bluuebunny/crossref_metadata_2025 huggingface dataset:
Management, Spirituality, and Religion (MSR) ways and means: a paper to encourage quality research
Authors: Tackney Charles Thomas , Chappell Stacie , Harris Dan , Pavlovich Kathryn , Egel Eleftheria , Major Richard , Finney Mary , Stoner James
Published: May 2017

Despite 15 years of functioning as an interest group, our domain of inquiry is relatively young and there are limited theoretical boundaries to support, shape, and assist our efforts. This metaphorical “blank canvas” is both empowering, in that so many inquiries are
open for exploration, and yet also limiting. In this document we highlight three critical elements to emphasize their importance in MSR research: (a) delineating and operationalizing the key terms of religion, spirituality, and workplace spirituality; (b) acknowledging the work to date in
the MSR corpus around definitions of these terms, and (c) being explicit about how ontological and epistemological assumptions inform our methods. The intention is to encourage growth in the quality and rigor of our individual and collective scholarship.
Tissue-resident T cells in hepatitis B: A new target for cure?
Authors: Bolte Fabian J. , Rehermann Barbara
Published: May 2017

A hallmark of chronic hepatitis B virus (HBV) infection is the functional impairment and depletion of antiviral T cells. In this issue of JEM, Pallett et al. (https://doi.org/10.1084/jem.20162115) identify a reservoir of functional HBV-specific T cells among liver-resident T cells.
On the apparent power law in CDM halo pseudo-phase space density profiles
Authors: Nadler Ethan O. , Oh S. Peng , Ji Suoqing
Published: May 2017

We investigate the apparent power-law scaling of the pseudo-phase space density (PPSD) in cold dark matter (CDM) haloes. We study fluid collapse, using the close analogy between the gas entropy and the PPSD in the fluid approximation. Our hydrodynamic calculations allow for a precise evaluation of logarithmic derivatives. For scale-free initial conditions, entropy is a power law in Lagrangian (mass) coordinates, but not in Eulerian (radial) coordinates. The deviation from a radial power law arises from incomplete hydrostatic equilibrium (HSE), linked to bulk inflow and mass accretion, and the convergence to the asymptotic central power-law slope is very slow. For more realistic collapse, entropy is not a power law with either radius or mass due to deviations from HSE and scale-dependent initial conditions. Instead, it is a slowly rolling power law that appears approximately linear on a log–log plot. Our fluid calculations recover PPSD power-law slopes and residual amplitudes similar to N-body simulations, indicating that deviations from a power law are not numerical artefacts. In addition, we find that realistic collapse is not self-similar; scalelengths such as the shock radius and the turnaround radius are not power-law functions of time. We therefore argue that the apparent power-law PPSD cannot be used to make detailed dynamical inferences or extrapolate halo profiles inwards, and that it does not indicate any hidden integrals of motion. We also suggest that the apparent agreement between the PPSD and the asymptotic Bertschinger slope is purely coincidental.
Changes in gait parameters after femoral derotational osteotomy in cerebral palsy patients with medial femoral torsion
Authors: Kim Ha Yong , Cha Yong Han , Byun Jae Yong , Chun Young Sub , Choy Won Sik
Published: May 2017

Medial femoral torsion (MFT) is a common pathologic gait in cerebral palsy (CP) children that can be corrected by femoral derotational osteotomy (FDO). It is not clearly known as to how much various gait parameters change after FDO. The aim of this study was to quantify changes in gait parameters after FDO. The study group included 19 young CP patients (28 limbs, age<20 years, average age: 13.2 years) with symptomatic MFT, treated with distal FDO. The study group was divided into two groups: the unilateral FDO group (UG) and the bilateral FDO group (BG). The mean degree of derotation was 24.6° (25.0° for UG, 24.4° for BG). Pre-FDO and post-FDO values of Staheli’s rotational profiles and kinematic data were compared. A paired t-test and Pearson’s correlation were used for statistical analysis. The mean internal hip rotation was 71.4±6.9° before surgery and 48.6±10.7° after surgery in the UG (P<0.05) and it was 63.8±15.8° before surgery and 40.9±9.2° after FDO in the BG (P<0.05). The change in the foot progression angle (FPA) was 12.9° in the UG group (P<0.05) and 12.6° in the BG group (P<0.05). The degree of FPA had changed by about a half of the surgical derotation angle. Changes in the mean hip rotation during gait were 14.8° in the UG (P<0.05) and 6.7° in the BG (P<0.05) groups. The overall pelvic rotation was not changed after surgery. However, in patients with preoperative compensatory pelvic rotation of more than 5°, there was a change of 5.3±4.8° in the UG and 6.6±1.54° in the BG after surgery (P<0.05). There was also a trend showing that the younger the patient, the more the pelvic rotation changed (P=0.069). In-toeing gait because of MFT improved with FDO in CP patients. The expected degree of postoperative correction of FPA and hip rotation is about a half of the FDO degree. The degree of compensatory pelvic rotation should be considered to determine the correction angle of FDO, especially in young patients with preoperative pelvic rotation of more than 5°.
Cardiac Abnormalities in Type 1 Facioscapulohumeral Muscular Dystrophy
Authors: Labombarda Fabien , Maurice Maxime , Simon Jean-Philippe , Legallois Damien , Guyant-Maréchal Lucie , Bedat-Millet Anne-Laure , Merle Philippe , Saloux Eric , Chapon Françoise , Milliez Paul
Published: May 2017

Objectives:

We conducted a retrospective study to characterize the cardiac complications in patients with genetically confirmed type 1 facioscapulohumeral dystrophy.

Methods:

We reviewed baseline cardiac investigations, including electrocardiogram, Holter electrocardiogram and echocardiogram, as well as cardiac complications that occurred during follow-up in 56 adult patients (37 men, mean duration of disease: 20 years).

Results:

Baseline evaluation revealed minor cardiac anomalies in 23 patients including incomplete right bundle branch block (iRBBB) in 13 patients (23%). Over a mean follow-up period of 7.2 years, there was no cardiac death, no patient developed cardiomyopathy, and 28 patients (50%) experienced cardiac anomalies. Among these patients, 3 had one or more major events (heart failure and/or atrial fibrillation). The remaining 25 patients presented minor cardiac anomalies of which iRBBB was the most frequent (25%).

Conclusions:

Cardiac anomalies identified during the follow-up of patients with type 1 facioscapulohumeral dystrophy are mainly minor anomalies, dominated by the iRBBB.
Immune Myopathy With Perimysial Pathology Associated With Interstitial Lung Disease and Anti-EJ Antibodies
Authors: Kwon Patrick M. , Zhou Lan , Motiwala Rajeev , Kerr Leslie D. , Shin Susan C.
Published: May 2017

Objectives:

We report a case of immune myopathy with perimysial pathology associated with anti-glycyl-transfer RNA synthetase (anti-EJ) antibody and an excellent treatment response.

Methods:

Chart review.

Results:

A 36-year-old woman presented with 3 months of fatigue, weight loss, progressive weakness in a scapuloperoneal distribution, and dysphagia. Nerve conduction studies, electromyography, and ultrasound suggested an irritable myopathy. She had marked elevations of creatine kinase and positive anti-glycyl-transfer RNA synthetase (anti-EJ) antibodies. A left biceps muscle biopsy revealed inflammation of the perimysium and surrounding perimysial blood vessels with focal fragmentation of the perimysium. Further evaluation revealed interstitial lung disease. Treatment with prednisone and mycophenolate mofetil led to marked clinical improvement of her symptoms.

Conclusions:

Our case adds to the growing spectrum of inflammatory myopathies and highlights the importance of performing a comprehensive, multisystem workup.
What's in the Literature?
Authors: Bromberg Mark , Silvestri Nicholas J. , Lacomis David
Published: May 2017

In this edition, we provide a detailed summary of an informative book, “GBS100: Celebrating a Century of Progress in Guillain–Barré Syndrome” developed by the Peripheral Nerve Society to honor the centenary of the original paper on Guillain–Barré Syndrome. We also review various studies in myasthenia gravis including: management with rituximab; the efficacy of early fast-acting treatment with corticosteroids; and various dosing strategies for tacrolimus. Finally, we review new studies including: the potential pathogenesis, risk factors, and functional decline of patients with inclusion body myositis; MxA immunoreactivity in dermatomyositis; diagnostic approaches for evaluating patients with myalgia, fatigue, and exercise intolerance; MRI patterns in genetic muscle disease; and MRI as an outcome measure in facioscapulohumeral muscular dystrophy.
LAMELLAR HOLE-ASSOCIATED EPIRETINAL PROLIFERATION IN LAMELLAR MACULAR HOLE AND FULL-THICKNESS MACULAR HOLE IN HIGH MYOPIA
Authors: Lai Tso-Ting , Yang Chung-May
Published: May 2017

Purpose:

To report findings and surgical outcomes of lamellar macular hole (LMH) or full-thickness macular hole (FTMH) accompanied by lamellar hole-associated epiretinal proliferation (LHEP) in eyes with high myopia (HM).

Methods:

Consecutive cases of HM with LMH or FTMH containing LHEP were retrospectively reviewed (study group, 43 cases). Cases of HM without LHEP (22) and those of non-HM with LHEP (30) served as Control A and B.

Results:

The study group showed larger (928.7 ± 381.9 μm) and deeper (remained base thickness: 79.7 ± 23.7 μm) LMH retinal defect than that in Control A (466.2 ± 179.1 and 99.9 ± 24.9) and B (647.1 ± 346.7 and 99.1 ± 38.1). Lamellar hole-associated epiretinal proliferation in the study group had a higher rate of wide extension (42.3%) and growing along the posterior hyaloid (PH, 53.8%). Patients with LMH who underwent surgery in the study group and Control A showed limited best corrected visual acuity (BCVA) improvement (0–1 and 1–2 ETDRS lines, respectively), while Control B had significant improvement (4–5 lines). For full-thickness macular holes, the study group was the youngest (50.0 ± 11.4) and LHEP was more likely to grow on the posterior hyaloid (23.5%); the postoperative best corrected visual acuity, however, was similar to that in Control A (20/63–20/80).

Conclusion:

Lamellar hole-associated epiretinal proliferation in HM tended to be more widespread and adherent to the posterior hyaloid than in eyes without HM. Visual outcomes after LMH repair in eyes with LHEP and HM are less favorable than eyes with LHEP and without HM, but similar to eyes with HM and without LHEP.
Easy Placement of Annular Sutures during Minimally Invasive Aortic Valve Replacement
Authors: Totsugawa Toshinori , Hiraoka Arudo , Tamura Kentaro , Yoshitaka Hidenori , Sakaguchi Taichi
Published: May 2017

Placing annular sutures at the right coronary cusp is difficult during minimally invasive aortic valve replacement. We propose the partial everting mattress method, whereby a prosthetic valve is implanted ina supra-annular position at the left coronary and noncoronary cusps, with pledgets on the left ventricular side, but in an intra-annular position at the right coronary cusp, with pledgets on the aortic side. Needles can be grasped in forehand pass at all three coronary cusps. Our method enables easy placement of annular stitches even in the small surgical field, without adversely influencing the hemodynamic performance of the prosthesis.
Oxidative lipidomics: applications in critical care
Authors: Anthonymuthu Tamil S. , Kim-Campbell Nahmah , Bayır Hülya
Published: May 2017

Purpose of review

Lipid peroxidation has long been established as a key player in the pathophysiology of critical illness. Recent developments in oxidative lipidomics have aided in deciphering the molecular mechanisms of lipid oxidation in health and disease. This review discusses recent achievements and recent developments in oxidative lipidomics and its contribution to the understanding of critical illness.

Recent findings

Most studies involving acute injury focus on identifying the end products of lipid peroxidation. This misses the early events and targets of peroxidation mechanisms. Recent developments in liquid chromatography tandem mass spectrometry-based oxidative lipidomics have enabled the identification of a wide variety of enzymatically generated lipid oxidation products. Such lipid mediators have been found to play an important role in injury, inflammation, and recovery in disease states such as sepsis or head trauma.

Multiple lipid oxidation products are formed either through enzymatic pathways or through random chemical reactions. These products are often biologically active and can contribute to the regulation of cellular signaling. Oxidative lipidomics has contributed to the identification and quantification of lipid peroxidation products, the mechanism and time course of their production after injury, and synergistic functioning with other regulatory processes in the body. These advances in knowledge will help guide the future development of interventions in critical illness.
Effects of the Insulin Sensitizer Metformin in Alzheimer Disease
Authors: Koenig Aaron M. , Mechanic-Hamilton Dawn , Xie Sharon X. , Combs Martha F. , Cappola Anne R. , Xie Long , Detre John A. , Wolk David A. , Arnold Steven E.
Published: May 2017

Epidemiological studies have identified a robust association between type II diabetes mellitus and Alzheimer disease (AD), and neurobiological studies have suggested the presence of central nervous system insulin resistance in individuals with AD. Given this association, we hypothesized that the central nervous system–penetrant insulin-sensitizing medication metformin would be beneficial as a disease-modifying and/or symptomatic therapy for AD, and conducted a placebo-controlled crossover study of its effects on cerebrospinal fluid (CSF), neuroimaging, and cognitive biomarkers. Twenty nondiabetic subjects with mild cognitive impairment or mild dementia due to AD were randomized to receive metformin then placebo for 8 weeks each or vice versa. CSF and neuroimaging (Arterial Spin Label MRI) data were collected for biomarker analyses, and cognitive testing was performed. Metformin was found to be safe, well-tolerated, and measureable in CSF at an average steady-state concentration of 95.6 ng/mL. Metformin was associated with improved executive functioning, and trends suggested improvement in learning/memory and attention. No significant changes in cerebral blood flow were observed, though post hoc completer analyses suggested an increase in orbitofrontal cerebral blood flow with metformin exposure. Further study of these findings is warranted.
Measuring compensation in neurodegeneration using MRI
Authors: Gregory Sarah , Long Jeffrey D. , Tabrizi Sarah J. , Rees Geraint
Published: May 2017

Purpose of review

Despite signs of cortical and subcortical loss, patients with prodromal and early-stage neurodegenerative disease are able to perform at a level comparable to the normal population. It is presumed that the onset of compensatory processes, that is changes in brain activation within a function-specific network or in the recruitment of a region outside of the task-network, underlies this maintenance of normal performance. However, in most studies to date, increased brain activity is not correlated with indices of both disease and performance and what appears to be compensation could simply be a symptom of neurodegeneration.

Recent findings

MRI studies have explored compensation in neurodegenerative disease, claiming that compensation is evident across a number of disorders, including Alzheimer's and Parkinson's disease, but generally always in early stages; after this point, compensation is generally no longer able to operate under the severe burden of disease. However, none of these studies explicitly adopted a particular model of compensation. Thus, we also discuss our recent attempts to operationalize compensation for empirical testing.

There is clear evidence of compensatory processes in the early stages of neurodegenerative disease. However, for a more complete understanding, this requires more explicit empirical modelling.
Structure-Function Analysis of Nonarteritic Anterior Ischemic Optic Neuropathy and Age-Related Differences in Outcome
Authors: Sun Ming-Hui , Liao Yaping Joyce
Published: May 2017

Background:

The optic nerve head is vulnerable to ischemia leading to anterior ischemic optic neuropathy (AION), the most common acute optic neuropathy in those older than 50 years of age.

Methods:

We performed a cross-sectional study of 55 nonarteritic anterior ischemic optic neuropathy (NAION) eyes in 34 patients to assess clinical outcome and perform structure-function correlations.

Results:

The peak age of NAION onset was between 50 and 55 years. Sixty-seven percent of patients presented with their first event between the ages of 40 and 60 years, and 32% presented at ≤50 years. Those with NAION onset at age ≤50 years did not have significantly better visual outcome per logMAR visual acuity, automated perimetric mean deviation (PMD) or optical coherence tomography (OCT) measurements. Kaplan–Meier survival curve and multivariate Cox proportional regression analysis showed that age >50 years at NAION onset was associated with greater risk of second eye involvement, with hazard ratio of 20. Older age at onset was significantly correlated with greater thinning of the ganglion cell complex (GCC) (P = 0.022) but not with logMAR visual acuity, PMD, or thinning of retinal nerve fiber layer (RNFL). Using area under receiver operating characteristic curve analyses, we found that thinning of RNFL and GCC was best able to predict visual outcome, and that mean RNFL thickness >65 μm or macular GCC thickness >55 μm significantly correlated with good visual field outcome.

Conclusions:

We showed that NAION onset at age >50 years had a greater risk of second eye involvement. Patients with OCT mean RNFL thickness >65 μm and mean macular ganglion cell complex thickness >55 μm had better visual outcomes.
A case of Vibrio vulnificus infection complicated with fulminant purpura: gene and biotype analysis of the pathogen
Authors: Hori Masatoshi , Nakayama Akifumi , Kitagawa Daisuke , Fukushima Hidetada , Asai Hideki , Kawai Yasuyuki , Okuchi Kazuo
Published: May 2017

Introduction.
Vibrio vulnificus (V. vulnificus) causes a severe infection that develops in the compromised host. Its pathophysiology is classified into three types: (1) primary septicaemia, (2) gastrointestinal illness pattern and (3) wound infection pattern. Of these, primary septicaemia is critical. V. vulnificus can be classified into three biotypes and two genotypes and its pathogenicity is type-dependent.

Case presentation. A 47-year-old man presented to a local hospital with chief complaints of fever, bilateral lower limb pain and diarrhoea. He had no history of foreign travel or known medical problems. He was in septic shock and developed fulminant purpura within 24 h of the onset. High-dose vasopressor and antibiotic administration failed to alter his status and he died 3 days after the onset of symptoms. V. vulnificus was isolated from blood, skin and nasal discharge cultures. Biotype and gene analysis of the microbe isolated identified it as Biotype 3, mainly reported in Israel in wound infections, and Genotype E, implicating an environmental isolate. These typing analyses indicated that the microbe isolated could be classified as a type with low pathogenicity.

Conclusion. This case highlighted that Biotype 3 and Genotype E can also cause primary septicaemia. Although the majority of reports on Biotype 3 have been from the Middle East, this experience with the present case provided evidence that the habitat of Biotype 3 V. vulnificus has been extending to East Asia as well.
Unsupervised multiple kernel learning for heterogeneous data integration
Authors: Mariette Jérôme , Villa-Vialaneix Nathalie
Published: May 2017

Recent high-throughput sequencing advances have expanded the breadth of available omics datasets and the integrated analysis of multiple datasets obtained on the same samples has allowed to gain important insights in a wide range of applications. However, the integration of various sources of information remains a challenge for systems biology since produced datasets are often of heterogeneous types, with the need of developing generic methods to take their different specificities into account.

We propose a multiple kernel framework that allows to integrate multiple datasets of various types into a single exploratory analysis. Several solutions are provided to learn either a consensus meta-kernel or a meta-kernel that preserves the original topology of the datasets. We applied our framework to analyse two public multi-omics datasets. First, the multiple metagenomic datasets, collected during theTARAOceans expedition, was explored to demonstrate that our method is able to retrieve previous findings in a single KPCA as well as to provide a new image of the sample structures when a larger number of datasets are included in the analysis. To perform this analysis, a generic procedure is also proposed to improve the interpretability of the kernel PCA in regards with the original data. Second, the multi-omics breast cancer datasets, provided by The Cancer Genome Atlas, is analysed using a kernel Self-Organizing Maps with both single and multi-omics strategies. The comparison of this two approaches demonstrates the benefit of our integration method to improve the representation of the studied biological system.

Proposed methods are available in the R packagemixKernel, released on CRAN. It is fully compatible with themixOmicspackage and a tutorial describing the approach can be found onmixOmicsweb sitehttp://mixomics.org/mixkernel/.
MOLECULAR CORRELATE OF MOUSE EXECUTIVE FUNCTION. TOP-DOWN AND BOTTOM-UP COMPLEMENTATIONS BY PRESYNAPTIC VERTEBRATE BRAIN-SPECIFIC Ntng GENE PARALOGS
Authors: Prosselkov Pavel , Zhang Qi , Goto Hiromichi , Polygalov Denis , McHugh Thomas J. , Itohara Shigeyoshi
Published: May 2017

Executive function (EF) is a regulatory construct of learning and general cognitive abilities. Genetic variations underlying the architecture of cognitive phenotypes are likely to affect EF and associated behaviors. Mice lacking one ofNtnggene paralogs, encoding the vertebrate brain-specific presynaptic Netrin-G proteins, exhibit prominent deficits in the EF control. Brain areas responsible for gating the bottom-up and top-down information flows differentially expressNtng1andNtng2, distinguishing neuronal circuits involved in perception and cognition. As a result, high and low cognitive demand tasks (HCD and LCD, respectively) modulateNtng1andNtng2associations either with attention and impulsivity (AI) or working memory (WM), in a complementary manner. During the LCDNtng2supported neuronal gating of AI and WM dominates over theNtng1-associated circuits. This is reversed during the HCD, when the EF requires a larger contribution of cognitive control, supported byNtng1, over theNtng2pathways. Since humanNTNGorthologs have been reported to affect human IQ (1), and an array of neurological disorders (2), we believe that mouseNtnggene paralogs serve an analogous role but influencing brain executive functioning.
Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa
Authors: Ashton Philip M. , Owen Sian V. , Kaindama Lukeki , Rowe Will P. M. , Lane Chris , Larkin Lesley , Nair Satheesh , Jenkins Claire , de Pinna Elizabeth , Feasey Nicholas , Hinton Jay C. D. , Dallman Tim
Published: May 2017

The ST313 sequence type of Salmonella enterica serovar Typhimurium causes invasive non-typhoidal salmonellosis amongst immunocompromised people in sub-Saharan Africa (sSA). Previously, two distinct phylogenetic lineages of ST313 have been described which have rarely been found outside sSA. Following the introduction of routine whole genome sequencing of Salmonella enterica by Public Health England in 2014, we have discovered that 2.7% (79/2888) of S. Typhimurium from patients in England and Wales are ST313. Of these isolates, 59/72 originated from stool and 13/72 were from extra-intestinal sites. The isolation of ST313 from extra-intestinal sites was significantly associated with travel to Africa (OR 12 [95% CI: 3,53]). Phylogenetic analysis revealed previously unsampled diversity of ST313, and distinguished UK-linked isolates causing gastroenteritis from African-associated isolates causing invasive disease. Bayesian evolutionary investigation suggested that the two African lineages diverged from their most recent common ancestors independently, circa 1796 and 1903. The majority of genome degradation of African ST313 lineage 2 is conserved in the UK ST313 lineages and only 10/44 pseudogenes were lineage 2-specific. The African lineages carried a characteristic prophage and antibiotic resistance gene repertoire, suggesting a strong selection pressure for these horizontally-acquired genetic elements in the sSA setting. We identified an ST313 isolate associated with travel to Kenya that carried a chromosomally-located blaCTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to selection pressure exerted by antibiotic usage.

The S. Typhimurium ST313 sequence type has been primarily associated with invasive disease in Africa. Here, we highlight the power of routine whole-genome-sequencing by public health agencies to make epidemiologically-significant deductions that would be missed by conventional microbiological methods. The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. We speculate that the niche specialization of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.
Zfp423, a Joubert syndrome gene, is a domain-specific regulator of cell cycle progression, DNA damage response and Purkinje cell development in the cerebellar primordium
Authors: Casonil Filippo , Crocil Laura , Bosonel Camilla , D’Ambrosio Roberta , Badaloni Aurora , Gaudesi Davide , Barilil Valeria , Sarna Justyna R. , Tessarollo Lino , Cremona Ottavio , Hawkes Richard , Warming Søren , Consalez G. Giacomo
Published: May 2017

Neurogenesis is a tightly regulated process whose success depends on the ability to balance the expansion/maintenance of an undifferentiated neural progenitor pool with the precisely timed birth of sequential generations of neurons. TheZfp423gene encodes a 30-Zn-finger transcription factor (TF) that acts as a scaffold in the assembly of complex transcriptional and cellular machineries regulating neural development. While null mutants forZfp423feature a severe cerebellar hypoplasia, the underlying mechanism is only partially characterized. Mutations of the human orthologZNF423have been identified in patients carrying cerebellar vermis hypoplasia (CVH) or Joubert Syndrome (JS), associated with other signs of classical ciliopathy outside the central nervous system (CNS). ZNF423 also plays a role in the DNA damage response (DDR). To further characterize the role of ZFP423 in cerebellar neurogenesis, with a focus on Purkinje cells (PC) development, we analyzed two previously undescribed mutant mouse lines carrying allelic in-frame deletions of the corresponding gene, selectively affecting two functionally characterized protein-protein interaction domains, affecting zinc (Zn) fingers 9-20 or 28-30. Some phenotypic defects are allele specific:Zfp423Δ9-20/Δ9-20mutants exhibit a depletion of the OLIG2+ PC progenitor pool in the cerebellar ventricular zone (VZ). In these mutants, M-phase progenitors display changes in spindle orientation indicative of a precocious switch from symmetric to asymmetric cell division. Conversely, theZfp423Δ28-30/Δ28-30primordium displays a sharp decrease in the expression of PC differentiation markers, including CORL2, despite an abundance of cycling PC progenitors. Moreover, and importantly, in both mutants VZ progenitor cell cycle progression is remarkably affected, and factors involved in the DDR are substantially upregulated in the VZ and in postmitotic precursors alike. Our in vivo evidence sheds light on the domain-specific roles played by ZFP423 in different aspects of PC progenitor development, and at the same time supports the emerging notion that an impaired DNA damage response may be a key factor in the pathogenesis of JS and other ciliopathies.
Hellbender Salamanders (Cryptobranchus alleganiensis) Exhibit an Ontogenetic Shift in Microhabitat Use in a Blue Ridge Physiographic Region Stream
Authors: Hecht K. A. , Freake M. J. , Nickerson M. A. , Colclough P.
Published: May 2017

Organisms that experience large changes in body size during the life span often exhibit differences in resource use among life stages. Ontogenetic shifts in habitat use reduce intraspecific competition and predation and are common in lotic organisms. Although information on the immature life stages of the Hellbender (Cryptobranchus alleganiensis) is limited, this aquatic salamander exhibits ontogenetic shifts in habitat use in some streams, with adults sheltering under large rocks and larvae utilizing interstitial spaces of gravel beds. Due to the geomorphology of Little River, Tennessee, however, limited interstitial spaces within the gravel are filled with sand. Therefore, we quantified microhabitat parameters for three life stages of Hellbenders (larvae, sub-adult, adult) to determine if an ontogenetic shift in microhabitat occurred in Little River. We found no significant differences in stream substrate at capture sites among the stages, but there was a positive correlation between rock shelters underlain with very coarse gravel and overall Hellbender occupancy. Although we found no difference in water quality parameters and streambed particle size among the stage classes at the sites of capture, there was a significant difference in the average shelter size among all stages, with larvae utilizing the smallest shelters. Based on these results, future Hellbender research and conservation efforts should consider differences in life stage habitat use as well as specific stream particle classes.
Direct modulation of aberrant brain network connectivity through real-time NeuroFeedback
Authors: Ramot Michal , Kimmich Sara , Gonzalez-Castillo Javier , Roopchansingh Vinai , Popal Haroon , White Emily , Gotts Stephen J. , Martin Alex
Published: May 2017

The existence of abnormal connectivity patterns between resting state networks in neuropsychiatric disorders, including Autism Spectrum Disorder (ASD), has been well established. Traditional treatment methods in ASD are limited, and do not address the aberrant network structure. Using real-time fMRI neurofeedback, we directly trained 3 brain nodes in participants with ASD, in which the aberrant connectivity has been shown to correlate with symptom severity. 17 ASD participants and 10 control participants were scanned over multiple sessions (123 sessions in total). Desired network connectivity patterns were reinforced in real-time, without participants’ awareness of the training taking place. This training regimen produced large, significant long-term changes in correlations at the network level, and whole brain analysis revealed that the greatest changes were focused on the areas being trained. These changes were not found in the control group. Moreover, changes in ASD resting state connectivity following the training were correlated to changes in behavior, suggesting that neurofeedback can be used to directly alter complex, clinically relevant network connectivity patterns.

Significance Statement

Many disorders are characterized by underlying abnormalities in network connectivity. These abnormalities are difficult to address with explicit training procedures (which are unlikely to target the specific abnormalities). Covert neurofeedback however, can directly target these networks, positively reinforcing the desired connections. We have developed a method for reinforcing correlations in real-time, and show that such training is effective, inducing significant, long-lasting changes in connectivity between aberrant networks in Autism Spectrum Disorder. This provides a potential mechanism for modulating aberrant correlation structures in other clinical groups as well.
Simulating the impact of sensorimotor deficits on reaching performance
Authors: Sketch Sean M. , Simpson Cole S. , Crevecoeur Frédéric , Okamura Allison M.
Published: May 2017

The healthy human nervous system accurately and robustly controls movements despite nonlinear dynamics, noise, and delays. After a stroke, motor ability frequently becomes impaired. To provide insight into the relative impact of specific sensorimotor deficits on motor performance, we modeled neural control of reaching with the human upper limb as a near-optimally feedback-controlled two-degree-of-freedom system with biologically based parameters. We added three sensorimotor impairments commonly associated with post-stroke hemiparesis—abnormal joint coupling, increased noise on internally modeled dynamics, and muscular weakness— and examined the impact on reaching performance. We found that abnormal joint coupling unknown to the system’s internal model caused systematic perturbations to trajectories, longer reach durations, and target overshoot. Increasing internal model noise and muscular weakness had little impact on motor performance unless model noise was increased by several orders of magnitude. Many reaches performed by our perturbed models replicate features commonly observed in reaches by hemiparetic stroke survivors. The sensitivity to unmodeled abnormal joint coupling agrees with experimental findings that abnormal coupling (possibly related to internal model errors) is the main cause of post-stroke motor impairment.
GenomeVIP: a cloud platform for genomic variant discovery and interpretation
Authors: Mashl R. Jay , Scott Adam D. , Huang Kuan-lin , Wyczalkowski Matthew A. , Yoon Christopher J. , Niu Beifang , DeNardo Erin , Yellapantula Venkata D. , Handsaker Robert E. , Chen Ken , Koboldt Daniel C. , Ye Kai , Fenyö David , Raphael Benjamin J. , Wendl Michael C. , Ding Li
Published: May 2017

Identifying genomic variants is a fundamental first step toward the understanding of the role of inherited and acquired variation in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional “download and analyze” paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis. Here, we introduce the Genome Variant Investigation Platform (GenomeVIP), an open-source framework for performing genomics variant discovery and annotation using cloud- or local high-performance computing infrastructure. GenomeVIP orchestrates the analysis of whole-genome and exome sequence data using a set of robust and popular task-specific tools, including VarScan, GATK, Pindel, BreakDancer, Strelka, and Genome STRiP, through a web interface. GenomeVIP has been used for genomic analysis in large-data projects such as the TCGA PanCanAtlas and in other projects, such as the ICGC Pilots, CPTAC, ICGC-TCGA DREAM Challenges, and the 1000 Genomes SV Project. Here, we demonstrate GenomeVIP's ability to provide high-confidence annotated somatic, germline, and de novo variants of potential biological significance using publicly available data sets.
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
Authors: Franke Vedran , Ganesh Sravya , Karlic Rosa , Malik Radek , Pasulka Josef , Horvat Filip , Kuzman Maja , Fulka Helena , Cernohorska Marketa , Urbanova Jana , Svobodova Eliska , Ma Jun , Suzuki Yutaka , Aoki Fugaku , Schultz Richard M. , Vlahovicek Kristian , Svoboda Petr
Published: May 2017

Retrotransposons are “copy-and-paste” insertional mutagens that substantially contribute to mammalian genome content. Retrotransposons often carry long terminal repeats (LTRs) for retrovirus-like reverse transcription and integration into the genome. We report an extraordinary impact of a group of LTRs from the mammalian endogenous retrovirus-related ERVL retrotransposon class on gene expression in the germline and beyond. In mouse, we identified more than 800 LTRs from ORR1, MT, MT2, and MLT families, which resemble mobile gene-remodeling platforms that supply promoters and first exons. The LTR-mediated gene remodeling also extends to hamster, human, and bovine oocytes. The LTRs function in a stage-specific manner during the oocyte-to-embryo transition by activating transcription, altering protein-coding sequences, producing noncoding RNAs, and even supporting evolution of new protein-coding genes. These functions result, for example, in recycling processed pseudogenes into mRNAs or lncRNAs with regulatory roles. The functional potential of the studied LTRs is even higher, because we show that dormant LTR promoter activity can rescue loss of an essential upstream promoter. We also report a novel protein-coding gene evolution—D6Ertd527e—in which an MT LTR provided a promoter and the 5′ exon with a functional start codon while the bulk of the protein-coding sequence evolved through a CAG repeat expansion. Altogether, ERVL LTRs provide molecular mechanisms for stochastically scanning, rewiring, and recycling genetic information on an extraordinary scale. ERVL LTRs thus offer means for a comprehensive survey of the genome's expression potential, tightly intertwining with gene expression and evolution in the germline.
Transfer properties of various compensation techniques for wireless power transfer system including parasitic effects
Authors: Kindl Vladimir , Frivaldsky Michal , Spanik Pavol , Piri Marek , Jaros Viliam
Published: May 2017

Purpose

This paper aims to develop mathematical models of variously compensated wireless energy transfer (WET) systems. Attention is primarily paid to the derivation of the most important energy transfer characteristics such as efficiency and amount of transferred power. This paper discusses the main advantages and disadvantages of various compensation techniques to show their possible application areas. On the basis of these results, a designer will be able to quickly identify which compensation type suites as the best solution to fulfill a given system’s requirements.

Design/methodology/approach

First, the current state in the field of mathematical modeling of WET systems is introduced. Next, the non-resonant magnetic-coupled circuit together with four most common resonant magnetic-coupled circuits is analyzed. The equivalent circuit models using loop currents methodology is applied to the analyses. The proposed methodology is experimentally verified by the laboratory measurement of selected circuit topology. The main contribution of the proposed methodology lies in its quick applicability on more complicated or extended systems while keeping a relatively good match with the real system’s behavior.

Findings

The authors have presented the usage of a simple and accurate methodology for investigating variously compensated WET systems. Electrical engineers who require effective and powerful tools for the identification of basic WET systems properties will find this methodology to be of extensive help.

Research limitations/implications

The analyses consider only the sinusoidal type of supply voltage; so, it is valid mainly for the close range of the resonant state. Nonlinearities cannot be taken into account.

Practical implications

This research may be applied in the field of WET systems.

Originality/value

Research in the area of power electronic systems, which provides a clear and straightforward procedure for WET system identification, will be helpful to most practical technicians who are not well versed in areas of physical-based phenomena.
Influence of curvature on air-gap magnetic field distribution and rotor losses in PM electric machines
Authors: Renedo Anglada Jaime , Sharkh Suleiman , Qazalbash Arfakhshand
Published: May 2017

Purpose

The purpose of this paper is to study the effect of curvature on the magnetic field distribution and no-load rotor eddy current losses in electric machines, particularly in high-speed permanent magnet (PM) machines.

Design/methodology/approach

The magnetic field distribution is obtained using conformal mapping, and the eddy current losses are obtained using a cylindrical multilayer model. The analytical results are validated using a two-dimensional finite element analysis. The analytical method is based on a proportional-logarithmic conformal transformation that maps the cylindrical geometry of a rotating electric machine into a rectangular configuration without modifying the length scale. In addition, the appropriate transformation of PM cylindrical domains into the rectangular domain is deduced. Based on this conformal transformation, a coefficient to quantify the effect of curvature is proposed.

Findings

Neglecting the effect of curvature can produce significant errors in the calculation of no-load rotor losses when the ratio between the air-gap length and the rotor diameter is large.

Originality/value

The appropriate transformation of PM cylindrical domains into the rectangular domain is deduced. The proportional-logarithmic transformation proposed provides an insight into the effect of curvature on the magnetic field distribution in the air-gap and no-load rotor losses. Furthermore, the proposed curvature coefficient gives a notion of the effect of curvature for any particular geometry without the necessity of any complicated calculation. The case study shows that neglecting the effect of curvature underestimates the rotor eddy-current losses significantly in machines with large gap-to-rotor diameter ratios.
RISE-backstepping-based robust control design for induction motor drives
Authors: Rkhissi-Kammoun Yosra , Ghommam Jawhar , Boukhnifer Moussa , Mnif Faiçal
Published: May 2017

Purpose

This paper aims to address the speed and flux tracking problem of an induction motor (IM) drive that propels an electric vehicle (EV). A new continuous control law is developed for an IM drive by using the backstepping design associated with the Robust Integral Sign of the Error (RISE) technique.

Design/methodology/approach

First, the rotor field-oriented IM dynamic model is derived. Then, a RISE-backstepping approach is proposed to compensate for the load torque disturbance under the assumptions that the disturbances are C2 class functions with bounded time derivatives.

Findings

The numerical validation results have presented good control performances in terms of speed and flux reference tracking. It is also robust against load disturbances rejection and IM parameters variation compared to the conventional Field-Oriented Control design. Besides, the asymptotic stability and the boundedness of the closed-loop signals is guaranteed in the context of Lyapunov.

Originality/value

A very relevant strategy based on a conjunction of the backstepping design with the RISE technique is proposed for an IM drive. The approach remains simple and can be scaled to different applications.
2-D quasi-static solution of a coil in relative motion to a conducting plate
Authors: Abdelqader Majd , Morelli Jordan , Palka Ryszard , Woronowicz Konrad
Published: May 2017

Purpose

The aim of this paper is to present a method for calculating the electromagnetic fields, forces and current density distribution using Fourier series for a two-dimensional quasi steady state model consisting of a conducting uniform plate moving relative to an arbitrary current source with time harmonic excitation.

Design/methodology/approach

The presented solution is valid for an arbitrary source. A specific source is chosen consisting of a single coil made up of two-time harmonic current filaments. The solutions are derived and presented in a form that allows its expansion to include an arbitrary number of spatially shifted coils conducting arbitrary harmonic currents.

Findings

The analytical solution is compared to simulations produced using commercial finite element analysis software, ANSYS Maxwell2D and COMSOL, and is found to be in good agreement. The analytical solution provides a direct method to analyze the spatial harmonics in the system and can be computationally significantly faster especially at high relative speeds between the primary source and conducting plate.

Originality/value

The presented Fourier series solution is applied to simple 2-D model of a single coil with AC current excitation moving relative to a conducting plate. An analytical solution and analysis of this system has not been presented before, to the authors’ knowledge, using Fourier series or any other method.
Analytical modeling of disc-type permanent magnet hysteresis motor in steady-state operational conditions
Authors: Behniafar Ali , Darabi Ahmad
Published: May 2017

Purpose

In this paper, a new structure for the permanent magnet hysteresis synchronous (PMHS) motor is introduced. Moreover, this paper aims to presents a new analytical method for modeling of a disc-type PMHS motor.

Design/methodology/approach

Because the hysteresis and permanent magnet motors have unique characteristics, a motor (the PMHS motor) with excellent performance features can be achieved by combining them. Choosing a disc-type slotless structure causes the major advantages of both motors to be preserved in the new motor. To analyze PMHS motor, mathematical equations are obtained by using Ampere’s circuital law, flux continuity law and Faraday’s law. Then the air-gap voltage and exciting current of the motor can be calculated. To implement this method, a new iterative algorithm is proposed. This algorithm consists of one-iteration loop for each input voltage to find the maximum flux density of the operational hysteresis loop of the motor.

Findings

Validity of the analytical approach is confirmed by experimental results. A reasonably close agreement between the two is shown and some outstanding performances of the PMHS motor are demonstrated.

Originality/value

A new structure for PMHS motor and also a new analytical method for performance prediction of this motor is presented.
Performance evaluation of MoM-based wide-band EM simulation with adaptive frequency sampling and Stöer-Bulirsch algorithm
Authors: Karwowski Andrzej
Published: May 2017

Purpose

The purpose of this paper is to examine the convergence, offered accuracy and efficiency of the bisectional adaptive frequency sampling (AFS) scheme combined with the Stöer-Bulirsch (SB) algorithm as a tool for supporting frequency-domain method-of-moments (MoM) in broadband electromagnetic (EM) simulations.

Design/methodology/approach

The AFS and SB procedures have been interfaced with the MoM code, and then, an extensive parametric study has been carried out to explore the performance of the numerical solution for the test problems of reconstructing frequency responses of the wire radiator and scatterer, respectively, over at least a decade bandwidth.

Findings

The results give evidence for the efficiency of the overall approach and its capability of constructing the approximation of multi-resonant responses with sharp resonant peaks from a substantially reduced number of EM samples (data points) compared to that of conventional uniform sampling.

Originality/value

Results of the study offer thorough insight into the performance of the AFS-SB technique, and the data given in this paper may be helpful in selecting the convergence criterion and the tolerance for the AFS-SB algorithm to achieve a possibly economical broadband simulation technique.