bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lennox–Gastaut Syndrome: A State of the Art Review
Authors: Mastrangelo Mario 
Published: March 2017

AbstractLennox–Gastaut syndrome (LGS) is a severe age-dependent epileptic encephalopathy usually with onset between 1 and 8 years of age. Functional neuroimaging studies recently introduced the concept of Lennox–Gastaut as “secondary network epilepsy” resulting from dysfunctions of a complex system involving both cortical and subcortical structures (default-mode network, corticoreticular connections, and thalamus). These dysfunctions are produced by different disorders including hypoxic–ischemic encephalopathies, meningoencephalitis, cortical malformations, neurocutaneous disorders, or tumors. The list of etiologies was expanded to pathogenic copy number variants at whole-genome array comparative genomic hybridization associated with late-onset cases or pathogenic mutations involving genes, such as GABRB3, ALG13, SCN8A, STXBP1, DNM1, FOXG1, or CHD2. Various clinical trials demonstrated the usefulness of different drugs (including rufinamide, clobazam, lamotrigine, topiramate, or felbamate), ketogenic diet, resective surgery, corpus callosotomy, and vagus nerve stimulation in the treatment of epileptic manifestations. The outcome of LGS often remains disappointing regarding seizure control or cognitive functioning. The realization of animal models, which are still lacking, and the full comprehension of molecular mechanisms involved in epileptogenesis and cognitive impairment would give a relevant support to further improvements in therapeutic strategies for LGS patients.
Politics, development and the instrumentalisation of (de)centralisation in Sierra Leone
Authors: Conteh Felix Marco 
Published: March 2017

ABSTRACT
The politics of decentralisation reforms in Sierra Leone are unpredictable and instructive. This article, based on fieldwork, analyses party politics within the context of decentralisation, arguing that the imperatives of post-conflict decentralisation are not necessarily embedded in technical considerations, but in processes of political compromise and accommodation. Decentralisation has helped facilitate the re-emergence of the old political order, in that the country’s main political parties have secured a consensus through which they have reconfigured the post-conflict state on their own terms. This study reveals that the narrative of a ‘divide’ within the political class is exaggerated, and illustrates the homogeneity and interconnectedness of its interests. The extent to which the ‘peace’ will be sustained by this compromise is uncertain, but this framing is useful in understanding the political economy in which ‘fragility’ and ‘peace’ co-exist, illuminating the political class’s agency, as well as its ability to ‘unite’ against ‘others’.
Inland Fisheries Habitat Management: Lessons Learned from Wildlife Ecology and a Proposal for Change
Authors: Sass Greg G. , Rypel Andrew L. , Stafford Joshua D. 
Published: March 2017

Abstract
The habitat concept in inland fisheries has been less studied than wildlife ecology. Since 1950, the cumulative number of publications about “freshwater or inland habitat and fisheries management” has been 60%–95% less than those considering “habitat and wildlife management.” The number of publications about “marine, river, and stream habitat and fisheries management” has also generally exceeded those for “lake habitat and fisheries management.” We provide a perspective comparing inland fish and wildlife habitat management systems and highlight lessons from wildlife ecology that could benefit inland fisheries. We reason that wildlife habitat management has become widespread and accepted because humans share habitats with wildlife and positive/negative responses to habitat restorations/loss are directly observable. We recommend that inland fisheries habitat studies and restorations include opportunities for humans to directly observe the ecological benefits of such practices. To support aquatic habitat management efforts, we suggest that dedicated funding solutions be considered to mitigate aquatic habitat loss. In theory, such a system would provide benefits to inland fish populations that parallel those provided to wildlife through state and federal stamps. Although aquatic habitat conservation and restoration may not solve management issues as rapidly, it will promote long-term sustainability and resiliency of diverse inland fish populations.
Estimating Fish Mortality Rates Using Telemetry and Multistate Models
Authors: Hightower Joseph E. , Harris Julianne E. 
Published: March 2017

Abstract
We simulated and evaluated multistate capture–recapture models to estimate mortality rates using telemetry data. Four field designs were considered: (A) fixed receivers to estimate total instantaneous mortality (Z), (B) manual searches to estimate instantaneous fishing (F) and natural (M) mortality, (C) fixed receivers combined with external high-reward tags to estimate F and M, and (D) manual searches combined with external high-reward tags to estimate M and fishing mortality rates associated with harvest (Fh) and catch-and-release death (Fcr) as well as the probability of death due to catch and release (α). Estimates generally appeared to be unbiased for a simulated study with five periods and releases of telemetered fish at the start of periods 1–4. Compared to estimating Z, larger sample sizes are needed to achieve reliable estimates of component rates (F and M). Estimates of component rates were more precise when that source of mortality was directly observed (M in design B, F in design C). The field design using fixed receivers and high-reward tags should be especially useful in practice, because manual searches are not required to estimate F and M. Multistate models are useful for clarifying the connection between field observations and ecological processes. Reliable estimates of mortality rates, coupled with information on behavior, habitat use, and movement, make telemetry a highly valuable tool for improving fisheries management and stock assessment.
Causes and Consequences of Straying into Small Populations of Pacific Salmon
Authors: Bett Nolan N. , Hinch Scott G. , Burnett Nicholas J. , Donaldson Michael R. , Naman Sean M. 
Published: March 2017

Abstract
Most Pacific salmon Oncorhynchus spp. migrate to their natal sites to spawn. Some, however, stray into nonnatal habitats and interact (e.g., reproduce) with individuals from other populations. Pacific salmon straying has been heavily studied for several decades, particularly from the perspective of the populations that donate the stray migrants. Conservation consequences are experienced primarily by the populations that receive strays, though, and there is recent evidence of significant levels of genetic introgression in small recipient populations, which could contribute to the loss of local adaptations. Straying may also provide the benefit of a demographic rescue effect that could save declining recipient populations from extirpation. We highlight the influence of population abundances on the magnitude of straying into recipient populations and demonstrate this using evidence we collected from a small population of Sockeye Salmon O. nerka in British Columbia, Canada. We also review potential factors that might promote higher donor stray rates and therefore recipient straying. Evidence of factors that affect straying is limited and we identify several knowledge gaps, as well as anthropogenic activities that could promote straying. We encourage further discussion and research on the potential effects of recipient straying and the factors that affect straying rates.
Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data
Authors: Shi Qianqian , Zhang Chuanchao , Peng Minrui , Yu Xiangtian , Zeng Tao , Liu Juan , Chen Luonan 
Published: March 2017

Abstract

Motivation
Integrating different omics profiles is a challenging task, which provides a comprehensive way to understand complex diseases in a multi-view manner. One key for such an integration is to extract intrinsic patterns in concordance with data structures, so as to discover consistent information across various data types even with noise pollution. Thus, we proposed a novel framework called ‘pattern fusion analysis’ (PFA), which performs automated information alignment and bias correction, to fuse local sample-patterns (e.g. from each data type) into a global sample-pattern corresponding to phenotypes (e.g. across most data types). In particular, PFA can identify significant sample-patterns from different omics profiles by optimally adjusting the effects of each data type to the patterns, thereby alleviating the problems to process different platforms and different reliability levels of heterogeneous data.

Results
To validate the effectiveness of our method, we first tested PFA on various synthetic datasets, and found that PFA can not only capture the intrinsic sample clustering structures from the multi-omics data in contrast to the state-of-the-art methods, such as iClusterPlus, SNF and moCluster, but also provide an automatic weight-scheme to measure the corresponding contributions by data types or even samples. In addition, the computational results show that PFA can reveal shared and complementary sample-patterns across data types with distinct signal-to-noise ratios in Cancer Cell Line Encyclopedia (CCLE) datasets, and outperforms over other works at identifying clinically distinct cancer subtypes in The Cancer Genome Atlas (TCGA) datasets.

Availability and implementation
PFA has been implemented as a Matlab package, which is available at http://www.sysbio.ac.cn/cb/chenlab/images/PFApackage_0.1.rar.

Supplementary information
Supplementary data are available at Bioinformatics online.
Relativistic radiative transfer and relativistic spherical flows: Relation between the mass-loss rate and terminal speed
Authors: Fukue Jun 
Published: March 2017

Abstract
Radiatively driven relativistic spherical flows are numerically investigated under the fully special relativistic treatment and relativistic radiative transfer. We first solve the relativistic radiative transfer equation for spherically symmetric outflows iteratively, using a trial velocity distribution, and obtain specific intensities as well as moment quantities, and the Eddington factor. Using the obtained comoving flux, we next solve the relativistic equation of motion, and obtain the refined velocity distribution, the mass-loss rate being determined as an eigenvalue. Until both the intensity and velocity distributions converge, we repeat these double iteration processes. We found that the flows are quickly accelerated near to the central lumious core to reach the terminal speed. The Eddington factor has a complicated behavior, depending on the optical depth and flow speed. We further found that a relation between the flow terminal speed βout normalized by the speed of light and the mass-loss rate $\dot{m}$ normalized by the critical one is roughly approximated as $\dot{m} \propto \tau _* \beta _{\rm out}^{-5/2}$, where τ* is a typical optical depth of the flow, whereas we can analytically derive the relation of $\dot{m} \propto \tau _* \beta _{\rm out}^{-2}$ using a back-of-the-envelope calculation in the nonrelativistic case.
Accurate cytogenetic biodosimetry through automation of dicentric chromosome curation and metaphase cell selection
Authors: Liu Jin , Li Yanxin , Wilkins Ruth , Flegal Farrah , Knoll Joan H. , Rogan Peter K. 
Published: March 2017

ABSTRACTSoftware to automate digital pathology relies on image quality and the rates of false positive and negative objects in these images. Cytogenetic biodosimetry detects dicentric chromosomes (DCs) that arise from exposure to ionizing radiation, and determines radiation dose received from the frequency of DCs. We present image segmentation methods to rank high quality cytogenetic images and eliminate suboptimal metaphase cell data based on novel quality measures. Improvements in DC recognition increase the accuracy of dose estimates, by reducing false positive (FP) DC detection. A set of chromosome morphology segmentation methods selectively filtered out false DCs, arising primarily from extended prometaphase chromosomes, sister chromatid separation and chromosome fragmentation. This reduced FPs by 55% and was highly specific to the abnormal structures (≥97.7%). Additional procedures were then developed to fully automate image review, resulting in 6 image-level filters that, when combined, selectively remove images with consistently unparsable or incorrectly segmented chromosome morphologies. Overall, these filters can eliminate half of the FPs detected by manual image review. Optimal image selection and FP DCs are minimized by combining multiple feature based segmentation filters and a novel image sorting procedure based on the known distribution of chromosome lengths. Applying the same segmentation filtering procedures to both calibration and test sample image data reduced the average dose estimation error from 0.4Gy to <0.2Gy, obviating the need to first manually review these images. This reliable and scalable solution enables batch processing multiple samples of unknown dose, and meets current requirements for triage radiation biodosimetry of high quality metaphase cell preparations.
Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells
Authors: Carter Stephen D. , Mageswaran Shrawan K. , Farino Zachary J. , Mamede João I. , Oikonomou Catherine M. , Hope Thomas J. , Freyberg Zachary , Jensen Grant J. 
Published: March 2017

AbstractCryogenic correlated light and electron microscopy (cryo-CLEM) is a valuable tool for studying biological processesin situ. In cryo-CLEM, a target protein of interest is tagged with a fluorophore and the location of the corresponding fluorescent signal is used to identify the structure in low-contrast but feature-rich cryo-EM images. To date, cryo-CLEM studies of mammalian cells have relied on very bright organic dyes or fluorescent protein tags concentrated in virus particles. Here we describe a method to expand the application of cryo-CLEM to cells harboring genetically-encoded fluorescent proteins. We discovered that a variety of mammalian cells exhibit strong punctate autofluorescence when imaged under cryogenic conditions (80K). Compared to fluorescent protein tags, these sources of autofluorescence exhibit a broader spectrum of fluorescence, which we exploited to develop a simple, robust approach to discriminate between the two. We validate this method in INS-1 E cells using a mitochondrial marker, and apply it to study the ultrastructural variability of secretory granules in a near-native state within intact INS-1E pancreatic cells by high-resolution 3D electron cryotomography.
Exome-capture RNA-sequencing of decade-old breast cancers and matched decalcified bone metastases identifies clinically actionable targets
Authors: Priedigkeit Nolan , Watters Rebecca J. , Lucas Peter C. , Basudan Ahmed , Bhargava Rohit , Horne William , Kolls Jay K. , Fang Zhou , Rosenzweig Margaret Q. , Brufsky Adam M. , Weiss Kurt R. , Oesterreich Steffi , Lee Adrian V. 
Published: March 2017

ABSTRACTBone metastases (BoM) are a significant cause of morbidity in patients with Estrogen-receptor (ER)-positive breast cancer, yet characterizations of human specimens are limited. In this study, exome-capture RNA-sequencing (ecRNA-seq) on aged (8-12 years), formalin-fixed paraffin-embedded (FFPE) and decalcified cancer specimens was first evaluated. Gene expression values and RNA-seq quality metrics from FFPE or decalcified tumor RNA showed minimal differences when compared to matched flash-frozen or non-decalcified tumors. ecRNA-seq was then applied on a longitudinal collection of 11 primary breast cancers and patient-matchedde novoor recurrent BoM. BoMs harbored shifts to more Her2 and LumB PAM50 intrinsic subtypes, temporally influenced expression evolution, recurrently dysregulated prognostic gene sets and altered expression of clinically actionable genes, particularly in the CDK-Rb-E2F and FGFR-signaling pathways. Taken together, this study demonstrates the use of ecRNA-seq on decade-old and decalcified specimens and defines expression-based tumor evolution in long-term, estrogen-deprived metastases that may have immediate clinical implications.Grant SupportResearch funding for this project was provided in part by a Susan G. Komen Scholar award to AVL and to SO, the Breast Cancer Research Foundation (AVL and SO), the Fashion Footwear Association of New York, the Magee-Women’s Research Institute and Foundation, and through a Postdoctoral Fellowship awarded to RJW from the Department of Defense (BC123242). NP was supported by a training grant from the NIH/NIGMS (2T32GM008424-21) and an individual fellowship from the NIH/NCI (5F30CA203095).Conflicts of Interest DisclosureNo relevant conflicts of interest disclosed for this study.Author ContributionsStudy concept and design (NP, RJW, SO, AVL); acquisition, analysis, or interpretation of data (all authors); drafting of the manuscript (NP, RJW, SO, AVL); critical revision of the manuscript for important intellectual content (all authors); administrative, technical, or material support (PCL, AB, RB, KRW, WH, JK, MR, ZF, AMB).
Task-dependent recurrent dynamics in visual cortex
Authors: Tajima Satohiro , Koida Kowa , Tajima Chihiro I. , Suzuki Hideyuki , Aihara Kazuyuki , Komatsu Hidehiko 
Published: March 2017

AbstractThe capacity for flexible sensory-action association in animals has been related to context-dependent attractor dynamics outside the sensory cortices. Here we report a line of evidence that flexibly modulated attractor dynamics during task switching are already present in the higher visual cortex in macaque monkeys. With a nonlinear decoding approach, we can extract the particular aspect of the neural population response that reflects the task-induced emergence of bistable attractor dynamics in a neural population, which could be obscured by standard unsupervised dimensionality reductions such as PCA. The dynamical modulation selectively increases the information relevant to task demands, indicating that such modulation is beneficial for perceptual decisions. A computational model that features nonlinear recurrent interaction among neurons with a task-dependent background input replicates the key properties observed in the experimental data. These results suggest that the context-dependent attractor dynamics involving the sensory cortex can underlie flexible perceptual abilities.
Multi-omics biomarker pipeline reveals elevated levels of protein-glutamine gamma-glutamyltransferase 4 in seminal plasma of prostate cancer patients
Authors: Drabovich Andrei P. , Saraon Punit , Drabovich Mikalai , Karakosta Theano D. , Dimitromanolakis Apostolos , Hyndman M. Eric , Jarvi Keith , Diamandis Eleftherios P. 
Published: March 2017

AbstractPurposeProstate-specific antigen, a blood serum biomarker of prostate cancer, lacks specificity and prognostic significance, so considerable efforts are devoted to developing novel biomarkers. Seminal plasma, due to its proximity to prostate, is a promising fluid for biomarker discovery and non-invasive diagnostics. In this study, we investigated if seminal plasma proteins could increase specificity of detecting primary prostate cancer and discriminate between high- and low-grade cancers.Experimental DesignTo select 148 most promising biomarker candidates, we combined proteins identified through five independent data mining or experimental approaches: tissue transcriptomics, seminal plasma proteomics, cell secretomics, tissue specificity and androgen regulation. A rigorous biomarker development pipeline based on targeted proteomics assays was designed to evaluate the most promising candidates.ResultsWe qualified 77 and verified 19 proteins in seminal plasma of 67 negative biopsy and 155 prostate cancer patients. Verification revealed a prostate-specific, secreted and androgen-regulated protein-glutamine gamma-glutamyltransferase 4 (TGM4), which could predict prostate cancer on biopsy and outperformed age and serum PSA. Machine-learning approaches also revealed improved multi-marker combinations for diagnosis and prognosis. In the independent verification set measured by an inhouse ELISA, TGM4 was up-regulated 3.7-fold (P=0.006) and revealed AUC 0.66 for detecting prostate cancer on biopsy for patients with serum PSA≥4 ng/mL and age≥50. Low levels of TGM4 (median 120 pg/mL) were detected in blood serum, but could not differentiate between negative biopsy, prostate cancer or prostate inflammation.ConclusionsPerformance of TGM4 warrants its further investigation within the distinct genomic subtypes and evaluation for the inclusion into emerging multi-biomarker panels.
The relevance of global sector influence in African sector portfolios
Authors: Boamah Nicholas Addai 
Published: March 2017

Purpose
The purpose of this paper is to examine the relative importance of global sector effects in African sector portfolios (ASPs). It explores the dynamics of the rate of change and the level of global sector effects in their respective ASPs.

Design/methodology/approach
The variance of African industry returns is decomposed to the component attributable to the corresponding global industry and the proportion that is African industry specific. The authors then scale the global component by the African sector-specific component to obtain the relative global sector influences in their corresponding ASP returns.

Findings
The evidence suggests that global sector effects are dominated by African industry-specific influences on the African markets; however, in the recent period the global sector influence has risen in importance. Additionally, the 2008 Global Financial Crisis had significant impact in the relative global sector effects in the ASPs. Turning points in the rate of change of and the relative importance of the corresponding global sector effects in the ASPs are identified. The findings infer time-varying global sector effects in their respective ASPs. The evidence suggests sector-level differences in the diversification gain of the ASPs.

Originality/value
The ASPs offer global investors the opportunity for diversification gains when included in geographically diversified portfolio within the same sector, although, global sector effects on the African markets have increased recently.
Can GBS be a preferable aid modality under SDGs?
Authors: Furukawa Mitsuaki , Takahata Junichiro 
Published: March 2017

Purpose
The purpose of this paper is to verify whether general budget support is a favorable aid modality under SDGs in developing countries.

Design/methodology/approach
The authors use panel data on government revenue, expenditure, and social indicators for the ten-year period from 1997 to 2006 to reflect the result for sustainable development goals (SDGs). The authors focus on the health sector as a representative social sector.

Findings
The results show that GBS in fact increases the budget allocation for the health sector more than tax revenue does. However, the effect of government health expenditure on health indicators is not necessarily improved by the introduction of GBS, which indicates that the introduction of GBS alone has limited impact.

Social implications
The paper suggests that the complementarity between GBS and projects/programs focusing on human and institutional capacity development should be seriously considered. These results shall be considered even under SDGs.

Originality/value
This paper attempts to assess the effect of GBS in developing countries by using panel data on government revenue, expenditure, and social indicators for the ten-year period from 1997 to 2006 to reflect the result for SDGs.