bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration method of large-scale photovoltaic system in distribution network based on improved multi-objective TLBO algorithm
Authors: Liu Shili , Yang Fan , Li Jianqing , Cheng Zhiyu , Zhang Tianzhong , Cheng Tingli , Guo Yuanjun
Published: January 2024

The increasing integration of distributed generations brings great challenges to the power grid. In this paper, a distributed photovoltaic (PV) integration methodology in distribution network is established for large-scale PV penetration. Firstly, a PV integration model was formulated with the aim of maximizing PV integration capacity and enhancing the voltage profile. Specially, the PV large-scale integration model for county-wide promotion is proposed by considering various typical integration scenarios. Additionally, a novel improved multi-objective Teaching-Learning based optimization (TLBO) algorithm, namely, IM-TLBO, was proposed to seek an optimal Pareto front of the PV integration model. The IM-TLBO algorithm innovatively incorporates the elite reverse learning search strategy to enhance exploration in the solution space. Moreover, the differentiated teaching guided by optimal individual and central location is employed to improve the efficiency of the “teaching” process. Meanwhile, a cyclic crowded sort deletion based on crowding distance is developed to enhance the diversity of elite individuals and the distribution characteristics of the Pareto Frontier. Finally, the performance of IM-TLBO is tested in benchmark functions. Also, a simulation case in IEEE 33 bus system is performed to verify the proposed PV integration method. It is observed that the proposed method in this paper can not only realize the overall optimal integration of roof distributed PV, but also improve voltage profile. The results of IM-TLBO are compared to other classical algorithms, and it is shown that IM-TLBO outperformed them in terms of convergence, distribution and diversity.
Numerical simulation of CO2-enhanced oil recovery in fractured shale reservoirs using discontinuous and continuous Galerkin finite element methods
Authors: Ma Tianran , Jiang Lintong , Liu Yanbao , Guo Chaobin , Shen Weijun , Xu Yongli
Published: January 2024

Introduction: This study explores the potential of enhancing shale oil recovery and reducing CO2 emissions through CO2 injection in fractured shale reservoirs. The importance of this approach lies in its dual benefit: improving oil extraction efficiency and addressing environmental concerns associated with CO2 emissions.

Method: We employed a discrete fracture-matrix model to simulate CO2 flooding in fractured shale reservoirs, utilizing both discontinuous Galerkin (DG) and continuous Galerkin (CG) finite element methods. The DG-CG FEM’s accuracy was validated against the McWhorter problem, ensuring the reliability of the simulation results. Our model also considered various factors, including reservoir heterogeneity, fracture permeability, CO2 injection volume, and gas injection patterns, to analyze their impact on shale oil recovery.

Result: Our simulations revealed that fractured reservoirs significantly enhance shale oil production efficiency compared to homogeneous reservoirs, with an approximate 48.9% increase in production. A notable increase in shale oil production, by 15.8%, was observed when fracture permeability was increased by two orders of magnitude. Additionally, a fourfold increase in CO2 injection rate resulted in a 31.5% rise in shale oil production. Implementing a step-by-step reduction in injection volume while maintaining the total CO2 injection constant proved to be more effective than constant-rate injections.

Discussion: The study demonstrates the effectiveness of CO2 flooding in fractured shale reservoirs for enhancing shale oil recovery.
Optimal scheduling of electric-gas-heat system considering dual virtual energy storage of gas network management and heat network storage
Authors: Yang Xiuyu , Liu Yuxuan , Zhang Hao , Guo Qi , Liu Xueyuan , Sun Jianshu
Published: January 2024

Aiming at the problem of wind curtailment caused by the lack of system flexibility, an optimal scheduling strategy for improving the flexibility of the electricity-gas-heat interconnection system by the coordinated operation of the gas network management and storage characteristics and the heat storage characteristics of the heat network is proposed. Firstly, the influence of gas network storage and heat network storage on improving flexibility is analyzed respectively. Then, an electricity-gas-heat interconnected system scheduling model considering the dynamic characteristics of gas network management and t the delay characteristics of heat storage in heat network, which greatly improves the imbalance between supply and demand of flexibility in space and time brought by the anti-peak regulation characteristics of wind power to the system. Finally, the IEEE-24 nodes power system, Belgium’s 20-node natural gas network and 6-node thermal network are used, for example, analysis. The results show that the proposed scheduling scheme improves the flexibility of the system while its operating cost and wind curtailment cost are the lowest, which promotes the consumption of wind power.
An attack-resilient distributed energy management strategy for integrated energy systems
Authors: Li Tong , Sun Feng , Chen Jian , Wang Lei , Yang Zhibin , Liu Ruitong , Qi Jun
Published: January 2024

The increasing integration of various energy sources and the adoption of smart grid technologies have revolutionized the way we generate, distribute, and consume energy. While these advancements offer numerous benefits, they also introduce vulnerabilities to cyber–physical attacks. To this aim, this paper investigates a resilient energy management strategy for integrated energy systems. By adopting a switched control approach and incorporating a local estimation mechanism, we have developed a resilient distributed energy management strategy to tackle the energy management problem (EMP) in integrated energy systems (IESs). This methodology demonstrates strong robustness and resilience, successfully detecting data integrity attacks and denial-of-service (DoS) attacks. Finally, we provide a case study to demonstrate the effectiveness of our proposed strategy in a real-world scenario.
Managing the challenge of fatigue for pilots operating ultra-long range flights
Authors: Signal T. L. , van den Berg M. J. , Zaslona J. L. , Wu L. , Hughes M. , Johnston B. , Dyer C. , Drane M. , Glover M.
Published: January 2024

Introduction

Ultra-long range (ULR) flights are defined as exceeding regulatory limits: normally 16 h flight time. They pose challenges due to long duty periods that could result in extended wakefulness and sleep loss, increasing the risk of fatigue. This study describes the mitigations used to manage fatigue in these operations. Two data collection phases were conducted on the Auckland-Chicago ULR route: when the route commenced (Study 1) and when the flight crew complement was altered (Study 2). Seasonal differences were also investigated.

Methods

Study 1 involved 72 crew who completed diaries and wore an actigraph to record sleep pre-departure, throughout the trip, and on return. In-flight, fatigue, sleepiness and workload were reported, and reaction time performance was measured. Study 2 involved 75 crew and data collection in the northern summer and northern winter. Crew completed diaries throughout the trip.

Results

Study 1 data found crew sleep longer than usual in the 24 h pre trip and post flights. On the shorter outbound flight in-flight sleep averaged 3.3 h and on the longer inbound flight, 3.3–3.8 h, with most crew taking 3 breaks. Ratings of sleepiness and fatigue increased, and reaction time performance declined across flights, with greater decrements on longer inbound flights. Pilots did not fully adjust their sleep patterns to local time during the layover and no seasonal differences were found. Comparisons between Study 1 and 2 showed no difference in ratings of fatigue and sleepiness or in-flight sleep duration with an altered crew complement. There was a trend for Captains to report greater workload and less in-flight sleep in Study 2.

Discussion

Mitigations that allow for preparation and recovery are well utilized by crew. In-flight sleep is relatively short and ways of increasing the amount of sleep obtained should be considered. The incomplete adaptation of sleep during the layover has implications for rest break strategies on the return flight. The altered crew complement did not result in higher levels of fatigue or sleepiness or less in-flight sleep on average, although findings suggest a need to understand the effects of changing the crew complement on workload and in-flight sleep for Captains.
Do financial development, urbanization, economic growth and renewable energy promote the emission mitigation agenda of Africa? Evidence from models that account for cross-sectional dependence and slope heterogeneity
Authors: Kong Yusheng , Donkor Mary , Jin Cheng , Musah Mohammed , Nkyi Joseph Akwasi
Published: January 2024

Carbon emissions from anthropogenic human activities are viewed as the major cause of pollution in the environment. The Paris Treaty came into effect to help minimize the galloping rate of global ecological pollution. The surge in global emissions has prompted other nations to change their environmental regulations to help them to attain their emission mitigation agenda. For instance, China, United States and India have improved their Nationally Determined Contributions they pledged as signatories to the Paris Accord to help them to achieve their sustainable development goals But, despite nations committing to the guidelines of this accord, ecological contamination continues to rise in the globe. To help curb the above menace, a study on the connection between financial development, urbanization, economic growth, renewable energy consumption, and environmental quality of 27 countries from North, South and East Africa over the period 1990 to 2019 was conducted. In attaining this goal, econometric techniques that are robust to heterogeneity and residual cross-sectional dependence were deemed appropriate. From the preliminary analysis, the panel was heterogeneous and cross-sectionally dependent. Also, all the series were stationary after first difference and cointegrated in the long-run. On the regression estimates via the common correlated effects mean group technique, financial development improved environmental quality in the North, South and Eastern regions by 0.56%, 0.42%, and 0.44% respectively. Also, renewable energy promoted ecological safety in the Northern and Eastern regions by 0.24% and 0.08% respectively, but degraded environmental sustainability in the Southern region by 0.66%. Besides, economic growth deteriorated the environment in the North by 0.66%, South by 0.41%, and East by 0.25%. However, urbanization enhanced ecological safety in the East by 0.63%, but had immaterial effect on environmental quality in the North and Southern regions of Africa. Some of the aforestated results are consistent to those under the dynamic common correlated effects mean group (DCCEMG) technique as an alternative estimator. Policy recommendations to help advance the carbon-neutrality target of the regions were proposed.
Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond (Prunus tenella)
Authors: Liu Xingyue , Zhang Dongdong , Yu Zhenfan , Zeng Bin
Published: January 2024

Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a “living fossil of plants.” It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees.

Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae.

Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.
Cancer incidence, mortality, and survivorship in African women: a comparative analysis (2016–2020)
Authors: Nwagwu Chibuikem Chrysogonus , Ogoke Uchenna Petronilla
Published: January 2024

Objectives

This research aims to provide concrete insight into cancer incidence, mortality, and survivorship dynamics among African women between 2016 and 2020.

Methods

The study computes the Mortality-to-Incidence Ratio (MIR) for 53 countries in Africa with available mortality and incidence data. It uses relevant Life Tables to obtain the 5-year Relative Survival rate for women in different age cohorts based on General Survival Rate and 5-year Cancer Prevalence data from the World Health Organization (WHO). The study performs an analysis of variance tests.

Results

The results of the initial data analysis show that women in the top economies in Africa have the highest cancer incidence and mortality. The study also finds that women in Northern and Southern African countries have higher relative survival rates and lower MIR than other African regions. ANOVA results confirm statistically significant differences in 5-year relative survival across the African regions. The relative survival at 5 years was an average of 45% across all age groups within the continent although relative survival is highest among females aged 5–19 and 80–84. The lowest relative survival rates are seen for infants (0–4), adolescents and young adults (25–29), and the very elderly (85+).

Conclusion

The study concludes that while cancer incidence in Africa is linked to affluence, survival is very challenging, especially for the least developed economies in Western, Eastern, and Central Africa. The results indicate the need for crucial intervention in the continent concerning awareness, research, and data collection methodology.
Delays in the decision to seek care and associated factors among mothers who delivered in rural health centers in Wolaita Zone, Southern Ethiopia
Authors: Gelaw Kelemu Abebe , Atalay Yibeltal Assefa , Zerefu Firehiwot , Gebeyehu Natnael Atnafu
Published: January 2024

Background

Delays in seeking care in health facilities during pregnancy and childbirth can potentially lead to adverse outcomes for women with obstetric complications. These complications lead to maternal mortality and morbidity in developing countries such as Ethiopia. The magnitude and underlying causes of maternal first delay in Ethiopia, particularly in rural areas of the country, are not well documented. This study aims to assess the magnitude of delay in the decision to seek care and associated factors among mothers who gave birth in rural health centers in Wolaita Zone, Southern Ethiopia.

Method and materials

A facility-based cross-sectional study was undertaken among mothers who gave birth in rural health centers of Wolaita Zone, Southern Ethiopia, from 30 June 2020 to 30 July 2022. A sample size of 410 study participants was selected from each public health center using the systematic random sampling method. Data were collected from a pretested and structured questionnaire using an Open Data Kit; analysis was carried out using SPSS version 25. The determining factors for the first delay were identified using binary logistic regression. Variables with a p-value of less than 0.25 in binary analysis were selected for a multivariable analysis. Variables with a p-value of less than 0.05 were considered statistically significant.

Results

The magnitude of delay in the decision to seek care in health facilities was 42.1% among mothers who gave birth in rural health centers in the Wolaita Zone, Southern Ethiopia. Unemployed mothers (Adjusted Odd Ratio, 2,529; 95% CI, 1.546, 4.136), husbands with no formal education (Adjusted Odd Ratio, 1.290; 95% CI, 1.029, 1.616), mothers who had negative attitudes towards seeking care in health facilities, and (Adjusted Odd Ratio; 1.695; 95% CI, 1.061, 2.709) were significantly associated with a delay in the decision to seek care at a health facility.

Conclusion

The magnitude of the first maternal decision to seek care at health facilities among mothers was high in the study area. Efforts should be made to strengthen the literacy level of the husbands of mothers and increase household income through various income-generating approaches. In addition, the dissemination of health information could effectively raise community awareness of the importance of institutional delivery.
Identity digitalization as dispossession and entrenched displacement: digitalization at the nexus of migration “management” and climate change in Thailand and Türkiye
Authors: Flaim Amanda , Nawyn Stephanie J.
Published: January 2024

Digitalizing technologies are increasingly heralded by a range of powerful actors and some human rights organizations as appropriate and necessary tools for ‘managing migration’ and mitigating climate change. Yet, just as exclusionary and marginalizing discourses of “migration problems” serve to justify the digital surveillance of vulnerable and precariously statused people, the context of climate change, accelerating contestation over land and water, and discourses of catastrophe prove fertile ground for entrenching these practices and technologies in multiple ways. Researchers are identifying the dispossessive power of digitalization in the arena of personal identification and in relation to resource and land mapping, yet these dynamics are rarely interrogated in connection. In this comparative analysis, we draw from sustained ethnographic engagement and insights in critical digitalization studies and political economy to analyze the consequences of state efforts to digitalize identity and resources in Thailand and Türkiye in the age of the Anthropocene. Our research points to a need for greater attention to the ways that state efforts to digitalize identification and registration of immigrant, refugee, and stateless people link with, and can facilitate, more efficient dispossessions and displacements of precariously statused communities from vital and contested lands.
Platelets modulate cardiac remodeling via the collagen receptor GPVI after acute myocardial infarction
Authors: Reusswig Friedrich , Dille Matthias , Krüger E. , Ortscheid J. , Feige Tobias , Gorressen S. , Fischer J.-W. , Elvers Margitta
Published: January 2024

Introduction

Platelets play an important role in cardiovascular diseases. After acute myocardial infarction, platelets display enhanced activation and migrate into the infarct zone. Furthermore, platelets trigger acute inflammation and cardiac remodeling leading to alterations in scar formation and cardiac function as observed in thrombocytopenic mice. GPVI is the major collagen receptor in platelets and important for platelet activation and thrombus formation and stability. Antibody induced deletion of GPVI at the platelet surface or treatment of mice with recombinant GPVI-Fc results in reduced inflammation and decreased infarct size in a mouse model of AMI. However, the role of GPVI has not been fully clarified to date.

Methods/Results

In this study, we found that GPVI is not involved in the inflammatory response in experimental AMI using GPVI deficient mice that were analyzed in a closed-chest model. However, reduced platelet activation in response to GPVI and PAR4 receptor stimulation resulted in reduced pro-coagulant activity leading to improved cardiac remodeling. In detail, GPVI deficiency in mice led to reduced TGF-β plasma levels and decreased expression of genes involved in cardiac remodeling such as Col1a1, Col3a1, periostin and Cthrc1 7 days post AMI. Consequently, collagen quality of the scar shifted to more tight and less fine collagen leading to improved scar formation and cardiac function in GPVI deficient mice at 21d post AMI.

Conclusion

Taken together, this study identifies GPVI as a major regulator of platelet-induced cardiac remodeling and supports the potential relevance of GPVI as therapeutic target to reduce ischemia reperfusion injury and to improve cardiac healing.
Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis
Authors: Ye Shuyu , Lyu Yongqing , Chen Libin , Wang Yiwei , He Yue , Li Quansi , Tian Li , Liu Fen , Wang Xiaoyan , Ai Feiyan
Published: January 2024

Background

Ulcerative colitis (UC) is a lifelong inflammatory disease affecting the rectum and colon with numerous treatment options that require an individualized treatment plan. Histone modifications regulate chromosome structure and gene expression, resulting in effects on inflammatory and immune responses. However, the relationship between histone modification-related genes and UC remains unclear.

Methods

Transcriptomic data from GSE59071 and GSE66407 were obtained from the Gene Expression Omnibus (GEO), encompassing colonic biopsy expression profiles of UC patients in inflamed and non-inflamed status. Differentially expressed gene (DEG) analyses, functional enrichment analyses, weighted gene co-expression network analysis (WGCNA), and random forest were performed to identify histone modification-related core genes associated with UC inflammation. Features were screened through the least absolute shrinkage and selection operator (LASSO) and support vector machine‐recursive feature elimination (SVM‐RFE), establishing a molecular inflammatory predictive model using logistic regression. The model was validated in the GSE107499 dataset, and the performance of the features was assessed using receiver operating characteristic (ROC) and calibration curves. Immunohistochemistry (IHC) staining of colonic biopsy tissues from UC patients treated with infliximab was used to further confirm the clinical application value. Univariate logistic regression on GSE14580 highlighted features linked to infliximab response.

Results

A total of 253 histone modification-related DEGs were identified between inflammatory and non-inflammatory patients with UC. Seven key genes (IL-1β, MSL3, HDAC7, IRF4, CAMK2D, AUTS2, and PADI2) were selected using WGCNA and random forest. Through univariate logistic regression, three core genes (CAMK2D, AUTS2, and IL-1β) were further incorporated to construct the molecular inflammatory predictive model. The area under the curve (AUC) of the model was 0.943 in the independent validation dataset. A significant association between CAMK2D protein expression and infliximab response was observed, which was validated in another independent verification set of GSE14580 from the GEO database.

Conclusion

The molecular inflammatory predictive model based on CAMK2D, AUTS2, and IL-1β could reliably distinguish the mucosal inflammatory status of UC patients. We further revealed that CAMK2D was a predictive marker of infliximab response. These findings are expected to provide a new evidence base for personalized treatment and management strategies for UC patients.
DEK deficiency suppresses mitophagy to protect against house dust mite-induced asthma
Authors: Bai Qiaoyun , Liu Ruobai , Quan Changlin , Han Xue , Wang Dandan , Wang Chongyang , Wang Zhiguang , Li Li , Li Liangchang , Piao Hongmei , Song Yilan , Yan Guanghai
Published: January 2024

DEK protein is highly expressed in asthma. However, the mechanism of DEK on mitophagy in asthma has not been fully understood. This study aims to investigate the role and mechanism of DEK in asthmatic airway inflammation and in regulating PINK1-Parkin-mediated mitophagy, NLRP3 inflammasome activation, and apoptosis. PINK1-Parkin mitophagy, NLRP3 inflammasome, and apoptosis were examined after gene silencing or treatment with specific inhibitors (MitoTEMPO, MCC950, and Ac-DEVD-CHO) in house dust mite (HDM) or recombinant DEK (rmDEK)-induced WT and DEK-/- asthmatic mice and BEAS-2B cells. The regulatory role of DEK on ATAD3A was detected using ChIP-sequence and co-immunoprecipitation. rmDEK promoted eosinophil recruitment, and co-localization of TOM20 and LC3B, MFN1 and mitochondria, LC3B and VDAC, and ROS generation, reduced protein level of MnSOD in HDM induced-asthmatic mice. Moreover, rmDEK also increased DRP1 expression, PINK1-Parkin-mediated mitophagy, NLRP3 inflammasome activation, and apoptosis. These effects were partially reversed in DEK-/- mice. In BEAS-2B cells, siDEK diminished the Parkin, LC3B, and DRP1 translocation to mitochondria, mtROS, TOM20, and mtDNA. ChIP-sequence analysis showed that DEK was enriched on the ATAD3A promoter and could positively regulate ATAD3A expression. Additionally, ATAD3A was highly expressed in HDM-induced asthma models and interacted with DRP1, and siATAD3A could down-regulate DRP1 and mtDNA-mediated mitochondrial oxidative damage. Conclusively, DEK deficiency alleviates airway inflammation in asthma by down-regulating PINK1-Parkin mitophagy, NLRP3 inflammasome activation, and apoptosis. The mechanism may be through the DEK/ATAD3A/DRP1 signaling axis. Our findings may provide new potential therapeutic targets for asthma treatment.
Glioma: bridging the tumor microenvironment, patient immune profiles and novel personalized immunotherapy
Authors: Mishchenko Tatiana A. , Turubanova Victoria D. , Gorshkova Ekaterina N. , Krysko Olga , Vedunova Maria V. , Krysko Dmitri V.
Published: January 2024

Glioma is the most common primary brain tumor, characterized by a consistently high patient mortality rate and a dismal prognosis affecting both survival and quality of life. Substantial evidence underscores the vital role of the immune system in eradicating tumors effectively and preventing metastasis, underscoring the importance of cancer immunotherapy which could potentially address the challenges in glioma therapy. Although glioma immunotherapies have shown promise in preclinical and early-phase clinical trials, they face specific limitations and challenges that have hindered their success in further phase III trials. Resistance to therapy has been a major challenge across many experimental approaches, and as of now, no immunotherapies have been approved. In addition, there are several other limitations facing glioma immunotherapy in clinical trials, such as high intra- and inter-tumoral heterogeneity, an inherently immunosuppressive microenvironment, the unique tissue-specific interactions between the central nervous system and the peripheral immune system, the existence of the blood-brain barrier, which is a physical barrier to drug delivery, and the immunosuppressive effects of standard therapy. Therefore, in this review, we delve into several challenges that need to be addressed to achieve boosted immunotherapy against gliomas. First, we discuss the hurdles posed by the glioma microenvironment, particularly its primary cellular inhabitants, in particular tumor-associated microglia and macrophages (TAMs), and myeloid cells, which represent a significant barrier to effective immunotherapy. Here we emphasize the impact of inducing immunogenic cell death (ICD) on the migration of Th17 cells into the tumor microenvironment, converting it into an immunologically “hot” environment and enhancing the effectiveness of ongoing immunotherapy. Next, we address the challenge associated with the accurate identification and characterization of the primary immune profiles of gliomas, and their implications for patient prognosis, which can facilitate the selection of personalized treatment regimens and predict the patient’s response to immunotherapy. Finally, we explore a prospective approach to developing highly personalized vaccination strategies against gliomas, based on the search for patient-specific neoantigens. All the pertinent challenges discussed in this review will serve as a compass for future developments in immunotherapeutic strategies against gliomas, paving the way for upcoming preclinical and clinical research endeavors.
DARTS: an open-source Python pipeline for Ca2+ microdomain analysis in live cell imaging data
Authors: Woelk Lena-Marie , Kovacevic Dejan , Husseini Hümeyra , Förster Fritz , Gerlach Fynn , Möckl Franziska , Altfeld Marcus , Guse Andreas H. , Diercks Björn-Philipp , Werner René
Published: January 2024

Ca2+ microdomains play a key role in intracellular signaling processes. For instance, they mediate the activation of T cells and, thus, the initial adaptive immune system. They are, however, also of utmost importance for activation of other cells, and a detailed understanding of the dynamics of these spatially localized Ca2+ signals is crucial for a better understanding of the underlying signaling processes. A typical approach to analyze Ca2+ microdomain dynamics is live cell fluorescence microscopy imaging. Experiments usually involve imaging a larger number of cells of different groups (for instance, wild type and knockout cells), followed by a time consuming image and data analysis. With DARTS, we present a modular Python pipeline for efficient Ca2+ microdomain analysis in live cell imaging data. DARTS (Deconvolution, Analysis, Registration, Tracking, and Shape normalization) provides state-of-the-art image postprocessing options like deep learning-based cell detection and tracking, spatio-temporal image deconvolution, and bleaching correction. An integrated automated Ca2+ microdomain detection offers direct access to global statistics like the number of microdomains for cell groups, corresponding signal intensity levels, and the temporal evolution of the measures. With a focus on bead stimulation experiments, DARTS provides a so-called dartboard projection analysis and visualization approach. A dartboard projection covers spatio-temporal normalization of the bead contact areas and cell shape normalization onto a circular template that enables aggregation of the spatiotemporal information of the microdomain detection results for the individual cells of the cell groups of interest. The dartboard visualization allows intuitive interpretation of the spatio-temporal microdomain dynamics at the group level. The application of DARTS is illustrated by three use cases in the context of the formation of initial Ca2+ microdomains after cell stimulation. DARTS is provided as an open-source solution and will be continuously extended upon the feedback of the community.

Code available at:10.5281/zenodo.10459243.
Minimal residual disease guided radical chemoradiotherapy combined with immunotherapy after neoadjuvant immunochemotherapy followed by adjuvant immunotherapy for esophageal squamous cell cancer (ECMRD-001): a study protocol for a prospective cohort study
Authors: Wang Hesong , Zhang Xueyuan , Zhao Xiaohan , Song Chunyang , Deng Wenzhao , Shen Wenbin
Published: January 2024

Introduction

For locally advanced, inoperable esophageal cancer, concurrent chemoradiotherapy (CCRT) becomes the norm. Combining immunotherapy with radiotherapy has been shown to improve efficacy. Circulating tumor DNA (ctDNA) is a strong predictor of effectiveness and tumor recurrence and is indicative of minimal residual disease (MRD). Patients with inoperable stage II-III esophageal squamous cell carcinoma (ESCC) are enrolled in the ECMRD-001 trial to evaluate changes in MRD status before and after CCRT combined with immunotherapy and adjuvant immunotherapy following neoadjuvant immunochemotherapy.

Methods and analysis

The ECMRD-001 trial is a prospective cohort study. Eligible patients will receive radical concurrent chemoradiotherapy combined with immunotherapy after neoadjuvant immunochemotherapy, followed by adjuvant immunotherapy for at least one year. Follow-up will be up to three years. MRD-related blood and tissue samples and T-cell immunohistobank related blood and tissue samples collected before, during and after treatment and follow-up will be grouped into sample collection time points. The relationship between MRD status at different time points and treatment efficacy is the primary outcome. Correlation between MRD status and immune microenvironment, radiotherapy dose, and tumor recurrence are the secondary outcomes. Examination of ctDNA mutations is the exploratory outcome.

Discussion

ctDNA-based MRD may be a potential predictive marker for the efficacy and tumor recurrence of inoperable ESCC patients. Elevated ctDNA-MRD may predict tumor recurrence earlier than imaging. ctDNA-based MRD analysis and ctDNA-based MRD guided diagnosis and treatment should be implemented into clinical practice to improve efficacy and reduce tumor recurrence of inoperable stage II-III ESCC.

Trial registration

The ECMRD-001 study has been registered at ClinicalTrials.gov as NCT05952661 (July 19, 2023), https://classic.clinicaltrials.gov/ct2/show/NCT05952661.
Click-click, who’s there? Acoustically derived estimates of sperm whale size distribution off western Ireland
Authors: Barile Cynthia , Berrow Simon , O’Brien Joanne
Published: January 2024

Understanding the structure of populations is a critical element to the establishment of management and conservation measures. Sperm whalesPhyseter macrocephalusare characterised by a demographic spatial segregation, associated with a conspicuous sexual dimorphism reflected in their vocalisations. These characteristics make acoustic techniques very relevant to the study of sperm whale population structure, especially in remote, challenging environments. The reliability of using inter-pulse intervals of sperm whale clicks to infer body size has long been verified and extensively used. We provide the first size structure estimates of the sperm whale population in an area where assumptions on population structure mainly relied on sparse observations at sea, whaling records and stranding data. Over 10,000 hours of acoustic data collected using both static acoustic recorders and towed hydrophone arrays in Irish offshore waters were processed using a machine learning-based tool aimed at automatically extracting inter-pulse intervals from sperm whale recordings. Our analyses suggested that, unlike previously thought, large males would not account for the majority of the animals recorded in the area. We showed that adult females/juvenile males (length 9-12 m) were predominant, accounting for 49% (n = 788) of the number of individuals recorded (n = 1,595), while the proportions of immature individuals (length<9 m) and adult males (length >12 m) were well balanced, accounting for 25% (n = 394) and 26% (n = 413) of the recorded whales, respectively. Our data also suggested some size segregation may be occurring within the area, with smaller individuals to the south. The implications of such findings are crucial to the management of the population and provide an important baseline to monitor changes in population structure, particularly relevant under changing habitat conditions.
Geomorphometric maps of Australia’s Marine Park estate and their role in improving the integrated monitoring and management of marine ecosystems
Authors: Lucieer Vanessa , Flukes Emma , Monk Jacquomo , Walsh Peter
Published: January 2024

The loss of marine biodiversity is a major global issue that needs to be prioritised. In Australia, a considerable proportion (48%) of its Exclusive Economic Zone is dedicated to marine protected areas. To effectively manage this network of marine protected areas Australia has recently introduced a Management Effectiveness system. This system is designed to identify, monitor, and manage natural values and the various activities and pressures affecting the Australian Marine Parks (AMPs). Key to this approach is the identification and accurate mapping of the location of these values and pressures acting on the seabed. The AusSeabed program is a national initiative in Australia aimed at improving access to bathymetric data and coordinating efforts to collect such data in Australian waters. This manuscript proposes a novel systematic processing method to create detailed and scalable geomorphometric maps from AusSeabed’s bathymetric data holdings, intended as a standard operating procedure for initial bathymetric data interpretation in the AMPs. Utilising this workflow, we produce seafloor geomorphometry maps across 37 AMPs within which sufficient bathymetric data has been collected. These maps can be used 1) for predictive mapping of biological assemblages; 2) in field sampling design for the collection of ‘ground truthing’ data (e.g. underwater imagery and sediment samples) to validate habitat maps from bathymetric datasets; and 3) as input datasets for subsequent geomorphological mapping with a deeper understanding of seafloor processes. This research highlights the importance of robust geomorphometry classification standards to ensure consistency in mapping Australia’s marine estate in preparation for the Decade of Oceans plans. The Seamap Australia program provides a stepwise approach to advancing Australia’s national collection of bathymetric data into derived products that can enable habitat mapping of Australian waters, providing a foundational tool for the adaptive management of AMPs.
Morphological and functional parameters in X-linked retinoschisis patients–A multicentre retrospective cohort study
Authors: Kiraly Peter , Seitz Immanuel P. , Abdalla Elsayed Maram E. A. , Downes Susan M. , Patel Chetan K. , Charbel Issa Peter , Birtel Johannes , Mautone Luca , Dulz Simon , Atiskova Yevgeniya , Herrmann Philipp , Vrabič Nika , Jarc-Vidmar Martina , Hawlina Marko , Fischer M. Dominik
Published: January 2024

Introduction

X-linked retinoschisis (XLRS) is a potential target for gene supplementation approaches. To establish potential structural and functional endpoints for clinical trials, a comprehensive understanding of the inter-eye symmetry, relationship between structural and functional parameters, and disease progression is vital.

Methods

In this retrospective multicentre study, 118 eyes of 59 XLRS patients with RS1 mutations were assessed. Information from center databases included: RS1 variant; age at presentation; best-corrected visual acuity (BCVA), central retinal thickness (CRT), macular volume (MV) at presentation and at the last follow up; full-field electroretinogram (ERG) findings; presence of peripheral retinoschisis and complications (vitreous hemorrhage, retinal detachment); treatment with systemic or topical carbonic anhydrase inhibitors (CAI).

Results

Inter-eye symmetry revealed strong correlation in CRT (r = 0.77; p < 0.0001) and moderate correlations in MV (r = 0.51, p < 0.0001) and BCVA (r = 0.49; p < 0.0001). Weak or no correlations were observed between BCVA and structural parameters (CRT, MV). Peripheral retinoschisis was observed in 40 (68%), retinal detachment in 9 (15%), and vitreous hemorrhage in 5 (8%) patients, respectively. Longitudinal examinations (mean, 4.3 years) showed no BCVA changes; however, a reduction of the CRT (p = 0.02), and MV (p = 0.01) was observed. Oral and/or topical CAI treatment did not significantly alter the CRT (p = 0.34).

Discussion

The XLRS phenotype demonstrates a strong CRT symmetry between the eyes within individual patients and stable BCVA over several years. BCVA exhibits a weak correlation with the morphological parameters of retinal thickness (CRT MV). In our cohort, longitudinal functional changes were not significant, likely attributed to the short average follow-up period. Furthermore, CAI treatment didn’t influence both morphological and functional outcomes.
Microbial transformation of soil organic matter under varying agricultural management systems in Ukraine
Authors: Symochko Lyudmyla , Demyanyuk Olena , Crisan Vlad , Dinca Lucian
Published: January 2024

Introduction

This paper presents comparative studies on the content and structure of organic matter (OM) and the activity of microbiological cellulose destruction in three types of Ukrainian soils intensively used in agricultural production.

Methods

The highest content of humus in the arable layer (4.9%), OM (410 t ha−1), and total carbon (30.9 mg C g−1 soil) was determined in chernic phaeozems, which is 2.2–2.5 times higher than in albic retisols. The soil of natural ecosystems is characterised by a high content of microbial carbon (Cmic) in the carbon fraction of organic soil compounds.

Results and discussion

In arable soils, the content and reserves of humus and soil organic matter (SOM) have decreased by an average of 1.5–2 times. The most considerable loss of humus reserves in the soil profile was identified in albic retisols (1.96–1.44 times) and the smallest in chernic phaeozems (1.27–1.81 times). During the long-term systematic application of mineral fertilisers, the Corg content decreased by 8-21% in chernic phaeozems, 12-33% in greyzemic phaeozems, and 6–38% in albic retisols. A significant difference of 2.1–8.0 times was determined regarding the number of aerobic cellulolytic microorganisms and 1.3–3.3 times in the potential cellulolytic activity of the studied soils. The high number of cellulose-destroying microorganisms is characteristic of chernic phaeozems with a high content of OM in the soil; the advantage over other types of studied soils was 1.4 times and 7.8 times for greyzemic phaeozems and albic retisols, respectively. Among the studied soil types, high values of CO2 emissions were identified in chernic phaeozems. Intensive agricultural practices in Ukrainian soils have significantly altered the content and composition of organic matter, leading to reduced humus and soil organic matter reserves. The study also underscores the importance of considering the abundance of cellulose-destroying microorganisms and their potential activity in assessing soil health and sustainability.
Molecular detection of Rickettsiales and a potential novel Ehrlichia species closely related to Ehrlichia chaffeensis in ticks (Acari: Ixodidae) from Shaanxi Province, China, in 2022 to 2023
Authors: Zhang Xue , Lv Wen , Teng Zhongqiu , Zhao Na , Zhou Yue , Ma Di , Ma Lin , Cheng Yuqing , Wei Jianjun , He Jia , Ma Wenke , Liu Dongli , Qin Tian
Published: January 2024

Important tick-borne diseases include spotted fever group Rickettsia (SFGR), Anaplasma, and Ehrlichia, which cause harm to animal and human health. Ixodidae are the primary vectors of these pathogens. We aimed to analyze the prevalence and genetic diversity of SFGR, Anaplasma, and Ehrlichia species in the Ixodidae in Shaanxi Province, China. Herein, 1,113 adult Ixodidae ticks were collected from domestic cattle and goats, and detected using nested PCR. A total of four Ixodidae species were collected and Ca. R. jingxinensis (20.58%, 229/1113), A. bovis (3.05%, 34/1113), A. capra (3.32%, 37/1113), A. marginale (0.18%, 2/1113), E. sp. Yonaguni138 (0.18%, 2/1113), and a potent novel Ehrlichia species named E. sp. Baoji96 (0.09%, 1/1113) were detected. A. marginale was detected for the first time in Rhipicephalus microplus. E. sp. Baoji96 was closely related to E. chaffeensis and was first identified in Haemaphysalis longicornis. In addition, co-infection with two Rickettsiales pathogens within an individual tick was detected in 10 (1.54%) ticks. This study provides a reference for the formulation of biological control strategies for ticks and tick-borne diseases in Shaanxi Province, and could lead to an improved control effect.
The analysis of low-dose glucocorticoid maintenance therapy in patients with primary nephrotic syndrome suffering from COVID-19
Authors: Li Yong-Qi , Wu Min , Wang Yu-Jia , Zhang Yu-Xia , Lu Jing , Zhao Yi-Nan , Ji Bo-Fan , Chen Zhi-Qing , Tang Ri-Ning , Liu Bi-Cheng
Published: January 2024

Objectives: This study aimed to describe the effects of low-dose (prednisolone acetate 2.5–7.5 mg/day) glucocorticoids (GCs) maintenance therapy in patients with primary nephrotic syndrome (NS) suffering from coronavirus disease 2019 (COVID-19).

Methods: A single-center retrospective study of NS patients with COVID-19 infection in Zhongda Hospital Affiliated to Southeast University from 1 February 2022 to 31 March 2023 was conducted. All enrolled patients underwent renal biopsy for the pathological diagnosis and reached complete remission (CR) or near-CR before COVID-19 infection. According to the maintained therapy regimen, patients were divided into low-dose GCs group and non-GCs group.

Results: A total of 125 patients were enrolled in the study. Their median age was 46.0 ± 15.6 years, and the median value of 24-h urine protein was 0.77 g. The majority of these patients received treatment for more than 6 months, with a significant portion achieving CR (29.6%) or near-CR (43.2%). The leading cause of NS was membranous nephropathy (52%). There were no significant differences in the baseline characteristics between low-dose GCs and non-GCs group. As compared to those in the non-GCs group, patients receiving low-dose GCs treatment showed less fatigue or muscle weakness, smell disorder, palpitations, decreased appetite, taste disorder, dizziness, sore throat or difficult to swallow and fever (p < 0.05). Moreover, patients in the low-dose GCs group were with higher median quality of life scores (85.0) than in the non-GCs group (p = 0.001). Further serum inflammatory factor analysis indicated that interleukin-6 (IL-6) levels in the non-GCs group were significantly higher than that in the low-dose GCs group (p < 0.05).

Conclusion: Patients with NS in low-dose GCs maintenance therapy stage showed milder symptom, higher quality of life and decreased serum IL-6 levels compared to those, who were not on GCs maintenance therapy. These results suggest the beneficial effect of low-dose GCs therapy in NS patients with CR/near-CR suffering from COVID-19 infection.
Identification and experimental validation of ferroptosis-related gene lactotransferrin in age-related hearing loss
Authors: Zeng Chaojun , Gu Xi , Chen Yuqing , Lin Yanchun , Chen Junying , Chen Zhifeng , Chen Chenyu , Yao Guangnan , Lin Chang
Published: January 2024

Objective

To reveal the relationship between ARHL and ferroptosis and screen ferroptosis-related genes (FRGs) in ARHL.

Methods

Bioinformatics were used to analyze the hub genes and molecular mechanism of ferroptosis in the aging cochleae. Senescence β-galactosidase staining, iron content detection, and micro malondialdehyde (MDA) assay kits were used to measure β-galactosidase activity, and expression of Fe2+ and MDA, respectively. Fluorescence microscope was used for immunofluorescence assay of hub genes. Western blot was used to verify the expression of hub genes in HEI-OC1 cells, cochlear explants, and cochleae of C57BL/6J mice. Data were expressed as mean ± SD of at least three independent experiments.

Results

The analysis of bioinformatics confirmed that lactotransferrin (LTF) is the hub gene and CEBPA-miR-130b-LTF network is the molecular mechanism for cochlear ferroptosis. Compared with the control group, the experiments proved that the indicators of ferroptosis, including Fe2+, MDA, and LTF were differentially expressed in aging HEI-OC1 cells, aging cochlear explants, and aging cochleae.

Conclusion

These results demonstrate that ferroptosis plays an important role in ARHL, and LTF is a potential therapeutic target for ARHL via regulating cochlear ferroptosis.