bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of severe anthropogenic disturbance on the heart rate and body temperature in free-living greylag geese (Anser anser)
Authors: Wascher Claudia A F , Arnold Walter , Kotrschal Kurt 
Published: August 2022

Abstract
Anthropogenic disturbances are a major concern for the welfare and conservation of wildlife. We recorded heart rate and body temperature of 20 free-living greylag geese in response to a major regularly re-occurring anthropogenic disturbance—New Year’s Eve fireworks. Heart rate and body temperature were significantly higher in the first and second hour of the new year, compared with the same hour on the 31st of December, the average during December and the average during January. Heart rate and body temperature was not significantly affected by sex or age. From 0200 to 0300 onwards, 1st of January heart rates did not significantly differ from the other periods; however, body temperatures were significantly increased until 0300–0400. From 0400 to 0500, heart rate was not affected by any of the investigated factors, whereas body temperature was significantly increased on the 1st of January compared with the 31st of December and the December average but not compared with the January average. To conclude, our results show that New Year’s Eve fireworks cause a substantial physiological response, indicative of a stress response in greylag geese, which is costly in terms of energy expenditure.
Natriuretic peptide pathways in heart failure: further therapeutic possibilities
Authors: Sangaralingham S Jeson , Kuhn Michaela , Cannone Valentina , Chen Horng H , Burnett John C 
Published: August 2022

Abstract
The discovery of the heart as an endocrine organ resulted in a remarkable recognition of the natriuretic peptide system (NPS). Specifically, research has established the production of atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) from the heart, which exert pleiotropic cardiovascular, endocrine, renal, and metabolic actions via the particulate guanylyl cyclase A receptor (GC-A) and the second messenger, cGMP. C-type natriuretic peptide (CNP) is produced in the endothelium and kidney and mediates important protective auto/paracrine actions via GC-B and cGMP. These actions, in part, participate in the efficacy of sacubitril/valsartan in heart failure (HF) due to the augmentation of the NPS. Here, we will review important insights into the biology of the NPS, the role of precision medicine, and focus on the phenotypes of human genetic variants of ANP and BNP in the general population and the relevance to HF. We will also provide an update of the existence of NP deficiency states, including in HF, which provide the rationale for further therapeutics for the NPS. Finally, we will review the field of peptide engineering and the development of novel designer NPs for the treatment of HF. Notably, the recent discovery of a first-in-class small molecule GC-A enhancer, which is orally deliverable, will be highlighted. These innovative designer NPs and small molecule possess enhanced and novel properties for the treatment of HF and cardiovascular diseases.
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?
Authors: Tang Anfu , Deléger Louise , Bossy Robert , Zweigenbaum Pierre , Nédellec Claire 
Published: August 2022

Abstract
Collecting relations between chemicals and drugs is crucial in biomedical research. The pre-trained transformer model, e.g. Bidirectional Encoder Representations from Transformers (BERT), is shown to have limitations on biomedical texts; more specifically, the lack of annotated data makes relation extraction (RE) from biomedical texts very challenging. In this paper, we hypothesize that enriching a pre-trained transformer model with syntactic information may help improve its performance on chemical–drug RE tasks. For this purpose, we propose three syntax-enhanced models based on the domain-specific BioBERT model: Chunking-Enhanced-BioBERT and Constituency-Tree-BioBERT in which constituency information is integrated and a Multi-Task-Learning framework Multi-Task-Syntactic (MTS)-BioBERT in which syntactic information is injected implicitly by adding syntax-related tasks as training objectives. Besides, we test an existing model Late-Fusion which is enhanced by syntactic dependency information and build ensemble systems combining syntax-enhanced models and non-syntax-enhanced models. Experiments are conducted on the BioCreative VII DrugProt corpus, a manually annotated corpus for the development and evaluation of RE systems. Our results reveal that syntax-enhanced models in general degrade the performance of BioBERT in the scenario of biomedical RE but improve the performance when the subject–object distance of candidate semantic relation is long. We also explore the impact of quality of dependency parses. [Our code is available at: https://github.com/Maple177/syntax-enhanced-RE/tree/drugprot (for only MTS-BioBERT); https://github.com/Maple177/drugprot-relation-extraction (for the rest of experiments)]
Database URL https://github.com/Maple177/drugprot-relation-extraction
Statistical primer: an introduction to the application of linear mixed-effects models in cardiothoracic surgery outcomes research—a case study using homograft pulmonary valve replacement data
Authors: Wang Xu , Andrinopoulou Eleni-Rosalina , Veen Kevin M , Bogers Ad J J C , Takkenberg Johanna J M 
Published: August 2022

Summary

OBJECTIVES
The emergence of big cardio-thoracic surgery datasets that include not only short-term and long-term discrete outcomes but also repeated measurements over time offers the opportunity to apply more advanced modelling of outcomes. This article presents a detailed introduction to developing and interpreting linear mixed-effects models for repeated measurements in the setting of cardiothoracic surgery outcomes research.

METHODS
A retrospective dataset containing serial echocardiographic measurements in patients undergoing surgical pulmonary valve replacement from 1986 to 2017 in Erasmus MC was used to illustrate the steps of developing a linear mixed-effects model for clinician researchers.

RESULTS
Essential aspects of constructing the model are illustrated with the dataset including theories of linear mixed-effects models, missing values, collinearity, interaction, nonlinearity, model specification, results interpretation and assumptions evaluation. A comparison between linear regression models and linear mixed-effects models is done to elaborate on the strengths of linear mixed-effects models. An R script is provided for the implementation of the linear mixed-effects model.

CONCLUSIONS
Linear mixed-effects models can provide evolutional details of repeated measurements and give more valid estimates compared to linear regression models in the setting of cardio-thoracic surgery outcomes research.
An orally administered drug prevents selection for antibiotic-resistant bacteria in the gut during daptomycin therapy
Authors: Morley Valerie J , Sim Derek G , Penkevich Aline , Woods Robert J , Read Andrew F 
Published: August 2022

Abstract

Background and objectives
Previously, we showed proof-of-concept in a mouse model that oral administration of cholestyramine prevented enrichment of daptomycin-resistant Enterococcus faecium in the gastrointestinal (GI) tract during daptomycin therapy. Cholestyramine binds daptomycin in the gut, which removes daptomycin selection pressure and so prevents the enrichment of resistant clones. Here, we investigated two open questions related to this approach: (i) can cholestyramine prevent the enrichment of diverse daptomycin mutations emerging de novo in the gut? and (ii) how does the timing of cholestyramine administration impact its ability to suppress resistance?

Methodology
Mice with GI E. faecium were treated with daptomycin with or without cholestyramine, and E. faecium was cultured from feces to measure changes in daptomycin susceptibility. A subset of clones was sequenced to investigate the genomic basis of daptomycin resistance.

Results
Cholestyramine prevented the enrichment of diverse resistance mutations that emerged de novo in daptomycin-treated mice. Whole-genome sequencing revealed that resistance emerged through multiple genetic pathways, with most candidate resistance mutations observed in the clsA gene. In addition, we observed that cholestyramine was most effective when administration started prior to the first dose of daptomycin. However, beginning cholestyramine after the first daptomycin dose reduced the frequency of resistant E. faecium compared to not using cholestyramine at all.

Conclusions and implications
Cholestyramine prevented the enrichment of diverse daptomycin-resistance mutations in intestinal E. faecium populations during daptomycin treatment, and it is a promising tool for managing the transmission of daptomycin-resistant E. faecium.
TcMYC2 regulates Pyrethrin biosynthesis in Tanacetum cinerariifolium
Authors: Zeng Tuo , Li Jia-Wen , Xu Zhi-Zhuo , Zhou Li , Li Jin-Jin , Yu Qin , Luo Jin , Chan Zhu-Long , Jongsma Maarten A , Hu Hao , Wang Cai-Yun 
Published: August 2022

Abstract
Pyrethrins constitute a class of terpene derivatives with high insecticidal activity and are mainly synthesized in the capitula of the horticulturally important plant, Tanacetum cinerariifolium. Treatment of T. cinerariifolium with methyl jasmonate (MeJA) in the field induces pyrethrin biosynthesis, but the mechanism linking MeJA with pyrethrin biosynthesis remains unclear. In this study, we explored the transcription factors involved in regulating MeJA-induced pyrethrin biosynthesis. A single spray application of MeJA to T. cinerariifolium leaves rapidly upregulated the expression of most known pyrethrin biosynthesis genes and subsequently increased the total pyrethrin content in the leaf. A continuous 2-week MeJA treatment resulted in enhanced pyrethrin content and increased trichome density. TcMYC2, a key gene in jasmonate signaling, was screened at the transcriptome after MeJA treatment. TcMYC2 positively regulated expression of the pyrethrin biosynthesis genes TcCHS, TcAOC, and TcGLIP by directly binding to E-box/G-box motifs in the promoters. The stable overexpression of TcMYC2 in T. cinerariifolium hairy roots significantly increased the expression of TcAOC and TcGLIP. Further transient overexpression and viral-induced gene-silencing experiments demonstrated that TcMYC2 positively promoted pyrethrin biosynthesis. Collectively, the results reveal a novel molecular mechanism for MeJA-induced pyrethrin biosynthesis in T. cinerariifolium involving TcMYC2.
Multi-omics analyses reveal MdMYB10 hypermethylation being responsible for a bud sport of apple fruit color
Authors: Liu Yu , Gao Xiu-hua , Tong Lu , Liu Mei-zi , Zhou Xiao-kang , Tahir Muhammad Mobeen , Xing Li-bo , Ma Juan-juan , An Na , Zhao Cai-ping , Yao Jia-Long , Zhang Dong 
Published: August 2022

Abstract
Apple bud sports offer a rich resource for clonal selection of numerous elite cultivars. The accumulation of somatic mutations as plants develop may potentially impact the emergence of bud sports. Previous studies focused on somatic mutation in the essential genes associated with bud sports. However, the rate and function of genome-wide somatic mutations that accumulate when a bud sport arises remain unclear. In this study, we identified a branch from a 10-year-old tree of the apple cultivar ‘Oregon Spur II’ as a bud sport. The mutant branch showed reduced red coloration on fruit skin. Using this plant material, we assembled a high-quality haplotype reference genome consisting of 649.61 Mb sequences with a contig N50 value of 2.04 Mb. We then estimated the somatic mutation rate of the apple tree to be 4.56 × 10 −8 per base per year, and further identified 253 somatic single-nucleotide polymorphisms (SNPs), including five non-synonymous SNPs, between the original type and mutant samples. Transcriptome analyses showed that 69 differentially expressed genes between the original type and mutant fruit skin were highly correlated with anthocyanin content. DNA methylation in the promoter of five anthocyanin-associated genes was increased in the mutant compared with the original type as determined using DNA methylation profiling. Among the genetic and epigenetic factors that directly and indirectly influence anthocyanin content in the mutant apple fruit skin, the hypermethylated promoter of MdMYB10 is important. This study indicated that numerous somatic mutations accumulated at the emergence of a bud sport from a genome-wide perspective, some of which contribute to the low coloration of the bud sport.
The BBX gene CmBBX22 negatively regulates drought stress tolerance in chrysanthemum
Authors: Liu Yanan , Cheng Hua , Cheng Peilei , Wang Chunmeng , Li Jiayu , Liu Ye , Song Aiping , Chen Sumei , Chen Fadi , Wang Likai , Jiang Jiafu 
Published: August 2022

Abstract
BBX transcription factors play vital roles in plant growth, development, and stress responses. Although BBX proteins have been studied in great detail in the model plant Arabidopsis, their roles in crop plants such as chrysanthemum are still largely uninvestigated. Here, we cloned CmBBX22 and further determined the function of CmBBX22 in response to drought treatment. Subcellular localization and transactivation assay analyses revealed that CmBBX22 was localized in the nucleus and possessed transactivation activity. Overexpression of CmBBX22 in chrysanthemum was found to reduce plant drought tolerance, whereas expression of the chimeric repressor CmBBX22-SRDX was found to promote a higher drought tolerance than that shown by wild-type plants, indicating that CmBBX22 negatively regulates drought tolerance in chrysanthemum. Transcriptome analysis and physiological measurements indicated the potential involvement of the CmBBX22-mediated ABA response, stomatal conductance, and antioxidant responses in the negative regulation of drought tolerance in chrysanthemum. Based on the findings of this study, we were thus able to establish the mechanisms whereby the transcriptional activator CmBBX22 negatively regulates drought tolerance in chrysanthemum via the regulation of the abscisic acid response, stomatal conductance, and antioxidant responses.
Comparative transcriptome and metabolome analysis reveal key regulatory defense networks and genes involved in enhanced salt tolerance of Actinidia (kiwifruit)
Authors: Abid Muhammad , Gu Shichao , Zhang Yong-Jie , Sun Shihang , Li Zhi , Bai Dan-Feng , Sun Leiming , Qi Xiu-Juan , Zhong Yun-Peng , Fang Jin-Bao 
Published: August 2022

Abstract
The Actinidia (kiwifruit) is an emerging fruit plant that is severely affected by salt stress in northern China. Plants have evolved several signaling network mechanisms to cope with the detrimental effects of salt stress. To date, no reported work is available on metabolic and molecular mechanisms involved in kiwifruit salt tolerance. Therefore, the present study aims to decipher intricate adaptive responses of two contrasting salt tolerance kiwifruit species Actinidia valvata [ZMH (an important genotype), hereafter referred to as R] and Actinidia deliciosa [‘Hayward’ (an important green-fleshed cultivar), hereafter referred to as H] under 0.4% (w/w) salt stress for time courses of 0, 12, 24, and 72 hours (hereafter refered to as h) by combined transcriptome and metabolome analysis. Data revealed that kiwifruit displayed specific enrichment of differentially expressed genes (DEGs) under salt stress. Interestingly, roots of R plants showed a differential expression pattern for up-regulated genes. The KEGG pathway analysis revealed the enrichment of DEGs related to plant hormone signal transduction, glycine metabolism, serine and threonine metabolism, glutathione metabolism, and pyruvate metabolism in the roots of R under salt stress. The WGCNA resulted in the identification of five candidate genes related to glycine betaine (GB), pyruvate, total soluble sugars (TSS), and glutathione biosynthesis in kiwifruit. An integrated study of transcriptome and metabolome identified several genes encoding metabolites involved in pyruvate metabolism. Furthermore, several genes encoding transcription factors were mainly induced in R under salt stress. Functional validation results for overexpression of a candidate gene betaine aldehyde dehydrogenase (AvBADH, R_transcript_80484) from R showed significantly improved salt tolerance in Arabidopsis thaliana (hereafter referred to as At) and Actinidia chinensis [‘Hongyang’ (an important red-fleshed cultivar), hereafter referred to as Ac] transgenic plants than in WT plants. All in all, salt stress tolerance in kiwifruit roots is an intricate regulatory mechanism that consists of several genes encoding specific metabolites.
Challenges of End-Stage Renal Disease Patients in Ethiopia
Authors: Atnafu Rahel , Selfako Andualem Hadero , Mishna Faye , Regehr Cheryl , Soklaridis Sophie , Kotecho Messay Gebremariam 
Published: August 2022

Abstract
Affecting all aspects of patients’ lives, end-stage renal disease (ESRD) presents significant challenges. Individuals with ESRD face biological, psychological, economic, and social issues. ESRD patients in Ethiopia bear multifaceted burdens of multiple medical conditions, including comorbid hypertension, diabetes, cardiac problems, anemia, gastrointestinal issues, and bone and mineral disorders. The aim of this study was to address the gap in research on patients in Ethiopia with ESRD and examine biopsychosocial and economic challenges. A qualitative hermeneutic phenomenology design was employed. In-depth interviews were held with 10 women and 10 men. Major themes include the physical corollary of ESRD (e.g., fatigue), and psychological (e.g., fear of loss of capacity and/or occupation) and socioeconomic challenges (e.g., difficulty obtaining social and economic support). Along with complications of ESRD and side effects of dialysis, patients face trauma and social and economic repercussions. Social workers are well positioned to help manage associated biopsychosocial and economic challenges. The findings indicate the need for policies that promote multidisciplinary teams in working with patients who are diagnosed with ESRD.
Long-term survival of single versus bilateral internal mammary artery grafting in patients under 70
Authors: Abreu Armando , Máximo José , Leite-Moreira Adelino 
Published: August 2022

Abstract

OBJECTIVES
As definitive data from randomized controlled trials comparing the effect on long-term survival of using single internal mammary artery (SIMA) or bilateral internal mammary artery (BIMA) grafting are not yet available, observational studies allow for long-term follow-up in large and representative populations, which might complement the information potentially derived from randomized trials. To compare long-term survival in patients under 70 years of age undergoing SIMA or BIMA grafting.

METHODS
Retrospective analysis of 3384 consecutive patients under 70 years undergoing primary isolated coronary artery bypass grafting, performed from 2000 to 2015, in a Portuguese level III Hospital. We identified 2176 and 1208 patients from the study population who underwent SIMA and BIMA grafting, respectively. The primary end point was all-cause mortality at 10 years. We employed inverse probability weighting to restrict confounding by indication.

RESULTS
The mean age of the study population was 59.4 (± 7.6) years, and 567 (16.8%) were females. Inverse probability weighting was effective in eliminating differences in all significant baseline characteristics. Follow-up was 99.88% complete. The median follow-up time was 12.82 (interquartile range, 9.65, 16.74) years: the primary end point of all-cause mortality at 10 years occurred in 463 patients (21.3%) and 166 (13.7%) in the SIMA and BIMA grafting groups, respectively (hazard ratio, 0.78; 95% confidence interval, 0.66–0.92; P = 0.004).

CONCLUSIONS
Bilateral internal mammary grafting is associated with lower long-term mortality than single internal mammary grafting. Moreover, this survival benefit comes at no increased perioperative morbidity or mortality cost.
Pollen interference emerges as a property from agent-based modelling of pollen competition in Arabidopsis thaliana
Authors: Beckford Charlotte , Ferita Montana , Fucarino Julie , Elzinga David C , Bassett Katherine , Carlson Ann L , Swanson Robert , Capaldi Alex 
Published: August 2022

Abstract
Differences in pollen performance, often revealed during pollen competition, have long been recognized as evolutionarily significant and agriculturally important. Though we have sophisticated models for the growth of individual pollen tubes, we have few robust models for larger-scale pollen competition, a process that has been linked with inbreeding avoidance, sexual selection, reproductive barrier reinforcement and speciation. Here we use existing data on pollen performance traits to develop an agent-based model of pollen competition. We calibrate our model parameters to empirical data found in the literature of seed siring proportions from mixed pollinations and pollen tube length distributions from single-accession pollinations. In this model, parameters that influence pollen tube movement and sensing of ovules were found to be primary factors in competition. Our model also demonstrates that interference competition emerges as a property of pollen competition, and suggests a potential mechanism for this phenomenon. This study integrates pollen performance measures with mathematical modelling conducted on a simplified and accessible system. This represents the first mechanistic agent-based model for pollen competition. Our model may be extended to predict seed siring proportions for other accessions of Arabidopsis thaliana given data on their pollen performance traits.
Understanding the Limits of Transnational NGO Power: Forms, Norms, and the Architecture
Authors: Schmitz Hans Peter , Mitchell George E 
Published: August 2022

AbstractA growing chorus of critics have called upon transnational nongovernmental organizations (TNGOs) from the Global North to “decolonize” their practices, to “shift the power” to the Global South, and to put an end to “white saviorism” by initiating a variety of significant organizational changes. Despite these repeated calls, the TNGO sector still struggles to reform. Explanations for TNGOs’ ongoing struggles from within the field of international relations have generally centered on TNGOs themselves and the ironies and paradoxes of organizational growth and financial success. This article introduces a different argument that TNGOs’ struggles to adapt in response to their critics are the result of TNGOs’ “nonprofitness.” By virtue of being nonprofit, TNGOs are embedded in an architecture consisting of forms and norms that inherently limit the extent to which they are able to change. Using the construct of the architecture, this article provides a novel account for the challenges that TNGOs confront as they attempt to close the gap between the rhetoric and reality of inclusive and transformational socioeconomic, political, or environmental change.