bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete reference genome for grapevine (Vitis viniferaL.) genetics and breeding
Authors: Shi Xiaoya , Cao Shuo , Wang Xu , Huang Siyang , Wang Yue , Liu Zhongjie , Liu Wenwen , Leng Xiangpeng , Peng Yanling , Wang Nan , Wang Yiwen , Ma Zhiyao , Xu Xiaodong , Zhang Fan , Xue Hui , Zhong Haixia , Wang Yi , Zhang Kekun , Velt Amandine , Avia Komlan , Holtgräwe Daniela , Grimplet Jérôme , Matus José Tomás , Ware Doreen , Wu Xinyu , Wang Haibo , Liu Chonghuai , Fang Yuling , Rustenholz Camille , Cheng Zongming , Xiao Hua , Zhou Yongfeng 
Published: April 2023

AbstractGrapevine is one of the most economically important crops worldwide. However, the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres, limiting the accessibility of the repetitive sequences, the centromeric and telomeric regions, and the study of inheritance of important agronomic traits in these regions. Here, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads. The T2T reference genome (PN_T2T) is 69 Mb longer with 9018 more genes identified than the 12X.v0 version. We annotated 67% repetitive sequences, 19 centromeres and 36 telomeres, and incorporated gene annotations of previous versions into the PN_T2T assembly. We detected a total of 377 gene clusters, which showed associations with complex traits, such as aroma and disease resistance. Even though PN40024 derives from nine generations of selfing, we still found nine genomic hotspots of heterozygous sites associated with biological processes, such as the oxidation–reduction process and protein phosphorylation. The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.
Revaluation of a selected segmental insufflation technique in total thoracoscopic lung segmentectomy
Authors: Suzuki Jun , Oizumi Hiroyuki , Watanabe Hikaru , Takamori Satoshi , Fujiwara Toshiya , Matsuura Motoki 
Published: April 2023

AbstractWe report selected insufflation technique using direct bronchial insufflation to visualize the intersegmental plane during total thoracoscopic segmentectomy. Following the transection of the bronchus using a stapler, a small incision was created in the dissected target bronchus, and direct air insufflation was performed at the small incision site. The target segment was inflated, while the preserved segments appeared to collapse, and a demarcating line was visualized between the inflated and deflated lung parenchyma. This technique quickly identifies the anatomic intersegmental plane without warranting special equipment such as jet ventilation or indocyanine green (ICG). Furthermore, this method saves time in creating inflation–deflation lines.
Machine-learning-based high-benefit approach versus conventional high-risk approach in blood pressure management
Authors: Inoue Kosuke , Athey Susan , Tsugawa Yusuke 
Published: April 2023

Abstract

Background
In medicine, clinicians treat individuals under an implicit assumption that high-risk patients would benefit most from the treatment (‘high-risk approach’). However, treating individuals with the highest estimated benefit using a novel machine-learning method (‘high-benefit approach’) may improve population health outcomes.

Methods
This study included 10 672 participants who were randomized to systolic blood pressure (SBP) target of either &lt;120 mmHg (intensive treatment) or &lt;140 mmHg (standard treatment) from two randomized controlled trials (Systolic Blood Pressure Intervention Trial, and Action to Control Cardiovascular Risk in Diabetes Blood Pressure). We applied the machine-learning causal forest to develop a prediction model of individualized treatment effect (ITE) of intensive SBP control on the reduction in cardiovascular outcomes at 3 years. We then compared the performance of high-benefit approach (treating individuals with ITE &gt;0) versus the high-risk approach (treating individuals with SBP ≥130 mmHg). Using transportability formula, we also estimated the effect of these approaches among 14 575 US adults from National Health and Nutrition Examination Surveys (NHANES) 1999–2018.

Results
We found that 78.9% of individuals with SBP ≥130 mmHg benefited from the intensive SBP control. The high-benefit approach outperformed the high-risk approach [average treatment effect (95% CI), +9.36 (8.33–10.44) vs +1.65 (0.36–2.84) percentage point; difference between these two approaches, +7.71 (6.79–8.67) percentage points, P-value &lt;0.001]. The results were consistent when we transported the results to the NHANES data.

Conclusions
The machine-learning-based high-benefit approach outperformed the high-risk approach with a larger treatment effect. These findings indicate that the high-benefit approach has the potential to maximize the effectiveness of treatment rather than the conventional high-risk approach, which needs to be validated in future research.
Global threshold dynamics of a spatial chemotactic mosquito-borne disease model
Authors: Wang Kai , Wang Hao , Zhao Hongyong 
Published: April 2023

AbstractIt is natural that mosquitoes move towards high human population density and environmental heterogeneity plays a pivotal role in disease transmission, and thus we formulate and analyse a mosquito-borne disease model with chemotaxis and spatial heterogeneity. The global existence and boundedness of solutions are proven to guarantee the solvability of the model and is challenging due to the model complexity. Under appropriate conditions, we demonstrate that the disease-free equilibrium is globally asymptotically stable provided that the basic reproduction number $\mathcal{R}_0$ is less than one, and the system is uniformly persistent and admits at least one endemic equilibrium if $\mathcal{R}_0$ is greater than one. Furthermore, we numerically explore the impacts of chemotactic effect, spatial heterogeneity and dispersal rates of infected individuals to provide a clear picture on disease severity. In particular, the mosquito chemotaxis causes mild disease in some regions but severe in others, which suggests developing targeted strategies to control mosquitoes in specific locations and achieve a deep understanding on the chemotaxis.
A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism
Authors: Chakrabarti Anob M , Iosub Ira A , Lee Flora C Y , Ule Jernej , Luscombe Nicholas M 
Published: April 2023

Abstract
The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences of this interplay. However, current transcriptome-wide experimental methods to chart these interactions are limited by their poor sensitivity. Here we extend the hiCLIP atlas of duplexes bound by Staufen1 (STAU1) ∼10-fold, through careful consideration of experimental assumptions, and the development of bespoke computational methods which we apply to existing data. We present Tosca, a Nextflow computational pipeline for the processing, analysis and visualisation of proximity ligation sequencing data generally. We use our extended duplex atlas to discover insights into the RNA selectivity of STAU1, revealing the importance of structural symmetry and duplex-span-dependent nucleotide composition. Furthermore, we identify heterogeneity in the relationship between transcripts with STAU1-bound 3′ UTR duplexes and metabolism of the associated RNAs that we relate to RNA structure: transcripts with short-range proximal 3′ UTR duplexes have high degradation rates, but those with long-range duplexes have low rates. Overall, our work enables the integrative analysis of proximity ligation data delivering insights into specific features and effects of RBP-RNA structure interactions.
The Problem of Interpretive Canons
Authors: Tan David 
Published: April 2023

Abstract
In this paper it is shown that interpretive canons are either constitutionally invalid because of the principles of interpretation it establishes, or a theory of interpretation can be made to be inconsistent: where a theory of interpretation says do p, then a new canon can say do not-p. This is called the Canon Dilemma. Whichever horn of the dilemma is taken as acceptable (accept invalidity or possible inconsistency), this shows that canons cause more problems for theorising about interpretation than currently realised. Some might interpret the Canon Dilemma as a process of theory change (p is replaced with not-p rather than being contradicted by it), but even then problems of incoherence still persist. This paper also shows a connection between debates on the constitutionality of interpretive canons and the descriptive accuracy of linguistic theories of interpretation.
Effectiveness Does Not Always Equate to Legislative Quality: The Case of the 15th Parliamentary Term in Greece
Authors: Primpas Ioannis 
Published: April 2023

Abstract
In the scientific debate about what quality means in legislation, the opinion has spread that legislation of good quality is synonymous with effective legislation. This article discusses that effectiveness does not always equate to legislative quality. The example of the 15th parliamentary term in Greece, amid the acute debt crisis, is typical. The most intense and numerous phenomena of ‘bad’, unconstitutional law-making in recent Greek parliamentary history were observed during this term. Nevertheless, the effects of this kind of legislation were remarkably positive since all the indicators of the Greek economy improved spectacularly. Yet, anti-democratic legislation is not qualitative legislation; even an authoritarian regime can enact effective laws. In a democratic rule of law, however, the law-making processes, the content, and the form of drafts must follow the Constitution and the Standing Orders of the Parliament; the legislature is obliged to produce law by the law. Particularly adherence to the prescribed procedures is of vital importance, as it functions as a guarantee of achieving good legislative quality. After all, no one can foresee the best quality content at the start of the legislative process since it is formed after creative fermentation and balancing of tendencies while following the prescribed procedures.
Circular RNA PDK1 targets miR‐4731‐5p to enhance TNXB expression in ligamentum flavum hypertrophy
Authors: Zhang Kai , Wang Xin , Zeng Li‐Ting , Yang Xiao , Cheng Xiao‐Fei , Tian Hai‐Jun , Chen Chen , Sun Xiao‐Jiang , Zhao Chang‐Qing , Ma Hui , Zhao Jie 
Published: April 2023

AbstractHypertrophic ligamentum flavum (LF) is a main factor responsible for lumbar spinal stenosis (LSS); however, the exact mechanisms of the pathogenesis of these processes remain unknown. This study aimed to elucidate whether circular RNAs and microRNAs regulate the pathogenesis of LF and LSS, especially focusing on circPDK1 (hsa_circ_0057105), a circRNA targeting pyruvate dehydrogenase kinase 1 and differentially expressed in LF tissues between lumbar disk herniation and LSS patients. The circPDK1/miR‐4731 and miR‐4731/TNXB (Tenascin XB) interactions were predicted and validated by luciferase reporter assay. Colony formation, wound‐healing, and MTT assays were used for estimating cell proliferation and migration. Protein expression levels were evaluated using Western blotting. TNXB expression was verified using immunohistochemistry (IHC). Overexpressing circPDK1 promoted the proliferation, migration, and expression of fibrosis‐related protein (alpha smooth muscle actin (α‐SMA), lysyl oxidase like 2 (LOXL2), Collagen I, matrix metalloproteinase‐2 (MMP‐2) and TNXB) in LF whereas miR‐4731‐5p showed opposite effects. The expression of TNXB was promoted by circPDK1; contrary results were observed with miR‐4731‐5p. Co‐overexpression of miR‐4731‐5p partially reversed the proliferative and fibrosis‐prompting effects of circPDK1 or TNXB. The circPDK1‐miR‐4731‐TNXB pathway may be proposed as a regulatory axis in LF hypertrophy, which might shed light on in‐depth research of LSS, as well as providing a novel therapeutic target for LF hypertrophy‐induced LSS.
An Investigation of Replication Practice in Nursing Education Research
Authors: Abbott Miriam R. B. , Nininger Jami 
Published: April 2023

Abstract

AIM
The project aims to explore replication, as a concept and practice, in nursing education research.

BACKGROUND
Replication practices are important features supporting the science of nursing education. The absence of replication studies in the wider education community raises questions about the potential for similar absences in nursing education. As such, an investigation into replication practices within nursing education provides directions for future discussion.

METHOD
Using Scopus and databases of nursing education journals, three search strategies were launched to assess replication practices using bibliometric data and content analysis.

RESULTS
Inconsistency in definitions of the term replication creates barriers to recognizing replication attempts in the body of literature. Based on bibliometric data and content analysis, conceptual replication appears to be common in highly cited nursing education research.

CONCLUSION
Within the academic nursing community, consensus on the meaning of the term and promotion of practices that support replication is recommended.
Defining Posterior Wall Fragments in Associated Both Column Acetabular Fractures (OTA/AO 62C)
Authors: Arthur D’Ann E. , Novak Avrey , Unno Florence , Mayo Keith , Agel Julie , Firoozabadi Reza , Githens Michael , Kleweno Conor P. 
Published: April 2023

Objective:
Associated both column acetabular fractures (OTA/AO 62C) with concomitant posterior wall fracture fragments (ABC + PW) have not been well-defined. The purpose of this study was to report on the incidence and morphology of ABC + PW fractures.

Methods:
A retrospective review of associated both column (ABC) fractures between 2014 and 2020 was performed. Computed tomography scans including 3-D surface rendered reformats for each were reviewed to determine whether a posterior wall (PW) fragment was present and its morphologic characteristics.

Results:
One hundred fifty-two ABC fractures were identified. Sixty-two fractures (41%) were identified as ABC + PW. 3D-computed tomographies were available on 58 fractures. Morphologic analysis was performed based on the relationship of the fracture to the gluteal pillar. Twenty PW fragments were posterior to the gluteal pillar, 19 extended into the gluteal pillar, and 19 extended anterior. Fifty-two fractures were treated with operative fixation; 32 (62%) were clamped and fixed with screws from the same anterior approach whereas 15 (29%) required a separate posterior approach; and no fixation was placed in 5 (9%). 29 of 32 PW fragments (91%) requiring fixation that extended into or anterior to the pillar were fixed from the anterior approach, and 7 of 15 posterior fractures (47%) required a separate posterior approach.

Conclusions:
A separate PW fragment was identified in 41% of ABC fractures. Their variation in morphology can be classified into 3 types based on the relation to the gluteal pillar that has potential implications for treatment from the anterior approach compared with requiring a separate posterior approach. We suggest these data could be used to update the 2018 OTA/AO Fracture Compendium.

Level of Evidence:
Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Spinal Versus General Anesthesia for Lumbar Decompression or Sequestrectomy in Patients Over 75 Years
Authors: Kindris Florinella , Zegarek Gregory , Krappel Ferdinand A. , Perrig Wolfgang N. , Schmid Samuel L. 
Published: April 2023

Background Context:
Decompression or sequestrectomy in the lumbar spine can be performed under general (GA) or regional anesthesia. In elderly patients, it is still not clear, which procedure should be chosen.

Objective:
To demonstrate that spinal anesthesia (SA) is a safe choice for lumbar decompression or sequestrectomy in elderly patients

Design:
Retrospective clinical single-center study.

Patients Sample:
We included 154 patients with ages over 75 years after lumbar decompression or sequestrectomy. The mean age of the patients was 81 years.

Outcome Measures:
Perioperative data (blood loss, dural tear, operative and perioperative time, delirium, urinary retention, and hospital stay) and the postoperative 1-year follow-up (visual analog scale and complication rate).

Patients and Methods:
Data were retrospectively collected from patients that underwent lumbar decompression or sequestrectomy between January 2019 and December 2020. The data from the GA and SA groups were compared.

Results:
SA was performed in 56 patients whereas 98 patients received a GA. There was no clinically relevant difference between both groups with comparable complication rates. The time of surgery, blood loss, perioperative time, and hospital stay time were significantly less in the SA group.

Conclusions:
SA and GA are both safe and reliable procedures for lumbar decompression or sequestrectomy in elderly patients with no clinically relevant difference.
Comparison of the survival outcomes between primary and secondary muscle-invasive bladder cancer: a propensity score-matched study
Authors: Lok Waichan , Zhang Jiapeng , Zheng Xiaonan , Lin Tianhai , Xu Hang , Tan Ping , Wei Qiang 
Published: April 2023

Abstract

Background:
Studies have classified muscle-invasive bladder cancer (MIBC) into primary (initially muscle-invasive, PMIBC) and secondary subtypes (initially non-muscle-invasive but progresses, SMIBC), for which controversial survival outcomes were demonstrated. This study aimed to compare the survival outcomes between PMIBC and SMIBC patients in China.

Methods:
Patients diagnosed with PMIBC or SMIBC at West China Hospital from January 2009 to June 2019 were retrospectively included. Kruskal–Wallis and Fisher tests were employed to compare clinicopathological characteristics. Kaplan–Meier curves and Cox competing proportional risk model were used to compare survival outcomes. Propensity score matching (PSM) was employed to reduce the bias and subgroup analysis was used to confirm the outcomes.

Results:
A total of 405 MIBC patients were enrolled, including 286 PMIBC and 119 SMIBC, with a mean follow-up of 27.54 and 53.30 months, respectively. The SMIBC group had a higher proportion of older patients (17.65% [21/119] vs. 9.09% [26/286]), chronic disease (32.77% [39/119] vs. 22.38% [64/286]), and neoadjuvant chemotherapy (19.33% [23/119] vs. 8.04% [23/286]). Before matching, SMIBC had a lower risk of overall mortality (OM) (hazard ratios [HR] 0.60, 95% confidence interval [CI] 0.41–0.85, P = 0.005) and cancer-specific mortality (CSM) (HR 0.64, 95% CI 0.44–0.94, P = 0.022) after the initial diagnosis. However, higher risks of OM (HR 1.47, 95% CI 1.02–2.10, P = 0.038) and CSM (HR 1.58, 95% CI 1.09–2.29, P = 0.016) were observed for SMIBC once it became muscle-invasive. After PSM, the baseline characteristics of 146 patients (73 for each group) were well matched, and SMIBC was confirmed to have an increased CSM risk (HR 1.83, 95% CI 1.09–3.06, P = 0.021) than PMIBC after muscle invasion.

Conclusions:
Compared with PMIBC, SMIBC, had worse survival outcomes once it became muscle-invasive. Specific attention should be paid to non-muscle-invasive bladder cancer with a high progression risk.
Effect of complete percutaneous revascularization on improving long-term outcomes of patients with chronic total occlusion and multi-vessel disease
Authors: Li Zeya , Zhou Ziru , Guo Lei , Zhong Lei , Xiao Jingnan , Meng Shaoke , Wang Yingdong , Ding Huaiyu , Zhang Bo , Zhu Hao , Zhou Xuchen , Huang Rongchong 
Published: April 2023

Abstract

Background:
Limited data are available on the clinical outcomes of complete vs. incomplete percutaneous coronary intervention (PCI) for patients with chronic total occlusion (CTO) and multi-vessel disease (MVD) remains unknown. The study aimed to compare their clinical outcomes.

Methods:
A total of 558 patients with CTO and MVD were divided into the optimal medical treatment (OMT) group (n = 86), incomplete PCI group (n = 327), and complete PCI group (n = 145). Propensity score matching (PSM) was performed between the complete and incomplete PCI groups as sensitivity analysis. The primary outcome was defined as the occurrence of major adverse cardiovascular events (MACEs), and unstable angina was defined as the secondary outcome.

Results:
At a median follow-up of 21 months, there were statistical differences among the OMT, incomplete PCI, and complete PCI groups in the rates of MACEs (43.0% [37/86] vs. 30.6% [100/327] vs. 20.0% [29/145], respectively, P = 0.016) and unstable angina (24.4% [21/86] vs. 19.3% [63/327] vs. 10.3% [15/145], respectively, P = 0.010). Complete PCI was associated with lower MACE compared with OMT (adjusted hazard ratio [HR] = 2.00; 95% confidence interval [CI] = 1.23–3.27; P = 0.005) or incomplete PCI (adjusted HR = 1.58; 95% CI = 1.04–2.39; P = 0.031). Sensitivity analysis of PSM showed similar results to the above on the rates of MACEs between complete PCI and incomplete PCI groups (20.5% [25/122] vs. 32.6% [62/190], respectively; adjusted HR = 0.55; 95% CI = 0.32–0.96; P = 0.035) and unstable angina (10.7% [13/122] vs. 20.5% [39/190], respectively; adjusted HR = 0.48; 95% CI = 0.24–0.99; P = 0.046).

Conclusions:
For treatment of CTO and MVD, complete PCI reduced the long-term risk of MACEs and unstable angina, as compared with incomplete PCI and OMT. Complete PCI in both CTO and non-CTO lesions can potentially improve the prognosis of patients with CTO and MVD.
How effective are lifestyle interventions for overweight women trying to conceive?
Authors: Hiller Roman Alexander Friedrich , Griesinger Georg 
Published: April 2023

Purpose of review
To summarize and critically review the current knowledge on the effectiveness of lifestyle modifications for overweight women trying to conceive.

Recent findings
Overweight is associated with a wide spectrum of disorders, which may directly or indirectly affect fertility [from menstrual cycle irregularities to a lower chance of live birth after assisted reproductive technology (ART) treatment]. Weight loss through nonpharmaceutical lifestyle interventions is achievable. Weight loss can normalize menstrual cycle irregularities and can increase fecundability. Pregnancy-associated risks, such as gestational diabetes can be decreased by preconception weight reduction.

Summary
Weight loss through lifestyle changes (i.e., lower caloric intake and increased physical activity), may increase fecundability and may have a positive impact on the course of pregnancy, delivery, and neonatal outcomes. Accordingly, women should be motivated to reduce their weight before conception. However, the effectiveness of life-style intervention programs for women actively seeking medical support in achieving pregnancy has not convincingly been demonstrated. In the few randomized controlled trials (RCTs), selection bias for trial participation by patient motivation may have been present, yet participant attrition was still high and mean effects were small, casting doubts on the utility of such programs in routine care. Pharmacological and surgical intervention may be more effective or necessary complements to lifestyle intervention programs.