bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of delay-adjusted all-cause excess mortality in the USA: March–December 2020
Authors: Akhmetzhanov Andrei R. 
Published: July 2021

AbstractWe estimate the delay-adjusted all-cause excess deaths across 53 US jurisdictions. Using provisional data collected from September through December 2020, we first identify a common mean reporting delay of 2.8 weeks, whereas four jurisdictions have prolonged reporting delays compared to the others: Connecticut (mean 5.8 weeks), North Carolina (mean 10.4 weeks), Puerto Rico (mean 4.7 weeks) and West Virginia (mean 5.5 weeks). After adjusting for reporting delays, we estimate the percent change in all-cause excess mortality from March to December 2020 with range from 0.2 to 3.6 in Hawaii to 58.4 to 62.4 in New York City. Comparing the March–December with September–December 2020 periods, the highest increases in excess mortality are observed in South Dakota (36.9–54.0), North Dakota (33.9–50.7) and Missouri (27.8–33.9). Our findings indicate that analysis of provisional data requires caution in interpreting the death counts in recent weeks, while one needs also to account for heterogeneity in reporting delays of excess deaths among US jurisdictions.
The frequency and efficacy of genetic testing in individuals with scimitar syndrome
Authors: Fick Tyler A. , Scott Daryl A. , Lupo Philip J. , Weigand Justin , Morris Shaine A. 
Published: July 2021

AbstractBackground:Scimitar syndrome is a rare CHD composed of partial anomalous pulmonary venous connection from the right lung, via a scimitar vein, to the inferior vena cava rather than the left atrium. Genetic conditions associated with scimitar syndrome have not been well investigated at present.Methods:Our study included patients with scimitar syndrome diagnosed at Texas Children’s Hospital from January 1987 to July 2020. Medical records were evaluated to determine if genetic testing was performed, including chromosomal microarray analysis or whole-exome sequencing. Copy number variants identified as pathogenic/likely pathogenic and variants of unknown significance were collected. Analyses of cardiac and extracardiac findings were performed via chart review.Results:Ninety-eight patients were identified with scimitar syndrome, 89 of which met inclusion criteria. A chromosome analysis or chromosomal microarray analysis was performed in 18 patients (20%). Whole-exome sequencing was performed in six patients following negative chromosomal microarray analysis testing. A molecular genetic diagnosis was made in 7 of 18 cases (39% of those tested). Ninety-six per cent of the cohort had some type of extracardiac finding, with 43% having asthma and 20% having a gastrointestinal pathology. Of the seven patients with positive genetic testing, all had extracardiac anomalies with all but one having gastrointestinal findings and 30% having congenital diaphragmatic hernia.Conclusions:Genetic testing revealed an underlying diagnosis in roughly 40% of those tested. Given the relatively high prevalence of pathogenic variants, we recommend chromosomal microarray analysis and whole-exome sequencing for patients with scimitar syndrome and extracardiac defects.
A CORRECTNESS PROOF FOR AL-BARAKĀT’S LOGICAL DIAGRAMS
Authors: HODGES WILFRID 
Published: July 2021

AbstractIn Baghdad in the mid twelfth century Abū al-Barakāt proposes a radical new procedure for finding the conclusions of premise-pairs in syllogistic logic, and for identifying those premise-pairs that have no conclusions. The procedure makes no use of features of the standard Aristotelian apparatus, such as conversions or syllogistic figures. In place of these al-Barakāt writes out pages of diagrams consisting of labelled horizontal lines. He gives no instructions and no proof that the procedure will yield correct results. So the reader has to work out what his procedure is and whether it is correct. The procedure turns out to be insightful and entirely correct, but this paper may be the first study to give a full description of the procedure and a rigorous proof of its correctness.
Electrical Resistivity Anomalies Offshore a Carbonate Coastline: Evidence for Freshened Groundwater?
Authors: Haroon Amir , Micallef Aaron , Jegen Marion , Schwalenberg Katrin , Karstens Jens , Berndt Christian , Garcia Xavier , Kühn Michel , Rizzo Enzo , Fusi Nicoletta Chiara , Ahaneku Chibuzo Valeria , Petronio Lorenzo , Faghih Zahra , Weymer Bradley A. , De Biase Michele , Chidichimo Francesco 
Published: July 2021

AbstractCarbonate lithologies host considerable quantities of the Earth's freshwater resources and partially supply a quarter of the global population with drinkable water. In addition, carbonates constitute substantial amounts of the global coastlines, yet it is not known if and how they can sustain freshened groundwater offshore. Here, we use controlled‐source electromagnetic, seismic reflection, and core sample data to derive a lithological model for the eastern margin of the Maltese Islands and identify four distinct resistivity anomalies within the Upper Coralline and Globigerina Limestone formations. The anomalies hosted in the former are likely associated with low porosities, whereas the anomaly within the latter is indicative of pore fluid freshening. Hydrogeological modeling suggests that freshened pore fluids, emplaced during sea‐level lowstands and preserved in low permeability units, are potentially still found within carbonate shelves. However, resource potential is low due to its relict nature and low permeability host environment.
Lithosphere Weakening During Arctic Ocean Opening: Evidence From Effective Elastic Thickness
Authors: Lu Yu , Lu Zhezhe , Li Chun‐Feng , Zhu Shuang , Audet Pascal 
Published: July 2021

AbstractEvolution of the Arctic Ocean lithosphere has involved multiple stages of opening with crustal stretching and thinning prior to lithospheric breakup. Mapping lateral variations in lithospheric rheology can help unravel the detailed tectonic history of the Arctic. Here we perform a wavelet analysis of gravity and bathymetry data to map the effective elastic thickness () of the lithosphere in the Arctic. The low overall suggests that large shear stresses and serpentinization weakened the lithosphere at Arctic passive margins during a multistage opening process. Moderately low values along the Gakkel Ridge imply a relatively cold ultraslow‐spreading center compared to typical mid‐ocean ridges.
India‐Tarim Lithospheric Mantle Collision Beneath Western Tibet Controls the Cenozoic Building of Tian Shan
Authors: Huangfu Pengpeng , Li Zhong‐Hai , Zhang Kai‐Jun , Fan Weiming , Zhao Junmeng , Shi Yaolin 
Published: July 2021

AbstractThe ongoing India‐Asia collision principally regulates the Cenozoic tectonic deformation of the Asian interior, and builds a far‐away but active spectacular intraplate orogen—Tian Shan. However, the deep processes and dynamics of far‐field deformation propagation and the resultant Tian Shan building remain ambiguous. Here, we construct systematic numerical models with variable thermo‐rheological properties of the orogen‐featured blocks and convergence rates, which reveal that the far‐field effect of India‐Asia collision on the Tian Shan building is strongly controlled by the direct collision of Indian lithospheric mantle with the rigid Tarim block beneath western Tibet. The model results, together with the well‐established geological and geophysical constraints, not only reconcile the first‐order crustal and lithospheric structures of the western Tibetan plateau and Tian Shan, but also confirm a >30 Myr time lag between the initial India‐Asia collision and the far‐field Tian Shan building.
Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers
Authors: Liu Juan , Chen Li-Yu , Zhou Ping , Liao Zhenyang , Lin Hai , Yu Qingyi , Ming Ray 
Published: July 2021

AbstractSex types of papaya are controlled by a pair of nascent sex chromosomes, but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still unclear. We performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers. A total of 1734 differentially expressed genes (DEGs) were identified, of which 923 showed female-biased expression and 811 showed male-biased expression. Functional annotation revealed that genes related to plant hormone biosynthesis and signaling pathways, especially in abscisic acid and auxin pathways, were overrepresented in the DEGs. Transcription factor binding motifs, such as MYB2, GAMYB, and AP2/EREBP, were enriched in the promoters of the hormone-related DEGs, and transcription factors with those motifs also exhibited differential expression between sex types. Among these DEGs, we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel development. Our results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional, epigenetic, and phytohormone regulation. Hormones, especially ABA and auxin, transcription factors, and genes in the non-recombination region of the sex chromosome could be involved in this process. Our findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.
The R2R3-type MYB transcription factor MdMYB90-like is responsible for the enhanced skin color of an apple bud sport mutant
Authors: Sun Chao , Wang Chunming , Zhang Wang , Liu Shuai , Wang Weiyao , Yu Xinyi , Song Tao , Yu Maxwell , Yu Weichang , Qu Shenchun 
Published: July 2021

AbstractThe anthocyanin content in apple skin determines its red coloration, as seen in a Fuji apple mutant. Comparative RNA-seq analysis was performed to determine differentially expressed genes at different fruit development stages between the wild-type and the skin color mutant. A novel R2R3-MYB transcription factor, MdMYB90-like, was uncovered as the key regulatory gene for enhanced coloration in the mutant. The expression of MdMYB90-like was 21.3 times higher in the mutant. MdMYB90-like regulates anthocyanin biosynthesis directly through the activation of anthocyanin biosynthesis genes and indirectly through the activation of other transcription factors that activate anthocyanin biosynthesis. MdMYB90-like bound to the promoters of both structural genes (MdCHS and MdUFGT) and other transcription factor genes (MdMYB1 and MdbHLH3) in the yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay. Transgenic analysis showed that MdMYB90-like was localized in the nucleus, and its overexpression induced the expression of other anthocyanin-related genes, including MdCHS, MdCHI, MdANS, MdUFGT, MdbHLH3, and MdMYB1. The mutant had reduced levels of DNA methylation in two regions (−1183 to −988 and −2018 to −1778) of the MdMYB90-like gene promoter, which might explain the enhanced expression of the gene and the increased anthocyanin content in the mutant apple skin.
Chloroplast and mitochondrial DNA editing in plants
Authors: Kang Beum-Chang , Bae Su-Ji , Lee Seonghyun , Lee Jeong Sun , Kim Annie , Lee Hyunji , Baek Gayoung , Seo Huiyun , Kim Jihun , Kim Jin-Soo 
Published: July 2021

AbstractPlant organelles including mitochondria and chloroplasts contain their own genomes, which encode many genes essential for respiration and photosynthesis, respectively. Gene editing in plant organelles, an unmet need for plant genetics and biotechnology, has been hampered by the lack of appropriate tools for targeting DNA in these organelles. In this study, we developed a Golden Gate cloning system1, composed of 16 expression plasmids (8 for the delivery of the resulting protein to mitochondria and the other 8 for delivery to chloroplasts) and 424 transcription activator-like effector subarray plasmids, to assemble DddA-derived cytosine base editor (DdCBE)2 plasmids and used the resulting DdCBEs to efficiently promote point mutagenesis in mitochondria and chloroplasts. Our DdCBEs induced base editing in lettuce or rapeseed calli at frequencies of up to 25% (mitochondria) and 38% (chloroplasts). We also showed DNA-free base editing in chloroplasts by delivering DdCBE mRNA to lettuce protoplasts to avoid off-target mutations caused by DdCBE-encoding plasmids. Furthermore, we generated lettuce calli and plantlets with edit frequencies of up to 99%, which were resistant to streptomycin or spectinomycin, by introducing a point mutation in the chloroplast 16S rRNA gene.
Targeted base editing in the plastid genome of Arabidopsis thaliana
Authors: Nakazato Issei , Okuno Miki , Yamamoto Hiroshi , Tamura Yoshiko , Itoh Takehiko , Shikanai Toshiharu , Takanashi Hideki , Tsutsumi Nobuhiro , Arimura Shin-ichi 
Published: July 2021

AbstractBacterial cytidine deaminase fused to the DNA binding domains of transcription activator-like effector nucleases was recently reported to transiently substitute a targeted C to a T in mitochondrial DNA of mammalian cultured cells1. We applied this system to targeted base editing in the Arabidopsis thaliana plastid genome. The targeted Cs were homoplasmically substituted to Ts in some plantlets of the T1 generation and the mutations were inherited by their offspring independently of their nuclear-introduced vectors.
Two separate, large cohorts reveal potential modifiers of age-associated variation in visual reaction time performance
Authors: Talboom J. S. , De Both M. D. , Naymik M. A. , Schmidt A. M. , Lewis C. R. , Jepsen W. M. , Håberg A. K. , Rundek T. , Levin B. E. , Hoscheidt S. , Bolla Y. , Brinton R. D. , Schork N. J. , Hay M. , Barnes C. A. , Glisky E. , Ryan L. , Huentelman M. J. 
Published: July 2021

AbstractTo identify potential factors influencing age-related cognitive decline and disease, we created MindCrowd. MindCrowd is a cross-sectional web-based assessment of simple visual (sv) reaction time (RT) and paired-associate learning (PAL). svRT and PAL results were combined with 22 survey questions. Analysis of svRT revealed education and stroke as potential modifiers of changes in processing speed and memory from younger to older ages (ntotal = 75,666, nwomen = 47,700, nmen = 27,966; ages 18–85 years old, mean (M)Age = 46.54, standard deviation (SD)Age = 18.40). To complement this work, we evaluated complex visual recognition reaction time (cvrRT) in the UK Biobank (ntotal = 158,249 nwomen = 89,333 nmen = 68,916; ages 40–70 years old, MAge = 55.81, SDAge = 7.72). Similarities between the UK Biobank and MindCrowd were assessed using a subset of MindCrowd (UKBb MindCrowd) selected to mirror the UK Biobank demographics (ntotal = 39,795, nwomen = 29,640, nmen = 10,155; ages 40–70 years old, MAge = 56.59, SDAge = 8.16). An identical linear model (LM) was used to assess both cohorts. Analyses revealed similarities between MindCrowd and the UK Biobank across most results. Divergent findings from the UK Biobank included (1) a first-degree family history of Alzheimer’s disease (FHAD) was associated with longer cvrRT. (2) Men with the least education were associated with longer cvrRTs comparable to women across all educational attainment levels. Divergent findings from UKBb MindCrowd included more education being associated with shorter svRTs and a history of smoking with longer svRTs from younger to older ages.
Spatial distribution of B cells and lymphocyte clusters as a predictor of triple-negative breast cancer outcome
Authors: Wortman Juliana C. , He Ting-Fang , Solomon Shawn , Zhang Robert Z. , Rosario Anthony , Wang Roger , Tu Travis Y. , Schmolze Daniel , Yuan Yuan , Yost Susan E. , Li Xuefei , Levine Herbert , Atwal Gurinder , Lee Peter P. , Yu Clare C. 
Published: July 2021

AbstractWhile tumor infiltration by CD8+ T cells is now widely accepted to predict outcomes, the clinical significance of intratumoral B cells is less clear. We hypothesized that spatial distribution rather than density of B cells within tumors may provide prognostic significance. We developed statistical techniques (fractal dimension differences and a box-counting method ‘occupancy’) to analyze the spatial distribution of tumor-infiltrating lymphocytes (TILs) in human triple-negative breast cancer (TNBC). Our results indicate that B cells in good outcome tumors (no recurrence within 5 years) are spatially dispersed, while B cells in poor outcome tumors (recurrence within 3 years) are more confined. While most TILs are located within the stroma, increased numbers of spatially dispersed lymphocytes within cancer cell islands are associated with a good prognosis. B cells and T cells often form lymphocyte clusters (LCs) identified via density-based clustering. LCs consist either of T cells only or heterotypic mixtures of B and T cells. Pure B cell LCs were negligible in number. Compared to tertiary lymphoid structures (TLS), LCs have fewer lymphocytes at lower densities. Both types of LCs are more abundant and more spatially dispersed in good outcomes compared to poor outcome tumors. Heterotypic LCs in good outcome tumors are smaller and more numerous compared to poor outcome. Heterotypic LCs are also closer to cancer islands in a good outcome, with LC size decreasing as they get closer to cancer cell islands. These results illuminate the significance of the spatial distribution of B cells and LCs within tumors.
TBK1 and TNFRSF13B mutations and an autoinflammatory disease in a child with lethal COVID-19
Authors: Schmidt Axel , Peters Sophia , Knaus Alexej , Sabir Hemmen , Hamsen Frauke , Maj Carlo , Fazaal Julia , Sivalingam Sugirthan , Savchenko Oleksandr , Mantri Aakash , Holzinger Dirk , Neudorf Ulrich , Müller Andreas , Ludwig Kerstin U. , Krawitz Peter M. , Engels Hartmut , Nöthen Markus M. , Bagci Soyhan 
Published: July 2021

AbstractAmong children, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are typically mild. Here, we describe the case of a 3.5-year-old girl with an unusually severe presentation of coronavirus disease (COVID-19). The child had an autoinflammatory disorder of unknown etiology, which had been treated using prednisolone and methotrexate, and her parents were half cousins of Turkish descent. After 5 days of nonspecific viral infection symptoms, tonic-clonic seizures occurred followed by acute cardiac insufficiency, multi-organ insufficiency, and ultimate death. Trio exome sequencing identified a homozygous splice-variant in the gene TBK1, and a homozygous missense variant in the gene TNFRSF13B. Heterozygous deleterious variants in the TBK1 gene have been associated with severe COVID-19, and the variant in the TNFRSF13B gene has been associated with common variable immunodeficiency (CVID). We suggest that the identified variants, the autoinflammatory disorder and its treatment, or a combination of these factors probably predisposed to lethal COVID-19 in the present case.
Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns
Authors: Bollen Yannik , Stelloo Ellen , van Leenen Petra , van den Bos Myrna , Ponsioen Bas , Lu Bingxin , van Roosmalen Markus J. , Bolhaqueiro Ana C. F. , Kimberley Christopher , Mossner Maximilian , Cross William C. H. , Besselink Nicolle J. M. , van der Roest Bastiaan , Boymans Sander , Oost Koen C. , de Vries Sippe G. , Rehmann Holger , Cuppen Edwin , Lens Susanne M. A. , Kops Geert J. P. L. , Kloosterman Wigard P. , Terstappen Leon W. M. M. , Barnes Chris P. , Sottoriva Andrea , Graham Trevor A. , Snippert Hugo J. G. 
Published: July 2021

AbstractCentral to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq—a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.
Charge and discharge profiles of repurposed LiFePO4 batteries based on the UL 1974 standard
Authors: Chung Hsien-Ching 
Published: July 2021

AbstractOwing to the popularization of electric vehicles worldwide and the development of renewable energy supply, Li-ion batteries are widely used from small-scale personal mobile products to large-scale energy storage systems. Recently, the number of retired power batteries has largely increased, causing environmental protection threats and waste of resources. Since most of the retired power batteries still possess about 80% of their initial capacity, their second use becomes a possible route to solve the emergent problem. Safety and performance are important when using these second-use repurposed batteries. Underwriters Laboratories (UL), a global safety certification company, published the standard for evaluating the safety and performance of repurposed batteries, i.e., UL 1974. In this work, the test procedures are designed according to UL 1974, and the charge and discharge profile datasets of the LiFePO4 repurposed batteries are provided. Researchers and engineers can use the characteristic curves to evaluate the quality of the repurposed batteries. Furthermore, the profile datasets can be applied in the model-based engineering of repurposed batteries, e.g., fitting the variables of an empirical model or validating the results of a theoretical model.