bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of the Error in the Calculation of the Pressure‐Strain Term: Application in the Terrestrial Magnetosphere
Authors: Roberts O. W. , Vörös Z. , Torkar K. , Stawarz J. , Bandyopadhyay R. , Gershman D. J. , Narita Y. , Kieokaew R. , Lavraud B. , Klein K. , Yang Y. , Nakamura R. , Chasapis A. , Matthaeus W. H. 
Published: August 2023

AbstractCalculating the pressure‐strain terms has recently been performed to quantify energy conversion between the bulk flow energy and the internal energy of plasmas. It has been applied to numerical simulations and satellite data from the Magnetospheric MultiScale Mission. The method requires spatial gradients of the velocity and the use of the full pressure tensor. Here we present a derivation of the errors associated with calculating the pressure‐strain terms from multi‐spacecraft measurements and apply it to previously studied examples of magnetic reconnection at the magnetopause and the magnetotail. The errors are small in a dense magnetosheath event but much larger in the more tenuous magnetotail. This is likely due to larger counting statistics in the dense plasma at the magnetopause than in the magnetotail. The propagated errors analyzed in this work are important to understand uncertainties of energy conversion measurements in space plasmas and have applications to current and future multi‐spacecraft missions.
Spatial and Seasonal Variations in Dissolved Methane Across a Large Lake
Authors: Peacock Mike , Davidson Scott J. , Kothawala Dolly N. , Segersten Joel , Futter Martyn N. 
Published: August 2023

AbstractLakes process large volumes of organic carbon (OC), are important sources of methane (CH4), and contribute to climatic warming. However, there is a lack of data from large lakes >500 km2, which creates uncertainty in global budgets. In this data article, we present dissolved CH4, OC bioreactivity measurements, water chemistry, and algal biovolumes at 11 stations across Lake Mälaren, the third largest (1,074 km2) Swedish lake. Total phosphorus concentrations show that during the study period the lake was classed as mesotrophic/eutrophic. Overall mean CH4 concentration from all stations, sampled five times to cover seasonal variation, was 2.51 μg l−1 (0.98–5.39 μg l−1). There was no significant seasonal variation although ranges were greatest during summer. Concentrations of CH4 were greatest in shallow waters close to anthropogenic nutrient sources, whilst deeper, central basins had lower concentrations. Methane correlated positively with measures of lake productivity (chlorophyll a, total phosphorus), and negatively to water depth and oxygen concentration, with oxygen emerging as the sole significant driver in a linear mixed effects model. We collated data from other lakes >500 km2 (n = 21) and found a significant negative relationship between surface area and average CH4 concentration. Large lakes remain an understudied contributor to the global CH4 cycle and future research efforts should aim to quantify the spatial and temporal variation in their diffusive and ebullitive emissions, and associated drivers.
miR-30e-5p-mediated FOXD1 promotes cell proliferation by blocking cellular senescence and apoptosis through p21/CDK2/Rb signaling in head and neck carcinoma
Authors: Wu Tong , Yang Zhongyuan , Chen Weichao , Jiang Mingjie , Xiao Zhichao , Su Xuan , Jiao Zan , Yu Yongchao , Chen Shuwei , Song Ming , Yang Ankui 
Published: August 2023

AbstractForkhead box D1 (FOXD1) belongs to the FOX protein family, which has been found to function as a oncogene in multiple cancer types, but its role in head and neck squamous cell carcinoma (HNSCC) requires further investigation. Our research aimed to investigate the function of FOXD1 in HNSCC. Bioinformatics analysis indicated that mRNA level of FOXD1 was highly expressed in HNSCC tissues, and over-expressed FOXD1 was related to poor prognosis. Moreover, FOXD1 knockdown increased the ratio of senescent cells but decreased the proliferation ability, while FOXD1 overexpression obtained the opposite results. In vitro experiments revealed that FOXD1 bound to the p21 promoter and inhibited its transcription, which blocked the cyclin dependent kinase 2 (CDK2)/retinoblastoma (Rb) signaling pathway, thus preventing senescence and accelerating proliferation of tumor cells. CDK2 inhibitor could reverse the process to some extent. Further research has shown that miR-3oe-5p serves as a tumor suppressant by repressing the translation of FOXD1 through combining with the 3’-untranslated region (UTR). Thus, FOXD1 resists cellular senescence and facilitates HNSCC cell proliferation by affecting the expression of p21/CDK2/Rb signaling, suggesting that FOXD1 may be a potential curative target for HNSCC.
How does diabetes mellitus impact on the prognosis of dental implants?
Authors: Baniulyte Gabriele , Ali Kamran 
Published: August 2023

Abstract
Data sources
Web of Science, Embase, PubMed and Cochrane Library databases were searched for publications up to August 2021.

Study selection
The study noted clear inclusion and exclusion criteria. Search terms were provided; only observational studies were considered.

Data extraction and synthesis
A total of 122 studies were identified through the search strategy. Following deduplication, two reviewers conducted the screening.

Results
A total of 21 observational studies were included, involving cohort, case–control, and cross-sectional study designs. A meta-analysis identified increased risk of peri-implantitis in patients with diabetes mellitus and in smokers when compared to non-diabetic subjects and non-smokers. No significant association was found between poor plaque control or periodontal history and peri-implantitis.

Conclusions
Patients with diabetes mellitus appear to have a higher risk of peri-implantitis.
Optical control of ultrafast structural dynamics in a fluorescent protein
Authors: Hutchison Christopher D. M. , Baxter James M. , Fitzpatrick Ann , Dorlhiac Gabriel , Fadini Alisia , Perrett Samuel , Maghlaoui Karim , Lefèvre Salomé Bodet , Cordon-Preciado Violeta , Ferreira Josie L. , Chukhutsina Volha U. , Garratt Douglas , Barnard Jonathan , Galinis Gediminas , Glencross Flo , Morgan Rhodri M. , Stockton Sian , Taylor Ben , Yuan Letong , Romei Matthew G. , Lin Chi-Yun , Marangos Jon P. , Schmidt Marius , Chatrchyan Viktoria , Buckup Tiago , Morozov Dmitry , Park Jaehyun , Park Sehan , Eom Intae , Kim Minseok , Jang Dogeun , Choi Hyeongi , Hyun HyoJung , Park Gisu , Nango Eriko , Tanaka Rie , Owada Shigeki , Tono Kensuke , DePonte Daniel P. , Carbajo Sergio , Seaberg Matt , Aquila Andrew , Boutet Sebastien , Barty Anton , Iwata So , Boxer Steven G. , Groenhof Gerrit , van Thor Jasper J. 
Published: August 2023

AbstractThe photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump–probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.
Bacterial amylases enable glycogen degradation by the vaginal microbiome
Authors: Jenkins Dominick J. , Woolston Benjamin M. , Hood-Pishchany M. Indriati , Pelayo Paula , Konopaski Alyssa N. , Quinn Peters M. , France Michael T. , Ravel Jacques , Mitchell Caroline M. , Rakoff-Nahoum Seth , Whidbey Christopher , Balskus Emily P. 
Published: August 2023

AbstractThe human vaginal microbiota is frequently dominated by lactobacilli and transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in the vagina. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both bacterial and human enzymes. Here we biochemically characterize six glycogen-degrading enzymes (GDEs), all of which are pullanases (PulA homologues), from vaginal bacteria that support the growth of amylase-deficient Lactobacillus crispatus on glycogen. We reveal variations in their pH tolerance, substrate preferences, breakdown products and susceptibility to inhibition. Analysis of vaginal microbiome datasets shows that these enzymes are expressed in all community state types. Finally, we confirm the presence and activity of bacterial and human GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.
Factors associated with healthy aging in Latin American populations
Authors: Santamaria-Garcia Hernando , Sainz-Ballesteros Agustín , Hernandez Hernán , Moguilner Sebastian , Maito Marcelo , Ochoa-Rosales Carolina , Corley Michael , Valcour Victor , Miranda J. Jaime , Lawlor Brian , Ibanez Agustin 
Published: August 2023

AbstractLatin American populations may present patterns of sociodemographic, ethnic and cultural diversity that can defy current universal models of healthy aging. The potential combination of risk factors that influence aging across populations in Latin American and Caribbean (LAC) countries is unknown. Compared to other regions where classical factors such as age and sex drive healthy aging, higher disparity-related factors and between-country variability could influence healthy aging in LAC countries. We investigated the combined impact of social determinants of health (SDH), lifestyle factors, cardiometabolic factors, mental health symptoms and demographics (age, sex) on healthy aging (cognition and functional ability) across LAC countries with different levels of socioeconomic development using cross-sectional and longitudinal machine learning models (n = 44,394 participants). Risk factors associated with social and health disparities, including SDH (β > 0.3), mental health (β > 0.6) and cardiometabolic risks (β > 0.22), significantly influenced healthy aging more than age and sex (with null or smaller effects: β < 0.2). These heterogeneous patterns were more pronounced in low-income to middle-income LAC countries compared to high-income LAC countries (cross-sectional comparisons), and in an upper-income to middle-income LAC country, Costa Rica, compared to China, a non-upper-income to middle-income LAC country (longitudinal comparisons). These inequity-associated and region-specific patterns inform national risk assessments of healthy aging in LAC countries and regionally tailored public health interventions.
Replication dynamics identifies the folding principles of the inactive X chromosome
Authors: Poonperm Rawin , Ichihara Saya , Miura Hisashi , Tanigawa Akie , Nagao Koji , Obuse Chikashi , Sado Takashi , Hiratani Ichiro 
Published: August 2023

AbstractChromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.
Droplet-based single-cell joint profiling of histone modifications and transcriptomes
Authors: Xie Yang , Zhu Chenxu , Wang Zhaoning , Tastemel Melodi , Chang Lei , Li Yang Eric , Ren Bing 
Published: August 2023

AbstractWe previously reported Paired-Tag, a combinatorial indexing-based method that can simultaneously map histone modifications and gene expression at single-cell resolution at scale. However, the lengthy procedure of Paired-Tag has hindered its general adoption in the community. To address this bottleneck, we developed a droplet-based Paired-Tag protocol that is faster and more accessible than the previous method. Using cultured mammalian cells and primary brain tissues, we demonstrate its superior performance at identifying candidate cis-regulatory elements and associating their dynamic chromatin state to target gene expression in each constituent cell type in a complex tissue.
Profile observations of the Arctic atmospheric boundary layer with the BELUGA tethered balloon during MOSAiC
Authors: Pilz Christian , Lonardi Michael , Egerer Ulrike , Siebert Holger , Ehrlich André , Heymsfield Andrew J. , Schmitt Carl G. , Shupe Matthew D. , Wehner Birgit , Wendisch Manfred 
Published: August 2023

AbstractDuring the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, the Balloon-bornE moduLar Utility for profilinG the lower Atmosphere (BELUGA) was deployed from an ice floe drifting in the Fram Strait from 29 June to 27 July 2020. The BELUGA observations aimed to characterize the cloudy Arctic atmospheric boundary layer above the sea ice using a modular setup of five instrument packages. The in situ measurements included atmospheric thermodynamic and dynamic state parameters (air temperature, humidity, pressure, and three-dimensional wind), broadband solar and terrestrial irradiance, aerosol particle microphysical properties, and cloud particle images. In total, 66 profile observations were collected during 33 balloon flights from the surface to maximum altitudes of 0.3 to 1.5 km. The profiles feature a high vertical resolution of 0.01 m to 1 m, including measurements below, inside, and above frequently occurring low-level clouds. This publication describes the balloon operations, instruments, and the obtained data set. We invite the scientific community for joint analysis and model application of the freely available data on PANGAEA.
Metagenome sequencing and 103 microbial genomes from ballast water and sediments
Authors: Xue Zhaozhao , Han Yangchun , Tian Wen , Zhang Wei 
Published: August 2023

AbstractThe great threat of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. Of these MAGs, 60 were ‘near complete’ (completeness >90%), 34 were >80% complete, and nine were >75% complete. Phylogenomic analysis revealed that over 70% (n = 74) of these MAGs represented new taxa at different taxonomical levels, including one order, three families, 12 genera, and 58 species. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 69), Bacteroidota (n = 17), and Actinobacteriota (n = 7). These draft genomes provided novel data on species diversity and function in the ballast-tank microbial community, which will facilitate ballast water and sediments management.
Investigation of the phytochemical composition, antioxidant, antibacterial, anti-osteoarthritis, and wound healing activities of selected vegetable waste
Authors: Salem Mohamed A. , Mohamed Osama G. , Mosalam Esraa M. , Elberri Aya Ibrahim , Abdel-Bar Hend Mohamed , Hassan Mariam , Al-Karmalawy Ahmed A. , Tripathi Ashootosh , Ezzat Shahira M. , Abo Mansour Hend E. 
Published: August 2023

AbstractAgri-food wastes, produced following industrial food processing, are mostly discarded, leading to environmental hazards and losing the nutritional and medicinal values associated with their bioactive constituents. In this study, we performed a comprehensive analytical and biological evaluation of selected vegetable by-products (potato, onion, and garlic peels). The phytochemical analysis included UHPLC-ESI-qTOF-MS/MS in combination with molecular networking and determination of the total flavonoid and phenolic contents. Further, the antimicrobial, anti-osteoarthritis and wound healing potentials were also evaluated. In total, 47 compounds were identified, belonging to phenolic acids, flavonoids, saponins, and alkaloids as representative chemical classes. Onion peel extract (OPE) showed the higher polyphenolic contents, the promising antioxidant activity, the potential anti-osteoarthritis activity, and promising antimicrobial activity, especially against methicillin-resistant Staphylococcus aureus (MRSA). Furthermore, OPE revealed to have promising in vivo wound healing activity, restoring tissue physiology and integrity, mainly through the activation of AP-1 signaling pathway. Lastly, when OPE was loaded with nanocapsule based hydrogel, the nano-formulation revealed enhanced cellular viability. The affinities of the OPE major metabolites were evaluated against both p65 and ATF-2 targets using two different molecular docking processes revealing quercetin-3,4′-O-diglucoside, alliospiroside C, and alliospiroside D as the most promising entities with superior binding scores. These results demonstrate that vegetable by-products, particularly, those derived from onion peels can be incorporated as natural by-product for future evaluation against wounds and osteoarthritis.
A novel organic semiconductor 4-phenylthiazol-2-yl-(phenylhydrazono) acetonitrile (PTPA) thin films: synthesis, optical and electrical properties
Authors: Abuelwafa Amr Attia , Elnobi Sahar , Santos M. Amélia , Alsoghier Hesham M. 
Published: August 2023

AbstractIn this study, 4-phenylthiazol-2-yl-(phenylhydrazono) acetonitrile (PTPA) azo dye was synthesized and studied from optical and electrical point of view. The tautomerization phenomenon of the PTPA dye was clarified using one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (1HNMR and 13C NMR), absorbance (UV-Vis), emission, and Fourier transform infrared spectroscopy (FT-IR). X-ray diffraction (XRD) evaluations were indicated that PTPA in powder and thin films crystallizes in a monoclinic system structure with nonstructural characteristics. Spectrophotometric measurements of absorbance A (λ), transmittance T (λ) and reflectance R (λ) at normal incidence light in the wavelength range 200–2500 nm were used to determine the optical band gap, extinction coefficient, k and refractive index, n. Also, non-linear optical parameters such as the third order non-linear susceptibility, χ(3) and nonlinear refractive index, n(2) of PTPA have revealed an awe-inspiring switching behavior, implying the possibility of using PTPA in optical switching systems. Finally, the electrical conductivity of the PTPA was shown to increase with rising temperature, indicating that it is a typical organic semiconductor. Mott’s parameters were determined and discussed at low temperatures. Thus, PTPA is a promising organic semiconductor with broad utility potential in organic electronics such as organic light-emitting diodes (OLEDs).
In vitro transcription of self-assembling DNA nanoparticles
Authors: Oh Chang Yong , Henderson Eric R. 
Published: August 2023

AbstractNucleic acid nanoparticles are playing an increasingly important role in biomolecular diagnostics and therapeutics as well as a variety of other areas. The unique attributes of self-assembling DNA nanoparticles provide a potentially valuable addition or alternative to the lipid-based nanoparticles that are currently used to ferry nucleic acids in living systems. To explore this possibility, we have assessed the ability of self-assembling DNA nanoparticles to be constructed from complete gene cassettes that are capable of gene expression in vitro. In the current report, we describe the somewhat counter-intuitive result that despite extensive crossovers (the stereochemical analogs of Holliday junctions) and variations in architecture, these DNA nanoparticles are amenable to gene expression as evidenced by T7 RNA polymerase-driven transcription of a reporter gene in vitro. These findings, coupled with the vastly malleable architecture and chemistry of self-assembling DNA nanoparticles, warrant further investigation of their utility in biomedical genetics.
Fine-grained cell-type specific association studies with human bulk brain data using a large single-nucleus RNA sequencing based reference panel
Authors: van den Oord Edwin J. C. G. , Aberg Karolina A. 
Published: August 2023

AbstractBrain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology but it is critical that expression is studied on a cell-type level. Cell-type specific association studies can be performed with bulk expression data using statistical methods that capitalize on cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we performed an integrated analysis of the seven largest single nucleus RNA-seq studies. Our panel included 17 cell-types that were robustly detected across all studies, subregions of the prefrontal cortex, and sex and age groups. To estimate the cell-type proportions, we used an empirical Bayes estimator that substantially outperformed three estimators recommended previously after a comprehensive evaluation of methods to estimate cell-type proportions from brain transcriptome data. This is important as being able to precisely estimate the cell-type proportions may avoid unreliable results in downstream analyses particularly for the multiple cell-types that had low abundances. Transcriptome-wide association studies performed with permuted bulk expression data showed that it is possible to perform transcriptome-wide association studies for even the rarest cell-types without an increased risk of false positives.
A novel approach to minimal reservoir computing
Authors: Ma Haochun , Prosperino Davide , Räth Christoph 
Published: August 2023

AbstractReservoir computers are powerful machine learning algorithms for predicting nonlinear systems. Unlike traditional feedforward neural networks, they work on small training data sets, operate with linear optimization, and therefore require minimal computational resources. However, the traditional reservoir computer uses random matrices to define the underlying recurrent neural network and has a large number of hyperparameters that need to be optimized. Recent approaches show that randomness can be taken out by running regressions on a large library of linear and nonlinear combinations constructed from the input data and their time lags and polynomials thereof. However, for high-dimensional and nonlinear data, the number of these combinations explodes. Here, we show that a few simple changes to the traditional reservoir computer architecture further minimizing computational resources lead to significant and robust improvements in short- and long-term predictive performances compared to similar models while requiring minimal sizes of training data sets.