bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method
Authors: Yu Ying , Zhang Naixin , Mai Yuanbang , Ren Luyao , Chen Qiaochu , Cao Zehui , Chen Qingwang , Liu Yaqing , Hou Wanwan , Yang Jingcheng , Hong Huixiao , Xu Joshua , Tong Weida , Dong Lianhua , Shi Leming , Fang Xiang , Zheng Yuanting 
Published: September 2023

Abstract
Background
Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are proposed to facilitate data integration. However, their respective advantages and limitations are not adequately assessed in terms of omics types, the performance metrics, and the application scenarios.

Results
As part of the Quartet Project for quality control and data integration of multiomics profiling, we comprehensively assess the performance of seven batch effect correction algorithms based on different performance metrics of clinical relevance, i.e., the accuracy of identifying differentially expressed features, the robustness of predictive models, and the ability of accurately clustering cross-batch samples into their own donors. The ratio-based method, i.e., by scaling absolute feature values of study samples relative to those of concurrently profiled reference material(s), is found to be much more effective and broadly applicable than others, especially when batch effects are completely confounded with biological factors of study interests. We further provide practical guidelines for implementing the ratio based approach in increasingly large-scale multiomics studies.

Conclusions
Multiomics measurements are prone to batch effects, which can be effectively corrected using ratio-based scaling of the multiomics data. Our study lays the foundation for eliminating batch effects at a ratio scale.
Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics
Authors: Tian Sha , Zhan Dongdong , Yu Ying , Wang Yunzhi , Liu Mingwei , Tan Subei , Li Yan , Song Lei , Qin Zhaoyu , Li Xianju , Liu Yang , Li Yao , Ji Shuhui , Wang Shanshan ,   Proteomic Massive Analysis and Quality Control Consortium, Qin Zhaoyu , He Qingyu , Yin Xingfeng , Dai Lunzhi , Deng Haiteng , Peng Chao , Wu Ping , Tan Minjia , Jiang Jing , Zhang Yaoyang , Li Yunxia , Liu Wenqin , Chen Wei , Wang Rui , Zi Jin , Li Qidan , Bai Mingzhou , Wang Zeng , Mei Zhanlong , Cheng Zhongyi , Zhu Jun , Wu Xuemei , Yang Xing , Zhou Yue , Zheng Yuanting , He Fuchu , Qin Jun , Ding Chen 
Published: September 2023

Abstract
Background
Quantitative proteomics is an indispensable tool in life science research. However, there is a lack of reference materials for evaluating the reproducibility of label-free liquid chromatography-tandem mass spectrometry (LC–MS/MS)-based measurements among different instruments and laboratories.

Results
Here, we develop the Quartet standard as a proteome reference material with built-in truths, and distribute the same aliquots to 15 laboratories with nine conventional LC–MS/MS platforms across six cities in China. Relative abundance of over 12,000 proteins on 816 mass spectrometry files are obtained and compared for reproducibility among the instruments and laboratories to ultimately generate proteomics benchmark datasets. There is a wide dynamic range of proteomes spanning about 7 orders of magnitude, and the injection order has marked effects on quantitative instead of qualitative characteristics.

Conclusion
Overall, the Quartet offers valuable standard materials and data resources for improving the quality control of proteomic analyses as well as the reproducibility and reliability of research findings.
Mottling as a prognosis marker in cardiogenic shock
Authors: Merdji Hamid , Bataille Vincent , Curtiaud Anais , Bonello Laurent , Roubille François , Levy Bruno , Lim Pascal , Schneider Francis , Khachab Hadi , Dib Jean-Claude , Seronde Marie-France , Schurtz Guillaume , Harbaoui Brahim , Vanzetto Gerald , Marchand Severine , Gebhard Caroline Eva , Henry Patrick , Combaret Nicolas , Marchandot Benjamin , Lattuca Benoit , Biendel Caroline , Leurent Guillaume , Gerbaud Edouard , Puymirat Etienne , Bonnefoy Eric , Meziani Ferhat , Delmas Clément 
Published: September 2023

Abstract
Aims
Impact of skin mottling has been poorly studied in patients admitted for cardiogenic shock. This study aimed to address this issue and identify determinants of 30-day and 1-year mortality in a large cardiogenic shock cohort of all etiologies.

Methods and results
FRENSHOCK is a prospective multicenter observational registry conducted in French critical care units between April and October, 2016. Among the 772 enrolled patients (mean age 65.7 ± 14.9 years; 71.5% male), 660 had skin mottling assessed at admission (85.5%) with almost 39% of patients in cardiogenic shock presenting mottling. The need for invasive respiratory support was significantly higher in patients with mottling (50.2% vs. 30.1%, p < 0.001) and likewise for the need for renal replacement therapy (19.9% vs. 12.4%, p = 0.09). However, the need for mechanical circulatory support was similar in both groups. Patients with mottling at admission presented a higher length of stay (19 vs. 16 days, p = 0.033), a higher 30-day mortality rate (31% vs. 23.3%, p = 0.031), and also showed significantly higher mortality at 1-year (54% vs. 42%, p = 0.003). The subgroup of patients in whom mottling appeared during the first 24 h after admission had the worst prognosis at 30 days.

Conclusion
Skin mottling at admission in patients with cardiogenic shock was statistically associated with prolonged length of stay and poor outcomes. As a perfusion-targeted resuscitation parameter, mottling is a simple, clinical-based approach and may thus help to improve and guide immediate goal-directed therapy to improve cardiogenic shock patients’ outcomes.

Graphical Abstract
Self-determination theory interventions versus usual care in people with diabetes: a systematic review with meta-analysis and trial sequential analysis
Authors: Mathiesen Anne Sophie , Zoffmann Vibeke , Lindschou Jane , Jakobsen Janus Christian , Gluud Christian , Due-Christensen Mette , Rasmussen Bodil , Marqvorsen Emilie Haarslev Schröder , Lund-Jacobsen Trine , Skytte Tine Bruhn , Thomsen Thordis , Rothmann Mette Juel 
Published: September 2023

Abstract
Background
Autonomy-supporting interventions, such as self-determination theory and guided self-determination interventions, may improve self-management and clinical and psychosocial outcomes in people with diabetes. Such interventions have never been systematically reviewed assessing both benefits and harms and concurrently controlling the risks of random errors using trial sequential analysis methodology. This systematic review investigates the benefits and harms of self-determination theory-based interventions compared to usual care in people with diabetes.

Methods
We used the Cochrane methodology. Randomized clinical trials assessing interventions theoretically based on guided self-determination or self-determination theory in any setting were eligible. A comprehensive search (latest search April 2022) was undertaken in CENTRAL, MEDLINE, Embase, LILACS, PsycINFO, SCI-EXPANDED, CINAHL, SSCI, CPCI-S, and CPCI-SSH to identify relevant trials. Two authors independently screened, extracted data, and performed risk-of-bias assessment of included trials using the Cochrane risk-of-bias tool 1.0. Our primary outcomes were quality of life, all-cause mortality, and serious adverse events. Our secondary outcomes were diabetes distress, depressive symptoms, and nonserious adverse events not considered serious. Exploratory outcomes were glycated hemoglobin and motivation (autonomy, controlled, amotivation). Outcomes were assessed at the end of the intervention (primary time point) and at maximum follow-up. The analyses were conducted using Review Manager 5.4 and Trial Sequential Analysis 0.9.5.10. Certainty of the evidence was assessed by GRADE.

Results
Our search identified 5578 potentially eligible studies of which 11 randomized trials (6059 participants) were included. All trials were assessed at overall high risk of bias. We found no effect of self-determination theory-based interventions compared with usual care on quality of life (mean difference 0.00 points, 95% CI −4.85, 4.86, I2 = 0%; 225 participants, 3 trials, TSA-adjusted CI −11.83, 11.83), all-cause mortality, serious adverse events, diabetes distress, depressive symptoms, adverse events, glycated hemoglobulin A1c, or motivation (controlled). The certainty of the evidence was low to very low for all outcomes. We found beneficial effect on motivation (autonomous and amotivation; low certainty evidence).

Conclusions
We found no effect of self-determination-based interventions on our primary or secondary outcomes. The evidence was of very low certainty.

Systematic review registration
PROSPERO CRD42020181144
Generation and characterization of a zebrafish knockout model of abcb4, a homolog of the human multidrug efflux transporter P-glycoprotein
Authors: Park Jinhee , Kim Hyosung , Alabdalla Leen , Mishra Smriti , Mchaourab Hassane 
Published: September 2023

AbstractThe ATP-binding cassette subfamily B member 1 (ABCB1), encoding a multidrug transporter referred to as P-glycoprotein (Pgp), plays a critical role in the efflux of xenobiotics in humans and is implicated in cancer resistance to chemotherapy. Therefore, developing high-throughput animal models to screen for Pgp function and bioavailability of substrates and inhibitors is paramount. Here, we generated and validated a zebrafish knockout line of abcb4, a human Pgp transporter homolog. CRISPR/Cas9 genome editing technology was deployed to generate a frameshift mutation in exon 4 of zebrafish abcb4. The zebrafish abcb4 homozygous mutant exhibited elevated accumulation of fluorescent rhodamine 123, a substrate of human Pgp, in the intestine and brain area of embryos. Moreover, abcb4 knockout embryos were sensitized toward toxic compounds such as doxorubicin and vinblastine compared to the WT zebrafish. Immunostaining for zebrafish Abcb4 colocalized in the endothelial brain cells of adult zebrafish. Transcriptome profiling using Gene Set Enrichment Analysis uncovered that the 'cell cycle process,' 'mitotic cell cycles,' and 'microtubule-based process' were significantly downregulated in the abcb4 knockout brain with age. This study establishes and validates the abcb4 knockout zebrafish as an animal model to study Pgp function in vivo. Unexpectedly it reveals a potentially novel role for zebrafish abcb4 in age-related changes in the brain. The zebrafish lines generated here will provide a platform to aid in the discovery of modulators of Pgp function as well as the characterization of human mutants thereof.
Identification of Fazael 2 (4000–3900 BCE) as first lost wax casting workshop in the Chalcolithic Southern Levant
Authors: Rose Thomas , Bar Shay , Asscher Yotam , Goren Yuval 
Published: September 2023

Abstract
Apart from many lost wax cast metal fragments, crucible fragments and several heated sediment nodules were found at the Chalcolithic site Fazael 2 (central Jordan Valley). Petrographic investigations on the heated sediment nodules revealed many features characteristic of the Chalcolithic Southern Levantine lost wax casting moulds. Heating temperatures were assessed using infrared spectroscopy, showing that casting did not vitrify the clay fraction in the moulds. Consequently, Fazael is the first identified Chalcolithic Southern Levant production site for lost wax cast metal items. These findings confirm the existence of a metallurgical tradition with lost wax casting in the Jordan Valley parallel to the unalloyed copper metallurgy in the Northern Negev. Moreover, crucibles and heated sediment nodules are made of local ferruginous loess, a material not mentioned in previous studies on lost wax casting mould fragments. Therefore, the existence of more than one such production site must be assumed.
Game-based learning in computer science education: a scoping literature review
Authors: Videnovik Maja , Vold Tone , Kiønig Linda , Madevska Bogdanova Ana , Trajkovik Vladimir 
Published: September 2023

AbstractUsing games in education has the potential to increase students’ motivation and engagement in the learning process, gathering long-lasting practical knowledge. Expanding interest in implementing a game-based approach in computer science education highlights the need for a comprehensive overview of the literature research. This scoping review aims to provide insight into current trends and identify research gaps and potential research topics concerning game-based learning in computer science. Using standard methodology for scoping review, we identified 113 articles from four digital libraries published between 2017 and 2021. Those articles were analyzed concerning the educational level, type of the game, computer science topic covered by the game, pedagogical strategies, and purpose for implementing this approach in different educational levels. The results show that the number of research articles has increased through the years, confirming the importance of implementing a game-based approach in computer science. Different kinds of games, using different technology, concerning different computer science topics are presented in the research. The obtained results indicate that there is no standardized game or standardized methodology that can be used for the creation of an educational game for computer science education. Analyzed articles mainly implement a game-based approach using learning by playing, and no significant focus is given to the effectiveness of learning by designing a game as a pedagogical strategy. Moreover, the approach is mainly implemented for developing computational thinking or programming skills, highlighting the need for its implementation in other topics beyond programming.
Unified earthquake catalogue and mapping of Gutenberg–Richter parameters for the East African Rift System
Authors: Letamo Alemayehu , Kavitha B. , Tezeswi T. P. 
Published: September 2023

Abstract
Background
The initial phase of earthquake hazard assessment involves the consolidation of diverse magnitude scales, thereby requiring the homogenization of various magnitudes. Moment magnitude (Mw) emerges as the preferred descriptor for a range of magnitudes, encompassing local magnitude (ML), teleseismic magnitude (e.g., mb and MS), duration magnitudes (MD), and other magnitude proxies. Unlike alternative scales, Mw does not exhibit saturation at high magnitudes, enhancing its reliability. To achieve uniformity in magnitude representation, diverse regression techniques are employed, with the General Orthogonal Regression (GOR) method being widely regarded as the most dependable, accounting for uncertainty in both independent and dependent variables.

Methods
This study utilized the International Seismological Centre (ISC) Catalogue (http://www.isc.ac.uk/) to compile an array of events related to the East Africa Rift System (EARS). Subsequently, the General Orthogonal Regression method was applied to merge and harmonize the collected data. Furthermore, the research computed Gutenberg-Richter b-values using the newly unified magnitude.

Results
Notably, the conversion relationships between magnitude proxies, including MS-mb, mb-Mw, MS-Mw, and ML-Mw, exhibited robust correlations, with coefficients of 0.86, 0.80, 0.88, and 0.94, respectively. In contrast, the relationship between ML and mb proxies revealed a notably weaker correlation, registering a coefficient of 0.54. Ultimately, the study identified a magnitude of completeness and a b-value of 3.8 and 0.71, respectively, for the EARS region, providing valuable insights for earthquake hazard assessment in this area.

Conclusion
Generally, the homogeneous catalogue is a step forward in seismicity assessment and geodynamic activities in the EARS. Hence, developing the empirical equations for the area is essential for future studies on seismic hazards and engineering applications due to the peculiarity of EARS’s geological and tectonic characteristics.
Inadvertent catheter misplacement into the subclavian artery during ultrasound-guided internal jugular venous catheterization: a case report
Authors: Kohyama Tomoki , Fujimaki Keisuke , Sasamori Hiroki , Tokumine Joho , Moriyama Kiyoshi , Yorozu Tomoko 
Published: September 2023

Abstract
Background
Ultrasound-guided central venous catheterization has become a standard procedure. However, mechanical complications are still reported.

Case presentation
An 85-year-old woman presented with coagulopathic bladder tamponade. Ultrasound-guided right internal jugular venous catheterization was planned because of difficult peripheral venous access. A guidewire was advanced through a needle inserted at the midpoint of the right carotid triangle. The guidewire was identified in the short axis, but not in the long-axis ultrasound view, leading to inadvertent insertion of the catheter into the right subclavian artery through the internal jugular vein. Stent graft insertion was performed for perforation closure. The patient exhibited no symptoms of cerebral ischemia following stent graft insertion.

Discussion
This case demonstrated that the needle-sticking site should not be placed close to the clavicle for ultrasound-guided internal jugular venous catheterization, as it may not confirm the position of guidewire in the long-axis ultrasound view.
Appraising the impact of COVID-19 on trading volume of selected vessel types in sub-Saharan Africa
Authors: Olapoju Olabisi Michael 
Published: September 2023

AbstractThe emergence and diffusion of coronavirus (COVID-19) have brought a lot of impacts on various spheres of human endeavours including maritime trading. This paper explores the effect of the lockdown on maritime port calls for selected vessels in the sub-Saharan African (SSA) regions (East, Middle, South, and West Africa). The study utilizes port calls data of the maritime profile of the global economies obtained from the United Nations Conference on Trade and Development Statistics between 2018 and 2021. Data include port calls for liquid bulk carrier, liquefied petroleum gas, dry bulk carrier, dry break bulk carrier, roll-on-roll-off, and container carrier. The analysis of data involves the use of exploratory technique to reveal dimensions of performance by various carriers across the regions. The results picture the kind of response of port calls in all the regions akin to the response from other regions of the world. However, the study observes that though responses to COVID-19 lockdown across the globe were similar, SSA regions were slow in recovering from the decline in port calls when compared to the developed and some rapidly developing economies of the world due to the region’s lack of economic resilience. Thus, since ports have been identified as vulnerable to economic, social, institutional, and environmental shocks, and to dynamic and highly unpredictable demand for port services, policymakers of various nationals in the SSA may need to examine the patterns of performance of vessels in the regions to manage trade flows more effectively as a way of responding to future dynamics in maritime trade in the region.
A mixed method analysis of the Botswana schistosomiasis control policy and plans using the policy triangle framework
Authors: Gabaake Kebabonye P. , Lucero-Prisno Don Eliseo , Thakadu Olekae T. , Phaladze Nthabiseng A. 
Published: September 2023

Abstract
Background
The present goal of the World Health Organization (WHO) 2021–2030 roadmap for Neglected Tropical Diseases is to eliminate schistosomiasis as a public health problem, and reduce its prevalence of heavy infections to less than 1%. Given the evolution and impact of schistosomiasis in the Ngamiland district of Botswana, the aim of this study was to analyze the control policies for the district using the Policy Triangle Framework.

Methods
The study used a mixed method approaches of an analysis of policy documents and interviews with 12 informants who were purposively selected. Although the informants were recruited from all levels of the NTD sector, the analysis of the program was predominantly from the Ngamiland district. Data were analyzed using Braun and Clarke’s approach to content analysis.

Results
The study highlights the presence of clear, objectives and targets for the Ngamiland control policy. Another theme was the success in morbidity control, which was realized primarily through cycles of MDA in schools. The contextual background for the policy was high morbidity and lack of programming data. The implementation process of the policy was centralized at the Ministry of Health (MOH) and WHO, and there was minimal involvement of the communities and other stakeholders. The policy implementation process was impeded by a lack of domestic resources and lack of comprehensive policy content on snail control and no expansion of the policy content beyond SAC. The actors were predominately MOH headquarters and WHO, with little representation of the district, local level settings, NGOs, and private sectors.

Conclusions
The lack of resources and content in the control of environmental determinants and exclusion of other at-risk groups in the policy, impeded sustained elimination of the disease. There is a need to guide the treatment of preschool-aged children and develop national guidelines on treating foci of intense transmission. Moreover, the dynamic of the environmental transmissions and reorientation of the schistosomiasis policy to respond to the burden of schistosomiasis morbidity, local context, and health system context are required.
Data-driven next-generation smart grid towards sustainable energy evolution: techniques and technology review
Authors: Ahsan Faiaz , Dana Nazia Hasan , Sarker Subrata K. , Li Li , Muyeen S. M. , Ali Md. Firoj , Tasneem Zinat , Hasan Md. Mehedi , Abhi Sarafat Hussain , Islam Md. Robiul , Ahamed Md. Hafiz , Islam Md. Manirul , Das Sajal K. , Badal Md. Faisal R. , Das Prangon 
Published: September 2023

AbstractMeteorological changes urge engineering communities to look for sustainable and clean energy technologies to keep the environment safe by reducing CO2 emissions. The structure of these technologies relies on the deep integration of advanced data-driven techniques which can ensure efficient energy generation, transmission, and distribution. After conducting thorough research for more than a decade, the concept of the smart grid (SG) has emerged, and its practice around the world paves the ways for efficient use of reliable energy technology. However, many developing features evoke keen interest and their improvements can be regarded as the next-generation smart grid (NGSG). Also, to deal with the non-linearity and uncertainty, the emergence of data-driven NGSG technology can become a great initiative to reduce the diverse impact of non-linearity. This paper exhibits the conceptual framework of NGSG by enabling some intelligent technical features to ensure its reliable operation, including intelligent control, agent-based energy conversion, edge computing for energy management, internet of things (IoT) enabled inverter, agent-oriented demand side management, etc. Also, a study on the development of data-driven NGSG is discussed to facilitate the use of emerging data-driven techniques (DDTs) for the sustainable operation of the SG. The prospects of DDTs in the NGSG and their adaptation challenges in real-time are also explored in this paper from various points of view including engineering, technology, et al. Finally, the trends of DDTs towards securing sustainable and clean energy evolution from the NGSG technology in order to keep the environment safe is also studied, while some major future issues are highlighted. This paper can offer extended support for engineers and researchers in the context of data-driven technology and the SG.