bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable machine learning for maximum corrosion depth and influence factor analysis
Authors: Song Yuhui , Wang Qinying , Zhang Xingshou , Dong Lijin , Bai Shulin , Zeng Dezhi , Zhang Zhi , Zhang Huali , Xi Yuchen 
Published: February 2023

AbstractWe have employed interpretable methods to uncover the black-box model of the machine learning (ML) for predicting the maximum pitting depth (dmax) of oil and gas pipelines. Ensemble learning (EL) is found to have higher accuracy compared with several classical ML models, and the determination coefficient of the adaptive boosting (AdaBoost) model reaches 0.96 after optimizing the features and hyperparameters. In this work, the running framework of the model was clearly displayed by visualization tool, and Shapley Additive exPlanations (SHAP) values were used to visually interpret the model locally and globally to help understand the predictive logic and the contribution of features. Furthermore, the accumulated local effect (ALE) successfully explains how the features affect the corrosion depth and interact with one another.
Polarized branched Actin modulates cortical mechanics to produce unequal-size daughters during asymmetric division
Authors: Daeden Alicia , Mietke Alexander , Derivery Emmanuel , Seum Carole , Jülicher Frank , Gonzalez-Gaitan Marcos 
Published: February 2023

AbstractThe control of cell shape during cytokinesis requires a precise regulation of mechanical properties of the cell cortex. Only few studies have addressed the mechanisms underlying the robust production of unequal-sized daughters during asymmetric cell division. Here we report that unequal daughter-cell sizes resulting from asymmetric sensory organ precursor divisions in Drosophila are controlled by the relative amount of cortical branched Actin between the two cell poles. We demonstrate this by mistargeting the machinery for branched Actin dynamics using nanobodies and optogenetics. We can thereby engineer the cell shape with temporal precision and thus the daughter-cell size at different stages of cytokinesis. Most strikingly, inverting cortical Actin asymmetry causes an inversion of daughter-cell sizes. Our findings uncover the physical mechanism by which the sensory organ precursor mother cell controls relative daughter-cell size: polarized cortical Actin modulates the cortical bending rigidity to set the cell surface curvature, stabilize the division and ultimately lead to unequal daughter-cell size.
Universal logic with encoded spin qubits in silicon
Authors: Weinstein Aaron J. , Reed Matthew D. , Jones Aaron M. , Andrews Reed W. , Barnes David , Blumoff Jacob Z. , Euliss Larken E. , Eng Kevin , Fong Bryan H. , Ha Sieu D. , Hulbert Daniel R. , Jackson Clayton A. C. , Jura Michael , Keating Tyler E. , Kerckhoff Joseph , Kiselev Andrey A. , Matten Justine , Sabbir Golam , Smith Aaron , Wright Jeffrey , Rakher Matthew T. , Ladd Thaddeus D. , Borselli Matthew G. 
Published: February 2023

AbstractQuantum computation features known examples of hardware acceleration for certain problems, but is challenging to realize because of its susceptibility to small errors from noise or imperfect control. The principles of fault tolerance may enable computational acceleration with imperfect hardware, but they place strict requirements on the character and correlation of errors1. For many qubit technologies2–21, some challenges to achieving fault tolerance can be traced to correlated errors arising from the need to control qubits by injecting microwave energy matching qubit resonances. Here we demonstrate an alternative approach to quantum computation that uses energy-degenerate encoded qubit states controlled by nearest-neighbour contact interactions that partially swap the spin states of electrons with those of their neighbours. Calibrated sequences of such partial swaps, implemented using only voltage pulses, allow universal quantum control while bypassing microwave-associated correlated error sources1,22–28. We use an array of six 28Si/SiGe quantum dots, built using a platform that is capable of extending in two dimensions following processes used in conventional microelectronics29. We quantify the operational fidelity of universal control of two encoded qubits using interleaved randomized benchmarking30, finding a fidelity of 96.3% ± 0.7% for encoded controlled NOT operations and 99.3% ± 0.5% for encoded SWAP. The quantum coherence offered by enriched silicon5–9,16,18,20,22,27,29,31–37, the all-electrical and low-crosstalk-control of partial swap operations1,22–28 and the configurable insensitivity of our encoding to certain error sources28,33,34,38 all combine to offer a strong pathway towards scalable fault tolerance and computational advantage.
Simultaneous sequencing of genetic and epigenetic bases in DNA
Authors: Füllgrabe Jens , Gosal Walraj S. , Creed Páidí , Liu Sidong , Lumby Casper K. , Morley David J. , Ost Tobias W. B. , Vilella Albert J. , Yu Shirong , Bignell Helen , Burns Philippa , Charlesworth Tom , Fu Beiyuan , Fordham Howerd , Harding Nicolas J. , Gandelman Olga , Golder Paula , Hodson Christopher , Li Mengjie , Lila Marjana , Liu Yang , Mason Joanne , Mellad Jason , Monahan Jack M. , Nentwich Oliver , Palmer Alexandra , Steward Michael , Taipale Minna , Vandomme Audrey , San-Bento Rita Santo , Singhal Ankita , Vivian Julia , Wójtowicz Natalia , Williams Nathan , Walker Nicolas J. , Wong Nicola C. H. , Yalloway Gary N. , Holbrook Joanna D. , Balasubramanian Shankar 
Published: February 2023

AbstractDNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Methods widely used to detect epigenetic DNA bases fail to capture common C-to-T mutations or distinguish 5-methylcytosine from 5-hydroxymethylcytosine. We present a single base-resolution sequencing methodology that sequences complete genetics and the two most common cytosine modifications in a single workflow. DNA is copied and bases are enzymatically converted. Coupled decoding of bases across the original and copy strand provides a phased digital readout. Methods are demonstrated on human genomic DNA and cell-free DNA from a blood sample of a patient with cancer. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. Simultaneous, phased reading of genetic and epigenetic bases provides a more complete picture of the information stored in genomes and has applications throughout biomedicine.
SpliceVault predicts the precise nature of variant-associated mis-splicing
Authors: Dawes Ruebena , Bournazos Adam M. , Bryen Samantha J. , Bommireddipalli Shobhana , Marchant Rhett G. , Joshi Himanshu , Cooper Sandra T. 
Published: February 2023

AbstractEven for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.
Potential roles of acyl homoserine lactones (AHLs) in nitrifying bacteria survival under certain adverse circumstances
Authors: Zeng Xiangguo , Hu Huizhi 
Published: February 2023

AbstractPotential roles of quorum sensing (QS) in nitrifying bacteria activity and ecology, particularly under adverse circumstances have been rarely reported. Herein, eight lab-scale nitrification sequencing batch reactors, with or without adding acyl homoserine lactones (AHLs) were operated under adverse circumstances respectively. The results indicated that the introduction of AHLs significantly enhanced the nitrogen removal efficiency in the presence of nitrification inhibitors (dicyandiamide, DCD), accelerated the low temperature (10 °C) group into stable stage, and improved the utilization efficiency of AHLs in these two groups. Community analysis and qPCR further confirmed that AHLs significantly increased the abundance of nitrifying bacteria in low temperature group and DCD group, especially AOB. For normal condition (28 °C, pH = 8) or low pH level (5.5), however, the AHLs had no significant effect. Canonical correspondence analysis showed that nitrifying bacteria positively responded to AHLs, indicating that adding AHLs was an effective strategy to regulate nitrification process. However, under acid conditions, the effect of this regulatory mechanism was not significant, indicating that the influence of pH on the system was greater than that of AHLs. This study demonstrated that exogenous AHLs could enhance the competitiveness of nitrifying bacteria to utilize more resource and occupy space under some adverse environmental conditions.
Quantifying human performance in chess
Authors: Chowdhary Sandeep , Iacopini Iacopo , Battiston Federico 
Published: February 2023

AbstractFrom sports to science, the recent availability of large-scale data has allowed to gain insights on the drivers of human innovation and success in a variety of domains. Here we quantify human performance in the popular game of chess by leveraging a very large dataset comprising of over 120 million games between almost 1 million players. We find that individuals encounter hot streaks of repeated success, longer for beginners than for expert players, and even longer cold streaks of unsatisfying performance. Skilled players can be distinguished from the others based on their gaming behaviour. Differences appear from the very first moves of the game, with experts tending to specialize and repeat the same openings while beginners explore and diversify more. However, experts experience a broader response repertoire, and display a deeper understanding of different variations within the same line. Over time, the opening diversity of a player tends to decrease, hinting at the development of individual playing styles. Nevertheless, we find that players are often not able to recognize their most successful openings. Overall, our work contributes to quantifying human performance in competitive settings, providing a first large-scale quantitative analysis of individual careers in chess, helping unveil the determinants separating elite from beginner performance.
Reduced cardiovascular reserve capacity in long-term allogeneic stem cell transplant survivors
Authors: Dillon Hayley T. , Foulkes Stephen , Horne-Okano Yuki A. , Kliman David , Dunstan David W. , Daly Robin M. , Fraser Steve F. , Avery Sharon , Kingwell Bronwyn A. , La Gerche Andre , Howden Erin J. 
Published: February 2023

AbstractPremature cardiovascular mortality is increased in long-term allogeneic stem cell transplant (allo-SCT) survivors, but little information exists regarding subclinical cardiovascular dysfunction in this population. We compared peak oxygen uptake ($${{\dot{\mathrm V}}}$$

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O2peak), a prognostic cardiovascular marker, and its determinants between long-term allo-SCT survivors and non-cancer controls. Fourteen allo-SCT survivors (mean ± SD, 44 ± 15 years, 50% male, median time since allo-SCT: 6.5 years [range 2–20]) and 14 age- and sex-matched controls (46 ± 13 years, 50% male) underwent cardiopulmonary exercise testing to quantify $${{\dot{\mathrm V}}}$$

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O2peak. Resting echocardiography (left-ventricular ejection fraction and strain), exercise cardiac MRI (peak cardiac and stroke volume index [CIpeak, SVIpeak]), biochemistry (hemoglobin, troponin-I, B-natriuretic peptide), dual-energy x-ray absorptiometry (lean [LM] and fat [FM] mass, percent body fat [%BF]) and Fick-principal calculation (arteriovenous oxygen difference) were also performed. Survivors exhibited impaired $${{\dot{\mathrm V}}}$$

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O2peak as compared with controls (25.9 ± 5.1 vs. 33.7 ± 6.5 ml kg−1 min−1, p = 0.002), which coincided with reduced CIpeak (6.6 ± 0.8 vs. 8.6 ± 1.9 L min−1 m−2; p = 0.001) secondary to reduced SVIpeak (48 ± 4 vs. 61 ± 8 ml m−2; p < 0.001) rather than chronotropic impairment, and higher %BF (difference, 7.9%, p = 0.007) due to greater FM (5.8 kg; p = 0.069) and lower LM (4.3 kg, p = 0.25). All other measures were similar between groups. Despite comparable resting cardiac function and biomarker profiles, survivors exhibited reduced $${{\dot{\mathrm V}}}$$

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O2peak and exercise cardiac function and increased %BF relative to controls. These results highlight potential therapeutic avenues and the utility of exercise-based cardiovascular assessment in unmasking cardiovascular dysfunction in allo-SCT survivors.
In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration
Authors: Ganne Akshatha , Balasubramaniam Meenakshisundaram , Ayyadevara Haarika , Kiaei Lily , Shmookler Reis Robert J. , Varughese Kottayil I. , Kiaei Mahmoud 
Published: February 2023

AbstractAmyotrophic lateral sclerosis (ALS) is an inexorably progressive and degenerative disorder of motor neurons with no currently-known cure. Studies to determine the mechanism of neurotoxicity and the impact of ALS-linked mutations (SOD1, FUS, TARDP, C9ORF72, PFN1, TUBA4A and others) have greatly expanded our knowledge of ALS disease mechanisms and have helped to identify potential targets for ALS therapy. Cellular pathologies (e.g., aggregation of mutant forms of SOD1, TDP43, FUS, Ubiqulin2, PFN1, and C9ORF72), mitochondrial dysfunction, neuroinflammation, and oxidative damage are major pathways implicated in ALS. Nevertheless, the selective vulnerability of motor neurons remains unexplained. The importance of tubulins for long-axon infrastructure, and the special morphology and function of motor neurons, underscore the central role of the cytoskeleton. The recent linkage of mutations to the tubulin α chain, TUBA4A, to familial and sporadic cases of ALS provides a new investigative opportunity to shed light on both mechanisms of ALS and the vulnerability of motor neurons. In the current study we investigate TUBA4A, a structural microtubule protein with mutations causal to familial ALS, using molecular-dynamic (MD) modeling of protein structure to predict the effects of each mutation and its overall impact on GTP binding, chain stability, tubulin assembly, and aggregation propensity. These studies predict that each of the reported mutations will cause notable structural changes to the TUBA4A (α chain) tertiary protein structure, adversely affecting its physical properties and functions. Molecular docking and MD simulations indicate certain α chain mutations (e.g. K430N, R215C, and W407X) may cause structural deviations that impair GTP binding, and plausibly prevent or destabilize tubulin polymerization. Furthermore, several mutations (including R320C and K430N) confer a significant increase in predicted aggregation propensity of TUBA4A mutants relative to wild-type. Taken together, these in silico modeling studies predict structural perturbations and disruption of GTP binding, culminating in failure to form a stable tubulin heterocomplex, which may furnish an important pathogenic mechanism to trigger motor neuron degeneration in ALS.
Joint use of location and acceleration data reveals influences on transitions among habitats in wintering birds
Authors: VonBank Jay A. , Schafer Toryn L. J. , Cunningham Stephanie A. , Weegman Mitch D. , Link Paul T. , Kraai Kevin J. , Wikle Christopher K. , Collins Daniel P. , Cao Lei , Ballard Bart M. 
Published: February 2023

AbstractQuantifying relationships between animal behavior and habitat use is essential to understanding animal decision-making. High-resolution location and acceleration data allows unprecedented insights into animal movement and behavior. These data types allow researchers to study the complex linkages between behavioral plasticity and habitat distribution. We used a novel Markov model in a Bayesian framework to quantify the influence of behavioral state frequencies and environmental variables on transitions among landcover types through joint use of location and tri-axial accelerometer data. Data were collected from 56 greater white-fronted geese (Anser albifrons frontalis) across seven ecologically distinct winter regions over two years in midcontinent North America. We showed that goose decision-making varied across landcover types, ecoregions, and abiotic conditions, and was influenced by behavior. We found that time spent in specific behaviors explained variation in the probability of transitioning among habitats, revealing unique behavioral responses from geese among different habitats. Combining GPS and acceleration data allowed unique study of potential influences of an ongoing large-scale range shift in the wintering distribution of a migratory bird across midcontinent North America. We anticipate that behavioral adaptations among variable landscapes is a likely mechanism explaining goose use of highly variable ecosystems during winter in ways which optimize their persistence.
Introduction of a cascaded segmentation pipeline for parametric T1 mapping in cardiovascular magnetic resonance to improve segmentation performance
Authors: Viezzer Darian , Hadler Thomas , Ammann Clemens , Blaszczyk Edyta , Fenski Maximilian , Grandy Thomas Hiroshi , Wetzl Jens , Lange Steffen , Schulz-Menger Jeanette 
Published: February 2023

AbstractThe manual and often time-consuming segmentation of the myocardium in cardiovascular magnetic resonance is increasingly automated using convolutional neural networks (CNNs). This study proposes a cascaded segmentation (CASEG) approach to improve automatic image segmentation quality. First, an object detection algorithm predicts a bounding box (BB) for the left ventricular myocardium whose 1.5 times enlargement defines the region of interest (ROI). Then, the ROI image section is fed into a U-Net based segmentation. Two CASEG variants were evaluated: one using the ROI cropped image solely (cropU) and the other using a 2-channel-image additionally containing the original BB image section (crinU). Both were compared to a classical U-Net segmentation (refU). All networks share the same hyperparameters and were tested on basal and midventricular slices of native and contrast enhanced (CE) MOLLI T1 maps. Dice Similarity Coefficient improved significantly (p < 0.05) in cropU and crinU compared to refU (81.06%, 81.22%, 72.79% for native and 80.70%, 79.18%, 71.41% for CE data), while no significant improvement (p < 0.05) was achieved in the mean absolute error of the T1 time (11.94 ms, 12.45 ms, 14.22 ms for native and 5.32 ms, 6.07 ms, 5.89 ms for CE data). In conclusion, CASEG provides an improved geometric concordance but needs further improvement in the quantitative outcome.
Plant miRNA osa-miR172d-5p suppressed lung fibrosis by targeting Tab1
Authors: Kumazoe Motofumi , Ogawa Fumiyo , Hikida Ai , Shimada Yu , Yoshitomi Ren , Watanabe Ryoya , Onda Hiroaki , Fujimura Yoshinori , Tachibana Hirofumi 
Published: February 2023

AbstractLung fibrosis, including idiopathic pulmonary fibrosis, is an intractable disease accompanied by an irreversible dysfunction in the respiratory system. Its pathogenesis involves the transforming growth factorβ (TGFβ)-induced overproduction of the extracellular matrix from fibroblasts; however, limited countermeasures have been established. In this study, we identified osa-miR172d-5p, a plant-derived microRNA (miR), as a potent anti-fibrotic miR. In silico analysis followed by an in vitro assay based on human lung fibroblasts demonstrated that osa-miR172d-5p suppressed the gene expression of TGF-β activated kinase 1 (MAP3K7) binding protein 1 (Tab1). It also suppressed the TGFβ-induced fibrotic gene expression in human lung fibroblasts. To assess the anti-fibrotic effect of osa-miR172d-5p, we established bleomycin-induced lung fibrosis models to demonstrate that osa-miR172d-5p ameliorated lung fibrosis. Moreover, it suppressed Tab1 expression in the lung tissues of bleomycin-treated mice. In conclusion, osa-miR172d-5p could be a potent candidate for the treatment of lung fibrosis, including idiopathic pulmonary fibrosis.
Association of polysialic acid serum levels with schizophrenia spectrum and bipolar disorder-related structural brain changes and hospitalization
Authors: Müller-Miny Louisa , Thiel Katharina , Meinert Susanne , Hahn Tim , Kircher Tilo , Nenadić Igor , Krug Axel , Hufschmidt Felix , Liao Huan , Neumann Harald , Dannlowski Udo , Lünemann Jan D. 
Published: February 2023

AbstractExpression of polysialic acid (polySia) in the adult brain is enriched in areas of continuous neurogenesis and plasticity such as the hippocampus. Genome-wide association studies identified variants of glycosylation enzyme-encoding genes, required for the generation of polySia, to be associated with the development of schizophrenia and bipolar disorder. Here, we report that serum levels of polySia are increased in patients with schizophrenia spectrum disorder compared to patients with major depressive disorders or demographically matched healthy controls. Furthermore, elevated polySia serum levels are associated with structural hippocampal gray matter decline in schizophrenia spectrum and bipolar disorder. In patients with schizophrenia spectrum disorder, polySia serum levels correlate with the number, duration of disease-related hospitalizations, early retirement and medical leave as estimators of detrimental long-term disease trajectories. Our data show that polySia serum levels are linked to structural hippocampal brain changes in schizophrenia spectrum and bipolar disorders, and suggest a contribution of polySia to the pathophysiology of these diseases.
A numerical study towards shape memory alloys application in orthotic management of pediatric knee lateral deviations
Authors: Alonso M. G. , Yawny A. , Bertolino G. 
Published: February 2023

AbstractExerting a constant load would likely improve orthosis effectiveness in treating knee lateral deviations during childhood and early adolescence. Shape memory alloys are potential candidates for such applications due to their so called pseudoelastic effect. The present study aims to quantitatively define the applicable mechanical loads, in order to reduce treatment duration while avoiding tissular damage and patient discomfort. This is essential for performing a more efficient design of correction devices. We use a patient-specific finite elements model of a pediatric knee to determine safe loading levels. The achievable correction rates are estimated using a stochastic three-dimensional growth model. Results are compared against those obtained for a mechanical stimulus decreasing in proportion to the achieved correction, emulating the behavior of conventional orthoses. A constant flexor moment of 1.1 Nm is estimated to change femorotibial angle at a rate of (7.4 ± 4.6) deg/year (mean ± std). This rate is similar to the achieved by more invasive growth modulation methods, and represents an improvement in the order of 25% in the necessary time for reducing deformities of (10 ± 5) deg by half, as compared with conventional orthoses.