bluuebunny/crossref_metadata_2025_split huggingface dataset:
“That Little Bit of Time”: Transition-to-Hospice Perspectives From Hospice Staff and Bereaved Family
Authors: Cross Sarah H , Ramkalawan Janel R , Ring Jackie F , Boucher Nathan A 
Published: January 2022

Abstract

Background and Objectives
Many patients lack understanding of hospice services and their preparation for the transition to hospice at home may be insufficient. This study explored how hospice admissions staff and caregivers of hospice patients perceive the hospice admission process and the transition to hospice at home.

Research Design and Methods
We conducted in-depth, semistructured interviews with 2 subgroups: hospice admissions staff (n = 15) and bereaved caregivers of former hospice patients (n = 20). We performed a 3-coder descriptive content analysis.

Results
There were 4 overall themes: (a) issues relating to the referring/prehospice provider, (b) issues relating to hospital discharge/care transition home, (c) issues relating to the first touch of hospice, and (d) the impact of coronavirus disease 2019 (COVID-19) on hospice admissions. Patients are often referred to hospice without clear prognostic understanding, at times placing staff in the uncomfortable position of breaking difficult news. Stigma may make patients and families fearful of enrolling in hospice, and misconceptions about hospice are common. Caregivers emphasize the need for increased attention to their emotional needs. Staff revealed the emotional challenges they experience conducting admissions. Both staff and caregivers indicate that the transition to hospice is often emotionally and logistically burdensome, especially when discharging home from the hospital. Both subgroups report insufficient caregiver preparation for taking care of a dying patient at home, particularly regarding medication management. COVID-19 created challenges yet prompted innovative changes to hospice admission processes.

Discussion and Implications
Findings demonstrate a need to improve the hospice admissions process, better supporting terminally ill patients and their families.
Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition
Authors: Zhao Jiantao , Sauvage Christopher , Bitton Frédérique , Causse Mathilde 
Published: January 2022

Abstract
Improving fruit quality traits such as metabolic composition remains a challenge for tomato breeders. To better understand the genetic architecture of these traits and decipher the demographic history of the loci controlling tomato quality traits, we applied an innovative approach using multiple haplotype-based analyses, aiming to test the potentials of haplotype based study in association and genomic prediction studies. We performed and compared haplotype vs SNP-based associations (hapQTL) with multi-locus mixed model (MLMM), focusing on tomato fruit weight and metabolite contents (i.e. sugars, organic acids and amino acids). Using a panel of 163 tomato accessions genotyped with 5995 SNPs, we detected a total of 784 haplotype blocks, with an average size of haplotype blocks ~58 kb. A total of 108 significant associations for 26 traits were detected thanks to Haplotype/SNP-based Bayes models. Haplotype-based Bayes model (97 associations) outperformed SNP-based Bayes model (50 associations) and MLMM (53 associations) in identifying marker-trait associations as well as in genomic prediction (especially for those traits with moderate to low heritability). To decipher the demographic history, we identified 24 positive selective sweeps using the integrated haplotype score (iHS). Most of the significant associations for tomato quality traits were located within selective sweeps (54.63% and 71.7% in hapQTL and MLMM models, respectively). Promising candidate genes were identified controlling tomato fruit weight and metabolite contents. We thus demonstrated the benefits of using haplotypes for evolutionary and genetic studies, providing novel insights into tomato quality improvement and breeding history.
Significant improvement of apple (Malus domestica Borkh.) transgenic plant production by pre-transformation with a Baby boom transcription factor.
Authors: Chen Jiajing , Tomes Sumathi , Gleave Andrew P , Hall Wendy , Luo Zhiwei , Xu Juan , Yao Jia-Long 
Published: January 2022

Abstract
BABY BOOM (BBM) is a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family and its expression has been shown to improve herbaceous plant transformation and regeneration. However, this improvement has not been shown clearly for tree species. This study demonstrated that the efficiency of transgenic apple (Malus domestica Borkh.) plant production was dramatically increased by ectopic expression of the MdBBM1 gene. “Royal Gala” apple plants were first transformed with a CaMV35S-MdBBM1 construct (MBM) under kanamycin selection. These MBM transgenic plants exhibited enhanced shoot regeneration from leaf explants on tissue culture media, with most plants displaying a close-to-normal phenotype compared with CaMV35S-GUS transgenic plants when grown under greenhouse conditions, the exception being that some plants had slightly curly leaves. Thin leaf sections revealed the MBM plants produced more cells than the GUS plants, indicating that ectopic-expression of MdBBM1 enhanced cell division. Transcriptome analysis showed that mRNA levels for cell division activators and repressors linked to hormone (auxin, cytokinin and brassinosteroid) signalling pathways were enhanced and reduced, respectively, in the MBM plants compared with the GUS plants. Plants of eight independent MBM lines were compared with the GUS plants by re-transforming them with an herbicide-resistant gene construct. The number of transgenic plants produced per 100 leaf explants was 0–3% for the GUS plants, 3–8% for five MBM lines, and 20–30% for three MBM lines. Our results provided a solution for overcoming the barriers to transgenic plant production in apple, and possibly in other trees.
Functional characterization of the tomato HAIRPLUS gene reveals the implication of the epigenome in the control of glandular trichome formation
Authors: Fonseca Rocío , Capel Carmen , Yuste-Lisbona Fernando J , Quispe Jorge L , Gómez-Martín Cristina , Lebrón Ricardo , Hackenberg Michael , Oliver José L , Angosto Trinidad , Lozano Rafael , Capel Juan 
Published: January 2022

Abstract
Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene HAIRPLUS (HAP) that controls glandular trichome density in tomato plants was characterised. HAP belongs to a group of proteins involved in histone tail modifications although some also bind methylated DNA. HAP loss of function promotes epigenomic modifications in the tomato genome reflected in numerous differentially methylated cytosines and causes transcriptomic changes in hap mutant plants. Taken together, these findings demonstrate that HAP links epigenome remodelling with multicellular glandular trichome development and reveal that HAP is a valuable genomic tool for pest resistance in tomato breeding.
Engineering CRISPR immune systems conferring GLRaV-3 resistance in grapevine
Authors: Jiao Bolei , Hao Xinyi , Liu Zhiming , Liu Mingbo , Wang Jingyi , Liu Lin , Liu Na , Song Rui , Zhang Junxiang , Fang Yulin , Xu Yan 
Published: January 2022

Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the causal agents of grapevine leafroll disease (GLD), which severely impacts grapevine production in most viticultural regions of the world. The development of virus-resistant plants is a desirable strategy for the efficient control of viral diseases. However, natural resistant resources have not been reported in the genus Vitis, and anti-GLRaV-3 research has been quite limited in grapevine. In this study, by expressing FnCas9 and LshCas13a, we established a highly effective transgenic construct screening system via an optimized Agrobacterium-mediated transient delivery system in grapevine plantlets. Our study indicated that CRISPR/FnCas9 and LshCas13a caused GLRaV-3 inhibition. Moreover, three vectors—pCR01-CP, pCR11-Hsp70h and pCR11-CP—exhibited the most robust inhibition efficiency compared to those targeting other sites and could be further engineered to generate GLRaV-3-resistant grapevine. In addition, the viral interference efficiency of FnCas9 was dependent on its RNA binding activity. The efficiency of virus inhibition was positively correlated with the level of Cas gene expression. Importantly, we demonstrated that LshCas13a had better interference efficiency against viruses than FnCas9. In summary, this study confirmed that these two RNA-targeting CRISPR mechanisms can confer immunity against viruses in grapevine, providing new avenues to control GLRaV-3 or other RNA viruses in fruit crops.
Photoprotection contributes to freezing tolerance as revealed by RNA-seq profiling ofRhododendronleaves during cold acclimation and deacclimation over time.
Authors: Liu Bing , Zhao Fang-Meng , Cao Yan , Wang Xiu-Yun , Li Zheng , Shentu Yuanyue , Zhou Hong , Xia Yi-Ping 
Published: January 2022

AbstractCold acclimation (CA) and deacclimation (DA), which are often accompanied by changes in freezing tolerance (FT), carbohydrates and hormones, are crucial for winter survival, especially under global warming. Plants with weak CA and premature DA caused by warm winters and/or unseasonal warm spells can be easily injured by adverse reactions to cold. Thus, understanding the molecular mechanisms of FT is imperative. In this study, we used high-throughput RNA-seq to profile the CA and DA of leaves of overwintering Rhododendron “Miyo-no-Sakae” over time; these leaves do not undergo dormancy but do undergo photoprotection during CA, and they do not grow during DA. Using Mfuzz and weighted gene coexpression network analysis, we identified specific transcriptional characteristics in each phase of CA and DA and proposed networks involving coexpressed genes and physiological traits. In particular, we discovered that the circadian rhythm is critical for obtaining the strongest FT, and high expression of circadian rhythm-related genes might be linked to sugar accumulation during winter. Furthermore, evergreen leaves exhibited robust photoprotection during winter, as revealed by high values of nonphotochemical quenching, high expression of transcripts annotated as “early light-induced proteins”, loss of granum stacks and destacking of thylakoids, all of which were alleviated during DA. The strong requirement of photoprotection could be the reason for decreased abscisic acid (ABA) and jasmonic acid (JA) contents during CA, and decreases in ABA and JA contents may contribute to decreases in lignin content. Our data suggest that the molecular mechanisms of FT in overwintering leaves are unique, which may be due to the high requirements for photoprotection during winter.
Function and transcriptional regulation of CsKCS20 in the elongation of very-long-chain fatty acids and wax biosynthesis in Citrus sinensis flavedo
Authors: Wang Yang , Yang Xianpeng , Chen Zhaoxing , Zhang Jin , Si Kai , Xu Rangwei , He Yizhong , Zhu Feng , Cheng Yunjiang 
Published: January 2022

Abstract
Cuticular wax on plant aerial surfaces plays a vital role in the defense against various stresses, and the genes related to wax metabolism have been well documented in several model plants. However, there is very limited research on the key enzymes and transcription factors (TFs) associated with carbon chain distribution and wax biosynthesis in citrus fruit. In this study, an analysis of wax metabolites indicated that even carbon-chain (C24-C28) metabolites are the dominant wax components in citrus fruit, and a 3-ketoacyl-CoA synthase (KCS) family gene (CsKCS20) plays an important role in the carbon chain distribution during wax biosynthesis in a wax-deficient mutant (MT). Expression of CsKCS20 in yeast indicated that CsKCS20 can catalyze the biosynthesis of C22 and C24 very-long-chain fatty acids (VLCFAs). In addition, transcriptome and sequence analysis indicated that the differential expression of CsKCS20 between the wild-type (WT) and MT fruit can be partly attributed to the regulation of CsMYB96, which was further confirmed by yeast one-hybrid (Y1H) assays, electrophoretic mobility shift assays (EMSAs) and dual luciferase assays. The functions of CsMYB96 and CsKCS20 in wax biosynthesis were further validated by heterologous expression in Arabidopsis. In summary, this study elucidates the important roles of CsKCS20 and CsMYB96 in regulating VLCFA elongation and cuticular wax biosynthesis, which provides new directions for the improvement of citrus fruit wax quality in genetic breeding programs.
Illuminating the lineage-specific diversification of resin glycoside acylsugars in the morning glory (Convolvulaceae) family using computational metabolomics
Authors: Kruse Lars H , Bennett Alexandra A , Mahood Elizabeth H , Lazarus Elena , Park Se Jin , Schroeder Frank , Moghe Gaurav D 
Published: January 2022

Abstract
Acylsugars are a class of plant defense compounds produced across many distantly related families. Members of the horticulturally important morning glory (Convolvulaceae) family produce a diverse subclass of acylsugars called resin glycosides (RGs), which comprise oligosaccharide cores, hydroxyacyl chain(s), and decorating aliphatic and aromatic acyl chains. While many RG structures are characterized, the extent of structural diversity of this class in different genera and species is not known. In this study, we asked whether there has been lineage-specific diversification of RG structures in different Convolvulaceae species that may suggest diversification of the underlying biosynthetic pathways. Liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) was performed from root and leaf extracts of 26 species sampled in a phylogeny-guided manner. LC–MS/MS revealed thousands of peaks with signature RG fragmentation patterns with one species producing over 300 signals, mirroring the diversity in Solanaceae-type acylsugars. A novel RG from Dichondra argentea was characterized using nuclear magnetic resonance spectroscopy, supporting previous observations of RGs with open hydroxyacyl chains instead of closed macrolactone ring structures. Substantial lineage-specific differentiation in utilization of sugars, hydroxyacyl chains, and decorating acyl chains was discovered, especially among Ipomoea and Convolvulus—the two largest genera in Convolvulaceae. Adopting a computational, knowledge-based strategy, we further developed a high-recall workflow that successfully explained ~72% of the MS/MS fragments, predicted the structural components of 11/13 previously characterized RGs, and partially annotated ~45% of the RGs. Overall, this study improves our understanding of phytochemical diversity and lays a foundation for characterizing the evolutionary mechanisms underlying RG diversification.
The reference genome of Camellia chekiangoleosa provides insights into Camellia evolution and tea oil biosynthesis
Authors: Shen Teng-fei , Huang Bin , Xu Meng , Zhou Peng-yan , Ni Zhou-xian , Gong Chun , Wen Qiang , Cao Fu-liang , Xu Li-An 
Published: January 2022

Abstract
Camellia oil extracted from Camellia seeds is rich in unsaturated fatty acids and secondary metabolites beneficial to human health. However, no oil-tea tree genome has yet been published, which is a major obstacle to investigating the heredity improvement of oil-tea trees. Here, using both Illumina and PicBio sequencing technologies, we present the first chromosome-level genome sequence of the oil-tea tree species Camellia chekiangoleosa Hu. (CCH). The assembled genome consists of 15 pseudochromosomes with a genome size of 2.73 Gb and a scaffold N50 of 185.30 Mb. At least 2.16 Gb of the genome assembly consists of repetitive sequences, and the rest involves a high-confidence set of 64 608 protein-coding gene models. Comparative genomic analysis revealed that the CCH genome underwent a whole-genome duplication event shared across the Camellia genus at ~57.48 MYA and a γ-WGT event shared across all core eudicot plants at ~120 MYA. Gene family clustering revealed that the genes involved in terpenoid biosynthesis have undergone rapid expansion. Furthermore, we determined the expression patterns of oleic acid accumulation- and terpenoid biosynthesis-associated genes in six tissues. We found that these genes tend to be highly expressed in leaves, pericarp tissues, roots, and seeds. The first chromosome-level genome of oil-tea trees will provide valuable resources for determining Camellia evolution and utilizing the germplasm of this taxon.
Outcomes of Ileoanal Pouch Anastomosis in Pediatric Ulcerative Colitis Are Worse in the Modern Era: A Time Trend Analysis Outcomes Following Ileal Pouch–Anal Anastomosis in Pediatric Ulcerative Colitis
Authors: Runde Joseph , Erondu Amarachi , Akiyama Shintaro , Traboulsi Cindy , Rai Victoria , Glick Laura R , Yi Yangtian , Ollech Jacob E , Cohen Russell D , Skowron Kinga B , Hurst Roger D , Umanskiy Konstatin , Shogan Benjamin D , Hyman Neil H , Rubin Michele A , Dalal Sushila R , Sakuraba Atsushi , Pekow Joel , Chang Eugene B , Rubin David T 
Published: January 2022

Abstract

Background
Despite significant differences in surgical outcomes between pediatric and adult patients with ulcerative colitis (UC) undergoing colectomy, counseling on pediatric outcomes has largely been guided by data from adults. We compared differences in pouch survival between pediatric and adult patients who underwent total proctocolectomy with ileal pouch–anal anastomosis (IPAA).

Methods
This was a retrospective single-center study of patients with UC treated with IPAA who subsequently underwent pouchoscopy between 1980 and 2019. Data were collected via electronic medical records. We stratified the study population based on age at IPAA. Differences between groups were assessed using t tests and chi-square tests. Kaplan-Meier curves were used to compare survival probabilities. Differences between groups were assessed using a log-rank test.

Results
We identified 53 patients with UC who underwent IPAA before 19 years of age and 329 patients with UC who underwent IPAA at or after 19 years of age. Subjects who underwent IPAA as children were more likely to require anti-tumor nerosis factor (TNF) postcolectomy compared with adults (41.5% vs 25.8%; P &lt; .05). Kaplan-Meier estimates revealed that pediatric patients who underwent IPAA in the last 10 years had a 5-year pouch survival probability that was 28% lower than that of those who underwent surgery in the 1990s or 2000s (72% vs 100%; P &lt; .001). Further, children who underwent IPAA and received anti-TNF therapies precolectomy had the most rapid progression to pouch failure when compared with anti-TNF–naive children and with adults who were either exposed or naive precolectomy (P &lt; .05).

Conclusions
There are lower rates of pouch survival for children with UC who underwent IPAA following the uptake of anti-TNF therapy compared with both historical pediatric control subjects and contemporary adults.
Biphasic mineralized collagen-based composite scaffold for cranial bone regeneration in developing sheep
Authors: Zheng Jingchuan , Zhao Zhijun , Yang Yongdong , Wang Shuo , Zhao Yonggang , Xiong Yang , Yang Shuhui , Qiu Zhiye , Song Tianxi , Zhang Chunyang , Wang Xiumei 
Published: January 2022

AbstractAppropriate mechanical support and excellent osteogenic capability are two essential prerequisites of customized implants for regenerating large-sized cranial bone defect. Although porous bone scaffolds have been widely proven to promote bone regeneration, their weak mechanical properties limit the clinical applications in cranioplasty. Herein, we applied two previously developed mineralized collagen-based bone scaffolds (MC), porous MC (pMC) and compact MC (cMC) to construct a biphasic MC composite bone scaffold (bMC) to repair the large-sized cranial bone defect in developing sheep. A supporting frame composed of cMC phase in the shape of tic–tac–toe structure was fabricated first and then embedded in pMC phase. The two phases had good interfacial bond, attributing to the formation of an interfacial zone. The in vivo performance of the bMC scaffold was evaluated by using a cranial bone defect model in 1-month-old sheep. The computed tomography imaging, X-ray scanning and histological evaluation showed that the pMC phase in the bMC scaffold, similar to the pMC scaffold, was gradually replaced by the regenerative bone tissues with comprehensively increased bone mineral density and complete connection of bone bridge in the whole region. The cMC frame promoted new bone formation beneath the frame without obvious degradation, thus providing appropriate mechanical protection and ensuring the structural integrity of the implant. In general, the sheep with bMC implantation exhibited the best status of survival, growth and the repair effect. The biphasic structural design may be a prospective strategy for developing new generation of cranioplasty materials to regenerate cranial bone defect in clinic.
Non-Ischemic, Non-Hypoxic Myocardial Injury, and Long-Term Mortality in Patients with Coronavirus Disease 2019: A Retrospective Cohort Study
Authors: Li Fajiu , Zhu Xijie , Zhu Ziyang , Yang Yinjian , Tian Zhuang , Wang Duolao , Chen Shi , Gao Xiaoyan , Xu Yalin , Zhang Bo , Yu Wei , Liu Min , Xu Xiqi , Li Chenghong , Zhang Shuyang 
Published: January 2022

Abstract

Objective:
Cardiac damage is commonly reported in patients with coronavirus disease 2019 (COVID-19) but its prevalence and impact on the long-term survival of patients remain uncertain. This study aimed to explore the prevalence of myocardial injury and assess its prognostic value in patients with COVID-19.

Methods:
A single-center, retrospective cohort study was performed at the Affiliated Hospital of Jianghan University. Data from 766 patients with confirmed COVID-19 who were hospitalized from December 27, 2019 to April 25, 2020 were collected. Demographic, clinical, laboratory, electrocardiogram, treatment data and all-cause mortality during follow-up were collected and analyzed.

Results:
Of the 766 patients with moderate to critically ill COVID-19, 86 (11.2%) died after a mean follow-up of 72.8 days. Myocardial injury occurred in 94 (12.3%) patients. The mortality rate was 64.9% (61/94) and 3.7% (25/672) in patients with and without myocardial injury, respectively. Cox regression showed that myocardial injury was an independent risk factor for mortality (hazard ratio: 8.76, 95% confidence interval: 4.76–16.11, P
< 0.001). Of the 90 patients with myocardial injury with electrocardiogram results, sinus tachycardia was present in 29, bundle branch block in 26, low voltage in 10, and abnormal T-wave in 53.

Conclusions:
COVID-19 not only involves pneumonia but also cardiac damage. Myocardial injury is a common complication and an independent risk factor for mortality in COVID-19 patients.