bluuebunny/crossref_metadata_2025 huggingface dataset:
Prehistoric psychotropic consumption in Andean Chilean mummies
Authors: Ogalde Juan , Arriaza Bernardo , Soto Elia
Published: July 2019

Hallucinogenic plants are often regarded as the main source of psychoactive drugs in antiquity to reach deep altered states of consciousness^1,2^. Many researchers believe this was particularly true during the Tiwanaku empire expansion, circa (500-1000 A.D.), along the Atacama Desert of Chile. Highly decorated snuffing tablets and tubes are often found as grave goods during this period^3,4,5,6,7,8^. Until now the type of drugs consumed in this paraphernalia has been unclear. From the modern city of Arica, naturally mummified human bodies with abundant hair provided a unique opportunity to test for hallucinogenic plants consumed in Andean prehistory. Analysis by gas chromatography and mass spectrometry demonstrated the presence of harmine. The Banisteriopsis vine, commonly called Ayahuasca, was the probable source. This is the first confirmed evidence of psychoactive plant consumption in pre-Hispanic Andean populations along the Atacama coastal region. Of the 32 mummy hair samples analyzed 3 males tested positive for harmine. This alkaloid aids in the catalysis and synergic effects of powerful hallucinogenic drugs. The consumption of harmine was likely related to medicinal practices and not exclusively ingested by shamans. Another important aspect of this evidence is that Banisteriopsis is an Amazon plant. It does not grow in the Atacama coastal region. Thus, our findings reveal extensive plant trade networks in antiquity between the coast, desert, highlands, and Amazon basin. The excellent preservation of human organic specimens, the use of gas chromatography and mass spectrometry allowed us to map and demonstrate the consumption of psychoactive compound plants in Andean prehistory. In addition, our findings open the door for future studies to debate the consumption and social role of ancient psychoactive and hallucinogenic plants.
Evolution of the Protein Universe. Time Scales and Selection
Authors: Cosentino Lagomarsino Marco , Sellerio Alessandro , Heijning Philip , Bassetti Bruno
Published: July 2019

The availability of many genome sequences gives us abundant information, which is, however, very difficult to decode. As a consequence, in order to advance our understanding of biological processes at the whole-cell scale, it becomes very important to develop higher-level, synthetic descriptions of the contents of a genome. At the protein level, an effective scale of description is provided by protein domains. Domains are independent unit-shapes (or "folds") forming proteins. They are structurally stable and have thermodynamic origin. A domain determines a set of potential functions and interactions for the protein that carries it, for example DNA- or protein-binding capability or catalytic sites. Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. A stochastic growth model with two universal parameters, related to a minimal number of domains and to the relative time-scale of innovation to duplication reproduces two important features of these distributions: (i) the populations of domain classes (the sets, related to homology classes, containing realizations of the same domain in different proteins) follow common power-laws whose diversity is related to genome size measured by the total number of proteins or protein domains and (ii) the number of domain families is sublinear in genome size. In this evolutionary process, selective pressure can enter both as a global constraint on the innovation time-scale, and as a regulator of the population of specific domain classes, related to their modularity: some shapes are common to all genomes, some are contextual. These two features are sufficient to obtain general quantitative agreement with data from hundreds of genomes, and show that robust self-organizing phenomena encase specific selective pressures during evolution.
Chorionic Structures in Maternal Blood
Authors: Luz Nilo Pereira
Published: July 2019

Chorionic villi are the exchange structures of the placenta where human fetuses receive oxygen and nutrients from maternal blood, this article reports an improvement of a published method to recover them from the blood of pregnant, women, quotes their number and illustrates their size and trypsin impregnation. The reasons to explain the presence of chorionic structures and villi in the circulating maternal blood, the possible significance of their existence in maternal blood and the mechanisms to remove them are discussed. Their size and trypsin impregnation are illustrated. This paper discusses the significance of the presence of such allogeneic structures in the circulating blood of pregnant women and presents a brief discussion on the role of trypsin and its inhibitor in pregnancy homeostasis.
Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle
Authors: Vilasi Silvia , Ragone Raffaele
Published: July 2019

The potent immunomodulatory, anti-inflammatory and procoagulant properties of theprotein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have beenpreviously found to be modulated by a supramolecular monomer-trimer equilibrium.More structural details that integrate experimental data into a predictive frameworkhave recently been reported. Unfortunately, homology modelling and fold-recognitionstrategies were not successful in creating a theoretical model of the structuralorganization of SV-IV. It was inferred that the global structure of SV-IV is not similarto any protein of known three-dimensional structure. Reversing the classical approachto the sequence-structure-function paradigm, in this paper we report on novelinformation obtained by comparing physicochemical parameters of SV-IV with twodatasets made of intrinsically unfolded and ideally globular proteins. In addition, wehave analysed the SV-IV sequence by several publicly available disorder-orientedpredictors. Overall, disorder predictions and a re-examination of existing experimentaldata strongly suggest that SV-IV needs large plasticity to efficiently interact with thedifferent targets that characterize its multifaceted biological function and should betherefore better classified as an intrinsically disordered protein.
TMEPAI, a transmembrane TGF-β-inducible protein, sequesters Smad proteins in TGF-β signaling
Authors: Itoh Susumu , Watanabe Yukihide , Satoh Kiyotoshi , Inamitsu Masako , Shi Liang , Nakano Naoko , Tanaka Aya , Wiercinska Eliza , Shibuya Hiroshi , ten Dijke Peter , Kato Mitsuyasu
Published: July 2019

Transforming growth factor-[beta] (TGF-[beta]) is a multifunctional cytokine of key importance for controlling embryogenesis and tissue homeostasis. How TGF-[beta] signals are attenuated and terminated is not well understood. Here, we show that TMEPAI, a direct target gene of TGF-[beta] signaling, antagonizes TGF-[beta] signaling by interfering with TGF-[beta] type I receptor (T[beta]RI)-induced R-Smad phosphorylation. TMEPAI can directly interact with R-Smads via a Smad interaction motif (SIM). TMEPAI competes with Smad anchor for receptor activation (SARA) for R-Smad binding, thereby sequestering R-Smads from T[beta]RI kinase activation. In mammalian cells, ectopic expression of TMEPAI inhibited TGF-[beta]-induced PAI-1 production, whereas specific siRNA-mediated knockdown of TMEPAI expression potentiated TGF-[beta]-induced Smad2 phosphorylation and cellular responsiveness by TGF-[beta]. Consistently, TMEPAI inhibits activin-mediated mesoderm formation in Xenopus embryos. Taken together, TMEPAI participates in a negative feedback loop to control the duration and intensity of TGF-[beta] signaling.
c-Myc induced changes in higher order rDNA structure accompany growth factor stimulation of quiescent cells
Authors: Shiue Chiou-Nan , Berkson Rachel , Wright Anthony
Published: July 2019

Human c-Myc is believed to be a high level coordinator of protein synthesis capacity and cell growth rate, capable of activating transcription by all three nuclear RNA Polymerases. Direct activation of rDNA transcription by c-Myc is functionally conserved in rat cells, despite high divergence in non-coding rDNA sequences, suggesting that this coordinating role is likely to be a general within mammals. Upon re-feeding of starved cells, c-Myc activity enhances the efficiency of RNA Polymerase I and SL1/TIF-1B recruitment to the rDNA and rapidly induces higher order gene loop structures in rDNA chromatin that juxtapose upstream and downstream rDNA sequences. Furthermore c-Myc induced gene-loop formation in rDNA genes occurs independently of rDNA transcription, implying that it may be an early step in the re-programming of quiescent cells as they enter the growth cycle.
Are plants with anti-cancer activity resistant to crown gall? : A test of hypothesis
Authors: Srirama R , Ramesha BT. , Ravikanth G. , Uma Shaanker R. , Ganeshaiah KN
Published: July 2019

The Crown gall tumour assay (CGTA) is one of several bench top bioassays recommended for the rapid screening of plants with anti-cancer activity. The rationale for the use of the bioassay is that the tumorogenic mechanism initiated in plant tissues by Agrobacterium tumefaciens is in many ways similar to that of animals. Several plant species with anti-cancer activity have already been discovered using this bioassay. However till date no explicit test of an association between anti-cancer activity of plants and their resistance to crown gall formation has been demonstrated. Demonstration of an association could have exploratory potential when searching for plants with anti-cancer activity. In this paper, we determined whether or not a statistically significant association between crown gall resistance and anti-cancer activity exists in plants found in existing published data sets. Our results indicate that plants with anti-cancer activity have a higher proportion of their species resistant to crown gall formation compared to a random selection of plants. We discuss the implications of our results especially when prospecting for newer sources of anti-cancer activity in plants.
Interleukin-10 containing normal human serum inhibits granzyme B release but not perforin release from alloreactive and EBV-specific T cell clones
Authors: Nishimura Motoko , Sato Hideya , Okazaki Hitoshi , Satake Masahiro , Tadokoro Kenji
Published: July 2019

Interleukin-10 (IL-10), also known as cytokine synthesis inhibitory factor, has pleiotropic effects in immunoregulation and inflammation. It is capable of inhibiting synthesis of pro-inflammatory cytokines like interferon γ (IFNγ), IL-2, IL-3, tumor necrosis factor α(TNFα) and granulocyte macrophage colony stimulating factor (GM-CSF) made by cells such as macrophages and T helper Type 1 cells. We observed that normal human serum, derived from a healthy individual but containing large amounts of IL-10 (arbitrarily designated as "IL-10 serum"), inhibited cytotoxic activity and interfered with granzyme B release from alloreactive cytotoxic T cell (CTL) clones in vitro, but did not affect perforin release. The addition of normal human serum containing high levels of anti-IL-10 IgG (arbitrarily designated as "anti-IL-10 IgG serum") neutralized the inhibitory effects of IL-10 serum. Moreover, we have identified that cytotoxic activity and granzyme B release from an Epstein-Barr virus (EBV)-specific CTL clone was similarly inhibited in the presence of IL-10 serum, while perforin release was unaffected. Anti-IL-10 IgG serum also appeared to neutralize the inhibitory effect of IL-10 serum on an EBV-specific CTL clone.
Sex-Related Moral Behavior
Authors: Priori Alberto , Fumagalli Manuela , Marceglia Sara , Ferrucci Roberta , Mameli Francesca , Zago Stefano , Barbieri Sergio , Sartori Giuseppe , Cappa Stefano
Published: July 2019

The moral sense is one of the most complex aspects of the human mind. While neurobiological, cognitive and behavioural gender-related differences are increasingly studied and verified, the common belief that morality differs between men and women has not been experimentally investigated. We assessed the impact of gender on moral choices by testing thirty men and thirty women with the Moral Sense Task (MST) (Greene et al. 2001, 2004; Koenigs et al. 2007). Whereas the two genders did not differ in utilitarian responses to non-moral dilemmas (NM) and to impersonal moral dilemmas (MI), men gave significantly more utilitarian answers to personal moral dilemmas (MP; i.e. that action whose endorsement involves highly emotional decision). These results suggest that the cognitive-emotional processes implied in the evaluation of personal moral dilemmas differ between men and women, possibly reflecting differences in the underlying neural mechanisms. The existence of sex-related determinants of moral judgement may be one of the factors responsible for gender differences in real-life behaviours involving power management, economic decision-making, leadership and aggressive and criminal behaviours.
Evolution of malaria virulence in cross-generation transmission through selective immune pressure
Authors: Gurarie David
Published: July 2019

Theoretical arguments and some mathematical models of host-parasite coevolution (e.g. [1- 6]) suggest host immunity as the driving source for the evolution of parasite virulence. Imperfect vaccines in particular, can play the role and recent work [7] sets to test these ideas experimentally, using the mouse malaria model, Plasmodium chabaudi. To this end the authors evolve parasite lines in immunized and nonimmunized (“naïve”) mice using serial passage of infected blood samples. They find parasite lines evolved in immunized mice become more virulent than those evolved in naive mice. Furthermore, this feature persisted even when the evolved strains were transmitted through mosquitoes. Here we develop a mathematical model of parasite dynamics that qualitatively reproduces the experimental results of [7]. Our model accounts for the basic in-host processes: (i) production and depletion of red blood cells (RBC); (ii) immune-modulated parasite growth/ replication, (iii) immune stimulation and clearing of parasite. Besides we introduce multiple parasite strains with variable levels of virulence, and allow random mutations during replication process. The virulence is represented by a single parameter – immune stimulation threshold. So more virulent strains have higher “tolerance levels”, hence increased RBC depletion (anemia). Numeric simulations with our model exhibit, as in [7] the overall evolution of virulence in serial passage of parasite strains, and its enhancement through partial (imperfect) immunization.
Changes in temperature-moisture covariance could increase soil carbon loss
Authors: Noormets Asko , Gavazzi Michael , Strickland Sara , Sun Ge , Chen Jiquan , King John , McNulty Steve
Published: July 2019

Soils store about 1.5x10^16 g of carbon (C), about as much as terrestrial vegetation and atmosphere combined 1. The complex interplay between factors that regulate C release from soil through respiration is not completely understood, but could potentially exert strong influence on global radiation balance and climate change2. Respiration exerts strong effect on the spatial heterogeneity of terrestrial C cycle 3 and its temporal variation remains more poorly understood compared to gross ecosystem production (GEP) 4. This variation can analytically be attributed to changes in environmental factors, but forecasting individual deviations remains a challenge 4. Here we propose that deviations of the typical covariance pattern of primary environmental drivers (temperature, T, and moisture, presented in this study as volumetric water content, VWC) may affect the deviations of respiratory C loss. Typically, T and VWC are inversely related, with warm periods being generally drier and vice versa, and therefore the stimulating effect of one factor is counterbalanced by unfavorable levels of the other 5. However, should the driving variables be positively related, respiratory carbon release can increase significantly (Supplementary Fig. 1a). This hypothesis is supported by two consecutive years of ecosystem-level and soil carbon exchange data that differed in rain fall periodicity and T-VWC-covariance. With changing climate patterns, including the intensity and frequency of rainfall events, there is the possibility that the covariance patterns of T and VWC may change, and more frequent periods of positive T-VWC covariance may lead to greater loss of soil carbon, and contribute to greater radiative forcing on Earth’s energy budget.
Estimation of the Multiple Testing Burden for Genomewide Association Studies of Common Variants
Authors: Pe'er Itsik , Yelensky Roman , Altshuler David , Daly Mark
Published: July 2019

Genomewide association studies are an exciting strategy in genetics, recently becoming feasible. While pioneering studies are being underway, it is already clear that the analytic issue of determining the significance of results presents a challenge to the wide community of researchers. Rather than each study engaging in independent evaluation, there is need in the community to have standards set for whole-genome significance. We have therefore undertaken the task of developing such standards, based on data collected with collaborators in the International Haplotype Map Consortium. We report an estimated burden of a million independent tests genomewide in Europeans, and twice that number in Africans. We further identify the sensitivity of the testing burden to the required significance level, with implications to staged design of association studies.
Epigrass: a tool to study disease spread in complex networks.
Authors: Coelho Flávio Codeço , Codeco Claudia , Cruz Oswaldo
Published: July 2019

The construction of complex statial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most if not all these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior. A Network epidemiological model representing the spread of a directly transmitted disease through a bus-transportation network connecting mid-size cities in Brazil. Results show that the topological context of the starting point of the epidemic is of great importance from both control and preventive perspectives.Epigrass is shown to facilitate greatly the construction, simulation and analysis of complex network models. The output of model results in standard GIS file formats facilitate the post-processing and analysis of results by means of sophisticated GIS software.
Quantification of Cell Movement Reveals Distinct Edge Motility Types During Cell Spreading
Authors: Dubin-Thaler Benjamin , Hofman Jake , Xenias Harry , Spielman Ingrid , Shneidman Anna , David Lawrence , Dobereiner Hans-Guenther , Wiggins Chris , Sheetz Michael
Published: July 2019

Actin-based motility is central to cellular processes such as migration, bacterial engulfment, and cancer metastasis, and requires precise spatial and temporal regulation of the cytoskeleton. We studied one such process, fibroblast spreading, which involves three temporal phases: early, middle, and late spreading, distinguished by differences in cell area growth. In these studies, aided by improved algorithms for analyzing edge movement, we observed that each phase was dominated by a single, kinematically and biochemically distinct cytoskeletal organization, or motility type. Specifically, early spreading was dominated by periodic blebbing; continuous protrusion occurred predominantly during middle spreading; and periodic contractions were prevalent in late spreading. Further characterization revealed that each motility type exhibited a distinct distribution of the actin-related protein VASP, while inhibition of actin polymerization by cytochalasin D treatment revealed different dependences on barbed-end polymerization. Through this detailed characterization and graded perturbation of the system, we observed that although each temporal phase of spreading was dominated by a single motility type, in general cells exhibited a variety of motility types in neighboring spatial domains of the plasma membrane edge. These observations support a model in which global signals bias local cytoskeletal biochemistry in favor of a particular motility type.
Application of a periodic table for the genetic code to influenza A/H3N2 virus
Authors: Morimoto Susumu
Published: July 2019

If biologists can utilize a table to have access to biological phenomena in the manner analogous to the periodic table for chemical elements, they may get hold of a directing post in life science. Currently the mutational rule of influenza viruses have remained perplexed and to reveal it should be now desired when avian influenza virus has just then threatened human beings. Here I examine the applicability of a novel periodic table for the genetic code to influenza A/H3N2 virus, while presenting two rules regarding single point mutations of its virus hemagglutinin gene. One rule is that non-synonymous single point mutations are intimately associated with the first or second base replacements between four groups (5, 6, 9, and 10) in the periodic table. Another rule is that there is a new index (inversion number) conserving in mutation. This paper will take the first step to such contribution of mutational reactions.
Reducing the Probability of False Positive Research Findings by Pre-Publication Validation - Experience with a Large Multiple Sclerosis Database
Authors: Daumer Martin , Held Ulrike , Ickstadt Katja , Heinz Moritz , Schach Siegfried , Ebers George
Published: July 2019

*Objective*

We have assessed the utility of a pre-publication validation policy in reducing the probability of publishing false positive research findings. *Study design and setting*The large database of the Sylvia Lawry Centre for Multiple Sclerosis Research was split in two parts: one for hypothesis generation and a validation part for confirmation of selected results. We present case studies from 5 finalized projects that have used the validation policy and results from a simulation study.

*Results*

In one project, the "relapse and disability" project as described in section II (example 3), findings could not be confirmed in the validation part of the database. The simulation study showed that the percentage of false positive findings can exceed 20% depending on variable selection. *Conclusion*We conclude that the validation policy has prevented the publication of at least one research finding that could not be validated in an independent data set (and probably would have been a "true" false-positive finding) over the past three years, and has led to improved data analysis, statistical programming, and selection of hypotheses. The advantages outweigh the lost statistical power inherent in the process.
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors: Hucka Michael , Finney Andrew , Hoops Stefan , Keating Sarah , Le Novere Nicolas
Published: July 2019

Not applicable
Visualization of and Access to CloudSat Vertical Data through Google Earth
Authors: Chen Aijun , Leptoukh Gregory , Di Liping , Nadeau Denis , Farley John , Lynnes Christopher , Kempler Steven
Published: July 2019

Online tools, pioneered by the Google Earth (GE), are facilitating the way in which scientists and general public interact with geospatial data in real three dimensions. However, even in Google Earth, there is no method for depicting vertical geospatial data derived from remote sensing satellites as an orbit curtain seen from above. Here, an effective solution is proposed to automatically render the vertical atmospheric data on Google Earth. The data are first processed through the Giovanni system, then, processed to be 15-second vertical data images. A generalized COLLADA model is devised based on the 15-second vertical data profile. Using the designed COLLADA models and satellite orbit coordinates, a satellite orbit model is designed and implemented in KML format to render the vertical atmospheric data in spatial and temporal ranges vividly. The whole orbit model consists of repeated model slices. The model slices, each representing 15 seconds of vertical data, are placed on the CloudSat orbit based on the size, scale, and angle with the longitude line that are precisely and separately calculated on the fly for each slice according to the CloudSat orbit coordinates. The resulting vertical scientific data can be viewed transparently or opaquely on Google Earth. Not only is the research bridged the science and data with scientists and the general public in the most popular way, but simultaneous visualization and efficient exploration of the relationships among quantitative geospatial data, e.g. comparing the vertical data profiles with MODIS and AIRS precipitation data, becomes possible.
Ecological control on micro-ornamentation of conodont elements
Authors: Zhuravlev Andrey
Published: July 2019

Conodonts are considered now as specific group of early Chordata or even Vertebrata. Fifteen tooth-like conodont elements of seven morphological types compose the oral apparatus of conodonts. The elements demonstrate complex morphology. All the elements bear polygonal micro-ornamentation. The ornamentation is considered as representing imprints of the epithelium cells. Ecological dependencies of the cell sizes are known for some recent organisms.The maximum cell sizes are characteristic of optimal environmental conditions. Thus, one can supposes that decreasing in cell imprint size in the conodonts marks disturbance in water temperature or/and oxygen content.
Heterogeneity in Ty1-copia group of retroelements in chickpea (Cicer arietinum) genome
Authors: Rajput Manoj , Upadhyaya Kailash
Published: July 2019

Retrotransposons constitute a major fraction of plant genomes and these elements may have played a significant role in evolution and sequence organization of genomes. In order to access the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequences were amplified from chickpea genome, using the primers derived from two conserved domains of RT region. Thirty-six RT regions from independent amplicons were cloned and sequenced. On the basis of homology of deduced amino acids, the RT sequences could be grouped into three major families. The intra-family divergence at amino acid level ranges from 2 to 19%. Though intra-family RT sequences were conserved but no two sequences were identical. The results indicate a high degree of heterogeneity among the Ty1-copia group of retroelements from chickpea. It was possible to isolate RT specific sequences from RNA isolated from stressed seedlings, indicating that some of the retroelements may be functional under certain stress conditions.
Homologous self-organising scale-invariant properties characterise long range species spread and cancer invasion
Authors: Marco Diana , Cannas Sergio , Montemurro Marcelo , Hu Bo , Cheng Shiyuan
Published: July 2019

The invariance of some system properties over a range of temporal and/or spatial scales is an attribute of many processes in nature1, often characterised by power law functions and fractal geometry2. In particular, there is growing consensus in that fat-tailed functions like the power law adequately describe long-distance dispersal (LDD) spread of organisms 3,4. Here we show that the spatial spread of individuals governed by a power law dispersal function is represented by a clear and unique signature, characterised by two properties: A fractal geometry of the boundaries of patches generated by dispersal with a fractal dimension D displaying universal features, and a disrupted patch size distribution characterised by two different power laws. Analysing patterns obtained by simulations and real patterns from species dispersal and cell spread in cancer invasion we show that both pattern properties are a direct result of LDD and localised dispersal and recruitment, reflecting population self-organisation.
PAL: A Perl Script for Rapidly Identifying the Active Site of Large Protein Families
Authors: Larrea Andres , Larrea Pablo
Published: July 2019

In the post-genomic era, with an ever-increasing amount of sequence information, it is critical to develop tools that assist in sifting through all the data to identify information amidst the noise. The two main steps in determining the functional sites in proteins are aligning a large set of homologous sequences and analyzing this large file to identify highly conserved residues. Although a number of tools exist for generating high quality alignments rapidly there are much fewer tools available for rapidly identifying conserved cores within that multiple sequence alignment. PAL, is a Perl script that rapidly identifies conserved residues present in a large alignment file. The strengths of PAL are: speed, flexibility and ease of use.
Remote estimation of carbon dioxide uptake of terrestrial ecosystems
Authors: Garbulsky Martin F. , Peñuelas Josep , Papale Dario , Filella Iolanda
Published: July 2019

The estimation of the carbon balance in ecosystems, regions, and the biosphere is currently one of the main concerns in the study of the ecology of global change. Current remote sensing methodologies for estimating gross primary productivity are not satisfactory because they rely too heavily on (i) the availability of climatic data, (ii) the definition of land-use cover, and (iii) the assumptions of the effects of these two factors on the radiation-use efficiency of vegetation (RUE). A new methodology is urgently needed that will actually assess RUE and overcome the problems associated with the capture of fluctuations in carbon absorption in space and over time. Remote sensing techniques such as the widely used reflectance vegetation indices (e.g., NDVI, EVI) allow green plant biomass and therefore plant photosynthetic capacity to be assessed. Nevertheless, detecting how much of this capacity is actually realized is a much more challenging goal. The Photochemical Reflectance Index (PRI) derived from freely available satellite information (MODIS sensor) presented an exponential relationship with the RUE. Thus, we show that it is possible to estimate RUE in real time and therefore actual carbon uptake at ecosystem, regional, and biosphere levels using the PRI. This conceptual and technological advancement avoids the need to rely on either the sometimes unreliable maximum RUE for each ecosystem, hard-to-obtain climate data, or on imprecise land-use/land-cover data.
Ajuvant effect of a Synthetic Aluminium - Magnesium Silicate on chloroquine phosphate, against Plasmodium berghei.
Authors: ezeibe madike , obianuju Okoroafor obianuju , elendu-eleke nnenna , Ngene Augustine
Published: July 2019

Abstract effect of a synthetic Aluminium - Magnesium Silicate (AMS) on antiplasmodial activity of chloroquine was tested. Plasmodium berghei-infected mice were treated with 7 mg/kg, 5 mg/kg and 3 mg/kg chloroquine, respectively. The two subgroups in each experiment were treated with chloroquine alone and with chloroquine in AMS respectively. Parasitaemia (%) of the group treated with 7 mg/kg was higher than that of the control. At 5 mg/kg, chloroquine treatment significantly reduced parasitaemia from 3.60 to 2.46 (P =0.01). Incorporating chloroquine in AMS significantly improved its ability to reduce P. berghei parasitaemia at 5 mgkg and at 3 mg/kg, from 2.46 0.21 to 1.57 0.25 (P = 0.01) and from 3.82 0.06 to 2.12 0.08 (P =0.01 ). It also increased mortality of mice treated at 7 mg/kg from 20 to 80 %.
Empirical predictions of an intrinsically disordered protein theory approach to glycan/lectin reaction kinetics
Authors: Wallace Rodrick
Published: July 2019

Newly-developed methods from the theory of intrinsically disordered proteins can be applied to the flexible glycan structures that coat cellular surfaces and provide rich channels for biological information transmission. Extension of a mechanistic 'arm-in-sleeve' model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated 'spectral' classifications in glycan/lectin interaction, parameterized by an appropriate index of glycan frond length or other index of topological complexity, possibly requiring groupoid classifications analogous to quasicrystals.
Chromium uptake by Fenugreek
Authors: D S Xanthate , Ch V R Murthy , S C S Rajan , D M R Sekhar
Published: July 2019

Fenugreek (Trigonella foenum- graecum) is both herb (leaves) and a spice (seed) belonging to the family Fabaceae. Fenugreek leaves and seeds are used in the cuisine of India. Fenugreek also has medicinal value. Fenugreek seeds are known to reduce serum glucose and improve glucose tolerance and hence are prescribed to diabetic patients. In the recent past supplemental Chromium is being prescribed to diabetic patients to activate (increased- insulin binding, insulin receptor number, insulin receptor phosphorylation) insulin. Plants can uptake substantial quantities of toxic metals from contaminated soils if these soils are well ameliorated.It is then probable that the medicinal efficacy of Fenugreek in the case of diabetes could be enhanced if it takes up chromium from the soil. Preliminary studies are being conducted to note the chromium uptake by Fenugreek from soils which are applied with potassium dichromate.
"Dark Mediators" of Proteins as Revealed by NMR in Water: Residue-selective Anion Bindings that are Masked by Pre-existing Buffer
Authors: Song Jianxing , Miao Linlin , Qin Haina
Published: July 2019

Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities, which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and consequently no longer negligible in establishing "postreductionist framework" for protein biochemistry.
Genetic incorporation of D-Lysine into diketoreductase in Escherichia coli cells
Authors: Liu Zhi Zhi , Yang Xin , Yi Denghuan , Wang Shuzhen , Chen Yijun
Published: July 2019

D-Lysine has been genetically introduced into diketoreductase in E. coli cells by utilization of an orthogonal Ph tRNA /Lysyl-tRNA synthetase pair. This is the first report on the genetic incoporation of D-amino acids into proteins, which may be generally applicable to a wide variety of applications.
Neural Coding of Green Flash in Retinal Bipolar Pathways
Authors: Hu Caiping
Published: July 2019

What visual information do the graded potentials among retinal bipolar pathways actually transmit from photoreceptors to ganglion cells? The answer does not exist. Even the graded electric signals have not been understood completely. Here, this paper tries to analyze the encoding mechanisms of graded signals among the parallel bipolar pathways in response to brief green flash. The typical ON, OFF and ON-OFF bipolar cells simultaneously abstracted vectors from green flash stimulus with sine-like functions on their dendritic plane. Atypical bipolar cell had the synchronously monopolar response in contrast to the bipolar responses of typical bipolar cells, they also annotated green flash with facilitated stochastic (asynchronous and rate-coded) responses. Some complex ON-OFF bipolar cells with large voltage-gated Na+ current could generate high-frequent asynchronous responses, others had synchronous ON-OFF responses to green flash. The green flash was synchronously and asynchronously represented by the multiple-dimension signaling space among the parallel bipolar pathways. These results unraveled the multiple-dimension neural codes for brief green flash, demonstrated the superior encoding capability of parallel bipolar pathways, and suggested the electrophysiological mechanisms of vision such as color space.
USP4 is regulated by Akt phosphorylation and deubiquitylates TGF-beta type I receptor
Authors: Sheppard Kelly-Ann , Lu Chris , ten Dijke Peter , Zhang Long , Zhou Fangfang , Drabsch Yvette , Snaar-Jagalska Ewa , Mickanin Craig , Huang Huizhe
Published: July 2019

Stability and membrane localization of Transforming growth factor-β (TGF-β) type I receptor (TβRI) is essential for controlling TGF-β signaling. TβRI is targeted for ubiquitination-mediated degradation by Smad7/Smurf2 complex. However, it is unclear whether polyubiquitin modified TβRI can be reversed. Here we performed a genome-wide gain of function screen and identified ubiquitin-specific protease (USP) 4 as a strong inducer of TGF-β signaling. Putative oncogenic USP4 was found to interact with TβRI as deubiquitinating enzyme thus maintains TβR1 levels at the plasma membrane. Depletion of USP4 mitigates TGF-β-induced breast cancer cell migration, epithelial to mesenchymal transition and metastasis. Importantly, Akt/Protein kinase B (PKB), which has been associated with poor prognosis in breast cancer, associates with and phosphorylates USP4. Akt mediated phosphorylation relocates USP4 to cytoplasm and membrane and is required for maintaining its protein stability. Moreover, Akt-induced breast cancer cell migration was inhibited by USP4 depletion and TβRI kinase inhibition. Our results identified USP4 as an important determinant for crosstalk between TGF-β and Akt, which provides new opportunities for cancer treatment.
A New Method for Characterization of Natural Zeolites and Organic Nanostructure using Atomic Force Microscopy
Authors: Fuoco Domenico
Published: July 2019

In order to study and develop an economic solution to environmental pollution in water, a wide variety of materials were investigated. Natural zeolites emerge from that research as the best in class of this category. Zeolites are natural materials relatively abundant and non biodegradable, economic and good to perform processes of environmental remediation. This paper contains a full description of a new method to characterize superficial properties of natural zeolites of exotic provenience (Caribbean Islets) with atomic force microscopy (AFM). AFM works with the optical microscope simplicity and the high resolution typical of a transmission electron microscope (TEM). Structural information of mesoporous material is obtained using scanning and transmission electron microscopy (SEM and TEM), only if the sample is conductive, otherwise the sample has to be processed through the grafitation technique, but this procedure induces errors of topography. Therefore, the existing AFM method, to observe zeolite powders, is made in a liquid cell-head scanner, but this work puts in evidence and confirms that it is possible to use an ambient air-head scanner to obtain a new kind of microtopography. Once optimized, this new method allows investigating of organic micelles, very soft nanostructure, of cetyltriammonium bromide (CTAB) upon an inorganic surface such as natural zeolites. It is shown some correlation between SEM microphotographies and AFM 3D images.
Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies
Authors: Hoyal Cuthill Jennifer , Charleston Michael
Published: July 2019

The unpalatable and warning-patterned butterflies Heliconius erato and Heliconius melpomene provide the best studied example of mutualistic Müllerian mimicry, thought – but rarely demonstrated – to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of H. erato and H. melpomene, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence) that argued against codivergence. We present the first explicit cophylogenetic test of codivergence between mimetic populations of H. erato and H. melpomene, and re-examine the timing of these radiations. We find statistically significant topological congruence between multilocus coalescent population phylogenies of H. erato and H. melpomene, supporting repeated codivergence of mimetic populations. Divergence time estimates, based on a Bayesian coalescent model, suggest that the evolutionary radiations of H. erato and H. melpomene occurred over the same time period, and are compatible with a series of temporally congruent codivergence events. This evidence supports a history of reciprocal coevolution between Müllerian co-mimics characterised by phylogenetic codivergence and parallel phenotypic change.
Donor mesenchymal stem cells trigger chronic graft-versus-host disease following minor antigen-mismatched bone marrow transplantation
Authors: Yaguchi Saori , Shimmura Shigeto , Inaba Takaaki , Matsuzaki Yumi , Okamoto Shinichiro , Kawakami Yutaka , Ogawa Yoko , Morikawa Satoru , Okano Hideyuki , Mabuchi Yo , Suzuki Sadafumi , Tsubota Kazuo , Yaguchi Tomonori
Published: July 2019

Chronic graft-versus-host disease (cGVHD) is a complication after minor antigen mismatched bone marrow transplantation (BMT) characterized by an autoimmune-type reaction in various organs. Aberration in T cell regulation is involved, with donor mesenchymal stem cells (MSCs) playing a possible role in immunomodulation. In a minor-antigen mismatched mouse BMT model, transplantation of mismatched, but not syngeneic MSCs triggered the onset of cGVHD, and was associated with fibrosis, increased IL-6 secretion, decreased Foxp3+ regulatory T cells and increased Th17 in the peripheral blood. Mismatched MSCs alone were sufficient to induce cGVHD, while removal of donor MSCs rescued mice from cGVHD. RAG2 knockout recipient mice did not suffer cGVHD, indicating that host T cells were involved. Residual host-derived T cells were significantly higher in cGVHD patients compared to non-cGVHD patients. In conclusion, donor MSCs react with residual host T cells to trigger the progression of cGVHD.
Oxidative Stress and Mitochondrial Injury in Chronic Multisymptom Conditions: From Gulf War Illness to Autism Spectrum Disorder
Authors: Golomb Beatrice
Published: July 2019

Background:

Overlapping chronic multisymptom illnesses (CMI) include Chronic Fatigue Syndrome (CFS), fibromyalgia, irritable bowel syndrome, multiple chemical sensitivity, and Gulf War illness (GWI), and subsets of autism spectrum disorder (ASD). GWI entails a more circumscribed set of experiences that may provide insights of relevance to overlapping conditions.

Objectives:

To consolidate evidence regarding a role for oxidative stress and mitochondrial dysfunction (OSMD), as primary mediators in CMI, using GWI as a departure point.

Methods:

Exposure relations, character, timecourse and multiplicity of symptoms, and objective correlates of GWI are compared to expectation for OSMD. Objective correlates of OSMD in GWI and overlapping conditions are examined.

Discussion:

OSMD is an expected consequence of known GWI exposures; is compatible with symptom characteristics observed; and accords with objective markers and health conditions linked to GWI, extending to autoimmune disease and infection. Emergent triangulating evidence directly supports OSMD in multisymptom “overlap” CMI conditions, with similarities to, and diagnosed at elevated rates in, GWI, suggesting a common role in each.

Conclusions:

GWI is compatible with a paradigm by which uncompensated exposure to oxidative/nitrative stressors accompanies and triggers mitochondrial dysfunction, cell energy compromise, and multiple downstream effects such as vulnerability to autoantibodies. This promotes a profile of protean symptoms with variable latency emphasizing but not confined to energy-demanding post-mitotic tissues, according with (and accounting for) known properties of multisystem overlap conditions. This advances understanding of GWI; health conditions attending GWI at elevated rates; and overlap conditions like CFS and ASD, providing prospects for vulnerability assessment, mitigation of progression, treatment, and future prevention – with implications germane to additive and excessive environmental oxidative stressor exposures in the civilian setting.
In-group/out-group bias in contagious yawning
Authors: Porter J. Ryan , Platek Steven
Published: July 2019

Bias for an in-group is a social phenomenon characterized by an affinity for one’s in-group over a perceived out-group. Activation in the amygdala, which is implicated in social and emotional processes, is increased when humans view other-race faces. This increase in activation is associated with implicit racial bias as indicated by scores on an implicit attitude test. Contagious yawning is a social process that appears to subserve empathic processes enabling the inferential modeling of the mental states of others and is exhibited in few species other than humans, including chimpanzees (Pan troglodytes), stumptail macaques (Macaca arctoides), dogs (Canis familiaris), and budgerigars (Melopsittacus undulatus). Despite these comparative data, little research has investigated intra-species variation in contagious yawning.
New insight into DNA damage by cisplatin at the atomic scale
Authors: Heyrovska Raji
Published: July 2019

Cisplatin is cis-diamminedichloroplatinum (II) of chemical formula, Pt(NH3)Cl2, abbreviated as cis-DDP and known commercially as platinol. It is used widely as an anticancer drug for various types of cancer, ever since its discovery two centuries ago and has become a target of extensive researches. Transplatin, trans-DDP on the other hand, is found to be less or ineffective to treat cancers. Cisplatin is known to interact mainly with the N(7) nitrogen of guanine in nucleic acids, after a water molecule takes away one of the chlorines by hydrolysis. This initiates the damage of nucleic acids and eventually leads to apoptosis. However the way how this happens and why transplatin is less effective is not completely clear. Here the author brings some new insights, using the precise structures of these molecules at the atomic level, how cisplatin can interact with the nitrogen of guanine and adenine and rupture the hydrogen bonding in the Watson Crick base pairs and damage the structure of DNA. It is hoped that the results presented here will contribute to a better atomistic insight into the structure, bonding and feasibility of the biochemical reactions involving these compounds and their derivates for the alleviation of cancer.
An albumin-derived peptide scaffold capable of binding and catalysis
Authors: Maurizio Elisa , Sgarra Riccardo , Sblattero Daniele , Berti Federico , Luisi Immacolata , Pavan Silvia , Fontanive Giampaolo , Tossi Alessandro , Benedetti Fabio , Savoini Adriano
Published: July 2019

We have identified a 101-amino-acid polypeptide derived from the sequence surrounding the IIA binding site of human albumin. The polypeptide contains residues that make contact with ligands as warfarin in the parent protein, and eight cysteine residues to form disulfide bridges, which stabilize the polypeptide structure. Seventy-four amino acids are located in six [alpha]-helical regions, with the remaining amino acids forming six connecting coil/loop regions. Codon usage optimization was used to express a GST fusion protein in E. coli in yields as high as 4 mg/l. This fusion protein retains its structural integrity and aldolase activity, the ability to direct the stereochemical outcome of a diketone reduction, and its binding capacity to warfarin and efavirenz. Notably, this newly cloned polypeptide represents a valuable starting point for the construction of libraries of binders and catalysts with improved proficiency.