bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteria have transient influences on marine corrosion of steel
Authors: Melchers Robert , Jeffrey Robert 
Published: July 2019

AbstractThe contribution of bacteria to the corrosion mass loss and to pitting of mild steel was observed over 2.5 years using parallel streams of unpolluted natural (biotic) and nominally sterilized (abiotic) Pacific Ocean coastal seawater. As also observed by others, in artificial laboratory exposures, corrosion mass loss within the first few days of exposure was much greater in the biotic stream. However, after only about 10 days the difference in mass losses were gradually reduced and were very similar up to about one year of exposure. Thereafter, the corrosion loss in the biotic stream again became more severe. Pitting corrosion in the biotic stream was more severe from the very first exposure throughout the 2.5 years. Corrosion in both seawater streams exhibited three distinct but transient time-dependent phases. Of these only the first and third obviously involve bacteria. Similar longer-term observations in real seawaters have not been described previously but are generally consistent with some long-term field data. The results show that longer-term corrosion behavior and possible microbial influences cannot be predicted from short-term laboratory observations, even if natural seawater is used.
Insights from the Structure of Estrogen Receptor into the Evolution of Estrogens: Implications for Endocrine Disruption
Authors: Baker Michael 
Published: July 2019

AbstractIn the last decade, there has been important progress in understanding the origins and evolution of receptors for adrenal steroids (aldosterone, cortisol) and sex steroids (estradiol, progesterone, testosterone) due to the sequencing of genomes from animals that are at key sites in vertebrate evolution. Although the estrogen receptor [ER] appears to be the ancestral vertebrate steroid receptor and estradiol [E2] is the physiological ligand for vertebrate ERs, the identity of the ancestral ligand(s) for the ER remains unknown. Here, using an analysis of crystal structures of human ER[alpha] with E2 and other chemicals and 3D models of human ER[alpha] with 27-hydroxycholesterol and 5-androsten-3[beta],17[beta]-diol, we propose that one or more [DELTA]5 steroids were the ancestral ligands for the ER, with E2 evolving later as the canonical estrogen. The evidence that chemicals with a [beta]-hydroxy at C3 in a saturated A ring can act as estrogens and the conformational flexibility of the vertebrate ER can explain the diversity of synthetic chemicals that disrupt estrogen responses by binding to vertebrate ERs.
p53 independent epigenetic-differentiation treatment in xenotransplant models of acute myeloid leukemia
Authors: Saunthararajah Yogen , Ebrahem Quteba , Negrotto Soledad , Mahfouz Reda , Link Kevin , Hu Zhenbo , Gu Xiaorong , Advani Anjali , Kalaycio Matt , Sobecks Ronald , Sekeres Mikkael , Copelan Edward , Radivoyevitch Tomas , Maciejewski Jaroslaw , Mulloy James C. , Ng Kwok-Peng 
Published: July 2019

AbstractSuppression of apoptosis by TP53 mutation contributes to resistance of acute myeloid leukemia (AML) to conventional cytotoxic treatment. Using differentiation to induce irreversible cell cycle exit in AML cells could be a p53-independent treatment alternative, however, this possibility requires evaluation. In vitro and in vivo regimens of the cytosine analogue decitabine that deplete the chromatin modifying enzyme DNA methyl-transferase 1 (DNMT1) without phosphorylating p53 or inducing early apoptosis were determined. These decitabine regimens but not equimolar DNA-damaging cytarabine up regulated the key late differentiation factors CEBP&x03B5; and p27/CDKN1B, induced cellular differentiation, and terminated AML cell-cycle, even in cytarabine-resistant p53- and p16/CDKN2A-null AML cells. Leukemia initiation by xeno-transplanted AML cells was abrogated but normal hematopoietic stem cell (HSC) engraftment was preserved. In vivo, the low toxicity allowed frequent drug administration to increase exposure, an important consideration for S-phase specific decitabine therapy. In xeno-transplant models of p53-null and relapsed/refractory AML, the non-cytotoxic regimen significantly extended survival compared to conventional cytotoxic cytarabine. Modifying in vivo dose and schedule to emphasize this pathway of decitabine action can bypass a mechanism of resistance to standard therapy.
Molecular modelling and Function Prediction of hABH7, human homologue of E. coli ALKB7
Authors: Shankaracharya Mr. , Das Saibal , Vidyarthi Ambarish Sharan 
Published: July 2019

AbstractHuman homologues of ALKB protein have shown the prime role in DNA damaging drugs, used for cancer therapy. Little is known about structure and function of hABH7, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeller 9v7 to predict the 3D structure of the hABH7 protein. The tertiary structure model of hABH7, ALKBH7.B99990002.pdb was predicted and evaluated. Validation results showed 97.8% residues in favored and additional allowed regions of Ramachandran plots. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, presence of a Phe120-Gly121-Gly122 conserved pattern in the functional domain was detected. In the predicted structural model of hABH7, amino acid residues, Arginine at 57, 58, 59 and 60 along with tyrosine at 61 were predicted in RNA binding sites of the model. The predicted and validated model of human homologue hABH7 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate the research on designing appropriate inhibitors aiding in chemotherapy and cancer related diseases.
Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Authors: Wallace Rodrick 
Published: July 2019

AbstractWe examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of 'herd infection' inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence.
Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Authors: Convertino Matteo , Donoghue Joseph , Chu-Agor Ma Librada , Kiker Gregory , Munoz-Carpena Rafael , Fischer Richard , Linkov Igor 
Published: July 2019

AbstractIn this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover	(PP)	(Charadrius	melodus )	and	Red	Knot	(RK)	(Calidris	canutus ).	Additionally, we investigated the potential differences between the SP breeding and wintering distributions using only regional-scale physiognomic variables and the recorded occur- rences. To quantify the relationship between past renourishment projects and shorebird species we used a Monte Carlo procedure to sample from the posterior distribution of the binomial probabilities that a region is not a nesting or a wintering ground conditional on the occurrence of a beach replenishment intervention in the same and the previous year. The results indicate that it was 2.3, 3.1, and 0.8 times more likely that a region was not a wintering ground following a year with a renourishment intervention for the SP, PP and RK respectively. For the SP it was 2.5. times more likely that a region was not a breeding ground after a renourishment event. Through a maximum entropy principle model we observed small differences in the habitat use of the SP during the breeding and the wintering season. However the habitats where RK was observed appeared quite different. While ecological niche models at the macro-scale are useful for determining habitat suitability ranges, the characterization of the species’ local niche is fundamentally important for adopting concrete multi-species management scenarios. Maintaining and creating optimal suitable habitats for SP characterized by sparse low vegetation in the foredunes areas, and uneven/low-slope beach surfaces, is the proposed conservation scenario to convert anthropic beach restorations and SP populations into a positive feedback without impacting other threatened shorebird species.
Replacement and late formation of atmospheric N2 on undifferentiated Titan by impacts
Authors: Sekine Yasuhito , Genda Hidenori , Sugita Seiji , Kadono Toshihiko , Matsui Takafumi 
Published: July 2019

AbstractSaturn’s moon, Titan, has remarkable surface features—a massive N2 atmosphere and hydrological cycle of CH4—that are often compared with that of Earth^1^. However, the origin and evolution of Titan’s atmosphere remains largely unknown. The proposed formation mechanisms for Titan’s N2 require a prolonged, warm proto-atmosphere during accretion^2-4^. These mechanisms accordingly would not have worked efficiently if Titan stayed cold, as indicated by the incompletely differentiated interior observed by Cassini^5^. Because formation of a massive secondary atmosphere on a planetary body would associate with a major differentiation of its sold body during accretion^6–8^, the presence of such an atmosphere on undifferentiated cold Titan poses a serious dilemma on our view of how planetary bodies develop atmospheres. Here we propose a new mechanism for the post-accretion formation of Titan’s N2 to resolve this problem: conversion and replenishment of N2 from NH3 contained in Titan by impacts during the late heavy bombardment (LHB)^9^. Our results show that Titan, regardless of its thermal history, would acquire sufficient N2 to account for the current atmosphere during the LHB and that most of the pre-LHB atmosphere would have replaced by impact-induced N2. This is the first scenario capable of generating a N2-rich and nearly primordial Ar-free atmosphere on undifferentiated cold Titan. We also suggest that Titan’s N2 was delivered from a different source in the solar nebula compared with Earth and that the origins of N2 on Titan and Triton are fundamentally different with that of N2 on Pluto.
Microarray Analysis of PBMC after Plasmodium falciparum Infection: Molecular Insights into Disease Pathogenesis
Authors: Hu Wan-Chung , Scott Alan , Wolfe Nathan , Singh Sher , Jedlicka Anne , Bourgeois August Louis 
Published: July 2019

AbstractOur laboratory’s previous microarray analysis of subjects with Plasmodium falciparum revealed up-regulation of Toll-like receptor, NF-kB, TNF-α, IFN-γ, IL-1β, p38 MAPK, and MHC molecules. We performed further time-course microarray analysis focusing on malaria pathogenesis by using peripheral leukocytes as a cellular model. We found up-regulation of coagulation-related genes (SERPINB2, thrombomodulin, thrombospondin), heat shock proteins, glycolytic enzymes, glucose transporters, and vacuolar H+-ATPases in acute febrile malaria. In early malaria, prior to detectable parasitemia, CD36 and ICAM1 were up-regulated. During acute malaria, a correlation was observed between IL-1ß and heat shock proteins, suggesting heat shock protein response may be in the febrile response induced by IL-1ß. CD163, a hemoglobin scavenger receptor, was up-regulated in acute malaria to potentially facilitate free hemoglobin up-take by peripheral leukocytes. In acute malaria, high MafB gene expression was negatively correlated with down-regulation of hemoglobin and platelet counts. Consistent with a down-regulation of hemoglobin expression, peripheral RBC counts tended to increase during the acute malaria. In our model, up-regulations of RBC and/or leucocyte binding mediators like CD36, ICAM1, thrombospondin, and thrombomodulin may contribute to the pathogenesis of cerebral malaria. Similarly, up-regulation of genes coding for glycolytic enzymes, glucose transporter and H+-ATPases may contribute to the hypoglycemia and metabolic acidosis frequently observed in seriously ill malaria patients. Overall gender effects on gene expression profiles between male and female subjects were not apparent, except that some hemoglobins were significantly down-regulated in male versus female; suggesting males may be more prone to the development of malaria associate anemia.
Extending Tlusty's method to the glycome: Tuning the repertoire of glycan determinants
Authors: Wallace Rodrick , Wallace Deborah 
Published: July 2019

AbstractWe apply Tlusty's information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Convergence of atmospheric and North Atlantic CO2 trends on multidecadal timescales
Authors: McKinley Galen , Fay Amanda , Takahashi Taro , Metzl Nicolas 
Published: July 2019

AbstractThe oceans’ carbon uptake substantially reduces the rate of anthropogenic carbon accumulation in the atmosphere1, and thus slows global climate change. Some diagnoses of trends in ocean carbon uptake have suggested a significant weakening in recent years2-8, while others conclude that decadal variability confounds detection of long-term trends9-11. Here, we study trends in observed surface ocean partial pressure of CO2 (pCO2) in three gyre-scale biomes of the North Atlantic, considering decadal to multidecadal timescales between 1981 and 2009. Trends on decadal timescales are of variable magnitudes and depend sensitively on the precise choice of years. As more years are considered, oceanic pCO2 trends begin to converge to the trend in atmospheric pCO2. North of 30oN, it takes 25 years for the influence of decadal-timescale climate variability to be overcome by a long-term trend that is consistent with the accumulation of anthropogenic carbon. In the permanently stratified subtropical gyre, warming has recently become a significant contributor to the observed increase in oceanic pCO2. This warming, previously attributed to both a multidecadal climate oscillation and anthropogenic climate forcing12,13, is beginning to reduce ocean carbon uptake.
Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
Authors: Fusi Nicolo , Stegle Oliver , Lawrence Neil 
Published: July 2019

AbstractExpression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown environmental influences. These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals.Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the effect of prominent genetic regulators. As a result, PANAMA can more accurately distinguish between true genetic association signals and confounding variation.We applied our model and compared it to existing methods on a variety of datasets and biological systems. PANAMA consistently performs better than alternative methods, and finds in particular substantially more trans regulators. Importantly, PANAMA not only identified a greater number of associations, but also yields hits that are biologically more plausible and can be better reproduced between independent studies.
Toxicological Assessment of Herbal Medicine in Rats
Authors: Perumal Samy Ramar , TK Chow Vincent 
Published: July 2019

AbstractProtein profiles analysis of liver, kidney and spleen by SDS-PAGE in aqueous leaf extract of Tragia involucrata L. (Euphorbiaceae) was injected intraperitoneally in albino rats for 30 days. The variation of protein changes was recorded. In liver, the aqueous leaf extracts treated (1500 mg/kg body/weight) group did not exhibit a marked increase in any of the polypeptides over control. But in the case of other treatments (250, 500, 1000 and 2000 mg/kg body weight doses) the profile showed significant increases in the accumulation of all polypeptides that were quantified using densitometry. This concludes that the aqueous leaf extract influenced the accumulation of polypeptide in higher concentration. Extra polypeptides may be responsible for the protective action.
In vitro Evolution and Engineering for Improved Ribozyme Polymerase Production
Authors: Khan Israr , Akktar Muhammad Waheed , Khan Ayaz Ali 
Published: July 2019

AbstractAccording to the "RNA World Hypothesis" the first self replicating molecule formed from the prebiotic chemicals is the ribozyme. A model compartmentalized self replicating system for ribozyme polymerases is designed and used to improve activity, fidelity and generality of the enzyme.
The universal "shape" of human languages: spectral analysis beyond speech
Authors: Moscoso del Prado Fermin 
Published: July 2019

AbstractA common recommendation for linguists is that, when analyzing language, they should take a "man-from-mars", know-nothing, perspective to describe the structures that they observe, if possible limiting themselves to the mechanical application of a set of well-defined techniques and criteria. Unfortunately, the complex nature of linguistic structures makes it difficult to adopt such a detached perspective. A language, as represented by a corpus of text, can be described macroscopically by the symbolic periodogram of the corpus, analogous to the spectrograms commonly used for describing speech. Here, I show that the periodogram exhibits a universal "shape" from human languages, and this shape originates in known properties of the human mind. Despite the universality of the overall pattern, subtle differences also reveal particularities of individual languages. These differences demonstrate the long-held --but unproven-- hypothesis that human languages balance the amount of structure contained in different levels of description so that the total amount of linguistic structure remains fairly constant across languages. The universal pattern found in the periodograms illustrates how the biological properties of the mind constrain the structure of human languages.
Proteomics in the Light of Integral Value Transformations
Authors: Hassan Sk. S. , Choudhury P. Pal 
Published: July 2019

AbstractIn this paper, Proteomics have been studied in the light of Integral Value Transformations (IVTs) which was introduced by Sk. S. Hassan et al in 2010. For case study, a Human olfactory receptor OR1D2 protein sequence has been taken and then different IVTs have been used to evolve OR1D2 into some other proteomic like sequences. It has been observed that some of the generated sequences have been mapped to another olfactory receptor in Human or in some other species. Also it has been corroborated through fractal dimension that some of the fundamental protein properties have been nearly intact, even after the mapping. This study will help to comprehend the proteomic evolutionary network with the help of IVTs.
Cancer and the social induction of aging
Authors: Wallace Rodrick , Wallace Deborah 
Published: July 2019

AbstractAge has long been known as the primary population 'risk factor' for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by 'small molecule' interventions at the individual level, but must involve comprehensive prevention strategies that lessen exposures to policies and cultural practices that accelerate senescence in vulnerable or targeted populations.
Conservation Pakage for Modal Ecorace
Authors: Sinha Ajit Kumar 
Published: July 2019

AbstractConserving biodiversity is about genetic variety, species, habitats and ecosystems. All are important, but it is often most appropriate, practical and effective to focus on species. With modern conservation awareness, there is a welcome and popular commitment to maintaining the diversity of species in India. Nevertheless, over the last 50 years, we have witnessed the severe decline of many once widespread and familiar species, such as tropical Tasar silkworm Antherea mylitta D. Conservation is not just about avoiding extinctions, but about restoring or recovering species populations to secure levels and preventing other species from reaching such a perilous situation in the first place. Species, by their very nature, have specific ecological requirements. They may appear to share the same habitat with many others but each has a different, specific niche. It is what sets them apart, and makes them what they are. Habitat loss has historically been a factor in species decline. However, the way existing habitats are managed is also important.
The effect of noise correlations in populations of diversely tuned neurons
Authors: Ecker Alexander , Berens Philipp , Tolias Andreas , Bethge Matthias 
Published: July 2019

AbstractThe amount of information encoded by networks of neurons critically depends on the correlation structure of their activity. Neurons with similar stimulus preferences tend to have higher noise correlations than others. In homogeneous populations of neurons this limited range correlation structure is highly detrimental to the accuracy of a population code. Therefore, reduced spike count correlations under attention, after adaptation or after learning have been interpreted as evidence for a more efficient population code. Here we analyze the role of limited range correlations in more realistic, heterogeneous population models. We use Fisher information and maximum likelihood decoding to show that reduced correlations do not necessarily improve encoding accuracy. In fact, in populations with more than a few hundred neurons, increasing the level of limited range correlations can substantially improve encoding accuracy. We found that this improvement results from a decrease in noise entropy that is associated with increasing correlations if the marginal distributions are unchanged. Surprisingly, for constant noise entropy and in the limit of large populations the encoding accuracy is independent of both structure and magnitude of noise correlations.