bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework
Authors: Loyer Gabriel , Reinharz Vladimir 
Published: January 2024

Abstract

Motivation
The prediction of RNA structure canonical base pairs from a single sequence, especially pseudoknotted ones, remains challenging in a thermodynamic models that approximates the energy of the local 3D motifs joining canonical stems. It has become more and more apparent in recent years that the structural motifs in the loops, composed of noncanonical interactions, are essential for the final shape of the molecule enabling its multiple functions. Our capacity to predict accurate 3D structures is also limited when it comes to the organization of the large intricate network of interactions that form inside those loops.

Results
We previously developed the integer programming framework RNA Motifs over Integer Programming (RNAMoIP) to reconcile RNA secondary structure and local 3D motif information available in databases. We further develop our model to now simultaneously predict the canonical base pairs (with pseudoknots) from base pair probability matrices with or without alignment. We benchmarked our new method over the all nonredundant RNAs below 150 nucleotides. We show that the joined prediction of canonical base pairs structure and local conserved motifs (i) improves the ratio of well-predicted interactions in the secondary structure, (ii) predicts well canonical and Wobble pairs at the location where motifs are inserted, (iii) is greatly improved with evolutionary information, and (iv) noncanonical motifs at kink-turn locations.

Availability and implementation
The source code of the framework is available at https://gitlab.info.uqam.ca/cbe/RNAMoIP and an interactive web server at https://rnamoip.cbe.uqam.ca/.
Prediction of cervical lymph node metastasis in differentiated thyroid cancer based on radiomics models
Authors: Mu Jingshi , Cao Yuan , Zhong Xiao , Diao Wei , Jia Zhiyun 
Published: January 2024

Abstract

Objective
The accurate clinical diagnosis of cervical lymph node metastasis plays an important role in the treatment of differentiated thyroid cancer (DTC). This study aimed to explore and summarize a more objective approach to detect cervical malignant lymph node metastasis of DTC via radiomics models.

Methods
PubMed, Web of Science, MEDLINE, EMBASE, and Cochrane databases were searched for all eligible studies. Articles using radiomics models based on ultrasound, computed tomography, or magnetic resonance imaging to assess cervical lymph node metastasis preoperatively were included. Characteristics and diagnostic accuracy measures were extracted. Bias and applicability judgments were evaluated by the revised QUADAS-2 tool. The estimates were pooled using a random-effects model. Additionally, the leave-one-out method was conducted to assess the heterogeneity.

Results
Twenty-nine radiomics studies with 6160 validation set patients were included in the qualitative analysis, and 11 studies with 3863 validation set patients were included in the meta-analysis. Four of them had an external independent validation set. The studies were heterogeneous, and a significant risk of bias was found in 29 studies. Meta-analysis showed that the pooled sensitivity and specificity for preoperative prediction of lymph node metastasis via US-based radiomics were 0.81 (95% CI, 0.73-0.86) and 0.87 (95% CI, 0.83-0.91), respectively.

Conclusions
Although radiomics-based models for cervical lymphatic metastasis in DTC have been demonstrated to have moderate diagnostic capabilities, broader data, standardized radiomics features, robust feature selection, and model exploitation are still needed in the future.

Advances in knowledge
The radiomics models showed great potential in detecting malignant lymph nodes in thyroid cancer.
Imaging characterization of paediatric tumours with the neurotrophic tyrosine receptor kinase fusion transcript
Authors: Hermann Anne-Laure , Lemelle Lauriane , Pierron Gaëlle , Gauthier Arnaud , Nicolas Nayla , Cardoen Liesbeth , Moalla Salma , Petit Philippe , Morel Baptiste , Ducou Le Pointe Hubert , Hassani Adnan , Fréneaux Paul , Guillemot Delphine , Carton Matthieu , Corradini Nadège , Rome Angélique , Castex Marie-Pierre , Defachelles Anne-Sophie , Schleiermacher Gudrun , Berlanga Pablo , Delattre Olivier , Orbach Daniel , Brisse Hervé J 
Published: January 2024

Abstract

Objectives
The neurotrophic tyrosine receptor kinase (NTRK) fusion transcript (FT) is a major genetic landmark of infantile fibrosarcoma (IFS) and cellular congenital mesoblastic nephroma (cCMN) but is also described in other tumours. The recent availability of NTRK-targeted drugs enhances the need for better identification. We aimed to describe the anatomic locations and imaging features of tumours with NTRK-FT in children.

Case series
Imaging characteristics of NTRK-FT tumours of 41 children (median age: 4 months; 63% &lt;1 year old; range: 0-188) managed between 2001 and 2019 were retrospectively analysed. The tumours were located in the soft tissues (n = 24, including 19 IFS), kidneys (n = 9, including 8 cCMN), central nervous system (CNS) (n = 5), lung (n = 2), and bone (n = 1). The tumours were frequently deep-located (93%) and heterogeneous (71%) with necrotic (53%) or haemorrhagic components (29%). Although inconstant, enlarged intratumoural vessels were a recurrent finding (70%) with an irregular distribution (63%) in the most frequent anatomical locations.

Conclusion
Paediatric NTRK-FT tumours mainly occur in infants with very variable histotypes and locations. Rich and irregular intra-tumoural vascularization are recurrent findings.

Advances in knowledge
Apart from IFS of soft tissues and cCMN of the kidneys, others NTRK-FT tumours locations have to be known, as CNS tumours. Better knowledge of the imaging characteristics may help guide the pathological and biological identification.
Incidence and outcomes of surgical pulmonary embolectomy in the UK
Authors: Argyriou Amerikos , Vohra Hunaid , Chan Jeremy , Ahmed Eltayeb Mohamed , Rajakaruna Cha , Angelini Gianni Davide , Fudulu Daniel Paul 
Published: January 2024

Abstract

Background
Surgical pulmonary embolectomy is rarely used for the treatment of massive acute pulmonary embolism. The aim of this study was to assess the incidence and outcomes of this operation by undertaking a retrospective analysis of a large national registry in the UK.

Methods
All acute pulmonary embolectomies performed between 1996 and 2018 were captured in the National Institute of Cardiovascular Outcomes Research central database. Trends in the number of operations performed during this interval and reported in-hospital outcomes were analysed retrospectively. Multivariable logistic regression was used to identify independent risk factors for in-hospital death.

Results
All 256 patients treated surgically for acute pulmonary embolism during the study interval were included in the analysis. Median age at presentation was 54 years, 55.9% of the patients were men, 48.0% had class IV heart failure symptoms, and 37.5% had preoperative cardiogenic shock. The median duration of bypass was 73 min, and median cross-clamp time was 19 min. Cardioplegic arrest was used in 53.1% of patients. The median duration of hospital stay was 11 days. The in-hospital mortality rate was 25%, postoperative stroke occurred in 5.4%, postoperative dialysis was required in 16%, and the reoperation rate for bleeding was 7.5%. Risk-adjusted multivariable analysis revealed cardiogenic shock (OR 2.54, 95% c.i. 1.05 to 6.21; P = 0.038), preoperative ventilation (OR 5.85, 2.22 to 16.35; P &lt; 0.001), and duration of cardiopulmonary bypass exceeding 89 min (OR 7.82, 3.25 to 20.42; P &lt; 0.001) as significant independent risk factors for in-hospital death.

Conclusion
Surgical pulmonary embolectomy is rarely performed in the UK, and is associated with significant mortality and morbidity. Preoperative ventilation, cardiogenic shock, and increased duration of bypass were significant predictors of in-hospital death.
An electronic nose can identify humans by the smell of their ear
Authors: Brener Stephanie , Snitz Kobi , Sobel Noam 
Published: January 2024

Abstract
Terrestrial mammals identify conspecifics by body odor. Dogs can also identify humans by body odor, and in some instances, humans can identify other humans by body odor as well. Despite the potential for a powerful biometric tool, smell has not been systematically used for this purpose. A question arising in the application of smell to biometrics is which bodily odor source should we measure. Breath is an obvious candidate, but the associated humidity can challenge many sensing devices. The armpit is also a candidate source, but it is often doused in cosmetics. Here, we test the hypothesis that the ear may provide an effective source for odor-based biometrics. The inside of the ear has relatively constant humidity, cosmetics are not typically applied inside the ear, and critically, ears contain cerumen, a potent source of volatiles. We used an electronic nose to identify 12 individuals within and across days, using samples from the armpit, lower back, and ear. In an identification setting where chance was 8.33% (1 of 12), we found that we could identify a person by the smell of their ear within a day at up to ~87% accuracy (~10 of 12, binomial P &lt; 10−5), and across days at up to ~22% accuracy (~3 of 12, binomial P &lt; 0.012). We conclude that humans can indeed be identified from the smell of their ear, but the results did not imply a consistent advantage over other bodily odor sources.
Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization
Authors: Deogharia Manisha , Venegas-Zamora Leslye , Agrawal Akanksha , Shi Miusi , Jain Abhinav K , McHugh Kevin J , Altamirano Francisco , Marian Ali J , Gurha Priyatansh 
Published: January 2024

AbstractAimsHuman pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.Methods and resultsKDM5A, B, and C proteins were mainly expressed in the early post-natal stages, and their expressions were progressively downregulated in the post-natal CMs and were absent in adult hearts and CMs. In contrast, KDM5 proteins were persistently expressed in the iPSC-CMs up to 60 days after the induction of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor, induced differential expression of 2372 genes, including upregulation of genes involved in fatty acid oxidation (FAO), OXPHOS, and myogenesis in the iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the cleavage under targets and release using nuclease assay showed enriched of the H3K4me3 peaks at the promoter regions of genes encoding FAO, OXPHOS, and sarcomere proteins. Consistent with the chromatin and gene expression data, KDM5 inhibition increased the expression of multiple sarcomere proteins and enhanced myofibrillar organization. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene and increased its RNA and protein levels. Knockdown of ESRRA in KDM5-C70-treated iPSC-CM suppressed expression of a subset of the KDM5 targets. In conjunction with changes in gene expression, KDM5 inhibition increased oxygen consumption rate and contractility in iPSC-CMs.ConclusionKDM5 inhibition enhances maturation of iPSC-CMs by epigenetically upregulating the expressions of OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
Asymptotic properties of endogeneity corrections using nonlinear transformations
Authors: Breitung Jörg , Mayer Alexander , Wied Dominik 
Published: January 2024

Summary
This paper studies the asymptotic properties of endogeneity corrections based on nonlinear transformations without external instruments, which were originally proposed by Park and Gupta (2012) and have become popular in applied research. In contrast to the original copula-based estimator, our approach is based on a nonparametric control function and does not require a conformably specified copula. Moreover, we allow for exogenous regressors, which may be (linearly) correlated with the endogenous regressor(s). We establish consistency, asymptotic normality, and validity of the bootstrap for the unknown model parameters. An empirical application on wage data of the US Current Population Survey demonstrates the usefulness of the method.
Clonal haematopoiesis of indeterminate potential and atrial fibrillation: an east Asian cohort study
Authors: Ahn Hyo-Jeong , An Hong Yul , Ryu Gangpyo , Lim Jiwoo , Sun Choonghyun , Song Han , Choi Su-Yeon , Lee Heesun , Maurer Taylor , Nachun Daniel , Kwon Soonil , Lee So-Ryoung , Lip Gregory Y H , Oh Seil , Jaiswal Siddhartha , Koh Youngil , Choi Eue-Keun 
Published: January 2024

Abstract

Background and Aims
Both clonal haematopoiesis of indeterminate potential (CHIP) and atrial fibrillation (AF) are age-related conditions. This study investigated the potential role of CHIP in the development and progression of AF.

Methods
Deep-targeted sequencing of 24 CHIP mutations (a mean depth of coverage = 1000×) was performed in 1004 patients with AF and 3341 non-AF healthy subjects. Variant allele fraction ≥ 2.0% indicated the presence of CHIP mutations. The association between CHIP and AF was evaluated by the comparison of (i) the prevalence of CHIP mutations between AF and non-AF subjects and (ii) clinical characteristics discriminated by CHIP mutations within AF patients. Furthermore, the risk of clinical outcomes—the composite of heart failure, ischaemic stroke, or death—according to the presence of CHIP mutations in AF was investigated from the UK Biobank cohort.

Results
The mean age was 67.6 ± 6.9 vs. 58.5 ± 6.5 years in AF (paroxysmal, 39.0%; persistent, 61.0%) and non-AF cohorts, respectively. CHIP mutations with a variant allele fraction of ≥2.0% were found in 237 (23.6%) AF patients (DNMT3A, 13.5%; TET2, 6.6%; and ASXL1, 1.5%) and were more prevalent than non-AF subjects [356 (10.7%); P &lt; .001] across the age. After multivariable adjustment (age, sex, smoking, body mass index, diabetes, and hypertension), CHIP mutations were 1.4-fold higher in AF [adjusted odds ratio (OR) 1.38; 95% confidence interval 1.10–1.74, P &lt; .01]. The ORs of CHIP mutations were the highest in the long-standing persistent AF (adjusted OR 1.50; 95% confidence interval 1.14–1.99, P = .004) followed by persistent (adjusted OR 1.44) and paroxysmal (adjusted OR 1.33) AF. In gene-specific analyses, TET2 somatic mutation presented the highest association with AF (adjusted OR 1.65; 95% confidence interval 1.05–2.60, P = .030). AF patients with CHIP mutations were older and had a higher prevalence of diabetes, a longer AF duration, a higher E/E′, and a more severely enlarged left atrium than those without CHIP mutations (all P &lt; .05). In UK Biobank analysis of 21 286 AF subjects (1297 with CHIP and 19 989 without CHIP), the CHIP mutation in AF is associated with a 1.32-fold higher risk of a composite clinical event (heart failure, ischaemic stroke, or death).

Conclusions
CHIP mutations, primarily DNMT3A or TET2, are more prevalent in patients with AF than non-AF subjects whilst their presence is associated with a more progressive nature of AF and unfavourable clinical outcomes.
Evaluation of data collection bias of third molar stages of mineralisation for age estimation in the living
Authors: de Oliveira Santos Inês , Baptista Isabel Poiares , da Silva Ricardo Henrique Alves , Cunha Eugénia 
Published: January 2024

Abstract
Age assessment of the living is a fundamental procedure in the process of human identification, in order to guarantee fair treatment of individuals, which has ethical, civil, legal, and medical repercussions. The careful selection of the appropriate methods requires evaluation of several parameters: accuracy, precision of the method, as well as its reproducibility. The approach proposed by Mincer et al. adapted from Demirjian et al. exploring third molar mineralisation, is one of the most frequently considered for age estimation of the living. Thus, this work aims to assess potential bias in the data collection when applying the classification stages for dental mineralisation adapted by Mincer et al. A total of 102 orthopantomographs, of clinical origin, belonging to individuals aged between 12 and 25 years ($ \bar{\textit x} $ = 20.12 years, SD = 3.49 years; 65 females, 37 males, all of Portuguese nationality) were included and a retrospective analysis performed by five observers with different levels of experience (high, average, and basic). The performance and agreement between five observers were evaluated using Weighted Cohen’s Kappa and the Intraclass Correlation Coefficient. To access the influence of impaction on third molar classification, variables were tested using ordinal logistic regression Generalised Linear Model. It was observed that there were variations in the number of teeth identified among the observers, but the agreement levels ranged from moderate to substantial (0.4–0.8). Upon closer examination of the results, it was observed that although there were discernible differences between highly experienced observers and those with less experience, the gap was not as significant as initially hypothesised, and a greater disparity between the classifications of the upper (0.24–0.49) and lower third molars (&gt;0.55) was observed. When bone superimposition is present, the classification process is not significantly influenced; however, variation in teeth angulation affects the assessment. The results suggest that with an efficient preparation, the level of experience as a factor can be overcome. Mincer and colleague's classification system can be replicated with ease and consistency, even though the classification of upper and lower third molars presents distinct challenges.
Genetic regulation of volatile production in two melon introgression line collections with contrasting ripening behavior
Authors: Mayobre Carlos , Santo Domingo Miguel , Özkan Elif Nur , Fernández-Borbolla Andrés , Ruiz-Lasierra Javier , Garcia-Mas Jordi , Pujol Marta 
Published: January 2024

Abstract
The importance of melon aroma in determining fruit quality has been highlighted in recent years. The fruit volatile profile is influenced by the type of fruit ripening. Non-climacteric fruits contain predominantly aldehydes, while climacteric fruits mainly produce esters. Several genes have been described to participate in volatile organic compounds (VOCs) biosynthesis pathways, but knowledge in this area is still incomplete. In this work we analysed the volatile profile of two reciprocal Introgression Line (IL) collections generated from a cross between ‘Piel de Sapo' (PS) and ‘Védrantais’ (VED) melons, differing in their aroma profile and ripening behaviour. SPME GC–MS was performed to identify genes responsible for VOCs formation. More than 1000 QTLs for many volatiles were detected taken together both populations. Introgressions on chromosomes 3, 5, 6, 7 and 8 modified ester-aldehyde balance and were correlated to ripening changes in both genetic backgrounds. Some previously identified QTLs for fruit ripening might be involved in these phenotypes, such as ETHQV8.1 on chromosome 8 and ETHQV6.3 on chromosome 6. PS alleles on chromosomes 2, 6, 10 and 11 were found to increase ester content when introgressed in VED melons. Terpenes showed to be affected by several genomic regions not related to ripening. In addition, several candidate genes have been hypothesized to be responsible for some of the QTLs detected. The analysis of volatile compounds in two reciprocal IL collections has increased our understanding of the relationship between ripening and aroma and offers valuable plant material to improve food quality in melon breeding programs.
Various combinations of living and deceased donors for lung retransplantation—a single institutional retrospective study
Authors: Ohsumi Akihiro , Tanaka Satona , Yamada Yoshito , Yutaka Yojiro , Hamaji Masatsugu , Nakajima Daisuke , Date Hiroshi 
Published: January 2024

Abstract

OBJECTIVES
Lung retransplantation has been performed as a treatment option mainly for chronic lung allograft dysfunction; however, the outcomes of lung retransplantation have been reported to be worse than those of primary lung transplantation. Because of the scarcity of deceased donors in our country, our lung transplant experience includes both living and deceased donors. Therefore, we have experienced lung retransplantation cases with various combinations of living and deceased donors. The aim of this study was to explore technical pitfalls and outcomes of lung retransplantation in this unique environment.

METHODS
We performed 311 lung transplantation procedures between April 2002 and October 2022. Eight lung retransplantation cases (2.6%) were analysed retrospectively.

RESULTS
At lung retransplantation, the age of the recipient patients ranged from 11 to 61 years (median, 33 years). The combinations of donor sources (primary lung transplantation/lung retransplantation) were as follows: 2 living/living, 2 deceased/living, 3 living/deceased and 1 deceased/deceased. Seven of 8 patients received lung retransplantation for chronic lung allograft dysfunction. Hospital death occurred in 2 patients (25.0%). The 1-, 3- and 5-year survival rates after lung retransplantation (n = 8) were 75.0%, 75.0% and 75.0%, respectively, while those after primary lung transplantation (n = 303) were 92.8%, 83.4% and 76.4%, respectively (P = 0.162).

CONCLUSIONS
Lung retransplantation with various combinations of living and deceased donors is a technically difficult but feasible procedure with acceptable outcomes.