bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cross-sectional analysis of meteorological factors and SARS-CoV-2 transmission in 409 cities across 26 countries
Authors: Sera Francesco , Armstrong Ben , Abbott Sam , Meakin Sophie , O’Reilly Kathleen , von Borries Rosa , Schneider Rochelle , Royé Dominic , Hashizume Masahiro , Pascal Mathilde , Tobias Aurelio , Vicedo-Cabrera Ana Maria ,   MCC Collaborative Research Network, Hu Wenbiao , Tong Shilu , Lavigne Eric , Correa Patricia Matus , Meng Xia , Kan Haidong , Kynčl Jan , Urban Aleš , Orru Hans , Ryti Niilo R. I. , Jaakkola Jouni J. K. , Cauchemez Simon , Dallavalle Marco , Schneider Alexandra , Zeka Ariana , Honda Yasushi , Ng Chris Fook Sheng , Alahmad Barrak , Rao Shilpa , Di Ruscio Francesco , Carrasco-Escobar Gabriel , Seposo Xerxes , Holobâcă Iulian Horia , Kim Ho , Lee Whanhee , Íñiguez Carmen , Ragettli Martina S. , Aleman Alicia , Colistro Valentina , Bell Michelle L. , Zanobetti Antonella , Schwartz Joel , Dang Tran Ngoc , Scovronick Noah , de Sousa Zanotti Stagliorio Coélho Micheline , Diaz Magali Hurtado , Zhang Yuzhou ,   CMMID COVID-19 Working Group, Russell Timothy W. , Koltai Mihaly , Kucharski Adam J. , Barnard Rosanna C. , Quaife Matthew , Jarvis Christopher I. , Lei Jiayao , Munday James D. , Chan Yung-Wai Desmond , Quilty Billy J. , Eggo Rosalind M. , Flasche Stefan , Foss Anna M. , Clifford Samuel , Tully Damien C. , Edmunds W. John , Klepac Petra , Brady Oliver , Krauer Fabienne , Procter Simon R. , Jombart Thibaut , Rosello Alicia , Showering Alicia , Funk Sebastian , Hellewell Joel , Sun Fiona Yueqian , Endo Akira , Williams Jack , Gimma Amy , Waterlow Naomi R. , Prem Kiesha , Bosse Nikos I. , Gibbs Hamish P. , Atkins Katherine E. , Pearson Carl A. B. , Jafari Yalda , Villabona-Arenas C. Julian , Jit Mark , Nightingale Emily S. , Davies Nicholas G. , van Zandvoort Kevin , Liu Yang , Sandmann Frank G. , Waites William , Abbas Kaja , Medley Graham , Knight Gwenan M. , Gasparrini Antonio , Lowe Rachel 
Published: October 2021

AbstractThere is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (Re) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on Re with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.
Specialized transendothelial dendritic cells mediate thymic T-cell selection against blood-borne macromolecules
Authors: Vollmann Elisabeth H. , Rattay Kristin , Barreiro Olga , Thiriot Aude , Fuhlbrigge Rebecca A. , Vrbanac Vladimir , Kim Ki-Wook , Jung Steffen , Tager Andrew M. , von Andrian Ulrich H. 
Published: October 2021

AbstractT cells undergo rigorous selection in the thymus to ensure self-tolerance and prevent autoimmunity, with this process requiring innocuous self-antigens (Ags) to be presented to thymocytes. Self-Ags are either expressed by thymic stroma cells or transported to the thymus from the periphery by migratory dendritic cells (DCs); meanwhile, small blood-borne peptides can access the thymic parenchyma by diffusing across the vascular lining. Here we describe an additional pathway of thymic Ag acquisition that enables circulating antigenic macromolecules to access both murine and human thymi. This pathway depends on a subset of thymus-resident DCs, distinct from both parenchymal and circulating migratory DCs, that are positioned in immediate proximity to thymic microvessels where they extend cellular processes across the endothelial barrier into the blood stream. Transendothelial positioning of DCs depends on DC-expressed CX3CR1 and its endothelial ligand, CX3CL1, and disrupting this chemokine pathway prevents thymic acquisition of circulating proteins and compromises negative selection of Ag-reactive thymocytes. Thus, transendothelial DCs represent a mechanism by which the thymus can actively acquire blood-borne Ags to induce and maintain central tolerance.
Temperature dependence of quantum oscillations from non-parabolic dispersions
Authors: Guo Chunyu , Alexandradinata A. , Putzke Carsten , Estry Amelia , Tu Teng , Kumar Nitesh , Fan Feng-Ren , Zhang Shengnan , Wu Quansheng , Yazyev Oleg V. , Shirer Kent R. , Bachmann Maja D. , Peng Hailin , Bauer Eric D. , Ronning Filip , Sun Yan , Shekhar Chandra , Felser Claudia , Moll Philip J. W. 
Published: October 2021

AbstractThe phase offset of quantum oscillations is commonly used to experimentally diagnose topologically nontrivial Fermi surfaces. This methodology, however, is inconclusive for spin-orbit-coupled metals where π-phase-shifts can also arise from non-topological origins. Here, we show that the linear dispersion in topological metals leads to a T2-temperature correction to the oscillation frequency that is absent for parabolic dispersions. We confirm this effect experimentally in the Dirac semi-metal Cd3As2 and the multiband Dirac metal LaRhIn5. Both materials match a tuning-parameter-free theoretical prediction, emphasizing their unified origin. For topologically trivial Bi2O2Se, no frequency shift associated to linear bands is observed as expected. However, the π-phase shift in Bi2O2Se would lead to a false positive in a Landau-fan plot analysis. Our frequency-focused methodology does not require any input from ab-initio calculations, and hence is promising for identifying correlated topological materials.
Mechanics-driven nuclear localization of YAP can be reversed by N-cadherin ligation in mesenchymal stem cells
Authors: Zhang Cheng , Zhu Hongyuan , Ren Xinru , Gao Bin , Cheng Bo , Liu Shaobao , Sha Baoyong , Li Zhaoqing , Zhang Zheng , Lv Yi , Wang Haohua , Guo Hui , Lu Tian Jian , Xu Feng , Genin Guy M. , Lin Min 
Published: October 2021

AbstractMesenchymal stem cells adopt differentiation pathways based upon cumulative effects of mechanosensing. A cell’s mechanical microenvironment changes substantially over the course of development, beginning from the early stages in which cells are typically surrounded by other cells and continuing through later stages in which cells are typically surrounded by extracellular matrix. How cells erase the memory of some of these mechanical microenvironments while locking in memory of others is unknown. Here, we develop a material and culture system for modifying and measuring the degree to which cells retain cumulative effects of mechanosensing. Using this system, we discover that effects of the RGD adhesive motif of fibronectin (representative of extracellular matrix), known to impart what is often termed “mechanical memory” in mesenchymal stem cells via nuclear YAP localization, are erased by the HAVDI adhesive motif of the N-cadherin (representative of cell-cell contacts). These effects can be explained by a motor clutch model that relates cellular traction force, nuclear deformation, and resulting nuclear YAP re-localization. Results demonstrate that controlled storage and removal of proteins associated with mechanical memory in mesenchymal stem cells is possible through defined and programmable material systems.
Quantitative 3D imaging of the cranial microvascular environment at single-cell resolution
Authors: Rindone Alexandra N. , Liu Xiaonan , Farhat Stephanie , Perdomo-Pantoja Alexander , Witham Timothy F. , Coutu Daniel L. , Wan Mei , Grayson Warren L. 
Published: October 2021

AbstractVascularization is critical for skull development, maintenance, and healing. Yet, there remains a significant knowledge gap in the relationship of blood vessels to cranial skeletal progenitors during these processes. Here, we introduce a quantitative 3D imaging platform to enable the visualization and analysis of high-resolution data sets (>100 GB) throughout the entire murine calvarium. Using this technique, we provide single-cell resolution 3D maps of vessel phenotypes and skeletal progenitors in the frontoparietal cranial bones. Through these high-resolution data sets, we demonstrate that CD31hiEmcnhi vessels are spatially correlated with both Osterix+ and Gli1+ skeletal progenitors during postnatal growth, healing, and stimulated remodeling, and are concentrated at transcortical canals and osteogenic fronts. Interestingly, we find that this relationship is weakened in mice with a conditional knockout of PDGF-BB in TRAP+ osteoclasts, suggesting a potential role for osteoclasts in maintaining the native cranial microvascular environment. Our findings provide a foundational framework for understanding how blood vessels and skeletal progenitors spatially interact in cranial bone, and will enable more targeted studies into the mechanisms of skull disease pathologies and treatments. Additionally, our technique can be readily adapted to study numerous cell types and investigate other elusive phenomena in cranial bone biology.
Effectiveness of ChAdOx1 vaccine in older adults during SARS-CoV-2 Gamma variant circulation in São Paulo
Authors: Hitchings Matt D. T. , Ranzani Otavio T. , Dorion Murilo , D’Agostini Tatiana Lang , de Paula Regiane Cardoso , de Paula Olivia Ferreira Pereira , de Moura Villela Edlaine Faria , Torres Mario Sergio Scaramuzzini , de Oliveira Silvano Barbosa , Schulz Wade , Almiron Maria , Said Rodrigo , de Oliveira Roberto Dias , Silva Patricia Vieira , de Araújo Wildo Navegantes , Gorinchteyn Jean Carlo , Andrews Jason R. , Cummings Derek A. T. , Ko Albert I. , Croda Julio 
Published: October 2021

AbstractA two-dose regimen of the Oxford-AstraZeneca (ChAdOx1) Covid-19 vaccine with an inter-dose interval of three months has been implemented in many countries with restricted vaccine supply. However, there is limited evidence for the effectiveness of ChAdOx1 by dose in elderly populations in countries with high prevalence of the Gamma variant of SARS-CoV-2. Here, we estimate ChAdOx1 effectiveness by dose against the primary endpoint of RT-PCR-confirmed Covid-19, and secondary endpoints of Covid-19 hospitalization and Covid-19-related death, in adults aged ≥60 years during an epidemic with high Gamma variant prevalence in São Paulo state, Brazil using a matched, test-negative case-control study. Starting 28 days after the first dose, effectiveness of a single dose of ChAdOx1 is 33.4% (95% CI, 26.4–39.7) against Covid-19, 55.1% (95% CI, 46.6–62.2) against hospitalization, and 61.8% (95% CI, 48.9–71.4) against death. Starting 14 days after the second dose, effectiveness of the two-dose schedule is 77.9% (95% CI, 69.2–84.2) against Covid-19, 87.6% (95% CI, 78.2–92.9) against hospitalization, and 93.6% (95% CI, 81.9–97.7) against death. Completion of the ChAdOx1 vaccine schedule affords significantly increased protection over a single dose against mild and severe Covid-19 outcomes in elderly individuals during widespread Gamma variant circulation.
The impact of the timely birth dose vaccine on the global elimination of hepatitis B
Authors: de Villiers Margaret J. , Nayagam Shevanthi , Hallett Timothy B. 
Published: October 2021

AbstractIn 2016 the World Health Organization set the goal of eliminating hepatitis B globally by 2030. Horizontal transmission has been greatly reduced in most countries by scaling up coverage of the infant HBV vaccine series, and vertical transmission is therefore becoming increasingly dominant. Here we show that scaling up timely hepatitis B birth dose vaccination to 90% of new-borns in 110 low- and middle-income countries by 2030 could prevent 710,000 (580,000 to 890,000) deaths in the 2020 to 2030 birth cohorts compared to status quo, with the greatest benefits in Africa. Maintaining this could lead to elimination by 2030 in the Americas, but not before 2059 in Africa. Drops in coverage due to disruptions in 2020 may lead to 15,000 additional deaths, mostly in South-East Asia and the Western Pacific. Delays in planned scale-up could lead to an additional 580,000 deaths globally in the 2020 to 2030 birth cohorts.
Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5
Authors: Linders Peter T. A. , Gerretsen Eveline C. F. , Ashikov Angel , Vals Mari-Anne , de Boer Rinse , Revelo Natalia H. , Arts Richard , Baerenfaenger Melissa , Zijlstra Fokje , Huijben Karin , Raymond Kimiyo , Muru Kai , Fjodorova Olga , Pajusalu Sander , Õunap Katrin , ter Beest Martin , Lefeber Dirk , van den Bogaart Geert 
Published: October 2021

AbstractThe SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein syntaxin-5 (Stx5) is essential for Golgi transport. In humans, the STX5 mRNA encodes two protein isoforms, Stx5 Long (Stx5L) from the first starting methionine and Stx5 Short (Stx5S) from an alternative starting methionine at position 55. In this study, we identify a human disorder caused by a single missense substitution in the second starting methionine (p.M55V), resulting in complete loss of the short isoform. Patients suffer from an early fatal multisystem disease, including severe liver disease, skeletal abnormalities and abnormal glycosylation. Primary human dermal fibroblasts isolated from these patients show defective glycosylation, altered Golgi morphology as measured by electron microscopy, mislocalization of glycosyltransferases, and compromised ER-Golgi trafficking. Measurements of cognate binding SNAREs, based on biotin-synchronizable forms of Stx5 (the RUSH system) and Förster resonance energy transfer (FRET), revealed that the short isoform of Stx5 is essential for intra-Golgi transport. Alternative starting codons of Stx5 are thus linked to human disease, demonstrating that the site of translation initiation is an important new layer of regulating protein trafficking.
Partially overlapping spatial environments trigger reinstatement in hippocampus and schema representations in prefrontal cortex
Authors: Zheng Li , Gao Zhiyao , McAvan Andrew S. , Isham Eve A. , Ekstrom Arne D. 
Published: October 2021

AbstractWhen we remember a city that we have visited, we retrieve places related to finding our goal but also non-target locations within this environment. Yet, understanding how the human brain implements the neural computations underlying holistic retrieval remains unsolved, particularly for shared aspects of environments. Here, human participants learned and retrieved details from three partially overlapping environments while undergoing high-resolution functional magnetic resonance imaging (fMRI). Our findings show reinstatement of stores even when they are not related to a specific trial probe, providing evidence for holistic environmental retrieval. For stores shared between cities, we find evidence for pattern separation (representational orthogonalization) in hippocampal subfield CA2/3/DG and repulsion in CA1 (differentiation beyond orthogonalization). Additionally, our findings demonstrate that medial prefrontal cortex (mPFC) stores representations of the common spatial structure, termed schema, across environments. Together, our findings suggest how unique and common elements of multiple spatial environments are accessed computationally and neurally.
Analyzing the performance of variational quantum factoring on a superconducting quantum processor
Authors: Karamlou Amir H. , Simon William A. , Katabarwa Amara , Scholten Travis L. , Peropadre Borja , Cao Yudong 
Published: October 2021

AbstractIn the near-term, hybrid quantum-classical algorithms hold great potential for outperforming classical approaches. Understanding how these two computing paradigms work in tandem is critical for identifying areas where such hybrid algorithms could provide a quantum advantage. In this work, we study a QAOA-based quantum optimization approach by implementing the Variational Quantum Factoring (VQF) algorithm. We execute experimental demonstrations using a superconducting quantum processor, and investigate the trade off between quantum resources (number of qubits and circuit depth) and the probability that a given biprime is successfully factored. In our experiments, the integers 1099551473989, 3127, and 6557 are factored with 3, 4, and 5 qubits, respectively, using a QAOA ansatz with up to 8 layers and we are able to identify the optimal number of circuit layers for a given instance to maximize success probability. Furthermore, we demonstrate the impact of different noise sources on the performance of QAOA, and reveal the coherent error caused by the residual ZZ-coupling between qubits as a dominant source of error in a near-term superconducting quantum processor.
Cognitive, creative, functional, and clinical symptom improvements in schizophrenia after an integrative cognitive remediation program: a randomized controlled trial
Authors: Sampedro Agurne , Peña Javier , Sánchez Pedro , Ibarretxe-Bilbao Naroa , Gómez-Gastiasoro Ainara , Iriarte-Yoller Nagore , Pavón Cristóbal , Tous-Espelosin Mikel , Ojeda Natalia 
Published: October 2021

AbstractThis study analyzed the effectiveness of an integrative cognitive remediation program (REHACOP) in improving neurocognition, social cognition, creativity, functional outcome, and clinical symptoms in patients with schizophrenia. In addition, possible mediators predicting improvement in functional outcomes were explored. The program combined cognitive remediation with social cognitive training and social and functional skill training over 20 weeks. The sample included 94 patients, 47 in the REHACOP group and 47 in the active control group (occupational activities). Significant differences were found between the two groups in change scores of processing speed, working memory, verbal memory (VM), inhibition, theory of mind, emotion processing (EP), figural creative strengths, functional competence, disorganization, excitement, and primary negative symptoms. A mediational analysis revealed that changes in VM, inhibition, and EP partially explained the effect of cognitive remediation on functional competence improvement. This study provides initial evidence of the effect of integrative cognitive remediation on primary negative symptoms and creativity.
Exploiting viral sensing mediated by Toll-like receptors to design innovative vaccines
Authors: Sartorius Rossella , Trovato Maria , Manco Roberta , D’Apice Luciana , De Berardinis Piergiuseppe 
Published: October 2021

AbstractToll-like receptors (TLRs) are transmembrane proteins belonging to the family of pattern-recognition receptors. They function as sensors of invading pathogens through recognition of pathogen-associated molecular patterns. After their engagement by microbial ligands, TLRs trigger downstream signaling pathways that culminate into transcriptional upregulation of genes involved in immune defense. Here we provide an updated overview on members of the TLR family and we focus on their role in antiviral response. Understanding of innate sensing and signaling of viruses triggered by these receptors would provide useful knowledge to prompt the development of vaccines able to elicit effective and long-lasting immune responses. We describe the mechanisms developed by viral pathogens to escape from immune surveillance mediated by TLRs and finally discuss how TLR/virus interplay might be exploited to guide the design of innovative vaccine platforms.
A SARS-CoV-2 spike ferritin nanoparticle vaccine protects hamsters against Alpha and Beta virus variant challenge
Authors: Wuertz Kathryn McGuckin , Barkei Erica K. , Chen Wei-Hung , Martinez Elizabeth J. , Lakhal-Naouar Ines , Jagodzinski Linda L. , Paquin-Proulx Dominic , Gromowski Gregory D. , Swafford Isabella , Ganesh Akshaya , Dong Ming , Zeng Xiankun , Thomas Paul V. , Sankhala Rajeshwer S. , Hajduczki Agnes , Peterson Caroline E. , Kuklis Caitlin , Soman Sandrine , Wieczorek Lindsay , Zemil Michelle , Anderson Alexander , Darden Janice , Hernandez Heather , Grove Hannah , Dussupt Vincent , Hack Holly , de la Barrera Rafael , Zarling Stasya , Wood James F. , Froude Jeffrey W. , Gagne Matthew , Henry Amy R. , Mokhtari Elham Bayat , Mudvari Prakriti , Krebs Shelly J. , Pekosz Andrew S. , Currier Jeffrey R. , Kar Swagata , Porto Maciel , Winn Adrienne , Radzyminski Kamil , Lewis Mark G. , Vasan Sandhya , Suthar Mehul , Polonis Victoria R. , Matyas Gary R. , Boritz Eli A. , Douek Daniel C. , Seder Robert A. , Daye Sharon P. , Rao Mangala , Peel Sheila A. , Joyce M. Gordon , Bolton Diane L. , Michael Nelson L. , Modjarrad Kayvon 
Published: October 2021

AbstractThe emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a SARS-CoV-2 spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the Alpha (B.1.1.7), and Beta (B.1.351) VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 μg) or low (0.2 μg) dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose vaccinations. Dose-dependent SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.
Scientific rationale for developing potent RBD-based vaccines targeting COVID-19
Authors: Kleanthous Harry , Silverman Judith Maxwell , Makar Karen W. , Yoon In-Kyu , Jackson Nicholas , Vaughn David W. 
Published: October 2021

AbstractVaccination of the global population against COVID-19 is a great scientific, logistical, and moral challenge. Despite the rapid development and authorization of several full-length Spike (S) protein vaccines, the global demand outweighs the current supply and there is a need for safe, potent, high-volume, affordable vaccines that can fill this gap, especially in low- and middle-income countries. Whether SARS-CoV-2 S-protein receptor-binding domain (RBD)-based vaccines could fill this gap has been debated, especially with regards to its suitability to protect against emerging viral variants of concern. Given a predominance for elicitation of neutralizing antibodies (nAbs) that target RBD following natural infection or vaccination, a key biomarker of protection, there is merit for selection of RBD as a sole vaccine immunogen. With its high-yielding production and manufacturing potential, RBD-based vaccines offer an abundance of temperature-stable doses at an affordable cost. In addition, as the RBD preferentially focuses the immune response to potent and recently recognized cross-protective determinants, this domain may be central to the development of future pan-sarbecovirus vaccines. In this study, we review the data supporting the non-inferiority of RBD as a vaccine immunogen compared to full-length S-protein vaccines with respect to humoral and cellular immune responses against both the prototype pandemic SARS-CoV-2 isolate and emerging variants of concern.