bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-ensemble-function relationships for disordered proteins in live cells
Authors: Holehouse Alex , Emenecker Ryan , Guadalupe Karina , Shamoon Nora , Sukenik Shahar 
Published: November 2023

Abstract
Intrinsically disordered protein regions (IDRs) are ubiquitous across all kingdoms of life and play a variety of essential cellular roles. IDRs exist in a collection of structurally distinct conformers known as an ensemble. IDR amino acid sequence determines its ensemble, which in turn can play an important role in dictating molecular function. Yet a clear link connecting IDR sequence, its ensemble properties, and its molecular function in living cells has not been systematically established. Here, we set out to test this sequence-ensemble-function paradigm using a novel computational method (GOOSE) that enables the rational design of libraries of IDRs by systematically varying specific sequence properties. Using ensemble FRET, we measured the ensemble dimensions of a library of rationally designed IDRs in human-derived cell lines, revealing how IDR sequence influences ensemble dimensions in situ. Furthermore, we show that the interplay between sequence and ensemble can tune an IDR’s ability to sense changes in cell volume - a de novomolecular function for these synthetic sequences. Our results establish biophysical rules for intracellular sequence-ensemble relationships, enable a new route for understanding how IDR sequences map to function in live cells, and set the ground for the design of synthetic IDRs with de novo function.
Physiological and molecular responses of basil (Ocimum basilicum) to silver stress: A comparison between silver nanoparticles and silver nitrate treatments
Authors: Zareei Ali , Abbaspour Hossein , Peyvandi Maryam , Majd Ahmad 
Published: November 2023

Abstract

With the extensive utilization of nanotechnology, silver nanoparticles (AgNPs) are prevalent nanomaterials that may entail ecological risks by their potential translocation into plant systems. The present study investigated the physiological and molecular responses of basil seedlings (Ocimum basilicum) subjected to AgNPs or silver nitrate (AgNO3) for 7 days. The seedlings were treated with 0, 4, 10, or 40 mg/L of AgNO3 or AgNPs in Hoagland’s solution. Both treatments resulted in significant accumulation of Ag in the roots and shoots, with higher levels in the roots of AgNO3-treated seedlings. AgNPs increased plant biomass at 4 mg/L, while AgNO3 decreased it at all concentrations. Both treatments reduced the total chlorophyll, carotenoids, and carbohydrates, with more pronounced effects in AgNO3-treated seedlings. Both treatments also induced oxidative stress, as indicated by increased levels of H2O2, MD, and proline, and enhanced activity of antioxidant enzymes SOD, CAT, and APX. However, these responses were more evident in AgNO3-treated seedlings, especially at higher concentrations. Quantitative real-time PCR analysis revealed that both treatments induced the upregulation of genes encoding oxidative stress tolerance-related enzymes, such as FSD1, MSD1, CSD1, CATa, CATb, APXa and APXb, in the basil seedling shoots. These results suggest that AgNPs are less toxic to basil plants than AgNO3 and that basil plants can activate physiological and molecular mechanisms to cope with Ag-induced oxidative stress.
Phosphoric Acid Network Induced by Surface Ligands Shifts the Selectivity for Uranium Extraction over Single Atom Modified TiO2 Catalysts
Authors: Yao Tao , Li Mingzhe , Zhang Fucheng , Dong Huanhuan , Chen Tao , Fu Jiang , Ding Tao , Zhu Wen-Kun 
Published: November 2023

Abstract

Photo-driven uranium extraction from fluorine-containing uranium wastewater is considered as a promising avenue to overcome the difficulty of uranium extraction in traditional uranium treatment technologies. Herein, we report a photocatalyst composed of Mn single atoms located at hollow TiO2 nanospheres with organophosphorus acid modification (Mn-SAs/TiO2@HEDP) for efficient uranium extraction from fluorine-containing uranium wastewater. Notably, the synergistic effect of the single-atoms and organophosphorus acid modification in the hollow TiO2 nanosphere significantly enhances the charge separation/transfer efficiency and photo-electron lifetime, thereby greatly boosting the photo-assisted uranium extraction activity. Accordingly, Mn-SAs/TiO2@HEDP show a considerable U(VI) removal rate of 94% in fluorine-containing uranium wastewater. By virtue of the reaction kinetics parameters and DFT calculation, we have confirmed that the phosphoric acid network induced by surface ligands over Mn SAC-TiO2 with Ti-O-P charge transfer channels can significantly enhance the selectivity and reaction kinetics for uranyl ions, relative to modifying inorganic phosphates. Relying on the X-ray absorption spectroscopy technique, we further confirm the dissociate uranyl ions were captured by the interlocking phosphate network to form the sturdy 2Oax-1U-4Oeq configuration, further verifying photo-driven fluorine uranium separation. This study provides a precedent for the design of advanced photocatalysts with specific recognition and a theoretical guide for the treatment of fluorine-containing uranium wastewater.
Study on molecular mechanisms related to hepatic fibrosis by Mendelian randomization combined with transcriptome analysis
Authors: HUANG LIANGJIANG , HUANG GUOCHU , WANG MENG , MAO DEWEN , WANG MINGGANG , ZHENG JINGHUI , ZHANG RONGZHEN , LONG FULI , YAO FAN , YAO CHUN 
Published: November 2023

Abstract
Background Recent studies have proved the association between the gut microbiota (GM) through gut-brain axis and liver diseases, including hepatic fibrosis (HF) and hepatic encephalopathy (HE). Nevertheless, the specific gut microbial taxa identified in these studies have shown variability. Furthermore, it's important to note that observational studies cannot definitively demonstrate causation.Our study aims to explain the potential causal relationship between gut flora and HF and HE through transcriptome and Mendelian randomization analysis.Methods: A Mendelian randomization study was conducted using pooled statistics from the MiBioGen database of genome-wide Association Studies (GWAS) of GM and HF. The main analytical method for evaluating causality was the inverse variance weighting (IVW) method. In addition, sensitivity analyses were performed using Cochrane's Q test, MR-Egger intercept test, MR-PRESSO global test and leave-one analysis. Subsequently, transcriptomic analysis was conducted to assess variations in gene expression in patients with HF, investigating their potential correlations with immune cell infiltration and immune factor levels. The relationship between these genes and HE was also investigated.Results: At the site significance level, it was found that the presence of Lachnospiraceae(OR = 1.981, 95%CI: 1.183 − 3.315, P = 0.009) may be associated with a high risk of HF, while Butyricicoccus(OR = 0.414, 95%CI: 0.227 − 0.756, P = 0.004) is associated with a low risk of HF. In addition, SNP-related genes were extracted in the expression profile of GSE57193, which were successively COPG2, KLF14 and TSGA13. Our study also revealed the differences in the expression of related genes in patients with HF, as well as correlations with levels of immune cell infiltration and immune factors. The results revealed that these genes are significantly associated with immune cells and immune factors and play an important role in the immune microenvironment. At the same time, this study also explored the relationship between these genes and hepatic encephalopathy and discovered that they are significantly correlated with the regulatory genes of HE and are regulated by multiple transcription factors and signaling pathways.Conclusion: Our study is the first to apply transcriptome and Mendelian randomization analysis to explain the potential causal relationship between gut flora and HF and HE. These findings shed new light on the molecular mechanisms between gut flora and HF and hepatic encephalopathy and may provide valuable insights into their underlying mechanisms for further investigation.
Comparison of clinical outcomes between sequestered cervical disc herniation and non- sequestered cervical disc herniation after anterior cervical decompression and fusion: a cohort study
Authors: Jin Lanbo , Sun Ke , Liu Gang , Yuan Wen , Chen Huajiang , Tian Ye 
Published: November 2023

Abstract
Background
The advantages of anterior cervical decompression and fusion (ACDF) were well published, while research on postoperative results in different subtypes of cervical disc herniation (CDH) still remain blank. This study aimed to explore the operational effect between sequestration and other types in CDH.
Methods
This retrospective cohort study enrolled 108 patients treated with ACDF in our hospital. The participants were divided into two groups according to the existence of sequestered disc. The Visual analog scale(VAS) score, the Japanese Orthopedics Association(JOA)score and the Neck disability index(NDI) score were used to evaluate postoperative outcome.
Results
Significant improvements were observed in both groups at every viewpoint(P < 0.001). The mean JOA was 15.04 ± 1.26 in sequestered disc group and was 14.45 ± 1.43 in non-sequestered disc group two months after operation (P = 0.026 < 0.05). The improvement of JOA in two months after ACDF showed statistical difference:46.58%±39.17% in sequestered disc group and 33.39%±28.82% in non-sequestered disc group(p = 0.047 < 0.05).32 patients in sequestered disc group (64%) and 19 patients in non-sequestered disc group (32.76%) were presented with high signal intensity of spinal cord on preoperative cervical T2-weighted MRI, with statistical difference (P < 0.001).
Conclusions
Patients with sequestered cervical disc seemed to have a higher degree of symptom improvement two months after ACDF. CDH with sequestered disc appears to be more likely to cause high signal intensity changes in the compressed cervical spine on T2-weighted MRI. We prefer early positive surgery in patients with sequestered cervical disc from the clinical point of view.
WITHDRAWN: Episodic intensification of marine phosphorus burial over the last 80 million years
Authors: Li Dengfeng , Peng Jin-zhou , Poulton Simon , Chew David , O'Sullivan Gary , Fu Yu , Sun Xiao-ming 
Published: November 2023

Abstract

Marine phosphatization events cause episodic carbonate fluorapatite (CFA) precipitation on seamounts, and are commonly linked to growth hiatuses in ferromanganese (Fe-Mn) crusts. However, the full record of these events and their paleoenvironmental implications remain poorly understood, in large part due to poor age constraints. Here, we apply U-Pb dating to CFA in Fe-Mn crusts from the Western Pacific seamounts, representing the Earth’s oldest oceanic crust. These data reveal six distinct phosphatization events, which are aligned with Sr isotope records in CFA and phosphorite from both the Western Pacific and the Atlantic. This newly established CFA chronology tightens the timespan of phosphatization events and refines the age framework of Fe-Mn crusts. We subsequently utilize a multiproxy approach to demonstrate that the phosphatization events occurred coeval with the expansion of oceanic oxygen minimum zones. The Western Pacific Fe-Mn crusts thus document major perturbations in global oceanic phosphorus cycling, which appear to have been driven by climate-induced increases in primary productivity.
Stablity Analysis of roadbed under Flood Scouring
Authors: Wang Rui , Tang Hongmei , Zhou Fuchuan 
Published: November 2023

Abstract
Roadbed along the river suffers from water erosion at the bottom and collapse at the top under flood scouring, which leads to the suspension of upper pavement slab. In order to ensure the safety of roadbed along the river, this study explored the development mechanism of roadbed damage by flood in actual cases, and proposed the evolution process of instability under roadbed scouring. The stability law of roadbed along the river under flood scouring was analyzed, and the stability safety factor was corrected to analyze the sensitivity of water depth, flow rate, river bending angle and stability safety factor K in working conditions. The sensitivity of width and height of roadbed after flood scouring to water depth, flow velocity, river bending angle was investigated. Moreover, numerical simulation was carried out to determine the displacement nephogram and maximum shear stress nephogram of roadbed along the river under the conditions of road surface and roadbed load, vehicle loading or constant change of water depth. By comparing the above theories and engineering cases, the water damage mechanism of roadbed along the river was further verified.
Interstate Air Pollution Governance in the United States: Exploring Clean Air Act Section 126
Authors: Underwood Alixandra , Marcantonio Richard , Wood Danielle , Crippa Paola 
Published: November 2023

Abstract

Toxic air pollution is arguably the most pressing human health concern today, accounting for approximately 7–9 million premature deaths worldwide. In the United States, more than 200,000 early deaths are attributable to air pollution and almost half of these are estimated to result from emissions originating in neighboring states–i.e., transboundary air pollution. Yet more than 40% of these deaths are assessed to be cause by air pollution produced by neighboring states. This article examines the governance mechanisms used by the US to address this transboundary issue, with a focus on section 126 of the Clean Air Act. All section 126 petitions submitted from 2000–2022 (N = 13), critical factors including case length, evidence used, and case outcome are compiled and assessed using comparative case analysis. From this analysis, four main issues and corresponding recommendations to enhance US governance mechanisms related to section 126 are developed: the need for policy and procedural reforms to adjust the burden of proof on petitioning states the need for clarity on the criteria for sufficient evidence for petitioners; potential practical measures to address challenges with response timelines in petitioning process; and the means by which section 126 petitioning capacity can be made accessible to all states. The article concludes with a discussion on the significance of modeling techniques employed in the petitioning process by the US EPA and states to facilitate informed–and fair–decision-making processes.
Assessing rainfall triggering of shallow landslides with an automatic tool generating rainfall thresholds: a case study in the Alpes Maritimes region, France
Authors: Barthélemy Sophie , Bernardie Séverine , Grandjean Gilles 
Published: November 2023

Abstract

In this work, we use a statistical approach for modeling shallow landslide rainfall thresholds (Caine 1980) with a case study for the Alpes-Maritimes region (France). Cumulated rainfall / duration (ED) thresholds are obtained with the CTRL-T algorithm (Melillo and al. 2018) for different non-exceedance probabilities from a landslide and two climate datasets. This tool allows to automatically define rainfall events that might trigger landslides, ensuring robustness and objectivity in this process. The first climate dataset stores high resolution gridded rainfall data (1km resolution, hourly), which provides rainfall data with high temporal and spatial accuracy. This dataset, coming from radar data, is calibrated with rainfall gauges, ensuring a higher accuracy of the rainfall measurements. It provides the rainfall records directly used in the threshold construction The second dataset contains lower resolution gridded rainfall, snow, temperature, and evapotranspiration data (8km resolution, daily); it enables to assess the region’s climate through parameters imported in CTRL-T. The thresholds are then validated using a method designed by Gariano and al. (2015). Several improvements are made to the initial method. First, evapotranspiration values approximated in the process are replaced by values from the second climate dataset, the result accounting best for the regional climate. Then, computing duration values used for isolating events and sub-events for each mesh point allows to consider the heterogeneity of the Alpes-Maritimes climate. Rainfall thresholds are eventually obtained, successively from a set of probable conditions (MRC) and a set of highly probable conditions (MPRC). The validation process strengthens the analysis as well as enables to identify best performing thresholds. This work represents novel scientific progress towards landslide reliable warning systems by (a) making a case study of empirical rainfall thresholds for Alpes-Maritimes, (b) using high-resolution rainfall data and (c) adapting the method to climatically heterogeneous zones.
Increased dependence on nitrogen-fixation of a native legume in response to alien plant invasion
Authors: Han Meixu , Zhang Haiyang , Liu Mingchao , Tang Jinqi , Guo Xiaocheng , Ren Weizheng , Zhao Yong , Yang Qingpei , Guo Binglin , Han Qinwen , Feng Yulong , Feng Zhipei , Yang Xitian , Kong Deliang 
Published: November 2023

Abstract
Background and aims
Inhibition of nutrient acquisition by roots or their symbiotic microorganisms, such as mycorrhizal fungi and rhizobium, is an important for the success of alien plants invasion. However, we know little about how the invasive and native plants interact regarding the ‘quantity’ and ‘activity’ of the strategies, both of which are essential for plant nutrient acquisition.
Methods
Here we conducted a pot experiment by monoculture and mixed plantings of an invasive plant, Xanthium strumarium, and a widespread native legume, Glycine max, and a suite of traits of fine roots and nodules as well as mycorrhizal colonization were measured.
Results
Compared with monoculture, fine root ‘quantity’ (biomass, and surface area) and ‘activity’ (root nitrogen (N) concentration and acid phosphatase activity) of G. max both decreased in mixture plantings; nodule ‘quantity’ (biomass) decreased by 45%, while nodule N-fixing ‘activity’ (nifH gene copies) increased by 106%; mycorrhizal colonization rate remained unchanged. Contribution of N-fixation to leaf N content (%Ndfa) in G. max increased after mixed plantings; this arised from lowered rhizosphere soil N of G. max in mixed planting. Increased root ‘quantity’ and ‘activity’ together with higher mycorrhizal colonization rate of X. strumarium was observed in the mixed planting.
Conclusion
Although the legume plant can produce plenty of N resource through N-fixing of nodules, the invasive plant does not scavenge nutrients directly from N-fixing nodules, but rather deplete rhizosphere soil N of the legume crop through root strategy of the invasive plant, thereby inhibiting native root strategy while enhancing N-fixation ‘activity’.
Loneliness, self-care and activities of daily living among older adults: A Partial Least Squares Model
Authors: Masoudi Nazanin , Sarbazi Ehsan , Soleimanpour Hassan , Abbasian Mehdi , Ghasemi Masouma , Rostami Zahra , Azizi Hosein , Soleimanpour Maryam 
Published: November 2023

Abstract

Background: This study was conducted with the aim of investigating the feelings of loneliness and its relationship with self-care and Activities of Daily Living (ADL) among the older adults of Tabriz city.
Methods:In this observational cross-sectional study, older adults were interviewed face-to-face. Participants were selected randomly from Iran’s Integrated Health System (IIHS) framework. Three questionnaires including de Jong Gierveld Loneliness Scale, Persian version of self-care scale, and ADL-Katz were used for data collection. The Partial Least Squares and Spearman’s correlation were used to investigate the relationships between demographic characteristics, loneliness, self-care, and ADL.
Results: The sample comprised 315 respondents 51.1% were female, 49.5% had a middle school literacy and 86% were married. A significant relationship was observed between loneliness and self-care (P<0.001 and r =-0.311). Demographic characteristics such as age and marital status negatively moderated the relationships between loneliness and self-care (path coefficient -0.07, P=0.044). ADL was positively associated with self-care (path coefficient 0.41, p =0.046) and also a direct and significant relationship was observed between ADL and daily self-care (P<0.001 and r=0.335).
Conclusion: The feeling of loneliness and its inverse relationship with self-care, which is more crucial in elderlies than other people, indicates the importance of studying the feeling of loneliness in the older adults, and further studies are necessary to investigate more and make a plan of action.
Study Protocol: Evaluation of a multisite community-based participatory project to achieve full childhood immunization coverage in Mozambique and Malawi (Let’s talk about vaccines project)
Authors: Shuro Linda , Lawrence Emily , Knight Lucia , Schneider Helen , Tabana Hanani 
Published: November 2023

Abstract

Background
Full coverage of childhood vaccines is a persistent challenge in low- and middle-income countries, with the emergence of the COVID-19 pandemic further worsening the situation. The complementary use of community-based participatory research (CBPR) and human-centered design (HCD) approaches has the potential to effectively create tailored solutions (interventions) to improve public health outcomes. The Let’s talk about vaccines! project is a multisite community-based participatory project by VillageReach which uses the human- centered design approach to identify the barriers and co-create solutions to address under- two routine immunization access and uptake in Malawi and Mozambique. There are a few examples of evaluations of interventions created through human-centered design. This manuscript outlines a study protocol describing the evaluation of VillageReach’s participatory solution development and solution implementation (intervention-Let’s talk about vaccines Project).
Methods
Guided by the RE-AIM (Reach Effectiveness Adoption Implementation Maintenance) framework, this three-year evaluation prospectively evaluates the effectiveness (on under-two immunization coverage) of VillageReach’s intervention and processes of implementation (reach, adoption, implementation and maintenance) in two districts in Mozambique and two in Malawi. This paper will also describe the theory of change for VillageReach’s intervention. Thematic analysis will be used to analyze the qualitative data, and interrupted time series analysis used to analyze the intervention’s effectiveness on specific under-two immunization outcomes. Complex systems thinking with consideration of constructs inherent in health systems strengthening will be applied in the overall analysis. Findings will inform the development of a comprehensive framework to guide scalability of community-based approaches on childhood immunization uptake and access into similar contexts.
Discussion
This study is among the few studies to evaluate a public health intervention (solution) created through CBPR and HCD. This protocol provides examples of methods to evaluate the use of these novel approaches in low- and middle-income countries. The evaluation will be fundamental in providing evidence of the solution impact as well as informing scalability of the solution(s) to similar contexts. It will also contribute to the evidence base on mechanisms that explain observed improvements in under- two immunization outcomes as a result of codesigned community-driven solutions.