bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct conversion of CO and H2O into liquid fuels under mild conditions
Authors: Xu Yao , Li Jing , Li Wenjing , Li Weizhen , Zhang Xiaochen , Zhao Yue , Xie Jinglin , Wang Xiaoping , Liu Xi , Li Yongwang , Xiao Dequan , Yin Zhen , Cao Yong , Ma Ding 
Published: March 2019

AbstractAlthough enormous progress has been made in C1 chemistry and CO2 conversion in recent years, it is still a challenge to develop new carbon resource transformation protocols especially those lead to the production of liquid fuels with high selectivity under mild conditions (e.g., under low temperature and using benign solvent). Herein, we present a novel and energy-efficient catalytic route to directly transform CO and H2O to liquid fuels (i.e., liquid hydrocarbons) at low temperature (≤200 °C) in aqueous phase (i.e., in a benign solvent), in which H2O served as both hydrogen source and solvent for the liquid fuel production. The key to the catalytic process is the construction of a highly efficient tandem catalyst Pt-Mo2C/C + Ru/C, which can directly convert CO and H2O in aqueous phase to liquid hydrocarbons with a production rate of 8.7 mol-CH2- molRu−1 h−1 and selectivity up to 68.4% of C5+ hydrocarbons at 200 °C.
The Parkinson’s phenome—traits associated with Parkinson’s disease in a broadly phenotyped cohort
Authors: Heilbron Karl , Noyce Alastair J. , Fontanillas Pierre , Alipanahi Babak , Nalls Mike A. ,   The 23andMe Research Team, Agee M. , Auton A. , Bell R. K. , Bryc K. , Elson S. L. , Furlotte N. A. , Hinds D. A. , McCreight J. C. , Huber K. E. , Kleinman A. , Litterman N. K. , McIntyre M. H. , Mountain J. L. , Noblin E. S. , Northover C. A. M. , Pitts S. J. , Sathirapongsasuti J. F. , Sazonova O. V. , Shelton J. F. , Shringarpure S. , Tian C. , Tung J. Y. , Vacic V. , Wilson C. H. , Cannon Paul 
Published: March 2019

AbstractIn order to systematically describe the Parkinson’s disease phenome, we performed a series of 832 cross-sectional case-control analyses in a large database. Responses to 832 online survey-based phenotypes including diseases, medications, and environmental exposures were analyzed in 23andMe research participants. For each phenotype, survey respondents were used to construct a cohort of Parkinson’s disease cases and age-matched and sex-matched controls, and an association test was performed using logistic regression. Cohorts included a median of 3899 Parkinson’s disease cases and 49,808 controls, all of European ancestry. Highly correlated phenotypes were removed and the novelty of each significant association was systematically assessed (assigned to one of four categories: known, likely, unclear, or novel). Parkinson’s disease diagnosis was associated with 122 phenotypes. We replicated 27 known associations and found 23 associations with a strong a priori link to a known association. We discovered 42 associations that have not previously been reported. Migraine, obsessive-compulsive disorder, and seasonal allergies were associated with Parkinson’s disease and tend to occur decades before the typical age of diagnosis for Parkinson’s disease. The phenotypes that currently comprise the Parkinson’s disease phenome have mostly been explored in relatively small purpose-built studies. Using a single large dataset, we have successfully reproduced many of these established associations and have extended the Parkinson’s disease phenome by discovering novel associations. Our work paves the way for studies of these associated phenotypes that explore shared molecular mechanisms with Parkinson’s disease, infer causal relationships, and improve our ability to identify individuals at high-risk of Parkinson’s disease.
Genome sequence and transcriptomic profiles of a marine bacterium, Pseudoalteromonas agarivorans Hao 2018
Authors: Shan Kai , Wang Chunlei , Liu Wenlin , Liu Kai , Jia Baolei , Hao Lujiang 
Published: March 2019

AbstractMembers of the marine genus Pseudoalteromonas have attracted great interest because of their ability to produce a large number of biologically active substances. Here, we report the complete genome sequence of Pseudoalteromonas agarivorans Hao 2018, a strain isolated from an abalone breeding environment, using second-generation Illumina and third-generation PacBio sequencing technologies. Illumina sequencing offers high quality and short reads, while PacBio technology generates long reads. The scaffolds of the two platforms were assembled to yield a complete genome sequence that included two circular chromosomes and one circular plasmid. Transcriptomic data for Pseudoalteromonas were not available. We therefore collected comprehensive RNA-seq data using Illumina sequencing technology from a fermentation culture of P. agarivorans Hao 2018. Researchers studying the evolution, environmental adaptations and biotechnological applications of Pseudoalteromonas may benefit from our genomic and transcriptomic data to analyze the function and expression of genes of interest.
Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Authors: Li Xiaoyong , Tian Geng G. , Zhao Yongqiang , Wu Ji 
Published: March 2019

AbstractGermline stem cells are germ cells at an early developmental stage, so their development is key to ensuring human reproduction. There is increasing evidence that long noncoding RNA (lncRNA) and circular RNA (circRNA) play important roles in the development of germ cells. This data descriptor provides unique lncRNA and circRNA transcriptomic information for mouse germline stem cells. Using the Illumina HiSeqx 2000 system, a total of 511,836,732 raw reads were generated. High-quality transcripts, lncRNAs, and circRNAs were identificated and quantified using the reads, and more precise annotations of lncRNAs (especially 9357 novel lncRNAs) and circRNAs were performed in the germline stem cells. We then analyzed the transcript structures, genetic variants, and the interaction between circRNA and microRNA to provide the basis for subsequent functional experiments. This comprehensive dataset will help advance data sharing and deepen our understanding of mouse germline stem cells, providing a theoretical foundation for research on germ cell development and human reproduction, among others.
Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat
Authors: Kitada Shuichi , Nakajima Kaori , Hamasaki Katsuyuki , Shishidou Hirotoshi , Waples Robin S. , Kishino Hirohisa 
Published: March 2019

AbstractRelease of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the size and genetic diversity of wild populations of one of the world’s largest marine stock enhancement programs–the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our analyses found that the stock enhancement program reduced genetic diversity of the population, but the genetic effect diminished with increased size of the wild population. Increases to the seaweed communities and reduced fishing efforts were the primary factors associated with the wild population recovery; effects of aquaculture were much smaller. Our results represent crucial evidence that hatcheries for enhancement and conservation of populations cannot be successful over the long term unless sufficient efforts are also made to reduce harvest rates and rehabilitate natural habitats.
Tumor Ensemble-Based Modeling and Visualization of Emergent Angiogenic Heterogeneity in Breast Cancer
Authors: Stamatelos Spyros K. , Bhargava Akanksha , Kim Eugene , Popel Aleksander S. , Pathak Arvind P. 
Published: March 2019

AbstractThere is a critical need for new tools to investigate the spatio-temporal heterogeneity and phenotypic alterations that arise in the tumor microenvironment. However, computational investigations of emergent inter- and intra-tumor angiogenic heterogeneity necessitate 3D microvascular data from ‘whole-tumors’ as well as “ensembles” of tumors. Until recently, technical limitations such as 3D imaging capabilities, computational power and cost precluded the incorporation of whole-tumor microvascular data in computational models. Here, we describe a novel computational approach based on multimodality, 3D whole-tumor imaging data acquired from eight orthotopic breast tumor xenografts (i.e. a tumor ‘ensemble’). We assessed the heterogeneous angiogenic landscape from the microvascular to tumor ensemble scale in terms of vascular morphology, emergent hemodynamics and intravascular oxygenation. We demonstrate how the abnormal organization and hemodynamics of the tumor microvasculature give rise to unique microvascular niches within the tumor and contribute to inter- and intra-tumor heterogeneity. These tumor ensemble-based simulations together with unique data visualization approaches establish the foundation of a novel ‘cancer atlas’ for investigators to develop their own in silico systems biology applications. We expect this hybrid image-based modeling framework to be adaptable for the study of other tissues (e.g. brain, heart) and other vasculature-dependent diseases (e.g. stroke, myocardial infarction).
Copper(II) complexes as potential anticancer and Nonsteroidal anti-inflammatory agents: In vitro and in vivo studies
Authors: Hussain Afzal , AlAjmi Mohamed Fahad , Rehman Md. Tabish , Amir Samira , Husain Fohad Mabood , Alsalme Ali , Siddiqui Maqsood Ahmad , AlKhedhairy Abdulaziz A. , Khan Rais Ahmad 
Published: March 2019

AbstractCopper-based compounds are promising entities for target-specific next-generation anticancer and NSAIDS therapeutics.In lieuof this, benzimidazole scaffold plays an important role, because of their wide variety of potential functionalizations and coordination modes. Herein, we report three copper complexes1–3with benzimidazole-derived scaffolds, a biocompatible molecule, and secondary ligands viz, 1–10-phenanthroline and 2,2′-bipyridyl. All the copper complexes have been designed, synthesized and adequately characterized using various spectroscopic techniques.In-vitro, human serum albumin (HSA) binding was also carried out using fluorescence technique andin-silicomolecular modeling studies, which exhibited significant binding affinities of the complexes with HSA. Furthermore, copper complexes1–3were tested for biological studies, i.e., anticancer as well as NSAIDS.In vitrocytotoxicity results were carried out on cultured MCF-7 cell lines. To get the insight over the mechanism of action, GSH depletion and change in lipid peroxidation were tested and thus confirmed the role of ROS generation, responsible for the cytotoxicity of the complexes1–3. Moreover, the copper complexes1–3were tested for potential to act as NSAIDS on albino rats and mice in animal studiesin-vivo. Additionally, we also predicted the mechanism of action of the copper complexes1–3using molecular modeling studies with COX-2 inhibitor.
Effects and possible mechanism of Ruyiping formula application to breast cancer based on network prediction
Authors: Xie Rui-Fang , Liu Sheng , Yang Ming , Xu Jia-Qi , Li Zhi-Cheng , Zhou Xin 
Published: March 2019

AbstractRuyiping (RYP), a Chinese herbal formula, can remove toxin and clear nodular, showing ability of preventing postoperative recurrence of breast cancer. In this study, network was performed to predict possible targets, genes and pathways associated with RYP and breast cancer. Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC) were used to quantitatively study RYP formula and its single herbs. MTT methods, Luciferase reporter systems, zebrafish model and western blotting were respectively adopted to verify network prediction. Results showed that the quality of RYP could be controlled and icariin could be selected as mark ingredient; RYP expressed anti-breast tumor effects, which could be associated with inhibiting expression of Transforming Growth Factor β (TGFβ), promoting cells apoptosis and anti-angiogenesis. Parts of these results were consistent with network predictions in some degree, but not all. Network can help us narrow areas, focus on crucial factors, save money as well as time, but the results predicted by network should be confirmed by further experiments.
Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments
Authors: Ling Lin , Li Xuexue , Wang Kangxu , Cai Mingli , Jiang Yang , Cao Cougui 
Published: March 2019

AbstractNitrogen (N) and carbon(C) metabolisms in plants were investigated to assess different responses of Bt and non-Bt rice to different N treatments. T2A-1 (Bt rice variety) inserted with Cry2A* protein to resist Lepidoptera and its parental line MH63 was adopted in this study. The total N accumulation presented no statistical difference. But nitrogen contents in different parts of rice plant were significantly different between the two lines, especially on leaf and spike part. This study revealed that the nitrogen in leaf of T2A-1 was far more than that of MH63; however, the nitrogen in spike of T2A-1 was less than that of MH63. In addition, MH63 assimilated more carbon than T2A-1. However, the distribution proportion of carbon in leaf, stem and spike of T2A-1 and MH63 were both 1:1:1. What’s more, our study of the difference in metabolism pathway based on proteomics analysis provided more insights on the responses of two lines of Bt and non-Bt rice to different N treatments. And amino acid metabolism, energy metabolism, and carbohydrate metabolism presented significant difference between two lines. In addition, the number of differentially expressed proteins with N deficiency treatment was almost twice as many as that with normal N treatment. It could be inferred that the insertion of Cry2A* in T2A-1 may bring about effects on carbon and nitrogen allocation and related metabolisms, especially under N deficiency environment.
Potential of fungi isolated from the dumping sites mangrove rhizosphere soil to degrade polythene
Authors: Sangale Manisha K. , Shahnawaz Mohd. , Ade Avinash B. 
Published: March 2019

AbstractPolythene is the most widely used plastic around the globe. Among the total plastic waste generated, polythene contributes the maximum share (64%). Various strategies/methods are being utilized to deal with the increasing rate of plastic waste, but among all the methods, bioremediation is regarded as the ecofriendly and widely accepted method. In the current investigation, we have attempted to discover the elite polythene deteriorating fungi (isolated from the rhizosphere soil ofAvicennia marina). From 12 different eco-geographical locations along the West Coast of India, total 109 fungal isolates were recorded. The polythene deteriorating fungi were screened at varied pH (3.5, 7 and 9.5) based on changes in weight and tensile strength of the treated polythene at ambient temperature with continuous shaking for 60 days. BAYF5 isolate (pH 7) results in maximum reduction in weight (58.51 ± 8.14) whereas PNPF15 (pH 3.5) recorded highest reduction in tensile strength (94.44 ± 2.40). Surprisingly, we have also reported weight gain, with highest percent weight gain (28.41 ± 6.99) with MANGF13 at pH 9.5. To test the reproducibility of the results, the elite polythene degrading fungal isolates based on weight loss and reduction in tensile strength were only used for repetition experiment and the results based on the reduction in tensile strength were found only reproducible. Polythene biodegradation was further confirmed using Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) analysis. The most efficient polythene deteriorating fungal isolates were identified asAspergillus terreusstrain MANGF1/WL andAspergillus sydowiistrain PNPF15/TS using both morphological keys and molecular tools.
Pattern separation of spiketrains in hippocampal neurons
Authors: Madar Antoine D. , Ewell Laura A. , Jones Mathew V. 
Published: March 2019

AbstractPattern separation is a process that minimizes overlap between patterns of neuronal activity representing similar experiences. Theoretical work suggests that the dentate gyrus (DG) performs this role for memory processing but a direct demonstration is lacking. One limitation is the difficulty to measure DG inputs and outputs simultaneously. To rigorously assess pattern separation by DG circuitry, we used mouse brain slices to stimulate DG afferents and simultaneously record DG granule cells (GCs) and interneurons. Output spiketrains of GCs are more dissimilar than their input spiketrains, demonstrating for the first time temporal pattern separation at the level of single neurons in the DG. Pattern separation is larger in GCs than in fast-spiking interneurons and hilar mossy cells, and is amplified in CA3 pyramidal cells. Analysis of the neural noise and computational modelling suggest that this form of pattern separation is not explained by simple randomness and arises from specific presynaptic dynamics. Overall, by reframing the concept of pattern separation in dynamic terms and by connecting it to the physiology of different types of neurons, our study offers a new window of understanding in how hippocampal networks might support episodic memory.
Heritable Epichloë symbiosis shapes fungal but not bacterial communities of plant leaves
Authors: Nissinen Riitta , Helander Marjo , Kumar Manoj , Saikkonen Kari 
Published: March 2019

AbstractKeystone microbial species have driven eco-evolutionary processes since the origin of life. However, due to our inability to detect the majority of microbiota, members of diverse microbial communities of fungi, bacteria and viruses have largely been ignored as keystone species in past literature. Here we tested whether heritable Epichloë species of pooidae grasses modulate microbiota of their shared host plant.
Alternative splicing events expand molecular diversity of camel CSN1S2 increasing its ability to generate potentially bioactive peptides
Authors: Ryskaliyeva Alma , Henry Céline , Miranda Guy , Faye Bernard , Konuspayeva Gaukhar , Martin Patrice 
Published: March 2019

AbstractIn a previous study on camel milk from Kazakhstan, we reported the occurrence of two unknown proteins (UP1 and UP2) with different levels of phosphorylation. Here we show that UP1 and UP2 are isoforms of camel αs2-CN (αs2-CNsv1 and αs2-CNsv2, respectively) arising from alternative splicing events. First described as a 178 amino-acids long protein carrying eight phosphate groups, the major camel αs2-CN isoform (called here αs2-CN) has a molecular mass of 21,906 Da. αs2-CNsv1, a rather frequent (35%) isoform displaying a higher molecular mass (+1,033 Da), is present at four phosphorylation levels (8P to 11P). Using cDNA-sequencing, αs2-CNsv1 was shown to be a variant arising from the splicing-in of an in-frame 27-nucleotide sequence encoding the nonapeptide ENSKKTVDM, for which the presence at the genome level was confirmed. αs2-CNsv2, which appeared to be present at 8P to 12P, was shown to include an additional decapeptide (VKAYQIIPNL) revealed by LC-MS/MS, encoded by a 3′-extension of exon 16. Since milk proteins represent a reservoir of biologically active peptides, the molecular diversity generated by differential splicing might increase its content. To evaluate this possibility, we searched for bioactive peptides encrypted in the different camel αs2-CN isoforms, using an in silico approach. Several peptides, putatively released from the C-terminal part of camel αs2-CN isoforms after in silico digestion by proteases from the digestive tract, were predicted to display anti-bacterial and antihypertensive activities.
Target detection increases pupil diameter and enhances memory for background scenes during multi-tasking
Authors: Swallow Khena M. , Jiang Yuhong V. , Riley Elizabeth B. 
Published: March 2019

AbstractAttending to targets in a detection task can facilitate memory for concurrently presented information, a phenomenon known as the attentional boost effect. One account of the attentional boost suggests that it reflects the temporal selection of behaviorally relevant moments, broadly facilitating the processing of information encountered at these times. Because pupil diameter increases when orienting to behaviorally relevant events and is positively correlated with increases in gain and activity in the locus coeruleus (a purported neurophysiological mechanism for temporal selection), we tested whether the attentional boost effect is accompanied by an increase in pupil diameter. Participants memorized a series of individually presented scenes. Whenever a scene appeared, a high or low pitched tone was played, and participants counted (and later reported) the number of tones in the pre-specified, target pitch. Target detection enhanced later memory for concurrently presented scenes. It was accompanied by a larger pupil response than was distractor rejection, and this effect was more pronounced for subsequently remembered rather than forgotten scenes. Thus, conditions that produce the attentional boost effect may also elicit phasic changes in neural gain and locus coeruleus activity.
Morphologic, molecular and metabolic characterization of Aspergillus section Flavi in spices marketed in Lebanon
Authors: Makhlouf Joya , Carvajal-Campos Amaranta , Querin Arlette , Tadrist Soraya , Puel Olivier , Lorber Sophie , Oswald Isabelle P. , Hamze Monzer , Bailly Jean-Denis , Bailly Sylviane 
Published: March 2019

AbstractSpices are used extensively in Lebanon not only to flavour foods but also for their medicinal properties. To date, no data are available regarding the nature of the toxigenic fungal species that may contaminate these products at the marketing stage in this country. Eighty samples corresponding to 14 different types of spices were collected throughout Lebanon to characterize the Aspergillus section Flavi contaminating spices marketed in Lebanon and the toxigenic potential of these fungal species. Most fungal genera and species were identified as belonging to Aspergillus section Flavi. Aspergillus flavus was the most frequent species, representing almost 80% of the isolates. Although identified as A. flavus by molecular analysis, some strains displayed atypical morphological features. Seven strains of A. tamarii and one A. minisclerotigenes were also isolated. Analyses of toxigenic potential demonstrated that almost 80% of strains were able to produce mycotoxins, 47% produced aflatoxins, and 72% produced cyclopiazonic acid, alone or in combination with aflatoxins.