bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Modeled Hyperspectral Infrared Spectra Against All‐Sky AIRS Observations Using Different Cloud Overlap Schemes
Authors: Le Tianhao , Natraj Vijay , Braverman Amy J. , Yung Yuk L. 
Published: June 2022

AbstractHyperspectral infrared sounding contains information about clouds, which plays an important role in modulating Earth's climate. However, there is a great deal of uncertainty in modeling the radiative effect of clouds due to its complex dependence on various parameters. Therefore, cloudy scenarios are often neglected in retrievals of infrared spectral measurements and in data assimilation. One‐dimensional radiative transfer (RT) models have a limited capability to represent the cloud three‐dimensional multilayer structure. This issue is typically resolved by using a multiple independent column approach, which is computationally demanding. Therefore, it is necessary to find a balance between computational speed and accuracy for infrared RT all‐sky radiance simulations. In this study, we utilize the Community Radiative Transfer Model with four different cloud overlap schemes and compare against observations made by the Atmospheric Infrared Sounder (AIRS) using a statistical metric called the first Wasserstein distance. Our results show that the average cloud overlap scheme performs the best and successfully predicts the overall probability distribution of brightness temperature over nonfrozen oceans for a wide range of wavelengths. The mean absolute differences are less than 0.7 K for 846 selected AIRS channels between 790 cm−1 and 1231 cm−1.
Immersion graded index optics: theory, design, and prototypes
Authors: Vaidya Nina , Solgaard Olav 
Published: June 2022

AbstractImmersion optics enable creation of systems with improved optical concentration and coupling by taking advantage of the fact that the luminance of light is proportional to the square of the refractive index in a lossless optical system. Immersion graded index optical concentrators, that do not need to track the source, are described in terms of theory, simulations, and experiments. We introduce a generalized design guide equation which follows the Pareto function and can be used to create various immersion graded index optics depending on the application requirements of concentration, refractive index, height, and efficiency. We present glass and polymer fabrication techniques for creating broadband transparent graded index materials with large refractive index ranges, (refractive index ratio)2 of ~2, going many fold beyond what is seen in nature or the optics industry. The prototypes demonstrate 3x optical concentration with over 90% efficiency. We report via functional prototypes that graded-index-lens concentrators perform close to the theoretical maximum limit and we introduce simple, inexpensive, design-flexible, and scalable fabrication techniques for their implementation.
Mobile genetic elements used by competing coral microbial populations increase genomic plasticity
Authors: Wang Pengxia , Zhao Yi , Wang Weiquan , Lin Shituan , Tang Kaihao , Liu Tianlang , Wood Thomas K , Wang Xiaoxue 
Published: June 2022

Abstract
Intraspecies diversification and niche adaptation by members of the Vibrio genus, one of the most diverse bacterial genera, is thought to be driven by horizontal gene transfer. However, the intrinsic driving force of Vibrio species diversification is much less explored. Here, by studying two dominant and competing cohabitants of the gastric cavity of corals, we found that a phenotype influencing island (named VPII) in Vibrio alginolyticus was eliminated upon coculturing with Pseudoalteromonas. The loss of VPII reduced the biofilm formation and phage resistance, but activated motility, which may allow V. alginolyticus to expand to other niches. Mechanistically, we discovered that the excision of this island is mediated by the cooperation of two unrelated mobile genetic elements harbored in Pseudoalteromonas spp., an integrative and conjugative element (ICE) and a mobilizable genomic island (MGI). More importantly, these mobile genetic elements are widespread in cohabitating Gram-negative bacteria. Altogether, we discovered a new strategy by which the mobilome is employed by competitors to increase the genomic plasticity of rivals.
An executive function subtype of PTSD with unique neural markers and clinical trajectories
Authors: Jagger-Rickels Audreyana , Rothlein David , Stumps Anna , Evans Travis Clark , Bernstein John , Milberg William , McGlinchey Regina , DeGutis Joseph , Esterman Michael 
Published: June 2022

AbstractPrevious work identified a cognitive subtype of PTSD with impaired executive function (i.e., impaired EF-PTSD subtype) and aberrant resting-state functional connectivity between frontal parietal control (FPCN) and limbic (LN) networks. To better characterize this cognitive subtype of PTSD, this study investigated (1) alterations in specific FPCN and LN subnetworks and (2) chronicity of PTSD symptoms. In a post-9/11 veteran sample (N = 368, 89% male), we identified EF subgroups using a standardized neuropsychological battery and a priori cutoffs for impaired, average, and above-average EF performance. Functional connectivity between two subnetworks of the FPCN and three subnetworks of the LN was assessed using resting-state fMRI (n = 314). PTSD chronicity over a 1–2-year period was assessed using a reliable change index (n = 175). The impaired EF-PTSD subtype had significantly reduced negative functional connectivity between the FPCN subnetwork involved in top-down control of emotion and two LN subnetworks involved in learning/memory and social/emotional processing. This impaired EF-PTSD subtype had relatively chronic PTSD, while those with above-average EF and PTSD displayed greater symptom reduction. Lastly, FPCN-LN subnetworks partially mediated the relationship between EF and PTSD chronicity (n = 121). This study reveals (1) that an impaired EF-PTSD subtype has a specific pattern of FPCN-LN subnetwork connectivity, (2) a novel above-average EF-PTSD subtype displays reduced PTSD chronicity, and (3) both cognitive and neural functioning predict PTSD chronicity. The results indicate a need to investigate how individuals with this impaired EF-PTSD subtype respond to treatment, and how they might benefit from personalized and novel approaches that target these neurocognitive systems.
Common genetic variation associated with Mendelian disease severity revealed through cryptic phenotype analysis
Authors: Blair David R. , Hoffmann Thomas J. , Shieh Joseph T. 
Published: June 2022

AbstractClinical heterogeneity is common in Mendelian disease, but small sample sizes make it difficult to identify specific contributing factors. However, if a disease represents the severely affected extreme of a spectrum of phenotypic variation, then modifier effects may be apparent within a larger subset of the population. Analyses that take advantage of this full spectrum could have substantially increased power. To test this, we developed cryptic phenotype analysis, a model-based approach that infers quantitative traits that capture disease-related phenotypic variability using qualitative symptom data. By applying this approach to 50 Mendelian diseases in two cohorts, we identify traits that reliably quantify disease severity. We then conduct genome-wide association analyses for five of the inferred cryptic phenotypes, uncovering common variation that is predictive of Mendelian disease-related diagnoses and outcomes. Overall, this study highlights the utility of computationally-derived phenotypes and biobank-scale cohorts for investigating the complex genetic architecture of Mendelian diseases.
Groundwater discharge as a driver of methane emissions from Arctic lakes
Authors: Olid Carolina , Rodellas Valentí , Rocher-Ros Gerard , Garcia-Orellana Jordi , Diego-Feliu Marc , Alorda-Kleinglass Aaron , Bastviken David , Karlsson Jan 
Published: June 2022

AbstractLateral CH4 inputs to Arctic lakes through groundwater discharge could be substantial and constitute an important pathway that links CH4 production in thawing permafrost to atmospheric emissions via lakes. Yet, groundwater CH4 inputs and associated drivers are hitherto poorly constrained because their dynamics and spatial variability are largely unknown. Here, we unravel the important role and drivers of groundwater discharge for CH4 emissions from Arctic lakes. Spatial patterns across lakes suggest groundwater inflows are primarily related to lake depth and wetland cover. Groundwater CH4 inputs to lakes are higher in summer than in autumn and are influenced by hydrological (groundwater recharge) and biological drivers (CH4 production). This information on the spatial and temporal patterns on groundwater discharge at high northern latitudes is critical for predicting lake CH4 emissions in the warming Arctic, as rising temperatures, increasing precipitation, and permafrost thawing may further exacerbate groundwater CH4 inputs to lakes.
Molecular mechanics underlying flat-to-round membrane budding in live secretory cells
Authors: Shin Wonchul , Zucker Ben , Kundu Nidhi , Lee Sung Hoon , Shi Bo , Chan Chung Yu , Guo Xiaoli , Harrison Jonathan T. , Turechek Jaymie Moore , Hinshaw Jenny E. , Kozlov Michael M. , Wu Ling-Gang 
Published: June 2022

AbstractMembrane budding entails forces to transform flat membrane into vesicles essential for cell survival. Accumulated studies have identified coat-proteins (e.g., clathrin) as potential budding factors. However, forces mediating many non-coated membrane buddings remain unclear. By visualizing proteins in mediating endocytic budding in live neuroendocrine cells, performing in vitro protein reconstitution and physical modeling, we discovered how non-coated-membrane budding is mediated: actin filaments and dynamin generate a pulling force transforming flat membrane into Λ-shape; subsequently, dynamin helices surround and constrict Λ-profile’s base, transforming Λ- to Ω-profile, and then constrict Ω-profile’s pore, converting Ω-profiles to vesicles. These mechanisms control budding speed, vesicle size and number, generating diverse endocytic modes differing in these parameters. Their impact is widespread beyond secretory cells, as the unexpectedly powerful functions of dynamin and actin, previously thought to mediate fission and overcome tension, respectively, may contribute to many dynamin/actin-dependent non-coated-membrane buddings, coated-membrane buddings, and other membrane remodeling processes.
A patatin-like phospholipase mediates Rickettsia parkeri escape from host membranes
Authors: Borgo Gina M. , Burke Thomas P. , Tran Cuong J. , Lo Nicholas T. N. , Engström Patrik , Welch Matthew D. 
Published: June 2022

AbstractRickettsia species of the spotted fever group are arthropod-borne obligate intracellular bacteria that can cause mild to severe human disease. These bacteria invade host cells, replicate in the cell cytosol, and spread from cell to cell. To access the host cytosol and avoid immune detection, they escape membrane-bound vacuoles by expressing factors that disrupt host membranes. Here, we show that a patatin-like phospholipase A2 enzyme (Pat1) facilitates Rickettsia parkeri infection by promoting escape from host membranes and cell-cell spread. Pat1 is important for infection in a mouse model and, at the cellular level, is crucial for efficiently escaping from single and double membrane-bound vacuoles into the host cytosol, and for avoiding host galectins that mark damaged membranes. Pat1 is also important for avoiding host polyubiquitin, preventing recruitment of autophagy receptor p62, and promoting actin-based motility and cell-cell spread.
Third harmonic characterization of antiferromagnetic heterostructures
Authors: Cheng Yang , Cogulu Egecan , Resnick Rachel D. , Michel Justin J. , Statuto Nahuel N. , Kent Andrew D. , Yang Fengyuan 
Published: June 2022

AbstractElectrical switching of antiferromagnets is an exciting recent development in spintronics, which promises active antiferromagnetic devices with high speed and low energy cost. In this emerging field, there is an active debate about the mechanisms of current-driven switching of antiferromagnets. For heavy-metal/ferromagnet systems, harmonic characterization is a powerful tool to quantify current-induced spin-orbit torques and spin Seebeck effect and elucidate current-induced switching. However, harmonic measurement of spin-orbit torques has never been verified in antiferromagnetic heterostructures. Here, we report harmonic measurements in Pt/α-Fe2O3 bilayers, which are explained by our modeling of higher-order harmonic voltages. As compared with ferromagnetic heterostructures where all current-induced effects appear in the second harmonic signals, the damping-like torque and thermally-induced magnetoelastic effect contributions in Pt/α-Fe2O3 emerge in the third harmonic voltage. Our results provide a new path to probe the current-induced magnetization dynamics in antiferromagnets, promoting the application of antiferromagnetic spintronic devices.
Potential long-term habitable conditions on planets with primordial H–He atmospheres
Authors: Mol Lous Marit , Helled Ravit , Mordasini Christoph 
Published: June 2022

AbstractCold super-Earths that retain their primordial, H–He-dominated atmosphere could have surfaces that are warm enough to host liquid water. This would be due to the collision-induced absorption of infrared light by hydrogen, which increases with pressure. However, the long-term potential for habitability of such planets has not been explored yet. Here we investigate the duration of this potential exotic habitability by simulating planets of different core masses, envelope masses and semi-major axes. We find that terrestrial and super-Earth planets with masses of ~1–10 M⊕ can maintain temperate surface conditions up to 5–8 Gyr at radial distances larger than ~2 au. The required envelope masses are ~10−4 M⊕ (which is 2 orders of magnitude more massive than Earth’s) but can be an order of magnitude smaller (when close-in) or larger (when far out). This result suggests that the concept of planetary habitability should be revisited and made more inclusive with respect to the classical definition.
HS3ST2 expression induces the cell autonomous aggregation of tau
Authors: Huynh M. B. , Rebergue N. , Merrick H. , Gomez-Henao W. , Jospin E. , Biard D. S. F. , Papy-Garcia D. 
Published: June 2022

AbstractHeparan sulfates have long been known to intracellularly accumulate in Alzheimer’s disease neurons, where they colocalize with neurofibrillary tangles made of abnormally phosphorylated and aggregated tau protein. However, the reasons and consequences of the heparan sulfates accumulation in the Alzheimer’s cells are not yet well understood. Previously, we showed that the neural heparan sulfate 3-O-sulfotransferase HS3ST2 is critical for the abnormal phosphorylation of tau in Alzheimer's disease-related tauopathy. Using cell models of tauopathy we showed that intracellular 3-O-sulfatated heparan sulfates interact with tau inducing its abnormal phosphorylation. However, it is unknown whether HS3ST2 expression induces the intracellular aggregation of tau in cells. Here, by using replicative pEBV plasmids, we engineered HEK293 cells to stably express HS3ST2 together with human tau carrying or not the P301S mutation. We show that HS3ST2 gain of function induces the cell autonomous aggregation of tau not only in cells expressing tauP301S, but also in cells expressing the wild type tau. Our engineered cells mimicked both the HS intracellular accumulation observed in neurons of Alzheimer’s disease and the tau aggregation characteristic of tauopathy development and evolution. These results give evidence that the neural HS3ST2 plays a critical role in the cell autonomous self-aggregation of tau.
In vivo closed-loop control of a locust’s leg using nerve stimulation
Authors: Zurita Francisco , Del Duca Fulvia , Teshima Tetsuhiko , Hiendlmeier Lukas , Gebhardt Michael , Luksch Harald , Wolfrum Bernhard 
Published: June 2022

AbstractActivity of an innervated tissue can be modulated based on an acquired biomarker through feedback loops. How to convert this biomarker into a meaningful stimulation pattern is still a topic of intensive research. In this article, we present a simple closed-loop mechanism to control the mean angle of a locust’s leg in real time by modulating the frequency of the stimulation on its extensor motor nerve. The nerve is interfaced with a custom-designed cuff electrode and the feedback loop is implemented online with a proportional control algorithm, which runs solely on a microcontroller without the need of an external computer. The results show that the system can be controlled with a single-input, single-output feedback loop. The model described in this article can serve as a primer for young researchers to learn about neural control in biological systems before applying these concepts in advanced systems. We expect that the approach can be advanced to achieve control over more complex movements by increasing the number of recorded biomarkers and selective stimulation units.
Alignment of the attitude of teleoperators with that of a semi-autonomous android
Authors: Kubota Tomonori , Ogawa Kohei , Yoshikawa Yuichiro , Ishiguro Hiroshi 
Published: June 2022

AbstractStudies on social robots that can communicate with humans are increasingly important. In particular, semi-aautonomous robots have shown potential for practical applications in which robot autonomy and human teleoperation are jointly used to accomplish difficult tasks. However, it is unknown how the attitude represented in the autonomous behavior of the robots affects teleoperators. Previous studies reported that when humans play a particular role, their attitudes align with that role. The teleoperators of semi-autonomous robots also play the role given to the robots and may assimilate their autonomous expression. We hypothesized that the attitude of teleoperators may align with that of robots through teleoperation. To verify this, we conducted an experiment with conditions under which a participant operated a part of the body of an android robot that autonomously expressed a preferential attitude toward a painting and a condition under which they did not. Experimental results demonstrated that the preferential attitude of participants who teleoperated the android aligned statistically significantly more with that of the robot in comparison to those who did not teleoperate it, thereby supporting our hypothesis. This finding is novel regarding attitude change in teleoperators of semi-autonomous robots and can support the implementation of effective human-robot collaboration systems.
Effects of human mobility and behavior on disease transmission in a COVID-19 mathematical model
Authors: Gutiérrez-Jara Juan Pablo , Vogt-Geisse Katia , Cabrera Maritza , Córdova-Lepe Fernando , Muñoz-Quezada María Teresa 
Published: June 2022

AbstractHuman interactions and perceptions about health risk are essential to understand the evolution over the course of a pandemic. We present a Susceptible-Exposed-Asymptomatic-Infectious-Recovered-Susceptible mathematical model with quarantine and social-distance-dependent transmission rates, to study COVID-19 dynamics. Human activities are split across different location settings: home, work, school, and elsewhere. Individuals move from home to the other locations at rates dependent on their epidemiological conditions and maintain a social distancing behavior, which varies with their location. We perform simulations and analyze how distinct social behaviors and restrictive measures affect the dynamic of the disease within a population. The model proposed in this study revealed that the main focus on the transmission of COVID-19 is attributed to the “home” location setting, which is understood as family gatherings including relatives and close friends. Limiting encounters at work, school and other locations will only be effective if COVID-19 restrictions occur simultaneously at all those locations and/or contact tracing or social distancing measures are effectively and strictly implemented, especially at the home setting.
Network analysis suggests changes in food web stability produced by bottom trawl fishery in Patagonia
Authors: Funes Manuela , Saravia Leonardo A. , Cordone Georgina , Iribarne Oscar O. , Galván David E. 
Published: June 2022

AbstractDemersal fisheries are one of the top anthropic stressors in marine environments. In the long term, some species are more vulnerable to fishery impacts than others, which can lead to permanent changes on the food web. The trophic relationships between predator and prey constitute the food web and it represents a network of the energy channels in an ecosystem. In turn, the network structure influences ecosystem diversity and stability. The first aim of this study was to describe for the first time the food web of the San Jorge Gulf (Patagonia Argentina) with high resolution, i.e. to the species level when information is available. The San Jorge Gulf was subject to intense fisheries thus our second aim is to analyse the food web structure with and without fishery to evaluate if the bottom-trawl industrial fishery altered the network structure and stability. We used several network metrics like: mean trophic level, omnivory, modularity and quasi-sign stability. We included these metrics because they are related to stability and can be evaluated using predator diets that can weight the links between predators and prey. The network presented 165 species organized in almost five trophic levels. The inclusion of a fishery node adds 69 new trophic links. All weighted and unweighted metrics showed differences between the two networks, reflecting a decrease in stability when fishery was included in the system. Thus, our results suggested a probable change of state of the system. The observed changes in species abundances since the fishery was established, could represent the state change predicted by network analysis. Our results suggests that changes in the stability of food webs can be used to evaluate the impacts of human activity on ecosystems.
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information
Authors: Sia Jayson , Zhang Wei , Jonckheere Edmond , Cook David , Bogdan Paul 
Published: June 2022

AbstractCellular biological networks represent the molecular interactions that shape function of living cells. Uncovering the organization of a biological network requires efficient and accurate algorithms to determine the components, termed communities, underlying specific processes. Detecting functional communities is challenging because reconstructed biological networks are always incomplete due to technical bias and biological complexity, and the evaluation of putative communities is further complicated by a lack of known ground truth. To address these challenges, we developed a geometric-based detection framework based on Ollivier-Ricci curvature to exploit information about network topology to perform community detection from partially observed biological networks. We further improved this approach by integrating knowledge of gene function, termed side information, into the Ollivier-Ricci curvature algorithm to aid in community detection. This approach identified essential conserved and varied biological communities from partially observed Arabidopsis protein interaction datasets better than the previously used methods. We show that Ollivier-Ricci curvature with side information identified an expanded auxin community to include an important protein stability complex, the Cop9 signalosome, consistent with previous reported links to auxin response and root development. The results show that community detection based on Ollivier-Ricci curvature with side information can uncover novel components and novel communities in biological networks, providing novel insight into the organization and function of complex networks.