bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new computational model captures fundamental architectural features of diverse biological networks
Authors: Al-Anzi Bader , Olsman Noah , Ormerod Christopher , Gerges Sherif , Piliouras Georgios , Ormerod John , Zinn Kai 
Published: April 2016

ABSTRACTComplex biological systems are often represented by network graphs; however, their structural features are not adequately captured by existing computational graph models, perhaps because the datasets used to assemble them are incomplete and contain elements that lack shared functions. Here, we analyze three large, near-complete networks that produce specific cellular or behavioral outputs: a molecular yeast mitochondrial regulatory protein network, and two anatomical networks of very different scale, the mouse brain mesoscale connectivity network, and theC. elegansneuronal network. Surprisingly, these networks share similar characteristics. All consist of large communities composed of modules with general functions, and topologically distinct subnetworks spanning modular boundaries responsible for their more specific phenotypical outputs. We created a new model, SBM-PS, which generates networks by combining communities, followed by adjustment of connections by a ‘path selection’ mechanism. This model captures fundamental architectural features that are common to the three networks.
Modification of plant regeneration medium decreases the time for recovery of Solanum lycopersicum cultivar M82 stable transgenic lines
Authors: Gupta Sarika , Van Eck Joyce 
Published: April 2016

AbstractTomato (Solanum lycopersicum) has rapidly become a valuable model species for a variety of studies including functional genomics. A high-throughput method to obtain transgenic lines sooner than standard methods would greatly advance gene function studies. The goal of this study was to optimize our current transformation method by investigating medium components that would result in a decreased time for recovery of transgenics. For this study, 6-day-old cotyledon explants from Solanum lycopersicum cultivar M82 in vitro-grown seedlings were infected with theAgrobacterium tumefaciensstrain LBA4404 containing the binary vector pBI121. This vector contains the β-glucuronidase reporter gene and the neomycin phosphotransferase II selectable marker gene that confers resistance to kanamycin. Modification of our standard plant regeneration medium with indole-3-acetic acid (IAA) at concentrations of either 0.05 mg/l or 0.1 mg/l decreased the recovery time for transgenic lines by 6 weeks as compared to our standard medium that contains zeatin as the only plant growth regulator. We observed 50% and 54% transformation efficiency on plant regeneration medium containing 0.05 mg/l and 0.1 mg/l IAA, respectively. Moreover, addition of 1 mg/l IAA to the root induction medium resulted in earlier root development than medium that did not contain IAA. Addition of IAA to the plant regeneration and rooting media did not have any negative effects on plant development. Recovery of transgenic lines in a shorter time results in higher throughput for the introduction of gene constructs and has the potential to decrease the time and resources needed to complete investigations of gene function.
Ethanol Toxicity During Brain Development: Alterations of Excitatory Synaptic Transmission in Immature Organotypic Hippocampal Slice Cultures
Authors: Gerace Elisabetta , Landucci Elisa , Totti Arianna , Bani Daniele , Guasti Daniele , Baronti Roberto , Moroni Flavio , Mannaioni Guido , Pellegrini‐Giampietro Domenico E. 
Published: April 2016

BackgroundThe developing brain is particularly vulnerable to alcohol: Drinking during pregnancy can lead to a number of physical, learning, and behavioral disorders in the newborn. It has been demonstrated that immature and mature brain tissues display a differential sensitivity to ethanol (EtOH) toxicity and that cerebral structure and function are diversely impaired according to the stage of synaptic maturation.MethodsRat organotypic hippocampal slice cultures were exposed for 7 days to EtOH (100 to 300 mM) after 2 days (immature) or 10 days (mature) of culture in vitro; EtOH was then removed from the medium, and 24 hours later, slices were analyzed by fluorescence microscopy, Western blotting, electrophysiology, and electron microscopy to explore the molecular mechanisms of EtOH toxicity in the developing hippocampus.ResultsEtOH withdrawal elicited a selective CA1 pyramidal cell injury in mature slices, but not in immature slices. A significant increase in the expression of pre‐ and postsynaptic proteins in mature slices revealed that slice maturation is presumably associated with the development of new synapses. Incubation with chronic EtOH for 7 days and its removal from the medium induced a significant decrease in GluA1 and GluA2 expression levels; a significant reduction in the expression of synaptophysin and GluN2A was observed only after EtOH withdrawal. Whole‐cell patch‐clamp recordings showed that incubation with EtOH for 7 days induced a significant decrease in spontaneous excitatory postsynaptic current (sEPSC) frequency in CA1 pyramidal cells of immature slices and a trend toward a decrease in sEPSC amplitude. Electron microscopy revealed a disorganization of neurotubuli in immature slices after chronic exposure to EtOH.ConclusionsThese results indicate that prolonged incubation with EtOH and its subsequent withdrawal from the medium induce an impairment of excitatory synaptic transmission and possibly an incorrect formation of neuronal circuits in developing hippocampus in vitro, which is suggestive of mechanisms that may lead to mental retardation in fetal alcohol spectrum disorders.
Taking the First Full Drink: Epidemiological Evidence on Male–Female Differences in the United States
Authors: Cheng Hui G. , Cantave Marven D. , Anthony James C. 
Published: April 2016

BackgroundThis research extends prior epidemiological estimates for the United States and re‐examines a previously described male excess in alcohol drinking. Its aim was to estimate fine‐grained age‐specific incidence of becoming a drinker among 12‐ to 24‐year‐old U.S. males and females, and to compare incidence estimates with prevalence proportions.MethodsThe study population is 12‐ to 24‐year‐old noninstitutionalized U.S. civilian residents. Estimates are from 12 successive U.S. National Surveys on Drug Use and Health (NSDUH), with nationally representative samples drawn each year from 2002 to 2013 and assessed via computer‐assisted self‐interviews (n ~ 390,000). Analysis‐weighted incidence and prevalence estimates are generated using the NSDUH Restricted Data Analysis System for 6 year‐pairs. Meta‐analysis‐derived summary estimates are provided, treating each year‐pair as a replication.ResultsIn this 21st century evidence, there no longer is male excess of incidence with respect to underage drinking. Indeed, in mid‐adolescence, there is a clear female excess for the risk of becoming an underage drinker. Meta‐analytic summaries disclosed no other male–female differences in incidence. Nevertheless, a male excess in the prevalence of recently active drinking can be seen after the age of 19 years.ConclusionsThis new evidence from the United States shows that the so‐called “gender gap” in risk of becoming a drinker has narrowed to the point of there being no gap at all. Indeed, in mid‐adolescence, risk of starting to drink is greater for females than for males.
Reconstruction of the environmental history of a coastal insular system using shallow marine records: the last three millennia of the Cíes Islands (Ría de Vigo,NWIberia)
Authors: Muñoz Sobrino Castor , García‐Moreiras Iria , Martínez‐Carreño Natalia , Cartelle Víctor , Insua Tania L. , Ferreiro Da Costa Javier , Ramil‐Rego Pablo , Fernández Rodríguez Carlos , Alejo Irene , García‐Gil Soledad 
Published: April 2016

The coastal lagoon‐beach complex at the Cíes Islands located at the opening of the Ría de Vigo (NWIberia) is an important ecosystem currently threatened by anthropogenic impacts and climate variations. We used multiproxy marine sediment analyses to reconstruct the millennial environmental dynamics of this insular system and, in particular, the recent history of its coastal lagoon. Geophysical surveys were used to obtain bathymetry and identify the major sedimentary units of its closest submarine basin as well as their sediment sources. Core samples were taken in the middle and distal parts of the sedimentary body, where several prograding sedimentary units are thinner, allowing continuous sampling of the facies. Lithological, textural, elemental and chronological analyses were carried out on two cores. The detailed palynological studies on one of the cores included the analyses of the pollen, non‐pollen palynomorphs and dinocysts dating back three millennia. Our results revealed noticeable environmental changes affecting this area during the last 3000 years, due mainly to changing climate and oceanic conditions but also to the impact of historic human occupation of the islands. Several cold events (the 2.8 kaBPevent and the Little Ice Age) characterized by enhanced upwelling alternated with warmer stormy periods of prevailing downwelling conditions in the ria. These circumstances altered the balance amongst the lacustrine, marsh, dune and lagoon systems, opening ephemeral inlets and modifying the trophic stage of the shallow waters surrounding the archipelago. Here we provide a background of the human and climatic impacts affecting these highly sensitive habitats, which may serve to improve their future management strategies.
Environmental context for the terminal Ediacaran biomineralization of animals
Authors: Cui H. , Kaufman A. J. , Xiao S. , Peek S. , Cao H. , Min X. , Cai Y. , Siegel Z. , Liu X.‐M. , Peng Y. , Schiffbauer J. D. , Martin A. J. 
Published: April 2016

AbstractIn terminal Ediacaran strata of South China, the onset of calcareous biomineralization is preserved in the paleontological transition from Conotubus to Cloudina in repetitious limestone facies of the Dengying Formation. Both fossils have similar size, funnel‐in‐funnel construction, and epibenthic lifestyle, but Cloudina is biomineralized, whereas Conotubus is not. To provide environmental context for this evolutionary milestone, we conducted a high‐resolution elemental and stable isotope study of the richly fossiliferous Gaojiashan Member. Coincident with the first appearance of Cloudina is a significant positive carbonate carbon isotope excursion (up to +6‰) and an increase in the abundance and 34S composition of pyrite. In contrast, δ34S values of carbonate‐associated sulfate remain steady throughout the succession, resulting in anomalously large (>70‰) sulfur isotope fractionations in the lower half of the member. The fractionation trend likely relates to changes in microbial communities, with sulfur disproportionation involved in the lower interval, whereas microbial sulfate reduction was the principal metabolic pathway in the upper. We speculate that the coupled paleontological and biogeochemical anomalies may have coincided with an increase in terrestrial weathering fluxes of sulfate, alkalinity, and nutrients to the depositional basin, which stimulated primary productivity, the spread of an oxygen minimum zone, and the development of euxinic conditions in subtidal and basinal environments. Enhanced production and burial of organic matter is thus directly connected to the carbon isotope anomaly, and likely promoted pyritization as the main taphonomic pathway for Conotubus and other soft‐bodied Ediacara biotas. Our studies suggest that the Ediacaran confluence of ecological pressures from predation and environmental pressures from an increase in seawater alkalinity set the stage for an unprecedented geobiological response: the evolutionary novelty of animal biomineralization.
A Fish of Weedy Waters: Golden Shiner Biology and Culture
Authors: Stone Nathan M. , Kelly Anita M. , Roy Luke A. 
Published: April 2016

AbstractThe golden shiner, Notemigonus crysoleucas, is a major bait and forage fish species in the USA. Farmers produce millions of golden shiners annually that are distributed live, many across state boundaries. Native over much of the eastern and central USA, this species is often present but rarely abundant in natural systems, as fish density is apparently controlled by predation rather than by food resources. Aquaculture of the golden shiner is a century‐old practice and culture methods have evolved over time, resulting in today's farm‐raised, certified specific pathogen– and aquatic nuisance species–free baitfish. Federal and state agencies and universities have a long history of developing culture methods and promoting baitfish culture to replace the indiscriminate and wasteful harvest of fish from natural waters. Despite advances in culture methods and the advantages of a farm‐raised species produced under controlled and biosecure conditions, golden shiner farming is only marginally profitable and remaining farmers survive on farm equity and increased market share from others exiting the business. Ironically, increasing regulations and restrictions leading to a reduction in the supply of farm‐raised baitfish could drive anglers back to harvesting bait from natural waters, the very concern that initiated government support for baitfish culture a century ago.
Unexpected Roles for Ciliary Kinesins and Intraflagellar Transport Proteins
Authors: Pooranachandran Niedharsan , Malicki Jarema J 
Published: April 2016

AbstractTransport of proteins in the ciliary shaft is driven by microtubule-dependent motors, kinesins. Prior studies suggested that the heterotrimeric ciliary kinesin may be dispensable for certain aspects of transport in specialized cilia of vertebrate photoreceptor cells. To test this possibility further, we analyzed the mutant phenotype of the zebrafish kif3a gene, which encodes the common motor subunit of heterotrimeric ciliary kinesins. Cilia are absent in all organs examined, leading to the conclusion that kif3a is indispensable for ciliogenesis in all cells, including photoreceptors. Unexpectedly, kif3a function precedes ciliogenesis as ciliary basal bodies are mispositioned in mutant photoreceptors. This phenotype is much less pronounced in intraflagellar transport (IFT) mutants and reveals that kif3a has a much broader role than previously assumed. Despite the severity of their basal body phenotype, kif3a mutant photoreceptors survive longer compared to those in IFT mutants, which display much weaker basal body mispositioning. This effect is absent in kif3a;IFT double mutants, indicating that IFT proteins have ciliary transport-independent roles, which add to the severity of their photoreceptor phenotype. kif3a is dispensable for basal body docking in otic vesicle sensory epithelia and, surprisingly, short cilia form in mechanosensory cristae even in the absence of kif3a. In contrast to Kif3a, the functions of the Kif3c-related protein, encoded by the kif3c-like (kif3cl) gene, and the homodimeric ciliary kinesin, kif17, are dispensable for photoreceptor morphogenesis. These studies demonstrate unexpected new roles for both ciliary heterotrimeric kinesins and IFT particle genes and clarify the function of kif17, the homodimeric ciliary kinesin gene.
An Approximate Markov Model for the Wright–Fisher Diffusion and Its Application to Time Series Data
Authors: Ferrer-Admetlla Anna , Leuenberger Christoph , Jensen Jeffrey D , Wegmann Daniel 
Published: April 2016

Abstract
The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional information for disentangling these effects may be obtained by observing changes in allele frequencies over multiple time points. Such data are common in experimental evolution studies, as well as in the comparison of ancient and contemporary samples. Leveraging this information, however, has been computationally challenging, particularly when considering multilocus data sets. To overcome these issues, we introduce a novel, discrete approximation for diffusion processes, termed mean transition time approximation, which preserves the long-term behavior of the underlying continuous diffusion process. We then derive this approximation for the particular case of inferring selection and demography from time series data under the classic Wright–Fisher model and demonstrate that our approximation is well suited to describe allele trajectories through time, even when only a few states are used. We then develop a Bayesian inference approach to jointly infer the population size and locus-specific selection coefficients with high accuracy and further extend this model to also infer the rates of sequencing errors and mutations. We finally apply our approach to recent experimental data on the evolution of drug resistance in influenza virus, identifying likely targets of selection and finding evidence for much larger viral population sizes than previously reported.
Analysis of land use and occupation in the water quality at two sub-basins of Caxias do Sul City
Authors: Cornelli Renata , Schneider Vania Elisabete , Bortolin Taison Anderson , Cemin Gisele , Dos Santos Geise Macedo 
Published: April 2016

The use and land cover can directly influence in the quality and in the availability of water resources, whether by accelerated urbanization, by the removal of vegetation and the agricultural use. The impacts may vary according the use, the organic load supply, metal nutrients and contaminants and the drag of sediment affecting the water quality and the balance of aquatic ecosystems. This research was aimed to evaluated the influence of use and land use on water quality of river basins of the rivers Piaí and Tega, in Caxias do Sul-RS. Analyzed for such the Water Quality Index (WQI) and Toxicity (TI) in 5 points from River Piaí (P1 to P5) and 12 from River Tega (T1 to T12). Were realized 12 campaigns between September / 2012 to July / 2014. To develop the maps the use and occupation land were used Landsat 8 satellite images combined with the supervised classification with the maximum likelihood algorithm and Gaussian screen scanning in trouble spots. For the classification of maps were defined 7 classes of use, as follows: native forest, field, forestry, agriculture, bare soil, urban and water depth. For the classification of maps were defined 7 classes of use, as follows: native forest, field, forestry, agriculture, bare soil, urban area and water depth. It was concluded that the low water quality of points as P3 and P4 from River Piaí and points T1 to T9 from River Tega is the reflection the use and occupation of the soil, the release of effluents from point sources, such as homes and industries that do not have effluent treatment plant or whose treatment is not sufficient to meet the discharge standards prescribed by the laws. http://dx.doi.org/10.18226/23185279.v4iss1p1
Experimental Analysis of a Medium-Sized Diesel Engine on Mono and Dual-Fuel Operation
Authors: Dos Santos Dener Fachinelli , Altafini Carlos Roberto , Costa Giovanni Acordi , Maino Henrique Bracht , Godinho Marcelo 
Published: April 2016

This work aims to analyze the performance of an engine operating in mono fuel mode with diesel oil (DO) and in dual fuel mode using compressed natural gas (CNG) as primary fuel, and DO as secondary fuel in the form of a pilot injection. In the dual fuel operation mode, CNG intake is made with combustion air, being the mixture compressed and is ignited after the DO ignition. The engine studied is a six-cylinder, Diesel cycle, and is turbocharged. Performance tests (torque, power, fuel specific consumption and gas emissions) of the engine have been conducted on a dynamometer whose brake (retarder) is an electromagnetic type air-cooled. The data of the tests were corrected in accordance with ISO 3046/1 standard. A first set of tests was conducted to evaluate the performance of the engine operating only with diesel oil. The trends of torque, power and fuel specific consumption curves versus the engine speed were similar to those of the manufacturer, but quantitatively the values fell short. The experiments in dual fuel mode (DO-CNG) were conducted at 1800 RPM and achieved a percentage of diesel oil replacement of about 73%, representing a reduction in fuel costs, especially OD, of almost 29%. With the highest percentage of DO replacement was also the largest engine thermal efficiency (31.1%) compared to the DO100 mode (25.6%). http://dx.doi.org/10.18226/23185279.v4iss1p38
Dynamic Mechanical Analysis (DMA) of Polymeric Composite Materials
Authors: Lorandi Natalia Pagnoncelli , Cioffi Maria Odila Hilário , Ornaghi Jr. Heitor 
Published: April 2016

Polymeric composite materials have been studied in many fields in materials science, with the aim of replacing other materials and reaching better performance when applied. Among the existing techniques, a great alternative to evaluate composites properties is dynamic mechanical analysis (DMA), especially when viscoelastic parameters need to be studied as a function of time, temperature or frequency. Important properties, such as storage modulus, loss modulus and transitions temperaturescan be determined by this technique. The present paper brings a review about DMA, the advantages of this technique compared to others thermal and mechanical analysis, the behavior of polymeric composite materials during the tests and the properties which can be determined by DMA. The importance of DMA in the study of engineering materialsis also presented, especially when applied in aircraft structures. http://dx.doi.org/10.18226/23185279.v4iss1p48
Ultrasound guided continuous transversus abdominis plane block for postoperative analgesia after caesarean delivery in a patient with Wolff-Parkinson-White syndrome
Authors: Yadav Rupesh Kumar , Rayamajhi Anuj Jung , Bhattarai Prajjwal Raj , Paudel Subash Chandra 
Published: April 2016

Ultrasound-guided transversus abdominis plane block is an extremely attractive technique ensuring adequate perioperative analgesia. The use of ultrasound has enhanced the accuracy of local anaesthetic deposition in the plane between internal oblique and transversus abdominis, thereby blocking the spinal nerves more effectively and hence enhancing the efficacy of analgesia. Pregnancy is associated with higher frequency of arrhythmias in Wolff-Parkinson-White syndrome and poor perioperative pain management may contribute to life threatening arrhythmias. We report a case of Wolff-Parkinson-White syndrome posted for elective caesarean section, managed successfully under regional anesthesia with transverses abdominis plane block. The block and catheter were deposited under ultrasound guidance with continuous infusion of 0.2% of ropivacaine was used for postoperative pain relief. Dexmetedomidine was also used as intravenous adjunct at titrated dose of 0.4-0.6 mics/kg/min to attenuate maternal hormonal and hemodynamics during surgery.
Chemical and bioactive diversities of marine sponge <i>Neopetrosia</i>
Authors: Qaralleh Haitham 
Published: April 2016

<p class="Abstract">The marine sponge <em>Neopetrosia</em> contains about 27 species that is highly distributed in Indian Ocean, Atlantic Ocean (Caribbean Sea) and Pacific Ocean. It has proven to be valuable to the discovery of medicinal products due to the presence of various types of compounds with variable bio-activities. More than 85 compounds including alkaloids, quinones, sterols and terpenoids were isolated from this genus. Moreover, the crude extracts and the isolated compounds revealed activities such as antimicrobial, anti-fouling, anti-HIV, cytotoxic, anti-tumor, anti-oxidant, anti-protozoal, anti-inflammatory. Because only 9 out of 27 species of the genus <em>Neopetrosia</em> have been chemically studied thus far, there are signiﬁcant opportunities to ﬁnd out new chemical constituents from this genus.</p><p> </p>