bluuebunny/crossref_metadata_2025_split huggingface dataset:
An integrated resource for functional and structural connectivity of the marmoset brain
Authors: Tian Xiaoguang , Chen Yuyan , Majka Piotr , Szczupak Diego , Perl Yonatan Sanz , Yen Cecil Chern-Chyi , Tong Chuanjun , Feng Furui , Jiang Haiteng , Glen Daniel , Deco Gustavo , Rosa Marcello G. P. , Silva Afonso C. , Liang Zhifeng , Liu Cirong 
Published: December 2022

AbstractComprehensive integration of structural and functional connectivity data is required to model brain functions accurately. While resources for studying the structural connectivity of non-human primate brains already exist, their integration with functional connectivity data has remained unavailable. Here we present a comprehensive resource that integrates the most extensive awake marmoset resting-state fMRI data available to date (39 marmoset monkeys, 710 runs, 12117 mins) with previously published cellular-level neuronal tracing data (52 marmoset monkeys, 143 injections) and multi-resolution diffusion MRI datasets. The combination of these data allowed us to (1) map the fine-detailed functional brain networks and cortical parcellations, (2) develop a deep-learning-based parcellation generator that preserves the topographical organization of functional connectivity and reflects individual variabilities, and (3) investigate the structural basis underlying functional connectivity by computational modeling. This resource will enable modeling structure-function relationships and facilitate future comparative and translational studies of primate brains.
The coordination of anti-phage immunity mechanisms in bacterial cells
Authors: Arias Clemente F. , Acosta Francisco J. , Bertocchini Federica , Herrero Miguel A. , Fernández-Arias Cristina 
Published: December 2022

AbstractBacterial cells are equipped with a variety of immune strategies to fight bacteriophage infections. Such strategies include unspecific mechanisms directed against any phage infecting the cell, ranging from the identification and cleavage of the viral DNA by restriction nucleases (restriction-modification systems) to the suicidal death of infected host cells (abortive infection, Abi). In addition, CRISPR-Cas systems generate an immune memory that targets specific phages in case of reinfection. However, the timing and coordination of different antiviral systems in bacterial cells are poorly understood. Here, we use simple mathematical models of immune responses in individual bacterial cells to propose that the intracellular dynamics of phage infections are key to addressing these questions. Our models suggest that the rates of viral DNA replication and cleavage inside host cells define functional categories of phages that differ in their susceptibility to bacterial anti-phage mechanisms, which could give raise to alternative phage strategies to escape bacterial immunity. From this viewpoint, the combined action of diverse bacterial defenses would be necessary to reduce the chances of phage immune evasion. The decision of individual infected cells to undergo suicidal cell death or to incorporate new phage sequences into their immune memory would be determined by dynamic interactions between the host’s immune mechanisms and the phage DNA. Our work highlights the importance of within-cell dynamics to understand bacterial immunity, and formulates hypotheses that may inspire future research in this area.
Intermittent scavenging of storage lesion from stored red blood cells by electrospun nanofibrous sheets enhances their quality and shelf-life
Authors: Pandey Subhashini , Mahato Manohar , Srinath Preethem , Bhutani Utkarsh , Goap Tanu Jain , Ravipati Priusha , Vemula Praveen Kumar 
Published: December 2022

AbstractTransfusion of healthy red blood cells (RBCs) is a lifesaving process. However, upon storing RBCs, a wide range of damage-associate molecular patterns (DAMPs), such as cell-free DNA, nucleosomes, free-hemoglobin, and poly-unsaturated-fatty-acids are generated. DAMPs can further damage RBCs; thus, the quality of stored RBCs declines during the storage and limits their shelf-life. Since these DAMPs consist of either positive or negative charged species, we developed taurine and acridine containing electrospun-nanofibrous-sheets (Tau-AcrNFS), featuring anionic, cationic charges and an DNA intercalating group on their surfaces. We show that Tau-AcrNFS are efficient in scavenging DAMPs from stored human and mice RBCs ex vivo. We find that intermittent scavenging of DAMPs by Tau-AcrNFS during the storage reduces the loss of RBC membrane integrity and reduces discocytes-to-spheroechinocytes transformation in stored-old-RBCs. We perform RBC-transfusion studies in mice to reveal that intermittent removal of DAMPs enhances the quality of stored-old-RBCs equivalent to freshly collected RBCs, and increases their shelf-life by ~22%. Such prophylactic technology may lead to the development of novel blood bags or medical device, and may therefore impact healthcare by reducing transfusion-related adverse effects.
Targeted A-to-G base editing of chloroplast DNA in plants
Authors: Mok Young Geun , Hong Sunghyun , Bae Su-Ji , Cho Sung-Ik , Kim Jin-Soo 
Published: December 2022

AbstractChloroplast DNA (cpDNA) encodes up to 315 (typically, 120–130) genes1, including those for essential components in photosystems I and II and the large subunit of RuBisCo, which catalyses CO2 fixation in plants. Targeted mutagenesis in cpDNA will be broadly useful for studying the functions of these genes in molecular detail and for developing crops and other plants with desired traits. Unfortunately, CRISPR–Cas9 and CRISPR-derived base editors, which enable targeted genetic modifications in nuclear DNA, are not suitable for organellar DNA editing2, owing to the difficulty of delivering guide RNA into organelles. CRISPR-free, protein-only base editors (including DddA-derived cytosine base editors3–8 and zinc finger deaminases9), originally developed for mitochondrial DNA editing in mammalian cells, can be used for C-to-T, rather than A-to-G, editing in cpDNA10–12. Here we show that heritable homoplasmic A-to-G edits can be induced in cpDNA, leading to phenotypic changes, using transcription activator-like effector-linked deaminases13.
Safety and efficacy of HSP90 inhibitor ganetespib for neoadjuvant treatment of stage II/III breast cancer
Authors: Lang Julie E. , Forero-Torres Andres , Yee Douglas , Yau Christina , Wolf Denise , Park John , Parker Barbara A. , Chien A. Jo , Wallace Anne M. , Murthy Rashmi , Albain Kathy S. , Ellis Erin D. , Beckwith Heather , Haley Barbara B. , Elias Anthony D. , Boughey Judy C. , Yung Rachel L. , Isaacs Claudine , Clark Amy S. , Han Hyo S. , Nanda Rita , Khan Qamar J. , Edmiston Kristen K. , Stringer-Reasor Erica , Price Elissa , Joe Bonnie , Liu Minetta C. , Brown-Swigart Lamorna , Petricoin Emanuel F. , Wulfkuhle Julia D. , Buxton Meredith , Clennell Julia L. , Sanil Ashish , Berry Scott , Asare Smita M. , Wilson Amy , Hirst Gillian L. , Singhrao Ruby , Asare Adam L. , Matthews Jeffrey B. , Melisko Michelle , Perlmutter Jane , Rugo Hope S. , Symmans W. Fraser , van ‘t Veer Laura J. , Hylton Nola M. , DeMichele Angela M. , Berry Donald A. , Esserman Laura J. 
Published: December 2022

AbstractHSP90 inhibitors destabilize oncoproteins associated with cell cycle, angiogenesis, RAS-MAPK activity, histone modification, kinases and growth factors. We evaluated the HSP90-inhibitor ganetespib in combination with standard chemotherapy in patients with high-risk early-stage breast cancer. I-SPY2 is a multicenter, phase II adaptively randomized neoadjuvant (NAC) clinical trial enrolling patients with stage II-III breast cancer with tumors 2.5 cm or larger on the basis of hormone receptors (HR), HER2 and Mammaprint status. Multiple novel investigational agents plus standard chemotherapy are evaluated in parallel for the primary endpoint of pathologic complete response (pCR). Patients with HER2-negative breast cancer were eligible for randomization to ganetespib from October 2014 to October 2015. Of 233 women included in the final analysis, 140 were randomized to the standard NAC control; 93 were randomized to receive 150 mg/m2 ganetespib every 3 weeks with weekly paclitaxel over 12 weeks, followed by AC. Arms were balanced for hormone receptor status (51–52% HR-positive). Ganetespib did not graduate in any of the biomarker signatures studied before reaching maximum enrollment. Final estimated pCR rates were 26% vs. 18% HER2-negative, 38% vs. 22% HR-negative/HER2-negative, and 15% vs. 14% HR-positive/HER2-negative for ganetespib vs control, respectively. The predicted probability of success in phase 3 testing was 47% HER2-negative, 72% HR-negative/HER2-negative, and 19% HR-positive/HER2-negative. Ganetespib added to standard therapy is unlikely to yield substantially higher pCR rates in HER2-negative breast cancer compared to standard NAC, and neither HSP90 pathway nor replicative stress expression markers predicted response. HSP90 inhibitors remain of limited clinical interest in breast cancer, potentially in other clinical settings such as HER2-positive disease or in combination with anti-PD1 neoadjuvant chemotherapy in triple negative breast cancer.Trial registration: www.clinicaltrials.gov/ct2/show/NCT01042379
Thermodynamical and topological properties of metastable Fe3Sn
Authors: Shen Chen , Samathrakis Ilias , Hu Kun , Singh Harish K. , Fortunato Nuno , Liu Huashan , Gutfleisch Oliver , Zhang Hongbin 
Published: December 2022

AbstractThe Fe–Sn-based kagome compounds attract intensive attention due to its attractive topological transport and rich magnetic properties. Combining experimental data, first-principles calculations, and Calphad assessment, thermodynamic and topological transport properties of the Fe–Sn system were investigated. Density functional theory (DFT) calculations were performed to evaluate the intermetallics’ finite-temperature heat capacity (Cp). A consistent thermodynamic assessment of the Fe–Sn phase diagram was achieved by using the experimental and DFT results, together with all available data from previous publications. Here, we report that the metastable phase Fe3Sn was introduced into the current metastable phase diagram, and corrected phase locations of Fe5Sn3 and Fe3Sn2 under the newly measured corrected temperature ranges. Furthermore, the anomalous Hall conductivity and anomalous Nernst conductivity of Fe3Sn were calculated, with magnetization directions and doping considered as perturbations to tune such transport properties. It was observed that the enhanced anomalous Hall and Nernst conductivities originate from the combination of nodal lines and small gap areas that can be tuned by doping Mn at Fe sites and varying magnetization direction.
Angiopoietin-like 3-derivative LNA043 for cartilage regeneration in osteoarthritis: a randomized phase 1 trial
Authors: Gerwin Nicole , Scotti Celeste , Halleux Christine , Fornaro Mara , Elliott Jimmy , Zhang Yunyu , Johnson Kristen , Shi Jian , Walter Sandra , Li Yufei , Jacobi Carsten , Laplanche Nelly , Belaud Magali , Paul Jochen , Glowacki Gustavo , Peters Thomas , Wharton Keith A. , Vostiar Igor , Polus Florine , Kramer Ina , Guth Sabine , Seroutou Abdelkader , Choudhury Subhajit , Laurent Didier , Gimbel Joseph , Goldhahn Jörg , Schieker Matthias , Brachat Sophie , Roubenoff Ronenn , Kneissel Michaela 
Published: December 2022

AbstractOsteoarthritis (OA) is a common, debilitating, chronic disease with no disease-modifying drug approved to date. We discovered LNA043—a derivative of angiopoietin-like 3 (ANGPTL3)—as a potent chondrogenesis inducer using a phenotypic screen with human mesenchymal stem cells. We show that LNA043 promotes chondrogenesis and cartilage matrix synthesis in vitro and regenerates hyaline articular cartilage in preclinical OA and cartilage injury models in vivo. LNA043 exerts at least part of these effects through binding to the fibronectin receptor, integrin α5β1on mesenchymal stem cells and chondrocytes. In a first-in-human (phase 1), randomized, double-blinded, placebo-controlled, single ascending dose, single-center trial (NCT02491281; sponsored by Novartis Pharmaceuticals), 28 patients with knee OA were injected intra-articularly with LNA043 or placebo (3:1 ratio) either 2 h, 7 d or 21 d before total knee replacement. LNA043 met its primary safety endpoint and showed short serum pharmacokinetics, cartilage penetration and a lack of immunogenicity (secondary endpoints). Post-hoc transcriptomics profiling of cartilage revealed that a single LNA043 injection reverses the OA transcriptome signature over at least 21 d, inducing the expression of hyaline cartilage matrix components and anabolic signaling pathways, while suppressing mediators of OA progression. LNA043 is a novel disease-modifying OA drug candidate that is currently in a phase 2b trial (NCT04864392) in patients with knee OA.
A Dataset with Multibeam Forward-Looking Sonar for Underwater Object Detection
Authors: Xie Kaibing , Yang Jian , Qiu Kang 
Published: December 2022

AbstractMultibeam forward-looking sonar (MFLS) plays an important role in underwater detection. There are several challenges to the research on underwater object detection with MFLS. Firstly, the research is lack of available dataset. Secondly, the sonar image, generally processed at pixel level and transformed to sector representation for the visual habits of human beings, is disadvantageous to the research in artificial intelligence (AI) areas. Towards these challenges, we present a novel dataset, the underwater acoustic target detection (UATD) dataset, consisting of over 9000 MFLS images captured using Tritech Gemini 1200ik sonar. Our dataset provides raw data of sonar images with annotation of 10 categories of target objects (cube, cylinder, tyres, etc). The data was collected from lake and shallow water. To verify the practicality of UATD, we apply the dataset to the state-of-the-art detectors and provide corresponding benchmarks for its accuracy and efficiency.
Mass cytometry analysis of blood from peanut-sensitized tolerant and clinically allergic infants
Authors: Tursi Amanda R. , Saba Nicholas K. , Dunham Diane , Manohar Monali , Peters Rachel L. , Saffery Richard , Koplin Jennifer J. , Nadeau Kari C. , Neeland Melanie R. , Andorf Sandra 
Published: December 2022

AbstractIgE-mediated food allergies in infants are a significant health concern, with peanut allergy being of particular interest due to its prevalence and severity. Among individuals who produce peanut-specific IgE some experience no adverse reaction on peanut consumption. This asymptomatic phenotype is known as sensitized tolerance. To elucidate the immune environment of peanut sensitized tolerant and clinically allergic one-year-olds, high-dimensional mass cytometry was conducted as part of the HealthNuts study. The resulting data includes peripheral blood mononuclear cells from 36 participants encompassing non-allergic, peanut sensitized with tolerance, and clinically peanut allergic infants. The raw mass cytometry data is described here and freely available for reuse through the Immunology Database and Analysis Portal (ImmPort). Additional allergy information and serum vitamin D levels of the participants were measured and are also included in the data upload. These high-dimensional mass cytometry data, when combined with clinical information, offer a broad immune profile of peanut allergic and sensitized tolerant infants.
The unpredictable nature of bubble evolution
Authors: Lawless Jack , Keeler Jack , Gaillard Antoine , Hazel Andrew , Juel Anne 
Published: December 2022

AbstractUnpredictable dynamics arising from a sensitivity to initial conditions is commonly associated with chaos. We demonstrate how similar unpredictability manifests in a nonlinear system that possesses a large number of long-term outcomes, namely the propagation of an air bubble within a viscous fluid-filled channel. The system under investigation supports various stable states of single-bubble propagation. In addition, bubbles can readily break up during their propagation. Upon subjecting steadily-propagating bubbles to finite-amplitude perturbations in the form of localised channel constrictions, we identify localised regions of the driving flow rate for which the resulting evolutions are unpredictable. Visibly-indistinguishable bubbles are observed to evolve towards a multitude of long-term outcomes, including each of the stable states available to the initial bubble and various states of permanently-changed bubble topology. By combining high-precision experimental results with simulations of a depth-averaged lubrication model of the system, we determine that this behaviour is driven by a sensitive dependence on initial conditions within the vicinity of an unstable periodic orbit.
Owl-like plaques of the Copper Age and the involvement of children
Authors: Negro Juan J. , Blanco Guillermo , Rodríguez-Rodríguez Eduardo , Díaz Núñez de Arenas Víctor M. 
Published: December 2022

AbstractIn the Copper Age, slate engraved plaques were produced massively in the southwestern corner of the Iberian Peninsula. Researchers have speculated about the function of these palm-sized stone objects for more than a century, although most have favored the idea that they represented goddesses, and served ritual purposes. The plaques are engraved with different designs of varying complexity. In some of them, the ones sporting two large frontal eyes, we clearly see owls modelled after two species present in the area: the little owl (Athene noctua), and the long-eared owl (Asio otus). These two species, living in semi-open habitats, were possibly the most abundant owls around the human settlements and surrounding cultivated fields of the Chalcolithic period. People must have been aware of the owl presence and possibly interacted with them. Why owls but no other animals have been the models may relate to the fact they are the most anthropomorphic of all animals, with large frontally-placed eyes in their enormous heads. In the iconography, owls are systematically represented, even today, with their two eyes staring at the observer, as opposed to the lateral view used for any other animal. Additionally, slate is one of the commonest surface rocks in southwestern Iberia, and it provides a blank canvas for engraving lines using pointed tools made of flint, quartz or copper. The way slates exfoliate makes easy to craft owl-looking plaques. To silhouette animals other than owls in a recognizable way would request extra carving abilities and specific tools. Plaque manufacture and design were simple and did not demand high skills nor intensive labor as demonstrated in replication experiments. Owl engravings could have been executed by youngsters, as they resemble owls painted today by elementary school students. This also suggests that schematic drawings are universal and timeless. We propose that the owl-like slate plaques are the remains of a set of objects used in both playful activities and in ritual ceremonies. The actual engraving of the plaques may have been part of the game. Owlish slate plaques were often perforated twice at the top. We interpret this as insertion points for actual bird feathers added to the plaques, right at the place where tufts emerge in live owls. The frontier among play and ritual is diffuse in liminal societies and there is no contradiction in playing with animal-like toys and, at some point, using them as offerings as part of community rituals related, for instance, to the colossal megalithic tombs so characteristic of the Copper Age.
Risk of SARS-CoV-2 reinfection: a systematic review and meta-analysis
Authors: Deng Luojia , Li Peiqi , Zhang Xuezhixing , Jiang Qianxue , Turner DeAnne , Zhou Chao , Gao Yanxiao , Qian Frank , Zhang Ci , Lu Hui , Zou Huachun , Vermund Sten H. , Qian Han-Zhu 
Published: December 2022

AbstractThis meta-analysis aims to synthesize global evidence on the risk of reinfection among people previously infected with SARS-CoV-2. We systematically searched PubMed, Scopus, Embase and Web of Science as of April 5, 2021. We conducted: (1) meta-analysis of cohort studies containing data sufficient for calculating the incidence rate of SARS-CoV-2 reinfection; (2) systematic review of case reports with confirmed SARS-CoV-2 reinfection cases. The reinfection incidence was pooled by zero-inflated beta distribution. The hazard ratio (HR) between reinfection incidence among previously infected individuals and new infection incidence among infection-naïve individuals was calculated using random-effects models. Of 906 records retrieved and reviewed, 11 studies and 11 case reports were included in the meta-analysis and the systematic review, respectively. The pooled SARS-CoV-2 reinfection incidence rate was 0.70 (standard deviation [SD] 0.33) per 10,000 person-days. The incidence of reinfection was lower than the incidence of new infection (HR = 0.12, 95% confidence interval 0.09–0.17). Our meta-analysis of studies conducted prior to the emergency of the more transmissible Omicron variant showed that people with a prior SARS-CoV-2 infection could be re-infected, and they have a lower risk of infection than those without prior infection. Continuing reviews are needed as the reinfection risk may change due to the rapid evolution of SARS-CoV-2 variants.
Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis)
Authors: Li Wanyu , Lan Yue , Wang Lei , He Lewei , Tang Ruixiang , Price Megan , Yue Bisong , Fan Zhenxin 
Published: December 2022

AbstractThe Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.