bluuebunny/crossref_metadata_2025 huggingface dataset:
Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the C1 through C8 perfluorinated alkylsulfonic and alkylcarboxylic acids
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

Organic carbon normalized soil and sediment-water partitioning (Koc) coefficients were estimated for all C1 through C8 perfluorinated alkylsulfonic acid (PFSA) and alkylcarboxylic acids (PFCA) congeners. The limited experimental Koc dataset for the straight chain C7 through C10 PFCAs and C8 and C10 PFSAs was correlated to SPARC and ALOGPS computationally estimated octanol-water partitioning constants and used to predict Koc values for both branched and linear C1 through C8 isomers. All branched and linear congeners in this homologue range are expected to have Koc values>1, leading to their accumulation in organic matter on sediments and soils, retardation during ground and pore water flow, and the preferential association with dissolved organic matter in aquatic systems. Both increasing perfluoroalkyl chain length and linearity increase Koc values with substantial intra- and inter-homologue variation and interhomologue mixing. Variability in Koc values among the PFCA and PFSA congeners will likely lead to an enrichment of more linear and longer chain isomers in organic matter fractions, resulting in aqueous phases fractionated towards shorter chain branched congeners. The expected magnitude of fractionation will require inclusion in source apportionment models and risk assessments. A comparison of representative established quantitative structure property relationships for estimated Koc values from octanol-water partitioning constants suggests that equilibrium partitioning frameworks may be applicable towards modeling PFCA and PFSA environmental fate processes and warrants further study using other partitioning coefficients for which suitable experimental data is available.
Adherence to cancer screenings: Is the telephone survey a good method of investigation?
Authors: Cucchi Alessandro , Bergamini Mauro
Published: July 2019

*INTRODUCTION* - In order to define subjective variables, the methodology on the assessment of the women participation to screening programs to prevent cervical cancer is presented.

*MATERIALS AND METHODS*

- The study was conducted using a structured questionnaire administered by telephone to a sample of women invited to screening, regardless of their real participation to the Pap test. The phone calls were made within 2 days prior to the Pap test session. The questionnaire contained 12 closed questions. *RESULTS* - We contacted a total of 1206 women: a total of 1100 women (93.70%) received the invitation letter and answered to the questionnaire.

*CONCLUSIONS*

- The chosen procedure obtained a high percentage of women who agreed to be interviewed.
Reward sharpens orientation coding independently on attention
Authors: Baldassi Stefano , Simoncini Claudio
Published: July 2019

Rewarding improves performance. Is it due to modulations of the output modules of the neural systems or are there mechanisms favoring more 'generous' inputs? Some recent study included V1 in the the circuitry of reward-based modulations, but the effects of reward can easily be confused with effects of attention. Here we address this issue with a psychophysical dual task to control attention while orientation sensitivity on targets associated to different levels of reward is measured. We found that different reward rates improve orientation discrimination and sharpen the internal response distributions. Data are unaffected by changing attentional load nor by dissociating the feature of the reward cue from the feature relevant for the task. This suggests that reward may act independently on attention by modulating the activity of early sensory stages, perhaps V1, through a SNR improvement of task-relevant channels. Reward acts like attention, but using separate channels.
An artificial spiking synapse made of molecules and nanoparticles
Authors: Alibart Fabien , Pleutin Stephane , Guerin David , Gamrat Christian , Vuillaume Dominique
Published: July 2019

Molecule-based devices are envisioned to complement silicon devices by providing new functions or already existing functions at a simpler process level and at a lower cost by virtue of their self-organization capabilities, moreover, they are not bound to von Neuman architecture and this may open the way to other architectural paradigms. Here we demonstrate a device made of conjugated molecules and metal nanoparticles (NPs) which behaves as a spiking synapse suitable for integration in neural network architectures. We demonstrate that this device exhibits the main behavior of a biological synapse. These results open the way to rate coding utilization of the NOMFET in perceptron and Hopfield networks. We can also envision the NOMFET as a building block of neuroelectronics for interfacing neurons or neuronal logic devices made from patterned neuronal cultures with solid-state devices and circuits.
Signaling via Alk5 Controls Ontogeny of Lung Clara Cells
Authors: Xing Yiming , Li Changgong , Li Aimin , Sridurongrit Somyoth , Tiozzo Caterina , Bellusci Saverio , Borok Zea , Kaartinen Vesa , Minoo Parviz
Published: July 2019

Clara cells, together with ciliated and pulmonary neuroendocrine cells, make up the epithelium of the bronchioles along the conducting airways. Clara cells are also known as Progenitor/Stem cells during lung regeneration after injury. The mechanisms of Clara cell differentiation are largely unknown. Transforming growth factor-beta is a multifunctional molecule with roles in normal development and disease pathogenesis. In this study, we deleted the TGF-&x03B2; type I receptor, Alk5 in the embryonic lung epithelium using Gata5-Cre mice. Absence of Alk5 blocked Clara cell differentiation but had no effect on ciliated or pulmonary neuroendocrine cells. Hairy/Enhancer of Split-1, which is expressed in Clara cell putative "progenitors" was found to be a downstream target of Alk5 in vivo and in vitro. Loss of Alk5-mediated signaling also stimulated Pten gene expression and inhibited ERK phosphorylation in vivo. Using lung epithelial cells, we show that Alk5-regulated Hes1 expression is stimulated through Pten, MEK/ERK and PI3K/AKT pathways. Thus, the signaling pathway by which TGF-&x03B2;/ALK5 regulates Clara cell differentiation may entail inhibition of Pten expression, which in turn activates ERK and AKT phosphorylation.
Over-Imitation in the Kalahari Desert and the Origins of Human Cultural Cognition
Authors: Nielsen Mark , Tomaselli Keyan
Published: July 2019

Children grow up in environments saturated with tools and objects which they must learn to use. One of the most efficient ways in which children do this is by imitating. Recent work has shown that, in contrast to non-human primates, when young children learn by imitating they focus more on reproducing the specific actions used than the actual outcomes achieved. From about 18 months of age children will routinely copy arbitrary and unnecessary actions. This puzzling behaviour is called 'over-imitation'. By documenting similarities exhibited by children from a large, industrialised city and children from remote Bushman communities in southern Africa, we provide here the first indication that over-imitation is a universal human trait. We also show that over-imitation is unaffected by the age of the child, testing environment, or familiarity of the demonstrating adult. Furthermore we argue that, although seemingly maladaptive, over-imitation reflects an evolutionary adaptation fundamental to the development and transmission of human culture.
Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget
Authors: Xu Huilei , Ma'ayan Avi
Published: July 2019

Results from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly useful for showing time-series trends in multi-dimensional data. The Flash-based Motion Chart Google Gadget available through GoogleDocs is a recent advance in multi-dimensional data visualization. The Motion Chart Gadget is a component of the Trendalyzer software, which was developed for web-based animation of statistical results. Here we demonstrate the use of this Gadget to visualize molecular biological data, the phosphoproteomics results published on the Data Center of the Signaling Gateway web-site.
Parallel routes of human carcinoma development: Implications of the age-specific incidence data
Authors: Brody James
Published: July 2019

The multi-stage hypothesis suggests that cancers develop through a single defined series of genetic alterations. This hypothesis was first suggested over 50 years ago based upon age-specific incidence data. However, recent molecular studies of tumors indicate that multiple routes exist to the formation of cancer, not a single route. This parallel route hypothesis has not been tested with age-specific incidence data.To test the parallel route hypothesis, I formulated it in terms of a mathematical equation, confirmed this equation with computer simulations, then tested whether this equation was consistent with age-specific incidence data compiled by the Surveillance Epidemiology and End Results (SEER) cancer registries since 1973. I used the chi-squared goodness of fit test to measure consistency.I found that the age-specific incidence data from most human carcinomas, including those of the colon, lung, prostate, and breast were consistent with the parallel route hypothesis. However, this hypothesis is only consistent if an immune sub-population exists, one that will never develop carcinoma. Furthermore, breast carcinoma has two distinct forms of the disease, and one of these occurs at significantly different rates in different racial groups.
Nanoscience and Nano-Technology: Cracking Prodigal Farming
Authors: Mukhopadhyay Siddhartha , Parshad Vir Rajinder , Gill Inderpreet
Published: July 2019

Nano-science coupled with nano-technology has emerged as possible cost-cutting measure to prodigal farming and environmental clean-up operations. It has ushered as a new interdisciplinary field by converging various science disciplines, and is highly relevant to agricultural and food systems. Environmental Protection Agency of USA defined nanotechnology as the understanding and control of matter at dimensions of roughly 1-100 nm, where unique physical properties make novel applications possible. By this definition all soil-clays, many chemicals derived from soil organic matter (SOM), several soil microorganisms fall into this category. Apart from native soil-materials, many new nanotech products are entering into soil system, some of which are used for agricultural production and some others for many other purposes.Nano-science (also nanotechnology) has found applications in controlling release of nitrogen, characterization of soil minerals, studies of weathering of soil minerals and soil development, micro-morphology of soils, nature of soil rhizosphere, nutrient ion transport in soil-plant system, emission of dusts and aerosols from agricultural soil and their nature, zeoponics, and precision water farming. In its stride, nanotechnology converges soil mineralogy with imaging techniques, artificial intelligence, and encompass bio molecules and polymers with microscopic atoms and molecules, and macroscopic properties (thermodynamics) with microscopic properties (kinetics, wave theory, uncertainty principles, etc.), to name a few. Some of the examples include clinoloptolite and other zeolite based substrates, and Fe-, Mn-, and Cu- substituted synthetic hydroxyapatites that have made it possible to grow crops in space stations and at Antarctica. This has eliminated costs of repeated launching of space crafts. A disturbing fact is that the fertilizer use efficiency is 20-50 percent for nitrogen, and 10-25 percent for phosphorus (<1% for rock phosphate in alkaline calcareous soils). With nano-fertilizers emerging as alternatives to conventional fertilizers, build ups of nutrients in soils and thereby eutrophication and drinking water contamination may be eliminated. In fact, nano-technology has opened up new opportunities to improve nutrient use efficiency and minimize costs of environmental protection. It has helped to divulge to recent findings that plant roots and microorganisms can directly lift nutrient ions from solid phase of minerals (that includes so-called susceptible (i.e., easily weatherable, as well as non-susceptible minerals).
When does right functional hemispheric lateralization arise? Evidence from preterm infants
Authors: Mento Giovanni , Suppiej Agnese , Bisiacchi Patrizia
Published: July 2019

In recent years, magnetic resonance imaging (MRI) has allowed researchers to individuate an earlier morphological development of the right hemisphere compared to the left hemisphere before birth. Anatomical asymmetry, however, does not necessarily mean functional asymmetry and whether the anatomical differences between hemispheres at this early age are paralleled by functional specializations is still unknown. Here we show electrophysiological evidence of an early functional right lateralization for pitch processing arising by 30 gestational weeks, not before, in preterm newborns.
The study of the umbilical system in planktonic foraminifera in relation with depth of the Abderaz Formation at type section, IRAN
Authors: Shafiee Ardestani Meysam , Ghasemi-Nejad Ebrahim
Published: July 2019

Prospect of changes in such umbilical structures as Lip, Portici and Tegilla throughout Turonian-Campanian was also investigated. The phylogenic trend show that Lip structure in primary morphogroups turns gradually to tegilla in more developed forms in which the opening become also entirely umbilical. Statistical an analysis showed that the trends of changes are correlatable with increase in water depth while a decrease in depth result in development of lip in the planktonic foraminifera studied. The changes are considered to be in accord with Pascal law.
Carrier cell-mediated cell lysis of squamous cell carcinoma by squamous cell carcinoma antigen 1 promoter-driven oncolytic adenovirus
Authors: Hamada Katsuyuki , Zhang Ting , Desaki Junzo , Nakashiro Koh-ichi , Ito Hiroshi , Tani Kenzaburo , Koyama Yoshiyuki , Hamakawa Hiroyuki
Published: July 2019

The squamous cell carcinoma antigen (SCCA) serves as a serological marker for squamous cell carcinomas. Molecular cloning of the SCCA genomic region has revealed the presence of two tandemly arrayed genes, SCCA1 and SCCA2. We examined the promoter activity of the 5'-flanking proximal region of the SCCA1 gene. Deletion analysis of SCCA1 promoter identified a 175-bp core promoter region and an enhancer region at -525 to -475 bp upstream of the transcription start site. The transcriptional activity of the SCCA1 promoter was up-regulated in squamous cell carcinoma cells, compared with normal keratinocyte, normal non-keratinocyte and adenocarcinoma cells. Five tandem repeats of enhancer increased SCCA1 promoter activity by 4-fold. Oncolytic adenovirus driven by the SCCA1 promoter with 5 tandem repeats of enhancer specifically killed squamous cell carcinoma cells in vitro and in vivo. A549 carrier cells infected with the oncolytic adenovirus induced complete regression of tumor by overcoming immunogenicity and adenovirus-mGM-CSF augmented the antitumor effect of carrier cells. These findings suggest that SCCA1 promoter is a potential target of gene therapy for squamous cell carcinoma.
Experimental demonstration of associative memory with memristive neural networks
Authors: Pershin Yuriy , Di Ventra Massimiliano
Published: July 2019

When someone mentions the name of a known person we immediately recall her face and possibly many other traits. This is because we possess the so-called associative memory - the ability to correlate different memories to the same fact or event. Associative memory is such a fundamental and encompassing human ability (and not just human) that the network of neurons in our brain must perform it quite easily. The question is then whether electronic neural networks - electronic schemes that act somewhat similarly to human brains - can be built to perform this type of function. Although the field of neural networks has developed for many years, a key element, namely the synapses between adjacent neurons, has been lacking a satisfactory electronic representation. The reason for this is that a passive circuit element able to reproduce the synapse behaviour needs to remember its past dynamical history, store a continuous set of states, and be "plastic" according to the pre-synaptic and post-synaptic neuronal activity. Here we show that all this can be accomplished by a memory-resistor (memristor for short). In particular, by using simple and inexpensive off-the-shelf components we have built a memristor emulator which realizes all required synaptic properties. Most importantly, we have demonstrated experimentally the formation of associative memory in a simple neural network consisting of three electronic neurons connected by two memristor-emulator synapses. This experimental demonstration opens up new possibilities in the understanding of neural processes using memory devices, an important step forward to reproduce complex learning, adaptive and spontaneous behaviour with electronic neural networks.
Sensorimotor states affect choice in the magnitude judgment of ambiguous durations
Authors: Vicario Carmelo , Pavone Enea Francesco , Fuggetta Giorgio
Published: July 2019

The statistics of the environment seem to exert optimal influence on the organization of functions subserving decision making. In order to make decisions about ambiguous sensory information, predictive coding models suggest that brain generate a template against which to match observed sensory evidence. Here we challenge this notion providing evidence that stochastic choices about the magnitude judgment of visual duration are triggered by bottom-up sensorimotor information.
Stochastic Resonance Can Drive Adaptive Physiological Processes
Authors: Alicea Bradly
Published: July 2019

Stochastic resonance (SR) is a concept from the physics and engineering communities that has applicability to both systems physiology and other living systems. In this paper, it will be argued that stochastic resonance plays a role in driving behavior in neuromechanical systems. The theory of stochastic resonance will be discussed, followed by a series of expected outcomes, and two tests of stochastic resonance in an experimental setting. These tests are exploratory in nature, and provide a means to parameterize systems that couple biological and mechanical components. Finally, the potential role of stochastic resonance in adaptive physiological systems will be discussed.
Screening Lactic Acid Bacteria for Antimicrobial Compound Production
Authors: Khalid Khalisanni , Hung Kiong Lee
Published: July 2019

Lactic Acid Bacteria was known as potential probiotic used in food industries and dairy products and probable to produce antimicrobial compound that inhibit variety of microorganisms. The objectives of the research are to determine the optimum condition and glucose utilization in relation to antimicrobial compound production. Two species of Lactic Acid Bacteria namely Lactococcus and Lactobacillus were used as probiotic. The Lactic Acid Bacteria were fermentated in different medium, initial substrate pH and incubation temperature for the production of antimicrobial compound. The test organisms such as E.coli and Salmonella were selected as test organisms. Amongst the two species of Lactic Acid Bacteria, Lactococcus produced the highest amount of antimicrobial compound than Lactobacillus.
Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Authors: Muller Anthonie
Published: July 2019

Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a larger span of the thermal gradient. At the glaciation's end the ATP-generating mechanisms reversed and used ATP to sustain movement. Lastly, by functioning as animal organs, these protists then through symbiogenesis^15-17^ brought forth the first animals. This simple and straightforward scenario for the emergence of animals accounts for their large organ and organism size and their use of ATP, embryo and epigenetic control of development. The presented hypothesis is testable by collecting organisms near today's submarine hydrothermal vents and studying their behaviour in thermal gradients easily constructed in the laboratory. The scenario is extended to a general model for the emergence of biological movement^18^.
Insular gigantism and dwarfism in a snake, adaptive response or spandrel to selection on gape size?
Authors: Vincent Shawn , Brandley Matthew , Kuriyama Takeo , Mori Akira , Herrel Anthony , Hasegawa Masami
Published: July 2019

In biology, spandrels are phenotypic traits that evolve through their underlying developmental, genetic, and/or structural links to another trait under selection^1, 2, 3^. Despite the importance of the concept of spandrels in biology, empirical examples of spandrels are exceedingly rare at the organismal level^2, 3^. Here we test whether body size evolution in insular populations of a snake (Elaphe quadrivirgata) is the result of an adaptive response to differences in available prey, or the result of a non-adaptive spandrel resulting from selection on gape size. In contrast to previous hypotheses, Mantel tests show that body size does not coevolve with diet. However, gape size tightly matches diet (birds vs. lizards) across populations, even after controlling for the effects of body size, genetic, and geographic distance. Moreover, gape and body size show a strong degree of phenotypic covariation. Thus, the dramatic insular body size variation among E. quadrivirgata populations is at least partially caused by its underlying phenotypic covariation with gape size rather than the result of direct selection on overall body size.
Varicella notification in immigrants: a brief report from Ferrara, Italy
Authors: Cucchi Alessandro , Atti Silvia , Bergamini Mauro
Published: July 2019

Background and Aim of the work - We conducted a survey of varicella cases' notifications in the immigrant population in the province of Ferrara, Italy.

Materials and Methods

– We collected notifications of infectious disease between 2002 and 2006.

Results and discussion

- At the end of 2006, the 4.5% (14252 subjects) of total population of the province of Ferrara and its province was represented of immigrants from foreign countries. In this context, between 2002 and 2006, a total of 1969 cases of varicella, including 3.1% related to migrants, were reported. Among immigrants, there were 36 cases in males, and 26 in females. The cases were notified in the 64.5% by the hospital emergency service, in the 16.1% by the paediatrician and in 19.4% by the general practitioner. The incidence appears similar in both populations in childhood: this fact could means an integration in the local epidemiology for varicella of the immigrant school-children.
A novel Drosophila transcriptomic and behavioral model detects potassium chloride with therapeutic potential
Authors: Mohammad Farhan , Singh Priyanka , Sharma Abhay
Published: July 2019

In a newly described Drosophila model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the chronic PTZ model. Both transcriptomic and behavioral analyses thus showed LEV- and NaVP- like neuroprotective effect of KCl. This is consistent with neuroprotective effect of KCl observed previously in mammalian system. The Drosophila model thus provides a unique opportunity to understand long term mechanisms of neuroactive compounds.
Can Vision Exist Without Somatosensation?
Authors: Muniyandi Manivannan , Suresh Pawan Kumar
Published: July 2019

The interconnection between vision and somatosensation is already well-established and is further supplemented by the evolutionary link between eyes and photoreceptors, and the functional connection between photosensation and thermoreception. However, our analysis hypothesizes a possibility that vision is not just linked to somatosensation, but may not exist without somatosensation. Surprisingly, our photoreceptor itself needs somatosensory proteins for its functioning, and our entire visual pathway depends on somatosensory cues for its functioning.
A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis
Authors: Singh Priyanka , Mohammad Farhan , Sharma Abhay
Published: July 2019

Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs after PTZ discontinuation exhibited normal climbing speed on 7th day, i.e., 14th day from the beginning of PTZ treatment. Time-series of microarray expression profiles of fly heads comparing control PTZ- and AED-untreated, and AED-untreated post PTZ withdrawal groups showed differentially expressed genes throughout. These genes enriched gene ontology (GO) molecular functions including transcription regulator and GTPase regulator activities. Interestingly, expression profiles of fly heads comparing control PTZ- and AED-untreated, and AED-treated post PTZ withdrawal groups showed neutralization of transcription regulator and GTPase regulator activities by the AEDs. Further transcriptomic analysis based on overinteraction in protein interactome and enrichment of miRNA targets implicated axon guidance and neuronal remodeling related perturbations in the fly model. Differential expression of genes belonging to transcription regulator and GTPase regulator activities have previously been reported in post-epileptogenesis in established rodent models. Also, axon guidance and neuronal remodeling related alterations have been implicated in epilepsy. The Drosophila model thus provides a unique opportunity to dissect long-term plasticity relevant in epileptogenesis at cellular and molecular levels. Besides, the model also offers an excellent system to efficiently screen agents with potential therapeutic activity.
Common Transactivation Motif 9aaTAD recruits multiple general co-activatorsTAF9, MED15, CBP and p300
Authors: Piskacek Martin
Published: July 2019

More than 2000 transcription factors are involved in the human gene regulation to provide cellular function and development. Transactivation domain, TAD, mediates the interaction of transcription factors with general transcriptional co-activators such as TAF9, MED15, CBP and p300. Recently reported NMR-data for interactions of these co-activators with transcription factors reveal tightly binding of KIX and TAZ domains to common 9aaTAD motif. Nine-amino-acid Trans-Activation Domain, 9aaTAD, defines a transactivation domain common to a large super-family of eukaryotic transcription factors represented in yeast by Gal4, Oaf1, Pdr1, Rtg3, Pho4, Gln3, Gcn4 and in mammals by p53, E2A, NFAT, NFkB, HSF1, NF-IL6, MLL, EBNA2, VP16. The 9aaTAD family was derived from the transcription factor Oaf1 and its close orthologs Gal4, Pdr1, Leu3, Tea1 and Cha4.
Effective denitrification scales predictably with water residence time across diverse systems
Authors: Green Mark , Wollheim Wilfred , Basu Nandita , Gettel Gretchen , Rao P. Suresh , Morse Nathaniel , Stewart Robert
Published: July 2019

Nitrogen provides a fundamental building block for life. However, some nitrogen species (e.g., NO~3~) cause water quality degradation and contribute to climatic warming as a greenhouse gas (e.g., N~2~O). Denitrification is a central process in the nitrogen cycle, transforming water-soluble nitrogen to gaseous nitrogen, thereby removing nitrogen from the system. The factors controlling denitrification are known, yet the general quantitative comparison of controls on denitrification remains a rich area of study. Understanding the relative importance of various controls over denitrification is critical given its biological importance, role in the Earth system, and the current perturbation of the global nitrogen cycle by human activity. We demonstrate that the 'effective' denitrification rate constant (first-order constant; k~e~ [T^-1^]) and advective water transport (mean residence time; [tau] [T]) scale inversely across diverse systems, ranging from hillslopes and groundwater to large lakes and estuaries. As a result, we observe a relatively constant nitrogen removal across nine orders of magnitude in transport time scales. A central question remains as to why k~e~ scales approximately linearly with [tau]. We suggest that the variability of k~e~ arises from hydrologic masking of an intrinsic denitrification rate constant (k~den~). A two-compartment model shows how k~e~ varies with the amount of advective water, and thus [tau], explaining how denitrification losses in the reactive zone of a system are controlled by mass transfer to that reactive zone. Our finding highlights mean residence time in the advective zone as a primary control on effective rates of denitrification, while other factors (e.g., nitrate and organic carbon concentrations) provide secondary controls. Furthermore, the relationship between k~e~ and [tau] demonstrates the strong coupling of the water and nitrogen cycles.
Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies
Authors: Blondé Ward , Antezana Erick , De Baets Bernard , Mironov Vladimir , Kuiper Martin
Published: July 2019

While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org.
Logarithmic laws of echoic memory and auditory change detection in humans
Authors: Inui Koji , Urakawa Tomokazu , Yamashiro Koya , Otsuru Naofumi , Takeshima Yasuyuki , Kakigi Ryusuke
Published: July 2019

The cortical mechanisms underlying echoic memory and change detection were investigated using an auditory change-related component (N100c) of event-related brain potentials. N100c was elicited by paired sound stimuli, a standard followed by a deviant, while subjects watched a silent movie. The amplitude of N100c elicited by a fixed sound pressure deviance (70 dB vs. 75 dB) was negatively correlated with the logarithm of the interval between the standard sound and deviant sound (1 ~ 1000 ms), while positively correlated with the logarithm of the duration of the standard sound (25 ~ 1000 ms), indicating that the temporal representation of echoic memory is logarithmic. The amplitude of N100c elicited by a deviance in sound pressure, sound frequency and sound location was correlated with the logarithm of the magnitude of physical differences between the standard and deviant sounds, suggesting that Weber-Fechner's law holds for the automatic cortical response to sound changes.
The Neuroanatomic Basis of the Acupuncture Principal Meridians
Authors: Dorsher Peter
Published: July 2019

Acupuncture involves treating illness by inserting needles at specified body locations (acupoints). The Principal meridians are pathways that join acupoints with related physiologic effects. Despite nearly 5000 years of continuous clinical study, an accepted anatomic or physiologic basis for acupuncture's clinical effects has remained elusive. Some acupoints overlie peripheral nerves, and fMRI studies demonstrate that acupoints have specific effects on central nervous system processing. Traditional Chinese Medicine (TCM) founders described the body's viscera based on anatomic dissections yet not a discrete nervous system. By applying computer graphics and virtual human imaging techniques to human developmental neuroanatomy, this paradox may potentially be explained: acupuncture Principal meridians likely are TCM's representation of the nervous system. This neuroanatomic model of the Principal meridians is consistent with acupuncture's known neurophysiologic effects, and may allow 5 millennia of accumulated TCM observations regarding human health and illness to be understood in modern anatomic and physiologic terms.
Public awareness of cancer in Britain: a population-based survey of adults
Authors: Robb K , Stubbings S , Ramirez A , Macleod U , Austoker J , Waller J , Hiom S , Wardle J
Published: July 2019

_Objective:_

To assess public awareness of cancer warning signs, anticipated delay, and perceived barriers to seeking medical advice in the British population. Methods: We carried out a population-based survey using face-to-face, computer-assisted interviews to administer the Cancer Awareness Measure (CAM), a newly-developed, validated measure of cancer awareness. The sample included 2216 adults (970 male and 1246 female) recruited as part of the Office for National Statistics Opinions Survey using stratified probability sampling.*Results:* Awareness of cancer warning signs was low when open-ended (recall) questions were used and higher with closed (recognition) questions; but on either measure, awareness was lower in those who were male, younger, and from lower socioeconomic status (SES) groups or ethnic minorities. The most commonly endorsed barriers to help-seeking were difficulty making an appointment, worry about wasting the doctor’s time and worry about what would be found. Emotional barriers were more prominent in lower SES groups and practical barriers (e.g. too busy) more prominent in higher SES groups. Anticipated delay was lower in ethnic minority and lower SES groups. In multivariate analysis, higher symptom awareness was associated with lower anticipated delay, and more barriers with greater anticipated delay.

Conclusions:

A combination of public education about symptoms and empowerment to seek medical advice, as well as support at primary care level, could enhance early presentation and improve cancer outcomes.
Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Chain helicity
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

Semiempirical, ab initio, and density functional theory (DFT) studies were conducted on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C~1~ (trifluoroacetic acid; TFA) to C~9~ (perfluorodecanoic acid). Regardless of perfluoroalkyl chain length and computational method and level employed, no significant change in the electrostatic or steric characteristics of the carboxylate head group was found between C~2~ and C~9~. Application of a thermodynamic cycle to calculations at the B3LYP/6-311++G(3df,2p) level provided an accurate prediction of the experimental monomeric pK~a~ for TFA. At this – and similar – levels of theory, monomeric pK~a~ values of longer straight chain PFCAs are expected to display no significant increase with increasing chain length, having a relatively constant pK~a~ value of about 0 that is in excellent agreement with earlier predictions and with recent experimental evidence. Contrary to previous claims, perfluoroalkyl chain helicity does not appear to result in increased monomeric PFCA pK~a~ values at chain lengths >5 perfluorocarbons.
Suppression of cell cycle progression by Jun dimerization protein (JDP2) involves down-regulation of cyclin A2
Authors: Pan Jianzhi , Nakade Koji , Masuzaki Satoko , Hasegawa Hitomi , Huang Yu-Chang , Murata Takehide , Yoshiki Atsushi , Yamaguchi Naoto , Obata Yuichi , Yokoyama Kazunari
Published: July 2019

We report here a novel role for Jun dimerization protein-2 (JDP2) as a regulator of the progression of normal cells through the cell cycle. To determine the role of JDP2 in vivo, we generated Jdp2 knock-out (Jdp2KO) mice by targeting exon 1 to disrupt the site of initiation of transcription. The healing of wounded skin of Jdp2KO mice proceeded more rapidly than that of control mice and more proliferating cells were found at wound margins. Fibroblasts derived from embryos of Jdp2KO mice proliferated more rapidly and formed more colonies than wild-type fibroblasts. JDP2 was recruited to the promoter of the gene for cyclin A2 (ccna2) at a previously unidentified AP-1 site. Cells lacking Jdp2 had elevated levels of cyclin A2 mRNA. Moreover, reintroduction of JDP2 resulted in repression of transcription of ccna2 and of cell cycle progression. Thus, transcription of the gene for cyclin A2 appears to be a direct target of JDP2 in the suppression of cell proliferation.
Persistence of Edge-State in Stacked Graphene and Nano-Graphene Materials
Authors: Harigaya Kikuo
Published: July 2019

Nano-carbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings.
Enzyme activity and dynamics in near-anhydrous conditions
Authors: Lopez Murielle , Kurkal-Siebert Vandana , Dunn Rachel , Tehei Moeava , Finney John , Smith Jeremy , Daniel Roy
Published: July 2019

Water is widely assumed to be essential for life 1, although the exact molecular basis of this requirement is unclear 2-4. Water facilitates protein motions 5-9 and although enzyme activity has been demonstrated at low hydrations in organic solvents 10-13, such non-aqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an esterase to catalyse alcoholysis as an anhydrous powder, using a closed reaction system in which the substrates and products of the enzyme reaction are gaseous 14-15, and where the water content can be well defined 16. At hydrations equivalent to 3 (&177;2) molecules of water per molecule of enzyme, activity is observed that is several orders of magnitude greater than non-enzymatic catalysis. Neutron spectroscopy indicates that the fast (&8804;nanosecond) global anharmonic dynamics of the anhydrous functional enzyme are heavily suppressed. The results indicate that neither hydration water nor the solvent-activated fast anharmonic dynamics are required for enzyme function. An implication of these results is that one of the essential requirements of water for life may lie with its role as a diffusion medium rather than any of its more specific properties.
Roman roads: The hierarchical endosymbiosis of cognitive modules
Authors: Wallace Rodrick
Published: July 2019

Serial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of 'Roman roads' constituting channels for the transmission of information between modules.
The Role of Neuregulin 1 in Schizophrenia: A Bioinformatics Approach
Authors: Dias Alvaro , Maracaja-Coutinho Vinicius , Lopo Artur
Published: July 2019

*Context:* Notwithstanding the great number of studies on the etiology and pathophysiology of schizophrenia, both issues remain far from being fully understood. Schizophrenia seems to be related to several biochemical abnormalities, which point to a multi-factor etiology and pathophysiology, as well as to the perspective that several etiologically diverse disorders might coexist within this nosographic entity. On the other hand, identical twins reveal a high concordance for schizophrenia. From that standpoint, the perspective that structurally-related proteins may play an important and yet non-deterministic role seems attractive. Among these proteins, it is suggestive that Neuregulin 1 exerts a pivotal role.

Objective:

This paper aims to uncover the most prominent relations that Neuregulin 1 establishes with schizophrenia. *Method:* Several bioinformatical methods are used in order to present: 1. A visual representation of Neuregulin 1’s main molecular pathways, associated with a discussion about their importance to schizophrenia research; 2. A new heatmap of Neuregulin 1 and its receptor’s expression in brain tissues most relevant to the understanding of schizophrenia, created after the development of new R programming scripts (described elsewhere), which facilitate the analysis of gene expression profiles in public datasets; 3. A conceptual map of the literature retrieved using the keywords ‘Neuregulin 1 and human’ in PubMed, followed by a discussion of the most relevant sub-topics.

Results:

Neuregulin 1 polymorphisms affect several brain tissues and contribute to the etiology and pathophysiology of schizophrenia. Suggestively, Neuregulin 1 partially bridges the 'molecular gap' that schizophrenia establishes in relation to bipolar disorder and Alzheimer disease, which involves genes that affect several brain networks, at the same time that they are highly dependent on noxious environmental variables to be triggered.
Application of space technology to the design of sustainable settlements in hot deserts: Bioregenerative life support systems
Authors: Polyakov Yuriy , Musaev Ibrahim , Polyakov Sergey
Published: July 2019

Water scarcity in hot deserts, which cover about one-fifth of the Earth’s land area, along with rapid expansion of hot deserts into arable lands is one of the key global environmental problems. This paper proposes and substantiates an interdisciplinary approach to sustainable settlements in hot deserts using the accomplishments in the design of closed bioregenerative life support systems (CBLSS) for beyond-Earth (Lunar, Martian) settlements. Extensive space technology experience in the design of CBLSSes, which simultaneously produce food, water, nutrients, and fertilizers, process wastes, and revitalize air, has been analyzed and systematized with application to hot deserts, which represent extreme habitats with high input of solar energy, poor organic life, and nutrient/mineral-rich soils. A general flow diagram and design principles for hot-desert bioregenerative life support systems (BLSS), which may be considered as solar-powered "bioreactors" with accelerated cycles of carbon and nutrients, are formulated. Research and design guidelines for BLSS solar energy utilization, accelerated food production, water production and recycling, and wastes processing are suggested. Environmental and socioeconomic benefits of building hot-desert BLSSes are discussed.
Drone congregation areas of red dwarf honeybee, Apis florea
Authors: Nagaraja Narayanappa , Brockmann Axel
Published: July 2019

The drones of dwarf honeybees assemble at the drone congregation areas close to small trees with dense leafage at the heights between 2 to 4 meters.
Evaluation of the Cell Ontology (CL)
Authors: Cowell Lindsay
Published: July 2019

An ontological representation of the entities relevant to biological research is urgently needed. The cell ontology developed by Bard and colleagues (CL) (Bard et al. 2005) makes a significant contribution towards fulfilling this need by providing an ontology of cell types. The CL has already proven useful for data annotation (e.g. Grumbling et al. 2006), although the ontology’s potential utility goes well beyond that specific application. For example, using the number of distinct cell types in an organism as a measure of biological complexity, Vogel and Chothia (2006) compared the proteomes of 38 organisms of varying complexity and identified patterns in the evolution and expansion of protein domain superfamilies. This work has implications for some of the fundamental questions in biology, such as understanding the processes by which physiology becomes more intricate, new cell types arise, and biological complexity increases. While Vogel and Chothia did not yet utilize the CL for this work, they cite Bard et al. (2005) and describe the ontology’s value for improving and extending their analysis. Thus, in addition to its great utility for database annotation, the CL has the potential to play a significant role in basic scientific inquiry.The prospect of using the CL (and other ontologies) for this type of scientific research is extremely exciting but also imposes requirements on the level of formal rigor applied in ontology development, on the adequacy of the ontology as a representation of reality, and on its adherence to community standards of best practice. It is with these things in mind that I examined the CL to determine whether any revision would be required before my research group could use it for scientific research.After carefully evaluating the CL, my overall impression is that it does not possess the rigor and exactness required of a reference ontology. Furthermore, the problems I see are significant enough that it would be difficult for my research group to use the CL as our application ontology. While some of the problems could be resolved by changing a relation or rewriting a definition, others would require careful rethinking of the ontology’s foundation, because they involve the scope and organizing principle of the ontology as a whole.