bluuebunny/crossref_metadata_2025_split huggingface dataset:
International Survey of Critically Ill Children With Acute Neurologic Insults: The Prevalence of Acute Critical Neurological Disease in Children: A Global Epidemiological Assessment Study*
Authors: Fink Ericka L. , Kochanek Patrick M. , Tasker Robert C. , Beca John , Bell Michael J. , Clark Robert S. B. , Hutchison Jamie , Vavilala Monica S. , Fabio Anthony , Angus Derek C. , Watson R. Scott 
Published: February 2017

Objective:
The international scope of critical neurologic insults in children is unknown. Our objective was to assess the prevalence and outcomes of children admitted to PICUs with acute neurologic insults.

Design:
Prospective study.

Setting:
Multicenter (n = 107 PICUs) and multinational (23 countries, 79% in North America and Europe).

Patients:
Children 7 days to 17 years old admitted to the ICU with new traumatic brain injury, stroke, cardiac arrest, CNS infection or inflammation, status epilepticus, spinal cord injury, hydrocephalus, or brain mass.

Interventions:
None.

Measurements and Main Results:
We evaluated the prevalence and outcomes of children with predetermined acute neurologic insults. Child and center characteristics were recorded. Unfavorable outcome was defined as change in pre-post insult Pediatric Cerebral Performance Category score greater than or equal to 2 or death at hospital discharge or 3 months, whichever came first. Screening data yielded overall prevalence of 16.2%. Of 924 children with acute neurologic insults, cardiac arrest (23%) and traumatic brain injury (19%) were the most common. All-cause mortality at hospital discharge was 12%. Cardiac arrest subjects had highest mortality (24%), and traumatic brain injury subjects had the most unfavorable outcomes (49%). The most common neurologic insult was infection/inflammation in South America, Asia, and the single African site but cardiac arrest in the remaining regions.

Conclusions:
Neurologic insults are a significant pediatric international health issue. They are frequent and contribute substantial morbidity and mortality. These data suggest a need for an increased focus on acute critical neurologic diseases in infants and children including additional research, enhanced availability of clinical resources, and the development of new therapies.
Systematic Review of Interventions to Reduce Psychiatric Morbidity in Parents and Children After PICU Admissions*
Authors: Baker Samantha C. , Gledhill Julia A. 
Published: February 2017

Objective:
To describe and evaluate interventions aimed at reducing psychiatric morbidity in parents and children discharged from PICU.

Data Sources:
A systematic review of the literature was undertaken, searching EMBASE, PSYCHinfo, MEDLINE, and CINAHL. Experts in the field were contacted to identify unpublished studies.

Study Selection:
Exclusion criteria: Studies with participants above age 18 or drawn from a neonatal ICU, studies not in English, and those not measuring psychopathology.

Data Extraction:
Seven hundred fifty-three articles initially identified were hand searched which identified three studies, with a further three studies found by contacting experts in the field. Of these, three were randomized controlled trials and three feasibility studies.

Data Synthesis:
The interventions primarily targeted parents (particularly mothers), with the aim of reducing psychopathology especially posttraumatic stress disorder. Findings from these few studies demonstrated that interventions can lead to a reduction in parent and child psychopathology. Key ingredients of these interventions included psychoeducation, parent support after discharge, offering intervention to those families at high risk of developing psychopathology as identified by screening at the point of discharge, follow-up of all families with the aim of case finding, and specific interventions to target posttraumatic stress disorder symptoms.

Conclusions:
Intervention studies are few but do lead to reductions in parent and child psychopathology. There is sufficient information to suggest some of these interventions could be supported and further evaluated.
Passage of Gallstones Into Common Bile Duct During Laparoscopic Cholecystectomy: Is It the Surgeon’s Responsibility?
Authors: Bani Hani Mohammed , Al Manasra Abdel Rahman , Qandeel Haitham 
Published: February 2017

Purpose:
Gallstones patients without preoperative history of jaundice, deranged liver function tests, or dilated bile ducts (BD) are unlikely to have BD stones. However, some of these patients in our series underwent endoscopic stone(s) removal after laparoscopic cholecystectomy (LC). We aim to find the incidence, possible intraoperative risk factors, and if the Surgeon can be blamed for this event.

Materials and Methods:
We studied LC cases over 12-year period at our university hospital and identified patients who did not have preoperative risk factors for BD stones but developed postoperative jaundice and/or persistent abdominal pain.

Results:
Only 16 (0.7%) of 2390 LC met the inclusion criteria. In 5/16 patients, cystic duct (CD) stones were felt Intraoperatively and likely passed into BD during surgery. After surgery, 14/16 patients underwent endoscopic stone(s) removal.

Conclusions:
If CD stone(s) are encountered during LC, we suggest that careful attention should be paid to make sure that patient does not develop complications from possible BD stone(s). Technical precautions during LC (ie, early CD clipping, avoiding excessive manipulation, and crushing the stones) are recommended.
Pattern separation of spiketrains in hippocampal neurons
Authors: Madar Antoine D. , Ewell Laura A. , Jones Mathew V. 
Published: February 2017

AbstractPattern separation is a process that minimizes overlap between patterns of neuronal activity representing similar experiences. Theoretical work suggests that the dentate gyrus (DG) performs this role for memory processing but a direct demonstration is lacking. One limitation is the difficulty to measure DG inputs and outputs simultaneously. To rigorously assess pattern separation by DG circuitry, we used mouse brain slices to stimulate DG afferents and simultaneously record DG granule cells (GCs) and interneurons. Output spiketrains of GCs are more dissimilar than their input spiketrains, demonstrating for the first time temporal pattern separation at the level of single neurons in the DG. Pattern separation is larger in GCs than in fast-spiking interneurons and hilar mossy cells, and is amplified in CA3 pyramidal cells. Analysis of the neural noise and computational modelling suggest that this form of pattern separation is not explained by simple randomness and arises from specific presynaptic dynamics. Overall, by reframing the concept of pattern separation in dynamic terms and by connecting it to the physiology of different types of neurons, our study offers a new window of understanding in how hippocampal networks might support episodic memory.
Rapid evolution slows extinctions in food webs
Authors: Zee Peter C. , terHorst Casey P. , Schreiber Sebastian J. 
Published: February 2017

AbstractHistorically, evolutionary changes have been thought to act on much longer time scales than ecological dynamics. However, a recent body of research has demonstrated that evolution that is rapid enough to dramatically affect ecological dynamics can lead to feedbacks between ecological and evolutionary processes. Thus, to understand the stability of ecological communities, we must also consider evolutionary change in the component species. Here, we use individual-based simulations of a quantitative genetic eco-evolutionary model to describe how trait evolution influences the stability of ecological communities. On short time scales, faster evolutionary rates decreased the probability of species extinctions as populations at low densities were rescued via trait evolution. However, on longer time scales, evolutionary had little effect on the number of extinctions. The extent of short-term evolutionary rescue depended on the source of trait variation; populations with variation generated through mutation experienced more rescue events and were less prone to extinction, relative to populations with only standing trait variation. Trait evolution leading to more rescued populations increased the stability of the community on timescales relevant to conservation. Our work highlights the importance of intraspecific trait variation and the evolutionary mechanisms maintaining this variation for community ecology, as well as management of declining populations in a community context.
The effect of smoking on the brain revealed by using electronic cigarettes with concurrent fMRI
Authors: Wall Matthew B , Mentink Alexander , Lyons Georgina , Kowalczyk Oliwia S , Demetriou Lysia , Newbould Rexford D 
Published: February 2017

AbstractCigarette addiction is driven partly by the physiological effects of nicotine, but also by the distinctive sensory and behavioural aspects of smoking, and understanding the neural effects of such processes is vital. There are many practical difficulties associated with subjects smoking in the modern neuroscientific laboratory environment, however electronic cigarettes obviate many of these issues, and provide a close simulation of smoking tobacco cigarettes. We have examined the neural effects of ‘smoking’ electronic cigarettes with concurrent functional Magnetic Resonance Imaging (fMRI). The results demonstrate the feasibility of using these devices in the MRI environment, and show brain activation in a network of cortical (motor cortex, insula, cingulate, amygdala) and sub-cortical (putamen, thalamus, globus pallidus, cerebellum) regions. Concomitant relative deactivations were seen in the ventral striatum and orbitofrontal cortex. These results reveal the brain processes involved in (simulated) smoking for the first time, and validate a novel approach to the study of smoking, and addiction more generally.
Recovery of genomes from metagenomes via a dereplication, aggregation, and scoring strategy
Authors: Sieber Christian M. K. , Probst Alexander J. , Sharrar Allison , Thomas Brian C. , Hess Matthias , Tringe Susannah G. , Banfield Jillian F. 
Published: February 2017

AbstractMicrobial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Further, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including novel lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems.
SIRT3-dependent mitochondrial oxidative stress in sodium fluoride-induced hepatotoxicity and salvage by melatonin
Authors: Song Chao , Zhao Jiamin , Zhang Jingcheng , Mao Tingchao , Fu Beibei , Wu Haibo , Zhang Yong 
Published: February 2017

AbstractOxidative stress induced by fluoride (F) is associated with fluorosis formation, but the underlying molecular mechanism remains unclear. In this study, Melatonin pretreatment suppressed F-induced hepatocyte injury in HepG2 cells. Melatonin increases the activity of superoxide dismutase (SOD2) by enhancing sirtuin 3 (SIRT3)-mediated deacetylation and promotes SOD2 gene expression via SIRT3-regulated DNA-binding activity of forkhead box O3 (FoxO3a), indicating that melatonin markedly enhanced mROS scavenging in F-exposed HepG2 cells. Notably, melatonin activated the peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α). PGC-1α interacted with the estrogen-related receptor alpha (ERRα) bound to the SIRT3 promoter, where it functions as a transcription factor to regulate SIRT3 expression. Furthermore, daily injection of melatonin for 30 days inhibited F-induced oxidative stress in mice liver, leading to improvement of liver function. Mechanistic study revealed that the protective effects of melatonin were associated with down-regulation of JNK1/2 phosphorylation in vitro and in vivo. Collectively, our data suggest a novel role of melatonin in preventing F-induced oxidative stress through activation of the SIRT3 pathway.
HTSvis: A web app for exploratory data analysis and visualization of arrayed high-throughput screens
Authors: Scheeder Christian , Heigwer Florian , Boutors Michael 
Published: February 2017

AbstractThe analysis and visualization of arrayed high-throughput screens (HTS), such as cell-based RNAi or small-molecule HTS experiments, requires specialized computational methods. Software packages such as the R/Bioconductor package cellHTS have been developed to support the analysis and are broadly used by the high-throughput screening community. However, exploratory data analysis and integration of screening results remains challenging due to the size of produced data tables in multi-channel experiments and the lack of user-friendly tools to integrate and visualize screening results. Here we present HTSvis, an R/Shiny open-source web application for interactive visualization and exploratory analysis of arrayed high-throughput data. Using a light-weight infrastructure suitable for desktop computers, HTSvis can be used to visualize raw data, perform quality control and interactively visualize screening results from single- to multi-channel measurements, such as image-based, screens. Input data can either be a result file obtained upon analysis with cellHTS or a generic table with raw or analyzed data from, e.g. a high-content microscopy screen. HTSvis can be downloaded fromhttp://github.com/boutroslab/HTSvis.
Variability in fitness effects and the limitations of fitness optimization
Authors: Graves Christopher J , Weinreich Daniel M 
Published: February 2017

AbstractEvolutionary biologists commonly assess the evolutionary advantage of an allele based on its effects on the lifetime survival and reproduction of individuals. However, alleles affecting traits like sex, evolvability, and cooperation can cause fitness effects that depend heavily on differences in the environmental, genetic, and social context of individuals carrying the allele. This variability makes it difficult to summarize the evolutionary fate of an allele based solely on its effects on any one individual. In this review we show how attempts to average over variability in the fitness effects of an allele can sometimes cause misleading results. We then describe a number of intriguing new evolutionary phenomena that have emerged in studies that explicitly model the fate of alleles that influence long-term lineage dynamics. We conclude with prospects for generalizations of population genetics theory and discuss how this theory might be applied to the evolution of infectious diseases.
PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data
Authors: Garneau Julian , Depardieu Florence , Fortier Louis-Charles , Bikard David , Monot Marc 
Published: February 2017

ABSTRACTBacteriophages are the most abundant viruses on earth and display an impressive genetic as well as morphologic diversity. Among those, the most common order of phages is the Caudovirales, whose viral particles packages linear double stranded DNA (dsDNA). In this study we investigated how the information gathered by high throughput sequencing technologies can be used to determine the DNA termini and packaging mechanisms of dsDNA phages. The wet-lab procedures traditionally used for this purpose rely on the identification and cloning of restriction fragment which can be delicate and cumbersome. Here, we developed a theoretical and statistical framework to analyze DNA termini and phage packaging mechanisms using next-generation sequencing data. Our methods, implemented in the PhageTerm software, work with sequencing reads in fastq format and the corresponding assembled phage genome.PhageTerm was validated on a set of phages with well-established packaging mechanisms representative of the termini diversity: 5’cos (lambda), 3’cos (HK97), pac (P1), headful without a pac site (T4), DTR (T7) and host fragment (Mu). In addition, we determined the termini of 9Clostridium difficilephages and 6 phages whose sequences where retrieved from the sequence read archive (SRA).A direct graphical interface is available as a Galaxy wrapper version athttps://galaxy.pasteur.frand a standalone version is accessible athttps://sourceforge.net/projects/phageterm/.
Health quality of seed potato and yield losses in Ecuador
Authors: Navarrete Israel , Panchi Nancy , Kromann Peter , Forbes Gregory A. , Andrade-Piedra Jorge L. 
Published: February 2017

AbstractLow potato productivity in Ecuador is partly attributed to the use of low quality seed tubers. However, seed health quality in Ecuador, and its interaction with altitude and yield has been poorly investigated. We surveyed 11 farmers’ fields in Ecuador in 2010 to determine incidence and severity of pathogens and pests affecting foliage and seed tubers, and to determine the influence of altitude and seed sources over seed health quality (pathogen and pest diversity in/on the seed tuber). Additionally, a field experiment was planted in CIP-Quito using assessed seed tubers collected from surveyed farmers’ fields, during 2010 and 2011, to determine yield responses to seed health quality. Results show that foliage was mainly affected by late blight and flea beetle damages while seed tubers were predominantly affected by black scurf, andean weevil damages, potato virus S and potato virus X. We found that seed health quality was similar among farmers’ seed sources, and detected that increase in altitude decreased seed-borne virus diversity. Only seed-borne pathogens and presence of mechanical damages were found to explain yield variation. Seed-borne pathogens affecting yield variation were black scurf on seed tubers, potato virus S, and potato yellow vein virus. However, these factors changed when regressions were performed per seed source or variety. The yield responses to seed health quality of each variety should be considered to fine-tune integrated pest management strategies.
Frequency-specific directed interactions in the human brain network for language
Authors: Schoffelen J. M. , Hultén A. , Lam N. , Marquand A. , Uddén J. , Hagoort P. 
Published: February 2017

AbstractThe brain’s remarkable capacity for language requires bidirectional interactions between functionally specialized brain regions. We used magnetoencephalography to investigate interregional interactions in the brain network for language, while 102 participants were reading sentences. Using Granger causality analysis, we identified inferior frontal cortex and anterior temporal regions to receive widespread input, and middle temporal regions to send widespread output. This fits well with the notion that these regions play a central role in language processing. Characterization of the functional topology of this network, using data-driven matrix factorization, which allowed for partitioning into a set of subnetworks, revealed directed connections at distinct frequencies of interaction. Connections originating from temporal regions peaked at alpha frequency, whereas connections originating from frontal and parietal regions peaked at beta frequency. These findings indicate that processing different types of linguistic information may depend on the contributions of distinct brain rhythms.One Sentence SummaryCommunication between language relevant areas in the brain is supported by rhythmic synchronization, where different rhythms reflect the direction of information flow.
China's Emergent City‐Region Governance: A New Form of State Spatial Selectivity through State‐orchestrated Rescaling
Authors: Wu Fulong 
Published: February 2017

AbstractThis article examines the emergence of city‐region governance as a specific state spatial selectivity in post‐reform China. The process has been driven by the state in response to the crisis of economic decentralization, and to vicious inter‐city competition and uncoordinated development. As part of the recentralization of state power, the development of urban clusters (chengshiqun) as interconnected city‐regions is now a salient feature of ‘new urbanization' policy. I argue in this article that the Chinese city‐region corresponds to specific logics of scale production. Economic globalization has led to the development of local economies and further created the need to foster ‘regional competitiveness'. To cope with regulatory deficit at the regional level, three mechanisms have been orchestrated by the state: administrative annexation, spatial plan preparation and regional institution building, which reflect recent upscaling in post‐reform governance.
Justice As Subject and Object of Planning
Authors: Lake Robert W. 
Published: February 2017

AbstractConsiderations of justice have moved to a central place in planning theory following Susan Fainstein's (2010) eloquent plea to elevate justice to the principal criterion for the evaluation of planning practice. Justice based on this understanding is the object of planning—the normative end that planning practice should strive to achieve. In this essay I explore the implications for planning theory and practice of making justice the subject rather than the object of planning. This formulation places justice at the center of rather than regarding it as the outcome of practice: what is of concern here is planning as the practice of justice rather than the justice of planning practice. The question for planning in this mode shifts from ‘Is this a just outcome?' to ‘What is justice in this situation?'. Based on John Dewey's pragmatist philosophy, this question transcends the dualisms between subject and object, and process and outcome, by understanding outcomes as already formulated (what Dewey called ends‐in‐view) in the process of their production. A planning process that takes justice as its subject is anti‐foundational and contextual rather than universal, anticipatory rather than retrospective, generative of solutions rather than evaluative of outcomes, culturally encompassing rather than project‐delimited, and inclusively democratic rather than expert‐driven. Examples from a variety of sources illustrate the practice of justice as the subject of planning.