bluuebunny/crossref_metadata_2025_split huggingface dataset:
Region of interest-specific loss functions improve T2 quantification with ultrafast T2 mapping MRI sequences in knee, hip and lumbar spine
Authors: Tolpadi Aniket A. , Han Misung , Calivà Francesco , Pedoia Valentina , Majumdar Sharmila 
Published: December 2022

AbstractMRI T2 mapping sequences quantitatively assess tissue health and depict early degenerative changes in musculoskeletal (MSK) tissues like cartilage and intervertebral discs (IVDs) but require long acquisition times. In MSK imaging, small features in cartilage and IVDs are crucial for diagnoses and must be preserved when reconstructing accelerated data. To these ends, we propose region of interest-specific postprocessing of accelerated acquisitions: a recurrent UNet deep learning architecture that provides T2 maps in knee cartilage, hip cartilage, and lumbar spine IVDs from accelerated T2-prepared snapshot gradient-echo acquisitions, optimizing for cartilage and IVD performance with a multi-component loss function that most heavily penalizes errors in those regions. Quantification errors in knee and hip cartilage were under 10% and 9% from acceleration factors R = 2 through 10, respectively, with bias for both under 3 ms for most of R = 2 through 12. In IVDs, mean quantification errors were under 12% from R = 2 through 6. A Gray Level Co-Occurrence Matrix-based scheme showed knee and hip pipelines outperformed state-of-the-art models, retaining smooth textures for most R and sharper ones through moderate R. Our methodology yields robust T2 maps while offering new approaches for optimizing and evaluating reconstruction algorithms to facilitate better preservation of small, clinically relevant features.
A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands
Authors: Allioux Maxime , Yvenou Stéven , Merkel Alexander , Cozannet Marc , Aubé Johanne , Pommellec Jolann , Le Romancer Marc , Lavastre Véronique , Guillaume Damien , Alain Karine 
Published: December 2022

AbstractThe Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.
A System for Converting and Recovering Texts Managed as Structured Information
Authors: Verdesoto Edgardo Samuel Barraza , Ortiz Marlly Yaneth Rojas , Herrera Richard de Jesus Gil 
Published: December 2022

AbstractThis paper introduces a system that incorporates several strategies based on scientific models of how the brain records and recovers memories. Methodologically, an incremental prototyping approach has been applied to develop a satisfactory architecture that can be adapted to any language. A special case is studied and tested regarding the Spanish language. The applications of this proposal are vast because, in general, information such as text way, reports, emails, and web content, among others, is considered unstructured and, hence, the repositories based on SQL databases usually do not handle this kind of data correctly and efficiently. The conversion of unstructured textual information to structured one can be useful in contexts such as Natural Language Generation, Data Mining, and dynamic generation of theories, among others.
Atomized droplet size prediction for supersonic atomized water drainage and natural gas extraction
Authors: Liu Chengting , He Liang 
Published: December 2022

AbstractIn the later stage of natural gas reservoir exploration, the wellbore pressure is reduced and the liquid accumulation is serious, in order to solve the problem of liquid accumulation and low production in low-pressure and low-yield gas wells, the supersonic atomization drainage gas recovery technology is used to improve the recovery rate. By studying the influence of working condition parameters of downhole nozzle atomization drainage gas recovery on atomization effect and liquid carrying rate, a new physical model of atomization nozzle is established, the back propagation (BP) neural network atomization model and BP neural network atomization model optimized by genetic algorithm (GA) is established, and the Matlab is used to train the 45 groups of data sets before the experiment. After the model training, the normalized atomization parameters are trained for sensitivity analysis. The relationship between the strength and weakness of the factors affecting Sotel's average droplet particle size (SMD) is as follows: gas flow (Qg) > liquid inlet diameter (d) > liquid phase flow (Ql). The last 15 sets of data sets outside the training samples were tested by BP model and BP neural model optimized by genetic algorithm (GA-BP), and the size of SMD was predicted. The experimental results show that the determination coefficient R2 of the established GA-BP network model to the experimental parameters is 0.979 and the goodness of fit is high; the mean square error (MSE), mean absolute error (MAE) and mean absolute percentage error (MAPE) of the predicted value of GA-BP atomization model and the experimental value are 4.471, 1.811 and 0.031 respectively, the error is small, the prediction accuracy is high, and the establishment of the model is accurate. The GA-BP model can efficiently predict SMD under different operating conditions, at present, the new supersonic atomizing nozzle has been successfully applied to the Xushen gas field block of Daqing Oilfield, which can improve the recovery rate of natural gas by 4.5–8.6%, alleviate the problem of effusion near the end of oil exploration, and has certain guiding significance for solving the problem of wellbore effusion and improving production efficiency.
The predictability of graft thickness for Descemet’s stripping automated endothelial keratoplasty using a mechanical microkeratome system
Authors: Nishisako Sota , Yamaguchi Takefumi , Kusano Yuki , Higa Kazunari , Aoki Dai , Sasaki Chiaki , Shimazaki Jun 
Published: December 2022

AbstractDescemet's stripping automated endothelial keratoplasty (DSAEK) is used for treating corneal endothelial dysfunction, and the postoperative visual acuity outcome depends on the thickness of the graft. We created a simple nomogram using factors affecting the cutting thickness during graft preparation via a mechanical microkeratome system for DSAEK. This retrospective study was conducted from May 2018 through October 2022 and included donor eyes cut by automatic methods. We measured the graft thickness, cutting accuracy, and assessed ten variables with donor/cornea-related factors potentially affecting the cutting thickness. Subsequently, we created a simple nomogram. We analyzed 81 donor tissues, and the donor median age was 76 years. The mean central graft thickness was 122.2 μm, with 62% of the grafts that could be cut within the target central graft thickness range. Comparatively, donor corneas from those with cardiac diseases were cut deeper (P = 0.007). The developed nomogram provided a 83% probability of estimating the post-cutting graft thickness within 25 µm. Our nomogram, which considers cause of death, enables reproducible production of graft of a desired thickness. A detailed analysis of donor tissues, including the cause of donor death and the characteristics from pressurization to cutting, will enable more precise DSAEK graft preparation.
New quantitative method for dental wear analysis of small mammals
Authors: Bañuls-Cardona Sandra , Blasco Ruth , Rosell Jordi , Rufà Anna , Vallverdú Josep , Rivals Florent 
Published: December 2022

AbstractThe application of dental wear study to murids has always been ruled out because of their omnivorous diet, which does not leave significant wear on the dentition. Nevertheless, in our work we select Apodemus sylvaticus (wood mouse) as the object of study for several reasons: its seasonal diet, its ability to resist the gastric juices of predators, the fact that it has not undergone major morphological changes since its appearance 3 million years ago, and its widespread distribution throughout much of Europe and part of Africa. The importance of this work lies in the modifications we make to the dental wear methodology for its application to murids. These enable us to obtain quantitative data on the entire tooth surface. The sample chosen was a total of 75 lower first molars from two different archaeological sites: Teixoneres cave and Xaragalls cave. The chronology of the samples chosen ranges from Marine Isotope Stages 5–3. The data obtained reveal that the part of the tooth that shows most wear is the distal part (entoconid). Furthermore, the results provide us with relevant information on the types of accumulations of remains in the caves (short vs. long term), as well as on the seasonality of Neanderthal occupations during the Upper Pleistocene (MIS5-3) of the northeastern Iberian Peninsula.
Adsorption of a water-soluble molecular rotor fluorescent probe on hydrophobic surfaces
Authors: Mirzahossein Elham , Grzelka Marion , Guerton Fabrice , Bonn Daniel , Brown Ross 
Published: December 2022

AbstractEnvironmentally sensitive molecular rotors are widely used to probe the local molecular environment in e.g. polymer solutions, polymer glasses, and biological systems. These applications make it important to understand its fluorescence properties in the vicinity of a solid surface, since fluorescence microscopy generically employs cover slides, and measurements are often done in its immediate vicinity. Here, we use a confocal microscope to investigate the fluorescence of (4-daspi) in glycerol/water solutions close to the interface using hydrophilic or hydrophobic cover slips. Despite the dye’s high solubility in water, the observed lengthening of the fluorescence lifetime close to the hydrophobic surface, implies a surprising affinity of the dye with the surface. Because the homogeneous solution and the refractive index mismatch reduces the optical sectioning power of the microscope, we quantify the affinity with the help of a simple model of the signal vs. depth of focus, exhibiting surface and bulk contributions. The model reduces artefacts due to refractive index mismatch, as supported by Monte Carlo ray tracing simulations.
The role of centrifugal partition chromatography in the removal of β-asarone from Acorus calamus essential oil
Authors: Szczeblewski Paweł , Wróblewski Mateusz , Borzyszkowska-Bukowska Julia , Bairamova Tetiana , Górska Justyna , Laskowski Tomasz , Samulewicz Anna , Kosno Michał , Sobiech Łukasz , Polit Justyna Teresa , Kukula-Koch Wirginia 
Published: December 2022

AbstractΒ-asarone is a phenylpropane derivative present in the rhizomes of Acorus calamus, that was proved to exhibit toxic effects in humans. Because of its presence the whole plant that is commonly used in traditional medicine for its sedative, anti-inflammatory, neuroprotective and other properties has limited application nowadays. In the study, qualitative and quantitative analysis of a collection of nine essential oil (EO) samples of European and Asian origin was performed. The final content of β-asarone in the tested samples ranged between 0.265 and 1.885 mg/mL. Having in mind a possible application of the EO as a biopesticide, this research aimed at the development of CPC-based purification protocol that could help remove β-asarone from EO. It was proved that the biphasic solvent system composed of n-hexane/EtOAc/MeOH/water, 9:1:9:1 (v/v/v/v) was capable of the removal of the toxic constituent in the CPC chromatograph operated in the ascending elution mode with 2200 rpm and a flow rate of 5 mL/min. The chromatographic analysis that lasted only 144 min effectively separated β-asarone (purity of 95.5%) and α-asarone (purity of 93.7%) directly from the crude Acorus calamus rhizome EO.
Body surface scan anthropometrics are related to cardiorespiratory fitness in the general population
Authors: Köhler Armin , Filges Berit , Völzke Henry , Felix Stephan B. , Ewert Ralf , Stubbe Beate , Markus Marcello R. P. , Groß Stefan , Dörr Marcus , Ittermann Till , Bahls Martin 
Published: December 2022

AbstractThe assessment of cardiorespiratory fitness (CRF) is an important tool for prognosis evaluation of cardiovascular events. The gold standard to measure CRF is cardiopulmonary exercise testing (CPET) to determine peak oxygen uptake (VO2peak). However, CPET is not only time consuming but also expensive and is therefore not widely applicable in daily practice. The aim of our study was to analyze, whether and which anthropometric markers derived from a 3D body scanner were related to VO2peak in a general population-based study. We analyzed data (SHIP-START-3) from 3D body scanner and CPET of 1035 subjects (529 women; 51.1%, age range 36–93). A total of 164 anthropometric markers were detected with the 3D body scanner VITUS Smart XXL using the software AnthroScan Professional. Anthropometric measurements were standardized and associated with CRF by sex-stratified linear regression models adjusted for age and height. Anthropometric markers were ranked according to the  − log- p values derived from these regression models. In men a greater left and right thigh-knee-ratio, a longer forearm-fingertip length, a greater left thigh circumference and greater left upper arm circumference were most strongly associated with a higher VO2peak. In women a greater left and right thigh circumference, left calf circumference, thigh thickness and right calf circumference were most strongly associated with a higher VO2peak. The detected VO2peak-related anthropometric markers could be helpful in assessing CRF in clinical routine. Commonly used anthropometric markers, e.g. waist and hip circumference, were not among the markers associated with VO2peak.
Alginate-like polymers from full-scale aerobic granular sludge: content, recovery, characterization, and application for cadmium adsorption
Authors: Cydzik-Kwiatkowska Agnieszka , Gusiatin Mariusz Z. , Zielińska Magdalena , Wojnowska-Baryła Irena , Kulikowska Dorota , Bernat Katarzyna 
Published: December 2022

AbstractAerobic granular sludge (AGS) is a proven resource for the recovery of biopolymers like alginate-like polymers (ALP). This is the first report on the dynamics of ALP produced by AGS (ALP-AGS) in a full-scale wastewater treatment plant (WWTP), optimization of ALP recovery from AGS, and adsorption of cadmium (Cd2+) by ALP. Recovery of ALP was highest when using 120 mL of 0.2 M Na2CO3 at 70 °C for 45 min. Seasonal (1.5 years, over 3100 cycles) and intra-cycle changes in ALP-AGS in the WWTP were monitored. The ALP content in AGS increased in the transition period between winter and spring, reaching over 150 mg/g MLSS. In the batch reactor cycle, the ALP-AGS level peaked 2 h after the start of aeration (mean peak level: 120 mg/g MLSS), then decreased about two-fold by the end of the cycle. The ALP-AGS had a small surface area and a lamellar structure with crystalline outgrowths. The optimal conditions of Cd2+ adsorption with ALP were a dosage of 7.9 g d.m./L, a pH of 4–8, and an equilibrium time of 60 min. Carboxyl and hydroxyl groups were the key functional groups involved in Cd2+ adsorption. According to the Sips model, the maximum Cd2+ adsorption capacity of ALP-AGS was 29.5 mg/g d.m., which is similar to that of commercial alginate. AGS is a richer source of ALP than activated sludge, which ensures the cost-effectiveness of ALP recovery and increases the sustainability of wastewater treatment. Information on the chemical properties and yields of ALP from full-scale WWTPs is important for downstream applications with the recovered ALP.
Risk factors for delayed gastric emptying in pancreaticoduodenectomy
Authors: Mao Shih-Hao , Shyr Bor-Shiuan , Chen Shih-Chin , Wang Shin-E , Shyr Yi-Ming , Shyr Bor-Uei 
Published: December 2022

AbstractThe study of robotic pancreaticouodenectomy (RPD) focusing on delayed gastric emptying (DGE) is seldom reported. This study explored the incidence of DGE in RPD with extracorporeal hand-sewn gastrojejunostomy involving downward positioning of the stomach. Patients with periampullary lesions undergoing RPD or open pancreaticouodenectomy (OPD) were included for comparison. A variety of clinical factors were evaluated for the risk of developing DGE. There were 409 (68.2%) RPD and 191 (31.8%) OPD in this study. DGE occurred in 7.7% of patients after pancreaticoduodenectomy, with 4.4% in RPD and 14.7% in OPD, p < 0.001. Nausea/vomiting (12.6% vs. 6.3%) and jaundice (9.9% vs. 5.2%) were significant preoperative risk factors for DGE, while malignancy (8.7% vs. 2.2%) and lymph node involvement (9.8% vs. 5.6%) were significant pathological risk factors. Intraoperative blood loss > 200 c.c. was the other factor related to DGE (11.2% vs. 4.4% in those with blood loss ≤ 200 c.c.). None of the postoperative complications was significantly associated with DGE. Hospital stay was significantly longer in the group with DGE (median, 37 vs. 20 days in the group without DGE). After multivariate analysis by binary logistic regression, compared with OPD, RPD was the only independent factor associated with a lower incidence of DGE. RPD with extracorporeal hand-sewn antecolic, antiperistaltic, and inframesocolic gastrojejunostomy via a small umbilical wound involving careful downward positioning of the stomach was associated with a low incidence of DGE and presented as the most powerful independent predictor of this condition.
Mutation analysis of the WFS1 gene in a Chinese family with autosomal-dominant non-syndrome deafness
Authors: Zhao Jing , Zhang Siqi , Jiang Yuan , Liu Yan , Wang Jiantao , Zhu QingWen 
Published: December 2022

AbstractTo analyse the pathogenic genes and mutations of a family with hereditary deafness. We recruited a three-generation family with NSHL. A detailed medical history inquiry and related examinations were performed. Next-generation sequencing (NGS) was used to confirm the gene mutation in the proband, and Sanger sequencing was used for verification. The effect of the WFS1 mutation on the function and structure of the wolframin protein was predicted by multiple computational software. From the Gene Expression Omnibus (GEO) database, we obtained GSE40585 dataset and performed enrichment analyses. The family clinically manifested as autosomal dominant NSHL. A novel WFS1 c.2421C>G (p.Ser807Arg) mutation was identified in four affected individuals in the pedigree . The p.Ser807Arg mutation is a highly conserved residue and causes an increase in protein stability. It had an important influence on not only amino acid size, charge and hydrophobicity but also protein intermolecular hydrogen bonding and spatial structure. There were differentially expressed genes (DEGs) in GSE40585 dataset. Enrichment analysis revealed that DEGs mainly functioned in amino acid metabolism, signal transduction and dephosphorylation. We reported a novel mutation c.2421C>G (p.Ser807Arg in WFS1. This study expands the mutation spectrum of WFS1.
Time-scale analysis of the long-term variability of human gut microbiota characteristics in Chinese individuals
Authors: Han Na , Zhang Tingting , Qiang Yujun , Peng Xianhui , Li Xiuwen , Zhang Wen 
Published: December 2022

AbstractStudying the dynamics and stability of the human gut microbiota over time is important for exploring their relationship with human health and developing treatment strategies for putative microbiome-related ailments. Here, we collected stool samples from seven healthy Chinese subjects at 1-month intervals between 2016 and 2020. Sequencing and bioinformatics analyses revealed that the bacteria in the collected fecal samples fluctuated over time, and the extent of these changes increased over time. Further, the average shared proportion value obtained using Sourcetracker2 was 63.5% for samples collected from the same individual in the preceding month, and over a 3-year period, this value decreased to 40.7%. Furthermore, the proportion of different bacteria in the gut microbiota of the different subjects fluctuated to varying degrees. Therefore, our results suggested that it is important to consider the effect of time on gut microbiota composition when it is used to evaluate health. Our study opens up a new field of microbiota research, considering not just the instantaneous microbiota, but also the change of the gut microbiota over time.
Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats
Authors: Jia Zhen , Gao Peng , Yin Feifan , Quilichini Teagen D. , Sheng Huajin , Song Jingpu , Yang Hui , Gao Jie , Chen Ting , Yang Bo , Kochian Leon V. , Zou Jitao , Patterson Nii , Yang Qingyong , Gillmor C. Stewart , Datla Raju , Li Qiang , Xiang Daoquan 
Published: December 2022

AbstractProduction of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.