bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application efficiency of new raw materials in the production of flour confectionery products with increased nutritional value
Authors: Yanova M A , Sharopatova A V , Roslyakov Yu F , Dzobelova V B 
Published: September 2020

Abstract
The article deals with the issues of efficiency in the production of flour confectionery products with increased nutritional value due to the introduction of developed technologies for the production of high-protein flour from wheat grain. A comparison for the norms of quality indicators for three-grade grinding flour and the high-protein fractions isolated from them is made. It was found that the isolation of a high-protein fraction at optimal technological parameters had virtually no effect on the main quality indicators of the main product. Calculations for the production efficiency of flour confectionery products (gingerbread) showed that the profit from the sale of 1 ton of finished developed products is higher than in the production of traditional gingerbread, the profitability of new products was 22.3 %. Adding high-protein flour to the gingerbread recipe increases the nutritional value of the finished product, increases the amount of proteins and B vitamins.
Thiabendazole vs difenoconazole in chemical control of seed-borne toxigenic fungi affecting wheat quality
Authors: Kukushkina K V , Keler V V , Eskova E N , Muchkina E Ya , Khizhnyak S V 
Published: September 2020

Abstract
Two common fungicides: Vial TrasT (60 g/l tebuconazole and 80 g/l thiabendazole) and Oplot (90 g/l difenoconazole and 45 g/l tebuconazole) were tested for effectiveness against seed-borne toxigenic fungi Fusarium spp. and Alternaria spp. using naturally infected wheat (Triricum aestivum L., cultivar Novosibirskaya-14) seeds collected from the field located near Krasnoyarsk, Russia. Treatment with Oplot statistically significantly reduced Fusarium infection by 10 percentage points (from 31.4% to 21.4%) and statistically significantly reduced Alternaria infection by 25.8 percentage points (from 42.9% to 17.1%). Treatment with Vial TrasT demonstrated no statistically significant effect in reducing infection both for Fusarium and Alternaria. The results demonstrates that populations of Fusarium spp. and Alternaria spp. in Middle Siberia have developed resistance to tebuconazole and thiabendazole, but not to difenoconazole.
Biocenosis of cold-water and warm-water biofilter in recirculating aquaculture system
Authors: Nikiforov-Nikishin A L , Nikiforov-Nikishin D L , Kochetkov N I , Tatarenko P Yu 
Published: September 2020

Abstract
This article presents data on the species composition of periphyton organisms in biofilms of cold-water biological filtration systems intended for the cultivation of rainbow trout (Oncorhynchus mykiss) and warm-water species for the cultivation of (Clarias gariepinus) in a recirculating aquaculture system. Data on the occurrence of certain groups of periphyton organisms are presented, and their role in the process of water purification is indicated. A significant difference in the species composition of biofilter biofilm organisms is shown, depending on: temperature regime and planting density of aquaculture objects. The species composition of aquasysets is similar to that in urban wastewater treatment systems.
Solvent induced charge transport mechanism for conducting polymer at higher temperature
Authors: Moiz S A , Khan I A , Younis W A , Masud M I , Ismail Y , Khawaja Y M 
Published: September 2020

Abstract
To elucidate the response of different solvents such as isopropyl-alcohol (IPA) and acetone for polyaniline-emeraldine-base (PANI), the charge transport mechanism is investigated as a function of temperature in the presence of different solvents. From SEM and XRD characterization, it is noted that each solvent improves the surface smoothness and negligible solvent traces were observed in the final thin-film devices. It is further observed that all devices follow space-charge-limited-current (SCLC) model to define their electrical responses. Conductivity was measured directly through four-probe method, while mobility was estimated from SCLC model and then both conductivity and mobility of PANI are compared with the given solvent at different temperatures. Similarly, it is also realized that the IPA solvent improves conductivity, mobility and degradation of PANI thin-film due to complex behaviour of solvent induced self-organization of molecular chains and reduction of residual traps as a function of temperature.
Large-scale preparation of 22.06% efficiency single-crystalline silicon solar cells with inverted pyramid microstructure through nanostructure rebuilding treatment
Authors: Gu Hongcheng , Guan Zisheng , Liu Yuchen 
Published: September 2020

Abstract
The inverted pyramid microstructures (IPMS) were fabricated jointly by metal-assisted chemical etching (MACE) technology with extremely low concentration of silver ions to formed nanopores and nanostructure rebuilding (NSR) treatment of NH4HF2 solution. The results show nanopores were achieved with the aid of Ag-MACE technology, which diameter was mainly affected by the action of Ag ions, and depth was yet mainly influenced by HF concentration. Textured IPMS single-crystalline silicon (sc-Si) solar cells with the diameter of 1 μm and reflectivity of 8.62% were large-scale prepared. Benefiting from better light-trapping ability, the photoelectric conversion efficiency of IPMS sc-Si solar cells in standard size of 156.75 × 156.75 mm2 achieved 22.06%. Simultaneously, the short-circuit current was increased by 71 mA. This promising technology could become a viable solution for industrial production of highly efficient sc-Si solar cells in the foreseeable future.
Active controlled dual-band unidirectional reflectionlessness by classical driving field in non-Hermitian quantum system
Authors: Yang Hang , Qiu De Xiu , Zou Xin Yu , An Chengshou , Zhang Ying Qiao , Jin Xing Ri 
Published: September 2020

Abstract
We propose a scheme to realize the active controlled dual-band unidirectional reflectionlessness at exceptional points by classical driving field in a non-Hermitian quantum system that consists of two Λ-type three-level quantum dots side coupled to a plasmonic waveguide. We demonstrate that the dual-band unidirectional reflectionlessness can be controlled by appropriately tuning classical driving field, phase shift between two quantum dots, dissipations of two quantum dots, and quantum dot-waveguide coupling strengths. Furthermore, the dual-band unidirectional reflectionlessness spectra with quality factors of ∼375.40 and ∼402.59 can be obtained in the forward and backward directions, respectively.
A straightforward derivation of the four-wave kinetic equation in action-angle variables
Authors: Onorato M , Dematteis G 
Published: September 2020

Abstract
Starting from action-angle variables and using a standard asymptotic expansion, we present an original and coincise derivation of the Wave Kinetic equation for a resonant process of the type

2
↔
2

. Despite not being more rigorous than others, our procedure has the merit of being straightforward; it allows for a direct control of the random phases and random action of the initial wave field. We show that the Wave Kinetic equation can be derived assuming only initial random phases. The random action approximation has to be taken only after the weak nonlinearity and large box limits are taken. The reason is that the oscillating terms in the evolution equation for the action contain, as an argument, the action-dependent nonlinear corrections which is dropped, using the large box limit. We also show that a discrete version of the Wave Kinetic Equation can be obtained for the Nonlinear Schrödinger equation; this is because the nonlinear frequency correction terms give a zero contribution and the large box limit is not needed. In our calculation we do not make an explicitly use of the Wick selection rule.
The Age of the Witness and the Age of Surveillance: Romani Holocaust Testimony and the Perils of Digital Scholarship
Authors: Joskowicz Ari 
Published: September 2020

Abstract
For over half a century, historians have made ample use of witness testimonies. Efforts to preserve the accounts of marginalized people in particular have broadened the range of voices available to us and significantly expanded the field. Yet we have paid too little attention to the potentially disturbing consequences of the creation and distribution of such testimonies. Focusing on the experiences of Romani Holocaust survivors, this essay argues that new practices of surveillance and victim-witnessing developed in tandem, from the mid-twentieth century to the present. Beginning in the 1960s, prosecutors asked Romani survivors to testify about the crimes committed against them under Nazism even as state authorities continued to criminalize and surveil Romanies across Europe. These and related experiences have meant that different Romani witnesses—or potential witnesses—have often had to balance the desire to have their stories heard against the fear of being listened in on. As surveillance becomes increasingly pervasive and as personal information is increasingly monetized, the lessons that European Romanies learned as early victims of targeted policing remain salient for historians today. Despite its potential to empower, victim-witnessing also creates new vulnerabilities—both those we can currently anticipate and those we can’t yet fully imagine.
TEnGExA: an R package based tool for tissue enrichment and gene expression analysis
Authors: Rawal Hukam C , Angadi Ulavappa , Mondal Tapan Kumar 
Published: September 2020

Abstract
RNA-seq data analysis with rapidly advancing high-throughput sequencing technology, nowadays provides large number of transcripts or genes to perform downstream analysis including functional annotation and pathway analysis. However for the data from multiple tissues, downstream analysis with tissue-specific or tissue-enriched transcripts is highly preferable. However, there is still a need of tool for quickly performing tissue-enrichment and gene expression analysis irrespective of number of input genes or tissues at various fragments per kilobase of transcript per million fragments mapped (FPKM) thresholds. To fulfill this need, we presented a freely available R package and web-interface tool, TEnGExA, which allows tissue-enrichment analysis (TEA) for any number of genes or transcripts for any species provided only a read-count or FPKM-value matrix as input. Based on the different FPKM value and fold thresholds, TEnGExA classifies the user provided gene lists into tissue-enriched or tissue-specific transcripts along with other standard classes. By analyzing the published sample data from human, plant and microorganism, we signifies that TEnGExA can easily handle complex or large data from any species to provided tissue-enriched gene list for downstream analysis in quick time. In summary, TEnGExA is quick, easy to use and an efficient tool for TEA. The R package is freely available at https://github.com/ubagithub/TEnGExA/ and the GUI web interface is accessible at http://webtom.cabgrid.res.in/tissue_enrich/.
DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes
Authors: Ruan Peifeng , Wang Shuang 
Published: September 2020

AbstractBiological network-based strategies are useful in prioritizing genes associated with diseases. Several comprehensive human gene networks such as STRING, GIANT and HumanNet were developed and used in network-assisted algorithms to identify disease-associated genes. However, none of these networks are disease-specific and may not accurately reflect gene interactions for a specific disease. Aiming to improve disease gene prioritization using networks, we propose a Disease-Specific Network Enhancement Prioritization (DiSNEP) framework. DiSNEP first enhances a comprehensive gene network specifically for a disease through a diffusion process on a gene–gene similarity matrix derived from disease omics data. The enhanced disease-specific gene network thus better reflects true gene interactions for the disease and may improve prioritizing disease-associated genes subsequently. In simulations, DiSNEP that uses an enhanced disease-specific network prioritizes more true signal genes than comparison methods using a general gene network or without prioritization. Applications to prioritize cancer-associated gene expression and DNA methylation signal genes for five cancer types from The Cancer Genome Atlas (TCGA) project suggest that more prioritized candidate genes by DiSNEP are cancer-related according to the DisGeNET database than those prioritized by the comparison methods, consistently across all five cancer types considered, and for both gene expression and DNA methylation signal genes.
Inference of viral quasispecies with a paired de Bruijn graph
Authors: Freire Borja , Ladra Susana , Paramá Jose R , Salmela Leena 
Published: September 2020

AbstractMotivationRNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterize the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available. Current methods for assembling viral quasispecies are either based on overlap graphs or on de Bruijn graphs. Overlap graph-based methods tend to be accurate but slow, whereas de Bruijn graph-based methods are fast but less accurate.ResultsWe present viaDBG, which is a fast and accurate de Bruijn graph-based tool for de novo assembly of viral quasispecies. We first iteratively correct sequencing errors in the reads, which allows us to use large k-mers in the de Bruijn graph. To incorporate the paired-end information in the graph, we also adapt the paired de Bruijn graph for viral quasispecies assembly. These features enable the use of long-range information in contig construction without compromising the speed of de Bruijn graph-based approaches. Our experimental results show that viaDBG is both accurate and fast, whereas previous methods are either fast or accurate but not both. In particular, viaDBG has comparable or better accuracy than SAVAGE, while being at least nine times faster. Furthermore, the speed of viaDBG is comparable to PEHaplo but viaDBG is able to retrieve also low abundance quasispecies, which are often missed by PEHaplo.Availability and implementationviaDBG is implemented in C++ and it is publicly available at https://bitbucket.org/bfreirec1/viadbg. All datasets used in this article are publicly available at https://bitbucket.org/bfreirec1/data-viadbg/.Supplementary informationSupplementary data are available at Bioinformatics online.
Block bootstrap optimality and empirical block selection for sample quantiles with dependent data
Authors: Kuffner T A , Lee S M S , Young G A 
Published: September 2020

Summary
We establish a general theory of optimality for block bootstrap distribution estimation for sample quantiles under mild strong mixing conditions. In contrast to existing results, we study the block bootstrap for varying numbers of blocks. This corresponds to a hybrid between the sub- sampling bootstrap and the moving block bootstrap, in which the number of blocks is between 1 and the ratio of sample size to block length. The hybrid block bootstrap is shown to give theoretical benefits, and startling improvements in accuracy in distribution estimation in important practical settings. The conclusion that bootstrap samples should be of smaller size than the original sample has significant implications for computational efficiency and scalability of bootstrap methodologies with dependent data. Our main theorem determines the optimal number of blocks and block length to achieve the best possible convergence rate for the block bootstrap distribution estimator for sample quantiles. We propose an intuitive method for empirical selection of the optimal number and length of blocks, and demonstrate its value in a nontrivial example.
A novel analysis of gene array data: yeast cell cycle
Authors: Sirovich Lawrence 
Published: September 2020

Abstract
Many gene array studies of the yeast cell cycle have been performed (Cho RJ, Campbell MJ, Winzeler EA et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998;2:65–73; Orlando DA, Lin CY, Bernard A et al. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 2008;453:944–7; Pramila T, Wu W, Miles S et al. The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev 2006;20:2266–78; Spellman PT, Sherlock G, Zhang MQ et al. Comprehensive identification of cell cycle–regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. MBoC 1998;9:3273–97). Largely, these studies contain elements drawn from laboratory experiments. The present investigation determines cell division cycle (CDC) genes solely from the data (Orlando DA, Lin CY, Bernard A et al. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 2008;453:944–7). It is shown by simple reasoning that the dynamics of the approximately 6000 yeast genes are described by an approximately six-dimensional space. This leads a precisely determined cell-cycle period, along with the quality and timing of the identified CDC genes. Convincing evidence for the role of the identified genes is obtained. While these show good agreement with standard CDC gene representatives (Orlando DA, Lin CY, Bernard A et al. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature 2008;453:944–7; Spellman PT, Sherlock G, Zhang MQ et al. Comprehensive identification of cell cycle–regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. MBoC 1998;9:3273–97; de Lichtenberg U, Jensen LJ, Fausbøll A et al. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 2005;21:1164–71) several hundred newly revealed CDC genes appear, which merit attention. The present approach employs an adaptation of a method introduced to study turbulent flows (Schmid PJ. Dynamic mode decomposition of numerical and experimental data. J Fluid Mech 2010;656:5–28), “dynamic mode decomposition” (DMD). From this, one can infer that singular value decomposition, analysis of the data entangles the underlying (gene) dynamics implicit in the data; and that DMD produces the disentangling transformation. It is the assertion of this study that a new tool now exists for the analysis of the gene array signals, and in particular for investigating the yeast cell cycle.
Impact of Christianity and Ancestral Beliefs on Black South Africans’ Decision-Making Regarding the Adoption of Abandoned Children
Authors: Gerrand P , Nkomo T 
Published: September 2020

Abstract
Annually, hundreds of African infants are abandoned in South Africa and become adoptable because rigorous efforts to trace their parents and family members are unsuccessful. Although domestic adoption is prioritised in terms of legislation, policy and practice, most abandoned children’s right to be permanently raised in a loving family is not being realised. The most promising source of potential adopters is black South Africans, but the number of black adopters is ever declining. To investigate factors affecting black South African’s decision-making regarding the legal adoption of abandoned children, a post-graduate study was undertaken. Thirty-nine black adults participated in the study consisting of adopters, adoption applicants in the screening process, potential adopters that did not enter the screening process, adoption of social workers and citizens. The theory emerging derived from concurrent data gathering and analysis as set out by Corbin and Strauss is: ‘Tensions surrounding adoption policy and practice, and perceptions and experiences of adoption’. This article focuses on a main category of this grounded theory; that African ancestral beliefs and modern Christian beliefs can both reinforce and discourage adoption abandoned children.
Thrombotic microangiopathies assessment: mind the complement
Authors: Blasco Miquel , Guillén Elena , Quintana Luis F , Garcia-Herrera Adriana , Piñeiro Gastón , Poch Esteban , Carreras Enric , Campistol Josep M , Diaz-Ricart Maribel , Palomo Marta 
Published: September 2020

Abstract
When faced with microangiopathic haemolytic anaemia, thrombocytopenia and organ dysfunction, clinicians should suspect thrombotic microangiopathy (TMA). The endothelial damage that leads to this histological lesion can be triggered by several conditions or diseases, hindering an early diagnosis and aetiological treatment. However, due to systemic involvement in TMA and its low incidence, an accurate early diagnosis is often troublesome. In the last few decades, major improvements have been made in the pathophysiological knowledge of TMAs such as thrombotic thrombocytopenic purpura [TTP, caused by ADAMTS-13 (a disintegrin and metalloproteinase with a thrombospondin Type 1 motif, member 13) deficiency] and atypical haemolytic uraemic syndrome (aHUS, associated with dysregulation of the alternative complement pathway), together with enhancements in patient management due to new diagnostic tools and treatments. However, diagnosis of aHUS requires the exclusion of all the other entities that can cause TMA, delaying the introduction of terminal complement blockers, which have shown high efficacy in haemolysis control and especially in avoiding organ damage if used early. Importantly, there is increasing evidence that other forms of TMA could present overactivation of the complement system, worsening their clinical progression. This review addresses the diagnostic and therapeutic approach when there is clinical suspicion of TMA, emphasizing complement evaluation as a potential tool for the inclusive diagnosis of aHUS, as well as for the improvement of current knowledge of its pathophysiological involvement in other TMAs. The development of both new complement activation biomarkers and inhibitory treatments will probably improve the management of TMA patients in the near future, reducing response times and improving patient outcomes.
Complement and protection from tissue injury in COVID-19
Authors: Ortiz Alberto 
Published: September 2020

Abstract
As the second wave of coronavirus disease 2019 (COVID-19) is well under way around the world, the optimal therapeutic approach that addresses virus replication and hyperinflammation leading to tissue injury remains elusive. This issue of Clinical Kidney Journal provides further evidence of complement activation involvement in COVID-19. Taking advantage of the unique repeat access to chronic haemodialysis patients, the differential time course of C3 and C5 activation in relation to inflammation and severity of disease have been characterized. This further points to complement as a therapeutic target. Indeed, clinical trials targeting diverse components of complement are ongoing. However, a unique case of COVID-19 in a patient with pre-existent atypical haemolytic syndrome on chronic eculizumab therapy suggests that even early eculizumab may fail to prevent disease progression to a severe stage. Finally, preclinical studies in endotoxaemia, another hyperinflammation syndrome characterized by lung and kidney injury, suggest that cilastatin, an inexpensive drug already in clinical use, may provide tissue protection against hyperinflammation in COVID-19.