bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of ocean stratification on submarine melting of a major Greenland outlet glacier
Authors: Straneo Fiammetta , Curry Ruth , Sutherland David , Hamilton Gordon , Cenedese Claudia , Vaage Kjetil , Stearns Leigh
Published: July 2019

Submarine melting is an important balance term for tidewater glaciers1,2 and recent observations point to a change in the submarine melt rate as a potential trigger for the widespread acceleration of outlet glaciers in Greenland3-5. Our understanding of the dynamics involved, and hence our ability to interpret past and predict future variability of the Greenland Ice Sheet, however, is severely impeded by the lack of measurements at the ice/ocean interface. To fill this gap, attempts to quantify the submarine melt rate and its variability have relied on a paradigm developed for tidewater glaciers terminating in fjords with shallow sills. In this case, the fjords’ waters are mostly homogeneous and the heat transport to the terminus, and hence the melt rate, is controlled by a single overturning cell in which glacially modified water upwells at the ice edge, driving an inflow at depth and a fresh outflow at the surface1. Greenland’s fjords, however, have deep sills which allow both cold, fresh Arctic and warm, salty Atlantic waters, circulating around Greenland, to reach the ice sheet margin3,6,7. Thus, Greenland’s glaciers flow into strongly stratified fjords and the generic tidewater glacier paradigm is not applicable. Here, using new summer data collected at the margins of Helheim Glacier, East Greenland, we show that melting is driven by both Atlantic and Arctic waters and that the circulation at the ice edge is organized in multiple, overturning cells that arise from their different properties. Multiple cells with different characteristics are also observed in winter, when glacial run off is at a minimum and there is little surface outflow. These results indicate that stratification in the fjord waters has a profound impact on the melting dynamics and suggest that the shape and stability of Greenland’s glaciers are strongly influenced by layering and variability in the Arctic and Atlantic waters.
Reassessing the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria
Authors: Swithers Kristen , Fournier Gregory , Gogarten J. Peter , Lapierre Pascal
Published: July 2019

In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria. The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, Archaea and Bacilli. Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings. While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the DM group is broken down into smaller subgroups. We conclude that the signal detected in James Lake’s analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer.
Pathogenesis of AD is similar to that of uremic encephalopathy of Homocysteic acid.
Authors: Hasegawa Tohru , Ichiba Masayoshi , Tabira Takeshi
Published: July 2019

Homocysteic acid (HA) has been established as a pathogen in Alzheimer's disease (AD) in 3xTg-AD model mice. However, it is not established whether HA is involved in the AD pathogenesis in humans. We investigated the relationship between urinary HA levels and Mini-Mental State Examination (MMSE) scores in patients with AD (n = 110, normal =22, AD=88) and found a positive, statistically significant relationship between the two variables (r = 0.39, p =0.00003, n = 110). This relationship was stronger in females. (r = 0.47, p = 0.00008, n = 65 in females; r = 0.39, p = 0.02, n =45 in males). The difference in the urinary HA level between normal and AD females was statistically significant (normal:18.4 + 10.6vsAD: 9.1 + 7.2 mM,p<0.01), but this difference in males was not statistically significant. (normal:12.7 + 6 vs AD8.8 + 7.8). Smoking, hypertension, and diabetes mellitus decreased urinary HA excretion. On the basis of these results, we showed that HA is usually excreted into urine in humans and did not affect brain function in normal individuals. However, when urinary HA excretion was decreased, HA was shown to damage brain function, particularly cognitive ability. To confirm our hypothesis, that is, when urinary HA is suppressed to be excreted into urine, the blood HA level will increase, we examined the relationship between the urinary HA level and blood HA level in 19 patients. The result was shown that the negative statistically significant relationship between them was observed (r=-0.6, p=0.007, n=19). From this result, the uremic encephalopathy of HA toxicity was confirmed. However there remains the question of how the blood HA affected the brain's cognitive function. The direct effect of green tea leaves ingestion on HA level and MMSE score were also observed. Ingested green tea leaves decreased HA level in blood and concomitantly increased MMSE score, suggesting that blood HA could affect cognitive function. But How? Some papers showed that exogenous NMDA including HA disrupted the blood brain barrier and entered into the brain and affected the cognitive function to decrease MMSE score. These results indicate that human AD pathogenesis is influenced by HA, and that HA is a human pathogen in AD, indicating that the pathogenesis of AD is similar to that of uremic encephalopathy. Also, urinary HA can be used as a biomarker for Alzheimer's disease.
SARS-CoV Regulates Immune Function-Related Gene Expressions in Human Monocytic Cells
Authors: Hu Wan-Jiung , Yen Yu-Ting , Singh Sher , Kao Chuan-Liang , Wu-Hsieh Betty A.
Published: July 2019

Background:

Severe Acute Respiratory Syndrome (SARS) is characterized by acute respiratory distress (ARDS) and pulmonary fibrosis, and the monocyte/macrophage is the key player in the pathogenesis of SARS.

Methods:

In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV) infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection and the gene expression was profiled by oligonucleotide-based microarray.

Results:

Analysis of immune-related gene expression profiles showed that 24 h after SARS-CoV infection, (i) IFN-alpha/beta-inducible and cathepsin/proteosome genes were down-regulated; (ii) the hypoxia/hyperoxia-related genes were up-regulated; and (iii) the TLR/TLR-signaling, cytokine/cytokine receptor-related, chemokine/chemokine receptor-related, the lysosome-related, MHC/chaperon-related, and fibrosis-related genes were differentially regulated.

Conclusion:

These results elucidate that monocyte/macrophage dysfunction and dysregulation of fibrosis-related genes are two important pathogenic events of SARS.
Collective Animal Behavior from Bayesian Estimation and Probability Matching
Authors: Perez-Escudero Alfonso , de Polavieja Gonzalo
Published: July 2019

Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is based on empirical fits to observations and we lack first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.In the first stage, each animal makes a Bayesian estimation of which behavior is best to perform taking into account personal information about the environment and social information collected by observing the behaviors of other animals. In the probability matching stage, each animal chooses a behavior with a probability given by the Bayesian estimation that this behavior is the most appropriate one. This model derives very simple rules of interaction in animal collectives that depend only on two types of reliability parameters, one that each animal assigns to the other animals and another given by the quality of the non-social information. We test our model by obtaining theoretically a rich set of observed collective patterns of decisions in three-spined sticklebacks, Gasterosteus aculeatus, a shoaling fish species. The quantitative link shown between probabilistic estimation and collective rules of behavior allows a better contact with other fields such as foraging, mate selection, neurobiology and psychology, and gives predictions for experiments directly testing the relationship between estimation and collective behavior.
Shaping neurons: how morphological constraints affect axonal polarity
Authors: Villard Catherine , Andrieux Annie
Published: July 2019

Neuronal differentiation is under the tight control of biochemical and physical information arising from micro-environment. Here, through a panel of poly-L-lysine micropatterns, we wished to assay how external geometrical constraints of neurons may modulate axonal polarization. Constraints applied to either the cell body or to the neurite directions revealed the existence of a differential mechanical tension between the nascent axon and other neurites. Also, we show that centrosome location is not predictive of axonal polarization but responds to the force exerted by the nascent axon. Using curved trajectories for neurite growth inhibited axonal differentiation and prevented formation of multiple axons normally induced by cytochalasin or taxol treatments. Finally we provide evidence that microtubules act as curvature sensors during neuronal differentiation. Thus, biomechanics coupled to physical constraints might be the first level of regulation during neuronal development, primary to biochemical and guidance regulations.
Evaluation of Antimicrobial Studies of Traditional Medicine
Authors: Perumal Samy Ramar , Ignacimuthu S. , TK Chow Vincent
Published: July 2019

Synthetic drugs, which are having serious side effects, are cytotoxic to human beings. Moreover, bacteria slowly become resistant against antibiotics. In order to overcome these problems, scientists are continuing to search for antibacterial and novel principles from plants. Zanthoxylum limonella has been popularly used in traditional systems of medicine for the treatment of dental caries, cardiac, respiratory diseases and stomach problems. The present study was therefore focused on finding out the medicinal properties of the bark of Z. limonella tested against some selected bacteria using disc-diffusion method at the concentration of 100, 200 and 300 mg/ml. The methanol and water extracts of the bark exhibited effective antibacterial activity against S. aureus at a concentration of 300 mg/ml compared to the other extracts. Phytochemcial screening results also support the present findings and proved the traditional usage of this plant by tribal healers in the Kolli hills of Tamil Nadu.
Novel associations for hypothyroidism include known autoimmune risk loci
Authors: Do Chuong , Eriksson Nicholas , Tung Joyce , Kiefer Amy , Hinds David , Francke Uta , Mountain Joanna
Published: July 2019

Hypothyroidism is the most common thyroid disorder, affecting about 5% of the general population. Here we present the first large genome-wide association study of hypothyroidism, in 2,564 cases and 24,448 controls from the customer base of 23andMe, Inc., a personal genetics company. We identify four genome-wide significant associations, two of which are well known to be involved with a large spectrum of autoimmune diseases: rs6679677 near PTPN22 and rs3184504 in SH2B3 (p-values 3.5e-13 and 3.0e-11, respectively). We also report associations with rs4915077 near VAV3 (p-value 8.3e-11), another gene involved in immune function, and rs965513 near FOXE1 (p-value 3.1e-14). Of these, the association with PTPN22 confirms a recent small candidate gene study, and FOXE1 was previously known to be associated with thyroid-stimulating hormone (TSH) levels. Although SH2B3 has been previously linked with a number of autoimmune diseases, this is the first report of its association with thyroid disease. The VAV3 association is novel. These results suggest heterogeneity in the genetic etiology of hypothyroidism, implicating genes involved in both autoimmune disorders and thyroid function. Using a genetic risk profile score based on the top association from each of the four genome-wide significant regions in our study, the relative risk between the highest and lowest deciles of genetic risk is 2.1.
Environmental Pursuits In Nanomaterial Systems Science With Indian Exemplars
Authors: Sen Ranen , Seth Dipankar , Roy Indrani , Dasgupta Debmalya , Goswami Arunava
Published: July 2019

The behavior and pattern of NPs of minerals in the evolutionary history of the earth vis – a –vis the environmental context are inquired into, with a riverine system as a model. The study of fractal dimensions of NPs of interest serves as an aid to obtain a comprehensive view of natural NPs in the model system. The present study combines inputs from work done on nanoparticles, derived from the Subanarekha River System and products of base metal mine effluents that are rich in NPs of minerals. The authors believe this study would help to establish certain universalities about NPs and provide an updated framework for understanding the current state of nanomineral science.
bioDBcore: overview of the checklist and steps towards implementation
Authors: Gaudet Pascale , Rocca-Serra Philippe
Published: July 2019

Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this “one-stop shop” for those seeking information about the standards and data sharing policies.This presentation illustrates the rational for BioDBcore(P Gaudet) and the progresses for its implementation (P Rocca-Serra), in particular, (i) how the core attributes and the BioSharing catalogues can be used in combination, and (ii) the work towards the exchange of the descriptors.
Parkinson’s disease is a TH17 dominant autoimmune disorder against accumulated alpha-synuclein
Authors: Hu Wanchung
Published: July 2019

Parkinson’s disease is a very common neurodegenerative disorder. Patients usually undergo destruction of substantia nigra to develop typical symptoms such as resting tremor, hypokinesia, and rigidity. However, the exact mechanism of Parkinson’s disease is still unknown, so it is called idiopathic Parkinsonism. According to my microarray analysis of peripheral blood leukocytes and substantia nigra brain tissue, I propose that Parkinson’s disease is actually a TH17 dominant autoimmune disease. The autoantigen is mainly alpha-synuclein. After knowing the exact disease pathophysiology, we can develop better drugs to prevent or control the detrimental disorder.
NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0
Authors: You Tiefeng , Baianu I.
Published: July 2019

The soybean-derived products are among the most important agricultural products in the USA and the world. Conventional analytical methods for soybean composition analysis are both time consuming and costly. Faster and less expensive methods are required for most practical applications. To improve the accuracy, reliability and sensitivity of NIR, major advancements in instrumentation, as well as, data analysis / calibration methodology are required. Novel NIR instruments, such as DA-NIR and FT-NIR spectrometers developed in recent years have the potential for improving significantly the quantification of soybean composition at a reasonable cost. We present representative calibrations and data for intact soybean composition analysis obtained at the University of Illinois at Urbana with cutting-edge NIR instrumentation that is currently commercially available.
Reduction of circulating histone toxicity is a major function of C-reactive protein after extensive tissue damage
Authors: Toh Cheng-Hock , Baluwa Florence , Zhang Nan , Manson Joanna , Dar Caroline , Wang Susan Siyu , Liu Tingting , Abrams Simon , Brohi Karim , Kipar Anja , Yu Weiping , Thachil Jecko , Alhamdi Yasir , Wang guozheng
Published: July 2019

C-reactive protein (CRP) is a major acute phase protein. Although known to interact with chromatin, nucleosomes and histones, its functional roles are not clearly understood. Using both in vitro and in vivo models and samples from patients, this study demonstrates for the first time that CRP plays important roles in reducing the toxic effects of histones released into the circulation after extensive cell death. CRP protects endothelial cells by preventing histone integration into the cell membrane and thus reducing Ca2+ influx. In vivo, circulating histones cause endothelial damage, increased microvascular permeability, coagulation activation and IL-6 secretion. The latter induces CRP production in hepatocytes to form a negative feedback loop, a possible evolutionally conserved mechanism to limit secondary damage after extensive tissue injury. However, CRP responses lagged behind the histone surge following severe trauma. This indicates a time window for histone toxicity and also for potential clinical interventions using anti-histone therapy.
Development of Novel Calibrations for FT-NIR Analysis of Protein, Oil, Carbohydrates and Isoflavones in Foods
Authors: Baianu I , Guo Jun
Published: July 2019

The development of calibration methodology for novel FT-NIRS analysis of soybean-based foods is presented together with high-precision NIRS spectra and composition measurements in terms of proteins, oil and carbohydrates in soybean-based foods/soy foods.
Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game
Authors: Basanta David , Scott Jacob , Fishman Mayer , Ayala Gustavo , Hayward Simon , Anderson Alexander
Published: July 2019

Background:

Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the cancer; (ii) early in its genesis the tumour acquires a highly malignant phenotype, growing rapidly and displacing the original stromal population (often referred to as small cell prostate cancer) - these less common aggressive tumours are relatively independent of the local microenvironment; and, (iii) the tumour co-opts the local stroma - taking on a classic stromagenic phenotype where interactions with the local microenvironment are critical to the cancer growth. METHODS: We present an evolutionary game theoretical construct that models the influence of tumour-stroma interactions in driving these outcomes. We consider three characteristic and distinct cellular populations: stromal cells, tumour cells that are self-reliant in terms of microenvironmental factors and tumour cells that depend on the environment for resources but can also co-opt stroma.

RESULTS:

Using evolutionary game theory we explore a number of different scenarios that elucidate the impact of tumour-stromal interactions on the dynamics of prostate cancer growth and progression and how different treatments in the metastatic setting can affect different types of tumors.

CONCLUSIONS:

The tumour microenvironment plays a crucial role selecting the traits of the tumour cells that will determine prostate cancer progression. Equally important, treatments like hormone therapy affect the selection of these cancer phenotypes making it very important to understand how they impact prostate cancer’s somatic evolution.
Targeted delivery of anti-inflammatory therapy to rheumatoid tissue by fusion proteins containing an IL-4-linked synovial targeting peptide
Authors: Bombardieri Michele , Nissim Ahuva , Mather Stephen , Chernajovsky Yuti , Wythe Sarah , DiCara Danielle , Taher Taher , Finucane Ciara , Jones Rita , Pitzalis Costantino , Man Y. K. Stella
Published: July 2019

We provide first-time evidence that the synovial endothelium-targeting peptide (SyETP) CKSTHDRLC successfully delivers conjugated IL-4 to human rheumatoid synovium transplanted into SCID mice. SyETP, previously isolated by in vivo phage display and shown to preferentially localize to synovial xenografts, was linked by recombinant technology to hIL-4 via an MMP-cleavable sequence. Both IL-4 and the MMP-cleavable sequence were shown to be functional. IL-4-SyETP augmented production of IL-1ra by synoviocytes stimulated with IL-1[beta] in a dose-dependent manner. In vivo imaging confirmed increased retention of SyETP-linked-IL-4 in synovial grafts which was enhanced by increasing number of copies (one to three) in the constructs. Strikingly, SyETP delivered bioactive IL-4 in vivo as demonstrated by increased pSTAT6 in synovial grafts. Thus, this study provides proof of concept for peptide-tissue-specific targeted immunotherapy in rheumatoid arthritis. This technology is potentially applicable to other biological therapies providing enhanced potency to inflammatory sites and reducing systemic toxicity.
Predicting Prostate Cancer Aggressiveness through a Nanoparticle Test
Authors: Huo Qun , Sullivan Shannon , Hallquist Hillari , Litherland Sally , Decker David , Rivera-Ramirez Inoel
Published: July 2019

Prostate cancer (PCa) is the most common malignancy and the second leading cause of cancer death in American men. Due to the lack of accurate tests to distinguish aggressive cancer from indolent tumor, prostate cancer is often over-treated. Post-surgery pathology analysis revealed that 30% of tumors removed by radical prostatectomy are deemed clinically insignificant and would not have required such invasive treatment.^1^ Over-diagnosis and treatment of low-risk prostate cancer has serious and long-lasting side effect: as high as 70% of the patients who receive radical prostatectomy treatment will suffer a loss of sexual potency that cannot be remedied by drugs such as sildenafil citrate.^2^ We herein report a simple nanoparticle-serum protein adsorption test that not only can distinguish prostate cancer from normal and benign conditions, but also is capable of predicting the aggressiveness of prostate cancer quantitatively. This new test could potentially deliver the long-expected and very much needed solution for better individualization of prostate cancer treatment.
Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the 'logic gate' spectrum
Authors: Wallace Rodrick
Published: July 2019

Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological 'logic gates' having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the general from the particular, the analysis adds weight to arguments that a fundamental defining characteristic of the living state is the operation of chemical or other cognitive processes at virtually every scale and level of organization.
Dynamical patterns of human postural responses to emotional stimuli
Authors: Perakakis Pandelis , Vila Jaime , Idrissi Sofia , Ivanov Plamen
Published: July 2019

Erotic scenes and images of mutilated bodies are emotional stimuli that have repeatedly shown to evoke specific neurophysiological responses associated with enhanced attention and perceptual processing. Remarkably however, only a handful of studies have investigated human motor reactions to emotional activation as a direct index of physical approximation or withdrawal. Given the inconclusive results of these studies, the approach-avoidance distinction, one of the most salient concepts in human motivational research, remains a broadly exploited hypothesis that has never been empirically demonstrated. Here, we investigate postural responses elicited by discrete emotional stimuli in healthy young adults. We discover that both positive and negative affective pictures induce a significant posterior deviation from postural baseline equilibrium. Further, we find that neutral pictures also evoke posterior deviation, although with a less pronounced amplitude. Exploring the dynamical evolution of postural responses to emotional pictures at high temporal resolution, we uncover a characteristic profile that remains stable for stimuli from all three affective categories. In contrast, the postural response amplitude is modulated by the emotional content of the stimulus. Our observations do not support the interpretation of postural responses to affective picture-viewing as approach-avoidance behavior. Instead, our findings indicate the involvement of a previously unrecognized motor component of the physiological mechanism underlying human orienting responses.
Low dose IR-induced IGF-1-sCLU expression: a p53-repressed expression cascade that interferes with TGF&x00DF;1 signaling to confer survival
Authors: Willson David , Boothman David , Klokov Dmitry , Leskov Konstantin , Araki Shinako , Zou Yonglong , Goetz Eva , Luo Xiuquan
Published: July 2019

To better understand tissue responses after low IR doses, we generated a reporter system using human clusterin promoter fused to firefly luciferase (hCLUp-Luc). Secretory clusterin (sCLU), an extra-cellular molecular chaperone, induced by low doses of cytotoxic agents, clears cell debris promoting survival. Low dose IR (>2 cGy) exposure induced hCLUp-Luc activity with peak levels at 96 h, consistent with endogenous sCLU levels. As doses increased (>1 Gy), sCLU induction amplitudes increased and time to peak response decreased. sCLU expression was stimulated by IGF-1, but suppressed by p53. Responses in transgenic hCLUp-Luc reporter mice after low IR doses showed that specific tissues (i.e., colon, spleen, mammary, thymus, bone marrow) of female mice induced hCLUp-Luc activity more than male mice after whole body >10 cGy. Tissue-specific, non-linear dose- and time-responses of hCLUp-Luc and endogenous sCLU levels were noted. Colon maintained homeostatic balance after 10 cGy. Bone marrow responded with delayed, but prolonged and elevated expression. Intraperitoneal administration of the &x03B1;-TGF&x00DF;1 (1D11) antibody, but not a control antibody (13C4), immediately following IR exposure abrogated CLU induction responses. Induction in vivo also correlated with Smad signaling via activated TGF&x00DF;1 after IR. Mechanistically, media with elevated sCLU levels suppressed signaling, blocked apoptosis and increased survival of TGF&x00DF;1-exposed tumor or normal cells. Thus, sCLU is a TGF-&x00DF;1-induced pro-survival, potential bystander factor expressed in certain exposed tissues that, in turn, abrogates TGF&x00DF;1 signaling and may promote wound healing and likely contributes to a pro-tumor growth microenvironment.
Variety in evolutionary strategies favours biodiversity in habitats of moderate productivity
Authors: Pierce Simon
Published: July 2019

The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource economics and reproductive timing, coinciding with intermediate biomass production, whilst each productivity extreme is associated with small numbers of specialised species with similar trait values. Our data demonstrate that evolution can generate a greater range of phenotypes where large, fast-growing species are prevented from attaining dominance and extreme adaptation to a harsh abiotic environment is not a prerequisite for survival.
The use of DCEEG to estimate functional and metabolic state of nervous tissue of the brain at hyper- and hypoventilation
Authors: Murik Sergey
Published: July 2019

A pilot study has been made of the simultaneous DC potential and total slow electrical activity changes during modeling various metabolic and functional states of the human brain. The multi-electrode DCEEG recordings have been performed during the hyperventilation (frequent deep one-minute long breathing motions) and the hypoventilation (voluntary breath holding). It has been shown that the ischemic state occurring in hyperventilation is accompanied by the negative shift of DC potential and increase in the EEG rhythms amplitude. A distention of brain vessels during hypoventilation (voluntary breath-hold) and an improvement of blood supply and thus improvement of vital and functional state of neurons gave rise to an increase in the EEG rhythm amplitude too, though against a background of a positive DC-potential shift. Obtained results are considered in context of the generation of the qualitatively different functional states of brain cells during hyper- and hypoventilation which is reflected in their resting potential and activity. The conducted study shows the prospects for DCEEG and the method we used for DCEEG data processing to understand the character of functional and metabolic changes in the nervous tissue.
Mining SOM expression portraits: Feature selection and integrating concepts of molecular function
Authors: Wirth Henry , von Bergen Martin , Binder Hans
Published: July 2019

Background:

Self organizing maps (SOM) enable the straightforward portraying of high-dimensional data of large sample collections in terms of sample-specific images. The analysis of their texture provides so-called spot-clusters of co-expressed genes which require subsequent significance filtering and functional interpretation. We address feature selection in terms of the gene ranking problem and the interpretation of the obtained spot-related lists using concepts of molecular function.

Results:

Different expression scores based either on simple fold change-measures or on regularized Students t-statistics are applied to spot-related gene lists and compared with special emphasis on the error characteristics of microarray expression data. The spot-clusters are analyzed using different methods of gene set enrichment analysis with the focus on overexpression and/or overrepresentation of predefined sets of genes. Metagene-related overrepresentation of selected gene sets was mapped into the SOM images to assign gene function to different regions. Alternatively we estimated set-related overexpression profiles over all samples studied using a gene set enrichment score. It was also applied to the spot-clusters to generate lists of enriched gene sets. We used the tissue body index data set, a collection of expression data of human tissues, as an illustrative example. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. In addition, we display special sets of housekeeping and of consistently weak and highly expressed genes using SOM data filtering.

Conclusions:

The presented methods allow the comprehensive downstream analysis of SOM-transformed expression data in terms of cluster-related gene lists and enriched gene sets for functional interpretation. SOM clustering implies the ability to define either new gene sets using selected SOM spots or to verify and/or to amend existing ones.
MAP7D2 is a brain expressing X-linked maternal imprinted gene in humans
Authors: Niida Yo , Yachie Akihiro
Published: July 2019

Increasing evidence suggests imprinted genes influence mouse and human behaviors and cognitive functions. Unlike autosomal imprinted genes, X-linked imprinted genes are expressed in a sex-dependent manner because of male hemizygosity. Therefore, these genes could directly affect sex-specific brain functions and sex-biased vulnerability to psychiatric disorders such as autism1. Comparing lymphoblastoid cell lines (LCL) and peripheral blood mononuclear cells (PBMC) from healthy adult male and females, we identified MAP7 domain containing 2 (MAP7D2) as the first human X-linked imprinted gene. Both in LCL and PBMC, MAP7D2 expression was significantly suppressed in males by maternal imprinting. In each female LCL clone, MAP7D2 was expressed higher in paternally derived allele and was affected by X-chromosome inactivation. In female PBMC, however, reactivation of maternal MAP7D2 alleles was observed. MAP7D2 was expressed specifically in the brain among human tissues with unique isoforms. These results predict a crucial role of MAP7D2 for human sex-dependent neurobiological traits.
Precise Molecular Structures of Cysteine, Cystine, Hydrogen-Bonded Dicysteine, Cysteine Dipeptide, Glutathione and Acetyl Cysteine Based on Additivity of Atomic Radii
Authors: Heyrovska Raji
Published: July 2019

Structures of molecules are usually represented by arbitrary line drawings, ball and stick or space filling models. In recent years, the author found that using the appropriate radii of atoms and ions, bond lengths in inorganic, organic and biomolecules and of hydrogen bonds are exact sums of the radii of the adjacent atoms and or ions. This additivity of atomic radii was shown to hold also for the bond lengths in the twenty essential amino acids. On this basis, the atomic structures of the very important molecules mentioned in the title, have been presented here for the first time. It is hoped that these precise structures and their dimensions will shed new light into their role in biochemistry, pharmaceutical chemistry, environmental chemistry, biomedicine and in the mechanism of protein folding.
Balancing noise and plasticity in gene expression
Authors: Bajic Djordje , Poyatos Juan
Published: July 2019

Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational mechanisms are the ones separating noise from plasticity in low-plastic genes, a pattern associated with the simplicity of their expression regulation. Neighboring genome architecture as modifier appears then only effective in highly plastic genes. This poses ultimately an interesting paradox between intergenic distances and modulation, with short intergenic distances both associated and not associated with noise at different plasticity levels. Balancing the coupling among different types of expression variability appears thus as a potential shaping force of genome architecture and regulation.
Post-meiotic apozygotic combinatory process in sugar beet (Beta vulgaris L.)
Authors: Levites Evgenii , Kirikovich Svetlana
Published: July 2019

The effect of colchicine on phenotypic classes ratio of the enzyme locus controlling alcohol dehydrogenase (ADH1) in sugar beet agamospermous progenies was analyzed. The obtained data are indicative of the thing that colchicine causes polytenization of homological chromosome regions carrying marker locus Adh1 alleles. Theoretical calculation of the formation of egg cell frequencies and those of further development of cells entering embryogenesis without fertilization, also the diminution calculation of excessive chromosome regions carrying marker locus alleles have been made. The coincidence of theoretical and experimental ratios of phenotypic classes indicates the existence of a post-meiotic apozygotic combinatory process in plants.
Oncogenic KIT mutations induce STAT3-dependent autophagy to support cell proliferation in acute myeloid leukemia
Authors: Larrue Clément , Heydt Quentin , Saland Estelle , Boutzen Héléna , Kaoma Tony , Sarry Jean-Emmanuel , Joffre Carine , Récher Christian
Published: July 2019

Autophagy is associated with both survival and cell death in myeloid malignancies. Therefore, deciphering its role in different genetically defined subtypes of acute myeloid leukemia (AML) is critical. Activating mutations of the KIT receptor tyrosine kinase are frequently detected in core-binding factor AML and are associated with a greater risk of relapse. Herein, we report that basal autophagy was significantly increased by the KITD816V mutation in AML cells and contributed to support their cell proliferation and survival. Invalidation of the key autophagy protein Atg12 strongly reduced tumor burden and improved survival of immunocompromised NSG mice engrafted with KITD816V TF-1 cells. Downstream of KITD816V, STAT3, but not AKT or ERK pathways, was identified as a major regulator of autophagy. Accordingly, STAT3 pharmacological inhibition or downregulation inhibited autophagy and reduced tumor growth both in vitro and in vivo. Taken together, our results support the notion that targeting autophagy or STAT3 opens up an exploratory pathway for finding new therapeutic opportunities for patients with CBF-AML or others malignancies with KITD816V mutations.
Quantum optical neural networks
Authors: Steinbrecher Gregory R. , Olson Jonathan P. , Englund Dirk , Carolan Jacques
Published: July 2019

Physically motivated quantum algorithms for specific near-term quantum hardware will likely be the next frontier in quantum information science. Here, we show how many of the features of neural networks for machine learning can naturally be mapped into the quantum optical domain by introducing the quantum optical neural network (QONN). Through numerical simulation and analysis we train the QONN to perform a range of quantum information processing tasks, including newly developed protocols for quantum optical state compression, reinforcement learning, black-box quantum simulation, and one-way quantum repeaters. We consistently demonstrate that our system can generalize from only a small set of training data onto inputs for which it has not been trained. Our results indicate that QONNs are a powerful design tool for quantum optical systems and, leveraging advances in integrated quantum photonics, a promising architecture for next-generation quantum processors.
Global perspectives on food fraud: results from a WHO survey of members of the International Food Safety Authorities Network (INFOSAN)
Authors: Spink John , Embarek Peter Ben , Savelli Carmen Joseph , Bradshaw Adam
Published: July 2019

This survey of International Food Safety Authorities Network (INFOSAN) members regarding food fraud prevention, management, education, and information sharing included 166 WHO member states that resulted in 175 responses. The respondents engage in food fraud prevention (70%) or are responsible for food fraud incident response (74%). Nearly all respondents acknowledged a desire for more guidance and information on best practices in managing the full range of “food safety events involving food fraud” (97%), but also for prevention of such events (97%), indicating a need to provide technical support beyond acute incident response. The scope of food fraud covered in the survey comprised the full range of fraudulent activities, including the addition of adulterant-substances, tampering (including mislabeling), theft, smuggling, gray market/diversion, and counterfeiting (intellectual property rights). Key needs included: capacity-building/education; a platform for information sharing; and utilization of INFOSAN as an interagency/intergovernmental collaboration point.
Extracellular vesicles from T cells overexpress miR-146b-5p in HIV-1 infection and repress endothelial activation
Authors: Balducci Estelle , Leroyer Aurélie S. , Lacroix Romaric , Robert Stéphane , Todorova Dilyana , Simoncini Stéphanie , Lyonnet Luc , Chareyre Corinne , Zaegel-Faucher Olivia , Micallef Joëlle , Poizot-Martin Isabelle , Roll Patrice , Dignat-George Françoise
Published: July 2019

Human immunodeficiency virus type 1 (HIV-1) infection promotes a generalized activation of host responses that involves not only CD4 T cells, but also cells of the microenvironment, which are not directly infected, such as endothelial cells. The mechanisms triggering HIV-1-associated vascular alterations remain poorly understood. Extracellular vesicles (EVs), implicated in cell-to-cell communication, have been recently described as carriers of microRNAs (miRNAs). Here, we show that miR-146b-5p is upregulated in both CD4 T cells, CD4 T cell-derived EVs and circulating EVs obtained from antiretroviral therapy-naive HIV-1-infected patients. We further demonstrate that EVs from T cell line overexpressing miR-146b-5p mimics (miR-146b-EVs): 1) protect their miRNA cargo from RNase degradation, 2) transfer miR-146b-5p mimics into endothelial cells and 3) reduce endothelial inflammatory responses in vitro and in vivo in the lungs of mice through the downregulation of nuclear factor-κB-responsive molecules. These data advance our understanding on chronic inflammatory responses affecting endothelial homeostasis, in infectious and non-infectious diseases and pave the way for potential new anti-inflammatory strategies.
Heroic music stimulates empowering thoughts during mind-wandering
Authors: Koelsch Stefan , Bashevkin Tobias , Kristensen Joakim , Tvedt Jonas , Jentschke Sebastian
Published: July 2019

It is generally well-known, and scientifically well established, that music affects emotions and moods. However, only little is known about the influence of music on thoughts. This scarcity is particularly surprising given the importance of the valence of thoughts for psychological health and well-being. We presented excerpts of heroic- and sad-sounding music to n = 62 individuals, and collected thought probes after each excerpt, assessing the valence and the nature of thoughts stimulated by the music. Our results show that mind-wandering emerged during listening to either type of music (heroic, sad), and that the type of music strongly influenced the thought contents during mind-wandering. Heroic-sounding music evoked more positive, exciting, constructive, and motivating thoughts, while sad-sounding music evoked more calm or demotivating thoughts. The results thus indicate that music has a strong effect on the valence of thought contents during mind-wandering, with heroic music evoking more empowering and motivating thoughts, and sad music more relaxing or depressive thoughts. These findings have important implications for the use of music in everyday life to promote health and well-being in both clinical populations and healthy individuals.
Genotypic trade-off between appetitive and aversive capacities in honeybees
Authors: Junca Pierre , Garnery Lionel , Sandoz Jean-Christophe
Published: July 2019

Honey bees can learn both appetitive and aversive associations, using two olfactory conditioning protocols. Appetitive conditioning of the proboscis extension response (PER) involves associating an odor, the conditioned stimulus (CS) with a sucrose solution, the unconditioned stimulus (US). Conversely, aversive conditioning of the sting extension response (SER) involves associating the odor CS with an electric or thermal shock US. Here, we investigated the relationship between bees’ appetitive and aversive learning capacities at the individual level and the influence of bees’ genotype. As learning performance was shown to depend on an individuals’ sensitivity to the US, we systematically measured four different traits in each individual bee: sensitivity to sucrose, PER learning performance with a sucrose US, sensitivity to temperature, SER learning with a temperature US. First, we confirmed for both conditioning types that learning performance correlates with US responsiveness. Second, we found a trade-off between appetitive and aversive learning performances: bees that were better appetitive learners (and had a lower sucrose US threshold) learned less efficiently in the aversive conditioning (and had a higher temperature US threshold). Because the honey bee queen typically mates with 15–20 males, the workers from a honey bee hive belong to as many different patrilines, allowing for the search of the genetic determinism of cognitive abilities. Using microsatellite analysis, we show that a genetic determinism underlies the trade-off between appetitive and aversive capacities, with appetitively vs aversively biased patrilines. The honey bee hive thus appears as a genetically structured cognitive community.
Bionanocomposites based on chitosan intercalation in designed swelling high-charged micas
Authors: Alba María D. , Cota Agustín , Osuna Francisco J. , Pavón Esperanza , Perdigón Ana C. , Raffin Florian
Published: July 2019

Bionanocomposites based on layered inorganic components, as clays, and polymers of biological origin, as chitosan, have a major impact in medical and environmental fields, being economical and environmentally friendly materials. Na-Mn micas (n = 2 and 4) with controlled surface charge, high cation exchange capacity and swelling behaviour, are attractive inorganic composite components that exhibit improved adsorption properties compared to other inorganic solids which makes them potentially useful for bionanocomposites. The goal of this research was to explore the potential use of those synthetic brittle micas to form eco-friendly bionanocomposites with chitosan biopolymer. Hence, chitosan-mica bionanocomposites were prepared by ion-exchange reaction between chitosan solution and synthetic high charge mica. X-ray diffraction, Fourier transform infrared spectroscopy, thermal analysis, MAS-NMR spectroscopy and zeta-potential have been employed for bionanocomposites characterization. The results showed that the adsorption of chitosan is effective, although a chitosan portion remains in the outer surface being hydrogen-bonded to the tetrahedral sheet of the silicate.