bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distribution and relative age of endemism across islands worldwide
Authors: Veron Simon , Haevermans Thomas , Govaerts Rafaël , Mouchet Maud , Pellens Roseli 
Published: August 2019

AbstractIslands have remarkable levels of endemism and contribute greatly to global biodiversity. Establishing the age of island endemics is important to gain insights into the processes that have shaped the biodiversity patterns of island biota. We investigated the relative age of monocots across islands worldwide, using different measures of phylogenetic endemism tested against null models. We compiled a species occurrence dataset across 4,306 islands, and identified 142 sites with neo-, paleo-, mixed and super-endemism. These sites were distributed across the world, although they tended to be more common at low latitudes. The most frequent types of endemism were mixed and super-endemism, which suggests that present-day island biodiversity has frequently been shaped by processes that took place at different points in times. We also identified the environmental factors that contributed most to different types of endemism; we found that latitude, habitat availability and climate stability had a significant impact on the persistence of ancient taxa and on recent diversification events. The islands identified here are irreplaceable both for the uniqueness and the evolutionary history of their flora, and because they are a source of “option values” and evolutionary potential. Therefore, our findings will help guide biodiversity conservation on a global scale.
Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial
Authors: He Xuan , Parenti Mariana , Grip Tove , Lönnerdal Bo , Timby Niklas , Domellöf Magnus , Hernell Olle , Slupsky Carolyn M. 
Published: August 2019

AbstractHuman milk delivers an array of bioactive components that safeguard infant growth and development and maintain healthy gut microbiota. Milk fat globule membrane (MFGM) is a biologically functional fraction of milk increasingly linked to beneficial outcomes in infants through protection from pathogens, modulation of the immune system and improved neurodevelopment. In the present study, we characterized the fecal microbiome and metabolome of infants fed a bovine MFGM supplemented experimental formula (EF) and compared to infants fed standard formula (SF) and a breast-fed reference group. The impact of MFGM on the fecal microbiome was moderate; however, the fecal metabolome of EF-fed infants showed a significant reduction of several metabolites including lactate, succinate, amino acids and their derivatives from that of infants fed SF. Introduction of weaning food with either human milk or infant formula reduces the distinct characteristics of breast-fed- or formula-fed- like infant fecal microbiome and metabolome profiles. Our findings support the hypothesis that higher levels of protein in infant formula and the lack of human milk oligosaccharides promote a shift toward amino acid fermentation in the gut. MFGM may play a role in shaping gut microbial activity and function.
Molecular marker dissection of stem rust resistance in Nebraska bread wheat germplasm
Authors: Mourad Amira M. I. , Sallam Ahmed , Belamkar Vikas , Wegulo Stephen , Bai Guihua , Mahdy Ezzat , Bakheit Bahy , Abo El-Wafa Atif , Jin Yue , Baenziger P. Stephen 
Published: August 2019

AbstractStem rust (caused byPuccinia graminisf. sp.tritici) is a major disease of wheat. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, a set of 330 genotypes representing two nurseries (DUP2015 and TRP2015) were evaluated for resistance to a Nebraska stem rust race (QFCSC) in two replications. The TRP2015 nursery was also evaluated for its resistance to an additional 13 stem rust races. The analysis of variance revealed significant variation among genotypes in both populations for stem rust resistance. Nine stem rust genes,Sr6,Sr31,Sr1RSAmigo,Sr24,Sr36,SrTmp,Sr7b,Sr9b, andSr38, were expected and genotyped using gene-specific markers. The results of genetic analysis confirmed the presence of seven stem rust resistance genes. One genotype (NE15680) contained targetalleles for five stem rust resistance genes and had a high level of stem rust resistance against different races. Single marker analysis indicated thatSr24andSr38were highly significantly associated with stem rust resistance in the DUP2015 and TRP2015 nurseries, respectively. Linkage disequilibrium analysis identified the presence of 17 SNPs in high linkage with theSr38-specific marker. These SNPs potentially tagging theSr38gene could be used in marker-assisted selection after validating them in additional genetic backgrounds.
Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
Authors: Mattucci Federica , Galaverni Marco , Lyons Leslie A. , Alves Paulo C. , Randi Ettore , Velli Edoardo , Pagani Luca , Caniglia Romolo 
Published: August 2019

AbstractThe survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
iW-Net: an automatic and minimalistic interactive lung nodule segmentation deep network
Authors: Aresta Guilherme , Jacobs Colin , Araújo Teresa , Cunha António , Ramos Isabel , van Ginneken Bram , Campilho Aurélio 
Published: August 2019

AbstractWe propose iW-Net, a deep learning model that allows for both automatic and interactive segmentation of lung nodules in computed tomography images. iW-Net is composed of two blocks: the first one provides an automatic segmentation and the second one allows to correct it by analyzing 2 points introduced by the user in the nodule’s boundary. For this purpose, a physics inspired weight map that takes the user input into account is proposed, which is used both as a feature map and in the system’s loss function. Our approach is extensively evaluated on the public LIDC-IDRI dataset, where we achieve a state-of-the-art performance of 0.55 intersection over union vs the 0.59 inter-observer agreement. Also, we show that iW-Net allows to correct the segmentation of small nodules, essential for proper patient referral decision, as well as improve the segmentation of the challenging non-solid nodules and thus may be an important tool for increasing the early diagnosis of lung cancer.
Contrast sensitivity isocontours of the central visual field
Authors: Choi Agnes Y. J. , Nivison-Smith Lisa , Phu Jack , Zangerl Barbara , Khuu Sieu K. , Jones Bryan W. , Pfeiffer Rebecca L. , Marc Robert E. , Kalloniatis Michael 
Published: August 2019

AbstractStandard automated perimetry (SAP), the most common form of perimetry used in clinical practice, is associated with high test variability, impacting clinical decision making and efficiency. Contrast sensitivity isocontours (CSIs) may reduce test variability in SAP by identifying regions of the visual field with statistically similar patterns of change that can be analysed collectively and allow a point (disease)-to-CSI (normal) comparison in disease assessment as opposed to a point (disease)-to-point (normal) comparison. CSIs in the central visual field however have limited applicability as they have only been described using visual field test patterns with low, 6° spatial sampling. In this study, CSIs were determined within the central 20° visual field using the 10-2 test grid paradigm of the Humphrey Field Analyzer which has a high 2° sampling frequency. The number of CSIs detected in the central 20° visual field was greater than previously reported with low spatial sampling and stimulus size dependent: 6 CSIs for GI, 4 CSIs for GII and GIII, and 3 CSIs for GIV and GV. CSI number and distribution were preserved with age. Use of CSIs to assess visual function in age-related macular degeneration (AMD) found CSI guided analysis detected a significantly greater deviation in sensitivity of AMD eyes from normal compared to a standard clinical pointwise comparison (−1.40 ± 0.15 dB vs −0.96 ± 0.15 dB; p < 0.05). This work suggests detection of CSIs within the central 20° is dependent on sampling strategy and stimulus size and normative distribution limits of CSIs can indicate significant functional deficits in diseases affecting the central visual field such as AMD.
Fibrinogen binding is affected by amino acid substitutions in C-terminal repeat region of fibronectin binding protein A
Authors: Casillas-Ituarte Nadia N. , DiBartola Alex C. , Broughton Megan J. , Pérez-Guzmán Lumarie , Wheeler Robert M. , Ibaraki Makoto , Lower B. Alexis , Dunn James A. , Lower Brian H. , Fowler Vance G. , Hӧӧk Magnus , McIntyre Lauren M. , Lower Steven K. , Sharma-Kuinkel Batu K. 
Published: August 2019

AbstractFibronectin-binding protein A (FnBPA), a protein displayed on the outer surface of Staphylococcus aureus, has a structured A-domain that binds fibrinogen (Fg) and a disordered repeat-region that binds fibronectin (Fn). Amino acid substitutions in Fn-binding repeats (FnBRs) have previously been linked to cardiovascular infection in humans. Here we used microtiter and atomic force microscopy (AFM) to investigate adhesion by variants of full-length FnBPA covalently anchored in the outer cell wall of Lactococcus lactis, a Gram-positive surrogate that otherwise lacks adhesins to mammalian ligands. Fn adhesion increased in five of seven FnBPA variants under static conditions. The bond targeting Fn increased its strength with load under mechanical dissociation. Substitutions extended bond lifetime (1/koff) up to 2.1 times for FnBPA-Fn. Weaker adhesion was observed for Fg in all FnBPA variants tested with microtiter. However, mechanical dissociation with AFM showed significantly increased tensile strength for Fg interacting with the E652D/H782Q variant. This is consistent with a force-induced mechanism and suggests that the dock, lock, and latch (DLL) mechanism is favored for Fg-binding under mechanical stress. Collectively, these experiments reveal that FnBPA exhibits bimodal, ligand-dependent adhesive behavior. Amino acid substitutions in the repeat-region of FnBPA impact binding to both ligands. This was unexpected for Fg since all variants have the same A-domain sequence, and the Fg-binding site is distant from the repeat region. This indicates that FnBRs may fold back on the A-domain in a way that impacts the DLL binding mechanism for Fg.
Major lithogenic contributions to the distribution and budget of iron in the North Pacific Ocean
Authors: Zheng Linjie , Sohrin Yoshiki 
Published: August 2019

AbstractRecent studies have elucidated that iron (Fe) is a critical trace metal that influences the productivity of marine ecosystems and the biogeochemical cycles of other elements in the modern ocean. However, our understanding of the biogeochemistry of Fe remains incomplete. Herein, we report basin-scale and full-depth sectional distributions of total dissolvable iron (tdFe), dissolved iron (dFe), and labile particulate iron (lpFe = tdFe – dFe) in the North Pacific Ocean, as observed during three cruises of the GEOTRACES Japan program. We found that lpFe dominates tdFe and is significantly correlated with labile particulate aluminum (lpAl): lpFe [nmol kg−1] = (0.544 ± 0.005) lpAl [nmol kg−1] + 0.11 ± 0.04, r2 = 0.968, n = 432. The results indicate a major lithogenic contribution to the distribution of particulate Fe. For dFe, the unique distribution is attributed to the combined effects of biogeochemical cycling, manganese reduction, and lithogenic contribution. Based on concurrent observations of Fe, Al, and manganese (Mn), we infer that the width of the boundary scavenging zone is approximately 500 km off the Aleutian shelf. We estimate the inventory of tdFe in the North Pacific as 1.1 × 1012 mol, which is approximately four times that of dFe. Our results emphasize the potential importance of lpFe in the ocean’s iron cycle.
Endothelial RhoA GTPase is essential for in vitro endothelial functions but dispensable for physiological in vivo angiogenesis
Authors: Zahra Fatema Tuz , Sajib Md Sanaullah , Ichiyama Yusuke , Akwii Racheal Grace , Tullar Paul E. , Cobos Christopher , Minchew Shelby A. , Doçi Colleen L. , Zheng Yi , Kubota Yoshiaki , Gutkind J. Silvio , Mikelis Constantinos M. 
Published: August 2019

AbstractImbalanced angiogenesis is a characteristic of several diseases. Rho GTPases regulate multiple cellular processes, such as cytoskeletal rearrangement, cell movement, microtubule dynamics, signal transduction and gene expression. Among the Rho GTPases, RhoA, Rac1 and Cdc42 are best characterized. The role of endothelial Rac1 and Cdc42 in embryonic development and retinal angiogenesis has been studied, however the role of endothelial RhoA is yet to be explored. Here, we aimed to identify the role of endothelial RhoA in endothelial cell functions, in embryonic and retinal development and explored compensatory mechanisms. In vitro, RhoA is involved in cell proliferation, migration and tube formation, triggered by the angiogenesis inducers Vascular Endothelial Growth Factor (VEGF) and Sphingosine-1 Phosphate (S1P). In vivo, through constitutive and inducible endothelial RhoA deficiency we tested the role of endothelial RhoA in embryonic development and retinal angiogenesis. Constitutive endothelial RhoA deficiency, although decreased survival, was not detrimental for embryonic development, while inducible endothelial RhoA deficiency presented only mild deficiencies in the retina. The redundant role of RhoA in vivo can be attributed to potential differences in the signaling cues regulating angiogenesis in physiological versus pathological conditions and to the alternative compensatory mechanisms that may be present in the in vivo setting.
Alterations in lipid metabolism of spinal cord linked to amyotrophic lateral sclerosis
Authors: Chaves-Filho Adriano Britto , Pinto Isabella Fernanda Dantas , Dantas Lucas Souza , Xavier Andre Machado , Inague Alex , Faria Rodrigo Lucas , Medeiros Marisa H. G. , Glezer Isaias , Yoshinaga Marcos Yukio , Miyamoto Sayuri 
Published: August 2019

AbstractAmyotrophic lateral sclerosis (ALS) is characterized by progressive loss of upper and lower motor neurons leading to muscle paralysis and death. While a link between dysregulated lipid metabolism and ALS has been proposed, lipidome alterations involved in disease progression are still understudied. Using a rodent model of ALS overexpressing mutant human Cu/Zn-superoxide dismutase gene (SOD1-G93A), we performed a comparative lipidomic analysis in motor cortex and spinal cord tissues of SOD1-G93A and WT rats at asymptomatic (~70 days) and symptomatic stages (~120 days). Interestingly, lipidome alterations in motor cortex were mostly related to age than ALS. In contrast, drastic changes were observed in spinal cord of SOD1-G93A 120d group, including decreased levels of cardiolipin and a 6-fold increase in several cholesteryl esters linked to polyunsaturated fatty acids. Consistent with previous studies, our findings suggest abnormal mitochondria in motor neurons and lipid droplets accumulation in aberrant astrocytes. Although the mechanism leading to cholesteryl esters accumulation remains to be established, we postulate a hypothetical model based on neuroprotection of polyunsaturated fatty acids into lipid droplets in response to increased oxidative stress. Implicated in the pathology of other neurodegenerative diseases, cholesteryl esters appear as attractive targets for further investigations.
Glycan-immobilized dual-channel field effect transistor biosensor for the rapid identification of pandemic influenza viral particles
Authors: Hideshima Sho , Hayashi Hiroki , Hinou Hiroshi , Nambuya Shunsuke , Kuroiwa Shigeki , Nakanishi Takuya , Momma Toshiyuki , Nishimura Shin-Ichiro , Sakoda Yoshihiro , Osaka Tetsuya 
Published: August 2019

AbstractPandemic influenza, triggered by the mutation of a highly pathogenic avian influenza virus (IFV), has caused considerable damage to public health. In order to identify such pandemic IFVs, antibodies that specifically recognize viral surface proteins have been widely used. However, since the analysis of a newly discovered virus is time consuming, this delays the availability of suitable detection antibodies, making this approach unsuitable for the early identification of pandemic IFVs. Here we propose a label-free semiconductor-based biosensor functionalized with sialic-acid-containing glycans for the rapid identification of the pandemic IFVs present in biological fluids. Specific glycans are able to recognize wild-type human and avian IFVs, suggesting that they are useful in discovering pandemic IFVs at the early stages of an outbreak. We successfully demonstrated that a dual-channel integrated FET biosensing system, which were modified with 6′-sialyllactose and 3′-sialyllactose for each gate area, can directly and specifically detect human H1N1 and avian H5N1 IFV particles, respectively, present in nasal mucus. Furthermore, to examine the possibility of identifying pandemic IFVs, the signal attributed to the detection of Newcastle disease virus (NDV) particles, which was selected as a prime model of a pandemic IFV, was clearly observed from both sensing gates. Our findings suggest that the proposed glycan-immobilized sensing system could be useful in identifying new pandemic IFVs at the source of an outbreak.
Worldwide human mitochondrial haplogroup distribution from urban sewage
Authors: Pipek Orsolya Anna , Medgyes-Horváth Anna , Dobos László , Stéger József , Szalai-Gindl János , Visontai Dávid , Kaas Rolf S. , Koopmans Marion , Hendriksen Rene S. , Aarestrup Frank M. , Csabai István 
Published: August 2019

AbstractCommunity level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonable agreement with both previous studies of ancient evolution or migration and current US census data; and are also readily reproducible and highly robust. Our approach presents a promising alternative for sample collection in studies focusing on the ethnic and genetic composition of populations or diseases associated with different mtDNA haplogroups and genotypes.
LncRNA SAMD12-AS1 promotes cell proliferation and inhibits apoptosis by interacting with NPM1
Authors: Liu Qi , Liu Ningning , Shangguan Qilin , Zhang Fang , Chai Wenjia , Tong Xiaomei , Zhao Xin , Li Zhiwei , Qi Dandan , Ye Xin 
Published: August 2019

AbstractChronic hepatitis B virus infection is a major risk factor for hepatocellular carcinoma. HBV infection affects lncRNA expression in infected cells, but the detailed mechanism and biological significance are not yet clear. In this study, we focused on exploring the function of the HBV-upregulated lncRNA SAMD12-AS1 in cell proliferation. We found that there is a higher level of SAMD12-AS1 expression in tumors than in adjacent nontumorous liver tissues. We showed that ectopic expression of SAMD12-AS1 promotes cell growth and blocks apoptosis, while knockdown of SAMD12-AS1 inhibits cell proliferation and enhances etoposide-induced apoptosis. Using RNA immunoprecipitation and mass spectrometry, we determined that SAMD12-AS1 interacts with NPM1 and confirmed that SAMD12-AS1(1-350) is required for the interaction with NPM1. As it is known that NPM1 interacts with the E3 ligase HDM2 and reduces HDM2-mediated p53 degradation, we examined whether SAMD12-AS1 can affect p53 stability. Overexpression of SAMD12-AS1 caused a reduction in p53 protein levels by shortening its half-life. Conversely, knockdown of SAMD12-AS1 prolonged the half-life of p53. We further demonstrated that SAMD12-AS1 increased the interaction of HDM2 and p53 and enhanced p53 ubiquitination. Our findings reveal that HBV-upregulated SAMD12-AS1 regulates cell proliferation and apoptosis via the NPM1-HDM2-p53 axis.
Pore water pressure responses in silty sediment bed under random wave action
Authors: Niu Jianwei , Xu Jishang , Dong Ping , Li Guangxue 
Published: August 2019

AbstractWe studied pore water pressure responses in silty seabed under random wave action through a series of experiments in a wide wave flume. Unlike previous experiments involving regular waves, we focus on random waves including wind-induced short waves and long waves so as to gain further insights into seabed responses and liquefaction risks posed by random waves. In particular, the study investigated how the secondary long waves that were induced by incident short wave groups affected the seabed responses. The test results revealed that these long waves could cause much larger seabed responses than the short waves (eight times larger in our flume tests). Although they had smaller wave heights than the short waves, the long waves were found to contribute much more significantly to the cumulative pore pressure than previously recognized. The likely reason is that the long waves are disproportionally effective in generating cumulative excess pore pressure, confirming qualitatively some of the earlier theoretical predictions. One of the implications from these research findings is that the existing design methods when applied to random waves could grossly underestimate liquefaction potential in silty sediment bed if either spectrum-based mean wave parameters or significant wave parameters were used.