bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methyl carbamates of phosphatidylethanolamines and phosphatidylserines reveal bacterial contamination in mitochondrial lipid extracts of mouse embryonic fibroblasts
Authors: Castellaneta Andrea , Porcelli Vito , Losito Ilario , Barile Serena , Maresca Alessandra , Del Dotto Valentina , Guadalupi Ludovica Sofia , Calvano Cosima Damiana , Carelli Valerio , Palmieri Luigi , Cataldi Tommaso R. I. 
Published: August 2023

AbstractThe occurrence of methyl carbamates of phosphatidylethanolamines and phosphatidylserines in the lipid extract of mitochondria obtained from mouse embryonic fibroblasts was ascertained by hydrophilic interaction liquid chromatography with electrospray ionization single and multi-stage mass spectrometry, performed using sinergically a high resolution (quadrupole-Orbitrap) and a low resolution (linear ion trap) spectrometer. Two possible routes to the synthesis of methyl carbamates of phospholipids were postulated and evaluated: (i) a chemical transformation involving phosgene, occurring as a photooxidation by-product in the chloroform used for lipid extraction, and methanol, also used for the latter; (ii) an enzymatic methoxycarbonylation reaction due to an accidental bacterial contamination, that was unveiled subsequently on the murine mitochondrial sample. A specific lipid extraction performed on a couple of standard phosphatidyl-ethanolamines/-serines, based on purposely photo-oxidized chloroform and deuterated methanol, indicated route (i) as negligible in the specific case, thus highlighting the enzymatic route related to bacterial contamination as the most likely source of methyl carbamates. The unambiguous recognition of the latter might represent the starting point toward a better understanding of their generation in biological systems and a minimization of their occurrence when an artefactual formation is ascertained.
Dynamical system analysis of interacting dark energy in LRS Bianchi type I cosmology
Authors: Rathore Shivangi , Singh S. Surendra 
Published: August 2023

AbstractThis paper deals with an interacting dark energy (DE) model in Locally rotationally symmetric (LRS) Bianchi type I cosmological model with scalar field in the form of an exponential potential. We reduce the transformation equations to an independent system of ordinary differential equations by appropriate alteration of the variables to setup the complementary dynamical system and after that we also calculate the critical points of the system. We get six critical points when our coupling parameter is positive. And we get two critical points when our coupling parameter is negative. And dark energy behaves like a perfect fluid for all the critical points. And after that we analyzed all the critical points by calculating the eigenvalues of the Jacobian matrix and we find out that out of these eight critical points, six critical points are stable, which shows that our Universe is accelerating. And two (2) critical points are unstable. We also present the phase plot analysis.
Neuronal diversity can improve machine learning for physics and beyond
Authors: Choudhary Anshul , Radhakrishnan Anil , Lindner John F. , Sinha Sudeshna , Ditto William L. 
Published: August 2023

AbstractDiversity conveys advantages in nature, yet homogeneous neurons typically comprise the layers of artificial neural networks. Here we construct neural networks from neurons that learn their own activation functions, quickly diversify, and subsequently outperform their homogeneous counterparts on image classification and nonlinear regression tasks. Sub-networks instantiate the neurons, which meta-learn especially efficient sets of nonlinear responses. Examples include conventional neural networks classifying digits and forecasting a van der Pol oscillator and physics-informed Hamiltonian neural networks learning Hénon–Heiles stellar orbits and the swing of a video recorded pendulum clock. Such learned diversity provides examples of dynamical systems selecting diversity over uniformity and elucidates the role of diversity in natural and artificial systems.
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Authors: Odom Aubrey R. , Faits Tyler , Castro-Nallar Eduardo , Crandall Keith A. , Johnson W. Evan 
Published: August 2023

AbstractMost experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon sequencing. However, the most-used bioinformatics tools cannot produce high quality genus-level or species-level taxonomic calls and may underestimate the potential accuracy of these calls. We used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, concentrating on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq. Profiling tools were compared using publicly available mock community data from several sources, comprising 136 samples with varied species richness and evenness, several different amplified regions within the 16S rRNA gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole-genome metagenomics, outperformed DADA2, QIIME 2 using the DADA2 plugin, and Mothur, which are theoretically specialized for 16S analyses. Evaluations of reference libraries identified the SILVA and RefSeq/Kraken 2 Standard libraries as superior in accuracy compared to Greengenes. These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.
Reproducibility of continuous glucose monitoring results under real-life conditions in an adult population: a functional data analysis
Authors: Matabuena Marcos , Pazos-Couselo Marcos , Alonso-Sampedro Manuela , Fernández-Merino Carmen , González-Quintela Arturo , Gude Francisco 
Published: August 2023

AbstractContinuous glucose monitoring systems (CGM) are a very useful tool to understand the behaviour of glucose in different situations and populations. Despite the widespread use of CGM systems in both clinical practice and research, our understanding of the reproducibility of CGM data remains limited. The present work examines the reproducibility of the results provided by a CGM system in a random sample of a free-living adult population, from a functional data analysis approach. Functional intraclass correlation coefficients (ICCs) and their 95% confidence intervals (CI) were calculated to assess the reproducibility of CGM results in 581 individuals. 62% were females 581 participants (62% women) mean age 48 years (range 18–87) were included, 12% had previously been diagnosed with diabetes. The inter-day reproducibility of the CGM results was greater for subjects with diabetes (ICC 0.46 [CI 0.39–0.55]) than for normoglycaemic subjects (ICC 0.30 [CI 0.27–0.33]); the value for prediabetic subjects was intermediate (ICC 0.37 [CI 0.31–0.42]). For normoglycaemic subjects, inter-day reproducibility was poorer among the younger (ICC 0.26 [CI 0.21–0.30]) than the older subjects (ICC 0.39 [CI 0.32–0.45]). Inter-day reproducibility was poorest among normoglycaemic subjects, especially younger normoglycaemic subjects, suggesting the need to monitor some patient groups more often than others.
Targeted gene expression profiling for accurate endometrial receptivity testing
Authors: Meltsov Alvin , Saare Merli , Teder Hindrek , Paluoja Priit , Arffman Riikka K. , Piltonen Terhi , Laudanski Piotr , Wielgoś Mirosław , Gianaroli Luca , Koel Mariann , Peters Maire , Salumets Andres , Krjutškov Kaarel , Palta Priit 
Published: August 2023

AbstractExpressional profiling of the endometrium enables the personalised timing of the window of implantation (WOI). This study presents and evaluates a novel analytical pipeline based on a TAC-seq (Targeted Allele Counting by sequencing) method for endometrial dating. The expressional profiles were clustered, and differential expression analysis was performed on the model development group, using 63 endometrial biopsies spanning over proliferative (PE, n = 18), early-secretory (ESE, n = 18), mid-secretory (MSE, n = 17) and late-secretory (LSE, n = 10) endometrial phases of the natural cycle. A quantitative predictor model was trained on the development group and validated on sequenced samples from healthy women, consisting of 52 paired samples taken from ESE and MSE phases and five LSE phase samples from 31 individuals. Finally, the developed test was applied to 44 MSE phase samples from a study group of patients diagnosed with recurrent implantation failure (RIF). In validation samples (n = 57), we detected displaced WOI in 1.8% of the samples from fertile women. In the RIF study group, we detected a significantly higher proportion of the samples with shifted WOI than in the validation set of samples from fertile women, 15.9% and 1.8% (p = 0.012), respectively. The developed model was evaluated with an average cross-validation accuracy of 98.8% and an accuracy of 98.2% in the validation group. The developed beREADY screening model enables sensitive and dynamic detection of selected transcriptome biomarkers, providing a quantitative and accurate prediction of endometrial receptivity status.
Experimental study on anisotropic unloading mechanical behavior of bedded sandstone
Authors: Fang Jingcheng , Deng Huafeng , Wang Wei , Li Jianlin , Assefa Eleyas 
Published: August 2023

AbstractSandstone is a kind of bedded rock mass commonly used in engineering. The deformation and strength of bedded sandstone impose some problems during excavation. In this study, triaxial unloading tests were conducted on rock specimens (considering seven different bedding angles (β)). The results revealed the following key points: (1) At a constant confining pressure, the elastic modulus was gradually increasing when the bedding angle increased. Furthermore, after initial decreasing, the deformation modulus was increased and had a U-shaped distribution. (2) During the unloading of the axial compression, the rate of axial strain variations was initially increased and then decreased while the bedding angle increased (it has exhibited an inverted U-shaped distribution). However, the peak strength, cohesion, and angle of internal friction of rock specimens showed an initial decreasing and then increasing trend. (3) During the loading and unloading stages, the confining pressure reduces the anisotropy of bedded rock masses. (4) In the triaxial unloading test, the failure of rock specimens can be classified into four modes. When there was a large intersection angle between the bedding plane and the unloading direction, failure developed at the bedding planes.
A novel binding site between the voltage-dependent calcium channel CaV1.2 subunit and CaVβ2 subunit discovered using a new analysis method for protein–protein interactions
Authors: Murakami Agnieszka M. , Nagatomo Katsuhiro , Miyoshi Ichro , Itagaki Shirou , Niwa Yasutaka , Murakami Manabu 
Published: August 2023

AbstractWe developed a new method to analyze protein–protein interactions using a dual-inducible prokaryotic expression system. To evaluate protein–protein binding, a chimeric fusion toxin gene was constructed using a DNase-treated short DNA fragment (epitope library) and CcdB, which encodes a DNA topoisomerase II toxin. Protein–protein interactions would affect toxin activity, resulting in colony formation. Using this novel system, we found a new binding site in the voltage-dependent calcium channel α1 subunit (CaV1.2) for the voltage-dependent calcium channel β2 subunit. Prokaryotic expression screening of the β2 subunit using an epitope library of CaV1.2 resulted in two overlapping clones of the C-terminal sequence of CaV1.2. In vitro overlay and immunoprecipitation analyses revealed preferential binding of the C-terminal sequences of CaV1.2 and β2.
Change of temperature field around different drainage structures in cold region tunnel based on model testing
Authors: Zhu Jinhuan , Zhang Xuelan , Liu Lanjun , Tan Lizhen , Liu Lulu 
Published: August 2023

AbstractImproper layout of drainage structures and inadequate insulation measures in cold tunnels can result in varying degrees of frost formation during operation. This study focuses on the Hongtoushan highway tunnel as an example, where the distribution characteristics of the temperature field around the lower drainage structure under different arrangements are investigated through indoor model testing. The results indicate that there is a significant hysteresis phenomenon in temperature changes across the cross-section as the burial depth increases. With an increase in the burial depth of the surrounding rock, the hysteresis time of temperature changes gradually elongates. The temperature variation pattern can be approximated by a cubic polynomial. In the vertical section, as the tunnel depth increases, the temperature of the surrounding rock in the lower part of the tunnel gradually rises while the amplitude of temperature change diminishes. The temperature near the centerline is relatively lower compared to the sides, where the temperature gradually increases moving away from the centerline.
Self-serving reward and punishment: evidence from the laboratory
Authors: Chen Jianing , Lian Zeng , Zheng Jie 
Published: August 2023

AbstractReward for altruism and punishment for selfishness are crucial components for the maintenance of society. Past studies have provided strong evidence that people are willing to incur costs to punish selfish behaviors and to reward altruistic behaviors, but how their willingness to do so depends on their relationship with the individuals conducting the anti-social or pro-social behaviors is much less explored. To probe into this question, we devised a three-stage experiment that combined a revised dictator game and third-party reward or punishment. We employed two payoff frameworks, alignment and conflict, and analyzed how third-party’s willingness to reward and punish differed when their interests were either aligned or in conflict with the first-party under observation. We found that due to considerations for personal interests, third-party’s reward and punishment levels deviated from what was deemed “legitimate” by society, that is, the level of reward and punishment that enhances society’s intrinsic motivations to comply with social norms and act pro-socially. When an anti-social behavior was observed, third-party punished less severely under the alignment framework than under the conflict framework; when a pro-social behavior was observed, third-party demonstrated self-serving reward under the alignment framework, but they rewarded altruistically under the conflict framework. These findings provided evidence for third-party’s self-serving reward and punishment.
ABCD2 score has equivalent stroke risk prediction for anterior circulation TIA and posterior circulation TIA
Authors: Cao Shuang , Zhao Lu , Pei Lulu , Gao Yuan , Fang Hui , Liu Kai , Liu Hao , Yang Shuxiang , Sun Shilei , Wu Jun , Song Bo , Xu Yuming 
Published: August 2023

AbstractTransient ischemic attack (TIA) was clinically divided into anterior circulation (AC) or posterior circulation (PC). Previous study reported that ABCD2 score could predict the stroke risk after AC-TIA but might have limitation for PC-TIA. We aimed to classify TIA depending on neuroimaging and assess the value of ABCD2 score for predicting stroke risk in different territories. Research data was from TIA database of the First Affiliated Hospital of Zhengzhou University. TIA patients with acute infarction on diffuse weighted imaging [that is, transient symptoms with infarction (TSI)] were divided into anterior and posterior circulation groups according to the location of infarction. The outcome was recurrent stroke within 7 and 90 days. The predictive power of ABCD2 score was determined using area under receiver operator characteristic curve (AUC) analyses. Overall, 382 AC-TSI and 112 PC-TSI patients were included. There were 38 (9.9%) AC-TSI patients and 11(9.8%) PC-TSI patients who had recurrent stroke at 7 days, and 66 (17.3%) AC-TSI patients and 19 (17.0%) PC-TSI patients who had recurrent stroke within 90 days. At 7 days, the AUC for ABCD2 score was 0.637 (95% confidence interval CI 0.554–0.720) in anterior circulation and 0.683 (95% CI 0.522–0.845) in posterior circulation. The C statistics for ABCD2 score in the two groups were not statistically significant (Z =  − 0.499; P = 0.62). Similar result was found when the outcome time-point was set at 90 days. ABCD2 score could predict the short-term risk of recurrent stroke after AC-TSI and PC-TSI, and had similar predictive abilities for AC-TSI and PC-TSI.
Integrated geotechnical and mineralogical evaluation of the subgrade of some failed pavements along Enugu-Onitsha expressway Southeastern Nigeria
Authors: Ukor Kelechi Paulinus , Igwe Ogbonnaya , Onwuka Obialo Solomon , Nzereogu Stella Kosi , Eze Kelechi Nnaji , Echezona Pearl Elochukwu 
Published: August 2023

AbstractThis research is focused on the constant pavement failure in parts of the Enugu-Onitsha expressway. The failed portions are constructed on the natural subgrade known to be the Shale of Enugu and Mamu formations southeastern Nigeria. Five samples each were obtained from the formations and were subjected to geotechnical test, mineralogical analysis, scanning electron microscopy (SEM) and, statistical analysis. The outcome of the geotechnical test revealed that the liquid limits (LL) are of high plasticity with values ranging from 57.69 to 62.61% and 53.57 to 56.24%, plasticity index (PI) values ranging from 20.32 to 24.37% and 13.37 to 15.32%, Slake durability index (SDI) values ranging from 0.55 to 31.8% and 63.4 to 71.6%, for Enugu and Mamu Shales respectively. From the Unconfined compressive strength (UCS) test, the cohesion (C) values ranged from 37.36 to 43.89 kPa and 24.22 to 27.07 kPa, soaked California bearing ratio (CBR) values ranged from 1.03 to 1.22% and 0.90 to 1.60% for Enugu and Mamu Shales, respectively. The test results are not in the range of specification of the Nigerian Federal Ministry of Works and Housing (FMWH) Nigeria standard for pavement construction. X-ray diffraction (XRD) analysis revealed major minerals to be quartz and kaolinite. Moreover, kaolinite disperses and migrates when moist hence geotechnical failure. Images from Scanning electron microscopy revealed the presence of micropores and fractures which can be used as an inference to the geotechnical test results. Statistical analysis of key geotechnical parameters such as SDI, PI, C, and CBR revealed a strong correlation either positively or negatively with each other. The evaluated results pointed out that the underlined natural subgrade is poor for pavement construction, and thus requires improvement.
Clonal dynamics and Stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma
Authors: Zhao Ruiying , Xu Yunhua , Chen Yedan , Zhang Jiajun , Teng Fei , Liao Sha , Chen Shengnan , Wu Qian , Xiang Chan , Pang Jiaohui , Shang Zhanxian , Zhao Jikai , Bao Hairong , Bao Hua , Shao Yang , Lu Shun , Han Yuchen 
Published: August 2023

AbstractThe genomic origin and development of the biphasic lung adenosquamous carcinoma (ASC) remain inconclusive. Here, we derived potential evolutionary trajectory of ASC through whole-exome sequencing, Stereo-seq, and patient-derived xenografts. We showed that EGFR and MET activating mutations were the main drivers in ASCs. Phylogenetically, these drivers and passenger mutations found in both components were trunk clonal events, confirming monoclonal origination. Comparison of multiple lesions also revealed closer genomic distance between lymph node metastases and the ASC component with the same phenotype. However, as mutational signatures of EGFR-positive lung squamous carcinomas (LUSCs) were more comparable to EGFR-positive ASCs than to wild-type LUSCs, we postulated different origination of these LUSCs, with ASC being the potential intermediate state of driver-positive LUSCs. Spatial transcriptomic profiling inferred transformation from adenocarcinoma to squamous cell carcinoma, which was then histologically captured in vivo. Together, our results explained the development of ASC and provided insights into future clinical decisions.
Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells
Authors: Sarma Sudeep , Catella Carly M. , San Pedro Ellyce T. , Xiao Xingqing , Durmusoglu Deniz , Menegatti Stefano , Crook Nathan , Magness Scott T. , Hall Carol K. 
Published: August 2023

AbstractInfections by Clostridioides difficile, a bacterium that targets the large intestine (colon), impact a large number of people worldwide. Bacterial colonization is mediated by two exotoxins: toxins A and B. Short peptides that can be delivered to the gut and inhibit the biocatalytic activity of these toxins represent a promising therapeutic strategy to prevent and treat C. diff. infection. We describe an approach that combines a Peptide Binding Design (PepBD) algorithm, molecular-level simulations, a rapid screening assay to evaluate peptide:toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells. One peptide, SA1, is found to block TcdA toxicity in primary-derived human colon (large intestinal) epithelial cells. SA1 binds TcdA with a KD of 56.1 ± 29.8 nM as measured by surface plasmon resonance (SPR).
Quantum reference frames for an indefinite metric
Authors: de la Hamette Anne-Catherine , Kabel Viktoria , Castro-Ruiz Esteban , Brukner Časlav 
Published: August 2023

AbstractThe current theories of quantum physics and general relativity on their own do not allow us to study situations in which the gravitational source is quantum. Here, we propose a strategy to determine the dynamics of objects in the presence of mass configurations in superposition, and hence an indefinite spacetime metric, using quantum reference frame (QRF) transformations. Specifically, we show that, as long as the mass configurations in the different branches are related via relative-distance-preserving transformations, one can use an extension of the current framework of QRFs to change to a frame in which the mass configuration becomes definite. Assuming covariance of dynamical laws under quantum coordinate transformations, this allows to use known physics to determine the dynamics. We apply this procedure to find the motion of a probe particle and the behavior of clocks near the mass configuration, and thus find the time dilation caused by a gravitating object in superposition. Comparison with other models shows that semi-classical gravity and gravitational collapse models do not obey the covariance of dynamical laws under quantum coordinate transformations.