bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Physical and Financial Approaches to Manage Environmental Financial Risk on the Great Lakes
Authors: Meyer Eliot S. , Foster Benjamin T. , Characklis Gregory W. , Brown Casey , Yates Andrew J. 
Published: January 2020

AbstractPhysical and financial approaches each provide different benefits for managing environmental financial risks. Index insurance contracts, a financial approach, have been proposed for managing numerous environmental financial risks. A method for testing when and how physical (dredging) and financial risk management strategies (index insurance) could be deployed in tandem to maximize improvements in utility for commercial shippers on the Great Lakes is developed using principles from the benefit‐cost analysis and expected utility theory. Using a utility function with a decreasing marginal utility of income explicitly models the risk aversion of commercial shippers. The probabilistic nature of future revenue and costs is modeled and combined with the utility function to determine a Net Option Value. This value represents the maximum amount commercial shippers would pay more than the cost for reduced variability in net revenues. Results indicate that while the Net Option Value for dredging exceeds the potential benefits of using insurance contracts alone, the combination of dredging and insurance can improve overall utility with less cost than dredging alone. The strong autocorrelation in lake levels over long periods reduces the value of index insurance, such that the results show a potential lower bound of the value of combining physical and financial approaches in highly variable systems.
Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus
Authors: Zou Cheng , Karn Avinash , Reisch Bruce , Nguyen Allen , Sun Yongming , Bao Yun , Campbell Michael S. , Church Deanna , Williams Stephen , Xu Xia , Ledbetter Craig A. , Patel Sagar , Fennell Anne , Glaubitz Jeffrey C. , Clark Matthew , Ware Doreen , Londo Jason P. , Sun Qi , Cadle-Davidson Lance 
Published: January 2020

AbstractTransferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
Functionalization of remote C(sp3)-H bonds enabled by copper-catalyzed coupling of O-acyloximes with terminal alkynes
Authors: Li Zhaodong , Torres-Ochoa Rubén O. , Wang Qian , Zhu Jieping 
Published: January 2020

AbstractTransition metal catalyzed Sonogashira cross-coupling of terminal alkynes with aryl(vinyl) (pseudo)halides has been successfully extended to alkyl halides for the synthesis of functionalized internal alkynes. The direct alkynylation of remote unfunctionalized sp3 carbon by terminal alkynes remains difficult to realize. We report herein an approach to this synthetic challenge by developing two catalytic remote sp3 carbon alkynylation protocols. In the presence of a catalytic amount of Cu(I) salt and a tridentate ligand (tBu3-terpyridine), O-acyloximes derived from cycloalkanones and acyclic ketones are efficiently coupled with terminal alkynes to afford a variety of γ- and δ-alkynyl nitriles and γ-alkynyl ketones, respectively. These reactions proceed through a domino sequence involving copper-catalyzed reductive generation of iminyl radical followed by radical translocation via either β-scission or 1,5-hydrogen atom transfer (1,5-HAT) and copper-catalyzed alkynylation of the resulting translocated carbon radicals. The protocols are applicable to complex natural products.
A chromosome-level reference genome of the hornbeam, Carpinus fangiana
Authors: Yang Xiaoyue , Wang Zefu , Zhang Lei , Hao Guoqian , Liu Jianquan , Yang Yongzhi 
Published: January 2020

AbstractBetulaceae, the birch family, comprises six living genera and over 160 species, many of which are economically valuable. To deepen our knowledge of Betulaceae species, we have sequenced the genome of a hornbeam, Carpinus fangiana, which belongs to the most species-rich genus of the Betulaceae subfamily Coryloideae. Based on over 75 Gb (~200x) of high-quality next-generation sequencing data, we assembled a 386.19 Mb C. fangiana genome with contig N50 and scaffold N50 sizes of 35.32 kb and 1.91 Mb, respectively. Furthermore, 357.84 Mb of the genome was anchored to eight chromosomes using over 50 Gb (~130x) Hi-C sequencing data. Transcriptomes representing six tissues were sequenced to facilitate gene annotation, and over 5.50 Gb high-quality data were generated for each tissue. The structural annotation identified a total of 27,381 protein-coding genes in the assembled genome, of which 94.36% were functionally annotated. Additionally, 4,440 non-coding genes were predicted.
The influence of AlN buffer layer on the growth of self-assembled GaN nanocolumns on graphene
Authors: Liudi Mulyo Andreas , Rajpalke Mohana K. , Vullum Per Erik , Weman Helge , Kishino Katsumi , Fimland Bjørn-Ove 
Published: January 2020

AbstractGaN nanocolumns were synthesized on single-layer graphene via radio-frequency plasma-assisted molecular beam epitaxy, using a thin migration-enhanced epitaxy (MEE) AlN buffer layer as nucleation sites. Due to the weak nucleation on graphene, instead of an AlN thin-film we observe two distinguished AlN formations which affect the subsequent GaN nanocolumn growth: (i) AlN islands and (ii) AlN nanostructures grown along line defects (grain boundaries or wrinkles) of graphene. Structure (i) leads to the formation of vertical GaN nanocolumns regardless of the number of AlN MEE cycles, whereas (ii) can result in random orientation of the nanocolumns depending on the AlN morphology. Additionally, there is a limited amount of direct GaN nucleation on graphene, which induces non-vertical GaN nanocolumn growth. The GaN nanocolumn samples were characterized by means of scanning electron microscopy, transmission electron microscopy, high-resolution X-ray diffraction, room temperature micro-photoluminescence, and micro-Raman measurements. Surprisingly, the graphene with AlN buffer layer formed using less MEE cycles, thus resulting in lower AlN coverage, has a lower level of nitrogen plasma damage. The AlN buffer layer with lowest AlN coverage also provides the best result with respect to high-quality and vertically-aligned GaN nanocolumns.
County-level analysis reveals a rapidly shifting landscape of insecticide hazard to honey bees (Apis mellifera) on US farmland
Authors: Douglas Margaret R. , Sponsler Douglas B. , Lonsdorf Eric V. , Grozinger Christina M. 
Published: January 2020

AbstractEach year, millions of kilograms of insecticides are applied to crops in the US. While insecticide use supports food, fuel, and fiber production, it can also threaten non-target organisms, a concern underscored by mounting evidence of widespread decline of pollinator populations. Here, we integrate several public datasets to generate county-level annual estimates of total ‘bee toxic load’ (honey bee lethal doses) for insecticides applied in the US between 1997–2012, calculated separately for oral and contact toxicity. To explore the underlying components of the observed changes, we divide bee toxic load into extent (area treated) and intensity (application rate x potency). We show that while contact-based bee toxic load remained relatively steady, oral-based bee toxic load increased roughly 9-fold, with reductions in application rate outweighed by disproportionate increases in potency (toxicity/kg) and extent. This pattern varied markedly by region, with the greatest increase seen in Heartland (121-fold increase), likely driven by use of neonicotinoid seed treatments in corn and soybean. In this “potency paradox”, farmland in the central US has become more hazardous to bees despite lower volumes of insecticides applied, raising concerns about insect conservation and highlighting the importance of integrative approaches to pesticide use monitoring.
Relationship between nerve fiber layer defect and the presence of epiretinal membrane in a Japanese population: The JPHC-NEXT Eye Study
Authors: Uchida Atsuro , Sasaki Mariko , Motomura Kaoru , Yuki Kenya , Kurihara Toshihide , Tomita Yohei , Ozawa Yoko , Yamagishi Kazumasa , Kawasaki Ryo , Hanyuda Akiko , Sawada Norie , Tsubota Kazuo , Tsugane Shoichiro , Iso Hiroyasu 
Published: January 2020

AbstractThe study subjects were residents of Chikusei city, Japan, aged 40 years or older who attended annual health check-up programs and participated in the JPHC-NEXT Eye Study which performed non-mydriatic fundus photography of both eyes. The relationship of glaucomatous fundus changes such as optic disc cupping (cup to disc ratio ≥ 0.7) and retinal nerve fiber layer defect (NFLD) with the presence of epiretinal membrane (ERM) were examined cross-sectionally. A total of 1990 persons gave consent to participate in this study in 2013. The overall prevalence of ERM was 12.9%. Of these, 1755 had fundus photographs of sufficient quality and no history of intraocular surgery (mean age: 62.3 ± 10.0 years). After adjusting for age, sex and refractive error, NFLD was positively associated with the presence of ERM (odds ratio [OR]: 2.48; 95% confidence interval [CI]: 1.24, 4.96; P = 0.010), but optic disc cupping was not (OR: 1.33; CI: 0.71, 2.48; P = 0.37). The results did not necessarily suggest an association between glaucoma and ERM, but indicated an association between NFLD and ERM.
Differential Abundance Analysis with Bayes Shrinkage Estimation of Variance (DASEV) for Zero-Inflated Proteomic and Metabolomic Data
Authors: Huang Zhengyan , Lane Andrew N. , Fan Teresa W-M. , Higashi Richard M. , Weiss Heidi L. , Yin Xiangrong , Wang Chi 
Published: January 2020

AbstractMass spectrometry (MS) is frequently used for proteomic and metabolomic profiling of biological samples. Data obtained by MS are often zero-inflated. Those zero values are called point mass values (PMVs). Zero values can be further grouped into biological PMVs and technical PMVs. The former type is caused by true absence of a compound and the later type is caused by a technical detection limit. Methods based on a mixture model have been developed to separate the two types of zeros and to perform differential abundance analysis comparing proteomic/metabolomic profiles between different groups of subjects. However, we notice that those methods may give unstable estimate of the model variance, and thus lead to false positive and false negative results when the number of non-zero values is small. In this paper, we propose a new differential abundance analysis method, DASEV, which uses an empirical Bayes shrinkage method to more robustly estimate the variance and enhance the accuracy of differential abundance analysis. Simulation studies and real data analysis show that DASEV substantially improves parameter estimation of the mixture model and outperforms current methods in identifying differentially abundant features.
Room Temperature Electrically Detected Nuclear Spin Coherence of NV Centres in Diamond
Authors: Morishita H. , Kobayashi S. , Fujiwara M. , Kato H. , Makino T. , Yamasaki S. , Mizuochi N. 
Published: January 2020

AbstractWe demonstrate electrical detection of the14N nuclear spin coherence of NV centres at room temperature. Nuclear spins are candidates for quantum memories in quantum-information devices and quantum sensors, and hence the electrical detection of nuclear spin coherence is essential to develop and integrate such quantum devices. In the present study, we used a pulsed electrically detected electron-nuclear double resonance technique to measure the Rabi oscillations and coherence time (T2) of14N nuclear spins in NV centres at room temperature. We observedT2≈ 0.9 ms at room temperature, however, this result should be taken as a lower limit due to limitations in the longitudinal relaxation time of the NV electron spins. Our results will pave the way for the development of novel electron- and nuclear-spin-based diamond quantum devices.
Lactobacillus plantarum LMT1-48 exerts anti-obesity effect in high-fat diet-induced obese mice by regulating expression of lipogenic genes
Authors: Choi Woo Jin , Dong Hye Jin , Jeong Hyun Uk , Ryu Dong Wook , Song Soo Min , Kim Yu Ri , Jung Hyun Ho , Kim Tai Hoon , Kim Yeung-Hyen 
Published: January 2020

AbstractObesity is a major health problem and is known to be closely associated with metabolic diseases. Abnormal hepatic accumulation of fat causes fatty liver or hepatic steatosis, and long-term consumption of a high-fat diet is known to be a key obesity-causing factor. Recent studies have demonstrated that probiotics such as Lactobacillus strains, exert an anti-obesity effect by regulating adipogenesis. However, it is still unknown how the consumption of probiotics can reduce abdominal fat volume by regulating the hepatic expression of lipogenic genes. Therefore, we evaluated the effect of long-term ingestion of L. plantarum LMT1-48 on the expression of lipogenic genes in high-fat diet (HFD)-fed mice. We observed that treatment of 3T3-L1 adipocytes with L. plantarum LMT1-48 extract inhibited their differentiation and lipid accumulation by downregulating lipogenic genes, namely, PPARγ, C/EBPα, FAS, and FABP4. Interestingly, administration of L. plantarum LMT1-48 reduced liver weight and liver triglycerides concurrently with the downregulation of the lipogenic genes PPARγ, HSL, SCD-1, and FAT/CD36 in the liver, resulting in the reduction of body weight and fat volume in HFD-fed obese mice. Notably, we also observed that the administration of at least 106 CFU of L. plantarum LMT1-48 significantly lowered body weight and abdominal fat volume in modified diet-fed mouse models. Collectively, these data suggest that L. plantarum LMT1-48 is a potential healthy food for obese people.
Preoperative %p2PSA and Prostate Health Index Predict Pathological Outcomes in Patients with Prostate Cancer Undergoing Radical Prostatectomy
Authors: Cheng Yung-Ting , Huang Chao-Yuan , Chen Chung-Hsin , Chiu Shih-Ting , Hong Jian-Hua , Pu Yeong-Shiau , Liu Shih-Ping , Lu Yu-Chuan , Chang Yi-Kai , Chang Hong-Chiang , Huang Kuo-How , Lee Yuan-Ju , Chow Po-Ming , Chiang I-Ni , Hung Shih-Chun , Chiang Chih-Hung 
Published: January 2020

AbstractTo evaluate the predictive accuracy of the %p2PSA and prostate health index (PHI) in predicting aggressive pathological outcomes in patients with prostate cancer (PCa) undergoing radical prostatectomy (RP), we enrolled 91 patients with organ-confined PCa who were treated with robot-assisted RP. p2PSA levels and the PHI were investigated for their ability to predict pathological results. The %p2PSA and PHI were both significantly higher in patients with ≥pT3 disease, high-risk disease, positive surgical margin, or seminal vesical invasion (SVI). In univariable analysis, p2PSA derivatives were significant predictors of the presence of ≥pT3 disease, high-risk disease, positive surgical margin, and SVI. To predict adverse pathological outcomes at a sensitivity of 90%, p2PSA derivatives had higher specificity than standard PSA derivatives. In multivariable analysis, additional increases in the area under the receiver operating characteristic curve (AUC) were observed with the %p2PSA and PHI for ≥pT3 disease, high-risk disease, and positive surgical margin (8.2% and 2.7%, 6.2% and 4.1%, and 8.6% and 5.4%, respectively). A PHI ≥61.26 enhanced the predictive accuracy of the model for SVI by increasing the AUC from 0.624 to 0.819 (p = 0.009). The preoperative %p2PSA and PHI accurately predict adverse pathological results and are useful for decision-making.
Reference gene validation for quantification of gene expression during ovarian development of turbot (Scophthalmus maximus)
Authors: Gao Yunhong , Gao Yuntao , Huang Bin , Meng Zhen , Jia Yudong 
Published: January 2020

AbstractQuantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a powerful and sensitive method used in gene expression analysis. Suitable reference genes, which are stable under all experimental circumstances and tissues significantly improve the accuracy of qRT-PCR data. In this study, the stability of six genes, namely, 18S ribosomal RNA (18s), beta-actin (actb), elongation factor 1-alpha (ef1α), glyceraldehyde-3-phosphate-dehydrogenase (gapdh), cathepsin D (ctsd), and beta-2-microglobulin (b2m) were evaluated as potential references for qRT-PCR analysis. The genes were examined in the hypothalamus-pituitary-ovary-liver (HPOL) axis throughout turbot ovarian development via using the geNorm, NormFinder and BestKeeper algorithms. Results showed that the most stable reference genes were ef1α, actb, and ctsd in the hypothalamus, pituitary, ovary and liver, respectively. The best-suited gene combinations for normalization were 18s, ef1α, and ctsd in the hypothalamus; actb, ctsd, and 18s in the pituitary; actb, and ctsd in the ovary; gapdh and ctsd in the liver. Moreover, the expression profile of estrogen receptor α (erα) manifested no significant difference normalization to the aforementioned best-suited gene during turbot ovarian development. However, no single gene or pair of genes is suitable as an internal control and account for the amplification differences among the four tissues during ovarian development. In summary, these results provide a basic data for the optimal reference gene selection and obtain highly accurate normalization of qRT-PCR data in HPOL axis-related gene expression analysis during turbot ovarian development.
Multiscale Process Modelling in Translational Systems Biology of Leishmania major: A Holistic view
Authors: Chauhan Nutan , Singh Shailza 
Published: January 2020

AbstractPresent work aims to utilize systems biology and molecular modelling approach to understand the inhibition kinetics ofLeishmania majorGLO I and identifying potential hit followed by their validation throughin vitroand animal studies. Simulation of GLO I inhibition has shown to affect reaction fluxes of almost all reactions in the model that led to increased production of various AGEs and free radicals. Further,in vitrotesting of C1 and C2, selected through molecular modelling revealed remarkable morphological alterations like size reduction, membrane blebbing and loss in motility of the parasite, however, only C1 showed better antileishmanial activity. Additionally, C1 showed apoptosis mediated leishmanicidal activity (apoptosis-like cell death) along with cell-cycle arrest at sub-G0/G1 phase and exhibited potent anti-leishmanial effect against intracellular amastigotes. Furthermore, decrease in parasite load was also observed in C1 treated BALB/c female mice. Our results indicate that C1 has healing effect in infected mice and effectively reduced the parasitic burden. Hence, we suggest C1 as a lead molecule which on further modification, may be used to develop novel therapeutics againstLeishmaniasis.
Comparison of methods for miRNA isolation and quantification from ovine plasma
Authors: Wright Kathryn , de Silva Kumudika , Purdie Auriol C. , Plain Karren M. 
Published: January 2020

AbstractmicroRNA (miRNA) are promising candidates for disease biomarkers as they are abundant in circulation, highly stable in biological fluids and may yield diagnostic biomarker signatures. The reported issues with miRNA isolation using traditional RNA reagents necessitates the optimisation of miRNA isolation from challenging samples. In this study we compared six commercial RNA extraction kits to evaluate their ability to isolate miRNA from ovine plasma. We also compared three methods for quantification of small RNA extracted from plasma to determine the most reliable. Using minimal sample inputs of fresh and frozen plasma from five sheep, we compared the six kits (Kit A-F) using quantitative PCR. Operational factors were also assessed for each kit. Kits A and B provided the best detection of the miRNA qPCR reference genes across fresh and frozen samples (p < 0.001) followed by Kit C. The Qubit and microRNA assay provided the least variation (% CV 5.47, SEM ± 0.07), followed by the NanoDrop (% CV 7.01, SEM ± 0.92) and Agilent Bioanalyzer (% CV 59.21, SEM ± 1.31). We identify Kit A to be optimal for isolating miRNA from small volumes of fresh and frozen ovine plasma, and Kit B the top performing kit taking into consideration miRNA detection and operational factors. The Qubit fluorometer using a microRNA assay was the most reliable miRNA quantification method.
Astrocyte Support for Oligodendrocyte Differentiation can be Conveyed via Extracellular Vesicles but Diminishes with Age
Authors: Willis Cory M. , Nicaise Alexandra M. , Bongarzone Ernesto R. , Givogri Maria , Reiter Cory R. , Heintz Olivia , Jellison Evan R. , Sutter Pearl A. , TeHennepe Gregg , Ananda Guruprasad , Vella Anthony T. , Crocker Stephen J. 
Published: January 2020

AbstractThe aging brain is associated with significant changes in physiology that alter the tissue microenvironment of the central nervous system (CNS). In the aged CNS, increased demyelination has been associated with astrocyte hypertrophy and aging has been implicated as a basis for these pathological changes. Aging tissues accumulate chronic cellular stress, which can lead to the development of a pro-inflammatory phenotype that can be associated with cellular senescence. Herein, we provide evidence that astrocytes aged in culture develop a spontaneous pro-inflammatory and senescence-like phenotype. We found that extracellular vesicles (EVs) from young astrocyte were sufficient to convey support for oligodendrocyte differentiation while this support was lost by EVs from aged astrocytes. Importantly, the negative influence of culture age on astrocytes, and their cognate EVs, could be countered by treatment with rapamycin. Comparative proteomic analysis of EVs from young and aged astrocytes revealed peptide repertoires unique to each age. Taken together, these findings provide new information on the contribution of EVs as potent mediators by which astrocytes can extert changing influence in either the disease or aged brain.