bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dataset of Finite Element Models of Normal and Deformed Thoracolumbar Spine
Authors: Rasouligandomani Morteza , del Arco Alejandro , Chemorion Francis Kiptengwer , Bisotti Marc-Antonio , Galbusera Fabio , Noailly Jérôme , González Ballester Miguel A. 
Published: May 2024

AbstractAdult spine deformity (ASD) is prevalent and leads to a sagittal misalignment in the vertebral column. Computational methods, including Finite Element (FE) Models, have emerged as valuable tools for investigating the causes and treatment of ASD through biomechanical simulations. However, the process of generating personalised FE models is often complex and time-consuming. To address this challenge, we present a dataset of FE models with diverse spine morphologies that statistically represent real geometries from a cohort of patients. These models are generated using EOS images, which are utilized to reconstruct 3D surface spine models. Subsequently, a Statistical Shape Model (SSM) is constructed, enabling the adaptation of a FE hexahedral mesh template for both the bone and soft tissues of the spine through mesh morphing. The SSM deformation fields facilitate the personalization of the mean hexahedral FE model based on sagittal balance measurements. Ultimately, this new hexahedral SSM tool offers a means to generate a virtual cohort of 16807 thoracolumbar FE spine models, which are openly shared in a public repository.
Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis
Authors: Kourtis Savvas , Cianferoni Damiano , Serrano Luis , Sdelci Sara 
Published: May 2024

AbstractProteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, are determined by proteoform states, such as mutations and post-translational modifications (PTMs), methods for determining the differential abundance of proteoforms across conditions are very limited. Classically, immunoprecipitation coupled with mass spectrometry (IP-MS) has been used to understand how the interactome (preys) of a given protein (bait) changes between conditions to elicit specific cellular functions. Reversing this concept, we present here a new workflow for IP-MS data analysis that focuses on identifying the differential peptidoforms of the bait protein between conditions. This method can provide detailed information about specific bait proteoforms, potentially revealing pathogenic protein states that can be exploited for the development of targeted therapies.
Integrated coupled assessment of geostorage and geothermal prospects in the oil fields of Upper Assam Basin
Authors: Dutta Anupal Jyoti , Gogoi Nababrot , Hussain Firdush Zallah , Kulkarni Sandeep D. 
Published: May 2024

AbstractThis study proposes an integrated approach of assessing CO2storage potential and geothermal energy prospect based on the data of seventeen depleted wells of Upper Assam Basin which could assist the global objective of net zero transition. The petrophysical properties of Tipam, Barail and Lakadong + Therria Formations from the seventeen wells have been utilised to perform the Monte Carlo simulation for probabilistic estimation of the CO2storage in the Upper Assam Basin. This preliminary work showed that the mean storage capacity of 18.8 ± 0.7 MT, 19.8 ± 0.9 MT and 4.5 ± 0.8 MT could potentially be stored in the three geological formations of the basin. The corrected bottom hole temperature values for the studied seventeen wells were determined using the well log data and Waples and Harrison method; these values provided a static geothermal gradient for each well, which varies widely from 0.017 to 0.033 °C/m. In order to enable geothermal prospectivity, static formation temperature maps have been generated for the studied wells. The probabilistic assessment of stored heat-in-place and formation temperature maps delimited five prospective sites for the extraction of geothermal energy in the basin. The study also presented a risk assessment for CO2storage development in the basin. Further, the study illustrated an economic analysis of the implementation of a CO2storage project and geothermal operations in the basin.
Vascular risk profile and changes of arterial hypertension after surgical revascularization in adult Moyamoya patients
Authors: Haas Patrick , Wiggenhauser Lucas Moritz , Tellermann Jonas , Hurth Helene , Feucht Daniel , Tatagiba Marcos , Khan Nadia , Roder Constantin 
Published: May 2024

AbstractMoyamoya disease (MMD) is a rare stenoocclusive cerebral vasculopathy often treated by neurosurgical revascularization using extracranial-intracranial bypasses to prevent ischemic or hemorrhagic events. Little is known about the vascular risk profile of adult MMD patients compared to the general population. We therefore analyzed 133 adult MMD patients and compared them with data from more than 22,000 patients from the German Health Update database. Patients with MMD showed an age- and sex-adjusted increased prevalence of arterial hypertension, especially in women between 30 and 44 years and in patients of both sexes between 45 and 64 years. Diabetes mellitus was diagnosed significantly more frequently in MMD patients with increasing age, whereas the vascular risk profile in terms of obesity, nicotine and alcohol consumption was similar to that of the general population. Antihypertensive medication was changed one year after surgical revascularization in 67.5% of patients with a tendency towards dose reduction in 43.2% of all patients. After revascularization, physicians need to be aware of a high likelihood of changes in arterial hypertension and should adjust all other modifiable systemic vascular risk factors to achieve the best treatment possible.
National prevalence of atopic dermatitis in Korean adolescents from 2009 to 2022
Authors: Kattih Mafaz , Lee Hojae , Jo Hyesu , Jeong Jinyoung , Kim Hyejun , Park Jaeyu , Yang Hwi , Nguyen Ann , Kim Hyeon Jin , Lee Hyeri , Kim Minji , Lee Myeongcheol , Kwon Rosie , Kim Sunyoung , Koyanagi Ai , Kim Min Seo , Rahmati Masoud , López Sánchez Guillermo F. , Dragioti Elena , Kim Ju Hee , Woo Selin , Cho Seong H. , Smith Lee , Yon Dong Keon 
Published: May 2024

AbstractPrevious studies have examined the prevalence of allergic diseases in adolescents 1–2 years after the emergence of the COVID-19 pandemic. However, more data is needed to understand the long-term impact of COVID-19 on allergic diseases. Thus, we aimed to examine the trend of the atopic dermatitis prevalence in Korean adolescents before and during the COVID-19 pandemic across 14 years. Additionally, we analyze the risk factors of atopic dermatitis (AD) based on the results. The Korean Disease Control and Prevention Agency conducted the Korea Youth Risk Behavior Web-based Survey from 2009 to 2022, from which the data for this study were obtained. Prevalence trends were compared across subgroups, and the β difference (βdiff) was calculated. We computed odds ratios to examine changes in the disease prevalence before and during the pandemic. This study included a total of 917,461 participants from 2009 to 2022. The prevalence of atopic dermatitis increased from 6.79% (95% CI 6.66–6.91) in 2009–2011 to 6.89% (95% CI 6.72–7.05) in 2018–2019, then decreased slightly to 5.82% (95% CI 5.60–6.04) in 2022. Across the 14 years, middle school student status, low parent’s highest education level, low household income, non-alcohol consumption, non-smoker smoking status, no suicidal thoughts, and no suicide attempts were associated with increased risk of atopic dermatitis, while female sex, rural residence, high BMI, low school performance, low household income, and no feelings of sadness and despair was associated with a small increase. This study examined the prevalence of atopic dermatitis across an 18-year, and found that the prevalence increased in the pre-pandemic then decreased during the start of the pandemic and remained constant throughout the pandemic. This trend could be explained mainly by the large scale social and political changes that occurred during the COVID-19 pandemic.
PET/MRI multimodality imaging to evaluate changes in glymphatic system function and biomarkers of Alzheimer’s disease
Authors: Okazawa Hidehiko , Nogami Munenobu , Ishida Shota , Makino Akira , Mori Tetsuya , Kiyono Yasushi , Ikawa Masamichi 
Published: May 2024

AbstractThe glymphatic system is considered to play a pivotal role in the clearance of disease-causing proteins in neurodegenerative diseases. This study employed MR diffusion tensor imaging (DTI) to evaluate glymphatic system function and its correlation with brain amyloid accumulation levels measured using [11C]Pittsburgh compound-B (PiB) PET/MRI. Fifty-six patients with mild cognitive impairment and early Alzheimer’s disease (AD: 70 ± 11 y) underwent [11C]PiB PET/MRI to assess amyloid deposition and were compared with 27 age-matched cognitively normal volunteers (CN: 69 ± 10y). All participants were evaluated for cognitive function using the Mini Mental State Examination (MMSE) before [11C]PiB PET/MRI. DTI images were acquired during the PET/MRI scan with several other MR sequences. The DTI analysis along the perivascular space index (DTI-ALPS index) was calculated to estimate the functional activity of the glymphatic system. Centiloid scale was applied to quantify amyloid deposition levels from [11C]PiB PET images. All patients in the AD group showed positive [11C]PiB accumulation, whereas all CN participants were negative. ALPS-index for all subjects linearly correlated with PiB centiloid, MMSE scores, and hippocampal volume. The correlation between the ALPS-index and PiB accumulation was more pronounced than with any other biomarkers. These findings suggest that glymphatic system dysfunction is a significant factor in the early stages of Alzheimer’s disease.
A novel approach to craniofacial analysis using automated 3D landmarking of the skull
Authors: Wilke Franziska , Matthews Harold , Herrick Noah , Dopkins Nichole , Claes Peter , Walsh Susan 
Published: May 2024

AbstractAutomatic dense 3D surface registration is a powerful technique for comprehensive 3D shape analysis that has found a successful application in human craniofacial morphology research, particularly within the mandibular and cranial vault regions. However, a notable gap exists when exploring the frontal aspect of the human skull, largely due to the intricate and unique nature of its cranial anatomy. To better examine this region, this study introduces a simplified single-surface craniofacial bone mask comprising of 6707 quasi-landmarks, which can aid in the classification and quantification of variation over human facial bone surfaces. Automatic craniofacial bone phenotyping was conducted on a dataset of 31 skull scans obtained through cone-beam computed tomography (CBCT) imaging. The MeshMonk framework facilitated the non-rigid alignment of the constructed craniofacial bone mask with each individual target mesh. To gauge the accuracy and reliability of this automated process, 20 anatomical facial landmarks were manually placed three times by three independent observers on the same set of images. Intra- and inter-observer error assessments were performed using root mean square (RMS) distances, revealing consistently low scores. Subsequently, the corresponding automatic landmarks were computed and juxtaposed with the manually placed landmarks. The average Euclidean distance between these two landmark sets was 1.5 mm, while centroid sizes exhibited noteworthy similarity. Intraclass coefficients (ICC) demonstrated a high level of concordance (> 0.988), with automatic landmarking showing significantly lower errors and variation. These results underscore the utility of this newly developed single-surface craniofacial bone mask, in conjunction with the MeshMonk framework, as a highly accurate and reliable method for automated phenotyping of the facial region of human skulls from CBCT and CT imagery. This craniofacial template bone mask expansion of the MeshMonk toolbox not only enhances our capacity to study craniofacial bone variation but also holds significant potential for shedding light on the genetic, developmental, and evolutionary underpinnings of the overall human craniofacial structure.
Prognostic factors and survival disparities in right-sided versus left-sided colon cancer
Authors: Asghari-Jafarabadi Mohammad , Wilkins Simon , Plazzer John Paul , Yap Raymond , McMurrick Paul John 
Published: May 2024

AbstractRight-sided colon cancer (RCC) and left-sided colon cancer (LCC) differ in features and outcomes because of variations in embryology, epidemiology, pathology, and prognosis. This study sought to identify significant factors impacting patient survival through Bayesian modelling. Data was retrospectively analysed from a colorectal neoplasia database. Data on demographics, perioperative risks, treatment, mortality, and survival was analysed from patients who underwent colon cancer surgery from January 2010 to December 2021. This study involved 2475 patients, with 58.7% having RCC and 41.3% having LCC. RCC patients had a notably higher mortality rate, and their overall survival (OS) rates were slightly lower than those with LCC (P < 0.05). RCC stages I–IV consistently exhibited worse OS and relapse-free survival (RFS) than LCC (P < 0.05). Factors like age, BMI, ASA score, cancer stage, and comorbidities had significant associations with OS and RFS. Poor and moderate differentiation, lower lymph node yield, and organ resection were linked to lower survival while receiving chemotherapy; higher BMI levels and elective surgery were associated with better survival (all P < 0.05). Our study reveals key differences between RCC and LCC, emphasising the impact of age, BMI, ASA score, cancer stage, and comorbidities on patient survival. These findings could inform personalised treatment strategies for colon cancer patients.
Molecular and biochemical characterizations of a Fasciola gigantica retinoid X receptor-α isoform A (FgRXRα-A)
Authors: Torungkitmangmi Nattaya , Chantree Pathanin , Chaimon Salisa , Prathaphan Parisa , Ruangtong Jittiporn , Geadkaew-Krenc Amornrat , Sornchuer Phornphan , Sanannam Bumpenporn , Thongsepee Nattaya , Pankao Viriya , Adisakwattana Poom , Martviset Pongsakorn 
Published: May 2024

AbstractFascioliasis is a parasitic infection in animals and humans caused by the parasitic flatworm genus Fasciola, which has two major species, F. hepatica and F. gigantica. A major concern regarding this disease is drug resistance, which is increasingly reported worldwide. Hence, the discovery of a novel drug as well as drug targets is crucially required. Therefore, this study aims to characterize the novel drug target in the adult F. gigantica. In the beginning, we hypothesized that the parasite might interact with some host molecules when it lives inside the liver parenchyma or bile ducts, specifically hormones and hormone-like molecules, through the specific receptors, primarily nuclear receptors (NRs), which are recognized as a major drug target in various diseases. The retinoid X receptor (RXR) is a member of subfamily 2 NRs that plays multitudinous roles in organisms by forming homodimers or heterodimers with other NRs. We obtained the full-length amino acid sequences of F. gigantica retinoid X receptor-alpha (FgRXRα-A) from the transcriptome of F. gigantica that existed in the NCBI database. The FgRXRα-A were computationally predicted for the basic properties, multiple aligned, phylogeny analyzed, and generated of 2D and 3D models. Moreover, FgRXRα-A was molecular cloned and expressed as a recombinant protein (rFgRXRα-A), then used for immunization for specific polyclonal antibodies. The native FgRXRα-A was detected in the parasite extracts and tissues, and the function was investigated by in vitro binding assay. The results demonstrated the conservation of FgRXRα-A to the other RXRs, especially RXRs from the trematodes. Interestingly, the native FgRXRα-A could be detected in the testes of the parasite, where the sex hormones are accumulated. Moreover, the binding assay revealed the interaction of 9-cis retinoic acid and FgRXRα-A, suggesting the function of FgRXRα-A. Our findings suggested that FgRXRα-A will be involved with the sexual reproduction of the parasite by forming heterodimers with other NRs, and it could be the potential target for further drug development of fascioliasis.
Cryo-EM analysis reveals human SID-1 transmembrane family member 1 dynamics underlying lipid hydrolytic activity
Authors: Hirano Yoshinori , Ohto Umeharu , Ichi Ikuyo , Sato Ryota , Miyake Kensuke , Shimizu Toshiyuki 
Published: May 2024

AbstractTwo mammalian homologs of systemic RNA interference defective protein 1 (SID-1) (SIDT1/2) are suggested to function as double-stranded RNA (dsRNA) transporters for extracellular dsRNA uptake or for release of incorporated dsRNA from lysosome to cytoplasm. SIDT1/2 is also suggested to be involved in cholesterol transport and lipid metabolism. Here, we determine the cryo-electron microscopy structures of human SIDT1, homodimer in a side-by-side arrangement, with two distinct conformations, the cholesterol-bound form and the unbound form. Our structures reveal that the membrane-spanning region of SIDT1 harbors conserved histidine and aspartate residues coordinating to putative zinc ion, in a structurally similar manner to alkaline ceramidases or adiponectin receptors that require zinc for ceramidase activity. We identify that SIDT1 has a ceramidase activity that is attenuated by cholesterol binding. Observations from two structures suggest that cholesterol molecules serve as allosteric regulator that binds the transmembrane region of SIDT1 and induces the conformation change and the reorientation of the catalytic residues. This study represents a contribution to the elucidation of the cholesterol-mediated mechanisms of lipid hydrolytic activity and RNA transport in the SID-1 family proteins.
Transgene removal using an in cis programmed homing endonuclease via single-strand annealing in the mosquito Aedes aegypti
Authors: Chae Keun , Contreras Bryan , Romanowski Joseph S. , Dawson Chanell , Myles Kevin M. , Adelman Zach N. 
Published: May 2024

AbstractWhile gene drive strategies have been proposed to aid in the control of mosquito-borne diseases, additional genome engineering technologies may be required to establish a defined end-of-product-life timeline. We previously demonstrated that single-strand annealing (SSA) was sufficient to program the scarless elimination of a transgene while restoring a disrupted gene in the disease vector mosquito Aedes aegypti. Here, we extend these findings by establishing that complete transgene removal (four gene cassettes comprising ~8-kb) can be programmed in cis. Reducing the length of the direct repeat from 700-bp to 200-bp reduces, but does not eliminate, SSA activity. In contrast, increasing direct repeat length to 1.5-kb does not increase SSA rates, suggesting diminishing returns above a certain threshold size. Finally, we show that while the homing endonuclease Y2-I-AniI triggered both SSA and NHEJ at significantly higher rates than I-SceI at one genomic locus (P5-EGFP), repair events are heavily skewed towards NHEJ at another locus (kmo), suggesting the nuclease used and the genomic region targeted have a substantial influence on repair outcomes. Taken together, this work establishes the feasibility of engineering temporary transgenes in disease vector mosquitoes, while providing critical details concerning important operational parameters.
Multiple environmental stressors affect predation pressure in a tropical freshwater system
Authors: Zanghi Costanza , Penry-Williams Iestyn L. , Genner Martin J. , Deacon Amy E. , Ioannou Christos C. 
Published: May 2024

AbstractEnvironmental change can alter predator-prey dynamics. However, studying predators in the context of co-occurring environmental stressors remains rare, especially under field conditions. Using in situ filming, we examined how multiple stressors, including temperature and turbidity, impact the distribution and behaviour of wild fish predators of Trinidadian guppies (Poecilia reticulata). The measured environmental variables accounted for 17.6% of variance in predator species composition. While predator species differed in their associations with environmental variables, the overall prevalence of predators was greatest in slow flowing, deeper, warmer and less turbid habitats. Moreover, these warmer and less turbid habitats were associated with earlier visits to the prey stimulus by predators, and more frequent predator visits and attacks. Our findings highlight the need to consider ecological complexity, such as co-occurring stressors, to better understand how environmental change affects predator-prey interactions.
Vimentin is a key regulator of cell mechanosensing through opposite actions on actomyosin and microtubule networks
Authors: Alisafaei Farid , Mandal Kalpana , Saldanha Renita , Swoger Maxx , Yang Haiqian , Shi Xuechen , Guo Ming , Hehnly Heidi , Castañeda Carlos A. , Janmey Paul A. , Patteson Alison E. , Shenoy Vivek B. 
Published: May 2024

AbstractThe cytoskeleton is a complex network of interconnected biopolymers consisting of actin filaments, microtubules, and intermediate filaments. These biopolymers work in concert to transmit cell-generated forces to the extracellular matrix required for cell motility, wound healing, and tissue maintenance. While we know cell-generated forces are driven by actomyosin contractility and balanced by microtubule network resistance, the effect of intermediate filaments on cellular forces is unclear. Using a combination of theoretical modeling and experiments, we show that vimentin intermediate filaments tune cell stress by assisting in both actomyosin-based force transmission and reinforcement of microtubule networks under compression. We show that the competition between these two opposing effects of vimentin is regulated by the microenvironment stiffness. These results reconcile seemingly contradictory results in the literature and provide a unified description of vimentin’s effects on the transmission of cell contractile forces to the extracellular matrix.
Prudent carbon dioxide removal strategies hedge against high climate sensitivity
Authors: Schaber Theresa , Ekholm Tommi , Merikanto Joonas , Partanen Antti-Ilari 
Published: May 2024

AbstractUncertainty in climate sensitivity has been shown to warrant early-on mitigation to limit global warming while anticipating future carbon dioxide removal creates mitigation deterrence. Here we use an integrated assessment model to quantify the impacts of under- or overestimating the cost and availability (feasibility) of carbon dioxide removal when limiting warming to 1.5 °C by 2100 under uncertain climate sensitivity. If climate sensitivity uncertainty is disregarded, initial assumptions on the feasibility have only minor effects on mitigation costs. However, the climate sensitivity risk compounds the impact of prior assumptions. Wrong assumptions on carbon dioxide removal feasibility can lead to lower costs under extreme realizations of climate sensitivity. Moreover, scenarios considering uncertainty in climate sensitivity rely less on carbon dioxide removal. A prudential strategy assuming low feasibility for carbon dioxide removal reduces the “double whammy” risk of overestimating carbon dioxide removal in combination with a realization of high climate sensitivity.