bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polyethylenimine-Modified Multiwalled Carbon Nanotubes for Plasmid DNA Gene Delivery
Authors: Yu Bo-Zhang , Ma Ji-Fei , Li Wen-Xin 
Published: July 2019

AbstractAn efficient molecular delivery technique based on the transporting high-molecular-weight PEI 600K-modified multiwalled carbon nanotubes (PEI 600K-MWCNTs) into cell membranes is reported. The PEI 600K-MWCNTs exhibit low cytotoxicity and its associated plasmid DNA (pDNA) is delivered to cells efficiently, and the green fluorescent protein (GFP) levels up to 18 times higher than that of naked DNA were observed.
The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Authors: Tiruneh Gizachew 
Published: July 2019

Abstract
*Objective*:
To investigate the best statistical models that describe the effect of physical activity on BMI.*Design*: Cross-sectional analyses of physical activity and BMI data. *Subjects*: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m2, respectively).*Measurements*: Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables were also statistically controlled.

*Results*:
Coefficients of determination, r-squared, showed the inverse logarithmic model is more accurate in describing the effect of physical activity on BMI than is the inverse linear model. The inverse logistic method also showed physical activity affects BMI.

*Conclusions*:
Although the inverse logarithmic method can be used in some cases, the inverse logistic model seems to be theoretically and empirically best suited in describing the relationship between physical activity and body weight.
3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol
Authors: Baker Michael , Chang David , Chandsawangbhuwana Charlie 
Published: July 2019

AbstractLamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor. A perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids. For example, 15[alpha]-hydroxy-estradiol [15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2). To investigate how 15[alpha]-OH-E2 binds lamprey ER, we constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2. Our 3D model shows that S[delta] on Met-409 can form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2. In human ER[alpha], the corresponding residue Ile-424 has a van der Waals contact with 15[alpha]-OH-E2. BLAST analysis of GenBank indicates that among vertebrate ERs, only lamprey ER contains a methionine at this position. Thus, the contact between S[delta] on Met-409 and 15[alpha]-OH-E2 is unique. Our 3D model of lamprey ER should prove useful in virtual screening of chemical libraries to identify compounds for controlling reproduction in sea lamprey, an environmental pest in the Great Lakes in the USA.
Bias in culture-independent assessments of microbial biodiversity in the global ocean
Authors: Temperton Ben , Oliver Anna , Field Dawn , Tiwari Bela , Muhling Martin , Joint Ian , Gilbert Jack 
Published: July 2019

AbstractOn the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast not a single SAR11 fosmid was identified in a pooled shotgun sequenced data set of 100 fosmid clones. This under-representation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation; functional metabolic profiling and fragment recruitment. Analysis revealed a similar under-representation of low-GC Flavobacteriaceae. We speculate that the fosmid bias may be due to DNA fragmentation during preparation due to the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that while fosmid libraries can be extremely useful, caution must be used when directly inferring community composition from metagenomic fosmid libraries.
Analysis of Endocrine Disruption in Southern California Coastal Fish using an Aquatic Multi-Species Microarray
Authors: Baker Michael , Ruggeri Barbara , Sprague James , Eckhardt Colleen , Lapira Jennifer , Wick Ivan , Soverchia Laura , Ubaldi Massimo , Polzonetti-Magni Alberta , Vidal-Dorsch Doris , Bay Steven , Gully Joseph , Reyes Jesus , Kelley Kevin , Schlenk Daniel , Breen Ellen , Šášik Roman , Hardiman Gary 
Published: July 2019

Abstract
Background:
Endocrine disruptors include plasticizers, pesticides, detergents and pharmaceuticals. Turbot and other flatfish are used to characterize the presence of chemicals in the marine environment. Unfortunately, there are relatively few genes of turbot and other flatfish in GenBank, which limits the use of molecular tools such as microarrays and qRT-PCR to study disruption of endocrine responses in sentinel fish captured by regulatory agencies.

OBJECTIVES:
A multi-gene cross species microarray was fabricated as a diagnostic tool to screen the effects of environmental chemicals in fish, for which there is minimal genomic information. The array included genes that are involved in the actions of adrenal and sex steroids, thyroid hormone, and xenobiotic responses. This will provide a sensitive tool for screening for the presence of chemicals with adverse effects on endocrine responses in coastal fish species.

METHODS:
A custom multi-species microarray was used to study gene expression in wild hornyhead turbot, collected from polluted and clean coastal waters and in laboratory male zebrafish following exposure to estradiol and 4-nonylphenol. Gene-specific expression in turbot liver was measured by qRT-PCR and correlated to microarray data.

RESULTS:
Microarray and qRT-PCR analyses of livers from turbot collected near municipal wastewater discharge areas revealed altered gene expression profiles compared to those from reference areas.

CONCLUSIONS:
The agreement between the array data and qRT-PCR analyses validates this multi-species microarray. The microarray measurement of gene expression in zebrafish, which are phylogenetically distant from turbot, indicates that this multi-species microarray will be useful for measuring endocrine responses in other fish.
Tracking patterns of body mass index and triceps skinfold thickness from childhood to young adulthood: a 12-year prospective cohort study in Slovenia
Authors: Starc Gregor , Strel Janko 
Published: July 2019

AbstractOBJECTIVE: To examine tracking patterns of body mass index (BMI), triceps skinfold thickness (TSF), height and weight from childhood to young adulthood in a rapidly developing society.
DESIGN:
Prospective 12-year cohort study of the Slovenian children, born during 1990-1991.

SUBJECTS:
A subsample of 4 833 Slovenian children from the 1990-1991 national cohort (n = 21 777) who were included in the SLOFIT monitoring system from 1997 to 2008, with complete data at age 7 and 18 y.

MEASUREMENTS:
Height, weight and TSF were measured at ages 7, 11, 14 and 18 y. The IOTF BMI cutoff points were used to identify overweight and obesity.

RESULTS:
Height, weight, and BMI at age 18 y were well predicted from childhood and grew more predictable with age, while TSF was not. Obese and overweight children had the greatest risk of becoming overweight or obese young adults, since tracking of overweight and obesity showed that 53.9% of overweight and 77.7% of obese 7-y old males remained overweight or obese at age 18 y in comparison with 32.1% of overweight and 62% of obese 7-y old females. History of obese 18-y olds showed that 40% of males and 48.6% of females had been obese already at age 7 y.

CONCLUSION:
The study confirmed the tracking of BMI from childhood to young adulthood. Overweight or obese Slovenian children are very likely to become overweight or obese adolescents and young adults, which calls for the need of early prevention and treatment of overweight and obesity.
Extending the semi-empirical PM6 method for carbon oxyacid pKa prediction to sulfonic acids: Application towards congener-specific estimates for the environmentally and toxicologically relevant C1 through C8 perfluoroalkyl derivatives
Authors: Rayne Sierra , Forest Kaya , Friesen Ken 
Published: July 2019

AbstractA positive bias in the semi-empirical PM6 method for estimating pKa values of sulfonic acids was corrected by a correlation developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl, and halogen substituted sulfonic acids. Application of this correction to PM6 values allows for extension of this computational method to a new acid functional group.
Biased amino acid composition in warm-blooded animals
Authors: Wang Guang-Zhong , Lercher Martin 
Published: July 2019

AbstractAmong eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.
Authors: Onizuka Kentaro 
Published: July 2019

AbstractThe Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational stability and transition because the calculation time for the analysis is as long as a few seconds, and the analysis can be done without knowing the 3D structures.
Evolution of Cooperation on Playing Prisoner&apos;s Dilemma Game in the Finite-Capacity Spot
Authors: Toyoizumi Hiroshi 
Published: July 2019

AbstractExplaining the evolution of cooperative behavior has been one of main challenges in evo- lutionary theory^1-6^. Cooperation may collapse a surge of defectors who enjoy the benefit without cooperation in situation called prisoner's dilemma. In the concept of evolutionary game theory, there are many proposals to explain the evolution of cooperation by adding further mechanism such as, kin selection^1^, reciprocity^7^, punishment^8,9^ and the finiteness of the population^6^. In evolutionary game theory, a pair is randomly picked from population, and play a prisoner's dilemma game. Here we also show the finiteness encourages cooperation but use different approach: in spite of random-pick, individuals join and leave a spot or territory with a limited capacity to form a pair and play prisoner's dilemma game during their stay in the spot. We use a simple finite-state continuous-time Markov chain to analyze the dynamics in the spot and find that, given large cooperation benefit, just leaving together from the spot is enough for cooperation to be emerged. Further, we show that the coexistence of cooperators and defectors may become stable in highly congested spots.
Enhanced anti-cancer activity of microglia by AAV2-mediated IL-12 in the therapy of glioblastoma multiforme
Authors: Chiu Tsung-Lang , Wang Mei-Jen , Su Chin-Cheng 
Published: July 2019

AbstractMicroglia has been found to diversify its function by cancerous cells or in a cancerous environment, thereby contributing to cancer growth and metastasis. Its immuno-activity, however, can be modulated by interleukin-12. So a strategy was designed using AAV2 carrying IL-12 to activate microglia then to eliminate cancerous cells. The transduction efficacy of AAV was evaluated with AAV2 encoding GFP and IL-12 on cancerous and CNS cells. The bioactivity of microglia modulated by IL-12 was examined and death receptors 4 and 5 were detected on cancerous cells. The effects of IL-12 and AAV2/IL-12 on microglial cytoxoxicity were evaluated too. The results demonstrated human cell line DBTRG, surgical specimen of GBM, and rat astrocyte expressed GFP quite well. Tremendous IL-12 secretion was detected in DBTRG, RG2, and astrocyte after transfection of AAV2/IL-12. TRAIL releasing and phagocytotic activity of microglia were significant, increasing (p<0.05) after the stimulation of IL-12. DR4 and DR5 were expressed in all of the examined GBM cells. MTT assay of microglial cytotoxicity elicited significant increase (p<0.05) when the IL-12 protein or RG2-secreting IL-12 could have contact with microglial cells. Conclusively, AAV2 is an effective vector in transferring therapeutic genes such as IL-12 to induce or enhance microglial anti-cancer activity.
Hybrid Extraction Method; Innovative Method to Produce Non Oxidative Tuna Oil
Authors: Ito Yoshinori 
Published: July 2019

AbstractSummary: The function of Polyunsaturated Fatty Acid such as DHA, EPA are now well known world widely through strong scientific evidences and the importance of nutritional value and popularity are increasing every day all over the world with the name of omega 3 fatty acids.^1,2,3^ However, the fish oil, the source of omega 3 fatty acid had been considered as very vulnerable to oxidation. Many papers say the reason why is because its very easy to oxidize fish oil. The greater the Polyunsaturated Fatty Acid contents in the fish oil is, the faster oxidation takes place.^4,5^ Here I show that tuna oil extracted from Albacore Tuna Head in closed circuit under low temperature, at first decompressing then pressurizing and heating in a container, is very stable against the oxidation and conserved natural contents of Vitamins richly. The oil ware kept in a transparent bottle under natural light and some time under the sun light, with room temperature and opened every day for the sensual odor test during three months. This oil showed a stability of Fatty Acid Composition, Acid Value and Peroxide Value. That mean omega 3 fatty acids are more easy to handle and ample use as food ingredient to put it in many foods such as in a ketchup, mayonnaise, bread and noodle, rather than use in the capsules only.
Networking Phylogeny for Indo-European and Austronesian Languages
Authors: Blanchard Philippe , Petroni Filippo , Serva Maurizio , Volchenkov Dimitri 
Published: July 2019

AbstractHarnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the ‘express train’ model of Austronesian expansion from South-East Asia, with an essential role for the Batanes islands located between the Philippines and Taiwan.
A comparative assessment of octanol-water partitioning and distribution constant estimation methods for perfluoroalkyl carboxylates and sulfonates
Authors: Rayne Sierra , Forest Kaya 
Published: July 2019

AbstractNew experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs, as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the perfluoroalkyl chain (Δ~hydrophobic~G~ow~). Only the SPARC log D method accurately predicted the electrostatic contributions of the carboxylate head group (Δ~electrostatic~G~ow~) towards octanol-water partitioning for PFCAs. Similar log D values and organic carbon normalized sediment-water partitioning coefficients (K~oc~) for PFCAs and PFSAs having equivalent perfluoroalkyl chain lengths suggests potentially equivalent Δ~electrostatic~G~ow~ and Δ~hydrophobic~G~ow~ contributions towards lipophilic partitioning for these two contaminant classes, regardless of head group identity. In contrast, there are potentially different Δ~electrostatic~G~ow~ and Δ~hydrophobic~G~ow~ contributions towards proteinophilic partitioning.
Annotation of SBML Models Through Rule-Based Semantic Integration
Authors: Lister Allyson , Lord Phillip , Pocock Matthew , Wipat Anil 
Published: July 2019

Abstract*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.
*Results:*
We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RBM
Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Authors: Muller Anthonie 
Published: July 2019

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

AbstractConservation reserves are one of the most important tools for managing biodiversity. Ever since Diamond, based on theory of island biogeography, proposed that a single large reserve was preferable to several small reserves of the same total area, there has been an enduring debate about the veracity of his assertion. The so-called SLOSS debate - should we have a Single Large reserve Or Several Small reserves - features in every conservation text book and is central to conservation theory. Population dynamic models suggest that the design that minimizes the risk of extinction of species is case-specific, with the optimal number of reserves ranging between one and very many. Uncertainty is pervasive in ecology, but, the previous analyses of the SLOSS debate have not considered how uncertainty in the model of extinction risk might influence the optimal design. Here we show that when uncertainty is considered, the SLOSS problem is simplified and driven more by the aspirations of the manager than the population dynamics of the species. For a given budget of land area to be reserved in a region, the optimal solution is to have on the order of twenty or fewer reserves for any species. This result shows counter-intuitively that considering uncertainty actually simplifies rather than complicates decisions about designing nature reserves.
Aqueous synthesis of CdTe quantum dot as biological fluorescent probe for monitoring methyl parathion by fluoro-immunosensor
Authors: Chouhan Raghuraj , Vinayaka Aaydha , Thakur Munna 
Published: July 2019

AbstractBioconjugation of quantum dots (QDs) provide high resolution in biological fluorescent labelling as a result of physical and optical properties of QDs. This intrinsic property of QDs can be made use of for sensitive detection of target analytes including food and environmental monitoring. In this investigation, we report the bioconjugation of thiol stabilized CdTe QD for the sensitive detection of methyl parathion (MP) at picogram level. The specificity in the analysis was attributed by highly specific competitive immunological reactions between free MP and CdTe QD bioconjugated MP (MP-BSA-CdTe) for immobilized anti-MP IgY antibodies in a simple flow injection system. We also report the possible resonance energy transfer phenomenon as a result of nanobiomolecular interaction obtained through the bioconjugation of CdTe QD with protein bovine serum albumin (BSA). This has resulted in a significant change in the photo-absorption of CdTe QD, which can be made use for future nanosensor development.