bluuebunny/crossref_metadata_2025_split huggingface dataset:
RespirAnalyzer: an R package for analyzing data from continuous monitoring of respiratory signals
Authors: Zhang Teng , Dong Xinzheng , Wang Dandan , Huang Chen , Zhang Xiaohua Douglas 
Published: January 2024

Abstract

Motivation
The analysis of data obtained from continuous monitoring of respiratory signals (CMRS) holds significant importance in improving patient care, optimizing sports performance, and advancing scientific understanding in the field of respiratory health.

Results
The R package RespirAnalyzer provides an analytic tool specifically for feature extraction, fractal and complexity analysis for CMRS data. The package covers a wide and comprehensive range of data analysis methods including obtaining inter-breath intervals (IBI) series, plotting time series, obtaining summary statistics of IBI series, conducting power spectral density, multifractal detrended fluctuation analysis (MFDFA) and multiscale sample entropy analysis, fitting the MFDFA results with the extended binomial multifractal model, displaying results using various plots, etc. This package has been developed from our work in directly analyzing CMRS data and is anticipated to assist fellow researchers in computing the related features of their CMRS data, enabling them to delve into the clinical significance inherent in these features.

Availability and implementation
The package for Windows is available from both Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/RespirAnalyzer/index.html and GitHub: https://github.com/dongxinzheng/RespirAnalyzer.
ClusterV-Web: a user-friendly tool for profiling HIV quasispecies and generating drug resistance reports from nanopore long-read data
Authors: Su Junhao , Li Shumin , Zheng Zhenxian , Lam Tak-Wah , Luo Ruibang 
Published: January 2024

Abstract

Summary
Third-generation long-read sequencing is an increasingly utilized technique for profiling human immunodeficiency virus (HIV) quasispecies and detecting drug resistance mutations due to its ability to cover the entire viral genome in individual reads. Recently, the ClusterV tool has demonstrated accurate detection of HIV quasispecies from Nanopore long-read sequencing data. However, the need for scripting skills and a computational environment may act as a barrier for many potential users. To address this issue, we have introduced ClusterV-Web, a user-friendly web-based application that enables easy configuration and execution of ClusterV, both remotely and locally. Our tool provides interactive tables and data visualizations to aid in the interpretation of results. This development is expected to democratize access to long-read sequencing data analysis, enabling a wider range of researchers and clinicians to efficiently profile HIV quasispecies and detect drug resistance mutations.

Availability and implementation
ClusterV-Web is freely available and open source, with detailed documentation accessible at http://www.bio8.cs.hku.hk/ClusterVW/. The standalone Docker image and source code are also available at https://github.com/HKU-BAL/ClusterV-Web.
HIVseqDB: a portable resource for NGS and sample metadata integration for HIV-1 drug resistance analysis
Authors: Ssekagiri Alfred , Jjingo Daudi , Bbosa Nicholas , Bugembe Daniel L , Kateete David P , Jordan I King , Kaleebu Pontiano , Ssemwanga Deogratius 
Published: January 2024

Abstract

Summary
Human immunodeficiency virus (HIV) remains a public health threat, with drug resistance being a major concern in HIV treatment. Next-generation sequencing (NGS) is a powerful tool for identifying low-abundance drug resistance mutations (LA-DRMs) that conventional Sanger sequencing cannot reliably detect. To fully understand the significance of LA-DRMs, it is necessary to integrate NGS data with clinical and demographic data. However, freely available tools for NGS-based HIV-1 drug resistance analysis do not integrate these data. This poses a challenge in interpretation of the impact of LA-DRMs, mainly for resource-limited settings due to the shortage of bioinformatics expertise. To address this challenge, we present HIVseqDB, a portable, secure, and user-friendly resource for integrating NGS data with associated clinical and demographic data for analysis of HIV drug resistance. HIVseqDB currently supports uploading of NGS data and associated sample data, HIV-1 drug resistance data analysis, browsing of uploaded data, and browsing and visualizing of analysis results. Each function of HIVseqDB corresponds to an individual Django application. This ensures efficient incorporation of additional features with minimal effort. HIVseqDB can be deployed on various computing environments, such as on-premises high-performance computing facilities and cloud-based platforms.

Availability and implementation
HIVseqDB is available at https://github.com/AlfredUg/HIVseqDB. A deployed instance of HIVseqDB is available at https://hivseqdb.org.
Predicting axillary metastasis in breast cancer using lymphatic contrast-enhanced ultrasound-guided fine-needle aspiration of one lymph node
Authors: Zhuang Lingling , Liu Jun , Xu Xiaoxiao , Sun Xing , Li Fan , Shi Qiusheng , Zhang Weituo , Du Lianfang , Jin Lifang 
Published: January 2024

Abstract

Objectives
Fine-needle aspiration (FNA) is a microinvasive method to diagnose lymph nodes. This study aims to determine the capability of lymphatic contrast-enhanced ultrasound (LCEUS)-guided FNA in predicting the axillary metastasis with the target of one lymph node (LN) in patients with breast cancer.

Methods
LCEUS was prospectively performed in 105 patients with breast cancer. The most suspicious LN was targeted based on the characters of LCEUS. FNA was performed in the LN, followed by localization using a guide wire. The detection of lymph cells and/or tumour cells was recognized as a puncture success. Cytologic diagnosis was compared with histologic diagnosis of wire-marked LN for diagnosing accuracy and compared with histologic diagnosis of axillary LNs for predicting accuracy.

Results
LCEUS-guided FNA was performed in all 105 female patients who underwent axillary dissection. The puncture success rates were 74.3%, 91.4%, and 97.1% for three sequential groups (P = .010). In diagnosing LN metastasis, the sensitivity, specificity, and accuracy values of LCEUS-guided FNA were 89.7%, 100%, and 95.7%, respectively. In predicting axillary metastasis, the sensitivity, specificity, and accuracy values of LCEUS-guided FNA were 81.4%, 100%, and 91.3%, respectively.

Conclusions
The microinvasive LCEUS-guided FNA of one lymph node can be an accurate method and may help predict axillary metastasis in patients with breast cancer.

Advances in knowledge
This study presented that LCEUS combined with FNA would be practical in clinic. The characters of LCEUS could indicate the suspicious LNs and promote the accuracy in predicting axillary metastasis.
Mal-positioned nasogastric feeding tubes: are medical students safe to identify them?
Authors: Chew Cindy , O’Dwyer Patrick J , Young David , Banziger Carina , Hope Sarah , Rodolfo Sana , Obaro Anu E 
Published: January 2024

Abstract

Objectives
Nasogastric tube (NGT) placement is listed against Clinical Imaging in the upcoming Medical Licensing Assessment—compulsory for every graduating UK medical student from 2025. This study aims to establish the ability of medical students to correctly identify the position of an NGT on Chest X-ray (CXR) and to evaluate a learning tool to improve student outcome in this area.

Methods
Fourth-year (MB4) and fifth-year (MB5) medical students were invited to view 20 CXRs with 14 correctly sited and 6 mal-positioned NGT. MB5 students (Intervention) were exposed to an online interactive learning tool, with MB4 students kept as control. One week later, both groups of students were invited to view 20 more CXRs for NGT placement.

Results
Only 12 (4.8%) of 249 MB5 students and 5 (3.1%) of 161 MB4 students correctly identified all the NGTs on CXRs. The number of students misidentifying 1 or more mal-positioned NGT as “safe to feed” was 129 (51.8%) for MB5 and 76 (47.2%) for MB4 students. This improved significantly (P &lt; .001) following exposure to the learning tool with 58% scoring all CXRs correctly, while 28% scored 1 or more mal-positioned NGT incorrectly. Students struggled to determine if the NGT tip had adequately passed into the stomach. However, they failed to identify an NG tube in the lung (“never event”) in just one out of 1,108 opportunities.

Conclusion
Medical students’ ability to determine if the NGT was in the stomach remains suboptimal despite exposure to over 60 CXRs. Feeding NGT should be formally reported before use.

Advances in knowledge
This is the first attempt at quantifying graduating medical students’, and by inference junior doctors’, competence in safely identifying misplaced nasogastric feeding tubes. An online, experiential learning resource significantly improved their ability.
Deep learning for acute rib fracture detection in CT data: a systematic review and meta-analysis
Authors: Lopez-Melia Manel , Magnin Virginie , Marchand-Maillet Stéphane , Grabherr Silke 
Published: January 2024

Abstract

Objectives
To review studies on deep learning (DL) models for classification, detection, and segmentation of rib fractures in CT data, to determine their risk of bias (ROB), and to analyse the performance of acute rib fracture detection models.

Methods
Research articles written in English were retrieved from PubMed, Embase, and Web of Science in April 2023. A study was only included if a DL model was used to classify, detect, or segment rib fractures, and only if the model was trained with CT data from humans. For the ROB assessment, the Quality Assessment of Diagnostic Accuracy Studies tool was used. The performance of acute rib fracture detection models was meta-analysed with forest plots.

Results
A total of 27 studies were selected. About 75% of the studies have ROB by not reporting the patient selection criteria, including control patients or using 5-mm slice thickness CT scans. The sensitivity, precision, and F1-score of the subgroup of low ROB studies were 89.60% (95%CI, 86.31%-92.90%), 84.89% (95%CI, 81.59%-88.18%), and 86.66% (95%CI, 84.62%-88.71%), respectively. The ROB subgroup differences test for the F1-score led to a p-value below 0.1.

Conclusion
ROB in studies mostly stems from an inappropriate patient and data selection. The studies with low ROB have better F1-score in acute rib fracture detection using DL models.

Advances in knowledge
This systematic review will be a reference to the taxonomy of the current status of rib fracture detection with DL models, and upcoming studies will benefit from our data extraction, our ROB assessment, and our meta-analysis.
Imaging spectrum and complications of otogenic infections: insights into delayed diagnosis
Authors: Lo Eugene Sean , Kwok Hoi Ming , Pan Nin Yuan 
Published: January 2024

Abstract
Skull base osteomyelitis (SBO) is a late manifestation of complicated otogenic infections that presents a diagnostic challenge. Delayed or missed diagnoses lead to high morbidity and mortality and can be attributed to non-specific symptoms, subtle early radiologic findings, radiologic mimicry of nasopharyngeal carcinoma (NPC), and under-recognition from clinician and radiologists. This pictorial review aims to emphasize on early imaging recognition and distinction between SBO and NPC.
Changes in lumbar muscle diffusion tensor indices with age
Authors: Weedall Andrew D , Dallaway Alexander , Hattersley John , Diokno Michael , Hutchinson Charles E , Wilson Adrian J , Wayte Sarah C 
Published: January 2024

Abstract

Objective
To investigate differences in diffusion tensor imaging (DTI) parameters and proton density fat fraction (PDFF) in the spinal muscles of younger and older adult males.

Methods
Twelve younger (19-30 years) and 12 older (61-81years) healthy, physically active male participants underwent T1W, T2W, Dixon and DTI of the lumbar spine. The eigenvalues (λ1, λ2, and λ3), fractional anisotropy (FA), and mean diffusivity (MD) from the DTI together with the PDFF were determined in the multifidus, medial and lateral erector spinae (ESmed, ESlat), and quadratus lumborum (QL) muscles. A two-way ANOVA was used to investigate differences with age and muscle and t-tests for differences in individual muscles with age.

Results
The ANOVA gave significant differences with age for all DTI parameters and the PDFF (P &lt; .01) and with muscle (P &lt; .01) for all DTI parameters except for λ1 and for the PDFF. The mean of the eigenvalues and MD were lower and the FA higher in the older age group with differences reaching statistical significance for all DTI measures for ESlat and QL (P &lt; .01) but only in ESmed for λ3 and MD (P &lt; .05).

Conclusions
Differences in DTI parameters of muscle with age result from changes in both in the intra- and extra-cellular space and cannot be uniquely explained in terms of fibre length and diameter.

Advances in knowledge
Previous studies looking at age have used small groups with uneven age spacing. Our study uses two well defined and separated age groups.
Legacies of salient environmental experiences—insights from chemosensation
Authors: Dias Brian G 
Published: January 2024

Abstract
Evidence for parental environments profoundly influencing the physiology, biology, and neurobiology of future generations has been accumulating in the literature. Recent efforts to understand this phenomenon and its underlying mechanisms have sought to use species like rodents and insects to model multi-generational legacies of parental experiences like stress and nutritional exposures. From these studies, we have come to appreciate that parental exposure to salient environmental experiences impacts the cadence of brain development, hormonal responses to stress, and the expression of genes that govern cellular responses to stress in offspring. Recent studies using chemosensory exposure have emerged as a powerful tool to shed new light on how future generations come to be influenced by environments to which parents are exposed. With a specific focus on studies that have leveraged such use of salient chemosensory experiences, this review synthesizes our current understanding of the concept, causes, and consequences of the inheritance of chemosensory legacies by future generations and how this field of inquiry informs the larger picture of how parental experiences can influence offspring biology.
Impact of HLA-DQA1*05 Genotype in Immunogenicity and Failure to Treatment with Tumour Necrosis Factor-alpha Antagonists in Inflammatory Bowel Disease: A Systematic Review and Meta-analysis
Authors: Rodríguez-Alcolado Leticia , Grueso-Navarro Elena , Arias Ángel , Lucendo Alfredo J , Laserna-Mendieta Emilio J 
Published: January 2024

Abstract

Background
HLA-DQA1*05 carriage has been associated with an increased risk of immunogenicity in patients with immune-mediated inflammatory diseases treated with tumour necrosis factor-alpha [TNF-a] antagonists. Results have shown an inconsistent association with a loss of response [LOR] in patients with inflammatory bowel disease [IBD], which could be modified when using proactive optimisation and association with immunomodulatory drugs.

Aims
To define the association of HLA-DQA1*05 on anti-drug antibody development and loss of response [LOR] to anti-TNF-a in IBD.

Methods
We searched MEDLINE, EMBASE, and SCOPUS, for the period up to August 2023, to identify studies reporting the risk of immunogenicity and/or LOR in IBD patients with HLA-DQA1*05 genotype.

Results
A total of 24 studies comprising 12 papers, 11 abstracts and one research letter, with a total of 5727 IBD patients, were included. In a meta-analysis of 10 studies [2984 patients; 41.9% with HLA-DQA1*05 genotype], HLA-DQA1*05 carriers had higher risk of immunogenicity compared with non-carriers (risk ratio, 1.54; 95% confidence interval [CI], 1.23 − 1.94; I2 = 62%) [low certainty evidence]. Lack of therapeutic drug monitoring [TDM] increased immunogenicity in the presence of risk human leukocyte antigen [HLA] [risk ratio 1.97; 95% CI, 1.35 − 2.88; I2 = 66%], whereas proactive TDM revoked this association [very low certainty of evidence]. A meta-analysis of six studies [765 patients] found that risk for secondary LOR was higher among HLA-DQA1*05 carriers [hazard ratio 2.21; 95% CI, 1.69 − 2.88; I2 = 0%] [very low certainty evidence], although definition and time to assessment varied widely among studies.

Conclusion
HLA-DQA1*05 carriage may be associated with an increased risk of immunogenicity and secondary LOR in IBD patients treated with TNF-a antagonists.
Effects of sodium-glucose co-transporter 2 inhibitors on heart failure events in chronic kidney disease: a systematic review and meta-analysis
Authors: Theodorakopoulou Marieta P , Alexandrou Maria-Eleni , Tsitouridis Alexandros , Kamperidis Vasileios , Pella Eva , Xanthopoulos Andrew , Ziakas Antonios , Triposkiadis Filippos , Vassilikos Vassilios , Papagianni Aikaterini , Sarafidis Pantelis 
Published: January 2024

Abstract

Aims
Sodium-glucose co-transporter 2 (SGLT-2) inhibitors significantly reduce the risk for hospitalizations for heart failure (HF) in patients with diabetes, and HF; findings in patients with chronic kidney disease (CKD) are not uniform. We aimed to perform a meta-analysis exploring the effect of SGLT-2 inhibitors on HF events in patients with CKD and across subgroups defined by baseline kidney function.

Methods and results
A systematic search in major electronic databases was performed. Randomized controlled trials (RCTs) providing data on the effect of SGLT-2 inhibitors on the primary outcome, time to hospitalization or urgent visit for worsening HF in patients with prevalent CKD at baseline or across subgroups stratified by baseline estimated glomerular-filtration-rate (eGFR) were included. Twelve studies (n = 89,191 participants) were included in the meta-analysis. In patients with CKD, treatment with SGLT-2 inhibitors reduced the risk for HF events by 32% compared to placebo [hazard ratio (HR) 0.68; 95% confidence interval (CI) 0.63–0.73]. Reduction in HF events with SGLT-2 inhibitors was more prominent in patients with eGFR &lt;60 ml/min/1.73 m2 (HR 0.68; 95% CI 0.62–0.74) than in those with eGFR ≥60 ml/min/1.73 m2 (HR 0.76; 95% CI 0.69–0.83). Subgroup analysis according to type of SGLT-2 inhibitor showed a consistent treatment effect across all studied agents (p-subgroup-analysis = 0.44). Sensitivity analysis including data from studies including only diabetic patients showed an even more pronounced effect in eGFR subgroup &lt;60 ml/min/1.73 m2 (HR 0.62; 95% CI 0.54–0.70).

Conclusion
Treatment with SGLT-2 inhibitors led to a significant reduction in HF events in patients with CKD. Such findings may change the landscape of prevention of HF events in patients with advanced CKD.
PROSPERO Registration number CRD42022382857.
Morphological risk of acute type A aortic dissection in the mildly to moderately dilated aorta
Authors: Sun Lianjie , Li Haoyou , Feng Xiangzhen , Li Xiao , Wang Guoqing , Sun Jianchao , Zhang Xiaoming , Zhang Wenfeng , Wang Jianxun , Niu Zhaozhuo , Liu Gaoli 
Published: January 2024

Abstract

OBJECTIVES
This study aimed to analyse and determine the role of aortic length and curvature in the pathogenesis of acute type A aortic dissection (ATAAD) with ascending aortic diameters (AADs) &lt;5 cm.

METHODS
We reviewed the clinical and imaging data of patients with ATAAD (n = 201) and ascending aortic dilation (n = 83). Thoracic aortic bending index (TABI) was used to quantify aortic curvature and analyse its role in ATAAD below the diameter risk threshold.

RESULTS
The AAD was &lt;5.0 and &lt;4.0 cm in 78% and 37% of patients with ATAAD, respectively. The median ascending aortic length (AAL) was 104.6 mm (Q1–Q3, 96.5–113.6 mm), and in 62.7% of patients, it was &lt;11 cm. The median TABI was 14.99 mm/cm (Q1–Q3, 14.18–15.86 mm/cm). Patients with ATAAD and those with aortic dilation were matched for AAD, age, sex, height and other clinical factors. After matched, the dissection group had higher AALs (median, 102.9 mm; Q1–Q3, 96.0–112.5 mm vs median, 88.2 mm; Q1–Q3, 83.7–95.9 mm; P &lt; 0.001) and TABI (median, 14.84 mm/cm; Q1–Q3, 14.06–15.83 mm/cm vs median, 13.55 mm/cm; Q1–Q3, 13.03–14.28 mm/cm; P &lt; 0.001). According to the regression analysis, the area under the curve required to distinguish patients with ATAAD from those with aortic dilation was 0.831 in AAL, 0.837 in TABI and 0.907 when AAL was combined with TABI.

CONCLUSIONS
The patients with ATAAD had higher AAL and TABI than those with aortic dilation. The combination of TABI and AAL might be a potential morphological marker for determining ATAAD risk below the current aortic diameter risk threshold.
Modified transmanubrial approach for complicated type 1 cervical rib resection requiring subclavian artery reconstruction
Authors: Petrella Francesco , Rossi Luca , Gatto Arianna , Segramora Vittorio Maria , Del Bene Massimo , Froio Alberto 
Published: January 2024

Abstract
The transmanubrial musculoskeletal sparing approach (TMA) is commonly used for resecting apical lung tumours with vascular involvement. Non-neoplastic conditions which might require surgical exploration of the thoracic outlet include the ‘cervical rib’, a clinical condition consisting of an additional rib forming above the first rib and growing from the base of the neck just above the clavicle. Type 1 cervical rib—when a complete cervical rib articulates with the first rib or manubrium of the sternum—is the most challenging scenario where the subclavian artery can be damaged by continuous compression due to the narrow space between clavicle, first rib and supernumerary cervical rib, requiring prosthetic reconstruction of the involved tract. Here, we describe a modified TMA in which the incision in the neck is conducted posteriorly to the sternocleidomastoid muscle, thus allowing safe dissection of the superior and middle trunk of the brachial plexus.
A semblance-based microseismic event detector for DAS data
Authors: Porras Juan , Pecci Davide , Bocchini Gian Maria , Gaviano Sonja , De Solda Michele , Tuinstra Katinka , Lanza Federica , Tognarelli Andrea , Stucchi Eusebio , Grigoli Francesco 
Published: January 2024

SUMMARY
Distributed acoustic sensing (DAS) is becoming increasingly popular in microseismic monitoring operations. This data acquisition technology converts fibre-optic cables into dense arrays of seismic sensors that can sample the seismic wavefield produced by active or passive sources with a high spatial density, over distances ranging from a few hundred metres to tens of kilometres. However, standard microseismic data analysis procedures have several limitations when dealing with the high spatial (intersensor spacing up to submetre scale) sampling rates of DAS systems. Here, we propose a semblance-based seismic event detection method that fully exploits the high spatial sampling of the DAS data. The detector identifies seismic events by computing waveform coherence of the seismic wavefield along geometrical hyperbolic trajectories for different curvatures and positions of the vertex, which are completely independent from external information (i.e. velocity models). The method detects a seismic event when the coherence values overcome a given threshold and satisfies our clustering criteria. We first validate our method on synthetic data and then apply it to real data from the FORGE geothermal experiment in Utah, USA. Our method detects about two times the number of events obtained with a standard method when applied to 24 hr of data.