bluuebunny/crossref_metadata_2025_split huggingface dataset:
Axial impairment and falls in Parkinson’s disease: 15 years of subthalamic deep brain stimulation
Authors: Zampogna Alessandro , Cavallieri Francesco , Bove Francesco , Suppa Antonio , Castrioto Anna , Meoni Sara , Pélissier Pierre , Schmitt Emmanuelle , Bichon Amélie , Lhommée Eugénie , Kistner Andrea , Chabardès Stephan , Seigneuret Eric , Fraix Valerie , Moro Elena 
Published: September 2022

AbstractIn this retrospective study, we longitudinally analyzed axial impairment and falls in people with Parkinson’s disease (PD) and subthalamic nucleus deep brain stimulation (STN-DBS). Axial scores and falling frequency were examined at baseline, and 1, 10, and 15 years after surgery. Preoperative demographic and clinical data, including PD duration and severity, phenotype, motor and cognitive scales, medications, and vascular changes on neuroimaging were examined as possible risk factors through Kaplan–Meier and Cox regression analyses. Of 302 individuals examined before and at 1 year after surgery, 102 and 57 were available also at 10 and 15 years of follow-up, respectively. Axial scores were similar at baseline and at 1 year but worsened at 10 and 15 years. The prevalence rate of frequent fallers progressively increased from baseline to 15 years. Preoperative axial scores, frontal dysfunction and age at PD onset were risk factors for axial impairment progression after surgery. Axial scores, akinetic/rigid phenotype, age at disease onset and disease duration at surgery predicted frequent falls. Overall, axial signs progressively worsened over the long-term period following STN-DBS, likely related to the progression of PD, especially in a subgroup of subjects with specific risk factors.
A comprehensive genomic and transcriptomic dataset of triple-negative breast cancers
Authors: Chen Qingwang , Liu Yaqing , Gao Yuechen , Zhang Ruolan , Hou Wanwan , Cao Zehui , Jiang Yi-Zhou , Zheng Yuanting , Shi Leming , Ma Ding , Yang Jingcheng , Shao Zhi-Ming , Yu Ying 
Published: September 2022

AbstractMolecular subtyping of triple-negative breast cancer (TNBC) is essential for understanding the mechanisms and discovering actionable targets of this highly heterogeneous type of breast cancer. We previously performed a large single-center and multiomics study consisting of genomics, transcriptomics, and clinical information from 465 patients with primary TNBC. To facilitate reusing this unique dataset, we provided a detailed description of the dataset with special attention to data quality in this study. The multiomics data were generally of high quality, but a few sequencing data had quality issues and should be noted in subsequent data reuse. Furthermore, we reconduct data analyses with updated pipelines and the updated version of the human reference genome from hg19 to hg38. The updated profiles were in good concordance with those previously published in terms of gene quantification, variant calling, and copy number alteration. Additionally, we developed a user-friendly web-based database for convenient access and interactive exploration of the dataset. Our work will facilitate reusing the dataset, maximize the values of data and further accelerate cancer research.
Biosynthesis of TiO2 nanoparticles by Caricaceae (Papaya) shell extracts for antifungal application
Authors: Saka Abel , Shifera Yohannes , Jule Leta Tesfaye , Badassa Bayissa , Nagaprasad N , Shanmugam R , Priyanka Dwarampudi L , Seenivasan Venkatesh , Ramaswamy Krishnaraj 
Published: September 2022

AbstractTitanium dioxide nanoparticles (TiO2NPs) were prepared byCaricaceae(Papaya) Shell extracts. The Nanoparticles were analyzed by UV–Vis spectrums, X-ray diffractions, and energy-dispersive X-rays spectroscopy analyses with a scanning electron microscope. An antifungal study was carried out for TiO2NP in contradiction of S.sclerotiorums, R.necatrixsand Fusarium classes that verified a sophisticated inhibitions ratio for S.sclerotiorums(60.5%). Germs of pea were individually preserved with numerous concentrations of TiO2NPs. An experience of TiO2NPs (20%, 40%, 80% and 100%), as well as mechanisms that instigated momentous alterations in seed germinations, roots interval, shoot lengths, and antioxidant enzymes, were investigated. Associated with controls, the supreme seeds germinations, roots and plant growth were perceived with the treatments of TiO2NPs. Super-oxide dis-mutase and catalase activities increased because of TiO2NPs treatments. This advocates that TiO2Nanoparticles may considerably change antioxidant metabolisms in seed germinations.
Energy-efficient production of vaccine protein against porcine edema disease from transgenic lettuce (Lactuca sativa L.)
Authors: Yokoyama Asuka , Oiwa Seika , Matsui Takeshi , Sawada Kazutoshi , Tasaka Yasushi , Matsumura Takeshi 
Published: September 2022

AbstractThe development of functional protein production systems using transgenic plants as hosts has been rapidly progressing in recent years. Lettuce (Lactuca sativa L.) has been studied as one such host, and it has been reported that the biomass of lettuce per area and target protein expression level can be increased by optimizing the cultivation conditions. Therefore, we investigated methods to minimize the input light energy per target protein to reduce production costs. Herein, we examined the yield of a nontoxic B subunit of Stx2e (Stx2eB) from transgenic lettuce under various cultivation conditions. Stx2eB acts as a vaccine against swine edema disease. The effects of photon flux densities (PPFDs), photoperiod, and light source on Stx2eB production were examined and the findings suggested that 400 μmol m−2 s−1, 24 h, and white LED lamps, respectively, contributed to energy-efficient Stx2eB production. In addition, Stx2eB was produced 1.4 times more efficiently per unit area time using a high plant density (228.5 plants m−2) than a common density (30.4 plants m−2). The findings of the present study can facilitate the development of energy-efficient and low-cost production processes for vaccine protein production, considering temporal and spatial perspectives.
Nomogram for predicted probability of cervical cancer and its precursor lesions using miRNA in cervical mucus, HPV genotype and age
Authors: Kotani Kiriko , Iwata Aya , Kukimoto Iwao , Nishio Eiji , Mitani Takeji , Tsukamoto Tetsuya , Ichikawa Ryoko , Nomura Hiroyuki , Fujii Takuma 
Published: September 2022

AbstractCervical cancer is the fourth most common cancer in women worldwide. Although cytology or HPV testing is available for screening, these techniques have their drawbacks and optimal screening methods are still being developed. Here, we sought to determine whether aberrant expression of miRNAs in cervical mucus could be an ancillary test for cervical neoplasms. The presence of miRNAs in 583 and 126 patients (validation and external cohorts) was determined by real-time RT-PCR. Performance of a combination with five miRNAs (miR-126-3p, -451a -144-3p, -20b-5p and -155-5p) was estimated by ROC curve analysis. Predicted probability (PP) was estimated by nomograms comprising -ΔCt values of the miRNAs, HPV genotype and age. A combination of five miRNAs showed a maximum AUC of 0.956 (95% CI: 0.933–0.980) for discriminating cancer. Low PP scores were associated with good prognosis over the 2-year observation period (p < 0.05). Accuracy for identifying cancer and cervical intraepithelial neoplasia (CIN) 3 + by nomogram was 0.983 and 0.966, respectively. PP was constant with different storage conditions of materials. We conclude that nomograms using miRNAs in mucus, HPV genotype and age could be useful as ancillary screening tests for cervical neoplasia.
Multi-scale-average-filter-assisted level set segmentation model with local region restoration achievements
Authors: Mabood Lutful , Badshah Noor , Ali Haider , Zakarya Muhammad , Ahmed Aftab , Khan Ayaz Ali , Rada Lavdie , Haleem Muhammad 
Published: September 2022

AbstractSegmentation of noisy images having light in the background it is a challenging task for the existing segmentation approaches and methods. In this paper, we suggest a novel variational method for joint restoration and segmentation of noisy images which are having intensity and inhomogeneity in the existence of high contrast light in the background. The proposed model combines statistical local region information of circular regions centered at each pixel with a multi-phase segmentation technique enabling inhomogeneous image restoration. The proposed model is written in the fuzzy set framework and resolved through alternating direction minimization approach of multipliers. Through experiments, we have tested the performance of the suggested approach on diverse types of synthetic and real images in the existence of intensity and in-homogeneity; and evaluate the precision, as well as, the robustness of the suggested model. Furthermore, the outcomes are, then, compared with other state-of-the-art models including two-phase and multi-phase approaches and show that our method has superiority for images in the existence of noise and inhomogeneity. Our empirical evaluation and experiments, using real images, evaluate and assess the efficiency of the suggested model against several other closest rivals. We observed that the suggested model can precisely segment all the images having brightness, diffuse edges, high contrast light in the background, and inhomogeneity.
Implications of the COVID-19 pandemic on self-reported health status and noise annoyance in rural and non-rural Canada
Authors: Michaud David S. , Marro Leonora , Denning Allison , Shackleton Shelley , Toutant Nicolas , Cameron-Blake Emily , McNamee James P. 
Published: September 2022

AbstractThe Canadian Perspectives on Environmental Noise Survey (CPENS), conducted between April 12th, 2021 and May 25th, 2021 coincided with the third wave of the COVID-19 pandemic. Canadians 18 years of age and older (n = 6647) reported the degree to which the pandemic affected their physical health, mental health, stress, annoyance toward environmental and indoor noise, and overall well-being. Depending on the outcome evaluated, between 18 and 67% of respondents reported the measure as “somewhat” or “much worse” due to the pandemic. Stress was most affected, followed by mental health, overall well-being, physical health, annoyance toward environmental noise and annoyance toward indoor noise. Logistic regression models indicated that province, geographic region (rural/remote, suburban, urban), age, gender, poor physical/mental health, heart disease, a history of high sleep disturbance (in general) or diagnosed sleep disorders, anxiety/depression, working/schooling from home, and being retired significantly impacted the odds of reporting a worsening by the pandemic to varying degrees and directions, depending on the outcome. Indigenous status was unrelated to any of the modelled outcomes. Future research could address some of the noted study limitations and provide the data to determine if the observations on the reported measures of health are temporary, or long-lasting.
A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies
Authors: Le Treut Guillaume , Huber Greg , Kamb Mason , Kawagoe Kyle , McGeever Aaron , Miller Jonathan , Pnini Reuven , Veytsman Boris , Yllanes David 
Published: September 2022

AbstractPropagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell-phone tracking data recorded in the USA between March 2020 and February 2021. We apply this model to the SARS-CoV-2 pandemic by fitting just one global parameter representing the frequency of interaction between individuals. We find that the predicted infections agree reasonably well with the reported cases. We clearly see the effect of “shelter-in-place” policies introduced at the onset of the pandemic. Interestingly, a model with uniform transmission rates produces similar results, suggesting that the epidemic transmission was deeply influenced by air travel. We then study the effect of alternative mitigation policies, in particular restricting long-range travel. We find that this policy is successful in decreasing the epidemic size and slowing down the spread, but less effective than the shelter-in-place policy. This policy can result in a pulled wave of infections. We express its velocity and characterize the shape of the traveling front as a function of the epidemiological parameters. Finally, we discuss a policy of selectively constraining travel based on an edge-betweenness criterion.
Prospective analysis of breast masses using the combined score for quantitative ultrasonography parameters
Authors: Lee Eun Ji , Chang Yun-Woo 
Published: September 2022

AbstractTo investigate the diagnostic value of combined SWE, SMI, and B-mode US scores for distinguishing between benign and malignant masses. A total of 450 breast masses that underwent US-guided core needle biopsies were prospectively enrolled. The breast masses were assessed based on the BI-RADS and quantitative SWE and SMI parameters. The SWEmax, SWEratio, and SMIVI cutoff value were determined using Youden’s index by comparison to the pathological results. The BI-RADS categories were scored on a scale from 1 to 5, and SWEmax, SWEratio, and SMIVI were dichotomized based on each cutoff values (0 or 1). The combined scores (1 to 8) were calculated as the sum of the BI-RADS score and the quantitative scores and compared to the pathologic results using AUROC analysis. The cutoff values were 52.25 kPa for SWEmax, 5.03 for SWEratio, and 2.15% for SMIVI. In AUROC, the combined scores showed significantly better diagnostic performance compared to BI-RADS alone (p < 0.001). The combined score showed significantly increased than BI-RADS alone in specificity (p < 0.001) and accuracy (p < 0.001), but a sensitivity decreased without significance (p = 0.082). When a combined score cutoff value of 4 was used, the false negative rate was 2.7%. Using the combined score, 76.4% of the C4a lesions were considered benign also pathologically diagnosed as benign. The combined scores showed improved diagnostic performance in differentiating between benign and malignant breast masses, which could be helpful for determining a breast biopsy eligibility.
Bell-Evans model and steered molecular dynamics in uncovering the dissociation kinetics of ligands targeting G-protein-coupled receptors
Authors: Akhunzada Muhammad Jan , Yoon Hyun Jung , Deb Indrajit , Braka Abdennour , Wu Sangwook 
Published: September 2022

AbstractRecently, academic and industrial scientific communities involved in kinetics-based drug development have become immensely interested in predicting the drug target residence time. Screening drug candidates in terms of their computationally predicted residence times, which is a measure of drug efficacy in vivo, and simultaneously assessing computational binding affinities are becoming inevitable. Non-equilibrium molecular simulation approaches are proven to be useful in this purpose. Here, we have implemented an optimized approach of combining the data derived from steered molecular dynamics simulations and the Bell-Evans model to predict the absolute residence times of the antagonist ZMA241385 and agonist NECA that target the A2A adenosine receptor of the G-protein-coupled receptor (GPCR) protein family. We have predicted the absolute ligand residence times on the timescale of seconds. However, our predictions were many folds shorter than those determined experimentally. Additionally, we calculated the thermodynamics of ligand binding in terms of ligand binding energies and the per-residue contribution of the receptor. Subsequently, binding pocket hotspot residues that would be important for further computational mutagenesis studies were identified. In the experiment, similar sets of residues were found to be in significant contact with both ligands under study. Our results build a strong foundation for further improvement of our approach by rationalizing the kinetics of ligand unbinding with the thermodynamics of ligand binding.
Traces of calcium oxalate biomineralization in fossil leaves from late Oligocene maar deposits from Germany
Authors: Malekhosseini Mahdieh , Ensikat Hans-Jürgen , McCoy Victoria E. , Wappler Torsten , Weigend Maximilian , Kunzmann Lutz , Rust Jes 
Published: September 2022

AbstractCalcium oxalate (CaOx) is one of the most common bio-mineral in extant plants and is believed to serve a variety of functions such as calcium storage and herbivore defense. However, traces of CaOx crystals have rarely been identified in fossil plants, and they are primarily known from fossil gymnosperms, where empty cavities of former CaOx crystals or ghost crystals have been reported from leaf cuticles of some Late Cretaceous and Cenozoic conifers. Here we investigate fossil angiosperm leaves from the late Oligocene Rott Fossil Lagerstätte and report ghost crystals of various shapes, sizes and topology (distribution patterns), and cavities. These micromorphological structures of fossil leaves are compared to CaOx deposits in leaves of extant plants: globular structures in fossil leaves resemble CaOx druses (crystal aggregates) in fresh leaves in size and distribution; and angular or brick-shaped structures in the vascular system of fossil leaves closely resemble prismatic CaOx crystals in the vascular system of extant leaves in both size and topology. Chemically, CaOx druses have survived fossilization as cavities only, and were replaced by organic matter and ghost minerals containing Ca, Si, Al, S, and Fe. The identification of former CaOx remains in leaf fossils provides novel insights on the fate of plant bio-minerals during fossilization. More importantly, it provides an additional aspect of the ecophysiology of fossil plants thus improving the accuracy of palaeoecological reconstructions and can provide a broader perspective on the evolution of CaOx and their rule in plant ecology across geological timescales. Alternative interpretations of the fossil microstructures are discussed but ruled out.
Longitudinal associations between physical activity and other health behaviours during the COVID-19 pandemic: a fixed effects analysis
Authors: Mitchell John J. , Bu Feifei , Fancourt Daisy , Steptoe Andrew , Bone Jessica K. 
Published: September 2022

AbstractGovernment enforced restrictions on movement during the COVID-19 pandemic are likely to have had profound impacts on the daily behaviours of many individuals, including physical activity (PA). Given the associations between PA and other health behaviours, changes in PA during the pandemic may have been detrimental for other health behaviours. This study aimed to evaluate whether changes in PA during and after the first national lockdown in the United Kingdom (UK) were associated with concurrent changes in alcohol consumption, sleep, nutrition quality, diet quantity and sedentary time. Data were derived from the UCL COVID-19 Social Study, in which 52,784 adults were followed weekly across 22 weeks of the pandemic from 23rd March to 23rd August 2020. Fixed effects regression models showed that greater PA was positively associated with improved sleep and nutrition quality. However, increases in PA also showed modest associations with increased alcohol consumption and sedentary time. Encouraging people to engage in PA may lead to wider changes in other health behaviours in times of adversity. These associations could be a result of increases in available leisure time for many people during COVID-19 restrictions and are of ongoing importance given the emerging long-term changes to lifestyle and working patterns.
Comparison of microscopic adsorption characteristics of Zn(II), Pb(II), and Cu(II) on kaolinite
Authors: Tian Li , Fu Kai-bin , Chen Shu , Yao Jun , Bian Liang 
Published: September 2022

AbstractIn this research, kaolinite was used to investigate the comparative adsorption of copper, lead, and zinc ions through batch control experiments and first principles calculations. Different adsorption conditions were considered as the effect of solution acidity, initial concentration of ions, and contact shaking time. The adsorption system isotherms and kinetic studies were better agreed with the Langmuir and pseudo-second-order kinetic models. They reached adsorption equilibrium within two hours and maximum adsorption capacities of Zn(II), Pb(II), and Cu(II) on kaolinite were 15.515, 61.523, and 44.659 mg/g, respectively. In addition, the microscopic adsorption changes of Zn(II), Pb(II), and Cu(II) on kaolinite were characterized using X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy with energy dispersive X-ray spectroscopy. The results showed that Zn(II), Pb(II), and Cu(II) were most likely to be adsorbed on the kaolinite surface. Furthermore, the adsorption mechanism of [Zn(OH)]+, [Pb(OH)]+, and [Cu(OH)]+ on the kaolinite (001) surface was systematically studied through first-principles density functional calculations. The adsorption characteristics of different ions were evaluated by calculating the adsorption energy of the equilibrium adsorption configuration, state density, and electron density. The adsorption energy of [Zn(OH)]+, [Pb(OH)]+, and [Cu(OH)]+ were − 0.49,  − 1.17, and − 1.64 eV, respectively. The simulation results indicated that new hybrid orbitals were formed between the metal ions and O atoms on the kaolinite surface, with electron transfer occurring the adsorption processes. The charge transfer direction for [Pb(OH)]+ was opposite those for [Zn(OH)]+ and [Cu(OH)]+. [Zn(OH)]+ was more likely to form polydentate complexes with hydroxyl groups on the kaolinite surface than [Cu(OH)]+ and [Pb(OH)]+. This work further elucidated the interaction mechanism between the adsorption systems and provided fundamental theoretical support for the structural modification and optimization of kaolinite, such as increasing the layer spacing of kaolinite and introducing other active groups on its surface to improve the adsorption capacity of heavy metal ions in water treatment and soil remediation.