bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust single-cell matching and multimodal analysis using shared and distinct features
Authors: Zhu Bokai , Chen Shuxiao , Bai Yunhao , Chen Han , Liao Guanrui , Mukherjee Nilanjan , Vazquez Gustavo , McIlwain David R. , Tzankov Alexandar , Lee Ivan T. , Matter Matthias S. , Goltsev Yury , Ma Zongming , Nolan Garry P. , Jiang Sizun 
Published: January 2023

AbstractThe ability to align individual cellular information from multiple experimental sources is fundamental for a systems-level understanding of biological processes. However, currently available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely on a large number of shared features across datasets for cell matching. This approach underperforms when applied to single-cell proteomic datasets due to the limited number of parameters simultaneously accessed and lack of shared markers across these experiments. Here, we introduce a cell-matching algorithm, matching with partial overlap (MARIO) that accounts for both shared and distinct features, while consisting of vital filtering steps to avoid suboptimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multimodal methods, including spatial techniques and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via codetection by indexing imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid by cellular indexing of transcriptomes and epitopes by sequencing, revealing unique immune responses within the lung microenvironment of patients with COVID.
Behavioral origin of sound-evoked activity in mouse visual cortex
Authors: Bimbard Célian , Sit Timothy P. H. , Lebedeva Anna , Reddy Charu B. , Harris Kenneth D. , Carandini Matteo 
Published: January 2023

AbstractSensory cortices can be affected by stimuli of multiple modalities and are thus increasingly thought to be multisensory. For instance, primary visual cortex (V1) is influenced not only by images but also by sounds. Here we show that the activity evoked by sounds in V1, measured with Neuropixels probes, is stereotyped across neurons and even across mice. It is independent of projections from auditory cortex and resembles activity evoked in the hippocampal formation, which receives little direct auditory input. Its low-dimensional nature starkly contrasts the high-dimensional code that V1 uses to represent images. Furthermore, this sound-evoked activity can be precisely predicted by small body movements that are elicited by each sound and are stereotyped across trials and mice. Thus, neural activity that is apparently multisensory may simply arise from low-dimensional signals associated with internal state and behavior.
Arbuscular mycorrhizal fungi in oat-pea intercropping
Authors: Lee Alan , Neuberger Patrick , Omokanye Akim , Hernandez-Ramirez Guillermo , Kim Keunbae , Gorzelak Monika A. 
Published: January 2023

AbstractArbuscular mycorrhizal fungal diversity can be altered by intercropping plant species, as well as N fertilizer applications. This study examined the effects of oat-pea intercropping and N fertilizer addition on the richness and diversity of mycorrhizal species, as well as identified the most common arbuscular mycorrhizal fungi (AMF) genera recruited for oats and peas in two growing seasons (2019 and 2020). The AMF diversity was higher in an intercropped system compared to their respective monocropping system. Under drier conditions in 2019, arbuscular mycorrhizal richness decreased with N fertilizer addition in sole peas and increased with N fertilizer addition in sole oats, but no significant change in richness was observed in oat-pea intercropping. During the wetter growing season 2020, arbuscular mycorrhizal diversity increased when oat and pea were intercropped, compared to either sole oat or sole pea. Diversispora in sole pea was a significant indicator differentiating the root associated AMF community from sole oat. Claroideoglomus richness increased in peas in 2020, thus this genus could be moisture dependent. Paraglomus richness in oat-pea intercropping was similar to sole oat in 2019, and similar to sole pea in 2020. This can suggest that Paraglomus is an indicator of plant stress under intercropping, as based on the premise that stressed plants release more exudates, and the subsequent mycorrhizal associations favor these plants with higher exudation. Future investigations can further reveal the functions and benefits of these mycorrhizal genera in annual monocrop and intercropping systems.
The changes of distance between nipples following correction of women pectus excavatum
Authors: Yoo Gyeol , Jeon Hui Hyung , Rha Eun Young , Ko Jun Gul , Baek Sang Oon , Lee Jun Yong , Jeong Jin Yong 
Published: January 2023

AbstractThe breasts in women pectus excavatum patients frequently appear to be slanting medially along the inclination of the distorted ribs. This study aims to evaluate changes in the distance between the nipples and to find out whether medially slanting breasts are corrected in women pectus excavatum patients following modified Nuss procedure. This case series analysis enrolled 22 young women patients with pectus excavatum between October 2011 and September 2020. We measured all the patients’ distances from the sternal midline to the right and left nipples, based on chest computerized tomography. We calculated the distances between nipples as being the sum of the right and left distances. The mean age of patients was 16.50 ± 4.73 years, and the follow-up periods were 35.59 ± 20.23 months. The postoperative Haller indices (2.89 ± 0.43) were significantly lower than the preoperative Haller indices (5.14 ± 1.96) (p = 0.000). The distances between the nipples before and after Nuss procedure were 145.17 ± 17.73 mm and 172.29 ± 19.11 mm, which is a significant increase following surgery. (p = 0.000). Our results demonstrated that skeletal correction with modified Nuss procedure in pectus excavatum increased the distance between nipples, indicating that medially slanting breasts had been corrected.
Analysis of cerebral glucose metabolism following experimental subarachnoid hemorrhage over 7 days
Authors: Schadt Fabian , Israel Ina , Beez Alexandra , Alushi Kastriot , Weiland Judith , Ernestus Ralf-Ingo , Westermaier Thomas , Samnick Samuel , Lilla Nadine 
Published: January 2023

AbstractLittle is known about changes in brain metabolism following SAH, possibly leading towards secondary brain damage. Despite sustained progress in the last decade, analysis of in vivo acquired data still remains challenging. The present interdisciplinary study uses a semi-automated data analysis tool analyzing imaging data independently from the administrated radiotracer. The uptake of 2-[18F]Fluoro-2-deoxy-glucose ([18F]FDG) was evaluated in different brain regions in 14 male Sprague–Dawley rats, randomized into two groups: (1) SAH induced by the endovascular filament model and (2) sham operated controls. Serial [18F]FDG-PET measurements were carried out. Quantitative image analysis was performed by uptake ratio using a self-developed MRI-template based data analysis tool. SAH animals showed significantly higher [18F]FDG accumulation in gray matter, neocortex and olfactory system as compared to animals of the sham group, while white matter and basal forebrain region showed significant reduced tracer accumulation in SAH animals. All significant metabolic changes were visualized from 3 h, over 24 h (day 1), day 4 and day 7 following SAH/sham operation. This [18F]FDG-PET study provides important insights into glucose metabolism alterations following SAH—for the first time in different brain regions and up to day 7 during course of disease.
Descriptive characteristics of continuous oximetry measurement in moderate to severe covid-19 patients
Authors: Sobel Jonathan A. , Levy Jeremy , Almog Ronit , Reiner-Benaim Anat , Miller Asaf , Eytan Danny , Behar Joachim A. 
Published: January 2023

AbstractNon-invasive oxygen saturation (SpO2) is a central vital sign used to shape the management of COVID-19 patients. Yet, there have been no report quantitatively describing SpO2 dynamics and patterns in COVID-19 patients using continuous SpO2 recordings. We performed a retrospective observational analysis of the clinical information and 27 K hours of continuous SpO2 high-resolution (1 Hz) recordings of 367 critical and non-critical COVID-19 patients hospitalised at the Rambam Health Care Campus, Haifa, Israel. An absolute SpO2 threshold of 93% most efficiently discriminated between critical and non-critical patients, regardless of oxygen support. Oximetry-derived digital biomarker (OBMs) computed per 1 h monitoring window showed significant differences between groups, notably the cumulative time below 93% SpO2 (CT93). Patients with CT93 above 60% during the first hour of monitoring, were more likely to require oxygen support. Mechanical ventilation exhibited a strong effect on SpO2 dynamics by significantly reducing the frequency and depth of desaturations. OBMs related to periodicity and hypoxic burden were markedly affected, up to several hours before the initiation of the mechanical ventilation. In summary, OBMs, traditionally used in the field of sleep medicine research, are informative for continuous assessment of disease severity and response to respiratory support of hospitalised COVID-19 patients. In conclusion, OBMs may improve risk stratification and therapy management of critical care patients with respiratory impairment.
Magnitude estimation and ground motion prediction to harness fiber optic distributed acoustic sensing for earthquake early warning
Authors: Lior Itzhak , Rivet Diane , Ampuero Jean-Paul , Sladen Anthony , Barrientos Sergio , Sánchez-Olavarría Rodrigo , Villarroel Opazo German Alberto , Bustamante Prado Jose Antonio 
Published: January 2023

AbstractEarthquake early warning (EEW) systems provide seconds to tens of seconds of warning time before potentially-damaging ground motions are felt. For optimal warning times, seismic sensors should be installed as close as possible to expected earthquake sources. However, while the most hazardous earthquakes on Earth occur underwater, most seismological stations are located on-land; precious seconds may go by before these earthquakes are detected. In this work, we harness available optical fiber infrastructure for EEW using the novel approach of distributed acoustic sensing (DAS). DAS strain measurements of earthquakes from different regions are converted to ground motions using a real-time slant-stack approach, magnitudes are estimated using a theoretical earthquake source model, and ground shaking intensities are predicted via ground motion prediction equations. The results demonstrate the potential of DAS-based EEW and the significant time-gains that can be achieved compared to the use of standard sensors, in particular for offshore earthquakes.
Energy, exergy and economic (3E) analysis of flat-plate solar collector using novel environmental friendly nanofluid
Authors: Amar Muhammad , Akram Naveed , Chaudhary Ghulam Qadar , Kazi Salim Newaz , Soudagar Manzoore Elahi M. , Mubarak Nabisab Mujawar , Kalam Md Abul 
Published: January 2023

AbstractThe use of solar energy is one of the most prominent strategies for addressing the present energy management challenges. Solar energy is used in numerous residential sectors through flat plate solar collectors. The thermal efficiency of flat plate solar collectors is improved when conventional heat transfer fluids are replaced with nanofluids because they offer superior thermo-physical properties to conventional heat transfer fluids. Concentrated chemicals are utilized in nanofluids' conventional synthesis techniques, which produce hazardous toxic bi-products. The present research investigates the effects of novel green covalently functionalized gallic acid-treated multiwall carbon nanotubes-water nanofluid on the performance of flat plate solar collectors. GAMWCNTs are highly stable in the base fluid, according to stability analysis techniques, including ultraviolet–visible spectroscopy and zeta potential. Experimental evaluation shows that the thermo-physical properties of nanofluid are better than those of base fluid deionized water. The energy, exergy and economic analysis are performed using 0.025%, 0.065% and 0.1% weight concentrations of GAMWCNT-water at varying mass flow rates 0.010, 0.0144, 0.0188 kg/s. The introduction of GAMWCNT nanofluid enhanced the thermal performance of flat plate solar collectors in terms of energy and exergy efficiency. There is an enhancement in efficiency with the rise in heat flux, mass flow rate and weight concentration, but a decline is seen as inlet temperature increases. As per experimental findings, the highest improvement in energy efficiency is 30.88% for a 0.1% weight concentration of GAMWCNT nanofluid at 0.0188 kg/s compared to the base fluid. The collector's exergy efficiency increases with the rise in weight concentration while it decreases with an increase in flow rate. The highest exergy efficiency is achieved at 0.1% GAMWCNT concentration and 0.010 kg/s mass flow rate. GAMWCNT nanofluids have higher values for friction factor compared to the base fluid. There is a small increment in relative pumping power with increasing weight concentration of nanofluid. Performance index values of more than 1 are achieved for all GAMWCNT concentrations. When the solar thermal collector is operated at 0.0188 kg/s and 0.1% weight concentration of GAMWCNT nanofluid, the highest size reduction, 27.59%, is achieved as compared to a flat plate solar collector with water as a heat transfer fluid.
Explainable machine learning aggregates polygenic risk scores and electronic health records for Alzheimer’s disease prediction
Authors: Gao Xiaoyi Raymond , Chiariglione Marion , Qin Ke , Nuytemans Karen , Scharre Douglas W. , Li Yi-Ju , Martin Eden R. 
Published: January 2023

AbstractAlzheimer’s disease (AD) is the most common late-onset neurodegenerative disorder. Identifying individuals at increased risk of developing AD is important for early intervention. Using data from the Alzheimer Disease Genetics Consortium, we constructed polygenic risk scores (PRSs) for AD and age-at-onset (AAO) of AD for the UK Biobank participants. We then built machine learning (ML) models for predicting development of AD, and explored feature importance among PRSs, conventional risk factors, and ICD-10 codes from electronic health records, a total of > 11,000 features using the UK Biobank dataset. We used eXtreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP), which provided superior ML performance as well as aided ML model explanation. For participants age 40 and older, the area under the curve for AD was 0.88. For subjects of age 65 and older (late-onset AD), PRSs were the most important predictors. This is the first observation that PRSs constructed from the AD risk and AAO play more important roles than age in predicting AD. The ML model also identified important predictors from EHR, including urinary tract infection, syncope and collapse, chest pain, disorientation and hypercholesterolemia, for developing AD. Our ML model improved the accuracy of AD risk prediction by efficiently exploring numerous predictors and identified novel feature patterns.
Effects of different straw returning amounts and fertilizer conditions on bacteria of rice’s different part in rare earth mining area
Authors: Jin Shulan , Huang Yizong , Dong Chengxu , Bai Yijun , Pan Huahua , Hu Zhongjun 
Published: January 2023

AbstractPot experiments were conducted to explore the effects of different rice straw returning soil on the community structure and function of bacteria in rice root, rhizosphere, leaf and phyllosphere under 7 conditions of rice straw combined with different fertilizers respectively. The results showed that: rice straw returning in different ways increased the content of soil pH and K, and reduced the accumulation of N, P and organic matter in soil, and different rice straw returning ways had different effects; rice straw returning reduced dry weight of rice grain, 2% of rice straw returning reduced rice grain greater than that of 1% rice straw returning; The reduction of NP combined fertilization is greater than that of NK combined fertilization and NPK combined fertilization. Except for the decrease of chao_1 index in rice root at maturity, rice straw returning significantly improved the abundance, diversity and evenness of bacteria in rice root, rhizosphere, leaf and phyllosphere. Rice straw returning increased the content of REEs in rice, and 2% of rice straw returning soil increased rare earth element (REE) content in rice grain greater than that of 1% rice straw returning soil. Different ways of rice straw returning soil reduced the abundance of Bacillus, while the abundance of Exiguobacterium in rice leaves was hundreds of times higher than that of the control group, and the genus in leaves was dozens of times higher than that of the control group, 2% of rice straw returning soil increased the abundance of harmful bacteria and pathogens of Acidovorax, Clostridium sensu stricto, Citrobacter, Curtobacterium, and 1% of rice straw returning soil promoted the abundance of nitrogen fixing bacteria, plant growth-promoting bacteria, stress resistant bacteria such as Lactobacillus, Azospira, Acinetobacter, Bradyrhizobium and Acidocella; Environmental factors such as available P, organic matter, total nitrogen, nitrate nitrogen, rare earth element content in rice roots, available K and soil moisture are important factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at tillering stage of the rice. pH, REE content in rice roots, shoots, organic matter, total nitrogen, nitrate nitrogen and soil moisture content are the main environmental factors affecting the community structure of bacteria in rice roots, rhizosphere, leaf and phyllosphere at maturity stage of rice. 2% rice straw returning soil promoted the formation of harmful bacteria, which may be an important reason for its significant reduction in the dry weight of rice grains.
Automatic detection and vascular territory classification of hyperacute staged ischemic stroke on diffusion weighted image using convolutional neural networks
Authors: Lee Kun-Yu , Liu Chia-Chuan , Chen David Yen-Ting , Weng Chi-Lun , Chiu Hung-Wen , Chiang Chen-Hua 
Published: January 2023

AbstractAutomated ischemic stroke detection and classification according to its vascular territory is an essential step in stroke image evaluation, especially at hyperacute stage where mechanical thrombectomy may improve patients’ outcome. This study aimed to evaluate the performance of various convolutional neural network (CNN) models on hyperacute staged diffusion-weighted images (DWI) for detection of ischemic stroke and classification into anterior circulation infarct (ACI), posterior circulation infarct (PCI) and normal image slices. In this retrospective study, 253 cases of hyperacute staged DWI were identified, downloaded and reviewed. After exclusion, DWI from 127 cases were used and we created a dataset containing total of 2119 image slices, and separates it into three groups, namely ACI (618 slices), PCI (149 slices) and normal (1352 slices). Two transfer learning based CNN models, namely Inception-v3, EfficientNet-b0 and one self-derived modified LeNet model were used. The performance of the models was evaluated and activation maps using gradient-weighted class activation mapping (Grad-Cam) technique were made. Inception-v3 had the best overall accuracy (86.3%), weighted F1 score (86.2%) and kappa score (0.715), followed by the modified LeNet (85.2% accuracy, 84.7% weighted F1 score and 0.693 kappa score). The EfficientNet-b0 had the poorest performance of 83.6% accuracy, 83% weighted F1 score and 0.662 kappa score. The activation map showed that one possible explanation for misclassification is due to susceptibility artifact. A sufficiently high performance can be achieved by using CNN model to detect ischemic stroke on hyperacute staged DWI and classify it according to vascular territory.
Numerical simulation of size effect of defective rock under compression condition
Authors: Hu Zeyu , Xie Liangfu , Qin Yongjun , Liu Xuejun , Qian Jiangu 
Published: January 2023

AbstractThe existence of various types of damage, small cracks, some large voids and the size of the sample in the rock will make the experimental results show great discreteness. In this paper, based on the results of laboratory experiments, a numerical model of large flawed rock samples is established by using particle flow software PFC2D, and the mechanical response of rocks with different length-diameter ratios and different flaw positions in uniaxial compression experiments is discussed. The results show that the specimen size has a significant effect on the crack characteristics, mechanical characteristics and energy characteristics of rock mass. From the perspective of energy and crack characteristics, the total number of cracks after the failure of the defective rock sample is slightly lower than that of the intact rock sample, resulting in a slightly lower peak strain energy during the rock failure process. From the mechanical properties of rock samples, the Poisson’s ratio of intact rock samples is slightly smaller than that of defective rock samples. The strength of the defective sample is weakened relative to the complete rock sample, and the relationship formula between the weakening range and the aspect ratio is obtained through analysis. Moreover, different defect locations lead to different crack processes and crack modes, resulting in different uniaxial compressive strength.
Screening of lactic acid bacteria strains isolated from Iranian traditional dairy products for GABA production and optimization by response surface methodology
Authors: Edalatian Dovom Mohammad Reza , Habibi Najafi Mohammad Bagher , Rahnama Vosough Paria , Norouzi Neda , Ebadi Nezhad Seyyed Javad , Mayo Baltasar 
Published: January 2023

AbstractA total of 50 lactic acid bacteria (LAB) isolates from Iranian traditional dairy products (Motal and Lighvan cheeses, and artisanal yogurt) were screened for gamma-aminobutyric acid (GABA) production. Firstly, a rapid colorimetric test was performed to evaluate the glutamate decarboxylase (GAD) activity among the LAB isolates examined. Thin layer chromatography (TLC) was then performed on selected strains to identify isolates with high/moderate GABA producing capacity, and a GABase micro-titer plate assay was employed to quantify GABA. Finally, two Lactococcus (Lac.) lactis strains were selected for GABA production optimization via Response Surface Methodology (RSM) following Central Composite Design (CCD). Forty-one out of the 50 isolates showed GAD activity according to the colorimetric assay. Eight isolates displayed strong GAD activity, while nine showed no activity; low to moderate GAD activity was scored for all other isolates. GABA production was confirmed by TLC in all isolates with high GAD activity and in four selected among isoaltes with moderate activity. Among the Lactococcus strains tested, Lac. lactis 311 and Lac. lactis 491 were the strongest GABA producers with amounts of 3.3 and 1.26 mM, respectively. These two strains were subjected to GABA production optimization applying RSM and CCD on three key variables: Monosodium glutamate concentration (MSG) (between 25 and 150 mM), incubation temperature (between 25 and 37 °C), and pH (between 4.0 and 5.0). Optimal conditions for GABA production by Lac. lactis 311 and Lac. lactis 491 of temperature, pH and MSG concentration were, respectively, 35.4 and 30 °C, pH 4.5 and 4.6, and MSG concentration of 89 and 147.4 mM, respectively. Under the above conditions, the amount of GABA produced by Lac. lactis 311 and Lac. lactis 491 was 0.395 and 0.179 mg/mL, respectively. These strains and the optimal culture conditions determined in this study could be used for the biotechnological production of GABA or applied in food fermentations for the development of naturally GABA-enriched foods.