bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex
Authors: Lei Ying , Cheng Mengnan , Li Zihao , Zhuang Zhenkun , Wu Liang , sun Yunong , Han Lei , Huang Zhihao , Wang Yuzhou , Wang Zifei , Xu Liqin , Yuan Yue , Liu Shang , Pan Taotao , Xie Jiarui , Liu Chuanyu , Volpe Giacomo , Ward Carl , Lai Yiwei , Xu Jiangshan , Wang Mingyue , Yu Hao , Sun Haixi , Yu Qichao , Wu Liang , Wang Chunqing , Wong Chi Wai , Liu Wei , Xu Liangzhi , Wei Jingkuan , Chen Dandan , Shang Zhouchun , Li Guibo , Ma Kun , Cheng Le , Ling Fei , Tan Tao , Chen Kai , Tasic Bosiljka , Dean Michael , Ji Weizhi , Yang Huanming , Gu Ying , Esteban Miguel A. , Li Yuxiang , Chen Ao , Niu Yuyu , Zeng Hongkui , Hou Yong , Liu Longqi , Liu Shiping , Xu Xun 
Published: November 2022

AbstractSingle cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.
Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3
Authors: Dolce Luciano G. , Zimmer Aubree A. , Tengo Laura , Weis Félix , Rubio Mary Anne T. , Alfonzo Juan D. , Kowalinski Eva 
Published: November 2022

AbstractThe essential deamination of adenosine A34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.
Single cell sequencing reveals that CD39 inhibition mediates changes to the tumor microenvironment
Authors: Liu Lilong , Hou Yaxin , Deng Changqi , Tao Zhen , Chen Zhaohui , Hu Junyi , Chen Ke 
Published: November 2022

AbstractSingle-cell sequencing technologies have noteworthily improved our understanding of the genetic map and molecular characteristics of bladder cancer (BC). Here we identify CD39 as a potential therapeutic target for BC via single-cell transcriptome analysis. In a subcutaneous tumor model and orthotopic bladder cancer model, inhibition of CD39 (CD39i) by sodium polyoxotungstate is able to limit the growth of BC and improve the overall survival of tumor-bearing mice. Via single cell RNA sequencing, we find that CD39i increase the intratumor NK cells, conventional type 1 dendritic cells (cDC1) and CD8 + T cells and decrease the Treg abundance. The antitumor effect and reprogramming of the tumor microenvironment are blockaded in both the NK cells depletion model and the cDC1-deficient Batf3−/− model. In addition, a significant synergistic effect is observed between CD39i and cisplatin, but the CD39i + anti-PD-L1 (or anti-PD1) strategy does not show any synergistic effects in the BC model. Our results confirm that CD39 is a potential target for the immune therapy of BC.
Magnetic NH2-MIL-101(Al)/Chitosan nanocomposite as a novel adsorbent for the removal of azithromycin: modeling and process optimization
Authors: Azari Ali , Malakoutian Mohammad , Yaghmaeain Kamyar , Jaafarzadeh Neemat , Shariatifar Nabi , Mohammadi Gholamabbas , Masoudi Mahmood Reza , Sadeghi Reza , Hamzeh Sanaz , Kamani Hossein 
Published: November 2022

AbstractIn the present study, the magnetic NH2-MIL-101(Al)/chitosan nanocomposite (MIL/Cs@Fe3O4 NCs) was synthesized and used in the removal of azithromycin (AZT) from an aqueous solution for the first time. The as-synthesized MIL/Cs@Fe3O4 NCs was characterized by SEM, TEM, XRD, FTIR, BET, and VSM techniques. The effect of various key factors in the AZT adsorption process was modeled and optimized using response surface methodology based on central composite design (RSM-CCD). The low value of p-value (1.3101e−06) and RSD (1.873) parameters, along with the coefficient of determination > 0.997 implied that the developed model was well fitted with experimental data. Under the optimized conditions, including pH: 7.992, adsorbent dose: 0.279 g/L, time: 64.256 min and AZT concentration: 10.107 mg/L, removal efficiency and AZT adsorption capacity were obtained as 98.362 ± 3.24% and 238.553 mg/g, respectively. The fitting of data with the Langmuir isotherm (R2: 0.998, X2: 0.011) and Pseudo-second-order kinetics (R2: 0.999, X2: 0.013) showed that the adsorption process is monolayer and chemical in nature. ΔH° > 0, ΔS° > 0, and ∆G° < 0 indicated that AZT removal was spontaneous and endothermic in nature. The effect of Magnesium on AZT adsorption was more complicated than other background ions. Reuse of the adsorbent in 10 consecutive experiments showed that removal efficiency was reduced by about 30.24%. The performance of MIL/Cs@Fe3O4 NCs under real conditions was also tested and promising results were achieved, except in the treatment of AZT from raw wastewater.
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants
Authors: McMillen Tracy , Jani Krupa , Robilotti Elizabeth V. , Kamboj Mini , Babady N. Esther 
Published: November 2022

AbstractThe Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4 and BA.5) variants of concern (VOC) share several mutations in their spike gene, including mutations resulting in the deletion of two amino acids at position 69 and 70 (del 69–70) in the Spike protein. Del 69–70 causes failure to detect the S gene target on a widely used, commercial test, the TaqPath SARS-CoV-2 RT-PCR (Thermo Fisher). The S gene target failure (SGTF) signature has been used to preliminarily infer the presence of Alpha and Omicron VOC. We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1–99.9%) and 98.6% (95% CI 99.2–99.8%) for the Alpha variant and 99.6% (95% CI 98.9–99.9%) and 99.8% (95% CI 99.4–99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. The accuracy of the SGTF signature was high, making this genomic signature a rapid and accurate proxy for identification of these variants in real-world laboratory settings.
Power quality approximation for household equipment load combinations using a stepwise growth in input parameters of AI models
Authors: Zjavka Ladislav 
Published: November 2022

AbstractDetached off-grids, subject to the generated renewable energy (RE), need to balance and compensate the unstable power supply dependent on local source potential. Power quality (PQ) is a set of EU standards that state acceptable deviations in the parameters of electrical power systems to guarantee their operability without dropout. Optimization of the estimated PQ parameters in a day-horizon is essential in the operational planning of autonomous smart grids, which accommodate the norms for the specific equipment and user demands to avoid malfunctions. PQ data for all system states are not available for dozens of connected / switched on household appliances, defined by their binary load series only, as the number of combinations grows exponentially. The load characteristics and eventual RE contingent supply can result in system instability and unacceptable PQ events. Models, evolved by Artificial Intelligence (AI) methods using self-optimization algorithms, can estimate unknown cases and states in autonomous systems contingent on self-supply of RE power related to chaotic and intermitted local weather sources. A new multilevel extension procedure designed to incrementally improve the applicability and adaptability to training data. The initial AI model starts with binary load series only, which are insufficient to represent complex data patterns. The input vector is progressively extended with correlated PQ parameters at the next estimation level to better represent the active demand of the power consumer. Historical data sets comprise training samples for all PQ parameters, but only the load sequences of the switch-on appliances are available in the next estimation states. The most valuable PQ parameters are selected and estimated in the previous algorithm stages to be used as supplementary series in the next more precise computing. More complex models, using the previous PQ-data approximates, are formed at the secondary processing levels to estimate the target PQ-output in better quality. The new added input parameters allow us to evolve a more convenient model form. The proposed multilevel refinement algorithm can be generally applied in modelling of unknown sequence states of dynamical systems, initially described by binary series or other insufficient limited-data variables, which are inadequate in a problem representation. Most AI computing techniques can adapt this strategy to improve their adaptive learning and model performance.
Mendelian randomization study reveals a causal relationship between adiponectin and LDL cholesterol in Africans
Authors: Meeks Karlijn A. C. , Bentley Amy R. , Doumatey Ayo P. , Adeyemo Adebowale A. , Rotimi Charles N. 
Published: November 2022

AbstractAdiponectin has been associated with cardiometabolic traits in observational studies across populations, yet it is unclear if these associations are causal. We performed Mendelian randomization (MR) analysis to assess the relationship between adiponectin and cardiometabolic traits in sub-Saharan Africans. We constructed a polygenic risk score (PRS) for adiponectin levels across 3354 unrelated sub-Saharan Africans. The PRS was used as the instrumental variable in two-stage least-squares MR analysis to assess its association with insulin resistance, HDL, LDL, total cholesterol, triglycerides, blood pressure, Type 2 Diabetes (T2D), and hypertension. The adiponectin PRS was causally related with LDL (β = 0.55, 95%CI 0.07–1.04, P-value = 0.024) but not the other traits. This association was observed in both overweight/obese and normal weight individuals, but only reached statistical significance among overweight/obese individuals (β = 0.55, 95%CI 0.01–1.08, P-value = 0.045). In normal weight individuals, the adiponectin PRS was associated with T2D (OR = 0.13, 95%CI 0.02–0.73, P-value = 0.021), and in men with HDL (β = 1.03, 95%CI 0.14–1.92, P-value = 0.023). The findings of this first MR study in sub-Saharan Africans support a causal relationship of adiponectin with LDL, with T2D in normal weight individuals only, and with HDL in men only. These observations add to the small but growing literature on adiponectin MR studies.
Efficient computation of the steady-state and time-domain solutions of the photon diffusion equation in layered turbid media
Authors: Helton Michael , Zerafa Samantha , Vishwanath Karthik , Mycek Mary-Ann 
Published: November 2022

AbstractAccurate and efficient forward models of photon migration in heterogeneous geometries are important for many applications of light in medicine because many biological tissues exhibit a layered structure of independent optical properties and thickness. However, closed form analytical solutions are not readily available for layered tissue-models, and often are modeled using computationally expensive numerical techniques or theoretical approximations that limit accuracy and real-time analysis. Here, we develop an open-source accurate, efficient, and stable numerical routine to solve the diffusion equation in the steady-state and time-domain for a layered cylinder tissue model with an arbitrary number of layers and specified thickness and optical coefficients. We show that the steady-state ($$< 0.1$$

<
0.1

ms) and time-domain ($$< 0.5$$

<
0.5

ms) fluence (for an 8-layer medium) can be calculated with absolute numerical errors approaching machine precision. The numerical implementation increased computation speed by 3 to 4 orders of magnitude compared to previously reported theoretical solutions in layered media. We verify our solutions asymptotically to homogeneous tissue geometries using closed form analytical solutions to assess convergence and numerical accuracy. Approximate solutions to compute the reflected intensity are presented which can decrease the computation time by an additional 2–3 orders of magnitude. We also compare our solutions for 2, 3, and 5 layered media to gold-standard Monte Carlo simulations in layered tissue models of high interest in biomedical optics (e.g. skin/fat/muscle and brain). The presented routine could enable more robust real-time data analysis tools in heterogeneous tissues that are important in many clinical applications such as functional brain imaging and diffuse optical spectroscopy.
Lack of the association between height and cardiovascular prognosis in hypertensive men and women: analysis of national real-world database
Authors: Kim Hack-Lyoung , Lee Yonggu , Lee Jun Hyeok , Shin Jeong-Hun , Shin Jinho , Sung Ki-Chul 
Published: November 2022

AbstractData on the association between height and cardiovascular risk are still conflicting. Moreover, no reports are showing this issue in hypertensive patients. This study was performed to investigate whether height affects cardiovascular prognosis in hypertensive patients using nation-wide real-world data. Using the Korean National Health Insurance Service database, we analyzed 461,492 Korean hypertensive patients without any prior history of cardiovascular disease between January 2002 and December 2017. The incidence of a composite of cardiovascular death, myocardial infarction, and stroke was assessed according to height quintiles. In univariable comparisons, the taller the patients, the younger the age and the higher the proportion of men. In multivariable cox regression analyses, height was not associated with the occurrence of cardiovascular events. Although the risk of clinical events increased in some height quintiles compared to the first height quintile, there was no tendency to increase the risk according to the increase in the height quintile. These results were similar even when men and women were analyzed separately. In the same quintile group of height, there were no significant differences in clinical outcomes between sexes. In Korean hypertensive patients, there was no association between height and the occurrence of cardiovascular events. This result did not differ by sex. The clinical use of height for CVD prediction seems to be still tricky in hypertensive patients.
Improved generalized ComBat methods for harmonization of radiomic features
Authors: Horng Hannah , Singh Apurva , Yousefi Bardia , Cohen Eric A. , Haghighi Babak , Katz Sharyn , Noël Peter B. , Kontos Despina , Shinohara Russell T. 
Published: November 2022

AbstractRadiomic approaches in precision medicine are promising, but variation associated with image acquisition factors can result in severe biases and low generalizability. Multicenter datasets used in these studies are often heterogeneous in multiple imaging parameters and/or have missing information, resulting in multimodal radiomic feature distributions. ComBat is a promising harmonization tool, but it only harmonizes by single/known variables and assumes standardized input data are normally distributed. We propose a procedure that sequentially harmonizes for multiple batch effects in an optimized order, called OPNested ComBat. Furthermore, we propose to address bimodality by employing a Gaussian Mixture Model (GMM) grouping considered as either a batch variable (OPNested + GMM) or as a protected clinical covariate (OPNested − GMM). Methods were evaluated on features extracted with CapTK and PyRadiomics from two public lung computed tomography (CT) datasets. We found that OPNested ComBat improved harmonization performance over standard ComBat. OPNested + GMM ComBat exhibited the best harmonization performance but the lowest predictive performance, while OPNested − GMM ComBat showed poorer harmonization performance, but the highest predictive performance. Our findings emphasize that improved harmonization performance is no guarantee of improved predictive performance, and that these methods show promise for superior standardization of datasets heterogeneous in multiple or unknown imaging parameters and greater generalizability.
Test–retest reliability of splenic volume assessment by ultrasonography
Authors: Holmström Pontus , Pernett Frank , Schagatay Erika 
Published: November 2022

AbstractWhile MRI and CT are the gold standards for assessments of splenic size in clinical settings, ultrasonography is particularly suited due to its portability, cost efficiency and easy utilization. However, ultrasonography is associated with subjective assessment, potentially resulting in increased variation. We used a test–retest design aiming to determine the reliability of splenic measurements assessed by ultrasonography during apnea. In addition, we compared reliability between different equations for volume calculations: Koga, Prolate ellipsoid and Pilström. Twelve healthy participants (6 women) performed two tests separated by 15 min, comprising a maximal voluntary apnea in a seated position. Splenic dimensions were measured via ultrasonography for 5 min before and immediately following apnea. Resting splenic volume displayed high test–retest reliability between tests (Pilström: 157 ± 39 mL vs 156 ± 34 mL, p = .651, ICC = .970, p < .001, CV = 2.98 ± 0.1%; Prolate ellipsoid: 154 ± 37 mL vs 144 ± 43 mL, p = .122, ICC = .942, p < .001, CV = 5.47 ± 0.3%; Koga: 142 ± 37 mL vs 140 ± 59 mL, p = .845, ICC = .859, p < .001, CV = 9.72 ± 1.4%). Apnea-induced volumes displayed similar reliability (127 ± 29 mL vs 129 ± 28 mL, p = .359, ICC = .967, p < .001, CV = 3.14 ± 3.1%). Reliability was also high between equations (Pilström vs Prolate ellipsoid: ICC = .818, p < .001, CV = 7.33 ± 0.3%, bias =  − 3.1 mL, LoA =  − 46.9 to 40.7 mL; Pilström vs Koga: ICC = .618, p < .01, CV = 11.83 ± 1.1%, bias =  − 14.8 mL, LoA =  − 76.9 to 47.3 mL). We conclude that splenic ultrasonographic measurements have practical applications during laboratory and field-based research as a reliable method detecting splenic volume change consistently between repeated tests. The Pilström equation displayed similar reliability compared to the prolate ellipsoid formula and slightly higher compared to the Koga formula and may be particularly useful to account for individual differences in splenic dimensions.
Analysis of Early Iron Age (2500 BP) and modern period (150 BP) starch grains in Western Central Africa
Authors: Cagnato Clarissa , Nlend Pascal , Ngouoh François , Oslisly Richard , de Saulieu Geoffroy 
Published: November 2022

AbstractStarch grain analysis carried out on 23 ceramic sherds from 6 refuse pits from the site of Nachtigal in central Cameroon is shedding light on a longstanding debate regarding ancient diets in Central Africa during the Iron Age (IA, 2500 years BP) but also more recently during the Modern Period (ca. 150 BP). The results indicate a varied, but balanced diet, consisting of cereals, legumes, oil-rich seeds, and tubers; the latter being very rarely documented in the region. Moreover, we underscore the presence of taxa still consumed today, or in recent times. Rescue archaeology, and the application of specialized methodologies, are critical to better nuancing past dietary practices in this region.
Photoredox C–H functionalization leads the site-selective phenylalanine bioconjugation
Authors: Weng Yue , Su Chun-Jen , Jiang Haoyang , Chiang Chien-Wei 
Published: November 2022

AbstractSite-selectively chemical bioconjugation of peptides and proteins can improve the therapeutic exploration of modified protein drugs. Only 3.8% natural abundance of phenylalanine in protein and nearly 90% of proteins contain at least one phenylalanine residue in their sequenced, showing the potential in biopharmaceutical utility of the phenylalanine bioconjugation. However, the covalent bioconjugation of native phenylalanine is one of the most challenging problems in protein modification. Herein, an approach to protein modification is described that relies on a photoredox method for the site-selective bioconjugation of phenylalanine. This methodology has been validated on peptides as well as protein insulin using a straightforward and mild condition. In addition, based on characterization by near-UV CD spectroscopy and small angle X-ray scattering (SAXS), this pyrazole labeling approach permitted the insulin hexamer to completely dissociate into the monomeric form, thus making it a potential candidate for use as rapid-acting insulin for the treatment of diabetes.