bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human brain atlas: miRNA version
Authors: Khara M , Zhou Z , Wong J , Renwick N 
Published: September 2019

Human brain is a complex organ comprising multiple cell types of differing function. Although histological evaluation remains the mainstay approach for evaluating tissue, comprehensive molecular characterization is now possible due to advanced -omic approaches. microRNAs (miRNAs) are small (~22 nt) RNA molecules that regulate gene expression and mediate cellular differentiation in normal brain development. miRNAs also make excellent tissue markers due to their abundance, cell-type and disease-stage specificity, and stability in solid/liquid clinical samples. To advance our knowledge of miRNA-mediated gene regulation in human brain, we generated comprehensive miRNA expression profiles from 117 fresh normal brain samples through barcoded small RNA sequencing; tissues included neocortex, allocortex, white matter, cerebellum, olfactory bulb, optic nerve, pineal gland and spinal cord. FASTQ sequence files were annotated using state-of-the-art sequence annotation available through the Renwick lab. Following data pre-processing, high expression analysis of miRNA profiles showed that miR-9 was the highest expressed miRNA in neocortex, cerebellum and olfactory bulb, whereas miR-22 was highest expressed in cingulate cortex, optic nerve and spinal cord; interestingly, miR-29 was the highest expressed miRNA in hippocampus. Our analyses showed a trend towards unique miRNA signatures in different anatomical areas of the brain. Our next step is to perform miRNA fluorescence in situ hybridization on formalin-fixed paraffin-embedded tissues using a novel method developed in the Renwick lab. Accurate miRNA characterization of normal tissues will provide a firm basis for understanding miRNA changes in neurological diseases.LEARNING OBJECTIVESThis presentation will enable the learner to:1.Describe the function of miRNAs and their suitability as tissue/cell specific signatures2.Describe the miRNA expression trends in profiling various anatomical regions of the central nervous system
Image Analysis in Neuropathology: Hue-Saturation-Intensity vs. Colour Deconvolution
Authors: Cosma D , Alturkustani M , Khan A , Hammond R 
Published: September 2019

As image analysis expands into clinical and basic applications it is important that users be aware of opportunities and limitations. A common image analysis workflow involves the digitization of stained tissue sections into a red-green-blue (RGB) colour model for quantitative interpretation. Upstream of the digital image, quality and variability can be degraded at each step (tissue handling, fixation, sectioning, staining, image acquisition). Digital image analysis presents additional steps where variables can affect data quality. Image analysis platforms are not uniform. Aside from interface preferences, some introduce unintended variability due to their processing architecture that may not be obvious to the end-user. One important component of this is colour space representation: hue-saturation-intensity (HSI) vs. colour deconvolution (CD). A potential weakness of analyses within the HSI colour space is the mis-identification of darkly stained pixels, particularly when more than one stain is present. We were interested to discover whether HSI or CD provided greater fidelity in a typical immunoperoxidase/hematoxylin dataset.Fifty-nine samples were processed using HSI- and CD-based analyses. Processed image pairs were compared with the original sample to determine which processed image provided a more accurate representation. CD proved superior to HSI in 94.9% of the analyzed image pairs. Where the option exists, CD-based image analysis is strongly recommended.LEARNING OBJECTIVESThis presentation will enable the learner to:1.To describe differences between HSI and CD colour spaces2.To explain limitations in the use of HSI-based analyses3.To be aware of recent developments in CD-based platforms
NTRK2 Fusion Driven Pediatric Glioblastoma: Identification of key molecular drivers by personalized oncology
Authors: Levine  , Shen Y , Mungall K , Serrano J , Snuderl M , Pleasance E , Jones SJM , Laskin J , Marra MA , Rassekh R , Deyell R , Yip S , Cheng S , Dunham C 
Published: September 2019

We describe the case of an 11-month-old girl with a rare cerebellar glioblastoma driven by a NACC2-NTRK2 (Nucleus Accumbens Associated Protein 2-Neurotrophic Receptor Tyrosine Kinase 2) fusion. Initial workup of our case demonstrated homozygous CDKN2A deletion, but immunohistochemistry for other driver mutations, including IDH1 R132H, BRAF V600E, and H3F3A K27M were negative, and ATRX was retained. Tissue was subsequently submitted for personalized oncogenomic analysis, including whole genome and whole transcriptome sequencing, which demonstrated an activating NTRK2 fusion, as well as high PD-L1 expression, which was subsequently confirmed by immunohistochemistry. Furthermore, H3 and IDH demonstrated wildtype status. These findings suggested the possibility of treatment with either NTRK- or immune checkpoint- inhibitors through active clinical trials. Ultimately, the family pursued standard treatment that involved Head Start III chemotherapy and proton radiotherapy. Notably, at most recent follow upapproximately two years from initial diagnosis, the patient is in disease remission and thriving, suggesting favorable biology despite histologic malignancy. This case illustrates the value of personalized oncogenomics, as the molecular profiling revealed two actionable changes that would not have been apparent through routine diagnostics. NTRK fusions are known oncogenic drivers in a range of cancer types, but this is the first report of a NACC2-NTRK2 fusion in a glioblastoma.LEARNING OBJECTIVESThis presentation will enable the learner to:1.Explore the current molecular landscape of pediatric high grade gliomas2.Recognize the value of personalized oncogenomic analysis, particularly in rare and/or aggressive tumors3.Discuss the current status of NTRK inhibitor clinical trials
Role of MacroH2A2 in the glioblastoma stem cell epigenome
Authors: Nikolic A , Ellestad K , Johnston M , Dirks PB , Zemp FJ , Gafiuk C , Mahoney DJ , Gallo M 
Published: September 2019

Glioblastoma is the most common primary malignant brain tumour in adults, and remains uniformly lethal. These tumours contain a subpopulation of glioblastoma stem cells (GSCs) that drive tumour recurrence and drug resistance. We find that MacroH2A2 is a histone variant that can stratify glioblastoma patients, with higher levels of this histone variant associated with better patient prognosis. Knockdown of macroH2A2 in GSCs is associated with increased self-renewal and an increased expression of stemness genes by RNA-seq. Our preliminary results suggest that macroH2A2 is a novel biomarker for glioblastoma and that macroH2A2 loss is a marker of GSC stemness and a poor prognostic marker in glioblastoma. This work identifies loss of macroH2A2 as a feature of GSCs and provides a framework for therapeutic modulation of this histone variant.LEARNING OBJECTIVESThis presentation will enable the learner to:1.Explain the role of epigenetics in glioblastoma pathophysiology
Assessing autolyzed foetal brains
Authors: Joseph JT 
Published: September 2019

Problem:Evaluating very soft foetal brains is problematic, since anatomic information is often lost when these collapse on a dissection board.Methods:Present cases of very soft foetal brains photographed under water, discuss technical details on this technique, and indicate how these data can be used to evaluate the brains.Results:Foetal brains from intrauterine foetal deaths and from foetal terminations that have a long death-to-delivery time are often very soft, even after fixation, and collapse under their own weight on a dissection board. To better evaluate these brains, they have been floated and photographed in water. When possible, the brain is photographed intact in ventral and dorsal views. After the brainstem with cerebellum is removed and hemispheres are separated, these are all photographed; hemispheres are imaged in both lateral and medial views. This technique records developmental data about cortical gyration, the presence of olfactory tracts/bulbs, corpus callosum posterior extension, cerebellum foliation, and brainstem, which can be compared to standard brain development references. Problems with this technique include fragmentation of autolyzed brain into water.Discussions:Photography of very soft foetal brains under water allows evaluation of brains that normally collapse under their own weight. In cases too soft for meaningful dissection, these data often provide the only available brain developmental information.LEARNING OBJECTIVESThis presentation will enable the learner to:1.Photograph foetal brain under water2.Evaluate key aspects of external examination using standard developmental literature
Magnetic anisotropy and debris-dependent rheological heterogeneity within stratified basal ice
Authors: Hopkins Nathan R. , Evenson Edward B. , Bilardello Dario , Alley Richard B. , Berti Claudio , Kodama Kenneth P. 
Published: September 2019

AbstractBasal ice of glaciers and ice sheets frequently contains a well-developed stratification of distinct, semi-continuous, alternating layers of debris-poor and debris-rich ice. Here, the nature and distribution of shear within stratified basal ice are assessed through the anisotropy of magnetic susceptibility (AMS) of samples collected from Matanuska Glacier, Alaska. Generally, the AMS reveals consistent moderate-to-strong fabrics reflecting simple shear in the direction of ice flow; however, AMS is also dependent upon debris content and morphology. While sample anisotropy is statistically similar throughout the sampled section, debris-rich basal ice composed of semi-continuous mm-scale layers (thestratified facies) possesses well-defined triaxial to oblate fabrics reflecting shear in the direction of ice flow, whereas debris-poor ice containing mm-scale star-shaped silt aggregates (thesuspended facies) possesses nearly isotropic fabrics. Thus, deformation within the stratified basal ice appears concentrated in debris-rich layers, likely the result of decreased crystal size and greater availability of unfrozen water associated with high debris content. These results suggest that variations in debris-content over small spatial scales influence ice rheology and deformation in the basal zone.
Comparing the availability of paid parental leave for same-sex and different-sex couples in 34 OECD countries
Authors: WONG ELIZABETH , JOU JUDY , RAUB AMY , HEYMANN JODY 
Published: September 2019

AbstractThe availability of paid family leave has been widely researched in the context of a two-parent household with one mother and one father, yet few studies have explored whether households with same-sex parents have access to equal benefits. Expanding on previous cross-country comparisons of parental leave policies, this study examines parental leave policies in 34 OECD countries to compare the total duration of paid parental leave available to same-sex and different-sex parent families within a country. We find that same-sex female and different-sex couples receive equal durations of leave in the majority of countries. However, same-sex male couples often receive shorter durations of paid parental leave compared to both different-sex and same-sex female couples. In addition to addressing the implications of laws and policies surrounding same-sex marriage and same-sex adoption on parental leave availability, we highlight specific aspects of paid leave policies that may explain the unequal durations of paid leave between same-sex and different-sex couples.
Large prime factors on short intervals
Authors: MERIKOSKI JORI 
Published: September 2019

AbstractWe show that for all large enough x the interval [x, x + x1/2 log1.39x] contains numbers with a prime factor p > x18/19. Our work builds on the previous works of Heath–Brown and Jia (1998) and Jia and Liu (2000) concerning the same problem for the longer intervals [x, x + x1/2 + ϵ]. We also incorporate some ideas from Harman’s book Prime-detecting sieves (2007). The main new ingredient that we use is the iterative argument of Matomäki and Radziwiłł (2016) for bounding Dirichlet polynomial mean values, which is applied to obtain Type II information. This allows us to take shorter intervals than in the above-mentioned previous works. We have also had to develop ideas to avoid losing any powers of log x when applying Harman’s sieve method.
Developing a national research agenda to reduce consumption of sugar-sweetened beverages and increase safe water access and consumption among 0- to 5-year-olds: a mixed methods approach
Authors: Duffy Emily W , Lott Megan M , Johnson Emily J , Story Mary T 
Published: September 2019

AbstractObjective:Sugar-sweetened beverage (SSB) consumption in early childhood is a public health concern. Adequate hydration in early childhood is also important. We developed a national research agenda to improve beverage consumption patterns among 0–5-year-olds. This article focuses on the process used to develop this research agenda.Design:A mixed methods, multi-step process was used to develop the research agenda, including: (i) a scientific advisory committee; (ii) systematic reviews on strategies to reduce SSB consumption and increase water access and consumption; (iii) two stakeholder surveys to first identify and then rank strategies to reduce SSB consumption and increase water access and consumption; (iv) key informant interviews to better understand determinants of beverage consumption and strategies to improve beverage consumption patterns among high-risk groups; (v) an in-person convening with experts; and (vi) developing the final research agenda.Setting:This process included research and stakeholders from across the United States.Participants:A total of 276 participants completed survey 1 and 182 participants completed survey 2. Key informant interviews were conducted with 12 stakeholders. Thirty experts attended the convening, representing academia, government, and non-profit sectors.Results:Thirteen key issue areas and 59 research questions were developed. Priority topics were beverage consumption recommendations, fruit-flavoured drink consumption, interventions tailored to high-risk groups, and family engagement in childcare.Conclusions:This research agenda lays the groundwork for research efforts to improve beverage patterns of young children. The methods used can be a template to develop research agendas for other public health issues.
Linking agroecosystems producing farmed seafood with food security and health status to better address the nutritional challenges in Bangladesh
Authors: de Roos Baukje , Roos Nanna , Mamun Abdullah-Al , Ahmed Tahmeed , Sneddon Alan A , Murray Francis , Grieve Eleonor , Little David C 
Published: September 2019

AbstractObjective:Aquaculture is one of the fastest-growing food production sectors in many low-income and food-deficit countries with aquatic ecozones. Yet its specific impact on nutrition and livelihood in local communities, where commercial and/or export-orientated aquaculture activities are developed, is largely unknown.Design:The present narrative and argumentative review aims to provide an overview of our current understanding of the connections between aquaculture agroecosystems, local and national fish production, fish consumption patterns and nutrition and health outcomes.Results:The agroecological dynamic in a coastal-estuarine zone, where the aquatic environment ranges from fully saline to freshwater, is complex, with seasonal and annual fluctuations in freshwater supply creating a variable salinity gradient which impacts on aquatic food production and on food production more generally. The local communities living in these dynamic aquatic ecozones are vulnerable to poverty, poor diet and health, while these ecosystems produce highly valuable and nutritious aquatic foods. Policies addressing the specific challenges of risk management of these communities are limited by the sectoral separation of aquatic food production – the fisheries and aquaculture sector, the broader food sector – and public health institutions.Conclusions:Here we provide an argument for the integration of these factors to improve aquaculture value chains to better address the nutritional challenges in Bangladesh.
Prepregnancy obesity is associated with lower psychomotor development scores in boys at age 3 in a low-income, minority birth cohort
Authors: Nichols Amy R. , Rundle Andrew G. , Factor-Litvak Pam , Insel Beverly J. , Hoepner Lori , Rauh Virginia , Perera Frederica , Widen Elizabeth M. 
Published: September 2019

AbstractWhether maternal obesity and gestational weight gain (GWG) are associated with early-childhood development in low-income, urban, minority populations, and whether effects differ by child sex remain unknown. This study examined the impact of prepregnancy BMI and GWG on early childhood neurodevelopment in the Columbia Center for Children’s Environmental Health Mothers and Newborns study. Maternal prepregnancy weight was obtained by self-report, and GWG was assessed from participant medical charts. At child age 3 years, the Psychomotor Development Index (PDI) and Mental Development Index (MDI) of the Bayley Scales of Infant Intelligence were completed. Sex-stratified linear regression models assessed associations between prepregnancy BMI and pregnancy weight gain z-scores with child PDI and MDI scores, adjusting for covariates. Of 382 women, 48.2% were normal weight before pregnancy, 24.1% overweight, 23.0% obese, and 4.7% underweight. At 3 years, mean scores on the PDI and MDI were higher among girls compared to boys (PDI: 102.3 vs. 97.2, P = 0.0002; MDI: 92.8 vs. 88.3, P = 0.0001). In covariate-adjusted models, maternal obesity was markedly associated with lower PDI scores in boys [b = −7.81, 95% CI: (−13.08, −2.55), P = 0.004], but not girls. Maternal BMI was not associated with MDI in girls or boys, and GWG was not associated with PDI or MDI among either sex (all-P > 0.05). We found that prepregnancy obesity was associated with lower PDI scores at 3 years in boys, but not girls. The mechanisms underlying this sex-specific association remain unclear, but due to elevated obesity exposure in urban populations, further investigation is warranted.
Surface Warming During the 2018/Mars Year 34 Global Dust Storm
Authors: Streeter Paul M. , Lewis Stephen R. , Patel Manish R. , Holmes James A. , Kass David M. 
Published: September 2019

AbstractThe impact of Mars's 2018 Global Dust Storm (GDS) on surface and near‐surface air temperatures was investigated using an assimilation of Mars Climate Sounder observations. Rather than simply resulting in cooling everywhere from solar absorption (average surface radiative flux fell 26 W/m2), the globally averaged result was a 0.9‐K surface warming. These diurnally averaged surface temperature changes had a novel, highly nonuniform spatial structure, with up to 16‐K cooling/19‐K warming. Net warming occurred in low thermal inertia regions, where rapid nighttime radiative cooling was compensated by increased longwave emission and scattering. This caused strong nightside warming, outweighing dayside cooling. The reduced surface‐air temperature gradient closely coupled surface and air temperatures, even causing local dayside air warming. Results show good agreement with Mars Climate Sounder surface temperature retrievals. Comparisons with the 2001 GDS and free‐running simulations show that GDS spatial structure is crucial in determining global surface temperature effects.
Effects of Topography and Orientation on the Nonlinear Equilibration of Baroclinic Instability
Authors: Brown Justin M. , Gulliver Larry T. , Radko Timour 
Published: September 2019

AbstractThis study attempts to identify the equilibration mechanisms of baroclinic instability and investigate the effects of the orientation of the background flow and topography on eddy‐induced transport. The analysis is based on growth rate balance theory, which assumes that nonlinear equilibration occurs when the growth rate of the primary baroclinic instability becomes comparable to that of the secondary instabilities of amplifying modes. Two‐layer quasi‐geostrophic numerical simulations are performed and compared to growth rate balance theory in order to analytically predict the cross‐stream fluxes of potential vorticity. The model performs remarkably well in predicting the effects of variation in zonal topographic slope and background flow orientation. We find that meridional topographic slopes affect the baroclinic instability in an inherently nonlinear way. A predictive model based on conservation of potential vorticity is developed for the optimal slope that maximizes the transport characteristics of the baroclinic instability.
A Novel Method for Abrupt Motions Estimation of Sparse Scatterers in Differential Tomography SAR Imaging
Authors: Wu Baolong , He Lei , Tong Ling , Li Jinxin 
Published: September 2019

AbstractIn urban areas with many buildings, the scatterers located within one pixel can be assumed to be discrete and sparse (m = 0, 1, or 2). When the abrupt motions of sparse scatterers only happen in a single synthetic aperture radar (SAR) acquisition, these motions cannot be calculated using 2‐D or 3‐D frequency spectrum estimation method based on traditional differential Tomography SAR model. In this paper, a novel approach is proposed to solve this issue. By compensating a phase factor from the acquisition which has an abrupt motion and then maximizing the 3D Elevation‐Linear motion‐Amplitude of periodic motion spectrum at the scatterers locations, the final abrupt motions of the scatterers could be calculated. For the scatterers simulated, the estimation accuracy of the locations along elevation direction, linear motions velocity, the amplitudes of seasonal periodic motions, the amplitudes of relative scattering values, and the abrupt motions in the last acquisition are shown. The simulation results demonstrate that the proposed method can achieve high accuracy for no‐noise situation. The root‐mean‐square errors of the abrupt motions estimation are also acceptable (about 1–2 mm) when the signal‐to‐noise ratio = 10 and 8 dB. Thus, the estimation accuracy of the proposed algorithm can also fulfill the practical applications requirement.