bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winds at the Mars 2020 Landing Site: 1. Near‐Surface Wind Patterns at Jezero Crater
Authors: Viúdez‐Moreiras D. , Lemmon M. , Newman C. E. , Guzewich S. , Mischna M. , Gómez‐Elvira J. , Herkenhoff K. , Sánchez‐Lavega A. , de la Torre M. , Rodríguez‐Manfredi J. A. , Lorenz R. D. , Pla‐García J. , Hueso R. , Richardson M. , Tamppari L. , Smith M. , Apéstigue V. , Toledo D. , Bell J. 
Published: December 2022

AbstractThis is the first part of a two‐part paper. NASA's Mars 2020 Perseverance rover measured winds on the Jezero crater floor close to the delta of an ancient river. A mostly repeatable diurnal cycle was observed and presented two regimes: (a) a convective regime, from dawn to sunset, with average easterly to southeasterly winds, during which maximum wind speeds were measured, and (b) a nighttime regime with westerly‐northwesterly winds followed by a relatively calm period with highly variable wind directions as a function of sol and time of night. The timing and magnitude of the observed regimes are consistent with primary control by regional and local slope flows. Data suggest that the surface circulation at Jezero region in northern spring and summer is highly unaffected by large‐scale circulation except during particular periods in the diurnal cycle or generally during dust storms, which is supported by MarsWRF model simulations. Consequently, the observed seasonal variability was weak. However, sol‐to‐sol and seasonal variability were measured, most of it during certain nighttime periods. Traveling waves consistent with baroclinic instability were clearly observed in surface winds at Ls ∼ 75°. The early MY36/2022A regional dust storm at Ls ∼ 153° disturbed the wind patterns with changes suggesting enhanced tidal flows. After sunset, the dust storm also produced detectable gravity wave activity, increasing the mixing in the nighttime planetary boundary layer during storm conditions. Inferred wind directions from dust devil movies strongly suggest that prevailing winds continued to be slope‐driven during the late summer, fall and early winter seasons.
Characterization of Subsurface Hydrogeological Structures With Convolutional Conditional Neural Processes on Limited Training Data
Authors: Cui Zhesi , Chen Qiyu , Liu Gang 
Published: December 2022

AbstractOne of the main issues in the application of statistical‐learning‐based methods to the characterization of hydrological phenomena is the complex parameterization of the high‐quality reconstruction. The difficulty of obtaining enough training data and generating multiple‐scale structures hinder the applications of deep‐learning‐based methods in hydrogeological modeling. Hydrogeological modeling problems can be regarded as stochastic processes, and we propose a novel hydrogeological modeling approach based on convolutional conditional neural processes (GM‐ConvCNPs), a meta‐learning approach for dealing with stochastic processes. In this work, GM‐ConvCNP is used to reconstruct the entire spatial structures of subsurface hydrological attributes and channels from a limited amount of conditioning data. To achieve 3‐D characterization of subsurface structures, 3‐D GM‐ConvCNP is proposed according to the spatial distribution characteristics of 3‐D conditioning data. Compared to other deep‐learning‐based methods, we use a small amount of training data and obtain positive model generalization capabilities. Four data sets of categorical and continuous hydrogeological structures are exploited in the experiments. Various validation tests including variograms, connectivity functions, and multi‐dimensional scaling (MDS) map are used to evaluate the quality of generated realizations. The proposed approach is able to significantly reduce training consumption and improve the performance of realizations compared to a set of different benchmark tests. The experiments confirm that the GM‐ConvCNP model can extract heterogeneous patterns by using meta‐learning from limited training data and reconstruct multiple‐scale hydrogeological structures. A case study demonstrates that our method can be applied to characterize multiple‐source hydrological variables.
First week of life respiratory management and pulmonary ventilation/perfusion matching in infants with bronchopulmonary dysplasia: a retrospective observational study
Authors: Kjellberg Malin , Sanchez-Crespo Alejandro , Jonsson Baldvin 
Published: December 2022

Abstract
Objective
To investigate the association between early neonatal respiratory management in infants with bronchopulmonary dysplasia (BPD) and the degree of pulmonary ventilation perfusion-matching (V/Q) at term.

Methods
30 preterm infants with a diagnosis of BPD who were initially treated with either controlled mechanical ventilation/continuous positive airway pressure (CMV/CPAP) (n = 14) or high-frequency oscillatory ventilation (HFOV) using a high lung-volume strategy (n = 16) were retrospectively included in this study. All infants underwent pulmonary V/Q single photon emission computed tomography at a median postmenstrual age of 37 weeks.

Results
Infants treated with HFOV had significantly larger proportion of the lung with matched V/Q as compared to infants treated with CMV/CPAP, median (interquartile range) 60.4% (55.5–66.0%) and 45.8% (37.8–53.1%) respectively (p = 0.01).

Conclusions
In infants who needed mechanical ventilation the first week of life and later developed BPD an association was observed between treatment with a HFOV and better pulmonary V/Q matching at near-term age.
Glutamatergic dysfunction leads to a hyper-dopaminergic phenotype through deficits in short-term habituation: a mechanism for aberrant salience
Authors: Panayi Marios C. , Boerner Thomas , Jahans-Price Thomas , Huber Anna , Sprengel Rolf , Gilmour Gary , Sanderson David J. , Harrison Paul J. , Walton Mark E. , Bannerman David M. 
Published: December 2022

AbstractPsychosis in disorders like schizophrenia is commonly associated with aberrant salience and elevated striatal dopamine. However, the underlying cause(s) of this hyper-dopaminergic state remain elusive. Various lines of evidence point to glutamatergic dysfunction and impairments in synaptic plasticity in the etiology of schizophrenia, including deficits associated with the GluA1 AMPAR subunit. GluA1 knockout (Gria1−/−) mice provide a model of impaired synaptic plasticity in schizophrenia and exhibit a selective deficit in a form of short-term memory which underlies short-term habituation. As such, these mice are unable to reduce attention to recently presented stimuli. In this study we used fast-scan cyclic voltammetry to measure phasic dopamine responses in the nucleus accumbens of Gria1−/− mice to determine whether this behavioral phenotype might be a key driver of a hyper-dopaminergic state. There was no effect of GluA1 deletion on electrically-evoked dopamine responses in anaesthetized mice, demonstrating normal endogenous release properties of dopamine neurons in Gria1−/− mice. Furthermore, dopamine signals were initially similar in Gria1−/− mice compared to controls in response to both sucrose rewards and neutral light stimuli. They were also equally sensitive to changes in the magnitude of delivered rewards. In contrast, however, these stimulus-evoked dopamine signals failed to habituate with repeated presentations in Gria1−/− mice, resulting in a task-relevant, hyper-dopaminergic phenotype. Thus, here we show that GluA1 dysfunction, resulting in impaired short-term habituation, is a key driver of enhanced striatal dopamine responses, which may be an important contributor to aberrant salience and psychosis in psychiatric disorders like schizophrenia.
Frequency dependent emotion differentiation and directional coupling in amygdala, orbitofrontal and medial prefrontal cortex network with intracranial recordings
Authors: Sonkusare Saurabh , Qiong Ding , Zhao Yijie , Liu Wei , Yang Ruoqi , Mandali Alekhya , Manssuer Luis , Zhang Chencheng , Cao Chunyan , Sun Bomin , Zhan Shikun , Voon Valerie 
Published: December 2022

AbstractThe amygdala, orbitofrontal cortex (OFC) and medial prefrontal cortex (mPFC) form a crucial part of the emotion circuit, yet their emotion induced responses and interactions have been poorly investigated with direct intracranial recordings. Such high-fidelity signals can uncover precise spectral dynamics and frequency differences in valence processing allowing novel insights on neuromodulation. Here, leveraging the unique spatio-temporal advantages of intracranial electroencephalography (iEEG) from a cohort of 35 patients with intractable epilepsy (with 71 contacts in amygdala, 31 in OFC and 43 in mPFC), we assessed the spectral dynamics and interactions between the amygdala, OFC and mPFC during an emotional picture viewing task. Task induced activity showed greater broadband gamma activity in the negative condition compared to positive condition in all the three regions. Similarly, beta activity was increased in the negative condition in the amygdala and OFC while decreased in mPFC. Furthermore, beta activity of amygdala showed significant negative association with valence ratings. Critically, model-based computational analyses revealed unidirectional connectivity from mPFC to the amygdala and bidirectional communication between OFC-amygdala and OFC-mPFC. Our findings provide direct neurophysiological evidence for a much-posited model of top-down influence of mPFC over amygdala and a bidirectional influence between OFC and the amygdala. Altogether, in a relatively large sample size with human intracranial neuronal recordings, we highlight valence-dependent spectral dynamics and dyadic coupling within the amygdala-mPFC-OFC network with implications for potential targeted neuromodulation in emotion processing.
Body shape phenotypes of multiple anthropometric traits and cancer risk: a multi-national cohort study
Authors: Sedlmeier Anja M. , Viallon Vivian , Ferrari Pietro , Peruchet-Noray Laia , Fontvieille Emma , Amadou Amina , Seyed Khoei Nazlisadat , Weber Andrea , Baurecht Hansjörg , Heath Alicia K. , Tsilidis Kostas , Kaaks Rudolf , Katzke Verena , Inan-Eroglu Elif , Schulze Matthias B. , Overvad Kim , Bonet Catalina , Ubago-Guisado Esther , Chirlaque María-Dolores , Ardanaz Eva , Perez-Cornago Aurora , Pala Valeria , Tumino Rosario , Sacerdote Carlotta , Pasanisi Fabrizio , Borch Kristin B. , Rylander Charlotta , Weiderpass Elisabete , Gunter Marc J. , Fervers Béatrice , Leitzmann Michael F. , Freisling Heinz 
Published: December 2022

Abstract
Background
Classical anthropometric traits may fail to fully represent the relationship of weight, adiposity, and height with cancer risk. We investigated the associations of body shape phenotypes with the risk of overall and site-specific cancers.

Methods
We derived four distinct body shape phenotypes from principal component (PC) analysis on height, weight, body mass index (BMI), waist (WC) and hip circumferences (HC), and waist-to-hip ratio (WHR). The study included 340,152 men and women from 9 European countries, aged mostly 35–65 years at recruitment (1990–2000) in the European Prospective Investigation into Cancer and Nutrition (EPIC) study. Cox proportional hazards regression was used to estimate multivariable-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs).

Results
After a median follow-up of 15.3 years, 47,110 incident cancer cases were recorded. PC1 (overall adiposity) was positively associated with the risk of overall cancer, with a HR per 1 standard deviation (SD) increment equal to 1.07 (95% confidence interval 1.05 to 1.08). Positive associations were observed with 10 cancer types, with HRs (per 1 SD) ranging from 1.36 (1.30–1.42) for endometrial cancer to 1.08 (1.03–1.13) for rectal cancer. PC2 (tall stature with low WHR) was positively associated with the risk of overall cancer (1.03; 1.02–1.04) and five cancer types which were not associated with PC1. PC3 (tall stature with high WHR) was positively associated with the risk of overall cancer (1.04; 1.03–1.05) and 12 cancer types. PC4 (high BMI and weight with low WC and HC) was not associated with overall risk of cancer (1.00; 0.99–1.01).

Conclusions
In this multi-national study, distinct body shape phenotypes were positively associated with the incidence of 17 different cancers and overall cancer.
Dual wavelength retinal vessel oximetry – influence of fundus pigmentation
Authors: Hirsch Katrin , Cubbidge Robert P. , Heitmar Rebekka 
Published: December 2022

Abstract
Background
Clinical methods examining oxygenation parameters in humans have been used in many different care settings, but concerns have been raised regarding their clinical utility when assessing people with darker skin pigmentation. While saturation values can be crucial in emergency medicine, they are equally valuable in assessing disease mechanisms and monitoring change in disease progression. Retinal pigmentation varies across individuals and hence, can impact on retinal oxygen parameters. The objective of this study was to quantify and eliminate the impact of retinal pigmentation on retinal vessel oxygen saturation parameters measured in the superficial retinal arterioles and venules.

Methods
105 healthy individuals of varying skin colour, iris colour and heritage were included. Following a full eye exam to exclude any ocular abnormality, all participants underwent intraocular pressure, systemic blood pressure measurements and dilated dual wavelength retinal photography. Rotation matrices were employed to minimise the dependency of retinal pigmentation on arterial and venous oxygen saturation measurements determined in a concentric measurement annulus.

Results
Retinal oxygen saturation in venules showed a linear correlation with retinal pigmentation (y = 0.34 × x + 38.598), whereas arterial saturation followed a polynomial pattern (y = 0.0089 × x2 + 0.7499 × x + 85.073). Both arterial and venous saturation values were corrected using local fundus pigmentation. Pre-correction retinal arterial and venous oxygen saturation were 89.0% (±13.1) and 43.7% (±11.5), respectively, and post- correction values were 94.8% (±8.7) for arteries and 56.3% (±7.0) veins.

Conclusions
When assessing multi-ethnic cohorts, it is important to consider the impact of pigmentation on imaging parameters and to account for it prior to clinical interpretation.
Efficient synthesis of primary and secondary amides via reacting esters with alkali metal amidoboranes
Authors: Guo Yu , Wang Ruo-Ya , Kang Jia-Xin , Ma Yan-Na , Xu Cong-Qiao , Li Jun , Chen Xuenian 
Published: December 2022

AbstractAmides are one of the most important organic compounds that are widely applied in medicine, biochemistry, and materials science. To find an efficient synthetic method of amides is a challenge for organic chemistry. We report here a facile synthesis method of primary and secondary amides through a direct amidation of esters with sodium amidoboranes (NaNHRBH3, R = H, Me), at room temperature without using catalysts and other reagents. This process is rapid and chemoselective, and features quantitative conversion and wide applicability for esters tolerating different functional groups. The experimental and theoretical studies reveal a reaction mechanism with nucleophilic addition followed by a swift proton transfer-induced elimination reaction.
Cancer gene mutation frequencies for the U.S. population
Authors: Mendiratta Gaurav , Ke Eugene , Aziz Meraj , Liarakos David , Tong Melinda , Stites Edward C. 
Published: December 2022

AbstractMutations play a fundamental role in the development of cancer, and many create targetable vulnerabilities. There are both public health and basic science benefits from the determination of the proportion of all cancer cases within a population that include a mutant form of a gene. Here, we provide the first such estimates by combining genomic and epidemiological data. We estimate KRAS is mutated in only 11% of all cancers, which is less than PIK3CA (13%) and marginally higher than BRAF (8%). TP53 is the most commonly mutated gene (35%), and KMT2C, KMT2D, and ARID1A are among the ten most commonly mutated driver genes, highlighting the role of epigenetic dysregulation in cancer. Analysis of major cancer subclassifications highlighted varying dependencies upon individual cancer drivers. Overall, we find that cancer genetics is less dominated by high-frequency, high-profile cancer driver genes than studies limited to a subset of cancer types have suggested.
Structures of the eukaryotic ribosome and its translational states in situ
Authors: Hoffmann Patrick C. , Kreysing Jan Philipp , Khusainov Iskander , Tuijtel Maarten W. , Welsch Sonja , Beck Martin 
Published: December 2022

AbstractRibosomes translate genetic information into primary structure. During translation, various cofactors transiently bind to the ribosome that undergoes prominent conformational and structural changes. Different translational states of ribosomes have been well characterized in vitro. However, to which extent the known translational states are representative of the native situation inside cells has thus far only been addressed in prokaryotes. Here, we apply cryo-electron tomography to cryo-FIB milled Dictyostelium discoideum cells combined with subtomogram averaging and classification. We obtain an in situ structure that is locally resolved up to 3 Angstrom, the distribution of eukaryotic ribosome translational states, and unique arrangement of rRNA expansion segments. Our work demonstrates the use of in situ structural biology techniques for identifying distinct ribosome states within the cellular environment.
Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes
Authors: Hwang Youra , Han Soeun , Yoo Chan Yul , Hong Liu , You Chenjiang , Le Brandon H. , Shi Hui , Zhong Shangwei , Hoecker Ute , Chen Xuemei , Chen Meng 
Published: December 2022

AbstractLight initiates chloroplast biogenesis in Arabidopsis by eliminating PHYTOCHROME-INTERACTING transcription FACTORs (PIFs), which in turn de-represses nuclear photosynthesis genes, and synchronously, generates a nucleus-to-plastid (anterograde) signal that activates the plastid-encoded bacterial-type RNA polymerase (PEP) to transcribe plastid photosynthesis genes. However, the identity of the anterograde signal remains frustratingly elusive. The main challenge has been the difficulty to distinguish regulators from the plethora of necessary components for plastid transcription and other essential chloroplast functions, such as photosynthesis. Here, we show that the genome-wide induction of nuclear photosynthesis genes is insufficient to activate the PEP. PEP inhibition is imposed redundantly by multiple PIFs and requires PIF3’s activator activity. Among the nuclear-encoded components of the PEP holoenzyme, we identify four light-inducible, PIF-repressed sigma factors as anterograde signals. Together, our results elucidate that light-dependent inhibition of PIFs activates plastid photosynthesis genes via sigma factors as anterograde signals in parallel with the induction of nuclear photosynthesis genes.
Quantum physics in connected worlds
Authors: Tindall Joseph , Searle Amy , Alhajri Abdulla , Jaksch Dieter 
Published: December 2022

AbstractTheoretical research into many-body quantum systems has mostly focused on regular structures which have a small, simple unit cell and where a vanishingly small fraction of the pairs of the constituents directly interact. Motivated by advances in control over the pairwise interactions in many-body simulators, we determine the fate of spin systems on more general, arbitrary graphs. Placing the minimum possible constraints on the underlying graph, we prove how, with certainty in the thermodynamic limit, such systems behave like a single collective spin. We thus understand the emergence of complex many-body physics as dependent on ‘exceptional’, geometrically constrained structures such as the low-dimensional, regular ones found in nature. Within the space of dense graphs we identify hitherto unknown exceptions via their inhomogeneity and observe how complexity is heralded in these systems by entanglement and highly non-uniform correlation functions. Our work paves the way for the discovery and exploitation of a whole class of geometries which can host uniquely complex phases of matter.
Reference panel guided topological structure annotation of Hi-C data
Authors: Zhang Yanlin , Blanchette Mathieu 
Published: December 2022

AbstractAccurately annotating topological structures (e.g., loops and topologically associating domains) from Hi-C data is critical for understanding the role of 3D genome organization in gene regulation. This is a challenging task, especially at high resolution, in part due to the limited sequencing coverage of Hi-C data. Current approaches focus on the analysis of individual Hi-C data sets of interest, without taking advantage of the facts that (i) several hundred Hi-C contact maps are publicly available, and (ii) the vast majority of topological structures are conserved across multiple cell types. Here, we present RefHiC, an attention-based deep learning framework that uses a reference panel of Hi-C datasets to facilitate topological structure annotation from a given study sample. We compare RefHiC against tools that do not use reference samples and find that RefHiC outperforms other programs at both topological associating domain and loop annotation across different cell types, species, and sequencing depths.
The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication
Authors: Devlin Anne M. , Shukla Ashutosh , Ruiz Julio C. , Barnes Spencer D. , Govindan Ashwin , Hunter Olga V. , Scarborough Anna M. , D’Orso Iván , Conrad Nicholas K. 
Published: December 2022

AbstractControl of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi’s sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS’ activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.
Tuning the Fermi liquid crossover in Sr2RuO4 with uniaxial stress
Authors: Chronister A. , Zingl M. , Pustogow A. , Luo Yongkang , Sokolov D. A. , Jerzembeck F. , Kikugawa N. , Hicks C. W. , Mravlje J. , Bauer E. D. , Thompson J. D. , Mackenzie A. P. , Georges A. , Brown S. E. 
Published: December 2022

AbstractWe perform nuclear magnetic resonance (NMR) measurements of the oxygen-17 Knight shifts for Sr2RuO4, while subjected to uniaxial stress applied along [100] direction. The resulting strain is associated with a strong variation of the temperature and magnetic field dependence of the inferred magnetic response. A quasiparticle description based on density-functional theory calculations, supplemented by many-body renormalizations, is found to reproduce our experimental results, and highlights the key role of a van-Hove singularity. The Fermi-liquid coherence scale is shown to be tunable by strain, and driven to low values as the associated Lifshitz transition is approached.