bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long Process Incus necrosis in Revision Stapedotomy: Retrospective Clinical Study
Authors: Massimilla Eva Aurora , Testa Domenico , Nunziata Michele , Donadio Anna , Romano Maria Loreto , Motta Gaetano 
Published: January 2021

Objectives: We describe our experience with long process incus (LPI) necrosis in revision stapedotomy and discuss the different management methods proposed in the literature to identify surgical techniques that can lead to satisfactory results over time. Methods: Twenty-two stapedotomy revisions, in 21 patients with the necrosis of the long process of the incus, are performed from 1997 to 2017. In cases of erosion or minimal necrosis of LPI, a new prosthesis of the same type or an angled prosthesis was applied higher on the residual incus stump. In cases of partial necrosis of LPI, a Donaldson type ventilation tube reshaped and placed on the residual incus stump to stabilize prosthesis, or glass ionomer bone cement was used. In cases of subtotal necrosis of LPI, a cup piston prosthesis in polycel was applied on incus residual stump. Pre- and postoperative (≥1 year) pure tone audiometry was performed for all cases. Air conduction threshold, bone conduction (BC) threshold, and air-bone gap (ABG) were documented according to the American Academy of Otolaryngology Head and Neck Surgery Committee of Hearing and Equilibrium guidelines. Results: At 1-year follow-up, postoperative ABG was reduced to ≤10 dB in 13 (59%) cases and ≤20 dB in 19 (86.4%) cases. The mean postoperative ABG significantly decreased in each group. There was no significant change in postoperative BC thresholds, and there were no cases with postoperative SNHL. Conclusion: Excellent functional results can also be achieved in cases of long incus process necrosis. The choice of technique should be considered according to the degree of necrosis. Piston replacement with the same type or angled type prosthesis, in cases of erosion or minimal LPI necrosis, and modified Donaldson type ventilation tube, in cases of partial LPI necrosis, provided excellent hearing results.
HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding
Authors: Solares Edwin A. , Tao Yuan , Long Anthony D. , Gaut Brandon S. 
Published: January 2021

Abstract
Background
Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

Results
Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb).

Conclusions
HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito’s largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.
Drug-induced cell viability prediction from LINCS-L1000 through WRFEN-XGBoost algorithm
Authors: Lu Jiaxing , Chen Ming , Qin Yufang 
Published: January 2021

Abstract
Background
Predicting the drug response of the cancer diseases through the cellular perturbation signatures under the action of specific compounds is very important in personalized medicine. In the process of testing drug responses to the cancer, traditional experimental methods have been greatly hampered by the cost and sample size. At present, the public availability of large amounts of gene expression data makes it a challenging task to use machine learning methods to predict the drug sensitivity.

Results
In this study, we introduced the WRFEN-XGBoost cell viability prediction algorithm based on LINCS-L1000 cell signatures. We integrated the LINCS-L1000, CTRP and Achilles datasets and adopted a weighted fusion algorithm based on random forest and elastic net for key gene selection. Then the FEBPSO algorithm was introduced into XGBoost learning algorithm to predict the cell viability induced by the drugs. The proposed method was compared with some new methods, and it was found that our model achieved good results with 0.83 Pearson correlation. At the same time, we completed the drug sensitivity validation on the NCI60 and CCLE datasets, which further demonstrated the effectiveness of our method.

Conclusions
The results showed that our method was conducive to the elucidation of disease mechanisms and the exploration of new therapies, which greatly promoted the progress of clinical medicine.
nanotatoR: a tool for enhanced annotation of genomic structural variants
Authors: Bhattacharya Surajit , Barseghyan Hayk , Délot Emmanuèle C. , Vilain Eric 
Published: January 2021

Abstract
Background
Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently labeled DNA molecules for de novo genome assembly and SV calling, has allowed for increased sensitivity and specificity in SV detection. However, compared to small variant annotation tools, OGM-based SV annotation software has seen little development, and currently available SV annotation tools do not provide sufficient information for determination of variant pathogenicity.

Results
We developed an R-based package, nanotatoR, which provides comprehensive annotation as a tool for SV classification. nanotatoR uses both external (DGV; DECIPHER; Bionano Genomics BNDB) and internal (user-defined) databases to estimate SV frequency. Human genome reference GRCh37/38-based BED files are used to annotate SVs with overlapping, upstream, and downstream genes. Overlap percentages and distances for nearest genes are calculated and can be used for filtration. A primary gene list is extracted from public databases based on the patient’s phenotype and used to filter genes overlapping SVs, providing the analyst with an easy way to prioritize variants. If available, expression of overlapping or nearby genes of interest is extracted (e.g. from an RNA-Seq dataset, allowing the user to assess the effects of SVs on the transcriptome). Most quality-control filtration parameters are customizable by the user. The output is given in an Excel file format, subdivided into multiple sheets based on SV type and inheritance pattern (INDELs, inversions, translocations, de novo, etc.).
nanotatoR passed all quality and run time criteria of Bioconductor, where it was accepted in the April 2019 release. We evaluated nanotatoR’s annotation capabilities using publicly available reference datasets: the singleton sample NA12878, mapped with two types of enzyme labeling, and the NA24143 trio. nanotatoR was also able to accurately filter the known pathogenic variants in a cohort of patients with Duchenne Muscular Dystrophy for which we had previously demonstrated the diagnostic ability of OGM.

Conclusions
The extensive annotation enables users to rapidly identify potential pathogenic SVs, a critical step toward use of OGM in the clinical setting.
Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data
Authors: Dzomba E. F. , Chimonyo M. , Pierneef R. , Muchadeyi F. C. 
Published: January 2021

AbstractBackgroundPopulation history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands.ResultsA total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns.ConclusionsOverall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.
Comparative transcriptomic analysis reveals female-biased olfactory genes potentially involved in plant volatile-mediated oviposition behavior of Bactrocera dorsalis
Authors: Xu Li , Tang Kai-Yue , Chen Xiao-Feng , Tao Yong , Jiang Hong-Bo , Wang Jin-Jun 
Published: January 2021

Abstract
Background
Olfactory systems take on important tasks to distinguish salient information from a complex olfactory environment, such as locating hosts, mating, aggression, selecting oviposition sites, and avoiding predators. The olfactory system of an adult insect consists of two pairs of main olfactory appendages on the head, the antennae, and the palps, which are covered with sensilla. Benzothiazole and 1-octen-3-ol could elicit oviposition behavior in gravid B. dorsalis are regarded as oviposition stimulants. However, the mechanism for how B. dorsalis percepts benzothiazole and 1-octen-3-ol still remains unknown.

Results
We conducted a comparative analysis of the antennal transcriptomes in different genders of B. dorsalis using Illumina RNA sequencing (RNA-seq). We identified a total of 1571 differentially expressed genes (DEGs) among the two sexes, including 450 female-biased genes and 1121 male-biased genes. Among these DEGs, we screened out 24 olfaction-related genes and validated them by qRT-PCR. The expression patterns of these genes in different body parts were further determined. In addition, we detected the expression profiles of the screened female-biased chemosensory genes in virgin and mated female flies. Furthermore, the oviposition stimulants-induced expression profilings were used to identify chemosensory genes potentially responsible for benzothiazole and 1-octen-3-ol perception in this fly.

Conclusions
The results from this study provided fundamental data of chemosensory DEGs in the B. dorsalis antenna. The odorant exposure assays we employed lay a solid foundation for the further research regarding the molecular mechanism of benzothiazole and 1-octen-3-ol mediated oviposition behavior in B. dorsalis.
Genome-wide identification of GH3 genes in Brassica oleracea and identification of a promoter region for anther-specific expression of a GH3 gene
Authors: Jeong Jiseong , Park Sunhee , Im Jeong Hui , Yi Hankuil 
Published: January 2021

AbstractBackgroundTheGretchen Hagen 3(GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors.GH3genes, especially Group III subgroup 6GH3genes, and their expression patterns in economically importantB. oleraceavar.oleraceahave not been systematically identified.ResultsAs a first step to understand regulation and molecular functions of Group III subgroup 6GH3genes, 34GH3genes including four subgroup 6 genes were identified inB. oleraceavar.oleracea. Synteny found around subgroup 6GH3genes inB. oleraceavar.oleraceaandArabidopsis thalianaindicated that these genes are evolutionarily related. Although expression of four subgroup 6GH3genes inB. oleraceavar.oleraceais not induced by auxin, gibberellic acid, or jasmonic acid, the genes show different organ-dependent expression patterns. Among subgroup 6GH3genes inB. oleraceavar.oleracea, onlyBoGH3.13–1is expressed in anthers when microspores, polarized microspores, and bicellular pollens are present, similar to two out of four syntenicA. thalianasubgroup 6GH3genes. Detailed analyses of promoter activities further showed thatBoGH3.13–1is expressed in tapetal cells and pollens in anther, and also expressed in leaf primordia and floral abscission zones.ConclusionsSixty-two base pairs (bp) region (− 340 ~ − 279 bp upstream from start codon) and about 450 bp region (− 1489 to − 1017 bp) inBoGH3.13–1promoter are important for expressions in anther and expressions in leaf primordia and floral abscission zones, respectively. The identified anther-specific promoter region can be used to develop male sterile transgenicBrassicaplants.
Galectins from Onchocerca ochengi and O. volvulus and their immune recognition by Wistar rats, Gudali zebu cattle and human hosts
Authors: Ngwasiri Ngwafu Nancy , Brattig Norbert W. , Ndjonka Dieudonné , Liebau Eva , Paguem Archile , Leusder Dustin , Kingsley Manchang Tanyi , Eisenbarth Albert , Renz Alfons , Daniel Achukwi Mbunkah 
Published: January 2021

AbstractBackgroundDuring the last two decades research on animal filarial parasites, especiallyOnchocerca ochengi,infecting cattle in savanna areas of Africa revealed thatO. ochengias an animal model has biological features that are similar to those ofO. volvulus,the aetiological agent of human onchocerciasis. There is, however, a paucity of biochemical, immunological and pathological data forO. ochengi. Galectins can be generated by parasites and their hosts. They are multifunctional molecules affecting the interaction between filarial parasites and their mammalian hosts including immune responses. This study characterizedO. ochengigalectin, verified its immunologenicity and established its immune reactivity and that ofOnchocerca volvulusgalectin.ResultsThe phylogenetic analysis showed the high degree of identity between the identifiedO. ochengiand theO. volvulusgalectin-1 (ß-galactoside-binding protein-1) consisting only in one exchange of alanine for serine.O. ochengigalectin induced IgG antibodies during 28 days after immunization of Wistar rats. IgG fromO. ochengi-infected cattle andO. volvulus-infected humans cross-reacted with the corresponding galectins. Under the applied experimental conditions in a cell proliferation test,O. ochengigalectin failed to significantly stimulate peripheral blood mononuclear cells (PBMCs) fromO. ochengi-infected cattle, regardless of their parasite load.ConclusionAnO. ochengigalectin gene was identified and the recombinantly expressed protein was immunogenic. IgG fromOnchocerca-infected humans and cattle showed similar cross-reaction with both respective galectins. The present findings reflect the phylogenetic relationship between the two parasites and endorse the appropriateness of the cattleO. ochengimodel forO. volvulusinfection research.
Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis
Authors: Ma Dongmei , Liu Bei , Ge Lingqiao , Weng Yinyin , Cao Xiaohui , Liu Fang , Mao Peisheng , Ma Xiqing 
Published: January 2021

Abstract
Background
Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the production of alfalfa hay and seeds. However, the underlying molecular mechanisms of flowering time regulation in alfalfa are not well understood.

Results
In this study, an early-flowering alfalfa genotype 80 and a late-flowering alfalfa genotype 195 were characterized for the flowering phenotype. Our analysis revealed that the lower jasmonate (JA) content in new leaves and the downregulation of JA biosynthetic genes (i.e. lipoxygenase, the 12-oxophytodienoate reductase-like protein, and salicylic acid carboxyl methyltransferase) may play essential roles in the early-flowering phenotype of genotype 80. Further research indicated that genes encode pathogenesis-related proteins [e.g. leucine rich repeat (LRR) family proteins, receptor-like proteins, and toll-interleukin-like receptor (TIR)-nucleotide-binding site (NBS)-LRR class proteins] and members of the signaling receptor kinase family [LRR proteins, kinases domain of unknown function 26 (DUF26) and wheat leucine-rich repeat receptor-like kinase10 (LRK10)-like kinases] are related to early flowering in alfalfa. Additionally, those involved in secondary metabolism (2-oxoglutarate/Fe (II)-dependent dioxygenases and UDP-glycosyltransferase) and the proteasome degradation pathway [really interesting new gene (RING)/U-box superfamily proteins and F-box family proteins] are also related to early flowering in alfalfa.

Conclusions
Integrated phenotypical, physiological, and transcriptomic analyses demonstrate that hormone biosynthesis and signaling pathways, pathogenesis-related genes, signaling receptor kinase family genes, secondary metabolism genes, and proteasome degradation pathway genes are responsible for the early flowering phenotype in alfalfa. This will provide new insights into future studies of flowering time in alfalfa and inform genetic improvement strategies for optimizing this important trait.
Targeted amplicon sequencing + next-generation sequencing–based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)
Authors: Takeshima Ryoma , Ogiso-Tanaka Eri , Yasui Yasuo , Matsui Katsuhiro 
Published: January 2021

Abstract
Background
Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines. However, genetic loci and selection markers associated with PHS in buckwheat have not been reported.

Results
By next-generation sequencing (NGS) of whole-genome of parental lines, we developed a genome-wide set of 300 markers. By NGS- based bulked segregant analysis (NGS-BSA), we developed 100 markers linked to PHS tolerance. To confirm the effectiveness of marker development from NGS-BSA data, we developed 100 markers linked to the self-compatibility (SC) trait from previous NGS-BSA data. Using these markers, we developed genetic maps with AmpliSeq technology, which can quickly detect polymorphisms by amplicon-based multiplex targeted NGS, and performed quantitative trait locus (QTL) analysis for PHS tolerance in combination with NGS-BSA. QTL analysis detected two major and two minor QTLs for PHS tolerance in a segregating population developed from a cross between the PHS-tolerant ‘Kyukei 29’ and the self-compatible susceptible ‘Kyukei SC7’. We found different major and minor QTLs in other segregating populations developed from the PHS-tolerant lines ‘Kyukei 28’ and ‘NARO-FE-1’. Candidate markers linked to PHS developed by NGS-BSA were located near these QTL regions. We also investigated the effectiveness of markers linked to these QTLs for selection of PHS-tolerant lines among other segregating populations.

Conclusions
We efficiently developed genetic maps using a method combined with AmpliSeq technology and NGS-BSA, and detected QTLs associated with preharvest sprouting tolerance in common buckwheat. This is the first report to identify QTLs for PHS tolerance in buckwheat. Our marker development system will accelerate genetic research and breeding in common buckwheat.