bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Rapid Numerical Method to Constrain 2D Focused Fluid Flow Rates Along Convergent Margins Using Dense BSR‐Based Temperature Field Data
Authors: Kunath Pascal , Chi Wu‐Cheng , Berndt Christian , Liu Char‐Shine 
Published: June 2021

AbstractEstimates of the sub‐seabed fluid flow rates are important for understanding hydrological budgets, biogeochemical cycles, and physical properties of the sediments. Fluid flow rates and directions, however, are difficult to measure, particularly beneath the seafloor. We developed a rapid method to estimate regional fluid migration rates using an extensive database of seismic reflection profiles taken offshore SW Taiwan. We observe bottom‐simulating reflector (BSR) that deflects toward the seafloor near thrust faults that indicate localized heat flow variations. At these sites, advecting warm pore fluids transport heat to shallower depths and force the BSR shallower. Our 2D steady‐state numerical method quantifies the fluid flow rates required to cause such thermal anomalies. We found that fluid flow rates near the trench of the accretionary wedge range between 0.1 and 16 m3 yr−1 m−1, with slower and faster rates generally associated with slope basin discontinuities and faults, respectively. To evaluate the fluid pattern evolution from subduction to collision, we studied three transects: one along the Manila subduction zone in the south and two in Taiwan's initial collision zone in the north. We quantified the fluid budget and partitioning of fluid flow between focused discharge through faults and diffusive flow through the wedge. Faults in Taiwan's accretionary wedge capture on average 25% of the total dewatering flux in the younger subduction zone and 38.5% in the tectonically mature collision zone. Our method provides estimates of fluid migration rates along convergent plate boundaries, and contributes to our understanding of focused fluid flow processes in many other regions.
The Effect of Resolution on Vertical Heat and Carbon Transports in a Regional Ocean Circulation Model of the Argentine Basin
Authors: Swierczek Stan , Mazloff Matthew R. , Morzfeld Matthias , Russell Joellen L. 
Published: June 2021

AbstractSimulations of the Argentine Basin have large uncertainties associated with quantities such as air‐sea exchanges of heat and carbon in current generation climate models and ocean reanalysis products. This is due to the complex topography, profound undersampling until recent years, and strong currents and mixing of subpolar and subtropical water masses in the basin. Because mixing of water masses is important here, model resolution is hypothesized to play an important role in estimating ocean quantities and determining overall budgets. We construct three regional ocean models with biogeochemistry at 1/3°, 1/6°, and 1/12° resolutions for the year 2017 to investigate heat and carbon dynamics in the region and determine the effect of model resolution on these dynamics. Initial conditions and boundary forcing from BSOSE (the Biogeochemical Southern Ocean State Estimate (Verdy & Mazloff, 2017), https://doi.org/10.1002/2016JC012650) and atmospheric forcing from ERA5 are used. The models are evaluated for accuracy by comparing output to Argo and BGC‐Argo float profiles, BSOSE, and other reanalyses and mapped products. We then quantify the effect of resolution on model upper ocean heat and carbon transport and the associated air‐sea exchanges. We determine that increasing the resolution from 1/3° to 1/12° enhances the upward vertical transport and surface exchanges of heat but causes no significant effect on surface carbon fluxes despite enhancing downward transport of anomalous DIC.
Calving Multiplier Effect Controlled by Melt Undercut Geometry
Authors: Slater D. A. , Benn D. I. , Cowton T. R. , Bassis J. N. , Todd J. A. 
Published: June 2021

AbstractQuantifying the impact of submarine melting on calving is central to understanding the response of marine‐terminating glaciers to ocean forcing. Modeling and observational studies suggest the potential for submarine melting to amplify calving (the calving multiplier effect), but there is little consensus as to under what conditions this occurs. Here, by viewing a marine‐terminating glacier as an elastic beam, we propose an analytical basis for understanding the presence or absence of the calving multiplier effect. We show that as a terminus becomes undercut it becomes more susceptible to both serac failure (calving only of ice that is undercut, driven by vertical imbalance) and rotational failure (full‐thickness calving of ice behind the grounding line, driven by rotational imbalance). By deriving analytical stress thresholds for these two forms of calving, we suggest that the dominant of the two calving styles is determined principally by the shape of melt‐undercutting. Uniform undercutting extending from the bed to the waterline promotes serac failure and no multiplier effect, while glaciers experiencing linear undercutting that is greatest at the bed and zero at the waterline are more likely to experience rotational failure and a multiplier effect. Our study offers a quantitative framework for understanding where and when the calving multiplier effect occurs, and, therefore, a route to parameterizing the effect in ice sheet‐scale models.
Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2
Authors: Roxhed Niclas , Bendes Annika , Dale Matilda , Mattsson Cecilia , Hanke Leo , Dodig-Crnković Tea , Christian Murray , Meineke Birthe , Elsässer Simon , Andréll Juni , Havervall Sebastian , Thålin Charlotte , Eklund Carina , Dillner Joakim , Beck Olof , Thomas Cecilia E. , McInerney Gerald , Hong Mun-Gwan , Murrell Ben , Fredolini Claudia , Schwenk Jochen M. 
Published: June 2021

AbstractSerological testing is essential to curb the consequences of the COVID-19 pandemic. However, most assays are still limited to single analytes and samples collected within healthcare. Thus, we establish a multianalyte and multiplexed approach to reliably profile IgG and IgM levels against several versions of SARS-CoV-2 proteins (S, RBD, N) in home-sampled dried blood spots (DBS). We analyse DBS collected during spring of 2020 from 878 random and undiagnosed individuals from the population in Stockholm, Sweden, and use classification approaches to estimate an accumulated seroprevalence of 12.5% (95% CI: 10.3%–14.7%). This includes 5.4% of the samples being IgG+IgM+ against several SARS-CoV-2 proteins, as well as 2.1% being IgG−IgM+ and 5.0% being IgG+IgM− for the virus’ S protein. Subjects classified as IgG+ for several SARS-CoV-2 proteins report influenza-like symptoms more frequently than those being IgG+ for only the S protein (OR = 6.1; p < 0.001). Among all seropositive cases, 30% are asymptomatic. Our strategy enables an accurate individual-level and multiplexed assessment of antibodies in home-sampled blood, assisting our understanding about the undiagnosed seroprevalence and diversity of the immune response against the coronavirus.
High-resolution light field prints by nanoscale 3D printing
Authors: Chan John You En , Ruan Qifeng , Jiang Menghua , Wang Hongtao , Wang Hao , Zhang Wang , Qiu Cheng-Wei , Yang Joel K. W. 
Published: June 2021

AbstractA light field print (LFP) displays three-dimensional (3D) information to the naked-eye observer under ambient white light illumination. Changing perspectives of a 3D image are seen by the observer from varying angles. However, LFPs appear pixelated due to limited resolution and misalignment between their lenses and colour pixels. A promising solution to create high-resolution LFPs is through the use of advanced nanofabrication techniques. Here, we use two-photon polymerization lithography as a one-step nanoscale 3D printer to directly fabricate LFPs out of transparent resin. This approach produces simultaneously high spatial resolution (29–45 µm) and high angular resolution (~1.6°) images with smooth motion parallax across 15 × 15 views. Notably, the smallest colour pixel consists of only a single nanopillar (~300 nm diameter). Our LFP signifies a step towards hyper-realistic 3D images that can be applied in print media and security tags for high-value goods.
Unravelling cytosolic delivery of cell penetrating peptides with a quantitative endosomal escape assay
Authors: Teo Serena L. Y. , Rennick Joshua J. , Yuen Daniel , Al-Wassiti Hareth , Johnston Angus P. R. , Pouton Colin W. 
Published: June 2021

AbstractCytosolic transport is an essential requirement but a major obstacle to efficient delivery of therapeutic peptides, proteins and nucleic acids. Current understanding of cytosolic delivery mechanisms remains limited due to a significant number of conflicting reports, which are compounded by low sensitivity and indirect assays. To resolve this, we develop a highly sensitive Split Luciferase Endosomal Escape Quantification (SLEEQ) assay to probe mechanisms of cytosolic delivery. We apply SLEEQ to evaluate the cytosolic delivery of a range of widely studied cell-penetrating peptides (CPPs) fused to a model protein. We demonstrate that positively charged CPPs enhance cytosolic delivery as a result of increased non-specific cell membrane association, rather than increased endosomal escape efficiency. These findings transform our current understanding of how CPPs increase cytosolic delivery. SLEEQ is a powerful tool that addresses fundamental questions in intracellular drug delivery and will significantly improve the way materials are engineered to increase therapeutic delivery to the cytosol.
A subterranean adaptive radiation of amphipods in Europe
Authors: Borko Špela , Trontelj Peter , Seehausen Ole , Moškrič Ajda , Fišer Cene 
Published: June 2021

AbstractAdaptive radiations are bursts of evolutionary species diversification that have contributed to much of the species diversity on Earth. An exception is modern Europe, where descendants of ancient adaptive radiations went extinct, and extant adaptive radiations are small, recent and narrowly confined. However, not all legacy of old radiations has been lost. Subterranean environments, which are dark and food-deprived, yet buffered from climate change, have preserved ancient lineages. Here we provide evidence of an entirely subterranean adaptive radiation of the amphipod genusNiphargus, counting hundreds of species. Our modelling of lineage diversification and evolution of morphological and ecological traits using a time-calibrated multilocus phylogeny suggests a major adaptive radiation, comprised of multiple subordinate adaptive radiations. Their spatio-temporal origin coincides with the uplift of carbonate massifs in South-Eastern Europe 15 million years ago. Emerging subterranean environments likely provided unoccupied, predator-free space, constituting ecological opportunity, a key trigger of adaptive radiation. This discovery sheds new light on the biodiversity of Europe.
Defective folate metabolism causes germline epigenetic instability and distinguishes Hira as a phenotype inheritance biomarker
Authors: Blake Georgina E. T. , Zhao Xiaohui , Yung Hong wa , Burton Graham J. , Ferguson-Smith Anne C. , Hamilton Russell S. , Watson Erica D. 
Published: June 2021

AbstractThe mechanism behind transgenerational epigenetic inheritance is unclear, particularly through the maternal grandparental line. We previously showed that disruption of folate metabolism in mice by the Mtrr hypomorphic mutation results in transgenerational epigenetic inheritance of congenital malformations. Either maternal grandparent can initiate this phenomenon, which persists for at least four wildtype generations. Here, we use genome-wide approaches to reveal genetic stability in the Mtrr model and genome-wide differential DNA methylation in the germline of Mtrr mutant maternal grandfathers. We observe that, while epigenetic reprogramming occurs, wildtype grandprogeny and great grandprogeny exhibit transcriptional changes that correlate with germline methylation defects. One region encompasses the Hira gene, which is misexpressed in embryos for at least three wildtype generations in a manner that distinguishes Hira transcript expression as a biomarker of maternal phenotypic inheritance.
Machine learning differentiates enzymatic and non-enzymatic metals in proteins
Authors: Feehan Ryan , Franklin Meghan W. , Slusky Joanna S. G. 
Published: June 2021

AbstractMetalloenzymes are 40% of all enzymes and can perform all seven classes of enzyme reactions. Because of the physicochemical similarities between the active sites of metalloenzymes and inactive metal binding sites, it is challenging to differentiate between them. Yet distinguishing these two classes is critical for the identification of both native and designed enzymes. Because of similarities between catalytic and non-catalytic metal binding sites, finding physicochemical features that distinguish these two types of metal sites can indicate aspects that are critical to enzyme function. In this work, we develop the largest structural dataset of enzymatic and non-enzymatic metalloprotein sites to date. We then use a decision-tree ensemble machine learning model to classify metals bound to proteins as enzymatic or non-enzymatic with 92.2% precision and 90.1% recall. Our model scores electrostatic and pocket lining features as more important than pocket volume, despite the fact that volume is the most quantitatively different feature between enzyme and non-enzymatic sites. Finally, we find our model has overall better performance in a side-to-side comparison against other methods that differentiate enzymatic from non-enzymatic sequences. We anticipate that our model’s ability to correctly identify which metal sites are responsible for enzymatic activity could enable identification of new enzymatic mechanisms and de novo enzyme design.
In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia
Authors: Cole Basiel , Lambrechts Laurens , Gantner Pierre , Noppe Ytse , Bonine Noah , Witkowski Wojciech , Chen Lennie , Palmer Sarah , Mullins James I. , Chomont Nicolas , Pardons Marion , Vandekerckhove Linos 
Published: June 2021

AbstractClonal expansion of HIV-infected cells contributes to the long-term persistence of the HIV reservoir in ART-suppressed individuals. However, the contribution from cell clones that harbor inducible proviruses to plasma viremia is poorly understood. Here, we describe a single-cell approach to simultaneously sequence the TCR, integration sites and proviral genomes from translation-competent reservoir cells, called STIP-Seq. By applying this approach to blood samples from eight participants, we show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5’-end of the genome, often involving the major splice donor site. TCR and integration site sequencing reveal that cell clones with predicted pathogen-specificity can harbor inducible proviruses integrated into cancer-related genes. Furthermore, we find several matches between proviruses retrieved with STIP-Seq and plasma viruses obtained during ART and upon treatment interruption, suggesting that STIP-Seq can capture clones that are responsible for low-level viremia or viral rebound.
Pan-cancer characterization of lncRNA modifiers of immune microenvironment reveals clinically distinct de novo tumor subtypes
Authors: Zhang Zicheng , Yan Congcong , Li Ke , Bao Siqi , Li Lei , Chen Lu , Zhao Jingting , Sun Jie , Zhou Meng 
Published: June 2021

AbstractThe emerging field of long noncoding RNA (lncRNA)-immunity has provided a new perspective on cancer immunity and immunotherapies. The lncRNA modifiers of infiltrating immune cells in the tumor immune microenvironment (TIME) and their impact on tumor behavior and disease prognosis remain largely uncharacterized. In the present study, a systems immunology framework integrating the noncoding transcriptome and immunogenomics profiles of 9549 tumor samples across 30 solid cancer types was used, and 36 lncRNAs were identified as modifier candidates underlying immune cell infiltration in the TIME at the pan-cancer level. These TIME lncRNA modifiers (TIL-lncRNAs) were able to subclassify various tumors into three de novo pan-cancer subtypes characterized by distinct immunological features, biological behaviors, and disease prognoses. Finally, a TIL-lncRNA-derived immune state index (TISI) that was reflective of immunological and oncogenic states but also predictive of patients’ prognosis was proposed. Furthermore, the TISI provided additional prognostic value for existing tumor immunological and molecular subtypes. By applying the TISI to tumors from different clinical immunotherapy cohorts, the TISI was found to be significantly negatively correlated with immune-checkpoint genes and to have the ability to predict the effectiveness of immunotherapy. In conclusion, the present study provided comprehensive resources and insights for future functional and mechanistic studies on lncRNA-mediated cancer immunity and highlighted the potential of the clinical application of lncRNA-based immunotherapeutic strategies in precision immunotherapy.
Microbiologically induced aesthetic and structural changes to dimension stone
Authors: Gaylarde Christine C. , Baptista-Neto Jose Antonio 
Published: June 2021

AbstractDimension stone is natural rock prepared for building use. It is rapidly colonised by microorganisms that cause discoloration (mainly cyanobacteria, algae and fungi) and structural damage. Microbial mobilisation of ions leads to new superficial or internal deposits, weakening the structure. Cyanobacteria and fungi may penetrate, filling pores or creating new spaces. Lichens, fungus/phototroph associations, colonise surfaces and damage stone through ingrowing rhizines and acid production. Initial degradation produces conditions suitable for germination of seeds of higher plants and further destruction. Emerging techniques to elucidate stone-cell interactions and control of initial biofilm formation that eventuates in stone disintegration are discussed.
Cellular human tissue-engineered skin substitutes investigated for deep and difficult to heal injuries
Authors: Sierra-Sánchez Álvaro , Kim Kevin H. , Blasco-Morente Gonzalo , Arias-Santiago Salvador 
Published: June 2021

AbstractWound healing is an important function of skin; however, after significant skin injury (burns) or in certain dermatological pathologies (chronic wounds), this important process can be deregulated or lost, resulting in severe complications. To avoid these, studies have focused on developing tissue-engineered skin substitutes (TESSs), which attempt to replace and regenerate the damaged skin. Autologous cultured epithelial substitutes (CESs) constituted of keratinocytes, allogeneic cultured dermal substitutes (CDSs) composed of biomaterials and fibroblasts and autologous composite skin substitutes (CSSs) comprised of biomaterials, keratinocytes and fibroblasts, have been the most studied clinical TESSs, reporting positive results for different pathological conditions. However, researchers’ purpose is to develop TESSs that resemble in a better way the human skin and its wound healing process. For this reason, they have also evaluated at preclinical level the incorporation of other human cell types such as melanocytes, Merkel and Langerhans cells, skin stem cells (SSCs), induced pluripotent stem cells (iPSCs) or mesenchymal stem cells (MSCs). Among these, MSCs have been also reported in clinical studies with hopeful results. Future perspectives in the field of human-TESSs are focused on improving in vivo animal models, incorporating immune cells, designing specific niches inside the biomaterials to increase stem cell potential and developing three-dimensional bioprinting strategies, with the final purpose of increasing patient’s health care. In this review we summarize the use of different human cell populations for preclinical and clinical TESSs under research, remarking their strengths and limitations and discuss the future perspectives, which could be useful for wound healing purposes.
First simultaneous detection of electron and positron bunches at the positron capture section of the SuperKEKB factory
Authors: Suwada Tsuyoshi , Rehman Muhammad Abdul , Miyahara Fusashi 
Published: June 2021

AbstractThe direct simultaneous detection of electron and positron bunch signals was successfully performed for the first time with wideband pickups and a detection system at the positron capture section of the SuperKEKB factory. The time interval between the electron and positron bunches, their bunch lengths, and bunch intensities depending on the phase of accelerating structures were measured to investigate their capture process and to maximally optimize the positron intensity. The results show that the time intervals were measured in the range of 135–265 ps, and the line-order switch of the electron and positron bunches in the axial direction was clearly observed as a function of the phase. The positron (electron) intensity was maximized at the optimal phase (180$$^{\circ }$$

∘

shifted from the optimum). These series of measurements have never been experimentally conducted so far. It is demonstrated that the positron intensity can be systematically optimized with this system as functions of beam parameters in multidimensional spaces for any positron capture section.
Changes in soil microbial community and activity caused by application of dimethachlor and linuron
Authors: Medo Juraj , Maková Jana , Medová Janka , Lipková Nikola , Cinkocki Renata , Omelka Radoslav , Javoreková Soňa 
Published: June 2021

AbstractSoil microorganisms and their activities are essential for maintaining soil health and fertility. Microorganisms can be negatively affected by application of herbicides. Although effects of herbicides on microorganisms are widely studied, there is a lack of information for chloroacetamide herbicide dimethachlor. Thus, dimethachlor and well known linuron were applied to silty-loam luvisol and their effects on microorganisms were evaluated during112 days long laboratory assay. Dimethachlor and linuron were applied in doses 1.0 kg ha−1 and 0.8 kg ha−1 corresponding to 3.33 mg kg−1 and 2.66 mg kg−1 respectively. Also 100-fold doses were used for magnification of impacts. Linuron in 100-fold dose caused minor increase of respiration, temporal increase of soil microbial biomass, decrease of soil dehydrogenase activity, and altered microbial community. Dimethachlor in 100-fold dose significantly increased respiration; microbial biomass and decreased soil enzymatic activities. Microbial composition changed significantly, Proteobacteria abundance, particularly Pseudomonas and Achromobacter genera increased from 7 to 28th day. In-silico prediction of microbial gene expression by PICRUSt2 software revealed increased expression of genes related to xenobiotic degradation pathways. Evaluated characteristics of microbial community and activity were not affected by herbicides in recommended doses and the responsible use of both herbicides will not harm soil microbial community.