bluuebunny/crossref_metadata_2025 huggingface dataset:
Key parameters of volcanic tuffs used as building stone: a statistical approach
Authors: Pötzl Christopher , Siegesmund Siegfried , López-Doncel Rubén , Dohrmann Reiner
Published: December 2021

Volcanic tuffs naturally show a strong heterogeneity in their petrography and petrophysical properties. The arrangement of the components in tuffs can create a very wide spectrum of porosities and fabrics, which in turn can lead to a highly differential weathering behavior. Considerable amounts of clay minerals and zeolites are common and can contribute to a high sensitivity to expansional processes and salt crystallization. Understanding the influence of the rock properties on material behavior and durability can help to make predictions on future material behavior and evaluate the suitability of the material for construction purposes. This study presents the petrographic and petrophysical data of 15 selected tuffs and 513 tuffs from the literature used as building stones. Regression analysis show if parameters are comparable and if key parameters can be identified. Key parameters can potentially be used for the estimation of the material behavior, without the use of expensive analytics or weathering simulations.
The social dilemma in artificial intelligence development and why we have to solve it
Authors: Strümke Inga , Slavkovik Marija , Madai Vince Istvan
Published: December 2021

While the demand for ethical artificial intelligence (AI) systems increases, the number of unethical uses of AI accelerates, even though there is no shortage of ethical guidelines. We argue that a possible underlying cause for this is that AI developers face a social dilemma in AI development ethics, preventing the widespread adaptation of ethical best practices. We define the social dilemma for AI development and describe why the current crisis in AI development ethics cannot be solved without relieving AI developers of their social dilemma. We argue that AI development must be professionalised to overcome the social dilemma, and discuss how medicine can be used as a template in this process.
The AI ethicist’s dilemma: fighting Big Tech by supporting Big Tech
Authors: Sætra Henrik Skaug , Coeckelbergh Mark , Danaher John
Published: December 2021

Assume that a researcher uncovers a major problem with how social media are currently used. What sort of challenges arise when they must subsequently decide whether or not to use social media to create awareness about this problem? This situation routinely occurs as ethicists navigate choices regarding how to effect change and potentially remedy the problems they uncover. In this article, challenges related to new technologies and what is often referred to as ‘Big Tech’ are emphasized. We present what we refer to as the AI ethicist’s dilemma, which emerges when an AI ethicist has to consider how their own success in communicating an identified problem is associated with a high risk of decreasing the chances of successfully remedying the problem. We examine how the ethicist can resolve the dilemma and arrive at ethically sound paths of action through combining three ethical theories: virtue ethics, deontological ethics and consequentialist ethics. The article concludes that attempting to change the world of Big Tech only using the technologies and tools they provide will at times prove to be counter-productive, and that political and other more disruptive avenues of action should also be seriously considered by ethicists who want to effect long-term change. Both strategies have advantages and disadvantages, and a combination might be desirable to achieve these advantages and mitigate some of the disadvantages discussed.
Poisoning After Ingestion of Mucuna pruriens Seeds on Reunion Island
Authors: Maillot Adrien , Schmitt Corinne , Marteau Adrien
Published: December 2021

Mucuna pruriens seeds contain levodopa, a dopamine precursor that composes the standard treatment to manage symptoms of Parkinson’s disease. Also known as velvet bean, this plant is often involved in cases of intense pruritus after contact with the hair that grows on its beans. This case report describes the effects in a 58-y-old woman after ingestion of 5 raw seeds of M pruriens on Reunion Island, a French tropical island territory close to Mauritius, in the Indian Ocean. About 40 min after ingesting the plant, the patient showed adverse digestive symptoms such as nausea, vomiting, and abundant diarrhea followed by a state of confusion, hallucinations, and amnesia. She was brought to the emergency department. After medical examination, her vitals were normal, and only her nausea lingered. The poison control center was contacted by the medical team. The plant, previously well described and known by the patient, was later picked from the garden and reviewed by the Indian Ocean toxicovigilance department. Expert botanists confirmed the plant species to be M pruriens. The patient ate the raw seeds after reading articles on the Internet, without confirming whether the seeds should have been cooked before consumption. This case highlights that ingesting raw, unprepared M pruriens seeds can cause severe digestive symptoms, possibly accompanied by neurologic disorders.
Multilocus-phylogeny of the lichen-forming genus Bacidia s. str. (Ramalinaceae, Lecanorales) with special emphasis on the Russian Far East
Authors: Gerasimova Julia V. , Ezhkin Aleksandr K. , Davydov Evgeny A. , Beck Andreas
Published: December 2021

To clarify deep relationships among species lineages within Bacidia s. str., and to investigate the robustness of the deeper branches, we combined data from three traditionally used RNA-coding genes (nrITS, nrLSU and mtSSU) with two protein-coding genes (RPB1 and RPB2). The multigene phylogeny contained 48 newly generated sequences from the Russian Far East and all Bacidia s. str. sequences from GenBank (131 sequences). We subjected the alignments for the single and concatenated data sets to Bayesian inference (BI) and two maximum likelihood (ML) analyses (RAxML and IQ-TREE). The topologies of phylogenetic trees recovered from BI and ML analyses were highly concordant. The multilocus phylogeny of Bacidia s. str. was congruent with previous results based on nrITS sequences from the Russian Far East but with considerably higher support values for most of the deeper branches. A correlation between the recovered clades and apothecial pigments in the upper part of the hymenium and lateral exciple was observed. Based on morphological and molecular evidence, Bacidia obtecta is described as new to science. It was recovered as the sister lineage of B. elongata. The two species are alike in having up to four enlarged lumina cells along the exciple edge, but B. obtecta differs in the abundant crystals found in the upper hymenium and lateral exciple, and by having spores with fewer septa.
Developmental change in children’s speech processing of auditory and visual cues: An eyetracking study
Authors: ZAMUNER Tania S. , RABIDEAU Theresa , MCDONALD Margarethe , YEUNG H. Henny
Published: December 2021

This study investigates how children aged two to eight years (N = 129) and adults (N = 29) use auditory and visual speech for word recognition. The goal was to bridge the gap between apparent successes of visual speech processing in young children in visual-looking tasks, with apparent difficulties of speech processing in older children from explicit behavioural measures. Participants were presented with familiar words in audio-visual (AV), audio-only (A-only) or visual-only (V-only) speech modalities, then presented with target and distractor images, and looking to targets was measured. Adults showed high accuracy, with slightly less target-image looking in the V-only modality. Developmentally, looking was above chance for both AV and A-only modalities, but not in the V-only modality until 6 years of age (earlier on /k/-initial words). Flexible use of visual cues for lexical access develops throughout childhood.
BioMimics 3D vascular stent system for femoropopliteal	interventions
Authors: Lichtenberg Michael , Zeller Thomas , Gaines Peter , Piorkowski Michael
Published: December 2021

Summary: Background: The MIMICS-3D study aimed to assess the safety and effectiveness of the BioMimics 3D Vascular Stent System for the treatment of symptomatic femoropopliteal artery disease in a real-world patient population. Patients and methods: Consecutive participants who were scheduled for implantation of the BioMimics 3D stent were enrolled in the prospective, observational, multicenter study. The primary effectiveness outcome was freedom from clinically driven target lesion revascularization at 12 months and the primary safety outcome was a composite of major adverse events comprising death, major target limb amputation, or clinically driven target lesion revascularization at 30 days. Outcomes through 24 months are reported. Results: A total of 507 patients (70±10 years, 65.5% male sex) were enrolled and treated with the study stent. 24.0% had critical limb-threatening ischemia, lesion length was 127±92 mm, and 56.8% of lesions were totally occluded. The Kaplan-Meier (KM) estimate of freedom from clinically driven target lesion revascularization at twelve-months was 90.6% (95% CI: 87.9%–93.3%) and the 30-day primary safety outcome occurred in 1.2% (95% CI: 0.5%–2.7%) of participants. At 24 months, clinical improvement was achieved in 86.6% and the KM estimate of freedom from clinically driven target lesion revascularization was 82.8% (95% CI: 79.4%–86.4%). The KM estimate of freedom from loss of primary patency according to PSVR >2.4 was 78.6% (95% CI: 74.7%–82.4%). Survival distribution functions regarding primary patency were lower with long lesions (>150 mm; log-rank p<0.001) but did not differ significantly between participants with or without critical limb-threatening ischemia (log-rank p=0.07). Conclusions: Endovascular treatment of atherosclerotic femoropopliteal lesions with the BioMimics 3D Vascular Stent System is efficacious and safe in a real-world setting.
Blended Learning mit Virtuellen Kindernotfallpatientinnen und -patienten für Studierende
Authors: Steiner Isabelle , Brandenberger Julia , Wagner Felicitas , Huwendiek Sören
Published: December 2021

Zusammenfassung. Die Behandlung von kritisch kranken Kindern stellt eine grosse Herausforderung für Lernende dar. Studierende fühlen sich häufig nicht adäquat auf diese Situationen vorbereitet, insbesondere im Hinblick auf ihre spätere Verantwortung für diese Patient_innen und Ärztinnen und Ärzte. Dieser Artikel beschreibt die Implementierung und Evaluation von Blended Learning mittels Virtuellen Patient_innen (VP) während des Blockpraktikums im Notfallzentrum für Kinder und Jugendliche am Inselspital Bern. In den Evaluationen bewerteten die Studierenden das Projekt als sehr gut und hilfreich und wünschen sich den Ausbau ins gesamte Medizinstudium.
CME/Antworten: Mechanische Reanimationshilfe bei Herz-Kreislauf-Stillstand
Authors: Oechslin Luca , Casso Gabriele , Wyss Christophe
Published: December 2021

Zusammenfassung. Eine möglichst frühzeitige und qualitativ hochwertige kardiopulmonale Reanimation ist die effektivste Massnahme zur Senkung der Mortalität und Verbesserung des neurolo-gischen Outcomes bei Herz-Kreislauf-Stillstand. Mit dem Ziel, die Reanimationsqualität zu verbessern, wurden verschiedene mechanische Reanimationshilfen (Assist Devices), die die manuelle Kompression ersetzen können, entwickelt. Wann diese eingesetzt werden können, ob sie zu einer Verbesserung des Outcomes führen und mit welchen Verletzungen sie einhergehen, wurde in mehreren Studien untersucht, worüber dieser Beitrag eine Übersicht schaffen soll.
CME-Rheumatologie 24/Antworten: DISH der Hand und undifferenzierte Polyarthritis
Authors: Tamborrini Giorgio , Kyburz Diego , Studler Ueli
Published: December 2021

Zusammenfassung. Wir stellen einen Fall mit undifferenzierter, bzw. nicht klassifizierter Polyarthritis und mit peripherer diffuser idiopathischer skelettaler Hyperostose (DISH) vor. Hierbei diskutieren wir die Differenzialdiagnosen der «seronegativen» Polyarthritis und erläutern die konventionelle Bildgebung der wenig bekannten peripheren Manifestation der DISH.
Effect of Upstream Dam Geometry on Peak Discharge During Overtopping Breach in Noncohesive Homogeneous Embankment Dams; Implications for Tailings Dams
Authors: Walsh A. , McDougall S. , Evans S. G. , Take W. A.
Published: December 2021

Tailings dams differ from conventional water‐retaining dams in design, materials retained behind the dam and used in construction of the dam, and the inclination of the upstream face of the dam. In this paper, we isolate the effect of upstream slope angle on behavior during overtopping breach. Six 1 m high homogeneous fine sand dams were constructed with upstream slope angles varying between 10.0° and 30.0° and brought to failure by V notch overtopping. Slope angle was observed to define the height of flow over the erosional breach crest hydraulic control structure that forms in the upstream face of the dam, with higher peak outflow corresponding to steeper upstream slope angles. A semiellipse was observed to be an excellent approximation of the geometry of the breach throughout the rising limb of the hydrograph to peak outflow. This observation permitted the use of the Ramanujan approximation for perimeter of an ellipse to define a mathematical relationship between breach width and arc length. A simplified method to predict the rising limb of the outflow hydrograph was then proposed based on the assumption of linear growth of breach width coupled with a semielliptical breach geometry. These findings show that hazard analysis for overtopping failure should consider the effect of upstream slope angle on peak outflow.
A National VS30 Model for South Korea to Combine Nationwide Dense Borehole Measurements With Ambient Seismic Noise Analysis
Authors: Kim Byeongwoo , Hong Tae‐Kyung
Published: December 2021

The average shear‐wave velocity within the top 30 m from the surface, VS30, represents site characteristics including the soil classification and site amplification that are essential information for building codes and seismic design. A novel method to determine a VS30 model based on a composite analysis of borehole standard penetration test numbers (SPT N) and horizontal‐to‐vertical (H/V) spectral ambient noise ratios is introduced. A national VS30 model for South Korea is determined using the method. The shear‐wave velocity structures beneath 20 nationwide broadband seismic stations are determined using the H/V analysis. The SPT N data are collected from 175,619 nationwide densely‐distributed boreholes. The shear‐wave velocity models from SPT N values are calibrated for the local reference velocity models from H/V analysis. A representative relationship between the SPT N values and shear‐wave velocities is introduced. A national VS30 model for South Korea is determined using the calibrated SPT N models at the nationwide boreholes. The VS30 model is verified by comparisons with local field measurements. The proposed model is consistent with the USGS model based on a surface slope analysis. The VS30 structure presents high correlation with geological and topographic features. The VS30 values are low in coastal (low topographic) areas, and high in mountain (high topographic) areas. Apparent linear relationship is observed between VS30 and topography. The western and southeastern coastal regions may be vulnerable to strong seismic shaking.
PetroChron Antarctica: A Geological Database for Interdisciplinary Use
Authors: Sanchez G. , Halpin J. A. , Gard M. , Hasterok D. , Stål T. , Raimondo T. , Peters S. , Burton‐Johnson A.
Published: December 2021

We present PetroChron Antarctica, a new relational database including petrological, geochemical and geochronological data sets along with computed rock properties from geological samples across Antarctica. The database contains whole‐rock geochemistry with major/trace element and isotope analyses, geochronology from multiple isotopic systems and minerals for given samples, as well as an internally consistent rock classification based on chemical analysis and derived rock properties (i.e., chemical indices, density, p‐velocity, and heat production). A broad range of meta‐information such as geographic location, petrology, mineralogy, age statistics and significance are also included and can be used to filter and assess the quality of the data. Currently, the database contains 11,559 entries representing 10,056 unique samples with varying amounts of geochemical and geochronological data. The distribution of rock types is dominated by mafic (36%) and felsic (33%) compositions, followed by intermediate (22%) and ultramafic (9%) compositions. Maps of age distribution and isotopic composition highlight major episodes of tectonic and thermal activity that define well known crustal heterogeneities across the continent, with the oldest rocks preserved in East Antarctica and more juvenile lithosphere characterizing West Antarctica. PetroChron Antarctica allows spatial and temporal variations in geology to be explored at the continental scale and integrated with other Earth‐cryosphere‐biosphere‐ocean data sets. As such, it provides a powerful resource ready for diverse applications including plate tectonic reconstructions, geological/geophysical maps, geothermal heat flow models, lithospheric and glacial isostasy, geomorphology, ice sheet reconstructions, biodiversity evolution, and oceanography.
Investigating the Impacts of a Wet Typhoon on Microseismicity: A Case Study of the 2009 Typhoon Morakot in Taiwan Based on a Template Matching Catalog
Authors: Zhai Qiushi , Peng Zhigang , Chuang Lindsay Y. , Wu Yih‐Min , Hsu Ya‐Ju , Wdowinski Shimon
Published: December 2021

Recent studies suggested that transient and long‐term stress changes caused by Earth's surface processes (e.g., extreme weather events, annual variations on groundwater storages) can affect earthquake activities in the subsurface. However, these studies may be limited by the completeness of standard earthquake catalogs, especially during or right after extreme weather events. Here we apply the template matching method to build a more complete earthquake catalog in Taiwan spanning seven months before and 12 months after 2009 typhoon Morakot, which brought the highest rainfall in southern Taiwan in the past 60 years and triggered numerous landslides. We then use the enhanced catalog to investigate possible influences of typhoon‐driven Earth's surface processes (atmospheric pressure, precipitation, and erosion) on local seismicity. We find that the seismicity rate of a 40‐day earthquake sequence in northeastern Taiwan was reduced significantly right after the passage of typhoon Morakot's eye center. In the typhoon‐triggered landslide zone in southern Taiwan, we find a slight increase in background seismicity rate in the next year after Morakot, matching the results of a recent study. However, we do not observe a clear change in the Gutenberg‐Richter b‐value in this zone, which is different from the recent study. Station outages during and right after Morakot prevents us from better understanding short‐term precipitation effect on local seismicity. Overall, except for a reduction in seismicity rate near the typhoon's low‐pressure eye center in northeastern Taiwan, we do not observe other clear seismicity changes that can be attributed to surface changes induced by typhoon Morakot.
Microscale Mechanical‐Chemical Modeling of Granular Salt: Insights for Creep
Authors: Hu Mengsu , Steefel Carl I. , Rutqvist Jonny
Published: December 2021

Microscale numerical modeling is potentially an effective approach for understanding salt creep, but it is quite challenging because natural salt grain boundaries can have complex and evolving geometry, and because contacts between these deformable salt mineral grains are dynamic as a result of compaction, chemical reaction, fluid flow, and heat transfer. In this study, we have overcome these challenges and developed a new microscale mechanical‐chemical (MC) model to analyze creep of salt at the microscale, accounting for coupled deformation, dynamic contacts, and chemical reaction in granular systems with realistic geometric representations. The MC model was realized by linking a new microscale mechanical code based on the numerical manifold method (NMM) to a reactive transport code named Crunch. We simulated the processes of reorganization of the salt grains, microfracturing, and pressure solution that contribute to creep at larger scales. Based on this first quantitative microscale model, we found that sharp corners of mineral grains can dominate the contact dynamics, microfracturing, and pressure solution when salt is compacted, thus governing the structural changes and porosity loss of the system. We found that pressure solution, which preferentially dissolves sharp corners and edges, can lead to relatively high porosity loss in the system, thus playing an important role in the creep of salt. Our analysis shows that the dynamic changes of salt granular systems involving grain relocation and pressure solution can occur repeatedly and continuously, thus contributing to longer‐term creep of salt at larger scales.
Tropical Cyclone Precipitation Response to Surface Warming in Aquaplanet Simulations With Uniform Thermal Forcing
Authors: Stansfield Alyssa M. , Reed Kevin A.
Published: December 2021

While many modeling studies have attempted to estimate how tropical cyclone (TC) precipitation is impacted by climate change, the multitude of analysis techniques and methodologies have resulted in varying conclusions. Simplified models may be able to help overcome this problem. Radiative‐convective equilibrium (RCE) model simulations have been used in various configurations to study fundamental aspects of Earth's climate. While many RCE modeling studies have focused on TC genesis, intensification, and size, limited work has been done using RCE to study TC precipitation. In this study, the response of TC precipitation to sea surface temperature (SST) change is analyzed in global Community Atmosphere Model (CAM) aquaplanet simulations run with Radiative‐Convective Equilibrium Model Intercomparison Project protocols, with the addition of planetary rotation. We expect that the insight gained about how TC precipitation responds to SST warming will help predict how TCs in the real world respond to climate change. In the CAM RCE simulations, the warmer SST simulations have less TCs on average, but the TCs tend to be larger in outer size and more intense. As simulation SST increases, more extreme precipitation rates occur within TCs, and more of the TC precipitation comes from these extreme rates. For extreme (99th percentile) TC precipitation, SST, and TC intensity increases dominate the 8.6% per K increase, while TC outer size changes have little impact. For accumulated TC precipitation, SST, and TC intensity contributions are still the majority, but TC outer size changes also contribute to the 6.6% per K increase.
Climate Drives Modeled Forest Carbon Cycling Resistance and Resilience in the Upper Great Lakes Region, USA
Authors: Dorheim Kalyn , Gough Christopher M. , Haber Lisa T. , Mathes Kayla C. , Shiklomanov Alexey N. , Bond‐Lamberty Ben
Published: December 2021

Forests dominate the global terrestrial carbon budget, but their ability to continue doing so in the face of a changing climate is uncertain. A key uncertainty is how forests will respond to (resistance) and recover from (resilience) rising levels of disturbance of varying intensities. This knowledge gap can optimally be addressed by integrating manipulative field experiments with ecophysiological modeling. We used the Ecosystem Demography‐2.2 (ED‐2.2) model to project carbon fluxes for a northern temperate deciduous forest subjected to a real‐world disturbance severity manipulation experiment. ED‐2.2 was run for 150 years, starting from near bare ground in 1900 (approximating the clear‐cut conditions at the time), and subjected to three disturbance treatments under an ensemble of climate conditions. Both disturbance severity and climate strongly affected carbon fluxes such as gross primary production (GPP), and interacted with one another. We then calculated resistance and resilience, two dimensions of ecosystem stability. Modeled GPP exhibited a two‐fold decrease in mean resistance across disturbance severities of 45%, 65%, and 85% mortality; conversely, resilience increased by a factor of two with increasing disturbance severity. This pattern held for net primary production and net ecosystem production, indicating a trade‐off in which greater initial declines were followed by faster recovery. Notably, however, heterotrophic respiration responded more slowly to disturbance, and it's highly variable response was affected by different drivers. This work provides insight into how future conditions might affect the functional stability of mature forests in this region under ongoing climate change and changing disturbance regimes.
High‐Resolution 3‐D Imaging of Daytime Sporadic‐E Over Japan by Using GNSS TEC and Ionosondes
Authors: Fu Weizheng , Ssessanga Nicholas , Yokoyama Tatsuhiro , Yamamoto Mamoru
Published: December 2021

A novel two‐step three‐dimensional (3‐D) computerized ionospheric tomography (CIT) technique has been developed to image the structure of daytime midlatitude sporadic‐E (Es). The CIT relies on total electron content (TEC) from a dense ground‐based Global Navigation Satellite System (GNSS) receiver network over the Japan area. First, on a coarse grid, the TEC data and a multiplicative algebraic reconstruction technique (MART) are used to reconstruct the F region from a smooth background. Then, on a fine grid and using singular value decomposition (SVD), the residues after deducting the F region contribution to TEC are utilized in reconstructing the E region, extending 80–180 km in altitude. To vertically constrain the E region solution, we introduced a family of subsets of time‐dependent empirical orthogonal functions (EOFs) from a Chapman model function tuned to manually scaled ionosonde observations. We analyzed three event days to validate the results. East‐West (E‐W) aligned frontal structures, spanning several hundred kilometers, migrating northward in the morning and southward in the afternoon, were observed. The new technique effectively tracks the Es‐height variation over time, which had proved difficult to reproduce in earlier tempts at 3‐D Es reconstructions.
Negative Pore Water Pressure in Aquitard Enhances Land Subsidence: Field, Laboratory, and Numerical Evidence
Authors: Liu Chun , Shi Bin , Gu Kai , Zhang Tiansheng , Tang Chaosheng , Wang Yue , Liu Suping
Published: December 2021

Land subsidence in the south Yangtze River delta area did not cease when the ground water table has risen during the last 20 years. This issue was generally interpreted as a result of the slow release of excess pore water pressure in the aquitards and the creep of soil. Recent distributed strain monitoring data in boreholes shows a great compressive strain in the aquitard above the main exploited aquifer. In laboratory tests, such great compressive strain also is observed in the clay layer during the draining of the underlying sand layer. Furthermore, a negative pore water pressure is observed in the clay layer, which significantly correlates with the change of the compressive strain. An improved discrete element model was used to simulate the deformation of soil layers under the effect of the negative pressure. The simulation results coincide with the tests, and the negative pressure enhances the compression of aquitard. Due to the effect of the negative pore water pressure, aquitards may be compressed during the draining and recharging cycles in the south Yangtze River delta area.
Sediment Reworking in Streambeds With Fine Sediment Deposits and Its Influence on Hyporheic Flow Regime
Authors: Shrivastava S. , Stewardson M. J. , Arora M.
Published: December 2021

The mobilization and mixing of sediments by the activities of in‐stream fauna, referred to as sediment reworking, constantly modifies the hydro‐physical properties of streambeds. This sediment‐organism interaction has been increasingly recognized to influence the hyporheic exchange flows in stream ecosystems, particularly in low flow environments (e.g., during base flow). In this work, we advance the knowledge of sediment reworking process by studying its impact on hyporheic exchange flows in streambeds with fine sediment deposits. Laboratory experiments are conducted in re‐circulating flumes following a control (only fine sediments) and treatment‐ (fine sediments + organisms) based design. The experiments involve studying the interaction of model organisms (Lumbriculus variegatus) with fine sediment (clay) deposits, and its subsequent influence on hyporheic flow regime in homogenous streambeds with fine sand, coarse sand, and gravel as substrate sediments. We observe that model organisms burrowed extensively into the fine sediment layer, mixed the clay particles with underlying grains, and eventually exposed the substrate sediments in the treatment flumes. Consequently, the treatment flumes exhibited greater solute penetration depth, shorter residence times, and higher hyporheic exchange flux compared to their respective control flumes. The results also suggest that the modification of hyporheic exchange flows depends on the overall reworking of the beds that is, the interaction of organisms with both substrate material and deposited fine sediments. It is critical to comprehend the influence of streambed inhabitants on mass and energy exchange across the sediment‐water interface as it has implications on the overall quality of both stream and groundwater.
Estimating Spatially Explicit Irrigation Water Use Based on Remotely Sensed Evapotranspiration and Modeled Root Zone Soil Moisture
Authors: Zhang Caijin , Long Di
Published: December 2021

Estimation of irrigation water use (IWU) is critical to assessing water use efficiency and optimizing water resource allocation. However, diversity in irrigation scheduling, irrigation system, and crop type has imposed restrictions on deriving the accurate spatial distribution of IWU. Existing approaches of deriving IWU may have large uncertainty, due mostly to methodological limitations, inadequate inputs, and the mismatch in spatiotemporal scale between IWU estimates and in situ counterparts. Remote sensing has the potential to provide valuable information on moisture transport, which could unravel water consumption by crops. First, we developed a robust relationship between root zone soil moisture (RZSM) and the ratio of actual evapotranspiration (ETa) to reference ET from the land components of European ReAnalysis‐5 (ERA5L) without an irrigation module across the Contiguous United States (CONUS). Second, RZSM under irrigation was derived from the developed relationship and remotely sensed ETa from the operational Simplified Surface Energy Balance (SSEBop) model during 2000–2020. Third, IWU over the two decades was derived based on increases in RZSM and ETa due to irrigation using remotely sensed and model‐based variables, along with our derived formulas considering groundwater recharge originating from irrigation. The IWU estimates were fairly reliable compared with reported IWU from the Farm and Ranch Irrigation Survey at the state‐level in four years, with the coefficient of determination ranging from 0.74 to 0.84, root mean square error ranging from 1.90 to 2.33 km3/yr, and bias ranging from −0.11 to 0.15 km3/yr. Integration of remotely sensed ETa with ERA5L output resulted in IWU estimates of much higher accuracy than published studies. The IWU estimates across the CONUS reflected an increasing trend (∼2.71 km3/yr2) during 2000–2007 but a decreasing trend (∼0.90 km3/yr2) during 2008–2020, due to efficient irrigation practices and increased precipitation.
Comprehensive transcriptomic characterization reveals core genes and module associated with immunological changes via 1619 samples of brain glioma
Authors: Zhang Ying , Ma Wenping , Fan Wenhua , Ren Changyuan , Xu Jianbao , Zeng Fan , Bao Zhaoshi , Jiang Tao , Zhao Zheng
Published: December 2021

Glioma is the most common primary malignant brain tumor with limited treatment options and poor prognosis. To investigate the potential relationships between transcriptional characteristics and clinical phenotypes, we applied weighted gene co-expression network analysis (WGCNA) to construct a free-scale gene co-expression network yielding four modules in gliomas. Turquoise and yellow modules were positively correlated with the most malignant glioma subtype (IDH-wildtype glioblastomas). Of them, genes in turquoise module were mainly involved in immune-related terms and were regulated by NFKB1, RELA, SP1, STAT1 and STAT3. Meanwhile, genes in yellow module mainly participated in cell-cycle and division processes and were regulated by E2F1, TP53, E2F4, YBX1 and E2F3. Furthermore, 14 genes in turquoise module were screened as hub genes. Among them, five prognostic hub genes (TNFRSF1B, LAIR1, TYROBP, VAMP8, and FCGR2A) were selected to construct a prognostic risk score model via LASSO method. The risk score of this immune-related gene signature is associated with clinical features, malignant phenotype, and somatic alterations. Moreover, this signature showed an accurate prediction of prognosis across different clinical and pathological subgroups in three independent datasets including 1619 samples. Our results showed that the high-risk group was characterized by active immune-related activities while the low-risk group enriched in neurophysiological-related pathway. Importantly, the high-risk score of our immune signature predicts an enrichment of glioma-associated microglia/macrophages and less response to immune checkpoint blockade (ICB) therapy in gliomas. This study not only provides new insights into the molecular pathogenesis of glioma, but may also help optimize the immunotherapies for glioma patients.
Rab35 and glucocorticoids regulate APP and BACE1 trafficking to modulate Aβ production
Authors: Zhuravleva Viktoriya , Vaz-Silva João , Zhu Mei , Gomes Patricia , Silva Joana M. , Sousa Nuno , Sotiropoulos Ioannis , Waites Clarissa L.
Published: December 2021

Chronic stress and elevated glucocorticoids (GCs), the major stress hormones, are risk factors for Alzheimer’s disease (AD) and promote AD pathomechanisms, including overproduction of toxic amyloid-β (Aβ) peptides and intraneuronal accumulation of hyperphosphorylated Tau protein. The latter is linked to downregulation of the small GTPase Rab35, which mediates Tau degradation via the endolysosomal pathway. Whether Rab35 is also involved in Aβ overproduction remains an open question. Here, we find that hippocampal Rab35 levels are decreased not only by stress/GC but also by aging, another AD risk factor. Moreover, we show that Rab35 negatively regulates Aβ production by sorting amyloid precursor protein (APP) and β-secretase (BACE1) out of the endosomal network, where they interact to produce Aβ. Interestingly, Rab35 coordinates distinct intracellular trafficking steps for BACE1 and APP, mediated by its effectors OCRL and ACAP2, respectively. Finally, we demonstrate that Rab35 overexpression prevents the amyloidogenic trafficking of APP and BACE1 induced by high GC levels. These studies identify Rab35 as a key regulator of APP processing and suggest that its downregulation may contribute to stress-related and AD-related amyloidogenesis.
Proactive and reactive accumulation-to-bound processes compete during perceptual decisions
Authors: Hernández-Navarro Lluís , Hermoso-Mendizabal Ainhoa , Duque Daniel , de la Rocha Jaime , Hyafil Alexandre
Published: December 2021

Standard models of perceptual decision-making postulate that a response is triggered in reaction to stimulus presentation when the accumulated stimulus evidence reaches a decision threshold. This framework excludes however the possibility that informed responses are generated proactively at a time independent of stimulus. Here, we find that, in a free reaction time auditory task in rats, reactive and proactive responses coexist, suggesting that choice selection and motor initiation, commonly viewed as serial processes, are decoupled in general. We capture this behavior by a novel model in which proactive and reactive responses are triggered whenever either of two competing processes, respectively Action Initiation or Evidence Accumulation, reaches a bound. In both types of response, the choice is ultimately informed by the Evidence Accumulation process. The Action Initiation process readily explains premature responses, contributes to urgency effects at long reaction times and mediates the slowing of the responses as animals get satiated and tired during sessions. Moreover, it successfully predicts reaction time distributions when the stimulus was either delayed, advanced or omitted. Overall, these results fundamentally extend standard models of evidence accumulation in decision making by showing that proactive and reactive processes compete for the generation of responses.
Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling
Authors: Coyote-Maestas Willow , Nedrud David , Suma Antonio , He Yungui , Matreyek Kenneth A. , Fowler Douglas M. , Carnevale Vincenzo , Myers Chad L. , Schmidt Daniel
Published: December 2021

Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions.
Single-cell analysis identifies a key role for Hhip in murine coronal suture development
Authors: Holmes Greg , Gonzalez-Reiche Ana S. , Saturne Madrikha , Motch Perrine Susan M. , Zhou Xianxiao , Borges Ana C. , Shewale Bhavana , Richtsmeier Joan T. , Zhang Bin , van Bakel Harm , Jabs Ethylin Wang
Published: December 2021

Craniofacial development depends on formation and maintenance of sutures between bones of the skull. In sutures, growth occurs at osteogenic fronts along the edge of each bone, and suture mesenchyme separates adjacent bones. Here, we perform single-cell RNA-seq analysis of the embryonic, wild type murine coronal suture to define its population structure. Seven populations at E16.5 and nine at E18.5 comprise the suture mesenchyme, osteogenic cells, and associated populations. Expression ofHhip, an inhibitor of hedgehog signaling, marks a mesenchymal population distinct from those of other neurocranial sutures. Tracing of the neonatalHhip-expressing population shows that descendant cells persist in the coronal suture and contribute to calvarial bone growth. InHhip−/−coronal sutures at E18.5, the osteogenic fronts are closely apposed and the suture mesenchyme is depleted with increased hedgehog signaling compared to those of the wild type. Collectively, these data demonstrate thatHhipis required for normal coronal suture development.
Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – targeting P-pocket by fragment screening
Authors: Singh Abhimanyu K. , Martinez Sergio E. , Gu Weijie , Nguyen Hoai , Schols Dominique , Herdewijn Piet , De Jonghe Steven , Das Kalyan
Published: December 2021

HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3’-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography that identifies two leads that bind the P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized, two of which show noticeable RT inhibition. An engineered RT/DNA aptamer complex could trap the transient P-pocket in solution, and structures of the RT/DNA complex were determined in the presence of an inhibitory fragment. A synthesized analog bound at P-pocket is further analyzed by single-particle cryo-EM. Identification of the P-pocket within HIV RT and the developed structure-based platform provide an opportunity for the design new types of polymerase inhibitors.
GPR180 is a component of TGFβ signalling that promotes thermogenic adipocyte function and mediates the metabolic effects of the adipocyte-secreted factor CTHRC1
Authors: Balazova Lucia , Balaz Miroslav , Horvath Carla , Horváth Áron , Moser Caroline , Kovanicova Zuzana , Ghosh Adhideb , Ghoshdastider Umesh , Efthymiou Vissarion , Kiehlmann Elke , Sun Wenfei , Dong Hua , Ding Lianggong , Amri Ez-Zoubir , Nuutila Pirjo , Virtanen Kirsi A. , Niemi Tarja , Ukropcova Barbara , Ukropec Jozef , Pelczar Pawel , Lamla Thorsten , Hamilton Bradford , Neubauer Heike , Wolfrum Christian
Published: December 2021

Activation of thermogenic brown and beige adipocytes is considered as a strategy to improve metabolic control. Here, we identify GPR180 as a receptor regulating brown and beige adipocyte function and whole-body glucose homeostasis, whose expression in humans is associated with improved metabolic control. We demonstrate that GPR180 is not a GPCR but a component of the TGFβ signalling pathway and regulates the activity of the TGFβ receptor complex through SMAD3 phosphorylation. In addition, using genetic and pharmacological tools, we provide evidence that GPR180 is required to manifest Collagen triple helix repeat containing 1 (CTHRC1) action to regulate brown and beige adipocyte activity and glucose homeostasis. In this work, we show that CTHRC1/GPR180 signalling integrates into the TGFβ signalling as an alternative axis to fine-tune and achieve low-grade activation of the pathway to prevent pathophysiological response while contributing to control of glucose and energy metabolism.
Changing impacts of Alaska-Aleutian subduction zone tsunamis in California under future sea-level rise
Authors: Dura Tina , Garner Andra J. , Weiss Robert , Kopp Robert E. , Engelhart Simon E. , Witter Robert C. , Briggs Richard W. , Mueller Charles S. , Nelson Alan R. , Horton Benjamin P.
Published: December 2021

The amplification of coastal hazards such as distant-source tsunamis under future relative sea-level rise (RSLR) is poorly constrained. In southern California, the Alaska-Aleutian subduction zone has been identified as an earthquake source region of particular concern for a worst-case scenario distant-source tsunami. Here, we explore how RSLR over the next century will influence future maximum nearshore tsunami heights (MNTH) at the Ports of Los Angeles and Long Beach. Earthquake and tsunami modeling combined with local probabilistic RSLR projections show the increased potential for more frequent, relatively low magnitude earthquakes to produce distant-source tsunamis that exceed historically observed MNTH. By 2100, under RSLR projections for a high-emissions representative concentration pathway (RCP8.5), the earthquake magnitude required to produce >1 m MNTH falls from ~Mw9.1 (required today) to Mw8.0, a magnitude that is ~6.7 times more frequent along the Alaska-Aleutian subduction zone.
Optogenetic relaxation of actomyosin contractility uncovers mechanistic roles of cortical tension during cytokinesis
Authors: Yamamoto Kei , Miura Haruko , Ishida Motohiko , Mii Yusuke , Kinoshita Noriyuki , Takada Shinji , Ueno Naoto , Sawai Satoshi , Kondo Yohei , Aoki Kazuhiro
Published: December 2021

Actomyosin contractility generated cooperatively by nonmuscle myosin II and actin filaments plays essential roles in a wide range of biological processes, such as cell motility, cytokinesis, and tissue morphogenesis. However, subcellular dynamics of actomyosin contractility underlying such processes remains elusive. Here, we demonstrate an optogenetic method to induce relaxation of actomyosin contractility at the subcellular level. The system, named OptoMYPT, combines a protein phosphatase 1c (PP1c)-binding domain of MYPT1 with an optogenetic dimerizer, so that it allows light-dependent recruitment of endogenous PP1c to the plasma membrane. Blue-light illumination is sufficient to induce dephosphorylation of myosin regulatory light chains and a decrease in actomyosin contractile force in mammalian cells and Xenopus embryos. The OptoMYPT system is further employed to understand the mechanics of actomyosin-based cortical tension and contractile ring tension during cytokinesis. We find that the relaxation of cortical tension at both poles by OptoMYPT accelerated the furrow ingression rate, revealing that the cortical tension substantially antagonizes constriction of the cleavage furrow. Based on these results, the OptoMYPT system provides opportunities to understand cellular and tissue mechanics.
Quantifying uncertainty in aggregated climate change risk assessments
Authors: Harrington Luke J. , Schleussner Carl-Friedrich , Otto Friederike E. L.
Published: December 2021

High-level assessments of climate change impacts aggregate multiple perils into a common framework. This requires incorporating multiple dimensions of uncertainty. Here we propose a methodology to transparently assess these uncertainties within the ‘Reasons for Concern’ framework, using extreme heat as a case study. We quantitatively discriminate multiple dimensions of uncertainty, including future vulnerability and exposure to changing climate hazards. High risks from extreme heat materialise after 1.5–2 °C and very high risks between 2–3.5 °C of warming. Risks emerge earlier if global assessments were based on national risk thresholds, underscoring the need for stringent mitigation to limit future extreme heat risks.