bluuebunny/crossref_metadata_2025_split huggingface dataset:
A predictive model of fractional land use
Authors: Kapitza Simon , Golding Nick , Wintle Brendan A. 
Published: December 2020

AbstractLand use change leads to shifts in species ranges and declines in biodiversity across the world. By mapping likely future land use under projections of socio-economic change, these ecological changes can be predicted to inform conservation decision-making.We present a land use modelling approach that enables ecologists to map changes in land use under various socio-economic scenarios at fine spatial resolutions. Its predictions can be used as a direct input to virtually all existing spatially-explicit ecological models.The most commonly used land use modelling approaches provide binary predictions of land use. However, continuous representations of land use have been shown to improve ecological models. Our approach maps the fractional cover of land use within each grid cell, providing higher information content than discrete classes at the same spatial resolution.When parametrized using data from 1990, the method accurately reproduced land use patterns observed in the Amazon from 1990 until 2018. Predictions were accurate in terms of the fractional amounts allocated across the landscape and the correct identification of areas with declines and increases in different land uses. A small case study showcases the successful application of our model to reproduce patterns of agricultural expansion and habitat decline.The model source code is provided as an open-source R package, making this new, open method available to ecologists to bridge the gap between socio-economic, land use and biodiversity modelling.
Wild red wolfCanis rufuspoaching risk
Authors: Agan Suzanne W. , Treves Adrian , Willey Lisabeth 
Published: December 2020

AbstractThe reintroduced red wolf population in northeastern North Carolina declined to 7 known wolves by October 2020. Poaching (illegal killing) is the major component of verified anthropogenic mortality in this and many other carnivore populations, but it is still not well understood. Poaching is often underestimated, partly as a result of cryptic poaching, when poachers conceal evidence. Cryptic poaching inhibits our understanding of the causes and consequences of anthropogenic mortality which is important to conservation as it can inform us about future population patterns within changing political and human landscapes. We estimate risk for marked adult red wolves of 5 causes of death (COD: legal, nonhuman, unknown, vehicle and poached) and disappearance, describe variation in COD in relation to hunting season, and compare time to disappearance or death. We include unknown fates in our risk estimates. We found that anthropogenic COD accounted for 0.724 – 0.787, including cryptic and reported poaching estimated at 0.510 – 0.635 of 508 marked animals. Risk of poaching and disappearance was significantly higher during hunting season. Mean time from collaring until nonhuman COD averaged 376 days longer than time until reported poached and 642 days longer than time until disappearance. Our estimates of risk differed from prior published estimates, as expected by accounting for unknown fates explicitly. We quantify the effects on risk for three scenarios for disappearances, which span conservative to most likely COD. Implementing proven practices that prevent poaching or hasten successful reintroduction may reverse the decline to extinction in the wild of this critically endangered population. Our findings add to a growing literature on endangered species protections and enhancing the science used to measure poaching worldwide.
Decoding Study-Independent Mind-Wandering from EEG using Convolutional Neural Networks
Authors: Jin Christina Yi , Borst Jelmer P. , van Vugt Marieke K. 
Published: December 2020

AbstractObjectiveMind-wandering is a mental phenomenon where the internal thought process disengages from the external environment periodically. In the current study, we trained EEG classifiers using convolutional neural networks (CNN) to track mind-wandering across studies.ApproachWe transformed the input from raw EEG to band-frequency information (power), singletrial ERP (stERP) patterns, and connectivity matrices between channels (based on inter-site phase clustering, ISPC). We trained CNN models for each input type from each EEG channel as the input model for the meta-learner. To verify the generalizability, we used leave-N-participant-out crossvalidations (N=6) and tested the meta-learner on the data from an independent study for across-study predictions.Main resultsThe current results show limited generalizability across participants and tasks. Nevertheless, our meta-learned trained with the stERPs performed the best among the state-of-theart neural networks. The mapping of each input model to the output of the meta-learner indicates the importance of each EEG channel.SignificanceOur study makes the first attempt to train study-independent mind-wandering classifiers. The results indicate that this remains challenging. The current proposed stacking neural network design allows an easy inspection of channel importance and feature maps.
Disentangling the shark and ray trade in Indonesia to reconcile conservation with food security
Authors: Prasetyo Andhika P. , McDevitt Allan D. , Murray Joanna M. , Barry Jon , Agung Firdaus , Muttaqin Efin , Mariani Stefano 
Published: December 2020

AbstractIndonesian marine resources are among the richest on the planet, sustaining highly diverse fisheries and includes the largest elasmobranch landings in the world, making Indonesia one of the world’s largest exporters of shark and ray products. Socio-economic and food security considerations pertaining to Indonesian communities add further layers of complexity to the management and conservation of these vulnerable species. This study investigates how shark and ray trade flows in and out of Indonesia and attempts to examine patterns and drivers of the current scenario. We identify substantial discrepancies between reported landings and declared exports, and between Indonesian exports in shark fin and meat products and the corresponding figures reported by importing countries. These mismatches are estimated to amount to over $43.6M and $20.9M for fins and meat, respectively, for the period between 2012 and 2018. Although the declared exports are likely to be an underestimation because of significant unreported or illegal trading activities, we find that domestic consumption of shark and ray products plays a significant role in explaining these discrepancies due to the increasing local demand for meat. The study also unearths a general scenario of unsystematic data collection and lack of granularity of product terminology, which is inadequate to meet the challenges of over-exploitation, illegal trade and food security in Indonesia. We discuss how to improve data transparency to support trade regulations and governance actions, by improving inspection measures, and conserving elasmobranch populations without neglecting the socio-economic dimension of this complex system.
Complete Protection of Nasal and Lung Airways Against SARS-CoV-2 Challenge by Antibody Plus Th1 Dominant N- and S-Specific T-Cell Responses to Subcutaneous Prime and Thermally-Stable Oral Boost Bivalent hAd5 Vaccination in an NHP Study
Authors: Gabitzsch Elizabeth , Safrit Jeffrey T. , Verma Mohit , Rice Adrian , Sieling Peter , Zakin Lise , Shin Annie , Morimoto Brett , Adisetiyo Helty , Wong Raymond , Bezawada Ashish , Dinkins Kyle , Balint Joseph , Peykov Victor , Garban Hermes , Liu Philip , Bone Pete , Bacon Andrew , Drew Jeff , Sanford Daniel C. , Spilman Patricia , Sender Lennie , Rabizadeh Shahrooz , Niazi Kayvan , Soon-Shiong Patrick 
Published: December 2020

ABSTRACTWe have developed a dual-antigen COVID-19 vaccine incorporating genes for a modified SARS-CoV-2 spike (S-Fusion) protein and the viral nucleocapsid (N) protein with an Enhanced T-cell Stimulation Domain (N-ETSD) with the potential to increase MHC class I/II responses. The adenovirus serotype 5 platform used, hAd5 [E1-, E2b-, E3-], previously demonstrated to be effective in the presence of Ad immunity, can be delivered in an oral formulation that overcomes cold-chain limitations. The hAd5 S-Fusion + N-ETSD vaccine was evaluated in rhesus macaques showing that a subcutaneous prime followed by oral boosts elicited both humoral and Th1 dominant T-cell responses to both S and N that protected the upper and lower respiratory tracts from high titer (1 x 106TCID50) SARS-CoV-2 challenge. Notably, viral replication was inhibited within 24 hours of challenge in both lung and nasal passages, becoming undetectable within 7 days post-challenge.ONE SENTENCE SUMMARYhAd5 spike + nucleocapsid SC prime/oral boost vaccine elicits humoral and T-cell responses and protects rhesus macaques from SARS-CoV-2 challenge.
Biologically informed deep neural network for prostate cancer classification and discovery
Authors: Elmarakeby Haitham A. , Hwang Justin , Liu David , AlDubayan Saud H. , Salari Keyan , Richter Camden , Arnoff Taylor E , Park Jihye , Hahn William C. , Van Allen Eliezer 
Published: December 2020

AbstractDetermination of molecular features that mediate clinically aggressive phenotypes in prostate cancer (PrCa) remains a major biological and clinical challenge. Here, we developed a biologically informed deep learning model (P-NET) to stratify PrCa patients by treatment resistance state and evaluate molecular drivers of treatment resistance for therapeutic targeting through complete model interpretability. Using a molecular cohort of 1,238 prostate cancers, we demonstrated that P-NET can predict cancer state using molecular data that is superior to other modeling approaches. Moreover, the biological interpretability within P-NET revealed established and novel molecularly altered candidates, such asMDM4andFGFR1, that were implicated in predicting advanced disease and validatedin vitro. Broadly, biologically informed fully interpretable neural networks enable preclinical discovery and clinical prediction in prostate cancer and may have general applicability across cancer types.
Host response to cholestyramine can be mediated by the gut microbiota
Authors: Newman Nolan K. , Monnier Philip M. , Rodrigues Richard R. , Gurung Manoj , Vasquez-Perez Stephany , Hioki Kaito A. , Greer Renee L. , Brown Kevin , Morgun Andrey , Shulzhenko Natalia 
Published: December 2020

AbstractThe gut microbiome has been implicated as a major factor contributing to metabolic diseases as well as being contributors to the response to drugs used for the treatment of such diseases. In this study, using a diet-induced obesity mouse model, we tested the effect of cholestyramine, a bile acid sequestrant, on the murine gut microbiome and mammalian metabolism. We also explored the hypothesis that some beneficial effects of this drug on systemic metabolism can be attributed to alterations in gut microbiota. First, we demonstrated that cholestyramine can decrease glucose and epidydimal fat levels. Next, while investigating gut microbiota we found increased alpha diversity of the gut microbiome of cholestyramine-treated mice, with fourteen taxa showing restoration of abundance to levels resembling those in mice fed with a control diet. Analyzing expression of genes known to be regulated by cholestyramine (including Cyp7a1), we confirmed the expected effect of this drug in the liver and ileum. Finally, using a transkingdom network analysis we inferredAcetatifactor murisandMuribaculum intestinaleas potential mediators/modifiers of cholestyramine effects on the mammalian host. In addition,A. muriscorrelated positively with glucagon (Gcg) expression in the ileum and negatively correlated with small heterodimer partner (Shp) expression in the liver. Interestingly,A. murisalso correlated negatively with glucose levels, further indicating the potential probiotic role forA. muris. In conclusion, our results indicate the gut microbiome has a role in the beneficial effects of cholestyramine and suggest specific microbes as targets of future investigations.
Non-Vertical Cultural Transmission, Assortment, and the Evolution of Cooperation
Authors: Cohen Dor , Lewin-Epstein Ohad , Feldman Marcus W. , Ram Yoav 
Published: December 2020

AbstractCultural evolution of cooperation under vertical and non-vertical cultural transmission is studied, and conditions are found for fixation and coexistence of cooperation and defection. The evolution of cooperation is facilitated by its horizontal transmission and by an association between social interactions and horizontal transmission. The effect of oblique transmission depends on the horizontal transmission bias. Stable polymorphism of cooperation and defection can occur, and when it does, reduced association between social interactions and horizontal transmission evolves, which leads to a decreased frequency of cooperation and lower population mean fitness. The deterministic conditions are compared to outcomes of stochastic simulations of structured populations. Parallels are drawn with Hamilton’s rule incorporating assortment and effective relatedness.
RAS specific protease Induces Irreversible Growth Arrest via p27 in several KRAS Mutant Colorectal Cancer cell lines
Authors: Stubbs Caleb K. , Biancucci Marco , Vidimar Vania , Satchell Karla J. F. 
Published: December 2020

ABSTRACTRas-specific proteases to degrade RAS within cancer cells are under active development as an innovative strategy to treat tumorigenesis. The naturally occurring biological toxin effector called RAS/RAP1-specific endopeptidase (RRSP) is known to cleave all RAS within a cell, including HRAS, KRAS, NRAS and mutant KRAS G13D. In the course of studies developing RRSP as an anti-cancer therapeutic, it was shown that cleavage of total RAS by RRSP results in a range of cell fates from cytotoxicity to moderate growth inhibition. Despite the considerable amount of evidence demonstrating RRSP anti-tumor effectsin vivo,our understanding of the mechanisms involved are unknown. Here, we first demonstrate, using isogenic mouse fibroblasts expressing a single isoform of RAS or mutant KRAS, that RRSP equally inactivates all isoforms of RAS as well as the major oncogenic KRAS mutants. The cleavage of RAS inhibited phosphorylation of ERK and cell proliferation regardless of the RAS isoform. To investigate further how RAS processing might lead to varying outcomes in cell fate within cancer cells, we tested RRSP against four colorectal cancer cell lines with a range of cell fates. While cell lines highly susceptible to RRSP (HCT116 and SW1463) undergo cytotoxic death, RRSP treatment of GP5d cells induces G1 cell cycle arrest, and SW620 cells instead induces growth inhibition through cell senescence. In three of four cell lines tested, growth effects were dictated by rescued expression of the tumor suppressor protein p27 (Kip1). The ability of RRSP to inactivate all RAS and inhibit cancer cell growth through a variety of mechanisms highlights the antitumor potential of RRSP, and further warrants investigation as a potential anti-tumor therapeutic.
Design of a radial multi-offset detection pattern forin vivophase contrast imaging of the retinal ganglion cells in humans
Authors: Gofas-Salas Elena , Rui Yuhua , Mecê Pedro , Zhang Min , Snyder Valerie C. , Vienola Kari V. , Lee Daniel , Sahel José-Alain , Grieve Kate , Rossi Ethan A. 
Published: December 2020

AbstractPrevious work has shown that multi-offset detection in adaptive optics scanning laser ophthalmoscopy (AOSLO) can be used to image retinal ganglion cells (RGCs) in monkeys and humans. However, though images of RGCs in anesthetized monkeys with high light levels produced high contrast images of RGCs, images from humans failed to reach the same contrast due to several drawbacks in the previous dual-wavelength multi-offset approach. Our aim here was to design and build a multi-offset detection pattern for humans at safe light levels that could reveal the retinal ganglion cell layer neurons with a contrast, robustness and acquisition time approaching results only previously obtained in monkeys. Here, we present a new imaging system using only one light source, compared to the previous dual-wavelength used on monkeys. Our single-wavelength solution allows for increased light power and eliminates problematic chromatic aberrations. Then, we demonstrate that a radial multi-offset detection pattern with an offset distance of 8-10 Airy Disk Diameter (ADD) is optimal to detect photons multiply scattered in all directions from RGCs thereby enhancing their contrast. This new setup and image processing pipeline led to improved imaging of retinal ganglion cells using multi-offset imaging in AOSLO.
Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways
Authors: Bowerman Samuel , Wereszczynski Jeff , Luger Karolin 
Published: December 2020

AbstractEukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ∼147 DNA base pairs into nucleosomes, archaeal histones form “nucleosome-like” complexes that continuously wind between 60 - 500 base pairs of DNA (“archaeasomes”), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90°out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.
Construction of a liquid-liquid phase separation system from the gel-sol transition of elongated protein microgels in a crowding agent
Authors: Xu Yufan , Qi Runzhang , Zhu Hongjia , Li Bing , Shen Yi , Krainer Georg , Klenerman David , Knowles Tuomas P. J. 
Published: December 2020

AbstractLiquid proteinaceous materials have been frequently found in cells or tissues and are crucial for various biological processes. Unlike their solid-state counterparts, liquid-state protein compartments are challenging to engineer and control at the microscale. Conventionally, gelation (sol-gel transition) of biological molecules has been thought to be the intermediate step between liquid-liquid phase separation (LLPS) states and insoluble aggregates that are related to protein functions, malfunctions and even diseases. However, the opposite process, i.e., the gel-sol transition of materials, has not been broadly explored. Here we describe a thermoresponsive gel-sol transition of a protein in a crowded environment that results in a demixed LLPS state, contradicting the common consequence of a one-phase protein solution by the end of such transition at elevated temperature without crowding agents. We also demonstrate a simple method to monitor the gel-sol transition by showing that elongated gelatin microgels can evolve towards a spherical morphology in the crowding agents because of interfacial tension. The LLPS system was explored for the diffusion of small particles for drug-release application scenarios. Our results demonstrate a route for the rapid construction of LLPS models, where the gel-sol transition of the protein-rich phase is monitorable. The models are featured with tunable size and dimensional monodispersity of dispersed condensates. The present study can be employed in biophysics and bioengineering with practices such as 3D printing and temperature sensing.
Relative water content consistently predicts drought mortality risk in seedling populations with different morphology, physiology, and times to death
Authors: Sapes Gerard , Sala Anna 
Published: December 2020

AbstractPredicted increases in forest drought mortality highlight the need for predictors of incipient drought-induced mortality (DIM) risk that enable proactive large-scale management. Such predictors should be consistent across plants with varying morphology and physiology. Because of their integrative nature, indicators of water status are promising candidates for real time monitoring of DIM, particularly if they standardize morphological differences among plants. We assessed the extent to which differences in morphology and physiology betweenPinus ponderosapopulations influence time to mortality and the predictive power of key indicators of DIM risk. Time to incipient mortality differed between populations but occurred at the same relative water content (RWC) and water potential (WP). RWC and WP were accurate predictors of drought mortality risk. These results highlight that variables related to water status capture critical thresholds during DIM and the associated dehydration processes. Both WP and RWC are promising candidates for large-scale assessments of DIM risk. RWC is of special interest because it allows comparisons across different morphologies and can be remotely sensed. Our results offer promise for real-time landscape-level monitoring of DIM and its global impacts in the near term.
The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Authors: Guo Chenxu , Tsai Shang-Jui , Ai Yiwei , Li Maggie , Pekosz Andrew , Cox Andrea , Atai Nadia , Gould Stephen J. 
Published: December 2020

AbstractThe spike D614G mutation increases SARS-CoV-2 infectivity, viral load, and transmission but the molecular mechanism underlying these effects remains unclear. We report here that spike is trafficked to lysosomes and that the D614G mutation enhances the lysosomal sorting of spike and the lysosomal accumulation of spike-positive punctae in SARS-CoV-2-infected cells. Spike trafficking to lysosomes is an endocytosis-independent, V-ATPase-dependent process, and spike-containing lysosomes drive lysosome clustering but display poor lysotracker labeling and reduced uptake of endocytosed materials. These results are consistent with a lysosomal pathway of coronavirus biogenesis and raise the possibility that a common mechanism may underly the D614G mutation’s effects on spike protein trafficking in infected cells and the accelerated entry of SARS-CoV-2 into uninfected cells.
Topological Insights into Mutant Huntingtin Exon 1 and PolyQ Aggregates by Cryo-Electron Tomography
Authors: Galaz-Montoya Jesús G. , Shahmoradian Sarah H. , Shen Koning , Frydman Judith , Chiu Wah 
Published: December 2020

ABSTRACTHuntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregatesin vitroare structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we observed some filaments in both types of aggregates under ∼2 nm in width, thinner than previously reported, while other regions form large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy, slab-shaped morphology in both aggregates, supportive of the “polyQ core” model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling and their identification in cells without fusion tags.