bluuebunny/crossref_metadata_2025 huggingface dataset:
Extensive Myocardial Calcification in Critically Ill Patients
Authors: Kapandji Natacha , Redheuil Alban , Fouret Pierre , Hékimian Guillaume , Lebreton Guillaume , Bréchot Nicolas , Luyt Charles-Edouard , Cluzel Philippe , Combes Alain , Schmidt Matthieu
Published: March 2018

Objectives:

To describe an unusual complication on extracorporeal membrane oxygenation.

Data Sources:

Clinical observation.

Study Selection:

Case report.

Data Extraction:

Relevant clinical information.

Data Synthesis:

We report the cases of three young patients who developed extensive myocardial calcifications on prolonged extracorporeal membrane oxygenation support for severe acute respiratory distress syndrome with septic cardiomyopathy, postresuscitation cardiogenic shock, and septic shock complicating severe acute respiratory distress syndrome, respectively. Extensive myocardial calcifications were confirmed by echocardiography, CT, and cardiac biopsy. The combination of multiple factors, for example, prolonged hemodynamic failure, profound acidosis, high vasopressor doses, and renal failure, may lead to this unusual and severe complication.

Conclusions:

Intensivists should be aware of this rare but rapid complication on extracorporeal membrane oxygenation support that may directly impact outcome. The precise role of extracorporeal membrane oxygenation support in the timing and frequency of new-onset diffuse myocardial calcification deserves further investigation.
Small Subset of Adenoid Cystic Carcinoma of the Skin Is Associated With Alterations of the MYBL1 Gene Similar to Their Extracutaneous Counterparts
Authors: Kyrpychova Liubov , Vanecek Tomas , Grossmann Petr , Martinek Petr , Steiner Petr , Hadravsky Ladislav , Belousova Irena E. , Shelekhova Ksenya V. , Svajdler Marian , Dubinsky Pavol , Michal Michal , Kazakov Dmitry V.
Published: March 2018

Adenoid cystic carcinoma (ACC) of the skin is a rare malignant neoplasm histologically identical to homonymous tumors in other organs. Cutaneous ACC has been found to harbor MYB gene activations, either through MYB chromosomal abnormalities or by generation of the MYB–NFIB fusion. In salivary gland ACC, in addition to the MYB gene, alterations in MYBL1, the gene closely related to MYB, have been reported. We studied 10 cases of cutaneous ACC (6 women, 4 men; and age range 51–83 years) for alterations in the MYB, NFIB, and MYBL1 genes, using FISH and PCR. MYB break-apart and NFIB break-apart tests were positive in 4 and 5 cases, respectively. MYB–NFIB fusions were found in 4 cases. The break of MYBL1 was found in 2 cases, and in one of them, the NFIB break-apart probe was positive, strongly indicating a MYBL1–NFIB fusion. In 2 cases, the MYB break-apart test was positive, whereas no MYB–NFIB was detected, strongly suggesting another fusion partner. It is concluded that MYBL1 alterations are detected in primary cutaneous ACC but are apparently less common compared with MYB and NFIB alterations.
Predictors of Intravenous Immunoglobulin Nonresponse and Racial Disparities in Kawasaki Disease
Authors: Clark Daniel E. , Denby Kara J. , Kaufman Laura M. , Fill Mary-Margaret A. , Piya Bhinnata , Krishnaswami Shanthi , Fonnesbeck Christopher , Halasa Natasha
Published: March 2018

Background:

Kawasaki disease (KD) is the most common cause of acquired heart disease in American children. Intravenous immunoglobulin (IVIG) nonresponse is a known risk factor for cardiac sequelae. Previously reported risk factors for nonresponse include age, male sex and laboratory abnormalities. We set out to identify additional risk factors for IVIG nonresponse in a racially diverse KD population.

Methods:

We conducted a retrospective chart review at a referral center in the Southeastern United States of children meeting ICD-9 (International Statistical Classification of Disease and Related Health Problems) criteria for KD and being treated with IVIG.

Results:

Four-hundred and fifty-nine children met inclusion criteria, 67 were excluded for subsequent rheumatologic diagnosis, unknown race, or failure to meet the American Heart Association guideline criteria. Our final cohort consisted of 392 subjects, with median age of 2.7 years, 65.1% male, 66.1% White, 24.2% Black, 4.9% Asian and 82.9% responded to a single dose of IVIG. Coronary ectasia or aneurysm developed in 27%; 7.4% developed aneurysms and 2.3% giant coronary aneurysms. Nonresponders were more likely to be Black, have higher white blood cell, erythrocyte sedimentation rate and C-reactive protein, lower hemoglobin, develop ectasia or aneurysm and require critical care and hospital readmission. Responders achieved echocardiographic normalization more often compared with nonresponders (81.3% vs. 60.9%, P = 0.002) and coronary artery pseudonormalization (87.2% vs. 69.7%, P = 0.03) at 1 year. Black nonresponders had the slowest normalization at 1 year (52.9%, P = 0.02).

Conclusions:

Nonresponders have higher rates and greater severity of coronary involvement than responders. Our study uniquely demonstrates Black race as a risk factor for nonresponse and for delayed normalization of cardiac involvement at 1-year follow-up.
Statistical Modeling for Quality Assurance of Human Papillomavirus DNA Batch Testing
Authors: Beylerian Emily N. , Slavkovsky Rose C. , Holme Francesca M. , Jeronimo Jose A.
Published: March 2018

Objectives

Our objective was to simulate the distribution of human papillomavirus (HPV) DNA test results from a 96-well microplate assay to identify results that may be consistent with well-to-well contamination, enabling programs to apply specific quality assurance parameters.

Materials and Methods

For this modeling study, we designed an algorithm that generated the analysis population of 900,000 to simulate the results of 10,000 microplate assays, assuming discrete HPV prevalences of 12%, 13%, 14%, 15%, and 16%. Using binomial draws, the algorithm created a vector of results for each prevalence and reassembled them into 96-well matrices for results distribution analysis of the number of positive cells and number and size of cell clusters (≥2 positive cells horizontally or vertically adjacent) per matrix.

Results

For simulation conditions of 12% and 16% HPV prevalence, 95% of the matrices displayed the following characteristics: 5 to 17 and 8 to 22 total positive cells, 0 to 4 and 0 to 5 positive cell clusters, and largest cluster sizes of up to 5 and up to 6 positive cells, respectively.

Conclusions

Our results suggest that screening programs in regions with an oncogenic HPV prevalence of 12% to 16% can expect 5 to 22 positive results per microplate in approximately 95% of assays and 0 to 5 positive results clusters with no cluster larger than 6 positive results. Results consistently outside of these ranges deviate from what is statistically expected and could be the result of well-to-well contamination. Our results provide guidance that laboratories can use to identify microplates suspicious for well-to-well contamination, enabling improved quality assurance.
Prevalence of Suspected Nonalcoholic Fatty Liver Disease in Lean Adolescents in the United States
Authors: Conjeevaram Selvakumar Praveen Kumar , Kabbany Mohammad Nasser , Lopez Rocio , Rayas Maria S , Lynch Jane L , Alkhouri Naim
Published: March 2018

Objectives:

Nonalcoholic fatty liver disease (NAFLD) can develop in lean subjects referred to as lean NAFLD. We aim to evaluate the prevalence and risk factors of NAFLD in lean adolescents in the United States (US).

Methods:

Cross sectional data from 1482 lean subjects (body mass index <85th percentile) ages between 12 and 18 years, who were enrolled in the National Health and Examination Survey during the 2005 to 2014 cycles were included. We defined suspected NAFLD as alanine aminotransferase >25.8 U/L for boys and >22.1 U/L for girls; hypertriglyceridemia as triglycerides ≥150 mg/dL; low HDL as HDL <40 mg/dL and insulin resistance (IR) as homeostatic model assessment of IR ≥3.

Results:

The mean weighted prevalence of suspected NAFLD among lean adolescents during 2005 to 2014 cycles was 8% (95% CI 6.2–9.9). Lean subjects with suspected NAFLD were significantly older compared with lean non‐NAFLD subjects (15.5 vs 15 years, P value <0.05). Low HDL (15.5% vs 6.8%; P value 0.016) and hypertriglyceridemia (10% vs 3.9%; P value 0.028) were also found to be more common among lean NAFLD subjects compared with their non‐NAFLD counterparts. Presence of IR increased the risk of having suspected NAFLD by 4‐fold among lean adolescents. Non‐Hispanic black lean adolescents were less likely to have suspected NAFLD compared with non‐Hispanic white lean adolescents.

Conclusions:

The estimated prevalence of suspected NAFLD among lean adolescents in the US was found to be 8% with evidence of metabolic derangements such as low HDL, hypertriglyceridemia, and IR.
H3K4 Methylation Regulates LPS-Induced Proinflammatory Cytokine Expression and Release in Macrophages
Authors: Zhao Shuqi , Zhong Yuyun , Fu Xiaoxia , Wang Yiqian , Ye Ping , Cai Junwei , Liu Yun , Sun Jiang , Mei Zhuzhong , Jiang Yong , Liu Jinghua
Published: March 2018

Histone methylation is an important epigenetic mechanism that plays an essential role in regulating gene expression in mammalian cells. To understand its influence on inflammation, methylation of H3K4, H3K9, H3K36, H3K79, and H4K20, the most common histones methylated in the inflammatory response was analyzed in murine RAW264.7 cells and bone marrow-derived macrophages (BMDMs) upon lipopolysaccharide (LPS) stimulation. LPS stimulation resulted in enhanced methylation at H3K4 and H3K9 in both RAW264.7 and BMDMs. To further confirm whether LPS-stimulated H3K4me2 and H3K9me2 were responsible for subsequent proinflammatory cytokine expression, the recruitment of H3K4me2 and H3K9me2 at the promoters of interleukin (IL)-6 and tumor necrosis factor-α (TNF-α) was assessed. H3K4me2, but not H3K9me2, was enriched at the promoters of both IL-6 and TNF-α. Furthermore, LPS-stimulated gene expression and release of IL-6 and TNF-α were markedly suppressed in macrophages by MTA, a specific inhibitor of H3K4 methylation. These results demonstrate that histone methylation, in particular H3K4me2, plays a critical role in the regulation of LPS-induced expression and release of IL-6 and TNF-α.
The Association of Abdominal Striae With Pelvic Organ Prolapse
Authors: Miranne Jeannine M. , Kramer MaryJo E. , Mete Mihriye , Iglesia Cheryl B.
Published: March 2018

Objective

Our objective was to estimate the prevalence of abdominal wall striae among women with and without pelvic organ prolapse (POP) in a population with pelvic floor disorders.

Methods

This cross-sectional study included nonpregnant women with urinary incontinence and POP presenting to a tertiary urogynecology practice between December 2012 and August 2013. Participants completed a nonvalidated questionnaire about striae, and the degree of abdominal wall striae was quantified on physical examination. Baseline demographics, clinical characteristics, and Pelvic Organ Prolapse Quantification (POP-Q) measurements were recorded.

Results

One hundred thirty-two women were approached for participation, of which 110 (83%) completed study questionnaires. Of these 110, 59 had POP defined at POP-Q stages 2–4, whereas 51 had normal pelvic support, POP-Q stages 0–1. The mean (SD) age was 55.5 (12) years, and most (78/110) were sexually active. Women with POP were more parous than women without POP (median 2 vs 1, respectively; P = 0.03). However, there was no difference in medical comorbidities, smoking status, or steroid use between groups (P > 0.05). More women with POP reported striae (42/59 [71%] vs 23/51 [45%], P = 0.006) and had quantifiable abdominal wall striae compared with women with normal support (39/59 [66%] vs 22/51 [44%], P = 0.02). On multivariate logistic regression, women with POP were 2.5 times more likely to have striae compared with women without POP after adjusting for skin type and smoking status (odds ratio, 2.5; 95% confidence interval, 1.03–6.06; P = 0.04).

Conclusion

Women with POP are more likely to have striae compared with women without POP.
Successful Treatment of Paradoxical Puborectalis Contraction and Intractable Anorectal Pain With Sacral Neuromodulation
Authors: Roth Ted M.
Published: March 2018

Background

Paradoxical puborectalis contraction (PPC) is a syndrome of obstructed defecation associated with a cluster of complaints including rectal pain, incomplete evacuatory sensation, prolonged repetitive straining with bowel movements, and the need for digital manipulation. Traditional treatment has yielded mixed results.

Case

We present a case of PPC successfully treated with staged sacral neuromodulation and review her diagnostic features, medical regimen, and prior unsuccessful interventions tried. Symptoms were analyzed using a visual analog scale pain score (0–10). Criteria to progress to implantation of the pulse generator included a pain score less than 3 during test stimulation and/or greater than 50% decrease in the pain score compared to baseline.

Our patient had a pain score of 0 (baseline 8) with stage 1 sacral neuromodulation. In addition, she had dramatic relief in her straining with bowel movements and need for digital manipulation. Her pulse generator was implanted after a 2-week trial, and she has experienced a lasting improvement at her follow-up of 2 years.

Conclusions

Sacral neuromodulation is an established therapy for overactive bladder syndrome, urinary retention, and fecal incontinence. In urology, the use of sacral neuromodulation has been described to benefit some patients with pelvic floor pain. Sacral neuromodulation can be a successful treatment for PPC and functional anorectal pain with resulting improvement in quality of life without the sequelae of an invasive and irreversible surgery.
Single-molecule optical mapping enables accurate molecular diagnosis of facioscapulohumeral muscular dystrophy (FSHD)
Authors: Dai Yi , Li Pidong , Wang Zhiqiang , Liang Fan , Yang Fan , Fang Li , Huang Yu , Huang Shangzhi , Zhou Jiapeng , Wang Depeng , Cui Liying , Wang Kai
Published: March 2018

Facioscapulohumeral Muscular Dystrophy (FSHD) is a common adult muscular dystrophy in which the muscles of the face, shoulder blades and upper arms are among the most affected. FSHD is the only disease in which “junk” DNA is reactivated to cause disease, and the only known repeat array-related disease where fewer repeats cause disease. More than 95% of FSHD cases are associated with copy number loss of a 3.3kb tandem repeat (D4Z4 repeat) at the subtelomeric chromosomal region 4q35, of which the pathogenic allele contains less than 10 repeats and has a specific genomic configuration called 4qA. Currently, genetic diagnosis of FSHD requires pulsed-field gel electrophoresis followed by Southern blot, which is labor-intensive, semi-quantitative and requires long turnaround time. Here, we developed a novel approach for genetic diagnosis of FSHD, by leveraging Bionano Saphyr single-molecule optical mapping platform. Using a bioinformatics pipeline developed for this assay, we found that the method gives direct quantitative measurement of repeat numbers, can differentiate 4q35 and the highly paralogous 10q26 regions, can determine the 4qA/4qB allelic configuration, and can quantitate levels of post-zygotic mosaicism. We evaluated this approach on 5 patients (including two with post-zygotic mosaicism) and 2 patients (including one with post-zygotic mosaicism) from two separate cohorts, and had complete concordance with Southern blots, but with improved quantification of repeat numbers resolved between haplotypes. We concluded that single-molecule optical mapping is a viable approach for molecular diagnosis of FSHD and may be applied in clinical diagnostic settings once more validations are performed.
Real-time analysis and visualization of pathogen sequence data
Authors: Neher Richard A. , Bedford Trevor
Published: March 2018

The rapid development of sequencing technologies has to led to an explosion of pathogen sequence data that are increasingly collected as part of routine surveillance or clinical diagnostics. In public health, sequence data is used to reconstruct the evolution of pathogens, anticipate future spread, and target interventions. In clinical settings whole genome sequences identify pathogens at the strain level, can be used to predict phenotypes such as drug resistance and virulence, and inform treatment by linking to closely related cases. However, the vast majority of sequence data are only used for specific narrow applications such as typing. Comprehensive analysis of these data could provide detailed insight into outbreak dynamics, but is not routinely done since fast, robust, and interpretable analysis work-flows are not in place. Here, we review recent developments in real-time analysis of pathogen sequence data with a particular focus on visualization and integration of sequence and phenotypic data.
Conservation and divergence in modules of the transcriptional programs of the human and mouse immune systems
Authors: Shay Tal , Jojic Vladimir , Zuk Or , Benoist Christophe , Koller Daphne , Regev Aviv ,   ImmGen consortium
Published: March 2018

Studies in mouse have shed important light on human hematopoietic differentiation and disease. However, substantial differences between the two species often limit the translation of findings from mouse to human.

Here, we compare previously defined modules of co-expressed genes in human and mouse immune cells based on compendia of genome-wide profiles. We show that the overall modular organization of the transcriptional program is conserved. We highlight modules of co-expressed genes in one species that dissolve or split in the other species. Many of the associated regulatory mechanisms – as reflected by computationally inferred trans regulators, or enriched cis-regulatory elements – are conserved between the species. Nevertheless, the degree of conservation in regulatory mechanism is lower than that of expression, suggesting that distinct regulation may underlie some of the conserved transcriptional responses.
Purge Haplotigs: Synteny Reduction for Third-gen Diploid Genome Assemblies
Authors: Roach Michael J , Schmidt Simon , Borneman Anthony R
Published: March 2018

Recent developments in third-gen long read sequencing and diploid-aware assemblers have resulted in the rapid release of numerous reference-quality assemblies for diploid genomes. However, assembling highly heterozygous genomes is still facing a major problem where the two haplotypes for a region are highly polymorphic and the synteny is not recognised during assembly. This causes issues with downstream analysis, for example variant discovery using the haploid assembly, or haplotype reconstruction using the diploid assembly. A new pipeline—Purge Haplotigs—was developed specifically for third-gen assemblies to identify and reassign the duplicate contigs. The pipeline takes a draft haplotype-fused assembly or a diploid assembly, and read alignments to produce an improved assembly. The pipeline was tested on a simulated dataset and on four recent diploid (phased) de novo assemblies from third-generation long-read sequencing. All assemblies after processing with Purge Haplotigs were less duplicated with minimal impact on genome completeness. The software is available at https://bitbucket.org/mroachawri/purge_haplotigs under a permissive MIT licence.
Topological linkage disequilibrium calculated from coalescent genealogies
Authors: Wirtz Johannes , Rauscher Martina , Wiehe Thomas
Published: March 2018

We revisit the classical concept of two-locus linkage disequilibrium (LD) and introduce a novel way of looking at haplotypes. In contrast to defining haplotypes as allele combinations at two marker loci, we concentrate on the clustering of sampled chromosomes induced by their coalescent genealogy. The root of a binary coalescent trees defines two clusters of chromosomes. At two different loci this assignment may be different as a result of recombination. We show that the amount of shared chromosomes among clusters at two different loci, measured by the squared correlation, constitutes a natural measure ofLD. We call thistopological LD(tLD) since it is induced by the topology of the coalescent tree. We find that its rate of decay decreases more slowly with distance between loci than that of conventionalLD. Furthermore,tLDhas a smaller coefficient of variation, which should render it more accurate for any kind of mapping purposes than conventionalLD. We conclude with a practical application to the LCT region in human populations.
Microtubule end tethering of a processive Kinesin-8 motor Kif18b is required for spindle positioning
Authors: McHugh Toni , Gluszek-Kustusz Agata , Welburn Julie P.I.
Published: March 2018

Mitotic spindle positioning specifies the plane of cell division during anaphase. Spindle orientation and positioning is therefore critical to ensure symmetric division in mitosis and asymmetric division during development. The control of astral microtubule length plays an essential role in positioning the spindle. Here we show using gene knockout that the Kinesin-8 Kif18b controls microtubule length to center the mitotic spindle at metaphase. Using an integrated approach, we reveal that Kif18b is a highly processive plus end-directed motor that uses a C-terminal non-motor microtubule-binding region to accumulate at growing microtubule plus ends. This region is regulated by phosphorylation to spatially control Kif18b accumulation at plus ends and is essential for Kif18b-dependent spindle positioning and regulation of microtubule length. Finally, we demonstrate that Kif18b shortens microtubules by increasing the catastrophe rate of dynamic microtubules. Overall, our work reveals that Kif18b utilizes its motile properties to reach microtubule ends where it regulates astral microtubule length to ensure spindle centering.
Distinct control of PERIOD2 degradation and circadian rhythms by the oncoprotein MDM2
Authors: Liu JingJing , Zou Xianlin , Gotoh Tetsuya , Brown Anne M. , Jiang Liang , Kim Jae Kyoung , Finkielstein Carla V.
Published: March 2018

The circadian clock relies on post-translational modifications to set the timing for degradation of core regulatory components and, thus, sets clock progression. Ubiquitin-modifying enzymes targeting clock components for degradation are known to mostly recognize phosphorylated substrates. A case in point is the circadian factorPERIOD2(PER2) whose phospho-specific turnover involves its recognition by β-transducin repeat containing proteins (β-TrCPs). Yet, the existence of this unique mode of regulation of PER2’s stability falls short of explaining persistent oscillatory phenotypes reported in biological systems lacking functional elements of the phospho-dependent PER2 degradation machinery.

In this study, we challenge the phosphorylation-centric view that PER2 degradation enhances circadian rhythm robustness byi) identifying the PER2:MDM2 endogenous complex,ii) establishing PER2 as a previously uncharacterized substrate for MDM2,iii) revealing an alternative phosphorylation-independent mechanism for PER2 ubiquitin-mediated degradation,iv) pinpointing residues for ubiquitin modification, andv) establishing the importance of MDM2-mediated PER2 turnover for defining the circadian period length. Our results not only expand MDM2’s suite of specific substrates beyond the cell cycle to include circadian components but also uncover novel regulatory players that likely impact our view of how other mechanisms crosstalk and modulate the clock itself.
Temperature explains broad patterns of Ross River virus transmission across Australia
Authors: Shocket Marta S. , Ryan Sadie J. , Mordecai Erin A.
Published: March 2018

Temperature impacts the physiology of ectotherms, including vectors that transmit disease. While thermal biology predicts nonlinear effects of temperature on vector and pathogen traits that drive disease transmission, the empirical relationship between temperature and transmission remains unknown for most vector-borne pathogens. We built a mechanistic model to estimate the thermal response of Ross River virus, an important mosquito-borne pathogen of humans in Australia, the Pacific Islands, and potentially emerging worldwide. Transmission peaks at moderate temperatures (26.4°C) and declines to zero at low (17.0°C) and high (31.5°C) temperatures. The model predicted broad patterns of disease across Australia. First, transmission is year-round endemic in the tropics and sub-tropics but seasonal in temperate zones. Second, nationwide human cases peak seasonally as predicted from population-weighted seasonal temperatures. These results illustrate the importance of nonlinear, mechanistic models for inferring the role of temperature in disease dynamics and predicting responses to climate change.
The Claustrum Coordinates Cortical Slow-Wave Activity
Authors: Narikiyo Kimiya , Mizuguchi Rumiko , Ajima Ayako , Mitsui Sachiko , Shiozaki Momoko , Hamanaka Hiroki , Johansen Joshua P. , Mori Kensaku , Yoshihara Yoshihiro
Published: March 2018

During sleep and awake rest, the neocortex generates large-scale slow-wave activity. Here we report that the claustrum, a poorly understood subcortical neural structure, coordinates neocortical slow-wave generation. We established a transgenic mouse line allowing genetic and electrophysiological interrogation of a subpopulation of claustral glutamatergic neurons. These claustral excitatory neurons received inputs from glutamatergic neurons in a large neocortical network. Optogenetic activation of claustral neurons in vitro induced excitatory post-synaptic responses in most neocortical neurons, but elicited action potentials primarily in inhibitory interneurons. Optogenetic activation of claustral neurons in vivo induced a Down-state featuring a prolonged silencing of neural acticity in all layers of many cortical areas, followed by a globally synchronized Down-to-Up state transition. These results demonstrate a crucial role of the claustrum in synchronizing inhibitory interneurons across the neocortex for spatiotemporal coordination of brain state. Thus, the claustrum is a major subcortical hub for the synchronization of neocortical slow-wave activity.
In vivo pulse-labeling of isochronic cohorts of cells in the central nervous system using FlashTag
Authors: Govindan Subashika , Oberst Polina , Jabaudon Denis
Published: March 2018

This protocol describes a fluorescence birthdating technique to label, track and isolate isochronic cohorts of newborn cells in the central nervous system in vivo. Injection of carboxyfluorescein esters into the cerebral ventricle allows pulse-labeling of M-phase progenitors in touch with the ventricle and their progeny across the central nervous system, a procedure we termed FlashTag. Labeled cells can be imaged ex vivo or in fixed tissue, targeted for electrophysiological experiments, or isolated using Fluorescence-Activated Cell Sorting (FACS) for cell culture or (single-cell) RNA-sequencing. The dye is retained for several weeks, allowing labeled cells to be identified postnatally. This protocol describes the labeling procedure using in utero injection, the isolation of live cells using FACS, as well as the processing of labeled tissue using immunohistochemistry.
Disrupted neural adaptation in autism spectrum disorder
Authors: Millin Rachel , Kolodny Tamar , Flevaris Anastasia V. , Kale Alex M. , Schallmo Michael-Paul , Gerdts Jennifer , Bernier Raphael A. , Murray Scott O.
Published: March 2018

There has been long-standing speculation that autism spectrum disorder (ASD) involves an increase in excitation relative to inhibition. However, there is little direct evidence of increased neural excitation in humans with ASD. Here we provide a potential explanation for this discrepancy: we show that increased neural excitation emerges only after repeated stimulation, manifesting as a deficit in neural adaptation. We measured fMRI responses induced by repeated audio-visual stimulation and button presses in early sensory-motor cortical areas. Across all cortical areas we show reduced adaptation in individuals with ASD compared to neurotypical individuals. The degree of adaptation is correlated between cortical areas and with button-press reaction times across subjects. These findings suggest that increased neural excitation in ASD, manifesting as dysregulated neural adaptation, is domain-general and behaviorally-relevant.
Iteratively improving Hi-C experiments one step at a time
Authors: Golloshi Rosela , Sanders Jacob , McCord Rachel Patton
Published: March 2018

The 3D organization of eukaryotic chromosomes affects key processes such as gene expression, DNA replication, cell division, and response to DNA damage. The genome-wide chromosome conformation capture (Hi-C) approach can characterize the landscape of 3D genome organization by measuring interaction frequencies between all genomic regions. Hi-C protocol improvements and rapid advances in DNA sequencing power have made Hi-C useful to diverse biological systems, not only to elucidate the role of 3D genome structure in proper cellular function, but also to characterize genomic rearrangements, assemble new genomes, and consider chromatin interactions as potential biomarkers for diseases. Yet, the Hi-C protocol is still complex and subject to variations at numerous steps that can affect the resulting data. Thus, there is still a need for better understanding and control of factors that contribute to Hi-C experiment success and data quality. Here, we evaluate recently proposed Hi-C protocol modifications as well as often overlooked variables in sample preparation and examine their effects on Hi-C data quality. We examine artifacts that can occur during Hi-C library preparation, including microhomology-based artificial template copying and chimera formation that can add noise to the downstream data. Exploring the mechanisms underlying Hi-C artifacts pinpoints steps that should be further optimized in the future. To improve the utility of Hi-C in characterizing the 3D genome of specialized populations of cells or small samples of primary tissue, we identify steps prone to DNA loss which should be optimized to adapt Hi-C to lower cell numbers.

Highlights

3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point)

Variability in Hi-C libraries can arise from early steps of cell preparation

Hi-C 2.0 changes to interaction capture steps also benefit 6-cutter libraries

Artificial molecule fusions can arise during end repair and PCR, increasing noise

Common causes of Hi-C DNA loss identified for future optimization
China’s urban-rural relationship: evolution and prospects
Authors: Zhang Zhenghe , Lu Yawen
Published: March 2018

Purpose

In the 69 years since the founding of the People’s Republic of China, especially the 40 years since the reform and opening-up, the relationship between urban and rural areas has undergone profound change. When the deepening reform of the urban-rural relationship is entering a critical period, it is necessary to reassess the evolution of the urban-rural relationship in China and draw a picture for that relationship in the future. The paper aims to discuss these issues.

Design/methodology/approach

This paper combs the policies on the urban and rural development since the founding of the People’s Republic of China, and analyzes macro data on the industries, population, personal income, and other aspects.

Findings

The study found that this urbanism affects individuals’ lives and the choices of society through the will of the state, and then provides feedback at the whole level of social values.

Originality/value

This paper divides the evolution of China’s urban-rural relationship into two major stages – nurturing cities with rural areas and leading rural areas with cities, which are then subdivided into five periods. The features of the relationship between the urban and rural areas in different periods are analyzed, and the future development of urban-rural relations is also considered.
Returns to public agricultural and rural investments in China
Authors: Fan Shenggen , Cho Emily EunYoung , Rue Christopher
Published: March 2018

Purpose

The purpose of this paper is to review China’s past returns in a period over the last 40 years to public agricultural and rural investments to highlight the importance for future strategic investments in China’s agri-food system and in rural areas.

Design/methodology/approach

The paper synthesizes research findings from previous studies and reviews more recent trends. Based on the main findings, the authors provide forward-looking guidance for China’s investments agriculture and rural areas in the context of emerging global and domestic trends in agriculture, food security, and nutrition.

Findings

Public investments in the agricultural research and development (R&D), rural education, and rural infrastructure have been shown to have significant positive returns to agricultural growth as well as to reductions in poverty and regional inequality. Returns to overall agricultural GDP were highest for agricultural R&D, followed by education, roads, and telephones. Investment in education had the greatest returns to poverty reduction, as well as to nonfarm GDP and overall rural GDP. Investment in agricultural R&D had the second greatest returns in term of poverty reduction, and was also a close second in returns to nonfarm GDP and overall rural GDP following education. The rural infrastructure spending also saw significant returns to poverty reduction, largely through growth in agricultural and nonagricultural sectors. Investments in agriculture and rural areas will continue to be important, as China and the world face emerging challenges amidst a changing global landscape, particularly regarding climate change, rapid urbanization, nutritional imbalances, and food safety concerns. In addressing these emerging challenges, continued support for agricultural R&D and innovations can play a key role.

Originality/value

The paper highlights research findings on key investment areas that will be increasingly important for China’s agri-food system, and provides guidance in the context of emerging trends impacting food security and nutrition.
Off-farm employment over the past four decades in rural China
Authors: Zhang Linxiu , Dong Yongqing , Liu Chengfang , Bai Yunli
Published: March 2018

Purpose

The purpose of this paper is to evaluate the trend of off-farm employment in rural China over the past four decades since the reform and opening-up.

Design/methodology/approach

Using two sets of panel survey data, the China National Rural Survey conducted in 2000 and 2008, and the China Rural Development Survey conducted in 2005, 2008, 2012 and 2016, this study offers a re-visit of China’s off-farm employment to give us the latest information about its evolution and whether rural labor markets have developed in a way that will allow them to facilitate the transformation of China’s economy more effectively. The evolution of off-farm employment is further examined through decomposition of types, destinations, industries, and population sub-groups as well as the change in the wage rate.

Findings

The data show the rapid increase in rural labor activities over the whole study period. Most notably, the authors findnd that a rapid rise in off-farm employment has continued even until after 2008 and into the mid-2010s, which is a time when some feared that macroeconomic conditions might keep rural residents on the farm or drive them back to the farm. In the disaggregation of labor market trends, the authors show that labor markets are acting consistently with an economy that is in transition from being dominated by agriculture to being dominated by other forms of production and with a population that is consistently becoming more urban.

Originality/value

The authors believe that the results will contribute positively to the exploration of answers to the question whether or not rural labor markets have developed in a way that will allow them to facilitate the transformation of China’s economy more effectively over the last four decades.
Knowledge hiding: impact of interpersonal behavior and expertise
Authors: Lanke Parijat
Published: March 2018

Purpose

This paper intends to put forward the role of interpersonal (in)justice among co-workers and their individual expertise as important factors contributing to knowledge hiding behavior. The paper is written with an intent to explain a conceptual model for practitioners’ benefit. The work is novel and covers the latest construct in the field of knowledge management and human resource management.

Design/methodology/approach

A conceptual framework is elaborated with a brief explanation of the theory that helps explain it. The framework although being novel in itself, the explanation has been drawn from existing literature.

Findings

If the co-workers do not treat each other with dignity and respect, it hampers their relationship. This in turn makes them hide knowledge from each other and at the same time if one of them holds an expertise power over the other, this behavior would be more enhanced. The whole relationship could be explained using social exchange theory. This holds implications for managers, especially when knowledge management is of paramount importance to a company for its sustenance.

Practical implications

This work provides new insights into knowledge hiding behavior by employees. Certain ways to reduce this behavior are proposed.

Originality/value

This paper is the one of the few written with an intent to bring knowledge hiding and its causes, to executives, in an easy to digest form. The concept is also newly introduced and these factors have not yet been brought up by any other researcher in the field.
Increasing the strategic role of HR: the importance of macro-economic conditions
Authors: Morris Adam
Published: March 2018

Purpose

The purpose of this paper is to introduce notions for increasing the strategic position of the HR function by outlining the influence that macro-economic trends play on the role of the function and the success of its initiatives. The main focus is on how HR can over time change with economic cycles to add tangible value and drive strategic conversations.

Design/methodology/approach

This argument is split into three sections: the importance of strategic considerations for change, macro-economic trends and HR, and HR’s increased input to business strategy. It looks at the work of key theorists in change management, analyzes the history of HR and develops these arguments into conclusions about how to improve HR’s strategic role.

Findings

Key theories of change management demonstrate that strategy is critical to the success of change projects. This means encompassing both internal and external factors affecting a business. By examining the historical development of HR it is clear to see that macro-economic trends are a significant external factor that is not often investigated by HR. If HR can harness this information, they will be able to implement proactive initiatives and drive strategic conversations.

Originality/value

The notions outlined in this paper identify a significant factor for the success of HR that is not often investigated by the function, allowing HR to implement more effective initiatives at optimal times.
The asymmetric price-volume relation revisited: evidence from Qatar
Authors: Ahmed Walid M.A.
Published: March 2018

Purpose

This study aims to revisit the stock price–volume relations, providing new evidence from the emerging market of Qatar. In particular, three main issues are examined using both aggregate market- and sector-level data. First, the return–volume relation and whether or not this relation is asymmetric. Second, the common characteristics of return volatility; and third, the nature of the relation between trading volume and return volatility.

Design/methodology/approach

The study uses the OLS and VAR modeling approaches to examine the contemporaneous and dynamic (causal) relations between index returns and trading volume, respectively, while an EGARCH-X(1,1) model is used to analyze the volatility–volume relation. The data set comprises daily index observations and the corresponding trading volumes for the entire market and the individual seven sectors of the Qatar Exchange (i.e. banks and financial services, consumer goods and services, industrials, insurance, real estate, telecommunications and transportation).

Findings

The empirical analysis reports evidence of a positive contemporaneous return–volume relation in all sectors barring transportation and insurance. This relation appears to be asymmetric for all sectors. For the market and almost all sectors, there is no significant causality between returns and volume. By and large, these findings lend support for the implications of the mixture of distributions hypothesis (MDH). Lastly, the information content of lagged volume seems to have an important role in predicting the future dynamics of return volatility in all sectors, with the industrials being the exception.

Practical implications

The findings provide important implications for portfolio managers and investors, given that the volume of transactions is generally found to be informative about the price movement of sector indices. Specifically, tracking the behavior of trading volume over time can give a broad portrayal of the future direction of market prices and volatility of equity, thereby enriching the information set available to investors for decision-making.

Originality/value

Based on both market- and sector-level data from the emerging stock market of Qatar, this study attempts to fill an important void in the literature by examining the return–volume and volatility–volume linkages.
Macroeconomic determinants of trade openness: empirical investigation of SAARC region
Authors: Tahir Muhammad , Hasnu SAF , Ruiz Estrada Mario
Published: March 2018

Purpose

Trade openness plays a significant role in the growth process of countries. The purpose of this paper is to examine the impact of macroeconomic determinants on the trade openness of countries.

Design/methodology/approach

The study focuses on the South Asian Association for Regional Cooperation (SAARC) member countries and the data used were from 1971 to 2011. Panel data econometrics techniques and two stages least square method (TSLS) are used to carry out empirical analysis and robustness testing.

Findings

The main finding of the paper is that macroeconomic determinants such as investment both in physical and human capital and per capita gross domestic product (GDP) positively affect trade openness. Further, the size of labour force and currency exchange rate has also impacted trade openness negatively and significantly.

Practical implications

It implies that efficient macroeconomic management matters for higher trade openness. The sampled developing countries are suggested to pay favourable attention to macroeconomic variables if they want to grow in the long run through outward-oriented policies.

Originality/value

This paper is an original contribution in the context of SAARC countries by focusing on the relationship between macroeconomic determinants and trade openness.
Multiplying the use of space and what it implies in practice: a cross-case analysis
Authors: Brinkoe Rikke , Nielsen Susanne Balslev
Published: March 2018

Purpose

Shared space is a design and engineering concept that gains attention in the context of both regeneration of, for example, former production sites and in the context of designing new building complex(es) with a multifunction strategy. But the practicalities of realising shared space are generally overlooked, despite its importance for the user experience and the degree of success with shared space initiatives. The purpose of this study is to increase the knowledge of shared space and the complex processes involved in realising multiple use of space.

Design/methodology/approach

To achieve the purpose stated, the paper presents a study of current literature and four cases of shared space, including a commercial building, a public sport facility, a public health centre and an educational building. The study draws on theory from the fields of property management, space management, urban design and architecture, as well as from the social sciences and geography, to provide an as complete picture as possible of the challenges related to shared spaces in practice.

Findings

The result of the study presented is increased knowledge of the processes involved in sharing space in a facilities management context, supported by specific recommendations regarding attention to issues of territoriality, involvement and practicalities.

Originality/value

Not much scientific work has been conducted on the topic of shared space in a facilities management context, and this study adds to the so far limited knowledge within the area.
Developing waqf land through crowdfunding-waqf model (CWM): the case of Malaysia
Authors: Mohd Thas Thaker Mohamed Asmy Bin , Allah Pitchay Anwar
Published: March 2018

Purpose

This paper aims to attempt to offer a viable alternative model of source of financing to develop waqf land, which is known as crowdfunding-waqf model (CWM).

Design/methodology/approach

The extant literature on the financing constraints faced by waqf institution in developing waqf land, and crowdfunding have been reviewed critically and used in the attempt of proposing an alternative model.

Findings

The paper has developed CWM as a source of financing for waqf institution in Malaysia. This model is expected to provide waqf institution in Malaysia to meet their liquidity constraint in developing waqf land. It also involves an involvement of crowdfunding platform.

Research limitations/implications

The paper is based on conceptual explorations of literature in the area of waqf and crowdfunding. This is a conceptual paper, so it did not use any empirical analysis.

Practical implications

The findings of this paper will provide waqf institution with an alternative source of financing to develop waqf land. The present study also has implications for government and policymakers. By involving crowdfunding, it helps the government to reduce its expenses for the development of waqf land in Malaysia.

Originality/value

This paper offers an additional literature on waqf and crowdfunding especially from the Malaysian context. The paper proposes a viable alternative model for waqf institution as a source of financing by using crowdfunding, to develop waqf land. This model incorporates donation-based crowdfunding model and reward-based crowdfunding model. This model is different with the existing way of raising Cash waqf, which is conducted also via online basis by financial institutions and state government agencies. Later, the collected Cash waqf fund is transformed into illiquid assets such as building of hospitals, educational institutions and purchasing machinery and assets. However, the nature of proposed model in this study is to assist waqf institution to develop waqf land. Crowdfunding model is used to raise fund to develop waqf land in Malaysia. The fund collected via crowdfunding model is based on donation and reward based, not based on the nature of Cash waqf.