bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics
Authors: Vatanparast Mohammad , Powell Adrian , Doyle Jeff J. , Egan Ashley N. 
Published: April 2018

Premise of the StudyThe development of pipelines for locus discovery has spurred the use of target enrichment for plant phylogenomics. However, few studies have compared pipelines from locus discovery and bait design, through validation, to tree inference. We compared three methods within Leguminosae (Fabaceae) and present a workflow for future efforts.MethodsUsing 30 transcriptomes, we compared Hyb‐Seq, MarkerMiner, and the Yang and Smith (Y&S) pipelines for locus discovery, validated 7501 baits targeting 507 loci across 25 genera via Illumina sequencing, and inferred gene and species trees via concatenation‐ and coalescent‐based methods.ResultsHyb‐Seq discovered loci with the longest mean length. MarkerMiner discovered the most conserved loci with the least flagged as paralogous. Y&S offered the most parsimony‐informative sites and putative orthologs. Target recovery averaged 93% across taxa. We optimized our targeted locus set based on a workflow designed to minimize paralog/ortholog conflation and thus present 423 loci for legume phylogenomics.ConclusionsMethods differed across criteria important for phylogenetic marker development. We recommend Hyb‐Seq as a method that may be useful for most phylogenomic projects. Our targeted locus set is a resource for future, community‐driven efforts to reconstruct the legume tree of life.
Review: Unmet Needs and the Path Forward in Joint Disease Associated With Calcium Pyrophosphate Crystal Deposition
Authors: Abhishek Abhishek , Neogi Tuhina , Choi Hyon , Doherty Michael , Rosenthal Ann K. , Terkeltaub Robert 
Published: April 2018

Calcium pyrophosphate (CPP) crystal deposition (CPPD) is prevalent and can be associated with synovitis and joint damage. The population of elderly persons predominantly affected by CPPD is growing rapidly. Since shortfalls exist in many aspects of CPPD, we conducted an anonymous survey of CPPD unmet needs, prioritized by experts from the Gout, Hyperuricemia and Crystal‐Associated Disease Network. We provide our perspectives on the survey results, and we propose several CPPD basic and clinical translational research pathways. Chondrocyte and cartilage culture systems for generating CPP crystals in vitro and transgenic small animal CPPD models are needed to better define CPPD mechanism paradigms and help guide new therapies. CPPD recognition, clinical research, and care would be improved by international consensus on CPPD nomenclature and disease phenotype classification, better exploitation of advanced imaging, and pragmatic new point‐of‐care crystal analytic approaches for detecting CPP crystals. Clinical impacts of CPP crystals in osteoarthritis and in asymptomatic joints in elderly persons remain major unanswered questions that are rendered more difficult by current inability to therapeutically limit or dissolve the crystal deposits and assess the consequent clinical outcome. Going forward, CPPD clinical research studies should define clinical settings in which articular CPPD does substantial harm and should include analyses of diverse clinical phenotypes and populations. Clinical trials should identify the best therapeutic targets to limit CPP crystal deposition and associated inflammation and should include assessment of intraarticular agents. Our perspective is that such advances in basic and clinical science in CPPD are now within reach and can lead to better treatments for this disorder.
Vanadium‐Doped WS2 Nanosheets Grown on Carbon Cloth as a Highly Efficient Electrocatalyst for the Hydrogen Evolution Reaction
Authors: Jiang Anning , Zhang Baohua , Li Zhonghao , Jin Guoxia , Hao Jingcheng 
Published: April 2018

AbstractTwo‐dimensional transition‐metal dichalcogenides have been widely studied as electrocatalysts for the hydrogen evolution reaction (HER). However, limited active sites and poor conductivity hinder their application. To solve these disadvantages, heteroatom doping has attracted wide attention because it can not only increase the active sites but also affect the intrinsic catalytic properties of the electrocatalyst. Herein, we grew vanadium‐doped WS2 nanosheets on carbon cloth (V‐WS2/CC) as an electrocatalyst for HER under acidic and alkaline conditions. With a proper vanadium doping concentration, the electrochemical surface areas of V0.065‐WS2/CC were 9.6 and 2.6 times as large as that of pure WS2 electrocatalyst under acidic and alkaline conditions, respectively. In addition, the charge‐transfer resistance also decreased with moderate vanadium doping. Based on this, the synthesized vanadium‐doped WS2 nanosheets exhibited good stability with high HER catalytic activity and could reach a current density of 10 mA cm−2 at overpotentials of 148 and 134 mV in 0.5 m H2SO4 and 1 m KOH, respectively. The corresponding Tafel slopes were 71 and 85 mV dec−1. Therefore, our synthesized vanadium‐doped WS2 nanosheets can be a promising electrocatalyst for the production of hydrogen over a wide pH range.
Simultaneous determination of 20(S)‐protopanaxadiol and its three metabolites in rat plasma by LC–MS/MS: application to their pharmacokinetic studies
Authors: Li Jin‐Qi , Wang Jia‐Feng , Li Jie , Zhang Shu‐han , He Dan , Tong Rong‐Sheng , She Shu‐Ya 
Published: April 2018

AbstractThe aim of this study was to develop an LC–MS/MS method for simultaneous determination of 20(S) protopanaxadiol (PPD) and its three metabolites, PPD‐glucuronide (M1), (20S,24S)‐epoxy‐dammarane‐3,12,25‐triol (M2) and (20S,24R)‐epoxydammarane‐3,12,25‐triol (M3), in rat plasma. Precipitation with acetonitrile was employed for sample preparation and chromatographic separations were achieved on a C18 column. The sample was detected using triple quadrupole tandem mass spectrometer with selected reaction monitoring mode. The monitored precursor‐to‐product ion transitions were m/z 459.4 → 375.3 for PPD, m/z 635.4 → 113.0 for M1, m/z 477.4 → 441.4 for M2 and M3 and m/z 475.4 → 391.3 for IS. The developed assay was validated according to the guidelines of the US Food and Drug Administration. The calibration curves showed good linearity over the tested concentration ranges (r > 0.9993), with the LLOQ being 1 ng/mL for all analytes. The intra‐ and inter‐day precisions (RSD) were < 9.51% while the accuracy (RE) ranged from −8.91 to 12.84%. The extraction recovery was >80% and no obvious matrix effect was detected. The analytes were stable in rat plasma with the RE ranging from −12.34 to 9.77%. The validated assay has been successfully applied to the pharmacokinetic study of PPD as well as its metabolites in rat plasma. According to the pharmacokinetic parameters, the in vivo exposures of M1, M2 and M3 were 11.91, 47.95 and 22.62% of that of PPD, respectively.
An analysis of the effect of statins on the risk of Non‐Hodgkin's Lymphoma in the Women’s Health Initiative cohort
Authors: Desai Pinkal , Wallace Robert , Anderson Matthew L. , Howard Barbara V. , Ray Roberta , Wu Chunyuan , Safford Monika , Martin Lisa W. , Schlecht Nicolas , Liu Simin , Cirillo Dominic , Jay Allison , Manson JoAnn E. , Simon Michael S. 
Published: April 2018

AbstractStatins have been shown to induce a phosphoprotein signature that modifies MYC (myelocytomatosis viral oncogene) activation and to have anti‐inflammatory activity that may impact the risk of Non‐Hodgkin's lymphoma (NHL). We analyzed the relationship between statins and risk of NHL using data from the Women's Health Initiative (WHI). The study population included 161,563 postmenopausal women ages 50–79 years from which 712 cases of NHL were diagnosed after 10.8 years of follow‐up. Information on statin use and other risk factors was collected by self‐ and interviewer‐administered questionnaires. Multivariable‐adjusted HR and 95% CI evaluating the relationship between statin use at baseline, as well as in a time‐dependent manner and risk of NHL, were computed from Cox proportional hazards analyses. A separate analysis was performed for individual NHL subtypes: diffuse large B‐Cell lymphoma (DLBCL) (n = 228), follicular lymphoma (n = 169), and small lymphocytic lymphoma (n = 74). All statistical tests were two‐sided. There was no significant association between use of statins at baseline and risk of NHL (HR 0.85, 95% C.I. 0.67–1.08). However, in the multivariable‐adjusted time‐dependent models, statin use was associated with a borderline lower risk of NHL (HR 0.81, 95% C.I. 0.66–1.00). Considering subtypes of NHL, statin use was associated with a lower risk of DLBCL (HR 0.62, 95% C.I. 0.42–0.91). This effect was driven by lipophilic statins (HR 0.62, 95% C.I. 0.40–0.96). In the WHI, statins were associated with a lower overall risk of DLBCL, particularly attributable to lipophilic statins. These results may have impact on primary or secondary prevention of NHL, particularly DLBCL.
Partner Selection, Interorganizational Coordination, and New Service Development Success in the Financial Service Industry
Authors: Tsou Hung‐Tai , Chen Ja‐Shen , Wang Zhi‐Qiang 
Published: April 2018

AbstractThis study aims to investigate the relationship between partner selection and new service development (NSD) success. We identified three partner selection factors based on partner selection theory: partner reliability, partner expertise, and partner compatibility, and suggested product‐market experience and technological experience as moderators. We developed a questionnaire and distributed it to 446 financial service companies in Taiwan. Overall, we received 122 usable pairs of responses from each firm's sales manager and marketing manager. The results indicate that interorganizational coordination contributes to NSD success. Among the three partner selection factors, partner reliability and partner compatibility were found to positively affect interorganizational coordination. In addition, product‐market experience enhances the positive effect of interorganizational coordination on NSD success. Copyright © 2018 ASAC. Published by John Wiley & Sons, Ltd.
Targeted and non‐targeted metabolite identification of MAM‐2201 in human, mouse, and rat hepatocytes
Authors: Kim Ju‐Hyun , Kong Tae Yeon , Moon Ju‐Yeon , Choi Kyung Ho , Cho Yong‐Yeon , Kang Han Chang , Lee Joo Young , Lee Hye Suk 
Published: April 2018

AbstractMAM‐2201 is a fluorinated naphthoylindole synthetic cannabinoid with potent psychoactive properties that has been detected as an active ingredient in herbal incense blends. To gain a greater understanding of MAM‐2201 metabolism and to compare its metabolic fate in humans with those in animals, the metabolism of MAM‐2201 in human, mouse, and rat hepatocytes was investigated using liquid chromatography–high‐resolution mass spectrometry combined with targeted and non‐targeted metabolite profiling approaches. Nineteen phase I metabolites (M1–M19) reported previously in human liver microsomes and 13 novel metabolites were identified in human, mouse, and rat hepatocytes: 1 phase I metabolite (M20) and 12 phase II metabolites including 6 glucuronides (G1–G6), 1 sulfate (S1), and 5 glutathione (GSH) conjugates (GS1–GS5) of MAM‐2201 metabolites. G3 was human‐specific, but M20, G1, G2, and 5 GSH conjugates were rat‐specific, indicating species‐related differences in MAM‐2201 metabolism. The findings in the present study can be useful for the experimental design and assessment of metabolism‐mediated toxic risk of MAM‐2201.
Edge disturbance drives liana abundance increase and alteration of liana–host tree interactions in tropical forest fragments
Authors: Campbell Mason J. , Edwards Will , Magrach Ainhoa , Alamgir Mohammed , Porolak Gabriel , Mohandass D. , Laurance William F. 
Published: April 2018

AbstractClosed‐canopy forests are being rapidly fragmented across much of the tropical world. Determining the impacts of fragmentation on ecological processes enables better forest management and improves species‐conservation outcomes. Lianas are an integral part of tropical forests but can have detrimental and potentially complex interactions with their host trees. These effects can include reduced tree growth and fecundity, elevated tree mortality, alterations in tree‐species composition, degradation of forest succession, and a substantial decline in forest carbon storage. We examined the individual impacts of fragmentation and edge effects (0–100‐m transect from edge to forest interior) on the liana community and liana–host tree interactions in rainforests of the Atherton Tableland in north Queensland, Australia. We compared the liana and tree community, the traits of liana‐infested trees, and determinants of the rates of tree infestation within five forest fragments (23–58 ha in area) and five nearby intact‐forest sites. Fragmented forests experienced considerable disturbance‐induced degradation at their edges, resulting in a significant increase in liana abundance. This effect penetrated to significantly greater depths in forest fragments than in intact forests. The composition of the liana community in terms of climbing guilds was significantly different between fragmented and intact forests, likely because forest edges had more small‐sized trees favoring particular liana guilds which preferentially use these for climbing trellises. Sites that had higher liana abundances also exhibited higher infestation rates of trees, as did sites with the largest lianas. However, large lianas were associated with low‐disturbance forest sites. Our study shows that edge disturbance of forest fragments significantly altered the abundance and community composition of lianas and their ecological relationships with trees, with liana impacts on trees being elevated in fragments relative to intact forests. Consequently, effective control of lianas in forest fragments requires management practices which directly focus on minimizing forest edge disturbance.
Strong population structure but no equilibrium yet: Genetic connectivity and phylogeography in the kelp Saccharina latissima (Laminariales, Phaeophyta)
Authors: Luttikhuizen Pieternella C. , van den Heuvel Freek H. M. , Rebours Céline , Witte Harry J. , van Bleijswijk Judith D. L. , Timmermans Klaas 
Published: April 2018

AbstractKelp aquaculture is globally developing steadily as human food source, along with other applications. One of the newer crop species is Saccharina latissima, a northern hemisphere kelp inhabiting temperate to arctic rocky shores. To protect and document its natural genetic variation at the onset of this novel aquaculture, as well as increase knowledge on its taxonomy and phylogeography, we collected new genetic data, both nuclear and mitochondrial, and combined it with previous knowledge to estimate genetic connectivity and infer colonization history. Isolation‐with‐migration coalescent analyses demonstrate that gene flow among the sampled locations is virtually nonexistent. An updated scenario for the origin and colonization history of S. latissima is developed as follows: We propose that the species (or species complex) originated in the northwest Pacific, crossed to the northeast Pacific in the Miocene, and then crossed the Bering Strait after its opening ~5.5 Ma into the Arctic and northeast Atlantic. It subsequently crossed the Atlantic from east to west. During the Pleistocene, it was compressed in the south with evidence for northern refugia in Europe. Postglacial recolonization led to secondary contact in the Canadian Arctic. Saccharina cichorioides is shown to probably belong to the S. latissima species complex and to derive from ancestral populations in the Asian North Pacific. Our novel approach of comparing inferred gene flow based on coalescent analysis versus Wright's island model suggests that equilibrium levels of differentiation have not yet been reached in Europe and, hence, that genetic differentiation is expected to increase further if populations are left undisturbed.
Temperature effects on ballistic prey capture by a dragonfly larva
Authors: Quenta Herrera Estefania , Casas Jérôme , Dangles Olivier , Pincebourde Sylvain 
Published: April 2018

AbstractUnderstanding the effects of temperature on prey–predator interactions is a key issue to predict the response of natural communities to climate change. Higher temperatures are expected to induce an increase in predation rates. However, little is known on how temperature influences close‐range encounter of prey–predator interactions, such as predator's attack velocities. Based on the speed–accuracy trade‐off concept, we hypothesized that the increase in predator attack velocity by increasing temperature reduces the accuracy of the attack, leading to a lower probability of capture. We tested this hypothesis on the dragonfly larvae Anax imperator and the zooplankton prey Daphnia magna. The prey–predator encounters were video‐recorded at high speed, and at three different temperatures. Overall, we found that (1) temperature had a strong effect on predator's attack velocities, (2) prey did not have the opportunity to move and/or escape due to the high velocity of the predator during the attack, and (3) neither velocity nor temperature had significant effects on the capture success. By contrast, the capture success mainly depended on the accuracy of the predator in capturing the prey. We found that (4) some 40% of mistakes were undershooting and some 60% aimed below or above the target. No lateral mistake was observed. These results did not support the speed–accuracy trade‐off hypothesis. Further studies on dragonfly larvae with different morphological labial masks and speeds of attacks, as well as on prey with different escape strategies, would provide new insights into the response to environmental changes in prey–predator interactions.
Seasonal variations in body melanism and size of the wolf spiderPardosa astrigera(Araneae: Lycosidae)
Authors: Yang Jinjian , Wu Qijia , Xiao Rong , Zhao Jupeng , Chen Jian , Jiao Xiaoguo 
Published: April 2018

AbstractVariations in species morphology and life‐history traits strongly correlate with geographic and climatic characteristics. Most studies on morphological variations in animals focus on ectotherms distributed on a large geographic scale across latitudinal and/or altitudinal gradient. However, the morphological variations of spiders living in the same habitats across different seasons have not been reported. In this study, we used the wolf spider,Pardosa astrigera, as a model to determine seasonal differences in adult body size, melanism, fecundity, and egg diameter both in the overwintering and the first generation for 2010 and 2016. The results showed that in 2010, both females and males of the overwintering generation were significantly darker than the first generation. Moreover, the overwintering females were markedly larger and produced more and bigger eggs than the first generation in both 2010 and 2016. Considering the overwinteringP. astrigeraexperiencing low temperature and/or desiccation stress, these results suggest that substantially darker and larger body of the overwintering generation is adaptive to adverse conditions.
Diversity and evolution of rice progenitors in Australia
Authors: Moner Ali M. , Furtado Agnelo , Chivers Ian , Fox Glen , Crayn Darren , Henry Robert J. 
Published: April 2018

AbstractIn the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.
Continuous purification of Candida antarctica lipase B using 3‐membrane adsorber periodic counter‐current chromatography
Authors: Brämer Chantal , Schreiber Sarah , Scheper Thomas , Beutel Sascha 
Published: April 2018

AbstractBatch chromatography has several disadvantages, such as insufficient utilization of the capacity of the resin, high buffer consumption and discontinuity. Considering the high costs for downstream processing, a continuously working chromatographic system with three membrane adsorber units was designed, tested and put into operation. The basic principle of the setup is periodic counter‐current chromatography (PCCC). The PCCC system was used for capturing and purifying Candida antarctica lipase B (CalB) directly from cell lysate in one single unit operation. The best purification result was achieved by means of anion‐exchange chromatography. The dynamic binding capacity with Sartobind® Q 75 amounted to 4.2 mg (56 g/cm2). After transferring the method to the 3MA‐PCCC, 0.22 g CalB (73 U/mg) were obtained from 0.9 L E. coli lysate within 6 h and a recovery of 80%. Compared to the batch process, the productivity could be increased by 36% and the buffer consumption could be reduced by about 20%. Although the purification of CalB from lysate by means of anion‐exchange chromatography was not selective and quantitative using the 3MA‐PCCC device, it could be shown that the concept of the system was successfully implemented and led to a significant improvement of CalB purification.
Theoretical link between rainfall and flood magnitude
Authors: Criss Robert E. 
Published: April 2018

AbstractThe rainfall–run‐off convolution integral is analytically solved for several models for the elementary hydrograph. These solutions can be combined with available rainfall frequency analyses to predict flood flows along streams for different recurrence intervals, using no free parameters for gauged streams and one estimable parameter for ungauged streams. Extreme discharge magnitudes at gauged sites can be typically estimated within a factor of two of actual records, using no historical data on extreme flows. The flow predictions reproduce several important characteristics of the flood phenomenon, such as the slope of the regression line between observed extreme flows and basin area on the conventional logQ versus logA plot. Importantly, for the models and data sets investigated, the storm duration of greatest significance to flooding was found to approximate the intrinsic transport timescale of the particular watershed, which increases with basin size. Thus, storms that deliver extraordinary amounts of rainfall over a particular time interval will most greatly activate basins whose time constants approximately equal that interval. This theoretical finding is supported by examination of the regional hydrological response to the massive storms of September 14, 2008, and April 28–30, 2017, which caused extraordinary record flooding of basins of about 5–100 km2 and 500–4,000 km2, respectively, but produced few records in basins that were larger or smaller than those ranges.