bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controls on Dense Shelf Water Formation in Four East Antarctic Polynyas
Authors: Portela Esther , Rintoul Stephen R. , Herraiz‐Borreguero Laura , Roquet Fabien , Bestley Sophie , van Wijk Esmee , Tamura Takeshi , McMahon Clive R. , Guinet Christophe , Harcourt Robert , Hindell Mark A. 
Published: November 2022

AbstractCoastal polynyas are key formation regions for dense shelf water (DSW) that ultimately contributes to the ventilation of the ocean abyss. However, not all polynyas form DSW. We examine how the physiographic setting, water‐mass distribution and transformation, water column stratification, and sea‐ice production regulate DSW formation in four East Antarctic coastal polynyas. We use a salt budget to estimate the relative contribution of sea‐ice production and lateral advection to the monthly change in salinity in each polynya. DSW forms in Mackenzie polynya due to a combination of physical features (shallow water depth and a broad continental shelf) and high sea‐ice production. Sea‐ice formation begins early (March) in Mackenzie polynya, counteracting fresh advection and establishing a salty mixed layer in autumn that preconditions the water column for deep convection in winter. Sea‐ice production is moderate in the other three polynyas, but saline DSW is not formed (a fresh variety is formed in the Barrier polynya). In the Shackleton polynya, brine rejection during winter is insufficient to overcome the very fresh autumn mixed layer. In Vincennes Bay, a strong inflow of modified Circumpolar Deep Water stratifies the water column, hindering deep convection and DSW formation. Our study highlights that DSW formation in a given polynya depends on a complex combination of factors, some of which may be strongly altered under a changing climate, with potentially important consequences for the ventilation of the deep ocean, the global meridional overturning circulation, and the transport of ocean heat to Antarctic ice shelves.
The Role of Massive Ice and Exposed Headwall Properties on Retrogressive Thaw Slump Activity
Authors: Hayes Samuel , Lim Michael , Whalen Dustin , Mann Paul J. , Fraser Paul , Penlington Roger , Martin James 
Published: November 2022

AbstractRetrogressive Thaw Slumps (RTSs), a highly dynamic form of mass wasting, are accelerating geomorphic change across ice‐cored permafrost terrain, yet the main controls on their activity are poorly constrained. Questions over the spatial variability of environmentally sensitive massive ice bodies and a paucity of high‐spatial and temporal resolution topographic data have limited our ability to project their development and wider impacts. This research addresses these key problems by investigating RTS processes on Peninsula Point—a well‐studied site for intra‐sedimental massive ice in the Western Canadian Arctic. Utilizing high‐resolution topographic data from drone surveys in 2016, 2017 and 2018 we (a) measure the temporal and spatial variations in headwall properties and retreat rates, (b) determine the spatial pattern of subsurface layering using passive seismic monitoring and (c) combine these to analyze and contextualize the factors controlling headwall retreat (HWR) rates. We find that headwall properties, namely massive ice and overburden thickness, are significant controls over rates of HWR. Where persistent massive ice exposures are present inland of the headwall, regardless of thickness, and overburden thickness remains <4 m, HWR is typically more than double that of other headwalls. Furthermore, a 3D site model was created by combining photogrammetric and passive seismic data, highlighting internal layering variability and demonstrating the limitations of extrapolations of internal layering based on headwall exposures. These results provide fresh insights into the in situ controls on HWR rates and new approaches to understanding their variability.
Generalization Ability of Deep Learning Algorithms Trained Using SEM Data for Objects Classification
Authors: Zaky Yasmina , Fortino Nicolas , Miramond Benoit , Dauvignac Jean‐Yves 
Published: November 2022

AbstractThis paper proposes an efficient method to determine the material of spherical objects and the location of the receiving antenna relative to the object in bi‐static measurements using supervised learning techniques. From a single observation, we compare classification performances resulting from the application of several classifiers on different data types: the Ultra‐Wide Band scattered field in time and frequency domains and pre‐processed data from the singularity expansion method (SEM) which has seldom been used in classification because it is considered to be noise sensitive. We selected a robust SEM technique which is vector fitting to decompose the frequency response into complex natural resonances (CNRs) and residues. Indeed, CNRs are aspect independent and therefore, can be used to discriminate the objects. However, the residues associated to each pole depend upon the aspect angle, and hence, they were never exploited. In this paper, we propose a novel use of those residues. Additionally, we construct an original data set using SEM data in order to further improve the robustness to noise and the generalization capacity of the learning algorithms. The advantages of using SEM data for object classification are highlighted by comparing it with raw scattered field data in time and frequency domains where the classification algorithms are optimized in each case. The results are very promising, especially in terms of generalization, robustness to noise, and computation time, which are all reasons to take an interest in SEM for these purposes.
Richards Equation at the Hillslope Scale: Can We Resolve the Heterogeneity of Soil Hydraulic Material Properties?
Authors: Bauser Hannes H. , Kim Minseok , Ng Wei‐Ren , Bugaj Aaron , Troch Peter A. 
Published: November 2022

AbstractProcess‐based modeling of soil water movement with the Richards equation requires the description of soil hydraulic material properties, which are highly uncertain and heterogeneous at all scales. This limits the applicability of the Richards equation at larger scales beyond the patch scale. The experimental capabilities of the three hillslopes of the Landscape Evolution Observatory (LEO) at Biosphere 2 provide a unique opportunity to observe the heterogeneity of hydraulic material properties at the hillslope scale. We performed a gravity flow experiment where through constant irrigation the water content increases until the hydraulic conductivity matches the irrigation flux above. The dense water content sensor network at LEO then allows mapping of the heterogeneity of hydraulic conductivity at a meter scale resolution. The experiment revealed spatial structures within the hillslopes, mainly a vertical trend with the lowest hydraulic conductivity close to the surface. However, the variation between neighboring sensors is high, showing that the heterogeneity cannot be fully resolved even at LEO. By representing the heterogeneity in models through Miller scaling we showed the impact on hillslope discharge. For the hillslope with the smallest heterogeneity, representing the dominant structures was sufficient. However, for the two hillslopes with the larger overall heterogeneity, adding further details of the local heterogeneity did impact the discharge further. This highlights the limitations of the Richards equation, which requires the heterogeneous field of material properties, at the hillslope scale and shows the relevance to improving our understanding of effective parameters to be able to apply the process‐based model to larger scales.
Inflammation, sex, blood pressure changes and hypertension in midlife: the Hordaland Health Study
Authors: Kringeland Ester , Gerdts Eva , Ulvik Arve , Tell Grethe S. , Igland Jannicke , Haugsgjerd Teresa R. , Ueland Per Magne , Midtbø Helga 
Published: November 2022

AbstractOur aim was to test sex-specific associations of circulating markers of inflammation with blood pressure (BP) and incident hypertension in midlife. Participants in the Hordaland Health study (n = 3280, 56% women, mean age 48 years) were examined at baseline and followed for 6 years. Circulating levels of inflammatory markers including high-sensitive C-reactive protein (hs-CRP), neopterin, and pyridoxic acid ratio (PAr) index were measured at follow-up. The associations with systolic/diastolic BP and incident hypertension were tested in sex-specific linear- or logistic-regression analyses adjusted for body mass index, serum triglycerides, creatinine, physical activity, smoking and diabetes. At follow-up, women had lower mean BP than men (124/72 vs. 130/78 mmHg, p < 0.001). Higher hs-CRP was significantly associated with greater systolic and diastolic BP (standardized β = 0.07 and β = 0.09, both p < 0.01) in women, but not in men. Higher neopterin was associated with higher diastolic BP in women and higher PAr index was associated with higher diastolic BP in women and higher systolic and diastolic BP in men (all p < 0.01). Compared to hs-CRP < 1 mg/l, higher levels of hs-CRP 1–<3 mg/l and hs-CRP ≥ 3 mg/l were associated with new-onset hypertension only in women (odds ratio (OR) 1.74, 95% CI 1.20–2.53 and OR 1.87, 95% CI 1.20–2.90). Sex-interactions were found for hs-CRP and neopterin in models on incident hypertension and diastolic BP, respectively (both p < 0.05). Higher levels of circulating markers of inflammation were associated with higher BP and incident hypertension in a sex-specific manner. Our results suggest a sex-specific interaction between cardiovascular inflammation and BP in midlife.
Carboxyl-terminal modulator protein facilitates tumor metastasis in triple-negative breast cancer
Authors: Lin Cheng-Han , Lin Wen-Der , Huang Yun-Chin , Chen Yu-Chia , Loh Zhu-Jun , Ger Luo-Ping , Lin Forn-Chia , Li Hao-Yi , Cheng Hui-Chuan , Lee Kuen-Haur , Hsiao Michael , Lu Pei-Jung 
Published: November 2022

AbstractCurrently, the survival rate for breast cancer is more than 90%, but once the cancer cells metastasize to distal organs, the survival rate is dramatically reduced, to less than 30%. Triple-negative breast cancer accounts for 15-20% of all breast cancers. Triple-negative breast cancer (TNBC) is associated with poor prognostic and diagnostic outcomes due to the limiting therapeutic strategies, relative to non-TNBC breast cancers. Therefore, the development of targeted therapy for TNBC metastasis remains an urgent issue. In this study, high Carboxyl-terminal modulator protein (CTMP) is significantly associated with recurrence and disease-free survival rate in TNBC patients. Overexpression of CTMP promotes migration and invasion abilities in BT549 cells. Down-regulating of CTMP expression inhibits migration and invasion abilities in MDA-MB-231 cells. In vivo inoculation of high-CTMP cells enhances distant metastasis in mice. The metastasis incidence rate is decreased in mice injected with CTMP-downregulating MDA-MB-231 cells. Gene expression microarray analysis indicates the Akt-dependent pathway is significantly enhanced in CTMP overexpressing cells compared to the parental cells. Blocking Akt activation via Akt inhibitor treatment or co-expression of the dominant-negative form of Akt proteins successfully abolishes the CTMP mediating invasion in TNBC cells. Our findings suggest that CTMP is a potential diagnostic marker for recurrence and poor disease-free survival in TNBC patients. CTMP promotes TNBC metastasis via the Akt-activation-dependent pathway.
Deletion of the Notch ligand Jagged1 during cochlear maturation leads to inner hair cell defects and hearing loss
Authors: Gilels Felicia A. , Wang Jun , Bullen Anwen , White Patricia M. , Kiernan Amy E. 
Published: November 2022

AbstractThe mammalian cochlea is an exceptionally well-organized epithelium composed of hair cells, supporting cells, and innervating neurons. Loss or defects in any of these cell types, particularly the specialized sensory hair cells, leads to deafness. The Notch pathway is known to play a critical role in the decision to become either a hair cell or a supporting cell during embryogenesis; however, little is known about how Notch functions later during cochlear maturation. Uniquely amongst Notch ligands, Jagged1 (JAG1) is localized to supporting cells during cell fate acquisition and continues to be expressed into adulthood. Here, we demonstrate that JAG1 in maturing cochlear supporting cells is essential for normal cochlear function. Specifically, we show that deletion of JAG1 during cochlear maturation disrupts the inner hair cell pathway and leads to a type of deafness clinically similar to auditory neuropathy. Common pathologies associated with disruptions in inner hair cell function, including loss of hair cells, synapses, or auditory neurons, were not observed in JAG1 mutant cochleae. Instead, RNA-seq analysis of JAG1-deficient cochleae identified dysregulation of the Rho GTPase pathway, known to be involved in stereocilia development and maintenance. Interestingly, the overexpression of one of the altered genes, Diaph3, is responsible for autosomal dominant auditory neuropathy-1 (AUNA1) in humans and mice, and is associated with defects in the inner hair cell stereocilia. Strikingly, ultrastructural analyses of JAG1-deleted cochleae revealed stereocilia defects in inner hair cells, including fused and elongated bundles, that were similar to those stereocilia defects reported in AUNA1 mice. Taken together, these data indicate a novel role for Notch signaling in normal hearing development through maintaining stereocilia integrity of the inner hair cells during cochlear maturation.
The Heterochromatin protein 1 is a regulator in RNA splicing precision deficient in ulcerative colitis
Authors: Mata-Garrido Jorge , Xiang Yao , Chang-Marchand Yunhua , Reisacher Caroline , Ageron Elisabeth , Guerrera Ida Chiara , Casafont Iñigo , Bruneau Aurelia , Cherbuy Claire , Treton Xavier , Dumay Anne , Ogier-Denis Eric , Batsché Eric , Costallat Mickael , Revêchon Gwladys , Eriksson Maria , Muchardt Christian , Arbibe Laurence 
Published: November 2022

AbstractDefects in RNA splicing have been linked to human disorders, but remain poorly explored in inflammatory bowel disease (IBD). Here, we report that expression of the chromatin and alternative splicing regulator HP1γ is reduced in ulcerative colitis (UC). Accordingly, HP1γ gene inactivation in the mouse gut epithelium triggers IBD-like traits, including inflammation and dysbiosis. In parallel, we find that its loss of function broadly increases splicing noise, favoring the usage of cryptic splice sites at numerous genes with functions in gut biology. This results in the production of progerin, a toxic splice variant of prelamin A mRNA, responsible for the Hutchinson-Gilford Progeria Syndrome of premature aging. Splicing noise is also extensively detected in UC patients in association with inflammation, with progerin transcripts accumulating in the colon mucosa. We propose that monitoring HP1γ activity and RNA splicing precision can help in the management of IBD and, more generally, of accelerated aging.
Switching nanoprecipitates to resist hydrogen embrittlement in high-strength aluminum alloys
Authors: Wang Yafei , Sharma Bhupendra , Xu Yuantao , Shimizu Kazuyuki , Fujihara Hiro , Hirayama Kyosuke , Takeuchi Akihisa , Uesugi Masayuki , Cheng Guangxu , Toda Hiroyuki 
Published: November 2022

AbstractHydrogen drastically embrittles high-strength aluminum alloys, which impedes efforts to develop ultrastrong components in the aerospace and transportation industries. Understanding and utilizing the interaction of hydrogen with core strengthening elements in aluminum alloys, particularly nanoprecipitates, are critical to break this bottleneck. Herein, we show that hydrogen embrittlement of aluminum alloys can be largely suppressed by switching nanoprecipitates from the η phase to the T phase without changing the overall chemical composition. The T phase strongly traps hydrogen and resists hydrogen-assisted crack growth, with a more than 60% reduction in the areal fractions of cracks. The T phase-induced reduction in the concentration of hydrogen at defects and interfaces, which facilitates crack growth, primarily contributes to the suppressed hydrogen embrittlement. Transforming precipitates into strong hydrogen traps is proven to be a potential mitigation strategy for hydrogen embrittlement in aluminum alloys.
A glutamine-based single α-helix scaffold to target globular proteins
Authors: Escobedo Albert , Piccirillo Jonathan , Aranda Juan , Diercks Tammo , Mateos Borja , Garcia-Cabau Carla , Sánchez-Navarro Macarena , Topal Busra , Biesaga Mateusz , Staby Lasse , Kragelund Birthe B. , García Jesús , Millet Oscar , Orozco Modesto , Coles Murray , Crehuet Ramon , Salvatella Xavier 
Published: November 2022

AbstractThe binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones
Authors: Kim Hyeong Jin , Black Mazzen , Edwards Ross A. , Peillard-Fiorente Flora , Panigrahi Rashmi , Klingler David , Eidelpes Reiner , Zeindl Ricarda , Peng Shiyun , Su Jikun , Omar Ayat R. , MacMillan Andrew M. , Kreutz Christoph , Tollinger Martin , Charpentier Xavier , Attaiech Laetitia , Glover J. N. Mark 
Published: November 2022

AbstractThe ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. The structure reveals specific recognition of the 3’ nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila. Structural analysis and RNA binding studies reveal that other ProQ/FinO domains also recognize related transcriptional terminators with different specificities for the length of the 3’ ssRNA tail.
Deep graph level anomaly detection with contrastive learning
Authors: Luo Xuexiong , Wu Jia , Yang Jian , Xue Shan , Peng Hao , Zhou Chuan , Chen Hongyang , Li Zhao , Sheng Quan Z. 
Published: November 2022

AbstractGraph level anomaly detection (GLAD) aims to spot anomalous graphs that structure pattern and feature information are different from most normal graphs in a graph set, which is rarely studied by other researchers but has significant application value. For instance, GLAD can be used to distinguish some different characteristic molecules in drug discovery and chemical analysis. However, GLAD mainly faces the following three challenges: (1) learning more comprehensive graph level representations to differ normal graphs and abnormal graphs, (2) designing an effective graph anomaly evaluation paradigm to capture graph anomalies from the local and global graph perspectives, (3) overcoming the number imbalance problem of normal and abnormal graphs. In this paper, we combine graph neural networks and contrastive learning to build an end-to-end GLAD framework for solving the three challenges above. We aim to design a new graph level anomaly evaluation way, which first utilizes the contrastive learning strategy to enhance different level representations of normal graphs from node and graph levels by a graph convolution autoencoder with perturbed graph encoder. Then, we evaluate the error of them with corresponding representations of the generated reconstruction graph to detect anomalous graphs. Extensive experiments on ten real-world datasets from three areas, such as molecular, protein and social network anomaly graphs, show that our model can effectively detect graph level anomaly from the majority and outperform existing advanced methods.
Towards the ionizing radiation induced bond dissociation mechanism in oxygen, water, guanine and DNA fragmentation: a density functional theory simulation
Authors: KC Santosh , Abolfath Ramin 
Published: November 2022

AbstractThe radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy and radio-biology, and critical to space projects. In this study, we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic acid (DNA) and the molecules surrounding DNA such as oxygen and water under non-equilibrium conditions using the first-principle calculations based on density functional theory (DFT). Our results reveal the structural stability of DNA bases and backbone that withstand up to a combined threshold of charge and hydrogen abstraction owing to simultaneously direct and indirect ionization processes. We show the hydrogen contents of the molecules significantly control the stability in the presence of radiation. This study provides comprehensive information on the impact of the direct and indirect induced bond dissociations and DNA damage and introduces a systematic methodology for fine-tuning the input parameters necessary for the large-scale Monte Carlo simulations of radio-biological responses and mitigation of detrimental effects of ionizing radiation.
Model-free phasor image analysis of quantitative myocardial T1 mapping
Authors: Franssen Wouter M. J. , Treibel Thomas A. , Seraphim Andreas , Weingärtner Sebastian , Terenzi Camilla 
Published: November 2022

AbstractModel-free phasor image analysis, well established in fluorescence lifetime imaging and only recently applied to qMRI $${T}_{2}$$

T
2

data processing, is here adapted and validated for myocardial qMRI $${T}_{1}$$

T
1

mapping. Contrarily to routine mono-exponential fitting procedures, phasor enables mapping the lifetime information from all image voxels to a single plot, without resorting to any regression fitting analysis, and describing multi-exponential qMRI decays without biases due to violated modelling assumptions. In this feasibility study, we test the performance of our recently developed full-harmonics phasor method for unravelling partial-volume effects, motion or pathological tissue alteration, respectively on a numerically-simulated dataset, a healthy subject scan, and two pilot patient datasets. Our results show that phasor analysis can be used, as alternative method to fitting analysis or other model-free approaches, to identify motion artifacts or partial-volume effects at the myocardium-blood interface as characteristic deviations, or delineations of scar and remote myocardial tissue in patient data.