bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil
Authors: Tong Di , Wang Youjing , Yu Haodan , Shen Haojie , Dahlgren Randy A , Xu Jianming 
Published: May 2023

Abstract
Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the “viral shuttle” exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net “carbon sink” vs. “carbon source” in soils.
P38 kinase in gastrointestinal cancers
Authors: Phan Thuy , Zhang Xu Hannah , Rosen Steven , Melstrom Laleh G. 
Published: May 2023

AbstractGastrointestinal cancers are a leading cause of cancer morbidity and mortality worldwide with 4.2 million new cases and 3.2 million deaths estimated in 2020. Despite the advances in primary and adjuvant therapies, patients still develop distant metastases and require novel therapies. Mitogen‑activated protein kinase (MAPK) cascades are crucial signaling pathways that regulate many cellular processes, including proliferation, differentiation, apoptosis, stress responses and cancer development. p38 Mitogen Activated Protein Kinases (p38 MAPKs) includes four isoforms: p38α (MAPK14), p38β (MAPK11), p38γ (MAPK12), and p38δ (MAPK13). p38 MAPK was first identified as a stress response protein kinase that phosphorylates different transcriptional factors. Dysregulation of p38 pathways, in particular p38γ, are associated with cancer development, metastasis, autophagy and tumor microenvironment. In this article, we provide an overview of p38 and p38γ with respect to gastrointestinal cancers. Furthermore, targeting p38γ is also discussed as a potential therapy for gastrointestinal cancers.
Revealing topology in metals using experimental protocols inspired by K-theory
Authors: Cheng Wenting , Cerjan Alexander , Chen Ssu-Ying , Prodan Emil , Loring Terry A. , Prodan Camelia 
Published: May 2023

AbstractTopological metals are conducting materials with gapless band structures and nontrivial edge-localized resonances. Their discovery has proven elusive because traditional topological classification methods require band gaps to define topological robustness. Inspired by recent theoretical developments that leverage techniques from the field of C∗-algebras to identify topological metals, here, we directly observe topological phenomena in gapless acoustic crystals and realize a general experimental technique to demonstrate their topology. Specifically, we not only observe robust boundary-localized states in a topological acoustic metal, but also re-interpret a composite operator—mathematically derived from the K-theory of the problem—as a new Hamiltonian whose physical implementation allows us to directly observe a topological spectral flow and measure the topological invariants. Our observations and experimental protocols may offer insights for discovering topological behaviour across a wide array of artificial and natural materials that lack bulk band gaps.
Leveraging generative adversarial networks to create realistic scanning transmission electron microscopy images
Authors: Khan Abid , Lee Chia-Hao , Huang Pinshane Y. , Clark Bryan K. 
Published: May 2023

AbstractThe rise of automation and machine learning (ML) in electron microscopy has the potential to revolutionize materials research through autonomous data collection and processing. A significant challenge lies in developing ML models that rapidly generalize to large data sets under varying experimental conditions. We address this by employing a cycle generative adversarial network (CycleGAN) with a reciprocal space discriminator, which augments simulated data with realistic spatial frequency information. This allows the CycleGAN to generate images nearly indistinguishable from real data and provide labels for ML applications. We showcase our approach by training a fully convolutional network (FCN) to identify single atom defects in a 4.5 million atom data set, collected using automated acquisition in an aberration-corrected scanning transmission electron microscope (STEM). Our method produces adaptable FCNs that can adjust to dynamically changing experimental variables with minimal intervention, marking a crucial step towards fully autonomous harnessing of microscopy big data.
Combining skin and olfactory α-synuclein seed amplification assays (SAA)—towards biomarker-driven phenotyping in synucleinopathies
Authors: Kuzkina A. , Rößle J. , Seger A. , Panzer C. , Kohl A. , Maltese V. , Musacchio T. , Blaschke S. J. , Tamgüney G. , Kaulitz S. , Rak K. , Scherzad A. , Zimmermann P. H. , Klussmann J. P. , Hackenberg S. , Volkmann J. , Sommer C. , Sommerauer M. , Doppler K. 
Published: May 2023

AbstractSeed amplification assays (SAA) are becoming commonly used in synucleinopathies to detect α-synuclein aggregates. Studies in Parkinson’s disease (PD) and isolated REM-sleep behavior disorder (iRBD) have shown a considerably lower sensitivity in the olfactory epithelium than in CSF or skin. To get an insight into α-synuclein (α-syn) distribution within the nervous system and reasons for low sensitivity, we compared SAA assessment of nasal brushings and skin biopsies in PD (n = 27) and iRBD patients (n = 18) and unaffected controls (n = 30). α-syn misfolding was overall found less commonly in the olfactory epithelium than in the skin, which could be partially explained by the nasal brushing matrix exerting an inhibitory effect on aggregation. Importantly, the α-syn distribution was not uniform: there was a higher deposition of misfolded α-syn across all sampled tissues in the iRBD cohort compared to PD (supporting the notion of RBD as a marker of a more malignant subtype of synucleinopathy) and in a subgroup of PD patients, misfolded α-syn was detectable only in the olfactory epithelium, suggestive of the recently proposed brain-first PD subtype. Assaying α-syn of diverse origins, such as olfactory (part of the central nervous system) and skin (peripheral nervous system), could increase diagnostic accuracy and allow better stratification of patients.
A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters
Authors: Anstett Julia , Plominsky Alvaro M. , DeLong Edward F. , Kiesser Alyse , Jürgens Klaus , Morgan-Lang Connor , Stepanauskas Ramunas , Stewart Frank J. , Ulloa Osvaldo , Woyke Tanja , Malmstrom Rex , Hallam Steven J. 
Published: May 2023

AbstractOxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.
Serum neutrophil gelatinase-associated lipocalin and lactate level during surgery predict acute kidney injury and early allograft dysfunction after liver transplantation
Authors: Cho Hyeyeon , Jung Ji-Yoon , Yoon Hyun-Kyu , Yang Seong-Mi , Lee Ho-Jin , Kim Won Ho , Jung Chul-Woo , Suh Kyung-Suk 
Published: May 2023

AbstractEarly allograft dysfunction (EAD) and acute kidney injury (AKI) are common and clinically important complications after liver transplantation. Serum lactate level at the end of surgery could predict EAD and neutrophil gelatinase-associated lipocalin (NGAL) is known as a biomarker for AKI after liver transplantation. The authors investigated whether the combination of these two laboratory tests could be used as an early predictor of these two complications of EAD and AKI. We reviewed cases undergoing living donor liver transplantation (n = 353). Lactate-adjusted NGAL level, a combination of these two predictors, was calculated as the sum of each value multiplied by the odds ratio for EAD or AKI. We evaluated whether this combined predictor at the end of surgery is significantly associated with both postoperative AKI or EAD. We compared the area under the receiver operating characteristic curve (AUC) between our multivariable regression models with and without NGAL, lactate, or lactate-adjusted NGAL. NGAL, lactate and lactate-adjusted NGAL are significant predictors for EAD and AKI. The regression model for EAD or AKI including lactate-adjusted NGAL showed a greater AUC (for EAD: odds ratio [OR] 0.88, 95% confidence interval [CI] 0.84–0.91; for AKI: OR 0.89, 95% CI 0.85–0.92) compared to the AUC of the models including lactate (for EAD: OR 0.84, 95% CI 0.81–0.88; for AKI: OR 0.79, 95% CI 0.74–0.83) or NGAL alone (for EAD: OR 0.82, 95% CI 0.77–0.86; for AKI: OR 0.84, 95% CI 0.80–0.88) or the model without lactate or NGAL (for EAD: OR 0.64, 95% CI 0.58–0.69, for AKI: OR 0.75, 95% CI 0.70–0.79). In conclusion, lactate-adjusted NGAL level at the end of surgery could be a reliable combined laboratory predictor for postoperative EAD or AKI after liver transplantation with a greater discriminative ability than lactate or NGAL alone.
Bioinspired 5-caffeoylquinic acid capped silver nanoparticles using Coffee arabica leaf extract for high-sensitive cysteine detection
Authors: Harsha Haridas E. S. , Bhattacharya Susmita , Varma M. K. Ravi , Chandra Goutam Kumar 
Published: May 2023

AbstractSelection of plant extracts as bioactive phytochemical source to synthesize nanoparticles is highly demanding due to the biocompatibility, nontoxicity, and cost-effectiveness over other available physical and chemical methods. Here, for the first time, Coffee arabica leaf extracts (CAE) were used to produce highly stable silver nanoparticles (AgNPs) and the corresponding bio reduction, capping and stabilization mechanism mediated by dominant isomer 5-caffeoylquinic acid (5-CQA) is discussed. UV–Vis, FTIR, μRaman spectroscopy, TEM, DLS and Zeta potential analyzer measurements were employed to characterize these green synthesized NPs. The affinity of 5-CQA capped CAE–AgNPs to thiol moiety of amino acid is utilized for the selective as well as sensitive detection of L-cysteine (L-Cys) to a low detection limit of 0.1 nM, as obtained from its μRaman spectra. Hence, the proposed novel, simple, eco-friendly, and economically sustainable method can provide a promising nanoplatform in the field of biosensors compliant with large-scale industrial production of AgNPs without aid of further instrumentation.
Multi-channel recordings reveal age-related differences in the sleep of juvenile and adult zebra finches
Authors: Yeganegi Hamed , Ondracek Janie M. 
Published: May 2023

AbstractDespite their phylogenetic differences and distinct pallial structures, mammals and birds show similar electroencephalography (EEG) traces during sleep, consisting of distinct rapid eye movement (REM) sleep and slow wave sleep (SWS) stages. Studies in human and a limited number of other mammalian species show that this organization of sleep into interleaving stages undergoes radical changes during lifetime. Do these age-dependent variations in sleep patterns also occur in the avian brain? Does vocal learning have an effect on sleep patterns in birds? To answer these questions, we recorded multi-channel sleep EEG from juvenile and adult zebra finches for several nights. Whereas adults spent more time in SWS and REM sleep, juveniles spent more time in intermediate sleep (IS). The amount of IS was significantly larger in male juveniles engaged in vocal learning compared to female juveniles, which suggests that IS could be important for vocal learning. In addition, we observed that functional connectivity increased rapidly during maturation of young juveniles, and was stable or declined at older ages. Synchronous activity during sleep was larger for recording sites in the left hemisphere for both juveniles and adults, and generally intra-hemispheric synchrony was larger than inter-hemispheric synchrony during sleep. A graph theory analysis revealed that in adults, highly correlated EEG activity tended to be distributed across fewer networks that were spread across a wider area of the brain, whereas in juveniles, highly correlated EEG activity was distributed across more numerous, albeit smaller, networks in the brain. Overall, our results reveal that significant changes occur in the neural signatures of sleep during maturation in an avian brain.
Predicting glycemic control status and high blood glucose levels through voice characteristic analysis in patients with cystic fibrosis-related diabetes (CFRD)
Authors: Suppakitjanusant Pichatorn , Kasemkosin Nittaya , Sivapiromrat Alisa K. , Weinstein Samuel , Ongphiphadhanakul Boonsong , Hunt William R. , Sueblinvong Viranuj , Tangpricha Vin 
Published: May 2023

AbstractCystic fibrosis-related diabetes (CFRD) is associated with reduced life expectancy in adults with cystic fibrosis (CF). Voice analysis may be a convenient method for diagnosing and monitoring CFRD. This study aims to determine the relationship between voice characteristics and markers of glucose and glycemic control and to identify if voice analysis can predict high blood glucose levels and glycemic control in adults with CFRD. We conducted a prospective cross-sectional study in adults with CF from March to December 2021. We recorded 3-second voice samples of a sustained /a/ vowel and analyzed voice characteristic using the Computerized Speech Lab with the Multi-Dimensional Voice Program. In female participants with CFRD, the noise-to-harmonic ratio was significantly lower in those with HbA1c ≥ 7. Furthermore, fundamental frequency variation was significantly lower in both male and female participants with CFRD who had a glucose level of 200 mg/dL or higher at the time of collection. This finding was also associated with a high level of point-of-care glucose. The human voice has potential as a non-invasive tool for measuring glucose levels and glycemic control status in CFRD patients in the future.
RNA-Seq–based transcriptome analysis of corneal endothelial cells derived from patients with Fuchs endothelial corneal dystrophy
Authors: Nakagawa Tatsuya , Tokuda Yuichi , Nakano Masakazu , Komori Yuya , Hanada Naoya , Tourtas Theofilos , Schlötzer-Schrehardt Ursula , Kruse Friedrich , Tashiro Kei , Koizumi Noriko , Okumura Naoki 
Published: May 2023

AbstractFuchs endothelial corneal dystrophy (FECD) is the most common inherited corneal disease. Fibrillar focal excrescences called guttae and corneal edema due to corneal endothelial cell death result in progressive vision loss. Multiple genetic variants have been reported, but the pathogenesis of FECD is not fully understood. In this study, we used RNA-Seq to analyze differential gene expression in the corneal endothelium obtained from patients with FECD. Differential expression analysis of transcriptomic profiles revealed that expression of 2366 genes (1092 upregulated and 1274 downregulated genes) was significantly altered in the corneal endothelium of patients with FECD compared to healthy subjects. Gene ontology analysis demonstrated an enrichment of genes involved in extracellular matrix (ECM) organization, response to oxidative stress, and apoptotic signaling. Several pathway analyses consistently indicated the dysregulation of ECM-associated pathways. Our differential gene expression findings support the previously proposed underlying mechanisms, including oxidative stress and apoptosis of endothelial cells, as well as the phenotypic clinical FECD hallmark of ECM deposits. Further investigation focusing on differentially expressed genes related to these pathways might be beneficial for elucidating mechanisms and developing novel therapies.
Kilohertz-frequency interferential current induces hypoalgesic effects more comfortably than TENS
Authors: Park Dahoon , Kim Yushin 
Published: May 2023

AbstractRecent research on transcutaneous electrical stimulation has shown that inhibiting nerve conduction with a kilohertz frequency is both effective and safe. This study primarily aims to demonstrate the hypoalgesic effect on the tibial nerve using transcutaneous interferential-current nerve inhibition (TINI), which injects the kilohertz frequency produced by the interferential currents. Additionally, the secondary objective was to compare the analgesic effect and comfort of TINI and transcutaneous electrical nerve stimulation (TENS). Thirty-one healthy adults participated in this cross-over repeated measures study. The washout period was set to 24 h or more. Stimulus intensity was set just below the pain threshold level. TINI and TENS were applied for 20 min each. The ankle passive dorsiflexion range of motion, pressure pain threshold (PPT), and tactile threshold were measured at the baseline, pre-test, test (immediately before ceasing intervention), and post-test (30 min after ceasing intervention) sessions. After the interventions, the participants evaluated the level of discomfort for TINI and TENS on a 10 cm visual analog scale (VAS). As the results, PPT significantly increased compared to baseline in test and posttest sessions of TINI, but not in those of TENS. Also, participants reported that TENS was 36% more discomfort than TINI. The hypoalgesic effect was not significantly different between TINI and TENS. In conclusion, we found that TINI inhibited mechanical pain sensitivity and that the inhibitory effect persisted long after electrical stimulation ceased. Our study also shows that TINI provides the hypoalgesic effect more comfortably than TENS.
Continuous cuffless blood pressure monitoring using photoplethysmography-based PPG2BP-net for high intrasubject blood pressure variations
Authors: Joung Jingon , Jung Chul-Woo , Lee Hyung-Chul , Chae Moon-Jung , Kim Hae-Sung , Park Jonghun , Shin Won-Yong , Kim Changhyun , Lee Minhyung , Choi Changwoo 
Published: May 2023

AbstractContinuous, comfortable, convenient (C3), and accurate blood pressure (BP) measurement and monitoring are needed for early diagnosis of various cardiovascular diseases. To supplement the limited C3 BP measurement of existing cuff-based BP technologies, though they may achieve reliable accuracy, cuffless BP measurement technologies, such as pulse transit/arrival time, pulse wave analysis, and image processing, have been studied to obtain C3 BP measurement. One of the recent cuffless BP measurement technologies, innovative machine-learning and artificial intelligence-based technologies that can estimate BP by extracting BP-related features from photoplethysmography (PPG)-based waveforms have attracted interdisciplinary attention of the medical and computer scientists owing to their handiness and effectiveness for both C3 and accurate, i.e., C3A, BP measurement. However, C3A BP measurement remains still unattainable because the accuracy of the existing PPG-based BP methods was not sufficiently justified for subject-independent and highly varying BP, which is a typical case in practice. To circumvent this issue, a novel convolutional neural network(CNN)- and calibration-based model (PPG2BP-Net) was designed by using a comparative paired one-dimensional CNN structure to estimate highly varying intrasubject BP. To this end, approximately $$70\%$$

70
%

, $$20\%$$

20
%

, and $$10\%$$

10
%

of 4185 cleaned, independent subjects from 25,779 surgical cases were used for training, validating, and testing the proposed PPG2BP-Net, respectively and exclusively (i.e., subject-independent modelling). For quantifying the intrasubject BP variation from an initial calibration BP, a novel ‘standard deviation of subject-calibration centring (SDS)’ metric is proposed wherein high SDS represents high intrasubject BP variation from the calibration BP and vice versa. PPG2BP-Net achieved accurately estimated systolic and diastolic BP values despite high intrasubject variability. In 629-subject data acquired after 20 minutes following the A-line (arterial line) insertion, low error mean and standard deviation of $$0.209\pm 7.509$$

0.209
±
7.509

and $$0.150\pm 4.549\;\textrm{mmHg}$$

0.150
±
4.549

mmHg

for highly varying A-line systolic and diastolic BP values, respectively, where their SDSs are 15.375 and 8.745. This study moves one step forward in developing the C3A cuffless BP estimation devices that enable the push and agile pull services.
Dynamic calibration with approximate Bayesian computation for a microsimulation of disease spread
Authors: Asher Molly , Lomax Nik , Morrissey Karyn , Spooner Fiona , Malleson Nick 
Published: May 2023

AbstractThe global COVID-19 pandemic brought considerable public and policy attention to the field of infectious disease modelling. A major hurdle that modellers must overcome, particularly when models are used to develop policy, is quantifying the uncertainty in a model’s predictions. By including the most recent available data in a model, the quality of its predictions can be improved and uncertainties reduced. This paper adapts an existing, large-scale, individual-based COVID-19 model to explore the benefits of updating the model in pseudo-real time. We use Approximate Bayesian Computation (ABC) to dynamically recalibrate the model’s parameter values as new data emerge. ABC offers advantages over alternative calibration methods by providing information about the uncertainty associated with particular parameter values and the resulting COVID-19 predictions through posterior distributions. Analysing such distributions is crucial in fully understanding a model and its outputs. We find that forecasts of future disease infection rates are improved substantially by incorporating up-to-date observations and that the uncertainty in forecasts drops considerably in later simulation windows (as the model is provided with additional data). This is an important outcome because the uncertainty in model predictions is often overlooked when models are used in policy.