bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ghost Lineages Highly Influence the Interpretation of Introgression Tests
Authors: Tricou Théo , Tannier Eric , de Vienne Damien M 
Published: February 2022

AbstractMost species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression, and admixture, are therefore likely to involve “ghosts,” that is extinct, unknown, or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario. [ABBA–BABA; D-statistic; gene flow; ghost lineage; introgression; simulation.]
The relationship between tree size and tree water-use: is competition for water size-symmetric or size-asymmetric?
Authors: Forrester David I , Limousin Jean-Marc , Pfautsch Sebastian 
Published: February 2022

Abstract
Relationships between tree size and water use indicate how soil water is partitioned between differently sized individuals, and hence competition for water. These relationships are rarely examined, let alone whether there is consistency in shape across populations. Competition for water among plants is often assumed to be size-symmetric, i.e., exponents (b1) of power functions (water use ∝ biomassb1) equal to 1, with all sizes using the same amount of water proportionally to their size. We tested the hypothesis that b1 actually varies greatly, and based on allometric theory, that b1 is only centered around 1 when size is quantified as basal area or sapwood area (not diameter). We also examined whether b1 varies spatially and temporally in relation to stand structure (height and density) and climate. Tree water use ∝ sizeb1 power functions were fitted for 80 species and 103 sites using the global SAPFLUXNET database. The b1 were centered around 1 when tree size was given as basal area or sapwood area, but not as diameter. The 95% confidence intervals of b1 included the theoretical predictions for the scaling of plant vascular networks. b1 changed through time within a given stand for the species with the longest time series, such that larger trees gained an advantage during warmer and wetter conditions. Spatial comparisons across the entire dataset showed that b1 correlated only weakly (R2 &lt; 12%) with stand structure or climate, suggesting that inter-specific variability in b1 and hence the symmetry of competition for water may be largely related to inter-specific differences in tree architecture or physiology rather than to climate or stand structure. In conclusion, size-symmetric competition for water (b1 ≈ 1) may only be assumed when size is quantified as basal area or sapwood area, and when describing a general pattern across forest types and species. There is substantial deviation in b1 between individual stands and species.
Investigation of Autologous Fat Transfer in Capsule Formation around Silicone Implants in a Rat Model
Authors: Papaconstantinou Anthony , Koletsa Triantafyllia , Demiri Efterpi , Tzorakoleftheraki Sofia-Eleni , Gasteratos Kostantinos , Pavlidis Leonidas , Dionyssiou Dimitrios , Spyropoulou Georgia-Alexandra 
Published: February 2022

Background:
In this experimental study, the authors investigated whether fat placement in the pocket during implant insertion affects capsule formation.

Methods:
Twenty albino Wistar rats, 400 g each, were used. The rats were divided into two groups, A and B, of 10 rats each. At the dorsum of each rat, four pockets (2 × 2 cm each) were dissected, two left and two right of the midline. In each pocket, a 1 × 1 × 1.5-cm silicone implant was inserted. In the two left pockets, only silicone implants were placed (control). In the two right pockets, 0.4 ml of fat was injected around the implant. Animals in group A were killed 2 months postoperatively, and those in group B were killed 4 months postoperatively. The implants were dissected with the capsule and sent for histopathologic examination.

Results:
The data of the fat transfer group was compared with control in groups A and B. Capsule thickness, neovascularization, myofibroblast layer thickness, and mast cell population demonstrated no statistically significant difference in either group A (p = 0.385, p = 0.862, p = 0.874, and p = 0.210, respectively) or group B (p = 0.338, p = 1.000, p = 0.288, and p = 0.344, respectively). Inflammation was statistically significantly less (p = 0.07) at 4 months (group B) in the fat transfer group compared to the control group. Likewise, cellularity was statistically significantly less (p = 0.019) at 4 months for the fat transfer group compared with the control group.

Conclusion:
Fat injection in the pocket during implant placement may reduce inflammation and cellularity of capsules and predispose to faster capsule maturation.

Clinical Relevance Statement:
Fat transfer around implants may positively affect implant-based breast reconstruction and/or breast augmentation.
Incorrect Knowledge of Event-Driven PrEP “2-1-1” Dosing Regimen Among PrEP-Experienced Gay and Bisexual Men in Australia
Authors: Chan Curtis , Vaccher Stefanie , Fraser Doug , Grulich Andrew E. , Holt Martin , Zablotska-Manos Iryna , Prestage Garrett P. , Bavinton Benjamin R. 
Published: February 2022

Background:
Event-driven pre-exposure prophylaxis (ED-PrEP), when taken according to the “2-1-1” dosing method, is highly effective at preventing HIV acquisition for gay, bisexual, and other men who have sex with men (GBM). Any missed doses when using ED-PrEP drastically reduce its effectiveness, so it is vital that people using this method know how to take it correctly. This study investigated Australian GBM's awareness of ED-PrEP and their knowledge of how to take it correctly.

Method:
We conducted a survey of 1471 PrEP-experienced GBM in Australia, between October 2019 and March 2020. The survey assessed awareness and knowledge of the 3 components of the “2-1-1” ED-PrEP dosing regimen (number of pills for loading dose, timing of loading dose, and number of days after sex to take PrEP pills) among GBM. Characteristics associated with ED-PrEP awareness and correct knowledge of how to take ED-PrEP were assessed with multivariate logistic regression.

Results:
Two-thirds (n = 1004, 68.4%) had heard of ED-PrEP, of whom only one-eighth (n = 125, 12.5%) knew the correct details of the “2-1-1” ED-PrEP method; one-third (n = 339, 33.8%) did not know any of the 3 key components. Awareness of ED-PrEP and correct knowledge was associated with greater belief in PrEP efficacy, university education, and intention to take a nondaily PrEP regimen in the next 6 months.

Conclusions:
Although ED-PrEP awareness was considerable, most participants did not know how to use ED-PrEP correctly. Further work is needed to increase awareness and knowledge of ED-PrEP among GBM.
Packing of elastic rings with friction
Authors: Alben S. 
Published: February 2022

We study the deformations of elastic filaments confined within slowly shrinking circular boundaries, under contact forces with friction. We perform computations with a spring-lattice model that deforms like a thin inextensible filament of uniform bending stiffness. Early in the deformation, two lobes of the filament make contact. If the friction coefficient is small enough, one lobe slides inside the other; otherwise, the lobes move together or one lobe bifurcates the other. There follows a sequence of deformations that is a mixture of spiralling and bifurcations, primarily the former with small friction and the latter with large friction. With zero friction, a simple model predicts that the maximum curvature and the total elastic energy scale as the wall radius to the

−
3

/

2

and

−
2

powers, respectively. With non-zero friction, the elastic energy follows a similar scaling but with a prefactor up to eight times larger, due to delayering and bending with a range of small curvatures. For friction coefficients as large as 1, the deformations are qualitatively similar with and without friction at the outer wall. Above 1, the wall friction case becomes dominated by buckling near the wall.
Single-Droplet Surface-Enhanced Raman Scattering Decodes the Molecular Language of Liquid-Liquid Phase Separation
Authors: Avni Anamika , Joshi Ashish , Walimbe Anuja , Pattanashetty Swastik G. , Mukhopadhyay Samrat 
Published: February 2022

AbstractBiomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease.
Taxonomic practice, creativity, and fashion: What’s in a spider name?
Authors: Mammola Stefano , Viel Nathan , Amiar Dylan , Mani Atishya , Hervé Christophe , Heard Stephen B. , Fontaneto Diego , Pétillon Julien 
Published: February 2022

ABSTRACTThere’s a secret pleasure in naming new species. Besides traditional etymologies recalling the sampling locality, habitat, or morphology of the species, etymologies may be tributes to some meaningful person (for example, the species’ collector, the author’s husband or wife, or a celebrity), pop culture references, and even exercises of enigmatography. The possibility of choosing witty or even playful names for new species departs from the otherwise impersonal and old-fashioned writing style that’s common in taxonomic papers; but, how has the descriptor’s choice for specific etymologies changed over the 300+ years since the introduction of the Linnaean binomial system of nomenclature? Using an unprecedented dataset of 48,464 etymologies (all valid species and subspecies of spiders described between 1757 and May 2020), we tested the hypothesis that species names given by taxonomists are deeply influenced by their cultural background. In particular, we asked whether naming practices change through space (continent in which the species was found) or have changed through time (year of description). We observed spatial and temporal differences in the way taxonomists name new species. In absolute terms, etymologies referring to morphology were the most frequently used. In relative terms, however, references to morphology peaked in 1850–1900 and then began to decline, with a parallel increase in etymologies dedicated to people and geography. Currently, these are the most widely used, with ∼38% of all etymologies of spider species described in the last ten years referring to geography, ∼25% to people, and ∼25% to morphology. Interestingly, there has been a dramatic increase in etymologies referring to pop culture and other cultural aspects in the last two decades, especially in Europe and the Americas. While such fashionable names often carry little or no biological information regarding the species itself, they help give visibility to the science of taxonomy, a discipline currently facing a profound crisis within academia. Taxonomy is among the most unchanged disciplines across the last centuries in terms of background, tools, rules, and writing style; but our analysis suggests that taxonomists remain deeply influenced by their living time and space.
Antibody and memory B-cell immunity in a heterogeneously SARS-CoV-2 infected and vaccinated population
Authors: Bednarski Eva , Rio Estrada Perla M Del , DaSilva Justin , Boukadida Celia , Zhang Fengwen , Luna-Villalobos Yara A , Rodríguez-Rangel Ximena , Pitén-Isidro Elvira , Luna-García Edgar , Rivera Dafne Díaz , López-Sánchez Dulce M , Tapia-Trejo Daniela , Soto-Nava Maribel , Astorga-Castañeda Myriam , Martínez-Moreno José O , Urbina-Granados Guadalupe S , Jiménez-Jacinto José A , Serna Alvarado Francisco J , Enriquez-López Yerania E , López-Arellano Oliva , Reyes-Teran Gustavo , Bieniasz Paul D. , Avila-Rios Santiago , Hatziioannou Theodora 
Published: February 2022

AbstractGlobal population immunity to SARS-CoV-2 is accumulating through heterogenous combinations of infection and vaccination. Vaccine distribution in low- and middle-income countries has been variable and reliant on diverse vaccine platforms. We studied B-cell immunity in Mexico, a middle-income country where five different vaccines have been deployed to populations with high SARS-CoV-2 incidence. Levels of antibodies that bound a stabilized prefusion spike trimer, neutralizing antibody titers and memory B-cell expansion correlated with each other across vaccine platforms. Nevertheless, the vaccines elicited variable levels of B-cell immunity, and the majority of recipients had undetectable neutralizing activity against the recently emergent omicron variant. SARS-CoV-2 infection, experienced prior to or after vaccination potentiated B-cell immune responses and enabled the generation of neutralizing activity against omicron and SARS-CoV for all vaccines in nearly all individuals. These findings suggest that broad population immunity to SARS-CoV-2 will eventually be achieved, but by heterogenous paths
psntools - a Python package for protein structure network analysis
Authors: Sora Valentina , Tiberti Matteo , Papaleo Elena 
Published: February 2022

AbstractThe application of network theory to investigate protein structures and conformational ensembles through Protein Structure Networks (PSNs) has proven particularly insightful to study protein dynamics, the potentially disruptive effects of disease-related mutations, and allosteric mechanisms. Here, we presentpsntools, a novel Python package for downstream analysis of PSNs.psntoolsis completely PSN-agnostic, in contrast with several available tools in the community.psntoolsrelies only on a few Python dependencies, most notably MDAnalysis and NetworkX, works without external software, and can be incorporated into Python-based analysis pipelines. We also present an example of the usage ofpsntoolson a case of study of biological interest, which helped produce novel insights on the structural details of the interaction between BCL-xL and the BH3 motif of BECLIN-1. Thepsntoolspackage and the data associated with the case study are available athttps://github.com/ELELAB/psntools.
The mechanism of RNA capping by SARS-CoV-2
Authors: Park Gina J. , Osinski Adam , Hernandez Genaro , Eitson Jennifer L. , Majumdar Abir , Tonelli Marco , Henzler-Wildman Katie , Pawłowski Krzysztof , Chen Zhe , Li Yang , Schoggins John W. , Tagliabracci Vincent S. 
Published: February 2022

AbstractThe SARS-CoV-2 RNA genome contains a 5’-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2’-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature
Authors: Correy Galen J. , Kneller Daniel W. , Phillips Gwyndalyn , Pant Swati , Russi Silvia , Cohen Aina E. , Meigs George , Holton James M. , Gahbauer Stefan , Thompson Michael C. , Ashworth Alan , Coates Leighton , Kovalevsky Andrey , Meilleur Flora , Fraser James S. 
Published: February 2022

AbstractThe NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
Myosin 10 supports mitotic spindle bipolarity by promoting PCM integrity and supernumerary centrosome clustering
Authors: Yim Yang-In , Pedrosa Antonio , Wu Xufeng , Cheney Richard E. , Hammer John A. 
Published: February 2022

AbstractMyosin 10 (Myo10) is a member of the MyTH4/FERM domain family of unconventional, actin-based motor proteins. Studies have implicated Myo10 in supporting cell adhesion via its integrin-binding FERM domain, and spindle positioning and spindle pole integrity via its microtubule-binding MyTH4 domain. Here we characterized Myo10’s contribution to mitosis using Myo10 knockout HeLa cells and MEFs isolated from a Myo10 knockout mouse. Most notably, both of these knockout cells exhibit a pronounced increase in the frequency of multipolar spindles. Staining of unsynchronized metaphase cells showed that the primary driver of spindle multipolarity in knockout MEFs and knockout HeLa cells lacking supernumerary centrosomes is PCM fragmentation, which creates y-tubulin-positive, centriole-negative microtubule asters that serve as additional spindle poles. For HeLa cells possessing supernumerary centrosomes, Myo10 depletion further accentuates spindle multipolarity by impairing centrosome clustering. These results argue, therefore, that Myo10 supports spindle bipolarity by maintaining PCM integrity in both normal and cancer cells, and by promoting supernumerary centrosome clustering in cancer cells. Finally, we present evidence that the defect in spindle pole integrity in Myo10 knockout cells is likely due to a defect in pole stability rather than pole maturation, and that Myo10 promotes supernumerary centrosome clustering at least in part by promoting cell adhesion during mitosis.
In situ study on the effect of stress on corrosion behavior of AZ91 magnesium alloy
Authors: Zhao Pengxiong , Wu Wei , Ma Zeyu , Dan Yong 
Published: February 2022

Purpose
This paper aims to investigate the corrosion evolution process of AZ91 magnesium alloy in 3.5 wt.% NaCl solution under different stresses by using in situ methods, thereby evaluate the influence of stress on the corrosion sensitivity of AZ91 magnesium alloy, and discuss the potential mechanism.

Design/methodology/approach
A four-point bending method was used to apply different loads to the magnesium alloy samples, a charge coupled device camera and electrochemical impedance spectroscopy test being used for in situ study. Scanning electron microscopy and X-ray diffraction (XRD) analysis were performed for corrosion product and morphology characteristics.

Findings
The observation results show that the corrosion of AZ91 magnesium alloy becomes more and more serious with the increase in the stress and generated many corrosion products. Originally, corrosion products prevented alloy matrix from contacting the corrosive medium. However, the increase in the stress facilitated the emergence of the corrosion holes in the corrosion products, which provided the microscopic channels for corrosive solution to attack the Mg alloy matrix, and accelerated the corrosion of the magnesium alloy, resulting in a lot of corrosion pits on the magnesium alloy surface under the corrosion product layer.

Originality/value
The evolution information of corrosion process is crucial to explore the mechanism of corrosion. Currently, most researches about corrosion of magnesium alloy used traditional testing techniques to obtain corrosion information, lacking the direct tracking and monitoring of the corrosion evolution process. Hence, this paper focuses on in situ corrosion study of AZ91 magnesium alloy. The technology with spatial resolution capability observed the changes in magnesium alloy surface at different times in the corrosion process in situ. Meanwhile, the in situ electrochemical technology was used to monitor the changes in micro-electrochemical signals during the corrosion process of magnesium alloy under different stresses.