bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers
Authors: Dong Xiaofeng , Penrice-Randal Rebekah , Goldswain Hannah , Prince Tessa , Randle Nadine , Donovan-Banfield I'ah , Salguero Francisco J , Tree Julia , Vamos Ecaterina , Nelson Charlotte , Clark Jordan , Ryan Yan , Stewart James P , Semple Malcolm G , Baillie J Kenneth , Openshaw Peter J M , Turtle Lance , Matthews David A , Carroll Miles W , Darby Alistair C , Hiscox Julian A 
Published: May 2022

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5′ sequence, the leader–transcriptional regulatory sequence gene junction (leader–TRS junction), that can be identified using sequencing. High-resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader–TRS junctions and can be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus or a future newly discovered coronavirus. LeTRS was tested on published data sets and novel clinical samples from patients and longitudinal samples from animal models with coronavirus disease 2019. LeTRS identified known leader–TRS junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, which can then subject to selection pressure. The data indicated multiphasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection but not at late points. This pattern is reflected in some human nasopharyngeal samples and therefore has implications for transmission models and nucleic acid–based diagnostics. LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and nonclinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.
Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce (Lactuca sativa L.)
Authors: Park Jee-Soo , Kang Min-Young , Shim Eun-Jo , Oh JongHee , Seo Kyoung-In , Kim Kyung Seok , Sim Sung-Chur , Chung Sang-Min , Park Younghoon , Lee Gung Pyo , Lee Won-Sik , Kim Minkyung , Jung Jin-Kee 
Published: May 2022

Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption
Authors: Xu Huimin , Wang Chunhua , Shao Guirong , Wu Shasha , Liu Peng , Cao Ping , Jiang Peng , Wang Shubin , Zhu Hong , Lin Xiao , Tauqeer Arfa , Lin Yizhang , Chen Wei , Huang Weiqun , Wen Qingfang , Chang Jiang , Zhong Fenglin , Wu Shuang 
Published: May 2022

Abstract
Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows a higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that long terminal repeat retrotransposon insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After whole-genome triplication, over-retained pakchoi genes escape stringent selection pressure, and among them a set of cuticle-related genes are retained. Using bulked-segregant analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that the heat-resistant pakchoi cultivar can mitigate heat-caused leaf damage by activating an unfolded protein response, as well as by inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.
Exploring the diversity and genetic structure of the U.S. National Cultivated Strawberry Collection
Authors: Zurn Jason D , Hummer Kim E , Bassil Nahla V 
Published: May 2022

Abstract
The cultivated strawberry (Fragaria ×ananassa) arose through a hybridization of two wild American octoploid strawberry species in a French garden in the 1750s. Since then, breeders have developed improved cultivars adapted to different growing regions. Diverse germplasm is crucial to meet the challenges strawberry breeders will continue to address. The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon maintains the U.S. strawberry collection. Recent developments in high-throughput genotyping for strawberry can provide new insights about the diversity and structure of the collection, germplasm management, and future breeding strategies. Genotyping was conducted on 539 F. ×ananassa accessions using either the iStraw35 or FanaSNP 50 K Axiom array. Data for markers shared by the two arrays were curated for call quality, missing data, and minor allele frequency resulting in 4033 markers for structure assessment, diversity analysis, pedigree confirmation, core collection development, and the identification of haplotypes associated with desirable traits. The F. ×ananassa collection was equally diverse across the different geographic regions represented. K-means clustering, sNMF, and UPGMA hierarchal clustering revealed seven to nine sub-populations associated with different geographic breeding centers. Two 100 accession core collections were created. Pedigree linkages within the collection were confirmed. Finally, accessions containing disease resistance-associated haplotypes for FaRCa1, FaRCg1, FaRMp1, and FaRPc2 were identified. These new core collections will allow breeders and researchers to more efficiently utilize the F. ×ananassa collection. The core collections and other accessions of interest can be requested for research from the USDA-ARS NCGR via the Germplasm Resources Information Network (https://www.ars-grin.gov/).
Utility of the surgical Apgar score for predicting the short- and long-term outcomes in non-small-cell lung cancer patients who undergo surgery
Authors: Nagoya Akihiro , Kanzaki Ryu , Kimura Kenji , Fukui Eriko , Kanou Takashi , Ose Naoko , Funaki Soichiro , Minami Masato , Fujii Makoto , Shintani Yasushi 
Published: May 2022

Abstract

OBJECTIVES
The surgical Apgar score (SAS) is a simple score that predicts postoperative complications based on 3 intraoperative valuables. The present study evaluated the association between the SAS and postoperative outcomes in non-small-cell lung cancer patients who underwent surgery.

METHODS
A total of 585 patients who underwent lung resection were enrolled in the present study. We calculated the SAS of each patient and investigated its influence on the short- and long-term outcomes.

RESULTS
Postoperative complications of any grade were detected in 164 cases (28%). The morbidity rate increased with decreasing SAS. When all the patients were divided into 2 groups (SAS &lt;7 vs ≥7), postoperative complications were observed more frequently in the SAS &lt;7 group than in the SAS ≥7 group (41% vs 25%, P &lt; 0.001). In the multivariate analysis, the SAS was an independent risk factor for postoperative complications (odds ratio: 1.64 [1.03–2.61], P = 0.036). In terms of long-term outcomes, the 5-year disease-free survival (54.1% vs 73.2%, P &lt; 0.001) and overall survival (73.8% vs 83.0%, P = 0.031) were significantly worse in the SAS &lt;7 group than in the SAS ≥7 group. In a multivariate analysis, however, the SAS was not found to be an independent prognostic factor for either disease-free survival (hazard ratio: 1.39 [0.97–2.00], P = 0.075) or overall survival (hazard ratio: 0.90 [0.57–1.42], P = 0.642).

CONCLUSIONS
The SAS reflected preoperative and intraoperative characteristics and was able to stratify the morbidity rate, suggesting it to be a useful predictor of short-term outcomes in non-small-cell lung cancer patients who undergo surgery.
Clinical significance of postoperative pulmonary complications in elderly patients with lung cancer
Authors: Okada Satoru , Shimomura Masanori , Ishihara Shunta , Ikebe Satoshi , Furuya Tatsuo , Inoue Masayoshi 
Published: May 2022

Abstract

OBJECTIVES
An increasing number of elderly patients with impaired immunity, malnutrition and comorbidities are considered surgical candidates. This study aimed to clarify the predictive factors and prognostic impact of postoperative pulmonary complications in elderly patients with lung cancer.

METHODS
This retrospective study included 188 patients (≥75 years) who underwent complete anatomical lung resection for non-small cell lung cancer between 2005 and 2019. Postoperative pulmonary complications graded ≥II in the Clavien-Dindo classification, occurring within 30-day post-surgery were evaluated. Multivariate logistic regression analyses and Cox proportional hazard models were used to analyse predictors and prognostic impact of complications.

RESULTS
Video-assisted thoracoscopic surgery was performed in 154 patients (81.9%). The 90-day mortality rate was 0.5%. Postoperative pulmonary complications including air leak, pneumonia, sputum retention, atelectasis, bronchopleural fistula and empyema occurred in 29 patients (15.4%). A lower prognostic nutritional index (&lt;45) and longer operative time were independent predictive factors of pulmonary complications, with 33.3% of patients experiencing both factors. Following a median follow-up of 48 months, the 5-year overall and relapse-free survival rates were significantly worse in patients with pulmonary complications than in those without them (54.4% vs 81.5% and 41.2% vs 74.9%). Pulmonary complications were significantly associated with worse overall and relapse-free survival [hazard ratio (95% confidence interval): 1.97 (1.01–3.66), P = 0.047 and 2.35 (1.28–4.12), P = 0.007, respectively] along with pathologic stage and carcinoembryonic antigen levels.

CONCLUSIONS
Postoperative pulmonary complications are associated with a lower prognostic nutritional index and prolonged operative time; the complications are independent adverse prognostic factors in elderly patients.
Time to review reflective practice?
Authors: Quilty Terry , Murphy Lyn 
Published: May 2022

Abstract

Background
Reflective practice is an integral part of modern healthcare. If done well, it can significantly improve the individual skills of health care practitioners. However, we hypothesize that extrapolating individual reflective practice into broader organization applications undermines its fundamental nature and inhibits objective benchmarking within the health sector.

Methods
We reflect on the nature and use of the reflective practice in healthcare.

Results
An organization that practices reflective practice may, in effect, create an environment where reflective practice is promoted but operates to homogenize thinking to a point where it turns into dysfunctional institutional navel-gazing. Homogenized thinking may inhibit the ability to move beyond practice to explore ideas that lead to change.

Conclusions
The collective approach to reflective practice can subvert the underlying process of self-analysis, which allows the critical examination of individual values, priorities, and evaluations. It can inhibit individual growth, favouring a homogenizing effect which is the antithesis of an innovative organization when measured against the original intent and must therefore be used with care.
Automatic anomaly detection and processing for long-term tension monitoring of stay cables based on vibration measurements
Authors: Wu Wen-Hwa , Chen Chien-Chou , Lin Shang-Li , Lai Gwolong 
Published: May 2022

Abstract
Stay cables are the crucial force-transmitting components of cable-stayed bridges. Consequently, effective cable tension monitoring is typically regarded as the most important issue in structural health monitoring for this type of bridge. In the long-term monitoring of structures, the occurrence of abnormal signals due to a variety of reasons such as sensor faults, a system malfunction, data loss in transmission, or the instability of power supply, are almost unavoidable and are highly likely to lead to a deterioration in the quality of subsequent analyses. The current paper presents the first phase of a project to develop an automatic monitoring system for cable tension based on ambient vibration signals for the Mao-Luo-Hsi Bridge. The results demonstrate that automatic anomaly detection and processing for cable vibration measurements can be achieved with a relatively simple algorithm using an appropriate threshold of maximum response value. In addition, the paper also reports the elimination of anomalies during testing of the monitoring system installation.
Update on Urine Adulterants and Synthetic Urine Samples to Subvert Urine Drug Testing
Authors: Vikingsson Svante , Krauss Shannon T , Winecker Ruth E , Flegel Ronald R , Hayes Eugene D 
Published: May 2022

Abstract
To avoid a positive urine drug test, donors might try to subvert the test, either by adulterating the specimen with a product designed to interfere with testing or by substituting the specimen for a synthetic urine. A market search conducted in December of 2020 identified 3 adulterants and 32 synthetic urines, and a selection was procured based on specific criteria. Samples prepared with the 3 adulterants and 10 synthetic urines were submitted for testing at five forensic drug testing laboratories to perform immunoassay screening, chromatographic confirmation analysis and specimen validity testing (SVT). One adulterant determined to contain iodate reduced THC-COOH concentrations by 65% and the concentrations of 6-acetylmorphine, morphine, oxycodone, oxymorphone, hydrocodone and hydromorphone by 6–27%. Another adulterant determined to contain nitrite reduced THC-COOH concentrations by 22%, while the third did not affect drug screening or confirmatory testing. Both active adulterants could be identified through positive oxidant screens as well as through signal suppression in cloned enzyme donor immunoassay (CEDIA). The synthetic urines could not be identified either through traditional SVT or by the AdultaCheck10 dipstick. The Synthetic UrineCheck dipstick produced a difference in response between the authentic urine specimen and the synthetic urine samples, but the difference was small and difficult to observe. While most synthetic urines now contain uric acid, magnesium and caffeine, the results indicated that a biomarker panel including endogenous and exogenous markers of authentic urine performed well and clearly demonstrated the absence of biomarkers in the synthetic urines. The SVT assay also offers potential targets for future screening assays.
A Comparison of High Drug Concentrations in Impaired Driving and Postmortem Casework in Harris County, TX
Authors: Dempsey Sara K , Gray Teresa R , Kelly Anna T , Stout Peter , Lee Dayong 
Published: May 2022

AbstractDrug-impaired driving is a growing public safety issue. Addressing impairment due to drugs other than ethanol can be challenging for forensic toxicologists as many factors need to be considered including the type of drug(s), drug−drug interaction, the dose(s) and the individual’s physiological condition and drug use history. Interpretation of blood drug test results is additionally difficult as drug concentrations in impaired driving cases may overlap levels typically viewed as toxic. This study compares blood concentrations of drugs in impaired driving cases to those in postmortem cases in Houston, TX, from 2014 to 2020. Blood drug concentrations from driving while intoxicated (DWI) or driving under the influence of drugs (DUID) cases submitted to Houston Forensic Science Center (HFSC) and Harris County Institute of Forensic Sciences (HCIFS) were compared to postmortem blood test results from HCIFS. Eight DWI/DUID cases had drugs that exceeded impaired driving concentrations reported in the literature. These drugs included fentanyl (220 ng/mL), oxycodone (680 ng/mL), hydrocodone (310 and 490 ng/mL), clonazepam (330 ng/mL), methamphetamine (3,500 and 7,100 ng/mL) and tetrahydrocannabinol (THC) (160 ng/mL). For oxycodone and hydrocodone, the presented DWI/DUID cases exceeded 91% and 96% of postmortem concentrations, respectively. The 7,100 ng/mL methamphetamine DWI/DUID result was greater than 98% of postmortem cases. The presented DWI/DUID concentrations were higher than all but one postmortem case for clonazepam and higher than all postmortem cases for THC. This study demonstrates that extremely high drug concentrations in DWI/DUID casework blur the line between therapeutic/recreational and toxic concentrations.
Palliative Care and Burn Care: Empirically Derived Referral Criteria
Authors: Grossoehme Daniel H , Shaner Valerie , Friebert Sarah , Brown Miraides , Steiner Stephanie , Khandelwal Anjay , Eickmeyer Shari W , Teo Esther , Brown Carrie , Lou Richard 
Published: May 2022

AbstractBurns frequently require complex interdisciplinary care. Specialist palliative care (PC) minimizes suffering, aids in decision making, and provides family support in addition to end-of-life care. Specialist PC is a limited resource, best conserved by identifying persons most likely to benefit from a PC referral. Little guidance is available for clinicians on whether and when to refer to PC. This study’s purpose was to identify referral criteria using a mixed-methods approach. Data were examined for between-group differences using Fisher’s exact, chi-square, or Wilcoxon Rank Sum tests. Qualitative thematic analysis was used to analyze PC provider notes to describe interventions provided. These data formed initial referral criteria, which were reviewed by an expert panel. Significant between-group differences included dying in the burn center; whether multiple patients were transported to the burn center from one event; and ventilator days. Four themes emerged from qualitative analysis. These included managing physical aspects of care; clarifying goals of care; managing end-of-life care; and managing patient/family psychosocial distress. Expert panel input clarified referral criteria language and supplemented the proposed criteria. We present empirically derived referral criteria to guide burn providers in referring persons for specialist PC. Subsequent testing is required to determine their efficacy in improving patient/family outcomes.
Current treatment status of older patients with gynecological cancers
Authors: Yunokawa Mayu , Onda Takashi , Ishikawa Mitsuya , Yaegashi Nobuo , Kanao Hiroyuki 
Published: May 2022

Abstract
The percentage of older patients with gynecological malignancies has recently been on the rise. Although prospective studies focusing on the treatment of older patients have been conducted for ovarian cancer, mainly in Europe, there have been scarce literature on cervical and endometrial cancers, and information on their treatment is currently lacking. One of the characteristics of older patients is that not only their performance status but also other factors, such as physical, mental and social factors, cause a large variability, and individual differences in their response to treatments. One of the major issues in the treatment of older patients is how to objectively measure these individual differences and link them to the appropriate treatment selection. In this review, clinical evidence for the guided treatment of older patients with gynecological cancer will be reviewed.
Recurrent chylopericardium in a patient with history of left leg sarcoma
Authors: Aboukheir-Aboukheir Aihab , Lugo-Perez Paloma M , Colon-Melendez Eduardo , Gonzalez-Cancel Ivan , Boodoodingh-Casiano Dev R 
Published: May 2022

Abstract
Chylopericardium is a rare condition that is characterized by the presence of chyle in the pericardial space due to idiopathic (primary) or secondary causes. We present a 43-year-old female with hypothyroidism and left lower extremity sarcoma which were treated with resection and adjuvant chemoradiotherapy that was found with moderate pericardial effusion in surveillance tests. The patient was initially treated with tube thoracostomy and conservative management but presented with recurrence. Eventually, she was treated with left thoracotomy, ligation of the thoracic duct and pericardiectomy.
Functions and mechanisms of the Ubc13-UEV complex and lysine 63-linked polyubiquitination in plants
Authors: Yang Kun , Xiao Wei 
Published: May 2022

Abstract
Ubiquitination is one of the best-known post-translational modifications in eukaryotes, in which different linkage types of polyubiquitination result in different outputs of the target proteins. Distinct from the well-characterized K48-linked polyubiquitination that usually serves as a signal for degradation of the target protein, K63-linked polyubiquitination often requires a unique E2 heterodimer Ubc13-UEV and alters the target protein activity instead of marking it for degradation. This review focuses on recent advances on the roles of Ubc13-UEV-mediated K63-linked polyubiquitination in plant growth, development, and response to environmental stresses.