bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple convergent supergene evolution events in mating-type chromosomes
Authors: Branco Sara , Carpentier Fantin , Rodríguez de la Vega Ricardo C. , Badouin Hélène , Snirc Alodie , Le Prieur Stéphanie , Coelho Marco A. , de Vienne Damien M. , Hartmann Fanny E. , Begerow Dominik , Hood Michael E. , Giraud Tatiana 
Published: May 2018

AbstractConvergent adaptation provides unique insights into the predictability of evolution and ultimately into processes of biological diversification. Supergenes (beneficial gene linkage) are striking examples of adaptation, but little is known about their prevalence or evolution. A recent study on anther-smut fungi documented supergene formation by rearrangements linking two key mating-type loci, controlling pre- and post-mating compatibility. Here further high-quality genome assemblies reveal four additional independent cases of chromosomal rearrangements leading to regions of suppressed recombination linking these mating-type loci in closely related species. Such convergent transitions in genomic architecture of mating-type determination indicate strong selection favoring linkage of mating-type loci into cosegregating supergenes. We find independent evolutionary strata (stepwise recombination suppression) in several species, with extensive rearrangements, gene losses, and transposable element accumulation. We thus show remarkable convergence in mating-type chromosome evolution, recurrent supergene formation, and repeated evolution of similar phenotypes through different genomic changes.
A workflow for the integrative transcriptomic description of molecular pathology and the suggestion of normalizing compounds, exemplified by Parkinson’s disease
Authors: Hamed Mohamed , Gladbach Yvonne , Möller Steffen , Fischer Sarah , Ernst Mathias , Struckmann Stephan , Storch Alexander , Fuellen Georg 
Published: May 2018

AbstractThe volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches. We propose here a workflow for the integrative transcriptomic description of the molecular pathology in Parkinsons’s Disease (PD), including suggestions of compounds normalizing disease-induced transcriptional changes as a paradigmatic example. We integrated gene expression profiles, miRNA signatures, and publicly available regulatory databases to specify a partial model of the molecular pathophysiology of PD. Six genetic driver elements (2 genes and 4 miRNAs) and several functional network modules that are associated with PD were identified. Functional modules were assessed for their statistical significance, cellular functional homogeneity, literature evidence, and normalizing small molecules. In summary, our workflow for the joint regulatory analysis of coding and non-coding RNA, has the potential to yield clinically as well as biologically relevant information, as demonstrated here on PD data.
A direct tissue-grafting approach to increasing endogenous brown fat
Authors: Blumenfeld Nicole R. , Kang Hwan June , Fenzl Anna , Song Ziwei , Chung Janice J. , Singh Ranjodh , Johnson Roshawn , Karakecili Ayse , Feranil Jun B. , Rossen Ninna S. , Zhang Vivian , Jaggi Sahir , McCarty Bret , Bessler Steven , Schwartz Gary J. , Grant Robert , Korner Judith , Kiefer Florian W. , Gillette Brian M. , Sia Samuel K. 
Published: May 2018

AbstractThere is widespread evidence that increasing functional mass of brown adipose tissue (BAT) via browning of white adipose tissue (WAT) could potentially counter obesity and diabetes. However, most current approaches focus on administration of pharmacological compounds which expose patients to highly undesirable side effects. Here, we describe a simple and direct tissue-grafting approach to increase BAT mass through ex vivo browning of subcutaneous WAT, followed by re-implantation into the host; this cell-therapy approach could potentially act synergistically with existing pharmacological approaches. With this process, entitled “exBAT”, we identified conditions, in both mouse and human tissue, that convert whole fragments of WAT to BAT via a single step and without unwanted off-target pharmacological effects. We show that ex vivo, exBAT exhibited UCP1 immunostaining, lipid droplet formation, and mitochondrial metabolic activity consistent with native BAT. In mice, exBAT exhibited a highly durable phenotype for at least 8 weeks. Overall, these results enable a simple and scalable tissue-grafting strategy, rather than pharmacological approaches, for increasing endogenous BAT and studying its effect on host weight and metabolism.
Differential protein profiling as a potential multi-marker approach for obese patients with heart failure: A retrospective study
Authors: Timotin Andrei , Cinato Mathieu , Boal Frederic , Dejean Sebastien , Anesia Rodica , Arnaut Oleg , Lagente Christine , Roncalli Jerome , Desmoulin Franck , Tronchere Helene , Kunduzova Oksana 
Published: May 2018

AbstractIdentification of novel circulating biomarkers predicting death and major cardio-metabolic events in obese patients with heart failure (HF) remains a research priority. In this study, we compared multi-marker profile of non-obese (NOB) and obese (OB) HF patients in relation to mortality outcome. The new multiplex proximity extension assay technology was used to analyze the levels of 92 proteins in plasma samples from HF patients according to body mass index (BMI) categories. At 2-year follow-up, all-cause mortality rates were significantly greater in NOB patients (BMI < 30 kg/m2) compared to the OB patients (BMI > 30 kg/m2) with HF (odds ratio 26; 95% CI: 1.14–624, p < 0,04). Quantitative proteomic analysis revealed thirteen distinct proteins expression profiles of OB and NOB HF patients. Among these proteins, RAGE, CXCL6, CXCL1, CD40, NEMO, VEGF-A, KLK6, PECAM1, PAR1, MMP1, BNP and NTproBNP were down-regulated, whereas leptin was up-regulated in OB HF patients. In addition, an inverse correlation between plasma BNP levels and leptin in OB HF patients was observed (r = −0.58 p = 0.02). This study identifies specific plasma protein signature in OB and NOB patients with HF in relation to mortality outcome.
Statistical machine learning of sleep and physical activity phenotypes from sensor data in 96,220 UK Biobank participants
Authors: Willetts Matthew , Hollowell Sven , Aslett Louis , Holmes Chris , Doherty Aiden 
Published: May 2018

AbstractCurrent public health guidelines on physical activity and sleep duration are limited by a reliance on subjective self-reported evidence. Using data from simple wrist-worn activity monitors, we developed a tailored machine learning model, using balanced random forests with Hidden Markov Models, to reliably detect a number of activity modes. We show that physical activity and sleep behaviours can be classified with 87% accuracy in 159,504 minutes of recorded free-living behaviours from 132 adults. These trained models can be used to infer fine resolution activity patterns at the population scale in 96,220 participants. For example, we find that men spend more time in both low- and high- intensity behaviours, while women spend more time in mixed behaviours. Walking time is highest in spring and sleep time lowest during the summer. This work opens the possibility of future public health guidelines informed by the health consequences associated with specific, objectively measured, physical activity and sleep behaviours.
Extremely Low Frequency Electromagnetic Fields impair the Cognitive and Motor Abilities of Honey Bees
Authors: Shepherd S. , Lima M. A. P. , Oliveira E. E. , Sharkh S. M. , Jackson C. W. , Newland P. L. 
Published: May 2018

AbstractExtremely low frequency electromagnetic field (ELF EMF) pollution from overhead powerlines is known to cause biological effects across many phyla, but these effects are poorly understood. Honey bees are important pollinators across the globe and due to their foraging flights are exposed to relatively high levels of ELF EMF in proximity to powerlines. Here we ask how acute exposure to 50 Hz ELF EMFs at levels ranging from 20–100 µT, found at ground level below powerline conductors, to 1000–7000 µT, found within 1 m of the conductors, affects honey bee olfactory learning, flight, foraging activity and feeding. ELF EMF exposure was found to reduce learning, alter flight dynamics, reduce the success of foraging flights towards food sources, and feeding. The results suggest that 50 Hz ELF EMFs emitted from powerlines may represent a prominent environmental stressor for honey bees, with the potential to impact on their cognitive and motor abilities, which could in turn reduce their ability to pollinate crops.
Genome-wide association study identified new susceptible genetic variants in HLA class I region for hepatitis B virus-related hepatocellular carcinoma
Authors: Sawai Hiromi , Nishida Nao , Khor Seik-Soon , Honda Masao , Sugiyama Masaya , Baba Natsumi , Yamada Kayoko , Sawada Norie , Tsugane Shoichiro , Koike Kazuhiko , Kondo Yuji , Yatsuhashi Hiroshi , Nagaoka Shinya , Taketomi Akinobu , Fukai Moto , Kurosaki Masayuki , Izumi Namiki , Kang Jong-Hon , Murata Kazumoto , Hino Keisuke , Nishina Sohji , Matsumoto Akihiro , Tanaka Eiji , Sakamoto Naoya , Ogawa Koji , Yamamoto Kazuhide , Tamori Akihiro , Yokosuka Osamu , Kanda Tatsuo , Sakaida Isao , Itoh Yoshito , Eguchi Yuichiro , Oeda Satoshi , Mochida Satoshi , Yuen Man-Fung , Seto Wai-Kay , Poovorawan Yong , Posuwan Nawarat , Mizokami Masashi , Tokunaga Katsushi 
Published: May 2018

AbstractWe have performed a genome-wide association study (GWAS) including 473 Japanese HBV (hepatitis B virus)-positive HCC (hepatocellular carcinoma) patients and 516 HBV carriers including chronic hepatitis and asymptomatic carrier individuals to identify new host genetic factors associated with HBV-derived HCC in Japanese and other East Asian populations. We identified 65 SNPs with P values < 10−4 located within the HLA class I region and three SNPs were genotyped in three independent population-based replication sets. Meta-analysis confirmed the association of the three SNPs (rs2523961: OR = 1.73, P = 7.50 × 10−12; rs1110446: OR = 1.79, P = 1.66 × 10−13; and rs3094137: OR = 1.73, P = 7.09 × 10−9). We then performed two-field HLA genotype imputation for six HLA loci using genotyping data to investigate the association between HLA alleles and HCC. HLA allele association testing revealed that HLA-A
*
33:03 (OR = 1.97, P = 4.58 × 10−4) was significantly associated with disease progression to HCC. Conditioning analysis of each of the three SNPs on the HLA class I region abolished the association of HLA-A*33:03 with disease progression to HCC. However, conditioning the HLA allele could not eliminate the association of the three SNPs, suggesting that additional genetic factors may exist in the HLA class I region.
Allergy immunotherapy restores airway epithelial barrier dysfunction through suppressing IL-25 -induced endoplasmic reticulum stress in asthma
Authors: Yuan Xiefang , Wang Junyi , Li Yin , He Xiang , Niu Bin , Wu Dehong , lan Nan , Wang Xiaoyun , Zhang Yun , Dai Xi , Wang Xing , Liu Zhigang , Li Guoping 
Published: May 2018

AbstractConstant exposure to allergen triggers destructive type 2 cell-mediated inflammation. The effect of allergen specific immunotherapy (SIT) in maintaining airway epithelial barrier function in asthma remains unknown. In the current study, we showed that SIT maintained airway epithelial homeostasis in mice exposed to dermatophagoides farinae (Der f), which induced increased expression of IL-25, endoplasmic reticulum (ER) stress and airway epithelial apoptosis. Meanwhile, SIT treatment ameliorated airway inflammatory infiltration and hyper-responsiveness in allergic mice. SIT treatment restored the airway epithelial integrity, attenuated Der f -induced airway epithelial ER stress and epithelial apoptosis. We also found that 4-PBA, an inhibitor of ER stress, suppressed airway epithelial ER stress and apoptosis in vitro. The pathological changes were partially induced by IL-25-induced ER stress, epithelial tight junction damage, and cell apoptosis in airways following allergen exposure. Furthermore, IL-25 induced ER stress in airway epithelial cells in vitro. The IL-25-induced airway epithelial apoptosis dependent on PERK activity was inhibited by 4-PBA. Taken together, we demonstrate that SIT is effective in allergic asthma and dependent on its depressive effect on the expression of IL-25, epithelial integrity damage, and epithelial ER stress.
Commercially Available Natural Benzyl Esters and Their Synthetic Analogs Exhibit Different Toxicities against Insect Pests
Authors: Feng Yan , Chen Jian , Zhang Aijun 
Published: May 2018

AbstractBenzyl methyl ester, also known as methyl benzoate (MB), is a volatile organic compound that exists naturally as a floral fragrance in many plants. Our behavioral bioassays show that MB and some of its naturally occurring and synthetic analogs kill insects at different life stages. Compared to commercial pesticides containing pyriproxyfen and acetamiprid, MB and some analogs are 1.3 to 3.4 times more toxic to gypsy moth larvae and brown marmorated stinkbug nymphs. The arthropod repellent DEET is also a benzyl ester, and shares the same chemical skeleton with MB. They differ by the diethylamide ester and a methyl group on the benzene ring in DEET. However, unlike MB, DEET does not kill insects; instead, it deters or repels them. Exactly how DEET causes the repellent effect in target organisms is still a mystery. Due to the MB’s structural similarity to DEET, exploring the structure – activity relationship (SAR) of the MB analogs will provide useful information for the discovery of the mode and mechanistic actions of DEET as an insect repellent. In addition, the SAR will allow researchers to modify the chemical structure of the MB molecule, leading to the development of more efficient, safe, and environmentally – friendly green pesticides.
Dependences of microstructure on electromagnetic interference shielding properties of nano-layered Ti3AlC2 ceramics
Authors: Tan Yongqiang , Luo Heng , Zhou Xiaosong , Peng Shuming , Zhang Haibin 
Published: May 2018

AbstractThe microstructure dependent electromagnetic interference (EMI) shielding properties of nano-layered Ti3AlC2ceramics were presented in this study by comparing the shielding properties of various Ti3AlC2ceramics with distinct microstructures. Results indicate that Ti3AlC2ceramics with dense microstructure and coarse grains are more favourable for superior EMI shielding efficiency. High EMI shielding effectiveness over 40 dB at the whole Ku-band frequency range was achieved in Ti3AlC2ceramics by microstructure optimization, and the high shielding effectiveness were well maintained up to 600 °C. A further investigation reveals that only the absorption loss displays variations upon modifying microstructure by allowing more extensive multiple reflections in coarse layered grains. Moreover, the absorption loss of Ti3AlC2was found to be much higher than those of highly conductive TiC ceramics without layered structure. These results demonstrate that nano-layered MAX phase ceramics are promising candidates of high-temperature structural EMI shielding materials and provide insightful suggestions for achieving high EMI shielding efficiency in other ceramic-based shielding materials.
Fabrication of aluminum alloy functionally graded material using directional solidification under an axial static magnetic field
Authors: Hu Shaodong , Gagnoud Annie , Fautrelle Yves , Moreau Rene , Li Xi 
Published: May 2018

AbstractAluminum alloy in situ functionally graded materials (FGMs) have been successfully fabricated using directional solidification under an axial static magnetic field. Al-Zn, Al-Ni and Al-Cu alloys with a hypereutectic composition were selected to produce FGMs. Experimental results show that the graded composition of the primary phases (i.e., Zn, Al3Ni and Al2Cu) is obvious along the longitudinal section of the sample. The graded composition of the primary phases could be controlled by the value of the magnetic field, growth rate and temperature gradient. A proposed model and simulations are carried out to explain the origin of the graded composition of the primary phases in FGMs during directional solidification under an axial static magnetic field. It should be attributed to the combined actions of heavier species migration under gravity force and thermoelectric (TE) magnetic convection under magnetic field. Furthermore, it can be found that the magnetic field can induce the columnar FGMs to change into equiaxed FGMs. This work not only presents a new approach to fabricate FGMs using the directional solidification under an axial static magnetic field but also deeply understands the effect of the solute migration and temperature distribution on the crystal growth during directional solidification.
Real-time precise point positioning-based zenith tropospheric delay for precipitation forecasting
Authors: Zhao Qingzhi , Yao Yibin , Yao Wanqiang , Li Zufeng 
Published: May 2018

AbstractGPS-based Zenith Tropospheric Delay (ZTD) estimation should be easily obtained in a cost-effective way, however, the most previous studies focus on post-processed ZTD estimates using satellite orbit and clock products with at least 3–9 hours latency provided by International GNSS Service (IGS), which limits the GNSS meteorological application for nowcasting. With the development of IGS’s real-time pilot project (RTPP), this limitation was removed by April, 2013 as real-time satellite orbit and clock products can be obtained on-line. In this paper, on the one hand, the GPS-derived ZTD estimation was evaluated using the IGS final and real-time satellite products based on independently developed PPP software. On the other hand, the analysis of the time series of GPS-derived ZTD by least-square fitting of a broken line tendency for a full year of observations, and a forecasting method for precipitation is proposed based on the ZTD slope in the ascending period. The agreement between ZTD slope and the ground rainfall records suggested that the proposed method is useful for the assisted forecasting, especially for short-term alarms.
The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression
Authors: Sen Onur , Saurin Adrian T. , Higgins Jonathan M. G. 
Published: May 2018

AbstractSiR-Hoechst (SiR-DNA) is a far-red fluorescent DNA probe being used widely for time-lapse imaging of living cells that is reported to be minimally toxic at concentrations as high as 10–25 µM. However, measuring nuclear import of Cyclin B1, inhibition of mitotic entry, and the induction of γH2AX foci in cultured human cells reveals that SiR-Hoechst induces DNA damage responses and G2 arrest at concentrations well below 1 µM. SiR-Hoechst is useful for live cell imaging, but it should be used with caution and at the lowest practicable concentration.
Effect of Plant Density, Boron Nutrition and Growth Regulation on Seed Mass, Emergence and Offspring Growth Plasticity in Cotton
Authors: Zohaib Ali , Tabassum Tahira , Jabbar Abdul , Anjum Shakeel Ahmad , Abbas Tasawer , Mehmood Azhar , Irshad Sohail , Kashif Muhammad , Nawaz Mohsin , Farooq Naila , Nasir Irfan Rasool , Rasool Tassadduq , Nadeem Mubashar , Ahmad Riaz 
Published: May 2018

AbstractSeed nutrients reserves have direct relationship with seed functional traits and influence offspring performance. Effects of plant density, foliage boron (B) nutrition and mepiquat chloride (MC) growth regulation on seed nutrients reserves, seed mass and production, and emergence and offspring growth traits of cotton were studied in two years field experiment. Seed nutrients reserves and seed mass were decreased at higher maternal plant density relative to lower plant density with concomitant decrease in emergence and offspring seedling growth. However, maternal foliage B nutrition and MC growth regulation enhanced seed nutrients reserves, seed mass, emergence and offspring seedling growth performance. There was a significant positive relationship between seed mass and seed nutrients reserves indicating that changes in nutrient availability/uptake in response to maternal ecological factors determine variation in seed functional traits. Nonetheless, seed mass was positively correlated with emergence percentage and negatively with emergence timing. Furthermore, variation in offspring seedling growth traits with seed mass indicated the significance of initial seed nutrients reserves for early seedling vigour and establishment. In conclusion, lower maternal plant density, B nutrition and MC growth regulation ensued in higher emergence and offspring seedling growth of cotton because of higher seed nutrient reserves and seed mass.
Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid
Authors: Isobe Yosuke , Itagaki Mai , Ito Yuko , Naoe Satoko , Kojima Kotoe , Ikeguchi Mitsunori , Arita Makoto 
Published: May 2018

AbstractMetabolites generated via oxygenation of the omega-3 double bond (omega-3 oxygenation) in eicosapentaenoic acid (EPA) have recently been identified as novel anti-inflammatory lipid mediators. Therefore, oxygenase(s) responsible for this metabolic pathway are of particular interest. We performed genome-wide screening of mouse cytochrome P450 (CYP) isoforms to explore enzymes involved in omega-3 oxygenation of EPA. As a result, 5 CYP isoforms (mouse Cyp1a2, 2c50, 4a12a, 4a12b, and 4f18) were selected and identified to confer omega-3 epoxidation of EPA to yield 17,18-epoxyeicosatetraenoic acid (17,18-EpETE). Stereoselective production of 17,18-EpETE by each CYP isoform was confirmed, and molecular modeling indicated that chiral differences stem from different EPA binding conformations in the catalytic domains of respective CYP enzymes.
Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota
Authors: Chalermwatanachai Thanit , Vilchez-Vargas Ramiro , Holtappels Gabriele , Lacoere Tim , Jáuregui Ruy , Kerckhof Frederiek-Maarten , Pieper Dietmar H. , Van de Wiele Tom , Vaneechoutte Mario , Van Zele Thibaut , Bachert Claus 
Published: May 2018

AbstractChronic rhinosinusitis with nasal polyp (CRSwNP) patients are often characterized by asthma comorbidity and a type-2 inflammation of the sinonasal mucosa. The mucosal microbiota has been suggested to be implicated in the persistence of inflammation, but associations have not been well defined. To compare the bacterial communities of healthy subjects with CRSwNP patients, we collected nasal swabs from 17 healthy subjects, 21 CRSwNP patients without asthma (CRSwNP−A), and 20 CRSwNP patients with co-morbid asthma (CRSwNP+A). We analysed the microbiota using high-throughput sequencing of the bacterial 16S rRNA. Bacterial communities were different between the three groups. Haemophilus influenzae was significantly enriched in CRSwNP patients, Propionibacterium acnes in the healthy group; Staphylococcus aureus was abundant in the CRSwNP−A group, even though present in 57% of patients. Escherichia coli was found in high amounts in CRSwNP+A patients. Nasal tissues of CRSwNP+A patients expressed significantly higher concentrations of IgE, SE-IgE, and IL-5 compared to those of CRSwNP−A patients. Co-cultivation demonstrated that P. acnes growth was inhibited by H. influenzae, E. coli and S. aureus. The nasal microbiota of healthy subjects are different from those of CRSwNP−A and CRSwNP+A patients. However, the most abundant species in healthy status could not inhibit those in CRSwNP disease.