bluuebunny/crossref_metadata_2025_split huggingface dataset:
Making Ecosystem Modeling Operational–A Novel Distributed Execution Framework to Systematically Explore Ecological Responses to Divergent Climate Trajectories
Authors: Steenbeek Jeroen , Ortega Pablo , Bernardello Raffaele , Christensen Villy , Coll Marta , Exarchou Eleftheria , Fuster‐Alonso Alba , Heneghan Ryan , Julià Melis Laura , Pennino Maria Grazia , Rivas David , Keenlyside Noel 
Published: March 2024

AbstractMarine Ecosystem Models (MEMs) are increasingly driven by Earth System Models (ESMs) to better understand marine ecosystem dynamics, and to analyze the effects of alternative management efforts for marine ecosystems under potential scenarios of climate change. However, policy and commercial activities typically occur on seasonal‐to‐decadal time scales, a time span widely used in the global climate modeling community but where the skill level assessments of MEMs are in their infancy. This is mostly due to technical hurdles that prevent the global MEM community from performing large ensemble simulations with which to undergo systematic skill assessments. Here, we developed a novel distributed execution framework constructed of low‐tech and freely available technologies to enable the systematic execution and analysis of linked ESM/MEM prediction ensembles. We apply this framework on the seasonal‐to‐decadal time scale, and assess how retrospective forecast uncertainty in an ensemble of initialized decadal ESM predictions affects a mechanistic and spatiotemporal explicit global trophodynamic MEM. Our results indicate that ESM internal variability has a relatively low impact on the MEM variability in comparison to the broad assumptions related to reconstructed fisheries. We also observe that the results are also sensitive to the ESM specificities. Our case study warrants further systematic explorations to disentangle the impacts of climate change, fisheries scenarios, MEM internal ecological hypotheses, and ESM variability. Most importantly, our case study demonstrates that a simple and free distributed execution framework has the potential to empower any modeling group with the fundamental capabilities to operationalize marine ecosystem modeling.
Myelodysplastic neoplasms dissected into indolent, leukaemic and unfavourable subtypes by computational clustering of haematopoietic stem and progenitor cells
Authors: van Spronsen Margot F. , Van Gassen Sofie , Duetz Carolien , Westers Theresia M. , Saeys Yvan , van de Loosdrecht Arjan A. 
Published: March 2024

AbstractMyelodysplastic neoplasms (MDS) encompass haematological malignancies, which are characterised by dysplasia, ineffective haematopoiesis and the risk of progression towards acute myeloid leukaemia (AML). Myelodysplastic neoplasms are notorious for their heterogeneity: clinical outcomes range from a near-normal life expectancy to leukaemic transformation or premature death due to cytopenia. The Molecular International Prognostic Scoring System made progress in the dissection of MDS by clinical outcomes. To contribute to the risk stratification of MDS by immunophenotypic profiles, this study performed computational clustering of flow cytometry data of CD34+ cells in 67 MDS, 67 AML patients and 49 controls. Our data revealed heterogeneity also within the MDS-derived CD34+ compartment. In MDS, maintenance of lymphoid progenitors and megakaryocytic-erythroid progenitors predicted favourable outcomes, whereas expansion of granulocyte-monocyte progenitors increased the risk of leukaemic transformation. The proliferation of haematopoietic stem cells and common myeloid progenitors with downregulated CD44 expression, suggestive of impaired haematopoietic differentiation, characterised a distinct MDS subtype with a poor overall survival. This exploratory study demonstrates the prognostic value of known and previously unexplored CD34+ populations and suggests the feasibility of dissecting MDS into a more indolent, a leukaemic and another unfavourable subtype.
Transient stimulated Raman scattering spectroscopy and imaging
Authors: Yu Qiaozhi , Yao Zhengjian , Zhou Jiaqi , Yu Wenhao , Zhuang Chenjie , Qi Yafeng , Xiong Hanqing 
Published: March 2024

AbstractStimulated Raman scattering (SRS) has been developed as an essential quantitative contrast for chemical imaging in recent years. However, while spectral lines near the natural linewidth limit can be routinely achieved by state-of-the-art spontaneous Raman microscopes, spectral broadening is inevitable for current mainstream SRS imaging methods. This is because those SRS signals are all measured in the frequency domain. There is a compromise between sensitivity and spectral resolution: as the nonlinear process benefits from pulsed excitations, the fundamental time-energy uncertainty limits the spectral resolution. Besides, the spectral range and acquisition speed are mutually restricted. Here we report transient stimulated Raman scattering (T-SRS), an alternative time-domain strategy that bypasses all these fundamental conjugations. T-SRS is achieved by quantum coherence manipulation: we encode the vibrational oscillations in the stimulated Raman loss (SRL) signal by femtosecond pulse-pair sequence excited vibrational wave packet interference. The Raman spectrum was then achieved by Fourier transform of the time-domain SRL signal. Since all Raman modes are impulsively and simultaneously excited, T-SRS features the natural-linewidth-limit spectral line shapes, laser-bandwidth-determined spectral range, and improved sensitivity. With ~150-fs laser pulses, we boost the sensitivity of typical Raman modes to the sub-mM level. With all-plane-mirror high-speed time-delay scanning, we further demonstrated hyperspectral SRS imaging of live-cell metabolism and high-density multiplexed imaging with the natural-linewidth-limit spectral resolution. T-SRS shall find valuable applications for advanced Raman imaging.
Cost-utility analysis and impact on the environment of videoconference in pressure injury. A randomized controlled trial in individuals with spinal cord injury
Authors: Irgens Ingebjørg , Kleven Linn , Midelfart-Hoff Jana , Jelnes Rolf , Alexander Marcalee , Stanghelle Johan K. , Rekand Tiina 
Published: March 2024

Abstract
Study design
A prospective randomized controlled trial (RCT) in persons with spinal cord injury (SCI) and ongoing pressure injury (PI).

Objectives
The main aim was to perform a cost-utility analysis (CUA) alongside the RCT comparing regular care to regular care with additional videoconference consultations. Secondary aims were to assess costs and greenhouse gas emission related to transportation in the two study groups.

Setting
Two spinal cord units in Norway.

Methods
Participants were allocated to a regular care group (RCG) and a regular care group with additional videoconference (VCG), in a 1-year follow-up between 2016 and 2018. Costs were prospectively collected, and health-related quality of life (HRQoL) data were collected at baseline and 12 months. The outcome was quality-adjusted life years (QALYs), derived from the EQ-5D-5L questionnaire. Results are reported as incremental cost-effectiveness ratio (ICER), expressed as the cost per additional QALY gained. Transportation related costs and environmental emissions were compared by t-tests.

Results
There were 56 participants included, 28 in each group. Of these 27 in the VCG and 26 in the RCG completed. Three participants died. The mean cost per patient was € 8819 in the VCG and € 3607 in the RCG, with 0.1 QALYs gained in the VCG. No significant differences were identified regarding HRQoL or secondary outcomes.

Conclusion
The VCG costs € 5212 more for an additional 0.1 QALYs, giving an ICER of € 52,120 per QALY. No significant differences were found regarding transportation-related costs, or emission of greenhouse gases.

Trial registration
www.ClinicalTrials.gov; NCT02800915, TeleSCIpi. CRISTIN.no. https://app.cristin.no/projects/show.jsf?id=545284. Sunnaas Rehabilitation hospital’s web page, available at https://www.sunnaas.no/fag-og-forskning/fagstoff/sar.
STING dependent BAX-IRF3 signaling results in apoptosis during late-stage Coxiella burnetii infection
Authors: Chauhan Manish , Osbron Chelsea A. , Koehler Heather S. , Goodman Alan G. 
Published: March 2024

AbstractSTING (STimulator of Interferon Genes) is a cytosolic sensor for cyclic dinucleotides (CDNs) and initiates an innate immune response upon binding to CDNs. Coxiella burnetii is a Gram-negative obligate intracellular bacterium and the causative agent of the zoonotic disease Q fever. The ability of C. burnetii to inhibit host cell death is a critical factor in disease development. Previous studies have shown that C. burnetii inhibits host cell apoptosis at early stages of infection. However, during the late-stages of infection, there is host cell lysis resulting in the release of bacteria to infect bystander cells. Thus, we investigated the role of STING during late-stages of C. burnetii infection and examined STING’s impact on host cell death. We show that the loss of STING results in higher bacterial loads and abrogates IFNβ and IL6 induction at 12 days post-infection. The absence of STING during C. burnetii infection significantly reduces apoptosis through decreased caspase-8 and -3 activation. During infection, STING activates IRF3 which interacts with BAX. BAX then translocates to the mitochondria, which is followed by mitochondrial membrane depolarization. This results in increased cytosolic mtDNA in a STING-dependent manner. The presence of increased cytosolic mtDNA results in greater cytosolic 2′-3′ cGAMP, creating a positive feedback loop and leading to further increases in STING activation and its downstream signaling. Taken together, we show that STING signaling is critical for BAX-IRF3-mediated mitochondria-induced apoptosis during late-stage C. burnetii infection.
Immune response induced by standard and fractional doses of 17DD yellow fever vaccine
Authors: Abdala-Torres Thais , Campi-Azevedo Ana Carolina , da Silva-Pereira Rosiane Aparecida , dos Santos Luara Isabela , Henriques Priscilla Miranda , Costa-Rocha Ismael Artur , Otta Dayane Andriotti , Peruhype-Magalhães Vanessa , Teixeira-Carvalho Andréa , Araújo Márcio Sobreira Silva , Fernandes Eder Gatti , Sato Helena Keico , Fantinato Francieli Fontana Sutile Tardetti , Domingues Carla Magda Allan Santos , Kallás Esper Georges , Tomiyama Helena Tomoko Iwashita , Lemos Jandira Aparecida Campos , Coelho-dos-Reis Jordana Grazziela , de Lima Sheila Maria Barbosa , Schwarcz Waleska Dias , de Souza Azevedo Adriana , Trindade Gisela Freitas , Ano Bom Ana Paula Dinis , da Silva Andrea Marques Vieira , Fernandes Camilla Bayma , Camacho Luiz Antônio Bastos , de Sousa Maia Maria de Lourdes ,   Collaborative Group for Studies of Yellow Fever Vaccine, Martins-Filho Olindo Assis , do Antonelli Lis Ribeiro do Valle 
Published: March 2024

AbstractThe re-emergence of yellow fever (YF) urged new mass vaccination campaigns and, in 2017, the World Health Organization approved the use of the fractional dose (FD) of the YF vaccine due to stock shortage. In an observational cross-sectional investigation, we have assessed viremia, antibodies, soluble mediators and effector and memory T and B-cells induced by primary vaccination of volunteers with FD and standard dose (SD). Similar viremia and levels of antibodies and soluble markers were induced early after immunization. However, a faster decrease in the latter was observed after SD. The FD led to a sustained expansion of helper T-cells and an increased expression of activation markers on T-cells early after vaccination. Although with different kinetics, expansion of plasma cells was induced upon SD and FD immunization. Integrative analysis reveals that FD induces a more complex network involving follicular helper T cells and B-cells than SD. Our findings substantiate that FD can replace SD inducing robust correlates of protective immune response against YF.
An optogenetic method for the controlled release of single molecules
Authors: Kashyap Purba , Bertelli Sara , Cao Fakun , Kostritskaia Yulia , Blank Fenja , Srikanth Niranjan A. , Schlack-Leigers Claire , Saleppico Roberto , Bierhuizen Dolf , Lu Xiaocen , Nickel Walter , Campbell Robert E. , Plested Andrew J. R. , Stauber Tobias , Taylor Marcus J. , Ewers Helge 
Published: March 2024

AbstractWe developed a system for optogenetic release of single molecules in cells. We confined soluble and transmembrane proteins to the Golgi apparatus via a photocleavable protein and released them by short pulses of light. Our method allows for a light dose-dependent delivery of functional proteins to the cytosol and plasma membrane in amounts compatible with single-molecule imaging, greatly simplifying access to single-molecule microscopy of any protein in live cells. We were able to reconstitute ion conductance by delivering BK and LRRC8/volume-regulated anion channels to the plasma membrane. Finally we were able to induce NF-kB signaling in T lymphoblasts stimulated by interleukin-1 by controlled release of a signaling protein that had been knocked out. We observed light-induced formation of functional inflammatory signaling complexes that triggered phosphorylation of the inhibitor of nuclear factor kappa-B kinase only in activated cells. We thus developed an optogenetic method for the reconstitution and investigation of cellular function at the single-molecule level.
A chromosome-level genome for the flower thrips Frankliniella intonsa
Authors: Song Wei , Wang Jia-Xu , Cao Li-Jun , Chen Jin-Cui , Bao Wen-Xue , Chen Min , Wei Shu-Jun 
Published: March 2024

AbstractThe flower thrips Frankliniella intonsa (Thysanoptera: Thripidae) is a common insect found in flowers of many plants. Sometimes, F. intonsa causes damage to crops through direct feeding and transmission of plant viruses. Here, we assembled a chromosomal level genome of F. intonsa using the Illumina, Oxford Nanopore (ONT), and Hi-C technologies. The assembled genome had a size of 209.09 Mb, with a contig N50 of 997 bp, scaffold N50 of 13.415 Mb, and BUSCO completeness of 92.5%. The assembled contigs were anchored on 15 chromosomes. A set of 14,109 protein-coding genes were annotated in the genome with a BUSCO completeness of 95.0%. The genome contained 491 non-coding RNA and 0.57% of interspersed repeats. This high-quality genome provides a valuable resource for understanding the ecology, genetics, and evolution of F. intonsa, as well as for controlling thrips pests.
Orbit constraint of a small bead on a rotating large circular hoop in a horizontal plane
Authors: Wang Yuan-Sheng 
Published: March 2024

AbstractOrbit constraint problems can be encountered in mechanical equipment and amusement equipment. Mechanics exercises generally consider the ideal physical model, and the practical problems also consider the influence of friction, which makes the problem more complex and and practical. The problem of the force and oscillation of objects on orbit needs to be deeply discussed. In order to simulate the orbital motion of objects more realistically and help students expand their theoretical mechanics beyond class, we study the orbit constraint of a small bead on a rotating large circular hoop in a horizontal plane about an axis passing through a point on the circumference. The coupling equations followed by the bead on the hoop are derived using Newton’s second law in a planar polar coordinate system and solved by numerical methods. We found that under the action of friction, when the initial angular velocity of the bead is greater than the critical angular velocity, the bead will rotate on the ring, and the number of rotations is related to the initial angular velocity and influenced by the friction coefficient. At different initial angular velocities, the number of oscillations of the bead on the hoop is basically the same and ultimately stops near the fixed point.
A proof-of-principle for decontamination of transplantation kidney through UV-C exposition of the perfusate solution
Authors: Goenaga-Mafud L. C. , Vollet-Filho J. D. , Costa C. , Inada N. M. , Netto A. S. , Kurachi C. , Bagnato V. S. 
Published: March 2024

AbstractKidney transplantation is a common yet highly demanding medical procedure worldwide, enhancing the quality of life for patients with chronic kidney disease. Despite its prevalence, the procedure faces a shortage of available organs, partly due to contamination by microorganisms, leading to significant organ disposal. This study proposes utilizing photonic techniques associated with organ support machines to prevent patient contamination during kidney transplantation. We implemented a decontamination system using ultraviolet-C (UV-C) irradiation on the preservation solution circulating through pigs' kidneys between harvest and implant. UV-C irradiation, alone or combined with ultrasound (US) and Ps80 detergent during ex-vivo swine organ perfusion in a Lifeport® Kidney Transporter machine, aimed to reduce microbiological load in both fluid and organ. Results show rapid fluid decontamination compared to microorganism release from the organ, with notable retention. By including Ps80 detergent at 0.5% during UV-C irradiation 3 log10 (CFU mL−1) of Staphylococcus aureus bacteria previously retained in the organ were successfully removed, indicating the technique's feasibility and effectiveness.
Modeling brain network flexibility in networks of coupled oscillators: a feasibility study
Authors: Chinichian Narges , Lindner Michael , Yanchuk Serhiy , Schwalger Tilo , Schöll Eckehard , Berner Rico 
Published: March 2024

AbstractModeling the functionality of the human brain is a major goal in neuroscience for which many powerful methodologies have been developed over the last decade. The impact of working memory and the associated brain regions on the brain dynamics is of particular interest due to their connection with many functions and malfunctions in the brain. In this context, the concept of brain flexibility has been developed for the characterization of brain functionality. We discuss emergence of brain flexibility that is commonly measured by the identification of changes in the cluster structure of co-active brain regions. We provide evidence that brain flexibility can be modeled by a system of coupled FitzHugh-Nagumo oscillators where the network structure is obtained from human brain Diffusion Tensor Imaging (DTI). Additionally, we propose a straightforward and computationally efficient alternative macroscopic measure, which is derived from the Pearson distance of functional brain matrices. This metric exhibits similarities to the established patterns of brain template flexibility that have been observed in prior investigations. Furthermore, we explore the significance of the brain’s network structure and the strength of connections between network nodes or brain regions associated with working memory in the observation of patterns in networks flexibility. This work enriches our understanding of the interplay between the structure and function of dynamic brain networks and proposes a modeling strategy to study brain flexibility.
Study on the influence of pore water pressure on shear mechanical properties and fracture surface morphology of sandstone
Authors: Cheng Jiaxin , Liu Yixin , Xu Chuanhua , Xu Jiang , Sun Mingzhi 
Published: March 2024

AbstractTo further investigate the weakening effect of pore water pressure on intact rock mechanics properties and characteristics of fracture surface after failure, direct shear tests of sandstone were conducted under different pore pressure. A 3D scanner was employed to digitize the morphology of the post-shear fracture surface. The variogram function was applied to quantify the anisotropic characteristics of post-shear fracture surface. The relationship between deformation during shear failure of intact rock and quantitative parameters of fracture surface after shear failure was initially established. It can be found that amplitudes of the sinusoidal surface determine the maximum value of variogram, and period affect lag distance that reach the maximum value of variogram. Test results revealed that the increase of pore pressure has obvious weakening effect on shear strength and deformation of rock. Moreover, the increase of pore pressure makes the shear fracture surface flatter. It can be obtained that both Sillmax and Rangemax are positively related to shear strain, but negatively related to normal strain.
Doppler ultrasonographic scan, gene expression and serum profile of immune, APPs and antioxidant markers in Egyptian buffalo–cows with clinical endometritis
Authors: El-Sayed Ahmed , Refaai Mohamed , Ateya Ahmed 
Published: March 2024

AbstractThe objective of this study was to elaborate Doppler ultrasonographic scan, genetic resistance and serum profile of markers associated with endometritis susceptibility in Egyptian buffalo–cows. The enrolled animals were designed as; twenty five apparently healthy buffalo–cows considered as a control group and twenty five infected buffalo with endometritis. There were significant (p < 0.05) increased of cervical diameter, endometrium thickness, uterine horn diameter, TAMEAN, TAMAX and blood flow through middle uterine artery with significant decrease of PI and RI values in endometritis buffalo–cows. Gene expression levels were considerably higher in endometritis-affected buffaloes than in resistant ones for the genes A2M, ADAMTS20, KCNT2, MAP3K4, MAPK14, FKBP5, FCAMR, TLR2, IRAK3, CCl2, EPHA4, and iNOS. The RXFP1, NDUFS5, TGF-β, SOD3, CAT, and GPX genes were expressed at substantially lower levels in endometritis-affected buffaloes. The PCR-DNA sequence verdicts of healthy and affected buffaloes revealed differences in the SNPs in the amplified DNA bases related to endometritis for the investigated genes. However, MAP3K4 elicited a monomorphic pattern. There was a significant decrease of red blood cells (RBCs) count, Hb and packed cell volume (PCV) with neutrophilia, lymphocytosis and monocytosis in endometritis group compared with healthy ones. The serum levels of Hp, SAA, Cp, IL-6, IL-10, TNF-α, NO and MDA were significantly (P˂0.05) increased, along with reduction of CAT, GPx, SOD and TAC in buffalo–cows with endometritis compared to healthy ones. The variability of Doppler ultrasonographic scan and studied genes alongside alterations in the serum profile of investigated markers could be a reference guide for limiting buffalo endometritis through selective breeding of natural resistant animals.