bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upper‐Tropospheric Troughs and North American Monsoon Rainfall in a Long‐Term Track Dataset
Authors: Igel Matthew R. , Ullrich Paul A. , Boos William R. 
Published: October 2021

AbstractThe North American monsoon is frequently affected by transient, propagating upper tropospheric vorticity anomalies. Sometimes called Tropical Upper‐Tropospheric Troughs (TUTTs), these features have been claimed to episodically enhance monsoon rainfall. Here, we track long‐lived TUTTs in 40 years of reanalysis data, producing composites and case studies from 340 TUTTs which last, on average, 7 days as they move westward across the North American monsoon region. TUTTs are thought to form from midlatitude Rossby wave breaking; case studies from our dataset support this theory. TUTTs move westward within the easterly upper‐level flow in which they are embedded. In vortex‐centered composites along the full tracks of long‐lived TUTTs, we find no detectable increase in rainfall within the main TUTT circulation. Instead, negative precipitation anomalies lie within about 500 km of the TUTT center. Quasi‐geostrophic ascent occurs in the southeast quadrant of TUTTs but is confined to the upper troposphere and does not appear to interact with precipitation. Positive anomalies of ascent and rainfall occur south and southeast of TUTTs but lie outside the main TUTT vortex, perhaps indicating concurrent variations in nearby climatological precipitation maxima. In contrast with previous case studies and subjective analyses that showed TUTTs enhance precipitation in parts of northwestern Mexico, our composites along the tracks of long‐lived TUTTs portray these systems, to first order, as strong vorticity anomalies trapped in the upper troposphere that interact only weakly and indirectly with precipitation.
Psilocin, LSD, mescaline, and DOB all induce broadband desynchronization of EEG and disconnection in rats with robust translational validity
Authors: Vejmola Čestmír , Tylš Filip , Piorecká Václava , Koudelka Vlastimil , Kadeřábek Lukáš , Novák Tomáš , Páleníček Tomáš 
Published: October 2021

AbstractSerotonergic psychedelics are recently gaining a lot of attention as a potential treatment of several neuropsychiatric disorders. Broadband desynchronization of EEG activity and disconnection in humans have been repeatedly shown; however, translational data from animals are completely lacking. Therefore, the main aim of our study was to assess the effects of tryptamine and phenethylamine psychedelics (psilocin 4 mg/kg, LSD 0.2 mg/kg, mescaline 100 mg/kg, and DOB 5 mg/kg) on EEG in freely moving rats. A system consisting of 14 cortical EEG electrodes, co-registration of behavioral activity of animals with subsequent analysis only in segments corresponding to behavioral inactivity (resting-state-like EEG) was used in order to reach a high level of translational validity. Analyses of the mean power, topographic brain-mapping, and functional connectivity revealed that all of the psychedelics irrespective of the structural family induced overall and time-dependent global decrease/desynchronization of EEG activity and disconnection within 1–40 Hz. Major changes in activity were localized on the large areas of the frontal and sensorimotor cortex showing some subtle spatial patterns characterizing each substance. A rebound of occipital theta (4–8 Hz) activity was detected at later stages after treatment with mescaline and LSD. Connectivity analyses showed an overall decrease in global connectivity for both the components of cross-spectral and phase-lagged coherence. Since our results show almost identical effects to those known from human EEG/MEG studies, we conclude that our method has robust translational validity.
Exploration of alcohol use disorder-associated brain miRNA–mRNA regulatory networks
Authors: Lim Yolpanhchana , Beane-Ebel Jennifer E. , Tanaka Yoshiaki , Ning Boting , Husted Christopher R. , Henderson David C. , Xiang Yangfei , Park In-Hyun , Farrer Lindsay A. , Zhang Huiping 
Published: October 2021

AbstractTranscriptomic changes in specific brain regions can influence the risk of alcohol use disorder (AUD), but the underlying mechanism is not fully understood. We investigated AUD-associated miRNA–mRNA regulatory networks in multiple brain regions by analyzing transcriptomic changes in two sets of postmortem brain tissue samples and ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons. miRNA and mRNA transcriptomes were profiled in 192 tissue samples (Set 1) from eight brain regions (amygdala, caudate nucleus, cerebellum, hippocampus, nucleus accumbens, prefrontal cortex, putamen, and ventral tegmental area) of 12 AUD and 12 control European Australians. Nineteen differentially expressed miRNAs (fold-change>2.0 &P < 0.05) and 97 differentially expressed mRNAs (fold-change>2.0 &P < 0.001) were identified in one or multiple brain regions of AUD subjects. AUD-associated miRNA–mRNA regulatory networks in each brain region were constructed using differentially expressed and negatively correlated miRNA–mRNA pairs. AUD-relevant pathways (includingCREB Signaling,IL-8 Signaling, andAxonal Guidance Signaling) were potentially regulated by AUD-associated brain miRNA–mRNA pairs. Moreover, miRNA and mRNA transcriptomes were mapped in additional 96 tissue samples (Set 2) from six of the above eight brain regions of eight AUD and eight control European Australians. Some of the AUD-associated miRNA–mRNA regulatory networks were confirmed. In addition, miRNA and mRNA transcriptomes were analyzed in hESC-derived cortical interneurons with or without ethanol exposure, and ethanol-influenced miRNA–mRNA regulatory networks were constructed. This study provided evidence that alcohol could induce concerted miRNA and mRNA expression changes in reward-related or alcohol-responsive brain regions. We concluded that altered brain miRNA–mRNA regulatory networks might contribute to AUD development.
Efficient generative modeling of protein sequences using simple autoregressive models
Authors: Trinquier Jeanne , Uguzzoni Guido , Pagnani Andrea , Zamponi Francesco , Weigt Martin 
Published: October 2021

AbstractGenerative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence databases. Here we propose simple autoregressive models as highly accurate but computationally efficient generative sequence models. We show that they perform similarly to existing approaches based on Boltzmann machines or deep generative models, but at a substantially lower computational cost (by a factor between 102 and 103). Furthermore, the simple structure of our models has distinctive mathematical advantages, which translate into an improved applicability in sequence generation and evaluation. Within these models, we can easily estimate both the probability of a given sequence, and, using the model’s entropy, the size of the functional sequence space related to a specific protein family. In the example of response regulators, we find a huge number of ca. 1068 possible sequences, which nevertheless constitute only the astronomically small fraction 10−80 of all amino-acid sequences of the same length. These findings illustrate the potential and the difficulty in exploring sequence space via generative sequence models.
Determinants of renal cell carcinoma invasion and metastatic competence
Authors: Kim Kangsan , Zhou Qinbo , Christie Alana , Stevens Christina , Ma Yuanqing , Onabolu Oreoluwa , Chintalapati Suneetha , Mckenzie Tiffani , Tcheuyap Vanina Toffessi , Woolford Layton , Zhang He , Singla Nirmish , Parida Pravat Kumar , Marquez-Palencia Mauricio , Pedrosa Ivan , Margulis Vitaly , Sagalowsky Arthur , Xie Zhiqun , Wang Tao , Durinck Steffen , Modrusan Zora , Seshagiri Somasekar , Kapur Payal , Brugarolas James , Malladi Srinivas 
Published: October 2021

AbstractMetastasis is the principal cause of cancer related deaths. Tumor invasion is essential for metastatic spread. However, determinants of invasion are poorly understood. We addressed this knowledge gap by leveraging a unique attribute of kidney cancer. Renal tumors invade into large vessels forming tumor thrombi (TT) that migrate extending sometimes into the heart. Over a decade, we prospectively enrolled 83 ethnically-diverse patients undergoing surgical resection for grossly invasive tumors at UT Southwestern Kidney Cancer Program. In this study, we perform comprehensive histological analyses, integrate multi-region genomic studies, generate in vivo models, and execute functional studies to define tumor invasion and metastatic competence. We find that invasion is not always associated with the most aggressive clone. Driven by immediate early genes, invasion appears to be an opportunistic trait attained by subclones with diverse oncogenomic status in geospatial proximity to vasculature. We show that not all invasive tumors metastasize and identify determinants of metastatic competency. TT associated with metastases are characterized by higher grade, mTOR activation and a particular immune contexture. Moreover, TT grade is a better predictor of metastasis than overall tumor grade, which may have implications for clinical practice.
Unveiling unconventional magnetism at the surface of Sr2RuO4
Authors: Fittipaldi R. , Hartmann R. , Mercaldo M. T. , Komori S. , Bjørlig A. , Kyung W. , Yasui Y. , Miyoshi T. , Olde Olthof L. A. B. , Palomares Garcia C. M. , Granata V. , Keren I. , Higemoto W. , Suter A. , Prokscha T. , Romano A. , Noce C. , Kim C. , Maeno Y. , Scheer E. , Kalisky B. , Robinson J. W. A. , Cuoco M. , Salman Z. , Vecchione A. , Di Bernardo A. 
Published: October 2021

AbstractMaterials with strongly correlated electrons often exhibit interesting physical properties. An example of these materials is the layered oxide perovskite Sr2RuO4, which has been intensively investigated due to its unusual properties. Whilst the debate on the symmetry of the superconducting state in Sr2RuO4 is still ongoing, a deeper understanding of the Sr2RuO4 normal state appears crucial as this is the background in which electron pairing occurs. Here, by using low-energy muon spin spectroscopy we discover the existence of surface magnetism in Sr2RuO4 in its normal state. We detect static weak dipolar fields yet manifesting at an onset temperature higher than 50 K. We ascribe this unconventional magnetism to orbital loop currents forming at the reconstructed Sr2RuO4 surface. Our observations set a reference for the discovery of the same magnetic phase in other materials and unveil an electronic ordering mechanism that can influence electron pairing with broken time reversal symmetry.
Neural heterogeneity promotes robust learning
Authors: Perez-Nieves Nicolas , Leung Vincent C. H. , Dragotti Pier Luigi , Goodman Dan F. M. 
Published: October 2021

AbstractThe brain is a hugely diverse, heterogeneous structure. Whether or not heterogeneity at the neural level plays a functional role remains unclear, and has been relatively little explored in models which are often highly homogeneous. We compared the performance of spiking neural networks trained to carry out tasks of real-world difficulty, with varying degrees of heterogeneity, and found that heterogeneity substantially improved task performance. Learning with heterogeneity was more stable and robust, particularly for tasks with a rich temporal structure. In addition, the distribution of neuronal parameters in the trained networks is similar to those observed experimentally. We suggest that the heterogeneity observed in the brain may be more than just the byproduct of noisy processes, but rather may serve an active and important role in allowing animals to learn in changing environments.
Household cooking fuel estimates at global and country level for 1990 to 2030
Authors: Stoner Oliver , Lewis Jessica , Martínez Itzel Lucio , Gumy Sophie , Economou Theo , Adair-Rohani Heather 
Published: October 2021

AbstractHousehold air pollution generated from the use of polluting cooking fuels and technologies is a major source of disease and environmental degradation in low- and middle-income countries. Using a novel modelling approach, we provide detailed global, regional and country estimates of the percentages and populations mainly using 6 fuel categories (electricity, gaseous fuels, kerosene, biomass, charcoal, coal) and overall polluting/clean fuel use – from 1990-2020 and with urban/rural disaggregation. Here we show that 53% of the global population mainly used polluting cooking fuels in 1990, dropping to 36% in 2020. In urban areas, gaseous fuels currently dominate, with a growing reliance on electricity; in rural populations, high levels of biomass use persist alongside increasing use of gaseous fuels. Future projections of observed trends suggest 31% will still mainly use polluting fuels in 2030, including over 1 billion people in Sub-Saharan African by 2025.
Enabling comprehensive optogenetic studies of mouse hearts by simultaneous opto-electrical panoramic mapping and stimulation
Authors: Rieger Michael , Dellenbach Christian , vom Berg Johannes , Beil-Wagner Jane , Maguy Ange , Rohr Stephan 
Published: October 2021

AbstractDuring the last decade, cardiac optogenetics has turned into an essential tool for investigating cardiac function in general and for assessing functional interactions between different myocardial cell types in particular. To advance exploitation of the unique research opportunities offered by this method, we develop a panoramic opto-electrical measurement and stimulation (POEMS) system for mouse hearts. The core of the experimental platform is composed of 294 optical fibers and 64 electrodes that form a cup which embraces the entire ventricular surface of mouse hearts and enables straightforward ‘drop&go’ experimentation. The flexible assignment of fibers and electrodes to recording or stimulation tasks permits a precise tailoring of experiments to the specific requirements of individual optogenetic constructs thereby avoiding spectral congestion. Validation experiments with hearts from transgenic animals expressing the optogenetic voltage reporters ASAP1 and ArcLight-Q239 demonstrate concordance of simultaneously recorded panoramic optical and electrical activation maps. The feasibility of single fiber optical stimulation is proven with hearts expressing the optogenetic voltage actuator ReaChR. Adaptation of the POEMS system to larger hearts and incorporation of additional sensors can be achieved by redesigning the system-core accordingly.
Protein identification by nanopore peptide profiling
Authors: Lucas Florian Leonardus Rudolfus , Versloot Roderick Corstiaan Abraham , Yakovlieva Liubov , Walvoort Marthe T. C. , Maglia Giovanni 
Published: October 2021

AbstractNanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification.
Atomic level fluxional behavior and activity of CeO2-supported Pt catalysts for CO oxidation
Authors: Vincent Joshua L. , Crozier Peter A. 
Published: October 2021

AbstractReducible oxides are widely used catalyst supports that can increase oxidation reaction rates by transferring lattice oxygen at the metal-support interface. There are many outstanding questions regarding the atomic-scale dynamic meta-stability (i.e., fluxional behavior) of the interface during catalysis. Here, we employ aberration-corrected operando electron microscopy to visualize the structural dynamics occurring at and near Pt/CeO2 interfaces during CO oxidation. We show that the catalytic turnover frequency correlates with fluxional behavior that (a) destabilizes the supported Pt particle, (b) marks an enhanced rate of oxygen vacancy creation and annihilation, and (c) leads to increased strain and reduction in the CeO2 support surface. Overall, the results implicate the interfacial Pt-O-Ce bonds anchoring the Pt to the support as being involved also in the catalytically-driven oxygen transfer process, and they suggest that oxygen reduction takes place on the highly reduced CeO2 surface before migrating to the interfacial perimeter for reaction with CO.
Current and projected regional economic impacts of heatwaves in Europe
Authors: García-León David , Casanueva Ana , Standardi Gabriele , Burgstall Annkatrin , Flouris Andreas D. , Nybo Lars 
Published: October 2021

AbstractExtreme heat undermines the working capacity of individuals, resulting in lower productivity, and thus economic output. Here we analyse the present and future economic damages due to reduced labour productivity caused by extreme heat in Europe. For the analysis of current impacts, we focused on heatwaves occurring in four recent anomalously hot years (2003, 2010, 2015, and 2018) and compared our findings to the historical period 1981–2010. In the selected years, the total estimated damages attributed to heatwaves amounted to 0.3–0.5% of European gross domestic product (GDP). However, the identified losses were largely heterogeneous across space, consistently showing GDP impacts beyond 1% in more vulnerable regions. Future projections indicate that by 2060 impacts might increase in Europe by a factor of almost five compared to the historical period 1981–2010 if no further mitigation or adaptation actions are taken, suggesting the presence of more pronounced effects in the regions where these damages are already acute.
Programmable nano-reactors for stochastic sensing
Authors: Jia Wendong , Hu Chengzhen , Wang Yuqin , Gu Yuming , Qian Guangrui , Du Xiaoyu , Wang Liying , Liu Yao , Cao Jiao , Zhang Shanyu , Yan Shuanghong , Zhang Panke , Ma Jing , Chen Hong-Yuan , Huang Shuo 
Published: October 2021

AbstractChemical reactions of single molecules, caused by rapid formation or breaking of chemical bonds, are difficult to observe even with state-of-the-art instruments. A biological nanopore can be engineered into a single molecule reactor, capable of detecting the binding of a monatomic ion or the transient appearance of chemical intermediates. Pore engineering of this type is however technically challenging, which has significantly restricted further development of this technique. We propose a versatile strategy, “programmable nano-reactors for stochastic sensing” (PNRSS), by which a variety of single molecule reactions of hydrogen peroxide, metal ions, ethylene glycol, glycerol, lactic acid, vitamins, catecholamines or nucleoside analogues can be observed directly. PNRSS presents a refined sensing resolution which can be further enhanced by an artificial intelligence algorithm. Remdesivir, a nucleoside analogue and an investigational anti-viral drug used to treat COVID-19, can be distinguished from its active triphosphate form by PNRSS, suggesting applications in pharmacokinetics or drug screening.
Wdr47, Camsaps, and Katanin cooperate to generate ciliary central microtubules
Authors: Liu Hao , Zheng Jianqun , Zhu Lei , Xie Lele , Chen Yawen , Zhang Yirong , Zhang Wei , Yin Yue , Peng Chao , Zhou Jun , Zhu Xueliang , Yan Xiumin 
Published: October 2021

AbstractThe axonemal central pair (CP) are non-centrosomal microtubules critical for planar ciliary beat. How they form, however, is poorly understood. Here, we show that mammalian CP formation requires Wdr47, Camsaps, and microtubule-severing activity of Katanin. Katanin severs peripheral microtubules to produce central microtubule seeds in nascent cilia. Camsaps stabilize minus ends of the seeds to facilitate microtubule outgrowth, whereas Wdr47 concentrates Camsaps into the axonemal central lumen to properly position central microtubules.Wdr47deficiency in mouse multicilia results in complete loss of CP, rotatory beat, and primary ciliary dyskinesia. Overexpression of Camsaps or their microtubule-binding regions induces central microtubules inWdr47−/−ependymal cells but at the expense of low efficiency, abnormal numbers, and wrong location. Katanin levels and activity also impact the central microtubule number. We propose that Wdr47, Camsaps, and Katanin function together for the generation of non-centrosomal microtubule arrays in polarized subcellular compartments.
Magnetic-field-controlled spin fluctuations and quantum criticality in Sr3Ru2O7
Authors: Lester C. , Ramos S. , Perry R. S. , Croft T. P. , Laver M. , Bewley R. I. , Guidi T. , Hiess A. , Wildes A. , Forgan E. M. , Hayden S. M. 
Published: October 2021

AbstractWhen the transition temperature of a continuous phase transition is tuned to absolute zero, new ordered phases and physical behaviour emerge in the vicinity of the resulting quantum critical point. Sr3Ru2O7 can be tuned through quantum criticality with magnetic field at low temperature. Near its critical field Bc it displays the hallmark T-linear resistivity and a $$T\,{{{{{{\mathrm{log}}}}}}}\,(1/T)$$
T

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(

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/
T

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electronic heat capacity behaviour of strange metals. However, these behaviours have not been related to any critical fluctuations. Here we use inelastic neutron scattering to reveal the presence of collective spin fluctuations whose relaxation time and strength show a nearly singular variation with magnetic field as Bc is approached. The large increase in the electronic heat capacity and entropy near Bc can be understood quantitatively in terms of the scattering of conduction electrons by these spin-fluctuations. On entering the spin-density-wave ordered phase present near Bc, the fluctuations become stronger suggesting that the order is stabilised through an “order-by-disorder” mechanism.
Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate
Authors: Krüger Lena , Albrecht Christoph J. , Schammann Hannah K. , Stumpf Florian M. , Niedermeier Marie L. , Yuan Yizhi , Stuber Katrin , Wimmer Josua , Stengel Florian , Scheffner Martin , Marx Andreas 
Published: October 2021

AbstractThe nucleotides diadenosine triphosphate (Ap3A) and diadenosine tetraphosphate (Ap4A) are formed in prokaryotic and eukaryotic cells. Since their concentrations increase significantly upon cellular stress, they are considered to be alarmones triggering stress adaptive processes. However, their cellular roles remain elusive. To elucidate the proteome-wide interactome of Ap3A and Ap4A and thereby gain insights into their cellular roles, we herein report the development of photoaffinity-labeling probes and their employment in chemical proteomics. We demonstrate that the identified ApnA interactors are involved in many fundamental cellular processes including carboxylic acid and nucleotide metabolism, gene expression, various regulatory processes and cellular response mechanisms and only around half of them are known nucleotide interactors. Our results highlight common functions of these ApnAs across the domains of life, but also identify those that are different for Ap3A or Ap4A. This study provides a rich source for further functional studies of these nucleotides and depicts useful tools for characterization of their regulatory mechanisms in cells.