bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting species abundance distributions by simultaneously using number and biomass as units of measurement
Authors: Henderson Peter , Magurran Anne
Published: July 2019

The universal observation that some species in an ecological community are common, but many more are rare, is neatly encapsulated in a species abundance distribution (SAD)1. However, the shape of the distribution can depend on the currency used to measure abundance 2. Here we show how the SADs for numerical abundance and biomass are related and how this relationship can be used to predict the form of the SAD. When plotted in log numerical abundance, log biomass space, species points lie within an approximately triangular area the limits of which are set by body size range, and the upper limit of abundance in both metrics. Under the simplifying, but reasonable, assumption that the observed scatter of species within this region is random, the shape of the SAD is immediately derived from simple geometrical considerations. For the SAD of numerical abundance this is a power curve. The biomass SAD can be either a power curve or, more frequently, a unimodal curve, which can approximate a log normal. This log triangular random placement model serves as a null hypothesis against which actual communities can be compared. Data from two intensively surveyed local communities indicate that it can give a good approximation, with species scattered within a triangle. Further, we can predict the consequences, for the SAD, of size-selective sampling protocols. We argue that mechanistic models of SADs must be able to account for the relative abundance of species in alternative currencies. Moreover, this approach will shed light on niche packing and may have application in environmental monitoring.
Cell Adhesion: A surprising cohesive force
Authors: Vasseur Hugues
Published: July 2019

When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a reacting "suction" force, due to the slow penetration of the surrounding fluid between the cell and the substrate, opposes to the dissociation. This force can overcome other known adhesive forces when the process is sufficiently violent (typically 10^5^ pN). Its maximal contribution to the total adhesive energy of the cell can then be estimated to 2 10^-3^ J/m2. The physical origin of this effect is quite simple, and it may be compared with that leaning a "suction-cup" against a bathroom wall. We address the consequences of this effect on (i) the separation energy, (ii) the motion of the fluid surrounding the cell, more especially, on the pumping of the fluid by moving cells, and (iii) the inhibition of cell motion.
Koffka's Ring Effect Depends on Thickness, Not Continuity
Authors: Huang Abigail , Hon Alice , Altschuler Eric
Published: July 2019

More than 70 years ago Gestalt psychologist Kurt Koffka described a fascinating effect1,2: When a contiguous grey ring is placed on a background half of one shade of grey (different from the ring) and half of another shade of grey, the ring appears to be a homogenous. However, if the ring is slightly divided, now the two halves of the ring appear different shades of grey with the half of the ring on the darker background appearing lighter than the half of the ring on the darker background. The Gestalt principle of continuity in visual perception is invoked to explain this effect. Here we show that in fact when the ring is made thinner it appears heterogeneous even when contiguous. Furthermore, when viewing a thick ring after first viewing a thin ring, the thick ring now too appears heterogenous! These effects are also demonstrated with a colored background and backgrounds with more than two regions. We show that standard simultaneous brightness and color contrast weaken with larger test patches. Thus, Koffka's ring effect is due to vanishingly weak simultaneous contrast for a sufficiently thick ring, not continuity.
The concentration of homocysteine-derived disulfides in human coronary artery
Authors: Iuliano Mauro , De Tommaso Gaetano , Ciavatta Liberato , Ragone Raffaele
Published: July 2019

*Background*

Based on previous findings, we have estimated that, in injured coronary artery tissue, the low molecular weight disulfides homocystine and cysteine-homocysteine, otherwise identified as oxidized homocysteine equivalents (OHcyE), may achieve a total concentration that is higher than the aqueous solubility of homocystine at room temperature. In order to verify whether or not OHcyE could reach their saturation limit in the vascular tissue, we have measured the solubility of homocystine in physiological-like condition.

*Materials and methods*

The solubility of homocystine has been measured in aqueous sodium chloride solutions at 37 °C by differential pulse polarography based on the reduction of homocystine to homocysteine.

*Results*

We have estimated that the concentration achieved by OHcyE in injured coronary artery tissue is at least near-saturating, because the solubility of homocystine in physiological-like condition, above which deposition of homocystine and/or cysteine-homocysteine as solid phase occurs, almost exactly matches its value. Near-saturation levels of OHcyE within the vascular tissue means that significant leakage of intracellular fluid can promote OHcyE crystallization in tissue fluids, which may serve to initiate inflammation.

*Conclusions*

We speculate that deposition of OHcyE crystals could damage blood vessels and act as a primer of homocysteine-triggered inflammation, thus being along the causal pathway that leads to vascular dysfunction.
Application of the Sensory Contact Model for Pharmacological Studies under Simulated Clinical Conditions
Authors: Kudryavtseva Natalia , Avgustinovich Damira , Bondar Natalia , Tenditnik Michael , Kovalenko Irina
Published: July 2019

The sensory contact model allows forming different psycho-pathological states (anxious depression, catalepsy, social withdrawal, pathological aggression, cognition disturbances, anhedonia, addictive states etc.) produced by repeated agonistic interactions in male mice and investigating the therapeutic and preventive properties of any drug as well as its efficiency under simulated clinical conditions. This approach can be useful for a better understanding of the drugs’ action in different stages of disease development in individuals. It is suggested that this behavioral approach and pharmacological designs may be applied for the screening of novel psychotropic drugs.
Iridium complex, a phosphorescent light-emitting diode material, serves as a novel chemical probe for imaging hypoxic tumor tissues
Authors: Zhang Shaojuan , Hosaka Masahiro , Yoshihara Toshitada , Iida Yasuhiko , Endo Keigo , Tobita Seiji , Takeuchi Toshiyuki
Published: July 2019

Iridium complex, a promising organic light-emitting diode for next generation television displays, emits phosphorescence. Phosphorescence is quenched by oxygen. We used this oxygen-quenching feature for imaging tumor hypoxia. Red light-emitting iridium complex Ir(btp)~2~(acac) (BTP) presented hypoxia-dependent light emission in culture cell lines, whose intensity was in parallel with HIF-1[alpha] expression. BTP was further applied to imaging five tumors (four from human origin and one from mouse origin) transplanted in athymic mice. All tumors presented a bright BTP-emitting image even 5 min after the injection. The BTP-dependent tumor image peaked at 1 to 2 h after the injection, and was then cleared from tumors within 24 h. The minimal BTP image recognition size was 3 to 4 mm in diameter. Compared with ^18^F-FDG/PET images, BTP delineated a clearer image for a tumor profile. We suggest that iridium complex has a vast potential for imaging hypoxic lesions such as tumor tissues.
The nitrite anion: the key intermediate in alkyl nitrates degradative mechanism.
Authors: Grossi Loris
Published: July 2019

Alkyl nitrates, in vivo, are metabolized to yield nitric oxide, and thiol groups are considered necessary cofactors. This statement is based on studies that underline how these species potentiate hemodynamic responsiveness to nitrates in patients with ischemic heart disease. However, the role of thiols might be mediated by the formation of corresponding S-nitrosothiols, and a redox process is responsible for the nitrates' degradation: an enzyme, probably the cytochrome P450, is involved in vivo. Here, we report evidence that, in vitro, no reaction between thiols and alkyl nitrates takes place, but that stronger reducing agents, such as iron (II) derivatives, are necessary: alkoxy radicals and the nitrite anion are the reaction intermediates. The latter, in slightly acidic conditions, for instance mimicking ischemic conditions, is shown to nitrosilate thiols to the corresponding S-nitrosothiols: the real NO suppliers. Therefore, the direct release of NO from nitrates is excluded. Finally, the in vivo role of thiols on depletion and tolerance is also accounted for.
Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Authors: Ma'ayan Avi
Published: July 2019

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function.
Angiotensinergic innervation of rat and human mesenteric resistant blood vessels
Authors: Patil Jaspal , Heiniger Eva , Schaffner Thomas , Muhlemann Oliver , Imboden Hans
Published: July 2019

In contrast to the current believe that angiotensin II (Ang II) only interacts with the sympathetic nervous system (SNS) as a circulating hormone, we document here the existence of an endogenous renin-angiotensin system (RAS) in the sympathetic coeliac ganglion and the angiotensinergic innervation with mesenteric resistant blood vessels. Our findings indicate that Ang II is synthesized inside the neurons of sympathetic coeliac ganglion and may act as an endogenous neurotransmitter locally on the mesenteric resistant blood vessels.
Effective Sample Size: Quick Estimation of the Effect of Related Samples in Genetic Case-Control Association Analyses
Authors: Yang Yaning , Remmers Elaine , Ogunwole Chukwuma , Kastner Daniel , Gregersen Peter , Li Wentian
Published: July 2019

Correlated samples have been frequently avoided in case-controlgenetic association studies in part because the methods for handling them are either noteasily implemented or not widely known. Weadvocate one method for case-control association analysis of correlatedsamples -- the effective sample size method -- as a simple andaccessible approach that does not require specialized computer programs.The effective sample size method captures the variance inflationof allele frequency estimation exactly, and can be used to modify thechi-square test statistic, p-value, and 95% confidence interval ofodds-ratio simply by replacing the apparent number of allele counts with theeffective ones. For genotype frequency estimation, although a singleeffective sample size is unable to completely characterize the variance inflation,an averaged one can satisfactorily approximate the simulated result.The effective sample size method is applied to the rheumatoid arthritissiblings data collected from the North American Rheumatoid Arthritis Consortium (NARAC)to establish a significant association with the interferon-inducedhelicasel gene (IFIH1) previously being identified as a type 1 diabetessusceptibility locus. Connections between the effective sample sizemethod and other methods, such as generalized estimation equation,variance of eigenvalues for correlation matrices, and genomic controls,are also discussed.
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Authors: Niman Henry , Boynton Bruce
Published: July 2019

Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current theory of “random mutation” through copy error, and are more easily explained by recombination with a common source. This conclusion is supported by additional polymorphisms shared by clade 2.2 isolates in Egypt and Germany.
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Authors: Niman Henry , Saad Magdi , Aly Mona , Tjaden Jeffery , Earhart Kenneth , Monteville Marshall , Mansour Moustafa , El-Sayed Nasr , Nayel Ahmed , Abdelghani Ahmed , Esmat Hala , Labib Emad , Ayoub Ehab , Arafa Abdelattar , Raczniak Gregory , Agyen-Frempong Mensah , Ampofo William , Boynton Bruce
Published: July 2019

Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current theory of “random mutation” through copy error, and are more easily explained by recombination with a common source. This conclusion is supported by additional polymorphisms shared by clade 2.2 isolates in Egypt and Germany.
The saltational model for the dawn of H. sapiens, chin, adolescence phase, complex language and modern behavior
Authors: NOYAN Omer Faruk , CAKIR Sahin
Published: July 2019

A new model may contribute to resolve the origin problem of H. sapiens. According to our new viewpoint, Neandertals were neither one of our direct ancestors nor a different species. Their origin was not in Europe 150-200 or 300 thousand years ago. As for the origin of H. sapiens, it was neither in Africa roughly 2 million years ago nor roughly 200 thousand years ago. In other words, both the Multiregional model and the recent African origin model seem wrong. Our own species arose in the Middle East approximately 150 thousand years ago and split into two subspecies: Moderns and Neandertals. Rapid and radial expansion of H. sapiens from the origin implies a revolution (see Figure 1). Complex language, modern behavior and even adolescence phase plus chin might be included into the revolution. This possibility seems consistent with the data and could also be tested via; 1-the origin of complex language based on the modern human form of FOXP2 gene 2-the origin of adolescence or adolescent growth spurt 3- the genetic origin of the Flores hobbits. If all of these three origins appeared in the Levant about 150 thousand years ago then our model is true in all aspects. This speciation seems an unexpected revolution or macroevolution occured in several thousand years. The last pre-sapiens hominids may be extinct due to OIS 6 namely without replacement by sapiens.
High-Value Phytochemicals from Grape Cane Waste: Potential Value-Added Viticultural Sources of Trans-Resveratrol and Trans-e-Viniferin with Medicinal and Anti-Phytopathogenic Applications
Authors: Rayne Sierra
Published: July 2019

Grape canes as agricultural waste from commercial viticultural activities represent a potentially important source of the well-known medicinal and anti-phytopathogenic stilbene compounds trans-resveratrol and trans-e-viniferin. Reports in the literature suggest that concentrations of these compounds range up to 5 mg/g dw and 2 mg/g dw, respectively, and can be quantitatively extracted from the cane residue using low-cost, environmental benign, and non-toxic aqueous alcoholic solvent systems such as ethanol:water mixtures. With current commercial values of these compounds between US$2,000 to US$3,000 per kg, established stilbene yields from cane waste could represent an agricultural coproduct valued at US$2,000 to US$3,000 per hectare of production. At the present worldwide wine grape production of 8,000,000 ha, the extraction of trans-resveratrol and trans-e-viniferin from grape cane waste would have an estimated global economic value of >$30 billion.
The folding fingerprint of visual cortex reveals the timing of human V1 and V2
Authors: Ales Justin , Carney Thom , Klein Stanley
Published: July 2019

Primate neocortex contains over 30 visual areas. Recent techniques such as functional magnetic resonance imaging (fMRI) have successfully identified many of these areas in the human brain, but have been of limited value for revealing the temporal dynamics between adjacent visual areas, a critical component of understanding visual cognition. The voltages recorded at the scalp, electroencephalography (EEG), is a direct measure of neural activity that reflects the summed activity across all brain areas. Identifying the cortical sources that contribute to the EEG is a difficult problem. We developed an anatomically constrained dipole search method that solves the traditional problems by combining fMRI, EEG and many stimuli that activate small cortical regions. The method provides a means to validate the extracted waveforms. Both V1 and V2 waveforms have similar onset latencies as well as dynamics that can explain previous controversial findings about the responses of these areas.
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Authors: Niman Henry , Saad Magdi , Tjaden Jeffery , Earhart Kenneth , Monteville Marshall , Aly Mona , Mansour Moustafa , El-Sayed Nasr , Nayel Ahmed , Abdelghani Ahmed , Esmat Hala , Labib Emad , Ayoub Ehab , Arafa Abdelattar , Raczniak Gregory , Agyen-Frempong Mensah , Ampofo William , Boynton Bruce
Published: July 2019

The evolution of H5N1 has attracted significant interest 1-4 due to linkages with avian 5,6 and human infections 7,8. The basic tenets of influenza genetics 9 attribute genetic drift to replication errors caused by a polymerase complex that lacks a proof reading function. However, recent analysis 10 of swine influenza genes identifies regions copied with absolute fidelity for more than 25 years. In addition, polymorphism tracing of clade 2.2 H5N1 single nucleotide polymorphisms identify concurrent acquisition 11 of the same polymorphism onto multiple genetic backgrounds in widely dispersed geographical locations. Here we show the aggregation of regional clade 2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa onto a human Nigerian H5N1 hemagglutinin (HA), implicating recombination in the dispersal and aggregation of single nucleotide polymorphisms from closely related genomes.
Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Authors: Niman Henry , Saad Magdi , Tjaden Jeffery , Earhart Kenneth , Monteville Marshall , Aly Mona , Mansour Moustafa , El-Sayed Nasr , Nayel Ahmed , Abdelghani Ahmed , Esmat Hala , Labib Emad , Ayoub Ehab , Arafa Abdelattar , Raczniak Gregory , Agyen-Frempong Mensah , Ampofo William , Boynton Bruce
Published: July 2019

The rapid evolution of the H5N1 serotype of avian influenza has been explained by a mechanism involving the selection of single nucleotide polymorphisms generated by copy errors. The recent emergence of H5N1 Clade 2.2 in fifty countries, offered a unique opportunity to view the acquisition of new polymorphism in these evolving genomes. We analyzed the H5N1 hemagglutinin gene from a fatal human case from Nigeria in 2007. The newly emerged polymorphisms were present in diverse H5N1 isolates from the previous year. The aggregation of these polymorphisms from clade 2.2 sub-clades was not supported by recent random mutations, and was most easily explained by recombination between closely related sequences.
Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
Authors: Ptitsyn Andrey , Gimble Jeffrey
Published: July 2019

*Background*

It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences.

*Results*

We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different regions within the 3’ end of the last exon. We demonstrate that in murine brown adipose tissue two downstream 3’ probe sets experience circadian baseline oscillation in counter-phase to the upstream probe set. Such differences in expression patterns are a telltale sign of alternative splicing within the last exon of SOCS3. In contrast, all three probe sets oscillated in a common phase in murine liver and white adipose tissue. This suggests that the regulation of SOCS3 expression in brown fat is tissue specific. Another component of the signaling pathway, Janus kinase (JAK), is directly regulated by SOCS and has alternative transcript probe sets oscillating in counter-phase in a white adipose tissue specific manner. *Conclusion*We hypothesize that differential oscillation of alternative transcripts may provide a mechanism to maintain steady levels of expression in spite of circadian baseline variation.
Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Authors: Good Benjamin , Kawas Edward , Wilkinson Mark
Published: July 2019

Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value. With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of meaningful annotations needed by modern biomedical science. We present E.D., the Entity Describer, a mashup of the Connotea social tagging system, an index of semantic web-accessible controlled vocabularies, and a new public RDF database for storing social semantic annotations.
Decrease of vanillin sucrose intake by victorious and defeated mice: development of anhedonia?
Authors: Kudryavtseva Natalia N. , Bondar Natalia P. , Kovalenko Irina L. , Avgustinovich Damira F.
Published: July 2019

Hedonic reactions to various rewards play a key role in various forms of motivated behavior. The influence of repeated experience of social victories or defeats in daily agonistic interactions between male mice on voluntary consumption of vanillin sucrose solution used as hedonic reinforcer was studied. Intake of vanillin sucrose solution was shown to decrease in the winners and losers exposed to social confrontations as compared with the controls. Three days of deprivation failed to restore the intake of vanillin sucrose solution to the control level in the losers and did so in the winners. The results obtained imply that similar reaction of animals to a hedonic non-drug reinforcer may have different motivational origin depending on positive or negative social experience.
Vesicles and lamella: outcome of the changing formation path of a sodium N-lauroylsarcosinate hydrate/1-decanol/water system
Authors: Akter Nasima , Mohamed Faizal , Radiman Shahidan , Reza Mohammad
Published: July 2019

Vesicles are closed bilayers that enclose a part of the continuous phase inside the core. In spherical shape, they attain the minimum free energy state. Conversely, lamella with maximum free energy remain in planer bilayer shape in the colloidal dispersion. Even with the same amphiphile concentration the colloidal structures depend on different parameters, many of these already addressed in different reports. However, the effect of mixing procedure as a formation path is unidentified. Here we reported water in 1-decanol and 1-decanol in water; these two different mixing procedures yield vesicles and lamella at the same point of the phase diagram of a sodium N-lauroylsarcosinate hydrate/1-decanol/water system. It was found that the favorable and unfavorable contact of water with the weak tertiary ammonium cation in amino-acid head-group plays the crucial role in this process. Moreover, this weak cationic property of this amphoteric surfactant can be exploited to carry DNA for gene therapy with a nontoxic system instead of cationic.
Studies on the Accumulation of Chromium in Fenugreek
Authors: D S Xanthate , Ch V R Murthy , S C S Rajan , D M R Sekhar
Published: July 2019

Studying Cr uptake by Fenugreek, we note that the maximum concentration of Cr takes place in the shells of the pods followed by leaves, stems and seeds in that order. Interestingly, applied higher doses of Cr does not increase accumulation of Cr in the stems, rather Cr content in the stems levels off. However, the maximum dispersal/distribution of Cr taken up is in the leaves.
Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans
Authors: Song Jianxing , Miao Linlin
Published: July 2019

We demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 µM in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 ºC, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Incidence response to a suddenly increased cancer risk
Authors: Hallberg Örjan
Published: July 2019

Incidence rates of several cancers, including melanoma of the skin and breast cancer, have increased since the middle of the 20th century in Western countries. Here, we developed a model for cancer incidence over time, when considering a suddenly increased cancer risk from an environmental change. A two parameter exponential function was used to simulate cancer risk over calendar time since birth, taking into account the time lapse since the environmental change took place. The calculated incidence for all age cohorts over calendar time was used to calculate the age-standardized rates. The best fit between calculated and reported age-standardized rates was sought by parameter variation. The model was tested using reported rates for melanoma and breast cancer. The best fit was obtained when an increased cancer risk took place from 1955 and with the starting age being that of puberty. Age-standardized rates of melanoma and breast cancer were easily modeled and fit well with reported data. In addition, age-specific rates fit well with reported data without further parameter adjustments. The good fit with reported data when using this simple exponential model strongly supports the hypothesis that an environmental change in the mid-20th century was the main cause of the cancer epidemic noted after 1955. Other forms of cancer should be analyzed in a similar manner.
Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31
Authors: Sardeshmukh N , Sanmukh S , Nakkeeran E
Published: July 2019

The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown proteins by using CELLO v 2.5 server. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural, functional and Sub-cellular localization of unknown proteins in Unclassified Halophilic archaeon DL31chromosome.
A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains coexpressed in normal samples in a tissue-specific manner
Authors: Cheng Weiyi , Anastassiou Dimitris
Published: July 2019

A recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3 and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12 (aka SDF1). The same subset of co-expressed genes is also strongly present even in normal samples in a tissue-specific manner, with lowest expression in brain tissues and highest expression in reproductive system tissues. The full signature, with prominent presence of COL11A1, THBS2 and INHBA appears to be triggered in solid cancers particularly when cancer cells encounter adipocytes.
Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against Salmonella gallinarum
Authors: Chikelu Ogechukwu , Ezeibe Madike , Anosa George , Okorie Okechi , Elendu-Eleke Nnenna , Okoroafor Obianuju , Ngene Augustine
Published: July 2019

Solutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate (AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10 mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 % reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved AT`s ability to clear the infection, in vivo.
Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Authors: Wallace Rodrick
Published: July 2019

Once cognitive biological phenomena are recognized as necessarily having 'dual' information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Biodiversity is a cauliflower under the sunlight
Authors: Gatti Cazzolla Roberto
Published: July 2019

For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater
Authors: Affan Md. Abu , Lee Dae-Won , Park Heung-Sik , Noh Jae-Hoon , Heo Soo-Jin , Oh Chulhong , Jeon Seon-Mi , Son Joo-Won , Son Seung-Gyu , Lee Hyi-Seung , Lee Hyeon Yong , Kang Do-Hyung
Published: July 2019

Carbon capture and storage have involved high cost and an earthquake threat. Coal in NaOH-natural seawater (NSW) can produce clean coal, and organic carbon enriched pretreated sweater (PSWS) can be used to grow Spirulina maxima. However, with freshwater shortage, high cost CO2 feedstock incurs S. maxima biomass production, and using PSWS should be considered as an alternative. NaHCO3 and Na2CO3 were used to sediment Mg2+ and Ca2+ of NSW to resolve turbidity and decreasing phosphate solubility. Here, we show that pre-combustion coal and NaOH concentration calculated by our devised formulae for any salinity could dilute volatile matter 19.8 Kg plus CO2 116.50 to 168.89 Kg Ton^-1^ coal in NaOH-NSW by sedimentation Mg2+ and Ca2+ of 99.91% and 32.52%, respectively, and clean coal will be produced. S. maxima biomass production cost was 3.35 times lower in PSWS medium than that of the standard. This method will be used for carbon sequestration and low cost biomass production.
Quantum probabilities in competing lizard communities
Authors: Aerts Diederik , Czachor Marek , D’Hooghe Bart , Kuna Maciej , Sinervo Barry , Sozzo Sandro
Published: July 2019

Despite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this ‘paradox of the plankton’ comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs, and thus could be overlooked. In more realistic scenarios, involving games ‘with ace in a sleeve’, the non-Kolmogorovian structure can be activated. Surprisingly, lizards occasionally do play such games. In consequence, the formalism of evolutionary games, similarly to quantum mechanics, should begin with density matrix equations. Implications of our finding extend beyond lizard communities, given that RPS games are common in nature and higher dimensional RPS games may be even more common in ecosystems.
Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition
Authors: Krylov Alexander , Zhdanov Renad
Published: July 2019

Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call "nucleic acid-protein fingerprints". The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells - biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases - 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins.
Dispersal of Aedes aegypti: field study in temperate areas and statistical approach
Authors: Bergero Paula , Ruggerio Carlos A. , Lombardo Rubén , Schweigmann Nicolás , Solari Hernán
Published: July 2019

We studied the dispersion of Aedes aegypti during egg laying in natural conditions. Two independent experiments involving mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms. We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with different oviposition activity were determined: a corridor surrounding the urbanized area, a second region between 10m and 25m and the third region extending from 30m to 45m from the urbanization. The landscape (plant cover) and the human activity in the area appear to have an influence in the dispersal of Aedes aegypti.
Inter-Tunneling Mechanism of Colliding Population Waves
Authors: Kalmykov Lev , Kalmykov Vyacheslav
Published: July 2019

Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
The phyogenetic principles of mma: A hypothetical biostratigraphic model
Authors: Czarnetzki Alfred , von Rautenfeld Dirk , Samii Madjid
Published: July 2019

Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.
Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven
Published: July 2019

We show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.
Aetiology and treatment of epidermal depigmentory disorder in humans
Authors: Sawhney S. S.
Published: July 2019

The epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa have been found as the renaturant of HES condition with the capacity to dislodge the denaturant hydrogen peroxide forming stronger hydrogen bonding with hydrogen peroxide than that of carbonyl molecular surface of melanolipoprotein, the epidermal colour determinant. The orally and topically defined plant based combined therapy advances the recovery time of HES condition.
Highly Efficient Gene Expression in B Lymphocytes Mediating by Lentivirus Vector
Authors: Tempaku Akira
Published: July 2019

Gene transduction and expression efficiencies among several type cell lines were compared by using vesicular stomatitis virus-glycoprotein (VSV-G) pseudotyped human immunodeficiency virus type-1 (HIV-1) based lentivirus vector. Large discrepancies of the efficiencies were shown among them. B lymphocytes showed high susceptibility of gene transduction and expression, while other cell lines marked lower potential. Variable gene transduction strategies have been assessed to apply immunological therapies. This study showed that B lymphocytes had facilities enough to support the gene transduction and expression by lentivirus vector. Our result suggested that the lentivirus vector would be a powerful tool to express exogenous genes in B lymphocytes.
Nitric oxide synthase in skeletal muscle fibres of patients with type 2 diabetes
Authors: Punkt Karla , Kandt Katharina , Oberbach Andreas , Adams Volker , Buchwalow Igor , Blueher Matthias
Published: July 2019

Muscle-derived nitric oxide (NO) mediates fundamental physiological actions on skeletal muscle including glucose uptake into muscle cells. Recently, we have shown that the altered glucose metabolism in skeletal muscle of patients with type 2 diabetes (T2D) is associated with changes in the metabolic profile of individual muscle fibres, but fibre-type specific changes in NO synthase (NOS) expression in skeletal muscle of T2D patients remain to be elucidated. Here we investigated fibre-type related NOS expression in vastus lateralis muscle of T2D patients compared with healthy individuals with normal glucose tolerance (NGT). Cytophotometrical assay and Western blotting did not reveal any quantitative differences between NOS expression in muscles from NGT and T2D subjects. Positive NOS immunoreactivity in vastus lateralis of T2D patients was found to be associated with fast-oxidative glycolytic (FOG) muscle phenotype. This indicates that NOS expression in T2D patients correlates both with skeletal muscle fibre type distribution and the activity of oxidative and glycolytic enzymes.
A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Authors: Baianu I.
Published: July 2019

A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several recent clinical studies have shown that gene expression data for cancer cells can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’ that will have to be validated through optimally designed clinical trials in cancer. A Human Cancer Genomes and Epigenetics Project is proposed that can provide the essential data required for the optimal design of clinical trials with the goal of achieving significant improvements of the survival rates of cancer patients participating in clinical trials for advanced cancer stages. The results of such a six-year Human Cancer Genomes and Epigenetics Project should also greatly aid with the accelerated, rational development of effective anti-cancer medicines and the chemoprevention of cancers.