bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial Trends and Drivers of Bedload and Suspended Sediment Fluxes in Global Rivers
Authors: Cohen Sagy , Syvitski Jaia , Ashley Thomas , Lammers Roderick , Fekete Balazs , Li Hong‐Yi 
Published: June 2022

AbstractBedload is notoriously challenging to measure and model; its dynamics, therefore, remains largely unknown in most fluvial systems worldwide. We present results from a global scale bedload flux model as part of the WBMsed modeling framework that well predict the distribution of water discharge, suspended sediment and bedload. The sensitivity of bedload predictions to river slope, particle size, discharge, river width, and suspended sediment were analyzed, showing the model to be most responsive to spatial dynamics in river discharge and slope. The relationship between bedload and total sediment flux is analyzed globally, and for representative longitudinal river profiles (Amazon, Mississippi, and Lena Rivers). The results show that while the proportion of bedload decreases from headwaters to the coasts, there is considerable variability between basins and along river corridors. The topographic and hydrological longitudinal profiles of rivers are shown to be the key drivers of bedload trends, with fluctuations in slope controlling its more local dynamics. Estimates of water and sediment fluxes to global oceans from 2,067 largest river outlets (draining 67% of the global continental area) are provided. Estimated water discharge at 30,579 km3/y corresponds well to past estimates; however, sediment flux is higher. Total global particulate load of 17.8 Gt/y is delivered to global oceans, 14.8 Gt/y as washload, 1.1 Gt/y as bedload, and 2.6 Gt/y as suspended bed material. The largest 25 rivers are predicted to transport more than half of the total sediment flux to global oceans.
A Systems Approach to Remediating Human Exposure to Arsenic and Fluoride From Overexploited Aquifers
Authors: Knappett P. S. K. , Farias P. , Miller G. R. , Hoogesteger J. , Li Y. , Mendoza‐Sanchez I. , Woodward R. T. , Hernandez H. , Loza‐Aguirre I. , Datta S. , Huang Y. , Carrillo G. , Roh T. , Terrell D. 
Published: June 2022

AbstractIn semiarid agricultural regions, aquifers have watered widespread economic development. Falling water tables, however, drive up energy costs and can make the water toxic for human consumption. The study area is located in central Mexico, where arsenic and fluoride are widely present at toxic concentrations in well water. We simulated the holistic outcomes from three pumping scenarios over 100 years (2020–2120); (S1) pumping rates increase at a similar rate to the past 40 years, (S2) remain constant, or (S3) decrease. Under scenario S1, by 2120, the depth to water table increased to 426 m and energy consumption for irrigation increased to 4 × 109 kWh/yr. Arsenic and fluoride concentrations increased from 14 to 46 μg/L and 1.0 to 3.6 mg/L, respectively. The combined estimated IQ point decrements from drinking untreated well water lowered expected incomes in 2120 by 27% compared to what they would be with negligible exposure levels. We calculated the 100‐year Net Present Value (NPV) of each scenario assuming the 2020 average crop value to water footprint ratio of 0.12 USD/m3. Without drinking water mitigation, S1 and S3 yielded relative NPVs of −5.96 × 109 and 1.51 × 109 USD, respectively, compared to the base case (S2). The relative NPV of providing blanket reverse osmosis treatment, while keeping pumping constant (S2), was 11.55 × 109 USD and this gain increased when combined with decreased pumping (S3). If a high value, low water footprint crop was substituted (broccoli, 1.51 USD/m3), the net gains from increasing pumping were similar in size to those of implementing blanket drinking water treatment.
Accelerating Ice Loss From Peripheral Glaciers in North Greenland
Authors: Khan Shfaqat A. , Colgan William , Neumann Thomas A. , van den Broeke Michiel R. , Brunt Kelly M. , Noël Brice , Bamber Jonathan L. , Hassan Javed , Bjørk Anders A. 
Published: June 2022

AbstractIn recent decades, Greenland's peripheral glaciers have experienced large‐scale mass loss, resulting in a substantial contribution to sea level rise. While their total area of Greenland ice cover is relatively small (4%), their mass loss is disproportionally large compared to the Greenland ice sheet. Satellite altimetry from Ice, Cloud, and land Elevation Satellite (ICESat) and ICESat‐2 shows that mass loss from Greenland's peripheral glaciers increased from 27.2 ± 6.2 Gt/yr (February 2003–October 2009) to 42.3 ± 6.2 Gt/yr (October 2018–December 2021). These relatively small glaciers now constitute 11 ± 2% of Greenland's ice loss and contribute to global sea level rise. In the period October 2018–December 2021, mass loss increased by a factor of four for peripheral glaciers in North Greenland. While peripheral glacier mass loss is widespread, we also observe a complex regional pattern where increases in precipitation at high altitudes have partially counteracted increases in melt at low altitude.
Directly wireless communication of human minds via mind-controlled programming metasurface
Authors: Luo Xiangang 
Published: June 2022

AbstractAn concept of electromagnetic brain-computer-metasurface (EBCM), and remotely mindcontrolled metasurface (RMCM) via brainwaves is reported in eLight. Rather than DC voltage from power supply or AC voltages from signal generators, such metasurfaces are controlled by brainwaves collected in real time and can transmit information wirelessly between human brains. Such platforms can lead to a promising approach for the service of disabled people.
Establishment of combined diagnostic models of Alzheimer’s disease in a Chinese cohort: the Chongqing Ageing & Dementia Study (CADS)
Authors: Fan Dong-Yu , Jian Jie-Ming , Huang Shan , Li Wei-Wei , Shen Ying-Ying , Wang Zhen , Zeng Gui-Hua , Yi Xu , Jin Wang-Sheng , Liu Yu-Hui , Zeng Fan , Bu Xian-Le , Chen Li-Yong , Mao Qing-Xiang , Xu Zhi-Qiang , Yu Jin-Tai , Wang Jun , Wang Yan-Jiang 
Published: June 2022

AbstractCerebrospinal fluid (CSF) biomarkers are essential for the accurate diagnosis of Alzheimer’s disease (AD), yet their measurement levels vary widely across centers and regions, leaving no uniform cutoff values to date. Diagnostic cutoff values of CSF biomarkers for AD are lacking for the Chinese population. As a member of the Alzheimer’s Association Quality Control program for CSF biomarkers, we aimed to establish diagnostic models based on CSF biomarkers and risk factors for AD in a Chinese cohort. A total of 64 AD dementia patients and 105 age- and sex-matched cognitively normal (CN) controls from the Chongqing Ageing & Dementia Study cohort were included. CSF Aβ42, P-tau181, and T-tau levels were measured by ELISA. Combined biomarker models and integrative models with demographic characteristics were established by logistic regression. The cutoff values to distinguish AD from CN were 933 pg/mL for Aβ42, 48.7 pg/mL for P-tau181 and 313 pg/mL for T-tau. The AN model, including Aβ42 and T-tau, had a higher diagnostic accuracy of 89.9%. Integrating age and APOE ε4 status to AN model (the ANA’E model) increased the diagnostic accuracy to 90.5% and improved the model performance. This study established cutoff values of CSF biomarkers and optimal combined models for AD diagnosis in a Chinese cohort.
Pilot study of bempegaldesleukin in combination with nivolumab in patients with metastatic sarcoma
Authors: D’Angelo Sandra P. , Richards Allison L. , Conley Anthony P. , Woo Hyung Jun , Dickson Mark A. , Gounder Mrinal , Kelly Ciara , Keohan Mary Louise , Movva Sujana , Thornton Katherine , Rosenbaum Evan , Chi Ping , Nacev Benjamin , Chan Jason E. , Slotkin Emily K. , Kiesler Hannah , Adamson Travis , Ling Lilan , Rao Pavitra , Patel Shreyaskumar , Livingston Jonathan A. , Singer Samuel , Agaram Narasimhan P. , Antonescu Cristina R. , Koff Andrew , Erinjeri Joseph P. , Hwang Sinchun , Qin Li-Xuan , Donoghue Mark T. A. , Tap William D. 
Published: June 2022

AbstractPD-1 blockade (nivolumab) efficacy remains modest for metastatic sarcoma. In this paper, we present an open-label, non-randomized, non-comparative pilot study of bempegaldesleukin, a CD122-preferential interleukin-2 pathway agonist, with nivolumab in refractory sarcoma at Memorial Sloan Kettering/MD Anderson Cancer Centers (NCT03282344). We report on the primary outcome of objective response rate (ORR) and secondary endpoints of toxicity, clinical benefit, progression-free survival, overall survival, and durations of response/treatment. In 84 patients in 9 histotype cohorts, all patients experienced ≥1 adverse event and treatment-related adverse event; 1 death was possibly treatment-related. ORR was highest in angiosarcoma (3/8) and undifferentiated pleomorphic sarcoma (2/10), meeting predefined endpoints. Results of our exploratory investigation of predictive biomarkers show: CD8 + T cell infiltrates and PD-1 expression correlate with improved ORR; upregulation of immune-related pathways correlate with improved efficacy; Hedgehog pathway expression correlate with resistance. Exploration of this combination in selected sarcomas, and of Hedgehog signaling as a predictive biomarker, warrants further study in larger cohorts.
Effective lifting of the topological protection of quantum spin Hall edge states by edge coupling
Authors: Stühler R. , Kowalewski A. , Reis F. , Jungblut D. , Dominguez F. , Scharf B. , Li G. , Schäfer J. , Hankiewicz E. M. , Claessen R. 
Published: June 2022

AbstractThe scientific interest in two-dimensional topological insulators (2D TIs) is currently shifting from a more fundamental perspective to the exploration and design of novel functionalities. Key concepts for the use of 2D TIs in spintronics are based on the topological protection and spin-momentum locking of their helical edge states. In this study we present experimental evidence that topological protection can be (partially) lifted by pairwise coupling of 2D TI edges in close proximity. Using direct wave function mapping via scanning tunneling microscopy/spectroscopy (STM/STS) we compare isolated and coupled topological edges in the 2D TI bismuthene. The latter situation is realized by natural lattice line defects and reveals distinct quasi-particle interference (QPI) patterns, identified as electronic Fabry-Pérot resonator modes. In contrast, free edges show no sign of any single-particle backscattering. These results pave the way for novel device concepts based on active control of topological protection through inter-edge hybridization for, e.g., electronic Fabry-Pérot interferometry.
Regional and seasonal partitioning of water and temperature controls on global land carbon uptake variability
Authors: Wang Kai , Bastos Ana , Ciais Philippe , Wang Xuhui , Rödenbeck Christian , Gentine Pierre , Chevallier Frédéric , Humphrey Vincent W. , Huntingford Chris , O’Sullivan Michael , Seneviratne Sonia I. , Sitch Stephen , Piao Shilong 
Published: June 2022

AbstractGlobal fluctuations in annual land carbon uptake (NEEIAV) depend on water and temperature variability, yet debate remains about local and seasonal controls of the global dependences. Here, we quantify regional and seasonal contributions to the correlations of globally-averaged NEEIAV against terrestrial water storage (TWS) and temperature, and respective uncertainties, using three approaches: atmospheric inversions, process-based vegetation models, and data-driven models. The three approaches agree that the tropics contribute over 63% of the global correlations, but differ on the dominant driver of the global NEEIAV, because they disagree on seasonal temperature effects in the Northern Hemisphere (NH, >25°N). In the NH, inversions and process-based models show inter-seasonal compensation of temperature effects, inducing a global TWS dominance supported by observations. Data-driven models show weaker seasonal compensation, thereby estimating a global temperature dominance. We provide a roadmap to fully understand drivers of global NEEIAV and discuss their implications for future carbon–climate feedbacks.
Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential
Authors: Nefzger Christian M. , Jardé Thierry , Srivastava Akanksha , Schroeder Jan , Rossello Fernando J. , Horvay Katja , Prasko Mirsada , Paynter Jacob M. , Chen Joseph , Weng Chen-Fang , Sun Yu B. Y. , Liu Xiaodong , Chan Eva , Deshpande Nikita , Chen Xiaoli , Li Y. Jinhua , Pflueger Jahnvi , Engel Rebekah M. , Knaupp Anja S. , Tsyganov Kirill , Nilsson Susan K. , Lister Ryan , Rackham Owen J. L. , Abud Helen E. , Polo Jose M. 
Published: June 2022

AbstractThe impact of aging on intestinal stem cells (ISCs) has not been fully elucidated. In this study, we identified widespread epigenetic and transcriptional alterations in old ISCs. Using a reprogramming algorithm, we identified a set of key transcription factors (Egr1, Irf1, FosB) that drives molecular and functional differences between old and young states. Overall, by dissecting the molecular signature of aged ISCs, our study identified transcription factors that enhance the regenerative capacity of ISCs.
Genome-wide association study of musical beat synchronization demonstrates high polygenicity
Authors: Niarchou Maria , Gustavson Daniel E. , Sathirapongsasuti J. Fah , Anglada-Tort Manuel , Eising Else , Bell Eamonn , McArthur Evonne , Straub Peter ,   23andMe Research Team, Aslibekyan Stella , Auton Adam , Bell Robert K. , Bryc Katarzyna , Clark Sarah K. , Elson Sarah L. , Fletez-Brant Kipper , Fontanillas Pierre , Furlotte Nicholas A. , Gandhi Pooja M. , Heilbron Karl , Hicks Barry , Huber Karen E. , Jewett Ethan M. , Jiang Yunxuan , Kleinman Aaron , Lin Keng-Han , Litterman Nadia K. , McCreight Jey C. , McIntyre Matthew H. , McManus Kimberly F. , Mountain Joanna L. , Mozaffari Sahar V. , Nandakumar Priyanka , Noblin Elizabeth S. , Northover Carrie A. M. , O’Connell Jared , Pitts Steven J. , Poznik G. David , Shastri Anjali J. , Shelton Janie F. , Shringarpure Suyash , Tian Chao , Tung Joyce Y. , Tunney Robert J. , Vacic Vladimir , Wang Xin , McAuley J. Devin , Capra John A. , Ullén Fredrik , Creanza Nicole , Mosing Miriam A. , Hinds David A. , Davis Lea K. , Jacoby Nori , Gordon Reyna L. 
Published: June 2022

AbstractMoving in synchrony to the beat is a fundamental component of musicality. Here we conducted a genome-wide association study to identify common genetic variants associated with beat synchronization in 606,825 individuals. Beat synchronization exhibited a highly polygenic architecture, with 69 loci reaching genome-wide significance (P < 5 × 10−8) and single-nucleotide-polymorphism-based heritability (on the liability scale) of 13%–16%. Heritability was enriched for genes expressed in brain tissues and for fetal and adult brain-specific gene regulatory elements, underscoring the role of central-nervous-system-expressed genes linked to the genetic basis of the trait. We performed validations of the self-report phenotype (through separate experiments) and of the genome-wide association study (polygenic scores for beat synchronization were associated with patients algorithmically classified as musicians in medical records of a separate biobank). Genetic correlations with breathing function, motor function, processing speed and chronotype suggest shared genetic architecture with beat synchronization and provide avenues for new phenotypic and genetic explorations.
A harmonized chemical monitoring database for support of exposure assessments
Authors: Isaacs Kristin K. , Wall Jonathan T. , Williams Ashley R. , Hobbie Kevin A. , Sobus Jon R. , Ulrich Elin , Lyons David , Dionisio Kathie L. , Williams Antony J. , Grulke Christopher , Foster Caroline A. , McCoy Josiah , Bevington Charles 
Published: June 2022

AbstractDirect monitoring of chemical concentrations in different environmental and biological media is critical to understanding the mechanisms by which human and ecological receptors are exposed to exogenous chemicals. Monitoring data provides evidence of chemical occurrence in different media and can be used to inform exposure assessments. Monitoring data provide required information for parameterization and evaluation of predictive models based on chemical uses, fate and transport, and release or emission processes. Finally, these data are useful in supporting regulatory chemical assessment and decision-making. There are a wide variety of public monitoring data available from existing government programs, historical efforts, public data repositories, and peer-reviewed literature databases. However, these data are difficult to access and analyze in a coordinated manner. Here, data from 20 individual public monitoring data sources were extracted, curated for chemical and medium, and harmonized into a sustainable machine-readable data format for support of exposure assessments.
A large, curated, open-source stroke neuroimaging dataset to improve lesion segmentation algorithms
Authors: Liew Sook-Lei , Lo Bethany P. , Donnelly Miranda R. , Zavaliangos-Petropulu Artemis , Jeong Jessica N. , Barisano Giuseppe , Hutton Alexandre , Simon Julia P. , Juliano Julia M. , Suri Anisha , Wang Zhizhuo , Abdullah Aisha , Kim Jun , Ard Tyler , Banaj Nerisa , Borich Michael R. , Boyd Lara A. , Brodtmann Amy , Buetefisch Cathrin M. , Cao Lei , Cassidy Jessica M. , Ciullo Valentina , Conforto Adriana B. , Cramer Steven C. , Dacosta-Aguayo Rosalia , de la Rosa Ezequiel , Domin Martin , Dula Adrienne N. , Feng Wuwei , Franco Alexandre R. , Geranmayeh Fatemeh , Gramfort Alexandre , Gregory Chris M. , Hanlon Colleen A. , Hordacre Brenton G. , Kautz Steven A. , Khlif Mohamed Salah , Kim Hosung , Kirschke Jan S. , Liu Jingchun , Lotze Martin , MacIntosh Bradley J. , Mataró Maria , Mohamed Feroze B. , Nordvik Jan E. , Park Gilsoon , Pienta Amy , Piras Fabrizio , Redman Shane M. , Revill Kate P. , Reyes Mauricio , Robertson Andrew D. , Seo Na Jin , Soekadar Surjo R. , Spalletta Gianfranco , Sweet Alison , Telenczuk Maria , Thielman Gregory , Westlye Lars T. , Winstein Carolee J. , Wittenberg George F. , Wong Kristin A. , Yu Chunshui 
Published: June 2022

AbstractAccurate lesion segmentation is critical in stroke rehabilitation research for the quantification of lesion burden and accurate image processing. Current automated lesion segmentation methods for T1-weighted (T1w) MRIs, commonly used in stroke research, lack accuracy and reliability. Manual segmentation remains the gold standard, but it is time-consuming, subjective, and requires neuroanatomical expertise. We previously released an open-source dataset of stroke T1w MRIs and manually-segmented lesion masks (ATLAS v1.2, N = 304) to encourage the development of better algorithms. However, many methods developed with ATLAS v1.2 report low accuracy, are not publicly accessible or are improperly validated, limiting their utility to the field. Here we present ATLAS v2.0 (N = 1271), a larger dataset of T1w MRIs and manually segmented lesion masks that includes training (n = 655), test (hidden masks, n = 300), and generalizability (hidden MRIs and masks, n = 316) datasets. Algorithm development using this larger sample should lead to more robust solutions; the hidden datasets allow for unbiased performance evaluation via segmentation challenges. We anticipate that ATLAS v2.0 will lead to improved algorithms, facilitating large-scale stroke research.
Improvement of eukaryotic protein predictions from soil metagenomes
Authors: Belliardo Carole , Koutsovoulos Georgios D. , Rancurel Corinne , Clément Mathilde , Lipuma Justine , Bailly-Bechet Marc , Danchin Etienne G. J. 
Published: June 2022

AbstractDuring the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI’s IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.
CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies
Authors: Neff Samuel L. , Hampton Thomas H. , Puerner Charles , Cengher Liviu , Doing Georgia , Lee Alexandra J. , Koeppen Katja , Cheung Ambrose L. , Hogan Deborah A. , Cramer Robert A. , Stanton Bruce A. 
Published: June 2022

AbstractResearchers studying cystic fibrosis (CF) pathogens have produced numerous RNA-seq datasets which are available in the gene expression omnibus (GEO). Although these studies are publicly available, substantial computational expertise and manual effort are required to compare similar studies, visualize gene expression patterns within studies, and use published data to generate new experimental hypotheses. Furthermore, it is difficult to filter available studies by domain-relevant attributes such as strain, treatment, or media, or for a researcher to assess how a specific gene responds to various experimental conditions across studies. To reduce these barriers to data re-analysis, we have developed an R Shiny application called CF-Seq, which works with a compendium of 128 studies and 1,322 individual samples from 13 clinically relevant CF pathogens. The application allows users to filter studies by experimental factors and to view complex differential gene expression analyses at the click of a button. Here we present a series of use cases that demonstrate the application is a useful and efficient tool for new hypothesis generation. (CF-Seq: http://scangeo.dartmouth.edu/CFSeq/)
Protective Policy Index (PPI) global dataset of origins and stringency of COVID 19 mitigation policies
Authors: Shvetsova Olga , Zhirnov Andrei , Adeel Abdul Basit , Bayar Mert Can , Bayrali Onsel Gurel , Catalano Michael , Catalano Olivia , Chu Hyoungrohk , Giannelli Frank , Muftuoglu Ezgi , Rosenberg Dina , Seyis Didem , Skopyk Bradley , VanDusky-Allen Julie , Zhao Tianyi 
Published: June 2022

AbstractWe have developed and made accessible for multidisciplinary audience a unique global dataset of the behavior of political actors during the COVID-19 pandemic as measured by their policy-making efforts to protect their publics. The dataset presents consistently coded cross-national data at subnational and national levels on the daily level of stringency of public health policies by level of government overall and within specific policy categories, and reports branches of government that adopted these policies. The data on these public mandates of protective behaviors is collected from media announcements and government publications. The dataset allows comparisons of governments’ policy efforts and timing across the world and can serve as a source of information on policy determinants of pandemic outcomes–both societal and possibly medical.