bluuebunny/crossref_metadata_2025_split huggingface dataset:
UQAM‐TCW: A Global Hybrid Tropical Cyclone Wind Model Based Upon Statistical and Coupled Climate Models
Authors: Carozza David A. , Boudreault Mathieu , Grenier Manuel , Caron Louis‐Philippe 
Published: March 2024

AbstractTropical cyclones (TCs) are among the most destructive natural hazards and yet, quantifying their financial impacts remains a significant methodological challenge. It is therefore of high societal value to synthetically simulate TC tracks and winds to assess potential impacts along with their probability distributions for example, land use planning and financial risk management. A common approach to generate TC tracks is to apply storm detection methodologies to climate model output, but such an approach is sensitive to the method and parameterization used and tends to underestimate intense TCs. We present a global TC model (the UQAM‐TCW model thereafter) that melds statistical modeling, to capture historical risk features, with a climate model large ensemble, to generate large samples of physically coherent TC seasons. Integrating statistical and physical methods, the model is probabilistic and consistent with the physics of how TCs develop. The model includes frequency and location of cyclogenesis, full trajectories with maximum sustained winds and the entire wind structure along each track for the six typical cyclogenesis basins from IBTrACS. Being an important driver of TCs globally, we also integrate ENSO effects in key components of the model. The global TC model thus belongs to a recent strand of literature that combines probabilistic and physical approaches to TC track generation. As an application of the model, we show global hazard maps for direct and indirect hits expressed in terms of return periods. The global TC model can be of interest to climate and environmental scientists, economists and financial risk managers.
Hydro‐Sedimentary Processes of a Plunging Hyperpycnal River Plume Revealed by Synchronized Remote Imagery and Gridded Current Measurements
Authors: Thorez Stan , Lemmin Ulrich , Barry D. Andrew , Blanckaert Koen 
Published: March 2024

AbstractThe present knowledge of plunging hyperpycnal river plumes is mainly based on two‐dimensional (confined) laboratory experiments. Several hypotheses on three‐dimensional (unconfined) flow processes have been made, but not tested in situ. In this field study, the dominant three‐dimensional hydro‐sedimentary processes related to unconfined plunging were elucidated by synchronizing autonomous time‐lapse camera images with boat‐towed acoustic Doppler current profiler measurements. It was found that the flow field complies with two‐dimensional conceptualizations along the plume centerline. Perpendicular to the centerline, the plume slumped laterally due to its density excess and simultaneously converged laterally due to its vertical divergence. This combination led to a narrowing of the plume near the surface, resulting in a sediment‐rich triangle‐shaped pattern on the surface near the inflow, and a rather stable width near the bed. The formation of secondary flow cells transporting riverine water and suspended particulate matter (SPM) away from the plume near the bed, up toward the surface and back toward the plume near the surface, was revealed. An increase of the average SPM concentration and the SPM flux in the main flow direction indicates net sediment erosion under the investigated conditions of high discharge and sediment load. This suggests transient storage of sediment during conditions of lower discharge and sediment load, and high morphological activity in the plunging area. These findings allowed extending a classical conceptual plunging model to laterally unconfined sediment‐laden plunging inflows for conditions of well‐mixed ambient water in the plunging region and inflow densimetric Froude numbers exceeding 1, common in nature.
A 3D-printed microhemispherical shell resonator with electrostatic tuning for a Coriolis vibratory gyroscope
Authors: Hou Baoyin , Zhu Ye , He Chaofan , Wang Weidong , Ding Zhi , He Wen , He Yong , Che Lufeng 
Published: March 2024

AbstractThe emergence of microhemispherical resonant gyroscopes, which integrate the advantages of exceptional stability and long lifetime with miniaturization, has afforded new possibilities for the development of whole-angle gyroscopes. However, existing methods used for manufacturing microhemispherical resonant gyroscopes based on MEMS technology face the primary drawback of intricate and costly processing. Here, we report the design, fabrication, and characterization of the first 3D-printable microhemispherical shell resonator for a Coriolis vibrating gyroscope. We remarkably achieve fabrication in just two steps bypassing the dozen or so steps required in traditional micromachining. By utilizing the intricate shaping capability and ultrahigh precision offered by projection microstereolithography, we fabricate 3D high-aspect-ratio resonant structures and controllable capacitive air gaps, both of which are extremely difficult to obtain via MEMS technology. In addition, the resonance frequency of the fabricated resonators can be tuned by electrostatic forces, and the fabricated resonators exhibit a higher quality factor in air than do typical MEMS microhemispherical resonators. This work demonstrates the feasibility of rapidly batch-manufacturing microhemispherical shell resonators, paving the way for the development of microhemispherical resonator gyroscopes for portable inertial navigation. Moreover, this particular design concept could be further applied to increase uptake of resonator tools in the MEMS community.
Reactivation of encoding ensembles in the prelimbic cortex supports temporal associations
Authors: Santos Thays Brenner , de Oliveira Coelho Cesar Augusto , Kramer-Soares Juliana Carlota , Frankland Paul W. , Oliveira Maria Gabriela Menezes 
Published: March 2024

AbstractFear conditioning is encoded by strengthening synaptic connections between the neurons activated by a conditioned stimulus (CS) and those activated by an unconditioned stimulus (US), forming a memory engram, which is reactivated during memory retrieval. In temporal associations, activity within the prelimbic cortex (PL) plays a role in sustaining a short-term, transient memory of the CS, which is associated with the US after a temporal gap. However, it is unknown whether the PL has only a temporary role, transiently representing the CS, or is part of the neuronal ensembles that support the retrieval, i.e., whether PL neurons support both transient, short-term memories and stable, long-term memories. We investigated neuronal ensembles underlying temporal associations using fear conditioning with a 5-s interval between the CS and US (CFC-5s). Controls were trained in contextual fear conditioning (CFC), in which the CS-US overlaps. We used Robust Activity Marking (RAM) to selectively manipulate PL neurons activated by CFC-5s learning and Targeted Recombination in Active Populations (TRAP2) mice to label neurons activated by CFC-5s learning and reactivated by memory retrieval in the amygdala, medial prefrontal cortex, hippocampus, perirhinal cortices (PER) and subiculum. We also computed their co-reactivation to generate correlation-based networks. The optogenetic reactivation or silencing of PL encoding ensembles either promoted or impaired the retrieval of CFC-5s but not CFC. CFC-5s retrieval reactivated encoding ensembles in the PL, PER, and basolateral amygdala. The engram network of CFC-5s had higher amygdala and PER centralities and interconnectivity. The same PL neurons support learning and stable associative memories.
Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing
Authors: Lynn Nicolas , Tuller Tamir 
Published: March 2024

AbstractCancer research has long relied on non-silent mutations. Yet, it has become overwhelmingly clear that silent mutations can affect gene expression and cancer cell fitness. One fundamental mechanism that apparently silent mutations can severely disrupt is alternative splicing. Here we introduce Oncosplice, a tool that scores mutations based on models of proteomes generated using aberrant splicing predictions. Oncosplice leverages a highly accurate neural network that predicts splice sites within arbitrary mRNA sequences, a greedy transcript constructor that considers alternate arrangements of splicing blueprints, and an algorithm that grades the functional divergence between proteins based on evolutionary conservation. By applying this tool to 12M somatic mutations we identify 8K deleterious variants that are significantly depleted within the healthy population; we demonstrate the tool’s ability to identify clinically validated pathogenic variants with a positive predictive value of 94%; we show strong enrichment of predicted deleterious mutations across pan-cancer drivers. We also achieve improved patient survival estimation using a proposed set of novel cancer-involved genes. Ultimately, this pipeline enables accelerated insight-gathering of sequence-specific consequences for a class of understudied mutations and provides an efficient way of filtering through massive variant datasets – functionalities with immediate experimental and clinical applications.
Fabrication of porous beta-cyclodextrin functionalized PVDF/Fe–MOF mixed matrix membrane for enhanced ciprofloxacin removal
Authors: Njaramba Lewis Kamande , Yoon Yeomin , Park Chang Min 
Published: March 2024

AbstractHerein, we demonstrate the synthesis of beta-cyclodextrin (β–CD) functionalized polyvinylidene fluoride (PVDF) and iron-based metal-organic framework (Fe–MOF) mixed matrix membrane (MMM) for the enhanced removal of ciprofloxacin (CIP) from water. The membranes were prepared using the phase inversion technique with PVDF as the polymer matrix, Fe–MOF as the filler, and polyvinylpyrrolidone (PVP) as the porogen. The optimized MMM with 7% wt. Fe–MOF exhibited excellent performance with 87.6% removal efficiency. Moreover, the maximum adsorption capacity was 6.43 mg g–1. The β–CD functionalization improved the MMM hydrophilicity exhibited by the water contact angle (WCA) analysis (WCA = 55°). Furthermore, excellent adsorption performance can be attributed to the large Fe–MOF specific surface area (682.5 m2 g–1), the high porosity (77%), and the average pore diameter (395 nm) of the membrane. The inclusion of PVP (1% wt.) enhanced the porous nature of the MMM and, consequently, the adsorption performance for CIP. Notably, the hydrophilic and macroporous membrane showed good reusability with over 70% removal efficiency after five sequential adsorption–desorption cycles. The insights from this study suggest that the PMC–7 membrane can be an excellent candidate for the remediation of organic contaminants from aquatic environments.
Clonal hematopoiesis of indeterminate potential is associated with acute kidney injury
Authors: Vlasschaert Caitlyn , Robinson-Cohen Cassianne , Chen Jianchun , Akwo Elvis , Parker Alyssa C. , Silver Samuel A. , Bhatraju Pavan K. , Poisner Hannah , Cao Shirong , Jiang Ming , Wang Yinqiu , Niu Aolei , Siew Edward , Van Amburg Joseph C. , Kramer Holly J. , Kottgen Anna , Franceschini Nora , Psaty Bruce M. , Tracy Russell P. , Alonso Alvaro , Arking Dan E. , Coresh Josef , Ballantyne Christie M. , Boerwinkle Eric , Grams Morgan , Zhang Ming-Zhi , Kestenbaum Bryan , Lanktree Matthew B. , Rauh Michael J. , Harris Raymond C. , Bick Alexander G. 
Published: March 2024

AbstractAge is a predominant risk factor for acute kidney injury (AKI), yet the biological mechanisms underlying this risk are largely unknown. Clonal hematopoiesis of indeterminate potential (CHIP) confers increased risk for several chronic diseases associated with aging. Here we sought to test whether CHIP increases the risk of AKI. In three population-based epidemiology cohorts, we found that CHIP was associated with a greater risk of incident AKI, which was more pronounced in patients with AKI requiring dialysis and in individuals with somatic mutations in genes other than DNMT3A, including mutations in TET2 and JAK2. Mendelian randomization analyses supported a causal role for CHIP in promoting AKI. Non-DNMT3A-CHIP was also associated with a nonresolving pattern of injury in patients with AKI. To gain mechanistic insight, we evaluated the role of Tet2-CHIP and Jak2V617F-CHIP in two mouse models of AKI. In both models, CHIP was associated with more severe AKI, greater renal proinflammatory macrophage infiltration and greater post-AKI kidney fibrosis. In summary, this work establishes CHIP as a genetic mechanism conferring impaired kidney function recovery after AKI via an aberrant inflammatory response mediated by renal macrophages.
Locoregional delivery of IL-13Rα2-targeting CAR-T cells in recurrent high-grade glioma: a phase 1 trial
Authors: Brown Christine E. , Hibbard Jonathan C. , Alizadeh Darya , Blanchard M. Suzette , Natri Heini M. , Wang Dongrui , Ostberg Julie R. , Aguilar Brenda , Wagner Jamie R. , Paul Jinny A. , Starr Renate , Wong Robyn A. , Chen Wuyang , Shulkin Noah , Aftabizadeh Maryam , Filippov Aleksandr , Chaudhry Ammar , Ressler Julie A. , Kilpatrick Julie , Myers-McNamara Paige , Chen Mike , Wang Leo D. , Rockne Russell C. , Georges Joseph , Portnow Jana , Barish Michael E. , D’Apuzzo Massimo , Banovich Nicholas E. , Forman Stephen J. , Badie Behnam 
Published: March 2024

AbstractChimeric antigen receptor T cell (CAR-T) therapy is an emerging strategy to improve treatment outcomes for recurrent high-grade glioma, a cancer that responds poorly to current therapies. Here we report a completed phase I trial evaluating IL-13Rα2-targeted CAR-T cells in 65 patients with recurrent high-grade glioma, the majority being recurrent glioblastoma (rGBM). Primary objectives were safety and feasibility, maximum tolerated dose/maximum feasible dose and a recommended phase 2 dose plan. Secondary objectives included overall survival, disease response, cytokine dynamics and tumor immune contexture biomarkers. This trial evolved to evaluate three routes of locoregional T cell administration (intratumoral (ICT), intraventricular (ICV) and dual ICT/ICV) and two manufacturing platforms, culminating in arm 5, which utilized dual ICT/ICV delivery and an optimized manufacturing process. Locoregional CAR-T cell administration was feasible and well tolerated, and as there were no dose-limiting toxicities across all arms, a maximum tolerated dose was not determined. Probable treatment-related grade 3+ toxicities were one grade 3 encephalopathy and one grade 3 ataxia. A clinical maximum feasible dose of 200 × 106 CAR-T cells per infusion cycle was achieved for arm 5; however, other arms either did not test or achieve this dose due to manufacturing feasibility. A recommended phase 2 dose will be refined in future studies based on data from this trial. Stable disease or better was achieved in 50% (29/58) of patients, with two partial responses, one complete response and a second complete response after additional CAR-T cycles off protocol. For rGBM, median overall survival for all patients was 7.7 months and for arm 5 was 10.2 months. Central nervous system increases in inflammatory cytokines, including IFNγ, CXCL9 and CXCL10, were associated with CAR-T cell administration and bioactivity. Pretreatment intratumoral CD3 T cell levels were positively associated with survival. These findings demonstrate that locoregional IL-13Rα2-targeted CAR-T therapy is safe with promising clinical activity in a subset of patients. ClinicalTrials.gov Identifier: NCT02208362.
PEARL-Neuro Database: EEG, fMRI, health and lifestyle data of middle-aged people at risk of dementia
Authors: Dzianok Patrycja , Kublik Ewa 
Published: March 2024

AbstractInterdisciplinary approaches are needed to understand the relationship between genetic factors and brain structure and function. Here we describe a database that includes genetic data on apolipoprotein E (APOE) and phosphatidylinositol binding clathrin assembly protein (PICALM) genes, both of which are known to increase the risk of late-onset Alzheimer's disease, paired with psychometric (memory, intelligence, mood, personality, stress coping strategies), basic demographic and health data on a cohort of 192 healthy middle-aged (50–63) individuals. Part of the database (~79 participants) also includes blood tests (blood counts, lipid profile, HSV virus) and functional neuroimaging data (EEG/fMRI) recorded with a resting-state protocol (eyes open and eyes closed) and two cognitive tasks (multi-source interference task, MSIT; and Sternberg's memory task). The data were validated and showed overall good quality. This open-science dataset is well suited not only for research relating to susceptibility to Alzheimer's disease but also for more general questions on brain aging or can be used as part of meta-analytical multi-disciplinary projects.
Successful topical treatment of human biofilms using multiple antibiotic elution from a collagen-rich hydrogel
Authors: Sharma Ayushi D. , Jarman Evan H. , Kuppalli Krutika , Murphy Matthew J. , Longaker Michael T. , Gurtner Geoffrey , Fox Paige M. 
Published: March 2024

AbstractChronic non-healing wounds significantly strain modern healthcare systems, affecting 1–2% of the population in developed countries with costs ranging between $28.1 and $96.8 billion annually. Additionally, it has been established that chronic wounds resulting from comorbidities, such as peripheral vascular disease and diabetes mellitus, tend to be polymicrobial in nature. Treatment of polymicrobial chronic wounds with oral and IV antibiotics can result in antimicrobial resistance, leading to more difficult-to-treat wounds. Ideally, chronic ulcers would be topically treated with antibiotic combinations tailored to the microbiome of a patient’s wound. We have previously shown that a topical collagen-rich hydrogel (cHG) can elute single antibiotics to inhibit bacterial growth in a manner that is nontoxic to mammalian cells. Here, we analyzed the microbiology of cultures taken from human patients diagnosed with diabetes mellitus suffering from chronic wounds present for more than 6 weeks. Additionally, we examined the safety of the elution of multiple antibiotics from collagen-rich hydrogel in mammalian cells in vivo. Finally, we aimed to create tailored combinations of antibiotics impregnated into cHG to successfully target and treat infections and eradicate biofilms cultured from human chronic diabetic wound tissue. We found that the majority of human chronic wounds in our study were polymicrobial in nature. The elution of multiple antibiotics from cHG was well-tolerated in mammalian cells, making it a potential topical treatment of the polymicrobial chronic wound. Finally, combinations of antibiotics tailored to each patient’s microbiome eluted from a collagen-rich hydrogel successfully treated bacterial cultures isolated from patient samples via an in vitro assay.
Bi-stability in femtosecond laser ablation by MHz bursts
Authors: Žemaitis Andrius , Gaidys Mantas , Gečys Paulius , Gedvilas Mindaugas 
Published: March 2024

AbstractIn this work, a bi-stable behavior of laser ablation efficiency and quality was controlled by fluence and burst length. The plasma shielding of incoming laser radiation caused sudden jumps with a significant decrease in ablation efficiency for every even number of pulses in the burst. The attenuation of incoming laser radiation by plasma created by the previous pulse was incorporated into the toy model of burst ablation efficiency. The mathematical recurrence relation has been derived for the first time, binding ablation efficiency for the next pulse with the efficiency of the previous pulse, which predicts bi-stability, as well as sudden jumps occurring in ablation efficiency depending on the number of pulses in burst with the response to changes of the control parameter of peak laser fluence in the pulse. The modeling results using new recurrence relation showed stable and bi-stable ablation efficiency depending on burst fluence and the number of pulses, which agreed well with experimental data. The extremely efficient laser ablation has been achieved by optimizing the shielding effect using three pulses in the burst.
Brain tumour microstructure is associated with post-surgical cognition
Authors: Aznarez-Sanado Maite , Romero-Garcia Rafael , Li Chao , Morris Rob C. , Price Stephen J. , Manly Thomas , Santarius Thomas , Erez Yaara , Hart Michael G. , Suckling John 
Published: March 2024

AbstractBrain tumour microstructure is potentially predictive of changes following treatment to cognitive functions subserved by the functional networks in which they are embedded. To test this hypothesis, intra-tumoural microstructure was quantified from diffusion-weighted MRI to identify which tumour subregions (if any) had a greater impact on participants’ cognitive recovery after surgical resection. Additionally, we studied the role of tumour microstructure in the functional interaction between the tumour and the rest of the brain. Sixteen patients (22–56 years, 7 females) with brain tumours located in or near speech-eloquent areas of the brain were included in the analyses. Two different approaches were adopted for tumour segmentation from a multishell diffusion MRI acquisition: the first used a two-dimensional four group partition of feature space, whilst the second used data-driven clustering with Gaussian mixture modelling. For each approach, we assessed the capability of tumour microstructure to predict participants’ cognitive outcomes after surgery and the strength of association between the BOLD signal of individual tumour subregions and the global BOLD signal. With both methodologies, the volumes of partially overlapped subregions within the tumour significantly predicted cognitive decline in verbal skills after surgery. We also found that these particular subregions were among those that showed greater functional interaction with the unaffected cortex. Our results indicate that tumour microstructure measured by MRI multishell diffusion is associated with cognitive recovery after surgery.
Observational retrospective clinical study on clinical features of macrolide-resistant Mycoplasma pneumoniae pneumonia in Chinese pediatric cases
Authors: Li Peng , Wang Wei , Zhang Xianhui , Pan Jie , Gong Lina 
Published: March 2024

AbstractThis study aimed to investigate differences in clinical characteristics and laboratory findings between children infected with Macrolide-Sensitive Mycoplasma pneumoniae (MSMP) and Macrolide-Resistant Mycoplasma pneumoniae (MRMP). Additionally, the research sought to identify laboratory markers for rapidly distinguishing refractory Mycoplasma pneumoniae pneumonia (RMPP) from ordinary Mycoplasma pneumoniae pneumonia (OMPP). In total, 265 Mycoplasma pneumoniae (MP) patients were included, with MRMP identified by specific point mutations in domain V of the 23S rRNA gene. A retrospective analysis compared the clinical courses and laboratory data, revealing that MRMP patients experienced prolonged febrile days (P = 0.004), elevated CRP levels (P < 0.001), and higher MP DNA loads than MSMP patients (P = 0.037). Based on clinical symptoms, MRMP was divided into RMPP (n = 56) and OMPP (n = 70), with RMPP demonstrating significantly increased IL-18, community-acquired respiratory distress syndrome (CARDS) toxins in nasopharyngeal aspirate, and serum CRP levels (P < 0.001; P = 0.006; P < 0.001). In conclusion, timely recognition of RMPP is crucial for enhancing prognosis. The identification of MRMP, coupled with proinflammatory cytokines such as IL-18, CARDS toxins, and CRP, emerges as promising markers with the potential to contribute significantly to diagnostic accuracy and prognosis assessment.