bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stereo Slant Discrimination of Planar 3D Surfaces: Standard vs. Planar Cross-Correlation
Authors: Oluk Can , Bonnen Kathryn , Burge Johannes , Cormack Lawrence K. , Geisler Wilson S. 
Published: March 2021

AbstractBinocular stereo cues are important for discriminating 3D surface orientation, especially at near distances. We devised a single-interval task where observers discriminated the slant of a densely textured planar test surface relative to a textured planar surround reference surface. Although surfaces were rendered with correct perspective, the stimuli were designed so that the binocular cues dominated performance. Slant discrimination performance was measured as a function of the reference slant and the level of uncorrelated white noise added to the test-plane images in the left and right eye. We compared human performance with an approximate ideal observer (planar cross correlation, PCC) and two sub-ideal observers. The PCC observer uses the image in one eye and back projection to predict the test image in the other eye for all possible slants, tilts, and distances. The estimated slant, tilt, and distance are determined by the prediction that most closely matches the measured image in the other eye. The first sub-ideal observer (local PCC, LPCC) applies planar cross correlation over local neighborhoods and then pools estimates across the test plane. The second sub-optimal observer (standard cross correlation, SCC), uses only positional disparity information. We find that the ideal observer (PCC) and the first sub-ideal observer (LPCC) outperform the second sub-ideal observer (SCC), demonstrating the benefits of structural disparities. We also find that all three model observers can account for human performance, if two free parameters are included: a fixed small level of internal estimation noise, and a fixed overall efficiency scalar on slant discriminability.PrecisWe measured human stereo slant discrimination thresholds for accurately-rendered textured surfaces designed so that performance is dominated by binocular-disparity cues. We compared human performance with an approximate ideal observer and two sub-ideal observers.
Generation of fluorescent HCV pseudoparticles to study early viral entry events-involvement of Rab1a in HCV entry
Authors: Bhattacharjee Chayan , Mukhopadhyay Aparna 
Published: March 2021

AbstractUnderstanding the early events in viral biology holds the key to the development of preventives. In this study fluorescent Hepatitis C Virus pseudoparticles have been generated where the envelope glycoprotein has a GFP tag. Using these pseudoparticles entry assays were conducted where the entry of the pseudoparticles was tracked via confocal microscopy. Using this system, fusion of host and viral membranes is predicted to occur within 15 minutes of entry in HCV. Using cells with a knockdown for Rab1a, HCV trafficking was observed to be altered, indicating a role of Rab1a in HCV trafficking. In conclusion, this study reports the generation and use of fluorescent pseudoparticles which may be used to understand the early events of viral entry. This system may be adapted for the study of other enveloped viruses as well.HighlightsFluorescent HCV pseudoparticles have been created to study early entry events.HCV entry tracking via confocal microscopy reveals fusion within 15 minutes.Rab1a is important for HCV trafficking within the cell.
Epigenetic switching outcompetes genetic mutations during adaptation to fluctuating environments
Authors: Stajic Dragan , Bank Claudia , Gordo Isabel 
Published: March 2021

AbstractEpigenetic inheritance allows for the emergence of phenotypic plasticity in clonal populations and enables the rapid stochastic switching between distinct phenotypes. In natural environments, where stress conditions can recurrently fluctuate, clones with an epigenetic control of genes targeted by selection should be fitter than clones that rely solely on genetic mutation. To test this prediction, we engineered switcher and non-switcher yeast strains, where the uracil biosynthesis geneURA3is under fluctuating selection. Competitions of clones with an epigenetically controlledURA3with clones without switching ability (SIR3knock-out), show that epigenetic switching dominates under rapidly changing stresses. We further show that this advantage depends both on the switching rate and the period of environmental fluctuations. Remarkably, epigenetic clones with a high, but not with a low, rate of switching can co-exist with non-switchers even under a constant selective pressure, consistent with different constraints on the evolution of the rate of epigenetic switching.
Profiling of cytokines, chemokines and growth factors in saliva and gingival crevicular fluid
Authors: Liu Yong , Zhao Renping , Reda Bashar , Yang Wenjuan , Hannig Matthias , Qu Bin 
Published: March 2021

AbstractIn saliva and gingival crevicular fluid (GCF) soluble factors such as cytokines, chemokines and growth factors have shown a great potential serving as biomarkers for early detection and/or diagnosis of oral and systemic diseases. However, GCF and saliva, which one is a better source is still under debate. This study aimed to gain an overview of cytokines, chemokines and growth factors in saliva and GCF to pave the way for selecting suitable oral fluids for oral and systemic diseases. Multiplex cytokine assay was conducted to determine concentrations of cytokines, chemokines and growth factors in saliva and GCF samples from healthy subjects. The protocol for sample collection was carefully optimized. Stabilization, repeatability, and donor variation of the profiles were analyzed. We found that for different donors, cytokine and chemokine profiles showed unique patterns in saliva but similar patterns in GCF. In terms of growth factors, the profiles were individualized in saliva and GCF. All profiles stayed stable for the same healthy individual. In saliva, profiles of cytokines, chemokines and growth factors are individualized for different donors. In GCF, profiles of cytokines and chemokines are similar. Other factors, such as growth factors and T helper-related cytokines, are highly variable in donors. Profiles of soluble factors are not correlated in saliva and GCF. The comprehensive cytokine profiles in saliva and GCF reported in this work would serve as a good base for choosing promising cytokines for developing biomarkers in oral fluids.
TNF Blockade Reduces Prostatic Hyperplasia and Inflammation while Limiting BPH Diagnosis in Patients with Autoimmune Disease
Authors: Vickman Renee E. , Aaron-Brooks LaTayia , Zhang Renyuan , Lanman Nadia A. , Lapin Brittany , Gil Victoria , Greenberg Max , Sasaki Takeshi , Cresswell Gregory M. , Broman Meaghan M. , Petkewicz Jacqueline , Talaty Pooja , Helfand Brian T. , Glaser Alexander P. , Wang Chi-Hsiung , Franco Omar E. , Ratliff Timothy L. , Nastiuk Kent L. , Crawford Susan E. , Hayward Simon W. 
Published: March 2021

AbstractBenign prostatic hyperplasia (BPH) is ostensibly linked to autoimmune (AI) diseases, but whether the prostate is a target of systemic inflammation associated with AI conditions is unknown. Prostatic inflammation is linked to fibrosis, hyperplasia, and reduced responses to BPH-related medical therapies. This study was conducted to determine if AI disease correlates with BPH diagnosis and whether systemic targeting of an inflammatory mediator limits prostatic inflammation and hyperplasia. Patient medical records (n=112,152) were evaluated to determine BPH prevalence among different AI diseases. Inflammatory cells from human BPH tissues were analyzed by single-cell (sc)RNA-seq and the tumor necrosis factor (TNF)α-antagonist etanercept was tested in two murine models of prostatic enlargement. BPH prevalence was significantly higher among patients with AI disease compared to unaffected individuals. However, AI patients treated with TNFα-antagonists had a significantly reduced incidence of BPH. Data from scRNA- seq identified macrophages as a dominant source of TNFα andin vitroassays confirmed that TNFα stimulates BPH-derived fibroblast proliferation. In the AI patient cohort and murine models, systemic treatment with TNFα-antagonists decreased prostatic epithelial proliferation, macrophage infiltration, and epithelial NFκB activation compared to control tissues. These studies are the first to show that patients with AI diseases have a heightened susceptibility to BPH and that the TNFα-signaling axis is important for BPH pathogenesis. Macrophage-secreted TNFα may mechanistically drive BPH via chronic activation of the signaling axis and NFκB. TNFα blockade appears to be a promising new pharmacological approach to target inflammation and suppress BPH.One sentence summaryPatient data and mouse models suggest that repurposing tumor necrosis factor alpha blockade reduces inflammation-mediated prostatic hyperplasia.
Embryo development inCarica papayaLinn
Authors: Acevedo-Benavides Miguel , Bolaños-Villegas Pablo 
Published: March 2021

ABSTRACTPapaya (Carica papayaLinn.) is a tropical plant whose draft genome has been sequenced. Papaya produces large fruits rich in vitamins A and C and is an important cash crop in developing countries. Nonetheless, little is known about how the female gametophyte develops, how it is fertilized and how it develops into a mature seed containing an embryo and an endosperm. The Papaya female gametophyte displays aPolygonum-type architecture consisting of two synergid cells, an egg cell, a central cell, and three antipodal cells. Reports are available of the presumed existence of varieties in which cross fertilization is bypassed and autonomous development of embryos occurs (e.g., apomixis). In this study, we analyzed the development of female gametophytes in a commercial Hawaiian parental line and in the presumed apomictic Costa Rican line L1. Samples were collected before and after anthesis to compare the overall structure, size and transcriptional patterns of several genes that may be involved in egg and endosperm cell fate and proliferation. These genes were the putative papaya homologs ofARGONAUTE9(AGO9),MEDEA(MEA),RETINOBLASTOMA RELATED-1(RBR1), andSLOW WALKER-1(SWA1). Our results suggest that its feasible to identify the contour of structural features ofPolygonum-type development, and that in bagged female flowers of line L1 we might have observed autonomous development of embryo-like structures. Possible downregulation of papaya homologs forAGO9, MEA, RBR1andSWA1was observed in embryo sacs from line L1 before and after anthesis, which may suggest a tentative link between suspected apomixis and transcriptional downregulation of genes for RNA-directed DNA methylation, histone remodelers, and rRNA processing. Most notably, the large size of the papaya embryo sac suggests that it could be a cytological alternative toArabidopsis thalianafor study. Significant variation in embryo sac size was observed between the varieties under study, suggesting wide differences in the genetic regulation of anatomical features.
NCoR1 and SMRT fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling
Authors: Jha Atimukta , Ahad Abdul , Mishra Gyan Prakash , Sen Kaushik , Smita Shuchi , Minz Aliva P , Biswas Viplov Kumar , Tripathy Archana , Senapati Shanti Bhushan , Gupta Bhawna , Orbea Hans Acha , Raghav Sunil Kumar 
Published: March 2021

AbstractDendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT (NCoR2) enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4+and CD8+T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic and transcriptomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion represses mTOR-STAT3-IL10 signaling in cDC1 by downregulating NR4A1. Besides,NfkbiaandSocs3were down-regulated inNcor2(Smrt) knockdown cDC1, supporting increased production of inflammatory cytokines. Moreover, studies in mice showed, adoptive transfer of SMRT knockdown cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8+T-cell frequency, respectively. We also depicted decreasedNcor2expression in Rheumatoid Arthritis, a Th1/Th17 disease.
Information flows from hippocampus to auditory cortex during replay of verbal working memory items
Authors: Dimakopoulos Vasileios , Mégevand Pierre , Stieglitz Lennart , Imbach Lukas , Sarnthein Johannes 
Published: March 2021

AbstractThe maintenance of items in working memory relies on a widespread network of cortical areas and hippocampus where synchronization between electrophysiological recordings reflects functional coupling.We investigated the direction of information flow between auditory cortex and hippocampus while participants heard and then mentally replayed strings of letters in working memory by activating their phonological loop. We recorded LFP from the hippocampus, reconstructed beamforming sources of scalp EEG, and - additionally in 3 participants – recorded from subdural cortical electrodes. When analyzing Granger causality, the information flow was from auditory cortex to hippocampus with a peak in the 4-8 Hz range while participants heard the letters. This flow was subsequently reversed during maintenance while participants maintained the letters in memory. The functional interaction between hippocampus and the cortex and the reversal of information flow provide a physiological basis for the encoding of memory items and their active replay during maintenance.
A PX-BAR protein Mvp1/SNX8 and a dynamin-like GTPase Vps1 drive endosomal recycling
Authors: Suzuki Sho W. , Oishi Akihiko , Nikulin Nadia , Jorgensen Jeff R. , Baile Matthew G. , Emr Scott D. 
Published: March 2021

SUMMARYMembrane protein recycling systems are essential for maintenance of the endosome-lysosome system. In yeast, retromer and Snx4 coat complexes are recruited to the endosomal surface where they recognize cargos. They sort cargo and deform the membrane into recycling tubules that bud from the endosome and target to the Golgi. Here, we reveal that the SNX-BAR protein, Mvp1, mediates an endosomal recycling pathway which is mechanistically distinct from the retromer and Snx4 pathways. Mvp1 deforms the endosomal membrane and sorts cargos containing a specific sorting motif into a membrane tubule. Subsequently, Mvp1 recruits the dynamin-like GTPase Vps1 to catalyze membrane scission and release of the recycling tubule. Similarly, SNX8, the human homolog of Mvp1, which has been also implicated in Alzheimer’s disease, mediates formation of an endosomal recycling tubule. Thus, we present evidence for a novel endosomal retrieval pathway that is conserved from yeast to humans.In BriefPX-BAR Mvp1 and dynamin-like GTPase Vps1 drive retromer independent endosomal recycling.HighlightsRetromer- and Snx4-independent endosomal recycling pathway discoveredSNX-BAR Mvp1 and dynamin-like GTPase Vps1 mediate cargo sorting into recycling tubules/vesicles in the absence of retromer functionMvp1 together with retromer and Snx4 complexes contribute to proper endosome functionMvp1 mediated recycling is evolutionary conserved from yeast to humansCharacters: 43,934/45,000 (including spaces and main figure legends but excluding STAR Methods text, supplemental item legends, and References section)
Dosage sensitivity in Pumilio1-related phenotypes reflects distinct disease mechanisms
Authors: Botta Salvatore , de Prisco Nicola , Chemiakine Alexei , Cabaj Maximilian , Patel Purvi , Doron-Mandel Ella , Treadway Colton J. , Jovanovic Marko , Brown Nicholas G. , Soni Rajesh K. , Gennarino Vincenzo A. 
Published: March 2021

AbstractMutations in the RNA-binding protein (RBP) Pumilio1 (PUM1) can cause dramatically different phenotypes. We previously noted that phenotypic severity tracked with protein dosage: a mild mutation that reduces PUM1 levels by 25% causes late-onset ataxia, whereas PUM1 haploinsufficiency causes developmental delay and seizures. Why this difference in expression should cause such different phenotypes has been unclear: PUM1 targets are de-repressed to equal degrees in both cases, and the more severe mutation does not hinder PUM1’s RNA-binding ability. We therefore developed a PUM1 interactome in the murine brain. We find that mild PUM1 loss de-represses PUM1-specific targets, but PUM1 haploinsufficiency disrupts several interactors and regulation of their targets. We validated these phenomena in patient-derived cell lines and show that normalizing PUM1 levels restores interactors and their targets to proper levels. We therefore propose that dosage sensitivity does not necessarily reflect a linear change in protein abundance but can involve distinct mechanisms. Studying the interactors of RBPsin vivowill be necessary to understand their functions in neurological diseases.
Reevaluating claims of ecological speciation inHalichoeres bivittatus
Authors: Warren Dan L. , Eytan Ron I. , Dornburg Alex , Iglesias Teresa L. , Brandley Matthew C. , Wainwright Peter C. 
Published: March 2021

AbstractUnderstanding the role of ecological processes in speciation has become one of the most active areas of research in marine population biology in recent decades. The traditional view was that allopatry was the primary driver of speciation in marine taxa, but the geography of the marine environment and the dispersal capabilities of many marine organisms render this view somewhat questionable. One of the earliest and most highly cited empirical examples of ecological speciation with gene flow in marine fishes is that of the slippery dick wrasse,Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep north-south divergence in a single mitochondrial locus, combined with a finding that these two haplotypes were associated with different habitat types in the Florida Keys and Bermuda, where they overlap. Here we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study, and find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations. These results severely undermine claims of ecological speciation with gene flow inHalichoeres bivittatus. We argue that future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.
Qualification of the UniBw protection concept in different rooms of the Obermenzinger high school
Authors: Kähler Christian J. , Fuchs Thomas , Hain Rainer 
Published: March 2021

AbstractCurrent research has shown that SARS-CoV-2 is transmitted via airborne particles. These particles are generated when infected persons exhale and they spread throughout the room, resulting in a high concentration and thus a high risk of infection of non-infected persons. One way to reduce the concentration of particles is to filter them using mobile room air cleaners, which can be easily set up and reduce the concentration of viruses or keep them at a low level. Since many studies are conducted in generic rooms, the question of the cleaning performance of such room air cleaners in real rooms arises. In order to investigate this, measurements of the effectiveness were carried out in a total of 4 different rooms of the “Obermenzinger Gymnasium” (Obermenzinger high school) in Munich. It can be shown that good effects of the room air cleaners are achieved even under realistic conditions. Even Plexiglas screens, which serve as protection against direct infection, have no negative influence.
Modelling, prediction and design of national COVID-19 lockdowns by stringency and duration
Authors: Mellone Alberto , Gong Zilong , Scarciotti Giordano 
Published: March 2021

AbstractThe implementation of lockdowns has been a key policy to curb the spread of COVID-19 and to keep under control the number of infections. However, quantitatively predicting in advance the effects of lockdowns based on their stringency and duration is a complex task, in turn making it difficult for governments to design effective strategies to stop the disease. Leveraging a novel mathematical “hybrid” approach, we propose a new epidemic model that is able to predict the future number of active cases and deaths when lockdowns with different stringency levels or durations are enforced. The key observation is that lockdown-induced modifications of social habits may not be captured by traditional mean-field compartmental models because these models assume uniformity of social interactions among the population, which fails during lockdown. Our model is able to capture the abrupt social habit changes caused by lockdowns. The results are validated on the data of Israel and Germany by predicting past lockdowns and providing predictions in alternative lockdown scenarios (different stringency and duration). The findings show that our model can effectively support the design of lockdown strategies by stringency and duration, and quantitatively forecast the course of the epidemic during lockdown.
Novel aluminophosphate Na6[Al3P5O20] with the original microporous crystal structure established in the study of a pseudomerohedric microtwin
Authors: Yakubovich Olga V. , Kiriukhina Galina V. , Volkov Anatoliy S. , Dimitrova Olga V. , Borovikova Elena Yu. 
Published: March 2021

The synthesis and characterization of a new aluminophosphate, Na6[Al3P5O20], obtained as single crystals in the same experiment together with Cl-sodalite, Na8[Al6Si6O24]Cl2, is reported. Na6[Al3P5O20], with a strongly pseudo-orthorhombic lattice, is described by the monoclinic crystal structure established in the study of a pseudomerohedric microtwin. The design of Na6[Al3P5O20] can be interpreted as an alternative to sodalite, with a monoclinic (pseudo-orthorhombic) 2×4×1 super-structure and unit-cell parameters multiples of those of sodalite: a ≃ 2a
s, b ≃ 4b
s and c ≃ c
s. The triperiodic framework is built by AlO6, AlO4 and PO4 polyhedra having vertex-bridging contacts. While all the oxygen vertices of the Al-centred octahedra and tetrahedra are shared with phosphate groups, some of the PO4 tetrahedra remain `pendant', e.g. containing vertices not shared with other polyhedra of the aluminophosphate construction. Na atoms occupy framework channels and cavities surrounded by eight-, six- and four-membered windows with maximal effective pore widths of 4.86 × 3.24 and 4.31 × 3.18 Å. The generalized framework density is equal to 19.8, which means that the compound may be classified as a microporous zeolite. The Na6[Al3P5O20] crystal structure is discussed as being formed from octahedral rods arranged in two perpendicular directions, similar to the rods elongated in one direction in the NASICON-type compounds, which have been intensively investigated as promising materials for batteries. Analogous properties can be expected for phases with a modified composition of the Na6Al3P5O20 topology, where the Al atoms at the centres of octahedra are replaced by Fe, V or Cr.