bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive approach to characterize navigation instruments for magnetic guidance in biological systems
Authors: Blümler Peter , Raudzus Fabian , Schmid Friederike 
Published: April 2024

AbstractAchieving non-invasive spatiotemporal control over cellular functions, tissue organization, and behavior is a desirable aim for advanced therapies. Magnetic fields, due to their negligible interaction with biological matter, are promising for in vitro and in vivo applications, even in deep tissues. Particularly, the remote manipulation of paramagnetic (including superparamagnetic and ferromagnetic, all with a positive magnetic susceptibility) entities through magnetic instruments has emerged as a promising approach across various biological contexts. However, variations in the properties and descriptions of these instruments have led to a lack of reproducibility and comparability among studies. This article addresses the need for standardizing the characterization of magnetic instruments, with a specific focus on their ability to control the movement of paramagnetic objects within organisms. While it is well known that the force exerted on magnetic particles depends on the spatial variation (gradient) of the magnetic field, the magnitude of the field is often overlooked in the literature. Therefore, we comprehensively analyze and discuss both actors and propose a novel descriptor, termed ‘effective gradient’, which combines both dependencies. To illustrate the importance of both factors, we characterize different magnet systems and relate them to experiments involving superparamagnetic nanoparticles. This standardization effort aims to enhance the reproducibility and comparability of studies utilizing magnetic instruments for biological applications.
RPA-CRISPR/Cas12a assay for the diagnosis of bovine Anaplasma marginale infection
Authors: Sutipatanasomboon Arpaporn , Wongsantichon Jantana , Sakdee Somsri , Naksith Piyaporn , Watthanadirek Amaya , Anuracpreeda Panat , Blacksell Stuart D. , Saisawang Chonticha 
Published: April 2024

AbstractAnaplasma marginale infection is one of the most common tick-borne diseases, causing a substantial loss in the beef and dairy production industries. Once infected, the pathogen remains in the cattle for life, allowing the parasites to spread to healthy animals. Since clinical manifestations of anaplasmosis occur late in the disease, a sensitive, accurate, and affordable pathogen identification is crucial in preventing and controlling the infection. To this end, we developed an RPA-CRISPR/Cas12a assay specific to A. marginale infection in bovines targeting the msp4 gene. Our assay is performed at one moderately high temperature, producing fluorescent signals or positive readout of a lateral flow dipstick, which is as sensitive as conventional PCR-based DNA amplification. This RPA-CRISPR/Cas12a assay can detect as few as 4 copies/μl of Anaplasma using msp4 marker without cross-reactivity to other common bovine pathogens. Lyophilized components of the assay can be stored at room temperature for an extended period, indicating its potential for field diagnosis and low-resource settings of anaplasmosis in bovines.
SOX11/PRDX2 axis modulates redox homeostasis and chemoresistance in aggressive mantle cell lymphoma
Authors: De Bolòs Anna , Sureda-Gómez Marta , Carreras-Caballé Maria , Rodríguez Marta-Leonor , Clot Guillem , Beà Silvia , Giné Eva , Campo Elias , Balsas Patricia , Amador Virginia 
Published: April 2024

AbstractMantle cell lymphoma (MCL) is an incurable B-cell neoplasm characterized by an aggressive behavior, short responses to conventional therapies and SOX11 overexpression, which is associated with aggressive disease features and inferior clinical outcome of patients. Oxidative stress is known to induce tumorigenesis and tumor progression, whereas high expression levels of antioxidant genes have been associated with chemoresistance in different cancers. However, the role of oxidative stress in MCL pathogenesis and the involvement of SOX11 regulating redox homeostasis in MCL cells are largely unknown. Here, by integrating gene set enrichment analysis of two independent series of MCL, we observed that SOX11+ MCL had higher reactive oxygen species (ROS) levels compared to SOX11− MCL primary tumors and increased expression of Peredoxine2 (PRDX2), which upregulation significantly correlated with SOX11 overexpression, higher ROS production and worse overall survival of patients. SOX11 knockout (SOX11KO) significantly reduced PRDX2 expression, and SOX11KO and PRDX2 knockdown (PRDX2KD) had increased ROS levels and ROS-mediated tumor cell death upon treatment with drugs, compared to control MCL cell lines. Our results suggest an aberrant redox homeostasis associated with chemoresistance in aggressive MCL through SOX11-mediated PRDX2 upregulation, highlighting PRDX2 as promising target for new therapeutic strategies to overcome chemoresistance in aggressive MCLs.
Cloning, functional expression, and pharmacological characterization of inwardly rectifying potassium channels (Kir) from Apis mellifera
Authors: Sourisseau Fabien , Chahine Chaimaa , Pouliot Valérie , Cens Thierry , Charnet Pierre , Chahine Mohamed 
Published: April 2024

AbstractPotassium channels belong to the super family of ion channels and play a fundamental role in cell excitability. Kir channels are potassium channels with an inwardly rectifying property. They play a role in setting the resting membrane potential of many excitable cells including neurons. Although putative Kir channel family genes can be found in the Apis mellifera genome, their functional expression, biophysical properties, and sensitivity to small molecules with insecticidal activity remain to be investigated. We cloned six Kir channel isoforms from Apis mellifera that derive from two Kir genes, AmKir1 and AmKir2, which are present in the Apis mellifera genome. We studied the tissue distribution, the electrophysiological and pharmacological characteristics of three isoforms that expressed functional currents (AmKir1.1, AmKir2.2, and AmKir2.3). AmKir1.1, AmKir2.2, and AmKir2.3 isoforms exhibited distinct characteristics when expressed in Xenopus oocytes. AmKir1.1 exhibited the largest potassium currents and was impermeable to cesium whereas AmKir2.2 and AmKir2.3 exhibited smaller currents but allowed cesium to permeate. AmKir1 exhibited faster opening kinetics than AmKir2. Pharmacological experiments revealed that both AmKir1.1 and AmKir2.2 are blocked by the divalent ion barium, with IC50 values of 10−5 and 10−6 M, respectively. The concentrations of VU041, a small molecule with insecticidal properties required to achieve a 50% current blockade for all three channels were higher than those needed to block Kir channels in other arthropods, such as the aphid Aphis gossypii and the mosquito Aedes aegypti. From this, we conclude that Apis mellifera AmKir channels exhibit lower sensitivity to VU041.
Orthotopic model for the analysis of melanoma circulating tumor cells
Authors: Pícková Markéta , Kahounová Zuzana , Radaszkiewicz Tomasz , Procházková Jiřina , Fedr Radek , Nosková Michaela , Radaszkiewicz Katarzyna Anna , Ovesná Petra , Bryja Vítězslav , Souček Karel 
Published: April 2024

AbstractMetastatic melanoma, a highly lethal form of skin cancer, presents significant clinical challenges due to limited therapeutic options and high metastatic capacity. Recent studies have demonstrated that cancer dissemination can occur earlier, before the diagnosis of the primary tumor. The progress in understanding the kinetics of cancer dissemination is limited by the lack of animal models that accurately mimic disease progression. We have established a xenograft model of human melanoma that spontaneously metastasizes to lymph nodes and lungs. This model allows precise monitoring of melanoma progression and is suitable for the quantitative and qualitative analysis of circulating tumor cells (CTCs). We have validated a flow cytometry-based protocol for CTCs enumeration and isolation. We could demonstrate that (i) CTCs were detectable in the bloodstream from the fourth week after tumor initiation, coinciding with the lymph node metastases appearance, (ii) excision of the primary tumor accelerated the formation of metastases in lymph nodes and lungs as early as one-week post-surgery, accompanied by the increased numbers of CTCs, and (iii) CTCs change their surface protein signature. In summary, we present a model of human melanoma that can be effectively utilized for future drug efficacy studies.
A distributed feature selection pipeline for survival analysis using radiomics in non-small cell lung cancer patients
Authors: Gottardelli Benedetta , Gouthamchand Varsha , Masciocchi Carlotta , Boldrini Luca , Martino Antonella , Mazzarella Ciro , Massaccesi Mariangela , Monshouwer René , Findhammer Jeroen , Wee Leonard , Dekker Andre , Gambacorta Maria Antonietta , Damiani Andrea 
Published: April 2024

AbstractPredictive modelling of cancer outcomes using radiomics faces dimensionality problems and data limitations, as radiomics features often number in the hundreds, and multi-institutional data sharing is ()often unfeasible. Federated learning (FL) and feature selection (FS) techniques combined can help overcome these issues, as one provides the means of training models without exchanging sensitive data, while the other identifies the most informative features, reduces overfitting, and improves model interpretability. Our proposed FS pipeline based on FL principles targets data-driven radiomics FS in a multivariate survival study of non-small cell lung cancer patients. The pipeline was run across datasets from three institutions without patient-level data exchange. It includes two FS techniques, Correlation-based Feature Selection and LASSO regularization, and Cox Proportional-Hazard regression with Overall Survival as endpoint. Trained and validated on 828 patients overall, our pipeline yielded a radiomic signature comprising "intensity-based energy" and "mean discretised intensity". Validation resulted in a mean Harrell C-index of 0.59, showcasing fair efficacy in risk stratification. In conclusion, we suggest a distributed radiomics approach that incorporates preliminary feature selection to systematically decrease the feature set based on data-driven considerations. This aims to address dimensionality challenges beyond those associated with data constraints and interpretability concerns.
Early gastric cancer detection and lesion segmentation based on deep learning and gastroscopic images
Authors: Zhang Kezhi , Wang Haibao , Cheng Yaru , Liu Hongyan , Gong Qi , Zeng Qian , Zhang Tao , Wei Guoqiang , Wei Zhi , Chen Dong 
Published: April 2024

AbstractGastric cancer is a highly prevalent disease that poses a serious threat to public health. In clinical practice, gastroscopy is frequently used by medical practitioners to screen for gastric cancer. However, the symptoms of gastric cancer at different stages of advancement vary significantly, particularly in the case of early gastric cancer (EGC). The manifestations of EGC are often indistinct, leading to a detection rate of less than 10%. In recent years, researchers have focused on leveraging deep learning algorithms to assist medical professionals in detecting EGC and thereby improve detection rates. To enhance the ability of deep learning to detect EGC and segment lesions in gastroscopic images, an Improved Mask R-CNN (IMR-CNN) model was proposed. This model incorporates a “Bi-directional feature extraction and fusion module” and a “Purification module for feature channel and space” based on the Mask R-CNN (MR-CNN). Our study includes a dataset of 1120 images of EGC for training and validation of the models. The experimental results indicate that the IMR-CNN model outperforms the original MR-CNN model, with Precision, Recall, Accuracy, Specificity and F1-Score values of 92.9%, 95.3%, 93.9%, 92.5% and 94.1%, respectively. Therefore, our proposed IMR-CNN model has superior detection and lesion segmentation capabilities and can effectively aid doctors in diagnosing EGC from gastroscopic images.
Genetic predisposition to childhood obesity does not influence the risk of developing skin cancer in adulthood
Authors: Keatley Jay , Law Matthew H. , Seviiri Mathias , Olsen Catherine M. , Pandeya Nirmala , Ong Jue-Sheng , MacGregor Stuart , Whiteman David C. , Dusingize Jean Claude 
Published: April 2024

AbstractThe relationship between body mass index (BMI) and melanoma and other skin cancers remains unclear. The objective of this study was to employ the Mendelian randomization (MR) approach to evaluate the effects of genetically predicted childhood adiposity on the risk of developing skin cancer later in life. Two-sample MR analyses were conducted using summary data from genome-wide association study (GWAS) meta-analyses of childhood BMI, melanoma, cutaneous squamous cell carcinoma (cSCC), and basal cell carcinoma (BCC). We used the inverse-variance-weighted (IVW) methods to obtain a pooled estimate across all genetic variants for childhood BMI. We performed multiple sensitivity analyses to evaluate the potential influence of various assumptions on our findings. We found no evidence that genetically predicted childhood BMI was associated with risks of developing melanoma, cSCC, or BCC in adulthood (OR, 95% CI: melanoma: 1.02 (0.93–1.13), cSCC 0.94 (0.79–1.11), BCC 0.97 (0.84–1.12)). Our findings do not support the conclusions from observational studies that childhood BMI is associated with increased risks of melanoma, cSCC, or BCC in adulthood. Intervening on childhood adiposity will not reduce the risk of common skin cancers later in life.
Temporal progression of pupil dilation and gaze behavior to emotion expressions in preschoolers with autism spectrum disorder
Authors: Polzer Leonie , Schenk Marc , Raji Naisan , Kleber Solvejg , Lemler Christian , Kitzerow-Cleven Janina , Kim Ziyon , Freitag Christine M. , Bast Nico 
Published: April 2024

AbstractPrevious work has shown divergent pupil dilation (PD) and gaze behavior in individuals with autism spectrum disorder (ASD), which may relate to the development of social difficulties in early life. Here, we investigated temporal dynamics of both phenotypes during naturalistic videos of a person displaying facial emotion expressions in 61 autistic and 61 non-autistic preschoolers. PD was segmented into three serial time components derived from a principal component analysis. Growth curve analysis was applied to analyze changes in looking time on eye and mouth regions over time. Groups did not differ in PD time components. Growth curve analysis revealed initially shorter looking times on the eyes and longer looking times on the mouth in autistic versus non-autistic preschoolers. However, a reversion of this pattern was observed over time, suggesting a delayed compensatory increase in eye attention during prolonged viewing periods in autistic children. Positive and negative associations of PD components and gaze behavior over time indicated a dynamic temporal relationship during emotion viewing. Our findings emphasize the need to apply time-sensitive measures in ecologically valid research, which may index etiological mechanisms of social difficulties in ASD.
A scalable blockchain based framework for efficient IoT data management using lightweight consensus
Authors: Haque Ehtisham Ul , Shah Adil , Iqbal Jawaid , Ullah Syed Sajid , Alroobaea Roobaea , Hussain Saddam 
Published: April 2024

AbstractRecent research has focused on applying blockchain technology to solve security-related problems in Internet of Things (IoT) networks. However, the inherent scalability issues of blockchain technology become apparent in the presence of a vast number of IoT devices and the substantial data generated by these networks. Therefore, in this paper, we use a lightweight consensus algorithm to cater to these problems. We propose a scalable blockchain-based framework for managing IoT data, catering to a large number of devices. This framework utilizes the Delegated Proof of Stake (DPoS) consensus algorithm to ensure enhanced performance and efficiency in resource-constrained IoT networks. DPoS being a lightweight consensus algorithm leverages a selected number of elected delegates to validate and confirm transactions, thus mitigating the performance and efficiency degradation in the blockchain-based IoT networks. In this paper, we implemented an Interplanetary File System (IPFS) for distributed storage, and Docker to evaluate the network performance in terms of throughput, latency, and resource utilization. We divided our analysis into four parts: Latency, throughput, resource utilization, and file upload time and speed in distributed storage evaluation. Our empirical findings demonstrate that our framework exhibits low latency, measuring less than 0.976 ms. The proposed technique outperforms Proof of Stake (PoS), representing a state-of-the-art consensus technique. We also demonstrate that the proposed approach is useful in IoT applications where low latency or resource efficiency is required.
VespAI: a deep learning-based system for the detection of invasive hornets
Authors: O’Shea-Wheller Thomas A. , Corbett Andrew , Osborne Juliet L. , Recker Mario , Kennedy Peter J. 
Published: April 2024

AbstractThe invasive hornet Vespa velutina nigrithorax is a rapidly proliferating threat to pollinators in Europe and East Asia. To effectively limit its spread, colonies must be detected and destroyed early in the invasion curve, however the current reliance upon visual alerts by the public yields low accuracy. Advances in deep learning offer a potential solution to this, but the application of such technology remains challenging. Here we present VespAI, an automated system for the rapid detection of V. velutina. We leverage a hardware-assisted AI approach, combining a standardised monitoring station with deep YOLOv5s architecture and a ResNet backbone, trained on a bespoke end-to-end pipeline. This enables the system to detect hornets in real-time—achieving a mean precision-recall score of ≥0.99—and send associated image alerts via a compact remote processor. We demonstrate the successful operation of a prototype system in the field, and confirm its suitability for large-scale deployment in future use cases. As such, VespAI has the potential to transform the way that invasive hornets are managed, providing a robust early warning system to prevent ingressions into new regions.
Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes
Authors: Kato Akira , Pipil Supriya , Ota Chihiro , Kusakabe Makoto , Watanabe Taro , Nagashima Ayumi , Chen An-Ping , Islam Zinia , Hayashi Naoko , Wong Marty Kwok-Shing , Komada Masayuki , Romero Michael F. , Takei Yoshio 
Published: April 2024

AbstractThe regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.
Dynamics of evolutionary succession and coordination between opposite adaptations in cuckoo hosts under antagonistic coevolution
Authors: Yang Canchao , Zhang Ziqi 
Published: April 2024

AbstractAdaptations are driven by specific natural selection pressures throughout biological evolution. However, these cannot inherently align with future shifts in selection dynamics, thus manifesting in opposing directions. We performed field experiments on cuckoo hosts to investigate the coexistence and conflict between two evolutionarily successive but opposing behavioral adaptations—egg retrieval and rejection. Our findings provide key insights. (1) Egg rejection against brood parasites in hosts reshapes egg retrieval to flexible reactions—retrieval, ignoring, or outright rejection of foreign eggs outside the nest cup, departing from instinctual retrieval. (2) Parasitism pressure and egg mimicry by parasites remarkably alter the proportions of the three host reactions. Host species with higher parasitism pressure exhibit frequent and rapid rejection of non-mimetic foreign eggs and reduced ignoring or retrieval responses. Conversely, heightened egg mimicry enhances retrieval behaviors while diminishing ignoring responses. (3) Cuckoos employ consistent mechanisms for rejecting foreign eggs inside or outside the nest cup. Direct rejection of eggs outside the nest cup shows that rejection precedes retrieval, indicating prioritization of specific adaptation over instinct. (4) Cuckoo hosts navigate the conflict between the intentions and motivations associated with egg rejection and retrieval by ignoring foreign eggs, a specific outcome of the rejection–retrieval tradeoff.
Recent reductions in aerosol emissions have increased Earth’s energy imbalance
Authors: Hodnebrog Øivind , Myhre Gunnar , Jouan Caroline , Andrews Timothy , Forster Piers M. , Jia Hailing , Loeb Norman G. , Olivié Dirk J. L. , Paynter David , Quaas Johannes , Raghuraman Shiv Priyam , Schulz Michael 
Published: April 2024

AbstractThe Earth’s energy imbalance is the net radiative flux at the top-of-atmosphere. Climate model simulations suggest that the observed positive imbalance trend in the previous two decades is inconsistent with internal variability alone and caused by anthropogenic forcing and the resulting climate system response. Here, we investigate anthropogenic contributions to the imbalance trend using climate models forced with observed sea-surface temperatures. We find that the effective radiative forcing due to anthropogenic aerosol emission reductions has led to a 0.2 ± 0.1 W m−2 decade−1 strengthening of the 2001–2019 imbalance trend. The multi-model ensemble reproduces the observed imbalance trend of 0.47 ± 0.17 W m−2 decade−1 but with 10-40% underestimation. With most future scenarios showing further rapid reductions of aerosol emissions due to air quality legislation, such emission reductions may continue to strengthen Earth’s energy imbalance, on top of the greenhouse gas contribution. Consequently, we may expect an accelerated surface temperature warming in this decade.