bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional Wait Times for Patients With Nonmelanoma Skin Cancer in Southwestern Ontario
Authors: Fan Stacy , Hackett Jesse , Lutz Kristina , Heaton Graham , Symonette Caitlin , Grant Aaron 
Published: October 2019

Background: Nonmelanoma skin cancer (NMSC) affects many Canadians. Although morbidity and mortality are rare, the burden to patients and the health-care system is significant. This study aims to evaluate current plastic surgery wait times and care pathways for patients with NMSC in Southwestern Ontario. Methods: A retrospective chart review of 225 patients treated in Ontario from 2015 to 2018 was conducted. Inclusion criteria included patients with an NMSC managed with surgical excision. Referral information was compared. Primary outcomes were wait times: from referral to consultation, referral to excision, and consultation to excision. Data were analyzed using Student t test with equal variance. Results: One-hundred forty-three patients were included from the academic cohort and 82 from the community cohort. Referrals to academic and community surgeons included lesion location (90% and 97.6%, respectively), but less frequently included size (18% and 29.2%, respectively). Most referrals to academic surgeons included biopsy results (78.6%), as opposed to community referrals (25.6%). Patients in the academic cohort waited 15.3 ± 12.7 weeks from referral to consultation, and 15.7 ± 13 weeks from referral to excision. Patients from the community cohort waited significantly shorter periods of 4.9 ± 3.1 ( P < .001) and 11.7 ± 9.9 weeks ( P = .016), respectively. However, patients of the academic cohort waited 2.4 ± 7.1 weeks from consultation to excision, while patients in the community cohort waited 6.7 ± 9.6 weeks ( P < .001). Rates of negative peripheral margins on pathology were similar between groups, at 89.5% of the academic cohort and 88.9% of the community cohort. Deep margins were positive 5.7% of the time at the academic sites and 6.2% of the time in the community. Conclusions: Patients referred to academic centres waited significantly longer periods of time in several parameters compared to those referred to a community surgeon. However, academic surgeons often had expedited consultation-to-excision time frame. This study provides important data for future quality improvement initiatives in NMSC care.
Alternate Measure of Disability Intensity: Modified Rankin Scale
Authors: Chakrabartty Satyendra Nath 
Published: October 2019

Objective: This study was aimed to propose an alternate method of scoring the intensity of disability in a patient, which will facilitate ranking and classifying a group of patients in mutually exclusive classes along with the quantification of progress made by a patient or the effect of interventions and also tracking the path of improvement of a patient and estimating the survival curve for drawing useful conclusions. Method: A nonparametric measure of disability intensity in terms of Cos θi for the ith patient is proposed to avoid limitations of the usual scoring of modified Rankin scale and satisfies many desired properties. Two measures of interrater agreement in terms of standard error of measurement and coefficient of variation are also proposed and their relationships with Cos θi are detailed. Illustration with hypothetical data involving 30 patients and 10 raters was undertaken. Results: Distribution of Cos θ was close to normal. Principal component analysis of Cos θ resulted in one factor explaining 64% of variance. Inconsistent raters were identified. Coefficient of variation appears to perform better than the standard error of measurement. Split-half reliability of raters in terms of angular association was higher. Similarly, split-half reliability of disability intensity (Cos θ) was higher. Average disability intensity [Formula: see text] showed similar empirical results with rigorous method of most preferred direction of a finite number of angles. Conclusions: The proposed simple measures will help the researchers and practitioners to make meaningful analysis and draw meaningful conclusions. Future studies may be undertaken to rescale Likert data to scales having properties of interval-level measurement and study the proposed measures in detail.
Evaluating the Trade, Revenue and Welfare Implication of Plantation Crops under ASEAN–India FTA
Authors: Jagdambe Subhash , Mouzam Shaikh Mohd 
Published: October 2019

This article examines the impact of ASEAN–India Free Trade Agreement on India’s special products categories, namely, coffee, tea and pepper based on partial equilibrium model. The Software for Market Analysis and Restrictive Trade (SMART) model has been used to estimate the trade creation (TC) and trade diversion (TD) effect, revenue effect and welfare effect for the above-mentioned commodities. The results from the SMART simulation analysis indicate that the increase in trade for both the scenarios is mainly driven by TC rather than TD. Further, the study also assesses how the total trade effect is distributed across the major ASEAN countries for each commodity and found that Indonesia and Vietnam are the biggest gainers in terms of TC effect in both the scenarios. JEL Classification: F13, F15, Q1
Chemical intolerance: involvement of brain function and networks after exposure to extrinsic stimuli perceived as hazardous
Authors: Azuma Kenichi , Uchiyama Iwao , Tanigawa Mari , Bamba Ikuko , Azuma Michiyo , Takano Hirohisa , Yoshikawa Toshikazu , Sakabe Kou 
Published: October 2019

AbstractBackgroundChemical intolerance (CI) is a chronic condition characterized by recurring and severe symptoms triggered by exposure to low levels of odorous or pungent substances. The etiology of CI has been a controversial subject for a long time. The aim of this review is to summarize findings on the neurological processing of sensory information during and after exposure to low levels of odorous or pungent substances in individuals with CI, focusing on the brain function and networks.MethodsScientific studies on CI published between 2000 and 2019 in academic peer-reviewed journals were systematically searched using medical and scientific literature databases. Only peer-reviewed articles reporting original research from experimental human studies directly associated with CI, and involving related neurological responses or brain imaging after exposure to odorous or pungent substances (i.e., in chemical provocation tests), were considered.ResultsForty-seven studies were found to be eligible for a full-text review. Twenty-three studies met the selection criteria and were included in this review. Evidence indicated that differences between subjects with CI and healthy controls were observed by brain imaging during and after exposure to odorous or pungent substances. Differences in brain imaging were also observed between initial exposure and after exposure to these substances. Neurological processing of sensory information after exposure to extrinsic stimuli in the limbic system and related cortices were altered in subjects with CI. A previous documentable exposure event was likely to be involved in this alteration.ConclusionsThis review documents consistent evidence for the altered neurological processing of sensory information in individuals with CI. Further neurophysiological research exploring the processing of extrinsic stimuli and cognition of sensation through the limbic system and related cortices in CI, and the appearance of symptoms in individuals with CI, are required.
Glycosylator: a Python framework for the rapid modeling of glycans
Authors: Lemmin Thomas , Soto Cinque 
Published: October 2019

Abstract

Background
Carbohydrates are a class of large and diverse biomolecules, ranging from a simple monosaccharide to large multi-branching glycan structures. The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N-linked glycosylation, plays an important role in the physiology of many living organisms. Most software for glycan modeling on a personal desktop computer requires knowledge of molecular dynamics to interface with specialized programs such as CHARMM or AMBER. There are a number of popular web-based tools that are available for modeling glycans (e.g., GLYCAM-WEB (http://https://dev.glycam.org/gp/) or Glycosciences.db (http://www.glycosciences.de/)). However, these web-based tools are generally limited to a few canonical glycan conformations and do not allow the user to incorporate glycan modeling into their protein structure modeling workflow.

Results
Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). The GUI provides a straightforward two-dimensional (2D) rendering of a glycoprotein that allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific three-dimensional (3D) glycans on a protein structure using a library of predefined templates.

Conclusions
Glycosylator was used to generate models of glycosylated protein without steric clashes. Since the molecular topology is based on the CHARMM force field, new complex sugar moieties can be generated without modifying the internals of the code. Glycosylator provides more functionality for analyzing and modeling glycans than any other available software or webserver at present. Glycosylator will be a valuable tool for the glycoinformatics and biomolecular modeling communities.
Diploid hybrid fish derived from the cross between female Bleeker’s yellow tail and male topmouth culter, two cyprinid fishes belonging to different subfamilies
Authors: Li Shengnan , Xie Lihua , Xiao Jun , Yuan Liujiao , Zhou Tian , Luo Kaikun , Zhang Chun , Zhao Rurong , Tao Min , Liu Shaojun 
Published: October 2019

Abstract

Background
Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT) and topmouth culter (Culter alburnus Basilewsky, TC) are both famous and important economic freshwater fish in China. YT, a kind of omnivorous fish, has strong resistance. TC, a kind of carnivorous fish, has high-quality meat but poor resistance. Distant hybridization can integrate the advantages of both parents. There has been no previous report regarding hybrid fish derived from female YT × male TC. It is expected that hybridization of these two kinds of fish will result in F1 hybrids with improved characteristics, such as faster growth rate, stronger resistance, and high-quality meat, which are of great significance in fish genetic breeding.

Results
In this study, we investigated the main biological characteristics of diploid hybrid fish derived from female YT × male TC. The hybrids had an intermediate number of upper lateral line scales between those for YT and TC. The hybrids were diploids with 48 chromosomes and had the same karyotype formula as their parents. The hybrids generated variations in 5S rDNA (designated class IV: 212 bp) and lost specific 5S rDNA derived from the maternal parent (designated class II: 221 bp), which might be related to hybridization. In terms of reproductive traits, all the tested female hybrids exhibited normal gonadal development, and the two-year-old F1 females produced mature eggs. However, all the tested testes of the male hybrids could not produce mature sperm. It is possible that the hybrid lineage will be established by back-crossing the fertile female hybrids and their parents.

Conclusions
Obtaining a fertile female hybrid fish made the creation of a new type of fish possible, which was significant in fish genetic breeding.
Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica
Authors: Yan Qi , Wu Fan , Ma Tiantian , Zong Xifang , Ma Qian , Li Jie , Zhao Yufeng , Wang Yanrong , Zhang Jiyu 
Published: October 2019

Abstract

Background
Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However, no information is available for the bZIP family in Cleistogenes songorica, which is an important xerophytic and allotetraploid grass in desert grasslands.

Results
In this study, 86 CsbZIPs were identified in the allotetraploid C. songorica genome. For location analysis, CsbZIPs were distributed evenly across two subgenomes of C. songorica. Phylogenetic tree analysis among three species indicated that CsbZIPs were evolutionarily more closely related to OsbZIPs than AtbZIPs. Syntenic and phylogenetic analyses confirmed that the CsbZIPs were mainly expanded by whole-genome duplication events. Furthermore, it was determined that rice and C. songorica might have undergone purified selection during their long evolutionary history by calculating the Ks values and Ka/Ks ratios of orthologous gene pairs. By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes. In shoots and roots, 79.1 and 87.2% of the CsbZIP genes, respectively, displayed transcript changes under at least one stress treatment, such as heat, cold, drought and salt. Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering. Co-expression network, GO annotation and real-time quantitative reverse transcription PCR (qRT-PCR) analyses revealed a close relationship between CL flowering-associated genes and abiotic stress-related genes.

Conclusions
BZIP TFs were comprehensively analysed and identified in allotetraploid C. songorica. Our results provide insights into the evolutionary history of the bZIP family in C. songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants.
Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation
Authors: Pasookhush Phongthana , Hindmarch Charles , Sithigorngul Paisarn , Longyant Siwaporn , Bendena William G. , Chaivisuthangkura Parin 
Published: October 2019

AbstractBackgroundMacrobrachium rosenbergii, is one of a major freshwater prawn species cultured in Southeast Asia. White tail disease (WTD), caused byMacrobrachium rosenbergiinodavirus (MrNV), is a serious problem in farm cultivation and is responsible for up to 100% mortality in the post larvae stage. Molecular data on howM. rosenbergiipost-larvae launches an immune response to an infection withMrNV is not currently available. We therefore compared the whole transcriptomic sequence ofM. rosenbergiipost-larvae before and afterMrNV infection.ResultsTranscriptome forM. rosenbergiipost-larvae demonstrated high completeness (BUSCO Complete: 83.4%, fragmentation: 13%, missing:3.3%, duplication:16.2%; highest ExN50 value: 94%). The assembled transcriptome consists of 96,362 unigenes with N50of 1308 bp. The assembled transcriptome was successfully annotated against the NCBI non-redundant arthropod database (33.75%), UniProt database (26.73%), Gene Ontology (GO) (18.98%), Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (EggNOG) (20.88%), and Kyoto Encyclopedia of Genes and Genome pathway (KEGG) (20.46%). GO annotations included immune system process, signaling, response to stimulus, and antioxidant activity. Differential abundance analysis using EdgeR showed 2413 significantly up-regulated genes and 3125 significantly down-regulated genes during the infection ofMrNV.ConclusionsThis study reported a highly complete transcriptome from the post-larvae stage of giant river prawn,M. rosenbergii.Differential abundant transcripts duringMrNV infection were identified and validated by qPCR, many of these differentially abundant transcripts as key players in antiviral immunity. These include known members of the innate immune response with the largest expression change occurring in theM. rosenbergiipost-larvae afterMrNV infection such as antiviral protein, C-type lectin, prophenol oxidase, caspase, ADP ribosylation factors, and dicer.
2-DE-based proteomic analysis of protein changes associated with etiolated mesocotyl growth in Zea mays
Authors: Niu Liangjie , Wu Zhaokun , Liu Hui , Wu Xiaolin , Wang Wei 
Published: October 2019

AbstractBackgroundThe mesocotyl connects the coleoptilar node and the basal part of the seminal root of maize (Zea mays) seedling. The mesocotyl pushes the shoot of the seedling out of the soil during seed germination; thus, its growth is highly related to deep-sowing tolerance. Although many studies on the maize mesocotyl have been carried out at physiological and molecular levels, the proteomic changes associated with cellular and physiological activities during mesocotyl growth are still unknown.ResultsIn the present study, the maize hybrid Zhengdan 958 was used to study mesocotyl growth and accompanying protein changes.The dark-grown etiolated mesocotyls exhibited a slow-fast-slow feature, with significant changes in the levels of indole-3-acetic acid (IAA) and cellulose and the activity of peroxidase (POD). In particular, POD activity increased with mesocotyl growth, showing higher activity at the mature (lower) end of the mesocotyl. For the proteomic analysis, soluble proteins were extracted from etiolated mesocotyls dark-grown for 48 h, 84 h, and 132 h, corresponding to the initial, rapid, and slow growth periods, respectively, and subjected to separation by two-dimensional gel electrophoresis (2-DE). As a result, 88 differentially abundant proteins (DAPs) were identified using MALDI-TOF-TOF analysis. At 48 h, most DAPs were stress proteins, heat shock proteins and storage proteins; at 84 h, oxidation/reduction proteins, carbohydrate biogenesis-related proteins and cytoskeleton-related proteins were highly accumulated; at 132 h, the most striking DAPs were those involved in the synthesis and modification of the cell wall and the biogenesis of carbohydrates. Gene ontology (GO) analysis showed that changes in the abundance and proportion of DAPs were consistent with cellular and physiological activities and biological processes during mesocotyl growth. The accumulation of nine DAPs of interest was verified by immunoblotting and RT-qPCR.ConclusionsThe present study revealed that the protein patterns in 2-D gels differed greatly with mesocotyl growth. At different growth periods, a specific set of DAPs participate in various biological processes and underlie the cellular and physiological activities of the mesocotyl. These results contributed to the understanding of mesocotyl growth and the cultivation of maize lines with deep-sowing tolerance.
Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya
Authors: Wang Gang , Lin Jingxian , Shi Yang , Chang Xiaoguang , Wang Yuanyuan , Guo Lin , Wang Wenhui , Dou Meijie , Deng Youjin , Ming Ray , Zhang Jisen 
Published: October 2019

Abstract

Background
Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.

Results
In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752 bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.

Conclusions
Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.
A Eurasia-wide polyploid species complex involving 6x Trifolium ambiguum, 2x T. occidentale and 4x T. repens produces interspecific hybrids with significance for clover breeding
Authors: Williams Warren M. , Verry Isabelle M. , Ansari Helal A. , Hussain S. Wajid , Ullah Ihsan , Ellison Nicholas W. 
Published: October 2019

AbstractBackgroundTrifolium ambiguumoccurs as a 2x, 4x, 6xpolyploid series in W Asia. The 6xform is the most agronomically desirable, having strong rhizomatous spread and drought tolerance. These traits would be potentially very valuable if they could be transferred to white clover (T. repens) which is the most important agronomic clover species. However, to-date, no fertile interspecific hybrids with 6x T. ambiguumare available. Previously, 2x T. occidentalefrom W Europe has produced synthetic fertile hybrids with both 2xand 4x T. ambiguumand these were inter-fertile with white clover. Here we ask whether 2x T. occidentalecan form fertile hybrids with 6x T. ambiguumand act as a genetic bridge to white clover and bring these species together as part of a common gene pool.ResultsTen verified F1(6x T. ambiguumx 2x T. occidentale) hybrids were produced by embryo rescue and seven were studied further. All four investigated for chromosome number were 2n = 4x = 32 and FISH confirmed the expected 21 T. ambiguumand 8 T. occidentalechromosomes. Hybrid fertility was extremely low but 2nfemale gametes functioned with white clover pollen to produce seeds. Derived plants were confirmed using FISH and were successfully backcrossed to white clover to produce partially fertile breeding populations.ConclusionsAlthoughT. occidentaleand 6x T. ambiguumare widely separated by geography and ecological adaptation they have maintained enough genomic affinity to produce partially fertile hybrids. Inter-fertility of the hybrids with allotetraploidT. repensshowed thatT. occidentalecan provide a genetic bridge between 6x T. ambiguumand white clover to produce plants with new phenotypes combining the traits of all three species. Use of this information should enable potentially valuable stress tolerance traits from 6x T. ambiguumto be used in white clover breeding for the first time.