bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpretation of Airborne Geophysical Data of Nsukka Area, Southeastern Nigeria
Authors: Obiora Daniel N. , Ossai Mirianrita N. , Okeke Francisca N. , Oha Andrew I.
Published: November 2016

Airborne geophysical (aeromagnetic and gravity) data of Nsukka area was interpreted qualitatively and quantitatively with the aim of determining the susceptibilities of rock types, depth/mass of the anomalous bodies, possible cause of the anomalies and type of mineralization prevalent in the area. The estimated depths from forward and inverse modeling of aeromagnetic data for profiles 1, 2, 3, 4 and 5 were 1200m, 1644m, 1972m, 2193m and 2285m respectively. The respective susceptibility values were 0.0031, 0.0073, 1.4493, 0.0069 and 0.0016. These indicate dominance of iron rich minerals like limonite, hematite, pyrrhotite, and pyrite and forms lateritic caps on sandstones. SPI depth result ranges from 151.6m minimum (shallow magnetic bodies) to 3082.7 m maximum (deep lying magnetic bodies). Euler depths for the four different structural index (SI = 0.5, 1, 2, 3) ranges from 7.99 to 128.93m which are depths of shallow magnetic sources resulting from lateritic bodies in the outcrops in the study area. From the gravity data interpretation, Euler depth estimation reveals that depth to anomalous bodies ranges from 89.13 to 2296.92m. Density of the causative body obtained from modeling results for profile 1 was 1498kg/m3, which is in the range of clay material and the depth was about 923m. From models 2, 4 and 5, the densities of the causative bodies were 3523, 4127 and 3707kg/m3, while depths to the surface were about 604, 815 and 1893m respectively. These density ranges correspond to that of ironstone. From model three, the density of causative body obtained was 2508kg/m3, located at a depth of about 268m below the surface. This work has shown that Nsukka area is underlain by thick strata of shales, sandstones and ironstones, which together are suitable for ceramic production, and sufficiently thick sediments suitable for hydrocarbon accumulation.
WEIGHT CHANGING OPERATORS FOR AUTOMORPHIC FORMS ON GRASSMANNIANS AND DIFFERENTIAL PROPERTIES OF CERTAIN THETA LIFTS
Authors: ZEMEL SHAUL
Published: November 2016

We define weight changing operators for automorphic forms on Grassmannians, that is, on orthogonal groups, and investigate their basic properties. We then evaluate their action on theta kernels, and prove that theta lifts of modular forms, in which the theta kernel involves polynomials of a special type, have some interesting differential properties.
The Critically Endangered Myanmar snub-nosed monkey Rhinopithecus strykeri found in the Salween River Basin, China
Authors: Yang Yin , Tian Ying-Ping , He Chen-Xiang , Huang Zhipang , Dong Shao-Hua , Wang Bin , Li Guang-Song , Xiang Zuo-Fu , Long Yong-Cheng , Xiao Wen
Published: November 2016

The Myanmar snub-nosed monkey Rhinopithecus strykeri was discovered in 2010 on the western slopes of the Gaoligong Mountains in the Irrawaddy River basin in Myanmar and subsequently in the same river basin in China, in 2011. Based on 2 years of surveying the remote and little disturbed forest of the Gaoligong Mountains National Nature Reserve in China, with outline transect sampling and infrared camera monitoring, a breeding group comprising > 70 individuals was found on the eastern slopes of the Gaoligong Mountains in the Salween River Basin. Given the Critically Endangered status of this primate (a total of < 950 individuals are estimated to remain in the wild), efforts to protect the relatively undisturbed habitat of this newly discovered population and to prevent hunting are essential for the long-term survival of this species.
Surviving Online Censorship in China: Three Satirical Tactics and their Impact
Authors: Lee Siu-yau
Published: November 2016

What accounts for online satirical campaigns that survive censorship in China where the state has formidable power to censor and manipulate online communication? Through comparative case studies of three attempts to challenge the policies or malpractices of the Chinese state in 2009, this article explains how different satirical tactics can influence the outcomes of online activism. It argues that online satirical campaigns are most likely to survive when activists adopt the tactic of “parodic satire,” whereby activists mimic a specific practice of the state and skilfully transplant it to other contexts. Since the language used by the activists resembles that of the powerful, the tactic allows netizens to exaggerate the internal contradictions of the policies or practices concerned without creating an easily identifiable symbol of resistance in the process. This tactic not only increases the cost to the state of censoring critical messages, but also restrains activists from extending their criticisms of the original subject to other areas. As a result, it increases the chance for the activists to exert insistent pressure on the state.
Compensation of Emergency Medical Technician (EMT)-Basics and Paramedics
Authors: Studnek Jonathan R.
Published: November 2016

Objectives

The objective of this paper is to identify factors associated with compensation for Emergency Medical Technician (EMT)-Basics and Paramedics and assess whether these associations have changed over the period 1999-2008.

Methods

Data obtained from the Longitudinal EMT Attributes and Demographic Study (LEADS) surveys, a mail survey of a random, stratified sample of nationally certified EMT-Basics and Paramedics, were analyzed. For the 1999-2003 period, analyses included all respondents providing Emergency Medical Services (EMS). With the addition of a survey in 2004 about volunteers, it was possible to exclude volunteers from these analyses.

Results

Over 60% of EMT-Basics reported being either compensated or noncompensated volunteers in the 2004-2008 period. This was substantially and significantly greater than the proportion of EMT-Paramedic volunteers (<25%). The EMT-Paramedics earned significantly more than EMT-Basics, with differentials of $11,000-$18,000 over the course of the study. The major source of earnings disparity was type of organization: respondents employed by fire-based EMS agencies reported significantly higher earnings than other respondents, at both the EMT-Basic and EMT-Paramedic levels. Males also earned significantly more than females, with annual earnings differentials ranging from $7,000 to $15,000.

Conclusions

There are a number of factors associated with compensation disparities within the EMS profession. These include type of service (ie, fire-based vs. other types of agencies) and gender. The reasons for these disparities warrant further investigation.

StudnekJR. Compensation of Emergency Medical Technician (EMT)-Basics and Paramedics. Prehosp Disaster Med. 2016;31(Suppl. 1):s87–s95.
The relationship between food insecurity and overweight/obesity differs by birthplace and length of US residence
Authors: Ryan-Ibarra Suzanne , Sanchez-Vaznaugh Emma V , Leung Cindy , Induni Marta
Published: November 2016

Objective

To examine whether the cross-sectional association between food insecurity and overweight/obesity varied according to birthplace and length of residence in the USA among California women.

Design

Using cross-sectional, population-based data from the California Women’s Health Survey (CWHS) 2009–2012, we examined whether the association between food insecurity and overweight or obesity varied by birthplace–length of US residence.

Setting

California, USA.

Subjects

Women (n16 008) aged 18 years or older.

Results

Among US-born women, very low food security (prevalence ratio (PR)=1·21; 95 % CI 1·11, 1·31) and low food security (PR=1·19; 95 % CI 1·10, 1·28) were significantly associated with higher prevalence of overweight/obesity, after controlling for age, marital status, race/ethnicity, poverty and education. Among immigrant women who lived in the USA for 10 years or longer, very low food security was significantly associated with higher prevalence of overweight/obesity, after controlling for covariates (PR=1·16; 95 % CI 1·07, 1·27). Among immigrant women who had lived in the USA for less than 10 years, low and very low food security were not significantly associated with overweight/obesity, after controlling for covariates.

Conclusions

Food insecurity may be an important pathway through which weight may increase with longer US residence among immigrant women. Public health programmes and policies should focus on increasing food security for all women, including immigrant women, as one strategy to reduce the prevalence of overweight/obesity.
The Galactic Club or Galactic Cliques? Exploring the limits of interstellar hegemony and the Zoo Hypothesis
Authors: Forgan Duncan H.
Published: November 2016

The Zoo solution to Fermi's Paradox proposes that extraterrestrial intelligences (ETIs) have agreed to not contact the Earth. The strength of this solution depends on the ability for ETIs to come to agreement, and establish/police treaties as part of a so-called ‘Galactic Club’. These activities are principally limited by the causal connectivity of a civilization to its neighbours at its inception, i.e. whether it comes to prominence being aware of other ETIs and any treaties or agreements in place. If even one civilization is not causally connected to the other members of a treaty, then they are free to operate beyond it and contact the Earth if wished, which makes the Zoo solution ‘soft’. We should therefore consider how likely this scenario is, as this will give us a sense of the Zoo solution's softness, or general validity. We implement a simple toy model of ETIs arising in a Galactic Habitable Zone, and calculate the properties of the groups of culturally connected civilizations established therein. We show that for most choices of civilization parameters, the number of culturally connected groups is >1, meaning that the Galaxy is composed of multiple Galactic Cliques rather than a single Galactic Club. We find in our models for a single Galactic Club to establish interstellar hegemony, the number of civilizations must be relatively large, the mean civilization lifetime must be several millions of years, and the inter-arrival time between civilizations must be a few million years or less.
From Settlement to Super-diversity: The Anglican Church and New Zealand’s Diversifying Population
Authors: Butcher Andrew
Published: November 2016

Anglicanism in New Zealand can be traced back to the beginning of New Zealand settlement itself. From its earliest days, the Anglican Church has deliberately set out to bridge divides between New Zealand’s indigenous population, Māori, and Europeans, though with mixed success. This article will illustrate that, even with this experience in bicultural engagement, the Anglican Church has not adapted well to the super-diverse multicultural New Zealand of the twenty-first century. Census data reveal that the Anglican Church has had a precipitous drop in numbers, and has a demographic profile that is much older and whiter than the general New Zealand, let alone Christian, population. This poses significant challenges for its ongoing sustainability. Given the common experience of super-diversity with other Western countries, this article provides a case study and a cautionary tale about the challenges and realities of the Anglican Church adjusting to a new multicultural society.
Transferrable single crystalline 4H-SiC nanomembranes
Authors: Kim Munho , Seo Jung-Hun , Zhao Deyin , Liu Shih-Chia , Kim Kwangeun , Lim Kangmook , Zhou Weidong , Waks Edo , Ma Zhenqiang
Published: November 2016

In this work, we demonstrate a transferrable single crystalline 4H-SiC nanomembrane (SiC NM) released from a SiC-on-insulator (SiCOI) wafer.
Effects of straw management, inorganic fertiliser, and manure amendment on soil microbial properties, nutrient availability, and root growth in a drip-irrigated cotton field
Authors: Pu X. Z. , Zhang G. J. , Zhang P. P. , Liu Y. J. , Zhang W. F.
Published: November 2016

Organic amendments not only improve soil conditions but also affect belowground biological processes. This study used a split plot design to investigate the effects of cotton straw management, inorganic fertiliser, and manure amendment on (i) soil nutrient content, (ii) soil microbial properties, and (iii) cotton root growth in a drip-irrigated cotton field. Straw return significantly increased soil inorganic nitrogen (N), N transformation rates, organic carbon (C), and urease activity. Straw return, however, had no significant effect on either root growth or activity. Inorganic fertiliser and/or manure amendment significantly increased inorganic N, N transformation rates, organic C, microbial biomass C, urease activity, and invertase activity. Inorganic fertiliser and/or manure also significantly increased fine root growth, triphenyltetrazolium chloride-reducing capacity, and specific root length. Moreover, the inorganic fertiliser plus manure treatment had the greatest soil inorganic N concentrations, N mineralisation rate, total carbon dioxide efflux, C mineralisation rate, soil organic C concentration, microbial biomass C concentration and enzyme activity, as well as root biomass, fine root : coarse root ratio, root triphenyltetrazolium chloride-reducing capacity and specific root length. Straw return to inorganically fertilised soil increased inorganic N concentrations by 11%, net N mineralisation rate by 59%, net nitrification by 59%, gross nitrification by 14%, denitrification by 39%, and urease activity by 25% compared with inorganic fertiliser alone. Taken together, the results indicated that straw return and manure application significantly promoted soil microbial activity and soil N transformation in the presence of inorganic fertiliser. The manure amendment enabled the crop to develop a more extensive root system, primarily by increasing the number of fine roots. Thus, organic amendments may improve the acquisition efficiency of inorganic fertiliser in drip-irrigated cotton fields.
Protein in culture and endogenous lipid interact with embryonic stages in vitro to alter calf birthweight after embryo vitrification and warming
Authors: Gómez E. , Carrocera S. , Uzbekova S. , Martín D. , Murillo A. , Alonso-Guervós M. , Goyache F. , Muñoz M.
Published: November 2016

Short-term protein removal in vitro improves long-term blastocyst competence to survive vitrification. We investigated the mechanisms and effects underlying protein removal. Day-6 morulae and early blastocysts were cultured individually with and without protein for 24 h. Development and lipid content were analysed in expanded blastocysts derived from morulae (M-XB) and from early blastocysts (EB-XB). Expression of genes involved in lipid metabolism, stress responses and apoptosis was analysed in fresh and vitrified–warmed M-XB produced with and without protein. Pregnancy rates, birth rates and birthweight (BW) were recorded after transfer of embryos. Day-7 EB-XB production rates (with, 66.9 ± 6.2 and without, 68.8 ± 6.0 protein) were higher than M-XB rates (with, 21.4 ± 4.6 and without, 9.4 ± 4.6 protein; P < 0.005). EB-XB showed fewer lipids than M-XB (P = 0.03). In fresh M-XB, expression of sterol regulatory element binding protein (SREBP1) was lower with (4.1 ± 2.2) than without (13.6 ± 2.2) protein, contrary to results obtained for Patatin-like phospholipase domain containing 2, Hormone-sensitive lipase and Bcl-2–associated X protein (P < 0.05). Protein did not affect pregnancy rates and birth phenotypes (P > 0.05). However, BW was higher (P < 0.01) in calves born from vitrified M-XB (48.6 ± 3.4 kg) than from EB-XB (39.8 ± 2.9 kg). Such effects were more pronounced in females (P < 0.001). Calves from fresh embryos did not show BW differences. These results indicate that embryonic kinetics and vitrification impact birth phenotypes, at least in females. Alterations might involve exogenous protein and mobilisation of lipid stocks.
Experimental investigation of thermophysical properties of eutectic Mo–C, graphite and tantalum at high temperatures
Authors: Senchenko V N , Belikov R S , Popov V S
Published: November 2016

An experimental technique based on fast electrical heating for investigation of thermophysical properties of refractory materials under high pressures and at high temperatures is considered. A set of thermophysical properties of refractory materials such as specific enthalpy, specific heat capacity, specific resistivity, melting heat of eutectic Mo-C and thermal expansion of graphite and tantalum were determined. The obtained temperature of eutectic melting of MoC0.82 shows close agreement with equilibrium Mo-C phase diagram.
Rheology of liquid n-triacontane: Molecular dynamics simulation
Authors: Kondratyuk N D , Norman G E , Stegailov V V
Published: November 2016

Molecular dynamics is applied to calculate diffusion coefficients of n-triacontane C30H62 using Einstein-Smoluchowski and Green-Kubo relations. The displacement 〈Δr2〉(t) has a subdiffusive part 〈Δr2〉 ∼ t
α, caused by molecular crowding at low temperatures. Longtime asymptotes of 〈v(0)v(t)〉 are collated with the hydrodynamic tail t-3/2 demonstrated for atomic liquids. The influence of these asymptotes on the compliance of Einstein-Smoluchowski and Green-Kubo methods is analyzed. The effects of the force field parameters on the diffusion process are treated. The results are compared with experimental data.
Ablation of gold irradiated by femtosecond laser pulse: Experiment and modeling
Authors: Ashitkov S I , Komarov P S , Zhakhovsky V V , Petrov Yu V , Khokhlov V A , Yurkevich A A , Ilnitsky D K , Inogamov N A , Agranat M B
Published: November 2016

We report on the ablation phenomena in gold sample irradiated by femtosecond laser pulses of moderate intensity. Dynamics of optical constants and expansion of a heated surface layer was investigated in a range from picosecond up to subnanosecond using ultrafast interferometry. Also morphology of the ablation craters and value of an ablation threshold (for absorbed fluence) were measured. The experimental data are compared with simulations of mass flows obtained by two-temperature hydrodynamics and molecular dynamics methods. Simulation shows evolution of a thin surface layer pressurized by a laser pulse. Unloading of the pressurized layer proceeds together with electron-ion thermalization, melting, cavitation and spallation of a part of surface liquid layer. The experimental and simulation results on two-temperature physics and on a fracture, surface morphology and strength of liquid gold at a strain rate ∼ 109 s-1 are discussed.
Equation of state of dense hydrogen plasma
Authors: Gabdullin M T , Ramazanov T S , Ismagambetova T N , Otarbay Zh Y
Published: November 2016

In this paper, dense non-ideal, non-isothermal plasma is considered. Effective screened interaction potentials taking into account the quantum-mechanical diffraction effect have been used. Pair correlation functions were studied in the exponential approximation. Thermodynamic properties for hydrogen plasma were calculated using the analytical expressions derived from these effective potentials.
Inference of evolutionary jumps in large phylogenies using Lévy processes
Authors: Duchen Pablo , Leuenberger Christoph , Szilágyi Sándor M. , Harmon Luke , Eastman Jonathan , Schweizer Manuel , Wegmann Daniel
Published: November 2016

While it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so called new adaptive zones, for instance after dispersal into a new geographic area, after rapid climatic changes, or following the appearance of an evolutionary novelty. Only recently, large, accurate and well calibrated phylogenies have become available that allow testing this hypothesis directly, yet inferring evolutionary jumps remains computationally very challenging. Here, we develop a computationally highly efficient algorithm to accurately infer the rate and strength of evolutionary jumps as well as their phylogenetic location. Following previous work we model evolutionary jumps as a compound process, but introduce a novel approach to sample jump configurations that does not require matrix inversions and thus naturally scales to large trees. We then make use of this development to infer evolutionary jumps inAnolislizards and Loriini parrots where we find strong signal for such jumps at the basis of clades that transitioned into new adaptive zones, just as postulated by Simpson's hypothesis.
Inference of Cell Type Composition from Human Brain Transcriptomic Datasets Illuminates the Effects of Age, Manner of Death, Dissection, and Psychiatric Diagnosis
Authors: Hagenauer Megan Hastings , Schulmann Anton , Li Jun Z. , Vawter Marquis P. , Walsh David M. , Thompson Robert C. , Turner Cortney A. , Bunney William E. , Myers Richard M. , Barchas Jack D. , Schatzberg Alan F. , Watson Stanley J. , Akil Huda
Published: November 2016

Psychiatric illness is unlikely to arise from pathology occurring uniformly across all cell types in affected brain regions. Despite this, transcriptomic analyses of the human brain have typically been conducted using macro-dissected tissue due to the difficulty of performing single-cell type analyses with donated post-mortem brains. To address this issue statistically, we compiled a database of several thousand transcripts that were specifically-enriched in one of 10 primary cortical cell types in previous publications. Using this database, we predicted the relative cell type composition for 833 human cortical samples using microarray or RNA-Seq data from the Pritzker Consortium (GSE92538) or publicly-available databases (GSE53987, GSE21935, GSE21138, CommonMind Consortium). These predictions were generated by averaging normalized expression levels across transcripts specific to each cell type using our R-packageBrainInABlender(validated and publicly-released:https://github.com/hagenaue/BrainInABlender). Using this method, we found that the principal components of variation in the datasets strongly correlated with the neuron to glia ratio of the samples.

This variability was not simply due to dissection – the relative balance of brain cell types appeared to be influenced by a variety of demographic, pre- and post-mortem variables. Prolonged hypoxia around the time of death predicted increased astrocytic and endothelial gene expression, illustrating vascular upregulation. Aging was associated with decreased neuronal gene expression. Red blood cell gene expression was reduced in individuals who died following systemic blood loss. Subjects with Major Depressive Disorder had decreased astrocytic gene expression, mirroring previous morphometric observations. Subjects with Schizophrenia had reduced red blood cell gene expression, resembling the hypofrontality detected in fMRI experiments. Finally, in datasets containing samples with especially variable cell content, we found that controlling for predicted sample cell content while evaluating differential expression improved the detection of previously-identified psychiatric effects. We conclude that accounting for cell type can greatly improve the interpretability of transcriptomic data.
Graph regularized, semi-supervised learning improves annotation ofde novotranscriptomes
Authors: Malik Laraib I. , Thatipally Shravya , Junneti Nikhil , Patro Rob
Published: November 2016

We present a new method, GRASS, for improving an initial annotation ofde novotranscriptomes. GRASS makes the shared-sequence relationships between assembled contigs explicit in the form of a graph, and applies an algorithm that performs label propagation to transfer annotations between related contigs and modifies the graph topology iteratively. We demonstrate that GRASS increases the completeness and accuracy of the initial annotation, allows for improved differential analysis, and is very efficient, typically taking 10s of minutes.
Gluten-Free Beer via Hydrodynamic Cavitation Assisted Brewing of Barley Malts
Authors: Albanese Lorenzo , Ciriminna Rosaria , Meneguzzo Francesco , Pagliaro Mario
Published: November 2016

We provide evidence that novel brewing technology based on controlled hydrodynamic cavitation greatly reduces gluten concentration in wort and finished beer. We advance the hypothesis that the degradation of proline, the most recalcitrant among gluten constituents, leads to gluten concentration reduction in the unfermented as well as in the fermenting wort and later during maturation. These findings are significant as the new cavitation-assisted technology could provide coeliac patients and gluten-intolerant people with gluten-free beer of high quality, offering an alternative to existing methods to lower the gluten concentration, which are detrimental to flavor and taste.
Can paid reviews promote scientific quality and offer novel career perspectives for young scientists?
Authors: Wurzbacher Christian , Grossart Hans-Peter , Kristiansson Erik , Nilsson R. Henrik , Unterseher Martin
Published: November 2016

We exemplify how community driven paid reviews could work in conjunction with a feed-back loop to young scientists. This would remove pressure from the conventional peer-review system and promote the integration of reviews into an academic career. This concept may eventually revive the community based journal type.
The Semantics of Adjective Noun Phrases in the Human Brain
Authors: Fyshe Alona , Sudre Gustavo , Wehbe Leila , Rafidi Nicole , Mitchell Tom M.
Published: November 2016

As a person reads, the brain performs complex operations to create higher order semantic representations from individual words. While these steps are effortless for competent readers, we are only beginning to understand how the brain performs these actions. Here, we explore semantic composition using magnetoencephalography (MEG) recordings of people reading adjective-noun phrases presented one word at a time. We track the neural representation of semantic information over time, through different brain regions. Our results reveal two novel findings: 1) a neural representation of the adjective is present during noun presentation, but this neural representation is different from that observed during adjective presentation 2) the neural representation of adjective semantics observed during adjective reading is reactivated after phrase reading, with remarkable consistency. We also note that while the semantic representation of the adjective during the reading of the adjective is very distributed, the later representations are concentrated largely to temporal and frontal areas previously associated with composition. Taken together, these results paint a picture of information flow in the brain as phrases are read and understood.
Inference of candidate germline mutator loci in humans from genome-wide haplotype data
Authors: Seoighe Cathal , Scally Aylwyn
Published: November 2016

The rate of germline mutation varies widely between species but little is known about the extent of variation in the germline mutation rate between individuals of the same species. Here we demonstrate that an allele that increases the rate of germline mutation can result in a distinctive signature in the genomic region linked to the affected locus, characterized by a number of haplotypes with a locally high proportion of derived alleles, against a background of haplotypes carrying a typical proportion of derived alleles. We searched for this signature in human haplotype data from phase 3 of the 1000 Genomes Project and report a number of candidate mutator loci, several of which are located close to or within genes involved in DNA repair or the DNA damage response. To investigate whether mutator alleles remained active at any of these loci, we usedde novomutation counts from human parent-offspring trios in the 1000 Genomes and Genome of the Netherlands cohorts, looking for an elevated number ofde novomutations in the offspring of parents carrying a candidate mutator haplotype at each of these loci. We found some support for two of the candidate loci, including one locus just upstream of theBRSK2gene, which is expressed in the testis and has been reported to be involved in the response to DNA damage.

Author Summary

Each time a genome is replicated there is the possibility of error resulting in the incorporation of an incorrect base or bases in the genome sequence. When these errors occur in cells that lead to the production of gametes they can be incorporated into the germline. Such germline mutations are the basis of evolutionary change; however, to date there has been little attempt to quantify the extent of genetic variation in human populations in the rate at which they occur. This is particularly important because new spontaneous mutations are thought to make an important contribution to many human diseases. Here we present a new way to identify genetic loci that may be associated with an elevated rate of germline mutation and report the application of this method to data from a large number of human genomes, generated by the 1000 Genomes Project. Several of the candidate loci we report are in or near genes involved in DNA repair and some were supported by direct measurement of the mutation rate obtained from parent-offspring trios.
Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy
Authors: Albuquerque Marco A. , Grande Bruno M. , Ritch Elie J. , Jessa Selin , Krzywinski Martin , Grewal Jasleen K. , Shah Sohrab P. , Boutros Paul C. , Morin Ryan D.
Published: November 2016

We present a collection of Galaxy tools representing many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We implemented methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability on cloud-based infrastructure and commodity hardware. Some tools represents extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate several of these to perform some standard data integration and visualization tasks are demonstrated on a cohort of 96 diffuse large B-cell lymphomas, enabling the discovery of multiple candidate lymphoma-related genes that have not been reported previously.
Statistical Quality Scale 6 (SQS-6)
Authors: Fausto de Morais José , Pereira Borges Gecilmar , Fernandes do Prado Gilmar
Published: November 2016

Context

The statistical analysis is an important part of the process of assessing the quality of randomized controlled trials, unfortunately it tends to be underestimated or even omitted by editors, in this sense, scales that cover this gap becomes necessary.

Objective

To build a definition and a scale for assessing the quality of statistical analysis in randomized controlled trials.

Methods

A content analysis on 16 biostatistics texts was considered in the building of the definition and of the scale. The indicators of quality were based on the description and presentation of results of articles.

Results

We identify 32 quality indicators grouping in six dimensions: randomization and management of lost; sample size computation; use of mean and median; statistical test; use and interpretation of confidence interval and P-values. The scale range from 0 to 6 and score greater than three identify article with appropriate statistical analysis.

Conclusions

The scale presented three dimensions linked to quality of description and three linked to quality of used strategy.
FlyLimbTracker: an active contour based approach for leg segment tracking in unmarked, freely behavingDrosophila
Authors: Uhlmann Virginie , Ramdya Pavan , Delgado-Gonzalo Ricard , Benton Richard , Unser Michael
Published: November 2016

Understanding the biological underpinnings of movement and action requires the development of tools for precise, quantitative, and high-throughput measurements of animal behavior.Drosophila melanogasterprovides an ideal model for developing such tools: the fly has unparalleled genetic accessibility and depends on a relatively compact nervous system to generate sophisticated limbed behaviors including walking, reaching, grooming, courtship, and boxing. Here we describe a method that uses active contours to semi-automatically track body and leg segments from video image sequences of unmarked, freely behavingDrosophila. We show that this approach is robust to wide variations in video spatial and temporal resolution and that it can be used to measure leg segment motions during a variety of locomotor and grooming behaviors. FlyLimbTracker, the software implementation of this method, is open-source and our approach is generalizable. This opens up the possibility of tracking leg movements in other species by modifications of underlying active contour models.

Author Summary

In terrestrial animals, including humans, fundamental actions like locomotion and grooming emerge from the displacement of multiple limbs through space. Therefore, precise measurements of limb movements are critical for investigating and, ultimately, understanding the neural basis for behavior. The vinegar fly,Drosophila melanogaster, is an attractive animal model for uncovering general principles about limb control since its genome and nervous system are easy to manipulate. However, existing methods for measuring leg movements in freely behavingDrosophilahave significant drawbacks: they require complicated experimental setups and provide limited information about each leg. Here we report a new method - and provide its open-source software implementation, FlyLimbTracker - for tracking the body and leg segments of freely behaving flies using only computational image processing approaches. We illustrate the power of this method by tracking fly limbs during five distinct walking and grooming behaviors and from videos across a wide range of spatial and temporal resolutions. Our approach is generalizable, allowing researchers to use and customize our software for limb tracking inDrosophilaand in other species.
Investigating side effect modules in the interactome and their use in drug adverse effect discovery
Authors: Guney Emre
Published: November 2016

One of the biggest challenges in drug development is increasing costs of bringing new drugs to the market. Many candidate drugs fail during phase II and III trials due to unexpected side effects and experimental methods remain cost ineffective for large scale discovery of adverse effects. Alternatively, computational methods are used to characterize drug side effects, but they often rely on training predictors based on drug and side effect similarity. Moreover, these methods are typically tailored to the underlying data set and provide little mechanistic insights on the predicted associations. In this study, we investigate the role of network topology in explaining observed side effects of drugs. We find that drug targets are closer in the interactome to the proteins inducing the known side effects of the drug compared to the proteins associated with the rest of the side effects. We show that the interactome based proximity can be used to identify side effects and we highlight a use case in which interactome-based side effect prediction can give insights on drug side effects observed in the clinic.
Physical models of spatial genome organization
Authors: Slanina S.V. , Aleshchenko A.V. , Eidelman Y.A. , Andreev S.G.
Published: November 2016

Remodeling of nuclear organization occurs during normal cell development, differentiation and cancer. One of the biggest gaps of knowledge remains how to link the information on chromatin and chromosome structural organization with genes activity. In this paper we introduce some physical ideas and a general computational method demonstrating how genome 3D architecture and its remodeling can be quantitatively modeled. We study a hypothetical scenario of alterations of chromosome territories positioning in the course of cell proliferation. On this basis we obtain quantitative information about chromosomal contacts in the nucleus. We predict changes of radial distributions of contacts between chromosomal megabase domains during proliferation. The proposed modeling approach may be helpful in integrating experimental data on nuclear reorganization associated with normal development and with various diseases. This predictive modeling may find applications in genome research of normal and cancer cells, stem cell biology, biology of aging,etc.
Global-scale structure of the eelgrass microbiome
Authors: Fahimipour Ashkaan K , Kardish Melissa R , Eisen Jonathan A , Lang Jenna M , Green Jessica L , Stachowicz John J
Published: November 2016

Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial plant species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrassZostera marinathroughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of their surrounding seawater and sediment communities, we uncovered the structure, composition and variability of microbial communities associated withZ. marina. We also investigated hypotheses about the mechanisms driving assembly of the eelgrass microbiome using a whole-genomic metabolic modeling approach. Our results reveal aboveground leaf communities displaying high variability and spatial turnover, that strongly mirror their adjacent coastal seawater microbiomes. In contrast, roots showed relatively low spatial turnover and were compositionally distinct from surrounding sediment communities — a result largely driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Metabolic modeling of enriched taxa was consistent with an assembly process whereby similarity in resource use drives taxonomic co-occurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a coreZ. marinaroot microbiome with putative functional roles and highlights potentially disparate processes influencing microbiome assembly on different plant compartments.
Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with thePax5promoter in a chicken B cell line
Authors: Fujita Toshitsugu , Kitaura Fusako , Yuno Miyuki , Suzuki Yutaka , Sugano Sumio , Fujii Hodaka
Published: November 2016

Chromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we identified genomic regions that physically bind to the promoter region of thePax5gene in the chicken B-cell line DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. Using insertional chromatin immunoprecipitation (iChIP) in combination with next-generation sequencing (NGS) (iChIP-Seq), we found that thePax5promoter bound to multiple genomic regions. The identified chromosomal interactions were independently confirmed byin vitroengineered DNA-binding molecule-mediated ChIP (in vitroenChIP) in combination with NGS (in vitroenChIP-Seq). Comparing chromosomal interactions in wild-type DT40 with those in a macrophage-like counterpart, we found that some of the identified chromosomal interactions were organized in a B cell–specific manner. In addition, deletion of a B cell–specific interacting genomic region in chromosome 11, which was marked by active enhancer histone modifications, resulted in moderate but significant down-regulation ofPax5transcription. Together, these results suggested thatPax5transcription in DT40 cells is regulated by inter-chromosomal interactions. Moreover, these analyses showed that iChIP-Seq andin vitroenChIP-Seq are useful for non-biased identification of functional genomic regions that physically interact with a locus of interest.
fMRI Correlates of Reaction Time Prolongation during intentional False Responding; an inter-individual difference study
Authors: Pishnamazi Morteza , Yeganeh Doost Maral , Ganjgahi Habib , Ekhtiari Hamed , Oghabian Mohammad Ali
Published: November 2016

Reaction time (RT) is chiefly longer when people lie. However, the baseline speed in answering questions and the amount of RT prolongation during lying show considerable amount of inter-individual variability. In the current study, we exploited this fact to glean insights on the contribution of each lie-related brain region to hampering of response speeds when people try to be deceitful. In an event-related fMRI session, participants were interrogated by yes-no autobiographical questions and were instructed to intentionally provide false responses to a pre-selected subset of questions. Data from twenty healthy volunteers were analyzed.Baseline speed[RTtruth] andrelative appended lie RT[(RTlie− RTtruth) ⁄ RTtruth] measures were calculated for each participant and were included in the group level analysis of [lie > truth] BOLD contrasts. Lying RTs were significantly longer than truth telling RTs. Lie-related increase in activity of right ventrolateral prefrontal cortex (VLPFC) and bilateral paracingulate cortex correlated with the baseline speed of participants, while the increase in activity of Left VLPFC, left lateral occipital cortex and bilateral anterior cingulate areas directly correlated with the amount of lying reaction time cost. Activity within bilateral posterior cingulate cortex and right insular cortex inversely correlated with lying RT-cost. Bilateral supplementary motor areas, internal capsule white matter and left angular gyrus showed lie-related increase in activity but did not correlate with either of behavioral measures. Provisional implications regarding the contribution of these regions to RT prolongation and their cognitive role in deceitful behavior are discussed.
Hyphal aggregation and surface attachment ofStreptomycesis governed by extracellular poly-β-1,6-N-acetylglucosamine
Authors: van Dissel Dino , Willemse Joost , Zacchetti Boris , Claessen Dennis , Pier Gerald B. , van Wezel Gilles P.
Published: November 2016

Streptomycetes are multicellular filamentous microorganisms, which are major producers of antibiotics, anticancer drugs and industrial enzymes. When grown in submerged cultures, the preferred enzyme producer,Streptomyces lividans, forms dense mycelial aggregates or pellets, which requires the activity of the proteins encoded by thematABandcslA-glxA. Here we show that matAB encodes the biosynthetic genes for the extracellular polymeric substance (EPS) poly-β-1,6-N-acetylglucosamine or PNAG. Heterologous expression of matAB in actinomycetes that naturally lack these genes was sufficient for PNAG production and induction of mycelial aggregation. Also, overexpression ofmatABin a non-pelletingcslAmutant restored pellet formation, which could effectively be antagonized by the PNAG-specific hydrolase, dispersin B. Extracellular accumulation of PNAG allowedStreptomycesto attach to hydrophilic surfaces, unlike attachment to hydrophobic surfaces, which involves a cellulase-degradable EPS produced by CslA. Altogether, our data support a model in which pellet formation depends on hydrophilic interactions mediated by PNAG and hydrophobic interactions involving the EPS produced by CslA. These new insights may be harnessed to improve growth and industrial exploitation of these highly versatile natural product and enzyme producers.
The Eurozone Crisis and Emerging‐Market Expansion: Capital Switching and the Uneven Geographies of Spanish Urbanization
Authors: Kutz William
Published: November 2016

The theory of capitalist urbanization posits that the built form serves as a crucial sink through which overaccumulated capital is ‘switched' from industrial production into long‐term investment in urban infrastructure. Since Harvey's (1978) deployment of the theory, researchers have attempted to empirically substantiate the switching thesis with limited success. Christophers (2011) revisited the debate with new data and methods to support the claim that significant investment had switched into the built environment at the onset of the 2007/08 financial crisis. However, Christophers' study overlooks how crises are also geographically displaced. This article analyses Spanish trade data for the years 1993 to 2013, the years prior and subsequent to the housing‐induced economic crisis (1997 to 2006). Two studies are undertaken. The first replicates Christophers' methodology to assess how and to what extent a sectoral switch into property investment occurred in Spain between 1997 and 2006. The second modifies the methodology to investigate the extent to which overaccumulated capital in Spain has been geographically displaced through investment in the Moroccan building industry since 2006. These approaches situate uneven development (geographical switching) and turnover time (sectoral switching) as the twin dynamics through which capitalist urbanization is spatio‐temporally fixed.
Reappearance of the Public: Placemaking, Minoritization and Resistance in Detroit
Authors: Montgomery Alesia
Published: November 2016

Recent studies of public space in US central cities tend to focus either on (1) market‐driven placemaking (privatized parks, hipster shops) in gentrifying enclaves or (2) street cultures (community gardens, hip‐hop) in low‐income neighborhoods. Neither focus adequately frames the ability of African Americans to shape public space as the white middle class returns to central cities. In this case study of downtown Detroit, I theorize a dialectic: the history of clashes between racial capitalism and social movements in public space reappears in the contradictory design of market‐driven placemaking, which suppresses and displays cultures of resistance. White business and real‐estate interests showcase downtown spaces to counter news of disinvestment and suffering in low‐income neighborhoods. The legal and political legacies of civil rights and black power struggles—combined with consumer demand (black culture sells)—force them to involve black entrepreneurs, professionals and artists in placemaking. This placemaking subordinates the black urban poor, even as it incorporates their street cultures. The contradictions of placemaking shape possibilities for resistance, as shown in mundane subversions and street protests that use the downtown spotlight to call for social justice citywide. This analysis contributes to research on public space at a time when new movements are challenging public order in the financial core of US cities.