bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trend analysis of drought indices in the eastern Slovakia
Authors: Nagy P , Purcz P , Galas S , Portela M M , Hlavatá Helena , Simonová Dorota 
Published: October 2020

Abstract
Extreme weather changes have been increasing in the recent times also in the eastern Slovakia. Extremely dry periods alternate with above-average precipitation. In the paper the drought indices were evaluated: Standardized Evapotranspiration Index (SPEI) and Standardized Precipitation Index (SPI). Using the non-parametric statistical Mann-Kendall test. The evaluated period was 1960 – 2015 at selected river and climatological stations in the eastern Slovakia. The results showed that no clean significant trends occurred in all evaluated indices and stations.
Computer modeling of flow on the object of the sewer network
Authors: Šutúš M , Hrudka J , Rózsa G , Škultétyová I 
Published: October 2020

Abstract
This work deals with the creation of a hydrodynamic model of the combined sewerage overflow chamber in Banská Bystrica. As an object on the sewer network, we chose a combined sewerage overflow chamber, because its correct functionality directly affects the quality of the environment in the recipient. Simulations were calculated in the program Ansys Workbench 19.2 – Fluid Flow (Fluent). The basis of the work was the creation of a 3D graphic model. The 3D model serves as a base for flow modeling. The core of the work are simulations in the combined sewerage overflow chamber that should correspond to real flow. The goal of our work is to compare the influence of inflow velocity and flow rakes on hydrodynamic flow.
The design of the technical flood protection measures on Svitava River, Czech Republic
Authors: Uhmannova H , Ondrejka Harbulakova V , Cetkovska L 
Published: October 2020

Abstract
The paper present the design of the technical flood protection measures on Svitava River in Březová above Svitava town. The current state of the study area was evaluated and determined based on related documents available for public as well as on the personal survey of the landscape. Technical solution as proposal of adjustment of the Svitava River (by composite trapezoid), extracting sediments and designing, stabilization of the bank and construction of the protective floodwall is shown in the paper. The riverbed slopes were fortified with a stone riprap with a sieve of grass mixture.
The treehouses
Authors: Vacenovská V 
Published: October 2020

Abstract
The goal of this research is to evaluate and find new solution in the area of wooden constructions placed in the treetops, which are interesting mainly due to their independence and amazing view among the treetops, and enable the utilization of the land below the treehouse itself. Treehouses can be constructed as a detached object without having to interfere with the trunk, or anchored into the trunk using special anchoring elements, where compact root system of surrounding trees is essential for healthy grow of the tree. Wood is also a specific natural material, which offers a possibility to create architecturally interesting and modern construction. This article is focused on evaluation of anchoring suitability of these constructions in treetops, evaluation of using these houses for recreational purposes as well as permanent living, effect of climate conditions on suitably chosen wood type and construction of these objects.
Building materials for 3D print
Authors: Wawrek I 
Published: October 2020

Abstract
The paper maps the current level of knowledge in 3D printing of construction objects. It introduces different approaches to creating wall structures of two world companies dealing with the problem of 3D print. It confronts their solution with the normative requirements for the territory of the Slovak Republic valid after 2021. It also presents proposals for possible improvement of the thermal-technical properties of the perimeter wall, modification of the design of the internal structure and properties of the printed material towards the normative requirements.
Associations of Maternal Androgen-Related Conditions With Risk of Autism Spectrum Disorder in Progeny and Mediation by Cardiovascular, Metabolic, and Fertility Factors
Authors: Rotem Ran S , Nguyen Vy T , Chodick Gabriel , Davidovitch Michael , Shalev Varda , Hauser Russ , Coull Brent A , Bellavia Andrea , Weisskopf Marc G 
Published: October 2020

AbstractFetal exposure to elevated androgens is thought to contribute to autism spectrum disorder (ASD) risk. However, data rely heavily on in utero androgens measurements, which also reflect fetal secretions. Thus, in utero hyperandrogenemia might indicate adverse autism-related neurogenesis that has already occurred affecting fetal androgen homeostasis, rather than being a cause of the disorder. Associations between maternal androgen-related conditions and ASD could more directly implicate androgens’ etiological role. We examined the association between maternal hyperandrogenemia-related conditions, focusing primarily on polycystic ovarian syndrome (PCOS), and progeny ASD, in an Israeli cohort of 437,222 children born in 1999–2013. Odds ratios and 95% confidence intervals were estimated using generalized estimating equations. Multiple mediation analyses using natural effect models were conducted to evaluate combined mediation of the PCOS effect by androgen-related cardiovascular, metabolic, and fertility factors. Results indicated that children of mothers with PCOS had higher ASD odds compared with children of mothers without PCOS (odds ratio = 1.42, 95% confidence interval: 1.24,1.64), and this effect was only partly mediated by the factors considered. Elevated odds were also observed for other hyperandrogenemia-related conditions. Findings provide support for direct involvement of maternal hyperandrogenemia in ASD etiology. Alternatively, findings might reflect shared genetic and/or environmental factors independently affecting maternal androgen homeostasis and fetal neurodevelopment.
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins
Authors: Pintado Carlos , Santos Jaime , Iglesias Valentín , Ventura Salvador 
Published: October 2020

Abstract

Summary
Polypeptides are exposed to changing environmental conditions that modulate their intrinsic aggregation propensities. Intrinsically disordered proteins (IDPs) constitutively expose their aggregation determinants to the solvent, thus being especially sensitive to its fluctuations. However, solvent conditions are often disregarded in computational aggregation predictors. We recently developed a phenomenological model to predict IDPs' solubility as a function of the solution pH, which is based on the assumption that both protein lipophilicity and charge depend on this parameter. The model anticipated solubility changes in different IDPs accurately. In this application note, we present SolupHred, a web-based interface that implements the aforementioned theoretical framework into a predictive tool able to compute IDPs aggregation propensities as a function of pH. SolupHred is the first dedicated software for the prediction of pH-dependent protein aggregation.

Availability and implementation
The SolupHred web server is freely available for academic users at: https://ppmclab.pythonanywhere.com/SolupHred. It is platform-independent and does not require previous registration.

Supplementary information
Supplementary data are available at Bioinformatics online.
Lipopolysaccharide-induced epididymitis modifies the transcriptional profile ofWfdcgenes in mice†
Authors: Andrade Alexandre D , Almeida Priscila G C , Mariani Noemia A P , Freitas Geanne A , Kushima Hélio , Filadelpho André L , Spadella Maria Angélica , Avellar Maria Christina W , Silva Erick J R 
Published: October 2020

AbstractWhey-acidic protein four-disulfide core domain (WFDC) genes display putative roles in innate immunity and fertility. In mice, a locus on chromosome 2 contains 5 and 11 Wfdc genes in its centromeric and telomeric subloci, respectively. Although Wfdc genes are highly expressed in the epididymis, their contributions to epididymal function remain elusive. Here, we investigated whether Wfdc genes are regulated in response to lipopolysaccharide (LPS)-induced epididymitis, an inflammatory condition that impairs male fertility. We induced epididymitis in mice via (i) interstitial LPS injection into epididymal initial segment and (ii) intravasal LPS injection into the vas deferens towards cauda epididymis. Interstitial and intravasal LPS induced a differential upregulation of inflammatory mediators (interleukin 1 beta, interleukin 6, tumor necrosis factor, interferon gamma, and interleukin 10) in the initial segment and cauda epididymis within 72 h post-treatment. These changes were accompanied by a time-dependent endotoxin clearance from the epididymis. In the initial segment, interstitial LPS upregulated all centromeric (Slpi, Wfdc5, Wfdc12, Wfdc15a, and Wfdc15b) and five telomeric (Wfdc2, Wfdc3, Wfdc6b, Wfdc10, and Wfdc13) Wfdc transcripts at 24 and 72 h. In the cauda epididymis, intravasal LPS upregulated Wfdc5 and Wfdc2 transcripts at 24 h, followed by a downregulation of Wfdc15b and three telomeric (Wfdc6a, Wfdc11, and Wfdc16) gene transcripts at 72 h. Pharmacological inhibition of nuclear factor kappa B activation prevented LPS-induced upregulation of centromeric and telomeric Wfdc genes depending on the epididymal region. We show that LPS-induced inflammation differentially regulated the Wfdc locus in the proximal and distal epididymis, indicating region-specific roles for the Wfdc family in innate immune responses during epididymitis.
Basis expansions for functional snippets
Authors: Lin Zhenhua , Wang Jane-Ling , Zhong Qixian 
Published: October 2020

SummaryEstimation of mean and covariance functions is fundamental for functional data analysis. While this topic has been studied extensively in the literature, a key assumption is that there are enough data in the domain of interest to estimate both the mean and covariance functions. We investigate mean and covariance estimation for functional snippets in which observations from a subject are available only in an interval of length strictly, and often much, shorter than the length of the whole interval of interest. For such a sampling plan, no data is available for direct estimation of the off-diagonal region of the covariance function. We tackle this challenge via a basis representation of the covariance function. The proposed estimator enjoys a convergence rate that is adaptive to the smoothness of the underlying covariance function, and has superior finite-sample performance in simulation studies.
Glioblastoma surgery related emotion recognition deficits are associated with right cerebral hemisphere tract changes
Authors: Sinha Rohitashwa , Dijkshoorn Aicha B C , Li Chao , Manly Tom , Price Stephen J 
Published: October 2020

Abstract
Patients with glioblastoma face abysmal overall survival, cognitive deficits, poor quality of life and limitations to social participation; partly attributable to surgery. Emotion recognition deficits mediated by pathophysiological mechanisms in the right inferior fronto-occipital fasciculus and right inferior longitudinal fasciculus have been demonstrated in traumatic brain injury and dementia, with negative associations for social participation. We hypothesise similar mechanisms occur in patients undergoing resection surgery for glioblastoma. Here, we apply tract-based spatial statistics using a combination of automated image registration methods alongside cognitive testing before and after surgery. In this prospective, longitudinal, observational study of 15 patients, surgery is associated with an increase of emotion recognition deficits (p = 0.009) and this is correlated with decreases in fractional anisotropy in the Inferior Longitudinal Fasciculus, Inferior Fronto-Occipital Fasciculus, Anterior Thalamic Radiation and Uncinate Fasciculus; all in the right hemisphere (p = 0.014). Methodologically, the combination of registration steps used demonstrate that tract-based spatial statistics can be applied in the context of large, scan distorting lesions such as glioblastoma. These results can inform clinical consultations with patients undergoing surgery, support consideration for social cognition rehabilitation and are consistent with theoretical mechanisms that implicate these tracts in emotion recognition deficits across different diseases.
Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function
Authors: Smercina Darian N , Evans Sarah E , Friesen Maren L , Tiemann Lisa K 
Published: October 2020

ABSTRACT
Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.
Climate sensitive growth models for predicting diameter growth of western Canadian boreal tree species
Authors: Oboite Felix O , Comeau Philip G 
Published: October 2020

Abstract
In the face of anticipated climate change, growth models require modifications to effectively model likely future growth and survival of trees and stands. To support incorporation of climate effects in the Mixedwood Growth Model (MGM), we developed climate-sensitive mixed effects models for lodgepole pine (Pinus contorta Douglas ex Loudon), jack pine (Pinus banksiana Lamb.), trembling aspen (Populus tremuloides Michx.), balsam poplar (Populus balsamifera L.) and white spruce (Picea glauca (Moench) Voss), and examined how tree size, intra- and interspecific competition and climate will influence individual-tree diameter growth. Remeasurement data from permanent growth and yield sample plots from across the western Canadian boreal forest were used for this study. Based on the model that we developed, tree size, competition and climate had varying effects on growth, among tree species. Although intraspecific competition had a stronger negative effect on growth for deciduous and white spruce trees, interspecific competition had a stronger negative effect on the growth of pine. Deciduous trees growing in stands having longer frost-free period experienced an increase in growth but a negative effect of frost-free period was observed for conifers. In addition, higher moisture was found to increase tree growth, but the influence of available moisture on growth was dependent on competition. Overall, these results suggest that, under climate warming, between-species differences in growth responses will contribute to our understanding of the stand dynamics in the western boreal region of Canada. Climate sensitive growth models developed in this study will be useful in the recalibration of MGM and other individual-tree models, and predictions will contribute to better-informed decisions about silvicultural treatments for these economically important boreal tree species.
Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage
Authors: Cooney Elizabeth C , Okamoto Noriko , Cho Anna , Hehenberger Elisabeth , Richards Thomas A , Santoro Alyson E , Worden Alexandra Z , Leander Brian S , Keeling Patrick J 
Published: October 2020

Abstract
Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron–sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.
A Chromosome-Level Genome Assembly of Dendrobium Huoshanense Using Long Reads and Hi-C Data
Authors: Han Bangxing , Jing Yi , Dai Jun , Zheng Tao , Gu Fangli , Zhao Qun , Zhu Fucheng , Song Xiangwen , Deng Hui , Wei Peipei , Song Cheng , Liu Dong , Jiang Xueping , Wang Fang , Chen Yanjun , Sun Chuanbo , Yao Houjun , Zhang Li , Chen Naidong , Chen Shaotong , Li Xiaoli , Wei Yuan , Ouyang Zhen , Yan Hui , Lu Jiangjie , Wang Huizhong , Guo Lanping , Kong Lingdong , Zhao Jing , Li Shaoping , Luo Lifen , Kristiansen Karsten , Feng Zhan , Sun Silong , Chen Cunwu , Yue Zhen , Chen Naifu 
Published: October 2020

Abstract
Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79 Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.
Assessing the performance of beneficiary targeting in Brazil’s More Doctors Programme
Authors: Özçelik Ece A , Massuda Adriano , McConnell Margaret , Castro Marcia C 
Published: October 2020

Abstract
Many countries employ strategies that rest on the use of an explicitly defined set of criteria to identify underserved communities. Yet, we know relatively little about the performance of community-level targeting in large-scale health programmes. To address this gap, we examine the performance of community targeting in the More Doctors Programme (MDP). Our analysis covers all 5570 municipalities in the period between 2013 and 2017 using publicly available data. We first calculate the rate at which vulnerable municipalities enrolled in the MDP. Next, we consider two types of mistargeting: (1) proportion of vulnerable municipalities that did not have any MDP physicians (i.e. under-coverage municipalities) and (2) proportion of MDP enrolees that did not fit the vulnerability criteria (i.e. non-target municipalities). We found that almost 70% of vulnerable municipalities received at least one MDP physician between 2013 and 2017; whereas non-target municipalities constituted 33% of beneficiaries. Targeting performance improved over time. Non-target municipalities had the highest levels of socioeconomic development and greater physician availability. The poverty rate among under-coverage municipalities was almost six times that in non-target municipalities. Under-coverage municipalities had the lowest primary care physician availability. They were also smaller and more sparsely populated. We also found small differences in the political party alignments of mayors and the President between under-coverage and non-target municipalities. Our results suggest that using community-level targeting approaches in large-scale health programmes is a complex process. Programmes using these approaches may face substantial challenges in beneficiary targeting. Our results highlight that policymakers who consider using these approaches should carefully study various municipal characteristics that may influence the implementation process, including the level of socioeconomic development, health supply factors, population characteristics and political party alignments.