bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying Carbon Cycle Extremes and Attributing Their Causes Under Climate and Land Use and Land Cover Change From 1850 to 2300
Authors: Sharma Bharat , Kumar Jitendra , Collier Nathan , Ganguly Auroop R. , Hoffman Forrest M. 
Published: June 2022

AbstractThe increasing atmospheric carbon dioxide (CO2) mole fraction affects global climate through radiative (trapping longwave radiation) and physiological effects (reduction of plant transpiration). We use the simulations of the Community Earth System Model (CESM1‐BGC) forced with Representative Concentration Pathway 8.5 to investigate climate‐vegetation feedbacks from 1850 to the year 2300. Human‐induced land use and land cover change (LULCC), through biogeochemical and biogeophysical processes, alter the climate and modify photosynthetic activity. The changing characteristics of extreme anomalies in photosynthesis, referred to as carbon cycle extremes, increase the uncertainty of terrestrial ecosystems to act as a net carbon sink. However, the role of LULCC in altering carbon cycle extremes under business‐as‐usual (continuously rising) CO2 emissions is unknown. Here we show that LULCC magnifies the intensity, frequency, and extent of carbon cycle extremes, resulting in a net reduction in expected photosynthetic activity in the future. We found that large temporally contiguous negative carbon cycle extremes are due to a persistent decrease in soil moisture, which is triggered by declines in precipitation. With LULCC and global warming, vegetation exhibits increased vulnerability to hot and dry environmental conditions, increasing the frequency of fire events and resulting in considerable losses in photosynthetic activity. While most regions show strengthening of negative carbon cycle extremes, a few locations show a weakening effect driven by declining vegetation cover or benign climate conditions for photosynthesis. Increasing hot, dry, and fire‐driven carbon cycle extremes are essential for improving carbon cycle modeling and estimation of ecosystem responses to LULCC and rising CO2 mole fractions. Moreover, large aberrations in vegetation productivity represent potential and growing threats to human lives, wildlife, and food security.
Optimizing the Management of Multireservoir Systems Under Shifting Flow Regimes
Authors: Espanmanesh Vahid , Tilmant Amaury 
Published: June 2022

AbstractOver the past few decades, significant research efforts have been devoted to the development of tools and techniques to improve the operational effectiveness of multireservoir systems. One of those efforts focuses on the incorporation of relevant hydrologic information into reservoir operation models. This effort is particularly relevant in regions characterized by low‐frequency climate signals, where time series of river discharges exhibit regime‐like behavior. Failure to properly capture such regime‐like behavior yields suboptimal operating policies, especially in systems characterized by large storage capacity such as large multireservoir systems. Hidden Markov Modeling is a class of hydrological models that can accommodate both overdispersion and serial dependence in time series, two essential hydrological properties that must be captured when modeling a system where the climate is switching between different states (e.g., dry, normal, and wet). In terms of reservoir operation, Stochastic Dual Dynamic Programming (SDDP) is one of the few optimization techniques that can accommodate both system and hydrologic complexity, that is, a large number of reservoirs and diverse hydrologic information. However, current SDDP formulations are unable to capture the long‐term persistence of the streamflow process found in some regions. In this paper, we present an extension of the SDDP algorithm that can handle the long‐term persistence and provide reservoir operating policies that explicitly capture regime shifts. Using the Senegal River Basin as a case study, we illustrate the potential gain associated with reservoir operating policies tailored to climate states.
Seasonal Photoacclimation in the North Pacific Transition Zone
Authors: Britten Gregory L. , Padalino Christine , Forget Gaël , Follows Michael J. 
Published: June 2022

AbstractThe Transition Zone Chlorophyll Front (TZCF) is a dynamic region of elevated chlorophyll concentrations in the Northeast Pacific that migrates from a southern winter (February) extent of approximately 30°N to a northern summer (August) extent of approximately 40°N. The transition zone has been highlighted as important habitat for marine animals and fisheries. We re‐examine the physical and biological drivers of seasonal TZCF variability using a variety of remote sensing, reanalysis, and in situ data sets. Satellite‐based remote sensing estimates of chlorophyll and carbon concentrations show that seasonal TZCF migration primarily reflects a seasonal increase in the chlorophyll to carbon ratio, rather than changes in phytoplankton carbon. We use our data compilation to demonstrate how the seasonality of light and nutrient fluxes decouple chlorophyll and carbon seasonality at the transition zone latitudes. Seasonal mixed‐layer‐averaged light availability is positively correlated with carbon and negatively correlated with chlorophyll through the transition zone, while climatological nitrate profiles show that chlorophyll to carbon ratios are facilitated by wintertime nitrate entrainment. These empirical results are consistent with physiological data and models describing elevated chlorophyll to carbon ratios in low light, nutrient‐replete environments, demonstrating the importance of latitudinal structure in interpreting seasonal chlorophyll dynamics at the basin scale.
Disease-Related Distress in Pediatric IBD: Development and Validation of the Crohn’s and Colitis Distress Scale
Authors: Stellway Jacklyn E. , Cummings Caroline , Paternostro Jennifer , Stoeckel Maggie , Muir Linda , Harris Michael A. 
Published: June 2022

Objective: Inflammatory bowel disease (IBD) is characterized by inflammation in the gastrointestinal tract with painful and distressing symptoms periods of exacerbations and remissions. Youth with IBD are at increased risk of experiencing challenges across psychosocial functioning. Mental health concerns (i.e., anxiety, depression) are commonly assessed in youth with IBD, but measures used to assess psychopathology may not fully capture emotional distress unique to living with IBD. There remains no well-validated measure of IBD-specific distress in pediatrics. Method: The Crohn’s and Colitis Distress Scale (CCDS), a newly developed measure of pediatric IBD-distress, was completed by 120 youth with IBD during routine care. The psychometric properties of the measure were examined. Results: The Cronbach’s alpha for the full scale was .94 and subscale internal consistency ranged from .66 to .90. Longer time since diagnosis and longer time since last flare was associated with lower IBD-distress. Further, greater IBD-distress was reported in girls with a diagnosis of ulcerative colitis, currently symptomatic, or currently flaring respective to their counterparts. Though moderately to largely correlated (.30 < r < .73), IBD-distress was found to be a distinct construct from global anxiety and depression. Conclusions: Data support the use of an instrument specific to IBD-distress, such as the CCDS, to allow for more accurate detection of risk for emotional distress in IBD. Further assessment of the reliability and validity of the measure within larger, more diverse samples is warranted. Such investigation should include assessment of the associations between IBD-distress and treatment engagement and health outcomes. Implications for Impact Statement Mental health concerns (e.g., anxiety, depression) are commonly assessed in youth with Inflammatory Bowel Disease (IBD), but the measures used do not fully capture emotional distress that is unique to living with IBD. The Crohn’s and Colitis Distress Scale (CCDS) is a newly developed measure assessing IBD-related emotional distress in youth. Our study found initial evidence for validating the CCDS, we identified 5 factors of IBD-distress, and we found that IBD-distress as a distinct construct from more global anxiety and depression.
Insights on the corrosion thermodynamics of chromium in molten LiF-NaF-KF eutectic salts
Authors: Chan Ho Lun , Romanovskaia Elena , Qiu Jie , Hosemann Peter , Scully John R. 
Published: June 2022

AbstractThe thermodynamic stability of chromium in the Cr0, Cr2+, and Cr3+ oxidation states considering various F− ion coordination compounds was investigated in molten LiF–NaF-KF (FLiNaK) eutectic salt. Potential fluoride ion activity (F− and CrF3−) diagrams were constructed to predict the most stable Cr oxidation states as a function of anion activity, solvation state of chromium ions and potential at 600 °C. The Gibbs free energies of these compounds were estimated by utilizing a combined cyclic voltammetry – Nernst theory analysis approach in FLiNaK salt. To verify the constructed diagrams, X-ray diffraction was utilized after exposure of Cr at various applied potentials to determine whether compounds detected in solidified FLiNaK salts agreed with thermodynamic calculations. This work aims to identify key thermodynamic factors that are significant to chromium corrosion for molten salt nuclear reactor applications. The F− stability region spans the entire region where spontaneous corrosion of Cr occurs. Cr may be oxidized to Cr2+ and Cr3+ in the presence HF (due to moisture as an impurity) spontaneously except some conditions of p1/2H2/aHF etc. This situation is not changed qualitatively for various states of solvation between oxidized Cr solute in F− solvent and this aspect is substantially similar for the two cases (pair 1: Cr0/CrF3−/ CrF63−; pair 2: Cr0/CrF42−/CrF52−) considered in this work.
Ancient genomes from the last three millennia support multiple human dispersals into Wallacea
Authors: Oliveira Sandra , Nägele Kathrin , Carlhoff Selina , Pugach Irina , Koesbardiati Toetik , Hübner Alexander , Meyer Matthias , Oktaviana Adhi Agus , Takenaka Masami , Katagiri Chiaki , Murti Delta Bayu , Putri Rizky Sugianto , Mahirta  , Petchey Fiona , Higham Thomas , Higham Charles F. W. , O’Connor Sue , Hawkins Stuart , Kinaston Rebecca , Bellwood Peter , Ono Rintaro , Powell Adam , Krause Johannes , Posth Cosimo , Stoneking Mark 
Published: June 2022

AbstractPrevious research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region’s demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600–250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
Putative rhythms in attentional switching can be explained by aperiodic temporal structure
Authors: Brookshire Geoffrey 
Published: June 2022

AbstractThe neural and perceptual effects of attention were traditionally assumed to be sustained over time, but recent work suggests that covert attention rhythmically switches between objects at 3–8 Hz. Here I use simulations to demonstrate that the analysis approaches commonly used to test for rhythmic oscillations generate false positives in the presence of aperiodic temporal structure. I then propose two alternative analyses that are better able to discriminate between periodic and aperiodic structure in time series. Finally, I apply these alternative analyses to published datasets and find no evidence for behavioural rhythms in attentional switching after accounting for aperiodic temporal structure. The techniques presented here will help clarify the periodic and aperiodic dynamics of perception and of cognition more broadly.
Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies
Authors: Gong Binsheng , Kusko Rebecca , Jones Wendell , Tong Weida , Xu Joshua 
Published: June 2022

AbstractThe lack of suitable reference genomic material to enable a transparent cross-lab study of oncopanels inspired the SEQC2 Oncopanel Sequencing Working Group to develop four reference samples, sequenced with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. This rich, publicly available dataset enabled performance assessment of the clinical applicability of oncopanels. In addition, this dataset present sample opportunities for developing specific and robust bioinformatics pipelines and fine-tuning parameters for more accurate variant calling, investigating ideal sequencing depth for variant calling of a given minimum VAF and variant type, and also recommending best use cases for Unique Molecular Identifier (UMI) technology.
CAN-SAR: A database of Canadian species at risk information
Authors: Naujokaitis-Lewis Ilona , Endicott Sarah , Guezen Jessica M. 
Published: June 2022

AbstractThreatened species lists describe the conservation status of species and are key tools used to inform decisions for biodiversity conservation. These lists are rich in information obtained during status assessment and recovery planning processes, ranging from biological attributes to actions that support recovery. Data compiled from species lists allow for analyses, including assessing trends in threats, prioritizing actions, and identifying barriers to achieving recovery objectives. For legally protected species at risk of extinction in Canada, such analyses are challenging owing to a lack of comprehensive and accessible data reflecting information compiled from listing and recovery documents. To encourage ongoing synthesis and minimise duplication of efforts, we initiated CAN-SAR: a database of Canadian Species at Risk information. This transparent, open-access, and searchable database contains information transcribed from listing documents, including listing date, and derived variables. Derived variables required interpretation for which we developed standardised criteria to record information, including classification of recovery actions. The CAN-SAR database is updateable, and will contribute towards improved recovery planning to safeguard species of conservation concern.
A global database of woody tissue carbon concentrations
Authors: Doraisami Mahendra , Kish Rosalyn , Paroshy Nicholas J. , Domke Grant M. , Thomas Sean C. , Martin Adam R. 
Published: June 2022

AbstractWoody tissue carbon (C) concentration is a key wood trait necessary for accurately estimating forest C stocks and fluxes, which also varies widely across species and biomes. However, coarse approximations of woody tissue C (e.g., 50%) remain commonplace in forest C estimation and reporting protocols, despite leading to substantial errors in forest C estimates. Here, we describe the Global Woody Tissue Carbon Concentration Database (GLOWCAD): a database containing 3,676 individual records of woody tissue C concentrations from 864 tree species. Woody tissue C concentration data—i.e., the mass of C per unit dry mass—were obtained from live and dead woody tissues from 130 peer-reviewed sources published between 1980–2020. Auxiliary data for each observation include tissue type, as well as decay class and size characteristics for dead wood. In GLOWCAD, 1,242 data points are associated with geographic coordinates, and are therefore presented alongside 46 standardized bioclimatic variables extracted from climate databases. GLOWCAD represents the largest available woody tissue C concentration database, and informs studies on forest C estimation, as well as analyses evaluating the extent, causes, and consequences of inter- and intraspecific variation in wood chemical traits.
Pancreatic cancer cells spectral library by DIA-MS and the phenotype analysis of gemcitabine sensitivity
Authors: Kong Ran , Qian Xiaohong , Ying Wantao 
Published: June 2022

AbstractData-independent acquisition (DIA)-mass spectrometry (MS)-based proteome strategies are increasingly used for detecting and validating protein biomarkers and therapeutic targets. Here, based on an in-depth proteome analysis of seven pancreatic cancer cell lines, we built a pancreas-specific mass spectrum library containing 10633 protein groups and 184551 peptides. The proteome difference among the seven pancreatic cancer cells was significant, especially for the divergent expression of proteins related to epithelial-mesenchymal transition (EMT). The spectra library was applied to explore the proteome difference of PANC-1 and BxPC-3 cells upon gemcitabine (GEM) treatment, and potential GEM targets were identified. The cytotoxicity test and GEM target analysis found that HPAC, CFPAC-1, and BxPC-3 were sensitive to GEM treatment, whereas PANC-1 and AsPC-1 were resistant. Finally, we found EMT was significant for CFPAC-1, AsPC-1, and PANC-1 cells, whereas BxPC-3 and HPAC cells showed more typical epithelial features. This library provides a valuable resource for in-depth proteomic analysis on pancreatic cancer cell lines, meeting the urgent demands for cell line-dependent protein differences and targeted drug analysis.
Clarifying the taxonomy of some cryptic blennies (Blenniidae) in their native and introduced range
Authors: Cabezas M. Pilar , Lasso-Alcalá Oscar M. , Quintero-T Elena , Xavier Raquel , Giarrizzo Tommaso , Nunes Jorge L. S. , Machado Fabiola S. , Gómez Jesús , Silva Pedroza Wellington , Jowers Michael J. 
Published: June 2022

AbstractOmobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identified to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the first genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least five distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confirmed that O. punctatus sensu stricto, O. dispar and O. sewalli correspond to different species that started to diverge about 2.6 Mya. Furthermore, O. sewalli was identified as the invasive species colonizing Atlantic shores. The existence of historical oceanographic barriers, such as the emergence of the Sunda Shelf in the Eastern Indian Ocean during the Pleistocene, and the biological traits of these blennies are the most likely factors responsible for their genetic differentiation and subsequent speciation.
Predicting compressive strength of high-performance concrete with high volume ground granulated blast-furnace slag replacement using boosting machine learning algorithms
Authors: Rathakrishnan Vimal , Bt. Beddu Salmia , Ahmed Ali Najah 
Published: June 2022

AbstractPredicting the compressive strength of concrete is a complicated process due to the heterogeneous mixture of concrete and high variable materials. Researchers have predicted the compressive strength of concrete for various mixes using machine learning and deep learning models. In this research, compressive strength of high-performance concrete with high volume ground granulated blast-furnace slag replacement is predicted using boosting machine learning (BML) algorithms, namely, Light Gradient Boosting Machine, CatBoost Regressor, Gradient Boosting Regressor (GBR), Adaboost Regressor, and Extreme Gradient Boosting. In these studies, the BML model’s performance is evaluated based on prediction accuracy and prediction error rates, i.e., R2, MSE, RMSE, MAE, RMSLE, and MAPE. Additionally, the BML models were further optimised with Random Search algorithms and compared to BML models with default hyperparameters. Comparing all 5 BML models, the GBR model shows the highest prediction accuracy with R2 of 0.96 and lowest model error with MAE and RMSE of 2.73 and 3.40, respectively for test dataset. In conclusion, the GBR model are the best performing BML for predicting the compressive strength of concrete with the highest prediction accuracy, and lowest modelling error.
Identification of bronchoalveolar and blood immune-inflammatory biomarker signature associated with poor 28-day outcome in critically ill COVID-19 patients
Authors: Voiriot Guillaume , Dorgham Karim , Bachelot Guillaume , Fajac Anne , Morand-Joubert Laurence , Parizot Christophe , Gerotziafas Grigorios , Farabos Dominique , Trugnan Germain , Eguether Thibaut , Blayau Clarisse , Djibré Michel , Elabbadi Alexandre , Gibelin Aude , Labbé Vincent , Parrot Antoine , Turpin Matthieu , Cadranel Jacques , Gorochov Guy , Fartoukh Muriel , Lamazière Antonin 
Published: June 2022

AbstractThe local immune-inflammatory response elicited by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is still poorly described, as well as the extent to which its characteristics may be associated with the outcome of critical Coronavirus disease 2019 (COVID-19). In this prospective monocenter study, all consecutive COVID-19 critically ill patients admitted from February to December 2020 and explored by fiberoptic bronchoscopy with bronchoalveolar lavage (BAL) were included. Biological assays, including digital ELISA cytokine profiling and targeted eicosanoid metabolomic analysis, were performed on paired blood and BAL fluid (BALF). Clinical outcome was assessed through the World Health Organization 10-point Clinical Progression Scale (WHO-CPS) at the 28th day (D28) following the admission to intensive care unit. A D28-WHO-CPS value higher than 5 defined a poor outcome. Seventy-six patients were included, 45 (59%) had a poor day-28 outcome. As compared to their counterparts, patients with D28-WHO-CPS > 5 exhibited a neutrophil-predominant bronchoalveolar phenotype, with a higher BALF neutrophil/lymphocyte ratio, a blunted local type I interferon response, a decompartimentalized immune-inflammatory response illustrated by lower BALF/blood ratio of concentrations of IL-6 (1.68 [0.30–4.41] vs. 9.53 [2.56–19.1]; p = 0.001), IL-10, IL-5, IL-22 and IFN-γ, and a biological profile of vascular endothelial injury illustrated by a higher blood concentration of VEGF and higher blood and/or BALF concentrations of several vasoactive eicosanoids. In critically ill COVID-19 patients, we identified bronchoalveolar and blood immune-inflammatory biomarker signature associated with poor 28-day outcome.