bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seeing the Invisible
Authors: Chuang Tzyy-Ling , Chen Yu-Ruei , Wang Yuh-Feng 
Published: August 2021

Abstract
A 76-year-old woman with uterine cervical cancer 20 years ago received right total hip replacement 3 months ago for right hip avascular necrosis without specific intraoperative finding. She reported persistent right hip pain after falling from bed. Pelvic x-ray showed right pubic ramus fracture. To evaluate prosthesis loosening, 99mTc-MDP 3-phase bone scan was arranged, showing diffusely and heterogeneously increased vascularity and tracer perfusion over the right hip, with intensely and heterogeneously increased metabolism in the right iliac bone and hip. SPECT/CT showed nearby swelling of calcified muscles. After debridement and synovectomy, the pathologic report showed chondroblastic osteosarcoma.
A Third Dose of SARS-CoV-2 Vaccine Increases Neutralizing Antibodies Against Variants of Concern in Solid Organ Transplant Recipients
Authors: Karaba Andrew H. , Zhu Xianming , Liang Tao , Wang Kristy H. , Rittenhouse Alex G. , Akinde Olivia , Eby Yolanda , Ruff Jessica E. , Blankson Joel N. , Abedon Aura T. , Alejo Jennifer L. , Cox Andrea L. , Bailey Justin R. , Thompson Elizabeth A. , Klein Sabra L. , Warren Daniel S. , Garonzik-Wang Jacqueline M. , Boyarsky Brian J. , Sitaras Ioannis , Pekosz Andrew , Segev Dorry L. , Tobian Aaron A.R. , Werbel William A. 
Published: August 2021

ABSTRACTVaccine-induced SARS-CoV-2 antibody responses are attenuated in solid organ transplant recipients (SOTRs) and breakthrough infections are more common. Additional SARS-CoV-2 vaccine doses increase anti-spike IgG in some SOTRs, but it is uncertain whether neutralization of variants of concern (VOCs) is enhanced. We tested 47 SOTRs for clinical and research anti-spike IgG, pseudoneutralization (ACE2 blocking), and live-virus neutralization (nAb) against VOCs before and after a third SARS-CoV-2 vaccine dose (70% mRNA, 30% Ad26.COV2.S) with comparison to 15 healthy controls after two mRNA vaccine doses. We used correlation analysis to compare anti-spike IgG assays and focused on thresholds associated with neutralizing activity. A third SARS-CoV-2 vaccine dose increased median anti-spike (1.6-fold) and receptor-binding domain (1.5-fold) IgG, as well as pseudoneutralization against VOCs (2.5-fold versus Delta). However, IgG and neutralization activity were significantly lower than healthy controls (p<0.001); 32% of SOTRs had zero detectable nAb against Delta after third vaccination. Correlation with nAb was seen at anti-spike IgG >4 AU on the clinical assay and >10^4 AU on the research assay. These findings highlight benefits of a third vaccine dose for some SOTRs and the need for alternative strategies to improve protection in a significant subset of this population.
International Completeness of Death Registration 2015-2019
Authors: Karlinsky Ariel 
Published: August 2021

AbstractDeath registration completeness, the share of deaths captured by countries’ vital registration systems, vary substantially across countries. Estimates of completeness, even recent ones, are outdated or contradictory for many countries. This paper presents the International Completeness of Death Registration (ICDR) dataset. ICDR contains the annual amount of deaths registered in 181 countries’ vital registration systems from 2015 to 2019. These counts allow derivation of the most up-to-date and consistent estimates of death registration completeness.
How big should this object be? Perceptual influences on viewing-size preferences
Authors: Chen (陳鴨嘉) Yi-Chia , Deza Arturo , Konkle Talia 
Published: August 2021

AbstractWhen viewing objects depicted in a frame, observers prefer to view large objects like cars in larger sizes and smaller objects like cups in smaller sizes. That is, the visual size of an object that “looks best” is linked to its typical physical size in the world. Why is this the case? One intuitive possibility is that these preferences are driven by semantic knowledge: For example, when we recognize a sofa, we access our knowledge about its real-world size, and this influences what size we prefer to view the sofa within a frame. However, might visual processing play a role in this phenomenon—that is, do visual features that are related to big and small objects look better at big and small visual sizes, respectively, even when observers do not have explicit access to semantic knowledge about the objects? To test this possibility, we used “texform” images, which are synthesized versions of recognizable objects, which critically retain local perceptual texture and coarse contour information, but are no longer explicitly recognizable. To test for visual size preferences, we first used a size adjustment task, and the results were equivocal. However, clear results were obtained using a two-interval forced choice task, in which each texform was presented at the preferred visual size of its corresponding original image, and a visual size slightly bigger or smaller. Observers consistently selected the texform presented at the canonical visual size as the more aesthetically pleasing one. An additional control experiment ruled out alternative explanations related to size priming effects. These results suggest that the preferred visual size of an object depends not only on explicit knowledge of its real-world size, but also can be evoked by mid-level visual features that systematically covary with an object’s real-world size.HighlightsWe prefer to view large objects like cars large, and small objects like cups smallIntuitively, such preferences may be driven by our knowledge of object sizesWe used unrecognizable texforms of objects that preserved mid-level visual featuresSimilar viewing size preferences can be revealed with these texformsSuch preferences thus arise not only from knowledge but also from visual processing
Measuring thousands of single vesicle leakage events reveals the mode of action of antimicrobial peptides
Authors: Nahas Kareem Al , Fletcher Marcus , Hammond Katharine , Nehls Christian , Cama Jehangir , Ryadnov Maxim G , Keyser Ulrich F 
Published: August 2021

AbstractHost defense or antimicrobial peptides hold promise for providing new pipelines of effective antimicrobial agents. Their activity quantified against model phospholipid membranes is fundamental to a detailed understanding of their structure-activity relationships. However, existing characterization assays lack the resolution necessary to achieve this insight. Leveraging a highly parallelized microfluidic platform for trapping and studying thousands of giant unilamellar vesicles, we conducted quantitative long-term microscopy studies to monitor the membrane-disruptive activity of archetypal antimicrobial peptides with a high spatiotemporal resolution. We described the modes of action of these peptides via measurements of the disruption of the vesicle population under the conditions of continuous peptide dosing using a range of concentrations, and related the observed modes with the molecular activity mechanisms of these peptides. The study offers an effective approach for characterizing membrane-targeting antimicrobial agents in a standardized manner, and for assigning specific modes of action to the corresponding antimicrobial mechanisms.
Robustness of trinucleosome compaction to A-tract mediated linker histone orientation
Authors: De Madhura , Würtz Martin , Müller Gabriele , Tóth Katalin , Wade Rebecca C. 
Published: August 2021

AbstractLinker histones (LH) have been shown to preferentially bind to AT-rich DNA, particularly A-tracts, contiguous stretches of adenines. Using spFRET (single pair Förster/Fluorescence Resonance Energy Transfer), we recently found that the globular domain (gH) ofXenopus laevisH1.0b LH orients towards A-tracts on the linker-DNA (L-DNA) while binding on-dyad in LH:mononucleosome complexes. Here, we investigate the impact of this A-tract-mediated orientation of the gH on the compaction of higher-order structures by studying trinucleosomes as minimal models for chromatin. Two 600 bp DNA sequences were constructed, each containing three consecutive Widom 601 core sequences connected by about 40 bp L-DNA but differing in the positioning of A-tracts on either the outer or the inner L-DNAs flanking the first and third Widom 601 sequences. The two inner L-DNAs were fluorescently labelled at their midpoints. Trinucleosomes were reconstituted using the doubly labelled DNA, core histone octamers and H1.0b. SpFRET was performed for a range of NaCl concentrations to measure the compaction and whether gH orientations affected the stability of the trinucleosomes to salt-induced dissociation. While the LH compacted the trinucleosomes, the extent of compaction and the stability were similar for the two DNA sequences. Modeling constrained by the measured FRET efficiency suggests that the structures adopted by the trinucleosomes correspond to the standard zig-zagged two-helical start arrangement with the first and third nucleosomes stacked on top of each other. In this arrangement, the first and third LHs are insufficiently close to interact and affect compaction. Thus, despite differences in the positioning of the A-tracts in the sequences studied, LH binding compacts the corresponding trinucleosomes similarly.Why it mattersThe compaction and three-dimensional structure of chromatin affect the exposure of the DNA and thus regulate gene expression. Linker histone proteins bind to nucleosomes and thereby contribute to chromatin compaction. We here investigated whether the DNA A-tract-mediated orientation of a linker histone globular domain affects chromatin structure by using a trinucleosome as a minimal model for chromatin. Our observations suggest that the trinucleosome structure and compaction are robust against differences in linker histone globular domain orientations.eTOC blurbWe investigate whether DNA sequences, such as adenine-tracts, and sequence-induced linker histone reorientation affect chromatin structure. Using trinucleosomes as model systems for chromatin, we demonstrate that the chromatin structure and compaction are robust to the studied DNA sequence differences and sequence-induced linker histone orientation.
Single-nucleus RNA-sequencing in pre-cellularizationDrosophila melanogasterembryos
Authors: Albright Ashley , Stadler Michael , Eisen Michael 
Published: August 2021

AbstractOur current understanding of the regulation of gene expression in the earlyDrosophila melanogasterembryo comes from observations of a few genes at a time, as within situhybridizations, or observation of gene expression levels without regards to patterning, as with RNA-sequencing. Single-nucleus RNA-sequencing however, has the potential to provide new insights into the regulation of gene expression for many genes at once while simultaneously retaining information regarding the position of each nucleus prior to dissociation based on patterned gene expression. In order to establish the practicality of single-nucleus RNA sequencing in the context of a real biological question, here we look at the difference in gene expression between control and an insulator protein, dCTCF, maternal null embryos during zygotic genome activation at nuclear cycle 14. We find that early embryonic nuclei can be grouped into distinct clusters according to gene expression. From both virtual and publishedin situhybridizations, we also find that these clusters correspond to spatial regions of the embryo. Lastly, we present multiple examples of differential gene expression between control and maternal CTCF null nuclei in one or more clusters, but not in bulk when grouping expression across all nuclei. These results highlight the potential for single-nucleus RNA-sequencing to reveal new insights into the regulation of gene expression in the earlyDrosophila melanogasterembryo.
Screening of cell-virus, cell-cell, gene-gene cross-talks among kingdoms of life at single cell resolution
Authors: Chen Dongsheng , Ou Zhihua , Zhu Jiacheng , Ding Peiwen , Wang Haoyu , Luo Lihua , Ding Xiangning , Lan Tianming , Wu Weiying , Yuan Yuting , Wu Wendi , Qiu Jiaying , Zhu Yixin , Jia Yi , Wei Yanan , Qin Qiuyu , Li Runchu , Sun Chengcheng , Zhao Wandong , Lv Zhiyuan , Pu Mingyi , Yang Shangchen , Chang Ashley , Wei Xiaofeng , Chen Fengzhen , Yang Tao , Wei Zhenyong , Yang Fan , Li Yuejiao , Hua Yan , Liu Huan 
Published: August 2021

AbstractThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) issued a significant and urgent threat to global health. The exact animal origin of SARS-CoV-2 remains obscure and understanding its host range is vital for preventing interspecies transmission. Previously, we have assessed the target cell profiles of SARS-CoV-2 in pets, livestock, poultry and wild animals. Herein, we expand this investigation to a wider range of animal species and viruses to provide a comprehensive source for large-scale screening of potential virus hosts. Single cell atlas for several mammalian species (alpaca, hamster, hedgehog, chinchilla etc.), as well as comparative atlas for lung, brain and peripheral blood mononuclear cells (PBMC) for various lineages of animals were constructed, from which we systemically analyzed the virus entry factors for 113 viruses over 20 species from mammalians, birds, reptiles, amphibians and invertebrates. Conserved cellular connectomes and regulomes were also identified, revealing the fundamental cell-cell and gene-gene cross-talks between these species. Overall, our study could help identify the potential host range and tissue tropism of SARS-CoV-2 and a diverse set of viruses and reveal the host-virus co-evolution footprints.
Nrf2 is a central regulator of the metabolic landscape in macrophages and finetunes their inflammatory response
Authors: Ryan Dylan G. , Knatko Elena V. , Casey Alva , Hukelmann Jens L. , Brenes Alejandro J. , Naidu Sharadha Dayalan , Higgins Maureen , Tronci Laura , Nikitopoulou Efterpi , O’Neill Luke A.J. , Frezza Christian , Lamond Angus I. , Abramov Andrey Y. , Cantrell Doreen A. , Murphy Michael P. , Dinkova-Kostova Albena T. 
Published: August 2021

AbstractTo overcome oxidative, inflammatory, and metabolic stress, cells have evolved networks of cytoprotective proteins controlled by nuclear factor erythroid 2 p45-related factor 2 (Nrf2) and its main negative regulator the Kelch-like ECH associated protein 1 (Keap1). Here, we used high-resolution mass-spectrometry to characterize the proteomes of macrophages with genetically altered Nrf2 status. Our analysis revealed significant differences among the genotypes in cellular metabolism and redox homeostasis, which we validated with respirometry and metabolomics, as well as in anti-viral immune pathways and the cell cycle. Nrf2 status significantly affected the proteome following lipopolysaccharide (LPS) stimulation, with alterations in redox, carbohydrate and lipid metabolism, and innate immunity observed. Of note, Nrf2 activation was found to promote mitochondrial fusion in inflammatory macrophages. The Keap1 inhibitor, 4-octyl itaconate (4-OI), a derivative of the mitochondrial immunometabolite itaconate, remodeled the inflammatory macrophage proteome, increasing redox and suppressing anti-viral immune effectors in a Nrf2-dependent manner. These data suggest that Nrf2 activation facilitates metabolic reprogramming and mitochondrial adaptation, and finetunes the innate immune response in macrophages.Graphical abstractHighlightsFirst high-resolution proteome of macrophages with genetically altered Nrf2 statusNrf2 is key regulator of macrophage redox and intermediary metabolismNrf2 finetunes the inflammatory response suppressing anti-viral immune and cytokine effectors, whilst promoting T cell activation factorsNrf2 regulates mitochondrial adaptation in inflammatory macrophages promoting the formation of a fused network4-octyl itaconate (4-OI) suppresses anti-viral immune effectors in inflammatory macrophages in a Nrf2-dependent manner
“Playing mysterious”: occurrence of Bio-duck calls in Brazil reveals a complex acoustic behaviour for the Antarctic minke whale (Balaenoptera bonaerensis)
Authors: Rossi-Santos Marcos R. , Filun Diego , Soares-Filho William , Paro Alexandre D. , Wedekin Leonardo L. 
Published: August 2021

AbstractAcoustic methods can provide important data on the occurrence and distribution of migratory species. Information about Antarctic Minke whale (Balaenoptera bonaerensis) occurrence in the winter breeding grounds is scarce, mostly limited to old records from whaling stations before 1960’s international moratory, such as Costinha Station in Northeastern Brazil (6° S / 34° W). This work describes the occurrence of the Antarctic minke whale (AMW) through Bio-duck acoustic detections in the Santos Basin, South-Southeastern Brazil (22° and 28° S / 42° and 48° W), registered between November 12 and December 19, 2015. AMW calls were detected for 12 days. We detected and classified 9 different Bio-duck calls in Brazilian coast waters, evidencing a high diverse acoustic behaviour for the minke whale breeding ground. This is the first study to describe the acoustic diversity of AMW vocalizations in lower latitudes, constituting important information to the conservation and management of cetaceans and their habitat. Therefore, our study presents the foremost acoustic evidence of the Antarctic minke whale in Brazil, utilizing high technological passive acoustic methods, such as autonomous underwater vehicle (SeaGlider) sampling.
Microtubule-associated proteins promote microtubule generation in the absence of γ-tubulin in human colon cancer cells
Authors: Tsuchiya Kenta , Goshima Gohta 
Published: August 2021

Abstractγ-Tubulin complex acts as the predominant microtubule (MT) nucleator that initiates MT formation and is therefore an essential factor for cell proliferation. Nonetheless, cellular MTs are formed after experimental depletion of the γ-tubulin complex, suggesting that cells possess other factors that drive MT nucleation. Here, by combining gene knockout, auxin-inducible degron, RNA interference, MT depolymerisation/regrowth assay, and live microscopy, we identified four microtubule-associated proteins (MAPs), ch-TOG, CLASP1, CAMSAPs, and TPX2, which are involved in γ-tubulin-independent MT generation in human colon cancer cells. In the mitotic MT regrowth assay, nucleated MTs organised non-centriolar MT organising centres (ncMTOCs) in the absence of γ-tubulin. Depletion of CLASP1 or TPX2 substantially delayed ncMTOC formation, suggesting that they promote MT nucleation in the absence of γ-tubulin. In contrast, depletion of CAMSAPs or ch-TOG did not affect the timing of ncMTOC appearance. CLASP1 also accelerates γ-tubulin-independent MT regrowth during interphase. Thus, MT generation can be promoted by MAPs without the γ-tubulin template.
Phase-locking patterns underlying effective communication in exact firing rate models of neural networks
Authors: Reyner-Parra David , Huguet Gemma 
Published: August 2021

AbstractMacroscopic oscillations in the brain have been observed to be involved in many cognitive tasks but their role is not completely understood. One of the suggested functions of the oscillations is to dynamically modulate communication between neural circuits. The Communication Through Coherence (CTC) theory establishes that oscillations reflect rhythmic changes in excitability of the neuronal populations. Thus, populations need to be properly phase-locked so that input volleys arrive at the peaks of excitability of the receiving population to communicate effectively. Here, we present a modeling study to explore synchronization between neuronal circuits connected with unidirectional projections. We consider an Excitatory-Inhibitory (E-I) network of quadratic integrate-and-fire neurons modeling a Pyramidal-Interneuronal Network Gamma (PING) rhythm. The network receives an external periodic input from either one or two sources, simulating the inputs from other oscillating neural groups. We use recently developed mean-field models which provide an exact description of the macroscopic activity of the spiking network. This low-dimensional mean field model allows us to use tools from bifurcation theory to identify the phase-locked states between the input and the target population as a function of the amplitude, frequency and coherence of the inputs. We identify the conditions for optimal phaselocking and selective communication. We find that inputs with high coherence can entrain the network for a wider range of frequencies. Besides, faster oscillatory inputs than the intrinsic network gamma cycle show more effective communication than inputs with similar frequency. Our analysis further shows that the entrainment of the network by inputs with higher frequency is more robust to distractors, thus giving them an advantage to entrain the network. Finally, we show that pulsatile inputs can switch between attended inputs in selective attention.Author summaryOscillations are ubiquitous in the brain and are involved in several cognitive tasks but their role is not completely understood. The Communication Through Coherence theory proposes that background oscillations in the brain regulate the information flow between neural populations. The oscillators that are properly phase-locked so that inputs arrive at the peaks of excitability of the receiving population communicate effectively. In this paper, we study the emerging phase-locking patterns of a network generating PING oscillations under external periodic forcing, simulating the oscillatory input from other neural groups. We identify the conditions for optimal phase-locking and selective communication. Namely, we find that inputs with higher frequency and coherence have an adavantage to entrain the network and we quantify how robust are to distractors. Furthermore, we show how selective attention can be implemented by means of phase locking and we show that pulsatile inputs can switch between attended inputs.
An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise
Authors: Van Wouwe Tom , Ting Lena H. , De Groote Friedl 
Published: August 2021

AbstractOptimal control simulations have shown that both musculoskeletal dynamics and physiological noise are important determinants of movement. However, due to the limited efficiency of available computational tools, deterministic simulations of movement focus on accurately modelling the musculoskeletal system while neglecting physiological noise, and stochastic simulations account for noise while simplifying the dynamics. We took advantage of recent approaches where stochastic optimal control problems are approximated using deterministic optimal control problems, which can be solved efficiently using direct collocation. We were thus able to extend predictions of stochastic optimal control as a theory of motor coordination to include muscle coordination and movement patterns emerging from non-linear musculoskeletal dynamics. In stochastic optimal control simulations of human standing balance, we demonstrated that the inclusion of muscle dynamics can predict muscle co-contraction as minimal effort strategy that complements sensorimotor feedback control in the presence of sensory noise. In simulations of reaching, we demonstrated that nonlinear multi-segment musculoskeletal dynamics enables complex perturbed and unperturbed reach trajectories under a variety of task conditions to be predicted. In both behaviors, we demonstrated how interactions between task constraint, sensory noise, and the intrinsic properties of muscle influence optimal muscle coordination patterns, including muscle co-contraction, and the resulting movement trajectories. Our approach enables a true minimum effort solution to be identified as task constraints, such as movement accuracy, can be explicitly imposed, rather than being approximated using penalty terms in the cost function. Our approximate stochastic optimal control framework predicts complex features, not captured by previous simulation approaches, providing a generalizable and valuable tool to study how musculoskeletal dynamics and physiological noise may alter neural control of movement in both healthy and pathological movements.