bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wood density and wood shrinkage in relation to initial spacing and tree growth in black spruce (Picea mariana)
Authors: Zhang Shu Yin , Ren Haiqing , Jiang Zehui 
Published: April 2021

AbstractThis study has quantified basic wood density and various types of wood shrinkage in relation to initial spacing (or initial planting density) and tree growth based on a 48-year-old black spruce (Picea mariana) spacing trial in eastern Canada. A total of 139 sample trees were collected from four initial spacings (3086, 2500, 2066, 1372 trees/ha) for this study. Analyses of variance (ANOVA) show that initial spacing is the most important parameter affecting wood density significantly, followed by tree diameter at breast height (DBH) class. With increasing spacing, wood density, radial and volumetric shrinkage tend to decrease, whereas longitudinal shrinkage tends to increase gradually. The largest spacing has the lowest wood density, the smallest transverse shrinkage and the largest longitudinal shrinkage. Path analysis indicates that wood density is the most important parameter affecting transverse shrinkage, followed by the distance from the pith. Furthermore, much of the variation of the transverse shrinkage with wood density may be due to the initial spacing and tree DBH class. Path analysis also reveals that longitudinal shrinkage is mainly related to log height and tree DBH class. With increasing log height, longitudinal shrinkage tends to increase, and transverse shrinkage tends to decrease. With increasing DBH class, the trees tend to have an increasing longitudinal shrinkage and a decreasing transverse shrinkage. Overall, this study suggests that a large increase in the initial spacing (e.g., 1372 trees/ha) might lead to a significant reduction in both wood density and transverse shrinkage, and a significant increase in longitudinal shrinkage in black spruce.
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations
Authors: Jiang Fan , Lin Ruiyi , Xiao Changyi , Xie Tanghui , Jiang Yaoxin , Chen Jianhai , Ni Pan , Sung Wing-Kin , Han Jianlin , Du Xiaoyong , Li Shijun 
Published: April 2021

AbstractBackgroundThe most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.ResultsBased on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8,THAP5, andDNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g.,ADCYAP1R1andPDC) and in genes that are associated with morphological traits such as cell growth (e.g.,IGF1R).ConclusionsOur findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.
TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes
Authors: Zhang Guanglan , Chitkushev Lou , Olsen Lars Rønn , Keskin Derin B. , Brusic Vladimir 
Published: April 2021

AbstractWe previously developed TANTIGEN, a comprehensive online database cataloging more than 1000 T cell epitopes and HLA ligands from 292 tumor antigens. In TANTIGEN 2.0, we significantly expanded coverage in both immune response targets (T cell epitopes and HLA ligands) and tumor antigens. It catalogs 4,296 antigen variants from 403 unique tumor antigens and more than 1500 T cell epitopes and HLA ligands. We also included neoantigens, a class of tumor antigens generated through mutations resulting in new amino acid sequences in tumor antigens. TANTIGEN 2.0 contains validated TCR sequences specific for cognate T cell epitopes and tumor antigen gene/mRNA/protein expression information in major human cancers extracted by Human Pathology Atlas. TANTIGEN 2.0 is a rich data resource for tumor antigens and their associated epitopes and neoepitopes. It hosts a set of tailored data analytics tools tightly integrated with the data to form meaningful analysis workflows. It is freely available athttp://projects.met-hilab.org/tadb.
Efficacy of 16S rRNA variable regions high-resolution melt analysis for bacterial pathogens identification in periprosthetic joint infections
Authors: Bourbour Samaneh , Emaneini Mohammad , Jabalameli Mahmoud , Mortazavi Seyed Mohammad Javad , Tahmasebi Mohamad Naghi , Taghizadeh Amirheckmat , Sharafatvaziri Arash , Beigverdi Reza , Jabalameli Fereshteh 
Published: April 2021

AbstractBackgroundAccurate and rapid identification of microorganisms causing periprosthetic joint infections (PJIs) are necessary for choosing an appropriate antibiotic therapy. Therefore, molecular techniques are suggested for diagnosis in suspected PJIs. The Broad-range PCR and High-Resolution Melt Analysis (HRMA) were evaluated for the identification of causative organisms of PJIs in this study.ResultsFor 47 of 63 specimens, both the culture and broad-range PCR were positive. The culture was found to be able of organism’s detection in 74.6% (47/63) of patients. Of 47 positive cultures, 11 (23.4%) were polymicrobial and 36 (76.59%) were monomicrobial cultures, in which 34 (91.89%) cases were detected by HRM assay. The sensitivity, specificity of HRMA vs monomicrobial culture were 91.89, 93.75%, respectively. The sensitivity, specificity of total HRMA (mono + poly) vs culture were 82.92, 93.75%.ConclusionsHRM assay coupled with broad-range PCR are effective screening, rapid, and relatively cost-effective methods for discrimination of PJIs especially in aiding culture method. Using computer programs such as the Matlab-2018b program for HRM data analysis is also valuable and helpful in diagnosis.
Small RNA sequencing provides candidate miRNA-target pairs for revealing the mechanism of apomixis in Zanthoxylum bungeanum
Authors: Fei Xitong , Lei Yu , Qi Yichen , Wang Shujie , Hu Haichao , Wei Anzhi 
Published: April 2021

Abstract
Background
Apomixis is a form of asexual reproduction that produces offspring without the need for combining male and female gametes, and the offspring have the same genetic makeup as the mother. Therefore, apomixis technology has great application potential in plant breeding. To identify the apomixis types and critical period, embryonic development at different flower development stages of Zanthoxylum bungeanum was observed by cytology.

Results
The results show that the S3 stage is the critical period of apomixis, during which the nucellar cells develop into an adventitious primordial embryo. Cytological observations showed that the type of apomixis in Z. bungeanum is sporophytic apomixis. Furthermore, miRNA sequencing, miRNA-target gene interaction, dual luciferase reporter assay, and RT-qPCR verification were used to reveal the dynamic regulation of miRNA-target pairs in Z. bungeanum apomixis. The miRNA sequencing identified 96 mature miRNAs, of which 40 were known and 56 were novel. Additionally, 29 differentially expressed miRNAs were screened according to the miRNAs expression levels at the different developmental stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses showed that the target genes of the differentially expressed miRNAs were mainly enriched in plant hormone signal transduction, RNA biosynthetic process, and response to hormone pathways.

Conclusions
During the critical period of apomictic embryonic development, miR172c significantly reduces the expression levels of TOE3 and APETALA 2 (AP2) genes, thereby upregulating the expression of the AGAMOUS gene. A molecular regulation model of miRNA-target pairs was constructed based on their interactions and expression patterns to further understand the role of miRNA-target pairs in apomixis. Our data suggest that miR172c may regulates AGAMOUS expression by inhibiting TOE3 in the critical period of apomixis.
Explore the gene network regulating the composition of fatty acids in cottonseed
Authors: Ma Lihong , Cheng Xinqi , Wang Chuan , Zhang Xinyu , Xue Fei , Li Yanjun , Zhu Qianhao , Sun Jie , Liu Feng 
Published: April 2021

AbstractBackgroundCottonseed is one of the major sources of vegetable oil. Analysis of the dynamic changes of fatty acid components and the genes regulating the composition of fatty acids of cottonseed oil is of great significance for understanding the biological processes underlying biosynthesis of fatty acids and for genetic improving the oil nutritional qualities.ResultsIn this study, we investigated the dynamic relationship of 13 fatty acid components at 12 developmental time points of cottonseed (Gossypium hirsutumL.) and generated cottonseed transcriptome of the 12 time points. At 5–15 day post anthesis (DPA), the contents of polyunsaturated linolenic acid (C18:3n-3) and saturated stearic acid (C18:0) were higher, while linoleic acid (C18:2n-6) was mainly synthesized after 15 DPA. Using 5 DPA as a reference, 15,647 non-redundant differentially expressed genes were identified in 10–60 DPA cottonseed. Co-expression gene network analysis identified six modules containing 3275 genes significantly associated with middle-late seed developmental stages and enriched with genes related to the linoleic acid metabolic pathway and α-linolenic acid metabolism. Genes (Gh_D03G0588andGh_A02G1788) encoding stearoyl-ACP desaturase were identified as hub genes and significantly up-regulated at 25 DPA. They seemed to play a decisive role in determining the ratio of saturated fatty acids to unsaturated fatty acids.FAD2genes (Gh_A13G1850andGh_D13G2238) were highly expressed at 25–50 DPA, eventually leading to the high content of C18:2n-6 in cottonseed. The content of C18:3n-3 was significantly decreased from 5 DPA (7.44%) to 25 DPA (0.11%) and correlated with the expression characteristics ofGh_A09G0848andGh_D09G0870.ConclusionsThese results contribute to our understanding on the relationship between the accumulation pattern of fatty acid components and the expression characteristics of key genes involved in fatty acid biosynthesis during the entire period of cottonseed development.
Predictive value of CHA2DS2-VASc score combined with hs-CRP for new-onset atrial fibrillation in elderly patients with acute myocardial infarction
Authors: Fu Yuan , Pan Yuxia , Gao Yuanfeng , Yang Xinchun , Chen Mulei 
Published: April 2021

Abstract
Background
New-onset atrial fibrillation (NOAF) is common during acute myocardial infarction (AMI) and independently associated with worse prognosis. We aimed to validate the discrimination performance of CHA2DS2-VASc score combined with hs-CRP in the prediction of NOAF after AMI in elderly Chinese population.

Methods
311 consecutive elderly patients (age ≥ 65 years old) with AMI from 1 January 2018 to 1 January 2019 without atrial fibrillation history were enrolled in our study. Univariable and multivariable logistic regression analyses were used to identify risk factors of NOAF. The discrimination performance of different score models were evaluated using ROC curve analysis and AUCs were compared using the Z test.

Results
30 (9.65%) patients developed NOAF during hospitalization. The NOAF group were older and had higher hs-CRP, initial Killip class, BNP, LAD, CHADS2 score, CHA2DS2-VASc score, in-hospital mortality and lower LVEF and ACEI/ARB use (P < 0.05 vs group without NOAF for all measures). In multivariate regression analyses, age (OR = 1.127, 95% CI 1.063–1.196, P < 0.001) and hs-CRP (OR = 1.034, 95% CI 1.018–1.05, P < 0.001) were independent predictors of NOAF. In ROC curve analyses, both CHADS2 score (AUC = 0.624, 95% CI 0.516–0.733, P = 0.026) and CHA2DS2-VASc score (AUC = 0.687, 95% CI 0.584–0.79, P = 0.001) had acceptable but unsatisfactory discrimination performance in predicting NOAF after AMI. The combined model with CHA2DS2-VASc score and hs-CRP showed a significant better predictive value (AUC = 0.791, 95% CI 0.692–0.891, P < 0.001) compared to that of the CHA2DS2-VASc score alone (Z test, P = 0.008).

Conclusion
The combined model with CHA2DS2-VASc score and hs-CRP had high accuracy in predicting post-AMI NOAF.
A case of intraductal tubulopapillary neoplasm of the pancreas in a branch duct: a rare case report and literature review
Authors: Yamaguchi Atsushi , Hamada Takuro , Wada Kaoru , Moriuchi Riho , Tao Kanae , Konishi Hirona , Tamaru Yuzuru , Kusunoki Ryusaku , Kuwai Toshio , Kouno Hirotaka , Ishiyama Kohei , Hadano Naoto , Sudo Takeshi , Toyota Naoyuki , Zaitsu Junichi , Kuraoka Kazuya , Kohno Hiroshi 
Published: April 2021

Abstract
Background
Intraductal tubulopapillary neoplasm (ITPN) of the pancreas is a new disease concept defined by the World Health Organization in 2010. ITPN progresses with tubulopapillary growth in the pancreatic duct and is known to have a fair prognosis. Localization in the main pancreatic duct (MPD) is one characteristic. There are few case reports of ITPN in a branch of the pancreatic duct (BD).

Case presentation
We encountered a case of ITPN localized in BD. An 85-year-old man was followed after colonic surgery for rectal carcinoma. An abdominal computed tomography scan revealed a cystic mass in the pancreatic head and further examination was done. A T2 weighted intension picture in magnetic resonance imaging showed a 20 mm cystic lesion with an internal mass of 15 mm. Duodenal papilla were slightly open and endoscopic retrograde pancreatography revealed mild and diffuse dilatation of the main pancreatic duct and mucin in the MPD. In consideration with the image examinations, we diagnosed the tumor as an intraductal papillary mucinous neoplasm with carcinoma because of its large mural nodule (> 10 mm in size) in a cyst. Consequently, a pancreaticoduodenectomy was performed. Macroscopically, a white solid tumor sized 2.5 × 1.8 × 1.0 was identified in the head of the pancreas. The cut surface of the resected pancreas showed a side-branch type intraductal tumor with tubulopapillary architecture without mucin secretion. Immunohistochemical staining was positive for MUC1, and negative for MUC2 and MUC5AC. The final diagnosis was determined to be pancreatic ITPN from BD. At the time of this report (48 months post-surgery), the patient remains disease-free without evidence of recurrence.

Conclusion
ITPNs localized in BD are rare and diagnosis prior to surgery is difficult. In our case, the shape was round, not papillary, and with little fluid. These characteristics are different from a branch duct type IPMN and can be a clue to suspect ITPN in BD.
Predictive value of geriatric-quickSOFA in hospitalized older people with sepsis
Authors: Remelli Francesca , Castellucci Federico , Vitali Aurora , Mattioli Irene , Zurlo Amedeo , Spadaro Savino , Volpato Stefano 
Published: April 2021

Abstract
Background
QuickSOFA, a prognostic score proposed for patients with infection, has shown a poor predictive value in the geriatric population, probably because of the inappropriateness of the Glasgow Coma Scale (GCS) in assessing acute alteration of mental status in older patients. Indeed, the GCS might result chronically low in older patient with pre-existing cognitive disorders. The aim of this study was to develop an alternative quickSOFA (geriatric-quickSOFA), using the presence of delirium, assessed according to DSM-5 criteria, instead of GCS assessment, to predict mortality in hospitalized older patients with sepsis.

Methods
Retrospective observational study in Acute Geriatrics Unit of St. Anna Hospital of Ferrara (Italy). The study enrolled 165 patients hospitalized between 2017 and 2018 with diagnosis of sepsis or septic shock. Demographic, clinical data and 30-day survival were collected for each patient. Based on arterial blood pressure, respiratory rate, and the presence of delirium, geriatric-quickSOFA was calculated at admission. Primary outcome was 30-day mortality.

Results
One hundred sixty-five patients were enrolled with a median age of 88 years; 60.6% were men. High quickSOFA score was not significantly correlated neither with in-hospital nor 30-day mortality. High geriatric-qSOFA score was significantly related to both in-hospital (13.3%vs 51.5%, p = 0.0003) and 30-day mortality (30.0%vs 84.3%, p < 0.00001).

Conclusion
Geriatric-quickSOFA is significantly associate with short-term mortality risk in older patients with sepsis. Geriatric quickSOFA seems to represent a more suitable and useful predictive tool than the traditional quickSOFA in the geriatric population.
European data sources for computing burden of (potential) vaccine-preventable diseases in ageing adults
Authors: Méroc Estelle , Fröberg Janeri , Almasi Timea , Winje Brita Askeland , Orrico-Sánchez Alejandro , Steens Anneke , McDonald Scott A. , Bollaerts Kaatje , Knol Mirjam J. 
Published: April 2021

Abstract
Background
To guide decision-making on immunisation programmes for ageing adults in Europe, one of the aims of the Vaccines and InfecTious diseases in the Ageing popuLation (IMI2-VITAL) project is to assess the burden of disease (BoD) of (potentially) vaccine-preventable diseases ((P)VPD). We aimed to identify the available data sources to calculate the BoD of (P)VPD in participating VITAL countries and to pinpoint data gaps. Based on epidemiological criteria and vaccine availability, we prioritized (P) VPD caused by Extra-intestinal pathogenic Escherichia coli (ExPEC), norovirus, respiratory syncytial virus, Staphylococcus aureus, and pneumococcal pneumonia.

Methods
We conducted a survey on available data (e.g. incidence, mortality, disability-adjusted life years (DALY), quality-adjusted life years (QALY), sequelae, antimicrobial resistance (AMR), etc.) among national experts from European countries, and carried out five pathogen-specific literature reviews by searching MEDLINE for peer-reviewed publications published between 2009 and 2019.

Results
Morbidity and mortality data were generally available for all five diseases, while summary BoD estimates were mostly lacking. Available data were not always stratified by age and risk group, which is especially important when calculating BoD for ageing adults. AMR data were available in several countries for S. aureus and ExPEC.

Conclusion
This study provides an exhaustive overview of the available data sources and data gaps for the estimation of BoD of five (P) VPD in ageing adults in the EU/EAA, which is useful to guide pathogen-specific BoD studies and contribute to calculation of (P)VPDs BoD.
Diagnostic value of MRI for detecting recurrent soft-tissue sarcoma in a long-term analysis at a multidisciplinary sarcoma center
Authors: Sedaghat Sam , Sedaghat Maya , Meschede Jens , Jansen Olav , Both Marcus 
Published: April 2021

AbstractBackgroundSoft-tissue sarcomas (STS) are rare tumors of the soft tissue. Recent diagnostic studies on STS mainly dealt with only few cases of STS and did not investigate the post-therapeutic performance of MRI in a routine clinical setting. Therefore, we assessed the long-term diagnostic accuracy of MRI for detecting recurrent STS at a multidisciplinary sarcoma center.MethodsIn all, 1055 postoperative follow-up MRIs of 204 patients were included in the study. MRI follow-up scans were systematically reviewed for diagnostic values (true-positive/−negative and false-positive/−negative results) in detecting recurrences. Pathological reports and follow-up MRIs were set as baseline references.ResultsThe median age of the patients was 55.3 ± 18.2 years. Of the patients, 34.8% presented with recurrences. Here, 65 follow-up scans were true positive, 23 false positive, 6 false negative, and 961 true negative. The overall sensitivity and specificity of MRI for detecting recurrences were 92 and 98%, respectively, with an accuracy of 97%. For intramuscular lesions and after surgery alone the sensitivity was higher (95 and 97%, respectively) than for subcutaneous lesions and surgery with additional radiation therapy (83 and 86%, respectively), at similarly high specificities (96–98%). The 6 false-negative results were found in streaky (n = 2) and small ovoid/nodular (n = 4) recurring lesions. The false-positive lesions imitated streaky (n = 14), ovoid/nodular (n = 8), and polycyclic/multilobulated recurring tumors (n = 1). All false-positive results were found in patients in whom the primary tumors were polycyclic/multilobulated in appearance.ConclusionMRI shows a high diagnostic accuracy for detecting recurrent STS, with a high sensitivity and specificity. The diagnostic accuracy decreases in subcutaneous lesions and after surgery with radiation therapy, compared to intramuscular lesions and surgery alone. Radiologists should pay particular attention to streaky and small ovoid/nodular recurring lesions and patients with polycyclic/multilobulated primary tumors.
Distribution of ocular biometric parameters and optimal model of anterior chamber depth regression in 28,709 adult cataract patients in China using swept‐source optical biometry
Authors: Lei Qiong , Tu Haixia , Feng Xi , Ortega-Usobiaga Julio , Cao Danmin , Wang Yong 
Published: April 2021

Abstract
Background
The purpose of this study was to evaluate the ocular biometric parameters in adult cataract patients from China and create an anterior chamber depth (ACD) regression model.

Methods
The ocular biometric records of 28,709 right eyes of cataract surgery candidates who were treated at Aier Eye Hospitals in nine cities from 2018 to 2019 were retrospectively analyzed. All measurements were taken with IOLMaster 700. We included patients who were at least 40 years old and were diagnosed with cataract.

Results
The mean age of the patients was 68.6 ± 11.0 years. The mean values recorded were as follows: axial length (AL), 24.17 ± 2.47 mm; mean keratometry (Km) value, 44.26 ± 1.70 D; corneal astigmatism (CA), 1.06 ± 0.96 D; ACD, 3.02 ± 0.45 mm; lens thickness (LT), 4.52 ± 0.45 mm; central corneal thickness (CCT), 0.534 ± 0.04 mm; and white to white (WTW) corneal diameter, 11.64 ± 0.46 mm. ACD correlated positively with AL (Spearman coefficient, 0.544) and WTW (0.300), but negatively with LT (-0.660) and age (-0.285) (all P < 0.01). In the multivariate regression analysis of ACD, which included LT, AL, WTW, sex, Km, CCT, and age, there was a reasonable prediction with adjusted R2 = 0.641.

Conclusions
Cataract patients with longer AL and wider WTW have deeper ACD. With increasing age and lens thickening ACD becomes shallower. Based on the standardized coefficients of ACD multivariate regression analysis from the study, LT is the main factor that affects ACD, and is followed by AL.