bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 anti-spike antibody levels following second dose of ChAdOx1 nCov-19 or BNT162b2 in residents of long-term care facilities in England (VIVALDI)
Authors: Stirrup Oliver , Krutikov Maria , Tut Gokhan , Palmer Tom , Bone David , Bruton Rachel , Fuller Chris , Azmi Borscha , Lancaster Tara , Sylla Panagiota , Kaur Nayandeep , Spalkova Eliska , Bentley Christopher , Amin Umayr , Jadir Azar , Hulme Samuel , Giddings Rebecca , Nacer-Laidi Hadjer , Baynton Verity , Irwin-Singer Aidan , Hayward Andrew , Moss Paul , Copas Andrew , Shallcross Laura 
Published: January 2022

AbstractBackgroundGeneral population studies have shown strong humoral response following SARS-CoV-2 vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations such as Long-Term Care Facility (LTCF) residents but published data are scarce.MethodsVIVALDI is a prospective cohort study in England which links serial blood sampling in LTCF staff and residents to routine healthcare records. We measured quantitative titres of SARS-CoV-2 anti-spike antibodies in residents and staff following second vaccination dose with ChAdOx1 nCov-19 (Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech). We investigated differences in peak antibody levels and rates of decline using linear mixed effects models.ResultsWe report on 1317 samples from 402 residents (median age 86 years, IQR 78-91) and 632 staff (50 years, 37-58), ≤280 days from second vaccination dose. Peak antibody titres were 7.9-fold higher after Pfizer-BioNTech vaccine compared to Oxford-AstraZeneca (95%CI 3.6-17.0; P<0.01) but rate of decline was increased, and titres were similar at 6 months. Prior infection was associated with higher peak antibody levels in both Pfizer-BioNTech (2.8-fold, 1.9-4.1; P<0.01) and Oxford-AstraZeneca (4.8-fold, 3.2-7.1; P<0.01) recipients and slower rates of antibody decline. Increasing age was associated with a modest reduction in peak antibody levels for Oxford-AstraZeneca recipients.ConclusionsDouble-dose vaccination elicits robust and stable antibody responses in older LTCF residents, suggesting comparable levels of vaccine-induced immunity to that in the general population. Antibody levels are higher after Pfizer-BioNTech vaccination but fall more rapidly compared to Oxford-AstraZeneca recipients and are enhanced by prior infection in both groups.
VEGF-C expression in TAMs rewires the metastatic fate of breast cancer cells
Authors: Banerjee Kaveri , Kerzel Thomas , Bekkhus Tove , de Souza Ferreira Sabrina , Wallmann Tatjana , Wallerius Majken , Landwehr Laura-Sophie , Agardy Dennis Alexander , Schauer Nele , Malmerfeldt Anna , Bergh Jonas , Bartish Margarita , Hartman Johan , Östman Arne , Squadrito Mario Leonardo , Rolny Charlotte 
Published: January 2022

SummaryExpression of pro-lymphangiogenic vascular endothelial growth factor C (VEGF-C) in primary tumors correlates with the occurrence of proximal lymph node metastasis in most solid cancer types. However, the role of VEGF-C in regulating tumor cell dissemination to distant organs is currently unclear. Perivascular tumor-associated macrophages (TAMs) are key regulators of hematogenous cancer cell spreading, forming tumor microenvironment of metastasis (TMEM) doorways for breast cancer cells to intravasate tumor blood vessels and fuel distant metastases. Using an experimental breast cancer (BC) model, we show here that TAMs expressing VEGF-C decrease cancer cell dissemination to the lung while enhancing lymph node metastasis. These TAMs express podoplanin and associate with normalized tumor blood vessels expressing VEGFR3. Further clinical data reveal that VEGF-C+TAMs correlate inversely with malignant grade and with the occurrence of TMEM complexes in a cohort of BC patients. Thus, our study displays an apparently paradoxical role of VEGF-C expressing TAMs in redirecting cancer cells to preferentially disseminate to the lymph nodes, at least in part, by normalizing tumor blood vessels and promoting lymphangiogenesis.
A pipeline to track unlabeled cells in wide migration chambers using pseudofluorescence
Authors: Paola Antonello , Thelen Marcus , Krause Rolf , Ulisse Pizzagalli Diego 
Published: January 2022

AbstractCell migration is a pivotal biological process, whose dysregulation is found in many diseases including inflammation and cancer. Advances in microscopy technologies allow now to study cell migration in vitro, within microenvironments that resemble in vivo conditions. However, when cells are observed within large 3D migration chambers at low magnification and for extended periods of time, data analysis becomes difficult. Indeed, cell detection and tracking are hampered due to the large pixel size, the possible low signal-to-noise ratio and distortions in the cell shape due to changes in the z-axis position. Although fluorescent staining can be used to facilitate cell detection, it may alter cell behavior and suffer from fluorescence loss over time (photobleaching).Here we describe the application of an image analysis pipeline based on deep learning to convert the transmitted light signal from unlabeled lymphoma cells to pseudofluorescence. Such pipeline confers a significant improvement in tracking accuracy while not suffering from photobleaching. This is reflected in the possibility of tracking cells for three-fold longer periods of time.
Genetic modifiers of Cep290-mediated retinal degeneration
Authors: Meyer K.J. , Whitmore S.S. , Burnight E.R. , Riker M. , Mercer H.E. , Ajose A. , Howell G.R. , Stone E.M. , Mullins R.F. , Tucker B.A. , Scheetz T.E. , Anderson M.G. 
Published: January 2022

ABSTRACTMutations in CEP290 cause up to 30% of cases of Leber congenital amaurosis (LCA), a severe childhood blindness resulting from abnormalities in the photoreceptor connecting cilia that lead to rapid retinal degeneration. Like many genetic diseases, CEP290-LCA has considerable variable expressivity, indicating the presence of other factors that influence phenotypic outcome. Here, we have undertaken a phenotype-driven approach in mice to identify genetic modifiers of CEP290-mediated retinal degeneration through backcrosses and intercrosses between BXD24-Cep290rd16 mice and the genetically distinct inbred CAST strain to introduce genetic variation. Optical coherence tomography was used to quantitatively measure retinal thickness as a surrogate indication of photoreceptor degeneration in the resulting rd16-mutant mice. It was readily apparent that CEP290-mediated retinal degeneration in the resulting mice is sensitive to genetic background, with some mice exhibiting relatively thick laminated retinas and others having thin retinas with advanced disease. Quantitative trait locus (QTL) analysis identified multiple genomic loci capable of influencing the retinal degeneration phenotype in Cep290-mutant mice that together account for 71.7% of the phenotypic variation in retinal thickness observed in our population. Following the QTL analysis, two suppressor loci were studied in detail through a combination of physical and molecular approaches to narrow the critical region for each QTL and identify the probable causative genetic variations.
Single-cell RNA sequencing identifies phenotypically, functionally, and anatomically distinct stromal niche populations in human bone marrow
Authors: Li Hongzhe , Bräunig Sandro , Dhapolar Parashar , Karlsson Göran , Lang Stefan , Scheding Stefan 
Published: January 2022

SummaryHematopoiesis is regulated by the bone marrow (BM) stroma. However, cellular identities and functions of the different BM stromal elements in humans remain poorly defined. Based on single-cell RNA sequencing, we systematically characterized the BM stromal compartment which led to the identification of six transcriptionally and functionally distinct stromal cell populations. Stromal cell differentiation hierarchy was recapitulated based on RNA velocity analysis, in vitro proliferation capacities and differentiation potentials. Potential key factors that govern the transition from stem and progenitor cells to fate- committed cells were identified. In silico cell-cell communication prediction and in situ localization analyses demonstrated distinct hematopoietic stromal cell niches in specific BM locations, which used either the CXCL12 or SPP1 axis as the major hematopoiesis-regulating mechanism. These findings provide the basis for a comprehensive understanding of the cellular complexity of the human BM microenvironment and the intricate stroma- hematopoiesis crosstalk mechanisms, thus refining our current view on hematopoietic niche organization.
A peptide-mediated, multilateral molecular dialogue for the coordination of pollen wall formation
Authors: Truskina Jekaterina , Brück Stefanie , Stintzi Annick , Boeuf Sophy , Doll Nicolas M. , Fujita Satoshi , Geldner Niko , Schaller Andreas , Ingram Gwyneth C. 
Published: January 2022

AbstractThe surface of pollen grains is reinforced by pollen wall components produced non-cell autonomously by tapetum cells that surround developing pollen within the male floral organ, the anther. Here we show that tapetum activity is regulated by the GASSHO (GSO) receptor-like kinase pathway, controlled by two sulfated peptides, CASPARIAN STRIP INTEGRITY FACTOR 3 (CIF3) and CIF4, the precursors of which are expressed in the tapetum itself. Coordination of tapetum activity with pollen grain development depends on the action of subtilases, including AtSBT5.4, which are produced stage-specifically by developing pollen grains. Tapetum-derived CIF precursors are processed by subtilases, triggering GSO-dependent tapetum activation. We show that the GSO receptors act from the middle layer, a tissue surrounding the tapetum and developing pollen. Three concentrically organized cell types therefore cooperate to coordinate pollen wall deposition through a multilateral molecular dialog.Significance StatementPollen viability depends on a tough external barrier called the pollen wall. Pollen wall components are produced by tapetum cells which surround developing pollen grains within the anther. Precise coordination of tapetum activity with pollen grain development is required to ensure effective pollen wall formation. Here we reveal that this is achieved through a multidirectional dialogue involving three distinct cell types. We show that peptide precursors from the tapetum are activated by proteases produced stage-specifically in developing pollen grains. Unexpectedly, we found that activated peptides are perceived not in the tapetum, but in the middle layer, which encloses the developing tapetum and pollen grains, revealing an unsuspected role for this enigmatic cell layer in the control of tapetum development.
Entorhinal layer 6b subplate neurons govern spatial learning and memory
Authors: Ben-Simon Yoav , Kaefer Karola , Velicky Philipp , Csicsvari Jozsef , Danzl Johann G. , Jonas Peter 
Published: January 2022

AbstractThe mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a “trisynaptic loop”, processing input originating from the superficial layers of the entorhinal cortex (EC) in a linear fashion, and sending it back to its deeper layers. Here, we show that contrary to this canonical view, excitatory neurons in the deepest layer of the mouse EC, exhibiting the unique morphology and molecular profile of layer 6b cortical subplate neurons (SPNs), project to all sub-regions comprising the HF, with a preference towards CA3 pyramidal neurons, and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory post-synaptic currents (EPSCs), capable of driving plateau-like potentials in their target cells. Optogenetic inhibition of the EC-6b pathway markedly affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide the first evidence of a functional role for the cortical layer 6b neurons in the adult brain and elucidate a critical novel element determining cortico-hippocampal activity patterns.
Fgfr2b signaling is essential for the maintenance of the alveolar epithelial type 2 lineage during lung homeostasis in mice
Authors: Ahmadvand Negah , Lingampally Arun , Khosravi Farhad , Vazquez-Armendariz Ivonne , Rivetti Stefano , Wilhelm Jochen , Herold Susanne , Barreto Guillermo , Koepke Janine , Samakovlis Christos , Carraro Gianni , Zhang Jin-San , Al Alam Denise , Bellusci Saverio 
Published: January 2022

ABSTRACTFibroblast growth factor receptor 2b (Fgfr2b) signaling is essential throughout lung development to form the alveolar epithelial lineage. However, its role in alveolar epithelial type 2 cells (AT2s) homeostasis was recently considered dispensable. SftpcCreERT2; tdTomatoflox/flox mice were used to delete Fgfr2b expression in cells belonging to the AT2 lineage, which contains mature AT2s and a novel SftpcLow lineage-traced population called “injury activated alveolar progenitors” or IAAPs. Upon continuous tamoxifen exposure for either one or two weeks to delete Fgfr2b, a shrinking of the AT2s is observed. Mature AT2s exit the cell cycle, undergo apoptosis and fail to form alveolospheres in vitro. However, the lung morphometry appears normal, suggesting the involvement of compensatory mechanisms. In mutant lungs, IAAPs which escaped Fgfr2b deletion expand, display enhanced alveolosphere formation in vitro and increase drastically their AT2 signature suggesting differentiation towards mature AT2s. Interestingly, a significant increase in AT2s and decrease in IAPPs occurs after a one-week tamoxifen exposure followed by an eight-week chase period. While mature AT2s partially recover their alveolosphere formation capabilities, the IAAPs no longer display this property. Single-cell RNA seq analysis confirms that AT2s and IAAPs represent stable and distinct cell populations and recapitulate some of their characteristics observed in vivo. Our results underscore the essential role played by Fgfr2b signaling in the maintenance of the AT2 lineage in the adult lung and suggest that the IAAPs could represent a new population of AT2 progenitors.
Interaction of the Proline-Rich Domain of Fission Yeast WASp (Ws1p1) with Actin Filaments
Authors: Rosenbloom Aaron D. , Pollard Thomas D. 
Published: January 2022

AbstractBackgroundThe Wiskott-Aldrich Syndrome protein (WASp) family of proteins plays a crucial role in the activation of the Arp2/3 (actin-related protein 2/3) complex to promote the branching of actin filaments. The proline-rich domain (PRD) of WASp is known to contribute to branching nucleation but was overlooked, until experiments showed that the PRD of budding yeast Las17 can bind actin filaments (1).MethodsWe purified recombinant proline-rich domains from fission yeast S. pombe Wsp1 and budding yeast S. cerevisiae Las17 to test in biochemical assays of actin binding and polymerization.ResultsThe PRD of the S. pombe Wsp1 binds actin filaments with micromolar affinity. The PRDs of both Wsp1 and Las17 slowed the rate of actin filament elongation by Mg-ATP-actin monomers by half and slowed the spontaneous polymerization of Mg-ATP-actin monomers modestly.ConclusionThe affinity of PRDs of WASp-family proteins for actin filaments is high enough to contribute to the reported stimulation of actin filament branching by Arp2/3 complex.
Anti-SARS-CoV-2 swine glyco-humanized polyclonal antibody XAV-19 retains neutralizing activity against SARS-CoV-2 B.1.1.529 (Omicron)
Authors: Vanhove Bernard , Marot Stéphane , Evanno Gwénaëlle , Malet Isabelle , Rouvray Gaëtane , Shneiker Françoise , Mevel Edwige , Ciron Carine , Rousse Juliette , Royer Pierre-Joseph , Lheriteau Elsa , Raffi François , Duvaux Odile , Marcelin Anne-Geneviève , Calvez Vincent 
Published: January 2022

AbstractB.1.1.529 is the SARS-CoV-2 variant designated Omicron by the WHO in November 2021. It is a highly divergent variant with a high number of mutations, including 26-32 mutations in the spike protein among which 15 in the Receptor Binding Domain (RBD) including at the human angiotensin converting enzyme 2 (ACE-2) receptor interacting interface. Because of a decreased affinity for the ACE-2 receptor and a geometric reorganization of the S1-S2 cleavage site, the Omicron variant is predicted to not have a significant infectivity advantage over the delta variant and to be less pathogenic than Delta. However, in Omicron, neutralizing epitopes are greatly affected, suggesting that current vaccines and neutralizing monoclonal antibodies might confer reduced protection against this variant. In contrast, we and others previously demonstrated that polyclonal antibodies against SARS-CoV-2 RBD obtained from hyperimmunized animal hosts do maintain their neutralizing properties against Alpha to Delta. Here, we confirmed these findings by showing that XAV-19, a swine glyco-humanized polyclonal antibody retains full neutralizing activity against Omicron.
Single-Cell Analysis Reveals Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary Hypertension
Authors: Viswanathan Gayathri , Kirshner Hélène Fradin , Nazo Nour , Ganapathi Asvin , Cummings Ian , Choi Issac , Warman Anmol , Almeida-Peters Susana , Haney John , Corcoran David , Yu Yen-Rei , Rajagopal Sudarshan 
Published: January 2022

AbstractChronic thromboembolic pulmonary hypertension (CTEPH) is a sequelae of acute pulmonary embolism (PE) in which the PE remodels into a chronic scar in the pulmonary arteries. This results in vascular obstruction, small vessel arteriopathy and pulmonary hypertension. Our current understanding of CTEPH pathobiology is primarily derived from cell-based studies limited by the use of specific cell markers or phenotypic modulation in cell culture. Here we used single cell RNA sequencing (scRNAseq) of tissue removed at the time of pulmonary thromboendarterectomy (PTE) surgery to identify the multiple cell types, including macrophages, T cells, and smooth muscle cells, that comprise CTEPH thrombus. Notably, multiple macrophage subclusters were identified but broadly split into two categories, with the larger group characterized by an upregulation of inflammatory signaling predicted to promote pulmonary vascular remodeling. Both CD4+ and CD8+ T cells were identified and likely contribute to chronic inflammation in CTEPH. Smooth muscle cells were a heterogeneous population, with a cluster of myofibroblasts that express markers of fibrosis and are predicted to arise from other smooth muscle cell clusters based on pseudotime analysis. Additionally, cultured endothelial, smooth muscle and myofibroblast cells isolated from CTEPH thrombus have distinct phenotypes from control cells with regards to angiogenic potential and rates of proliferation and apoptosis. Lastly, our analysis identified protease-activated receptor 1 (PAR1) as a potential therapeutic target that links thrombosis to chronic PE in CTEPH, with PAR1 inhibition decreasing smooth muscle cell and myofibroblast proliferation and migration. These findings suggest a model for CTEPH similar to atherosclerosis, with chronic inflammation promoted by macrophages and T cells driving vascular remodeling through smooth muscle cell modulation, and suggest new approaches for pharmacologically targeting this disease.
Temperature modulates PVN pre-sympathetic neurones via transient receptor potential ion channels
Authors: O’Brien Fiona , Feetham Claire , Staunton Caroline , Hext Katharine , Barrett-Jolley Richard 
Published: January 2022

AbstractBackground and purposeThe paraventricular nucleus (PVN) of the hypothalamus plays a vital role in maintaining homeostasis and controls cardiovascular function via autonomic pre-sympathetic neurones. We have previously shown that coupling between transient receptor potential cation channel subfamily V member 4 (Trpv4) and small-conductance calcium-activated potassium channels (SK) in the PVN facilitate osmosensing. TRP channels are also thermosensitive and therefore, in this report we investigated the temperature sensitivity of PVN neurones.Experimental approachWe identified TRP channel mRNA in mouse PVN using quantitative reverse transcription-PCR (RT-PCR). Using cell-attached patch-clamp electrophysiology, we characterised the thermosensitivity of Trpv4-like ion channels on mouse PVN neurones. Following recovery of temperature sensitive single channel kinetic schema, we constructed a novel and predictive stochastic mathematical model of these neurones. We then validated this model with electrophysiological recordings of action current frequency from mouse PVN neurones.ResultsWe identified 7 TRP channel genes in the PVN with known thermosensitive capabilities. Trpv4 was the most abundant of these and was easily identified at the single channel level using cell-attached patch-clamp electrophysiology on PVN neurones. We investigated the thermosensitivity of these Trpv4-like channels; open probability (Po) markedly decreased when temperature was decreased, mediated by a decrease in mean open dwell times. Our neuronal model predicted that PVN spontaneous action current frequency (ACf) would increase as temperature is decreased and in our electrophysiological experiments, we found that ACf from PVN neurones was significantly higher at lower temperatures. The broad-spectrum channel blocker, gadolinium (100 μM), was used to block the warm-activated Ca2+-permeable Trpv4 and Trpv3 channels. In the presence of gadolinium (100 μM), the temperature effect was largely retained. Using econazole (10 μM), a blocker of Trpm2, we found there were significant increases in overall ACf and the temperature effect was inhibited.ConclusionOur work identified Trpv4 mRNA as an abundantly expressed thermosensitive TRP channel gene in the PVN and this ion channel contributes to the intrinsic thermosensitive properties of PVN neurones. At physiological temperatures (37°C), we observed relatively low ACf primarily due to the activity of Trpm2 channels, whereas at room temperature, where most of the previous characterisation of PVN neuronal activity has been performed, ACf is much higher, and appears to be predominately due to reduced Trpv4 activity. This work gives insight into the fundamental mechanisms by which the body decodes temperature signals and maintains homeostasis.