bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotype–Phenotype Correlations for ATX‐TBP (SCA17): MDSGene Systematic Review
Authors: Rossi Malco , Hamed Moath , Rodríguez‐Antigüedad Jon , Cornejo‐Olivas Mario , Breza Marianthi , Lohmann Katja , Klein Christine , Rajalingam Rajasumi , Marras Connie , van de Warrenburg Bart P. 
Published: November 2022

ABSTRACTSpinocerebellar ataxia type 17 or ATX‐TBP is a CAG/CAA repeat expansion disorder characterized by marked clinical heterogeneity. Reports of affected carriers with subthreshold repeat expansions and of patients with Parkinson's disease (PD) with expanded repeats have cast doubt on the established cutoff values of the expansions and the phenotypic spectrum of this disorder. The objective of this systematic review was to explore the genotype–phenotype relationships for repeat expansions in TBP to delineate the ATX‐TBP phenotype and reevaluate the pathological range of repeat expansions. The International Parkinson and Movement Disorder Society Genetic Mutation Database (MDSGene) standardized data extraction protocol was followed. Clinically affected carriers of reported ATX‐TBP expansions were included. Publications that contained repeat sizes in screened cohorts of patients with PD and/or healthy individuals were included for a separate evaluation of cutoff values. Phenotypic and genotypic data for 346 ATX‐TBP patients were curated. Overall, 97.7% of the patients had ≥41 repeats, while 99.6% of patients with PD and 99.9% of healthy individuals had ≤42 repeats, with a gray zone of reduced penetrance between 41 and 45 repeats. Pure parkinsonism was more common in ATX‐TBP patients with 41 to 45 repeats than in the group with ≥46 repeats, which conversely more often presented with a complex phenotype with mixed movement disorders. An updated genotype–phenotype assessment for ATX‐TBP is provided, and new repeat expansion cutoff values of reduced penetrance (41–45 expanded repeats) and full penetrance (46–66 expanded repeats) are proposed. These adjusted cutoff values will have diagnostic and counseling implications and may guide future clinical trial protocol. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
FSDscore: An Effective Target‐focused Scoring Criterion for Virtual Screening
Authors: Hua Yi , Huang Dingfang , Liang Li , Qian Xu , Dai Xiaowen , Xu Yuan , Qiu Haodi , Lu Tao , Liu Haichun , Chen Yadong , Zhang Yanmin 
Published: November 2022

AbstractImproving screening efficiency is one of the most challenging tasks of virtual screening (VS). In this work, we propose an effective target‐focused scoring criterion for VS and apply it to the screening of a specific target scaffold replacement library constructed by enumeration of suitable substitution fragments and R‐groups of known ligands. This criterion is based on both ligand‐ and structure‐based scoring methods, which includes feature maps, 3D shape similarity, and the pairwise distance information between proteins and ligands (FSDscore). It is precisely due to the hybrid advantages of ligand‐ and structure‐based approaches that FSDscore performs far better on the validation dataset than other scoring methods. We apply FSDscore to the VS of different kinase targets, MERTK (Mer tyrosine kinase) and ABL1 (tyrosine‐protein kinase ABL1) in order to avoid occasionality. Finally, a VS case study shows the potential and effectiveness of our scoring criterion in drug discovery and molecular dynamics simulation further verifies its powerful ability.
Parameter estimation for WMTI‐Watson model of white matter using encoder–decoder recurrent neural network
Authors: Diao Yujian , Jelescu Ileana 
Published: November 2022

PurposeBiophysical modeling of the diffusion MRI (dMRI) signal provides estimates of specific microstructural tissue properties. Although non‐linear least squares (NLLS) is the most widespread fitting method, it suffers from local minima and high computational cost. Deep learning approaches are steadily replacing NLLS, but come with the limitation that the model needs to be retrained for each acquisition protocol and noise level. In this study, a novel fitting approach was proposed based on the encoder–decoder recurrent neural network (RNN) to accelerate model estimation with good generalization to various datasets.MethodsThe white matter tract integrity (WMTI)‐Watson model as an implementation of the Standard Model of diffusion in white matter derives its parameters indirectly from the diffusion and kurtosis tensors (DKI). The RNN‐based solver, which estimates the WMTI‐Watson model from DKI, is therefore more readily translatable to various data, irrespective of acquisition protocols as long as the DKI was pre‐computed from the signal. An embedding approach was also used to render the model insensitive to potential differences in distributions between training data and experimental data. The analytical solution, NLLS, RNN‐, and a multilayer perceptron (MLP)‐based methods were evaluated on synthetic and in vivo datasets of rat and human brain.ResultsThe proposed RNN solver showed highly reduced computation time over the analytical solution and NLLS, with similar accuracy but improved robustness, and superior generalizability over MLP.ConclusionThe RNN estimator can be easily applied to various datasets without retraining, which shows great potential for a widespread use.
In vivo T1 mapping of neonatal brain tissue at 64 mT
Authors: Padormo Francesco , Cawley Paul , Dillon Louise , Hughes Emer , Almalbis Jennifer , Robinson Joanna , Maggioni Alessandra , Botella Miguel De La Fuente , Cromb Dan , Price Anthony , Arlinghaus Lori , Pitts John , Luo Tianrui , Zhang Dingtian , Deoni Sean C. L. , Williams Steve , Malik Shaihan , O′Muircheartaigh Jonathan , Counsell Serena J. , Rutherford Mary , Arichi Tomoki , Edwards A. David , Hajnal Joseph V. 
Published: November 2022

PurposeUltralow‐field (ULF) point‐of‐care MRI systems allow image acquisition without interrupting medical provision, with neonatal clinical care being an important potential application. The ability to measure neonatal brain tissue T1 is a key enabling technology for subsequent structural image contrast optimization, as well as being a potential biomarker for brain development. Here we describe an optimized strategy for neonatal T1 mapping at ULF.MethodsExaminations were performed on a 64‐mT portable MRI system. A phantom validation experiment was performed, and a total of 33 in vivo exams were acquired from 28 neonates with postmenstrual age ranging from 31+4 to 49+0 weeks. Multiple inversion‐recovery turbo spin‐echo sequences were acquired with differing inversion and repetition times. An analysis pipeline incorporating inter‐sequence motion correction generated proton density and T1 maps. Regions of interest were placed in the cerebral deep gray matter, frontal white matter, and cerebellum. Weighted linear regression was used to predict T1 as a function of postmenstrual age.ResultsReduction of T1 with postmenstrual age is observed in all measured brain tissue; the change in T1 per week and 95% confidence intervals is given by dT1 = −21 ms/week [−25, −16] (cerebellum), dT1 = −14 ms/week [−18, −10] (deep gray matter), and dT1 = −35 ms/week [−45, −25] (white matter).ConclusionNeonatal T1 values at ULF are shorter than those previously described at standard clinical field strengths, but longer than those of adults at ULF. T1 reduces with postmenstrual age and is therefore a candidate biomarker for perinatal brain development.
Quantification of GABA concentration measured noninvasively in the human posterior cingulate cortex with 7 T ultra‐short‐TE MR spectroscopy
Authors: Genovese Guglielmo , Deelchand Dinesh K. , Terpstra Melissa , Marjańska Małgorzata 
Published: November 2022

PurposeThe increased spectral dispersion achieved at ultra‐high field permits quantification of γ‐aminobutyric acid (GABA) concentrations at ultra‐short‐TE without editing. This work investigated the influence of spectral quality and different LCModel fitting approaches on quantification of GABA. Additionally, the sensitivity with which cross‐sectional and longitudinal variations in GABA concentrations can be observed was characterized.MethodsIn ‐ vivo spectra were acquired in the posterior cingulate cortex of 10 volunteers at 7 T using a STEAM sequence. Synthetically altered spectra with different levels of GABA signals were used to investigate the reliability of GABA quantification with different LCModel fitting approaches and different realizations of SNR. The synthetically altered spectra were also used to characterize the sensitivity of GABA quantification.ResultsThe best LCModel fitting approach used stiff spline baseline, no soft constraints, and measured macromolecules in the basis set. With lower SNR, coefficients of variation increased dramatically. Longitudinal and cross‐sectional variations in GABA of 10% could be detected with 79 and 48 participants per group, respectively. However, the small cohort may bias the calculation of the coefficients of variation and of the sample size that would be needed to detect variations in GABA.ConclusionReliable quantification of normal and abnormal GABA concentrations was achieved for high quality 7 T spectra using LCModel fitting.
B1+$$ {B}_1^{+} $$‐correction of magnetization transfer saturation maps optimized for 7T postmortem MRI of the brain
Authors: Lipp Ilona , Kirilina Evgeniya , Edwards Luke J. , Pine Kerrin J. , Jäger Carsten , Gräßle Tobias ,   EBC Consortium, Weiskopf Nikolaus , Helms Gunther 
Published: November 2022

PurposeMagnetization transfer saturation () is a useful marker to probe tissue macromolecular content and myelination in the brain. The increased ‐inhomogeneity at  T and significantly larger saturation pulse flip angles which are often used for postmortem studies exceed the limits where previous correction methods are applicable. Here, we develop a calibration‐based correction model and procedure, and validate and evaluate it in postmortem 7T data of whole chimpanzee brains.TheoryThe dependence of was investigated by varying the off‐resonance saturation pulse flip angle. For the range of saturation pulse flip angles applied in typical experiments on postmortem tissue, the dependence was close to linear. A linear model with a single calibration constant is proposed to correct bias in by mapping it to the reference value of the saturation pulse flip angle.Methods was estimated voxel‐wise in five postmortem chimpanzee brains. “Individual‐based global parameters” were obtained by calculating the mean within individual specimen brains and “group‐based global parameters” by calculating the means of the individual‐based global parameters across the five brains.ResultsThe linear calibration model described the data well, though was not entirely independent of the underlying tissue and . Individual‐based correction parameters and a group‐based global correction parameter () led to visible, quantifiable reductions of ‐biases in high‐resolution maps.ConclusionThe presented model and calibration approach effectively corrects for inhomogeneities in postmortem 7T data.
Dynamics of triboelectric nanogenerators: A review
Authors: Xu Guoqiang , Li Chuanyang , Chen Chaojie , Fu Jingjing , Hou Tingting , Zi Yunlong 
Published: November 2022

AbstractTriboelectric nanogenerators (TENGs) represent a promising next‐generation renewable energy technology. TENGs have become increasingly popular for harvesting vibration energy in the environment due to their advantages of lightweight, broad range of material choices, low cost, and no pollution. However, issues such as input force irregularity, working bandwidth, efficiency calculation, and dynamic modeling hinder the use of TENGs in industrial or practical applications. In this paper, the modeling process of the dynamical system of a TENG is reviewed from the perspective of energy flow. In addition, this paper reviews the main contributions made in recent years to achieve optimized output based on springs, magnetic forces, and pendulums, and introduces different ways to increase the bandwidth of TENGs. Finally, the main problems of TENGs in the process of harvesting vibration energy are discussed. This review may serve as a practical reference for methods to convert irregular mechanical input sources into optimized output performance toward the commercialization of TENGs.
In situ stress assessment based on plastic behavior of borehole breakouts and machine learning
Authors: Garavand Aboozar , Hadavimoghaddam Fahime 
Published: November 2022

AbstractThe accurate estimation of in situ stress tensor has an inevitable role in solving problems facing the development of oil and gas fields. Two components of three, vertical stress () and minimum horizontal stress (), could be computed through direct methods. The last and most challenging component, maximum horizontal stress (), is commonly computed based on the elastic theory assumptions and shape of the borehole breakouts from well‐logging data. Due to the abundance of borehole breakouts data, methods based on the shape of breakouts are highly valued. Field observations show that such breakouts commonly occur in the weak layers, which contradict elastic assumptions. Furthermore, finding the consistent relationship between the shape of the breakouts and loading conditions remains the main issue for such approaches. The process's initiation and development until stabilization have been simulated by borehole breakout modeling considering inelastic deformation. Machine learning algorithms have been implemented to ascertain the relationship between applied in situ stress and obtained borehole breakouts. In this paper, first using the finite element method and elastoplastic model, a set of in situ stress and their corresponding shape of borehole breakouts is obtained. Then, the data set is used to train four machine learning algorithms (XGBoost, LightGBM, CatBoost, and AdaBoost) to find the relationship between the in situ stress and the shape of breakouts. Finally, employing the inversed analysis to the trained algorithms, the in situ stress is estimated from the shape of breakouts. Even though, the numerical experiments show that all four algorithms are promising for predicting the in situ stress, the XGBoost algorithm indicates more accuracy than the others.
Acrylic‐urethane/modified Rhodamine‐B eco‐friendly UV‐curable anticounterfeiting ink
Authors: Gharieh Ali , Abdollahi Amin , Sohrabi Laleh 
Published: November 2022

AbstractCounterfeiting is an ever‐growing global problem challenging companies, governments, and customers. In recent decades, as a potential remedy, anticounterfeiting technology and information security have gained a great deal of attention from academia and industry. In this work and for the first time, Rhodamine B (RhB), an efficient and enticing fluorescent material, was modified and used as a reactive stimuli‐responsive component in the formulation of an eco‐friendly ink. Additionally, a UV‐curable polyurethane dispersion (UCPUD) with zero volatile organic compound was synthesized and employed as the matrix for the fluorescent ink. The modified RhB and UCPUD were thoroughly characterized using Fourier‐transform infrared and proton nuclear magnetic resonance analyses. Exploiting the fluorescent monomer in the ink formulations could enhance the absorption intensity (λmax = 552 nm) of the prepared ink up to 7 with respect to its solution (λmax = 519 nm). The printed pattern was immediately illuminated with brilliant red‐pink fluorescence emission upon UV irradiation. It has been shown that the prepared fluorescent ink has potential applications in the encryption, security marking, and optical authentication of confidential cellulose substrates.
Cancer‐associated fibroblasts potentiate colorectal cancer progression by crosstalk of the IGF2–IGF1R and Hippo–YAP1 signaling pathways
Authors: Zhang Jinglin , Chen Bonan , Li Hui , Wang Yifei , Liu Xiaoli , Wong Kit Yee , Chan Wai Nok , Chan Aden KY , Cheung Alvin HK , Leung Kam Tong , Dong Yujuan , Pan Yi , Ke Huixing , Liang Li , Zhou Zhaocai , Xiao Jianyong , Wong Chi Chun , Wu William KK , Cheng Alfred SL , Ma Brigette BY , Yu Jun , Lo Kwok Wai , Kang Wei ,   Ka Fai To
Published: November 2022

AbstractColorectal cancer (CRC) is one of the most common cancers worldwide. The tumor microenvironment exerts crucial effects in driving CRC progression. Cancer‐associated fibroblasts (CAFs) serve as one of the most important tumor microenvironment components promoting CRC progression. This study aimed to elucidate the novel molecular mechanisms of CAF‐secreted insulin‐like growth factor (IGF) 2 in colorectal carcinogenesis. Our results indicated that IGF2 was a prominent factor upregulated in CAFs compared with normal fibroblasts. CAF‐derived conditioned media (CM) promoted tumor growth, migration, and invasion of HCT 116 and DLD‐1 cells. IGF1R expression is significantly increased in CRC, serving as a potent receptor in response to IGF2 stimulation and predicting unfavorable outcomes for CRC patients. Apart from the PI3K–AKT pathway, RNA‐seq analysis revealed that the YAP1‐target signature serves as a prominent downstream effector to mediate the oncogenic signaling of IGF2–IGF1R. By single‐cell RNA sequencing (scRNA‐seq) and immunohistochemical validation, IGF2 was found to be predominantly secreted by CAFs, whereas IGF1R was expressed mainly by cancer cells. IGF2 triggers the nuclear accumulation of YAP1 and upregulates YAP1 target signatures; however, these effects were abolished by either IGF1R knockdown or inhibition with picropodophyllin (PPP), an IGF1R inhibitor. Using CRC organoid and in vivo studies, we found that cotargeting IGF1R and YAP1 with PPP and verteporfin (VP), a YAP1 inhibitor, enhanced antitumor effects compared with PPP treatment alone. In conclusion, this study revealed a novel molecular mechanism by which CAFs promote CRC progression. The findings highlight the translational potential of the IGF2–IGF1R–YAP1 axis as a prognostic biomarker and therapeutic target for CRC. © 2022 The Pathological Society of Great Britain and Ireland.
Dynamic response of Nomex honeycomb sandwich panels subjected to aluminum foam projectile impact–An experimental study
Authors: Deng Yunfei , Hu Xiaoyu , Yang Xiaoyue , Huang Ziqiang , Wang Yuetong , Zhou Chunping 
Published: November 2022

AbstractThe impact resistance of the Nomex honeycomb sandwich structure subjected to strong dynamic loading of lightweight and deformable projectiles was studied experimentally. The deformation process and failure modes of the sandwich panels were investigated by using a first‐state gas gun to launch aluminum foam projectiles. 3D‐DIC was presented to investigate the dynamic response in terms of response rate and deflection‐profile history. And the impact resistance of three structures, namely single‐layer sandwich, rubber‐honeycomb sandwich and double‐layer sandwich, was compared in relation to the load intensity. The results show that the dynamic response process of the sandwich panel can be divided into discrete deformation stage, concentrated deformation stage，elastic stage, vibration stage and stabilization stage. As the impulse increases, the maximum deflection of the back face‐sheet continues to increase. Under the strong load of a light and deformable projectile, both rubber‐honeycomb and double‐layer honeycomb sandwich structures can effectively reduce the deflection change of the back face‐sheet and improve the load‐bearing capacity of the structure. Qualitatively analyzing the relationship between structure, loading, and performance can be carried out to provide guidance for structural design.
Enhanced mechanical, thermal, and barrier properties of poly(lactic acid)/starch composite films using gelatinized starch acetate‐functionalized montmorillonite
Authors: Chen Haifeng , Dai Chunfa , Long Yue , Zeng Shaohua , Xia Ru 
Published: November 2022

AbstractA nanostructured starch acetate–montmorillonite (SA–Mt) hybrid, where gelatinized SA was attached on the exfoliated Mt through Mt hydration expansion, ion exchange between Mt and quaternary ammonium salt, and SA intercalation, was designed and further used for reinforcing poly(lactic acid)/starch acetate (PLA/SA) composite films. Making use of the synergistic effect of SA and Mt, considerable enhancement in mechanical, thermal, and barrier properties for PLA/SA composite films was achieved. The effect of SA–Mt hybrids on structure–property relationships of PLA/SA composite films was investigated. Under an optimal loading of 7 wt% SA–Mt (SA:Mt = 1:1, w/w), the tensile strength, Young's modulus and elongation at break of SA–Mt‐filled composite films were significantly enhanced, about 104%, 73%, and 98% higher than those of PLA/SA, respectively, revealing the synergistic strengthening/toughening effect of SA and Mt; the thermal decomposition temperature and degradation activation energy of such composite film were also enhanced, implying their superior thermal stability. Moreover, the obtained PLA‐based composite films with good water/oxygen barrier performance and excellent biodegradability provide a potential for use as packaging materials.
Registration of the PI 173438/WA 8137 wheat doubled haploid mapping population
Authors: Phipps Savannah N. , Balow Kerry , Burke Adrienne B. , Stowe Anna , Smith Jared H. , Murray Timothy , Carter Arron H. 
Published: November 2022

AbstractA doubled haploid mapping population was developed from a cross between the hard red winter wheat (Triticum aestivum L. subsp. aestivum) landrace PI 173438 and WA 8137, a soft white winter wheat breeding line developed by the Washington State University winter wheat breeding program in Pullman, WA. The PI 173438/WA 8137 (Reg. no. MP‐16, NSL 543858 MAP) population consists of 437 individuals, with 358 of these individuals used to identify quantitative trait loci associated with snow mold (Typhula spp.) tolerance in PI 173438. Genotypic information was gathered on these individuals using genotype‐by‐sequencing and processed using a pipeline developed by the USDA Eastern Regional Small Grains Genotyping Laboratory. Twenty‐three linkage groups covering the whole genome with groups for the long and short arms of chromosomes 3D and 7D were constructed using 4,029 single nucleotide polymorphisms from the sequenced individuals. Quantitative trait loci associated with snow mold tolerance and snow mold recovery attributed to PI 173438 were successfully identified in this population. PI 173438 has also been used to identify other traits associated with snow mold tolerance, such as freezing tolerance and carbohydrate reserves, and has been important in research investigating dwarf and common bunt. This population may continue to expand current knowledge in these areas, and, given the landrace status of PI 173438, the population may be useful in identifying other novel traits of interest.