bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Competition on Motivation to Fake in Employment Interviews
Authors: Ho Jordan L. , Powell Deborah M. , Barclay Pat , Gill Harjinder
Published: July 2019

Abstract. Many applicants fake, or intentionally misrepresent information, in employment interviews. Recent theories of faking propose that applicants may fake more when there are situational cues that signal intense competition for the job. We tested this proposition by manipulating the number of competitors and selection ratio in selection scenarios, and assessed individuals’ faking intentions. We also examined whether Honesty-Humility moderated the relation between competition and faking intentions. Hypotheses were tested using a between-subjects study with 775 participants. Results show that faking intentions increased with few competitors and a small selection ratio. Honesty-Humility did not moderate the relation between competition and faking intentions. Findings support competition as a situational predictor of faking intentions, lending support to models of faking.
A Path‐Tracing Monte Carlo Library for 3‐D Radiative Transfer in Highly Resolved Cloudy Atmospheres
Authors: Villefranque Najda , Fournier Richard , Couvreux Fleur , Blanco Stéphane , Cornet Céline , Eymet Vincent , Forest Vincent , Tregan Jean‐Marc
Published: July 2019

Interactions between clouds and radiation are at the root of many difficulties in numerically predicting future weather and climate and in retrieving the state of the atmosphere from remote sensing observations. The broad range of issues related to these interactions, and to three‐dimensional interactions in particular, has motivated the development of accurate radiative tools able to compute all types of radiative metrics, from monochromatic, local, and directional observables to integrated energetic quantities. Building on this community effort, we present here an open‐source library for general use in Monte Carlo algorithms. This library is devoted to the acceleration of ray tracing in complex data, typically high‐resolution large‐domain grounds and clouds. The main algorithmic advances embedded in the library are related to the construction and traversal of hierarchical grids accelerating the tracing of paths through heterogeneous fields in null‐collision (maximum cross‐section) algorithms. We show that with these hierarchical grids, the computing time is only weakly sensitive to the refinement of the volumetric data. The library is tested with a rendering algorithm that produces synthetic images of cloud radiances. Other examples of implementation are provided to demonstrate potential uses of the library in the context of 3‐D radiation studies and parameterization development, evaluation, and tuning.
Large Fugitive Methane Emissions From Urban Centers Along the U.S. East Coast
Authors: Plant Genevieve , Kort Eric A. , Floerchinger Cody , Gvakharia Alexander , Vimont Isaac , Sweeney Colm
Published: July 2019

Urban emissions remain an underexamined part of the methane budget. Here we present and interpret aircraft observations of six old and leak‐prone major cities along the East Coast of the United States. We use direct observations of methane (CH4), carbon dioxide (CO2), carbon monoxide (CO), ethane (C2H6), and their correlations to quantify CH4 emissions and attribute to natural gas. We find the five largest cities emit 0.85 (0.63, 1.12) Tg CH4/year, of which 0.75 (0.49, 1.10) Tg CH4/year is attributed to natural gas. Our estimates, which include all thermogenic methane sources including end use, are more than twice that reported in the most recent gridded EPA inventory, which does not include end‐use emissions. These results highlight that current urban inventory estimates of natural gas emissions are substantially low, either due to underestimates of leakage, lack of inclusion of end‐use emissions, or some combination thereof.
Subtropical Cyclone Anita's Potential to Tropical Transition Under Warmer Sea Surface Temperature Scenarios
Authors: Reboita M. S. , Oliveira D. M. , da Rocha R. P. , Dutra L. M. M.
Published: July 2019

On 6 March 2010, Anita, the first subtropical cyclone observed over the South Atlantic Ocean, formed near the southeastern coast of Brazil, and during its life cycle, Anita almost acquired a tropical structure. The potential of Anita to undergo tropical transition in scenarios of increased sea surface temperature (SST) was investigated through a set of numerical sensitivity experiments. The results show that, if the SST had been 2°C warmer throughout Anita's life cycle, the system would have undergone tropical transition in its maturity stage; however, if the SST had increased only during Anita's quasi‐stationary period, the tropical transition completion would have occurred only with higher values of SST (6°C).
A Large Source of Atomic Chlorine From ClNO2 Photolysis at a U.K. Landfill Site
Authors: Bannan Thomas J. , Khan M. Anwar H. , Le Breton Michael , Priestley Michael , Worrall Stephen D. , Bacak Asan , Marsden Nicholas A. , Lowe Douglas , Pitt Joe , Allen Grant , Topping David , Coe Hugh , McFiggans Gordon , Shallcross Dudley E. , Percival Carl J.
Published: July 2019

Nitryl chloride (ClNO2) acts as a source of highly reactive chlorine atoms as well as an important NOx reservoir. Measurements of ClNO2 at an operational U.K. landfill site are reported here for the first time. A peak concentration of 4 ppb of ClNO2 was found with a peak mean nighttime maximum of 0.9 ppb. Using models based upon the photolysis of observed ClNO2 and atmospheric chlorine chemistry, chlorine atom concentrations reaching in excess of 1.20 × 105 molecules/cm3 in the early morning following sunrise are calculated. These concentrations are approximately 10 times higher than previously reported in the United Kingdom, suggesting a significant impact on the oxidizing capacity around such sites. Given the ubiquity of landfill sites regionally and globally, and the large abundances of Cl atoms from the photolysis of ClNO2, chlorine chemistry has a significant impact on ozone formation and volatile organic compounds oxidation as shown by WRF‐Chem modeling.
Plasma Pressures in the Heliosheath From Cassini ENA and Voyager 2 Measurements: Validation by the Voyager 2 Heliopause Crossing
Authors: Dialynas Konstantinos , Krimigis Stamatios M. , Decker Robert B. , Mitchell Donald G.
Published: July 2019

We report “ground truth,” 28‐ to 3,500‐keV in situ ion and 5.2‐ to 55‐keV remotely sensed ENA measurements from Voyager 2/Low Energy Charged Particle detector and Cassini/Ion and Neutral Camera, respectively, that assess the components of the ion pressure in the heliosheath. In this process, we predict an interstellar neutral hydrogen density of ∼0.12 cm−3 and an interstellar magnetic field strength of ∼0.5‐nT upstream of the heliopause in the direction of V2, that is, consistent with the measured magnetic field and neutral density measurements at Voyager 1 from August 2012, when the spacecraft entered interstellar space, to date. Further, this analysis results in an estimated heliopause crossing by V2 of ∼119 AU, as observed, suggesting that the parameters deduced from the pressure analysis are valid. The shape of the >5.2‐keV ion energy spectra play a critical role toward determining the pressure balance and acceleration mechanisms inside the heliosheath.
Modeling of ARS-interacting multifunctional proteins p18 and p38.
Authors: Deineko Viktor
Published: July 2019

ARS-interacting multifunctional proteins (auxiliary components) – are nonezymatic proteins, associated with aminoacyl-tRNA synthetases – enzymes that catalyse the joining of amino acids with their corresponding tRNAs. All these proteins are complexed into large macromolecular multisynthetase complex in eukaryotes. It includes nine different ARSs and three auxiliary components. Their spatial structures precisely defined by X-ray analysis are still not known. Nevertheless, it very useful to have this structure while making biochemical studies. Bioinformatical tools were used to create structural models of two auxiliary components of multisynthetase complex – p18 and p38.
South Dakota Diversity of Temperature: Pictures from Statistical Analysis
Authors: Shmagin Boris , Todey Dennis
Published: July 2019

The regional diversity of monthly temperature was analyzed based on long-term data obtained for South Dakota (SD) from the High Plains Regional Climate Center. Multidimensional statistical methods were used and the principal results presented as a sequence of 2- and 3-dimensional scatterplot pictures depicting the quantitative results. System hierarchical model of landscape was used for research tasks formulation. Initial matrixes for three research tasks were compiled for the state. The first set of initial matrices of time series {Xt*n}, where t = number of years and n = number of meteorological stations, contains two matrixes: X1(67*29) and X2(33*94). The second set -{Xt*m}, where t = number of years and m = number of months in a year: X3(113*12), X4(110*12), and X5(102*12). The third set - {Xn*m}, where n = number of meteorological stations and m = number of months in a year, contains two matrixes: X6(29*12) and X7(94*12). Statistical analysis allowed us to differentiate weather stations by temporal trends and spatial distribution for the time interval 1932-1998. The most variable stations (Brookings, Camp Crook, and Highmore) were determined; their seasonality was described (the most variable months and correlation among months during the year) and their seasonal regime determined. The average annual and monthly temperature distributions were presented for South Dakota based on 29 and 94 stations for the time intervals 1932-1998 and 1963-1995.
PlnTFDB: Plant Transcription Factor Database – Update
Authors: Riaño-Pachón Diego Mauricio , Guedes Correa Luiz Gustavo , Mueller-Roeber Bernd
Published: July 2019

PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss Physcomitrella patens and the rice Oryza sativa spp indica. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte algae Galdieria sulphuraria and Cyanidioschyzon merolae, and the diatom Thalassiosira pseudonana. This will allow acquiring a better knowledge of plant evolution and on differentiation events. Moreover, the inclusion of large EST collections (i.e., Hordeum vulgare) have further extended the range of this resource to species whose genome are not yet sequenced but that have, nevertheless, highthroughput EST sequencing projects ongoing.
Current status of herbal and their future perspectives
Authors: Samy Ramar Perumal , Gopalakrishnakone Ponnampalam
Published: July 2019

Traditional medicine is the synthesis of therapeutic experience of generations of practicing physicians of indigenous systems of medicine. Throughout the history of mankind, many infectious diseases have been treated with herbals. The traditional medicine is increasingly solicited through the tradipractitioners and herbalists in the treatment of infectious diseases. Among the remedies used, plant drugs constitute an important part. A number of scientific investigations have highlighted the importance and the contribution of many plant families i.e. Asteraceae, Liliaceae, Apocynaceae, Solanaceae, Caesalpinaceae, Rutaceae, Piperaceae, Sapotaceae used as medicinal plants. Medicinal plants play a vital role for the development of new drugs (export and import diverse parts or bioactive compounds in the current market). The bioactive extract should be standardized on the basis of active compound. The bioactive extract should undergo limited safety studies.
Kinase independent inhibition of NFκB transcriptional activity by GRK5 through IκBα stabilization.
Authors: Sorriento Daniela , Ciccarelli Michele , Santulli Gaetano , Campanile Alfonso , Altobelli Giovanna Giuseppina , Cimini Vincenzo , Galasso Gennaro , Astone Dalila , Piscione Federico , Pastore Lucio , Trimarco Bruno , Iaccarino Guido
Published: July 2019

Members of the G protein receptor kinase (GRK) family that regulates receptor desensitization and members of the nuclear transcription factors family NF[kappa]B have been recently and convincingly demonstrated to interact, although the effects on transcription and gene expression have not yet been described. Using overexpression, knockdown (small interfering RNA) and mutagenesis experiments, we demonstrate that GRK5 couples to and stabilizes the NF[kappa]B inhibitor I[kappa]B[alpha], and inhibits NF[kappa]B activity. Studies with minigenes suggest that the N-terminal Regulation of G protein Signaling (RGS) homology (RH) domain confers GRK5 such ability. GRK5-RH domain overexpression affects NF[kappa]B dependent phenotypes, such as apoptosis protection, cytokine production and inflammation and tissue regeneration. Our results reveal a novel, unexpected role of GRK5 in NF[kappa]B transcription activity regulation that represents a possible target for diagnostic and therapeutics.
Transient-mediated fate determination in a transcriptional circuit of HIV
Authors: Weinberger Leor , Dar Roy , Simpson Michael
Published: July 2019

Steady-state behavior and bistability have been proposed as mechanisms for decision-making in gene circuits. However, transient gene expression has also been proposed to control cell fate with the decision arbitrated by the lifetime of the expression transient. Here, we report that transcriptional positive-feedback plays a critical role in determining HIV infected cell-fate by extending the duration of Tat expression transients far beyond what protein half-life modulation can achieve. To directly quantify feedback strength and its effects on the duration of Tat transcriptional pulses, we exploit the noise inherent to gene-expression and measure shifts in the autocorrelation of expression noise. The results indicate that transcriptional positive-feedback extends the single-cell Tat expression lifetime by ~6-fold for both minimal Tat circuits and full-length, actively-replicating HIV-1. Importantly, artificial weakening of Tat positive-feedback shortened the duration of Tat expression transients and biased the probability in favor of latency. Thus, transcriptional positive-feedback appears to modulate transient expression lifetime and thereby control cell-fate in HIV.
A new dynamic property of human consciousness
Authors: Lee UnCheol , Kim Seunghwan , Noh Gyu-Jeong , Choi Byung-Moon
Published: July 2019

As pointed out by William James, "the consciousness is a dynamic process, not a thing" , during which short term integration is succeeded by another differentiated neural state through the continual interplay between the environment, the body, and the brain itself. Thus, the dynamic structure underlying successive states of the brain is important for understanding human consciousness as a process. In order to investigate the dynamic property of human consciousness, we developed a new method to reconstruct a state space from electroencephalogram(EEG), in which a trajectory, reflecting states of consciousness, is constructed based on the global information integration of the brain. EEGs were obtained from 14 subjects received an intravenous bolus of propopol. Here we show that the degree of human consciousness is directly associated with the information integration capacity of gamma wave, which is significantly higher in the conscious state than in the unconscious state. And we found a new time evolutional property of human consciousness. The conscious state showed a lower dimensional dynamic process which changed to a random-like process after loss of consciousness. This characteristic dynamic property, appeared only in the gamma band, might be used as an indicator to distinguish the conscious and unconscious states and also considered as an important fact for the human consciousness model.
Reciprocal homeostatic reactions to chronic excitatory synaptic receptor inactivation in developing cerebral cortex networks
Authors: Corner Michael
Published: July 2019

Chronic blockade of actively excitatory glutamatergic synaptic receptors in co-cultured organotypic rodent neocortex explants leads to a compensatory up-regulation of otherwise inactive input channels so as to maintain almost normal levels of ongoing bursts of action potentials. We report here that this homeostatic return of spontaneous (now kainate receptor driven) firing is accompanied by a reciprocal down-regulation of blocked AMPA and NMDA receptors, such that the developing cortical network is protected against becoming hyperactive when those synaptic inputs are again able to transmit normally.
Ecological optimum of ectothermic organisms: static-dynamical approach
Authors: Verbitsky Vladimir , Verbitskaya Tamara
Published: July 2019

During 20th century the majority of researchers interpreted ecological optimum as a certain combination of ambient factors which is optimal for growth, existence and reproduction of an organism. However, it was revealed in many species, that the maximum rates of various processes in an organism are achieved at various combinations of values of different factors, and under variable regimes as opposite to constant regimes. One may state that there is no well defined general concept which takes into account a bulk of data that do not conform the traditional definition of ecological optimum. Here, we show that it is necessary to make distinction between concepts of "static" and "dynamic" optima. It is needed for definition of real ecological optimum and creation of optimum conditions for given factor. We show also that it is necessary to take into account so-called delayed effects of factors. Basing on the analysis of responses of zooplankton to various temperatures and phosphoric load, we show that an optimum has "dynamic" characteristics besides previously known "static" ones, like a range of factor values on tolerance curve or a doze of factor. These "dynamic" characteristics are cyclic and stepwise changes of a factor, a directionality of factor's dynamics in case of stepwise changes and additionally, we reveal stimulating and inhibiting delayed effects of factors. Our results allow for a more detailed concept of ecological optimum, and also may stimulate investigations of quantitative contribution of various parameters of environmental factors to an ecological optimum of an organism or population.
Cryopreservation of a whole liver
Authors: Gavish Zohar , Arav Amir , Ben-Haim Menahem
Published: July 2019

Preservation of vascularized organs such as the liver is limited to 24hrs. before destructive processes disqualify it for transplantation. This narrow time window prevents surgeons from performing optimal pathogen screening and matching tests which often lead to re-transplantation. Numerous problems are associated with viably freezing and thawing a whole liver: complicated geometry, poor heat transfer, release of latent heat and the difficulty of generating a uniform cooling rate. Our past success led us to apply our novel freezing technique to a larger solid organ, the liver. Whole livers were frozen/thawed using a directional solidification apparatuses; viability was tested by means of integrity and functionality in vitro and in auxiliary liver transplantation. Thawed livers were intact with over 80% viability; histology revealed normal architecture, bile production and blood flow following auxillary transplantation where normal. Our results suggest a novel cryopreservation method and may enable better organ donor-recipient matching in the future
Bio-communication of Plants
Authors: Witzany Guenther
Published: July 2019

Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns – mediated by signs.
Effects of Pre- and Post-natal smoke exposure on airway neural responses
Authors: Wu Zhong.-Xin , Kish Vincent , Batchelor Thomas , Dey Richard
Published: July 2019

Abundant epidemiological data shows that maternal smoking during pregnancy or second-hand smoke exposure during neonatal life and infancy increases the incidence of respiratory illnesses later in life. However, underlying mechanisms initiated in early life but affecting adult disease remain undefined. Neurotrophins, including nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), are neurotrophic factors essential in promoting and maintaining differentiation, growth, and survival of central and peripheral nervous system. The goal of this proposal is to examine the potential role of neurotrophin release in mediating long-term effects of prenatal and early postnatal smoke exposure. Our studies showed that an initial exposure to smoke during prenatal and early postnatal periods significantly changed lung function, substance P (SP) innervation in trachea and the level of NGF in BAL fluid after re-exposure to smoke on adult (postnatal day (PD) 60). In controls, smoke exposure (PD 28) with a subsequent re-exposure at PD 60 did not affect lung function or SP innervation or NGF levels. PCR array revealed enhanced expression of multiple genes including NGF and its receptor by smoke exposure only during early prenatal periods. These data suggest that a critical period of exposure exists in early periods of development. Increased expression of NGF and its receptor in airway caused by smoke exposure may enhance susceptibility to respiratory illnesses in adult. These findings have obvious and significant implication both for smoking during pregnancy and the effects of second hand tobacco smoke exposure. The study provides evidence that prenatal and early postnatal life are periods of enhanced susceptibility to detrimental effects of cigarette smoke. These effects appear to be mediated through the release of neurotrophic factors like NGF which regulate growth and maturation of the airway during these susceptible periods.
Requirement of Activation for Hepatitis B Virus Infection
Authors: Bruns Michael , Maenz Claudia
Published: July 2019

Although _in vitro_ models of human hepatitis B virus replication are established, so far none could approximate infection efficiency as expected from in vivo observations. Susceptibility for HBV infections has only been reported for primary hepatocytes of human, chimpanzee or Tupaia belangeri and the cell line HepaRG. Here we show that the insusceptible human hepatoma cell line HepG2 can be infected, when the virus was beforehand activated by passage over whole duck liver cell cultures. That suggests an activation step to be performed by specialized liver cells.
Intracellular Regulatory Networks are close to Monotone Systems
Authors: Ma'ayan Avi , Iyengar Ravi , Sontag Eduardo
Published: July 2019

Several meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast transcriptional networks and a mammalian signaling network contain far more sign-consistent feedback and feed-forward loops than expected for shuffled networks. Inconsistent loops with negative links can be more easily removed from real regulatory networks as compared to shuffled networks. This topological feature in real networks emerges from the presence of hubs that are enriched for either negative or positive links, and is not due to a preference for double negative links in paths. These observations indicate that intracellular regulatory networks may be close to monotone systems and that this network topology contributes to the dynamic stability.
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Authors: Shi Leming , Jones Wendell , Jensen Roderick , Harris Stephen , Perkins Roger , Goodsaid Federico , Guo Lei , Croner Lisa , Boysen Cecilie , Fang Hong , Amur Shashi , Bao Wenjun , Barbacioru Catalin , Bertholet Vincent , Cao Xiaoxi Megan , Chu Tzu-Ming , Collins Patrick , Fan Xiao-hui , Frueh Felix , Fuscoe James , Guo Xu , Han Jing , Herman Damir , Hong Huixiao , Kawasaki Ernest , Li Quan-Zhen , Luo Yuling , Ma Yunqing , Mei Nan , Peterson Ron , Puri Raj , Qian Feng , Shippy Richard , Su Zhenqiang , Sun Yongming Andrew , Sun Hongmei , Thorn Brett , Turpaz Yaron , Wang Charles , Wang Sue-Jane , Warrington Janet , Willey James , Wu Jie , Xie Qian , Zhang Liang , Zhang Lu , Zhong Sheng , Wolfinger Russell , Tong Weida
Published: July 2019

Reproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity.
Swine Influenza A Evolution via Recombination - Genetic Drift Reservoir
Authors: Niman Henry
Published: July 2019

The looming influenza pandemic has focused attention^1-4^ on the rapid evolution of H5N1 and other human and avian serotypes. The basic tenets of influenza genetics^5^ define gradual changes as drifts caused by point mutations created by a polymerase that lacks a proof reading function. More abrupt changes have been linked to reassortment, which shuffles the eight sub-genomic segments of the influenza genome in dually infected host. The complex evolution of these viruses has created a challenge in vaccine development. Swine influenza isolates from 2003 and 2004 have been identified^6^ that have acquired a human influenza gene, PB1. My analysis of the eight gene segments found large portions of two genes, PB2 and PA, which were identical matches with 1977 swine isolates^7,8^. Additional regions were exact matches with 1998 and 2002 isolates,^9,10^ demonstrating homologous recombination between earlier genomes. The absolute fidelity discounts the role of point mutations in gene drift. Moreover the human PB1 gene represented a reservoir for acquisition of polymorphisms in human seasonal flu. These observations challenge the basic tenets of influenza genetics and provide a method for predicting the changes in seasonal and pandemic influenza, as well as other rapidly evolving genomes.
A Three dimesional stochastic spatio-temporal model of cell spreading
Authors: Xiong Yuguang , Rangamani Padmini , Dubin-Thaler Benjamin , Sheetz Michael , Iyengar Ravi
Published: July 2019

Cell motility is important for many physiological processes and the underlyingbiochemical reactions motility have been well-characterized. Mathematical models, usingthe biochemical reactions and focused on different types of spreading behavior have beenconstructed and analyzed. In this study, we build on these previous models to develop athree-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell spreading behavior. We analyzed the effects of varying branching reaction rates, membrane resistance forces and capping protein concentrations on the dynamics of isotropic spreading. The simulations allowed us to identify the range within which branching reaction rates and membrane force values cooperate to yield isotropic spreading behavior. The model predicts increasing capping protein concentration would lead to a linear decrease in average peripheral velocity. We tested this prediction experimentally using varying concentrations of a pharmacologic agent (Cytochalasin D)that caps growing actin filaments. We find that the experimental results agree with the numerical simulations. Thus, a spatio-temporally complex model made up of a simple set of stochastic reactions near the cell surface, when constrained by membrane forces, can yield deterministic behavior as characterized by isotropic cell spreading.
Concentrations of Polychlorinated Biphenyls (PCBs), Polychlorinated Dibenzo-p-dioxins and Furans (PCDD/Fs), and Polybrominated Diphenyl Ethers (PBDEs) as Functions of Sample Depth in Killer Whale (Orcinus orca) Blubber
Authors: Ikonomou Michael , Rayne Sierra , Crewe Norman
Published: July 2019

Concentrations of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and polybrominated diphenyl ethers (PBDEs) were examined as a function of depth in killer whale (Orcinus orca) blubber samples. Lipid-normalized concentrations of PCBs, PCDD/Fs, and PBDEs did not display significant variation with depth in three distinct blubber layers (outer, central, and inner). Significantly more variation in contaminant concentrations were observed with depth on a wet weight basis for the killer whale sample. The current study indicates that non-invasive microdart biopsy sampling methods commonly used for monitoring contaminants in marine mammals yield representative details on contaminant burdens for chlorinated and brominated aromatic compounds in marine mammal blubber, regardless of the quantity and type of blubber sampled, provided that lipid normalization is performed on resulting analytical determinations.
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

We 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

Proteins 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

*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

Different 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

We 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'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

Western 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

RNA-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.
Universality of a mesenchymal transition signature in invasive solid cancers
Authors: Anastassiou Dimitris
Published: July 2019

In this brief communication, additional computational validation is provided consistent with the unifying hypothesis that a shared biological mechanism of mesenchymal transition, reflected by a precise gene expression signature, may be present in all types of solid cancers when they reach a particular stage of invasiveness.
Quantization makes relativity compatible with superluminal phenomena
Authors: Zhang Qi-Ren
Published: July 2019

News 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

In 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

Genome-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

We 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

Complex 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