bluuebunny/crossref_metadata_2025_split huggingface dataset:
From RNA sequencing measurements to the final results: A practical guide to navigating the choices and uncertainties of gene set analysis
Authors: Wünsch Milena , Sauer Christina , Callahan Patrick , Hinske Ludwig Christian , Boulesteix Anne‐Laure 
Published: February 2024

AbstractGene set analysis (GSA), a popular approach for analyzing high‐throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last years, a multitude of methods have been developed for this task. However, clear guidance is lacking: choosing the right method is the first hurdle a researcher is confronted with. No less challenging than overcoming this so‐called method uncertainty is the procedure of preprocessing, from knowing which steps are required to selecting a corresponding approach from the plethora of valid options to create the accepted input object (data preprocessing uncertainty), with clear guidance again being scarce. Here, we provide a practical guide through all steps required to conduct GSA, beginning with a concise overview of a selection of established methods, including Gene Set Enrichment Analysis and Database for Annotation, Visualization, and Integrated Discovery (DAVID). We thereby lay a special focus on reviewing and explaining the necessary preprocessing steps for each method under consideration (e.g., the necessity of a transformation of the RNA sequencing data)—an essential aspect that is typically paid only limited attention to in both existing reviews and applications. To raise awareness of the spectrum of uncertainties, our review is accompanied by an extensive overview of the literature on valid approaches for each step and illustrative R code demonstrating the complex analysis pipelines. It ends with a discussion and recommendations to both users and developers to ensure that the results of GSA are, despite the above‐mentioned uncertainties, replicable and transparent.This article is categorized under:
Statistical and Graphical Methods of Data Analysis > Analysis of High Dimensional Data
Data: Types and Structure > Data Preparation and Processing
Applications of Computational Statistics > Genomics/Proteomics/Genetics
A trans‐Canadian positive deviance seminar for paraesophageal hernia surgery: Reporting national postoperative outcomes and consensus recommendations
Authors: Tankel James , Safieddine Najib , Malthaner Rick , French Danny , Johnston Brian , Finley Christian , Darling Gail , Ferri Lorenzo , Seely Andrew , Gowing Stephen 
Published: February 2024

AbstractBackgroundThe incidence of adverse events (AEs) and length of stay (LOS) varies significantly following paraesophageal hernia surgery. We performed a Canadian multicenter positive deviance (PD) seminar to review individual center and national level data and establish holistic perioperative practice recommendations.MethodsA national virtual PD seminar was performed in October 2021. Recent best evidence focusing on AEs and LOS was presented. Subsequently, anonymized center‐level AE and LOS data collected between 01/2017 and 01/2021 from a prospective, web‐based database that tracks postoperative outcomes was presented. The top two performing centers with regards to these metrics were chosen and surgeons from these hospitals discussed elements of their treatment pathways that contributed to these outcomes. Consensus recommendations were then identified with participants independently rating their level of agreement.ResultsTwenty‐eight surgeons form 8 centers took part in the seminar across 5 Canadian provinces. Of the 680 included patients included, Clavien‐Dindo grade I and II/III/IV/V complications occurred in 121/39/12/2 patients (17.8%/5.7%/1.8%/0.3%). Respiratory complications were the most common (effusion 12/680, 1.7% and pneumonia 9/680, 1.3%). Esophageal and gastric perforation occurred in 7 and 4/680, (1.0% and 0.6% respectively). Median LOS varied significantly between institutions (1 day, range 1‐3 vs. 7 days, 3‐8, p < 0.001). A strong level of agreement was achieved for 10/12 of the consensus statements generated.ConclusionPD seminars provide a supportive forum for centers to review best evidence and experience and generate recommendations based on expert opinion. Further research is ongoing to determine if this approach effectively accomplishes this objective.
Conformal quantum mechanics, holomorphic factorisation, and ultra-spinning black holes
Authors: Dorey Nick , Mouland Rishi 
Published: February 2024

Abstract
We study a limit in which a relativistic CFT reduces to conformal quantum mechanics, and relate the partition functions of the two theories. When the initial CFT is holographic, our limit coincides with an ultra-spinning limit in the gravity dual. We therefore propose that ultra-spinning black holes are dual to an appropriate ensemble in finite-dimensional conformal quantum mechanics. The limit is studied in detail for SCFTs in four and six dimensions. These theories have a superconformal index which can be computed by gluing together two or more blocks. Applying our limit to the index effectively isolates a single such block. Our results therefore suggest that ultra-spinning black holes play the role of blocks in the gravitational dual of holomorphic factorisation.
Optimization and improving of the production capacity of a flexible tyre painting cell
Authors: Santos Adriano A. , Pereira Filipe , Felgueiras Carlos 
Published: February 2024

Abstract
Optimization of industrial processes is a constant concern and a main task for many companies in several industry sectors. Based on optimized solutions, the company can decrease manufacturing costs, lead times or, more generally, increase benefit. However, when developing a new process, you must be sure that the new solution will add more value to the initial solution. This, among many others, is one of the main reasons why companies opt, in addition to experimentation, for the use of tools that allow for the virtual prototyping, simulation, and integration of complex and sophisticated processes. Experimentation requires approximation testing, searching for the ideal values of quantity, temperature, etc.; simulation provides industrial processes with test support ranging from flows to robotic systems such as the intelligent software. This simulation software allows to develop programs, add Computer Aided Design (CAD) layouts, and simulate the cycle times of the different tasks to be performed. In this paper, an experimental approach is presented with atomization and fan spray pressure as the study basis and a simulation of the robot-based handling solution used in a tyre production line. The result is an improvement of the painting process, optimisation of the amount of fluid deposited on the tyre, of the processed product, as well as of the running times of the robot.
A modified pull-through approach with a pedicled bone flap for oral and oropharyngeal cancer resection: a feasibility study
Authors: Neckel Norbert , Neckel Peter H. , Hirt Bernhard , Doll Christian , Hofmann Elena , Nahles Susanne , Heiland Max , Kreutzer Kilian , Koerdt Steffen 
Published: February 2024

Abstract
Purpose
Compromised swallowing, speaking, and local complications are the major disadvantages of established approaches to the posterior tongue and oropharynx. The mandibular split involves an esthetically unpleasant bipartition of the lower lip and is prone to bony non-union or sequestration. The conventional pull-through technique on the other hand lacks the secure reattachment of the lingually released soft tissues.

Methods
The feasibility of a new modified pull-through approach was tested on three anatomical specimens. CAD/CAM cutting guides were used to design a retentive bone flap to properly refixate the genioglossus and geniohyoid muscles after the procedure. The radiographic assessment and treatment planning was performed on 12 cadavers. The entire procedure was tested surgically via dissection in three of those cases. This procedure was then applied in a clinical case.

Results
Precise repositioning and dynamic compression of bony segments was possible reproducibly and without injury to adjacent structures. In all dissected cases, a median lingual foramen was found and in two cases vessels entering it could be dissected Radiologic anatomical landmarks were sufficient in all 12 cases to perform the clinical planning procedure. Clinically, the osteotomized segment demonstrated good blood supply and plateless repositioning was verified postoperatively via cone beam scan.

Conclusion
The method presented is safe and easy to perform. Individual cutting guides improve the safety and accuracy of the procedure, potentially eliminating the need for osteosynthesis. We provide the anatomical and radiologic basis for clinical evaluation of this pedicled bone flap procedure and present the clinical application of this modified pull-through approach.
Umfrage zur blutverdünnenden Therapie bei Patienten mit altersabhängiger Makuladegeneration
Authors: Weber Constance , Tedt Jezabel , Husser Oliver , Holz Frank G. , Liegl Raffael 
Published: February 2024

Zusammenfassung
Hintergrund
Patienten mit altersabhängiger Makuladegeneration (AMD) erhalten häufig zeitgleich systemische blutverdünnende Medikamente. Diese erhöhen bekanntermaßen das Risiko für schwere Blutungen, unter anderem auch im Rahmen der AMD, sodass es zu extensiven subretinalen Blutungen kommen kann.

Ziel der Arbeit
In dieser Studie soll untersucht werden, wie hoch der Anteil an Patienten mit AMD und blutverdünnender Therapie ist und welche blutverdünnenden Medikamente eingenommen werden.

Methoden
Diese Umfrage wurde prospektiv an der Universitäts-Augenklinik Bonn durchgeführt. Freiwillige wurden in der Netzhaut-Sprechstunde sowie der Sprechstunde für intravitreale Injektionen (IVOM) rekrutiert.

Ergebnisse
Insgesamt konnten 178 Fragebögen von 178 Patienten ausgewertet werden, bei denen der Fragebogen vollständig ausgefüllt wurde. Das Durchschnittsalter betrug 81,7 Jahre (58 bis 100); 101 Patienten (57,7 %) nahmen eine blutverdünnende Therapie ein. Die Mehrheit der Patienten nahm Thrombozytenaggregationshemmer (n = 59; 58,4 %), insbesondere ASS (n = 55; 54,5 %) ein. Direkte orale Antikoagulanzien (DOAK) wurden von 33 Patienten (32,7 %) eingenommen, darunter am häufigsten Apixaban (17,8 %). Vitamin-K-Antagonisten (VKA) wurde von 4 Patienten (4 %) eingenommen. Als häufigster Grund für eine blutverdünnende Therapie wurde ein VHF benannt (n = 32, 31,7 %), gefolgt von einer Stentimplantation (n = 20, 19,8 %) und einem Schlaganfallgeschehen (n = 12, 11,9 %); 13 Patienten (12,9 %) wussten nicht, warum sie eine blutverdünnende Therapie einnahmen. Bei 31 Patienten (30,7 %) lag eine nicht eindeutig nachvollziehbare Indikation vor.

Diskussion
In unserer Kohorte nahm ein Großteil der Patienten mit AMD eine blutverdünnende Therapie ein. Nicht bei jedem Patienten liegt jedoch eine eindeutige Indikation zur Einnahme vor. Hier sollte die Einnahme aufgrund des erhöhten Blutungsrisikos in enger Zusammenarbeit mit Hausärzten und Kardiologen kritisch hinterfragt werden.
Clinical and serological characterization of acute pleuropericarditis suggests an autoinflammatory pathogenesis and highlights risk factors for recurrent attacks
Authors: Kaudewitz Dorothee , John Lukas , Meis Jan , Frey Norbert , Lorenz Hanns-Martin , Leuschner Florian , Blank Norbert 
Published: February 2024

Abstract
Purpose
We describe the manifestations and course of patients with pleuropericarditis (PP). Serum parameters were analyzed to evaluate the contribution of autoimmune and autoinflammatory mechanisms to PP pathogenesis. Finally, we outline risk factors for recurrent PP attacks.

Methods
Electronic medical records of the University Hospital Heidelberg were screened for PP diagnosis between the years 2009 and 2021. A total of 164 patients were detected and compared to patients suffering from systemic lupus erythematosus (SLE)-associated PP. Follow-up data were collected until January 2023.

Results
In 57.3% of a total of 164 PP cases, no trigger was identified (idiopathic PP). The clinical manifestations were similar in subgroups with different triggers (idiopathic, post-cardiac injury and post-infectious). None of the patients in the idiopathic-PP (i-PP) group fulfilled the diagnostic criteria of an autoimmune disease and the i-PP group could be clearly discriminated by clinical, epidemiological and serological means from the control cohort of SLE-associated PP. After a median follow-up of 1048 days, the majority of PP patients (72.7%) had at least one PP relapse. Univariate analyses showed that CRP, SAA (serum amyloid A), troponin T, NT-BNP and post-cardiac injury were negatively correlated, while the presence of fever and an idiopathic trigger were positively correlated with recurrence of PP. Multivariate analyses showed that fever, an idiopathic trigger and low SAA values were risk factors for PP recurrence.

Conclusion
This study highlights that most cases of PP are idiopathic and PP cases with various triggers have an identical clinical phenotype. Our data suggest that the clinical, epidemiological and serological characteristics of idiopathic PP considerably differ from patients with PP caused by autoimmune disease like SLE. We further demonstrate that PP has a high risk of recurrence and identify factors associated with this risk, allowing for a targeted secondary prophylaxis.

Graphical Abstract
Frailty, periinterventional complications and outcome in patients undergoing percutaneous mitral and tricuspid valve repair
Authors: Schäfer Matthieu , Nöth Hannah , Metze Clemens , Iliadis Christos , Körber Maria Isabel , Halbach Marcel , Baldus Stephan , Pfister Roman 
Published: February 2024

Abstract
Background
Frailty is common in elderly and multimorbid patients and associated with increased vulnerability to stressors.

Methods
In a single centre study frailty according to Fried criteria was assessed in consecutive patients before transcatheter mitral and tricuspid valve repair. Postprocedural infections, blood transfusion and bleeding and renal failure were retrospectively assessed from records. Median follow-up time for survival was 560 days (IQR: 363 to 730 days).

Results
90% of 626 patients underwent mitral valve repair, 5% tricuspid valve repair, and 5% simultaneous mitral and tricuspid valve repair. 47% were classified as frail. Frailty was associated with a significantly increased frequency of bleeding (16 vs 10%; p = 0.016), blood transfusions (9 vs 3%; p =  < 0.001) and infections (18 vs 10%; p = 0.006), but not with acute kidney injury (20 vs 20%; p = 1.00). Bleeding and infections were associated with longer hospital stays, with a more pronounced effect in frail patients (interaction test p < 0.05, additional 3.2 and 4.1 days in frail patients, respectively). Adjustment for the occurrence of complications did not attenuate the increased risk of mortality associated with frailty (HR 2.24 [95% CI 1.62–3.10]; p < 0.001).

Conclusions
Bleeding complications and infections were more frequent in frail patients undergoing transcatheter mitral and tricuspid valve repair and partly explained the longer hospital stay. Albeit some of the complications were associated with higher long-term mortality, this did not explain the strong association between frailty and mortality. Further research is warranted to explore interventions targeting periprocedural complications to improve outcomes in this vulnerable population.

Graphical abstract
Comparison of Arctic Front Advance Pro and POLARx cryoballoons for ablation therapy of atrial fibrillation: an intraprocedural analysis
Authors: Knappe Vincent , Lahrmann Caroline , Funken Maximilian , Zietzer Andreas , Gestrich Christopher , Nickenig Georg , Schrickel Jan W. , Beiert Thomas 
Published: February 2024

Abstract

Introduction
Cryoballoon (CB) ablation has become a popular method for pulmonary vein isolation (PVI) in atrial fibrillation (AF) treatment. This study aimed to compare the intraprocedural ablation characteristics of two cryoballoons, Arctic Front Advance Pro™ (AFA-Pro, Medtronic) and POLARx™ (Boston Scientific).

Methods and results
In this retrospective single-center study, 230 symptomatic paroxysmal or persistent AF patients underwent CB ablation with either AFA-Pro or POLARx. Propensity-score matching resulted in two cohorts of 114 patients each. Baseline and procedural characteristics were comparable between both CBs. POLARx achieved lower minimal temperatures (e.g., left superior pulmonary vein, LSPV: AFA-Pro − 49.0 °C vs. POLARx − 59.5 °C) and lower temperatures at time-to-isolation (TTI). Additionally, POLARx reached lower temperatures faster, as evidenced by lower temperatures after 40 and 60 s, and a larger mean temperature change between 20 and 40 s. POLARx also had a greater area under the curve below 0 °C and a longer thawing phase. Both CBs achieved comparable high rates of final PV-isolation.
TTI, minimal esophagus temperature, and first-pass isolation rates were similar between groups. Periprocedural complications, including phrenic nerve injuries, were comparable. Troponin levels in the left atrium were elevated with both systems. Values and change in troponin were numerically higher in the POLARx group (delta troponin: AFA-Pro 36.3 (26.4, 125.4) ng/L vs. POLARx 104.9 (49.5, 122.2) ng/L), p = 0.077).

Conclusion
AFA-Pro and POLARx are both highly effective and safe CB systems for PVI. POLARx exhibited significant faster and lower freezing characteristics, and numerically higher troponin levels might indicate greater myocardial injury. However, these differences did not translate into improved performance, procedural efficiency, or safety.

Graphical abstract
Developmental characteristics of the permanent upper lateral incisor in unilateral cleft lip and palate
Authors: Knüppe Tim B. A. , Haj Mona , Strabbing Elske M. , Wolvius Eppo B. , Carvajal Monroy Paola L. 
Published: February 2024

Abstract
Objectives
This study aims to provide insights into the developmental characteristics of the upper lateral incisor in individuals with unilateral clefts.

Materials and methods
Panoramic radiographs of a consistent group of Caucasian children taken over time (ages 6, 9, and 12) were extensively reviewed. The study assessed the distribution pattern, eruption path, tooth development, and crown size of the upper lateral incisor within the cleft region.

Results
The most commonly observed distribution pattern was the lateral incisor located distal to the cleft, accounting for 49.2% of cases. Furthermore, a significant delay in tooth development of the upper lateral incisor on the cleft side was noted at ages 6 and 9 (p > 0.001). Compared with the non-cleft side, these incisors often erupted along the alveolar cleft and exhibited microdontia (88.3%, p < 0.041).

Conclusion
Lateral incisors on the cleft side display unique distribution patterns, microdontia, and delayed tooth development. Careful monitoring of the cuspid eruption is essential, as it can influence the eruption of the lateral incisor.

Clinical relevance
A comprehensive understanding of the development of the upper lateral incisor relative to the cleft is vital for determining its prognosis over time. The position of the upper lateral incisor can also influence the timing and prognosis of secondary alveolar bone grafting. Preserving the upper lateral incisor favors arch length, perimeter, and symmetry in individuals with unilateral clefts.
A comparison of brain retraction mechanisms using finite element analysis and the effects of regionally heterogeneous material properties
Authors: Griffiths Emma , Jayamohan Jayaratnam , Budday Silvia 
Published: February 2024

AbstractFinite element (FE) simulations of the brain undergoing neurosurgical procedures present us with the great opportunity to better investigate, understand, and optimize surgical techniques and equipment. FE models provide access to data such as the stress levels within the brain that would otherwise be inaccessible with the current medical technology. Brain retraction is often a dangerous but necessary part of neurosurgery, and current research focuses on minimizing trauma during the procedure. In this work, we present a simulation-based comparison of different types of retraction mechanisms. We focus on traditional spatulas and tubular retractors. Our results show that tubular retractors result in lower average predicted stresses, especially in the subcortical structures and corpus callosum. Additionally, we show that changing the location of retraction can greatly affect the predicted stress results. As the model predictions highly depend on the material model and parameters used for simulations, we also investigate the importance of using region-specific hyperelastic and viscoelastic material parameters when modelling a three-dimensional human brain during retraction. Our investigations demonstrate how FE simulations in neurosurgical techniques can provide insight to surgeons and medical device manufacturers. They emphasize how further work into this direction could greatly improve the management and prevention of injury during surgery. Additionally, we show the importance of modelling the human brain with region-dependent parameters in order to provide useful predictions for neurosurgical procedures.
Improved honey badger algorithm based on elementary function density factors and mathematical spirals in polar coordinate systema
Authors: Zhang Si-Wen , Wang Jie-Sheng , Li Yi-Xuan , Zhang Shi-Hui , Wang Yu-Cai , Wang Xiao-Tian 
Published: February 2024

AbstractThe Honey Badger Algorithm (HBA) is a new swarm intelligence optimization algorithm by simulating the foraging behavior of honey badgers in nature. To further improve its convergence speed and convergence accuracy, an improved HBA based on the density factors with the elementary functions and the mathematical spirals in the polar coordinate system was proposed. The algorithm proposes six density factors for attenuation states based on elementary functions, and introduces mathematical expressions of the polar diameters and angles of seven mathematical spirals (Fibonacci spiral, Butterfly curve, Rose spiral, Cycloid, Archimedean spiral, Hypotrochoid and Cardioid) in the polar coordinate system based on the density factors with the best synthesized effect to replace the foraging strategy of honey badger digging pattern in HBA. By using 23 benchmark test functions, the above improvements are sequentially compared with the original HBA, and the optimization algorithm with the best improvement, α4CycρHBA, is selected to be compared with SOA, MVO, DOA, CDO, MFO, SCA, BA, GWO and FFA. Finally, four engineering design problems (pressure vessel design, three-bar truss design, cantilever beam design and slotted bulkhead design) were solved. The simulation experiments results show that the proposed improved HBA based on the density factors with the elementary functions and the mathematical spirals of the polar coordinate system has the characteristics of balanced exploration and expiration, fast convergence and high accuracy, and is able to solve the function optimization and engineering optimization problems in a better way.