bluuebunny/crossref_metadata_2025_split huggingface dataset:
The metabolic function of pyruvate kinase M2 regulates reactive oxygen species production and microbial killing by neutrophils
Authors: Toller-Kawahisa Juliana Escher , Hiroki Carlos Hiroji , Silva Camila Meirelles de Souza , Nascimento Daniele Carvalho , Públio Gabriel Azevedo , Martins Timna Varela , Damasceno Luis Eduardo Alves , Veras Flávio Protásio , Viacava Paula Ramos , Sukesada Fábio Yuji , Day Emily Anne , Zotta Alessia , Ryan Tristram Alexander Jasper , Moreira da Silva Rodrigo , Cunha Thiago Mattar , Lopes Norberto Peporine , Cunha Fernando de Queiroz , O’Neill Luke Anthony John , Alves-Filho José Carlos 
Published: July 2023

AbstractNeutrophils rely predominantly on glycolytic metabolism for their biological functions, including reactive oxygen species (ROS) production. Although pyruvate kinase M2 (PKM2) is a glycolytic enzyme known to be involved in metabolic reprogramming and gene transcription in many immune cell types, its role in neutrophils remains poorly understood. Here, we report that PKM2 regulates ROS production and microbial killing by neutrophils. Zymosan-activated neutrophils showed increased cytoplasmic expression of PKM2. Pharmacological inhibition or genetic deficiency of PKM2 in neutrophils reduced ROS production andStaphylococcus aureuskilling in vitro. In addition, this also resulted in phosphoenolpyruvate (PEP) accumulation and decreased dihydroxyacetone phosphate (DHAP) production, which is required for de novo synthesis of diacylglycerol (DAG) from glycolysis. In vivo, PKM2 deficiency in myeloid cells impaired the control of infection withStaphylococcus aureus. Our results fill the gap in the current knowledge of the importance of lower glycolysis for ROS production in neutrophils, highlighting the role of PKM2 in regulating the DHAP and DAG synthesis to promote ROS production in neutrophils.
A renal YY1-KIM1-DR5 axis regulates the progression of acute kidney injury
Authors: Yang Chen , Xu Huidie , Yang Dong , Xie Yunhao , Xiong Mingrui , Fan Yu , Liu XiKai , Zhang Yu , Xiao Yushuo , Chen Yuchen , Zhou Yihao , Song Liangliang , Wang Chen , Peng Anlin , Petersen Robert B. , Chen Hong , Huang Kun , Zheng Ling 
Published: July 2023

AbstractAcute kidney injury (AKI) exhibits high morbidity and mortality. Kidney injury molecule-1 (KIM1) is dramatically upregulated in renal tubules upon injury, and acts as a biomarker for various renal diseases. However, the exact role and underlying mechanism of KIM1 in the progression of AKI remain elusive. Herein, we report that renal tubular specific knockout ofKim1attenuates cisplatin- or ischemia/reperfusion-induced AKI in male mice. Mechanistically, transcription factor Yin Yang 1 (YY1), which is downregulated upon AKI, binds to the promoter ofKIM1and represses its expression. Injury-induced KIM1 binds to the ECD domain of death receptor 5 (DR5), which activates DR5 and the following caspase cascade by promoting its multimerization, thus induces renal cell apoptosis and exacerbates AKI. Blocking the KIM1-DR5 interaction with rationally designed peptides exhibit reno-protective effects against AKI. Here, we reveal a YY1-KIM1-DR5 axis in the progression of AKI, which warrants future exploration as therapeutic targets.
Impact of cognitive performance and negative symptoms on psychosocial functioning in Czech schizophrenia patients
Authors: Kalisova L. , Michalec J. , Dechterenko F. , Silhan P. , Hyza M. , Chlebovcova M. , Brenova M. , Bezdicek O. 
Published: July 2023

AbstractSchizophrenia has a profound influence on the real-life functioning of patients. There are several factors inherent to the disease course affecting the level of psychosocial functioning. Our study focused on the impact of cognitive deficit and severity of negative symptoms (i.e., the experiential domain (avolition, asociality, and anhedonia) and the expressive domain (blunted affect and alogia)) to explore psychosocial functioning in schizophrenia. Schizophrenia patients (n = 211) were tested for the presence of cognitive impairment using the NIMH-MATRICS: Measurement and Treatment Research to Improve Cognition in Schizophrenia Consensus Cognitive Cattery (MCCB; MATRICS Consensus Cognitive Battery) and the extent of negative symptoms using the PANSS (PANSS; Positive and Negative Syndrome Scale—selected items). The level of psychosocial functioning was measured with the Personal and Social Performance Scale (PSP). The path analysis using three regression models was used to analyse variables influencing psychosocial functioning (PSP). One of these models analyzed influence of cognitive functioning (MCCB) and negative schizophrenia symptoms (PANSS selected items reflecting expressive and experiential deficits) as predictors and NART/CRT and disease length as confounders. R2 was 0.54. The direct effect of the MCCB (β = 0.09) on the PSP was suppressed by the strong effect of the negative symptoms (β = −0.64). The presence of cognitive deficits and negative symptoms in our sample of schizophrenia patients significantly influences the level of their psychosocial functioning, a key factor in remission and recovery.
Short-term high-fat diet consumption impairs synaptic plasticity in the aged hippocampus via IL-1 signaling
Authors: González Olmo Brigitte M. , Bettes Menaz N. , DeMarsh James W. , Zhao Fangli , Askwith Candice , Barrientos Ruth M. 
Published: July 2023

AbstractMore Americans are consuming diets higher in saturated fats and refined sugars than ever before. These trends could have serious consequences for the older population because high-fat diet (HFD) consumption, known to induce neuroinflammation, has been shown to accelerate and aggravate memory declines. We have previously demonstrated that short-term HFD consumption, which does not evoke obesity-related comorbidities, produced profound impairments to hippocampal-dependent memory in aged rats. These impairments were precipitated by increases in proinflammatory cytokines, primarily interleukin-1 beta (IL-1β). Here, we explored the extent to which short-term HFD consumption disrupts hippocampal synaptic plasticity, as measured by long-term potentiation (LTP), in young adult and aged rats. We demonstrated that (1) HFD disrupted late-phase LTP in the hippocampus of aged, but not young adult rats, (2) HFD did not disrupt early-phase LTP, and (3) blockade of the IL-1 receptor rescued L-LTP in aged HFD-fed rats. These findings suggest that hippocampal memory impairments in aged rats following HFD consumption occur through the deterioration of synaptic plasticity and that IL-1β is a critical driver of that deterioration.
Robust estimation of cortical similarity networks from brain MRI
Authors: Sebenius Isaac , Seidlitz Jakob , Warrier Varun , Bethlehem Richard A. I. , Alexander-Bloch Aaron , Mallard Travis T. , Garcia Rafael Romero , Bullmore Edward T. , Morgan Sarah E. 
Published: July 2023

AbstractStructural similarity is a growing focus for magnetic resonance imaging (MRI) of connectomes. Here we propose Morphometric INverse Divergence (MIND), a new method to estimate within-subject similarity between cortical areas based on the divergence between their multivariate distributions of multiple MRI features. Compared to the prior approach of morphometric similarity networks (MSNs) onn > 11,000 scans spanning three human datasets and one macaque dataset, MIND networks were more reliable, more consistent with cortical cytoarchitectonics and symmetry and more correlated with tract-tracing measures of axonal connectivity. MIND networks derived from human T1-weighted MRI were more sensitive to age-related changes than MSNs or networks derived by tractography of diffusion-weighted MRI. Gene co-expression between cortical areas was more strongly coupled to MIND networks than to MSNs or tractography. MIND network phenotypes were also more heritable, especially edges between structurally differentiated areas. MIND network analysis provides a biologically validated lens for cortical connectomics using readily available MRI data.
Clinical relevance of deep learning models in predicting the onset timing of cancer pain exacerbation
Authors: Bang Yeong Hak , Choi Yoon Ho , Park Mincheol , Shin Soo-Yong , Kim Seok Jin 
Published: July 2023

AbstractCancer pain is a challenging clinical problem that is encountered in the management of cancer pain. We aimed to investigate the clinical relevance of deep learning models that predict the onset of cancer pain exacerbation in hospitalized patients. We defined cancer pain exacerbation (CPE) as the pain with a numerical rating scale (NRS) score of ≥ 4. We investigated the performance of the deep learning models using the Matthews correlation coefficient (MCC) with different input lengths and time binning. All the pain records were obtained from the electronic medical records of the hematology-oncology wards in a Samsung Medical Center between July 2016 and February 2020. The model was externally validated using the holdout method with 20% of the datasets. The most common type of cancer was lung cancer (n = 745, 21.7%), and the median CPE per day was 1.01. The NRS pain records showed circadian patterns that correlated with NRS pain patterns of the previous days. The correlation of the NRS scores showed a positive association with the closeness of the NRS pattern of the day with forecast date and size of time binning. The long short-term memory-based model exhibited a good performance by demonstrating 9 times the best performance and 8 times the second-best performance among 21 different settings. The best performance was achieved with 120 h input and 12 h bin lengths (MCC: 0.4927). Our study demonstrated the possibility of predicting CPE using deep learning models, thereby suggesting that preemptive cancer pain management using deep learning could potentially improve patients’ daily life.
Explainable ML models for a deeper insight on treatment decision for localized prostate cancer
Authors: Han Jang Hee , Lee Sungyup , Lee Byounghwa , Baek Ock-kee , Washington Samuel L. , Herlemann Annika , Lonergan Peter E. , Carroll Peter R. , Jeong Chang Wook , Cooperberg Matthew R. 
Published: July 2023

AbstractAlthough there are several decision aids for the treatment of localized prostate cancer (PCa), there are limitations in the consistency and certainty of the information provided. We aimed to better understand the treatment decision process and develop a decision-predicting model considering oncologic, demographic, socioeconomic, and geographic factors. Men newly diagnosed with localized PCa between 2010 and 2015 from the Surveillance, Epidemiology, and End Results Prostate with Watchful Waiting database were included (n = 255,837). We designed two prediction models: (1) Active surveillance/watchful waiting (AS/WW), radical prostatectomy (RP), and radiation therapy (RT) decision prediction in the entire cohort. (2) Prediction of AS/WW decisions in the low-risk cohort. The discrimination of the model was evaluated using the multiclass area under the curve (AUC). A plausible Shapley additive explanations value was used to explain the model’s prediction results. Oncological variables affected the RP decisions most, whereas RT was highly affected by geographic factors. The dependence plot depicted the feature interactions in reaching a treatment decision. The decision predicting model achieved an overall multiclass AUC of 0.77, whereas 0.74 was confirmed for the low-risk model. Using a large population-based real-world database, we unraveled the complex decision-making process and visualized nonlinear feature interactions in localized PCa.
Simple algorithm for judging equivalence of differential-algebraic equation systems
Authors: Kato Shota , Zhang Chunpu , Kano Manabu 
Published: July 2023

AbstractMathematical formulas play a prominent role in science, technology, engineering, and mathematics (STEM) documents; understanding STEM documents usually requires knowing the difference between equation groups containing multiple equations. When two equation groups can be transformed into the same form, we call the equation groups equivalent. Existing tools cannot judge the equivalence of two equation groups; thus, we develop an algorithm to judge such an equivalence using a computer algebra system. The proposed algorithm first eliminates variables appearing only in either equation group. It then checks the equivalence of the equations one by one: the equations with identical algebraic solutions for the same variable are judged equivalent. If each equation in one equation group is equivalent to an equation in the other, the equation groups are judged equivalent; otherwise, non-equivalent. We generated 50 pairs of equation groups for evaluation. The proposed method accurately judged the equivalence of all pairs. This method is expected to facilitate comprehension of a large amount of mathematical information in STEM documents. Furthermore, this is a necessary step for machines to understand equations, including process models.
Assessing environmental and radiological impacts and lithological mapping of beryl-bearing rocks in Egypt using high-resolution sentinel-2 remote sensing images
Authors: Khaleal Farrage M. , El-Bialy Mohammed Z. , Saleh Gehad M. , Lasheen El Saeed R. , Kamar Mohamed S. , Omar Mohamed M. , El-dawy Mohamed N. , Abdelaal Ahmed 
Published: July 2023

AbstractEmerald and other beryls represent a family of the most valuable gemstone around the world and particularly in Egypt. Beryllium (Be) contents in beryl-bearing bedrocks in south Sinai (Wadi Ghazala and Wadi Sedri), and in central and south Eastern Desert of Egypt (Igla area, Zabara-Um Addebaa belt, Homret Akarem, and Homret Mukpid) were investigated in this study. The environmental risk levels of Be, associated major ions, and heavy metals in groundwater nearby to beryl-bearing mineralization were also evaluated. Results showed that Be contents ranged from 1 to 374 ppm in beryl-bearing bedrocks, while in nearby groundwater, Be content has a range of 0.0001–0.00044 mg/L with an average of 0.00032 mg/L, which is within the permissible levels and below (0.004) the U.S. EPA maximum contaminant level (MCL). Most levels of heavy metals (e.g., Be, B, Ni, V, Fe, and Al) in the investigated groundwater of central and south Eastern Desert and south Sinai are within the permissible levels and below their corresponding U.S. EPA MCLs. This study also investigated the radiological risk of natural radionuclides distributed in beryl-bearing bedrocks in the study area using gamma spectrometry; Sodium Iodide [NaI(Tl)] scintillation detector. Among the estimated mean 238U, 232Th, and 226Ra activity concentrations of the studied beryl-bearing rocks, Homret Mukpid (79, 87.15, 60.26 Bq kg−1) and Homret Akarem (111.6, 51.17, 85.1 Bq kg−1) contain the highest values. This may be attributed to their highly fractionated granitic rocks that host uranium and thorium reservoir minerals such as zircon, allanite, and monazite. The estimated data of multi-radiological parameters such as absorbed gamma dose, outdoor and indoor annual effective dose, radium equivalent activity, internal and external indices, index of excess cancer, and effective dose to human organs reflecting no significant impacts from the emitted natural gamma radiation.
Silver decorated lithium niobat nanostructure by UV activation method for silver–lithium niobate/silicon heterojunction device
Authors: Salim Evan T. , Khalef Wafaa K. , Fakhri Makram A. , Fadhil Rawan B. , Azzahrani Ahmad S. , Ibrahim Raed Khalid , Ismail Raid A. 
Published: July 2023

AbstractLithium niobite (LiNbO3) nanostructure were successfully synthesized by chemical bath deposition method (CBD) and then decorated with silver nitrate (AgNO3) through UV activation method at different immersion durations (5, 15, 25, 35, and 45 s). The silver nanoparticles (AgNPs) effects on the optical and structural properties were studied and analyzed using various scientific devices and technique. X-ray diffraction (XRD) results showed that all the samples have a hexagonal structure with a maximum diffraction peak at the (012), and the existence of silver atoms could be recognized at 2θ = 38.2° which corresponds to the (111) diffraction plane. The optical absorption of nanocomposites depicted the presence of plasma peak related to silver (Ag) at 350 nm. The estimated energy gap from the optical absorption revealed a reduction in the Eg value from (3.97 eV) to (3.59 eV) with the presence of Ag atom. The Photolumincence (PL) peaks were observed at around 355 nm for pure LiNbO3/Si and 358, 360, 363, 371, 476 nm for different immersion durations respectively, in the visible region of the electromagnetic spectrum. The scanning electron microscopy (SEM) study illustrated that with increasing the immersion time, especially at 45 s, a change in the particle morphology was observed (LiNbO3 NRs structure). Atomic force microscopy (AFM) displayed that the surface roughness decreases from 80.71 nm for pure sample to 23.02 nm for the decorated sample as the immersion time is increased. FT-IR manifested a noticeable increase in the intensity of the peaks of samples decorated with AgNPs. Raman spectroscopy elucidated that the peaks shifted to higher intensity due to the plasmonic effect of Ag nanoparticles. Ag–LiNbO3/Si heterojunction nano-devices were fabricated successfully and enhanced the optoelectronic properties in comparison with the pure LiNbO3/Si heterojunction device.
Identification of immune biomarkers in recent active pulmonary tuberculosis
Authors: Shaukat Sobia Naz , Eugenin Eliseo , Nasir Faizan , Khanani Rafiq , Kazmi Shahana Urooj 
Published: July 2023

AbstractTuberculosis (TB) has remained an unsolved problem and a major public health issue, particularly in developing countries. Pakistan is one of the countries with the highest tuberculosis infection rates globally. However, methods or biomarkers to detect early signs of TB infection are limited. Here,we characterized the mRNA profiles of immune responses in unstimulatedPeripheral blood mononuclear cellsobtained fromtreatment naïve patientswith early signsof active pulmonary tuberculosis without previous history of clinical TB. We identified a unique mRNA profile in active TB compared to uninfected controls, including cytokines such as IL-27, IL-15, IL-2RA, IL-24, and TGFβ, transcription factors such as STAT1 and NFATC1 and immune markers/receptors such as TLR4, IRF1, CD80, CD28, and PTGDR2 from an overall 84 different transcripts analyzed. Among 12 significant differentially expressed transcripts, we identified five gene signatures which included three upregulated IL-27, STAT1, TLR4 and two downregulated IL-24andCD80 that best discriminate between active pulmonary TB and uninfected controls with AUC ranging from 0.9 to 1. Our data identified a molecular immune signature associated with theearly stages of active pulmonary tuberculosis and it could be further investigated as a potential biomarker of pulmonary TB.
MRI evaluation of foraminal changes in the cervical spine with assistance of a novel compression device
Authors: Hutchins J. , Lagerstrand K. , Stävlid E. , Svensson P-A. , Rennerfelt K. , Hebelka H. , Brisby H. 
Published: July 2023

AbstractStandard supine Magnetic Resonance Imaging (MRI) does not acquire images in a position where most patients with intermittent arm radiculopathy have symptoms. The aim of this study was to test the feasibility of a new compression device and to evaluate image quality and foraminal properties during a Spurling test under MRI acquisition. Ten asymptomatic individuals were included in the study (6 men and 4 women; age range 27 to 55 years). First, the subjects were positioned in the cervical compression device in a 3 T MRI scanner, and a volume T2 weighted (T2w) sequence was acquired in a relaxed supine position (3 min). Thereafter, the position and compressive forces on the patient’s neck (provocation position) were changed by maneuvering the device from the control room, with the aim to simulate a Spurling test, causing a mild foraminal compression, followed by a repeated image acquisition (3 min). A radiologist measured the blinded investigations evaluating cervical lordosis (C3–C7), foraminal area on oblique sagittal images and foraminal cross-distance in the axial plane. A total of three levels (C4–C7) were measured on the right side on each individual. Measurements were compared between the compressed and relaxed state. Reliability tests for inter- and intraclass correlation were performed. The device was feasible to use and well tolerated by all investigated individuals. Images of adequate quality was obtained in all patients. A significant increase (mean 9.4, p = 0.013) in the cervical lordosis and a decreased foraminal cross-distance (mean 32%, p < 0.001) was found, during the simulated Spurling test. The area change on oblique sagittal images did not reach a statistically significant change. The reliability tests on the quantitative measures demonstrated excellent intraobserver reliability and moderate to good interobserver reliability. Applying an individualized provocation test on the cervical spine, which simulates a Spurling test, during MRI acquisition was feasible with the novel device and provided images of satisfactory quality. MRI images acquired with and without compression showed changes in cervical lordosis and foraminal cross distance indicating the possibility of detecting changes of the foraminal properties. As a next step, the method is to be tested on symptomatic patients.
Genome sequencing and application of Taiwanese macaque Macaca cyclopis
Authors: Chiu Kuo-Ping , Stuart Lutimba , Ooi Hong Sain , Yu John , Smith David Glenn , Pei Kurtis Jai-Chyi 
Published: July 2023

AbstractFormosan macaque (Macaca cyclopis) is the only non-human primate in Taiwan Island. We performed de novo hybrid assembly for M. cyclopis using Illumina paired-end short reads, mate-pair reads and Nanopore long reads and obtained 5065 contigs with a N50 of 2.66 megabases. M. cyclopis contigs >  = 10 kb were assigned to chromosomes using Indian rhesus macaque (Macaca mulatta mulatta) genome assembly Mmul_10 as reference, resulting in a draft of M. cyclopis genome of 2,846,042,475 bases, distributed in 21 chromosomes. The draft genome contains 23,462 transcriptional origins (genes), capable of expressing 716,231 exons in 59,484 transcripts. Genome-based phylogenetic study using the assembled M. cyclopis genome together with genomes of four other macaque species, human, orangutan and chimpanzee showed similar result as previously reported. However, the M. cyclopis species was found to diverge from Chinese M. mulatta lasiota about 1.8 million years ago. Fossil gene analysis detected the presence of gap and pol endogenous viral elements of simian retrovirus in all macaques tested, including M. fascicularis, M. m. mulatta and M. cyclopis. However, M. cyclopis showed ~ 2 times less in number and more uniform in chromosomal locations. The constrain in foreign genome disturbance, presumably due to geographical isolation, should be able to simplify genomics-related investigations, making M. cyclopis an ideal primate species for medical research.