bluuebunny/crossref_metadata_2025 huggingface dataset:
Immersion graded index optics: theory, design, and prototypes
Authors: Vaidya Nina , Solgaard Olav
Published: June 2022

Immersion 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

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

Previous 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

Clinical 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

Lateral 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

Membrane 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

Rickettsia 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

Electrical 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

Cold 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

Heparan 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

Activity 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

Studies 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

Human 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

Demersal 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

Cellular 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.
A unifying physically meaningful relativistic action
Authors: Friedman Yaakov
Published: June 2022

The motion of an object under the influence of force fields and/or media is described by means of a world-line with least action in its influenced spacetime. For any spacetime point x and a four-vector u, measured in the frame of an inertial observer, a unifying and physically meaningful action function L(x, u) generating the action is defined. To ensure independence of the observer and of the parametrization on the world-line, L(x, u) must be Lorentz invariant and positive homogeneous of order 1 in u. The simplest such L(x, u) depends on two four-potentials. In most cases, these potentials can be defined directly from the sources of the fields without the need for field equations. The unified dynamics equation resulting from this action, properly describes the motion in any electromagnetic field, in any static gravitational field, in a combined electromagnetic and gravitational field, as well as the propagation of light and charges in isotropic media.
Individuals of high socioeconomic status are altruistic in sharing money but egoistic in sharing time
Authors: Liebe Ulf , Schwitter Nicole , Tutić Andreas
Published: June 2022

The questions of whether and how socioeconomic status (SES) predicts prosocial behavior have sparked an interest from different disciplines, yet experimental evidence is inconclusive. We embedded two types of dictator games in a web survey with 7772 participants from Germany, Poland, Sweden, and the US. Each participant was asked to split a sum of money and a fixed amount of time between themself and a recipient. While higher-SES individuals are more generous than lower-SES individuals in the money game, they are more egoistic in the time game. In addition, the SES of the recipient matters more in the money game than in the time game. These results point towards the relevancy of a situationally contingent social norm of redistribution in studying the relationship between SES and prosocial behavior.
A hands-free stool sampling system for monitoring intestinal health and disease
Authors: Grego Sonia , Welling Claire M. , Miller Graham H. , Coggan Peter F. , Sellgren Katelyn L. , Hawkins Brian T. , Ginsburg Geoffrey S. , Ruiz Jose R. , Fisher Deborah A. , Stoner Brian R.
Published: June 2022

Analysis of stool offers simple, non-invasive monitoring for many gastrointestinal (GI) diseases and access to the gut microbiome, however adherence to stool sampling protocols remains a major challenge because of the prevalent dislike of handling one’s feces. We present a technology that enables individual stool specimen collection from toilet wastewater for fecal protein and molecular assay. Human stool specimens and a benchtop test platform integrated with a commercial toilet were used to demonstrate reliable specimen collection over a wide range of stool consistencies by solid/liquid separation followed by spray-erosion. The obtained fecal suspensions were used to perform occult blood tests for GI cancer screening and for microbiome 16S rRNA analysis. Using occult blood home test kits, we found overall 90% agreement with standard sampling, 96% sensitivity and 86% specificity. Microbiome analysis revealed no significant difference in within-sample species diversity compared to standard sampling and specimen cross-contamination was below the detection limit of the assay. Furthermore, we report on the use of an analogue turbidity sensor to assess in real time loose stools for tracking of diarrhea. Implementation of this technology in residential settings will improve the quality of GI healthcare by facilitating increased adherence to routine stool monitoring.
A unique antigen against SARS-CoV-2, Acinetobacter baumannii, and Pseudomonas aeruginosa
Authors: Rahbar Mohammad Reza , Mubarak Shaden M. H. , Hessami Anahita , Khalesi Bahman , Pourzardosht Navid , Khalili Saeed , Zanoos Kobra Ahmadi , Jahangiri Abolfazl
Published: June 2022

The recent outbreak of COVID-19 has increased hospital admissions, which could elevate the risk of nosocomial infections, such asA. baumanniiandP. aeruginosainfections. Although effective vaccines have been developed against SARS-CoV-2, no approved treatment option is still available against antimicrobial-resistant strains ofA. baumanniiandP. aeruginosa.In the current study, an all-in-one antigen was designed based on an innovative, state-of-the-art strategy. In this regard, experimentally validated linear epitopes of spike protein (SARS-CoV-2), OmpA (A. baumannii), and OprF (P. aeruginosa) were selected to be harbored by mature OmpA as a scaffold. The selected epitopes were used to replace the loops and turns of the barrel domain in OmpA; OprF311–341replaced the most similar sequence within the OmpA, and three validated epitopes of OmpA were retained intact. The obtained antigen encompasses five antigenic peptides of spike protein, which are involved in SARS-CoV-2 pathogenicity. One of these epitopes, viz. QTQTNSPRRARSV could trigger antibodies preventing super-antigenic characteristics of spike and alleviating probable autoimmune responses. The designed antigen could raise antibodies neutralizing emerging variants of SARS-CoV-2 since at least two epitopes are consensus. In conclusion, the designed antigen is expected to raise protective antibodies against SARS-CoV-2,A. baumannii,andP. aeruginosa.
Classification of the plant-associated lifestyle of Pseudomonas strains using genome properties and machine learning
Authors: Poncheewin Wasin , van Diepeningen Anne D. , van der Lee Theo A. J. , Suarez-Diez Maria , Schaap Peter J.
Published: June 2022

The rhizosphere, the region of soil surrounding roots of plants, is colonized by a unique population of Plant Growth Promoting Rhizobacteria (PGPR). Many important PGPR as well as plant pathogens belong to the genus Pseudomonas. There is, however, uncertainty on the divide between beneficial and pathogenic strains as previously thought to be signifying genomic features have limited power to separate these strains. Here we used the Genome properties (GP) common biological pathways annotation system and Machine Learning (ML) to establish the relationship between the genome wide GP composition and the plant-associated lifestyle of 91 Pseudomonas strains isolated from the rhizosphere and the phyllosphere representing both plant-associated phenotypes. GP enrichment analysis, Random Forest model fitting and feature selection revealed 28 discriminating features. A test set of 75 new strains confirmed the importance of the selected features for classification. The results suggest that GP annotations provide a promising computational tool to better classify the plant-associated lifestyle.
Acute kidney injury secondary to urinary tract infection in kidney transplant recipients
Authors: Królicki Tomasz , Bardowska Klaudia , Kudla Tobiasz , Królicka Anna , Letachowicz Krzysztof , Mazanowska Oktawia , Krajewski Wojciech , Poznański Paweł , Krajewska Magdalena , Kamińska Dorota
Published: June 2022

Acute kidney injury (AKI) in kidney transplant recipients (KTRs) is a common, yet poorly investigated, complication of urinary tract infections (UTI) and urosepsis. A retrospective comparative analysis was performed, recruiting 101 KTRs with urosepsis, 100 KTRs with UTI, and 100 KTRs without history of UTI or sepsis. The incidences of AKI in the urosepsis and UTI groups were 75.2% and 41%, respectively. The urosepsis group has also presented with a significantly higher prevalence of AKI stage 2 and 3 than the UTI group. The rates of recovery from AKI stages 1, 2 and 3, were 75,6%, 55% and 26.1%, respectively. Factors independently associated with renal recovery from AKI were: AKI severity grade (AKI stage 2 with OR = 0.25 and AKI stage 3 with OR = 0.1), transfusion of red blood cells (RBC) (OR = 0.22), and the use of steroid bolus in the acute phase of treatment (OR = 4). The septic status (urosepsis vs UTI) did not influence the rates of renal recovery from AKI after adjustment for the remaining variables. The dominant cause of RBC transfusions in the whole population was upper GI-bleeding. In multivariable analyses, the occurrence of AKI was also independently associated with a greater decline of eGFR at 1-year post-discharge and with a greater risk of graft loss. In KTRs with both urosepsis and UTI, the occurrence of AKI portends poor transplantation outcomes. The local transfusion policy, modulation of immunosuppression and stress ulcer prophylaxis (which is not routinely administered in KTRs) in the acute setting may be modifiable factors that significantly impact long-term transplantation outcomes.
TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq
Authors: Shichino Shigeyuki , Ueha Satoshi , Hashimoto Shinichi , Ogawa Tatsuro , Aoki Hiroyasu , Wu Bin , Chen Chang-Yu , Kitabatake Masahiro , Ouji-Sageshima Noriko , Sawabata Noriyoshi , Kawaguchi Takeshi , Okayama Toshitugu , Sugihara Eiji , Hontsu Shigeto , Ito Toshihiro , Iwata Yasunori , Wada Takashi , Ikeo Kazuho , Sato Taka-Aki , Matsushima Kouji
Published: June 2022

Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell–cell interaction networks from scRNA-seq data. However, droplet- and plate-based scRNA-seq techniques have cell sampling bias that could affect the cell composition of scRNA-seq datasets. Here we developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform. TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell–cell interactions and expression of growth factors/interleukins in cell subsets than 10X Chromium v2 and Smart-seq2. Expanding TAS-Seq application will improve understanding and atlas construction of lung biology at the single-cell level.
Molecular insights into intra-complex signal transmission during stressosome activation
Authors: Miksys Algirdas , Fu Lifei , Madej M. Gregor , Guerreiro Duarte N. , Kaltwasser Susann , Conway Maria , Ejder Sema , Bruckmann Astrid , Marles-Wright Jon , Lewis Richard J. , O’Byrne Conor , Pané-Farré Jan , Ziegler Christine
Published: June 2022

The stressosome is a pseudo-icosahedral megadalton bacterial stress-sensing protein complex consisting of several copies of two STAS-domain proteins, RsbR and RsbS, and the kinase RsbT. Upon perception of environmental stress multiple copies of RsbT are released from the surface of the stressosome. Free RsbT activates downstream proteins to elicit a global cellular response, such as the activation of the general stress response in Gram-positive bacteria. The molecular events triggering RsbT release from the stressosome surface remain poorly understood. Here we present the map of Listeria innocua RsbR1/RsbS complex at resolutions of 3.45 Å for the STAS domain core in icosahedral symmetry and of 3.87 Å for the STAS domain and N-terminal sensors in D2 symmetry, respectively. The structure reveals a conformational change in the STAS domain linked to phosphorylation in RsbR. Docking studies indicate that allosteric RsbT binding to the conformationally flexible N-terminal sensor domain of RsbR affects the affinity of RsbS towards RsbT. Our results bring to focus the molecular events within the stressosome complex and further our understanding of this ubiquitous signaling hub.
Discovery of the deep-sea NEOM Brine Pools in the Gulf of Aqaba, Red Sea
Authors: Purkis Sam J. , Shernisky Hannah , Swart Peter K. , Sharifi Arash , Oehlert Amanda , Marchese Fabio , Benzoni Francesca , Chimienti Giovanni , Duchâtellier Gaëlle , Klaus James , Eberli Gregor P. , Peterson Larry , Craig Andrew , Rodrigue Mattie , Titschack Jürgen , Kolodziej Graham , Abdulla Ameer
Published: June 2022

Deep-sea brine pools represent hypersaline environments famed for their extremophile microbes. With anoxia entirely excluding bioturbating megafauna, brine pools are also conducive to the pristine preservation of sedimentary sequences. Here we use bathymetric and geophysical observations to locate a complex of brine pools in the Gulf of Aqaba consisting of one 10,000 m2pool and three minor pools of less than 10 m2. We further conduct sediment coring and direct sampling of the brine to confirm the sedimentary and environmental characteristics of these pools. We find that the main pool preserves a stratigraphy which spans at least 1200 years and contains a combination of turbidites, likely resulting from flashfloods and local seismicity, and tsunamigenic terrestrial sediment. The NEOM Brine Pools, as we name them, extend the known geographical range of Red Sea brine pools, and represent a unique preservational environment for the sedimentary signals of regional climatic and tectonic events.
Testing and isolation to prevent overloaded healthcare facilities and reduce death rates in the SARS-CoV-2 pandemic in Italy
Authors: Bandyopadhyay Arnab , Schips Marta , Mitra Tanmay , Khailaie Sahamoddin , Binder Sebastian C. , Meyer-Hermann Michael
Published: June 2022

Background

During the first wave of COVID-19, hospital and intensive care unit beds got overwhelmed in Italy leading to an increased death burden. Based on data from Italian regions, we disentangled the impact of various factors contributing to the bottleneck situation of healthcare facilities, not well addressed in classical SEIR-like models. A particular emphasis was set on the undetected fraction (dark figure), on the dynamically changing hospital capacity, and on different testing, contact tracing, quarantine strategies.

Methods

We first estimated the dark figure for different Italian regions. Using parameter estimates from literature and, alternatively, with parameters derived from a fit to the initial phase of COVID-19 spread, the model was optimized to fit data (infected, hospitalized, ICU, dead) published by the Italian Civil Protection.

Results

We show that testing influenced the infection dynamics by isolation of newly detected cases and subsequent interruption of infection chains. The time-varying reproduction number (Rt) in high testing regions decreased to <1 earlier compared to the low testing regions. While an early test and isolate (TI) scenario resulted in up to ~31% peak reduction of hospital occupancy, the late TI scenario resulted in an overwhelmed healthcare system.

Conclusions

An early TI strategy would have decreased the overall hospital usage drastically and, hence, death toll (∼34% reduction in Lombardia) and could have mitigated the lack of healthcare facilities in the course of the pandemic, but it would not have kept the hospitalization amount within the pre-pandemic hospital limit.
Enzyme-active liquid coacervate microdroplets as artificial membraneless organelles for intracellular ROS scavenging
Authors: Chen Yufeng , Yuan Min , Zhang Yanwen , Zhou Shaohong , Wang Kemin , Wu Zhenjun , Liu Jianbo
Published: June 2022

Catalase-containing coacervate microdroplets, developed as artificial membraneless organelles with unique liquid compartments, were integrated into living cells to scavenge intracellular massive reactive oxygen species and recover cell viability.
Size effect of Ru particles on the self-reforming-driven hydrogenolysis of a lignin model compound
Authors: Guo Zhiruo , Li Lingxiao , Guo Yong , Liu Xiaohui , Wang Yanqin
Published: June 2022

The size effect of Ru/NiAl2O4 catalysts on the self-reforming-driven hydrogenolysis of a lignin model compound is investigated.
Glycopeptoid nanospheres: glycosylation-induced coacervation of poly(sarcosine)
Authors: Okuno Yota , Nishimura Tomoki , Sasaki Yoshihiro , Akiyoshi Kazunari
Published: June 2022

Conjugation of maltopentaose to water-soluble homo-poly(sarcosine) induced self-association and formed nanospheres (−150 nm) in water although homo-poly(sarcosine) was water-soluble and did not form any aggregates.
Microporous carbon in the selective electro-oxidation of molecular biomarkers: uric acid, ascorbic acid, and dopamine
Authors: Rattanaumpa Tidapa , Maensiri Santi , Ngamchuea Kamonwad
Published: June 2022

Herein, we demonstrate the superior electrocatalytic activities of microporous carbon in the oxidation of three molecular biomarkers, ascorbic acid (AA), dopamine (DA), and uric acid (UA), which are co-present in biological fluids.
From a Möbius-aromatic interlocked Mn2B10H10 wheel to the metal-doped boranaphthalenes M2@B10H8 and M2B5 2D-sheets (M = Mn and Fe): a molecules to materials continuum using DFT studies
Authors: Ghorai Sagar , Jemmis Eluvathingal D.
Published: June 2022

The design of (1) Möbius aromatic interlocked boron wheel Mn2B10H10, (2) Hückel aromatic boron analogs of naphthalene (M2@B10H8; M = Mn and Fe), and (3) metal boride monolayers (FeB5 and Fe2B5), creating a molecules to materials continuum.
N-Cyanorhodamines: cell-permeant, photostable and bathochromically shifted analogues of fluoresceins
Authors: Heynck Lukas , Matthias Jessica , Bossi Mariano L. , Butkevich Alexey N. , Hell Stefan W.
Published: June 2022

N-Cyanorhodamines – photostable, cell-permeant analogues of fluoresceins – provide fast labelling kinetics with the HaloTag protein and background-free images in multicolour super-resolution microscopy.
Changing charge transfer mode with cobalt–molybdenum bimetallic atomic pairs for enhanced nitrogen fixation
Authors: Li Xin , Liu Jin , Zhang Yizhen , Leung Michael K. H.
Published: June 2022

An electrocatalyst based on atomically dispersed Co–Mo pairs anchored on N-doped carbon frameworks (Co–Mo-SA/NC) successfully enhances nitrogen fixation by “donation–donation” charge transfer mode and modification of the d-band center.
Phosphorus-triggered activation of PdPb nanoflowers for enhanced oxygen reduction electrocatalysis
Authors: Wang Ziqiang , Tian Pengjun , Zhang Hugang , Deng Kai , Yu Hongjie , Wang Xin , Xu You , Wang Hongjing , Wang Liang
Published: June 2022

We present a one-pot wet-chemical pathway to synthesize P-doped PdPb nanoflowers for enhanced oxygen reduction electrocatalysis in alkaline electrolye.
Solvent co-assembly in lead-free perovskite scintillators for stable and large-area X-ray imaging
Authors: Liu Lulu , Li Weijun , Pan Wanting , Wei Haotong , Yang Bai
Published: June 2022

We report two 0D lead-free perovskite structures co-assembled from solvent molecules. The solvent co-assembled perovskite single-crystal exhibits excellent moisture stability and the wafer shows potential applications in large area X-ray imaging.
Active-matrix micro-light-emitting diode displays driven by monolithically integrated dual-gate oxide thin-film transistors
Authors: Yang Junghoon , Park HyunWoo , Kim Baul , Cho Yong-Hoon , Park Sang-Hee Ko
Published: June 2022

We present the first monolithic fabrication of a-IGZO TFTs on a GaN-based micro-LED array at a low temperature to overcome the weak thermal endurance constraint of the organic planarization layer for high resolution and stable low-cost LED displays.
Double discrete‐time‐switch protocol for SWIPT at the energy harvesting relays: Protocol design and optimization
Authors: Hu Yifan , Zhu Dong
Published: June 2022

Here, the energy harvesting (EH) relaying node which needs to complete the simultaneous wireless information and power transfer (SWIPT) is considered. The EH relaying node uses the EH technique to get the energy supply and uses the directional transmission to improve the performance of SWIPT. The double discrete‐time‐switch (D‐DTS) based energy harvesting–power transfer–information transmission (EH–PT–IT) protocol is designed. One of the discrete‐time‐switch (DTS) controls the receiver of the EH relaying node and the other controls the transmitter. The performance is analysed by considering the average information rate and the average transferred power. The expressions of the average information rate and the average transferred power are derived analytically. The balanced maximization is considered, and the optimal parameters are obtained analytically. The simulations are presented to verify the analytical results and compare the performance. Comparing with previous works, the SWIPT performance using D‐DTS protocol in this work is better.
Pulse width modulation voltage source deadtime effect on partial discharge and lifetime of inverter‐fed motor insulation
Authors: Akram Shakeel , Wang Peng , Meng Pengfei , Montanari Gian Carlo , Malik Farhan Hameed
Published: June 2022

This paper analyses the impact of square wave pulse voltage deadtime on the partial discharge (PD) and the lifetime of turn‐to‐turn insulation. A bipolar repetitive pulse voltage with a deadtime of 0–10 μs is produced using double half‐bridge solid‐state switches having push–pull technology controlled by a field‐programmable gate array. The mechanism of the discharge process at rising and falling edges of the pulse voltage before and after deadtime is analysed in detail. The discharge amplitude and PD probability at the rising/falling edges of the voltage waveform increase as the deadtime increases from 0 to 10 μs due to the remanent charges. The number of PD and their intensity is higher at the first rising/falling edges of pulse voltage as compared to the second rising/falling edges for all deadtimes 0–10 μs. As the deadtime increases beyond 2 μs, the number of PDs increases and concentrates at a specific phase angle of rising/falling edges. These localise discharges degrade the insulation material and reduce its lifetime. This study helps to identify the inverter‐fed motor insulation faults due to deadtime. It can provide guidelines to motor insulation designers to determine the limit value of deadtime to compensate PD and ensure the safer operation of such motors.
Review of Grid Codes and Implementation for Wind Farm Frequency Regulation
Authors: Bao Xianwen , Zhang Lirong
Published: June 2022

With the increase of wind power and the construction of UHVDC transmission, the wind turbines must actively participate in the system frequency regulation through inertia response and primary frequency regulation to ensure the safe and stable operation of the power system. However, the wind power penetration rate and the grid structure of each regional power grid are different, so that the corresponding power grid codes are also slightly different. Firstly, this paper introduces the specific requirements of wind power grid guidelines in typical countries and regions, and with reference to the experience of international frequency regulation codes, it puts forward the proposed implementation mode of active support new energy frequency regulation suitable for domestic power grid, and the recommended parameter for wind farm frequency regulation. Secondly, this paper summarizes the frequency modulation implementation schemes of the main wind turbine manufacturers in the world, and demonstrates the potential frequency modulation capability of the wind turbine. Finally, the challenges and realizable solutions of virtual inertia and primary frequency regulation of wind farms are prospected, and some suggestions are given.
Experience and enlightenment of urban waterlogging disaster prevention in foreign countries
Authors: Lu Jifeng , Li Fang , Wang Yingruo
Published: June 2022

As an important type of disaster, urban waterlogging has become a great challenge for urban governance around the world, threatening people’s lives, health and safety and property safety. The United States, Britain, Japan, Singapore and other countries have accumulated rich experience in the prevention and control of urban waterlogging. Foreign countries have strengthened the prevention and control of urban waterlogging disasters mainly in terms of condensing concepts and awareness, improving laws and regulations, paying attention to planning and construction, using scientific and technological means, strengthening knowledge popularization, strengthening risk assessment and early warning, implementing project-driven and active participation of multiple subjects, and achieved certain results. It is of reference and enlightening significance. In terms of the current and future urban waterlogging prevention and control in China, we should continuously improve the concept and awareness of urban waterlogging prevention and control, scientifically and systematically plan and construct the city; comprehensively use various policies and scientific and technological effective means to improve the effectiveness of urban waterlogging prevention; pay attention to waterlogging Risk assessment and disaster early warning work to realize the advancement of waterlogging disaster governance; strengthen knowledge promotion, popularization and multi-subject participation, create a joint force in urban waterlogging prevention and governance, and promote the modernization of urban waterlogging management systems and capabilities.