bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gas Emission Characteristics and Tectonic Implications in the Southernmost Okinawa Trough From Split‐Beam Echo Sounder Observations
Authors: Lin Yi Chin , Lin Jing‐Yi , Hsu Shu‐Kun , Chen Song‐Chuen , Lin Shiao‐Shan , Tsai Ching‐Hui 
Published: March 2024

AbstractTraditionally, single‐beam echo sounder (SBES) data are used to determine the position of emission structures in the form of a two‐dimensional profile, which may not be straightforward enough to correlate the data of adjacent profiles and determine the exact discharge area. In this study, we develop semiautomatic software to remove noise and select possible flare signals to enhance the speed and precision of the data processing. The program also allows for the transformation of the data into a three‐dimensional point cloud distribution by computing the receiving angle of the data. By applying this method to investigate the distribution and mechanism of gas emission structures in the South Okinawa Trough (SOT), we determine four high flux areas and 22 isolated plumes with roots. Widespread gas flares usually occur in areas with large‐scale volcanic activity or gas‐enriched structures. Isolated gas plumes could be found for a single knoll outcrop and normal faulting structures. The energy of the flares around the knoll area is generally stronger than that observed along the normal faults. Compared with other geophysical data, we find that the widespread distribution of gas flares generally implies a larger hydrothermal potential, which may not be revealed by single‐profile acoustic image observations. We also find that the direction of flares is strongly influenced by tides, and the height of the flare represents the thermocline as a strong boundary for bubbles composited by carbon dioxide.
Spatial Inhomogeneity of Synoptic‐Induced Precipitation in a Region of Steep Topographic Relief: A Case Study
Authors: Zhang Mengke , Li Jian , Li Nina , Sun Wei , Li Puxi , Zhao Yin 
Published: March 2024

AbstractThe topography plays an essential role in the initiation and development of precipitating clouds, therefore has a profound effect on the ultimate spatial distribution of precipitation. This study investigates the fine‐scale characteristics of a synoptic‐induced precipitation event in Southwest China, a region characterized by a sequence of steep mountains aligned roughly north‐south. The convection‐permitting simulation successfully reproduces the observed rainband induced by a synoptic‐scale shear line. The spatial distribution of accumulated precipitation over three small‐scale mountains (named M1, M2, and M3 from east to west) exhibits distinct inhomogeneity. The accumulated precipitation is significantly enhanced on the western slope of M1, the high‐altitude area of M2, and the eastern slope of M3. The low‐level vortex generated on the western slope of M1, as well as the convergence established over M2 and the eastern slope of M3, dynamically contributes to the enhanced precipitation over the various mountain locations. As the highest of the three mountains, M2 exhibits pronounced blocking effects on the mesoscale circulations. Additional sensitivity experiment demonstrates that the mesoscale circulations and corresponding precipitation are sensitive to the highest elevation in the continuous mountains. The rainfall accumulation over M2 (M3) could decrease (increase) by 54.3% (63.4%), when the terrain of M2 is reduced to the comparable height of surrounding mountains. With more upslope wind flowing over M2, the convergence over M3 is strengthened. The more intense upward motion and stronger potential instability both contribute to the notable increase of precipitation over M3. This study implies the possible mechanisms of the inhomogeneous precipitation over Southwest China and could deepen the current understanding of the topographic effects on precipitation over complex terrains.
ECMWF and UK Met Office Offshore Blowing Winds: Impact of Horizontal Resolution and Coastal Orography
Authors: Cavaleri L. , Balsamo G. , Beljaars A. , Bertotti L. , Davison S. , Edwards J. , Kanehama T. , Wedi N. 
Published: March 2024

AbstractWe analyze the performance of the European Centre for Medium‐Range Weather Forecasts (ECMWF) and UK Met Office (UKMO) meteorological models in predicting offshore blowing wind in coastal areas. Our attention is mainly on the Mediterranean coast, up to 200 km distance from the shore. We compare forecast neutral winds with Advanced Scatterometer measurements. The results indicate that the ECMWF forecasts systematically underestimate wind speed with respect to scatterometer data, while the UKMO model tends to overestimate. A cross‐analysis suggests that, better than fetch, model biases are a function of the model horizontal discretization, hence of the number of grid steps the wind runs over the sea. The steepness and roughness of the land orography before entering the sea, together with the related drag parameters, appear to have a strong role in determining the coastal offshore wind values. Surface drag over land tends to reduce the related wind speed, and it takes a few grid points to adjust to the smooth sea surface conditions. This is supported by a detailed study with a high resolution grid, but different orography resolutions. In these simulations, practically identical coastal wind speed distributions are found when the subgrid orography schemes are switched off. Vertical cross‐sections of potential temperature and wind in bora and mistral conditions illustrate the strong role of gravity waves, wind channeling and turbulent diffusion in coastal numerical weather prediction. Besides local wave modeling, this may be relevant for offshore wind farms, typically situated within 5–50 km from the coast.
Constraints on Southern Ocean Shortwave Cloud Feedback From the Hydrological Cycle
Authors: Tan Chuyan , McCoy Daniel T. , Elsaesser Gregory S. 
Published: March 2024

AbstractShifts in Southern Ocean (SO, 40–85°S) shortwave cloud feedback (SWFB) toward more positive values are the dominant contributor to higher effective climate sensitivity (ECS) in Coupled Model Intercomparison Project Phase 6 (CMIP6) models. To provide an observational constraint on the SO SWFB, we use a simplified physical model to connect SO SWFB with the response of column‐integrated liquid water mass (LWP) to warming and the susceptibility of albedo to LWP in 50 CMIP5 and CMIP6 GCMs. In turn, we predict the responses of SO LWP using a cloud‐controlling factor (CCF) model. The combination of the CCF model and radiative susceptibility explains about 50% of the variance in the GCM‐simulated SWFB in the SO. Observations of SW radiation fluxes, LWP, and CCFs from reanalysis are used to constrain the SO SWFB. Observations suggest a SO LWP increase in response to warming and albedo susceptibility to LWP that is on the lower end relative to GCMs. The overall constraint on the contribution of SO to global mean SWFB is −0.168 to +0.051 W m−2 K−1, relative to −0.277 to +0.270 Wm−2 K−1. In summary, observations suggest SO SWFB is less likely to be as extremely positive as predicted by some CMIP6 GCMs, but more likely to range from moderately negative to weakly positive.
Protective effect of PDE4B subtype-specific inhibition in an App knock-in mouse model for Alzheimer’s disease
Authors: Armstrong Paul , Güngör Hüseyin , Anongjanya Pariya , Tweedy Clare , Parkin Edward , Johnston Jamie , Carr Ian M. , Dawson Neil , Clapcote Steven J. 
Published: March 2024

AbstractMeta-analysis of genome-wide association study data has implicated PDE4B in the pathogenesis of Alzheimer’s disease (AD), the leading cause of senile dementia. PDE4B encodes one of four subtypes of cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase-4 (PDE4A–D). To interrogate the involvement of PDE4B in the manifestation of AD-related phenotypes, the effects of a hypomorphic mutation (Pde4bY358C) that decreases PDE4B’s cAMP hydrolytic activity were evaluated in the AppNL-G-F knock-in mouse model of AD using the Barnes maze test of spatial memory, 14C-2-deoxyglucose autoradiography, thioflavin-S staining of β-amyloid (Aβ) plaques, and inflammatory marker assay and transcriptomic analysis (RNA sequencing) of cerebral cortical tissue. At 12 months of age, AppNL-G-F mice exhibited spatial memory and brain metabolism deficits, which were prevented by the hypomorphic PDE4B in AppNL-G-F/Pde4bY358C mice, without a decrease in Aβ plaque burden. RNA sequencing revealed that, among the 531 transcripts differentially expressed in AppNL-G-F versus wild-type mice, only 13 transcripts from four genes – Ide, Btaf1, Padi2, and C1qb – were differentially expressed in AppNL-G-F/Pde4bY358C versus AppNL-G-F mice, identifying their potential involvement in the protective effect of hypomorphic PDE4B. Our data demonstrate that spatial memory and cerebral glucose metabolism deficits exhibited by 12-month-old AppNL-G-F mice are prevented by targeted inhibition of PDE4B. To our knowledge, this is the first demonstration of a protective effect of PDE4B subtype-specific inhibition in a preclinical model of AD. It thus identifies PDE4B as a key regulator of disease manifestation in the AppNL-G-F model and a promising therapeutic target for AD.
Long-term outcomes of physical activity counseling in in-patients with major depressive disorder: results from the PACINPAT randomized controlled trial
Authors: Kreppke Jan-Niklas , Cody Robyn , Beck Johannes , Brand Serge , Donath Lars , Eckert Anne , Faude Oliver , Hatzinger Martin , Imboden Christian , Lang Undine E. , Ludyga Sebastian , Mans Sarah , Mikoteit Thorsten , Oswald Anja , Schweinfurth-Keck Nina , Holsboer-Trachsler Edith , Zahner Lukas , Gerber Markus 
Published: March 2024

AbstractMajor depressive disorder (MDD) is an increasingly common psychiatric illness associated with a high risk of insufficient physical activity, which in turn is associated with negative mental and physical health outcomes. Theory-based, individually tailored, in-person and remote physical activity counseling has the potential to increase physical activity levels in various populations. Given this, the present study investigated the effect of such a physical activity intervention on the physical activity behavior of in-patients with MDD. This was a multi-center, two-arm randomized controlled trial including initially insufficiently physically active adult in-patients with MDD from four study sites in Switzerland. The sample consisted of 220 participants (Mage = 41 ± 12.6 years, 52% women), 113 of whom were randomized to the intervention group and 107 to the control group. The main outcome, moderate-to-vigorous physical activity (MVPA), was assessed at three time points via hip-worn accelerometer. According to accelerometer measures, there was no significant difference in minutes spent in MVPA over a 12-month intervention period when comparing the intervention with the control group (β = −1.02, 95% CI = −10.68 to 8.64). Higher baseline physical activity significantly predicted physical activity at post and follow-up. This study showed that it is feasible to deliver an individually tailored, theory-based physical activity counseling intervention to in-patients with MDD, however yielding no significant effects on accelerometer-based MVPA levels. Further efforts are warranted to identify efficacious approaches.Trial registration: ISRCTN, ISRCTN10469580, registered on 3rd September 2018, https://www.isrctn.com/ISRCTN10469580.
FBXO22 promotes glioblastoma malignant progression by mediating VHL ubiquitination and degradation
Authors: Shen Zhigang , Dong Tao , Yong Hongmei , Deng Chuyin , Chen Changxiu , Chen Xintian , Chen Miaolei , Chu Sufang , Zheng Junnian , Li Zhongwei , Bai Jin 
Published: March 2024

AbstractGlioblastoma (GBM) is the most common malignant primary brain tumor. Despite comprehensive treatment with traditional surgery, radiotherapy, and chemotherapy, the median survival rate is <14.6% and the 5-year survival rate is only 5%. FBXO22, a substrate receptor of the SCF ubiquitin ligases, has been reported to play a promoting role in melanoma, liver cancer, cervical cancer, and other cancers. However, the function of FBXO22 in GBM has not been reported. In the present study, we demonstrate that FBXO22 is highly expressed in glioma and is positively correlated with worse pathological features and shorter survival of GBM patients. We revealed that FBXO22 promotes GBM cell proliferation, angiogenesis, migration, and tumorigenesis in vitro and in vivo. In terms of mechanism, we reveal that FBXO22 decreases VHL expression by directly mediating VHL ubiquitination degradation, which ultimately increases HIF-1α and VEGFA expression. In addition, our data confirm that there are positive correlations among FBXO22, HIF-1α, and VEGFA expression, and there is a negative correlation between FBXO22 and VHL protein expression in glioma patients. Our study strongly indicates that FBXO22 is a promising diagnostic marker and therapeutic target for glioma patients.
Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria
Authors: Hernandez-Beltran J. Carlos R. , Rodríguez-Beltrán Jerónimo , Aguilar-Luviano Oscar Bruno , Velez-Santiago Jesús , Mondragón-Palomino Octavio , MacLean R. Craig , Fuentes-Hernández Ayari , San Millán Alvaro , Peña-Miller Rafael 
Published: March 2024

AbstractThe rise of antibiotic resistance is a critical public health concern, requiring an understanding of mechanisms that enable bacteria to tolerate antimicrobial agents. Bacteria use diverse strategies, including the amplification of drug-resistance genes. In this paper, we showed that multicopy plasmids, often carrying antibiotic resistance genes in clinical bacteria, can rapidly amplify genes, leading to plasmid-mediated phenotypic noise and transient antibiotic resistance. By combining stochastic simulations of a computational model with high-throughput single-cell measurements of blaTEM-1 expression in Escherichia coli MG1655, we showed that plasmid copy number variability stably maintains populations composed of cells with both low and high plasmid copy numbers. This diversity in plasmid copy number enhances the probability of bacterial survival in the presence of antibiotics, while also rapidly reducing the burden of carrying multiple plasmids in drug-free environments. Our results further support the tenet that multicopy plasmids not only act as vehicles for the horizontal transfer of genetic information between cells but also as drivers of bacterial adaptation, enabling rapid modulation of gene copy numbers. Understanding the role of multicopy plasmids in antibiotic resistance is critical, and our study provides insights into how bacteria can transiently survive lethal concentrations of antibiotics.
Expression of USP25 associates with fibrosis, inflammation and metabolism changes in IgG4-related disease
Authors: Jiang Panpan , Jing Yukai , Zhao Siyu , Lan Caini , Yang Lu , Dai Xin , Luo Li , Cai Shaozhe , Zhu Yingzi , Miller Heather , Lai Juan , Zhang Xin , Zhao Xiaochao , Wu Yonggui , Yang Jingzhi , Zhang Wen , Guan Fei , Zhong Bo , Umehara Hisanori , Lei Jiahui , Dong Lingli , Liu Chaohong 
Published: March 2024

AbstractIgG4-related disease (IgG4-RD) has complex clinical manifestations ranging from fibrosis and inflammation to deregulated metabolism. The molecular mechanisms underpinning these phenotypes are unclear. In this study, by using IgG4-RD patient peripheral blood mononuclear cells (PBMCs), IgG4-RD cell lines and Usp25 knockout mice, we show that ubiquitin-specific protease 25 (USP25) engages in multiple pathways to regulate fibrotic and inflammatory pathways that are characteristic to IgG4-RD. Reduced USP25 expression in IgG4-RD leads to increased SMAD3 activation, which contributes to fibrosis and induces inflammation through the IL-1β inflammatory axis. Mechanistically, USP25 prevents ubiquitination of RAC1, thus, downregulation of USP25 leads to ubiquitination and degradation of RAC1. Decreased RAC1 levels result in reduced aldolase A release from the actin cytoskeleton, which then lowers glycolysis. The expression of LYN, a component of the B cell receptor signalosome is also reduced in USP25-deficient B cells, which might result in B cell activation deficiency. Altogether, our results indicate a potential anti-inflammatory and anti-fibrotic role for USP25 and make USP25 a promising diagnostic marker and potential therapeutic target in IgG4-RD.
Programming mechanics in knitted materials, stitch by stitch
Authors: Singal Krishma , Dimitriyev Michael S. , Gonzalez Sarah E. , Cachine A. Patrick , Quinn Sam , Matsumoto Elisabetta A. 
Published: March 2024

AbstractKnitting turns yarn, a 1D material, into a 2D fabric that is flexible, durable, and can be patterned to adopt a wide range of 3D geometries. Like other mechanical metamaterials, the elasticity of knitted fabrics is an emergent property of the local stitch topology and pattern that cannot solely be attributed to the yarn itself. Thus, knitting can be viewed as an additive manufacturing technique that allows for stitch-by-stitch programming of elastic properties and has applications in many fields ranging from soft robotics and wearable electronics to engineered tissue and architected materials. However, predicting these mechanical properties based on the stitch type remains elusive. Here we untangle the relationship between changes in stitch topology and emergent elasticity in several types of knitted fabrics. We combine experiment and simulation to construct a constitutive model for the nonlinear bulk response of these fabrics. This model serves as a basis for composite fabrics with bespoke mechanical properties, which crucially do not depend on the constituent yarn.
Velocities of transmission eigenchannels and diffusion
Authors: Genack Azriel Z. , Huang Yiming , Maor Asher , Shi Zhou 
Published: March 2024

AbstractThe diffusion model is used to calculate both the time-averaged flow of particles in stochastic media and the propagation of waves averaged over ensembles of disordered static configurations. For classical waves exciting static disordered samples, such as a layer of paint or a tissue sample, the flux transmitted through the sample may be dramatically enhanced or suppressed relative to predictions of diffusion theory when the sample is excited by a waveform corresponding to a transmission eigenchannel. Even so, it is widely assumed that the velocity of waves is irretrievably randomized in scattering media. Here we demonstrate in microwave measurements and numerical simulations that the statistics of velocity of different transmission eigenchannels are distinct and remains so on all length scales and are identical on the incident and output surfaces. The interplay between eigenchannel velocities and transmission eigenvalues determines the energy density within the medium, the diffusion coefficient, and the dynamics of propagation. The diffusion coefficient and all scattering parameters, including the scattering mean free path, oscillate with the width of the sample as the number and shape of the propagating channels in the medium change.
Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair
Authors: Perez-Bermejo Juan A. , Efagene Oghene , Matern William M. , Holden Jeffrey K. , Kabir Shaheen , Chew Glen M. , Andreoletti Gaia , Catton Eniola , Ennis Craig L. , Garcia Angelica , Gerstenberg Trevor L. , Hill Kaisle A. , Jain Aayami , Krassovsky Kristina , Lalisan Cassandra D. , Lord Daniel , Quejarro B. Joy , Sales-Lee Jade , Shah Meet , Silva Brian J. , Skowronski Jason , Strukov Yuri G. , Thomas Joshua , Veraz Michael , Vijay Twaritha , Wallace Kirby A. , Yuan Yue , Grogan Jane L. , Wienert Beeke , Lahiri Premanjali , Treusch Sebastian , Dever Daniel P. , Soros Vanessa B. , Partridge James R. , Seim Kristen L. 
Published: March 2024

AbstractHomology Directed Repair (HDR) enables precise genome editing, but the implementation of HDR-based therapies is hindered by limited efficiency in comparison to methods that exploit alternative DNA repair routes, such as Non-Homologous End Joining (NHEJ). In this study, we develop a functional, pooled screening platform to identify protein-based reagents that improve HDR in human hematopoietic stem and progenitor cells (HSPCs). We leverage this screening platform to explore sequence diversity at the binding interface of the NHEJ inhibitor i53 and its target, 53BP1, identifying optimized variants that enable new intermolecular bonds and robustly increase HDR. We show that these variants specifically reduce insertion-deletion outcomes without increasing off-target editing, synergize with a DNAPK inhibitor molecule, and can be applied at manufacturing scale to increase the fraction of cells bearing repaired alleles. This screening platform can enable the discovery of future gene editing reagents that improve HDR outcomes.
Defect-induced helicity dependent terahertz emission in Dirac semimetal PtTe2 thin films
Authors: Chen Zhongqiang , Qiu Hongsong , Cheng Xinjuan , Cui Jizhe , Jin Zuanming , Tian Da , Zhang Xu , Xu Kankan , Liu Ruxin , Niu Wei , Zhou Liqi , Qiu Tianyu , Chen Yequan , Zhang Caihong , Xi Xiaoxiang , Song Fengqi , Yu Rong , Zhai Xuechao , Jin Biaobing , Zhang Rong , Wang Xuefeng 
Published: March 2024

AbstractNonlinear transport enabled by symmetry breaking in quantum materials has aroused considerable interest in condensed matter physics and interdisciplinary electronics. However, achieving a nonlinear optical response in centrosymmetric Dirac semimetals via defect engineering has remained a challenge. Here, we observe the helicity dependent terahertz emission in Dirac semimetal PtTe2 thin films via the circular photogalvanic effect under normal incidence. This is activated by a controllable out-of-plane Te-vacancy defect gradient, which we unambiguously evidence with electron ptychography. The defect gradient lowers the symmetry, which not only induces the band spin splitting but also generates the giant Berry curvature dipole responsible for the circular photogalvanic effect. We demonstrate that the THz emission can be manipulated by the Te-vacancy defect concentration. Furthermore, the temperature evolution of the THz emission features a minimum in the THz amplitude due to carrier compensation. Our work provides a universal strategy for symmetry breaking in centrosymmetric Dirac materials for efficient nonlinear transport.