bluuebunny/crossref_metadata_2025 huggingface dataset:
Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Authors: Piffer Davide
Published: July 2019

Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings support the hypothesis that evening preference in males is a sexually selected trait.
Evaluation of effective parameters on fabrication of BSA nanoparticles
Authors: Rahimnejad Mostafa , Najafpour Ghasem , Jahanshahi Mohsen
Published: July 2019

Coacervation technique was implemented in fabrication of BSA nanoparticle for the purpose of drug delivery system. Nanoparticle was purified with 48,800 g centrifuge, and then followed by dialysis, micro and ultra filtration. The fabricated nanoparticles were subjected to physical, morphological and biochemical characterization. The analyzed samples by SEM and AFM proved the semi-spherically shape of the particles whilst the size distribution was measured by photon correlation spectroscopy. Fourier transforms infra-red spectroscopy (FTIR) spectrum indicated that the fabricated nanoparticles were pure. The impact of various parameters upon the particle size was extensively investigated. The concentration of glutaraldehyde at fixed temperature had absolutely no significant effect on the size of particles. The affecting parameter was modeled to predict the size of nanoparticle. At low temperature (4{degree sign}C), the nanoparticle size of 89.3nm was fabricated with pure BSA concentration of 20 mg.ml-1.
Evolvability of Chaperonin Substrate Proteins
Authors: Raineri Emanuele , Ribeca Paolo , Serrano Luis , Maier Tobias
Published: July 2019

Molecular chaperones ensure that their substrate proteins reach the functional native state, and prevent their aggregation. Recently, an additional function was proposed for molecular chaperones: they serve as buffers (capacitors) for evolution by permitting their substrate proteins to mutate and at the same time still allowing them to fold productively.Using pairwise alignments of E. coli genes with genes from other gamma-proteobacteria, we showed that the described buffering effect cannot be observed among substrate proteins of GroEL, an essential chaperone in E. coli. Instead, we find that GroEL substrate proteins evolve less than other soluble E. coli proteins. We analyzed several specific structural and biophysical properties of proteins to assess their influence on protein evolution and to find out why specifically GroEL substrates do not show the expected higher divergence from their orthologs.Our results culminate in four main findings: *1.* We find little evidence that GroEL in E. coli acts as a capacitor for evolution in vivo. *2.* GroEL substrates evolved less than other E. coli proteins. *3.* Predominantly structural features appear to be a strong determinant of evolutionary rate. *4.* Besides size, hydrophobicity is a criterion for exclusion for a protein as a chaperonin substrate.
Novel determinants describe chaperonin substrate proteins
Authors: Raineri Emanuele , Ribeca Paolo , Serrano Luis , Maier Tobias
Published: July 2019

Molecular chaperones ensure that their substrate proteins reach the functional native state and prevent their aggregation. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level. Its substrate proteins in E. coli have been identified and characterized. However, a long standing and yet unresolved question in the field is: what makes a protein a chaperone substrate?Here we demonstrate with a bioinformatics-based approach that a simple set of criteria is sufficient to describe the GroEL substrate proteome to unprecedented accuracy. We define two novel parameters differentiating GroEL substrates from other cellular proteins: evolutionary rate and hydrophobicity. We demonstrate their conjunct applicability and explain why they are suitable descriptors. Combining them with other specific features of proteins, such as structure and size, we manage to identify the subset of GroEL substrate proteins with high confidence. We verify the applicability of our findings by correctly predicting a number of known heterologous GroEL substrate proteins.Furthermore, our results show that in vivo, the proposed buffering capacity of chaperones does not appear to be a dominant effect. Instead, the observed lower evolutionary rates among substrate proteins could be explained by their energetically unfavorable folding pathways not allowing for additional destabilizing mutations to occur.We show that a combination of simple parameters is sufficient to accurately describe the GroEL substrate proteome and to successfully predict known heterologous substrates. Our approach can potentially be used to predict chaperonin usage for any given polypeptide chain. Observed low evolutionary rates of GroEL substrates suggest that constraints in the folding pathways of the respective proteins do not allow for the accumulation of mutations.
Seasonal patterns of presentation in primary malignant brain tumors and metastases based on a retrospective neuropathologic database
Authors: Ehsani Sepehr , Croul Sidney , Knight Keith , Kiehl Tim-Rasmus
Published: July 2019

Seasonal variation in the occurrence of several classes of cancer has been observed in the past. However, evidence for such trends in adult central nervous system tumors is scant. We have analyzed the monthly occurrence rates of glioblastomas as well as carcinomas metastatic to the brain in 6,154 neurosurgical patients in Toronto selected from the University Health Network neuropathologic database over a seven-year period (July 2001 to June 2008). The electronic repository was representative of the patient population in southern Ontario, and the case accession dates in the database reflected the onset patterns of the selected tumor groups. A modification to Nam's alternative method to the Roger test was developed to statistically quantify the differences. The results demonstrated significant cyclical occurrence rates of glioblastomas with seasonal peaks in March, June, September and December. Moreover, significant increases in the rates of carcinomas metastatic to the brain were found for January, April and August. Surprisingly, the monthly frequency for the two tumor groups resembled each other in peak/trough topology. Semiquantitative comparison of major histologic features between glioblastomas from a peak (March) and trough (November) month in the seven-year period was performed, revealing differences in the amount of perivascular lymphocytic inflammation. This novel observation may have profound implications for the understanding of the biology of adult central nervous system tumors.
Pyrolysis of asphaltenes and biomarkers for the fingerprinting of the Amoco Cadiz oil spill after 23 years
Authors: Oudot Jean , Chaillan Frédéric
Published: July 2019

The chemical composition of the petroleum products accidently or deliberately released in the environment varies considerably with time under the action of biological (biodegradation) and physico-chemical (photo-oxidation) processes. It becomes more and more difficult to trace the origin of the oil spilled. A technique widely used for monitoring ancient oil pollutions is the study of oil biomarkers like terpanes and steranes^1,2^. Here we show that the geochemical technique of asphaltenes pyrolysis can be successfully applied to environmental samples. This method allows the reconstitution of the original oil from the asphaltenes fraction of severely degraded oil residues. We applied the two techniques: biomarkers analysis and pyrolysis of asphaltenes to the long-term characterisation of the Amoco Cadiz oil 23 years after the spill in the salt marshes of Ile Grande, Northern Brittany, France. The results show that the oil reached the ultimate degradation stage. The total biodegradation rate was 60% relatively to initial oil. The asphaltenes pyrolysis generated a gas-chromatographic profile very similar to the original Amoco Cadiz oil. In the biomarkers fraction, gas chromatographic/mass spectrometric (GC/MS) analyses demonstrated that terpanes were conserved whereas steranes were partly degraded. We also showed that the class of seco-hopanes biomarkers are conserved and can be used in the long term monitoring of oil pollutions.
The beauty of the mammalian vascular system
Authors: Gil Julio , Lahoz-Beltra Rafael , Gimeno Miguel , Laborda Jesús , Nubiala Javier
Published: July 2019

Beauty is a characteristic of objects that provides a perceptual experience of pleasure. In nature, aesthetic appreciation thereof has given rise to the mathematical search for good series (e.g. the Fibonacci series) and proportions (e.g. the Golden proportion) as important elements of beauty. In 1928 the mathematician George David Birkhoff introduced a formula for aesthetic measurement of an object. Birkhoff equation defines the aesthetic value as the amount of order divided by the complexity of the product. These two features can be measured easily in poetry, music, painting, architecture, etc. In the fine arts, it is the artist who manipulates both these features, but how does nature manage order and complexity in living organisms or their parts? Here we show how Birkhoff equation, applied to the mammalian vascular system of eight representative animals, results in new insights into the organization of the animal vascular system. We found that order and complexity are highly correlated in the mammalian vascular system (R^2^=0.9511). Accordingly, in nature both features are not independently managed in the manner of artists. We found significant differences among the Birkhoff aesthetic values in the mammalian arterial system, whereas no such differences exist in the venous system. We anticipate our approach to be useful in the study of morphogenesis and evolution of tree-like structures, employing the Birkhoff aesthetic value as a simple tool for conducting such studies.
Examining the PM6 semiempirical method for pKa prediction across a wide range of oxyacids
Authors: Rayne Sierra , Forest Kaya , Friesen Ken
Published: July 2019

The pK~a~ estimation ability of the semiempirical PM6 method was evaluated across a broad range of oxyacids and compared to results obtained using the SPARC software program. Compound classes under consideration included acetic acids, alicyclic and aromatic heterocyclic acids, benzoic acids, boronic acids, hydroxamic acids, oximes, peroxides, peroxyacids, phenols, α-saturated acids, α-saturated alcohols, sulfinic acids, α-unsaturated acids, and α-unsaturated alcohols. PM6 accurately predicts the acidity of acetic and benzoic acids and their derivatives, but is less reliable for alicyclic and aromatic heterocyclic acids and phenols. α-Saturated acids are reliably modeled by PM6 except for polyacid derivatives with α-alcohol moieties. α-Saturated alcohols only appear to yield reliable PM6 results where an α-hydroxy or α-alkoxy moiety is absent. Carboxylic acids with simple α-alkene unsaturation are well approximated by PM6 except where alkyne α-unsaturation or α-carboxylation are also present. The PM6 and SPARC methods exhibit approximately equal pKa prediction performance for the acetic, alicyclic, and benzoic acids. SPARC outperforms PM6 on the peroxides, peroxyacids, phenols, and α-saturated acids and α-saturated alcohols. pKa values for boron, nitrogen, and sulfur oxyacids do not appear to be reliably estimated by either the PM6 or SPARC methods. The findings will help guide the potential appropriateness of results from the PM6 pK~a~ estimation method for waste treatment and environmental fate investigations.
Population Dynamics
Authors: Nielsen Ron
Published: July 2019

Explicit assumption that the use of natural resources promoting and sustaining growth is proportional to the number of people living on the planet at any given time leads to a model, which reproduces the population data remarkably well.
Protective vaccination in the horse against Streptococcus equi with recombinant antigens
Authors: Guss Bengt , Flock Margareta , Frykberg Lars , Waller Andrew , Robinson Carl , Smith Ken , Flock Jan-Ingmar
Published: July 2019

Streptococcus equi subspecies equi (S. equi) is a clonal, equine host-adapted pathogen of global importance that causes a highly contagious suppurative lymphodendopathy of the head and neck, more commonly known as Strangles. The disease is highly prevalent, can be severe and spread easily by visibly infected animals or by carrier animals that show no clinical signs of disease. Antibiotic treatment is usually ineffective. However, the majority of horses develop immunity to re-infection, suggesting that vaccination should be a feasible way to prevent the infection. Live attenuated vaccine strains of S. equi are available but adverse reactions have been reported and they suffer from a short duration of immunity. Thus, a safe and effective vaccine against S. equi is highly desirable. In this report, Welsh mountain ponies vaccinated with a combination of seven recombinant S. equi proteins, were significantly protected from experimental infection by S. equi, resembling the spontaneous disease. The protective antigens consisted of five surface localized proteins and two IgG endopeptidases. The results from a second vaccination trial indicate that the endopeptidases were important for good protection. The similarity of S. equi to other pyogenic streptococci suggests that our findings have broader implications for the prevention of streptococcal infections.
Study on the effect of toxicity under highly arsenic prone zone in Nadia district of West Bengal in India
Authors: Rana Tanmoy , Sarkar Samar , Mandal Tapan , Batabyal Subhasis , Datta Bakul , De Sumanta , Sikdar Sourav
Published: July 2019

The present study was carried out on the basis of status of arsenic in soil, drinking water and plants, blood, urine and faeces of animals at arsenic prone zone. Within the ambit with the environment, the examination of animals was taken into consideration. They were screened and categorised on the degree of As toxicity. For field works animals were randomly selected from arsenic prone zone. The external manifestation indicated a complex syndrome and characteristic signs such as increased heart rate and respiratory rate, red urine, congested mucous membrane, anorexia, absence of ruminal motility, diarrhoea with blood, polyuria and unusual weight loss. The haematobiochemical changes such as low Hb level, decreased level of TEC, TLC and increased level ALT, AST, BUN and creatinine. Increased level of arsenic in urine, blood and faeces than the value of control animals could be the confirmatory indication of arsenic toxicity.
Glucose-6-phosphate-dehydrogenase deficiency as a risk factor in proliferative disorder development
Authors: Mandas Antonella , Peiretti Enrico , Cocco Pierluigi , Norfo Claudia , Abete Claudia , Angius Fabrizio , Pani Alessandra , Diaz Giacomo , Dessì Sandra , Fossarello Maurizio
Published: July 2019

Glucose-6-phosphate dehydrogenase (G6PD) is an important site of metabolic control in the pentose phosphate pathway (PPP) which provides reducing power (NADPH) and pentose phosphates. The former is mainly involved in the detoxification of chemical reactive species; the latter in the regulation of cell proliferation. G6PD deficiency is the most common enzymopathy in the human population, characterized by decreased G6PD activity, mainly in red blood cells, but actually also in nucleated cells. This decreased activity is not due to enzyme synthesis impairment, but rather to reduced enzyme stability, which leads to a shortening of its half-life. Therefore, a major problem is to understand the underlying mechanisms linking G6PD deficiency to oxidative stress and cell proliferation. In order to address this issue, in the present study we utilized, as an experimental model, fibroblasts isolated from pterygium, an ocular proliferative lesion, from G6PD normal and deficient (PFs+ and PFs-, respectively) patients. Our choice was determined by the fact that pterygium is believed to be caused by chronic oxidative stress induced by UV exposure, and that pterygium fibroblasts resemble a tumorigenic phenotype. As controls we utilized fibroblasts isolated from conjunctiva from G6PD normal and deficient patients (NCFs+ and NCFs-, respectively) who had undergone cataract surgery. Growth rate analysis revealed that PFs grow faster than NCFs, but while NCFs- grow more slowly than NCFs+, PFs- and PFs+ grow at the same rate. This was associated with significantly lower G6PD activity in NCFs+ compared to NCFs-, while no significant differences in the G6PD activity of PFs+ and PFs- were noted. This result was supported by the finding that in PFs-, G6PD mRNA levels were significantly higher than in PFs+. Another interesting finding of this study was increased green autofluorescence in both NCFs- and PFs- compared to corresponding positive cells, indicative of pronounced oxidative stress in deficient cells. Finally, abnormal accumulation of neutral lipids, mainly cholesterol esters was observed both in PFs- and PFs+ compared to NCFs- and NCFs+. Though further studies are necessary for better understanding the exact mechanism which links G6PD to oxidative stress and cell proliferation, our data allow to speculate on the role of G6PD on tumorigenesis, and to consider G6PD-deficient subjects at major risk to develop common and dreaded proliferative disorders, such as atherosclerosis and cancer.
Description of variation of genlculate's features of Phyllodiaptomustunguidus shen et Tai and sex-linked inheritance of Calanoida in freshwater
Authors: Long Sheng-Xing , Gou Xiao-Ming , Xia Pin-Hua , Ren Qi-Fei , Wan San , Chen Chuan
Published: July 2019

In the present paper, variation of genlculate's features of Phyllodiaptomustunguidus shen et Tai of Calanoida are described.The authors find that the right first antenna of female species has changed into genlculate and first antenna of male species changed into genlculate, which can be explained by X-sex-linked inheritance. This isn't a disease but a genetic characteristic that is better for the living of the species.
Population genetic structure of the pelagic goby, Sufflogobius bibarbatus, in the Northern Benguela ecosystem, based on PCR-RFLP analysis of the mitochondrial control region and the ND 3 and 4 region (Dissertation).
Authors: De Silva Pallagae
Published: July 2019

Polymorphism within the mitochondrial NADH-3,4 dehydrogenase(ND-3/4) and control region (D-Loop) was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of Sufflogobius bibarbatus (Pelagic Goby) population in the Northern Benguela ecosystem. Three major geographical areas representing the north-south axis (Ludritz, Walvis Bay and North of Ambrose Bay) were selected. Polymorphism was detected using three and two restriction enzymes respectively in ND- 3 / 4 and D-Loop regions, and a total number of 25 composite haplotypes were identified. The most common haplotype accounted for 36% of 238 individuals. Recorded haplotype diversities were quite high, ranging 0.70 to 0.86.The highest haplotype diversity was found in Walvis Bay followed by Ludritz and North of Ambrose Bay. Pairwise Fst values among regions indicated that significantly population differentiation existing. The Monte Carlo test revealed a significant difference among three geographical areas (P <0.05). Pairwise comparisons based on haplotype frequencies revealed significant differences between Ludritz and Walvis Bay (P < 0.05) and Ludritz and North of Ambrose Bay (P < 0.01) while no difference was found between Walvis Bay and North of Ambrose Bay (P >0.05).Similar observations were found by Exact test for haplotype frequencies. This study has shown existence of population subdivision of the pelagic goby in the Northern Benguela. Combination of factors like complex circulation pattern, physical barrier around Moeb Bay and adaptive selection can be contributed to the observed divergence. Identified population sub structure will be vital in future decision and policy making of the proposed ecosystem based management in the Benguela region.
Prey capture and meat-eating by the wild colobus monkey Rhinopithecus bieti in Yunnan, China
Authors: Ren Baoping , Li Dayong , Liu Zhijin , Wu Hua , Li Ming
Published: July 2019

If it is true that extant primates evolved from an insectivorous ancestor, then primate entomophagy would be a primitive trait. Many taxa, however, have undergone a dietary shift from entomophagy to phytophagy, evolving a specialised gut and dentition and becoming exclusive herbivores. The exclusively herbivorous taxa are the Malagasy families Indriidae and Lepilemuridae, and the Old World Monkey subfamily Colobinae, and among these meat-eating has not been observed except as an anomaly, with the sole exception of the Hanuman langur (Semnopithecus entellus), which feeds on insects seasonally, and a single observation of a nestling bird predated by wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana). Here, we describe the regular capture of warm-blooded animals and the eating of meat by a colobine, the critically endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). This monkey engages in scavenge hunting as a male-biased activity that may, in fact, be related to group structure and spatial spread. In this context, meat-eating can be regarded as an energy/nutrient maximization feeding strategy rather than as a consequence of any special characteristic of meat itself. The finding of meat-eating in forest-dwelling primates might provide new insights into the evolution of dietary habits in early humans.
A Therapeutically Relevant Difference in Leukemia and Normal Stem Cell Self Renewal
Authors: Negrotto Soledad , Hu Zhenbo , Link Kevin , Ng Kwok Peng , Bodo Juraj , Duong Hien , Schade Andrew , Hsi Eric , Lindner Daniel , Maciejewski Jaroslaw , Mulloy James , Saunthararajah Yogen
Published: July 2019

Abnormal self-renewal and differentiation are defining features of acute myeloid leukemia (AML). Using models of hematopoiesis, we show that persistent self-renewal that ignores differentiation signals can be produced through two distinct pathways. One pathway prevents repression of stem cell genes, producing daughter cells that resemble parental stem cells despite differentiation inducing lineage-specifying factor or cytokines. Runx1 deficiency, a frequent abnormality in AML, demonstrates the second pathway, which allows cytokine/lineage-specifying factor mediated repression of stem cell genes but impairs subsequent activation of differentiation genes that terminate transit-amplification, producing self-renewal in daughter cells that do not resemble the parental stem cell. Use of this pathway by AML cells has therapeutic relevance: cell-fate regulation by the chromatin-modifying protein DNMT1 is differentiation-phase dependent. In the post lineage-commitment differentiation-phase at which AML cell self-renewal occurs, DNMT1 has an opposite role than in normal stem cells. Consequently, DNMT1 depletion, using a clinically applicable method, terminates AML cell self-renewal but increases normal stem cell self-renewal.
Talin1 Promotes Prostate Cancer Invasion and Metastasis via AKT Signaling and Anoikis Resistance
Authors: Sakamoto Shinichi , McCann Richard , Kyprianou Natasha
Published: July 2019

Talin1 is an integrin regulatory protein that mediates integrin interactions with the extracellular matrix (ECM). This study investigated the significance of talin1 in prostate cancer progression to metastasis in vitro and in vivo. Talin1 overexpression enhanced prostate cancer cell adhesion, migration and invasion by activating survival signals and anoikis resistance. ShRNA-mediated talin1 loss led to a significant suppression of prostate cancer cell migration and transendothelial invasion in vitro and a significant inhibition of prostate cancer metastasis in vivo. Talin1 regulates cell survival signals via phosphorylation of focal adhesion kinase (FAK) and AKT. Targeting AKT activation led to a significant reduction of talin1-mediated prostate cancer cell invasion. Furthermore, talin1 expression was determined by immunostaining in prostate tissue from the TRAMP mouse model and in human prostate cancer specimens. Talin1 levels directly correlated with prostate tumor progression to metastasis in TRAMP mice. Talin1 profiling in human prostate specimens revealed a significantly higher expression of cytoplasmic talin1 in metastatic tissue compared to primary prostate tumors and benign prostate tissue (P<0.0001). This evidence suggests a potential value for talin1 as a marker of prostate cancer metastasis and implies that disrupting talin1 mediated signaling may have therapeutic significance in the treatment of metastatic disease.
Transduction Pathways Regulating The Trophic effects of Saccharomyces boulardii in Rat small intestinal mucosa
Authors: Buts Jean-Paul , De Keyser Nadine
Published: July 2019

S . boulardii is a probiotic yeast widely prescribed in a lyophilized form that determines in human and rat small intestine several effects including endoluminal secretion of enzymes and of polyamines, stimulation of microvillous enzymes, of sIgA ,increased production of the receptor for polymeric immunoglobulins by crypt cells, and enhanced D-glucose uptake.Aim: The objective of this study was to determine the pathway(s) by which these effects generated by the yeast are transduced into the cell.

Methods:

Litters of 6 growing Wistar rats each (30 days post partum) were treated with S .boulardii (50[micro]g per g body wt) or with saline during 72 hours. For each animal, the cytosol was prepared from the whole mucosa after the fat cake was discarded. Several known intestinal substrates were immunoprecipitated and immunoblotted using specific antibodies recognizing the non-, mono- or diphosphorylated forms of these substrates. The signals were detected using ECL and were measured by optodensitometry.

Results:

treatement with S.boulardii enhanced markedly the RAS-GAP-RAF-ERK1,2 pathway with participation of GRB2, SHC, SOS, and CRKII. Unit p85a of Pi-3 kinase ,tested in its phosporylated form, was also enhanced by the probiotic compared to control samples. In rats treated with an inhibitor of RAF-1 and of ERK 1,2 (PD098059) the expression of mucosal disaccharidases was inhibited by about 50%. Conclusion: The probiotic S. boulardii generates in vivo mitogen and metabolic signals which are transduced into intestinal cells downstream from the apical membrane to the nuclei, using recruitment substrates and serine, threonine, or tyrosine kinases .
Design of selective peptide antibiotics by using the sequence moment concept
Authors: Juretic Davor , Ilic Nada , Vukicevic Damir , Antcheva Nikolinka , Tossi Alessandro
Published: July 2019

New antibiotics against multidrug-resistant bacteria are urgently needed, but rapid acquisition of resistance limits their usefulness. Endogenous antimicrobial peptides (AMPs) with moderate selectivity, but multimodal mechanism of action, have remained effective against bacteria for millions of years. Their therapeutic application, however, requires optimizing the balance between antibacterial activity and selectivity, so that rational design methods for increasing selectivity are highly desirable. We have created training (n=36) and testing (n=37) sets from frog-derived AMPs with determined therapeutic index (TI). The 'sequence moments' concept then enabled us to find a one-parameter linear model resulting in a good correlation between measured and predicted TI (r2=0.83 and 0.64 for each set, respectively). The concept was then used in the AMP-Designer algorithm to propose primary structures for highly selective AMPs against Gram-negative bacteria. Testing the activity of one such peptide produced a TI>200 as compared to the best AMP in the data-base, with TI=125.
bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Authors: Page Roderic
Published: July 2019

Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. bioGUID is available at "http://bioguid.info/":http://bioguid.info/. Source code is available from "Google Code":http://code.google.com/p/bioguid/.
Validated, Ultra Violet Spectroscopy Method for the Dissolution Study of Mycophenolate Mofetil Immediate Release 500mg Tablets
Authors: Verma Surajpal , Alam Ozair , Mullick Pooja , Siddiqui Nadeem , Khan Suroor
Published: July 2019

A simple, selective and precise dissolution method was developed and validated for the Mycophenolate mofetil immediate release tablets. The method employed dissolution medium 0.1N HCl (pH1.2) and volume 900ml with USP-II apparatus (Paddle). Detection was made by measuring the absorbance on UV at the λ~max~ 250nm. The method show the linearity in the range of conc. 5[mu]g/ml to 40[mu]g/ml with r^2^=0.999. The method is also validated as per International Conference of Harmonization guidelines. The method showed the specificity with standard deviation 0.00. The method is repeatable, selective and accurate for the dissolution study of Mycophenolate mofetil immediate release tablets.
On the 7-azaindole in acetonitrile anhydrous solutions as an inappropriate photophysical model for DNA base pairs
Authors: Catalán Javier
Published: July 2019

Multiple Hydrogen-bonding is a fundamental issue to explain base-pairing in DNA structures, which was firstly described by Watson and Crick^1^ using stable keto tautomer forms. In their analysis, they considered the possibility of mutations via proton transfer reactions within a base pair. Such reactions can be induced by electronic excitation, for example, adenine-cytosine mispairing may be caused by double-proton phototautomerism.^2^ The 7-azaindole (7AI) doubly-hydrogen bonded dimer was firstly proposed as a suitable model for explaining the DNA base mispairing owing to excited state two-proton phototautomerization in 1969 by Taylor et al.^3^ The concerted nature of this excited state biprotonic transfer has been strongly supported by available evidence (see references 4-6 and references therein). Recently, Kwon and Zewail^7^ (K&Z) have reported femtosec time-resolved evidence on the stepwise mechanism in polar solvents, using very concentrated solutions of 7AI (0.1 M) in anhydrous acetonitrile, diethylether and dichloromethane on excitation at 320 nm. However, based on a careful spectroscopic analysis of the absorption and emission spectra of anhydrous 0.1 M 7-azaindole solutions in acetonitrile and butyronitrile, we demonstrate in this letter that the 7AI molecule does not form the doubly hydrogen bonded dimer at room temperature (rt) in acetonitrile, but it does generate another aggregate which emits fluorescence at ca. 500 nm. Consequently, the assertion of Kwon and Zewail^7,8^ that the rate of proton transfer in 7-azaindole dimers is significantly dependent on the solvent polarity and its stepwise mechanism for the process is not rightly stated as no C~2h~ dimer is formed in the medium used to record their femtosecond time resolved and fluorescence spectroscopic evidence (viz. 7-azaindole 0.1 M solution in acetonitrile at rt).
DNA sequences classification and computation scheme based on the symmetry principle
Authors: Song Xiao-Gang , Qiu Wen-Yuan
Published: July 2019

The DNA sequences containing multifarious novel symmetrical structure frequently play crucial role in how genomes work. Here we present a new scheme for understanding the structural features and potential mathematical rules of symmetrical DNA sequences using a method containing stepwise classification and recursive computation. By defining the symmetry of DNA sequences, we classify all sequences and conclude a series of recursive equations for computing the quantity of all classes of sequences existing theoretically; moreover, the symmetries of the typical sequences at different levels are analyzed. The classification and quantitative relation demonstrate that DNA sequences have recursive and nested properties. The scheme may help us better discuss the formation and the growth mechanism of DNA sequences because it has a capability of educing the information about structure and quantity of longer sequences according to that of shorter sequences by some recursive rules. Our scheme may provide a new stepping stone to the theoretical characterization, as well as structural analysis, of DNA sequences.
Assessing the Genotypic Differences for Seed Set and Seed Abortion in Tomato Genotypes
Authors: Reddy Chalapathy , Narayana Ganeshaiah , Shaanker Uma
Published: July 2019

Tomato (Lycopersicon esculentum Mill.) is one of the most popular fruit vegetable around the world. Seed abortion where in only a small proportion of ovules in an ovary develops into matured seeds, is a wide spread phenomenon in multi-ovulated species. In agriculturally important crops such as chickpea, groundnut, Brassica, pigeon pea and field bean seed abortion substantially reduces their productivity. Tomato genotypes exhibited seed abortion where in only some proportion of ovules developed into matured seeds. Seed abortion in tomato cultivars would increase the cost of hybrid seed production. In this study, we have analyzed 19 genotypes for number of ovules, seed set and seed abortion. Tomato genotypes differed significantly for number of ovules per ovary, seed set per fruit and per cent seed abortion. The ovules, matured seeds and seed abortion ranged from 52 to 412 per ovary; 50.90 to 240.76 per fruit and 6.06 to 24.44 per cent respectively. Strong positive correlation was observed in genotypes with higher number of ovules showed higher percentage of seed abortion.
Characteristics of Uremic Cardiomyopathy with Reversible Systolic Dysfunction
Authors: Adhyapak Srilakshmi , Iyengar Shamanna
Published: July 2019

Background:

There exists a sub group of patients with uremic cardiomyopathy who experience resolution of heart failure following hemodialysis. It has been hypothesized that these patients are fluid overloaded, and following hemodialysis, show improvements in cardiac geometry and function. We wanted to study their clinical, biochemical and echocardiographic features to define any other additional characteristics.Aim: To define characteristics of reversible systolic dysfunction.Methods: We studied 72 patients with chronic kidney disease on hemodialysis of whom 52 presented with congestive heart failure, over a period of 190 days. We studied their echocardiographic profile and blood biochemistry parameters including troponin I and C reactive protein.

Results:

There were 29 patients with systolic dysfunction (LVEF≤40%). Twenty three patients with preserved systolic function, had diastolic dysfunction. Of the 29 patients with systolic dysfunction, 10 patients had significant improvement in NYHA functional class, and left ventricular dimensions (LVIDd:59.8±2.6 mm to 55.9±2 mm and LVIDs:51.8±1.8 mm to 34±1.2 mm; p<0.001) with significant increase in left ventricular ejection fraction (30.5±5% to 50.1±4%; p<0.001). These patients had the highest serum levels of troponin I (p=0.024) which decreased significantly with recovery of cardiac function. In the patients with persistent systolic dysfunction and in the patients with diastolic function, the troponin I remained high. The troponin I was significantly lesser in the control group (p=0.002).

Conclusions:

A sub group of patients with uremic cardiomyopathy demonstrated reversible left ventricular systolic dysfunction, and high levels of serum troponin I levels at presentation, which regressed with recovery of ventricular function.
Biodiversity Quality: a paradigm for biodiversity
Authors: Feest Alan , Aldred Timothy , Jedamzik Katrin
Published: July 2019

The internationally accepted definition of biodiversity creates difficulty in measuring difference and change. The authors suggest that well-sampled data can be used to generate a range of numerical indices reflecting species group characteristics/functionality (Species Richness, Simposons Index, Population Density, Biomass and Species Conservation Value) that can be viewed in combination to create a picture of biodiversity quality. This overall approach has considerable advantages over the currently accepted Convention on biological Diversity definition based on the "variability" of genes, species and ecosystems, since the numerical expression of the indices allows the probability of difference between biodiversity quality trends and values over time and between sites or taxonomic groups, to be assessed for statistical inference.
In silico Protein Structural Modeling and Active binding site Evaluation of Streptococcus pneumoniae
Authors: Balakrishnan M. , Srivastava R.C. , Ramachandran M.
Published: July 2019

Structure function relation of glucose kinese in Streptococcus pneumoniae. However, a solved structure for Streptococcus pneumoniae glucose kinese is not available at the protein data bank. Glucose kinase is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression system. So, we created a model of glucose kinese from Streptococcus pnemoniae using the X-ray crystallography structure of glucose kinese enzymes from Enterobacteria faecalis as template with Molsoft ICM v3.5 software. The model was validated using protein structure checking tools such as PROCHECK, WHAT IF: for reliability. The active site amino acid "Asp114" in the template is retained in S. pneumoniae Glucose kinese model "Asp115". Solvent accessible surface area analysis of the glucose kinese model showed that known key residues playing important role in active site for ligand binding and metal ion binding are buried and hence not accessible to solvent. The information thus discussed provides insight to the molecular understanding of Streptococcus pneumoniae in glucose kinase.
Coupling of capillary RBC flow failure with neuronal depolarization
Authors: Tomita Minoru , Tomita Yutaka , Toriumi Haruki , Unekawa Miyuki , Suzuki Norihiro
Published: July 2019

RBC (oxygen-carrier) behaviour in the cerebrocortical microvasculature during K^+^-induced cortical spreading depression (CSD) was examined in urethane-anesthetized male Wistar rats (n=10). The movements of FITC-labeled RBCs in single capillaries in the cortical region were traced with a high-speed camera laser scanning confocal fluorescence microscope and analyzed with Matlab domain software, KEIO-IS2, to obtain the velocities of all labeled RBCs appearing in local capillaries during CSD wave propagation. We found that CSD induced periodic decreases in both RBC number and velocity until RBCs halted or disappeared for 3.3 +/- 2.3 s, and then RBC flow was restored. The RBC flow stall was statistically significant (P < 0.05). During capillary flow failure in association with CSD spread, systemic arterial blood pressure remained unchanged. We conclude that RBCs are transiently sieved and stalled in capillaries during neuronal depolarization, and we suggest that this neuro-capillary coupling involves a hemorheological (viscosity-related) mechanism.
A conceptual framework for the evolutionary selection of biologically 'essential' elements
Authors: Conyers Mark
Published: July 2019

Standard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential and nonessential nutrients for plants is not always clear. When animals and 'lower' organisms are considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of monovalent elements (bar H^+^) and divalent elements (bar O2^-^) involves a trade-off between low atomic mass and low ionic potential. The essentiality of Mo and non-essentiality of As remain a problem for this model. This conceptual framework provides a basis for re-evaluating the function of an element in the nutrition of plants, animals and 'lower' organisms.
An evolutionary approach to Function
Authors: Lord Phillip
Published: July 2019

The distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for applying these definitions in practice.
Developing ontologies in decentralised settings
Authors: Garcia Alexander , O’Neill Kieran , Garcia Leyla , Lord Phillip , Stevens Robert , Corcho Oscar , Gibson Frank
Published: July 2019

This paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.
Why are Male IQ Scores More Variable?
Authors: Strauss Bernard , Strauss Jacob
Published: July 2019

The male female difference in the variance of quantitative traits including IQ can be accounted for by the observation of the concentration of genes involved in brain development on the X chromosome and by the mechanism of sex determination in mammals. Females have two X chromosomes with one randomly inactivated. Males have a single X chromosome, which results in increased variance. It is shown that these factors are sufficient to account for the observed differences.
Ustilago and the accidental domestication of maize
Authors: Martinez-Soriano Juan Pablo , Avina-Padilla Katia
Published: July 2019

Maize is the essential crop of the Americas. Maize appeared suddenly about 8,500 years ago as domesticated teosinte; however, there is no evidence (genetical, archaeological, linguistic or ethnobotanical) able to support a gradual transformation from the teosinte ear into the corn ear. Teosinte has never been cultivated by Americans, nor did they ever attempt to domesticate it. Its grains were not used as food, making unrealistic the assumption that prehispanics created something edible from seeds that were not so. Plant domestication is a slow process in almost every known crop but maize evolution might not be the case. Teosinte has a brittle cob, whereas maize forms solid ones that do not release their seeds 2. The latter are soft, while in teosinte they are enclosed in hard inedible cases. Why would the prehispanic natives even think of modifying those hard seeds, if they were not used as food in the first place?. The switch from teosinte to maize were due to important mutations, occurring in a relatively short period so that natives immediately noticed if they were well aware of the importance of teosinte (or its parasites) and rescued the resultant newborn maize.Teosinte-maize hybrids were highly susceptible to the fungus Ustilago maydis (known in Mexico as huitlacoche) under natural conditions. Consequently, this parasite was found to infect every part of the hybrid plant.Huitlacoche is well known as a food delicacy and it has been important to Mexicans since prehispanic times and it might have been very likely used as food taken from infected teosinte at the same time it was changing into maize. Ustilago maydis probably played a vital role on the domestication process of maize, since the change from teosinte to maize was noticed by humans, who then rescued it from nature
Variation in PNPLA3 is associated with outcomes in alcoholic liver disease
Authors: Tian Chao , Stokowski Renee , Kershenobich David , Ballinger Dennis , Hinds David
Published: July 2019

Two recent genome-wide association studies have described associations of SNP variants in PNPLA3 with nonalcoholic fatty liver and plasma liver enzyme levels in population based cohorts. We investigated the contributions of these variants to clinical outcomes in Mestizo subjects with a history of excessive alcohol consumption. We show that non-synonymous variant rs738409[G] (I148M) in PNPLA3 is strongly associated with alcoholic liver disease and progression to alcoholic cirrhosis (unadjusted OR = 2.25, P = 1.7x10^-10^; ancestry-adjusted OR = 1.79, P = 1.9x10^-5^).