bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oxygen depletion recorded in upper waters of the glacial Southern Ocean
Authors: Lu Zunli , Hoogakker Babette A. A. , Hillenbrand Claus-Dieter , Zhou Xiaoli , Thomas Ellen , Gutchess Kristina M. , Lu Wanyi , Jones Luke , Rickaby Rosalind E. M. 
Published: March 2016

AbstractOxygen depletion in the upper ocean is commonly associated with poor ventilation and storage of respired carbon, potentially linked to atmospheric CO2 levels. Iodine to calcium ratios (I/Ca) in recent planktonic foraminifera suggest that values less than ∼2.5 μmol mol−1 indicate the presence of O2-depleted water. Here we apply this proxy to estimate past dissolved oxygen concentrations in the near surface waters of the currently well-oxygenated Southern Ocean, which played a critical role in carbon sequestration during glacial times. A down-core planktonic I/Ca record from south of the Antarctic Polar Front (APF) suggests that minimum O2 concentrations in the upper ocean fell below 70 μmol kg−1 during the last two glacial periods, indicating persistent glacial O2 depletion at the heart of the carbon engine of the Earth’s climate system. These new estimates of past ocean oxygenation variability may assist in resolving mechanisms responsible for the much-debated ice-age atmospheric CO2 decline.
Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system
Authors: Speth Daan R. , in ’t Zandt Michiel H. , Guerrero-Cruz Simon , Dutilh Bas E. , Jetten Mike S. M. 
Published: March 2016

AbstractPartial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.
Identification of chemicals that mimic transcriptional changes associated with autism, brain aging and neurodegeneration
Authors: Pearson Brandon L. , Simon Jeremy M. , McCoy Eric S. , Salazar Gabriela , Fragola Giulia , Zylka Mark J. 
Published: March 2016

AbstractEnvironmental factors, including pesticides, have been linked to autism and neurodegeneration risk using retrospective epidemiological studies. Here we sought to prospectively identify chemicals that share transcriptomic signatures with neurological disorders, by exposing mouse cortical neuron-enriched cultures to hundreds of chemicals commonly found in the environment and on food. We find that rotenone, a pesticide associated with Parkinson’s disease risk, and certain fungicides, including pyraclostrobin, trifloxystrobin, famoxadone and fenamidone, produce transcriptional changesin vitrothat are similar to those seen in brain samples from humans with autism, advanced age and neurodegeneration (Alzheimer’s disease and Huntington’s disease). These chemicals stimulate free radical production and disrupt microtubules in neurons, effects that can be reduced by pretreating with a microtubule stabilizer, an antioxidant, or with sulforaphane. Our study provides an approach to prospectively identify environmental chemicals that transcriptionally mimic autism and other brain disorders.
Osteosarcoma: prognosis plateau warrants retinoblastoma pathway targeted therapy
Authors: Ballatori Sarah E , Hinds Philip W 
Published: March 2016

AbstractOsteosarcoma (OS) is the most common primary bone cancer in children and adolescents, affecting ~560 young patients in the United States annually. The term OS describes a diverse array of subtypes with varying prognoses, but the majority of tumors are high grade and aggressive. Perhaps because the true etiology of these aggressive tumors remains unknown, advances in OS treatment have reached a discouraging plateau, with only incremental improvements over the past 40 years. Thus, research surrounding the pathogenesis of OS is essential, as it promises to unveil novel therapeutic targets that can attack tumor cells with greater specificity and lower toxicity. Among the candidate molecular targets in OS, the retinoblastoma (RB) pathway demonstrates the highest frequency of inactivation and thus represents a particularly promising avenue for molecular targeted therapy. This review examines the present thinking and practices in OS treatment and specifically highlights the relevance of the RB pathway in osteosarcomagenesis. Through further investigation into RB pathway-related novel therapeutic targets, we believe that a near-term breakthrough in improved OS prognosis is possible.
The influence of polymer purification on the efficiency of poly(3-hexylthiophene):fullerene organic solar cells
Authors: Bannock James H. , Treat Neil D. , Chabinyc Michael , Stingelin Natalie , Heeney Martin , de Mello John C. 
Published: March 2016

AbstractWe report the influence of different polymer purification procedures on the photovoltaic performance of bulk heterojunction solar cells formed from binary blends of poly(3-hexylthiophene) (P3HT) and fullerenes. Selective Soxhlet extractions and metal scavenging agents were used to remove residual monomer, magnesium salt by-products and catalyst from high-weight P3HT (Mw 121 kg/mol, PDI 1.8, RR 99%) synthesised by the Grignard metathesis (GRIM) polymerization route. Using phenyl-C61-butyric acid methyl ester (PC60BM) as an electron acceptor, we observed an increase in average power conversion efficiency from 2.3 to 4.8% in going from crude to fully purified material. Using indene-C60 bisadduct (IC60BA) in place of PC60BM, we observed a further increase to an average value of 6.6% - high for a bulk heterojunction formed from a binary blend of P3HT and C60 fullerene derivatives.
Structure Based Docking and Molecular Dynamic Studies of Plasmodial Cysteine Proteases against a South African Natural Compound and its Analogs
Authors: Musyoka Thommas M. , Kanzi Aquillah M. , Lobb Kevin A. , Tastan Bishop Özlem 
Published: March 2016

AbstractIdentification of potential drug targets as well as development of novel antimalarial chemotherapies with unique mode of actions due to drug resistance by Plasmodium parasites are inevitable. Falcipains (falcipain-2 and falcipain-3) of Plasmodium falciparum, which catalyse the haemoglobin degradation process, are validated drug targets. Previous attempts to develop peptide based drugs against these enzymes have been futile due to the poor pharmacological profiles and susceptibility to degradation by host enzymes. This study aimed to identify potential non-peptide inhibitors against falcipains and their homologs from other Plasmodium species. Structure based virtual docking approach was used to screen a small non-peptidic library of natural compounds from South Africa against 11 proteins. A potential hit, 5α-Pregna-1,20-dien-3-one (5PGA), with inhibitory activity against plasmodial proteases and selectivity on human cathepsins was identified. A 3D similarity search on the ZINC database using 5PGA identified five potential hits based on their docking energies. The key interacting residues of proteins with compounds were identified via molecular dynamics and free binding energy calculations. Overall, this study provides a basis for further chemical design for more effective derivatives of these compounds. Interestingly, as these compounds have cholesterol-like nuclei, they and their derivatives might be well tolerated in humans.
Dynamic in situ observation of voltage-driven repeatable magnetization reversal at room temperature
Authors: Gao Ya , Hu Jia-Mian , Nelson C. T. , Yang T. N. , Shen Y. , Chen L. Q. , Ramesh R. , Nan C. W. 
Published: March 2016

AbstractPurely voltage-driven, repeatable magnetization reversal provides a tantalizing potential for the development of spintronic devices with a minimum amount of power consumption. Substantial progress has been made in this subject especially on magnetic/ferroelectric heterostructures. Here, we report the in situ observation of such phenomenon in a NiFe thin film grown directly on a rhombohedral Pb(Mg1/3Nb2/3)0.7Ti0.3O3(PMN-PT) ferroelectric crystal. Under a cyclic voltage applied perpendicular to the PMN-PT without a magnetic field, the local magnetization of NiFe can be repetitively reversed through an out-of-plane excursion and then back into the plane. Using phase field simulations we interpret magnetization reversal as a synergistic effect of the metastable ferroelastic switching in the PMN-PT and an electrically rotatable local exchange bias field arising from the heterogeneously distributed NiO clusters at the interface.
Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses
Authors: Shankar Rama , Bhattacharjee Annapurna , Jain Mukesh 
Published: March 2016

AbstractDrought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.
Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes
Authors: Lee JunMo , Kim Kyeong Mi , Yang Eun Chan , Miller Kathy Ann , Boo Sung Min , Bhattacharya Debashish , Yoon Hwan Su 
Published: March 2016

AbstractThe integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.
Anti-Müllerian hormone: a new actor of sexual dimorphism in pituitary gonadotrope activity before puberty
Authors: Garrel Ghislaine , Racine Chrystèle , L’Hôte David , Denoyelle Chantal , Guigon Céline J. , di Clemente Nathalie , Cohen-Tannoudji Joëlle 
Published: March 2016

AbstractAnti-Müllerian hormone (AMH) contributes to male sexual differentiation and acts on gonads of both sexes. Identification of AMH receptivity in both pituitary and brain has led to the intriguing idea that AMH participates to the hypothalamic-pituitary control of reproduction, however in vivo experimental evidence is still lacking. We show that AMH stimulates secretion and pituitary gene expression of the gonadotropin FSH in vivo in rats. AMH action is sex-dependent, being restricted to females and occurring before puberty. Accordingly, we report higher levels of pituitary AMH receptor transcripts in immature females. We show that AMH is functionally coupled to the Smad pathway in LβT2 gonadotrope cells and dose-dependently increases Fshb transcript levels. Furthermore, AMH was shown to establish complex interrelations with canonical FSH regulators as it cooperates with activin to induce Fshb expression whereas it reduces BMP2 action. We report that GnRH interferes with AMH by decreasing AMH receptivity in vivo in females. Moreover, AMH specifically regulates FSH and not LH, indicating that AMH is a factor contributing to the differential regulation of gonadotropins. Overall, our study uncovers a new role for AMH in regulating gonadotrope function and suggests that AMH participates in the postnatal elevation of FSH secretion in females.
Long-term Changes in Extreme Air Pollution Meteorology and the Implications for Air Quality
Authors: Hou Pei , Wu Shiliang 
Published: March 2016

AbstractExtreme air pollution meteorological events, such as heat waves, temperature inversions and atmospheric stagnation episodes, can significantly affect air quality. Based on observational data, we have analyzed the long-term evolution of extreme air pollution meteorology on the global scale and their potential impacts on air quality, especially the high pollution episodes. We have identified significant increasing trends for the occurrences of extreme air pollution meteorological events in the past six decades, especially over the continental regions. Statistical analysis combining air quality data and meteorological data further indicates strong sensitivities of air quality (including both average air pollutant concentrations and high pollution episodes) to extreme meteorological events. For example, we find that in the United States the probability of severe ozone pollution when there are heat waves could be up to seven times of the average probability during summertime, while temperature inversions in wintertime could enhance the probability of severe particulate matter pollution by more than a factor of two. We have also identified significant seasonal and spatial variations in the sensitivity of air quality to extreme air pollution meteorology.
Bioengineering of Tobacco Mosaic Virus to Create a Non-Infectious Positive Control for Ebola Diagnostic Assays
Authors: Lam Patricia , Gulati Neetu M. , Stewart Phoebe L. , Keri Ruth A. , Steinmetz Nicole F. 
Published: March 2016

AbstractThe 2014 Ebola epidemic is the largest to date. There is no cure or treatment for this deadly disease; therefore there is an urgent need to develop new diagnostics to accurately detect Ebola. Current RT-PCR assays lack sensitive and reliable positive controls. To address this critical need, we devised a bio-inspired positive control for use in RT-PCR diagnostics: we encapsulated scrambled Ebola RNA sequences inside of tobacco mosaic virus to create a biomimicry that is non-infectious, but stable and could therefore serve as a positive control in Ebola diagnostic assays. Here, we report the bioengineering and validation of this probe.
Clinical spectrum and survival analysis of 145 cases of HIV-negative Castleman’s disease: renal function is an important prognostic factor
Authors: Zhang Lu , Li Zhiyuan , Cao Xinxin , Feng Jun , Zhong Dingrong , Wang Shujie , Zhou Daobin , Li Jian 
Published: March 2016

AbstractCastleman’s disease (CD) is a rare lymphoproliferative disorder with clinical features and prognostic factors that are incompletely characterized. This retrospective single-center study reviewed the largest HIV-negative CD patient cohort (n = 145) to date. By clinical classification, we identified 69 patients (47.6%) as unicentric CD (UCD) and 76 patients (52.4%) as multicentric CD (MCD). Pathological classification identified 74 patients (51.0%) with the hyaline-vascular variant, 51 patients (35.2%) with the plasma-cell variant and 20 patients (13.8%) with a mixed variant. After a median follow-up duration of 58 months (range, 1–180 months), the 1-year and 5-year survival rates were 95.1% and 91.0%, respectively. UCD patients exhibited significantly better survival (1-year and 5-year survival rates of 98.5% and 97.1%, respectively) compared with MCD patients (1-year and 5-year survival rates of 92.1% and 85.5%, respectively; p = 0.005). By univariate and multivariate Cox regression analyses, the estimated glomerular filtration rate < 60 ml/min (with the MDRD equation; hazard ratio = 4.60; 95% confidence interval, 1.50–14.12; p = 0.008) was clinically significant and represented an independent predictor for death in MCD patients. In summary, this large-scale study suggests that UCD patients enjoy better survival than MCD patients and that renal function is an important prognostic factor for MCD patients.
Single crystalline cylindrical nanowires – toward dense 3D arrays of magnetic vortices
Authors: Ivanov Yurii P. , Chuvilin Andrey , Vivas Laura G. , Kosel Jurgen , Chubykalo-Fesenko Oksana , Vázquez Manuel 
Published: March 2016

AbstractMagnetic vortex-based media have recently been proposed for several applications of nanotechnology; however, because lithography is typically used for their preparation, their low-cost, large-scale fabrication is a challenge. One solution may be to use arrays of densely packed cobalt nanowires that have been efficiently fabricated by electrodeposition. In this work, we present this type of nanoscale magnetic structures that can hold multiple stable magnetic vortex domains at remanence with different chiralities. The stable vortex state is observed in arrays of monocrystalline cobalt nanowires with diameters as small as 45 nm and lengths longer than 200 nm with vanishing magnetic cross talk between closely packed neighboring wires in the array. Lorentz microscopy, electron holography and magnetic force microscopy, supported by micromagnetic simulations, show that the structure of the vortex state can be adjusted by varying the aspect ratio of the nanowires. The data we present here introduce a route toward the concept of 3-dimensional vortex-based magnetic memories.
Prevalence and Risk Factors of Carotid Plaque Among Middle-aged and Elderly Adults in Rural Tianjin, China
Authors: Zhan Changqing , Shi Min , Yang Ying , Pang Hongbo , Fei Shizao , Bai Lingling , Liu Bin , Tu Jun , Huo Yong , Ning Xianjia , Zhang Yan , Wang Jinghua 
Published: March 2016

AbstractCarotid plaque (CP) is associated with cardiovascular and cerebrovascular events. However, population-based studies with a large sample are rare in China, particularly those in the low-income population. We aimed to determine the prevalence of CP and the associated risk factors in the rural areas of northern China. Between April 2014 and June 2014, we recruited 3789 residents aged ≥45 years. B-mode ultrasonography was performed to measure the extent of CP. The prevalence of CP was 40.3% overall, 47.1% in men and 35.4% in women (P < 0.001). The prevalence of CP increased with increasing age (P < 0.001). The participants with CP were more likely to have hypertension, diabetes, high total cholesterol (TC) levels and high low-density lipoprotein-cholesterol levels and be a current smoker; however, they were less likely to be obese. Multiple logistic regression analysis, adjusted for confounders, indicated that age, male sex, hypertension, diabetes, current smoking and high LDL-C levels were the independent risk factors for CP. There was a lower risk of CP with alcohol consumption. The findings suggest that managing the conventional risk factors is crucial to reduce the burden of cardiovascular and cerebrovascular diseases in the low-income population in China.
Functional brain networks associated with eating behaviors in obesity
Authors: Park Bo-yong , Seo Jongbum , Park Hyunjin 
Published: March 2016

AbstractObesity causes critical health problems including diabetes and hypertension that affect billions of people worldwide. Obesity and eating behaviors are believed to be closely linked but their relationship through brain networks has not been fully explored. We identified functional brain networks associated with obesity and examined how the networks were related to eating behaviors. Resting state functional magnetic resonance imaging (MRI) scans were obtained for 82 participants. Data were from an equal number of people of healthy weight (HW) and non-healthy weight (non-HW). Connectivity matrices were computed with spatial maps derived using a group independent component analysis approach. Brain networks and associated connectivity parameters with significant group-wise differences were identified and correlated with scores on a three-factor eating questionnaire (TFEQ) describing restraint, disinhibition, and hunger eating behaviors. Frontoparietal and cerebellum networks showed group-wise differences between HW and non-HW groups. Frontoparietal network showed a high correlation with TFEQ disinhibition scores. Both frontoparietal and cerebellum networks showed a high correlation with body mass index (BMI) scores. Brain networks with significant group-wise differences between HW and non-HW groups were identified. Parts of the identified networks showed a high correlation with eating behavior scores.
Recombination spot identification Based on gapped k-mers
Authors: Wang Rong , Xu Yong , Liu Bin 
Published: March 2016

AbstractRecombination is crucial for biological evolution, which provides many new combinations of genetic diversity. Accurate identification of recombination spots is useful for DNA function study. To improve the prediction accuracy, researchers have proposed several computational methods for recombination spot identification. k-mer is one of the commonly used features for recombination spot identification. However, when the value of k grows larger, the dimension of the corresponding feature vectors increases rapidly, leading to extremely sparse vectors. In order to overcome this disadvantage, recently a new feature called gapped k-mer was proposed (Ghandi et al., PloS Computational Biology, 2014). That study showed that the gapped k-mer feature can improve the predictive performance of regulatory sequence prediction. Motived by its success, in this study we applied gapped k-mer to the field of recombination spot identification, and a computational predictor was constructed. Experimental results on a widely used benchmark dataset showed that this predictor outperformed other highly related predictors.