bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal plasma proteomics reveals biomarkers of alveolar-capillary barrier disruption in critically ill COVID-19 patients
Authors: Duijvelaar Erik , Gisby Jack , Peters James E. , Bogaard Harm Jan , Aman Jurjan 
Published: January 2024

AbstractThe pathobiology of respiratory failure in COVID-19 consists of a complex interplay between viral cytopathic effects and a dysregulated host immune response. In critically ill patients, imatinib treatment demonstrated potential for reducing invasive ventilation duration and mortality. Here, we perform longitudinal profiling of 6385 plasma proteins in 318 hospitalised patients to investigate the biological processes involved in critical COVID-19, and assess the effects of imatinib treatment. Nine proteins measured at hospital admission accurately predict critical illness development. Next to dysregulation of inflammation, critical illness is characterised by pathways involving cellular adhesion, extracellular matrix turnover and tissue remodelling. Imatinib treatment attenuates protein perturbations associated with inflammation and extracellular matrix turnover. These proteomic alterations are contextualised using external pulmonary RNA-sequencing data of deceased COVID-19 patients and imatinib-treated Syrian hamsters. Together, we show that alveolar capillary barrier disruption in critical COVID-19 is reflected in the plasma proteome, and is attenuated with imatinib treatment. This study comprises a secondary analysis of both clinical data and plasma samples derived from a clinical trial that was registered with the EU Clinical Trials Register (EudraCT 2020–001236–10, https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-001236-10/NL) and Netherlands Trial Register (NL8491, https://www.trialregister.nl/trial/8491).
Uncovering supramolecular chirality codes for the design of tunable biomaterials
Authors: Klawa Stephen J. , Lee Michelle , Riker Kyle D. , Jian Tengyue , Wang Qunzhao , Gao Yuan , Daly Margaret L. , Bhonge Shreeya , Childers W. Seth , Omosun Tolulope O. , Mehta Anil K. , Lynn David G. , Freeman Ronit 
Published: January 2024

AbstractIn neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.
Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection
Authors: Panda Sudhasini , Morgan Jeffrey , Cheng Catherine , Saito Mayuko , Gilman Robert H. , Ciobanu Nelly , Crudu Valeriu , Catanzaro Donald G. , Catanzaro Antonino , Rodwell Timothy , Perera Judy S. B. , Chathuranga Teshan , Gunasena Bandu , DeSilva Aruna D. , Peters Bjoern , Sette Alessandro , Lindestam Arlehamn Cecilia S. 
Published: January 2024

AbstractThere is still incomplete knowledge of which Mycobacterium tuberculosis (Mtb) antigens can trigger distinct T cell responses at different stages of infection. Here, a proteome-wide screen of 20,610 Mtb-derived peptides in 21 patients mid-treatment for active tuberculosis (ATB) reveals IFNγ-specific T cell responses against 137 unique epitopes. Of these, 16% are recognized by two or more participants and predominantly derived from cell wall and cell processes antigens. There is differential recognition of antigens, including TB vaccine candidate antigens, between ATB participants and interferon-gamma release assay (IGRA + /−) individuals. We developed an ATB-specific peptide pool (ATB116) consisting of epitopes exclusively recognized by ATB participants. This pool can distinguish patients with pulmonary ATB from IGRA + /− individuals from various geographical locations, with a sensitivity of over 60% and a specificity exceeding 80%. This proteome-wide screen of T cell reactivity identified infection stage-specific epitopes and antigens for potential use in diagnostics and measuring Mtb-specific immune responses.
Aqueous amine enables sustainable monosaccharide, monophenol, and pyridine base coproduction in lignocellulosic biorefineries
Authors: Xu Li , Cao Meifang , Zhou Jiefeng , Pang Yuxia , Li Zhixian , Yang Dongjie , Leu Shao-Yuan , Lou Hongming , Pan Xuejun , Qiu Xueqing 
Published: January 2024

AbstractThought-out utilization of entire lignocellulose is of great importance to achieving sustainable and cost-effective biorefineries. However, there is a trade-off between efficient carbohydrate utilization and lignin-to-chemical conversion yield. Here, we fractionate corn stover into a carbohydrate fraction with high enzymatic digestibility and reactive lignin with satisfactory catalytic depolymerization activity using a mild high-solid process with aqueous diethylamine (DEA). During the fractionation, in situ amination of lignin achieves extensive delignification, effective lignin stabilization, and dramatically reduced nonproductive adsorption of cellulase on the substrate. Furthermore, by designing a tandem fractionation-hydrogenolysis strategy, the dissolved lignin is depolymerized and aminated simultaneously to co-produce monophenolics and pyridine bases. The process represents the viable scheme of transforming real lignin into pyridine bases in high yield, resulting from the reactions between cleaved lignin side chains and amines. This work opens a promising approach to the efficient valorization of lignocellulose.
Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function
Authors: Lazzeri-Barcelo Francesca , Oliva-Vilarnau Nuria , Baniol Marion , Leibiger Barbara , Bergmann Olaf , Lauschke Volker M. , Leibiger Ingo B. , Moruzzi Noah , Berggren Per-Olof 
Published: January 2024

AbstractLongitudinal monitoring of liver function in vivo is hindered by the lack of high-resolution non-invasive imaging techniques. Using the anterior chamber of the mouse eye as a transplantation site, we have established a platform for longitudinal in vivo imaging of liver spheroids at cellular resolution. Transplanted liver spheroids engraft on the iris, become vascularized and innervated, retain hepatocyte-specific and liver-like features and can be studied by in vivo confocal microscopy. Employing fluorescent probes administered intravenously or spheroids formed from reporter mice, we showcase the potential use of this platform for monitoring hepatocyte cell cycle activity, bile secretion and lipoprotein uptake. Moreover, we show that hepatic lipid accumulation during diet-induced hepatosteatosis is mirrored in intraocular in vivo grafts. Here, we show a new technology which provides a crucial and unique tool to study liver physiology and disease progression in pre-clinical and basic research.
MVA-based vaccine candidates encoding the native or prefusion-stabilized SARS-CoV-2 spike reveal differential immunogenicity in humans
Authors: Mayer Leonie , Weskamm Leonie M. , Fathi Anahita , Kono Maya , Heidepriem Jasmin , Krähling Verena , Mellinghoff Sibylle C. , Ly My Linh , Friedrich Monika , Hardtke Svenja , Borregaard Saskia , Hesterkamp Thomas , Loeffler Felix F. , Volz Asisa , Sutter Gerd , Becker Stephan , Dahlke Christine , Addo Marylyn M. 
Published: January 2024

AbstractIn response to the COVID-19 pandemic, multiple vaccines were developed using platforms such as viral vectors and mRNA technology. Here, we report humoral and cellular immunogenicity data from human phase 1 clinical trials investigating two recombinant Modified Vaccinia virus Ankara vaccine candidates, MVA-SARS-2-S and MVA-SARS-2-ST, encoding the native and the prefusion-stabilized SARS-CoV-2 spike protein, respectively. MVA-SARS-2-ST was more immunogenic than MVA-SARS-2-S, but both were less immunogenic compared to licensed mRNA- and ChAd-based vaccines in SARS-CoV-2 naïve individuals. In heterologous vaccination, previous MVA-SARS-2-S vaccination enhanced T cell functionality and MVA-SARS-2-ST boosted the frequency of T cells and S1-specific IgG levels when used as a third vaccination. While the vaccine candidate containing the prefusion-stabilized spike elicited predominantly S1-specific responses, immunity to the candidate with the native spike was skewed towards S2-specific responses. These data demonstrate how the spike antigen conformation, using the same viral vector, directly affects vaccine immunogenicity in humans.
Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding
Authors: Quaresma Andreia , Ankenbrand Markus J. , Garcia Carlos Ariel Yadró , Rufino José , Honrado Mónica , Amaral Joana , Brodschneider Robert , Brusbardis Valters , Gratzer Kristina , Hatjina Fani , Kilpinen Ole , Pietropaoli Marco , Roessink Ivo , van der Steen Jozef , Vejsnæs Flemming , Pinto M. Alice , Keller Alexander 
Published: January 2024

AbstractOne of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
Rapid measurement of epidermal thickness in OCT images of skin
Authors: Lin Chieh-Hsi , Lukas Brandon E , Rajabi-Estarabadi Ali , May Julia Rome , Pang Yanzhen , Puyana Carolina , Tsoukas Maria , Avanaki Kamran 
Published: January 2024

AbstractEpidermal thickness (ET) changes are associated with several skin diseases. To measure ET, segmentation of optical coherence tomography (OCT) images is essential; manual segmentation is very time-consuming and requires training and some understanding of how to interpret OCT images. Fast results are important in order to analyze ET over different regions of skin in rapid succession to complete a clinical examination and enable the physician to discuss results with the patient in real time. The well-known CNN-graph search (CNN-GS) methodology delivers highly accurate results, but at a high computational cost. Our objective was to build a computational core, based on CNN-GS, able to accurately segment OCT skin images in real time. We accomplished this by fine-tuning the hyperparameters, testing a range of speed-up algorithms including pruning and quantization, designing a novel pixel-skipping process, and implementing the final product with efficient use of core and threads on a multicore central processing unit (CPU). We name this product CNN-GS-skin. The method identifies two defined boundaries on OCT skin images in order to measure ET. We applied CNN-GS-skin to OCT skin images, taken from various body sites of 63 healthy individuals. Compared with CNN-GS, our described method reduced computation time by 130 $$\times$$
×
with minimal reduction in ET determination accuracy (from 96.38 to 94.67%).
Composition and vertical distribution of organic matter in Central Indian Ocean sediment cores
Authors: Thalayappil Sruthi , Mullungal Muhammed Nayeem , Peediyakkathodi Sajna , C. S. Ratheesh Kumar , Panikkaveettil Resmi , P. M. Salas , C. H. Sujatha 
Published: January 2024

AbstractThis study aimed to investigate the quality and quantity of organic matter (OM) using biochemical components (protein, carbohydrate and lipids) in the sediment cores collected from the Central Indian Ocean (CIOB) under the program Equatorial Indian Ocean Process Study Dynamics and Biogeochemistry (EIOPS). Total organic carbon (TOC) and biochemical parameters (carbohydrate, lipid, protein, Tannin and lignin) were determined in core I and core II, respectively. Total carbohydrates varied from 4.66 to 2557.32 mg/kg (average 459.31 mg/kg) and 142.23 to 821.56 mg/kg (average 380.01 mg/kg) in core I and II, respectively. In core I, PRT varied from 70.95 to 107.05 mg/kg, and the minimum and maximum content of CHO was 143.23 and 822.56 mg/kg. The maximum and minimum concentrations of BPC in core II were 786.32 and 381.07 at 0–10 cm depth, respectively, which corresponded to the concentrations of PRT, CHO, LPD, and Tannin. The results showed that PRT was statistically significant with the TOC and negatively correlated with the LPD and CHO, while LPD was highly significant with clay and silt grains. In most of the samples, the ratio of LPD to CHO ratio was > 1, which indicated higher productivity of benthic organisms inhabiting the CIOB.
Dietary patterns, untargeted metabolite profiles and their association with colorectal cancer risk
Authors: Bodén Stina , Zheng Rui , Ribbenstedt Anton , Landberg Rikard , Harlid Sophia , Vidman Linda , Gunter Marc J. , Winkvist Anna , Johansson Ingegerd , Van Guelpen Bethany , Brunius Carl 
Published: January 2024

AbstractWe investigated data-driven and hypothesis-driven dietary patterns and their association to plasma metabolite profiles and subsequent colorectal cancer (CRC) risk in 680 CRC cases and individually matched controls. Dietary patterns were identified from combined exploratory/confirmatory factor analysis. We assessed association to LC–MS metabolic profiles by random forest regression and to CRC risk by multivariable conditional logistic regression. Principal component analysis was used on metabolite features selected to reflect dietary exposures. Component scores were associated to CRC risk and dietary exposures using partial Spearman correlation. We identified 12 data-driven dietary patterns, of which a breakfast food pattern showed an inverse association with CRC risk (OR per standard deviation increase 0.89, 95% CI 0.80–1.00, p = 0.04). This pattern was also inversely associated with risk of distal colon cancer (0.75, 0.61–0.96, p = 0.01) and was more pronounced in women (0.69, 0.49–0.96, p = 0.03). Associations between meat, fast-food, fruit soup/rice patterns and CRC risk were modified by tumor location in women. Alcohol as well as fruit and vegetables associated with metabolite profiles (Q2 0.22 and 0.26, respectively). One metabolite reflecting alcohol intake associated with increased CRC risk, whereas three metabolites reflecting fiber, wholegrain, and fruit and vegetables associated with decreased CRC risk.
Alkyl deoxyglycoside-polymyxin combinations against critical priority carbapenem-resistant gram-negative bacteria
Authors: de Matos Ana M. , Calado Patrícia , Miranda Mónica , Almeida Rita , Rauter Amélia P. , Oliveira M. Conceição , Manageiro Vera , Caniça Manuela 
Published: January 2024

AbstractThe escalating antimicrobial resistance crisis urges the development of new antibacterial treatments with innovative mechanisms of action, particularly against the critical priority carbapenem-resistant Acinetobacter baumannii (CRAB), Pseudomonas aeruginosa (CRPA) and Enterobacteriaceae (CRE). Membrane-disrupting dodecyl deoxyglycosides have been reported for their interesting phosphatidylethanolamine-associated bactericidal activity against Gram-positive strains; however, their inability to penetrate the Gram-negative outer membrane (OM) renders them useless against the most challenging pathogens. Aiming to repurpose alkyl deoxyglycosides against Gram-negative bacteria, this study investigates the antimicrobial effects of five reference compounds with different deoxygenation patterns or anomeric configurations in combination with polymyxins as adjuvants for enhanced OM permeability. The generation of the lead 4,6-dideoxy scaffold was optimized through a simultaneous dideoxygenation step and applied to the synthesis of a novel alkyl 4,6-dideoxy C-glycoside 5, herein reported for the first time. When combined with subtherapeutic colistin concentrations, most glycosides demonstrated potent antimicrobial activity against several multidrug-resistant clinical isolates of CRAB, CRE and CRPA exhibiting distinct carbapenem resistance mechanisms, together with acceptable cytotoxicity against human HEK-293T and Caco-2 cells. The novel 4,6-dideoxy C-glycoside 5 emerged as the most promising prototype structure for further development (MIC 3.1 μg/mL when combined with colistin 0.5 μg/mL against CRPA or 0.25 μg/mL against several CRE and CRAB strains), highlighting the potential of C-glycosylation for an improved bioactive profile. This study is the first to show the potential of IM-targeting carbohydrate-based compounds for the treatment of infections caused by MDR Gram-negative pathogens of clinical importance.
Aircraft observations in a tropical supercluster over the equatorial Indian Ocean during MISO-BOB field campaign
Authors: Phadtare Jayesh , Fernando Harindra J. S. , Black Garrett , McLaughlin Kaitlyn , Dehart Jeremy , Krishnamurthy Raghavendra , Bhat G. S. , Shroyer Emily , Tandon Amit , Pérez Valentín Jaynise M. , Jinadasa S. U. P. 
Published: January 2024

AbstractThe Monsoon Intra-Seasonal Oscillations in the Bay of Bengal (MISO-BOB) field campaign was conducted in the Indian Ocean during the 2018 and 2019 summer monsoon seasons. WC-130J aircraft of the 53rd Weather Reconnaissance Squadron of the US Air Force participated in the campaign in June 2018. The dropsonde observations across a tropical supercluster showed zonal wind variations in association with the structure of the convectively coupled Kelvin wave (CCKW). Within the supercluster, easterlies (westerlies) were observed in the upper (lower) troposphere; this transformation occurred just below the 0$$^{\circ }$$

∘

C level. The cold pool had an easterly component throughout, and it was coldest (by 2.5$$^{\circ }$$

∘

C) at the center of the supercluster, deepest ($$\sim$$
∼
$$1000\,\hbox {m}$$

1000

m

) at its rear/western end, and shallowest ($$\sim$$
∼
300 m) at the front/eastern end. The level of free convection (LFC) at the front end was at $$897\,\hbox {m}$$

897

m

altitude. At the eastern flank of the supercluster, zonal convergence in the lower troposphere occurred between 500-1500 m levels above the surface between the westerlies within the supercluster and opposing ambient easterlies. Thus, the uplifting of conditionally unstable air parcels above LFC to the east of the supercluster was likely to occur due to this convergence rather than the cold pool influence. Conversely, the western flank of the supercluster had low-level zonal divergence. These observations support the notion of ‘self-similarity’ among the mesoscale convective systems and large-scale waves.
Response of skin temperature, blood ammonia and lactate during incremental exercise until exhaustion in elite athletes
Authors: Korman Paweł , Kusy Krzysztof , Straburzyńska-Lupa Anna , Kantanista Adam , Quintana Manuel Sillero , Zieliński Jacek 
Published: January 2024

AbstractThe study aimed to evaluate the lower limb skin temperature (Tsk) and blood concentrations of lactate (LA) and ammonia (NH3) during exercise and recovery. Eleven elite sprint athletes (25 ± 3.4 yrs) and 11 elite endurance athletes (24.45 ± 5.4 yrs) performed an incremental running test until exhaustion. Body composition was estimated using the DXA method. Thermograms of the anterior and posterior surfaces of the lower limbs were recorded at rest, before each test stage (every 3 min, starting from 10 km h−1 and increasing by 2 km h−1), and in the 5th, 10th, 15th, 20th, and 30th minute of recovery. Endurance athletes had a higher maximum oxygen uptake than sprint athletes (5.0 ± 0.7 vs 4.3 ± 0.4 l·kg−1, p = 0.018), lower percentage of lean content (79 ± 2 vs 83 ± 2%, p < 0.001), and a higher percentage of fat content in the lower limbs (17 ± 2 vs 12 ± 2%, p < 0.001). In both groups, a significant decrease in Tsk was observed compared to resting value (endurance athletes—31.5 ± 0.6 °C; sprint athletes—32.3 ± 0.6 °C), during exercise (p < 0.001) and rewarming during recovery (p < 0.001). However, endurance athletes had a lower Tsk than sprint athletes at the exhaustion point (30.0 ± 1.1 vs 31.6 ± 0.8 °C, p < 0.05) and the pattern of change in Tsk differed between groups (p < 0.001). Tsk in the endurance athletes group decreased throughout the exercise protocol and returned more rapidly to initial values during recovery, while Tsk in the sprint group stabilised between moderate intensity and exhaustion, recovering more slowly after exercise. Both LA (endurance athletes—max 10.2 ± 1.5; sprint athletes—max 10.1 ± 1.4 mmol⋅L−1, p < 0.001) and NH3 (endurance athletes—max 75.6 ± 11.5; sprint athletes—max 76.7 ± 9.0 mmol⋅L−1, p < 0.001) increased during exercise and decreased during recovery (p < 0.001). During exercise, lower levels and slower increases in LA were observed during exercise in the endurance athletes’ group (p < 0.05). A negative correlation was revealed between Tsk and fat percentage (r = −0.43 to −0.71, p < 0.05). Tsk was positively correlated with LA during recovery (r = 0.43 to 0.48, p < 0.05), and negatively during recovery (r = −0.45 to −0.54, p < 0.05). Differences between groups in maximum aerobic capacity, the pattern of change in Tsk, and the correlation between Tsk and LA suggest that individuals who decrease less Tsk during exercise and higher Tsk during recovery are those with better aerobic capacity. In addition, athletes with less body fat dissipate heat from their tissues more efficiently.
Potholes and traffic signs detection by classifier with vision transformers
Authors: Satti Satish Kumar , Rajareddy Goluguri N. V. , Mishra Kaushik , Gandomi Amir H. 
Published: January 2024

AbstractDetecting potholes and traffic signs is crucial for driver assistance systems and autonomous vehicles, emphasizing real-time and accurate recognition. In India, approximately 2500 fatalities occur annually due to accidents linked to hidden potholes and overlooked traffic signs. Existing methods often overlook water-filled and illuminated potholes, as well as those shaded by trees. Additionally, they neglect the perspective and illuminated (nighttime) traffic signs. To address these challenges, this study introduces a novel approach employing a cascade classifier along with a vision transformer. A cascade classifier identifies patterns associated with these elements, and Vision Transformers conducts detailed analysis and classification. The proposed approach undergoes training and evaluation on ICTS, GTSRDB, KAGGLE, and CCSAD datasets. Model performance is assessed using precision, recall, and mean Average Precision (mAP) metrics. Compared to state-of-the-art techniques like YOLOv3, YOLOv4, Faster RCNN, and SSD, the method achieves impressive recognition with a mAP of 97.14% for traffic sign detection and 98.27% for pothole detection.