bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural Hazards and Their Governance in Sub-Saharan Africa
Authors: van Niekerk Dewald , Nemakonde Livhuwani David
Published: October 2017

The sub-Saharan Africa (SSA) region, along with the rest of the African continent, is prone to a wide variety of natural hazards. Most of these hazards and the associated disasters are relatively silent and insidious, encroaching on life and livelihoods, increasing social, economic, and environmental vulnerability even to moderate events. With the majority of SSA’s disasters being of hydrometeorological origin, climate change through an increase in the frequency and magnitude of extreme weather events is likely to exacerbate the situation. Whereas a number of countries in SSA face significant governance challenges to effectively respond to disasters and manage risk reduction measures, considerable progress has been made since the early 2000s in terms of policies, strategies, and/or institutional mechanisms to advance disaster risk reduction and disaster risk management. As such, most countries in SSA have developed/reviewed policies, strategies, and plans and put in place institutions with dedicated staffs and resources for natural hazard management. However, the lack of financial backing, limited skills, lack of coordination among sectors, weak political leadership, inadequate communication, and shallow natural hazard risk assessment, hinders effective natural hazard management in SSA.

The focus here is on the governance of natural hazards in the sub-Saharan Africa region, and an outline of SSA’s natural hazard profile is presented. Climate change is increasing the frequency and magnitude of extreme weather events, thus influencing the occurrence of natural hazards in this region. Also emphasized are good practices in natural hazard governance, and SSA’s success stories are described. Finally, recommendations on governance arrangements for effective implementation of disaster risk reduction initiatives and measures are provided.
A Historical Perspective of Unconventional Oil and Gas Extraction and Public Health
Authors: Haynes Erin N. , McKenzie Lisa , Malin Stephanie A. , Cherrie John W.
Published: October 2017

Technological advances in directional well drilling and hydraulic fracturing have enabled extraction of oil and gas from once unobtainable geological formations. These unconventional oil and gas extraction (UOGE) techniques have positioned the United States as the fastest-growing oil and gas producer in the world. The onset of UOGE as a viable subsurface energy abstraction technology has also led to the rise of public concern about its potential health impacts on workers and communities, both in the United States and other countries where the technology is being developed. Herein we review in the national and global impact of UOGE from a historical perspective of occupational and public health. Also discussed are the sociological interactions between scientific knowledge, social media, and citizen action groups, which have brought wider attention to the potential public health implications of UOGE.
Aerosols and Their Impact on Radiation, Clouds, Precipitation, and Severe Weather Events
Authors: Li Zhanqing , Rosenfeld Daniel , Fan Jiwen
Published: October 2017

Aerosols (tiny solid or liquid particles suspended in the atmosphere) have been in the forefront of environmental and climate change sciences as the primary atmospheric pollutant and external force affecting Earth’s weather and climate. There are two dominant mechanisms by which aerosols affect weather and climate: aerosol-radiation interactions (ARIs) and aerosol-cloud interactions (ACIs). ARIs arise from aerosol scattering and absorption, which alter the radiation budgets of the atmosphere and surface, while ACIs are connected to the fact that aerosols serve as cloud condensation nuclei and ice nuclei. Both ARIs and ACIs are coupled with atmospheric dynamics to produce a chain of complex interactions with a large range of meteorological variables that influence both weather and climate. Elaborated here are the impacts of aerosols on the radiation budget, clouds (microphysics, structure, and lifetime), precipitation, and severe weather events (lightning, thunderstorms, hail, and tornadoes). Depending on environmental variables and aerosol properties, the effects can be both positive and negative, posing the largest uncertainties in the external forcing of the climate system. This has considerably hindered the ability to project future climate changes and make accurate numerical weather predictions.
Environmental Change, Migration, and Population Health
Authors: McMichael Celia
Published: October 2017

Global environmental change amplifies and creates pressures that shape human migration. In the 21st century, there has been increasing focus on the complexities of migration and environmental change, including forecasts of the potential scale and pace of so-called environmental migration, identification of geographic sites of vulnerability, policy implications, and the intersections of environmental change with other drivers of human migration. Migration is increasingly viewed as an adaptive response to climatic and environmental change, particularly in terms of livelihood vulnerability and risk diversification. Yet the adaptive potential of migration will be defined in part by health outcomes for migrating populations. There has been limited examination, however, of the health consequences of migration related to environmental change.

Migration related to environmental change includes diverse types of mobility, including internal migration to urban areas, cross-border migration, forced displacement following environmental disaster, and planned relocation—migration into sites of environmental vulnerability; much-debated links between environmental change, conflict, and migration; immobile or “trapped” populations; and displacement due to climate change mitigation and decarbonization action. Although health benefits of migration may accrue, such as increased access to health services or migration away from sites of physical risk, migration—particularly irregular (undocumented) migration and forced displacement—can amplify vulnerabilities and present risks to health and well-being. For diverse migratory pathways, there is the need to anticipate, respond to, and ameliorate population health burdens among migrants.
Evidence-Based Practice in Arab Societies
Authors: Helal Ahmed T.
Published: October 2017

The concept of evidence-based practice (EBP) was introduced in social work by Mary Richmond, who had the revolutionary notion of adopting a more direct practice with clients.

The origins of EBP in the United States are traced, as well as its emergence in the Arab world. Discussed are various Arab faculties and departments of social work that include EBP among their academic courses. Social work settings that apply EBP in professional interventions with clients are examined. Barriers and challenges to the processes of both teaching and learning EBP in Arab society are highlighted. The future outlook for EBP in Arab schools of social work is explored.
Energy Economics
Authors: Tyner Wallace E , Herath Nisal
Published: October 2017

Energy economics is a vast topic. Many applied and agricultural economists today work on fuel economy, fossil fuel energy issues, energy sector economic analysis, electricity sector economic and policy issues, techno‐economic analyses of energy alternatives as well as agricultural energy issues such as biofuels, and energy use in agriculture. Energy economists also employ a wide variety of modeling and analytical tools. We cover six broad topics: externalities, policy analysis, energy demand and supply analyses, electricity pricing, biofuels, and techno‐economic analysis. Applied and agricultural economists have made and will continue to make major contributions to the literature and policy analysis in these areas.
Detecting hidden batch factors through data-adaptive adjustment for biological effects
Authors: Yi Haidong , Raman Ayush T , Zhang Han , Allen Genevera I , Liu Zhandong
Published: October 2017

Motivation

Batch effects are one of the major source of technical variations that affect the measurements in high-throughput studies such as RNA sequencing. It has been well established that batch effects can be caused by different experimental platforms, laboratory conditions, different sources of samples and personnel differences. These differences can confound the outcomes of interest and lead to spurious results. A critical input for batch correction algorithms is the knowledge of batch factors, which in many cases are unknown or inaccurate. Hence, the primary motivation of our paper is to detect hidden batch factors that can be used in standard techniques to accurately capture the relationship between gene expression and other modeled variables of interest.

Results

We introduce a new algorithm based on data-adaptive shrinkage and semi-Non-negative Matrix Factorization for the detection of unknown batch effects. We test our algorithm on three different datasets: (i) Sequencing Quality Control, (ii) Topotecan RNA-Seq and (iii) Single-cell RNA sequencing (scRNA-Seq) on Glioblastoma Multiforme. We have demonstrated a superior performance in identifying hidden batch effects as compared to existing algorithms for batch detection in all three datasets. In the Topotecan study, we were able to identify a new batch factor that has been missed by the original study, leading to under-representation of differentially expressed genes. For scRNA-Seq, we demonstrated the power of our method in detecting subtle batch effects.

Availability and implementation

DASC R package is available via Bioconductor or at https://github.com/zhanglabNKU/DASC.

Supplementary information

Supplementary data are available at Bioinformatics online.
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies
Authors: Sun Hequan , Ding Jia , Piednoël Mathieu , Schneeberger Korbinian
Published: October 2017

Motivation

Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation.

Results

We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations. In an application with 71 female and 71 male human individuals, findGSE delivered an average of 3039 Mb as haploid human GS, while female genomes were on average 41 Mb larger than male genomes, in astonishing agreement with size difference of the X and Y chromosomes. Further analysis showed that human GS variations link to geographical patterns and significant differences between populations, which can be explained by variable abundances of LINE-1 retrotransposons.

Availability and implementation

R package of findGSE is freely available at https://github.com/schneebergerlab/findGSE and supported on linux and Mac systems.

Supplementary information

Supplementary data are available at Bioinformatics online.
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis
Authors: Chandak Shubham , Tatwawadi Kedar , Weissman Tsachy
Published: October 2017

Motivation

New Generation Sequencing (NGS) technologies for genome sequencing produce large amounts of short genomic reads per experiment, which are highly redundant and compressible. However, general-purpose compressors are unable to exploit this redundancy due to the special structure present in the data.

Results

We present a new algorithm for compressing reads both with and without preserving the read order. In both cases, it achieves 1.4×–2× compression gain over state-of-the-art read compression tools for datasets containing as many as 3 billion Illumina reads. Our tool is based on the idea of approximately reordering the reads according to their position in the genome using hashed substring indices. We also present a systematic analysis of the read compression problem and compute bounds on fundamental limits of read compression. This analysis sheds light on the dynamics of the proposed algorithm (and read compression algorithms in general) and helps understand its performance in practice. The algorithm compresses only the read sequence, works with unaligned FASTQ files, and does not require a reference.

Supplementary information

Supplementary material are available at Bioinformatics online. The proposed algorithm is available for download at https://github.com/shubhamchandak94/HARC.
Sovereignty, Territory, and Population in Jean Bodin’s
République
Authors: Miglietti Sara
Published: October 2017

This article offers a re-interpretation of Jean Bodin’s
Six livres de la République
(1576), a work that deeply transformed European political discourse at the time of the French Wars of Religion and that had important repercussions on the later ‘reason of state’ tradition. Highlighting the ties between Bodin’s definition of sovereignty in Book 1 and his discussion of demographic growth and territorial expansion in Books 4, 5, and 6, the article shows that Bodin’s critical contribution to early modern political thought, far from being limited to his reframing of the juristic concept of
souveraineté
or
maiestas
, extends to his novel understanding of the territory as a non-juridical ‘technologie politique’ (Michel Foucault). Through an examination of Bodin’s work and its later reception, the article argues that Bodin’s insights about territorial and demographic matters played a fundamental role in the early modern ‘territorialisation de la politique’ (Romain Descendre), in that they helped redefine the very terms in which the notion of territory would be understood and discussed in the following decades.
Escape rate for cod (Gadus morhua) from the codend during buffer towing
Authors: Brinkhof Jesse , Herrmann Bent , Larsen Roger B , Sistiaga Manu
Published: October 2017

The high abundances of Northeast Arctic cod (Gadus morhua) in the Barents Sea have led to the development of a new fishing tactic called buffer towing. On factory trawlers, the trawl is deployed immediately after taking the catch onboard, a tactic used to ensure a continuous supply of fish is being processed. If the desired amount of fish is caught before the catch from the previous haul has been fully processed, the trawl is lifted off the seabed and towed at a given depth at low speed. This is called buffer towing. Cod that escape from the codend when the trawl is shallower than the initial fishing depth are exposed to an increased likelihood of barotrauma-related injuries, increased disease susceptibility, and predation, which could be lethal, or affect growth and reproduction capability. Therefore, this study quantified the escape rate and size selectivity during buffer towing of cod. A new analytical method was applied that allows using the same trawl configuration as applied during commercial fishing and avoids potential bias in the assessment of buffer towing size selection. Our results demonstrated a significant size selection for cod during buffer towing where cod measuring up to at least 42 cm in length were proven to escape. In particular, at least 60% of cod measuring 20 cm were estimated to escape during buffer towing. For cod measuring 30 and 40 cm, at least 53 and 45% were estimated to escape during buffer towing, respectively.
Gene Expression Assays for Early-Stage Hormone Receptor–Positive Breast Cancer: Understanding the Differences
Authors: Nunes Ana Tablante , Collyar Deborah E , Harris Lyndsay N
Published: October 2017

Biomarkers are frequently used to guide decisions for treatment of early-stage estrogen (ER) and progesterone (PR) receptor–positive (ER/PR+) invasive breast cancers and have been incorporated into guidelines. The American Society of Clinical Oncology (ASCO) 2016 guideline and a 2017 update were recently published to help clinicians use the tests available. ASCO currently recommends five tests that show evidence of clinical utility based on the parameters defined in the guideline. These include the 21-gene assay (Oncotype DX), Prediction of Analysis of Microarray-50 (PAM50), 12-gene risk score (Endopredict), Breast Cancer Index (BCI), and, most recently, the 70-gene assay (Mammaprint). However, discordance is often seen when the results of these gene assays are compared in a particular patient, for a number of reasons: the assays were initially developed to answer different questions, and the molecular makeup of each signature reflects this; the patient populations that were studied also differed and may not reflect the patient being tested; furthermore, the study design and statistical analysis varied between each test, leading to different scoring scales that may not be comparable. In this review, the background on the development and validation of these assays is discussed, and studies comparing them are reviewed. To provide guidance on which test to choose, the studies that support the level of evidence for clinical utility are presented. However, the choice of a particular test will also be influenced by socioeconomic factors, clinical factors, and patient preferences. We hope that a better understanding of the scientific and clinical rationale for each test will allow patients and providers to make optimal decisions for treatment of early-stage ER/PR+ breast cancer.
Enteric Microbiome Markers as Early Predictors of Clinical Outcome in Allogeneic Hematopoietic Stem Cell Transplant: Results of a Prospective Study in Adult Patients
Authors: Mancini Nicasio , Greco Raffaella , Pasciuta Renée , Barbanti Maria Chiara , Pini Giacomo , Morrow Olivia Beatrice , Morelli Mara , Vago Luca , Clementi Nicola , Giglio Fabio , Lupo Stanghellini Maria Teresa , Forcina Alessandra , Infurnari Laura , Marktel Sarah , Assanelli Andrea , Carrabba Matteo , Bernardi Massimo , Corti Consuelo , Burioni Roberto , Peccatori Jacopo , Sormani Maria Pia , Banfi Giuseppe , Ciceri Fabio , Clementi Massimo
Published: October 2017

Background

Infections and graft-vs-host disease (GvHD) still represent major, not easily predictable complications in allogeneic hematopoietic stem cell transplant (allo-HSCT). Both conditions have been correlated to altered enteric microbiome profiles during the peritransplant period. The main objective of this study was to identify possible early microbiome-based markers useful in pretransplant risk stratification.

Methods

Stool samples were collected from 96 consecutive patients at the beginning of the pretransplant conditioning regimen (T0) and at 10 (T1) and 30 (T2) days following transplant. When significant in univariate analysis, the identified microbiome markers were used in multivariate regression analyses, together with other significant clinical variables for allo-HSCT-related risk stratification. Four main outcomes were addressed: (1) septic complications, (2) GvHD, (3) relapse of the underlying disease, and (4) mortality.

Results

The presence of >5% proinflammatory Enterobacteriaceae at T0 was the only significant marker for the risk of microbiologically confirmed sepsis. Moreover, ≤10% Lachnospiraceae at T0 was the only significant factor for increased risk of overall mortality, including death from both infectious and noninfectious causes.

Finally, a low bacterial alpha-diversity (Shannon index ≤ 1.3) at T1 was the only variable significantly correlating with an increased risk of GvHD within 30 days.

Conclusions

Microbiome markers can be useful in the very early identification of patients at risk for major transplant-related complications, offering new tools for individualized preemptive or therapeutic strategies to improve allo-HSCT outcomes.
First In-Human Experience With Complete Integration of Neuromodulation Device Within a Customized Cranial Implant
Authors: Gordon Chad R , Santiago Gabriel F , Huang Judy , Bergey Gregory K , Liu Shuya , Armand Mehran , Brem Henry , Anderson William S
Published: October 2017

BACKGROUND

Neuromodulation devices have the potential to transform modern day treatments for patients with medicine-resistant neurological disease. For instance, the NeuroPace System (NeuroPace Inc, Mountain View, California) is a Food and Drug Administration (FDA)-approved device developed for closed-loop direct brain neurostimulation in the setting of drug-resistant focal epilepsy. However, current methods require placement either above or below the skull in nonanatomic locations. This type of positioning has several drawbacks including visible deformities and scalp pressure from underneath leading to eventual wound healing difficulties, micromotion of hardware with infection, and extrusion leading to premature explantation.

OBJECTIVE

To introduce complete integration of a neuromodulation device within a customized cranial implant for biocompatibility optimization and prevention of visible deformity.

METHODS

We report a patient with drug-resistant focal epilepsy despite previous seizure surgery and maximized medical therapy. Preoperative imaging demonstrated severe resorption of previous bone flap causing deformity and risk for injury. She underwent successful responsive neurostimulation device implantation via complete integration within a clear customized cranial implant.

RESULTS

The patient has recovered well without complication and has been followed closely for 180 d. Device interrogation with electrocorticographic data transmission has been successfully performed through the clear implant material for the first time with no evidence of any wireless transmission interference.

CONCLUSION

Cranial contour irregularities, implant site infection, and bone flap resorption/osteomyelitis are adverse events associated with implantable neurotechnology. This method represents a novel strategy to incorporate all future neuromodulation devices within the confines of a low-profile, computer-designed cranial implant and the newfound potential to eliminate contour irregularities, improve outcomes, and optimize patient satisfaction.
Temporal relations between magnetic bright points and the solar sunspot cycle
Authors: Utz Dominik , Muller Richard , Van Doorsselaere Tom
Published: October 2017

The Sun shows a global magnetic field cycle traditionally best visible in the photosphere as a changing sunspot cycle featuring roughly an 11-year period. In addition we know that our host star also harbours small-scale magnetic fields often seen as strong concentrations of magnetic flux reaching kG field strengths. These features are situated in inter-granular lanes, where they show up bright as so-called magnetic bright points (MBPs). In this short paper we wish to analyse an homogenous, nearly 10-year-long synoptic Hinode image data set recorded from 2006 November up to 2016 February in the G-band to inspect the relationship between the number of MBPs at the solar disc centre and the relative sunspot number. Our findings suggest that the number of MBPs at the solar disc centre is indeed correlated to the relative sunspot number, but with the particular feature of showing two different temporal shifts between the decreasing phase of cycle 23 including the minimum and the increasing phase of cycle 24 including the maximum. While the former is shifted by about 22 months, the latter is only shifted by less than 12 months. Moreover, we introduce and discuss an analytical model to predict the number of MBPs at the solar disc centre purely depending on the evolution of the relative sunspot number as well as the temporal change of the relative sunspot number and two background parameters describing a possibly acting surface dynamo as well as the strength of the magnetic field diffusion. Finally, we are able to confirm the plausibility of the temporal shifts by a simplistic random walk model. The main conclusion to be drawn from this work is that the injection of magnetic flux, coming from active regions as represented by sunspots, happens on faster time scales than the removal of small-scale magnetic flux elements later on.
Multiethnic meta-analysis identifies new loci for pulmonary function
Authors: Wyss Annah B. , Sofer Tamar , Lee Mi Kyeong , Terzikhan Natalie , Nguyen Jennifer N. , Lahousse Lies , Latourelle Jeanne C. , Smith Albert Vernon , Bartz Traci M. , Feitosa Mary F. , Gao Wei , Ahluwalia Tarunveer S. , Tang Wenbo , Oldmeadow Christopher , Duan Qing , Jong Kim de , Wojczynski Mary K. , Wang Xin-Qun , Noordam Raymond , Hartwig Fernando Pires , Jackson Victoria E. , Wang Tianyuan , Obeidat Ma’en , Hobbs Brian D. , Huan Tianxiao , Kichaev Gleb , Jin Jianping , Graff Mariaelisa , Harris Tamara B. , Kalhan Ravi , Heckbert Susan R. , Paternoster Lavinia , Burkart Kristin M. , Liu Yongmei , Holliday Elizabeth G. , Wilson James G. , Vonk Judith M. , Sanders Jason , Barr R. Graham , Mutsert Renée de , Menezes Ana Maria Baptista , Adams Hieab H. H. , Berge Maarten van den , Joehanes Roby , Launer Lenore J. , Morrison Alanna C. , Sitlani Colleen M. , Celedón Juan C. , Kritchevsky Stephen B. , Scott Rodney J. , Christensen Kaare , Rotter Jerome I. , Bonten Tobias N. , César Wehrmeister Fernando , Bossé Yohan , Franceschini Nora , Brody Jennifer A. , Kaplan Robert C. , Lohman Kurt , McEvoy Mark , Province Michael A. , Rosendaal Frits R. , Taylor Kent D. , Nickle David C. , North Kari E. , Fornage Myriam , Psaty Bruce M. , Myers Richard H. , O’Connor George , Hansen Torben , Laurie Cathy C. , Cassano Pat , Sung Joohon , Kim Woo Jin , Attia John R. , Lange Leslie , Boezen H. Marike , Thyagarajan Bharat , Rich Stephen S. , Mook-Kanamori Dennis O. , Horta Bernardo Lessa , Uitterlinden André G , Sin Don D. , Im Hae Kyung , Cho Michael H. , Brusselle Guy G. , Gharib Sina A. , Dupuis Josée , Manichaikul Ani , London Stephanie J.
Published: October 2017

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N=60,552), African (N=8,429), Asian (N=9,959), and Hispanic/Latino (N=11,775) ethnicities. We identified over 50 novel loci at genome-wide significance in ancestry-specific and/or multiethnic meta-analyses. Recent fine mapping methods incorporating functional annotation, gene expression, and/or differences in linkage disequilibrium between ethnicities identified potential causal variants and genes at known and newly identified loci. Sixteen of the novel genes encode proteins with predicted or established drug targets, includingKCNK2andCDK12.
Defining the Layers of a Sensory Cilium with STORM and Cryo-Electron Nanoscopies
Authors: Robichaux Michael A. , Potter Valencia L. , Zhang Zhixian , He Feng , Schmid Michael F. , Wensel Theodore G.
Published: October 2017

Primary cilia are cylindrical organelles extending from the surface of most animal cells that have been implicated in a host of signaling and sensory functions. Genetic defects in their component molecules, known as “ciliopathies” give rise to devastating symptoms, ranging from defective development, to kidney disease, to progressive blindness. The detailed structures of these organelles and the true functions of proteins encoded by ciliopathy genes are poorly understood because of the small size of cilia and the limitations of conventional microscopic techniques. We describe the combination of cryo-electron tomography, enhanced by sub-tomogram averaging, with super-resolution stochastic reconstruction microscopy (STORM) to define substructures and subdomains within the light-sensing rod sensory cilium of the mammalian retina. Longitudinal and radial domains are demarcated by structural features such as the axoneme and its connections to the ciliary membrane, and are correlated with molecular markers of these compartments, including Ca2+-binding protein centrin-2 in the lumen of the axoneme, acetylated tubulin forming the axoneme, the glycocalyx extending outward from the surface of the plasma membrane, and molecular residents of the space between axoneme and ciliary membrane, including Arl13B, intraflagellar transport proteins, BBS5, and syntaxin-3. Within this framework we document that deficiencies in the ciliopathy proteins BBS2, BBS7 and BBS9 lead to inappropriate accumulation of proteins in rod outer segments while largely preserving their sub-domain localization within the connecting cilium region, but alter the distribution of syntaxin-3 clusters.
Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions
Authors: Press Maximilian O. , Wiser Andrew H. , Kronenberg Zev N. , Langford Kyle W. , Shakya Migun , Lo Chien-Chi , Mueller Kathryn A. , Sullivan Shawn T. , Chain Patrick S. G. , Liachko Ivan
Published: October 2017

The assembly of high-quality genomes from mixed microbial samples is a long-standing challenge in genomics and metagenomics. Here, we describe the application of ProxiMeta, a Hi-C-based metagenomic deconvolution method, to deconvolve a human fecal metagenome. This method uses the intra-cellular proximity signal captured by Hi-C as a direct indicator of which sequences originated in the same cell, enabling culture-free de novo deconvolution of mixed genomes without any reliance on a priori information. We show that ProxiMeta deconvolution provides results of markedly high accuracy and sensitivity, yielding 50 near-complete microbial genomes (many of which are novel) from a single fecal sample, out of 252 total genome clusters. ProxiMeta outperforms traditional contig binning at high-quality genome reconstruction. ProxiMeta shows particularly good performance in constructing high-quality genomes for diverse but poorly-characterized members of the human gut. We further use ProxiMeta to reconstruct genome plasmid content and sharing of plasmids among genomes—tasks that traditional binning methods usually fail to accomplish. Our findings suggest that Hi-C-based deconvolution can be useful to a variety of applications in genomics and metagenomics.
Matrix stiffness modulates infection of endothelial cells byListeria monocytogenesvia expression of cell surface vimentin
Authors: Bastounis Effie E. , Yeh Yi-Ting , Theriot Julie A.
Published: October 2017

Extracellular matrix (ECM) stiffness is one of many mechanical forces acting on mammalian adherent cells that influence cellular function. We have addressed the open question of how ECM stiffness might alter the susceptibility of host cells to infection by bacterial pathogens. We manufactured hydrogels of varying physiologically-relevant stiffness and seeded human microvascular endothelial cells (HMEC-1) on them. We then infected HMEC-1 with the bacterial pathogenListeria monocytogenes(Lm) and found that adhesion of Lm onto host cells increases monotonically with increasing matrix stiffness, an effect that requires the activity of focal adhesion kinase (FAK). We identified cell surface vimentin as a candidate surface receptor mediating stiffness-dependent adhesion of Lm to HMEC-1, and demonstrated that bacterial infection of these host cells is decreased when surface vimentin is perturbed. Our results provide the first evidence that ECM stiffness can mediate the susceptibility of host cells to bacterial infection.
Oscillatory Networks of High-Level Mental Alignment: A Perspective-Taking MEG Study
Authors: Seymour, R.A , Wang, H. , Rippon, G. , Kessler, K.
Published: October 2017

Mentally imagining another’s perspective is a high-level social process, reliant on manipulating internal representations of the self in an embodied manner. Recently Wang et al., (1) showed that theta-band (3-7Hz) brain oscillations within the right temporo-parietal junction (rTPJ) and brain regions coding for motor/body schema contribute to the process of perspective-taking. Using a task requiring participants to engage in embodied perspective-taking, we set out to unravel the extended functional brain network and its connections in detail. We found that increasing the angle of disparity between self and other perspective was accompanied by longer reaction times and increases in theta power within rTPJ, right lateral pre-frontal cortex (PFC) and right anterior cingulate cortex (ACC). Using nonparametric Granger-causality, we showed that during later stages of perspective-taking, the lateral PFC and ACC exert top-down influences over rTPJ, indicative of executive control processes required for managing conflicts between self and other perspectives. Finally, we quantified patterns of whole-brain phase coupling (imaginary coherence) in relation to rTPJ during high-level perspective taking. Results suggest that rTPJ increases its theta-band phase synchrony with brain regions involved in mentalizing and regions coding for motor/body schema; whilst decreasing its synchrony to visual regions. Implications for neurocognitive models are discussed, and it is proposed that rTPJ acts as a ‘hub’ to route bottom-up visual information to internal representations of the self during perspective-taking, co-ordinated by theta-band oscillations. The self is then projected onto the other’s perspective via embodied motor/body schema transformations, regulated by top-down cingulo-frontal activity.

Significance Statement

High-level social processing, such as the ability to imagine another’s visuospatial experience of the world (perspective taking), is a core part of what makes us human. Building on a substantial body of converging previous evidence, our study reveals how concerted activity across the cortex in low frequencies (theta: 3-7 Hz) implements this crucial human process. We found that oscillatory power and connectivity (imaginary coherence, nonparametric Granger causality) at theta frequency linked functional sub-networks of executive control, mentalizing, and sensorimotor/body schema via a main hub located in the right temporo-parietal junction (rTPJ). Our findings inform neurocognitive models of social cognition by describing the co-ordinated changes in brain network connectivity, mediated by theta oscillations, during perspective-taking.
Oncogenic RAS-MET signal interactions are modulated by P53 status in NF1-related MPNSTs
Authors: Pridgeon Matthew G. , Tovar Elizabeth A. , Essenburg Curt J. , Madaj Zachary , Boguslawski Elissa A. , Dischinger Patrick S. , Peacock Jacqueline D. , Maina Flavio , Dono Rosanna , Winn Mary E. , Graveel Carrie R. , Steensma Matthew R.
Published: October 2017

We previously reported that cooperative RAS-MET signaling drives disease progression in NF1-related MPNSTs, and that MET inhibition results in downstream inhibition of RAS/MAPK in the context ofMETamplification. This study revealed that response to MET inhibition appeared to be modulated byP53gene status. It is currently unclear how P53 function affects kinome signaling and response to kinase inhibition. Here we utilized genetically engineered mouse models with variable levels ofMetandHgfamplification and differentialp53status (NF1fl/KO;lox-stop-loxMETtg/+;Plp-creERTtg/+;NF1+/KO;p53R172H;Plp-creERTtg/+; andNF1+/KO;Plp-creERTtg/+t). These NF1-MPNST models were used to assess a novel MET/MEK (i.e. RAS-MET) inhibition strategy and investigate the adaptive kinome response to MET and MEK inhibition. We demonstrate that combination MET (capmatinib) and MEK (trametinib) inhibition fully suppresses MET, RAS/MAPK, and PI3K/AKT activation in P53 wild type tumors, whereas P53-mutant tumors demonstrated sustained CRAF, BRAF, and AKT activation in the presence of combined MET and MEK inhibition. Interestingly, trametinib therapy alone strongly activates MET signaling inMETandHGF-amplified tumors regardless of P53 status, an effect that was abrogated by the addition of capmatinib. We conclude that P53 alters RAS-MET signaling interactions that drive therapy resistance in NF1-related MPNSTs.
Phylostratigraphic analysis of tumor and developmental transcriptomes reveals relationship between oncogenesis, phylogenesis and ontogenesis
Authors: Zhou Joseph X. , Cisneros Luis , Knijnenburg Theo , Trachana Kalliopi , Davies Paul , Huang Sui
Published: October 2017

The question of the existence of cancer is inadequately answered by invoking somatic mutations or the disruptions of cellular and tissue control mechanisms. As such uniformly random events alone cannot account for the almost inevitable occurrence of an extremely complex process such as cancer. In the different epistemic realm, an ultimate explanation of cancer is that cancer is a reversion of a cell to an ancestral pre-Metazoan state, i.e. a cellular form of atavism. Several studies have suggested that genes involved in cancer have evolved at particular evolutionary time linked to the unicellular-multicellular transition. Here we used a refined phylostratigraphic analysis of evolutionary ages of the known genes/pathways associated with cancer and the genes differentially expressed between normal and cancer tissue as well as between embryonic and mature (differentiated) cells. We found that cancer-specific transcriptomes and cancer-related pathways were enriched for genes that evolved in the pre-Metazoan era and depleted of genes that evolved in the post-Metazoan era. By contrast an opposite relation was found for cell maturation: the age distribution frequency of the genes expressed in differentiated epithelial cells were enriched for post-Metazoan genes and depleted of pre-Metazoan ones. These findings support the atavism theory that cancer cells manifest the reactivation of an ancient ancestral state featuring unicellular modalities. Thus our bioinformatics analyses suggest that not only does oncogenesis recapitulate ontogenesis, and ontogenesis recapitulates phylogenesis, but also oncogenesis recapitulates phylogenesis. This more encompassing perspective may offer a natural organizing framework for genetic alterations in cancers and point to new treatment options that target the genes controlling the atavism transition.

One Sentence Summary

Tracing cancer gene evolutionary ages revealed that cancer reverts to a pre-existing early Metazoan state.
Gestational low-protein intake enhances the whole kidney miR-192 and miR-200 family expression and epithelial-to-mesenchymal transition in adult male offspring
Authors: Sene Letícia B , Gonçalves Rizzi Victor Hugo , Gontijo José AR , Boer Patricia A
Published: October 2017

Background

Studies have been showed that maternal protein-restricted adult offspring, present pronounced reduction of nephron number associated with decreased fractional urinary sodium excretion and arterial hypertension. Also, recent advances in our understanding of the molecular pathways that govern the association of gestational nutritional restriction, intrauterine growth retardation inflammation with impaired nephrogenesis, nephron underdosing and kidney fibrosis point to the epithelial to mesenchymal transition (EMT) as the common.

Method

In the current study, the protein and sodium urinary excretion rates were evaluated and immunohistochemistry and western blot techniques were used to characterize the whole kidney structure changes in 16-wk old male LP offspring compared with age-matched controls. We also verify the expression of miRNAs, mRNAs and proteins markers of fibrosis and epithelial-to-mesenchymal transition in entire kidney prepared from LP offspring.

Results

In the current study, we may assume that arterial hypertension and long-term hyperfiltration process manifests, itself by proteinuria was accompanied by increased whole kidney mRNA expression of TGF-β1, ZEB1, type I collagen and, fibronectin in parallel to decreased expression of E-cadherin in 16-wk old LP offspring. Surprisingly, the renal tissue miR-129, miR-141, miR-200c and miR-429 were significantly upregulated in LP offspring compared to age-matched NP rats.

Conclusion

Considering that the overload in remaining nephrons, we may state that hypertension and proteinuria development following maternal protein restriction, may be a preponderant factor for the development of EMT and fibrous process and altered kidney ultrastructure in rat offspring. However, further studies are required to assess the contribution of miRNAs on renal injury progression in gestational protein-restricted model of fetal programming.
Computational model of brainstem circuit for state-dependent control of hypoglossal motoneurons
Authors: Naji Mohsen , Komarov Maxim , Krishnan Giri P. , Malhotra Atul , Powell Frank , Rukhadze Irma , Fenik Victor B. , Bazhenov Maxim
Published: October 2017

In patients with obstructive sleep apnea (OSA) the pharyngeal muscles become relaxed during sleep, which leads to a partial or complete closure of upper airway. Empirical studies suggest that withdrawal of noradrenergic and serotonergic drives importantly contribute to depression of hypoglossal motoneurons during rapid eye-movement (REM) sleep and, therefore, may contribute to OSA pathophysiology; however, specific cellular and synaptic mechanisms remain unknown. It was recently suggested that, in order to explain experimental observations, the neuronal network for monoaminergic control of excitability of hypoglossal motoneurons has to include excitatory and inhibitory perihypoglossal interneurons that would mediate noradrenergic and serotonergic drives to the motoneurons. In this study, we applied a biophysical network model to validate the rationality of the proposed circuit and to investigate the dynamics of its neuronal populations during REM sleep-induced withdrawal of noradrenergic and serotonergic drives. The state-dependent activity of the model hypoglossal motoneurons during simulated REM sleep with or without a virtual application of noradrenergic and serotonergic drugs was in qualitative agreement with in vivo data. The study predicts the dynamics of the perihypoglossal interneurons during these conditions and corroborates the hypothesis that the excitatory interneurons may integrate both noradrenergic and serotonergic drives. The latter drive has to be mediated by the inhibitory interneurons. The study suggests that perihypoglossal interneurons may serve as novel potential targets for pharmacological treatment of OSA.
Enigmatic Diphyllatea eukaryotes: Culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution
Authors: Orr Russell J.S. , Sen Zhao , Dag Klaveness , Akinori Yabuki , Keiji Ikeda , Watanabe Makoto M. , Kamran Shalchian-Tabrizi
Published: October 2017

Diphyllatea is an ancient and enigmatic lineage of unicellular eukaryotes that possesses morphological features common to other deeply diverging eukaryotes, such as Amoebozoa and Excavata. In reconstruction of the evolutionary processes underlying diversification and morphological innovation among eukaryotes, Diphyllatea plays a key role together with other orphan lineages. Despite being of evolutionary significance, only three species of Diphyllatea have descripted morphology, with molecular data available from fewer. The lack of data means that the actual diversity of this key lineage of eukaryotes remains unresolved. We here present a first attempt to understand the species diversity and higher order structure of the Diphyllatea phylogeny. We have cultured several new strains, described these morphologically, and amplified their rRNA. We have sampled DNA from multiple globally distributed sites, using these as templates in a Diphyllatea-specific PCR. In contrast to recent diversity studies, which use short variable gene regions, we amplify nearly the whole 18S rRNA gene, and sequence using PacBio RS II technology, to provide enough information to resolve historically ancient speciation events. Phylogenetic inference of Diphyllatea rRNA reveals three deeply branching and distinct clades of Diphyllatea, here named Diphy I – III. Diphy I and II include the generaDiphylleiaandCollodictyon. Notably, Diphy III is here shown as novel phylogenetic clade with all strains investigated having a congruent morphology toCollodictyon triciliatum(Diphy II). Altogether, Diphyllatea seems to constitute two morphotypes, a biflagellate (i.e. Diphy I) and a quadraflagellate (i.e. Diphy II and III) form, congruent with earlier descriptions ofDiphylleia and Collodictyon.Further, our targeted environmental sequencing approach, which includes specific PCR primers, reveals a wider global distribution of Diphyllatea than earlier known. Altogether, the described protocol shows the usefulness of combining long amplicon high-throughput sequencing and lineage-specific PCR approach in surveys of enigmatic eukaryote lineages.
Rare earth-based quaternary Heusler compoundsMCoVZ(M= Lu, Y;Z= Si, Ge) with tunable band characteristics for potential spintronic applications
Authors: Wang Xiaotian , Cheng Zhenxiang , Liu Guodong , Dai Xuefang , Khenata Rabah , Wang Liying , Bouhemadou Abdelmadjid
Published: October 2017

Magnetic Heusler compounds (MHCs) have recently attracted great attention since these types of material provide novel functionalities in spintronic and magneto-electronic devices. Among the MHCs, some compounds have been predicted to be spin-filter semiconductors [also called magnetic semiconductors (MSs)], spin-gapless semiconductors (SGSs) or half-metals (HMs). In this work, by means of first-principles calculations, it is demonstrated that rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formulaMCoVZ(M= Lu, Y;Z= Si, Ge) are new spin-filter semiconductors with total magnetic moments of 3 µB. Furthermore, under uniform strain, there are physical transitions from spin-filter semiconductor (MS) → SGS → HM for EQH compounds with the formula LuCoVZ, and from HM → SGS → MS → SGS → HM for EQH compounds with the formula YCoVZ. Remarkably, for YCoVZEQH compounds there are not only diverse physical transitions, but also different types of spin-gapless feature that can be observed with changing lattice constants. The structural stability of these four EQH compounds is also examined from the points of view of formation energy, cohesive energy and mechanical behaviour. This work is likely to inspire consideration of rare earth-based EQH compounds for application in future spintronic and magneto-electronic devices.
The science is in the data
Authors: Helliwell John R. , McMahon Brian , Guss J. Mitchell , Kroon-Batenburg Loes M. J.
Published: October 2017

Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a `digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided.