bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo chromosome level assembly of a plant genome from long read sequence data
Authors: Sharma Priyanka , Masouleh Ardashir Kharabian , Topp Bruce , Furtado Agnelo , Henry Robert J. 
Published: November 2021

SUMMARYRecent advances in the sequencing and assembly of plant genomes have allowed the generation of genomes with increasing contiguity and sequence accuracy. Chromosome level genome assemblies using sequence contigs generated from long read sequencing have involved the use of proximity analysis (Hi‐C) or traditional genetic maps to guide the placement of sequence contigs within chromosomes. The development of highly accurate long reads by repeated sequencing of circularized DNA (HiFi; PacBio) has greatly increased the size of contigs. We now report the use of HiFiasm to assemble the genome of Macadamia jansenii, a genome that has been used as a model to test sequencing and assembly. This achieved almost complete chromosome level assembly from the sequence data alone without the need for higher level chromosome map information. Eight of the 14 chromosomes were represented by a single large contig (six with telomere repeats at both ends) and the other six assembled from two to four main contigs. The small number of chromosome breaks appears to be the result of highly repetitive regions including ribosomal genes that cannot be assembled by these approaches. De novo assembly of near complete chromosome level plant genomes now appears possible using these sequencing and assembly tools. Further targeted strategies might allow these remaining gaps to be closed.
Comparison of iridocorneal angle parameters measured by spectral domain optical coherence tomography and ultrasound biomicroscopy in dogs
Authors: Shim Jaeho , Kang Seonmi , Jeong Youngseok , Lee Eunji , Jeong Dajeong , Seo Kangmoon 
Published: November 2021

AbstractObjectiveTo compare the measurements of iridocorneal angle parameters between spectral domain optical coherence tomography (SD‐OCT) and ultrasound biomicroscopy (UBM) in dogs.Animals studied and proceduresA total of 47 eyes of dogs were scanned at the temporal limbus using SD‐OCT and UBM. Iridocorneal angle (ICA) and angle opening distance (AOD) were measured from the obtained images accordingly. The intra‐observer and inter‐observer reproducibility were evaluated using the intraclass correlation coefficient. To evaluate intra‐observer reproducibility, measurements of the first and second grading from the first examiner were compared. To evaluate inter‐observer reproducibility, measurements between the two examiners were compared. Agreement between ICA and AOD for SD‐OCT and UBM was evaluated using Bland‐Altman plots.ResultsIn the first grading, the mean ICA and AOD for SD‐OCT were 31.4 ± 6.4° and 641.4 ± 270.8 µm, respectively. The mean ICA and AOD for UBM were 32.0 ± 4.8° and 700.4 ± 238.8 µm, respectively. For ICA and AOD measurements, intra‐observer reproducibility was excellent for both devices, whereas inter‐observer reproducibility was excellent for SD‐OCT and good for UBM. The mean difference in ICA between SD‐OCT and UBM was 0.6° with a limit of agreement (LoA) span of 18.9°. The mean difference in AOD between SD‐OCT and UBM was 58.9 µm with a LoA span of 804.4 µm.ConclusionsSpectral domain optical coherence tomography is an effective non‐contact imaging modality for the evaluation of canine iridocorneal angle parameters in a clinical setting. Reproducibility of measurements obtained is comparable or superior to UBM, but values obtained by SD‐OCT and UBM for AOD are not interchangeable between devices.
Association Between Lower Trapezius Isometric Strength and Y-Balance Test Upper Quarter Performance in College Volleyball Players
Authors: Mendez-Rebolledo Guillermo , Cools Ann M. , Ramirez-Campillo Rodrigo , Quiroz-Aldea Elias , Habechian Fernanda A.P. 
Published: November 2021

Context: Knowing the possible association between the isometric strength of the shoulder rotators, scapular muscles, and the Y-balance test upper quarter (YBT-UQ) performance could help identify which indicators of shoulder stability should be considered in this field test. This study aimed to determine whether the isometric strength of the shoulder rotators and scapular muscles is associated with the YBT-UQ performance of the dominant upper limb in amateur volleyball players. Design: Cross-sectional study. Methods: A convenience sample of 22 male and 18 female volleyball players (≥12 h of training/week) between 18 and 26 years of age. The isometric strength of the middle trapezius, lower trapezius, serratus anterior, internal, and external rotator muscles was assessed with a handheld dynamometer. Participants performed the YBT-UQ in the superolateral, medial, and inferolateral directions. The absolute isometric peak force (in Newtons) was normalized to body weight (in Newtons per kilogram) for each muscle test. For each YBT-UQ direction, the distance (in centimeters) was normalized for upper limb length (in percentage). A backward multiple linear regression analysis was used to determine the associations between variables. Results: The analysis revealed that the isometric strength of the lower trapezius (β = 26.82; 95% confidence interval, 21.24–32.40) is associated with inferolateral YBT-UQ performance (adjusted R2 = .706; P < .001). This factor explains 70% of the variability of the YBT-UQ in the inferolateral direction. Conclusions: Lower trapezius isometric strength is associated with inferolateral YBT-UQ performance of the dominant upper limb in amateur volleyball players. These findings could help in the development of more specific training programs and rehabilitation goals according to the performance of the athletes in the test.
Comparing organ donation decisions for next-of-kin versus the self: results of a national survey
Authors: Liu Christopher Weiyang , Chen Lynn N , Anwar Amalina , Lu Zhao Boyu , Lai Clin K Y , Ng Wei Heng , Suhitharan Thangavelautham , Ho Vui Kian , Liu Jean C J 
Published: November 2021

ObjectivesIntensive care audits point to family refusal as a major barrier to organ donation. In this study, we sought to understand refusal by accounting for the decision-maker’s mindset. This focused on: (1) how decisions compare when made on behalf of a relative (vs the self); and (2) confidence in decisions made for family members.DesignCross-sectional survey in Singapore.SettingParticipants were recruited from community settings via door-to-door sampling and community eateries.Participants973 adults who qualified as organ donors in Singapore.ResultsAlthough 68.1% of participants were willing to donate their own organs, only 51.8% were willing to donate a relative’s organs. Using machine learning, we found that consistency was predicted by: (1) religion, and (2) fears about organ donation. Conversely, participants who were willing to donate their own organs but not their relative’s were less driven by these factors, and may instead have resorted to heuristics in decision-making. Finally, we observed how individuals were overconfident in their decision-making abilities: although 78% had never discussed organ donation with their relatives, the large majority expressed high confidence that they would respect their relatives’ wishes on death.ConclusionsThese findings underscore the distinct psychological processes involved when donation decisions are made for family members. Amidst a global shortage of organ donors, addressing the decision-maker’s mindset (eg, overconfidence, the use of heuristics) may be key to actualizing potential donors identified in intensive care units.
ANA positivity and complement level in pleural fluid are potential diagnostic markers in discriminating lupus pleuritis from pleural effusion of other aetiologies
Authors: Chen Der-Yuan , Huang Yen-Hsiang , Chen Yi-Ming , Chen Jeremy J W , Yang Tsung-Ying , Chang Gee-Chen , Tang Kuo-Tung 
Published: November 2021

ObjectiveLupus pleuritis is the most common pulmonary manifestation of systemic lupus erythematosus (SLE). We aimed to compare various biomarkers in discriminating between pleural effusions due to lupus pleuritis and other aetiologies.MethodsWe determined in 59 patients (16 patients with SLE and 43 patients without SLE) pleural fluid levels of high-mobility group box 1, soluble receptor for advanced glycation end products (sRAGE), adenosine deaminase (ADA), interleukin (IL) 17A, tumour necrosis factor-α, antinuclear antibodies (ANA), and complements C3 and C4.ResultsWe found significant differences in the pleural fluid level of sRAGE, ADA, IL-17A, C3 and C4, and in the proportion of ANA positivity, among lupus pleuritis and other groups with pleural effusion. Specifically, ANA positivity (titre ≥1: 80) achieved a high sensitivity of 91%, specificity of 83% and negative predictive value (NPV) of 97% in discriminating lupus pleuritis from non-lupus pleural effusion. A parallel combination of the level of C3 (<24 mg/dL) and C4 (<3 mg/dL) achieved a sensitivity of 82%, specificity of 89% and NPV of 93% in discriminating lupus pleuritis from non-lupus exudative pleural effusion.ConclusionsIn conclusion, ANA, C3 and C4 in pleural fluid are useful in discriminating lupus pleuritis from pleural effusion due to other aetiologies with high NPV.
The Effect of Liraglutide on Epicardial Adipose Tissue in Type 2 Diabetes
Authors: Zhao Na , Wang Xiaoying , Wang Yongbo , Yao Junjie , Shi Chunhong , Du Jianling , Bai Ran 
Published: November 2021

Objective. To study the effect of liraglutide on the thickness of epicardial adipose tissue (EAT) in type 2 diabetes mellitus (T2DM) patients with abdominal obesity. Methods. Abdominal obesity T2DM patients with poor glycemic control were collected and treated with liraglutide. The changes of blood glucose, blood lipid, waist circumference, body mass index (BMI), and EAT thickness were compared after 3 months of treatment with liraglutide. Cardiac magnetic resonance imaging (MRI) was used to measure EAT thickness. Results. After 3 months of treatment with liraglutide, glycosylated hemoglobin (HbA1c) decreased from

9.81
±
1.46

% to

6.94
±
1.29

% (

95
%
CI
=
2.14
–
3.59

,

p
<
0.001

). The weight decreased from

91.67
±
16.29

kg to

87.29
±
16.43

kg (

95
%
CI
=
2.97
–
5.79

,

p
<
0.001

). Waist circumference before treatment was

103.69
±
9.14

cm, and after treatment was

96.42
±
8.42

cm (

95
%
CI
=
5.04
–
9.50

,

p
<
0.001

). Total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were significantly lower than those before treatment. TC decreased from

5.34
±
1.05

mmol/L to

4.86
±
0.97

mmol/L (

95
%
CI
=
0.15
–
0.82

,

p
<
0.001

). TG was 1.89 (1.48-3.17) and then to

1.92
±
0.69

(

p
=
0.03

). LDL-C decreased from

3.39
±
0.84

mmol/L to

3.01
±
0.74

mmol/L (

95
%
CI
=
0.17
–
0.59

,

p
=
0.001

). HDL-C increased by 1.7% after treatment, with no significant difference (

p
=
0.062

). More importantly, the thickness of EAT decreased from 5.0 (5.0-7.0) mm to

3.95
±
1.43

mm (

p
<
0.001

) after liraglutide administered for 3 months. Conclusion. Liraglutide significantly reduces EAT thickness in T2DM with abdominal obesity, which provides theoretical support for the cardiovascular benefits of liraglutide.
Evaluation between vitamin D serum level and Herpes Simplex Virus Type 1 in the field of dentistry
Authors: Parvaie Parvin , Baghan Saideh Ebrahimian , Osmani Freshteh 
Published: November 2021

Objectives: Our study sought to evaluate the association between HSV1 and serum 25-hydroxyvitamin D (25(OH) D) levels among dental students. Materials & Methods: This is a cross-sectional study with a quantitative approach conducted in Birjand, state of Khorasan Jonoobi, Iran, from July 2018 to April 2019. A peripheral blood sample (5 ml) and an anti-virus antibody along with Serum 25-hydroxyvitamin D (1,25(OH)2D3) levels were measured using an Anti-Herpes-1 IgG kit with ELISA by a pathologist. Pearson and chi-square tests were applied in the significance level of 5%. Results: The prevalence of HSV1 was 41%. The serum 25-hydroxyvitamin D3 levels mean was 23.22 ± 13.09. The prevalence of HSV1 antibody in pre-clinical and clinical levels was higher than in basic science, also, the results represented that a negative relation between vitamin D deficiency and the presence of HSV1, but it was not a significant association. Conclusion: Any association between vitamin D and herpes viruses remains inconclusive. Further studies in the general population are needed.
Adeus, Pirandello e a Grosse Fuge - Aproximações entre o romance de Marco Lucchesi e a op. 133 de Ludwig van Beethoven
Authors: Marzullo Alexandre 
Published: November 2021

O escritor Marco Lucchesi, em seu romance Adeus, Pirandello, realiza, ao longo de sua intrincada e multifária narrativa, com fortes matizes autobiográficos, uma série de menções pungentes e simbólicas ao compositor Ludwig van Beethoven e sua obra – em especial, à sua tardia op. 133, também chamada de Grosse Fuge (Grande Fuga). Esta composição, principalmente nos momentos finais do livro, contribui para a consolidação de um ambiente narrativo já tenso e polifônico, sinuoso e eivado de angústia desde os primeiros capítulos. O presente texto pretende apontar a presença de linhas comuns entre a estrutura narrativa do romance de Marco Lucchesi e a poética da Grande Fuga, ambas, “obras de invenção”, sob a perspectiva de uma correspondência sígnica e estrutural.
Palavras-chave: Marco Lucchesi; Ludwig van Beethoven; Adeus, Pirandello; Grosse Fuge; romance; fuga; crítica literária.
Cheng and Gadamer: Daoist Phenomenology
Authors: Goulding Jay 
Published: November 2021

Abstract
Two immense influences on my work originate from the seminal philosophers Hans-Georg Gadamer and Chung-ying Cheng. My academic career begins with personal interactions with the hermeneutics philosopher Gadamer at McMaster University in Hamilton, Canada whose guiding hand shapes my vision around the idea of merging horizons; Cheng enhances this rich and most provocative beginning with a unique East-West phenomenology of onto-generative hermeneutics. Both scholars provide fresh eyes for Martin Heidegger’s engagement with Daoism in what I call Daoist Phenomenology, and the forgotten “o”: the move from the saying of the Da of Da-sein to the waying of Da(o).
“So Many Mothers, So Little Love”: Discourse of Motherly Love and Parental Governance in 2019 Hong Kong Protests
Authors: Guo Ting 
Published: November 2021

Abstract
This paper focuses on Hong Kong Chief Executive Carrie Lam Cheng Yuet-ngor’s discourse of motherly love during the 2019 mass protests, examining it in relation to the politicization of Confucianism taking place in China today. This politicization results from a new cult of personality centered on President Xi Jinping and his wife Peng Liyuan which reinforces patriarchal authoritarianism and familial nationalism through an explicit emphasis on Confucianism and traditional values. Through this process, authoritarian power has been reconfigured and legitimized as Confucian duty, with the result that political leaders are made to appear firm but benevolent parents while the protestors are cast in the role of children requiring discipline. Lam’s discourse of motherly love is further complicated by the fact that she is the first woman to assume such a leadership role in modern Chinese history, which further illuminates Hong Kong’s struggle against both patriarchal authoritarianism and the gendered legacy of coloniality.
Muḥammad ibn Sulaymān al-Jazūlī and the Place of Dalāʾil al-Khayrāt in Jazūlite Sufism
Authors: Cornell Vincent J. 
Published: November 2021

Abstract
This article discusses the career of Muḥammad ibn Sulaymān al-Jazūlī (d. 869/1465), his compilation of Dalāʾil al-Khayrāt, and the place of this work in Jazūlite Sufism. The teachings of the Jazūliyya Sufi order emphasized intense spiritual devotion to the Prophet Muḥammad as a means of access to the Divine. As a manual of prayers and invocations on behalf of the Prophet, Dalāʾil al-Khayrāt became one of the most popular works of Islamic devotional literature. This widespread popularity was partly due to the Jazūliyya’s doctrinal connections with the Qādiriyya and Shādhiliyya Sufi orders. In Jazūliyya Sufi practice, the recitation of Dalāʾil al-Khayrāt and the prayers and litanies of the order were used to instill a “Muḥammadan” consciousness in the mind of the disciple. This higher consciousness was meant to serve as a compass of spiritual guidance for the “true seeker of God” (al-murīd al-ṣādiq), who aspired to the highest levels of Sufi knowledge.
Paths of Prayers in Ottoman North Africa
Authors: Beyazit Deniz 
Published: November 2021

Abstract
This article discusses The Met’s unpublished Dalāʾil al-khayrāt—2017.301—(MS New York, TMMA 2017.301), together with a group of comparable manuscripts. The earliest known dated manuscript within the corpus, it introduces several iconographic elements that are new to the Dalāʾil, and which compare with the traditions developing in the Mashriq and the Ottoman world in particular. The article discusses Dalāʾil production in seventeenth-century North Africa and its development in the Ottoman provinces, Tunisia, and/or Algeria. The manuscripts illustrate how an Ottoman visual apparatus—among which the theme of the holy sanctuaries at Mecca and Medina, appearing for the first time in MS New York, TMMA 2017.301—is established for Muhammadan devotion in Maghribī Dalāʾils. The manuscripts belong to the broader historic, social, and artistic contexts of Ottoman North Africa. Our analysis captures the complex dynamics of Ottomanization of the North African provinces of the Ottoman Empire, remaining strongly rooted in their local traditions, while engaging with Ottoman visual idioms.
Coping
Authors: Bovens Luc 
Published: November 2021

Coping and Philosophy is a collection of philosophical essays on how we deal with life’s challenges. We hope for better times, but what is hope and is it a good thing to hope? How do we look back and make sense of our lives in the face of death? What is the nature of love and how do we deal with its hardships? What makes for a genuine apology and is there too much or too little apologizing in this world? Can we effect changes in ourselves to adapt to our circumstances? And how can we sense of all the counsel that people have: be grateful, don’t cry over spilled milk, eat well, …
This volume is a perfect companion text for courses such as Philosophy of Life, The Meaning of Life, or for a moral psychology component in an Ethics course. The material is written for readers who are new to philosophy and progresses in short blog-style sections. It draws on literature, music, podcasts, and news items. Each chapter has a set of questions for discussion or essay writing and suggestions for material to explore the topic further.
Major Salivary Gland Cancer With Distant Metastasis Upon Presentation: Patterns, Outcomes, and Imaging Implications
Authors: Benchetrit Liliya , Mehra Saral , Mahajan Amit , Rahmati Rahmatullah W. , Judson Benjamin L. , Edwards Heather A. 
Published: November 2021

ObjectivesGiven limited data availability on distant metastasis (DM) in major salivary gland (MSG) malignancy presentation, we aimed to evaluate the rate, histologic patterns, location, and predictors of DM at first MSG cancer presentation and suggest potential implications on diagnostic workup.Study DesignRetrospective cohort.SettingCommission on Cancer–accredited hospitals.MethodsWe included patients in the National Cancer Database (2010‐2016) with MSG malignancy. Site and rate of DM were stratified by histologic subtype. Factors predictive of DM at presentation were determined by multivariate regression analysis. Survival analyses were conducted via the Kaplan‐Meier method, log‐rank test, and Cox regression analysis.ResultsOf 5776 patients with MSG carcinoma, 333 (5.8%) presented with DM. The most common DM site was the lung (57.1%), followed by bone (46.8%) and liver (19.5%). DM was most common in adenocarcinoma–not otherwise specified (15.1%, 132/874) and salivary duct carcinoma (10.4%, 30/288). High‐grade mucoepidermoid carcinoma had the highest rate of lung metastases (81.6%, 31/38). Conversely, myoepithelial carcinoma had the highest rate of bone metastases (85.7%, 6/7). DM at presentation was independently associated with an increased mortality risk (hazard ratio, 1.62; 95% CI, 1.40‐1.90).ConclusionWe identified a DM rate of 5.8% in MSG malignancy at presentation. Overall 43% of patients presented without DM to the lung but with DM to the bones, liver, and/or brain. The most common metastatic sites differed by tumor histology. Staging with computed tomography neck and chest alone may fail to detect sites of DM; this work can be used for patient counseling in the clinical setting.
Breathing exercises versus strength exercises through telerehabilitation in coronavirus disease 2019 patients in the acute phase: A randomized controlled trial
Authors: Rodríguez-Blanco Cleofas , Bernal-Utrera Carlos , Anarte-Lazo Ernesto , Saavedra-Hernandez Manuel , De-La-Barrera-Aranda Elena , Serrera-Figallo Maria Angeles , Gonzalez-Martin Maribel , Gonzalez-Gerez Juan Jose 
Published: November 2021

Objective To compare the effectiveness of two different exercise-based programs through telerehabilitation in patients with coronavirus disease 2019. Design Randomized, controlled, parallel, double-blinded, three-arm clinical trial. Setting Patients’ homes through telerehabilitation devices. Subjects Subjects with coronavirus disease 2019 in the acute phase. Interventions Subjects were divided into three groups: breathing exercises group, strength exercises group or no treatment/control group. Main measures We analysed visual analogue scale for fatigue, 6-minute walking test, 30-seconds sit-to-stand test, multidimensional dyspnoea-12 questionnaire and Borg scale at baseline and 14 days later. Results From 93 subjects recruited, 88 were enrolled, and 77 patients (mean [SD] age 39.40 [11.71]) completed the 14-days intervention and were included in the analysis: 26 in strength exercises group, 29 in breathing exercises group and 22 in control group. The intergroup analysis shows significant differences between the study groups and control group in all variables ( p < 0.05); Borg scale, multidimensional dyspnoea-12 questionnaire (pre–post intervention score: strength exercises group: 7.85 [6.82] – 4.54[4.82], breathing exercises group: 11.04 [6.49] – 5.32 [3.63], control group: 10.27 [6.49] – 10.59[6.58]), visual analogue scale for fatigue, 6-minute walking test and 30-seconds sit-to-stand test (pre–post intervention score: strength exercises group: 12.19 [4.42] – 13.58 [5.37], breathing exercises group: 11.18 [3.42] – 12.79 [4.00], control group: 10.45 [2.15] – 9.86[1.88]). The greatest effect sizes were found in the variables Borg Scale ( R2 = 0.548) and multidimensional dyspnoea-12 questionnaire ( R2 = 0.475). Conclusions Strength exercises group and breathing exercises group obtained significant improvements in fatigue, dyspnoea, perceived effort, and physical state, compared to control group, although the greatest benefits were found for dyspnoea and aerobic capacity in breathing exercises group.