bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron Microprobe Chemical Dating of Uraninite as a Reconnaissance Tool for Leucogranite Geochronology
Authors: Hurtado Jose , Chatterjee Nilanjan , Ramezani Jahandar , Hodges Kip , Bowring Samuel 
Published: July 2019

AbstractWe suggest that electron microprobe techniques may be employed to date Tertiary samples of uraninite (UO~2~), which can contain very high concentrations of radiogenic Pb after only a few million of years of U and Th decay. Although uraninite is regarded as a rare accessory mineral, it is relatively abundant in leucogranitic rocks such as those found in the Himalayan orogen. We apply the U-Th-total Pb electron microprobe chemical dating method to a uraninite crystal from a ca. 18.3 Ma dike of the Mugu granite from the Upper Mustang region of central Nepal. With this technique, we calculate a mean chemical date that is consistent with isotope-dilution thermal ionization mass spectrometry (ID-TIMS) U-Pb dates obtained from seven other uraninite grains and a monazite crystal from the same sample. Electron microprobe chemical dating yields results that typically will be an order of magnitude less precise than conventional dates: in the specific case of the Mugu granite, single point chemical dates each have ca. 1.5 Ma 2[sigma] (95%) confidence level uncertainties. However, the mean chemical date of 15 point analyses of the crystal we study has a 2SE (2 standard error) uncertainty of ca. 400 ka, comparable to uncertainties obtained with ID-TIMS. These results show that electron microprobe chemical dating of uraninite has substantial promise as a reconnaissance tool for the geochronology of young granitic rocks. The electron microprobe work also reveals substantial chemical complexity within uraninite that must be taken into account. The analyzed crystal displays a texturally and chemically distinctive core and rim that suggests episodic growth. Concentration gradients in U, Th, and Y across the boundary imply diffusive modification. We estimate the diffusivity of U, Th, and Y in uraninite at ca. 700 °C to be > 10-7 cm2 s-1. In contrast, Pb shows no distinctive concentration gradient across the core-rim boundary, implying that Pb has a much higher diffusivity in uraninite than U, Th, or Y. We estimate that Pb loss of as much as ca. 8.9% has occurred in the uraninite grains we analyzed by ID-TIMS.
Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks
Authors: Ackbarow Theodor , Buehler Markus 
Published: July 2019

AbstractProteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro. Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved. Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules. In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and diversity – in the following referred to as the universality-diversity paradigm (UDP) – is an overarching feature in protein materials. This paradigm is a paradox: How can a structure be universal and diverse at the same time? In protein materials, the coexistence of universality and diversity is enabled by utilizing hierarchies, which serve as an additional dimension beyond the 3D or 4D physical space. This may be crucial to understand how their structure and properties are linked, and how these materials are capable of combining seemingly disparate properties such as strength and robustness. Here we illustrate how the UDP enables to unify universal building blocks and highly diversified patterns through formation of hierarchical structures that lead to multi-functional, robust yet highly adapted structures. We illustrate these concepts in an analysis of three types of intermediate filament proteins, including vimentin, lamin and keratin.
Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications
Authors: Leitner Gabriel , Anug Ana-Maria , Merin Uzi , Silanikove Nissim 
Published: July 2019

Abstract
*Background*
Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.*Methodology/Principal Findings*We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the lobular-alveolar structure, as expected in involution stage II.

*Conclusions/Significance*
We conclude that lack of histological evidence for the appearance of involution stage II in the vast majority of modern cow's population is related to the peculiar modern dairy husbandry, in which dairy cows are induced into involution still pregnant. Because retardation of involution stage II in pregnant mammals is most likely a general physiological phenomena, it might occurs in other mammals, particularly in lactating humans. Thus, based on basic comparative physiology considerations, we suggest that concurrent lactation and pregnancy should be considered as an independent risk factor for breast cancer.
Mushroom-bodies mediate hierarchical interactions between fact- and skill-learning in Drosophila
Authors: Brembs Björn , Plendl Wolfgang 
Published: July 2019

AbstractDifferent brain circuits mediate the acquisition of skills and habits (via operant/instrumental learning) and the acquisition of facts (via classical/Pavlovian learning). Realistic learning situations always comprise interactions of skill- and fact-learning components (composite learning). So far, these interactions have escaped thorough scrutiny. Fixed flying Drosophila melanogaster at the torque meter provide one of the very few systems where the relationship of operant and classical predictors in composite learning can be studied with sufficient rigor. Experiments with wildtype, mutant and transgenic flies show that there is an interaction between predictive stimuli (classical component) and goal-directed actions (operant component) which makes composite conditioning more effective than the operant and classical components alone. Rutabaga (rut) mutants are impaired in learning about the (classical) stimuli, but show improved (operant) behavior learning. This is the first evidence that operant and classical conditioning differ not only at the circuit, but also at the molecular level. The interaction between operant and classical components is reciprocal and hierarchical, such that an impaired classical component (in rut flies) suppresses retrieval and an intact classical component suppresses acquisition of the operant component. Experiments with transgenic flies demonstrate that this suppression of operant acquisition is mediated by the mushroom-bodies and serves to ensure that the classical memories can be generalized for access by other behaviors. Extended training can overcome this suppression and transforms goal-directed actions into habitual responses. In conclusion, composite conditioning consists of two components with reciprocal, hierarchical interactions. Acquisition of the rut-dependent classical component suppresses acquisition of the rut-independent operant component via the mushroom-bodies. The operant component facilitates acquisition of the classical component via unknown, non-mushroom-body pathways. This interaction leads to efficient learning, enables generalization and prevents premature habit-formation. Habit formation after extended training reveals the gate-keeping role of the mushroom-bodies, allowing only well-rehearsed behaviors to consolidate into habits.
Unique for human centromeric regions of interphase chromatin homing (CENTRICH) govern dynamic features of chromatin fractal globules
Authors: Glinsky Gennadi 
Published: July 2019

AbstractWe report the results of the genome-wide alignment of inter- and intra-chromosomal chromatin interactions within the context of interphase chromatin binding to nuclear lamina and nucleolus. For all human chromosomes, a significant correlation exists between binding of chromosomal loci to nuclear lamina and segregation into spatially-defined distinct compartments of genome-wide chromatin interactions identified by Hi-C method. We report identification of near-centromeric intergenic regions on human chromosomes (chr2; chr10; chr17; chr1), which are highly enriched for interphase chromatin homing sites and function as attractors of long-range physical interactions (Centromeric Regions of Interphase Chromatin Homing, CENTRICH). CENTRICH are engaged in 397-1526 pair-wise interactions per 1 Kb distance, which represents 199 - 716-fold enrichment of interphase chromatin homing sites compared to genome-wide average (2-tail Fisher&apos;s exact test p values range 2.10E-101 - 1.08E-292). CENTRICH represent unique for human highly homologous DNA sequences of 3.9 - 22.4 Kb in size which are: 1) associated with nucleolus; 2) exhibit remarkably diverse regulatory protein contexts of chromatin state maps; 3) bind multiple intergenic disease-associated genomic loci (IDAGL) with documented long-range enhancer activities and established links to increased risk of developing epithelial malignancies and other common human disorders. For cancer, coronary artery disease, and type 2 diabetes, there is a statistically significant inverse correlation between the genome-wide association studies (GWAS)-defined odds ratios of increased risk of a disease and distances of SNP loci homing sites to the middle-point genomic coordinates of CENTRICH. We conclude that interactions with nucleolus and nuclear lamina may have a physiologically and pathologically significant global impact on 3D genome architecture by governing a dynamic transition of large segments of interphase human chromosomes from the open loop to folded fractal globule conformations. We propose that emergence of CENTRICH in genome's architecture during the evolution contributes to distinct phenotypic features of H.sapiens.
Medicine beyond magic bullets: a formal case for multilevel interventions
Authors: Wallace Rodrick 
Published: July 2019

AbstractWestern medicine's paradigmatic search for 'magic bullet' interventions is facing increasing difficulty: Between 1950 and 2010 the inflation-adjusted cost per USFDA-approved drug has increased exponentially in time, a draconian inverse of the famous Moore's Law of computing. A sequence of empirically-oriented statistical models suggests that carefully designed synergistic multifactorial and multiscale strategies might evade this relationship.
Detecting differential usage of exons from RNA-Seq data
Authors: Anders Simon , Reyes Alejandro , Huber Wolfgang 
Published: July 2019

AbstractRNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present DEXSeq, a statistical method to test for differential exon usage in RNA-Seq data. DEXSeq employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package.
Quantization makes relativity compatible with superluminal phenomena
Authors: Zhang Qi-Ren 
Published: July 2019

AbstractNews shocked the physicist society that neutrinos may move faster than light. Most physicists affirm that this is impossible, according to the well-established relativity. Some try to find a new theory other than relativity to explain the phenomena. In the following we show it may be explained within relativity, if the quantum theory is also taken into account.
Integrative Approach - New Level Knowledge of Functions: Opportunities and Prospects
Authors: Pokrovskii Vladimir 
Published: July 2019

AbstractIn this article, the example of the mechanisms of heart rhythmogenesis in the intact organism is used to demonstrate the new capabilities provided by an integrative approach. It is shown that the rhythm is formed in the brain, transmitted to the heart in the form of signals along the vagus nerves and reproduces the heart. Evidence: the heart rhythm reproduces the natural efferent signals in the vagus nerves in the cardio-respiratory synchronism and in the intact organism sino-atrial node performs the functions of the latent pacemaker. Integration of the two hierarchical levels of rhythmogenesis (brain and intracardiac) provides the reliability and functional perfection of cardiac rhythm generation in the body. It is expedient to extend the presented methodology for scientific analysis to other organism systems.
AntEpiSeeker2.0: extending epistasis detection to epistasis-associated pathway inference using ant colony optimization
Authors: Wang Yupeng , Liu Xinyu , Rekaya Romdhane 
Published: July 2019

AbstractGenome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking at pheromone distribution across pathways, epistasis-associated pathways can be easily identified. The effectiveness of AntEpiSeeker2.0 in inferring epistasis-associated pathways is demonstrated through a simulation study and a real data application. AntEpiSeeker 2.0 was designed to provide efficient inference of epistasis-associated pathways based on ant colony optimization and is freely available at http://lambchop.ads.uga.edu/antepiseeker2/.
Ecological connection between fish preference in the diet of Siberian cranes and their incubation period in tundra zone
Authors: Vladimirtseva Maria , Bysykatova Inga , Sleptsov Sergey 
Published: July 2019

AbstractWe researched the ecology of the third rarest crane species, Siberian crane, which breeds in northern-eastern Siberian tundra. Nesting in places near great lakes, this crane appears to be an indicator of the global warming processes that affect lake growth as a result of the permafrost situation close to the surface in tundra. Research has shown that these birds are presumably fish-eating during their incubation period, coinciding with the flooding season when fish come to areas around great lakes. Such a diet may be explained by the necessity of high-energy food during the incubating period as well as the particularity of this species for leaving plant resources around the nest point for the period of the first days after chick hatching. This situation emphasizes tight connections in the vulnerable northern ecosystems. If the water level in tundra lakes starts to be higher due to global warming, all these links may be destroyed.
Complex Systems Biology of Organisms
Authors: Baianu I. 
Published: July 2019

AbstractComplex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine's logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Metabolic, Replication and Genomic Category of Systems in Biology, Bioinformatics and Medicine
Authors: Baianu I. 
Published: July 2019

AbstractMetabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life’s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth. Genomic systems are also considered as molecular realizations of (M,R)-system subcatgeories.
Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Authors: Bisai Samiran , Bose Kaushik 
Published: July 2019

AbstractThis paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa. The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars. Height and weight were measured following standard techniques. The body mass index (BMI) was computed following standard equation. Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI. We followed the World Health Organization's classification (1995) of the public health problem of low BMI, based on adult populations worldwide. Our results show that, in general, among the tribes studied:i)Both sexes had very low levels of BMI ii)There existed high rates of CED indicating a critical nutritional condition iii)Women experienced greater nutritional stress iv)The nutritional situation is similar in both West Bengal as well as Orissa.
Direct observation and impact of co-segregated atoms in magnesium having multiple alloying elements
Authors: Zhao Xiaojun , Chen Houwen , Wilson Nick , Liu Qing , Nie Jian-Feng 
Published: July 2019

AbstractModern engineering alloys contain multiple alloying elements, but their direct observation when segregated at the atomic scale is challenging because segregation is susceptible to electron beam damage. This is very severe for magnesium alloys, especially when solute atoms segregate to form single atomic columns. Here we show that we can image segregation in magnesium alloys with atomic-resolution X-ray dispersive spectroscopy at a much lower electron voltage. We report a co-segregation pattern at twin boundaries in a magnesium alloy with both larger and smaller solutes forming alternating columns that fully occupy the twin boundary, in contrast to previous observations of half occupancy where mixed-solute columns alternate with magnesium. We further show that the solute co-segregation affects the twin migration mechanism and increases the twin boundary pinning. Our work demonstrates that the atomic-scale analysis of the structure and chemistry of solute segregation in metallic alloys with complex compositions is now possible.
Tunable ferromagnetic Weyl fermions from a hybrid nodal ring
Authors: Zheng Baobing , Xia Bowen , Wang Rui , Zhao Jinzhu , Chen Zhongjia , Zhao Yujun , Xu Hu 
Published: July 2019

AbstractRealization of nontrivial band topology in condensed matter systems is of great interest in recent years. Using first-principles calculations and symmetry analysis, we propose an exotic topological phase with tunable ferromagnetic Weyl fermions in a half-metallic oxide CrP2O7. In the absence of spin–orbit coupling (SOC), we reveal that CrP2O7 possesses a hybrid nodal ring. When SOC is present, the spin-rotation symmetry is broken. As a result, the hybrid nodal ring shrinks to discrete nodal points and forms different types of Weyl points. The Fermi arcs projected on the (100) surface are clearly visible, which can contribute to the experimental study for the topological properties of CrP2O7. In addition, the calculated quasiparticle interference patterns are also highly desirable for the experimental study of CrP2O7. Our findings provide a good candidate of ferromagnetic Weyl semimetals, and are expected to realize related topological applications with their attracted features.
Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors
Authors: Moyes Catherine L. , Wiebe Antoinette , Gleave Katherine , Trett Anna , Hancock Penelope A. , Padonou Germain Gil , Chouaïbou Mouhamadou S. , Sovi Arthur , Abuelmaali Sara A. , Ochomo Eric , Antonio-Nkondjio Christophe , Dengela Dereje , Kawada Hitoshi , Dabire Roch K. , Donnelly Martin J. , Mbogo Charles , Fornadel Christen , Coleman Michael 
Published: July 2019

AbstractThe impact of insecticide resistance in malaria vectors is poorly understood and quantified. Here a series of geospatial datasets for insecticide resistance in malaria vectors are provided, so that trends in resistance in time and space can be quantified, and the impact of resistance found in wild populations on malaria transmission in Africa can be assessed. Specifically, data have been collated and geopositioned for the prevalence of insecticide resistance, as measured by standard bioassays, in representative samples of individual species or species complexes. Data are provided for the Anopheles gambiae species complex, the Anopheles funestus subgroup, and for nine individual vector species. Data are also given for common genetic markers of resistance to support analyses of whether these markers can improve the ability to monitor resistance in low resource settings. Allele frequencies for known resistance-associated markers in the Voltage-gated sodium channel (Vgsc) are provided. In total, eight analysis-ready, standardised, geopositioned datasets encompassing over 20,000 African mosquito collections between 1957 and 2017 are released.
Biological parameters, life table and thermal requirements of Thaumastocoris peregrinus (Heteroptera: Thaumastocoridae) at different temperatures
Authors: Barbosa L. R. , Santos F. , Soliman E. P. , Rodrigues A. P. , Wilcken C. F. , Campos J. M. , Zanuncio A. J. V. , Zanuncio J. C. 
Published: July 2019

AbstractTemperature affects the development, population dynamics, reproduction and population size of insects.Thaumastocoris peregrinusCarpintero et Dellape (Heteroptera: Thaumastocoridae) is a eucalyptus pest. The objective of this study was to determine biological and life table parameters ofT.peregrinusonEucalyptus benthamiiat five temperatures (18 °C; 22 °C; 25 °C; 27 °C and 30 °C) with a relative humidity (RH) of 70 ± 10% and photoperiod of 12 hours. The duration of each instar and the longevity of this insect were inversely proportional to the temperature, regardless of sex. The nymph stage ofT.peregrinuswas 36.4 days at 18 °C and 16.1 days at 30 °C. The pre-oviposition period was 5.1 days at 30 °C and 13.1 days at 18 °C and that of oviposition was 7.6 days at 30 °C and 51.2 days at 22 °C. The generation time (T) ofT.peregrinuswas 27.11 days at 22 °C and 8.22 days at 30 °C. Lower temperatures reduced the development and increased the life stage duration ofT.peregrinus. Optimum temperatures forT.peregrinusdevelopment and reproduction were 18 and 25 °C, respectively.