bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinct dynein complexes defined by DYNLRB1 and DYNLRB2 regulate mitotic and male meiotic spindle bipolarity
Authors: He Shuwen , Gillies John P. , Zang Juliana L. , Córdoba-Beldad Carmen M. , Yamamoto Io , Fujiwara Yasuhiro , Grantham Julie , DeSantis Morgan E. , Shibuya Hiroki
Published: March 2023

Spindle formation in male meiosis relies on the canonical centrosome system, which is distinct from acentrosomal oocyte meiosis, but its specific regulatory mechanisms remain unknown. Herein, we report that DYNLRB2 (Dynein light chain roadblock-type-2) is a male meiosis-upregulated dynein light chain that is indispensable for spindle formation in meiosis I. In Dynlrb2 KO mouse testes, meiosis progression is arrested in metaphase I due to the formation of multipolar spindles with fragmented pericentriolar material (PCM). DYNLRB2 inhibits PCM fragmentation through two distinct pathways; suppressing premature centriole disengagement and targeting NuMA (nuclear mitotic apparatus) to spindle poles. The ubiquitously expressed mitotic counterpart, DYNLRB1, has similar roles in mitotic cells and maintains spindle bipolarity by targeting NuMA and suppressing centriole overduplication. Our work demonstrates that two distinct dynein complexes containing DYNLRB1 or DYNLRB2 are separately used in mitotic and meiotic spindle formations, respectively, and that both have NuMA as a common target.
Structural and functional analysis of human pannexin 2 channel
Authors: He Zhihui , Zhao Yonghui , Rau Michael J. , Fitzpatrick James A. J. , Sah Rajan , Hu Hongzhen , Yuan Peng
Published: March 2023

The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of PANX2 channel function remains largely unknown. Here, we present a cryo-electron microscopy structure of human PANX2, which reveals pore properties contrasting with those of the intensely studied paralog PANX1. The extracellular selectivity filter, defined by a ring of basic residues, more closely resembles that of the distantly related volume-regulated anion channel (VRAC) LRRC8A, rather than PANX1. Furthermore, we show that PANX2 displays a similar anion permeability sequence as VRAC, and that PANX2 channel activity is inhibited by a commonly used VRAC inhibitor, DCPIB. Thus, the shared channel properties between PANX2 and VRAC may complicate dissection of their cellular functions through pharmacological manipulation. Collectively, our structural and functional analysis provides a framework for development of PANX2-specific reagents that are needed for better understanding of channel physiology and pathophysiology.
Functional comparison of metabolic networks across species
Authors: Ramon Charlotte , Stelling Jörg
Published: March 2023

Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history and environmental adaptation shape these phenotypes is an open problem. Especially for microbes, which are metabolically diverse and often interact in complex communities, few phenotypes can be determined directly. Instead, potential phenotypes are commonly inferred from genomic information, and rarely were model-predicted phenotypes employed beyond the species level. Here, we propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and thereby link genotype and environment to phenotype. We show that these correlations provide a consistent functional complement to genomic information by capturing how network context shapes gene function. This enables, for example, phylogenetic inference across all domains of life at the organism level. For 245 bacterial species, we identify conserved and variable metabolic functions, elucidate the quantitative impact of evolutionary history and ecological niche on these functions, and generate hypotheses on associated metabolic phenotypes. We expect our framework for the joint interpretation of metabolic phenotypes, evolution, and environment to help guide future empirical studies.
Unraveling a bifunctional mechanism for methanol-to-formate electro-oxidation on nickel-based hydroxides
Authors: Zhu Botao , Dong Bo , Wang Feng , Yang Qifeng , He Yunpeng , Zhang Cunjin , Jin Peng , Feng Lai
Published: March 2023

For nickel-based catalysts, in-situ formed nickel oxyhydroxide has been generally believed as the origin for anodic biomass electro-oxidations. However, rationally understanding the catalytic mechanism still remains challenging. In this work, we demonstrate that NiMn hydroxide as the anodic catalyst can enable methanol-to-formate electro-oxidation reaction (MOR) with a low cell-potential of 1.33/1.41 V at 10/100 mA cm−2, a Faradaic efficiency of nearly 100% and good durability in alkaline media, remarkably outperforming NiFe hydroxide. Based on a combined experimental and computational study, we propose a cyclic pathway that consists of reversible redox transitions of NiII-(OH)2/NiIII-OOH and a concomitant MOR. More importantly, it is proved that the NiIII-OOH provides combined active sites including NiIIIand nearby electrophilic oxygen species, which work in a cooperative manner to promote either spontaneous or non-spontaneous MOR process. Such a bifunctional mechanism can well account for not only the highly selective formate formation but also the transient presence of NiIII-OOH. The different catalytic activities of NiMn and NiFe hydroxides can be attributed to their different oxidation behaviors. Thus, our work provides a clear and rational understanding of the overall MOR mechanism on nickel-based hydroxides, which is beneficial for advanced catalyst design.
Neuraminidase 1 promotes renal fibrosis development in male mice
Authors: Chen Qian-Qian , Liu Kang , Shi Ning , Ma Gaoxiang , Wang Peipei , Xie Hua-Mei , Jin Si-Jia , Wei Ting-Ting , Yu Xiang-Yu , Wang Yi , Zhang Jun-Yuan , Li Ping , Qi Lian-Wen , Zhang Lei
Published: March 2023

The functions of the influenza virus neuraminidase has been well documented but those of the mammalian neuraminidases remain less explored. Here, we characterize the role of neuraminidase 1 (NEU1) in unilateral ureteral obstruction (UUO) and folic acid (FA)-induced renal fibrosis mouse models. We find that NEU1 is significantly upregulated in the fibrotic kidneys of patients and mice. Functionally, tubular epithelial cell-specific NEU1 knockout inhibits epithelial-to-mesenchymal transition, inflammatory cytokines production, and collagen deposition in mice. Conversely, NEU1 overexpression exacerbates progressive renal fibrosis. Mechanistically, NEU1 interacts with TGFβ type I receptor ALK5 at the 160-200aa region and stabilizes ALK5 leading to SMAD2/3 activation. Salvianolic acid B, a component of Salvia miltiorrhiza, is found to strongly bind to NEU1 and effectively protect mice from renal fibrosis in a NEU1-dependent manner. Collectively, this study characterizes a promotor role for NEU1 in renal fibrosis and suggests a potential avenue of targeting NEU1 to treat kidney diseases.
The small GTPase Rit2 modulates LRRK2 kinase activity, is required for lysosomal function and protects against alpha-synuclein neuropathology
Authors: Obergasteiger Julia , Castonguay Anne-Marie , Pizzi Sara , Magnabosco Stefano , Frapporti Giulia , Lobbestael Evy , Baekelandt Veerle , Hicks Andrew A. , Pramstaller Peter P. , Gravel Claude , Corti Corrado , Lévesque Martin , Volta Mattia
Published: March 2023

In Parkinson’s disease (PD) misfolded alpha-synuclein (aSyn) accumulates in the substantia nigra, where dopaminergic neurons are progressively lost. The mechanisms underlying aSyn pathology are still unclear, but they are hypothesized to involve the autophagy-lysosome pathway (ALP). LRRK2 mutations are a major cause of familial and sporadic PD, and LRRK2 kinase activity has been shown to be involved in pS129-aSyn inclusion modulation. We observed selective downregulation of the novel PD risk factor RIT2 in vitro and in vivo. Rit2 overexpression in G2019S-LRRK2 cells rescued ALP abnormalities and diminished aSyn inclusions. In vivo, viral mediated overexpression of Rit2 operated neuroprotection against AAV-A53T-aSyn. Furthermore, Rit2 overexpression prevented the A53T-aSyn-dependent increase of LRRK2 kinase activity in vivo. On the other hand, reduction of Rit2 levels leads to defects in the ALP, similar to those induced by the G2019S-LRRK2 mutation. Our data indicate that Rit2 is required for correct lysosome function, inhibits overactive LRRK2 to ameliorate ALP impairment, and counteracts aSyn aggregation and related deficits. Targeting Rit2 could represent an effective strategy to combat neuropathology in familial and idiopathic PD.
Symptoms assessment and decision to treat patients with advanced Parkinson’s disease based on wearables data
Authors: Virbel-Fleischman Clara , Mousin Flavien , Liu Shuo , Hardy Sébastien , Corvol Jean-Christophe , Benatru Isabelle , Bendetowicz David , Béreau Matthieu , De Cock Valérie Cochen , Drapier Sophie , Frismand Solène , Giordana Caroline , Devos David , Rétory Yann , Grabli David
Published: March 2023

Body-worn sensors (BWS) could provide valuable information in the management of Parkinson’s disease and support therapeutic decisions based on objective monitoring. To study this pivotal step and better understand how relevant information is extracted from BWS results and translated into treatment adaptation, eight neurologists examined eight virtual cases composed of basic patient profiles and their BWS monitoring results. Sixty-four interpretations of monitoring results and the subsequent therapeutic decisions were collected. Relationship between interrater agreements in the BWS reading and the severity of symptoms were analyzed via correlation studies. Logistic regression was used to identify associations between the BWS parameters and suggested treatment modifications. Interrater agreements were high and significantly associated with the BWS scores. Summarized BWS scores reflecting bradykinesia, dyskinesia, and tremor predicted the direction of treatment modifications. Our results suggest that monitoring information is robustly linked to treatment adaptation and pave the way to loop systems able to automatically propose treatment modifications from BWS recordings information.
A survey on dogs with valvular disease flying to Japan for operation
Authors: Takahashi Arane , Takeuchi Sayaka , Chen Ayaka , Uechi Masami
Published: March 2023

In small-breed dogs, myxomatous mitral valve disease (MMVD) is a common disease which may lead to chronic heart failure. Mitral valve repair is an optimal surgical treatment that is currently available in limited veterinary facilities globally because it requires a special surgery team and specific devices. Therefore, some dogs must travel overseas to undergo this surgery. However, a question arises regarding the safety of dogs when traveling by air with a heart disease. We aimed to evaluate the effect of flight journey on dogs with mitral valve disease, including survival rates, symptoms during the trip, laboratory test results, and operational outcomes. All dogs stayed near the owner in the cabin during the flight. The survival rate after the flight was 97.5% in 80 dogs. The surgical survival rates (96.0% and 94.3%) and hospitalization periods (7 days and 7 days) were similar between overseas and domestic dogs. This report shows that taking air flights in the cabin may not have a significant effect on dogs with MMVD, on the premise that their overall conditions are stable under cardiac medication.
Terrestrial planet and asteroid belt formation by Jupiter–Saturn chaotic excitation
Authors: Lykawka Patryk Sofia , Ito Takashi
Published: March 2023

The terrestrial planets formed by accretion of asteroid-like objects within the inner solar system’s protoplanetary disk. Previous works have found that forming a small-mass Mars requires the disk to contain little mass beyond ~ 1.5 au (i.e., the disk mass was concentrated within this boundary). The asteroid belt also holds crucial information about the origin of such a narrow disk. Several scenarios may produce a narrow disk. However, simultaneously replicating the four terrestrial planets and the inner solar system properties remains elusive. Here, we found that chaotic excitation of disk objects generated by a near-resonant configuration of Jupiter–Saturn can create a narrow disk, allowing the formation of the terrestrial planets and the asteroid belt. Our simulations showed that this mechanism could typically deplete a massive disk beyond ~ 1.5 au on a 5–10 Myr timescale. The resulting terrestrial systems reproduced the current orbits and masses of Venus, Earth and Mars. Adding an inner region disk component within ~ 0.8–0.9 au allowed several terrestrial systems to simultaneously form analogues of the four terrestrial planets. Our terrestrial systems also frequently satisfied additional constraints: Moon-forming giant impacts occurring after a median ~ 30–55 Myr, late impactors represented by disk objects formed within 2 au, and effective water delivery during the first 10–20 Myr of Earth’s formation. Finally, our model asteroid belt explained the asteroid belt’s orbital structure, small mass and taxonomy (S-, C- and D/P-types).
Root cause prediction for failures in semiconductor industry, a genetic algorithm–machine learning approach
Authors: Rammal Abbas , Ezukwoke Kenneth , Hoayek Anis , Batton-Hubert Mireille
Published: March 2023

Failure analysis has become an important part of guaranteeing good quality in the electronic component manufacturing process. The conclusions of a failure analysis can be used to identify a component’s flaws and to better understand the mechanisms and causes of failure, allowing for the implementation of remedial steps to improve the product’s quality and reliability. A failure reporting, analysis, and corrective action system is a method for organizations to report, classify, and evaluate failures, as well as plan corrective actions. These text feature datasets must first be preprocessed by Natural Language Processing techniques and converted to numeric by vectorization methods before starting the process of information extraction and building predictive models to predict failure conclusions of a given failure description. However, not all-textual information is useful for building predictive models suitable for failure analysis. Feature selection has been approached by several variable selection methods. Some of them have not been adapted for use in large data sets or are difficult to tune and others are not applicable to textual data. This article aims to develop a predictive model able to predict the failure conclusions using the discriminating features of the failure descriptions. For this, we propose to combine a Genetic Algorithm with supervised learning methods for an optimal prediction of the conclusions of failure in terms of the discriminant features of failure descriptions. Since we have an unbalanced dataset, we propose to apply an F1 score as a fitness function of supervised classification methods such as Decision Tree Classifier and Support Vector Machine. The suggested algorithms are called GA-DT and GA-SVM. Experiments on failure analysis textual datasets demonstrate the effectiveness of the proposed GA-DT method in creating a better predictive model of failure conclusion compared to using the information of the entire textual features or limited features selected by a genetic algorithm based on a SVM. Quantitative performances such as BLEU score and cosine similarity are used to compare the prediction performance of the different approaches.
Exploiting machine learning models to identify novel Alzheimer’s disease biomarkers and potential targets
Authors: Alamro Hind , Thafar Maha A. , Albaradei Somayah , Gojobori Takashi , Essack Magbubah , Gao Xin
Published: March 2023

We still do not have an effective treatment for Alzheimer's disease (AD) despite it being the most common cause of dementia and impaired cognitive function. Thus, research endeavors are directed toward identifying AD biomarkers and targets. In this regard, we designed a computational method that exploits multiple hub gene ranking methods and feature selection methods with machine learning and deep learning to identify biomarkers and targets. First, we used three AD gene expression datasets to identify 1/ hub genes based on six ranking algorithms (Degree, Maximum Neighborhood Component (MNC), Maximal Clique Centrality (MCC), Betweenness Centrality (BC), Closeness Centrality, and Stress Centrality), 2/ gene subsets based on two feature selection methods (LASSO and Ridge). Then, we developed machine learning and deep learning models to determine the gene subset that best distinguishes AD samples from the healthy controls. This work shows that feature selection methods achieve better prediction performances than the hub gene sets. Beyond this, the five genes identified by both feature selection methods (LASSO and Ridge algorithms) achieved an AUC = 0.979. We further show that 70% of the upregulated hub genes (among the 28 overlapping hub genes) are AD targets based on a literature review and six miRNA (hsa-mir-16-5p, hsa-mir-34a-5p, hsa-mir-1-3p, hsa-mir-26a-5p, hsa-mir-93-5p, hsa-mir-155-5p) and one transcription factor, JUN, are associated with the upregulated hub genes. Furthermore, since 2020, four of the six microRNA were also shown to be potential AD targets. To our knowledge, this is the first work showing that such a small number of genes can distinguish AD samples from healthy controls with high accuracy and that overlapping upregulated hub genes can narrow the search space for potential novel targets.
CRISPR-assisted test for Schistosoma haematobium
Authors: Cherkaoui Dounia , Mesquita Silvia G. , Huang Da , Lugli Elena B. , Webster Bonnie L. , McKendry Rachel A.
Published: March 2023

Schistosomiasis is a major neglected tropical disease targeted for elimination as a public health issue by 2030, however there is an urgent need for more sensitive and specific diagnostic tests suitable to resource-limited settings. Here we developed CATSH, a CRISPR-assisted diagnostic test for Schistosoma haematobium, utilising recombinase polymerase amplification, Cas12a-targeted cleavage and portable real-time fluorescence detection. CATSH showed high analytical sensitivity, consistent detection of a single parasitic egg and specificity for urogenital Schistosoma species. Thanks to a novel CRISPR-compatible sample preparation developed using simulated urine samples containing parasitic eggs, CATSH had a sample-to-result within 2 h. The components of CATSH can be lyophilised, reducing cold chain dependence and widening access to lower and middle-income countries. This work presents a new application of CRISPR diagnostics for highly sensitive and specific detection of parasitic pathogens in remote areas and could have a significant impact on the elimination of neglected tropical diseases.
Striatal dopamine D2-like receptors availability in obesity and its modulation by bariatric surgery: a systematic review and meta-analysis
Authors: Ribeiro Gabriela , Maia Ana , Cotovio Gonçalo , Oliveira Francisco P. M. , Costa Durval C. , Oliveira-Maia Albino J.
Published: March 2023

There is significant evidence linking a ‘reward deficiency syndrome’ (RDS), comprising decreased availability of striatal dopamine D2-like receptors (DD2lR) and addiction-like behaviors underlying substance use disorders and obesity. Regarding obesity, a systematic review of the literature with a meta-analysis of such data is lacking. Following a systematic review of the literature, we performed random-effects meta-analyses to determine group differences in case–control studies comparing DD2lR between individuals with obesity and non-obese controls and prospective studies of pre- to post-bariatric surgery DD2lR changes. Cohen's d was used to measure effect size. Additionally, we explored factors potentially associated with group differences in DD2lR availability, such as obesity severity, using univariate meta-regression. In a meta-analysis including positron emission tomography (PET) and single-photon emission computed tomography (SPECT) studies, striatal DD2lR availability did not significantly differ between obesity and controls. However, in studies comprising patients with class III obesity or higher, group differences were significant, favoring lower DD2lR availability in the obesity group. This effect of obesity severity was corroborated by meta-regressions showing inverse associations between the body mass index (BMI) of the obesity group and DD2lR availability. Post-bariatric changes in DD2lR availability were not found, although a limited number of studies were included in this meta-analysis. These results support lower DD2lR in higher classes of obesity which is a more targeted population to explore unanswered questions regarding the RDS.
Transcriptome analysis reveals association of carotenoid metabolism pathway with fruit color in melon
Authors: Diao Qiannan , Tian Shoubo , Cao Yanyan , Yao Dongwei , Fan Hongwei , Zhang Yongping
Published: March 2023

Flesh color is an important quality of melon (Cucumis meloL.) and is determined mainly by carotenoid content, awarding them with colors, aromas, and nutrients. enhancing the nutritional and health benefits of fruits and vegetables for humans. In this study, we performed transcriptomic analysis of two melon inbred line “B-14” (orange-flesh) and “B-6” (white-flesh) at three developmental stages. We observed that the β-carotene content of inbred line “B-6” (14.232 μg/g) was significantly lower than that of inbred line “B-14” (0.534 μg/g). RNA-sequencing and quantitative reverse transcription PCR analyses were performed to identify differentially expressed genes (DEGs) between the two inbred lines at different stages; the DEGs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). We identified 33 structural DEGs in different developmental periods of the two lines that were related to carotenoid metabolism. Among them,PSY,Z-ISO,ZDS,CRTISO,CCD4,VDE1, andNCED2were highly correlated with carotenoid content. Thus, this study provides a basis for molecular mechanism of carotenoid biosynthesis and flesh color in melon fruit.
Cross over to collective rearrangements near the dry-wet transition in two-dimensional foams
Authors: Yanagisawa Naoya , Kurita Rei
Published: March 2023

Liquid foams respond plastically to external perturbations over some critical magnitude. This rearrangement process is directly related to the mechanical properties of the foams, playing a significant role in determining foam lifetime, deformability, elasticity, and fluidity. In this paper, we experimentally investigate the rearrangement dynamics of foams near a dry-wet transition. When a foam transforms from a dry state to a wet state, it is found that considering collective events, separated T1 events propagate in dry foams, while T1 events occur simultaneously in wet foams. This cross over to collective rearrangements is closely related to the change in local bubble arrangements and mobility. Furthermore, it is also found that a probability of collective rearrangement events occurring follows a Poisson distribution, suggesting that there is little correlation between discrete collective rearrangement events. These results constitute progress in understanding the dynamical properties of soft jammed systems, relevant for biological and material sciences as well as food science.
The spatial spillover effect of higher SO2 emission tax rates on PM2.5 concentration in China
Authors: Wang Kaifeng , Liu Yu , Wang Shaochen , Li Chengpeng
Published: March 2023

In this paper, the adoption of SO2emission tax rates higher than the legal minimum standard is regarded as a noteworthy policy reform in China (quasi-natural experiment), and a spatial Difference-in-Differences (Spatial-DID) model is constructed to test the direct effects (local effects) and indirect effects (spatial spillover effects) of SO2emission tax policy reform on PM2.5concentrations in the atmosphere of 285 China’s cities. The estimation and calculation results of the Spatial-DID model show that the SO2emission tax policy reform can significantly reduce local PM2.5concentration and significantly promote PM2.5concentration in surrounding areas. The results of heterogeneity analysis show that the SO2emission tax policy reform can produce a relatively more beneficial spatial spillover effect in eastern cities and higher administrative level cities, while the pollutants emission rights trading and the reform of NOxemission tax rates can produce beneficial spatial spillover effects when cooperating with the reform of SO2emission tax rates. The results of the mediation effect analysis show that the higher SO2emission tax rate can aggravate the surrounding PM2.5pollution by promoting the aggregation level of industrial production factors and the industrial SO2emission intensity in the surrounding areas, which can support the existence of the pollution heaven effect.
Endocannabinoid administration affects taste preference and the expression of cannabinoid and opioid receptors in the amygdala of early lactating cows
Authors: Schwerdtfeger Jessica , Krause Annika , Kalbe Claudia , Mazzuoli-Weber Gemma , Eggert Anja , Puppe Birger , Kuhla Björn , Röttgen Volker
Published: March 2023

The aim of the study was to investigate the influence of intraperitoneal N-arachidonoylethanolamide (AEA) on taste preference for feed and water, tongue taste receptor signalling (TAS1R2, GNAT3), and endocannabinoid (CNR1, CNR2, GPR55) and opioid (OPRD1, OPRK1, OPRM1, OPRL1) receptors in the amygdala and nucleus accumbens in periparturient cows. We conducted taste preference tests using unaltered, umami-tasting, and sweet-tasting water and feed, before and after calving. After calving, eight cows received AEA injections (3 µg/(kg bodyweight × day), 25 days), whereas eight control (CON) cows received saline injections. Tissue was sampled 30 days after calving. Before calving, both cow groups preferred sweet-tasting feed and umami-tasting water. After calving, only the AEA-treated group preferred sweet-tasting feed, whereas the CON group showed no clear taste preference. In the amygdala, the mRNA expression of CNR1, OPRD1 (left hemisphere) and OPRK1 (right hemisphere) was lower in AEA animals than in CON animals, whereas no differences were found in the nucleus accumbens and tongue taste receptor expression. In conclusion, AEA administration enhanced existing taste preferences and reduced the expression of specific endocannabinoid and opioid receptors in the amygdala. The results support endocannabinoid-opioid interactions in the control of taste-dependent feed preference in early lactating cows.
Magnetothermal-based non-invasive focused magnetic stimulation for functional recovery in chronic stroke treatment
Authors: Kim Hohyeon , Kim Jihye , Kim Jahae , Oh Seungjun , Choi Kangho , Yoon Jungwon
Published: March 2023

Magnetic heat-based brain stimulation of specific lesions could promote the restoration of impaired motor function caused by chronic stroke. We delivered localized stimulation by nanoparticle-mediated heat generation within the targeted brain area via focused magnetic stimulation. The middle cerebral artery occlusion model was prepared, and functional recovery in the chronic-phase stroke rat model was demonstrated by the therapeutic application of focused magnetic stimulation. We observed a transient increase in blood–brain barrier permeability at the target site of < 4 mm and metabolic brain activation at the target lesion. After focused magnetic stimulation, the rotarod score increased by 390 ± 28% (p < 0.05) compared to the control group. Standardized uptake value in the focused magnetic stimulation group increased by 2063 ± 748% (p < 0.01) compared to the control group. Moreover, an increase by 24 ± 5% (p < 0.05) was observed in the sham group as well. Our results show that non-invasive focused magnetic stimulation can safely modulate BBB permeability and enhance neural activation for chronic-phase stroke treatment in the targeted deep brain area.
Radial-tangential mode of single-wall carbon nanotubes manifested by Landau regulation: reinterpretation of low- and intermediate-frequency Raman signals
Authors: Hembram K. P. S. S. , Kim Jin-Gyu , Lee Sang-Gil , Park Jeongwon , Lee Jae-Kap
Published: March 2023

The low-frequency Raman signals of single-wall carbon nanotubes (SWNTs), appearing in the range of 100–300 cm−1, have been interpreted as radial-breathing mode (RBM) comprising pure radial Eigenvectors. Here, we report that most of the low-frequency and intermediate-frequency signals of SWNTs are radial-tangential modes (RTMs) coexisting radial and tangential Eigenvectors, while only the first peak at the low-frequency side is the RBM. Density functional theory simulation for SWNTs of ~ 2 nm in diameter shows that dozens of RTMs exhibit following the RBM (~ 150 cm−1) up to G-mode (~ 1592 cm−1) in order with Landau regulation. We specify the RBM and the RTM on Raman spectra obtained from SWNTs, where both appear as prominent peaks between 149 and 170 cm−1 and ripple-like peaks between 166 and 1440 cm−1, respectively. We report that the RTMs have been regarded as RBM (~ 300 cm−1) and ambiguously named as intermediate-frequency mode (300–1300 cm−1) without assignment. The RTMs gradually interlink the RBM and the G-mode resulting in the symmetric Raman spectra in intensity. We reveal high-resolution transmission microscope evidence for a helical structure of SWNTs, informing the typical diameter of commercial SWNTs to be 1.4–2 nm.
Shotgun proteomics of quinoa seeds reveals chitinases enrichment under rainfed conditions
Authors: Poza-Viejo Laura , Redondo-Nieto Miguel , Matías Javier , Granado-Rodríguez Sara , Maestro-Gaitán Isaac , Cruz Verónica , Olmos Enrique , Bolaños Luis , Reguera Maria
Published: March 2023

Quinoa is an Andean crop whose cultivation has been extended to many different parts of the world in the last decade. It shows a great capacity for adaptation to diverse climate conditions, including environmental stressors, and, moreover, the seeds are very nutritious in part due to their high protein content, which is rich in essential amino acids. They are gluten-free seeds and contain good amounts of other nutrients such as unsaturated fatty acids, vitamins, or minerals. Also, the use of quinoa hydrolysates and peptides has been linked to numerous health benefits. Altogether, these aspects have situated quinoa as a crop able to contribute to food security worldwide. Aiming to deepen our understanding of the protein quality and function of quinoa seeds and how they can vary when this crop is subjected to water-limiting conditions, a shotgun proteomics analysis was performed to obtain the proteomes of quinoa seeds harvested from two different water regimes in the field: rainfed and irrigated conditions. Differentially increased levels of proteins determined in seeds from each field condition were analysed, and the enrichment of chitinase-related proteins in seeds harvested from rainfed conditions was found. These proteins are described as pathogen-related proteins and can be accumulated under abiotic stress. Thus, our findings suggest that chitinase-like proteins in quinoa seeds can be potential biomarkers of drought. Also, this study points to the need for further research to unveil their role in conferring tolerance when coping with water-deficient conditions.
Application of machine learning in predicting non-alcoholic fatty liver disease using anthropometric and body composition indices
Authors: Razmpour Farkhondeh , Daryabeygi-Khotbehsara Reza , Soleimani Davood , Asgharnezhad Hamzeh , Shamsi Afshar , Bajestani Ghasem Sadeghi , Nematy Mohsen , Pour Mahdiyeh Razm , Maddison Ralph , Islam Sheikh Mohammed Shariful
Published: March 2023

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease, which can progress from simple steatosis to advanced cirrhosis and hepatocellular carcinoma. Clinical diagnosis of NAFLD is crucial in the early stages of the disease. The main aim of this study was to apply machine learning (ML) methods to identify significant classifiers of NAFLD using body composition and anthropometric variables. A cross-sectional study was carried out among 513 individuals aged 13 years old or above in Iran. Anthropometric and body composition measurements were performed manually using body composition analyzer InBody 270. Hepatic steatosis and fibrosis were determined using a Fibroscan. ML methods including k-Nearest Neighbor (kNN), Support Vector Machine (SVM), Radial Basis Function (RBF) SVM, Gaussian Process (GP), Random Forest (RF), Neural Network (NN), Adaboost and Naïve Bayes were examined for model performance and to identify anthropometric and body composition predictors of fatty liver disease. RF generated the most accurate model for fatty liver (presence of any stage), steatosis stages and fibrosis stages with 82%, 52% and 57% accuracy, respectively. Abdomen circumference, waist circumference, chest circumference, trunk fat and body mass index were among the most important variables contributing to fatty liver disease. ML-based prediction of NAFLD using anthropometric and body composition data can assist clinicians in decision making. ML-based systems provide opportunities for NAFLD screening and early diagnosis, especially in population-level and remote areas.
Importance of ipsilateral residual hearing for spatial hearing by bimodal cochlear implant users
Authors: Thomas Mathew , Galvin John J. , Fu Qian-Jie
Published: March 2023

Bimodal cochlear implant (CI) listeners have difficulty utilizing spatial cues to segregate competing speech, possibly due to tonotopic mismatch between the acoustic input frequency and electrode place of stimulation. The present study investigated the effects of tonotopic mismatch in the context of residual acoustic hearing in the non-CI ear or residual hearing in both ears. Speech recognition thresholds (SRTs) were measured with two co-located or spatially separated speech maskers in normal-hearing adults listening to acoustic simulations of CIs; low frequency acoustic information was available in the non-CI ear (bimodal listening) or in both ears. Bimodal SRTs were significantly better with tonotopically matched than mismatched electric hearing for both co-located and spatially separated speech maskers. When there was no tonotopic mismatch, residual acoustic hearing in both ears provided a significant benefit when maskers were spatially separated, but not when co-located. The simulation data suggest that hearing preservation in the implanted ear for bimodal CI listeners may significantly benefit utilization of spatial cues to segregate competing speech, especially when the residual acoustic hearing is comparable across two ears. Also, the benefits of bilateral residual acoustic hearing may be best ascertained for spatially separated maskers.
Indicator-based approach for fluvial flood risk assessment at municipal level in Slovakia
Authors: Vojtek Matej
Published: March 2023

The article focuses on the mapping and assessment of fluvial flood risk at municipal level of Slovakia. The fluvial floods risk index (FFRI), composed of a hazard component and a vulnerability component, was computed for 2927 municipalities using spatial multicriteria analysis and geographic information systems (GIS). The fluvial flood hazard index (FFHI) was computed based on eight physical-geographical indicators and land cover representing the riverine flood potential and also the frequency of flood events in individual municipalities. The fluvial flood vulnerability index (FFVI) was calculated using seven indicators representing the economic and social vulnerability of municipalities. All of the indicators were normalized and weighted using the rank sum method. By aggregating the weighted indicators, we obtained the FFHI and FFVI in each municipality. The final FFRI is a result of a synthesis of the FFHI and FFVI. The results of this study can be used mainly in the framework of flood risk management at national spatial scale, but also for local governments and periodic update of the Preliminary Flood Risk Assessment document, which is carried out at the national level under the EU Floods Directive.
Development of a risk prediction score and equation for chronic kidney disease: a retrospective cohort study
Authors: Kawasoe Shin , Kubozono Takuro , Salim Anwar Ahmed , Yoshimine Haruhito , Mawatari Seiichi , Ojima Satoko , Kawabata Takeko , Ikeda Yoshiyuki , Miyahara Hironori , Tokushige Koichi , Ido Akio , Ohishi Mitsuru
Published: March 2023

Chronic kidney disease (CKD) is a risk factor for end-stage renal disease and contributes to increased risk of cardiovascular disease morbidity and mortality. We aimed to develop a risk prediction score and equation for future CKD using health checkup data. This study included 58,423 Japanese participants aged 30–69 years, who were randomly assigned to derivation and validation cohorts at a ratio of 2:1. The predictors were anthropometric indices, life style, and blood sampling data. In derivation cohort, we performed multivariable logistic regression analysis and obtained the standardized beta coefficient of each factor that was significantly associated with new-onset CKD and assigned scores to each factor. We created a score and an equation to predict CKD after 5 years and applied them to validation cohort to assess their reproducibility. The risk score ranged 0–16, consisting of age, sex, hypertension, dyslipidemia, diabetes, hyperuricemia, and estimated glomerular filtration rate (eGFR), with area under the curve (AUC) of 0.78 for the derivation cohort and 0.79 for the validation cohort. The CKD incidence gradually and constantly increased as the score increased from ≤ 6 to ≥ 14. The equation consisted of the seven indices described above, with AUC of 0.88 for the derivation cohort and 0.89 for the validation cohort. We developed a risk score and equation to predict CKD incidence after 5 years in Japanese population under 70 years of age. These models had reasonably high predictivity, and their reproducibility was confirmed through internal validation.
Cloning, characterization, and heterologous expression of a candidate Hirudin gene from the salivary gland transcriptome of Hirudo nipponia
Authors: Shi Ping , Wei Jian , You Huajian , Chen Shijiang , Tan Fayin , Lu Zenghui
Published: March 2023

Hirudin is a pharmacologically active substance in leeches with potent blood anticoagulation properties. Although recombinant hirudin production isolated from Hirudo medicinalis Linnaeus and Hirudinaria manillensis Lesson is known, to our knowledge, this study is the first to report recombinant hirudin expression and production from Hirudo nipponia Whitman. Thus, the present study aimed to clone and characterize the full-length cDNA of a candidate hirudin gene (c16237_g1), which is localized on the salivary gland transcriptome of H. nipponia, and further evaluate its recombinant production using a eukaryotic expression system. The 489-bp cDNA possessed several properties of the hirudin “core” motifs associated with binding to the thrombin catalytic pocket. A fusion expression vector (pPIC9K-hirudin) was constructed and successfully transformed into Pichia pastoris strain GS115 via electroporation. Sodium dodecyl sulphate–polyacrylamide gel electrophoresis and western blot analysis confirmed hirudin expression. The recombinant protein was expressed with a yield of 6.68 mg/L culture. Mass spectrometry analysis further confirmed target protein expression. The concentration and antithrombin activity of purified hirudin were 1.67 mg/mL and 14,000 ATU/mL, respectively. These findings provide a basis for further elucidating the molecular anticoagulation mechanism of hirudin, and address China’s growing market demand for engineered H. nipponia-derived hirudin and hirudin-based drugs.
Genome-wide association study of population-standardised cognitive performance phenotypes in a rural South African community
Authors: Soo Cassandra C. , Brandenburg Jean-Tristan , Nebel Almut , Tollman Stephen , Berkman Lisa , Ramsay Michèle , Choudhury Ananyo
Published: March 2023

Cognitive function is an indicator for global physical and mental health, and cognitive impairment has been associated with poorer life outcomes and earlier mortality. A standard cognition test, adapted to a rural-dwelling African community, and the Oxford Cognition Screen-Plus were used to capture cognitive performance as five continuous traits (total cognition score, verbal episodic memory, executive function, language, and visuospatial ability) for 2,246 adults in this population of South Africans. A novel common variant, rs73485231, reached genome-wide significance for association with episodic memory using data for ~14 million markers imputed from the H3Africa genotyping array data. Window-based replication of previously implicated variants and regions of interest support the discovery of African-specific associated variants despite the small population size and low allele frequency. This African genome-wide association study identifies suggestive associations with general cognition and domain-specific cognitive pathways and lays the groundwork for further genomic studies on cognition in Africa.
A neurophysiological perspective on the integration between incidental learning and cognitive control
Authors: Takacs Adam , Beste Christian
Published: March 2023

Adaptive behaviour requires interaction between neurocognitive systems. Yet, the possibility of concurrent cognitive control and incidental sequence learning remains contentious. We designed an experimental procedure of cognitive conflict monitoring that follows a pre-defined sequence unknown to participants, in which either statistical or rule-based regularities were manipulated. We show that participants learnt the statistical differences in the sequence when stimulus conflict was high. Neurophysiological (EEG) analyses confirmed but also specified the behavioural results: the nature of conflict, the type of sequence learning, and the stage of information processing jointly determine whether cognitive conflict and sequence learning support or compete with each other. Especially statistical learning has the potential to modulate conflict monitoring. Cognitive conflict and incidental sequence learning can engage in cooperative fashion when behavioural adaptation is challenging. Three replication and follow-up experiments provide insights into the generalizability of these results and suggest that the interaction of learning and cognitive control is dependent on the multifactorial aspects of adapting to a dynamic environment. The study indicates that connecting the fields of cognitive control and incidental learning is advantageous to achieve a synergistic view of adaptive behaviour.
Defect engineering of silicon with ion pulses from laser acceleration
Authors: Redjem Walid , Amsellem Ariel J. , Allen Frances I. , Benndorf Gabriele , Bin Jianhui , Bulanov Stepan , Esarey Eric , Feldman Leonard C. , Ferrer Fernandez Javier , Garcia Lopez Javier , Geulig Laura , Geddes Cameron R. , Hijazi Hussein , Ji Qing , Ivanov Vsevolod , Kanté Boubacar , Gonsalves Anthony , Meijer Jan , Nakamura Kei , Persaud Arun , Pong Ian , Obst-Huebl Lieselotte , Seidl Peter A. , Simoni Jacopo , Schroeder Carl , Steinke Sven , Tan Liang Z. , Wunderlich Ralf , Wynne Brian , Schenkel Thomas
Published: March 2023

Defect engineering is foundational to classical electronic device development and for emerging quantum devices. Here, we report on defect engineering of silicon with ion pulses from a laser accelerator in the laser intensity range of 1019 W cm−2 and ion flux levels of up to 1022 ions cm−2 s−1, about five orders of magnitude higher than conventional ion implanters. Low energy ions from plasma expansion of the laser-foil target are implanted near the surface and then diffuse into silicon samples locally pre-heated by high energy ions from the same laser-ion pulse. Silicon crystals exfoliate in the areas of highest energy deposition. Color centers, predominantly W and G-centers, form directly in response to ion pulses without a subsequent annealing step. We find that the linewidth of G-centers increases with high ion flux faster than the linewidth of W-centers, consistent with density functional theory calculations of their electronic structure. Intense ion pulses from a laser-accelerator drive materials far from equilibrium and enable direct local defect engineering and high flux doping of semiconductors.
A UPLC-Q-TOF/MS and network pharmacology method to explore the mechanism of Anhua fuzhuan tea intervention in nonalcoholic fatty liver disease
Authors: Tian Feng-Ming , Yi Jian , Tang Yan , Chen Bo-Wei , Long Hong-Ping , Liu Ying-Fei , Ou-yang Yin , Zhang Wen-Jiang , Tang Rong-Mei , Liu Bai-Yan
Published: March 2023

The possible mechanism by which the active components of Anhua fuzhuan tea act on FAM in NAFLD lesions was investigated.
First direct observation of the built-in electric field and oxygen vacancy migration in ferroelectric Hf0.5Zr0.5O2 film during electrical cycling
Authors: Chen Liang , Liang Zhongxin , Shao Shixuan , Huang Qianqian , Tang Kechao , Huang Ru
Published: March 2023

By combining differential phase contrast scanning transmission electron microscope (DPC-STEM) and Energy Disperse Spectroscopy (EDS) analysis, the migration of oxygen vacancies and the evolution of the built-in field in ferroelectric HfO2 are observed for the first time.
Insights into the mechanism of the symmetry dependent SHG properties in low dimensional KNbO3 structures
Authors: Wu Tianhui , Yin Baipeng , Bian Zhenpan , Gao Yahui , Gu Jianmin , Wang Desong
Published: March 2023

The second harmonic generation (SHG) response of low-dimensional nanomaterials is potential dependence on structural symmetry and high-density surface defects, e.g., body contribution and surface contribution.
Enhancement of photovoltaic performance in ferrocenyl π-extended multi donor–π–acceptor (D–D′–π–A) dyes using chenodeoxycholic acid as a dye co-adsorbent for dye sensitized solar cells
Authors: Prabu Selvam , Viswanathan Thamodharan , David Ezhumalai , Jagadeeswari Sivanadanam , Palanisami Nallasamy
Published: March 2023

Enhanced DSSC efficiencies were attained in the presence of chenodeoxycholic acid (CDCA) as a co-adsorbent in multi-donor ferrocenyl dyes.
Geometry-dependent valence tautomerism, magnetism, and electrical conductivity in 1D iron–tetraoxolene chains
Authors: Kamin Ashlyn A. , Moseley Ian P. , Oh Jeewhan , Brannan E. J. , Gannon Paige M. , Kaminsky Werner , Zadrozny Joseph M. , Xiao Dianne J.
Published: March 2023

Here we show how a simple change in the geometry of 1D iron–tetraoxolene chains dramatically alters the observed physical properties, including the presence of valence tautomerism, strong magnetic coupling, and electrical conductivity.
A self-assembled molecularly triboelectronegative cellulose nanofiber material with ultrahigh contact triboelectrification for the design of green triboelectric nanogenerators
Authors: Li Yang , Wang Nannan , Wang Sheng , Li Bofan , Ye Enyi , Loh Xianjun , Li Zibiao
Published: March 2023

A novel green TENG with modified CNF as the electronegative tribolayer was prepared and can be used as a self-powered power module for wearable electronics.
Recent advances of two-dimensional lubricating materials: from tunable tribological properties to applications
Authors: Zhang Xiaole , Ren Tianhui , Li Zhipeng
Published: March 2023

2D nanomaterial lubricants have received increasing attention as mild and environmentally friendly friction and wear moderators. They can act as promising industrial antiwear agents to alleviate problems of energy loss and resource waste caused by wear of mechanical parts.
Pulsed-waveform electrocatalytic detoxification of hexavalent chromium promoted by pseudocapacitive effects
Authors: Xin Huaijia , Wang Hang , Zhang Wei , Liu Yang , Zhang Jun , Zhang Gong , Ji Qinghua , Liu Huijuan , Qu Jiuhui
Published: March 2023

We report a pulsed-voltage method using a pseudocapacitive electrode to improve the efficiency of the electrochemical reaction for aqueous Cr(vi) detoxification.