bluuebunny/crossref_metadata_2025_split huggingface dataset:
Best Practice Guideline – Empfehlungen der DEGUM zur Durchführung und Beurteilung der Mammasonografie
Authors: Vogel-Minea Claudia Maria , Bader Werner , Blohmer Jens-Uwe , Duda Volker , Eichler Christian , Fallenberg Eva Maria , Farrokh André , Golatta Michael , Gruber Ines , Hackelöer Bernhard-Joachim , Heil Jörg , Madjar Helmut , Marzotko Ellen , Merz Eberhard , Müller-Schimpfle Markus , Mundinger Alexander , Ohlinger Ralf , Peisker Uwe , Schäfer Fritz KW , Schulz-Wendtland Ruediger , Solbach Christine , Warm Mathias , Watermann Dirk , Wojcinski Sebastian , Dudwiesus Heiko , Hahn Markus 
Published: December 2023

Die Mammasonografie hat sich seit vielen Jahren neben der Mammografie als wichtige Methode zur Abklärung von Brustbefunden etabliert.Der Arbeitskreis Mammasonografie der DEGUM beabsichtigt mit der „Best Practice Guideline“ den senologisch tätigen Kolleginnen und Kollegen neben dem in Teil I publizierten aktuellen Dignitätskriterien- und Befundungskatalog in dem vorliegenden Teil II die additiven und fakultativen Anwendungsmodalitäten zur Abklärung von Brustbefunden zu beschreiben und dazu DEGUM-Empfehlungen zu äußern, um die Differenzialdiagnose von unklaren Läsionen zu erleichtern.Die vorliegende „Best Practice Guideline“ hat sich zum Ziel gesetzt, den Anforderungen zur Qualitätssicherung und der Gewährleistung einer qualitätskontrollierten Durchführung der Mammasonografie nachzukommen. Die wichtigsten Aspekte der Qualitätssicherung werden in diesem Teil II der Best Practice Guideline erläutert.
Cluster Preface: Functional Dyes
Authors: Yang Youjun , Fan Jiangli 
Published: December 2023

Youjun Yang (left) received his BS (2002) from the University of Science and Technology of China, and his PhD (2007) with Prof. Robert M. Strongin at Louisiana State University. Then, he joined the Anslyn group at UT Austin as a postdoc. In 2010, he joined the faculty of the school of pharmacy, East China University of Science and Technology (ECUST). His research interests include NIR fluorescent dyes, photo-responsive dyes, and fluorescent molecular probes.
Jiangli Fan (right) obtained her PhD at Dalian University of Technology (2005). Now she is a Professor at the School of Chemical Engineering at Dalian University of Technology, and she received the Distinguished Young Scholars of NSFC (2019). Her research interests mainly focus on the development of functional dyes for biomedical analysis and disease treatment.
Uterine Microbiome: Does the Sampling Technique Matter?
Authors: Lüll Kreete , Org Elin 
Published: December 2023

AbstractStudies have proven the significance of microbial communities in various parts of the human body for health. In recent years it has been discovered that the uterine cavity is not sterile, and endometrium has its own microbiome which appears to have an impact on female fertility and gynecological pathologies. Lactobacillus has shown to dominate the microbial profile in the uterus and is considered an indicator of a healthy uterine environment. Yet, many argue that the Lactobacillus dominance is due to vaginal contamination during the sampling process. To date there is no clearly defined healthy endometrial microbial profile, which is largely due to the fact that determining the microbial community from the endometrium is complicated, and there is currently no consensus on sampling methods for the endometrial microbiome. As a result, this restricts ability to replicate discoveries made in other cohorts. Here we aim to give an overview of the sampling methods used and discuss what impedes the endometrial microbiome studies as well as how to reach a consensus on the study design. This knowledge could be incorporated into the future research and the knowledge on endometrial microbiome could be included into the diagnostics and treatment of female reproductive health.
Anorectal Abscess
Authors: Kata Anna , Abelson Jonathan S. 
Published: December 2023

AbstractAnorectal abscesses are a common colorectal emergency. The hallmark of treatment is obtaining source control while avoiding injury to the underlying sphincter complex. Understanding the anatomy of an anorectal abscess is critical to planning the appropriate drainage strategy and decreasing the risk of complex fistula formation. Use of antibiotics should be reserved for those with extensive cellulitis, signs of systemic infection, or patients who are immunocompromised. Whether antibiotics prevent future fistula formation is an area of active research. Primary fistulotomy at time of the index drainage is controversial; however, there may be situations where it is appropriate. It is important to counsel patients that after effective drainage of an anorectal abscess, they have a 30 to 50% chance of developing an anal fistula that will then require further treatment.
Research on metaphor processing during the past five decades: a bibliometric analysis
Authors: Peng Zhibin , Khatin-Zadeh Omid 
Published: December 2023

AbstractMetaphor processing has been the subject of extensive research over the past five decades. A systematic review of metaphor processing publications through bibliometric tools can provide a clear overview of research on metaphor processing. In this study, we used the CiteSpace bibliometric tool to conduct a systematic review of publications related to metaphor processing. A total of 3271 works published and indexed in the Web of Science (WoS) were gathered. These works had been published between 1970 and 2022. We analyzed the co-citations of these works by CiteSpace to identify the most influential publications in metaphor processing research. A co-occurrence term analysis was done to identify dominant topics in this area of research. The results of this analysis showed that Language, comprehension, metaphor, figurative language, and context were the most frequent keywords. The most prominent clusters were students, figurative language, right hemisphere, embodied cognition, comprehension, N400, and anger. Based on the results of this analysis, we suggest that task properties such as response format and linguistic features should be carefully taken into account in future studies on metaphor processing.
Evaluation of the impact of a pharmacy transitions of care program
Authors: Dalton Heather , Hinely Molly T , Kostelic Emily M 
Published: December 2023

Abstract

Purpose
Pharmacist-driven transitions of care interventions have been shown to improve patient clinical outcomes. However, the evidence in the literature on the impact of pharmacy transitions of care services on hospitalization and emergency department visit rates is inconclusive. The purpose of this study is to determine the impact of a pharmacist-driven transitions of care program on hospitalization and emergency department visit rates at an academic medical center.

Methods
This retrospective observational cohort study was conducted via pre- and postintervention analyses. The data collection period included 30 days before the date of pharmacist intervention and 30 days after the date of intervention. The study evaluated patients who were enrolled in the Transitional Inpatient Rounding Experience (TIRE) program at Wake Forest Baptist Health between August 2017 and September 2020. Patients excluded were less than 18 years old, in hospice care, discharged to long-term care, or did not have a hospitalization within 90 days of intervention. The Wilcoxon signed rank test was utilized to analyze continuous data. Standard descriptive statistics were used for categorical data.

Results
One hundred patients met the inclusion criteria for this study. For the primary outcome, the TIRE intervention resulted in a reduction of 31 hospitalizations, or 50% (62 prior hospitalizations in the 30 days before the intervention vs 31 admissions in the 30 days after the intervention; P &lt; 0.001). There were significant reductions in the secondary outcomes of 90-day hospitalizations (24% fewer with intervention; P = 0.028) and 30-day emergency department visits (65% fewer with intervention; P =0.006). For the outcome of 90-day emergency department visits, there was a 36% reduction (P = 0.240).

Conclusion
The results of the study demonstrate that a pharmacy transitions of care program may lead to a reduction in hospitalization and emergency department visit rates. The study also found potential cost savings associated with a pharmacy transitions of care program.
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning
Authors: Stourac Jan , Borko Simeon , Khan Rayyan T , Pokorna Petra , Dobias Adam , Planas-Iglesias Joan , Mazurenko Stanislav , Pinto Gaspar , Szotkowska Veronika , Sterba Jaroslav , Slaby Ondrej , Damborsky Jiri , Bednar David 
Published: December 2023

Abstract
PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.
RMTLysPTM: recognizing multiple types of lysine PTM sites by deep analysis on sequences
Authors: Chen Lei , Chen Yuwei 
Published: December 2023

AbstractPost-translational modification (PTM) occurs after a protein is translated from ribonucleic acid. It is an important living creature life phenomenon because it is implicated in almost all cellular processes. Identification of PTM sites from a given protein sequence is a hot topic in bioinformatics. Lots of computational methods have been proposed, and they provide good performance. However, most previous methods can only tackle one PTM type. Few methods consider multiple PTM types. In this study, a multi-label classification model, named RMTLysPTM, was developed to recognize four types of lysine (K) PTM sites, including acetylation, crotonylation, methylation and succinylation. The surrounding sites of a lysine site were selected to constitute a peptide segment, representing the lysine at the center. Deep analysis was conducted to count the distribution of 2-residues with fixed location across the four types of lysine PTM sites. By aggregating the distribution information of 2-residues in one peptide segment, the peptide segment was encoded by informative features. Furthermore, a prediction engine that can precisely capture the traits of the above representations was designed to recognize the types of lysine PTM sites. The cross-validation results on two datasets (Qiu and CPLM training datasets) suggested that the model had extremely high performance and RMTLysPTM had strong generalization ability by testing it on protein Q16778 and CPLM testing datasets. The model was found to be generally superior to all previous models and those using popular methods and features. A web server was set up for RMTLysPTM, and it can be accessed at http://119.3.127.138/.
MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules
Authors: Liu Jian , Ma Fubin , Zhu Yongdi , Zhang Naiqian , Kong Lingming , Mi Jia , Cong Haiyan , Gao Rui , Wang Mingyi , Zhang Yusen 
Published: December 2023

Abstract

Motivation
Cancer is caused by the accumulation of somatic mutations in multiple pathways, in which driver mutations are typically of the properties of high coverage and high exclusivity in patients. Identifying cancer driver genes has a pivotal role in understanding the mechanisms of oncogenesis and treatment.

Results
Here, we introduced MaxCLK, an algorithm for identifying cancer driver genes, which was developed by an integrated analysis of somatic mutation data and protein–protein interaction (PPI) networks and further improved by an information entropy index. Tested on pancancer and single cancers, MaxCLK outperformed other existing methods with higher accuracy. About pancancer, we predicted 154 driver genes and 787 driver modules. The analysis of co-occurrence and exclusivity between modules and pathways reveals the correlation of their combinations. Overall, our study has deepened the understanding of driver mechanism in PPI topology and found novel driver genes.

Availability and implementation
The source codes for MaxCLK are freely available at https://github.com/ShandongUniversityMasterMa/MaxCLK-main.
The function of red and banded patterns in snakes: the ophiophagy hypothesis
Authors: Mouy Henri 
Published: December 2023

Abstract
The functions of bright bands in coral and other snakes have long been a puzzle. The most common opinion is that coral snakes display aposematic marks and that other red and black banded snakes in the Americas are mimics of coral snakes. I previously found that this prevailing opinion is weakly supported and unlikely, that red and bands had probably evolved independently or conjointly many times, and that a present selection for bands and red seems to exist in a significant fraction of the world. Here, I review the potential selective forces for red and bands in snakes. I find that snakes as predators are a priori plausible selective agents. I find that ophiophagy appears to be an exceptionally high risk in snakes that are themselves ophiophagous. Testing the working hypothesis that bands and red are protective against snake predators via their association with ophiophagy, as ophiophagous snakes are at higher risk, I find that the consumption of elongate vertebrates predicts band and red coloration with a very high level of confidence: red and bands are probably defensive against snake predators. Noting an apparent correlation of coloration with specific defensive behaviours and ontogenetic colour changes, I review both and find that ophiophagous snakes are remarkable for using stereotypical defences and not being aggressive, while ontogenetic colour changes seem to affect red and bands in snakes disproportionately. Defence against ophidian predators may be an unexpected natural selection shaping the appearance and behaviours of many snakes.
Vestibular damage affects the precision and accuracy of navigation in a virtual visual environment
Authors: Chari Divya A , Ahmad Maimuna , King Susan , Boutabla Anissa , Fattahi Cameron , Panic Alexander S , Karmali Faisal , Lewis Richard F 
Published: December 2023

Abstract
Vestibular information is available to the brain during navigation, as are the other self-generated (idiothetic) and external (allothetic) sensorimotor cues that contribute to central estimates of position and motion. Rodent studies provide strong evidence that vestibular information contributes to navigation but human studies have been less conclusive. Furthermore, sex-based differences have been described in human navigation studies performed with the head stationary, a situation where dynamic vestibular (and other idiothetic) information is absent, but sex differences in the utilization of vestibular information have not been described. Here, we studied men and women with severe bilateral vestibular damage as they navigated through a visually barren virtual reality environment and compared their performance to normal men and women. Two navigation protocols were employed, which either activated dynamic idiothetic cues (‘dynamic task’, navigate by turning, walking in place) or eliminated them (‘static task’, navigate with key presses, head stationary). For both protocols, we employed a standard ‘triangle completion task’ in which subjects moved to two visual targets in series and then were required to return to their perceived starting position without localizing visual information. The angular and linear ‘accuracy’ (derived from response error) and ‘precision’ (derived from response variability) were calculated. Comparing performance ‘within tasks’, navigation on the dynamic paradigm was worse in male vestibular-deficient patients than in normal men but vestibular-deficient and normal women were equivalent; on the static paradigm, vestibular-deficient men (but not women) performed better than normal subjects. Comparing performance ‘between tasks’, normal men performed better on the dynamic than the static paradigm while vestibular-deficient men and both normal and vestibular-deficient women were equivalent on both tasks. Statistical analysis demonstrated that for the angular precision metric, sex had a significant effect on the interaction between vestibular status and the test paradigm. These results provide evidence that humans use vestibular information when they navigate in a virtual visual environment and that men and women may utilize vestibular (and visual) information differently. On our navigation paradigm, men used vestibular information to improve navigation performance, and in the presence of severe vestibular damage, they utilized visual information more effectively. In contrast, we did not find evidence that women used vestibular information while navigating on our virtual task, nor did we find evidence that they improved their utilization of visual information in the presence of severe vestibular damage.
Identification of biomarkers for the early detection of non-small cell lung cancer: a systematic review and meta-analysis
Authors: Mohamed Eithar , García Martínez Daniel J , Hosseini Mohammad-Salar , Yoong Si Qi , Fletcher Daniel , Hart Simon , Guinn Barbara-ann 
Published: December 2023

Abstract
Lung cancer (LC) causes few symptoms in the earliest stages, leading to one of the highest mortality rates among cancers. Low-dose computerised tomography (LDCT) is used to screen high-risk individuals, reducing the mortality rate by 20%. However, LDCT results in a high number of false positives and is associated with unnecessary follow-up and cost. Biomarkers with high sensitivities and specificities could assist in the early detection of LC, especially in patients with high-risk features. Carcinoembryonic antigen (CEA), cytokeratin 19 fragments and cancer antigen 125 have been found to be highly expressed during the later stages of LC but have low sensitivity in the earliest stages. We determined the best biomarkers for the early diagnosis of LC, using a systematic review of eight databases. We identified 98 articles that focussed on the identification and assessment of diagnostic biomarkers and achieved a pooled area under curve of 0.85 (95% CI 0.82–0.088), indicating that the diagnostic performance of these biomarkers when combined was excellent. Of the studies, 30 focussed on single/antigen panels, 22 on autoantibodies, 31 on miRNA and RNA panels, and 15 suggested the use of circulating DNA combined with CEA or neuron-specific enolase (NSE) for early LC detection. Verification of blood biomarkers with high sensitivities (Ciz1, exoGCC2, ITGA2B), high specificities (CYFR21-1, antiHE4, OPNV) or both (HSP90α, CEA) along with miR-15b and miR-27b/miR-21 from sputum may improve early LC detection. Further assessment is needed using appropriate sample sizes, control groups that include patients with non-malignant conditions, and standardised cut-off levels for each biomarker.
Multiple Cardiac Biomarkers to Improve Prediction of Cardiovascular Events: Findings from the Generation Scotland Scottish Family Health Study
Authors: Welsh Paul , Kimenai Dorien M , Shah Anoop S V , Gadd Danni A , Marioni Riccardo E , Woodward Mark , Sudlow Cathie L M , Campbell Archie , Cleland John G F , Pellicori Pierpaolo , Hayward Caroline , Mills Nicholas L , Sattar Naveed 
Published: December 2023

Abstract

Background
Many studies have investigated whether single cardiac biomarkers improve cardiovascular risk prediction for primary prevention but whether a combined approach could further improve risk prediction is unclear. We aimed to test a sex-specific, combined cardiac biomarker approach for cardiovascular risk prediction.

Methods
In the Generation Scotland Scottish Family Health Study, N-terminal pro-B-type natriuretic peptide (NT-proBNP), growth differentiation factor-15 (GDF-15), cardiac troponin I (cTnI), cardiac troponin T (cTnT), and C-reactive protein (CRP) were measured in stored serum using automated immunoassays. Sex-specific Cox models that included SCORE2 risk factors evaluated addition of single and combined biomarkers for prediction of major adverse cardiovascular events (MACE). Combined biomarker models were compared to a baseline model that included SCORE2 risk factors.

Results
The study population comprised 18 383 individuals (58.9% women, median age of 48 years [25th–75th percentile, 35–58 years]). During the median follow up of 11.6 (25th–75th percentile, 10.8–13.0) years, MACE occurred in 942 (5.1%) individuals. The greatest increase in discrimination with addition of individual biomarkers to the base model was for women GDF-15 and for men NT-proBNP (change in c-index: + 0.010 for women and +0.005 for men). For women, combined biomarker models that included GDF-15 and NT-proBNP (+0.012) or GDF-15 and cTnI (+0.013), but not CRP or cTnT, further improved discrimination. For men, combined biomarker models that included NT-proBNP and GDF-15 (+0.007), NT-proBNP and cTnI (+0.006), or NT-proBNP and CRP (+0.008), but not cTnT, further improved discrimination.

Conclusions
A combined biomarker approach, particularly the use of GDF-15, NT-proBNP and cTnI, further refined cardiovascular risk estimates.
Privacy-Preserving Image Retrieval with Multi-Modal Query
Authors: Zhou Fucai , Zhang Zongye , Hou Ruiwei 
Published: December 2023

Abstract
The ever-growing multi-modal images pose great challenges to local image storage and retrieval systems. Cloud computing provides a solution to large-scale image data storage but suffers from privacy issues and lacks the support for multi-modal image retrieval. To address these, a searchable encryption-empowered privacy-preserving multi-modal image retrieval method is proposed. First, we design a hybrid image retrieval framework that fuses visual features and textual features at a decision level and further supports similar image retrieval and multi-keyword image retrieval. Second, we construct a new hybrid inverted index structure to distinguish high-frequency terms from low-frequency terms and index them through hierarchical index trees and data blocks, respectively, which greatly improves query efficiency. Third, we design a prime encoding-based multi-keyword query method that converts mapping operations in bloom filters into inner product calculations, and further implements secure multi-keyword image query. Experiments against the Baseline schemes are conducted to verify the performance of the scheme in terms of high efficiency.