bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphatase protector alpha4 (α4) is involved in adipocyte maintenance and mitochondrial homeostasis through regulation of insulin signaling
Authors: Sakaguchi Masaji , Okagawa Shota , Okubo Yuma , Otsuka Yuri , Fukuda Kazuki , Igata Motoyuki , Kondo Tatsuya , Sato Yoshifumi , Yoshizawa Tatsuya , Fukuda Takaichi , Yamagata Kazuya , Cai Weikang , Tseng Yu-Hua , Sakaguchi Nobuo , Kahn C. Ronald , Araki Eiichi 
Published: October 2022

AbstractInsulin signaling is mediated via a network of protein phosphorylation. Dysregulation of this network is central to obesity, type 2 diabetes and metabolic syndrome. Here we investigate the role of phosphatase binding protein Alpha4 (α4) that is essential for the serine/threonine protein phosphatase 2A (PP2A) in insulin action/resistance in adipocytes. Unexpectedly, adipocyte-specific inactivation of α4 impairs insulin-induced Akt-mediated serine/threonine phosphorylation despite a decrease in the protein phosphatase 2A (PP2A) levels. Interestingly, loss of α4 also reduces insulin-induced insulin receptor tyrosine phosphorylation. This occurs through decreased association of α4 with Y-box protein 1, resulting in the enhancement of the tyrosine phosphatase protein tyrosine phosphatase 1B (PTP1B) expression. Moreover, adipocyte-specific knockout of α4 in male mice results in impaired adipogenesis and altered mitochondrial oxidation leading to increased inflammation, systemic insulin resistance, hepatosteatosis, islet hyperplasia, and impaired thermogenesis. Thus, the α4 /Y-box protein 1(YBX1)-mediated pathway of insulin receptor signaling is involved in maintaining insulin sensitivity, normal adipose tissue homeostasis and systemic metabolism.
Solving the MCM paradox by visualizing the scaffold of CMG helicase at active replisomes
Authors: Polasek-Sedlackova Hana , Miller Thomas C. R. , Krejci Jana , Rask Maj-Britt , Lukas Jiri 
Published: October 2022

AbstractGenome duplication is safeguarded by constantly adjusting the activity of the replicative CMG (CDC45-MCM2-7-GINS) helicase. However, minichromosome maintenance proteins (MCMs)—the structural core of the CMG helicase—have never been visualized at sites of DNA synthesis inside a cell (the so-called MCM paradox). Here, we solve this conundrum by showing that anti-MCM antibodies primarily detect inactive MCMs. Upon conversion of inactive MCMs to CMGs, factors that are required for replisome activity bind to the MCM scaffold and block MCM antibody binding sites. Tagging of endogenous MCMs by CRISPR-Cas9 bypasses this steric hindrance and enables MCM visualization at active replisomes. Thus, by defining conditions for detecting the structural core of the replicative CMG helicase, our results explain the MCM paradox, provide visual proof that MCMs are an integral part of active replisomes in vivo, and enable the investigation of replication dynamics in living cells exposed to a constantly changing environment.
Concerted expansion and contraction of immune receptor gene repertoires in plant genomes
Authors: Ngou Bruno Pok Man , Heal Robert , Wyler Michele , Schmid Marc W. , Jones Jonathan D. G. 
Published: October 2022

AbstractRecent reports suggest that cell-surface and intracellular immune receptors function synergistically to activate robust defence against pathogens, but whether they co-evolve is unclear. Here we determined the numbers of cell-surface and intracellular immune receptors in 350 species. Surprisingly, the number of receptor genes that are predicted to encode cell-surface and intracellular immune receptors is strongly correlated. We suggest this is consistent with mutual potentiation of immunity initiated by cell-surface and intracellular receptors being reflected in the concerted co-evolution of the size of their repertoires across plant species.
Amplitude and frequency modulation of subthalamic beta oscillations jointly encode the dopaminergic state in Parkinson’s disease
Authors: Averna Alberto , Marceglia Sara , Priori Alberto , Foffani Guglielmo 
Published: October 2022

AbstractBrain states in health and disease are classically defined by the power or the spontaneous amplitude modulation (AM) of neuronal oscillations in specific frequency bands. Conversely, the possible role of the spontaneous frequency modulation (FM) in defining pathophysiological brain states remains unclear. As a paradigmatic example of pathophysiological resting states, here we assessed the spontaneous AM and FM dynamics of subthalamic beta oscillations recorded in patients with Parkinson’s disease before and after levodopa administration. Even though AM and FM are mathematically independent, they displayed negatively correlated dynamics. First, AM decreased while FM increased with levodopa. Second, instantaneous amplitude and instantaneous frequency were negatively cross-correlated within dopaminergic states, with FM following AM by approximately one beta cycle. Third, AM and FM changes were also negatively correlated between dopaminergic states. Both the slow component of the FM and the fast component (i.e. the phase slips) increased after levodopa, but they differently contributed to the AM-FM correlations within and between states. Finally, AM and FM provided information about whether the patients were OFF vs. ON levodopa, with partial redundancy and with FM being more informative than AM. AM and FM of spontaneous beta oscillations can thus both separately and jointly encode the dopaminergic state in patients with Parkinson’s disease. These results suggest that resting brain states are defined not only by AM dynamics but also, and possibly more prominently, by FM dynamics of neuronal oscillations.
Giant Berry curvature dipole density in a ferroelectric Weyl semimetal
Authors: Zhang Cheng-Long , Liang Tian , Kaneko Yoshio , Nagaosa Naoto , Tokura Yoshinori 
Published: October 2022

AbstractThe nonlinear Hall effect (NLHE) reflects Berry-curvature-related properties in non-centrosymmetric but time-reversal-symmetric materials. So far, the NLHE of the investigated systems remains a tiny effect due to the lack of Weyl point as magnetic monopoles in 2D systems or to the high carrier concentration in 3D systems. Here, we report large NLHE due to gigantic Berry curvature dipole density as generated by tilted Weyl cones near the Fermi level in a model ferroelectric Weyl semimetal In-doped Pb1−xSnxTe. By systematically lowering the carrier concentration down to ~1016 cm−3, the Berry curvature dipole density reaches values around 10−21 m3, 102–107 times higher than the previously reported ones. Furthermore, NLHE exhibits a power law of carrier concentration and follows the k−2 relation of the Berry curvature expression derived from the monopole. The present study establishes giant NLHE in a ferroelectric Weyl semimetal, promising for future applications such as current rectification.
Fine-scale population spatialization data of China in 2018 based on real location-based big data
Authors: Chen Mingxing , Xian Yue , Huang Yaohuan , Zhang Xiaoping , Hu Maogui , Guo Shasha , Chen Liangkan , Liang Longwu 
Published: October 2022

AbstractAccurate location-based big data has a high resolution and a direct interaction with human activities, allowing for fine-scale population spatial data to be realized. We take the average of Tencent user location big data as a measure of ambient population. The county-level statistical population data in 2018 was used as the assigned input data. The log linear spatially weighted regression model was used to establish the relationship between location data and statistical data to allocate the latter to a 0.01° grid, and the ambient population data of mainland China was obtained. Extracting street-level (lower than county-level) statistics for accuracy testing, we found that POP2018 has the best fit with the actual permanent population (R2 = 0.91), and the error is the smallest (MSEPOP2018 = 22.48 <MSEWorldPop = 37.24 <MSELandScan = 100.91). This research supplemented in the refined spatial distribution data of people between census years, as well as presenting the application technique of big data in ambient population estimation and zoning mapping.
A novel approach to measure brain-to-brain spatial and temporal alignment during positive empathy
Authors: Toppi J. , Siniatchkin M. , Vogel P. , Freitag C. M. , Astolfi L. , Ciaramidaro A. 
Published: October 2022

AbstractEmpathy is defined as the ability to vicariously experience others’ suffering (vicarious pain) or feeling their joy (vicarious reward). While most neuroimaging studies have focused on vicarious pain and describe similar neural responses during the observed and the personal negative affective involvement, only initial evidence has been reported for the neural responses to others’ rewards and positive empathy. Here, we propose a novel approach, based on the simultaneous recording of multi-subject EEG signals and exploiting the wavelet coherence decomposition to measure the temporal alignment between ERPs in a dyad of interacting subjects. We used the Third-Party Punishment (TPP) paradigm to elicit the personal and vicarious experiences. During a positive experience, we observed the simultaneous presence in both agents of the Late Positive Potential (LPP), an ERP component related to emotion processing, as well as the existence of an inter-subject ERPs synchronization in the related time window. Moreover, the amplitude of the LPP synchronization was modulated by the presence of a human-agent. Finally, the localized brain circuits subtending the ERP-synchronization correspond to key-regions of personal and vicarious reward. Our findings suggest that the temporal and spatial ERPs alignment might be a novel and direct proxy measure of empathy.
A rapid change in magma plumbing taps porphyry copper deposit-forming magmas
Authors: Carter Lawrence C. , Tapster Simon R. , Williamson Ben J. , Buret Yannick , Selby David , Rollinson Gavyn K. , Millar Ian , Parvaz Daniel B. 
Published: October 2022

AbstractPorphyry-type deposits are a vital source of green technology metals such as copper and molybdenum. They typically form in subduction-related settings from large, long-lived magmatic systems. The most widely accepted model for their formation requires that mantle-derived magmas undergo an increase in volatiles and ore-forming constituents in mid- to lower crustal reservoirs over millions of years, however, this is mostly based on observations from shallow, sporadically exposed parts of porphyry systems. To examine this paradigm, we have evaluated the timeframe and geochemical signatures of magmatism in a ~ 8 km palaeodepth cross-section through plutonic and volcanic rocks of the classic Yerington magmatic system, Nevada. We show that the magmas in the upper parts of the system (< 8 km) underwent a major and rapid change in chemistry over a period of < 200 kyrs that is coincident with the initiation of ore formation. We attribute this change to a shift from extraction of quartz monzodiorite and quartz monzonite magmas evolving in mid-crustal reservoirs, and that had relatively poor ore-forming potential, to extraction of volatile-rich granitic magmas from greater (~ 30 km) depths. As the granites crystallised, late stage melts were intruded through the carapace as aplite dykes which contain traceable expressions of the porphyry deposit-forming fluids. The rapid nature of the shift in ore-forming potential narrows the temporal-geochemical footprint of magmas associated with porphyry mineralisation and provides new constraints for exploration models.
Two-stage variable-fidelity modeling of antennas with domain confinement
Authors: Pietrenko-Dabrowska Anna , Koziel Slawomir , Golunski Lukasz 
Published: October 2022

AbstractSurrogate modeling has become the method of choice in solving an increasing number of antenna design tasks, especially those involving expensive full-wave electromagnetic (EM) simulations. Notwithstanding, the curse of dimensionality considerably affects conventional metamodeling methods, and their capability to efficiently handle nonlinear antenna characteristics over broad ranges of the system parameters is limited. Performance-driven (or constrained) modeling frameworks may be employed to mitigate these issues by considering a construction of surrogates from the standpoint of the antenna performance figures rather than directly geometry parameters. This permits a significant reduction of the model setup cost without restricting its design utility. This paper proposes a novel modeling framework, which capitalizes on the domain confinement concepts and also incorporates variable-fidelity EM simulations, both at the surrogate domain definition stage, and when rendering the final surrogate. The latter employs co-kriging as a method of blending simulation data of different fidelities. The presented approach has been validated using three microstrip antennas, and demonstrated to yield reliable models at remarkably low CPU costs, as compared to both conventional and performance-driven modeling procedures.
A novel and robust method for counting components within bio-molecular complexes using fluorescence microscopy and statistical modelling
Authors: Mersmann Sophia F. , Johns Emma , Yong Tracer , McEwan Will A. , James Leo C. , Cohen Edward A. K. , Grove Joe 
Published: October 2022

AbstractCellular biology occurs through myriad interactions between diverse molecular components, many of which assemble in to specific complexes. Various techniques can provide a qualitative survey of which components are found in a given complex. However, quantitative analysis of the absolute number of molecules within a complex (known as stoichiometry) remains challenging. Here we provide a novel method that combines fluorescence microscopy and statistical modelling to derive accurate molecular counts. We have devised a system in which batches of a given biomolecule are differentially labelled with spectrally distinct fluorescent dyes (label A or B), and mixed such that B-labelled molecules are vastly outnumbered by those with label A. Complexes, containing this component, are then simply scored as either being positive or negative for label B. The frequency of positive complexes is directly related to the stoichiometry of interaction and molecular counts can be inferred by statistical modelling. We demonstrate this method using complexes of Adenovirus particles and monoclonal antibodies, achieving counts that are in excellent agreement with previous estimates. Beyond virology, this approach is readily transferable to other experimental systems and, therefore, provides a powerful tool for quantitative molecular biology.
Investigation of radiomics based intra-patient inter-tumor heterogeneity and the impact of tumor subsampling strategies
Authors: Henry T. , Sun R. , Lerousseau M. , Estienne T. , Robert C. , Besse B. , Robert C. , Paragios N. , Deutsch E. 
Published: October 2022

AbstractWhile radiomics analysis has been applied for localized cancer disease, its application to the metastatic setting involves a non-exhaustive lesion subsampling strategy which may sidestep the intrapatient tumoral heterogeneity, hindering the reproducibility and the therapeutic response performance. Our aim was to evaluate if radiomics features can capture intertumoral intrapatient heterogeneity, and the impact of tumor subsampling on the computed heterogeneity. To this end, We delineated and extracted radiomics features of all visible tumors from single acquisition pre-treatment computed tomography of patients with metastatic lung cancer (cohort L) and confirmed our results on a larger cohort of patients with metastatic melanoma (cohort M). To quantify the captured heterogeneity, the absolute coefficient of variation (CV) of each radiomics index was calculated at the patient-level and a sensitivity analysis was performed using only a subset of all extracted features robust to the segmentation step. The extent of information loss by six commonly used tumor sampling strategies was then assessed. A total of 602 lesions were segmented from 43 patients (median age 57, 4.9% female). All robust radiomics indexes exhibited at least 20% of variation with significant heterogeneity both in heavily and oligo metastasized patients, and also at the organ level. None of the segmentation subsampling strategies were able to recover the true tumoral heterogeneity obtained by exhaustive tumor sampling. Image-based inter-tumor intra-patient heterogeneity can be successfully grasped by radiomics analyses. Failing to take into account this kind of heterogeneity will lead to inconsistent predictive algorithms. Guidelines to standardize the tumor sampling step and/or AI-driven tools to alleviate the segmentation effort are required.
Brief overview of dietary intake, some types of gut microbiota, metabolic markers and research opportunities in sample of Egyptian women
Authors: Hassan Nayera E. , El Shebini Salwa M. , El-Masry Sahar A. , Ahmed Nihad H. , Kamal Ayat N. , Ismail Ahmed S. , Alian Khadija M. , Mostafa Mohammed I. , Selim Mohamed , Afify Mahmoud A. S. 
Published: October 2022

AbstractMetabolic syndrome (MetS) is a phenotype caused by the interaction of host intrinsic factors such as genetics and gut microbiome, and extrinsic factors such as diet and lifestyle. To demonstrate the interplay of intestinal microbiota with obesity, MetS markers, and some dietary ingredients among samples of Egyptian women. This study was a cross-sectional one that included 115 Egyptian women; 82 were obese (59 without MetS and 23 with MetS) and 33 were normal weight. All participants were subjected to anthropometric assessment, 24 h dietary recall, laboratory evaluation of liver enzymes (AST and ALT), leptin, short chain fatty acids (SCFA), C-reactive protein, fasting blood glucose, insulin, and lipid profile, in addition to fecal microbiota analysis for Lactobacillus, Bifidobacteria, Firmicutes, and Bacteroid. Data showed that the obese women with MetS had the highest significant values of the anthropometric and the biochemical parameters. Obese MetS women consumed a diet high in calories, protein, fat, and carbohydrate, and low in fiber and micronutrients. The Bacteroidetes and Firmicutes were the abundant bacteria among the different gut microbiota, with low Firmicutes/Bacteroidetes ratio, and insignificant differences between the obese with and without MetS and normal weight women were reported. Firmicutes/Bacteroidetes ratio significantly correlated positively with total cholesterol and LDL-C and negatively with SCFA among obese women with MetS. Findings of this study revealed that dietary factors, dysbiosis, and the metabolic product short chain fatty acids have been implicated in causing metabolic defects.
KIR-HLA gene diversities and susceptibility to lung cancer
Authors: Hematian Larki Marjan , Ashouri Elham , Barani Shaghik , Ghayumi Seiyed Mohammad Ali , Ghaderi Abbas , Rajalingam Raja 
Published: October 2022

AbstractKiller-cell immunoglobulin-like receptors (KIR) are essential for acquiring natural killer (NK) cell effector function, which is modulated by a balance between the net input of signals derived from inhibitory and activating receptors through engagement by human leukocyte antigen (HLA) class I ligands. KIR and HLA loci are polygenic and polymorphic and exhibit substantial variation between individuals and populations. We attempted to investigate the contribution ofKIRcomplex andHLA class Iligands to the genetic predisposition to lung cancer in the native population of southern Iran. We genotyped 16KIRgenes for a total of 232 patients with lung cancer and 448 healthy controls (HC), among which 85 patients and 178 HCs were taken into account for evaluating combinedKIR-HLAassociations.KIR2DL2and2DS2were increased significantly in patients than in controls, individually (OR 1.63, and OR 1.42, respectively) and in combination withHLA-C1ligands (OR 1.99, and OR 1.93, respectively).KIR3DS1(OR 0.67) and2DS1(OR 0.69) were more likely presented in controls in the absence of their relative ligands. The incidence of CxTx subset was increased in lung cancer patients (OR 1.83), and disease risk strikingly increased by more than fivefold among genotype ID19 carriers (a CxTx genotype that carries2DL2in the absence of2DS2, OR 5.92). We found that genotypes withiKIRs > aKIRs(OR 1.67) were more frequently presented in lung cancer patients. Additionally, patients with lung cancer were more likely to carry the combination of CxTx/2DS2compared to controls (OR 2.04), andiKIRs > aKIRsgenotypes in the presence of2DL2(OR 2.05) increased the likelihood of lung cancer development. Here we report new susceptibility factors and the contribution ofKIRandHLA-Iencoding genes to lung cancer risk, highlighting an array of genetic effects and disease setting which regulates NK cell responsiveness. Our results suggest that inheritedKIRgenes andHLA-Iligands specifying the educational state of NK cells can modify lung cancer risk.
Methods and reference data for middle ear transfer functions
Authors: Koch M. , Eßinger T. M. , Maier H. , Sim J. H. , Ren L. , Greene N. T. , Zahnert T. , Neudert M. , Bornitz M. 
Published: October 2022

AbstractHuman temporal bone specimens are used in experiments measuring the sound transfer of the middle ear, which is the standard method used in the development of active and passive middle ear implants. Statistical analyses of these experiments usually require that the TB samples are representative of the population of non-pathological middle ears. Specifically, this means that the specimens must be mechanically well-characterized. We present an in-depth statistical analysis of 478 data sets of middle ear transfer functions (METFs) from different laboratories. The data sets are preprocessed and various contributions to the variance of the data are evaluated. We then derive a statistical range as a reference against which individual METF measurements may be validated. The range is calculated as the two-sided 95% tolerance interval at audiological frequencies. In addition, the mean and 95% confidence interval of the mean are given as references for assessing the validity of a sample group. Finally, we provide a suggested procedure for measuring METFs using the methods described herein.
Rapid adsorption of selenium removal using iron manganese-based micro adsorbent
Authors: Qureshi Sundus Saeed , Memon Sheeraz Ahmed , Rafi-ul-Zaman  , Ram Nanik , Saeed Sumbul , Mubarak Nabisab Mujawar , Karri Rama Rao 
Published: October 2022

Abstract
Selenium in wastewater is of particular concern due to its increasing concentration, high mobility in water, and toxicity to organisms; therefore, this study was carried out to determine the removal efficiency of selenium using iron and manganese-based bimetallic micro-composite adsorbents. The bimetallic micro-composite adsorbent was synthesized by using the chemical reduction method. Micro-particles were characterized by using energy-dispersive X-ray spectroscopy for elemental analysis after adsorption, which confirms the adsorption of selenium on the surface of the micro-composite adsorbent, scanning electron microscopy, which shows particles are circular in shape and irregular in size, Brunauer–Emmett–Teller which results from the total surface area of particles were 59.345m2/g, Zeta particle size, which results from average particles size were 39.8 nm. Then it was applied to remove selenium ions in an aqueous system. The data revealed that the optimum conditions for the highest removal (95.6%) of selenium were observed at pH 8.5, adsorbent dosage of 25 mg, and contact time of 60 min, respectively, with the initial concentration of 1 ppm. The Langmuir and Freundlich isotherm models match the experimental data very well. The results proved that bimetallic micro-composite could be used as an effective selenium adsorbent due to the high adsorption capacity and the short adsorption time needed to achieve equilibrium. Regarding the reusability of bimetallic absorbent, the adsorption and desorption percentages decreased from 50 to 45% and from 56 to 53%, respectively, from the 1st to the 3rd cycle.