bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Analysis of Osteoblast Activity Identifies Zbtb40 as a Regulator of Osteoblast Activity and Bone Mass
Authors: Doolittle Madison L. , Calabrese Gina M , Mesner Larry D. , Godfrey Dana A. , Maynard Robert D. , Ackert-Bicknell Cheryl L. , Farber Charles R. 
Published: November 2019

ABSTRACTOsteoporosis is a genetic disease characterized by progressive reductions in bone mineral density (BMD) leading to an increased risk of fracture. Over the last decade, genome-wide association studies (GWASs) have identified over 1000 associations for BMD. However, as a phenotype BMD is challenging as bone is a multicellular tissue affected by both local and systemic physiology. Here, we focused on a single component of BMD, osteoblast-mediated bone formation in mice, and identified associations influencing osteoblast activity on mouse Chromosomes (Chrs) 1, 4, and 17. The locus on Chr. 4 was in an intergenic region between Wnt4 and Zbtb40, homologous to a locus for BMD in humans. We tested both Wnt4 and Zbtb40 for a role in osteoblast activity and BMD. Knockdown of Zbtb40, but not Wnt4, in osteoblasts drastically reduced mineralization. Additionally, loss-of-function mouse models for both genes exhibited reduced BMD. Our results highlight that investigating the genetic basis of in vitro osteoblast mineralization can be used to identify genes impacting bone formation and BMD.
DeepACSON: Automated Segmentation of White Matter in 3D Electron Microscopy
Authors: Abdollahzadeh Ali , Belevich Ilya , Jokitalo Eija , Sierra Alejandra , Tohka Jussi 
Published: November 2019

ABSTRACTAutomated segmentation techniques are essential to tracing the entirety of ultrastructures in large three-dimensional electron microscopy (3D-EM) images of the brain tissue. Current automated techniques use deep convolutional neural networks (DCNNs) and rely on high-contrast cellular membranes to trace a small number of neuronal processes in very high-resolution EM datasets. We developed DeepACSON to segment large field-of-view, low-resolution 3D-EM datasets of white matter where tens of thousands of myelinated axons traverse the tissue. DeepACSON performs DCNN-based semantic segmentation and shape decomposition-based instance segmentation. With its top-down design, DeepACSON manages to account for severe membrane discontinuities inescapable with the low-resolution imaging. In particular, the instance segmentation of DeepACSON uses the tubularity of myelinated axons, decomposing an under-segmented myelinated axon into its constituent axons. We applied DeepACSON to ten serial block-face scanning electron microscopy datasets of rats after sham-operation or traumatic brain injury, segmenting hundreds of thousands of long-span myelinated axons, thousands of cell nuclei, and millions of mitochondria with excellent evaluation scores. DeepACSON quantified the morphology and spatial aspects of white matter ultrastructures, capturing nanoscopic morphological alterations five months after the injury.
Illuminance affects epidemiological parameters of banana Yellow Sigatoka in Brazil
Authors: Santana-Filho Djalma M. , da Silva Milene C. , de Souza Jorge T. , Cordeiro Zilton J. M. , Rocha Hermínio S. , Laranjeira Francisco F. 
Published: November 2019

ABSTRACTThe Sigatoka leaf spots are among the most important banana diseases. Although less damaging than black sigatoka, yellow sigatoka (Pseudocercospora musae) still prevails in some regions. This study aimed at testing the hypothesis of light interference in monocyclic parameters of yellow sigatoka epidemics. Grande Naine plantlets kept under contrasting shading conditions had their leaves 1 and 2 inoculated. Evaluations were performed for 60 days. For each inoculated leaf, the time until symptom onset (incubation), presence of infectious lesions (latency), and disease severity (extensive leaf necrosis) according to Stover’s scale modify per Gauhl (1994), called here only Stover’s scale, were registered. Logistic regression was used to assess the relative occurrence risk and survival analysis was used to check the effects of variables on relevant epidemiological parameters. The risks of sporulation and of reaching high severities were lower for plants kept under shading regardless of the acclimation conditions and no effect of leaf age was detected. The logistic regression showed symptoms appearing in both conditions (p=0,85), but have significance difference in occurrence of latent lesions (p=0,013) and necrosis (p<0,0001). The necrosis risk in non-shaded environment arrived 66%. The survival analysis showed significance difference in the time to appear the symptom evaluated in all tested variables (p<0,0001) in function of the cropping system. Lower illuminance negatively affected the incubation, latency and infectious periods, and severity. A shaded system could be tested to produce organic bananas in areas of high risk of occurrence of Yellow sigatoka disease.Significance and Impact of the StudyYellow Sigatoka (Pseudocercospora musae) is a banana disease that can cause severe damage if left uncontrolled. Its control is based mostly on fungicides.Our results show that shading downregulates the epidemiological parameters of that disease such as incubation, latent and infectious periods, and symptom’s severity. These results can be the basis for testing alternative cropping systems and producing organic bananas.
5’ splice site GC>GT variants differ from GT>GC variants in terms of their functionality and pathogenicity
Authors: Lin Jin-Huan , Masson Emmanuelle , Boulling Arnaud , Hayden Matthew , Cooper David N. , Férec Claude , Liao Zhuan , Chen Jian-Min 
Published: November 2019

ABSTRACTIn the human genome, most 5’ splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the non-canonical GC dinucleotide. The functionality and pathogenicity of 5’ splice site GT>GC (i.e., +2T>C) variants have been extensively studied but we still know very little about 5’ splice site GC>GT (+2C>T) variants. Herein, we sought to address this deficiency by performing a meta-analysis of identified +2C>T pathogenic variants together with a functional analysis of +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish a proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and pathogenicity and suggest that, in sharp contrast with +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants but might also improve our understanding of the evolutionary basis of switching between GT and GC 5’ splice sites in mammalian genomes.
Longest protein, longest transcript or most expression, for accurate gene reconstruction of transcriptomes?
Authors: Gilbert Donald G. 
Published: November 2019

AbstractMethods of transcript assembly and reduction filters are compared for recovery of reference gene sets of human, pig and plant, including longest coding sequence with EvidentialGene, longest transcript with CD-HIT, and most RNA-seq with TransRate. EvidentialGene methods are the most accurate in recovering reference genes, and maintain accuracy for alternate transcripts and paralogs. In comparison, filtering large over-assemblies by longest RNA measures, and most RNA-seq expression measures, discards a large portion of accurate models, especially alternates and paralogs. Accuracy of protein calculations is compared, with errors found in popular methods, as is accuracy of transcript assemblers. Gene reconstruction accuracy depends upon the underlying measurements, where protein criteria, including homology among species, have the strength of evolutionary biology that other criteria lack. EvidentialGene provides a gene reconstruction algorithm that is consistent with genome biology.
Reproduction has different costs for immunity and parasitism in a wild mammal
Authors: Albery Gregory F. , Watt Kathryn A. , Keith Rosie , Morris Sean , Morris Alison , Kenyon Fiona , Nussey Daniel H. , Pemberton Josephine M. 
Published: November 2019

Abstract

Life history theory predicts that reproductive allocation draws resources away from immunity, resulting in increased parasitism. However, studies of reproductive trade‐offs rarely examine multiple measures of reproduction, immunity and parasitism. It is therefore unclear whether the immune costs of reproductive traits correlate with their resource costs, and whether increased parasitism emerges from weaker immunity.

We examined these relationships in wild female red deer (Cervus elaphus) with variable reproductive allocation and longitudinal data on mucosal antibody levels and helminth parasitism. We noninvasively collected faecal samples, counting propagules of strongyle nematodes (order: Strongylida), the common liver fluke Fasciola hepatica and the red deer tissue nematode Elaphostrongylus cervi. We also quantified both total and anti‐strongyle mucosal IgA to measure general and specific immune allocation.

Contrary to our predictions, we found that gestation was associated with decreased total IgA but with no increase in parasitism. Meanwhile, the considerable resource demand of lactation had no further immune cost but was associated with higher counts of strongyle nematodes and E. cervi. These contrasting costs arose despite a negative correlation between antibodies and strongyle count, which implied that IgA was indicative of protective immunity.

Our findings suggest that processes other than classical resource allocation trade‐offs are involved in mediating observed relationships between reproduction, immunity and parasitism in wild mammals. In particular, reproduction–immunity trade‐offs may result from hormonal regulation or maternal antibody transfer, with parasitism increasing as a result of increased exposure arising from resource acquisition constraints. We advocate careful consideration of resource‐independent mechanistic links and measurement of both immunity and parasitism when investigating reproductive costs.

A free Plain Language Summary can be found within the Supporting Information of this article.
S wave attenuation based on Stokes boundary layer
Authors: Li Guangquan 
Published: November 2019

ABSTRACTBiot theory was based on two ideas: the coupling factor to quantify the kinetic energy of fluid and Darcy permeability to quantify the dissipation function. As Biot theory did not well predict attenuation of ultrasonic S wave, we modify the theory to better characterize the S wave attenuation. The range of the coupling factor is at first estimated in view of fluid mechanics. Application of the original theory to water‐saturated Boise sandstone and brine‐saturated Berea sandstone shows that the model prediction significantly underestimates the S wave attenuation ultrasonically measured. For this reason, we replace Darcy permeability with variable permeability to improve the fluid momentum equation. The new model yields predictions of phase velocity and the quality factor both close to the ultrasonic measurements. The reason why the improved model is superior to Biot theory is that variable permeability is based on the Stokes boundary layer at the fluid–solid interface, thus accurately quantifying the viscous stress between the two phases. Finally, the length scale of the viscous stress is calculated in the mesoscopic sense.
Survival and life table parameters of soybean pod borer Maruca vitrata (Geyer) (Lepidoptera: Crambidae) on leguminous crop cultivars
Authors: Yi Hwijong , Bae Soondo , Jung Jin Kyo , Kim Gil‐Hah , Kim Yonggyun , Yoon Youngnam , Jang Yunwoo , Jung Tae‐Wook , Maharjan Rameswor 
Published: November 2019

AbstractThe soybean pod borer, Maruca vitrata is one of the key insect pests of tropical legumes. It damages tender leaf axils, flower buds, flowers and pods by webbing and boring clusters of flowers and pods. In this study, we investigated the survival and life table parameters of M. vitrata on several leguminous crops; soybean (cvs. Daewon, Poongsannamool and Socheongja), azuki bean (cv. Hongeon), mung bean (cv. Sanpo), and cowpea (cv. Jangchae), compared to artificial diet to assess the antibiosis resistance to M. vitrata. The life‐variables of M. vitrata were significantly affected by the tested legume cultivars. None of the larvae fed cowpea cultivar Jangchae survived. The azuki bean cultivar Hongeon and mung bean cultivar Sanpo were found susceptible to M. vitrata, whereas cowpea cultivar Jangchae and soybean cultivar Daewon showed antibiosis resistance to M. vitrata. Further studies should examine the chemicals associated with leguminous crop cultivars and its mechanism to develop a control method against M. vitrata.
Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria)
Authors: Dumack Kenneth , Fiore‐Donno Anna Maria , Bass David , Bonkowski Michael 
Published: November 2019

AbstractWe have compiled a database of functional traits for two widespread and ecologically important groups of protists, Cercozoa and Endomyxa (Rhizaria). The functional traits of microorganisms are crucially important for interpreting results from environmental sequencing surveys. Linking morphological and ecological traits to environmental factors is common practice in studies involving micro‐ and macroorganisms, but is rarely applied to protists. Our database provides functional and ecologically significant traits linked to morphology, nutrition, locomotion and habitats. We discuss how the use of functional traits may help to unveil underlying ecosystem processes. This database is intended as a common reference for the molecular ecology community and will boost the understanding of ecosystem functions, especially those driven by biological interactions.
A probabilistic model for designing and assessing the performance of eDNA sampling protocols
Authors: Song Jeffery W. , Schultz Martin T. , Casman Elizabeth A. , Bockrath Katherine D. , Mize Erica , Monroe Emy M. , Tuttle‐Lau Maren , Small Mitchell J. 
Published: November 2019

AbstractEnvironmental DNA (eDNA) sampling, the detection of species‐specific genetic material in water samples, is an emerging tool for monitoring aquatic invasive species. Optimizing eDNA sampling protocols can be challenging because there is imperfect understanding of how each step of the protocol influences its sensitivity. This paper develops a probabilistic model that characterizes each step of an eDNA sampling protocol to evaluate the protocol's overall detection sensitivity for one sample. The model is then applied to analyse how changes over time made to the eDNA sampling protocol to detect bighead (BH) and silver carp (SC) eDNA have influenced its sensitivity, and hence interpretation of the results. The model shows that changes to the protocol have caused the sensitivity of the protocol to fluctuate. A more efficient extraction method in 2013, new species‐specific markers with a qPCR assay in 2014, and a more efficient capture method in 2015 have improved the sensitivity, while switching to a larger elution volume in 2013 and a smaller sample volume in 2015 have reduced the sensitivity. Overall, the sensitivity of the current protocol is higher for BH eDNA detection and SC eDNA detection compared to the original protocol used from 2009 to 2012. The paper shows how this model of eDNA sampling can be used to evaluate the effect of proposed changes in an eDNA sampling and analysis protocol on the sensitivity of that protocol to help researchers optimize their design.
Using stable isotope analysis to answer fundamental questions in invasion ecology: Progress and prospects
Authors: McCue Marshall D. , Javal Marion , Clusella‐Trullas Susana , Le Roux Johannes J. , Jackson Michelle C. , Ellis Allan G. , Richardson David M. , Valentine Alex J. , Terblanche John S. 
Published: November 2019

Abstract

What makes some species successful invaders while others fail, and why some invaders have major impacts in invaded ecosystems are pivotal questions that are attracting major research effort. The increasing availability of high resolution, georeferenced stable isotope landscapes (‘isoscapes’), coupled with the commercialization of stable isotope‐enriched tracer molecules and the development of new analytical approaches, is facilitating novel applications of stable isotope techniques in ecology. We can now address ecological questions that were previously intractable.

We review and discuss how stable isotope analysis (SIA) can complement fundamental research themes in the study of biological invasions, especially in answering questions relating to the physiological and ecological mechanisms underlying invasion processes and invader impacts.

SIA was first used for simply describing the diet of invaders but, more recently, SIA‐informed metrics of population and community trophic structure have been advanced. These approaches now permit the comparison of diets across space and time and provide quantitative tools to compare food webs across different stages of invasion.

SIA has also been pivotal in quantifying competition for resources between native and non‐native species (e.g. competition for food, water, or nutrient use). Specific questions related to modes of dispersal (e.g. origin and distance/direction travelled) and mechanisms of establishment can also be addressed using SIA in diverse taxa.

An overarching goal is to highlight examples of recent studies that have used SIA in key areas of invasion ecology and use these to synthesize testable predictions where SIA could be applied to future studies. We conclude by highlighting several paths forward and describing how unresolved challenges in quantifying the rates, impacts, and mechanisms underlying invasions could potentially benefit from the use of SIA.
Polypharmacy at discharge in older hospitalised patients in Vietnam and its association with frailty
Authors: Nguyen Thanh Xuan , Nguyen Tu N. , Nguyen Anh Trung , Nguyen Huong Thi Thu , Nguyen Thu Thi Hoai , Nguyen Tam Ngoc , Pham Thang , Vu Huyen Thi Thanh 
Published: November 2019

AbstractObjectivesTo investigate the prevalence of polypharmacy and the common drugs prescribed at discharge in frail and non‐frail older inpatients, and to examine whether frailty is significantly associated with polypharmacy.MethodsCross‐sectional analysis from data of a study about the prevalence of frailty in older inpatients in Vietnam in 2015. Polypharmacy was defined as using ≥5 medications. Frailty was defined by Fried's frailty criteria.ResultsThere were 382 participants, mean age 76.4, 56.5% female and 35.9% frail. At discharge, 59.2% had polypharmacy (62.8% in the frail and 57.1% in the non‐frail). Vitamin/supplements were the most common drugs prescribed, followed by antiplatelets. Frailty was not significantly associated with polypharmacy (adjusted OR 1.45, 95% CI 0.89‐2.34).ConclusionsThe prevalence of polypharmacy at discharge was high in both frail and non‐frail participants. The association between frailty and polypharmacy needs to be investigated further in multicentre studies with larger sample sizes in Vietnam.
The association between family history of diabetes mellitus and offspring long‐term neurological hospitalisation
Authors: Moscovici Khen , Wainstock Tamar , Sheiner Eyal , Pariente Gali 
Published: November 2019

AbstractAimThe aim of the present study was to determine whether being born to non‐diabetic mother with a family history of diabetes mellitus (DM) is associated with higher rates of long‐term neurological hospitalisations of the offspring.MethodsA retrospective analysis of all live births and paediatric hospitalisations at Soroka University Medical Center between 1991 and 2014 was performed. Family history of DM was collected from prepartum women using anamnesis. During the study period, 208 728 deliveries met the inclusion criteria, and of them 8.2% (n = 17 040) were of non‐diabetic mothers with family history of DM. Rates of neurological hospitalisation with or without family history were analysed.ResultsOffspring born to non‐diabetic mothers with family history of DM had higher rates of neurological hospitalisations. The cumulative incidence of long‐term neurological hospitalisations was higher as compared with those without family history of DM (log‐rank test P = .007). Neurological hospitalisations was higher by 13% in the study group, after controlling for confounders such as maternal age, maternal obesity, hypertensive disorders, birth weight and caesarean delivery. (adjusted odds ratio 1.13, 95% confidence interval 1.04‐1.23).ConclusionBeing born to a non‐diabetic mother with a family history of DM is independently associated with higher long‐term neurological hospitalisations of the offspring.
A family‐oriented intervention programme to curtail obesity from five years of age had no effect over no intervention
Authors: Donkor Hilde Mjell , Grundt Jacob Holter , Júlíusson Petur Benedikt , Eide Geir Egil , Hurum Jørgen , Bjerknes Robert , Markestad Trond 
Published: November 2019

AbstractAimTo examine the effect of a family‐oriented multidisciplinary intervention programme to curtail weight increase in young children with obesity.MethodsChildren who weighed more than one kilogram above the 97th percentile for height at the preschool assessment in Oppland County, Norway, were identified. Parents residing in one part of the county were invited to participate in a group‐based three‐year intervention programme while the rest had no interventions. Body mass index (BMI) and family characteristics at entry and measurements at birth were explanatory variables, and change in BMI standard deviation score (SDS) the outcome measure. For the intervention group, outcome was also related to skinfold thicknesses, waist‐to‐height ratio and physical ability.ResultsThe programme was completed by 31 families in the intervention and 33 in the control group. At entry, the respective median (interquartile) age was 5.83 (0.36) and 5.74 (0.66) years, and the BMI SDS 2.35 (1.06) and 1.95 (0.49), P = .012. The median decrease in BMI SDS was 0.19 in both groups. The decline increased with increasing BMI SDS at entry, but irrespective of group. Social or behavioural factor or other anthropometric measures were not associated with outcome.ConclusionThe intervention programme had no effect on BMI SDS.
Heat‐related changes in skin tissue dielectric constant (TDC)
Authors: Mayrovitz Harvey N. , Berdichevskiy Garry , Lorenzo‐Valido Cindy , Clavijo Fernandez Marcos 
Published: November 2019

SummaryThe impact of 20 min of whole‐body heating (WBH) on the tissue dielectric constant (TDC) of forearm and hand skin was evaluated in 24 young adults. TDC was measured in triplicate at 300 MHz using an open‐ended transmission line method in which the effective measurement depth was about 2 mm. TDC measurements are an effective way to assess and track localized oedema and lymphoedema. The underlying hypothesis was that heat‐induced eccrine gland activation would increase TDC values via an increase in fluid within the TDC measurement volume. The goal was to test this concept and to determine the magnitude of the change when environmental temperatures were elevated to near 42°C and to estimate TDC recovery time. The practical aspect of this research is motivated by the fact that patients in whom such measurements are made may arrive at the clinic in various states of sweat gland activation. Thus, knowledge of the effect of such activation on measured TDC values permits better understanding of possible relationships between such activation and TDC values. Results showed that increasing environmental temperature from 23·3 ± 1·6 to 41·5 ± 1·3°C increased forearm and thenar eminence skin temperatures to 37·8 ± 0·5 and 37·9 ± 0·4°C, respectively. These changes were associated with increases in TDC at arm from 30·7 ± 4·6 to 36·3 ± 5·7 (18·2%) and at hand from 34·7 ± 4·9 to 45·1 ± 5·5 (30%). Based on calculated TDC recovery rates, it is concluded that temperature‐related TDC variability can be minimized using a wait time of at least 15 min after bandage removal prior to TDC measurements in affected limbs.