:4), 2-hexenoylcarnitine, beta-D-glucopyranuronicacid, DG(38:9), MG(20:3), LysoPC(18:2) and LysoPC(16:0). These candidate metabolites indicated disrupted lipid metabolism in AIS, including glycerophospholipid, glycerolipid and fatty acid metabolism. Elevated expressions of adipose triglyceride lipase and hormone sensitive lipase in adipose tissue further corroborated our findings of increased lipid metabolism in AIS. Our findings suggest that differential metabolites discovered in AIS could be used as potential diagnostic biomarkers and that lipid metabolism plays a role in the pathogenesis of AIS.
Evolving Methanococcoides burtonii archaeal Rubisco for improved photosynthesis and plant growth
Authors: Wilson Robert H. , Alonso Hernan , Whitney Spencer M. 
Published: March 2016

AbstractIn photosynthesis Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the often rate limiting CO2-fixation step in the Calvin cycle. This makes Rubisco both the gatekeeper for carbon entry into the biosphere and a target for functional improvement to enhance photosynthesis and plant growth. Encumbering the catalytic performance of Rubisco is its highly conserved, complex catalytic chemistry. Accordingly, traditional efforts to enhance Rubisco catalysis using protracted “trial and error” protein engineering approaches have met with limited success. Here we demonstrate the versatility of high throughput directed (laboratory) protein evolution for improving the carboxylation properties of a non-photosynthetic Rubisco from the archaea Methanococcoides burtonii. Using chloroplast transformation in the model plant Nicotiana tabacum (tobacco) we confirm the improved forms of M. burtonii Rubisco increased photosynthesis and growth relative to tobacco controls producing wild-type M. burtonii Rubisco. Our findings indicate continued directed evolution of archaeal Rubisco offers new potential for enhancing leaf photosynthesis and plant growth.
Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions
Authors: Yokogawa Mariko , Tsushima Takashi , Noda Nobuo N. , Kumeta Hiroyuki , Enokizono Yoshiaki , Yamashita Kazuo , Standley Daron M. , Takeuchi Osamu , Akira Shizuo , Inagaki Fuyuhiko 
Published: March 2016

AbstractRegnase-1 is an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. Here, we report the structures of four domains of Regnase-1 from Mus musculus—the N-terminal domain (NTD), PilT N-terminus like (PIN) domain, zinc finger (ZF) domain and C-terminal domain (CTD). The PIN domain harbors the RNase catalytic center; however, it is insufficient for enzymatic activity. We found that the NTD associates with the PIN domain and significantly enhances its RNase activity. The PIN domain forms a head-to-tail oligomer and the dimer interface overlaps with the NTD binding site. Interestingly, mutations blocking PIN oligomerization had no RNase activity, indicating that both oligomerization and NTD binding are crucial for RNase activity in vitro. These results suggest that Regnase-1 RNase activity is tightly controlled by both intramolecular (NTD-PIN) and intermolecular (PIN-PIN) interactions.
Vitamin D improves endothelial dysfunction and restores myeloid angiogenic cell function via reduced CXCL-10 expression in systemic lupus erythematosus
Authors: Reynolds John A. , Haque Sahena , Williamson Kate , Ray David W. , Alexander M. Yvonne , Bruce Ian N. 
Published: March 2016

AbstractPatients with systemic lupus erythematosus (SLE) have accelerated cardiovascular disease and dysfunctional endothelial repair mechanisms. Myeloid angiogenic cells (MACs), derived from circulating monocytes, augment vascular repair by paracrine secretion of pro-angiogenic factors. We observed that SLE MACs are dysfunctional and secrete pro-inflammatory cytokines. We also found that the vitamin D receptor was transiently expressed during MAC differentiation and that in vitro, calcitriol increased differentiation of monocytes into MACs in both SLE and in a model using the prototypic SLE cytokine, interferon-alpha. The active form of vitamin D (calcitriol) restored the SLE MAC phenotype towards that of healthy subjects with reduced IL-6 secretion and normalised surface marker expression. Calcitriol also augmented the angiogenic capacity of MACs via the down-regulation of CXCL-10. In SLE patients treated with cholecalciferol for 12 weeks, the improvement in endothelial function correlated with increase in serum 25(OH)D concentrations independently of disease activity. We also show that MACs were able to positively modulate eNOS expression in human endothelial cells in vitro, an effect further enhanced by calcitriol treatment of SLE MACs. The results demonstrate that vitamin D can positively modify endothelial repair mechanisms and thus endothelial function in a population with significant cardiovascular risk.
Obesity impairs lactation performance in mice by inducing prolactin resistance
Authors: Buonfiglio Daniella C. , Ramos-Lobo Angela M. , Freitas Vanessa M. , Zampieri Thais T. , Nagaishi Vanessa S. , Magalhães Magna , Cipolla-Neto Jose , Cella Nathalie , Donato Jose 
Published: March 2016

AbstractObesity reduces breastfeeding success and lactation performance in women. However, the mechanisms involved are not entirely understood. In the present study, female C57BL/6 mice were chronically exposed to a high-fat diet to induce obesity and subsequently exhibited impaired offspring viability (only 15% survival rate), milk production (33% reduction), mammopoiesis (one-third of the glandular area compared to control animals) and postpartum maternal behaviors (higher latency to retrieving and grouping the pups). Reproductive experience attenuated these defects. Diet-induced obese mice exhibited high basal pSTAT5 levels in the mammary tissue and hypothalamus and an acute prolactin stimulus was unable to further increase pSTAT5 levels above basal levels. In contrast, genetically obese leptin-deficient females showed normal prolactin responsiveness. Additionally, we identified the expression of leptin receptors specifically in basal/myoepithelial cells of the mouse mammary gland. Finally, high-fat diet females exhibited altered mRNA levels of ERBB4 and NRG1, suggesting that obesity may involve disturbances to mammary gland paracrine circuits that are critical in the control of luminal progenitor function and lactation. In summary, our findings indicate that high leptin levels are a possible cause of the peripheral and central prolactin resistance observed in obese mice which leads to impaired lactation performance.
Genetic polymorphisms in circadian negative feedback regulation genes predict overall survival and response to chemotherapy in gastric cancer patients
Authors: Qu Falin , Qiao Qing , Wang Nan , Ji Gang , Zhao Huadong , He Li , Wang Haichao , Bao Guoqiang 
Published: March 2016

AbstractCircadian negative feedback loop (CNFL) genes play important roles in cancer development and progression. To evaluate the effects of single nucleotide polymorphisms (SNPs) in CNFL genes on the survival of GC patients, 13 functional SNPs from 5 CNFL genes were genotyped in a cohort of 1030 resected GC patients (704 in the training set, 326 in the validation set) to explore the association of SNPs with overall survival (OS). Among the 13 SNPs, three SNPs (rs1056560 in CRY1, rs3027178 in PER1 and rs228729 in PER3) were significantly associated with OS of GC in the training set, and verified in the validation set and pooled analysis. Furthermore, a dose-dependent cumulative effect of these SNPs on GC survival was observed, and survival tree analysis showed higher order interactions between these SNPs. In addition, protective effect conferred by adjuvant chemotherapy (ACT) on GC was observed in patients with variant alleles (TG/GG) of rs1056560, but not in those with homozygous wild (TT) genotype. Functional assay suggested rs1056560 genotypes significantly affect CRY1 expression in cancer cells. Our study presents that SNPs in the CNFL genes may be associated with GC prognosis, and provides the guidance in selecting potential GC patients most likely responsive to ACT.
A novel approach of chemical mechanical polishing using environment-friendly slurry for mercury cadmium telluride semiconductors
Authors: Zhang Zhenyu , Wang Bo , Zhou Ping , Guo Dongming , Kang Renke , Zhang Bi 
Published: March 2016

AbstractA novel approach of chemical mechanical polishing (CMP) is developed for mercury cadmium telluride (HgCdTe or MCT) semiconductors. Firstly, fixed-abrasive lapping is used to machine the MCT wafers and the lapping solution is deionized water. Secondly, the MCT wafers are polished using the developed CMP slurry. The CMP slurry consists of mainly SiO2 nanospheres, H2O2 and malic and citric acids, which are different from previous CMP slurries, in which corrosive and toxic chemical reagents are usually employed. Finally, the polished MCT wafers are cleaned and dried by deionized water and compressed air, respectively. The novel approach of CMP is environment-friendly. Surface roughness Ra and peak-to-valley (PV) values of 0.45 and 4.74 nm are achieved, respectively on MCT wafers after CMP. The first and second passivating processes are observed in electrochemical measurements on MCT wafers. The fundamental mechanisms of CMP are proposed according to the X-ray photoelectron spectroscopy (XPS) and electrochemical measurements. Malic and citric acids dominate the first passivating process and the CMP slurry governs the second process. Te4+3d peaks are absent after CMP induced by the developed CMP slurry, indicating the removing of oxidized films on MCT wafers, which is difficult to achieve using single H2O2 and malic and citric acids solutions.
Discovering communities in complex networks by edge label propagation
Authors: Liu Wei , Jiang Xingpeng , Pellegrini Matteo , Wang Xiaofan 
Published: March 2016

AbstractThe discovery of the community structure of real-world networks is still an open problem. Many methods have been proposed to shed light on this problem, and most of these have focused on discovering node community. However, link community is also a powerful framework for discovering overlapping communities. Here we present a novel edge label propagation algorithm (ELPA), which combines the natural advantage of link communities with the efficiency of the label propagation algorithm (LPA). ELPA can discover both link communities and node communities. We evaluated ELPA on both synthetic and real-world networks, and compared it with five state-of-the-art methods. The results demonstrate that ELPA performs competitively with other algorithms.
The hGFAP-driven conditional TSPO knockout is protective in a mouse model of multiple sclerosis
Authors: Daugherty Daniel J. , Chechneva Olga , Mayrhofer Florian , Deng Wenbin 
Published: March 2016

AbstractThe mitochondrial translocator protein (TSPO) has been implicated in CNS diseases. Here, we sought to determine the specific role of TSPO in experimental autoimmune encephalomyelitis (EAE), the most studied animal model of multiple sclerosis (MS). To fundamentally elucidate the functions of TSPO, we first developed a viable TSPO knockout mouse. A conditional TSPO knockout mouse was generated by utilizing the Cre-Lox system. We generated a TSPO floxed mouse and then crossed this mouse with a Cre recombinase expressing mouse driven by the human glial fibrillary acidic protein (hGFAP) promoter. The resultant mouse was a neural linage line specific TSPO knockout. The loss of TSPO in the CNS did not result in overt developmental defects or phenotypes. The TSPO−/− mouse showed a decrease in GFAP expression, correlating with a decrease in astrogliosis in response to neural injury during EAE. This decrease in astrogliosis was also witnessed in the lessening of severity of EAE clinical scoring, indicating an in vivo functional role for TSPO in suppressing EAE. The TSPO−/− mouse could be a useful tool in better understanding the role of TSPO in CNS disease and our results implicate TSPO as a potential therapeutic target in MS.
Ageing of 100Cr6 steel: Synchrotron X-ray diffraction and dimensional analysis investigation
Authors: Lejay V. , Sidoroff C. , Le Bourlot C. , Perez M. , Dierickx P. 
Published: February 2016

Thermal ageing of 100Cr6 with different initial austenitisings was studied using the combination of synchrotron X-ray diffraction and dimensional variation measurements. Synchrotron X-ray diffraction provided the phase volume fractions and their carbon content through the analysis of the lattice parameters. Dimensional measurements were obtained in situ in a quench dilatometer also used to realise the heat treatment. The combined analysis of these data provides a better understanding of phase evolutions. For the different austenitising treatments investigated, the dimensional variations were found to be easily linked to the phase parameters measured by X-ray diffraction. This paper is part of a Themed Issue on Recent developments in bearing steels.
Martensitic transformation cracking in high carbon steels for bearings
Authors: Bai M. K. , Pang J. C. , Wang G. D. , Yi H. L. 
Published: February 2016

Cracking generates usually due to the internal stress during martensitic transformation in high carbon steels, for instance the ‘1C–1.5Cr’ bearing steels. A novel low-density ‘1.2C–1.5Cr–5Al’ alloy has been designed recently for bearing application in previous research. The effect of morphology of martensite plates on the transformation cracking has been proposed and investigated in comparison between the ‘1.2C–1.5Cr–5Al’ and ‘1C–1.5Cr’ steels in this research. Based on the mechanisms proposed, the tendency for transformation cracking in the novel alloy with more carbon addition has been discussed compared with the ‘1C–1.5Cr’ steel. This paper is part of a Themed Issue on Recent developments in bearing steels.
Demosthenes as Text: Classical Reception and British Rhetorical History
Authors: Agnew Lois 
Published: March 2016

ABSTRACT
British rhetorical theorists demonstrate a persistent interest in Demosthenes, but their interpretations of his significance reflect different understandings of rhetoric. This article uses reception theory to illuminate how British depictions of Demosthenes at different moments in history reflect writers’ values and rhetorical aims. The focus on Demosthenes as a model of rhetorical prowess becomes particularly important for nineteenth-century British theorists who conceive of rhetoric as an individualistic display of linguistic virtuosity. Viewing Demosthenes through the lens of reception history reveals the inherent instability of a disciplinary history that is not only shaped by important figures, but also constructs those figures in ways that reflect shifting scholarly values.
Do faster swimmers spend longer underwater than slower swimmers at World Championships?
Authors: Veiga Santiago , Roig Andreu , Gómez‐Ruano Miguel A. 
Published: March 2016

AbstractThe main objectives of the present research were (1) to examine the relationships between the distances travelled underwater during the start and turn segments with swimming race performance at the elite level and (2) to determine if the individualised‐distance start and turn parameters affect the overall race performance. The race parameters of the 100 and 200 m events during 2013 World Championships were measured by an innovative image‐processing system (InThePool® 2.0). Overall, 100 m race times were largely related to faster start velocities in men's breaststroke and freestyle events. Conversely, overall, 200 m race times were largely related to longer starting distances in the women's butterfly events, to longer turn distances in men's and women's backstroke and women's butterfly events and to shorter turn distances in women's freestyle events. Changes on the start or turn velocities could represent moderate time improvements in most of the 100 m events, whereas modifications on the start or turn distances (especially in the last turn) could provide elite swimmers with time improvements of practical importance on the 200 m events. The evaluation of races by individualised‐distance parameters should be provided to elite swimmers in order to decide the most appropriate race segment configuration for each event.