bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision arbovirus serology with a pan-arbovirus peptidome
Authors: Morgenlander William R. , Chia Wan Ni , Parra Beatriz , Monaco Daniel R. , Ragan Izabela , Pardo Carlos A. , Bowen Richard , Zhong Diana , Norris Douglas E. , Ruczinski Ingo , Durbin Anna , Wang Lin-Fa , Larman H. Benjamin , Robinson Matthew L. 
Published: July 2024

AbstractArthropod-borne viruses represent a crucial public health threat. Current arboviral serology assays are either labor intensive or incapable of distinguishing closely related viruses, and many zoonotic arboviruses that may transition to humans lack any serologic assays. In this study, we present a programmable phage display platform, ArboScan, that evaluates antibody binding to overlapping peptides that represent the proteomes of 691 human and zoonotic arboviruses. We confirm that ArboScan provides detailed antibody binding information from animal sera, human sera, and an arthropod blood meal. ArboScan identifies distinguishing features of antibody responses based on exposure history in a Colombian cohort of Zika patients. Finally, ArboScan details epitope level information that rapidly identifies candidate epitopes with potential protective significance. ArboScan thus represents a resource for characterizing human and animal arbovirus antibody responses at cohort scale.
High throughput platform technology for rapid target identification in personalized phage therapy
Authors: Bayat Fereshteh , Hilal Arwa , Thirugnanasampanthar Mathura , Tremblay Denise , Filipe Carlos D. M. , Moineau Sylvain , Didar Tohid F. , Hosseinidoust Zeinab 
Published: July 2024

AbstractAs bacteriophages continue to gain regulatory approval for personalized human therapy against antibiotic-resistant infections, there is a need for transformative technologies for rapid target identification through multiple, large, decentralized therapeutic phages biobanks. Here, we design a high throughput phage screening platform comprised of a portable library of individual shelf-stable, ready-to-use phages, in all-inclusive solid tablets. Each tablet encapsulates one phage along with luciferin and luciferase enzyme stabilized in a sugar matrix comprised of pullulan and trehalose capable of directly detecting phage-mediated adenosine triphosphate (ATP) release through ATP bioluminescence reaction upon bacterial cell burst. The tablet composition also enhances desiccation tolerance of all components, which should allow easier and cheaper international transportation of phages and as a result, increased accessibility to therapeutic phages. We demonstrate high throughput screening by identifying target phages for select multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Staphylococcus aureus with targets identified within 30-120 min.
‘Rewritable’ and ‘liquid-specific’ recognizable wettability pattern
Authors: Dhar Manideepa , Sarkar Debasmita , Das Avijit , Rahaman S. K. Asif , Ghosh Dibyendu , Manna Uttam 
Published: July 2024

AbstractBio-inspired surfaces with wettability patterns display a unique ability for liquid manipulations. Sacrificing anti-wetting property for confining liquids irrespective of their surface tension (γLV), remains a widely accepted basis for developing wettability patterns. In contrast, we introduce a ‘liquid-specific’ wettability pattern through selectively sacrificing the slippery property against only low γLV (<30 mN m−1) liquids. This design includes a chemically reactive crystalline network of phase-transitioning polymer, which displays an effortless sliding of both low and high γLV liquids. Upon its strategic chemical modification, droplets of low γLV liquids fail to slide, rather spill arbitrarily on the tilted interface. In contrast, droplets of high γLV liquids continue to slide on the same modified interface. Interestingly, the phase–transition driven rearrangement of crystalline network allows to revert the slippery property against low γLV liquids. Here, we report a ‘rewritable’ and ‘liquid-specific’ wettability pattern for high throughput screening, separating, and remoulding non-aqueous liquids.
Turn-on protein switches for controlling actin binding in cells
Authors: Effiong Unyime M. , Khairandish Hannah , Ramirez-Velez Isabela , Wang Yanran , Belardi Brian 
Published: July 2024

AbstractWithin a shared cytoplasm, filamentous actin (F-actin) plays numerous and critical roles across the cell body. Cells rely on actin-binding proteins (ABPs) to organize F-actin and to integrate its polymeric characteristics into diverse cellular processes. Yet, the multitude of ABPs that engage with and shape F-actin make studying a single ABP’s influence on cellular activities a significant challenge. Moreover, without a means of manipulating actin-binding subcellularly, harnessing the F-actin cytoskeleton for synthetic biology purposes remains elusive. Here, we describe a suite of designed proteins, Controllable Actin-binding Switch Tools (CASTs), whose actin-binding behavior can be controlled with external stimuli. CASTs were developed that respond to different external inputs, providing options for turn-on kinetics and enabling orthogonality and multiplexing. Being genetically encoded, we show that CASTs can be inserted into native protein sequences to control F-actin association locally and engineered into structures to control cell and tissue shape and behavior.
Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI-1805 TOT-HER3 trial and biological determinants of early response
Authors: Brasó-Maristany Fara , Ferrero-Cafiero Juan Manuel , Falato Claudette , Martínez-Sáez Olga , Cejalvo Juan Miguel , Margelí Mireia , Tolosa Pablo , Salvador-Bofill Francisco Javier , Cruz Josefina , González-Farré Blanca , Sanfeliu Esther , Òdena Andreu , Serra Violeta , Pardo Francisco , Luna Barrera Ana María , Arumi Miriam , Guerra Juan Antonio , Villacampa Guillermo , Sánchez-Bayona Rodrigo , Ciruelos Eva , Espinosa-Bravo Martín , Izarzugaza Yann , Galván Patricia , Matito Judith , Pernas Sonia , Vidal Maria , Santhanagopal Anu , Sellami Dalila , Esker Stephen , Fan Pang-Dian , Suto Fumitaka , Vivancos Ana , Pascual Tomás , Prat Aleix , Oliveira Mafalda 
Published: July 2024

AbstractPatritumab deruxtecan (HER3-DXd) exhibits promising efficacy in breast cancer, with its activity not directly correlated to baseline ERBB3/HER3 levels. This research investigates the genetic factors affecting HER3-DXd’s response in women with early-stage hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer. In the SOLTI-1805 TOT-HER3 trial, a single HER3-DXd dose was administered to 98 patients across two parts: 78 patients received 6.4 mg/kg (Part A), and 44 received a lower 5.6 mg/kg dose (Part B). The CelTIL score, measuring tumor cellularity and infiltrating lymphocytes from baseline to day 21, was used to assess drug activity. Part A demonstrated increased CelTIL score after one dose of HER3-DXd. Here we report CelTIL score and safety for Part B. In addition, the exploratory analyses of part A involve a comprehensive study of gene expression, somatic mutations, copy-number segments, and DNA-based subtypes, while Part B focuses on validating gene expression. RNA analyses show significant correlations between CelTIL responses, high proliferation genes (e.g., CCNE1, MKI67), and low expression of luminal genes (e.g., NAT1, SLC39A6). DNA findings indicate that CelTIL response is significantly associated with TP53 mutations, proliferation, non-luminal signatures, and a distinct DNA-based subtype (DNADX cluster-3). Critically, low HER2DX ERBB2 mRNA, correlates with increased HER3-DXd activity, which is validated through in vivo patient-derived xenograft models. This study proposes chemosensitivity determinants, DNA-based subtype classification, and low ERBB2 expression as potential markers for HER3-DXd activity in HER2-negative breast cancer.
Direct presentation of inflammation-associated self-antigens by thymic innate-like T cells induces elimination of autoreactive CD8+ thymocytes
Authors: You Yuanyuan , Dunst Josefine , Ye Kewei , Sandoz Patrick A. , Reinhardt Annika , Sandrock Inga , Comet Natalia R. , Sarkar Rupak Dey , Yang Emily , Duprez Estelle , Agudo Judith , Brown Brian D. , Utz Paul J. , Kastenmüller Wolfgang , Gerlach Carmen , Prinz Immo , Önfelt Björn , Kreslavsky Taras 
Published: July 2024

AbstractUpregulation of diverse self-antigens that constitute components of the inflammatory response overlaps spatially and temporally with the emergence of pathogen-derived foreign antigens. Therefore, discrimination between these inflammation-associated self-antigens and pathogen-derived molecules represents a unique challenge for the adaptive immune system. Here, we demonstrate that CD8+ T cell tolerance to T cell-derived inflammation-associated self-antigens is efficiently induced in the thymus and supported by redundancy in cell types expressing these molecules. In addition to thymic epithelial cells, this included thymic eosinophils and innate-like T cells, a population that expressed molecules characteristic for all major activated T cell subsets. We show that direct T cell-to-T cell antigen presentation by minute numbers of innate-like T cells was sufficient to eliminate autoreactive CD8+ thymocytes. Tolerance to such effector molecules was of critical importance, as its breach caused by decreased thymic abundance of a single model inflammation-associated self-antigen resulted in autoimmune elimination of an entire class of effector T cells.
Lipidome changes due to improved dietary fat quality inform cardiometabolic risk reduction and precision nutrition
Authors: Eichelmann Fabian , Prada Marcela , Sellem Laury , Jackson Kim G. , Salas Salvadó Jordi , Razquin Burillo Cristina , Estruch Ramon , Friedén Michael , Rosqvist Frederik , Risérus Ulf , Rexrode Kathryn M. , Guasch-Ferré Marta , Sun Qi , Willett Walter C. , Martinez-Gonzalez Miguel Angel , Lovegrove Julie A. , Hu Frank B. , Schulze Matthias B. , Wittenbecher Clemens 
Published: July 2024

AbstractCurrent cardiometabolic disease prevention guidelines recommend increasing dietary unsaturated fat intake while reducing saturated fats. Here we use lipidomics data from a randomized controlled dietary intervention trial to construct a multilipid score (MLS), summarizing the effects of replacing saturated fat with unsaturated fat on 45 lipid metabolite concentrations. In the EPIC-Potsdam cohort, a difference in the MLS, reflecting better dietary fat quality, was associated with a significant reduction in the incidence of cardiovascular disease (−32%; 95% confidence interval (95% CI): −21% to −42%) and type 2 diabetes (−26%; 95% CI: −15% to −35%). We built a closely correlated simplified score, reduced MLS (rMLS), and observed that beneficial rMLS changes, suggesting improved dietary fat quality over 10 years, were associated with lower diabetes risk (odds ratio per standard deviation of 0.76; 95% CI: 0.59 to 0.98) in the Nurses’ Health Study. Furthermore, in the PREDIMED trial, an olive oil-rich Mediterranean diet intervention primarily reduced diabetes incidence among participants with unfavorable preintervention rMLS levels, suggestive of disturbed lipid metabolism before intervention. Our findings indicate that the effects of dietary fat quality on the lipidome can contribute to a more precise understanding and possible prediction of the health outcomes of specific dietary fat modifications.
Unfolding the downloads of datasets: A multifaceted exploration of influencing factors
Authors: Liu Zhifeng , Luo Pengcheng , Tang Xinglong , Wang Jimin , Nie Lei 
Published: July 2024

AbstractScientific data are essential to advancing scientific knowledge and are increasingly valued as scholarly output. Understanding what drives dataset downloads is crucial for their effective dissemination and reuse. Our study, analysing 55,473 datasets from 69 data repositories, identifies key factors driving dataset downloads, focusing on interpretability, reliability, and accessibility. We find that while lengthy descriptive texts can deter users due to complexity and time requirements, readability boosts a dataset’s appeal. Reliability, evidenced by factors like institutional reputation and citation counts of related papers, also significantly increases a dataset’s attractiveness and usage. Additionally, our research shows that open access to datasets increases their downloads and amplifies the importance of interpretability and reliability. This indicates that easy access enhances the overall attractiveness and usage of datasets in the scholarly community. By emphasizing interpretability, reliability, and accessibility, this study offers a comprehensive framework for future research and guides data management practices toward ensuring clarity, credibility, and open access to maximize the impact of scientific datasets.
Population based study on the progress in survival of primarily metastatic lung cancer patients in Germany
Authors: Tzschoppe Therese , Ohlinger Julia , Vordermark Dirk , Bedir Ahmed , Medenwald Daniel 
Published: July 2024

AbstractLung cancer is known for its high mortality; many patients already present with metastases at the time of diagnosis. The aim of this study is to assess the impact of new treatment strategies on the survival of primarily metastatic lung cancer patients and to analyze the differences in outcomes between non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) patients. Population-based data, provided by the Robert-Koch Institute in Germany, was used and patients diagnosed between 2007 and 2018 were included in the study. We differentiated between NSCLC and SCLC patients and analyzed the survival over time for both sexes separately, using the Kaplan–Meier method. To evaluate survival advantages, we calculated multivariable hazard ratios. In total, 127,723 patients were considered for the study. We observed a moderate increase in survival over time. All patients showed an increased survival rate when undergoing chemotherapy. Minimal to no increase in survival was shown in NSCLC patients when receiving radiotherapy, whereas SCLC patients’ survival time did benefit from it. NSCLC patients receiving immunotherapy showed an increase in survival as well. It can be concluded that advancements in radiotherapy, the application of chemotherapy, and the introduction of immunotherapies lead to an increased survival time of both NSCLC and SCLC primarily metastatic lung cancer patients.
Few-shot RUL prediction for engines based on CNN-GRU model
Authors: Sun Shuhan , Wang Jiongqi , Xiao Yaqi , Peng Jian , Zhou Xuanying 
Published: July 2024

AbstractIn the realm of prognosticating the remaining useful life (RUL) of pivotal components, such as aircraft engines, a prevalent challenge persists where the available historical life data often proves insufficient. This insufficiency engenders obstacles such as impediments in performance degradation feature extraction, inadequacies in capturing temporal relationships comprehensively, and diminished predictive accuracy. To address this issue, a 1D CNN-GRU prediction model for few-shot conditions is proposed in this paper. In pursuit of more comprehensive data feature extraction and enhanced RUL prognostication precision, the Convolutional Neural Network (CNN) is selected for its capacity to discern high-dimensional features amid the intricate dynamics of the data. Concurrently, the Gated Recurrent Unit (GRU) network is leveraged for its robust capability in extracting temporal features inherent within the data. We combine the two to construct a CNN-GRU hybrid network. Moreover, the integration of data distribution alongside correlation and monotonicity indices is employed to winnow the input of multi-sensor monitoring parameters into the CNN-GRU network. Finally, the engine RULs are predicted by the trained model. In this paper, experiments are conducted on a sub-dataset of the National Aeronautics and Space Administration (NASA) C-MAPSS multi-constraint dataset to validate the effectiveness of the method. Experimental results have demonstrated that this method has high accuracy in RUL prediction tasks, which can powerfully demonstrate its effectiveness.
Using torsional wave elastography to evaluate spring pot parameters in skin tumor mimicking phantoms
Authors: Almashakbeh Yousef , Shamimi Hirad , Callejas Antonio , Rus Guillermo 
Published: July 2024

AbstractEstimating the tissue parameters of skin tumors is crucial for diagnosis and effective therapy in dermatology and related fields. However, identifying the most sensitive biomarkers require an optimal rheological model for simulating skin behavior this remains an ongoing research endeavor. Additionally, the multi-layered structure of the skin introduces further complexity to this task. In order to surmount these challenges, an inverse problem methodology, in conjunction with signal analysis techniques, is being employed. In this study, a fractional rheological model is presented to enhance the precision of skin tissue parameter estimation from the acquired signal from torsional wave elastography technique (TWE) on skin tumor-mimicking phantoms for lab validation and the estimation of the thickness of the cancerous layer. An exhaustive analysis of the spring-pot model (SP) solved by the finite difference time domain (FDTD) is conducted. The results of experiments performed using a TWE probe designed and prototyped in the laboratory were validated against ultrafast imaging carried out by the Verasonics Research System. Twelve tissue-mimicking phantoms, which precisely simulated the characteristics of skin tissue, were prepared for our experimental setting. The experimental data from these bi-layer phantoms were measured using a TWE probe, and the parameters of the skin tissue were estimated using inverse problem-solving. The agreement between the two datasets was evaluated by comparing the experimental data obtained from the TWE technique with simulated data from the SP- FDTD model using Pearson correlation, dynamic time warping (DTW), and time-frequency representation. Our findings show that the SP-FDTD model and TWE are capable of determining the mechanical properties of both layers in a bilayer phantom, using a single signal and an inverse problem approach. The ultrafast imaging and the validation of TWE results further demonstrate the robustness and reliability of our technology for a realistic range of phantoms. This fusion of the SP-FDTD model and TWE, as well as inverse problem-solving methods has the potential to have a considerable impact on diagnoses and treatments in dermatology and related fields.
Enhancing agriculture through real-time grape leaf disease classification via an edge device with a lightweight CNN architecture and Grad-CAM
Authors: Karim Md. Jawadul , Goni Md. Omaer Faruq , Nahiduzzaman Md. , Ahsan Mominul , Haider Julfikar , Kowalski Marcin 
Published: July 2024

AbstractCrop diseases can significantly affect various aspects of crop cultivation, including crop yield, quality, production costs, and crop loss. The utilization of modern technologies such as image analysis via machine learning techniques enables early and precise detection of crop diseases, hence empowering farmers to effectively manage and avoid the occurrence of crop diseases. The proposed methodology involves the use of modified MobileNetV3Large model deployed on edge device for real-time monitoring of grape leaf disease while reducing computational memory demands and ensuring satisfactory classification performance. To enhance applicability of MobileNetV3Large, custom layers consisting of two dense layers were added, each followed by a dropout layer, helped mitigate overfitting and ensured that the model remains efficient. Comparisons among other models showed that the proposed model outperformed those with an average train and test accuracy of 99.66% and 99.42%, with a precision, recall, and F1 score of approximately 99.42%. The model was deployed on an edge device (Nvidia Jetson Nano) using a custom developed GUI app and predicted from both saved and real-time data with high confidence values. Grad-CAM visualization was used to identify and represent image areas that affect the convolutional neural network (CNN) classification decision-making process with high accuracy. This research contributes to the development of plant disease classification technologies for edge devices, which have the potential to enhance the ability of autonomous farming for farmers, agronomists, and researchers to monitor and mitigate plant diseases efficiently and effectively, with a positive impact on global food security.
Sex-specific alterations in functional connectivity and network topology in patients with degenerative cervical myelopathy
Authors: Oughourlian Talia C. , Rizvi Shan , Wang Chencai , Kostiuk Alex , Salamon Noriko , Holly Langston T. , Ellingson Benjamin M. 
Published: July 2024

AbstractPatients with degenerative cervical myelopathy (DCM) experience structural and functional brain reorganization. However, few studies have investigated the influence of sex on cerebral alterations. The present study investigates the role of sex on brain functional connectivity (FC) and global network topology in DCM and healthy controls (HCs). The resting-state functional MRI data was acquired for 100 patients (58 males vs. 42 females). ROI-to-ROI FC and network topological features were characterized for each patient and HC. Group differences in FC and network topological features were examined. Compared to healthy counterparts, DCM males exhibited higher FC between vision-related brain regions, and cerebellum, brainstem, and thalamus, but lower FC between the intracalcarine cortex and frontal and somatosensory cortices, while DCM females demonstrated higher FC between the thalamus and cerebellar and sensorimotor regions, but lower FC between sensorimotor and visual regions. DCM males displayed higher FC within the cerebellum and between the posterior cingulate cortex (PCC) and vision-related regions, while DCM females displayed higher FC between frontal regions and the PCC, cerebellum, and visual regions. Additionally, DCM males displayed significantly greater intra-network connectivity and efficiency compared to healthy counterparts. Results from the present study imply sex-specific supraspinal functional alterations occur in patients with DCM.