bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of focal radiotherapy boost for prostate cancer and perceived barriers toward its implementation: a survey
Authors: Zhong Allison Y. , Lui Asona J. , Katz Matthew S. , Berlin Alejandro , Kamran Sophia C. , Kishan Amar U. , Murthy Vedang , Nagar Himanshu , Seible Daniel , Stish Bradley J. , Tree Alison C. , Seibert Tyler M. 
Published: February 2023

AbstractBackgroundIn a recent phase III randomized control trial (FLAME), delivering a focal radiotherapy (RT) boost to tumors visible on MRI was shown to improve outcomes for prostate cancer patients without increasing toxicity. The aim of this study was to assess how widely this technique is being applied in current practice as well as physicians’ perceived barriers toward its implementation.MethodsAn online survey assessing the use of intraprostatic focal boost was conducted in December 2022 and February 2023. The survey link was distributed to radiation oncologists worldwide via email list, group text platform, and social media.ResultsThe survey initially collected 205 responses from various countries over a two-week period in December 2022. The survey was then reopened for one week in February 2023 to allow for more participation, leading to a total of 263 responses. The highest-represented countries were the United States (42%), Mexico (13%), and the United Kingdom (8%). The majority of participants worked at an academic medical center (52%) and considered their practice to be at least partially genitourinary (GU)-subspecialized (74%).57% of participants reportednotroutinely using intraprostatic focal boost. Even among complete subspecialists, a substantial proportion (39%) do not routinely use focal boost. Less than half of participants in both high-income and low-to-middle-income countries were shown to routinely use focal boost. The most commonly cited barriers were concerns about registration accuracy between MRI and CT (37%), concerns about risk of additional toxicity (35%), and challenges to accessing high-quality MRI (29%).ConclusionDespite level 1 evidence from the FLAME trial, most radiation oncologists surveyed are not routinely offering focal RT boost. Adoption of this technique might be accelerated by increased access to high-quality MRI, better registration algorithms of MRI to CT simulation images, physician education on benefit-to-harm ratio, and training on contouring prostate lesions on MRI.
Stomatal dynamics are regulated by leaf hydraulic traits and guard cell anatomy in nine true mangrove species
Authors: Qie Ya-Dong , Zhang Qi-Wei , McAdam Scott A. M. , Cao Kun-Fang 
Published: February 2023

AbstractStomatal regulation is critical for mangroves to survive water deficits and highly fluctuating ambient water availability in the hyper-saline intertidal zone. Despite the importance of stomatal regulation in mangroves very little is known about stomatal sensitivity to vapour pressure deficit (VPD), and the co-ordination of this trait with stomatal morphology and leaf hydraulic traits in these species.We measured the stomatal response to a step increase in vapour pressure deficit (VPD)in situ, stomatal anatomy, leaf hydraulic vulnerability and pressure-volume traits in nine true mangrove species of five families. We aimed to answer two questions: (1) Does stomatal morphology determine stomatal dynamics in response to a high VPD in mangroves and (2) do leaf hydraulic traits influence stomatal sensitivity to VPD in mangroves?We found that the stomata of mangrove plants highly sensitive to VPD, and that species with higher maximum stomatal conductance had slower stomatal responses to an increase in VPD, and that stomatal density and size were correlated with the speed of stomatal closure at high VPD across the closely-related species. We also found that a higher leaf capacitance (Cleaf) and more resistance to leaf hydraulic vulnerability were associated with slower stomatal responses to an increase in VPD.Our results demonstrate that the dynamics of the stomatal response to an increase in VPD are regulated by leaf hydraulic traits and stomatal morphology. Our work provides a quantitative framework to better understand stomatal regulation in mangroves in an environment with highly dynamic water availability.
Calcium transients trigger switch-like discharge of prostaglandin E2in an extracellular signal-regulated kinase-dependent manner
Authors: Watabe Tetsuya , Yamahira Shinya , Takakura Kanako , Thumkeo Dean , Narumiya Shuh , Matsuda Michiyuki , Terai Kenta 
Published: February 2023

AbstractProstaglandin E2(PGE2) is a key player in a plethora of physiological and pathological events. Nevertheless, little is known about the dynamics of PGE2secretion from a single cell and its effect on the neighboring cells. Here, by observing confluent Madin-Darby canine kidney (MDCK) epithelial cells expressing fluorescent biosensors we demonstrate that calcium transients in a single cell cause PGE2-mediated radial spread of PKA activation (RSPA) in neighboring cells. Byin vivoimaging, RSPA was also observed in the basal layer of the mouse epidermis. Experiments with an optogenetic tool revealed a switch-like PGE2discharge in response to the increasing cytoplasmic Ca2+concentrations. The cell density of MDCK cells correlated with the frequencies of calcium transients and the following RSPA. The extracellular signal-regulated kinase (ERK) activation also enhanced the frequency of RSPA in MDCK andin vivo. Thus, the PGE2discharge is regulated temporally by calcium transients and ERK activity.
Deep brain stimulation does not modulate fMRI resting-state functional connectivity in essential tremor
Authors: Awad Amar , Grill Filip , Blomstedt Patric , Nyberg Lars , Eriksson Johan 
Published: February 2023

AbstractBackgroundWhile the effectiveness of deep brain stimulation (DBS) in alleviating essential tremor (ET) is well-established, the underlying mechanisms of the treatment are unclear. ET, as characterised by tremor during action, is proposed to be driven by a dysfunction in the cerebello-thalamo-cerebral circuit that is evident not only during motor actions but also during rest.MethodsDBS effects on resting-state functional connectivity were investigated by functional MRI in 16 ET patients with fully implanted DBS in the caudal zona incerta during On and Off therapeutic stimulation, in a counterbalanced design. Functional connectivity was calculated between different constellations of sensorimotor as well as non-sensorimotor regions (as derived from seed-based and data-driven approaches), and compared between On and Off DBS.ResultsWe found that DBS did not modulate resting-state functional connectivity in ET.ConclusionsThe lack of DBS modulation during resting-state, in combination with previously demonstrated effects on the cerebello-thalamo-cerebral circuit during motor tasks, suggest an action-dependent modulation of DBS.
Comparison of Bayesian methods for incorporating adult clinical trial data to improve certainty of treatment effect estimates in children
Authors: Walker R , Phillips B , Dias S 
Published: February 2023

AbstractThere are challenges associated with recruiting children to take part in randomised clinical trials and as a result, compared to adults, in many disease areas we are less certain about which treatments are most safe and effective. This can lead to weaker recommendations about which treatments to prescribe in practice. However, it may be possible to ‘borrow strength’ from adult evidence to improve our understanding of which treatments work best in children, and many different statistical methods are available to conduct these analyses. In this paper we discuss Bayesian methods for extrapolating adult clinical trial evidence to children. Using an exemplar dataset, we compare the effect of modelling assumptions on the estimated treatment effect and associated heterogeneity. We finally discuss the appropriateness of different modelling assumptions in the context of estimating treatment effect in children.
Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes
Authors: Tagirdzhanova Gulnara , Saary Paul , Cameron Ellen S. , Garber Arkadiy I. , Díaz Escandón David , Goyette Spencer , Nogerius Veera Tuovinen , Passo Alfredo , Mayrhofer Helmut , Holien Håkon , Tønsberg Tor , Stein Lisa Y. , Finn Robert D. , Spribille Toby 
Published: February 2023

AbstractLichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobiont, no global census of lichen organismal composition has been undertaken. Here, we analyze the genome content of 437 lichen metagenomes from six continents, and show that four bacterial lineages occur in the majority of lichen symbioses, at a frequency on par with algal photobionts. A single bacterial genus,Lichenihabitans, occurs in nearly one-third of all lichens sampled. Genome annotations from the most common lichen bacterial symbionts suggest they are aerobic anoxygenic photoheterotrophs and produce essential vitamins, but do not fix nitrogen. We also detected secondary basidiomycete symbionts in about two-thirds of analyzed metagenomes. Our survey suggests a core set of four to seven microbial symbionts are involved in forming and maintaining lichen symbioses.
The consequence of ATP synthase dimer angle on mitochondrial morphology studied by cryo-electron tomography
Authors: Buzzard Emma , McLaren Mathew , Bragoszewski Piotr , Brancaccio Andrea , Ford Holly , Daum Bertram , Kuwabara Patricia , Collinson Ian , Gold Vicki A.M. 
Published: February 2023

AbstractMitochondrial ATP synthases form rows of dimers, which induce membrane curvature to give cristae their characteristic lamellar or tubular morphology. The angle formed between the central stalks of ATP synthase dimers varies between species. Using cryo-electron tomography and sub-tomogram averaging, we determined the structure of the ATP synthase dimer from the nematode wormC. elegansand show that the dimer angle differs from previously determined structures. The consequences of this species-specific difference at the dimer interface were investigated by comparingC. elegansandS. cerevisiaemitochondrial morphology. We reveal thatC. eleganshas a larger ATP synthase dimer angle with more lamellar (flatter) cristae when compared to yeast. The underlying cause of this difference was investigated by generating an atomic model of theC. elegansATP synthase dimer by homology modelling. A comparison of ourC. elegansmodel to an existingS. cerevisiaestructure reveals the presence of extensions and rearrangements inC. eleganssubunits associated with maintaining the dimer interface. We speculate that increasing dimer angles could provide an advantage for species that inhabit variable-oxygen environments by forming flatter more energetically efficient cristae.
Discovery of a unique pathway for glutathione utilization in Francisella
Authors: Wang Yaxi , Ledvina Hannah E. , Tower Catherine A. , Kambarev Stanimir , Liu Elizabeth , Charity James C. , Kreuk Lieselotte S.M. , Chen Qiwen , Gallagher Larry A. , Radey Matthew C. , Rerolle Guilhem F. , Li Yaqiao , Penewit Kelsi M. , Turkarslan Serdar , Skerrett Shawn J. , Salipante Stephen J. , Baliga Nitin S. , Woodward Joshua J. , Dove Simon L. , Peterson S. Brook , Celli Jean , Mougous Joseph D. 
Published: February 2023

AbstractGlutathione (GSH) is an abundant metabolite that can act as a signal, a nutrient source, or serve in a redox capacity for intracellular pathogens. For Francisella, GSH is thought to be a critical in vivo source of cysteine; however, the cellular pathways permitting GSH utilization by Francisella differ between strains and have remained poorly understood. Using genetic screening, we discovered a unique pathway for GSH utilization in Francisella spp. Whereas prior work suggested GSH catabolism initiates in the periplasm, the pathway we define consists of a major facilitator superfamily member that transports intact GSH and a previously unrecognized bacterial cytoplasmic enzyme that catalyzes the first step of GSH degradation. Interestingly, we find that the transporter gene for this pathway is pseudogenized in pathogenic Francisella, explaining phenotypic discrepancies in GSH utilization among Francisella spp. and revealing a critical role for GSH in the environmental niche of these bacteria.
Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques
Authors: Song Kaiyuan , Xu Honglin , Shi Yi , Hao Jie , Da Lin-Tai , Zou Xin 
Published: February 2023

AbstractThe molecular mechanisms underlying the recognition of epitopes by T cell receptors (TCRs) are critical for activating T cell immune responses and rationally designing TCR-based therapeutics. Single-cell sequencing techniques vastly boost the accumulation of TCR sequences, while the limitation of available TCR-pMHC structures hampers further investigations. In this study, we proposed a comprehensive strategy that incorporates structural information and single-cell sequencing data to investigate the epitope-recognition mechanisms of TCRs. By antigen specificity clustering, we mapped the epitope sequences between epitope-known and epitope-unknown TCRs from COVID-19 patients. One reported SARS-CoV-2 epitope, NQKLIANQF (S919-927), was identified for a TCR expressed by 614 T cells (TCR-614). Epitope screening also identified a potential cross-reactive epitope, KLKTLVATA (NSP31790-1798), for a TCR expressed by 204 T cells (TCR-204). According to the molecular dynamics (MD) simulations, we revealed the detailed epitope-recognition mechanisms for both TCRs. The structural motifs responsible for epitope recognition revealed by the MD simulations are consistent with the sequential features recognized by the sequence-based clustering method. This strategy will facilitate the discovery and optimization of TCR-based therapeutics. In addition, the comprehensive strategy can also promote the development of cancer vaccines in virtue of the ability to discover neoepitopes and epitope-recognition mechanisms.
Multi-species polyploidization, chromosome shuffling, and genome extraction inZea/Tripsacumhybrids
Authors: Iqbal Muhammad Zafar , Wen Xiaodong , Xu Lulu , Zhao Yanli , Li Jing , Jiang Weiming , Cheng Mingjun , Li Huaxiong , Li Yinzheng , Li Xiaofeng , He Ruyu , He Jianmei , Ali Asif , Peng Yan , Rong Tingzhao , Tang Qilin 
Published: February 2023

AbstractBy hybridization and special sexual reproduction, we sequentially aggregatedZea mays, Zea perennis,andTripsacum dactyloidesin an allohexaploid, backcrossed it with maize, derived self-fertile allotetraploids of maize andZ. perennisby natural genome extraction, extended their first six selfed generations, and finally constructed amphitetraploid maize using nascent allotetraploids as a genetic bridge. Transgenerational chromosome inheritance, subgenomes stability, chromosome pairings and rearrangements, and their impacts on an organism’s fitness were investigated by fertility phenotyping and molecular cytogenetics techniques GISH and FISH. Results showed that diversified sexual reproductive methods produced highly differentiated progenies (2n=35-84) with varying proportions of subgenomic chromosomes, of which one individual (2n=54, MMMPT) overcame self-incompatibility barriers and produced self-fertile nascent near-allotetraploid by preferentially eliminatingTripsacumchromosomes. Nascent near-allotetraploid progenies showed persistent chromosome changes, intergenomic translocations, and rDNA variations for at least up to the first six selfed generations; however, ploidy tended to stabilize at near-tetraploid level (2n=40) with full integrity of 45SrDNA pairs, and a trend of decreasing variations by advancing generations with an average of 25.53, 14.14, and 0.37 maize,Z. perennis,andT. dactyloideschromosomes, respectively. The mechanisms for three genome stabilities and karyotype evolution for formatting new polyploid species were discussed.
Single-cell RNA sequencing reveals cellular and molecular heterogeneity in fibrocartilaginous enthesis formation
Authors: Zhang Tao , Liyang Wan , Han Xiao , Wang Linfeng , Hu Jianzhong , Lu Hongbin 
Published: February 2023

AbstractThe attachment site of the rotator cuff (RC) is a classic fibrocartilaginous enthesis, which is the junction between bone and tendon with typical characteristics of a fibrocartilage transition zone. Enthesis development has historically been studied with lineage tracing of individual genes selected a priori, which does not allow for the determination of single-cell landscapes yielding mature cell types and tissues. Here, we applied Single-cell RNA sequencing (scRNA-seq) to delineate the comprehensive postnatal RC enthesis growth and the temporal atlas from as early as embryonic day 15 up to postnatal week 4. In summary, we compared the development pattern between enthesis and tendon or articular cartilage, then deciphered the cellular heterogeneity and the molecular dynamics during fibrocartilage differentiation. This data provides a transcriptional resource that will support future investigations of enthesis development at the mechanistic level and may shed light on the strategies for enhanced RC healing outcomes.
PerTurboID: A targeted in situ method to measure changes in a local protein environment reveals the impact of kinase deletion on cytoadhesion in malaria causing parasites
Authors: Davies Heledd , Belda Hugo , Broncel Malgorzata , Dalimot Jill , Treeck Moritz 
Published: February 2023

ABSTRACTReverse genetics is key to understanding protein function, but the mechanistic connection between a gene of interest and the observed phenotype is not always clear. Here we describe the use of proximity labeling using TurboID and site-specific quantification of biotinylated peptides to measure changes to the local protein environment of selected targets upon perturbation. We apply this technique, which we call PerTurboID, to understand how theP. falciparumexported kinase, FIKK4.1, regulates the function of the major virulence factor of the malaria causing parasite, PfEMP1. We generated independent TurboID fusions of 2 proteins that are predicted substrates of FIKK4.1 in a FIKK4.1 conditional KO parasite line. Comparing the abundance of site-specific biotinylated peptides between wildtype and kinase deletion lines reveals the differential accessibility of proteins to biotinylation, indicating changes to localization, protein-protein interactions, or protein structure which are mediated by FIKK4.1 activity. We further show that FIKK4.1 is likely the only FIKK kinase that controls surface levels of PfEMP1, but not other surface antigens, on the infected red blood cell under standard culture conditions. We believe PerTurboID is broadly applicable to study the impact of genetic or environmental perturbation on a selected cellular niche.
A simple Turing reaction-diffusion model can explain how mother centrioles break symmetry to generate a single daughter
Authors: Wilmott Zachary M. , Goriely Alain , Raff Jordan W. 
Published: February 2023

AbstractCentrioles duplicate when a mother centriole gives birth to a daughter that grows from its side. Polo-like-kinase 4 (PLK4), the master regulator of centriole duplication, is recruited symmetrically around the mother centriole, but it then concentrates at a single focus that defines the daughter centriole assembly site. How PLK4 breaks symmetry is unclear. Here, we propose that phosphorylated and unphosphorylated species of PLK4 form the two components of a classical Turing reaction-diffusion system. These two components bind-to/unbind-from the surface of the mother centriole at different rates, allowing a slow-diffusing activator species of PLK4 to accumulate at a single site on the mother, while a fast-diffusing inhibitor species of PLK4 suppresses activator accumulation around the rest of the centriole. This “short-range activation/long-range inhibition”, inherent to Turing-systems, can drive PLK4 symmetry breaking on a continuous centriole surface, with PLK4 overexpression producing multiple PLK4 foci and PLK4 kinase inhibition leading to uniform PLK4 accumulation—as observed experimentally.
Identification and characterization ofDICER-LIKEgenes and their roles inMarchantia polymorphadevelopment and stress adaptation
Authors: Csicsely Erika , Oberender Anja , Georgiadou Anastasia-Styliani , Gutsche Nora , Zachgo Sabine , Top Oguz , Frank Wolfgang 
Published: February 2023

AbstractDICER-LIKE (DCL) proteins have a central role in plant small RNA (sRNA) biogenesis. TheMarchantia polymorphagenome encodes four DCL proteins: two DCL1 homologs, MpDCL1a and MpDCL1b, MpDCL3 and MpDCL4. While MpDCL1a, MpDCL3 and MpDCL4 show high similarities to their orthologs inPhyscomitrium patensandArabidopsis thaliana, MpDCL1b shares only a limited homology with PpDCL1b, but it is very similar, in terms of functional domains, to orthologs inAnthoceros agrestisandSalvinia cucullata. We generated Mpdclgemutant lines via the CRISPR/Cas9 system and performed comprehensive phenotypic analyses of these mutant lines, under control and salt stress conditions as well as upon exogenous naphthaleneacetic acid (NAA) and abscisic acid (ABA) treatments to gain insights into the respective MpDCL functions. While Mpdcl1agemutants display severe developmental aberrations throughout their development, no adverse phenotypic changes are detectable in Mpdcl1bgeand Mpdcl4gemutants except the development of less and smaller male sexual organs (antheridiophores) when they are cultivated under photoperiod conditions supplemented with far-red light. Mpdcl3gemutants display rosette-shaped thallus formation and overall faster development, but are not able to form antheridiophores. The rosette-shaped thallus development of Mpdcl3gecan be reverted to a wild-type-like thallus growth upon NAA treatment. Mpdcl1bgemutants can tolerate high levels of salt, whereas Mpdcl4gemutants show higher salt sensitivity. Moreover, Mpdcl1ageand Mpdcl3gemutants show an ABA-hypersensitive phenotype. It can be concluded that the observed phenotypic alterations, under normal or treatment conditions, are linked to the mutations in the respective MpDCLsand hence to defective or altered sRNA biogenesis pathways inM. polymorpha. In conclusion, MpDCLs and their associated sRNAs regulate development, abiotic stress and phytohormonal response inM. polymorpha.
Mechanisms of SARS-CoV-2 Inactivation using UVC Laser Radiation
Authors: Devitt George , Johnson Peter B. , Hanrahan Niall , Lane Simon I.R. , Vidale Magdalena C. , Sheth Bhavwanti , Allen Joel D. , Humbert Maria V. , Spalluto Cosma M. , Hervé Rodolphe C. , Staples Karl , West Jonathan J. , Forster Robert , Divecha Nullin , McCormick Christopher J , Crispin Max , Hempler Nils , Malcolm Graeme P. A. , Mahajan Sumeet 
Published: February 2023

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-Cov-2) has had a tremendous impact on humanity. Prevention of transmission by disinfection of surfaces and aerosols through a chemical-free method is highly desirable. Ultraviolet C (UVC) light is uniquely positioned to achieve inactivation of pathogens. We report the inactivation of SARS-CoV-2 virus by UVC radiation and explore its mechanisms. A dose of 50mJ/cm2using a UVC laser at 266nm achieved an inactivation efficiency of 99.89%, whilst infectious virions were undetectable at 75mJ/cm2indicating >99.99% inactivation. Infection by SARS-CoV-2 involves viral entry mediated by the spike glycoprotein (S), and viral reproduction, reliant on translation of its genome. We demonstrate that UVC radiation damages ribonucleic acid (RNA) and provide in-depth characterisation of UVC-induced damage of the S protein. We find that UVC severely impacts SARS-CoV-2 spike protein’s ability to bind human angiotensin-converting enzyme 2 (hACE2) and this correlates with loss of native protein conformation and aromatic amino acid integrity. This report has important implications for the design and development of rapid and effective disinfection systems against the SARS-CoV-2 virus and other pathogens.