bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers
Authors: Huang Shi 
Published: July 2019

AbstractInterpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results. This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution. The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction. Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny. A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time. This ‘slow clock’ method showed that humans are genetically more distant to orangutans than African apes are and separated from the pongid clade (containing orangutan and African apes) 17.3 million years ago. Also, tarsiers are genetically closer to lorises than simian primates are, suggesting a tarsier-loris clade to the exclusion of simian primates. The validity and internal coherence of the primate phylogeny here were independently verified. The molecular split time of human and pongid calibrated from the fossil record of gorilla, or the fossil times for the radiation of anthropoids/mammals at the K/T boundary and for the Eutheria-Metatheria split in the Early Cretaceous, were independently confirmed from molecular dating calibrated using the fossil split times of tarsier-loris and two other pairs of mammals (mouse-rat and opossum-kangaroo). This remarkable and unprecedented concordance between molecules and fossils provides the latest confirmation of the inseparable unity of genotype and phenotype and the unmatched value of MGD in a coherent interpretation of life history.
Factors influencing impala distribution patterns in Nairobi National Park, Kenya
Authors: Obade Vincent , Clercq Eva 
Published: July 2019

AbstractMonitoring the distribution of wild animals using appropriate methods and survey techniques is essential not only for sustainable management but also to avoid wastage of resources. This study applied remote sensing to investigate the factors influencing the distribution of herbivores in Nairobi National Park, Kenya. Impala was selected as indicator specie for the herbivores within the park, because the population of impala had drastically reduced over time. The influence of food availability, water and disturbance on herbivore presence was investigated. A positive significant statistical relationship between impala population density and feed availability was observed. However, the correlation between impala population density and water distance was negative, indicating less impalas as the distance from water sources increase. An interesting finding was the expectation of greater impala population presence next to roads. The study demonstrated a rapid method for gaining information useful for conservation and land use planning practices, such as in the determination of the carrying capacity or even for redistributing animals within the park.
A novel strategy for the targeted analysis of protein and peptide metabolites
Authors: Williamson Nicholas , Reilly Charles , Tan Chor-Teck , Ramarathinam Sri-Harsha , Jones Alun , Hunter Christie , Rooney Francis , Purcell Anthony 
Published: July 2019

AbstractThe detection and quantitation of exogenously administered biological macromolecules (e.g. vaccines, peptide and protein therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related compounds. We describe a method that incorporates stable isotope labeling of the compound of interest allowing the selective screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low molecular weight fragment ions produced during MS/MS that distinguish isotopically labelled material from related endogenous compounds. All isotopically labelled substances can be selected using this scanning technique for further analysis whilst other unlabelled and irrelevant substances are ignored. The potential for this technique to be used in metabolism and pharmacokinetic experiments is discussed with specific examples looking at the metabolism of &x03B1;-synuclein in serum and the brain.
New methods for analyzing serological data with applications to influenza surveillance
Authors: Ndifon Wilfred 
Published: July 2019

AbstractTwo important challenges to the use of serological assays for influenza surveillance include the substantial amount of experimental effort involved, and the inherent noisiness of serological data. Here, informed by the observation that log-transformed serological data (obtained from the hemagglutination-inhibition assay) exist in an effectively one-dimensional space, computational methods are developed for accurately and efficiently recovering unmeasured serological data from a sample of measured data, and systematically minimizing noise found in the measured data. Careful application of these methods would enable the collection of better-quality serological data on a greater number of circulating influenza viruses than is currently possible, and improve the ability to identify potential epidemic/pandemic viruses before they become widespread. Although the focus here is on influenza surveillance, the described methods are more widely applicable.
A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation
Authors: Arjunan Satya , Tomita Masaru 
Published: July 2019

AbstractMany important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization patterns of molecules in fluorescence microscopy images with simulation, we devised a visualization method that mimics the microphotography process by showing the trajectory of simulated molecules averaged according to the camera exposure time. In the rod-shaped bacterium Escherichia coli, the division site is suppressed at the cell poles by periodic pole-to-pole oscillations of the Min proteins (MinC, MinD and MinE) arising from carefully orchestrated RD in both cytoplasm and membrane compartments. Using Spatiocyte we could model and reproduce the in vivo MinDE localization dynamics by accounting for the established properties of MinE. Our results suggest that the MinE ring, which is essential in preventing polar septation, is largely composed of MinE that is transiently attached to the membrane independently after recruited by MinD. Overall, Spatiocyte allows simulation and visualization of complex spatial and reaction-diffusion mediated cellular processes in volumes and surfaces. As we showed, it can potentially provide mechanistic insights otherwise difficult to obtain experimentally.
A Comparative Study of the Magnitude, Frequency and Distribution of Intense Rainfall in the United Kingdom
Authors: Rodda John , Little Max , Rodda Harvey , McSharry Patrick 
Published: July 2019

AbstractDuring the 1960s, a study was made of the magnitude, frequency and distribution of intense rainfall over the UK, employing data from more than 120 daily-read rain gauges covering the period 1911 to 1960. Using the same methodology, that study was recently updated utilizing data for the period 1961 to 2006 for the same gauges, or from those nearby. This paper describes the techniques applied to ensure consistency of data and statistical modelling. It presents a comparison of patterns of extreme rainfalls for the two periods and discusses the changes that have taken place. Most noticeably, increases up to 20% have occurred in the north west of the country and in parts of East Anglia. There have also been changes in other areas, including decreases of the same magnitude over central England. The implications of these changes are considered.
Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program
Authors: Shan Yunfeng , Gras Robin 
Published: July 2019

AbstractThe origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the Bayesian method under the coalescence model with the latest program (BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear genes encoding amino acid residues with the jackknife method for taxon sub-sampling. The results, combined with those of other three genome-scale approaches, successfully prove the hypothesis that lungfishes and coelacanths form a monophyletic sister group and are equally related to tetrapods supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.
Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case
Authors: Rybarczyk José Luiz , Castro Mauro , Dalmolin Rodrigo , Moreira José , Brunnet Leonardo , de Almeida Rita 
Published: July 2019

AbstractA genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms.
Regulated peristalsis into the acidic region of the Drosophila larval midgut is controlled by a novel component of the Autonomic Nervous System
Authors: LaJeunesse Dennis Richard , Johnson Brooke Ann , Presnell Jason , Catignas Kathleen , Zapotoczny Grzegorz 
Published: July 2019

AbstractThe underlying cellular and molecular mechanisms that regulate and coordinate critical physiological processes such as peristalsis are complex, often cryptic, and involve the integration of multiple tissues and organ systems within the organism. We have identified a completely novel component of the larval autonomic nervous system in the Drosophila larval midgut that is essential for the peristaltic movement of food from the anterior midgut into the acidic region of the midgut. We have named this region the Superior Cupric Autonomic Nervous System or SCANS. Located at the junction of the anterior and the acidic portions of the midgut, the SCANS is characterized by a cluster of a novel neuro-enteroendocrine cells that we call Lettuce Head Cells, a valve, and two anterior muscular tethers to the dorsal gastric caeca. Using cell ablation and ectopic activation via expression of the Chlamydomonas reinhardtii blue-light activated channelrhodopsin, we demonstrate that the SCANS and in particular the Lettuce Head Cells are both necessary and sufficient for peristalsis and perhaps serve a larger role by coordinating digestion throughout the anterior midgut with development and growth.
In vitro synergistic anti-prion effect of cholesterol ester modulators
Authors: Orrù Christina Doriana , Cannas Maria Dolores , Vascellari Sarah , Angius Fabrizio , Cocco Pier Luigi , Norfo Claudia , Mandas Antonella , La Colla Paolo , Dessì Sandra , Pani Alessandra 
Published: July 2019

Abstract
Background.
Our studies on the role of cholesterol in prion infection/replication showed that brains and peripheral cells of sheep susceptible to or suffering from Scrapie were characterized by an altered cholesterol homeostasis compared to animals with a scrapie-resistant genotype, and that drugs influencing cholesterol esterification were endowed with selective anti-prion activity in N2a cell lines infected with the 22L and RML prion strains. Results. In prion-infected N2a cell lines we now report increased anti-prion activity of dual-drug combinations consisting of cholesterol ester modulators associated with prion inhibitors Synergism was obtained with the cholesterol ester modulators everolimus, pioglitazone, progesterone, and verapamil associated with the anti-prion chlorpromazine, and with everolimus and pioglitazone associated with the anti-prion quinacrine. Comparative lipid analyses in prion-infected and non-infected N2a cells by colorimetric, enzymatic, and chemical means, clearly demonstrated a derangement of type and distribution of cholesterol esters, free cholesterol, and triglycerides in the infected N2a cells. Although single-drug treatments influenced lipid syntheses, only the combined-drug treatments appeared to restore a lipid profile similar to that of untreated-uninfected cells.

Conclusions.
We conclude that the anti-prion synergistic effect of cholesterol ester modulators with the cholesterol metabolism interfering anti-prion drugs chlorpromazine and quinacrine may arise from the ability of combined drugs to re-establish the intracellular lipid profile of untreated-uninfected cells. Overall, these data suggest that inhibition of prion replication can be readily potentiated by combinatorial drug treatments, and that steps of cholesterol/cholesterol ester metabolism may represent suitable targets.
The Origin and Evolution of Viruses as Molecular Organisms
Authors: Bandea Claudiu 
Published: July 2019

AbstractViruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for their origin from parasitic cellular species that fused with their host cells. By losing their membrane and cellular structure within the host cell, these new types of parasitic species gained full access to precursors for the synthesis of their specific molecules and to the host’s information processing machineries, such as translation, which created unique parasitic and evolutionary opportunities. To identify viruses during their intracellular stage of their life cycle, in which their specific molecules are free or dispersed within the host cell, this paper introduces the concept of “molecular structure” and labels viruses as “molecular organisms.” Among the extant viruses, the life cycle of poxviruses and other complex viruses that fuse with their host cells provides compelling evidence for the fusion model. One of the most remarkable implications of fusion model is that new viral lineages originated from parasitic cellular species throughout the history of life, and that this process might still be active. Surprisingly, it appears that several parasitic cellular species are currently evolving into molecular organisms. More remarkably though, according to this model, several parasites that are currently classified as cellular organisms are in fact genuine molecular organisms. The current evidence for the fusion hypothesis is strong and it is fully testable using both experimental and phylogenetic approaches. The academic and research implications of this model, which supports the inclusion of viruses in the Tree of Life, are highly significant. Some of these implications are discussed in more detail in two other articles of this series, which presents a unifying model for the origin and evolution of cellular and viral domains, including the origin of life.
The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?
Authors: Wallace Rodrick 
Published: July 2019

AbstractWe extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of human biology into the center of biological psychiatry. The cultural and epigenetic systems of heritage may well provide the 'missing' heritability of complex diseases now under so much intense discussion.
16S rRNA based identification of Aeromonas sp. kumar by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar
Authors: Kumar P. , Ramakritinan C. M. , Kumaraguru A. K. 
Published: July 2019

AbstractA bacterial strain, designated Aeromonas sp. kumar, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were studied using BPROM tool. In genetics, a promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters are typically located near the genes they regulate, on the same strand and upstream (towards the 5' region of the sense strand). The objective of the study is to predict the regulatory elements which are -10 box, -35box and three Transcription Factors (rpoD19, rpoD17 and araC) with their binding sites in the 16S rRNA gene of Aeromonas sp. kumar. The gene bank accession number for 16S rRNA gene of Aeromonas sp. kumar is FJ896014.
Natural Selection In Utero Contributes to the Male Longevity Deficit in Contemporary Human Populations
Authors: Catalano Ralph 
Published: July 2019

AbstractMuch literature invokes natural selection to explain the pervasive deficit in the average lifespan of men compared to women.^1^ The explanation assumes that mothers, not fathers, provisioned children over much of human existence, and that women who lived long enough to help their children and grand children survive to reproductive age had more grandchildren and great-grandchildren than did shorter-lived women.^2^ Although this argument implies that natural selection would conserve mutations that conferred longevity on mothers but not fathers,^3,4^ it offers no explanation of the considerable changes over historic time in the male longevity deficit thereby implying that these arise solely from culture.^5^ I show, however, that natural selection in utero empirically predicts variability over time in the deficit. This mechanism spontaneously aborts less fit fetuses during stressful times and reportedly selects more against males than females. My finding suggests that natural selection interacts with culture to predictably affect both the life span and sex ratio of contemporary human populations.
Voluntary universal testing and treatment is unlikely to lead to HIV elimination: a modeling analysis
Authors: Wagner Bradley , Blower Sally 
Published: July 2019

AbstractRecently Granich et al. at the World Health Organization (WHO) concluded, using mathematical modeling, that HIV epidemics could be eliminated within a decade. They assumed all individuals would be tested annually and every infected individual (regardless of stage of infection) would be put on treatment. Based on this modeling study the WHO is considering using universal testing and treatment as an HIV elimination strategy. Here we examine the study by Granich et al. and assess its validity. We present new analyses of their model by varying assumptions and parameter values. We find that under certain very optimistic assumptions HIV elimination would be (theoretically) possible, but it would take at least 70 years. To obtain this result we assumed ~65% of symptomatic and ~20% of asymptomatic individuals would be treated per year; ARVs would reduce infectivity of treated individuals a hundred fold, and only 5% of symptomatic individuals would give up treatment per year. Even under optimistic assumptions we find elimination to be unlikely. For example, we show if ~65% of symptomatic individuals are treated per year and treated individuals are completely noninfectious, HIV will remain endemic with a prevalence of 34% and an incidence of 2% per year. We conclude that the model developed by Granich et al., when used with realistic parameter values, does not show HIV elimination is possible. However our modeling results show treatment could act as an effective prevention tool and significantly reduce transmission, even if only symptomatic individuals receive ARVs. Treatment should first, and foremost, be used for therapeutic purposes. Hence, we recommend – when resources are limited - targeting those in need of treatment. Such a strategy would be ethical, feasible and epidemiologically sound. We advise that models used as health policy tools should be carefully evaluated and their results interpreted with caution.