bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of flow rate of continuous bladder irrigation according to the height of the irrigation infusion set
Authors: Yang Boeun , Han Jeongwon 
Published: November 2023

AbstractThis is a control volume analysis to examine the flow rate of irrigation fluid according to the size of indwelling catheter and the height of the fluid bag in consideration of the temperature of irrigation fluid and intra-bladder pressure during continuous bladder irrigation. In case of minimum bladder pressure with room temperature, the flow rates were − 0.045 to 0.993 cc/sec for 18Fr, − 0.053 to 1.176 cc/sec for 20Fr, − 0.055 to 1.227 cc/sec for 22Fr, and − 0.055 to 1.243 cc/sec for 24Fr. In case of maximum bladder pressure with room temperature, the flow rates were − 0.180 to 0.868 cc/sec for 18Fr, − 0.212 to 1.028 cc/sec for 20Fr, − 0.220 to 1.072 cc/sec for 22Fr, and − 0.223 to 1.086 cc/sec for 24Fr. In case of minimum bladder pressure with cold fluid, the flow rates were − 0.028 to 0.365 cc/sec for 18Fr, − 0.033 to 0.749 cc/sec for 20Fr, − 0.034 to 0.781 cc/sec for 22Fr, and − 0.035 to 0.791 cc/sec for 24Fr. In case of maximum bladder pressure with cold fluid, the flow rates were − 0.112 to 0.553 cc/sec for 18Fr, − 0.131 to 0.653 cc/sec for 20Fr, − 0.137 to 0.681 cc/sec for 22Fr, and − 0.139 to 0.689 cc/sec for 24Fr. This study is significant in that it utilized a fluid dynamics approach to provide basic data for continuous bladder wash care. Through the findings of this study, nurses can plan the exchange time of irrigation fluid and the pattern of urinary drainage when performing continuous bladder irrigation. It is also inferred that there may be an advantage in not having to calculate additional material costs for using an infusion pump for patients by determining the hourly injection rate of irrigation fluid based on the height of the infusion set's drop chamber.
Survey on the scheme evaluation, opportunities and challenges of software defined‐information centric network
Authors: Ai Zhengyang , Zhang Ming , Zhang Weiting , Kang Jiawen , Tong Lingling , Duan Yunqiang 
Published: November 2023

AbstractAs a promising architecture of next‐generation network, software defined‐information centric network (SD‐ICN) inherits the advantages of software defined network (SDN) and information‐centric network (ICN) to enable flexible and fast content retrieval, especially in the current era of artificial intelligence. However, the existing researches mainly focus on a single respective in this field, which motivates in comprehensively providing a forward‐looking guidance and development direction for scholars and engineers. To this end, the latest developments of SD‐ICN is presented. First, the widely‐accepted concepts and impacts on traditional networks are introduced. Second, the shortcomings of SDN and ICN over conventional networks are respectively analyzed to illustrate the necessity of SD‐ICN. Third, based on extensive analysis and deep deliberation, a methodical taxonomy for existing combination studies is proposed. They are divided into SDN over ICN, ICN over SDN, and mutual immersive pattern. Fourth, the performances of three integration categories are compared and the limitations of related works are highlighted. Fifth, the maturity index from six development indicators are evaluated. Further, the maturity and practicality of these schemes are generalized. Based on the above studies and comparisons, the lessons learned by SDN and ICN developments are concluded. Finally, future research directions and opportunities are discussed for the readers.
oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data
Authors: Ullrich Kristian K , Glytnasi Nikoleta E 
Published: November 2023

Abstract

Summary
For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species’ ontogeny, and soon, they will be standard even for nonmodel species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context.

Availability and implementation
oggmap source code is available at https://github.com/kullrich/oggmap, documentation is available at https://oggmap.readthedocs.io/en/latest/. oggmap can be installed via PyPi or directly used via a docker container.
Penalized regression with multiple sources of prior effects
Authors: Rauschenberger Armin , Landoulsi Zied , van de Wiel Mark A , Glaab Enrico 
Published: November 2023

Abstract

Motivation
In many high-dimensional prediction or classification tasks, complementary data on the features are available, e.g. prior biological knowledge on (epi)genetic markers. Here we consider tasks with numerical prior information that provide an insight into the importance (weight) and the direction (sign) of the feature effects, e.g. regression coefficients from previous studies.

Results
We propose an approach for integrating multiple sources of such prior information into penalized regression. If suitable co-data are available, this improves the predictive performance, as shown by simulation and application.

Availability and implementation
The proposed method is implemented in the R package transreg (https://github.com/lcsb-bds/transreg, https://cran.r-project.org/package=transreg).
Testing serial independence of object-valued time series
Authors: Jiang Feiyu , Gao Hanjia , Shao Xiaofeng 
Published: November 2023

Summary
We propose a novel method for testing serial independence of object-valued time series in metric spaces, which are more general than Euclidean or Hilbert spaces. The proposed method is fully nonparametric, free of tuning parameters and can capture all nonlinear pairwise dependence. The key concept used in this paper is the distance covariance in metric spaces, which is extended to the autodistance covariance for object-valued time series. Furthermore, we propose a generalized spectral density function to account for pairwise dependence at all lags and construct a Cramér–von Mises-type test statistic. New theoretical arguments are developed to establish the asymptotic behaviour of the test statistic. A wild bootstrap is also introduced to obtain the critical values of the nonpivotal limiting null distribution. Extensive numerical simulations and two real data applications on cumulative intraday returns and human mortality data are conducted to illustrate the effectiveness and versatility of our proposed test.
Evaluation of objective tools and artificial intelligence in robotic surgery technical skills assessment: a systematic review
Authors: Boal Matthew W E , Anastasiou Dimitrios , Tesfai Freweini , Ghamrawi Walaa , Mazomenos Evangelos , Curtis Nathan , Collins Justin W , Sridhar Ashwin , Kelly John , Stoyanov Danail , Francis Nader K 
Published: November 2023

Abstract

Background
There is a need to standardize training in robotic surgery, including objective assessment for accreditation. This systematic review aimed to identify objective tools for technical skills assessment, providing evaluation statuses to guide research and inform implementation into training curricula.

Methods
A systematic literature search was conducted in accordance with the PRISMA guidelines. Ovid Embase/Medline, PubMed and Web of Science were searched. Inclusion criterion: robotic surgery technical skills tools. Exclusion criteria: non-technical, laparoscopy or open skills only. Manual tools and automated performance metrics (APMs) were analysed using Messick's concept of validity and the Oxford Centre of Evidence-Based Medicine (OCEBM) Levels of Evidence and Recommendation (LoR). A bespoke tool analysed artificial intelligence (AI) studies. The Modified Downs–Black checklist was used to assess risk of bias.

Results
Two hundred and forty-seven studies were analysed, identifying: 8 global rating scales, 26 procedure-/task-specific tools, 3 main error-based methods, 10 simulators, 28 studies analysing APMs and 53 AI studies. Global Evaluative Assessment of Robotic Skills and the da Vinci Skills Simulator were the most evaluated tools at LoR 1 (OCEBM). Three procedure-specific tools, 3 error-based methods and 1 non-simulator APMs reached LoR 2. AI models estimated outcomes (skill or clinical), demonstrating superior accuracy rates in the laboratory with 60 per cent of methods reporting accuracies over 90 per cent, compared to real surgery ranging from 67 to 100 per cent.

Conclusions
Manual and automated assessment tools for robotic surgery are not well validated and require further evaluation before use in accreditation processes.
PROSPERO: registration ID CRD42022304901
CircCDK17 promotes the proliferation and metastasis of ovarian cancer cells by sponging miR-22-3p to regulate CD147 expression
Authors: Qu Bin , Sun Lisha , Xiao Ping , Shen Haoming , Ren Yuxi , Zhang Jing 
Published: November 2023

Abstract
Ovarian cancer (OC) is a common malignancy in women of reproductive age. Circular RNAs (circRNAs) are emerging players in OC progression. We investigated the function and mechanism of circular RNA hsa_circ_0027803 (circCDK17) in OC pathogenesis. Real‑time PCR (RT-qPCR) and western blot were utilized for gene and protein expression analysis, respectively. Cell counting kit‑8 (CCK-8), EdU and Transwell assays investigated OC cell proliferation, migration and invasion. The associations between circCDK17, miR-22-3p and CD147 were examined by dual-luciferase reporter and RNA-protein immunoprecipitation (RIP) assays. The in vivo model of OC nude mice was constructed to explore the role of circCDK17. CircCDK17 was increased in OC tissue and cells, and patients with higher expression of circCDK17 had a shorter survival. CircCDK17 downregulation inhibited OC cell proliferation, migration and invasion, and reduced epithelial-mesenchymal transition (EMT)-related markers. In vivo experiments showed that circCDK17 silencing inhibited OC tumor growth and metastasis. CircCDK17 depletion reduced CD147 level via sponging miR-22-3p. MiR-22-3p knockdown overturned effect of circCDK17 depletion on OC cell proliferation, migration and invasion. Meanwhile, overexpressed CD147 restored functions of circCDK17 downregulation on OC development. CircCDK17 is an important molecule that regulates OC pathogenic process through miR-22-3p/CD147.
The CXCL10-CXCR3 axis plays an important role in Kawasaki disease
Authors: Hosaka Sho , Imagawa Kazuo , Yano Yusuke , Lin Lisheng , Shiono Junko , Takahashi-Igari Miho , Hara Hideki , Hayashi Daisuke , Imai Hironori , Morita Atsushi , Fukushima Hiroko , Takada Hidetoshi 
Published: November 2023

Abstract
The precise pathogenesis of Kawasaki disease remains unknown. In an attempt to elucidate the pathogenesis of KD through the analysis of acquired immunity, we comprehensively examined the immunophenotypic changes in immune cells such as lymphocytes and monocytes along with various cytokines, focusing on differences between pre- and post- treatment samples. We found high levels of CXCL9 and CXCL10 chemokines that decreased with treatment, which coincided with a post-treatment expansion of Th1 cells expressing CXCR3. Our results show that the CXCL10-CXCR3 axis plays an important role in the pathogenesis of KD.
FooDrugs: a comprehensive food–drug interactions database with text documents and transcriptional data
Authors: Lacruz-Pleguezuelos Blanca , Piette Oscar , Garranzo Marco , Pérez-Serrano David , Milešević Jelena , Espinosa-Salinas Isabel , Ramírez de Molina Ana , Laguna Teresa , Carrillo de Santa Pau Enrique 
Published: November 2023

Abstract
Food–drug interactions (FDIs) occur when a food item alters the pharmacokinetics or pharmacodynamics of a drug. FDIs can be clinically relevant, as they can hamper or enhance the therapeutic effects of a drug and impact both their efficacy and their safety. However, knowledge of FDIs in clinical practice is limited. This is partially due to the lack of resources focused on FDIs. Here, we describe FooDrugs, a database that centralizes FDI knowledge retrieved from two different approaches: a natural processing language pipeline that extracts potential FDIs from scientific documents and clinical trials and a molecular similarity approach based on the comparison of gene expression alterations caused by foods and drugs. FooDrugs database stores a total of 3 430 062 potential FDIs, with 1 108 429 retrieved from scientific documents and 2 321 633 inferred from molecular data. This resource aims to provide researchers and clinicians with a centralized repository for potential FDI information that is free and easy to use.
Database URL: https://zenodo.org/records/8192515
Database DOI: https://doi.org/10.5281/zenodo.6638469
PlantIntronDB: a database for plant introns that host functional elements
Authors: Wang Weiping , Hu Jiming , Li Han , Yan Jun , Sun Xiaoyong 
Published: November 2023

Abstract
Although more and more attention has been focused on introns and the important role of plant introns in plant growth and development has been discovered, there is still a lack of an open and comprehensive database on plant introns with functional elements in current research. In order to make full use of large-scale sequencing data and help researchers in related fields to achieve high-throughput functional verification of identified plant introns with functional elements, we designed a database containing five plant species, PlantIntronDB and systematically analyzed 358, 59, 185, 210 and 141 RNA-seq samples from Arabidopsis thaliana (Arabidopsis), Gossypium raimondii (cotton), Zea mays (maize), Brassica napus (oilseed rape) and Oryza sativa Japonica Group (rice). In total, we found 100 126 introns that host functional elements in these five species. Specifically, we found that among all species, the number of introns with functional elements on the positive and negative strands is similar, with a length mostly smaller than 1500 bp, and the Adenine/Thymine (A/T) content is much higher than that of Guanine/Cytosine (G/C). In addition, the distribution of functional elements in introns varies among different species. All the above data can be downloaded for free in this database. This database provides a concise, comprehensive and user-friendly web interface, allowing users to easily retrieve target data based on their needs, using relevant organizational options. The database operation is simple and convenient, aiming to provide strong data support for researchers in related fields to study plant introns that host functional elements, including circular RNAs, lncRNAs, etc.
Database URL: http://deepbiology.cn/PlantIntronDB/
Fluctuating selection facilitates the discovery of broadly effective but difficult to reach adaptive outcomes in yeast
Authors: Fasanello Vincent J , Liu Ping , Fay Justin C , Botero Carlos A 
Published: November 2023

Abstract
Evolutionary compromises are thought to be common under fluctuating selection because the mutations that best enable adaptation to one environmental context can often be detrimental to others. Yet, prior experimental work has shown that generalists can sometimes perform as well as specialists in their own environments. Here we use a highly replicated evolutionary experiment (N = 448 asexual lineages of the brewer’s yeast) to show that even though fluctuation between two environmental conditions often induces evolutionary compromises (at least early on), it can also help reveal difficult to reach adaptive outcomes that ultimately improve performance in both environments. Specifically, we begin by showing that yeast adaptation to chemical stress can involve fitness trade-offs with stress-free environments and that, accordingly, lineages that are repeatedly exposed to occasional stress tend to respond by trading performance for breadth of adaptation. We then show that on rare occasions, fluctuating selection leads to the evolution of no-cost generalists that can even outcompete constant selection specialists in their own environments. We propose that the discovery of these broader and more effective adaptive outcomes under fluctuating selection could be partially facilitated by changes in the adaptive landscape that result from having to deal with fitness trade-offs across different environmental conditions. Overall, our findings indicate that reconciling the short- and long-term evolutionary consequences of fluctuating selection could significantly improve our understanding of the evolution of specialization and generalism.
Hybridization and its impact on the ontogenetic allometry of skulls in macaques
Authors: Ito Tsuyoshi , Kimura Ryosuke , Wakamori Hikaru , Tanaka Mikiko , Tezuka Ayumi , Nagano Atsushi J , Hamada Yuzuru , Kawamoto Yoshi 
Published: November 2023

Abstract
The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (Macaca fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, that is, the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and nonadditive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.
Genome-wide identification of the histone acetyltransferase gene family in Citrus clementina and its potential roles in citrate metabolism
Authors: Lin Xiahui , Shi Yanna , Liu Shengchao , Liu Xincheng , Zhang Minglei , Zhang Bo , Li Shaojia , Chen Kunsong 
Published: November 2023

Abstract
Histone acetyltransferase (HAT) catalyzes histone acetylation and is involved in plant growth and development and stress responses. Here, 37 CitHAT genes were identified in Citrus clementina. Their physicochemical properties, chromosomal location, gene structure, conserved domain and motif, and cis-acting elements were characterized. CitHATs were classified into four subfamilies based on protein sequence homology, which was strongly supported by gene structure, conserved domain, and motif analysis. The cis-acting elements in gene promoter regions were predicted to be associated with the regulation of plant growth, stress resistance, and response to hormones. Phenotypic and transcriptomic analyses of citrus callus with mock treatment and HAT inhibitor treatment revealed that increased citric acid content in inhibitor treatment may be attributed to differential expression of CitPEPCK2 and CitGS2, which may be due to the hypo-acetylation of histone H3. The expression patterns of CitHATs in citrus fruit development stages showed that CitHAG11 and CitHAG28 exhibited a negative correlation with citric acid content. Our study associates the potential function of histone acetyltransferases in citrate metabolism and extends the molecular mechanism of citrate metabolism in fruits.
Fate of ochratoxin A in dried red chilies during roasting process
Authors: Xiao Xiao , Chen Jiang , Zhu Qiujin , Wan Jing 
Published: November 2023

Abstract
Dried red chilies are widely used globally and are susceptible to contamination by fungi and fungal toxins. Roasting is a common way of processing dried red chilies. This study explored the effects of Aspergillus niger and ochratoxin A (OTA) contamination on the quality of roasted chilies, and the fate of OTA during the roasting process. Three optimum roasting conditions (140 °C×8 min, 160 °C×6 min, and 180 °C×4 min) were screened out by a combination of instrumental and manual sensory evaluations. Under these roasting conditions, A. niger and OTA contamination diminished the quality and taste of roasted chilies. With increasing roasting temperature and time duration, OTA content and mold counts gradually decreased, together with the DNA degradation of OTA biosynthesis-related genes of A. niger in roasted chilies. The roasting condition at 180 °C×4 min showed the greatest decomposition effect on OTA, while also maintaining good sensory quality of roasted chilies. This study shed light on the fate of OTA during the chili roasting process.
Assessing midwifery services in Iran via the balanced scorecard framework
Authors: Rezaei GholamReza , SadeghzadehMaharluie Mohammad , Ebrahimi Maedeh , Ebrahimi Marziyeh 
Published: November 2023

AbstractThis study investigates the impact of intra-organizational information, midwife job satisfaction and performance assessment on the quality of midwife services. The questions are empirically tested with survey data obtained from 276 midwives, specialist doctors and nurses, and mothers who recently gave birth in a cross-section of Iranian public healthcare organizations. The results from a structural equation model suggest that an improved performance assessment system leads to higher quality midwife services. In addition, the results indicate that midwife job satisfaction and intra-organizational information increases the quality of midwife services, both directly and indirectly, through the mediating effect of a performance assessment system. Our study contributes to the growing research exploring the interface between accounting and health issues by recognizing the importance of a performance assessment system of midwifery services via the balanced scorecard framework for understanding the quality of midwife services.