bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heating and Drying of Autoclaved Aerated Concrete Blocks for Defects of Buildings by Application of Microwave Radiation
Authors: Sobotka Jindřich , Smolka Radim 
Published: February 2020

Abstract
Experiments of heating and drying of autoclaved aerated concrete blocks were divided into several areas, in which the depth of heating in relation to irradiation time intervals was checked. The impact of individual heating phases on the distribution of the irradiated field and comparison of drying rate at different lengths of the cycle “heating-cooling”. Theoretical potential of construction materials rehabilitation with the use of microwave radiation has been known for many years. This technique has been used by a number of companies in the construction practice. However, obtaining accurate information on suitable devices, procedures of their use, remedial action technique, positives and negatives and potential risks when using microwave radiation is very demanding since the findings obtained from practice are protected by individual companies for their own needs. It is understood that it is part of their “know-how”. The long-term research based on close cooperation between Civil Engineering Faculty, BUT Brno, and S. P. UNI company, tries to make accessible enough information on potential and suitable use of the microwave technology in practice, based on laboratory and in-situ experiments.
Reduction of Light Transmission by Glazing with Atmospheric Pollutants
Authors: Machová Petra , Vajkay František 
Published: February 2020

Abstract
Daylight has been used for centuries as the main source of light in interiors and has always been an implicit part of architecture ever since buildings exist. Daylight is an irreplaceable environmental factor and is a prerequisite for a healthy stay in buildings. Ensuring daylight access to the interior is a challenge when designing buildings. The aim is to provide enough daylight for the visual work that indoor building users do. The deposition of air pollutants on the glazing can significantly affect the transmission of daylight into buildings located in urban areas. This study shows the impact of air pollution on glazing permeability in three cities in the Czech Republic. The throughput was measured on a total of 9 windows for half a year. Air purity, exposure to rain, the slope of glazing and use of rooms are factors influencing the final permeability of the glazing. Where glazing is exposed to rain, dirt on the outside of the windows tends to accumulate. The final reduction in throughput is usually 4-8%, with some exceptions.
Mechanical, structural, and thermodynamic properties of TaC-ZrC ultra-high temperature ceramics using first principle methods
Authors: Farhadizadeh Ali Reza , Ghomi Hamid 
Published: February 2020

Abstract
In this research, a systematic investigation of the properties of stoichiometric ultra-high temperature ceramics

Z

r

x

T

a

8
−
x

C

8

is carried out. The mechanical properties including elastic constants, shear modulus, bulk modulus, Zener ratio, Poisson ratio, Pugh’s index are calculated and then the hardness (H) and

H

3

/

E

2

based on a semi-empirical approach are estimated. It exhibits that TaC possesses the lowest hardness equal to 22 GPa that increases to maximum hardness 30 GPa when a single Zr atom is substituted with Ta

(
Z

r

1

T

a

7

C

8

)
.

Afterwards, the partial density of states (PDOS) of mentioned ceramics was calculated and plotted. Since the density of states at the Fermi level has some value, it is inferred that they all are electrical conductors. The p-d hybridization, the states at the Fermi level and the Mulliken charges of each atom indicate that the covalent, metallic and ionic nature of bonding exist simultaneously among constituent elements.
Tax bargaining, fiscal contracts, and fiscal capacity in Ghana: A long-term perspective
Authors: Aboagye Prince Young , Hillbom Ellen 
Published: February 2020

Abstract
Many Sub-Saharan African countries are unable to generate sufficient tax revenues for public purposes. While it is widely accepted that governments’ ability to tax is shaped by politics, the precise mechanisms through which this relationship takes place in practice remain elusive. Based on a historical analysis of four major tax reforms in Ghana from the 1850s to the late 1990s, this article captures the various ways in which taxpayers negotiate with the state in an attempt to limit the extent of taxation, especially in cases where state reciprocity falls short of what people expect. Our evidence suggests that, far from being a recent development, effective taxation in Ghana has long depended on the ability of the state to convince taxpayers that tax revenues will be used for the public benefit. A history of misappropriation of tax revenues, overt corruption, and profligacy diminished taxpayers’ support for governments’ tax efforts. More generally, the article points to the importance of understanding how tax bargaining works in practice and people’s perceptions of their governments over the long term to overcome resistance to tax reforms.
Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas
Authors: Cenci Alberto , Sardos Julie , Hueber Yann , Martin Guillaume , Breton Catherine , Roux Nicolas , Swennen Rony , Carpentier Sebastien Christian , Rouard Mathieu 
Published: February 2020

Abstract

Background and Aims
Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security.

Methods
Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes.

Key Results
Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups.

Conclusions
The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
Local conspecific density does not influence reproductive output in a secondary cavity-nesting songbird
Authors: Hoover Jeffrey P , Davros Nicole M , Schelsky Wendy M , Brawn Jeffrey D 
Published: February 2020

AbstractDensity dependence is a conceptual cornerstone of avian population biology and, in territorial songbirds, past research has emphasized interactions among food limitation, density, and reproduction. Documenting the importance of density effects is central to understanding how selective forces shape life histories and population dynamics. During the 2008–2011 breeding seasons, we nearly doubled overall conspecific breeding densities on study sites, and manipulated nest box spacing to increase local breeding densities (defined as the number of pairs breeding within 200 m of a pair’s nest) of a secondary cavity-nesting songbird, the Prothonotary Warbler (Protonotaria citrea). Our primary objective was to test for effects of food limitation, as mediated by conspecific local densities, on measures of productivity. We monitored breeding pairs and recorded the total number of fledglings produced along with several components of reproductive output (clutch size, hatching success, nestling survival, and probability of attempting a second brood), rates of nestling provisioning, and nestling body condition prior to fledging. We predicted that if the availability of food were affected by local densities, then one or more of these parameters measuring reproduction would be affected negatively. We did not detect an effect of local density on total reproductive output or its components despite our vast range of local densities (1–27 pairs; i.e. 0.16–2.23 pairs ha–1). Further, we also did not detect differences in nestling provisioning rates and nestling body condition relative to local density. By breeding in a productive ecosystem rich in food resources, these warblers appear to avoid reduced reproductive output when breeding in high densities. Whereas density-dependent food limitation may commonly reduce reproductive output in many species, the ecological circumstances underlying when it does not occur merit further investigation and may provide new insights into what is driving territoriality and what are the primary factors affecting individual fitness.
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace
Authors: Singh Natesh , Chaput Ludovic , Villoutreix Bruno O 
Published: February 2020

AbstractThe interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.
Integrating multi-network topology for gene function prediction using deep neural networks
Authors: Peng Jiajie , Xue Hansheng , Wei Zhongyu , Tuncali Idil , Hao Jianye , Shang Xuequn 
Published: February 2020

Abstract

Motivation
The emergence of abundant biological networks, which benefit from the development of advanced high-throughput techniques, contributes to describing and modeling complex internal interactions among biological entities such as genes and proteins. Multiple networks provide rich information for inferring the function of genes or proteins. To extract functional patterns of genes based on multiple heterogeneous networks, network embedding-based methods, aiming to capture non-linear and low-dimensional feature representation based on network biology, have recently achieved remarkable performance in gene function prediction. However, existing methods do not consider the shared information among different networks during the feature learning process.

Results
Taking the correlation among the networks into account, we design a novel semi-supervised autoencoder method to integrate multiple networks and generate a low-dimensional feature representation. Then we utilize a convolutional neural network based on the integrated feature embedding to annotate unlabeled gene functions. We test our method on both yeast and human datasets and compare with three state-of-the-art methods. The results demonstrate the superior performance of our method. We not only provide a comprehensive analysis of the performance of the newly proposed algorithm but also provide a tool for extracting features of genes based on multiple networks, which can be used in the downstream machine learning task.

Availability
DeepMNE-CNN is freely available at https://github.com/xuehansheng/DeepMNE-CNN

Contact
jiajiepeng@nwpu.edu.cn; shang@nwpu.edu.cn; jianye.hao@tju.edu.cn
GPS-Palm: a deep learning-based graphic presentation system for the prediction ofS-palmitoylation sites in proteins
Authors: Ning Wanshan , Jiang Peiran , Guo Yaping , Wang Chenwei , Tan Xiaodan , Zhang Weizhi , Peng Di , Xue Yu 
Published: February 2020

AbstractAs an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating various biological processes and is associated with human diseases. Besides experimental assays, computational prediction of S-palmitoylation sites can efficiently generate helpful candidates for further experimental consideration. Here, we reviewed the current progress in the development of S-palmitoylation site predictors, as well as training data sets, informative features and algorithms used in these tools. Then, we compiled a benchmark data set containing 3098 known S-palmitoylation sites identified from small- or large-scale experiments, and developed a new method named data quality discrimination (DQD) to distinguish data quality weights (DQWs) between the two types of the sites. Besides DQD and our previous methods, we encoded sequence similarity values into images, constructed a deep learning framework of convolutional neural networks (CNNs) and developed a novel algorithm of graphic presentation system (GPS) 6.0. We further integrated nine additional types of sequence-based and structural features, implemented parallel CNNs (pCNNs) and designed a new predictor called GPS-Palm. Compared with other existing tools, GPS-Palm showed a &gt;31.3% improvement of the area under the curve (AUC) value (0.855 versus 0.651) for general prediction of S-palmitoylation sites. We also produced two species-specific predictors, with corresponding AUC values of 0.900 and 0.897 for predicting human- and mouse-specific sites, respectively. GPS-Palm is free for academic research at http://gpspalm.biocuckoo.cn/.
Bio2Rxn: sequence-based enzymatic reaction predictions by a consensus strategy
Authors: Zhang Tong , Tian Yu , Yuan Le , Chen Fu , Ren Ailin , Hu Qian-Nan 
Published: February 2020

Abstract

Summary
The development of sequencing technologies has generated large amounts of protein sequence data. The automated prediction of the enzymatic reactions of uncharacterized proteins is a major challenge in the field of bioinformatics. Here, we present Bio2Rxn as a web-based tool to provide putative enzymatic reaction predictions for uncharacterized protein sequences. Bio2Rxn adopts a consensus strategy by incorporating six types of enzyme prediction tools. It allows for the efficient integration of these computational resources to maximize the accuracy and comprehensiveness of enzymatic reaction predictions, which facilitates the characterization of the functional roles of target proteins in metabolism. Bio2Rxn further links the enzyme function prediction with more than 300 000 enzymatic reactions, which were manually curated by more than 100 people over the past 9 years from more than 580 000 publications.

Availability and implementation
Bio2Rxn is available at: http://design.rxnfinder.org/bio2rxn/.

Contact
qnhu@sibs.ac.cn

Supplementary information
Supplementary data are available at Bioinformatics online.
Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer
Authors: Donald Kirsten M , McCulloch Graham A , Dutoit Ludovic , Spencer Hamish G 
Published: February 2020

AbstractWe examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).
NDRG1 deficiency is associated with regional metastasis in oral cancer by inducing epithelial–mesenchymal transition
Authors: de Lima Jefferson Muniz , Morand Grégoire B , Macedo Carolina Carneiro Soares , Diesel Luciana , Hier Michael P , Mlynarek Alex , Kowalski Luiz P , Maschietto Mariana , Alaoui-Jamali Moulay A , da Silva Sabrina Daniela 
Published: February 2020

Abstract
Regional metastasis is the single most important prognostic factor in oral squamous cell carcinoma (OSCC). Abnormal expression of N-myc downstream-regulated genes (NDRGs) has been identified to occur in several tumor types and to predict poor prognosis. In OSCC, the clinical significance of deregulated NDRG expression has not been fully established. In this study, NDRG1 relevance was assessed at gene and protein levels in 100 OSCC patients followed up by at least 10 years. Survival outcome was analyzed using a multivariable analysis. Tumor progression and metastasis was investigated in preclinical model using oral cancer cell lines (HSC3 and SCC25) treated with epidermal growth factor (EGF) and orthotopic mouse model of metastatic murine OSCC (AT84). We identified NDRG1 expression levels to be significantly lower in patients with metastatic tumors compared with patients with local disease only (P = 0.001). NDRG1 expression was associated with MMP-2, -9, -10 (P = 0.022, P = 0.002, P = 0.042, respectively) and BCL2 (P = 0.035). NDRG1 lower expression was able to predict recurrence and metastasis (log-rank test, P = 0.001). In multivariable analysis, the expression of NDRG1 was an independent prognostic factor (Cox regression, P = 0.013). In invasive OSCC cells, NDRG1 expression is diminished in response to EGF and this was associated with a potent induction of epithelial–mesenchymal transition phenotype. This result was further confirmed in an orthotopic OSCC mouse model. Together, this data support that NDRG1 downregulation is a potential predictor of metastasis and approaches aimed at NDRG1 signaling rescue can serve as potential therapeutic strategy to prevent oral cancer progression to metastasis.
Mutations in long-lived epithelial stem cells and their clonal progeny in pre-malignant lesions and in oral squamous cell carcinoma
Authors: Melis Marta , Zhang Tuo , Scognamiglio Theresa , Gudas Lorraine J 
Published: February 2020

Abstract
Oral squamous cell carcinomas (OSCCs) are the most common cancers of the oral cavity, but the molecular mechanisms driving OSCC carcinogenesis remain unclear. Our group previously established a murine OSCC model based on a 10-week carcinogen [4-nitroquinoline 1-oxide (4-NQO)] treatment. Here we used K14CreERTAM;Rosa26LacZ mice to perform lineage tracing to delineate the mutational profiles in clonal cell populations resulting from single, long-lived epithelial stem cells, here called LacZ+ stem cell clones (LSCCs). Using laser-capture microdissection, we examined mutational changes in LSCCs immediately after the 10-week 4-NQO treatment and &gt;17 weeks after 4-NQO treatment. We found a 1.8-fold ±0.4 (P = 0.009) increase in single-nucleotide variants and insertions/deletions (indels) in tumor compared with pre-neoplastic LSCCs. The percentages of indels and of loss of heterozygosity events were 1.3-fold±0.3 (P = 0.02) and 2.2-fold±0.7 (P = 0.08) higher in pre-neoplastic compared with tumor LSCCs. Mutations in cell adhesion- and development-associated genes occurred in 83% of the tumor LSCCs. Frequently mutated genes in tumor LSCCs were involved in planar cell polarity (Celsr1, Fat4) or development (Notch1). Chromosomal amplifications in 50% of the tumor LSCCs occurred in epidermal growth factor receptor, phosphoinositide 3-kinase and cell adhesion pathways. All pre-neoplastic and tumor LSCCs were characterized by key smoking-associated changes also observed in human OSCC, C&gt;A and G&gt;T. DeconstructSigs analysis identified smoking and head and neck cancer as the most frequent mutational signatures in pre-neoplastic and tumor LSCCs. Thus, this model recapitulates a smoking-associated mutational profile also observed in humans and illustrates the role of LSCCs in early carcinogenesis and OSCCs.
Design, challenges, and the potential of transcriptomics to understand social behavior
Authors: Lim Wen Kin , Mathuru Ajay S 
Published: February 2020

Abstract
Rapid advances in Ribonucleic Acid sequencing (or RNA-seq) technology for analyzing entire transcriptomes of desired tissue samples, or even of single cells at scale, have revolutionized biology in the past decade. Increasing accessibility and falling costs are making it possible to address many problems in biology that were once considered intractable, including the study of various social behaviors. RNA-seq is opening new avenues to understand long-standing questions on the molecular basis of behavioral plasticity and individual variation in the expression of a behavior. As whole transcriptomes are examined, it has become possible to make unbiased discoveries of underlying mechanisms with little or no necessity to predict genes involved in advance. However, researchers need to be aware of technical limitations and have to make specific decisions when applying RNA-seq to study social behavior. Here, we provide a perspective on the applications of RNA-seq and experimental design considerations for behavioral scientists who are unfamiliar with the technology but are considering using it in their research.