bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Downward Surface Longwave Flux Estimates Using Meteosat Cloud Observations
Authors: Lopes Francisco M. , Dutra Emanuel , Trigo Isabel F. , Wild Martin 
Published: March 2024

AbstractThe downward surface longwave flux (DSLF) plays a relevant role in the Earth’s surface radiative budget, which is crucial to monitor, understand and model the impact of changes at local and global scales on surface temperature and surface conditions. This study focuses on the evaluation and intercomparison of four DSLF products: (a) a recently developed all‐weather DSLF product based on the multivariate adaptive regression splines (MARS) algorithm driven by satellite cloud information from the Meteosat Second Generation (MSG) and ERA5 reanalysis screen variables; (b) the Satellite Application Facility on Land Surface Analysis (LSA SAF); (c) CERES Synoptic top‐of‐atmosphere and surface fluxes and clouds (CERES‐SYN1deg) and (d) ERA5 reanalysis. The study covers the period 2005–2021 and the MSG region focusing on monthly means. The evaluation performed against 48 ground stations from the Baseline Surface Radiation Network (BSRN) and FLUXNET2015 networks showed that the MARS product outperforms the remaining products, particularly the LSA SAF, while ERA5 and CERES show similar performance metrics. The fours products are intercompared in terms of their mean spatial variability and temporal mean annual cycles and inter‐annual variability in four selected regions, showing a high level of agreement, particularly between MARS, ERA5 and CERES. Our results highlight the clear added value of MARS with respect to LSA SAF, while providing higher spatial resolution (0.05°), constrained by satellite cloud information, when compared with ERA5 (0.25°) or CERES (1°).
The Eμ-Ret mouse is a novel model of hyperdiploid B-cell acute lymphoblastic leukemia
Authors: Farrokhi Ali , Atre Tanmaya , Rever Jenna , Fidanza Mario , Duey Wendy , Salitra Samuel , Myung Junia , Guo Meiyun , Jo Sumin , Uzozie Anuli , Baharvand Fatemeh , Rolf Nina , Auer Franziska , Hauer Julia , Grupp Stephan A. , Eydoux Patrice , Lange Philipp F. , Seif Alix E. , Maxwell Christopher A. , Reid Gregor S. D. 
Published: March 2024

AbstractThe presence of supernumerary chromosomes is the only abnormality shared by all patients diagnosed with high-hyperdiploid B cell acute lymphoblastic leukemia (HD-ALL). Despite being the most frequently diagnosed pediatric leukemia, the lack of clonal molecular lesions and complete absence of appropriate experimental models have impeded the elucidation of HD-ALL leukemogenesis. Here, we report that for 23 leukemia samples isolated from moribund Eμ-Ret mice, all were characterized by non-random chromosomal gains, involving combinations of trisomy 9, 12, 14, 15, and 17. With a median gain of three chromosomes, leukemia emerged after a prolonged latency from a preleukemic B cell precursor cell population displaying more diverse aneuploidy. Transition from preleukemia to overt disease in Eμ-Ret mice is associated with acquisition of heterogeneous genomic abnormalities affecting the expression of genes implicated in pediatric B-ALL. The development of abnormal centrosomes in parallel with aneuploidy renders both preleukemic and leukemic cells sensitive to inhibitors of centrosome clustering, enabling targeted in vivo depletion of leukemia-propagating cells. This study reveals the Eμ-Ret mouse to be a novel tool for investigating HD-ALL leukemogenesis, including supervision and selection of preleukemic aneuploid clones by the immune system and identification of vulnerabilities that could be targeted to prevent relapse.
“The forest and the trees”: a narrative medicine curriculum by residents for residents
Authors: Sinha Anoushka , Slater Carly S. , Lee Alyson , Sridhar Harini , Gowda Deepthiman 
Published: March 2024

Abstract
A 7-session narrative medicine (NM) curriculum was designed and facilitated by pediatrics residents for pediatrics residents in order to unpack challenging experiences during clinical training and strengthen relationships with colleagues and patients. The primary facilitator, a resident with a master’s degree in NM, provided facilitator training to her co-residents with whom she co-led the workshops in the curriculum. We conducted, transcribed, and analyzed individual interviews of 15 residents, with three resultant themes: reflection on personal and professional identity; connection to others and community building; and reconceptualization of medical practice. Residents shared that they experienced greater solidarity, professional fulfillment, appreciation for multiple facets of their identities, recognition of holding space for vulnerability, and advocacy for marginalized populations. Our study highlights the feasibility and effectiveness of peer-led NM workshops to enhance clinical training through self-reflection, inclusion of persons from underrecognized backgrounds, and promotion of values consistent with humanistic care.

Impact

A novel narrative medicine curriculum was designed and facilitated by pediatrics residents for pediatrics residents.

The curriculum was feasible and acceptable to pediatrics residents and required a facilitator with content and methodology expertise in narrative medicine to train additional facilitators.

Three themes emerged from resident interviews: reflection on personal and professional identity; connection to others and community building; and reconceptualization of medical practice on individual and global levels.
Diindoles produced from commensal microbiota metabolites function as endogenous CAR/Nr1i3 ligands
Authors: Liu Jiabao , Malekoltojari Ainaz , Asokakumar Anjana , Chow Vimanda , Li Linhao , Li Hao , Grimaldi Marina , Dang Nathanlown , Campbell Jhenielle , Barrett Holly , Sun Jianxian , Navarre William , Wilson Derek , Wang Hongbing , Mani Sridhar , Balaguer Patrick , Anakk Sayeepriyadarshini , Peng Hui , Krause Henry M. 
Published: March 2024

AbstractNumerous studies have demonstrated the correlation between human gut bacteria and host physiology, mediated primarily via nuclear receptors (NRs). Despite this body of work, the systematic identification and characterization of microbe-derived ligands that regulate NRs remain a considerable challenge. In this study, we discover a series of diindole molecules produced from commensal bacteria metabolites that act as specific agonists for the orphan constitutive androstane receptor (CAR). Using various biophysical analyses we show that their nanomolar affinities are comparable to those of synthetic CAR agonists, and that they can activate both rodent and human CAR orthologues, which established synthetic agonists cannot. We also find that the diindoles, diindolylmethane (DIM) and diindolylethane (DIE) selectively up-regulate bona fide CAR target genes in primary human hepatocytes and mouse liver without causing significant side effects. These findings provide new insights into the complex interplay between the gut microbiome and host physiology, as well as new tools for disease treatment.
Defective mitochondria remodelling in B cells leads to an aged immune response
Authors: Iborra-Pernichi Marta , Ruiz García Jonathan , Velasco de la Esperanza María , Estrada Belén S. , Bovolenta Elena R. , Cifuentes Claudia , Prieto Carro Cristina , González Martínez Tamara , García-Consuegra José , Rey-Stolle María Fernanda , Rupérez Francisco Javier , Guerra Rodriguez Milagros , Argüello Rafael J. , Cogliati Sara , Martín-Belmonte Fernando , Martínez-Martín Nuria 
Published: March 2024

AbstractThe B cell response in the germinal centre (GC) reaction requires a unique bioenergetic supply. Although mitochondria are remodelled upon antigen-mediated B cell receptor stimulation, mitochondrial function in B cells is still poorly understood. To gain a better understanding of the role of mitochondria in B cell function, here we generate mice with B cell-specific deficiency in Tfam, a transcription factor necessary for mitochondrial biogenesis. Tfam conditional knock-out (KO) mice display a blockage of the GC reaction and a bias of B cell differentiation towards memory B cells and aged-related B cells, hallmarks of an aged immune response. Unexpectedly, blocked GC reaction in Tfam KO mice is not caused by defects in the bioenergetic supply but is associated with a defect in the remodelling of the lysosomal compartment in B cells. Our results may thus describe a mitochondrial function for lysosome regulation and the downstream antigen presentation in B cells during the GC reaction, the dysruption of which is manifested as an aged immune response.
InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data
Authors: Liu Xiaochuan , Chen Hao , Li Zekun , Yang Xiaoxiao , Jin Wen , Wang Yuting , Zheng Jian , Li Long , Xuan Chenghao , Yuan Jiapei , Yang Yang 
Published: March 2024

AbstractAlternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has been implicated in diverse biological processes and diseases, as it can produce noncoding transcripts or transcripts with truncated coding regions. However, a reliable method is required to accurately characterize IPA. Here, we propose a computational method called InPACT, which allows for the precise characterization of IPA from conventional RNA-seq data. InPACT successfully identifies numerous previously unannotated IPA transcripts in human cells, many of which are translated, as evidenced by ribosome profiling data. We have demonstrated that InPACT outperforms other methods in terms of IPA identification and quantification. Moreover, InPACT applied to monocyte activation reveals temporally coordinated IPA events. Further application on single-cell RNA-seq data of human fetal bone marrow reveals the expression of several IPA isoforms in a context-specific manner. Therefore, InPACT represents a powerful tool for the accurate characterization of IPA from RNA-seq data.
Photoswitchable polyynes for multiplexed stimulated Raman scattering microscopy with reversible light control
Authors: Yang Yueli , Bai Xueyang , Hu Fanghao 
Published: March 2024

AbstractOptical imaging with photo-controllable probes has greatly advanced biological research. With superb chemical specificity of vibrational spectroscopy, stimulated Raman scattering (SRS) microscopy is particularly promising for super-multiplexed optical imaging with rich chemical information. Functional SRS imaging in response to light has been recently demonstrated, but multiplexed SRS imaging with reversible photocontrol remains unaccomplished. Here, we create a multiplexing palette of photoswitchable polyynes with 16 Raman frequencies by coupling asymmetric diarylethene with super-multiplexed Carbow (Carbow-switch). Through optimization of both electronic and vibrational spectroscopy, Carbow-switch displays excellent photoswitching properties under visible light control and SRS response with large frequency change and signal enhancement. Reversible and spatial-selective multiplexed SRS imaging of different organelles are demonstrated in living cells. We further achieve photo-selective time-lapse imaging of organelle dynamics during oxidative stress and protein phase separation. The development of Carbow-switch for photoswitchable SRS microscopy will open up new avenues to study complex interactions and dynamics in living cells with high spatiotemporal precision and multiplexing capability.
Brain atrophy in normal older adult links tooth loss and diet changes to future cognitive decline
Authors: Nakamura Hiroyuki , Noguchi-Shinohara Moeko , Ishimiya-Jokaji Mai , Kobayashi Yutaka , Isa Mikana , Ide Kentaro , Kawano Toshihiro , Kawashiri Shuichi , Uchida Kazuhiro , Tatewaki Yasuko , Taki Yasuyuki , Ohara Tomoyuki , Ninomiya Toshiharu , Ono Kenjiro 
Published: March 2024

AbstractSeveral studies have found associations between poor oral health, particularly tooth loss and cognitive decline. However, the specific brain regions affected by tooth loss and the probable causes remain unclear. We conducted a population-based longitudinal cohort study in Nakajima, Nanao City, Japan. Between 2016 and 2018, 2454 residents aged ≥60 participated, covering 92.9% of the local age demographics. This study used comprehensive approach by combining detailed dental examinations, dietary assessments, magnetic resonance imaging (MRI) analysis, and cognitive evaluations. Tooth loss, even in cognitively normal individuals, is associated with parahippocampal gyrus atrophy and increased WMH volume, both of which are characteristics of dementia. Tooth loss was associated with altered dietary patterns, notably a reduction in plant-based food intake and an increase in fatty, processed food intake. This study highlights a possible preventative pathway where oral health may play a significant role in preventing the early neuropathological shifts associated with dementia.
De novo and somatic structural variant discovery with SVision-pro
Authors: Wang Songbo , Lin Jiadong , Jia Peng , Xu Tun , Li Xiujuan , Liu Yuezhuangnan , Xu Dan , Bush Stephen J. , Meng Deyu , Ye Kai 
Published: March 2024

Abstract
Long-read-based de novo and somatic structural variant (SV) discovery remains challenging, necessitating genomic comparison between samples. We developed SVision-pro, a neural-network-based instance segmentation framework that represents genome-to-genome-level sequencing differences visually and discovers SV comparatively between genomes without any prerequisite for inference models. SVision-pro outperforms state-of-the-art approaches, in particular, the resolving of complex SVs is improved, with low Mendelian error rates, high sensitivity of low-frequency SVs and reduced false-positive rates compared with SV merging approaches.
UVB induced reactivation leads to HSV1 in the corneas of virtually all latently infected mice and requires STING to develop corneal disease
Authors: Yin Xiao-Tang , Hartman Alexis , Sirajuddin Nadia , Shukla Deepak , Leger Anthony St. , Keadle Tammie L. , Stuart Patrick M. 
Published: March 2024

AbstractReactivation of latent herpes simplex type 1 results in virus returning to the cornea leading to recurrent herpetic stromal keratitis (rHSK). We compare two competing models to reactivate viruses from latency, UV-B irradiation and cyclophosphamide (CP). Results revealed that while both result in corneal recrudescence, only UV-B irradiation results in rHSK. To better understand the dynamics of reactivation, we analyzed corneas for both the presence of infectious viruses and the dynamics of exposure to multiple reactivations using UV-B. We noted that multiple reactivations result in progressively worse corneal disease. We also noted that expression of IFNα and STING, surragate markers for the presence of virus, are induced by the presence of reactivated virus. Studies to determine the importance of STING to the development of HSK revealed that in the absence of STING, mice do not develop significant HSK and the magnitude of the infiltrate of CD45+ cells in these corneas is significantly reduced. The resulting paucity of CD45+CD11b+GR-1+F4/80-neutrophils, and to a lesser extent CD45+CD11b+GR-1-F4/80+ macrophages in B6-STING KO mice following reactivation is likely the underlying cause for lack of rHSK as has been noted by ourselves and others. These results underscore the critical importance of STING’s role in developing rHSK.
Smartphone-based device for point-of-care diagnostics of pulmonary inflammation using convolutional neural networks (CNNs)
Authors: Ghaderinia Mohammadreza , Abadijoo Hamed , Mahdavian Ashkan , Kousha Ebrahim , Shakibi Reyhaneh , Taheri S. Mohammad-Reza , Simaee Hossein , Khatibi Ali , Moosavi-Movahedi Ali Akbar , Khayamian Mohammad Ali 
Published: March 2024

AbstractIn pulmonary inflammation diseases, like COVID-19, lung involvement and inflammation determine the treatment regime. Respiratory inflammation is typically arisen due to the cytokine storm and the leakage of the vessels for immune cells recruitment. Currently, such a situation is detected by the clinical judgment of a specialist or precisely by a chest CT scan. However, the lack of accessibility to the CT machines in many poor medical centers as well as its expensive service, demands more accessible methods for fast and cheap detection of lung inflammation. Here, we have introduced a novel method for tracing the inflammation and lung involvement in patients with pulmonary inflammation, such as COVID-19, by a simple electrolyte detection in their sputum samples. The presence of the electrolyte in the sputum sample results in the fern-like structures after air-drying. These fern patterns are different in the CT positive and negative cases that are detected by an AI application on a smartphone and using a low-cost and portable mini-microscope. Evaluating 160 patient-derived sputum sample images, this method demonstrated an interesting accuracy of 95%, as confirmed by CT-scan results. This finding suggests that the method has the potential to serve as a promising and reliable approach for recognizing lung inflammatory diseases, such as COVID-19.
A quantitative comparison of virtual and physical experimental paradigms for the investigation of pedestrian responses in hostile emergencies
Authors: Shipman Alastair , Majumdar Arnab , Feng Zhenan , Lovreglio Ruggiero 
Published: March 2024

AbstractModern experiments investigating human behaviour in emergencies are often implemented in virtual reality (VR), due to the increased experimental control and improved ethical viability over physical reality (PR). However, there remain questions regarding the validity of the results obtained from these environments, and no full validation of VR experiments has yet appeared. This study compares the results of two sets of experiments (in VR and PR paradigms) investigating behavioural responses to knife-based hostile aggressors. This study quantitatively analyses these results to ascertain whether the different paradigms generate different responses, thereby assessing the use of virtual reality as a data generating paradigm for emergencies. The results show that participants reported almost identical psychological responses. This study goes on to identify minimal differences in movement responses across a range of predictors, noting a difference in responses between genders. As a result, this study concludes that VR can produce similarly valid data as physical experiments when investigating human behaviour in hostile emergencies, and that it is therefore possible to conduct realistic experimentation through VR environments while retaining confidence in the resulting data. This has major implications for the future of this type of research, and furthermore suggests that VR experimentation should be performed for both existing and new critical infrastructure to understand human responses in hostile scenarios.
Effect of different salinity on seed germination, growth parameters and biochemical contents of pumpkin (Cucurbita pepo L.) seeds cultivars
Authors: Irik Hasan Ali , Bikmaz Gülsah 
Published: March 2024

AbstractSoil and water salinity is an important limiting factor affecting yield and production levels in arid and semi-arid areas. Salt tolerance during germination is an important parameter that also affects the other plant development stages. In this respect, this study was designed to determine the responses of pumpkin seed varieties (Develi, Ürgüp, Hybrid) to different NaCl salinities. The study was carried out in 2022 in the laboratory of Biosystems Engineering Department of Erciyes University in randomized plots design with 3 replications. Experiments were conducted with 5 different water salinity. Germination percentage (GP), germination index (GI), mean germination time (MGT), seedling vigor index (SVI), ion leakage (Il), radicula length (RL) and plumule length (PL), root and shoot fresh and dry weights and some mineral composition (Na, K, Ca) were examined. Proline, antioxidant capacity, total phenolic and DPPH content were significantly affected by salinity. In scatter plot correlation analysis SVI a positive correlation was observed between GP (r2 = 0.774), GI (r2 = 0.745), RL (r2 = 0.929), FRW (r2 = 0.837), FSW (r2 = 0.836), DRW (r2 = 0.894), AC (r2 = 0.747), TP (r2 = 0.640) and DPPH (r2 = 0.635). It was determined that there were negative correlations between SVI and MGT (r2 = − 0.902), II (r2 = − 0.588), DSW (r2 = − 0.682) and PR (r2 = − 0.344). Present findings revealed that investigated parameters were significantly affected by increasing salinity levels. While Hybrid cultivar was the most affected by salinity, Develi cultivar was found to be resistant to saline conditions.
Effect of the temporal coordination and volume of cyclic mechanical loading on human Achilles tendon adaptation in men
Authors: Tsai Meng-Shiuan , Domroes Theresa , Pentidis Nikolaos , Koschinski Sophia , Schroll Arno , Bohm Sebastian , Arampatzis Adamantios , Mersmann Falk 
Published: March 2024

AbstractHuman tendons adapt to mechanical loading, yet there is little information on the effect of the temporal coordination of loading and recovery or the dose–response relationship. For this reason, we assigned adult men to either a control or intervention group. In the intervention group, the two legs were randomly assigned to one of five high-intensity Achilles tendon (AT) loading protocols (i.e., 90% maximum voluntary contraction and approximately 4.5 to 6.5% tendon strain) that were systematically modified in terms of loading frequency (i.e., sessions per week) and overall loading volume (i.e., total time under loading). Before, at mid-term (8 weeks) and after completion of the 16 weeks intervention, AT mechanical properties were determined using a combination of inverse dynamics and ultrasonography. The cross-sectional area (CSA) and length of the free AT were measured using magnetic resonance imaging pre- and post-intervention. The data analysis with a linear mixed model showed significant increases in muscle strength, rest length-normalized AT stiffness, and CSA of the free AT in the intervention group (p < 0.05), yet with no marked differences between protocols. No systematic effects were found considering the temporal coordination of loading and overall loading volume. In all protocols, the major changes in normalized AT stiffness occurred within the first 8 weeks and were mostly due to material rather than morphological changes. Our findings suggest that—in the range of 2.5–5 sessions per week and 180–300 s total high strain loading—the temporal coordination of loading and recovery and overall loading volume is rather secondary for tendon adaptation.
Combined effects of biochar and biodegradable mulch film on chromium bioavailability and the agronomic characteristics of tobacco
Authors: Tang Yuan , Zuo Fumin , Li Changhong , Zhang Qinghai , Gao Weichang , Cheng Jianzhong 
Published: March 2024

AbstractBiochar (BC) and biodegradable mulch film (BMF) are both commonly used means of production in agriculture. In recent years, most studies have focused on the effects of BC or BMF on soil heavy metal pollution, while they have neglected the combined effects. In this study, a pot experiment was conducted to examine the impacts of BMF, BC, and combined BMF and BC (CMB) on the mobility of chromium (Cr) and the agronomic characteristics of flue-cured tobacco. Compared with the control, BMF, BC, and CMB significantly reduced the concentrations of diethylenetriamine pentaacetic acid (DTPA) extractable Cr in soils by 29.07–29.75%, 45.35–48.54%, and 34.21–37.92%, respectively. In comparison to the application of BMF and BC alone, co-application reduced the availability of Cr in soil via increasing the adsorption of soil Cr and soil enzyme activity, which resulted in the decrease of Cr content and bioconcentration factor and in plants. Moreover, the combined application increased the plant height, stem diameter, leaf area, total root area, root tip number, and root activity of tobacco, which leaded to increase in leaf and root biomass by 11.40–67.01% and 23.91–50.74%, respectively. Therefore, the application of CMB can reduce the heavy metal residues in tobacco leaves and improve tobacco yield and quality.