bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collection of X-ray micro computed tomography images of shells of planktic foraminifera with curated taxonomy
Authors: Siccha Michael , Morard Raphaël , Meilland Julie , Iwasaki Shinya , Kucera Michal , Kimoto Katsunori 
Published: October 2023

AbstractCalcite shells of planktic foraminifera (Protista, Rhizaria) constitute a large portion of deep-sea sediments. The shells are constructed by sequential addition of partly overlapping chambers with diverse shapes, resulting in complex shell architectures, which are genetically fixed and diagnostic at the species level. The characterisation of the complete architecture requires three-dimensional imaging of the shell, including the partially or entirely covered juvenile chambers. Here we provide reconstructed x-ray micro computed tomography image stacks of 179 specimens of extant planktic foraminifera collected from plankton tows, sediment traps and surface sediments. The specimens have fully resolved and curated taxonomy and represent 43 of the currently recognised 48 holoplanktic species and subspecies. The image stacks form a basis for further applications, such as the characterisation of the architectural morphospace of the extant taxa, allowing studies of species functional ecology, calcification intensity and reconstructions of phylogenetic relationships.
Long- and short-read RNA sequencing from five reproductive organs of boar
Authors: Liu Zhipeng , Zhang Xia , Huang Libin , Huo Hailong , Wang Pei , Li Weizhen , Dai Hongmei , Yang Fuhua , Fu Guowen , Zhao Guiying , Sun Yu H. , Huo Jinlong 
Published: October 2023

AbstractThe production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE). We identified 110,996 full-length isoforms from 22,298 genes, and classified the alternative splicing (AS) events in these five glands. Transcriptome-wide variation analysis indicated that the number of single nucleotide polymorphisms (SNPs) in five tissues of BMI was significantly lower than that in the non-inbred pig, DSE, revealing the effect of inbreeding on BMI. Additionally, we performed small-RNA sequencing and identified 299 novel miRNAs across all glands. Overall, our findings provide a comprehensive overview of the RNA landscape within these five glands, paving the path for future investigations on reproductive biology and the impact of inbreeding on pig transcriptome.
An angiopoietin 2, FGF23, and BMP10 biomarker signature differentiates atrial fibrillation from other concomitant cardiovascular conditions
Authors: Chua Winnie , Cardoso Victor R. , Guasch Eduard , Sinner Moritz F. , Al-Taie Christoph , Brady Paul , Casadei Barbara , Crijns Harry J. G. M. , Dudink Elton A. M. P. , Hatem Stéphane N. , Kääb Stefan , Kastner Peter , Mont Lluis , Nehaj Frantisek , Purmah Yanish , Reyat Jasmeet S. , Schotten Ulrich , Sommerfeld Laura C. , Zeemering Stef , Ziegler André , Gkoutos Georgios V. , Kirchhof Paulus , Fabritz Larissa 
Published: October 2023

AbstractEarly detection of atrial fibrillation (AF) enables initiation of anticoagulation and early rhythm control therapy to reduce stroke, cardiovascular death, and heart failure. In a cross-sectional, observational study, we aimed to identify a combination of circulating biomolecules reflecting different biological processes to detect prevalent AF in patients with cardiovascular conditions presenting to hospital. Twelve biomarkers identified by reviewing literature and patents were quantified on a high-precision, high-throughput platform in 1485 consecutive patients with cardiovascular conditions (median age 69 years [Q1, Q3 60, 78]; 60% male). Patients had either known AF (45%) or AF ruled out by 7-day ECG-monitoring. Logistic regression with backward elimination and a neural network approach considering 7 key clinical characteristics and 12 biomarker concentrations were applied to a randomly sampled discovery cohort (n = 933) and validated in the remaining patients (n = 552). In addition to age, sex, and body mass index (BMI), BMP10, ANGPT2, and FGF23 identified patients with prevalent AF (AUC 0.743 [95% CI 0.712, 0.775]). These circulating biomolecules represent distinct pathways associated with atrial cardiomyopathy and AF. Neural networks identified the same variables as the regression-based approach. The validation using regression yielded an AUC of 0.719 (95% CI 0.677, 0.762), corroborated using deep neural networks (AUC 0.784 [95% CI 0.745, 0.822]). Age, sex, BMI and three circulating biomolecules (BMP10, ANGPT2, FGF23) are associated with prevalent AF in unselected patients presenting to hospital. Findings should be externally validated. Results suggest that age and different disease processes approximated by these three biomolecules contribute to AF in patients. Our findings have the potential to improve screening programs for AF after external validation.
Morphological analysis of three-dimensional MR images of patellofemoral joints in asymptomatic subjects
Authors: Katano Hisako , Ozeki Nobutake , Mizuno Mitsuru , Endo Kentaro , Okanouchi Noriya , Fujita Jo , Masumoto Jun , Koga Hideyuki , Sekiya Ichiro 
Published: October 2023

AbstractThe existing methods for analyzing patellofemoral (PF) osteoarthritis (OA) are limited. Our purpose was to clarify the frequency, localization, and morphological progression of PFOA by observing three-dimensional (3D) magnetic resonance (MR) images from a cohort population. The subjects were 561 patients aged 30–79 years from the Kanagawa Knee Study who had not visited a hospital for more than three consecutive months for knee symptoms. MR images of the PF joints, separated into the medial and lateral types, were presented in order of the highest to lowest patella cartilage area ratios. Cartilage defects in the patella were detected in 37 subjects (6.6%). Medial lesions (4.6%) were significantly more frequent than lateral lesions (2.0%) (p < 0.01). For both medial and lateral lesions, the patellar cartilage defects were divided into confined and unconfined types. The 3D MR images of the PF joint showed that the patellar cartilage defect occurred along each ridge of the femoral trochlea. The 3D MR images revealed a 6.6% prevalence of patellar cartilage defects, higher in the medial than lateral regions. The 3D MR images can easily determine PF morphology and cartilage defect location, making them useful in understanding the pathophysiology and etiology of PFOA.
Chemical analysis of pottery reveals the transition from a maritime to a plant-based economy in pre-colonial coastal Brazil
Authors: Admiraal Marjolein , Colonese Andre C. , Milheira Rafael G. , da Rocha Bandeira Dione , Demathe Alexandro , Pereira dos Santos Adriana M. , Fossile Thiago , Talbot Helen M. , Bondetti Manon , Lucquin Alexandre , Montalvo-Cabrera Javier , Prates Luciano , Serna Alejandro , Craig Oliver E. 
Published: October 2023

AbstractUnderstanding long-term dynamics of past socio-ecological systems is essential for their future management. The southern Atlantic Forest coast of Brazil with its biodiverse littoral zone and artisanal fishing communities, is a priority for conservation. Traditional maritime knowledge is thought to have a deep-history and indeed, marine exploitation can be traced back to the middle Holocene. As part of one of South America’s largest diasporas, Guarani groups reached the southern Brazilian coast at around 1000 years ago. Their impact on the long-standing coastal economy is unknown, due to poor preservation of organic remains. Through the first organic residue study on Guarani pottery, we show that maize rather than aquatic foods was the most dominant product in pottery at this time. By developing a mixing model based on carbon isotope values of saturated and mono-unsaturated fatty acids we propose new criteria for the identification of maize, opening up avenues for future research. Our data confirms the importance of maize to the pre-colonial Guarani, even in a highly productive coastal environment. The Guarani occupation of this region marks a significant departure from previous socio-economic systems, potentially leading to loss of traditional knowledge and alleviating anthropogenic pressure, albeit temporarily, on the marine environment.
Assessment of the electro-mechanical equipment’s weight of the European hydropower fleet
Authors: Quaranta Emanuele 
Published: October 2023

AbstractHydropower structures are typically made of materials that are available in most parts of the world, such as steel, concrete, and—to a lesser extent—copper, and do not use critical materials. The weight of hydropower structures is an important input data, as it is used to perform Life Cycle Assessments and to estimate the cost and the economic value of materials, both during the design and in case of dismantling or retrofitting. The weight of material is of interest also for policy-making purposes and for strategic development planning, for example to estimate impacts on resources. In this study, available literature equations are, for the first time, applied at a regional scale (the European Union) to estimate the weight of the hydropower fleet’s electro-mechanical (steel-made) equipment. The total weight of the electro-mechanical equipment (runner, distributor, generator, draft tube and casing) amounts to 877 ktons. The average ratio of weight to installed power is R = 5.7 ton/MW and it is lower in mountainous countries (R = 4–6 in alpine areas, R = 30 in Denmark), where hydropower plants exploit high heads and low discharges.
The mental health impact of school bullying among young carers in Australia: a causal mediation analysis
Authors: Alfonzo Ludmila Fleitas , Singh Ankur , Disney George , King Tania 
Published: October 2023

AbstractInformal care can exert adverse effects on the mental health of young people. Bullying victimisation is an important determinant of mental disorders. Young carers are at elevated risk of bullying. We quantify the mental health effects of informal care among Australian adolescents and the extent to which these effects are transmitted through school bullying. We used data from the Longitudinal Study of Australian Children. Participants were classified as non-carers, light carers (caring for < 10 h/week) and moderate-to-heavy carers (caring for 10 + h/week). Mental health was measured using the Kessler Psychological Distress Scale (K10). Using a counterfactual approach to mediation analysis, total effects (TE) of informal care on mental health were decomposed into natural direct effects (NDE—mental health effects not transmitted through school bullying) and natural indirect effects (NIE—mental health effects transmitted through school bullying). The TE of informal caring was 0.71 (95%CI − 0.03, 1.49) for light carers and 1.72 (95%CI 0.45, 3.02) for moderate-to-heavy carers. While school bullying explained 27% of the TE among moderate-to-heavy carers (NIE: 0.46; 95%CI 0.12, 0.91) there was weak evidence of mediation for light carers. Our findings indicate that the mental health effects of moderate-to-heavy caregiving can be reduced by school bullying interventions.
Behavior-related health risk factors, mental disorders and mortality after 20 years in a working aged general population sample
Authors: John Ulrich , Rumpf Hans-Jürgen , Hanke Monika , Meyer Christian 
Published: October 2023

AbstractMortality is predicted by the sum of behavior-related health risk factors (BRFs: tobacco smoking, alcohol drinking, body overweight, and physical inactivity). We analyzed degrees and combinations of BRFs in their relation to mortality and adjusted for mental disorders. In a random sample of the general population in northern Germany aged 18–64, BRFs and mental disorders had been assessed in 1996–1997 by the Munich Composite International Diagnostic Interview. A sum score including eight ranks of the behavior-related health risk factors was built. Death and its causes were ascertained 2017–2018 using residents’ registration files and death certificates. Relations of the sum score and combinations of the BRFs at baseline with all-cause, cancer, and cardiovascular mortality 20 years later were analyzed. The sum score and combinations predicted all-cause, cardiovascular and cancer mortality. The odds ratio of the sum score was 1.38 (95% confidence interval 1.31–1.46) after adjustment for age, gender, and mental disorder. In addition to the BRFs, mood, anxiety or somatoform disorders were not related to mortality. We concluded that the sum score and combinations of behavior-related health risk factors predicted mortality, even after adjustment for mental disorders.
Design of hypoxia responsive CRISPR-Cas9 for target gene regulation
Authors: An Yan , Talwar Chandana S. , Park Kwang-Hyun , Ahn Woo-Chan , Lee Su-Jin , Go Seong-Ryeong , Cho Jin Hwa , Kim Do Yon , Kim Yong-Sam , Cho Sayeon , Kim Jeong-Hoon , Kim Tae-Jip , Woo Eui-Jeon 
Published: October 2023

AbstractThe CRISPR–Cas9 system is a widely used gene-editing tool, offering unprecedented opportunities for treating various diseases. Controlling Cas9/dCas9 activity at specific location and time to avoid undesirable effects is very important. Here, we report a conditionally active CRISPR–Cas9 system that regulates target gene expression upon sensing cellular environmental change. We conjugated the oxygen-sensing transcription activation domain (TAD) of hypoxia-inducing factor (HIF-1α) with the Cas9/dCas9 protein. The Cas9-TAD conjugate significantly increased endogenous target gene cleavage under hypoxic conditions compared with that under normoxic conditions, whereas the dCas9-TAD conjugate upregulated endogenous gene transcription. Furthermore, the conjugate system effectively downregulated the expression of SNAIL, an essential gene in cancer metastasis, and upregulated the expression of the tumour-related genes HNF4 and NEUROD1 under hypoxic conditions. Since hypoxia is closely associated with cancer, the hypoxia-dependent Cas9/dCas9 system is a novel addition to the molecular tool kit that functions in response to cellular signals and has potential application for gene therapeutics.
Effects of MRI scanner manufacturers in classification tasks with deep learning models
Authors: Kushol Rafsanjany , Parnianpour Pedram , Wilman Alan H. , Kalra Sanjay , Yang Yee-Hong 
Published: October 2023

AbstractDeep learning has become a leading subset of machine learning and has been successfully employed in diverse areas, ranging from natural language processing to medical image analysis. In medical imaging, researchers have progressively turned towards multi-center neuroimaging studies to address complex questions in neuroscience, leveraging larger sample sizes and aiming to enhance the accuracy of deep learning models. However, variations in image pixel/voxel characteristics can arise between centers due to factors including differences in magnetic resonance imaging scanners. Such variations create challenges, particularly inconsistent performance in machine learning-based approaches, often referred to as domain shift, where the trained models fail to achieve satisfactory or improved results when confronted with dissimilar test data. This study analyzes the performance of multiple disease classification tasks using multi-center MRI data obtained from three widely used scanner manufacturers (GE, Philips, and Siemens) across several deep learning-based networks. Furthermore, we investigate the efficacy of mitigating scanner vendor effects using ComBat-based harmonization techniques when applied to multi-center datasets of 3D structural MR images. Our experimental results reveal a substantial decline in classification performance when models trained on one type of scanner manufacturer are tested with data from different manufacturers. Moreover, despite applying ComBat-based harmonization, the harmonized images do not demonstrate any noticeable performance enhancement for disease classification tasks.
Defect engineering for enhanced optical and photocatalytic properties of ZnS nanoparticles synthesized by hydrothermal method
Authors: Jubeer E. Muhammed , Manthrammel M. Aslam , Subha P. A. , Shkir Mohd , Biju K. P. , AlFaify S. A. 
Published: October 2023

AbstractDefect engineering is a promising method for improving light harvesting in photocatalytic materials like Zinc sulphide (ZnS). By altering the S/Zn molar ratio during hydrothermal processes, Zn and S defects are successfully introduced into the ZnS crystal. The band structures can be modified by adding defects to the crystal structure of ZnS samples. During the treatment process, defects are formed on the surface. XRD and Raman studies are used for the confirmation of the crystallinity and phase formation of the samples. Using an X-ray peak pattern assessment based on the Debye Scherer model, the Williamson-Hall model, and the size strain plot, it was possible to study the influence of crystal defect on the structural characteristics of ZnS nanoparticles. The band gap (Eg) values were estimated using UV–Vis diffuse spectroscopy (UV–Vis DRS) and found that the Eg is reduced from 3.28 to 3.49 eV by altering the S/Zn molar ratio. Photoluminescence study (PL) shows these ZnS nanoparticles emit violet and blue radiations. In keeping with the results of XRD, TEM demonstrated the nanoscale of the prepared samples and exhibited a small agglomeration of homogenous nanoparticles. Scanning electron microscopy (SEM) was used to examine the surface morphology of the ZnS particles. Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) and X-ray photoelectron spectroscopy (XPS) were used to evaluate and validate the elemental composition. XPS results indicate the presence of defects on the prepared ZnS nanoparticles. For the investigation of vacancy-dependent catalytic activity under exposure to visible light, defective ZnS with different quantities of Zn and S voids are used as catalysts. The lowest S/Zn sample, ZnS0.67 and the highest S/Zn sample, ZnS3, show superior photocatalytic activity.
Advancing chirality analysis through enhanced enantiomer characterization and quantification via fast Fourier transform capacitance voltammetry
Authors: Ebrahimi Mehrnaz , Norouzi Parviz , Ghasemi Jahan B. , Moosavi-Movahedi Ali Akbar , Noroozifar Meissam , Salahandish Razieh 
Published: October 2023

AbstractThe exploration of the chiral configurations of enantiomers represents a highly intriguing realm of scientific inquiry due to the distinct roles played by each enantiomer (D and L) in chemical reactions and their practical utilities. This study introduces a pioneering analytical methodology, termed fast Fourier transform capacitance voltammetry (FFT-CPV), in conjunction with principal component analysis (PCA), for the identification and quantification of the chiral forms of tartaric acid (TA), serving as a representative model system for materials exhibiting pronounced chiral characteristics. The proposed methodology relies on the principle of chirality, wherein the capacitance signal generated by the adsorption of D-TA and L-TA onto the surface of a platinum electrode (Pt-electrode) in an acidic solution is harnessed. The capacitance voltammograms were meticulously recorded under optimized experimental conditions. To compile the final dataset for the analyte, the average of the FFT capacitance voltammograms of the acidic solution (without the presence of the analyte) was subtracted from those containing the analyte. A distinct arrangement was obtained by employing PCA as a linear data transformation method, representing D-TA and L-TA in a two/three-dimensional space. The outcomes of the study reveal the successful detection of the two chiral forms of TA with a considerable degree of precision and reproducibility. Moreover, the proposed method facilitated the establishment of two linear response ranges for the concentration values of each enantiomer, spanning from 1 to 20 µM, and 50 to 500 µM. The respective detection limits were also determined to be 0.4 µM for L-TA and 1.3 µM for D-TA. These findings underscore the satisfactory sensitivity and efficiency of the proposed method in both qualitative and quantitative assessments of the chiral forms of TA.
Characterization and application of tannase and gallic acid produced by co-fungi of Aspergillus niger and Trichoderma viride utilizing agro-residues substrates
Authors: Ahmed Alshaymaa I. , Abou-Taleb Khadiga A. A. , Abd-Elhalim Basma T. 
Published: October 2023

AbstractBioconversion using fungi, as natural factory of many applicable bioactive compounds, as enzymes utilizing agro-residue substrates as a solid, abundant, low-cost growth and enzyme production media. This study characterized and applied a tannase enzyme (308 U/mg) from Aspergillus niger A8 + Trichoderma viride co-cultures utilizing pomegranate peels. The partially purified enzyme showed maximal relative activity at 37–65 °C for 10 min and kinetics of thermal inactivation energy at a high point at 60 °C for 0.040/min. The half-life was 37 °C for 58.6 min, temperature coefficient Q10 of tannase was maximal for 1.38 between 40 and 50 °C, and the activation energy was 17.42 kJ/mol. The enzyme activity peaked in the pH range of 4–8, and the maximum relative activity (100.6%) for tannase was achieved at pH 6. The Km and Vmax values for purified enzymes using tannic acid were 7.3 mg/mL and 3333.33 U/mL, respectively. The enzyme reduced the total tannin content in all tannin-rich substrates after 12h. The gallic acid (GA) had total phenols of 77.75 ppm and antioxidant activity of 82.91%. It was observed that the GA as antimicrobial influencer exhibited the largest inhibitory zone diameter (IZD) of 31 ± 1.0 mm against Pseudomonas aeruginosa ATCC27853. The GA minimum inhibitory concentration value was ranged from 7770.0–121.41 µg/mL. The obtained GA showed a bactericidal effect against all bacterial strains except Shigella sonnei DSM5570 and Salmonella typhi DSM17058, which showed bacteriostatic behavior.
Zn salts incorporated polyurethane/polyacrylonitrile electrospinning fiber membrane for high porosity polymer electrolyte in Zn ion battery
Authors: Likitaporn Chutiwat , Okhawilai Manunya , Senthilkumar Nangan , Wongsalam Tawan , Tanalue Nattapon , Kasemsiri Pornnapa , Qin Jiaqian , Uyama Hiroshi 
Published: October 2023

AbstractSo far, a large variety of polymer molecule architectures have been explored in the electrolyte field. Polymer electrolytes have gathered research efforts as an interesting alternative to conventional liquid electrolytes due to their advantages of low probability of leakage and low volatility of liquid solvent, lightweight, flexibility, inertness, high durability, and thermal stability. In this work, a polymer electrolyte developed from a polyurethane/polyacrylonitrile (PU/PAN) electrospinning fiber membrane was added with different zinc (Zn) salts, namely, Zn(CH3CO2)2, ZnSO4, and Zn(OTf)2. The samples with the Zn salt presented many different properties; especially, the high Zn(OTf)2 sample showed gradually bundle morphology in its structure. Characterization revealed improved properties in contact angle, water uptake, and thermal resistance. Namely, the 15 wt% Zn(OTf)2) sample exhibited an outstandingly high ionic conductivity of 3.671 mS cm−1, which is 10 times higher than that of the neat PU/PAN membrane.