bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seabird Supertrees: Combining Partial Estimates of Procellariiform Phylogeny
Authors: Kennedy Martyn , Page Roderic D. M. 
Published: September 2019

Abstract
The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exist, we need to combine different hypotheses in a way that provides the best estimate of the phylogeny for that group. Here, we combine seven seabird phylogenies (based on behavioral, DNA–DNA hybridization, isozyme, life history, morphological, and sequence data) to generate a comprehensive supertree for the Procellariiformes using matrix representation with parsimony. This phylogeny contains 122 taxa and represents a conservative estimate of combined relationships presented in the original seven source trees. We compared the supertree with results of a combined sequence data supermatrix for 103 seabird taxa. Results of the two approaches are broadly concordant, but matrix representation with parsimony provides a more comprehensive and more conservative estimate of the phylogeny of the group because it is less influenced by the largest of the source studies (which uses a single, relatively quickly evolving gene). Genetic data sets that can be combined in a supermatrix approach are currently less likely to be available than phylogenies that can be combined using some form of supertree approach. Although there are limitations to both of those approaches, both would be simpler if all phylogenetic studies made both their data sets and trees they generate available through databases such as TREEBASE.
Western Sandpipers (Calidris Mauri) During the Nonbreeding Season: Spatial Segregation on a Hemispheric Scale
Authors: Nebel Silke , Lank David B. , O'Hara Patrick D. , Fernández Guillermo , Haase Ben , Delgado Francisco , Estela Felipe A. , Ogden Lesley J. Evans , Harrington Brian , Kus Barbara E. , Lyons James E. , Mercier Francine , Ortego Brent , Takekawa John Y. , Warnock Nils , Warnock Sarah E. 
Published: September 2019

Abstract
The nonbreeding distribution of Western Sandpipers (Calidris mauri) was documented using 19 data sets from 13 sites along the Pacific and Atlantic coasts of the Americas. Western Sandpipers showed latitudinal segregation with regard to sex and age. Females wintered farther south than males. A “U” shaped pattern was found with respect to age, with juveniles occurring at higher proportions at both the northern and southern ends of the range. Distribution of sexes might be affected by differences in bill length and a latitudinal trend in depth distribution of prey. For age class distribution, two different life-history tactics of juveniles might exist that are related to the higher cost of feather wear for juveniles compared to adults. Most juveniles complete three long-distance migrations on one set of flight feathers whereas adults complete two. Juveniles may winter either far north, thereby reducing feather wear induced by ultraviolet light, migration, or both, or far south and spend the summer on the nonbreeding area.
scds: computational annotation of doublets in single-cell RNA sequencing data
Authors: Bais Abha S , Kostka Dennis 
Published: September 2019

Abstract

Motivation
Single-cell RNA sequencing (scRNA-seq) technologies enable the study of transcriptional heterogeneity at the resolution of individual cells and have an increasing impact on biomedical research. However, it is known that these methods sometimes wrongly consider two or more cells as single cells, and that a number of so-called doublets is present in the output of such experiments. Treating doublets as single cells in downstream analyses can severely bias a study’s conclusions, and therefore computational strategies for the identification of doublets are needed.

Results
With scds, we propose two new approaches for in silico doublet identification: Co-expression based doublet scoring (cxds) and binary classification based doublet scoring (bcds). The co-expression based approach, cxds, utilizes binarized (absence/presence) gene expression data and, employing a binomial model for the co-expression of pairs of genes, yields interpretable doublet annotations. bcds, on the other hand, uses a binary classification approach to discriminate artificial doublets from original data. We apply our methods and existing computational doublet identification approaches to four datasets with experimental doublet annotations and find that our methods perform at least as well as the state of the art, at comparably little computational cost. We observe appreciable differences between methods and across datasets and that no approach dominates all others. In summary, scds presents a scalable, competitive approach that allows for doublet annotation of datasets with thousands of cells in a matter of seconds.

Availability and implementation
scds is implemented as a Bioconductor R package (doi: 10.18129/B9.bioc.scds).

Supplementary information
Supplementary data are available at Bioinformatics online.
Neural crest-derived tumor neuroblastoma and melanoma share 1p13.2 as susceptibility locus that shows a long-range interaction with the SLC16A1 gene
Authors: Avitabile Marianna , Succoio Mariangela , Testori Alessandro , Cardinale Antonella , Vaksman Zalman , Lasorsa Vito Alessandro , Cantalupo Sueva , Esposito Matteo , Cimmino Flora , Montella Annalaura , Formicola Daniela , Koster Jan , Andreotti Virginia , Ghiorzo Paola , Romano Maria Fiammetta , Staibano Stefania , Scalvenzi Massimiliano , Ayala Fabrizio , Hakonarson Hakon , Corrias Maria Valeria , Devoto Marcella , Law Matthew H , Iles Mark M , Brown Kevin , Diskin Sharon , Zambrano Nicola , Iolascon Achille , Capasso Mario 
Published: September 2019

Abstract
Neuroblastoma (NB) and malignant cutaneous melanoma (CMM) are neural crest cells (NCC)-derived tumors and may have a shared genetic basis, but this has not been investigated systematically by genome-wide association studies (GWAS). We took a three-staged approach to conduct cross-disease meta-analysis of GWAS for NB and CMM (2101 NB cases and 4202 controls; 12 874 CMM cases and 23 203 controls) to identify shared loci. Findings were replicated in 1403 NB cases and 1403 controls of European ancestry and in 636 NB, 508 CMM cases and 2066 controls of Italian origin. We found a cross-association at locus 1p13.2 (rs2153977, odds ratio = 0.91, P = 5.36 × 10−8). We also detected a suggestive (P &lt; 10−7) NB-CMM cross-association at 2q37.1 with opposite effect on cancer risk. Pathway analysis of 110 NB-CMM risk loci with P &lt; 10−4 demonstrated enrichment of biological processes such as cell migration, cell cycle, metabolism and immune response, which are essential of human NCC development, underlying both tumors. In vitro and in silico analyses indicated that the rs2153977-T protective allele, located in an NB and CMM enhancer, decreased expression of SLC16A1 via long-range loop formation and altered a T-box protein binding site. Upon depletion of SLC16A1, we observed a decrease of cellular proliferation and invasion in both NB and CMM cell lines, suggesting its role as oncogene. This is the largest study to date examining pleiotropy across two NC cell-derived tumors identifying 1p13.2 as common susceptibility locus for NB and CMM risk.
We demonstrate that combining genome-wide association studies results across cancers with same origins can identify new loci common to neuroblastoma and melanoma arising from tissues which originate from neural crest cells. Our results also show 1p13.2 confer risk to neuroblastoma and melanoma by regulating SLC16A1.
Neural Representations of Abstract Concepts: Identifying Underlying Neurosemantic Dimensions
Authors: Vargas Robert , Just Marcel Adam 
Published: September 2019

Abstract
The abstractness of concepts is sometimes defined indirectly as lacking concreteness, this view provides little insight into their cognitive or neural basis. Multivariate pattern analytic techniques applied to functional magnetic resonance imaging data were used to characterize the neural representations of 28 individual abstract concepts. A classifier trained on the concepts’ neural signatures reliably decoded their neural representations in an independent subset of data for each participant. There was considerable commonality of the neural representations across participants as indicated by the accurate classification of each participant’s concepts based on the neural signatures obtained in other participants. Group-level factor analysis revealed 3 semantic dimensions underlying the 28 concepts, suggesting a brain-based ontology for this set of abstract concepts. The 3 dimensions corresponded to 1) the degree a concept was Verbally Represented; 2) whether a concept was External (or Internal) to the individual, and 3) whether the concept contained Social Content. Further exploration of the Verbal Representation dimension suggests that the degree a concept is verbally represented can be construed as a point on a continuum between language faculties and perceptual faculties. A predictive model, based on independent behavioral ratings of the 28 concepts along the 3 factor dimensions, provided converging evidence for the interpretations.
The United States under President Trump: Gravedigger of International Law
Authors: Talmon Stefan 
Published: September 2019

Abstract
The United States’ recognition of Israeli sovereignty over the Syrian Golan has been widely considered a flagrant breach of international law. This illegal act gives reason to examine the relationship between the United States under President Trump and international law more generally. Unlike its predecessors, the Trump administration has not just violated international law whenever U.S. economic, political, or strategic interests demanded it to do so, it has rather challenged international law and its institutions as such, and has actively undermined them. The attitude of the Trump administration towards international law and its institutions is marked by an unparalleled contempt or disdain. This article delivers a powerful “J’accuse” against this international law nihilism.
Lopinavir-Ritonavir Impairs Adrenal Function in Infants
Authors: Kariyawasam Dulanjalee , Peries Marianne , Foissac Frantz , Eymard-Duvernay Sabrina , Tylleskär Thorkild , Singata-Madliki Mandisa , Kankasa Chipepo , Meda Nicolas , Tumwine James , Mwiya Mwiya , Engebretsen Ingunn , Flück Christa E , Hartmann Michaela F , Wudy Stefan A , Hirt Deborah , Treluyer Jean Marc , Molès Jean-Pierre , Blanche Stéphane , Van De Perre Philippe , Polak Michel , Nagot Nicolas ,   ANRS 12174 Trial Group, Nagot N , Vallo R , Marechal V , Neveu D , Peries M , Van de Perre P , Kankasa C , Mwiya M , Siuluta C , Rutagwera D , Tumwine J K , Kwagala M , Ndeezi G , Meda N , Traore H , Some E , Neboua D , Hofmeyr G J , Sunday A , Singata M , Hofmeyr G J , Sunday A , Jackson D , Engebretsen I M S , Sommerfelt H , Tylleskar T , Lombard C , Blanche S , Sommerfelt H , Rekacewicz C 
Published: September 2019

AbstractBackgroundPerinatal treatment with lopinavir boosted by ritonavir (LPV/r) is associated with steroidogenic abnormalities. Long-term effects in infants have not been studied.MethodsAdrenal-hormone profiles were compared at weeks 6 and 26 between human immunodeficiency virus (HIV)-1–exposed but uninfected infants randomly assigned at 7 days of life to prophylaxis with LPV/r or lamivudine (3TC) to prevent transmission during breastfeeding. LPV/r in vitro effect on steroidogenesis was assessed in H295R cells.ResultsAt week 6, 159 frozen plasma samples from Burkina Faso and South Africa were assessed (LPV/r group: n = 92; 3TC group: n = 67) and at week 26, 95 samples from Burkina Faso (LPV/r group: n = 47; 3TC group: n = 48). At week 6, LPV/r-treated infants had a higher median dehydroepiandrosterone (DHEA) level than infants from the 3TC arm: 3.91 versus 1.48 ng/mL (P &lt; .001). Higher DHEA levels (&gt;5 ng/mL) at week 6 were associated with higher 17-OH-pregnenolone (7.78 vs 3.71 ng/mL, P = .0004) and lower testosterone (0.05 vs 1.34 ng/mL, P = .009) levels in LPV/r-exposed children. There was a significant correlation between the DHEA and LPV/r AUC levels (ρ = 0.40, P = .019) and Ctrough (ρ = 0.40, P = .017). At week 26, DHEA levels remained higher in the LPV/r arm: 0.45 versus 0.13 ng/mL (P = .002). Lopinavir, but not ritonavir, inhibited CYP17A1 and CYP21A2 activity in H295R cells.ConclusionsLopinavir was associated with dose-dependent adrenal dysfunction in infants. The impact of long-term exposure and potential clinical consequences require evaluation.Clinical Trials RegistrationNCT00640263
Developmental competence and ultrastructural changes of heat-stressed mouse early blastocysts produced in vitro
Authors: Qu Pingping , Tian Wenru , Li Tao , Jiang Zhongling , Gao Shansong , Tian Zhongjie , Wang Mingzhi 
Published: September 2019

Abstract
Mouse early blastocysts were exposed to temperatures of 39°C and 41°C for 2 h, respectively, to determine their developmental competence and ultrastructural changes. The results showed that heat stress at 41°C for 2 h, significantly reduced the percentages of expanded and hatched blastocysts, but not at 39°C for 2 h. The average cell numbers in expanded blastocysts, which developed from early blastocysts heat-stressed at temperatures of 39°C and 41°C, were significantly reduced. The average cell numbers in hatched blastocysts subjected to heat stress were no different from those in the control group cultured at 37°C. The mitochondria of the early blastocysts heat-stressed at 39°C for 2 h, were slightly swollen, but they had recovered after culturing at 37°C for 2 h. However, the mitochondria in the blastocysts heat stressed at 41°C for 2 h were severely swollen, and their number increased. The ribosomes shed from the rough endoplasmic reticulum, and the number of secondary lysosomes in the plasma increased. The integrity of desmosomes was disrupted. The space between the nuclear envelope and the perivitelline membrane enlarged. The fibre fraction and the particulate fraction of nucleoli were separated. The heterochromatin in nucleoli was also increased in its quantity. There were some lamellar-shape structures and heterogeneous dense materials exhibiting in the cytoplasm. The ultrastructural changes induced by heat shock at 41°C for 2 h were not reversible. In conclusion, the damage of heat stress to mitochondria, lysosomes, ribosomes and cell nucleus, may be one of the most important factors that inhibit the normal development of mouse early blastocysts.
Adjustment of the annual cycle to climatic change in a long-lived migratory bird species
Authors: Møller A. P. , Flensted-Jensen E. , Mardal W. 
Published: September 2019

Abstract
Climate change has advanced the phenology of many organisms. Migratory animals face particular problems because climate change in the breeding and the wintering range may be asynchronous, preventing rapid response to changing conditions. Advancement in timing of spring migration may have carry-over effects to other parts of the annual cycle, simply because advancement of one event in the annual cycle also advances subsequent events, gradually causing a general shift in the timing of the entire annual cycle. Such a phenotypic shift could generate accumulating effects over the years for individuals, but also across generations. Here we test this novel hypothesis of phenotypic response to climate change by using long-term data on the Arctic tern Sterna paradisaea. Mean breeding date advanced by almost three weeks during the last 70 years. Annual arrival date at the breeding grounds during a period of 47 years was predicted by environmental conditions in the winter quarters in the Southern Ocean near the Antarctic and by mean breeding date the previous year. Annual mean breeding date was only margiually determined by timing of arrival the current year, but to a larger extent by arrival date and breeding date the previous year. Learning affected arrival date as shown by a positive correlation between arrival date in year (i + 1) relative to breeding date in year (i) and the selective advantage of early breeding in year (i). This provides a mechanism for changes in arrival date being adjusted to changing environmental conditions. This study suggests that adaptation to changing climatic conditions can be achieved through learning from year to year.
Prophylactic effect of vitamin E against hepatotoxicity, nephrotoxicity, haematological indices and histopathology induced by diazinon insecticide in mice
Authors: El-Shenawy Nahla S. , Al-Eisa Rasha A. , El-Salmy Fawzia , Salah Omema 
Published: September 2019

Abstract
Considering that the involvement of reactive oxygen species (ROS) has been implicated in the toxicity of various pesticides, this study was designed to study the ameliorative effect of Vitamin E (100 mg/kg body weight) on mice (25 - 30 mg) treated with diazinon (32.5 or 16.25 mg/kg body weight) organophosphate insecticide for 14 days. Subchronic DZN exposure and the protective effects of vitamins E (vitE) were evaluated for their effects on haematological indices, the enzymes concerning liver damage [plasma alanine aminotransferase (ALT), aspartate aminotaransferase (AST), alkaline phosphatise (AIP), and some parameters of kidney function (urea and creatinine) in mice. Additionally, the histopathological changes in liver and kidney tissue were examined. The high dose of diazinon (DZNH) decreased the body weight significantly at the end of experiment. Additionally, the liver and kidney were examines for histopathological changes. The high dose of diazinon decreased body weight significantly. Moreover, there was a statistically significant decrease in haemoglobin (Hb), red blood cell (RBC) and hematocrit (Hct) in diazinon-treated mice compared to controls. This decrease was partially remedied in the diazinon-treated group that also received vitE. Damage in the liver and kidney tissues was also evident as elevated plasma ALT, AST, ALP, urea and creatinine. VitE partially counteracts the toxic effect of DZN and repairs tissue damage in the liver and kidney, especially when supplemented to 1/4 LD50 intoxicated animals. Histopathological changes in liver and kidney were observed only in 32.5 mg/kg DZN given group. These results suggest that the effects of DZN are dose dependent. No pathological findings were observed in vitE + DZN treated groups. According to the present study, we conclude that vitE can reduce the detrimental impacts of diazinon on haematological indicies, as well as liver and kidney function.
Life cycle of Craspedacusta sowerbyi xinyangensis
Authors: Xu Shanliang , Wang Danli 
Published: September 2019

Abstract
To explore the life cycle of Craspedacusta, the authors collected male and female specimens of the Craspedacusta sowerbyi xinyangensis in a small fire-fighting pond in Ningbo, Zhejiang Province in July, 2005 and 2006. The development of C. sowerbyi xinyangensis was studied from zygote to medusa by means of light microscopy and digital camera. The zygotes of C. sowerbyi xinyangensis are globular and smooth (90 - 105 μm diameter) and have an equal, total cleavage to the two-cell stage 15 min after fertilization. The embryos enter the four-cell stage after another 15 min and become multicellular embryos after 3h 15 min. At this stage the embryos have a diameter similar to fertilized eggs but have uneven surfaces that are distinct from the smooth surfaces of the uncleaved zygotes. Solid gastrulae are formed 7 h after fertilization. These are spherical planulae with short surface cilia that begin to swim in slow clockwise circles. After 12 h, they lose their cilia, cease swimming and become elongated planulae with one end larger than the other. Rod-like planulae, similar in thickness at both ends, are formed after an additional 7 h. After 4 days, the planulae develop into tiny polyps having two germ layers and a gastrovascular cavity. The polyp mouth is 50 - 62 µm in diameter, lacking tentacles but having nematocysts around the mouth. Planulae become mature polyps after 10 days (15 days after fertilization). Medusa buds (45 - 88 μm diameter) are formed by polyp budding, which soon become free-living medusae with 8 tentacles (380 - 620 μm diameters). Sometimes, the movement of frustules, which are formed by the polyps and similar to planulae in morphology can also be observed.
Mechanisms of species divergence through visual adaptation and sexual selection: Perspectives from a cichlid model system
Authors: Maan Martine E. , Seehausen Ole 
Published: September 2019

Abstract
The theory of ecological speciation suggests that assortative mating evolves most easily when mating preferences are directly linked to ecological traits that are subject to divergent selection. Sensory adaptation can play a major role in this process, because selective mating is often mediated by sexual signals: bright colours, complex song, pheromone blends and so on. When divergent sensory adaptation affects the perception of such signals, mating patterns may change as an immediate consequence. Alternatively, mating preferences can diverge as a result of indirect effects: assortative mating may be promoted by selection against intermediate phenotypes that are maladapted to their (sensory) environment. For Lake Victoria cichlids, the visual environment constitutes an important selective force that is heterogeneous across geographical and water depth gradients. We investigate the direct and indirect effects of this heterogeneity on the evolution of female preferences for alternative male nuptial colours (red and blue) in the genus Pundamilia. Here, we review the current evidence for divergent sensory drive in this system, extract general principles, and discuss future perspectives.
Can color vision variation explain sex differences in invertebrate foraging by capuchin monkeys?
Authors: Melin Amanda D. , Fedigan Linda M. , Young Hilary C. , Kawamura Shoji 
Published: September 2019

Abstract
Invertebrates are the main source of protein for many small-to-medium sized monkeys. Prey vary in size, mobility, degree of protective covering, and use of the forest, i.e. canopy height, and whether they are exposed or embed themselves in substrates. Sex-differentiation in foraging patterns is well documented for some monkey species and recent studies find that color vision phenotype can also affect invertebrate foraging. Since vision phenotype is polymorphic and sex-linked in most New World monkeys - males have dichromatic vision and females have either dichromatic or trichromatic vision - this raises the possibility that sex differences are linked to visual ecology. We tested predicted sex differences for invertebrate foraging in white-faced capuchins Cebus capucinus and conducted 12 months of study on four free-ranging groups between January 2007 and September 2008. We found both sex and color vision effects. Sex: Males spent more time foraging for invertebrates on the ground. Females spent more time consuming embedded, colonial invertebrates, ate relatively more “soft” sedentary invertebrates, and devoted more of their activity budget to invertebrate foraging. Color Vision: Dichromatic monkeys had a higher capture efficiency of exposed invertebrates and spent less time visually foraging. Trichromats ate relatively more “hard” sedentary invertebrates. We conclude that some variation in invertebrate foraging reflects differences between the sexes that may be due to disparities in size, strength, reproductive demands or niche preferences. However, other intraspecific variation in invertebrate foraging that might be mistakenly attributed to sex differences actually reflects differences in color vision.