bluuebunny/crossref_metadata_2025_split huggingface dataset:
Submesoscale‐Permitting Physical/Biogeochemical Future Projections for the Main Hawaiian Islands
Authors: Friedrich T. , Powell B. S. , Gunnarson J. L. , Liu G. , Giardina S. F. , Stuecker M. F. , Hošeková L. , Feloy K. , Stock C. A. 
Published: February 2024

AbstractGlobal climate models provide useful tools to forecast large‐scale anthropogenic trends and the impacts on ocean physics and marine biology and chemistry. Due to coarse spatial resolution, they typically lack the ability to represent important regional processes while underestimating mesoscale variability and vertical mixing. This means they provide limited value when it comes to regional climate projections. We developed a regional submesoscale‐permitting physical/biogeochemical model to dynamically downscale the output of a CMIP6 Earth System Model for three different Socioeconomic Pathways for the main Hawaiian Islands. We describe the methodology for downscaling the CMIP6 ocean physics and biogeochemistry along with atmospheric conditions in order to offline nest a regional model. We expect the large‐scale spatial and temporal features of the global model to be retained by the regional model, while adding representation of the regional processes that are crucial to understanding climate change on a local scale. We compare the regional model representation against both observed data and a regional reanalysis over the first two decades of the century. We show that the regional model maintains the large‐scale trends and interannual variability provided by the CMIP6 model while well‐representing the regional dynamics that drive the short‐term variability. To better illustrate the benefit of the downscaling, we present preliminary analysis of the downscaled results to examine climate impacts on the island corals that are not resolved by the global models. This analysis reveals that coastal corals are likely to experience unprecedented ocean acidification and substantial warming over the course of the century.
Tunable VO2 cavity enables multispectral manipulation from visible to microwave frequencies
Authors: Wei Hang , Gu Jinxin , Zhao Tao , Yan Zhiyuan , Xu He-Xiu , Dou Shuliang , Qiu Cheng-Wei , Li Yao 
Published: February 2024

AbstractOptical materials capable of dynamically manipulating electromagnetic waves are an emerging field in memories, optical modulators, and thermal management. Recently, their multispectral design preliminarily attracts much attention, aiming to enhance their efficiency and integration of functionalities. However, the multispectral manipulation based on these materials is challenging due to their ubiquitous wavelength dependence restricting their capacity to narrow wavelengths. In this article, we cascade multiple tunable optical cavities with selective-transparent layers, enabling a universal approach to overcoming wavelength dependence and establishing a multispectral platform with highly integrated functions. Based on it, we demonstrate the multispectral (ranging from 400 nm to 3 cm), fast response speed (0.9 s), and reversible manipulation based on a typical phase change material, vanadium dioxide. Our platform involves tandem VO2-based Fabry–Pérot (F-P) cavities enabling the customization of optical responses at target bands independently. It can achieve broadband color-changing capacity in the visible region (a shift of ~60 nm in resonant wavelength) and is capable of freely switching between three typical optical models (transmittance, reflectance, and absorptance) in the infrared to microwave regions with drastic amplitude tunability exceeding 0.7. This work represents a state-of-art advance in multispectral optics and material science, providing a critical approach for expanding the multispectral manipulation ability of optical systems.
Highly-sensitive wafer-scale transfer-free graphene MEMS condenser microphones
Authors: Pezone Roberto , Anzinger Sebastian , Baglioni Gabriele , Wasisto Hutomo Suryo , Sarro Pasqualina M. , Steeneken Peter G. , Vollebregt Sten 
Published: February 2024

AbstractSince the performance of micro-electro-mechanical system (MEMS)-based microphones is approaching fundamental physical, design, and material limits, it has become challenging to improve them. Several works have demonstrated graphene’s suitability as a microphone diaphragm. The potential for achieving smaller, more sensitive, and scalable on-chip MEMS microphones is yet to be determined. To address large graphene sizes, graphene-polymer heterostructures have been proposed, but they compromise performance due to added polymer mass and stiffness. This work demonstrates the first wafer-scale integrated MEMS condenser microphones with diameters of 2R = 220–320 μm, thickness of 7 nm multi-layer graphene, that is suspended over a back-plate with a residual gap of 5 μm. The microphones are manufactured with MEMS compatible wafer-scale technologies without any transfer steps or polymer layers that are more prone to contaminate and wrinkle the graphene. Different designs, all electrically integrated are fabricated and characterized allowing us to study the effects of the introduction of a back-plate for capacitive read-out. The devices show high mechanical compliances Cm = 0.081–1.07 μmPa−1 (10–100 × higher than the silicon reported in the state-of-the-art diaphragms) and pull-in voltages in the range of 2–9.5 V. In addition, to validate the proof of concept, we have electrically characterized the graphene microphone when subjected to sound actuation. An estimated sensitivity of S1kHz = 24.3–321 mV Pa−1 for a Vbias = 1.5 V was determined, which is 1.9–25.5 × higher than of state-of-the-art microphone devices while having a ~9 × smaller area.
SIRT7: a novel molecular target for personalized cancer treatment?
Authors: Ianni Alessandro , Kumari Poonam , Tarighi Shahriar , Braun Thomas , Vaquero Alejandro 
Published: February 2024

AbstractThe Sirtuin family of NAD+-dependent enzymes assumes a pivotal role in orchestrating adaptive responses to environmental fluctuations and stress stimuli, operating at both genomic and metabolic levels. Within this family, SIRT7 emerges as a versatile player in tumorigenesis, displaying both pro-tumorigenic and tumor-suppressive functions in a context-dependent manner. While other sirtuins, such as SIRT1 and SIRT6, exhibit a similar dual role in cancer, SIRT7 stands out due to distinctive attributes that sharply distinguish it from other family members. Among these are a unique key role in regulation of nucleolar functions, a close functional relationship with RNA metabolism and processing -exceptional among sirtuins- and a complex multienzymatic nature, which provides a diverse range of molecular targets. This review offers a comprehensive overview of the current understanding of the role of SIRT7 in various malignancies, placing particular emphasis on the intricate molecular mechanisms employed by SIRT7 to either stimulate or counteract tumorigenesis. Additionally, it delves into the unique features of SIRT7, discussing their potential and specific implications in tumor initiation and progression, underscoring the promising avenue of targeting SIRT7 for the development of innovative anti-cancer therapies.
Deep phenotyping of post-infectious myalgic encephalomyelitis/chronic fatigue syndrome
Authors: Walitt Brian , Singh Komudi , LaMunion Samuel R. , Hallett Mark , Jacobson Steve , Chen Kong , Enose-Akahata Yoshimi , Apps Richard , Barb Jennifer J. , Bedard Patrick , Brychta Robert J. , Buckley Ashura Williams , Burbelo Peter D. , Calco Brice , Cathay Brianna , Chen Li , Chigurupati Snigdha , Chen Jinguo , Cheung Foo , Chin Lisa M. K. , Coleman Benjamin W. , Courville Amber B. , Deming Madeleine S. , Drinkard Bart , Feng Li Rebekah , Ferrucci Luigi , Gabel Scott A. , Gavin Angelique , Goldstein David S. , Hassanzadeh Shahin , Horan Sean C. , Horovitz Silvina G. , Johnson Kory R. , Govan Anita Jones , Knutson Kristine M. , Kreskow Joy D. , Levin Mark , Lyons Jonathan J. , Madian Nicholas , Malik Nasir , Mammen Andrew L. , McCulloch John A. , McGurrin Patrick M. , Milner Joshua D. , Moaddel Ruin , Mueller Geoffrey A. , Mukherjee Amrita , Muñoz-Braceras Sandra , Norato Gina , Pak Katherine , Pinal-Fernandez Iago , Popa Traian , Reoma Lauren B. , Sack Michael N. , Safavi Farinaz , Saligan Leorey N. , Sellers Brian A. , Sinclair Stephen , Smith Bryan , Snow Joseph , Solin Stacey , Stussman Barbara J. , Trinchieri Giorgio , Turner Sara A. , Vetter C. Stephenie , Vial Felipe , Vizioli Carlotta , Williams Ashley , Yang Shanna B. ,   Center for Human Immunology, Autoimmunity, and Inflammation (CHI) Consortium, Nath Avindra 
Published: February 2024

AbstractPost-infectious myalgic encephalomyelitis/chronic fatigue syndrome (PI-ME/CFS) is a disabling disorder, yet the clinical phenotype is poorly defined, the pathophysiology is unknown, and no disease-modifying treatments are available. We used rigorous criteria to recruit PI-ME/CFS participants with matched controls to conduct deep phenotyping. Among the many physical and cognitive complaints, one defining feature of PI-ME/CFS was an alteration of effort preference, rather than physical or central fatigue, due to dysfunction of integrative brain regions potentially associated with central catechol pathway dysregulation, with consequences on autonomic functioning and physical conditioning. Immune profiling suggested chronic antigenic stimulation with increase in naïve and decrease in switched memory B-cells. Alterations in gene expression profiles of peripheral blood mononuclear cells and metabolic pathways were consistent with cellular phenotypic studies and demonstrated differences according to sex. Together these clinical abnormalities and biomarker differences provide unique insight into the underlying pathophysiology of PI-ME/CFS, which may guide future intervention.
Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation
Authors: Sharma Harshita , Valentine Matthew N. Z. , Toki Naoko , Sueki Hiromi Nishiyori , Gustincich Stefano , Takahashi Hazuki , Carninci Piero 
Published: February 2024

AbstractRNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA–RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
Increased CO2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast
Authors: Qin Ning , Li Lingyun , Wan Xiaozhen , Ji Xu , Chen Yu , Li Chaokun , Liu Ping , Zhang Yijie , Yang Weijie , Jiang Junfeng , Xia Jianye , Shi Shuobo , Tan Tianwei , Nielsen Jens , Chen Yun , Liu Zihe 
Published: February 2024

AbstractCO2 fixation plays a key role to make biobased production cost competitive. Here, we use 3-hydroxypropionic acid (3-HP) to showcase how CO2 fixation enables approaching theoretical-yield production. Using genome-scale metabolic models to calculate the production envelope, we demonstrate that the provision of bicarbonate, formed from CO2, restricts previous attempts for high yield production of 3-HP. We thus develop multiple strategies for bicarbonate uptake, including the identification of Sul1 as a potential bicarbonate transporter, domain swapping of malonyl-CoA reductase, identification of Esbp6 as a potential 3-HP exporter, and deletion of Uga1 to prevent 3-HP degradation. The combined rational engineering increases 3-HP production from 0.14 g/L to 11.25 g/L in shake flask using 20 g/L glucose, approaching the maximum theoretical yield with concurrent biomass formation. The engineered yeast forms the basis for commercialization of bio-acrylic acid, while our CO2 fixation strategies pave the way for CO2 being used as the sole carbon source.
Swept coded aperture real-time femtophotography
Authors: Liu Jingdan , Marquez Miguel , Lai Yingming , Ibrahim Heide , Légaré Katherine , Lassonde Philippe , Liu Xianglei , Hehn Michel , Mangin Stéphane , Malinowski Grégory , Li Zhengyan , Légaré François , Liang Jinyang 
Published: February 2024

AbstractSingle-shot real-time femtophotography is indispensable for imaging ultrafast dynamics during their times of occurrence. Despite their advantages over conventional multi-shot approaches, existing techniques confront restricted imaging speed or degraded data quality by the deployed optoelectronic devices and face challenges in the application scope and acquisition accuracy. They are also hindered by the limitations in the acquirable information imposed by the sensing models. Here, we overcome these challenges by developing swept coded aperture real-time femtophotography (SCARF). This computational imaging modality enables all-optical ultrafast sweeping of a static coded aperture during the recording of an ultrafast event, bringing full-sequence encoding of up to 156.3 THz to every pixel on a CCD camera. We demonstrate SCARF’s single-shot ultrafast imaging ability at tunable frame rates and spatial scales in both reflection and transmission modes. Using SCARF, we image ultrafast absorption in a semiconductor and ultrafast demagnetization of a metal alloy.
Structure of the recombinant RNA polymerase from African Swine Fever Virus
Authors: Pilotto Simona , Sýkora Michal , Cackett Gwenny , Dulson Christopher , Werner Finn 
Published: February 2024

AbstractAfrican Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.
Large language models streamline automated machine learning for clinical studies
Authors: Tayebi Arasteh Soroosh , Han Tianyu , Lotfinia Mahshad , Kuhl Christiane , Kather Jakob Nikolas , Truhn Daniel , Nebelung Sven 
Published: February 2024

AbstractA knowledge gap persists between machine learning (ML) developers (e.g., data scientists) and practitioners (e.g., clinicians), hampering the full utilization of ML for clinical data analysis. We investigated the potential of the ChatGPT Advanced Data Analysis (ADA), an extension of GPT-4, to bridge this gap and perform ML analyses efficiently. Real-world clinical datasets and study details from large trials across various medical specialties were presented to ChatGPT ADA without specific guidance. ChatGPT ADA autonomously developed state-of-the-art ML models based on the original study’s training data to predict clinical outcomes such as cancer development, cancer progression, disease complications, or biomarkers such as pathogenic gene sequences. Following the re-implementation and optimization of the published models, the head-to-head comparison of the ChatGPT ADA-crafted ML models and their respective manually crafted counterparts revealed no significant differences in traditional performance metrics (p ≥ 0.072). Strikingly, the ChatGPT ADA-crafted ML models often outperformed their counterparts. In conclusion, ChatGPT ADA offers a promising avenue to democratize ML in medicine by simplifying complex data analyses, yet should enhance, not replace, specialized training and resources, to promote broader applications in medical research and practice.
Unraveling the role of vaporization momentum in self-jumping dynamics of freezing supercooled droplets at reduced pressures
Authors: Yan Xiao , Au Samuel C. Y. , Chan Sui Cheong , Chan Ying Lung , Leung Ngai Chun , Wu Wa Yat , Sin Dixon T. , Zhao Guanlei , Chung Casper H. Y. , Mei Mei , Yang Yinchuang , Qiu Huihe , Yao Shuhuai 
Published: February 2024

AbstractSupercooling of water complicates phase change dynamics, the understanding of which remains limited yet vital to energy-related and aerospace processes. Here, we investigate the freezing and jumping dynamics of supercooled water droplets on superhydrophobic surfaces, induced by a remarkable vaporization momentum, in a low-pressure environment. The vaporization momentum arises from the vaporization at droplet’s free surface, progressed and intensified by recalescence, subsequently inducing droplet compression and finally self-jumping. By incorporating liquid-gas-solid phase changes involving vaporization, freezing recalescence, and liquid-solid interactions, we resolve the vaporization momentum and droplet dynamics, revealing a size-scaled jumping velocity and a nucleation-governed jumping direction. A droplet-size-defined regime map is established, distinguishing the vaporization-momentum-dominated self-jumping from evaporative drying and overpressure-initiated levitation, all induced by depressurization and vaporization. Our findings illuminate the role of supercooling and low-pressure mediated phase change in shaping fluid transport dynamics, with implications for passive anti-icing, advanced cooling, and climate physics.
Plant trait and vegetation data along a 1314 m elevation gradient with fire history in Puna grasslands, Perú
Authors: Halbritter Aud H. , Vandvik Vigdis , Cotner Sehoya H. , Farfan-Rios William , Maitner Brian S. , Michaletz Sean T. , Oliveras Menor Imma , Telford Richard J. , Ccahuana Adam , Cruz Rudi , Sallo-Bravo Jhonatan , Santos-Andrade Paul Efren , Vilca-Bustamante Lucely L. , Castorena Matiss , Chacón-Labella Julia , Christiansen Casper Tai , Duran Sandra M. , Egelkraut Dagmar D. , Gya Ragnhild , Haugum Siri Vatsø , Seltzer Lorah , Silman Miles R. , Strydom Tanya , Spiegel Marcus P. , Barros Agustina , Birkeli Kristine , Boakye Mickey , Chiappero Fernanda , Chmurzynski Adam , Garen Josef C. , Gaudard Joseph , Gauthier Tasha-Leigh J. , Geange Sonya R. , Gonzales Fiorella N. , Henn Jonathan J. , Hošková Kristýna , Isaksen Anders , Jessup Laura H. , Johnson Will , Kusch Erik , Lepley Kai , Lift Mackenzie , Martyn Trace E. , Muñoz Mazon Miguel , Middleton Sara L. , Quinteros Casaverde Natalia L. , Navarro Jocelyn , Zepeda Verónica , Ocampo-Zuleta Korina , Palomino-Cardenas Andrea Carmeli , Pastor Ploskonka Samuel , Pierfederici Maria Elisa , Pinelli Verónica , Rickenback Jess , Roos Ruben E. , Rui Hilde Stokland , Sanchez Diaz Eugenia , Sánchez-Tapia Andrea , Smith Alyssa , Urquiaga-Flores Erickson , von Oppen Jonathan , Enquist Brian J. 
Published: February 2024

AbstractAlpine grassland vegetation supports globally important biodiversity and ecosystems that are increasingly threatened by climate warming and other environmental changes. Trait-based approaches can support understanding of vegetation responses to global change drivers and consequences for ecosystem functioning. In six sites along a 1314 m elevational gradient in Puna grasslands in the Peruvian Andes, we collected datasets on vascular plant composition, plant functional traits, biomass, ecosystem fluxes, and climate data over three years. The data were collected in the wet and dry season and from plots with different fire histories. We selected traits associated with plant resource use, growth, and life history strategies (leaf area, leaf dry/wet mass, leaf thickness, specific leaf area, leaf dry matter content, leaf C, N, P content, C and N isotopes). The trait dataset contains 3,665 plant records from 145 taxa, 54,036 trait measurements (increasing the trait data coverage of the regional flora by 420%) covering 14 traits and 121 plant taxa (ca. 40% of which have no previous publicly available trait data) across 33 families.
Association between serum uric acid and bone mineral density in males from NHANES 2011–2020
Authors: Wang Renwei , Gao Yao , Wang Peng , He Chunru , Lu Hao 
Published: February 2024

AbstractCurrently, the relationship between serum uric acid (SUA) and bone mineral density (BMD) in men remains controversial. This study aims to investigate the relationship between SUA and lumbar spine BMD in American men using data from the National Health and Nutrition Examination Survey (NHANES). A total of 6254 male subjects aged 12–80 years (mean age 35.52 ± 14.84 years) in the NHANES from 2011 to 2020 were analyzed. SUA was measured by DxC using the timed endpoint method, and lumbar spine BMD was measured by dual-energy X-ray absorptiometry (DXA). Multivariate linear regression models were used to explore the relationship between SUA and BMD by adjusting for age, race/Hispanic origin, drinking behavior, smoking behavior, physical activity, body mass index (BMI), poverty-to-income ratio (PIR), total protein, serum calcium, cholesterol, serum phosphorus, and blood urea nitrogen. After correcting for the above confounders, it was found that SUA was positively associated with lumbar spine BMD in the range of SUA < 5 mg/dL (β = 0.006 95% CI 0.003–0.009, P < 0.001), and BMD of individuals in the highest quartile of SUA was 0.020 g/cm2 higher than those in the lowest quartile of SUA (β = 0.020 95% CI 0.008–0.032, P = 0.003). This study showed that SUA was positively correlated with lumbar spine BMD in American men within a certain range. This gives clinicians some insight into how to monitor SUA levels to predict BMD levels during adolescence when bone is urgently needed for growth and development and during old age when bone loss is rapid.