bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overestimated Terrestrial Carbon Uptake in the Future Owing to the Lack of Spatial Variations CO2 in an Earth System Model
Authors: Peng Jing , Wang Yongli , Dan Li , Feng Jinming , Yang Fuqiang , Tang Xiba , Wu Qizhong , Tian Jing 
Published: March 2022

AbstractAtmospheric carbon dioxide (CO2) would be increasing much more if it were not for terrestrial carbon (C) uptake, fueling the drawdown of atmospheric CO2 in vegetation and soil on decadal to centennial time scales. Here, we used a global Earth system model (BNU‐ESM) with two different CO2 data sets (i.e., uniform CO2 vs. non‐uniform CO2 data sets) to simulate the responses of the C balance, particularly to the non‐uniform CO2 effect. Under future conditions of 2071–2100, accounting for spatial variations of CO2 concentrations resulted in 0.51 Pg C yr−1 or 19% additional global net ecosystem production (NEP) inductions relative to the uniform conditions. The reduction in NEP in the future was mostly caused by the reduction in the Northern Hemisphere, within which summer was the season that accounted for the largest fraction of this reduction. Changes in NEP under future conditions differed largely to those under present conditions, resulting from changes in the circulation caused by the non‐uniform CO2—for example, reductions in evapotranspiration limit water vapor contributions to the lower atmosphere, and substantially diminish convective precipitation, which led to decreased precipitation. Our findings call for more attention to be paid to the influence of spatial variations in CO2 concentration—particularly in the Northern Hemisphere—to better constrain the projected C uptake under future conditions. Also, it highlights the fundamental importance of non‐uniform CO2 in determining the pattern, response, and magnitude of C uptake through to 2100.
Possible Causes of Anomalous Glacier Mass Balance in the Western Kunlun Mountains
Authors: Zhu Meilin , Yao Tandong , Yang Wei , Wu Guanjian , Li Shenghai , Zhao Huabiao , Thompson Lonnie G. 
Published: March 2022

AbstractUnder current global warming, most glaciers on the Tibetan Plateau have shown significant mass loss during 2000–2019. However, the average glacier mass balance in the western Kunlun Mountains (WKM) was positive during this period. The causes of these opposing average status and the temporal glacier mass changes over the last several decades in the WKM continue to be the subject of active debate. The long‐term mass balance of the Guliya Ice Cap (Guliya) in the WKM during 1970–2019 was reconstructed using an energy and mass balance model and calibrated ERA5 data, which was calibrated and validated by in situ measurements and geodetic mass balances. Guliya showed a positive mean mass balance during 2000–2019 because annual snowfall was larger than low ablation‐season meltwater caused by low air temperature (T

a
). At interannual scales, annual mass balances were equally controlled by ablation‐season precipitation and T

a
during 1970–2019. From 1970s–1990s to 1990s–2010s, most Tibetan glaciers showed decreased mass balance due to increased ablation season T

a
, while the WKM glaciers experienced increased mass balance due to increased ablation‐season precipitation related to changes in the Silk Road Pattern. However, during 2000–2019, the annual mass balance of Guliya followed a decreasing trend due to increasing ablation‐season T

a
. The positive mass balance of the WKM glaciers will cease under future warming due to annual snowfall decreasing below ablation‐season meltwater. These changes will threaten lives and livelihoods in the Tarim Basin, whilst also jeopardizing ice core‐derived climate histories from the WKM glaciers.
Exploring Radiation Biases Over the Tropical and Subtropical Oceans Based on Treatments of Frozen‐Hydrometeor Radiative Properties in CMIP6 Models
Authors: Li J.‐L. F. , Xu Kuan‐Man , Lee Wei‐Liang , Jiang J. H. , Fetzer Eric , Stephens Graeme , Wang Yi‐Hui , Yu Jia‐Yuh 
Published: March 2022

AbstractTo explore the impacts of hydrometeor radiative effects over subtropical and tropical Pacific and Atlantic Oceans, we quantify the mean radiation biases in historical climate simulations based on how frozen‐hydrometeors radiative properties are calculated in CMIP6 models. CMIP6 models are divided with cloud ice only (NOS), with combined (SON1), and with separate treatments (SON2) of cloud ice and falling ice (snow) radiative properties. Over the deep convective regions, NOS models overestimate outgoing longwave radiation (RLUT) and surface shortwave irradiance (RSDS), while underestimate top‐of‐atmosphere reflected shortwave radiation (RSUT). SON2 models reduce these biases by 4–14 W m−2. However, this improvement is not seen in SON1 against NOS. Spatially averaged absolute biases in radiative fluxes for SON1 models are larger than those of NOS, suggesting that the SON1 approach of falling ice radiative effects may not produce the expected hydrometeor–radiation interactions. Over the south Pacific trade‐wind regions, both SON2 and SON1 show similar improvements in RLUT, RSUT, and RSDS with positive absolute bias differences up to 20 W m−2 against NOS, leading to improvement of CMIP6 over CMIP5 ensembles. The seasonal cycles are consistent with the annual means over these two regions except with larger differences between subsets of models during January–May than during June–December. In general, improvement from CMIP5 to CMIP6 due to more participating SON2 models is limited because of offset by SON1. These results suggest that a separate treatment of frozen‐hydrometeor radiative properties may be critical for reducing the spread of CMIP models.
Covalently grafting first-generation PAMAM dendrimers onto MXenes with self-adsorbed AuNPs for use as a functional nanoplatform for highly sensitive electrochemical biosensing of cTnT
Authors: Liu Xin , Qiu Yong , Jiang Deming , Li Fengheng , Gan Ying , Zhu Yuxuan , Pan Yuxiang , Wan Hao , Wang Ping 
Published: March 2022

Abstract2D MXene-Ti3C2Tχhas demonstrated promising application prospects in various fields; however, it fails to function properly in biosensor setups due to restacking and anodic oxidation problems. To expand beyond these existing limitations, an effective strategy to for modifying the MXene by covalently grafting first-generation poly(amidoamine) dendrimers onto an MXene in situ (MXene@PAMAM) was reported herein. When used as a conjugated template, the MXene not only preserved the high conductivity but also conferred a specific 2D architecture and large specific surface areas for anchoring PAMAM. The PAMAM, an efficient spacer and stabilizer, simultaneously suppressed the substantial restacking and oxidation of the MXene, which endowed this hybrid with improved electrochemical performance compared to that of the bare MXene in terms of favorable conductivity and stability under anodic potential. Moreover, the massive amino terminals of PAMAM offer abundant active sites for adsorbing Au nanoparticles (AuNPs). The resulting 3D hierarchical nanoarchitecture, AuNPs/MXene@PAMAM, had advanced structural merits that led to its superior electrochemical performance in biosensing. As a proof of concept, this MXene@PAMAM-based nanobiosensing platform was applied to develop an immunosensor for detecting human cardiac troponin T (cTnT). A fast, sensitive, and highly selective response toward the target in the presence of a [Fe(CN)6]3−/4−redox marker was realized, ensuring a wide detection of 0.1–1000 ng/mL with an LOD of 0.069 ng/mL. The sensor’s signal only decreased by 4.38% after 3 weeks, demonstrating that it exhibited satisfactory stability and better results than previously reported MXene-based biosensors. This work has potential applicability in the bioanalysis of cTnT and other biomarkers and paves a new path for fabricating high-performance MXenes for biomedical applications and electrochemical engineering.
Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors in Vibrio cholerae
Authors: Tang Ming-Xuan , Pei Tong-Tong , Xiang Qi , Wang Zeng-Hang , Luo Han , Wang Xing-Yu , Fu Yang , Dong Tao 
Published: March 2022

Abstract
Vibrio cholerae, the etiological pathogen of cholera, employs its type VI secretion system (T6SS) as an effective weapon to survive in highly competitive communities. Antibacterial and anti-eukaryotic functions of the T6SS depend on its secreted effectors that target multiple cellular processes. However, the mechanisms that account for effector diversity and different effectiveness during interspecies competition remain elusive. Here we report that environmental cations and temperature play a key role in dictating cellular response and effector effectiveness during interspecies competition mediated by the T6SS of V. cholerae. We found that V. cholerae could employ its cell-wall-targeting effector TseH to outcompete the otherwise resistant Escherichia coli and the V. cholerae immunity deletion mutant ∆tsiH when Mg2+ or Ca2+ was supplemented. Transcriptome and genetic analyses demonstrate that the metal-sensing PhoPQ two-component system is important for Mg2+-dependent sensitivity. Competition analysis in infant mice shows that TseH was active under in vivo conditions. Using a panel of V. cholerae single-effector active mutants, we further show that E. coli also exhibited variable susceptibilities to other T6SS effectors depending on cations and temperatures, respectively. Lastly, V. cholerae effector VasX could sensitize Pseudomonas aeruginosa to its intrinsically resistant antibiotic irgasan in a temperature-dependent manner. Collectively, these findings suggest that abiotic factors, that V. cholerae frequently encounters in natural and host environments, could modulate cellular responses and dictate the competitive fitness conferred by the T6SS effectors in complex multispecies communities.
Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
Authors: Hong Rui , Koga Yusuke , Bandyadka Shruthi , Leshchyk Anastasia , Wang Yichen , Akavoor Vidya , Cao Xinyun , Sarfraz Irzam , Wang Zhe , Alabdullatif Salam , Jansen Frederick , Yajima Masanao , Johnson W. Evan , Campbell Joshua D. 
Published: March 2022

AbstractSingle-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, various technical artifacts can be present in scRNA-seq data and should be assessed before performing downstream analyses. While several tools have been developed to perform individual quality control (QC) tasks, they are scattered in different packages across several programming environments. Here, to streamline the process of generating and visualizing QC metrics for scRNA-seq data, we built the SCTK-QC pipeline within thesingleCellTKR package. The SCTK-QC workflow can import data from several single-cell platforms and preprocessing tools and includes steps for empty droplet detection, generation of standard QC metrics, prediction of doublets, and estimation of ambient RNA. It can run on the command line, within the R console, on the cloud platform or with an interactive graphical user interface. Overall, the SCTK-QC pipeline streamlines and standardizes the process of performing QC for scRNA-seq data.
Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans
Authors: Toukach Philip V. , Egorova Ksenia S. 
Published: March 2022

AbstractThe Carbohydrate Structure Database (CSDB, http://csdb.glycoscience.ru/) is a free curated repository storing various data on glycans of bacterial, fungal and plant origins. Currently, it maintains a close-to-full coverage on bacterial and fungal carbohydrates up to the year 2020. The CSDB web-interface provides free access to the database content and dedicated tools. Still, the number of these tools and the types of the corresponding analyses is limited, whereas the database itself contains data that can be used in a broader scope of analytical studies. In this paper, we present CSDB source data files and a self-contained SQL dump, and exemplify their possible application in glycan-related studies. By using CSDB in an SQL format, the user can gain access to the chain length distribution or charge distribution (as an example) in a given set of glycans defined according to specific structural, taxonomic, or other parameters, whereas the source text dump files can be imported to any dedicated database with a specific internal architecture differing from that of CSDB.
A citizen centred urban network for weather and air quality in Australian schools
Authors: Ulpiani Giulia , Hart Melissa Anne , Di Virgilio Giovanni , Maharaj Angela M. , Lipson Mathew J. , Potgieter Julia 
Published: March 2022

AbstractHigh-quality, standardized urban canopy layer observations are a worldwide necessity for urban climate and air quality research and monitoring. The Schools Weather and Air Quality (SWAQ) network was developed and distributed across the Greater Sydney region with a view to establish a citizen-centred network for investigation of the intra-urban heterogeneity and inter-parameter dependency of all major urban climate and air quality metrics. The network comprises a matrix of eleven automatic weather stations, nested with a web of six automatic air quality stations, stretched across 2779 km2, with average spacing of 10.2 km. Six meteorological parameters and six air pollutants are recorded. The network has a focus on Sydney’s western suburbs of rapid urbanization, but also extends to many eastern coastal sites where there are gaps in existing regulatory networks. Observations and metadata are available from September 2019 and undergo routine quality control, quality assurance and publication. Metadata, original datasets and quality-controlled datasets are open-source and available for extended academic and non-academic use.
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
Authors: Van Puyvelde Bart , Daled Simon , Willems Sander , Gabriels Ralf , Gonzalez de Peredo Anne , Chaoui Karima , Mouton-Barbosa Emmanuelle , Bouyssié David , Boonen Kurt , Hughes Christopher J. , Gethings Lee A. , Perez-Riverol Yasset , Bloomfield Nic , Tate Stephen , Schiltz Odile , Martens Lennart , Deforce Dieter , Dhaenens Maarten 
Published: March 2022

AbstractIn the last decade, a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics was unfolded with the introduction of dozens of novel instruments that incorporate additional data dimensions through innovative acquisition methodologies, in turn inspiring specialized data analysis pipelines. Simultaneously, a growing number of proteomics datasets have been made publicly available through data repositories such as ProteomeXchange, Zenodo and Skyline Panorama. However, developing algorithms to mine this data and assessing the performance on different platforms is currently hampered by the lack of a single benchmark experimental design. Therefore, we acquired a hybrid proteome mixture on different instrument platforms and in all currently available families of data acquisition. Here, we present a comprehensive Data-Dependent and Data-Independent Acquisition (DDA/DIA) dataset acquired using several of the most commonly used current day instrumental platforms. The dataset consists of over 700 LC-MS runs, including adequate replicates allowing robust statistics and covering over nearly 10 different data formats, including scanning quadrupole and ion mobility enabled acquisitions. Datasets are available via ProteomeXchange (PXD028735).
Adsorption behavior and performance of ammonium onto sorghum straw biochar from water
Authors: Xu Huajie , Wang Bing , Zhao Ruohan , Wang Xiangui , Pan Changbin , Jiang Yuting , Zhang Xueyang , Ge Banggui 
Published: March 2022

AbstractSorghum has been widely used for liquor production and brewing, but how to make efficiently utilize sorghum straw (SS) has become an urgent problem. Meanwhile, the wastewater produced by winemaking is typical organic wastewater with a high ammonium concentration. To solve the problem of resource utilization of SS and remove ammonium from water, SS was used to prepare biochar as an adsorbent for ammonium adsorption. Batch adsorption experiments were carried out to study the influencing factors and adsorption mechanisms of ammonium onto sorghum straw biochar (SSB). The results showed that the adsorption capacity of SSB was much higher than that of SS. The SSB pyrolyzed at 300 °C had the highest adsorption capacity. The favorable pH was 6–10, and the optimal dosage was 2.5 g/L. The adsorption process and behavior conformed to the pseudo-second-order kinetic and Langmuir isotherm adsorption models. The maximum ammonium adsorption capacity of SSB at 45 °C was 7.09 mg/g, which was equivalent to 7.60 times of SS. The ammonium adsorption of SS and SSB was mainly chemical adsorption. The regeneration test indicated that SSB had good regeneration performance after three adsorption-regeneration cycles. This work suggests that SSB could be potentially applied to sewage treatment containing ammonium to achieve the purpose of resource recycling.
Synergies and prospects for early resolution of the neutrino mass ordering
Authors: Cabrera Anatael , Han Yang , Obolensky Michel , Cavalier Fabien , Coelho João , Navas-Nicolás Diana , Nunokawa Hiroshi , Simard Laurent , Bian Jianming , Nayak Nitish , Ochoa-Ricoux Juan Pedro , Roskovec Bedřich , Chimenti Pietro , Dusini Stefano , Bongrand Mathieu , Karaparambil Rebin , Lebrin Victor , Viaud Benoit , Yermia Frederic , Asquith Lily , Bezerra Thiago J. C. , Hartnell Jeff , Lasorak Pierre , Ling Jiajie , Liao Jiajun , Yu Hongzhao 
Published: March 2022

AbstractThe measurement of neutrino mass ordering (MO) is a fundamental element for the understanding of leptonic flavour sector of the Standard Model of Particle Physics. Its determination relies on the precise measurement of $$\Delta m^2_{31}$$

Δ

m
31
2

and $$\Delta m^2_{32}$$

Δ

m
32
2

using either neutrino vacuum oscillations, such as the ones studied by medium baseline reactor experiments, or matter effect modified oscillations such as those manifesting in long-baseline neutrino beams (LB$$\nu$$
ν
B) or atmospheric neutrino experiments. Despite existing MO indication today, a fully resolved MO measurement ($$\ge 5\sigma$$

≥
5
σ

) is most likely to await for the next generation of neutrino experiments: JUNO, whose stand-alone sensitivity is $$\sim 3\sigma$$

∼
3
σ

, or LB$$\nu$$
ν
B experiments (DUNE and Hyper-Kamiokande). Upcoming atmospheric neutrino experiments are also expected to provide precious information. In this work, we study the possible context for the earliest full MO resolution. A firm resolution is possible even before 2028, exploiting mainly vacuum oscillation, upon the combination of JUNO and the current generation of LB$$\nu$$
ν
B experiments (NOvA and T2K). This opportunity is possible thanks to a powerful synergy boosting the overall sensitivity where the sub-percent precision of $$\Delta m^2_{32}$$

Δ

m
32
2

by LB$$\nu$$
ν
B experiments is found to be the leading order term for the MO earliest discovery. We also found that the comparison between matter and vacuum driven oscillation results enables unique discovery potential for physics beyond the Standard Model.
Aerobic exercise promotes the expression of ATGL and attenuates inflammation to improve hepatic steatosis via lncRNA SRA
Authors: Wu Baoai , Xu Chong , Tian Yiming , Zeng Yu , Yan Feng , Chen AnPing , Zhao Jinfeng , Chen Longchang 
Published: March 2022

AbstractThe role of aerobic exercise in preventing and improving non-alcoholic fatty liver has been widely established. SRA is a long non-coding RNA, which has received increasing attention due to its important role in lipid metabolism. However, it is unclear whether aerobic exercise can prevent and treat hepatic lipid accumulation via SRA. The mice were randomly divided into four groups as follows, normal control group, normal aerobic exercise group, high-fat diet group (HFD), and high-fat diet plus aerobic exercise (8 weeks, 6 days/week, 18 m/min for 50 min, 6% slope) group (HAE). After 8 weeks, the mice in the HAE group showed significant improvement in hepatic steatosis. Body weight as well as blood TC, LDL-C, and liver TG levels were significantly lower in the HAE group than in the HFD group. Compared with the HFD group, the expression of SRA was markedly suppressed and the expression of ATGL was significantly increased in the HAE group. Additionally, the JNK/P38 signaling was inhibited, the pro-inflammatory factors were down-regulated, and the anti-inflammatory factor was increased. In addition to this, the same results were shown in experiments with overexpression of SRA. The results of this study provided new support for aerobic exercise to improve hepatic lipid metabolism via lncRNA.
Gluten consumption and inflammation affect the development of celiac disease in at-risk children
Authors: Auricchio Renata , Calabrese Ilaria , Galatola Martina , Cielo Donatella , Carbone Fortunata , Mancuso Marianna , Matarese Giuseppe , Troncone Riccardo , Auricchio Salvatore , Greco Luigi 
Published: March 2022

AbstractGene expression, lipidomic and growth impairment findings suggest that the natural history of celiac disease (CD) starts before the gluten-induced immune response. Gluten intake in the first years of life is a controversial risk factor. We aimed to estimate the risk of developing CD associated with the amount of gluten intake and the serum inflammatory profile in genetically predisposed infants. From an Italian cohort of children at risk for CD, we enrolled 27 children who developed CD (cases) and 56 controls matched by sex and age. A dietary interview at 9, 12, 18, 24 and 36 months was performed. Serum cytokines (INFγ, IL1β, IL2, IL4, IL6, IL10 IL12p70, IL17, and TNFα) were analysed at 4 and 36 months. Infants who developed CD by 6 years showed an increase in serum cytokines (INFγ, IL1β, IL2, IL6, IL10, IL12p70 and TNFα) at 4 months of age before gluten introduction. CD cases ate significantly more gluten in the second year of life than controls, and gluten intake in the second year of life was strongly correlated with serum cytokines (INFγ, IL2, IL4, IL12p70, IL17) at 36 months only in CD cases. The dietary pattern of infants who developed CD was characterized by high consumption of biscuits and fruit juices and low intake of milk products, legumes, vegetables and fruits. Genetically predisposed infants who developed CD showed a unique serum cytokine profile at 4 months before gluten consumption. The amount of gluten was strongly correlated with an inflammatory profile in serum cytokines at 36 months only in infants who developed CD.