bluuebunny/crossref_metadata_2025_split huggingface dataset:
Top-down mass spectrometry of native proteoforms and their complexes: A community study
Authors: Lermyte Frederik , Habeck Tanja , Brown Kyle , Des Soye Benjamin , Lantz Carter , Zhou Mowei , Alam Novera , Hossain Md Amin , Jung Wonhyeuk , Keener James , Volny Michael , Wilson Jesse , Ying Yujia , Agar Jeffrey , Danis Paul , Ge Ying , Kelleher Neil , Li Huilin , Loo Joseph , Marty Michael , Pasa-Tolic Ljiljana , Sandoval Wendy 
Published: August 2023

Abstract

The combination of native electrospray ionisation with top-down fragmentation in mass spectrometry allows simultaneous determination of the stoichiometry of noncovalent complexes and identification of their component proteoforms and co-factors. While this approach is powerful, both native mass spectrometry and top-down mass spectrometry are not yet well standardised, and only a limited number of laboratories regularly carry out this type of research. To address this challenge, the Consortium for Top-Down Proteomics (CTDP) initiated a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. The outcomes are summarised in this report to provide robust benchmarks and a valuable entry point for the scientific community.
Evidence against stimulus-effect priming as the source of modality pairing effects in task-switching
Authors: Schacherer Jonathan , Hazeltine Eliot 
Published: August 2023

Abstract

Task-switch costs are affected by the pairings of stimulus and response modalities. For example, switch costs are reduced when switching between visual-manual and auditory-vocal tasks compared to switching between visual-vocal and auditory-manual tasks. These modality pairing effects are generally interpreted as reflecting increased crosstalk between the stimuli and response-related action effects for the two tasks. However, the exact mechanism by which this crosstalk operates—stimulus-effect priming or conflict between central operations—is unclear. In four experiments, we manipulated the modality compatibility between stimuli and experimentally-induced action effects, such that tasks overlapped in the stimulus modalities, effect modalities, both, or neither. Experiment 1 conceptually replicated prior reports of modality pairing effects in task-switching in which switch costs were reduced when similar stimulus and effect modalities were encapsulated within tasks. In Experiments 2a, 2b, and 3, symmetrical switch costs across tasks provided evidence against the stimulus-effect priming account, instead suggesting that modality pairing effects stem from interference between the representations engaged by central operations. These results help to characterize the mechanism underlying modality pairing effects in task-switching and add to a growing body of work illustrating how relationships between stimuli and response-related action effects influence response selection processes.
Season and depth differences of soil moisture use for tree growth across wet and dry gradients in the Tibetan Plateau
Authors: Li Qian , Jiao Liang , Xue Ruhong , Chen Xichen , Zhang Peng , Wang Xuge , Yuan Xin 
Published: August 2023

Abstract
Soil moisture has an important influence on tree growth in climate-sensitive regions. However, the seasonality of soil moisture utilization by trees in the Tibetan Plateau, a typical climate-sensitive region, and the mechanisms of depth of uptake are still unclear. Therefore, the spatial and temporal differences in the soil moisture use dynamics of tree growth were analyzed under wet and dry gradients on the Tibetan Plateau using tree-ring δ18O (δ18OTR). The results showed that: 1) soil moisture during the growing season was the main influencing factor on tree growth under different wet and dry gradients on the Tibetan Plateau. 2) The response of δ18OTR to soil moisture had a lag in arid areas than in wet areas. 3) In wet areas, trees absorbed the soil moisture in surface, while absorbed the soil moisture in deep in arid areas. And meanwhile, trees could develop more lateral and deep root systems using soil moisture from all soil layers to cope with climatic stress. In the future, more lateral and deep root systems of trees will be better suited to survive in complex habitats on the Tibetan Plateau, and that monitoring of trees in single water use areas should be enhanced. Further, it is of great significance to study soil water use strategies of tree growth under different wet and dry gradients for predicting forest ecosystem changes in complex environments.
Deciphering core microbiomes and community assembly of table grapes
Authors: Xie Muxi , Jia Jiyu , Luan Dongdong , Li Ruipeng , Zhang Jiangzhou , Zhang Junling 
Published: August 2023

Abstract
Aims
Understanding the assemblage of microbial communities is important for the health maintenance and post-harvest quality of fruit crops. However, systematic studies on the core microbiomes of table grapes and microbial community assembly of soil-plant continuum are still rare.
Methods
We collected samples from different compartments (bulk soil, rhizosphere soil of new roots and old roots, endosphere of new and old roots, and the endosphere of leaves and fruits) of five table grape varieties of Victoria, Balado Black, Fujimino, Jingya and Kyoho at the swelling stage and harvest stage. Microbial communities were analyzed using 16S rRNA and ITS rRNA high-throughput sequencing.
Results
The compartment was the major factor attributable to the variations in both bacterial and fungal communities. The alpha-diversity of both bacterial and fungal community decreased significantly along the compartment continuum from soil to fruit endosphere, but did not differ among the five varieties across all samples. We used the occupancy-abundance distribution to define core microbiomes for rhizosphere soil and endosphere. Functional annotations of the rhizospheric core bacteria were mainly associated with the redox process, while endophytic bacteria were mainly fermentative and symbiotic. Rhizospheric core fungi were saprophytic and the endophytic fungi were putatively pathogens. The null models indicated that the relative contribution of deterministic processes especially homogeneous selection gradually increased along the soil-plant continuum.
Conclusion
Our findings highlight niche-specific microbial communities are observed in different grape varieties. The deterministic processes contribute more to the assembly of microbial communities in the aboveground than in the belowground.
Exploring study for inverted planer perovskite solar cell: impact of PANI:PSS as a hole transport material
Authors: Moustafa Mohamed , yasin shadi , Waar Ziad Abu 
Published: August 2023

Abstract
This study explores the impact of PANI:PSS as a hole transport material in the perovskite based solar cell. This impact is tracked by numerical analysis using the one-dimensional solar cell capacitance simulator (SCAPS-1D). The effect of tuning several physical parameters of PANI:PSS, such as charge carrier density, charge carrier mobility, and defect density, on the solar cell performance, were analyzed and discussed. In addition, the role of the shunt and series resistance is investigated. The initial obtained power conversion efficiency is 4.94%, which agrees well with the reported experimental results in the literature. Increasing the charge carrier density of PANI:PSS from \(1\times {10}^{12}\) cm-3 to 1\(\times {10}^{22}\) cm-3 paved the solar cell toward high performance revealing \({V}_{OC}\) of 0.7 V, \({J}_{SC}\) of 21.7 mA/cm2, FF of 43% and \(PCE\) of 7.44%. Increasing the charge carrier mobility of PANI:PSS implied undesirable performance, with a stable performance above mobility of 50 cm2/Vs. The high defect density of PANI-PSS showed a harsh effect on the device performance. The efficiency decreased by 62% upon increasing the defect density from \(1\times {10}^{13}\) cm-3 to 1\(\times {10}^{22}\) cm-3. Finally, increasing the shunt resistance of the device is found to promote the cell’s performance. This could be due to the creation of alternative paths for the photogenerated charge carriers. Conversely, a huge drop in the solar cell performance is found upon increasing the series resistance due to a reduction of the current flow due to increasing the recombination rate.
Increased Level of Serum Leucine-Rich-Alpha-2-Glycoprotein 1 in Patients with Clear Cell Renal Cell Carcinoma
Authors: Nakanishi Shotaro , Goya Masato , Suda Tetsuji , Yonamine Tomoko , Sugawa Ai , Saito Seiichi 
Published: August 2023

Abstract

Background
There are currently no useful serum markers for clear cell renal cell carcinoma (ccRCC). Therefore, early detection may be difficult because diagnosis is based only on imaging tests. There is also the problem of radiation exposure because multiple CT examinations are required to follow up on the course of treatment. In addition, the histological types of renal cell carcinoma (RCC) are roughly divided into ccRCC and non-clear cell RCC (non-ccRCC), but the treatment response to medications differs between the two, and it is important to distinguish between them. Therefore, we aimed to find a novel serum marker for RCC.
Methods
We measured the serum level of leucine-rich-alpha-2-glycoprotein 1 (LRG1) in 64 patients with clear cell RCC (ccRCC) and 22 patients with non-clear cell RCC (non-ccRCC) who underwent radical or partial nephrectomy, as well as 63 patients without cancer, by enzyme-linked immunosorbent assay.
Results
Median values of serum LRG1 and their inter-quartile ranges were 63.2 (42.8–94.2) µg/mL in ccRCC, 23.4 (17.7–29.6) µg/mL in non-ccRCC, and 36.0 (23.7–56.7) µg/mL in patients without cancer, respectively (ccRCC vs. non-ccRCC or patients without cancer: P < 0.001). In ccRCC, C-reactive protein (CRP) (P = 0.0015), anaemia (P = 0.0368), hypercalcemia (P = 0.0233), and grade (P = 0.0315) were independent predictors of serum LRG1 levels. To assess diagnostic performance, the area under the receiver operating characteristic curve of serum LRG1 was used to differentiate ccRCC from non-cancer and non-ccRCC, yielding values of 0.73 (95% CI: 0.6439–0.8169) and 0.91 (95% CI: 0.8195–0.9614), respectively.
Conclusions
LRG1 is a serum marker associated with inflammation as indicated by CRP, anaemia and hypercalcemia, and malignant potential in ccRCC. Clinically, the serum level of LRG1 may help differentiate ccRCC from non-ccRCC with excellent diagnostic accuracy.
Wet Deposition of Total Nitrogen, Dissolved Organic Carbon and Heavy Metals Investigating Role of Long-Range Transport at Two Sites in Delhi
Authors: Kanojia Sunaina , Kulshrestha Umesh Chandra 
Published: August 2023

Abstract
Precipitation is one of the significant phenomena for various nitrogen, carbon and metal fractions depositions. In the current study, Total nitrogen (TN), Dissolved organic carbon (DOC) and metal concentrations were measured during different seasons in 2018 and 2019 to find out their potential sources at two sites in Delhi region having distinct land use pattern. The total nitrogen (TN) mean concentration was found to be 16 mg/l and 7 mg/l for DG and JN site respectively. Whereas the dissolved organic carbon (DOC) mean concentration was found to be 3.8 mg/l and 2.5 mg/l at DG and JN site respectively. The sequence for the metal concentrations was recorded as Ca>Na>K>Mg> Fe>Al>Cu>Mn>Zn>As for DG site whereas at JN site recorded different sequence i.e., Ca> Na> K>Mg>Fe>Al>Mn>Zn>Cu>As. Different source can be attributed to the influence of anthropogenic activities (agriculture, animal husbandry) on nitrogenous species and biomass burning on dissolved organic carbon species. The wind rose plots indicated that local and regional sources located in the north-western direction influenced the wet deposition of the species while air-mass back trajectory analysis implied the influence of air masses originating from the Bay of Bengal, This study bridges the data gap in the less studied part of the Delhi region and provides new information for policy makers to deal with pollution control.
An improved Shapley value algorithm based on fuzzy interval number
Authors: Xia Caoli , zhu Shijie , Wang Tonghui , Wei Guo 
Published: August 2023

Abstract
The unreasonable benefit distribution, which is often affected by uncertain factors, will affect the stability of the alliance. In this paper, an improved Shapley value algorithm with fuzzy interval number is designed to solve this problem. First, a competitive cooperative alliance with network architecture is constructed. Second, considering the uncertainty of alliance returns, an interval return function is established by using triangular fuzzy number. Third, weights of participants are changed by the improved coefficient of variation method combined with fuzzy interval number Shapley value, so that the stability evaluation of different methods is given. For the illustration of our new method, called coefficient of variation and shapley value (CV-SV) method. Last, a real data application is applied for numerical verification of our new method. The results show that both the individual marginal contribution rate and individual characteristics of each participant (participating in alliance cooperation) are considered in the new method, so it is more reasonable and stable
A critical examination of crop-yield data on vegetables, maize (Zea mays L) and tea (Camellia sinensis) for Sri Lankan biofilm biofertilizers
Authors: Dharma-wardana M. W. C. , Waidyanatha Parakrama , Renuka K. A. , Abeysiriwardena D. Sumith S. , Marambe Buddhi 
Published: August 2023

Abstract
With increasing global interest in microbial methods for agriculture, the commercialization of biofertilizers in Sri Lanka is of general interest. The use of a biofilm-biofertilizer (BFBF) commercialized in Sri Lanka is claimed to reduce chemical fertilizer (CF) usage by ~ 50% while boosting harvest by 20–30%. Many countries have explored the potential of biofilm biofertilizers, but have so far found mixed results. Here we review the BFBF commercialized in Sri Lanka and approved for national use. We show in detail that the improved yields claimed for this BFBF fall within the uncertainties (error bars) of the harvest. Theoretical models that produce a seemingly reduced CF scenario with an “increase” in harvests, although this is in fact not so, are presented. While BFBF usage seems to improve soil quality in some instances, the currently available BFBF promoted in Sri Lanka appears to have negligible impact on crop yields. We also briefly consider the potentially negative effects of large-scale adoption of microbial methods. The manner whereby a poorly-tested but product of biotechnology gained government and institutional acceptance is of global relevance in the rush to adopt new climate-mitigating technologies.
Inference on a Zero-inflated Bivariate Binomial Distribution Applicable to Baseball Data
Authors: Kim Seong , Kim Kipum , Lee Jaeyong , Hwang Beom Seuk 
Published: August 2023

Abstract
It is common to encounter situations where two success probabilities are parameters of interest based on nested (two-stage) binary data that commonly occur in sports data. Under these circumstances two correlated and nested binomial random variables can be utilized for analysis. Analysis of discrete count data with excessive zeros has been developed using different zero-inflated statistical models that allow for frequent zero-valued observations. The zero-inflated binomial distribution is one of the models that can be adequate when the underlying data generation of non-zero values is based on a sequence of independent Bernoulli trials. In this article, we propose a zero-inflated bivariate binomial distribution that can be applied to nested bivariate data when both components are zero-inflated. Some theoretical properties of the model are investigated and default Bayesian procedures regarding prior elicitation are also addressed. Moreover, the Bayesian predictive distribution is derived based on a three-fold distribution to see how a future observation behaves. Extensive simulation studies are performed to support the theoretical results, and real datasets for Major League Baseball players are analyzed to illustrate the methodology developed in this paper.
LncRNA SNHG6 binds to EEF1D through COPS5/P27 pathway to affect the cycle and proliferation of hepatocellular carcinoma
Authors: Ma Weijie , Liu Bin , Li Xiaomian , Guo Yonghua , Gao Meng , Hao Xingyuan , Liu Fusheng , Zhang Yang-Wen-Qing , Zhou Jitong , Yuan Yufeng 
Published: August 2023

Abstract
Our previous work had suggested that LncRNA SNHG6 interacted with COPS5 and their expression was positively correlated in hepatocellular carcinoma(HCC). In this study we found that SNHG6 and COPS5 was upregulated in HCC patients, and patients with high expression of SNHG6 and COPS5 had worse overall survival(OS). After RNA pulldown experiments and mass spectrometry analysis of SNHG6, and CO-IP experiments and mass spectrometry analysis of COPS5, we finally determined that EEF1D interacted both SNHG6 and COPS5. EEF1D, which had high expression in HCC tissues and cell lines, was related to poor prognosis. Meanwhile, SNHG6, EEF1D and COPS5 could affect the cell cycle and promote proliferation of HCC. Subcutaneous tumors grown from SNHG6-knockdown cells were inhibited compared to control cells. Knocking down SNHG6 or EEF1D leads to faster degradation of COPS5 protein, and activate COPS5/P27 pathway. The first domain leucine zipper of EEF1D was the binding site to COPS5. Eventually, SNHG6 binds to EEF1D and stabilize COPS5 and activate the P27 pathway, affecting the cell cycle to accelerate cell proliferation. SNHG6 may serve as a new target for the diagnosis and treatment of HCC.
Sea Level Variability and Predictions Using Artificial Neural Networks and Machine Learning Techniques in the Gulf of Guinea
Authors: Ayinde Akeem Shola , YU Huaming , WU Kejian 
Published: August 2023

Abstract

The rising sea level due to climate change poses a critical threat, particularly affecting vulnerable low-lying coastal areas such as the Gulf of Guinea (GoG). This impact necessitates precise sea level prediction models to guide planning and mitigation efforts for safeguarding coastal communities and ecosystems. This study presents a comprehensive analysis of mean sea level anomaly (MSLA) trends in the GoG between 1993 and 2020. The assessment covers three distinct periods (1993–2002, 2003–2012, and 2013–2020) and investigates connections between interannual sea level variability and large-scale oceanic and atmospheric forcings. Additionally, the performance of artificial neural networks (LSTM and MLPR) and machine learning techniques (MLR, GBM, and RFR) is evaluated to optimize sea level predictions. The findings reveal a consistent rise in MSLA linear trends across the basin, particularly pronounced in the north, with a total linear trend of 88 mm/year over the entire period. The highest decadal trend (38.7 mm/year) emerged during 2013–2020, and the most substantial percentage increment (100%) occurred in 2003–2012. Spatial variation in decadal sea-level trends was influenced by subbasin physical forcings. Strong interannual signals in the spatial sea level distribution were identified, linked to large-scale oceanic and atmospheric phenomena. Seasonal variations in sea level trends are attributed to seasonal changes in the forcing factors. Model evaluation indicates RFR and GBR as accurate methods, reproducing interannual sea level patterns with 97% and 96% accuracy, respectively. These findings contribute essential insights for effective coastal management and climate adaptation strategies in the GoG.
Longitudinal association of oral function and dementia in Japanese elderly people
Authors: Iwai Komei , Azuma Tetsuji , Yonenaga Takatoshi , Sasai Yasuyuki , Nomura Taketsugu , Sugiura Iwane , Inagawa Yujo , Matsumoto Yusuke , Nakashima Seiji , Abe Yoshikazu , Tomofuji Takaaki 
Published: August 2023

Abstract
The relationship between oral function and dementia was examined in 7384 elderly people (age ≥ 75 years) who visited a dental clinic in Gifu, Japan. Participants without dementia in a baseline survey in April 2018 were followed until March 2021. As oral functions, chewing function, tongue and lip function, and swallowing function were assessed by self-administered questionnaire, by oral diadochokinesis test, and by repetitive saliva swallowing test, respectively. The presence of systemic diseases was based on data obtained from the National Database of Health Insurance of Japan (NDB). At follow-up, 415 (6%) participants were diagnosed with dementia. Multivariate logistic regression analyses showed the presence of dementia at follow-up was associated with female (odds ratio [OR], 1.386; 95% confidence interval [CI], 1.117–1.719), elderly (OR, 1.078; CI, 1.056–1.101), regular dental checkups (absence; OR, 1.452; CI, 1.180–1.788), brushing frequency ≥ twice/day (absence; OR, 1.510; CI, 1.194–1.911), decayed teeth (presence; OR, 1.328; CI, 1.071–1.648), swallowing function (poor; OR, 1.484; CI, 1.135–1.939) at baseline. It was found that poor swallowing function was associated with the future onset of dementia.
Inequality in exposure and knowledge drives vulnerability to rat-associated leptospirosis among Chicago communities
Authors: Dyer Alexandre , Byers Kaylee A. , Buckley Jacqueline Y. , German Danielle , Murray Maureen H. 
Published: August 2023

Abstract
To predict and prevent public health risks from urban rats, studies often examine zoonotic pathogen prevalence in rats in different urban environments. However, human exposure to rats and their awareness of the associated risks are poorly understood. In this study, we aimed to identify factors associated with two aspects of vulnerability to leptospirosis as a model rat-associated disease: 1) exposure to rat urine in the home and 2) lack of awareness that rats carry leptospirosis. To collect data on residents’ experiences and knowledge about rats, we mailed a survey to randomly-selected households along an income gradient in Chicago. Of 432 complete cases, 36% had observed rat urine in the home and 73% were unaware that rats carry leptospirosis. Using logistic regression, we found that non-white respondents had over three times higher odds of observing rat urine in the home than white respondents. Dog owners and respondents who sought out information about rats, regardless of source, were more likely to be aware that rats carry leptospirosis. When we examined both aspects of vulnerability simultaneously using multinomial regression, we found that residents most vulnerable to leptospirosis (who had been exposed to urine and were not aware that rats carry leptospirosis) were significantly less likely to be white and less likely to be dog owners. Our results suggest that more public education is needed about rat-associated diseases spread through feces and urine and that exposure to rats should be considered another environmental health burden that is disproportionately persistent in underserved communities of color.