bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health
Authors: Bui Thi Phuong Nam , Mannerås-Holm Louise , Puschmann Robert , Wu Hao , Troise Antonio Dario , Nijsse Bart , Boeren Sjef , Bäckhed Fredrik , Fiedler Dorothea , deVos Willem M. 
Published: August 2021

AbstractWe describe the anaerobic conversion of inositol stereoisomers to propionate and acetate by the abundant intestinal genus Anaerostipes. A inositol pathway was elucidated by nuclear magnetic resonance using [13C]-inositols, mass spectrometry and proteogenomic analyses in A. rhamnosivorans, identifying 3-oxoacid CoA transferase as a key enzyme involved in both 3-oxopropionyl-CoA and propionate formation. This pathway also allowed conversion of phytate-derived inositol into propionate as shown with [13C]-phytate in fecal samples amended with A. rhamnosivorans. Metabolic and (meta)genomic analyses explained the adaptation of Anaerostipes spp. to inositol-containing substrates and identified a propionate-production gene cluster to be inversely associated with metabolic biomarkers in (pre)diabetes cohorts. Co-administration of myo-inositol with live A. rhamnosivorans in western-diet fed mice reduced fasting-glucose levels comparing to heat-killed A. rhamnosivorans after 6-weeks treatment. Altogether, these data suggest a potential beneficial role for intestinal Anaerostipes spp. in promoting host health.
Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM
Authors: Antanasijevic Aleksandar , Sewall Leigh M. , Cottrell Christopher A. , Carnathan Diane G. , Jimenez Luis E. , Ngo Julia T. , Silverman Jennifer B. , Groschel Bettina , Georgeson Erik , Bhiman Jinal , Bastidas Raiza , LaBranche Celia , Allen Joel D. , Copps Jeffrey , Perrett Hailee R. , Rantalainen Kimmo , Cannac Fabien , Yang Yuhe R. , de la Peña Alba Torrents , Rocha Rebeca Froes , Berndsen Zachary T. , Baker David , King Neil P. , Sanders Rogier W. , Moore John P. , Crotty Shane , Crispin Max , Montefiori David C. , Burton Dennis R. , Schief William R. , Silvestri Guido , Ward Andrew B. 
Published: August 2021

AbstractEngineered ectodomain trimer immunogens based on BG505 envelope glycoprotein are widely utilized as components of HIV vaccine development platforms. In this study, we used rhesus macaques to evaluate the immunogenicity of several stabilized BG505 SOSIP constructs both as free trimers and presented on a nanoparticle. We applied a cryoEM-based method for high-resolution mapping of polyclonal antibody responses elicited in immunized animals (cryoEMPEM). Mutational analysis coupled with neutralization assays were used to probe the neutralization potential at each epitope. We demonstrate that cryoEMPEM data can be used for rapid, high-resolution analysis of polyclonal antibody responses without the need for monoclonal antibody isolation. This approach allowed to resolve structurally distinct classes of antibodies that bind overlapping sites. In addition to comprehensive mapping of commonly targeted neutralizing and non-neutralizing epitopes in BG505 SOSIP immunogens, our analysis revealed that epitopes comprising engineered stabilizing mutations and of partially occupied glycosylation sites can be immunogenic.
Spin-state reconfiguration induced by alternating magnetic field for efficient oxygen evolution reaction
Authors: Zhou Gang , Wang Peifang , Li Hao , Hu Bin , Sun Yan , Huang Rong , Liu Lizhe 
Published: August 2021

AbstractOxygen evolution reaction (OER) plays a determining role in electrochemical energy conversion devices, but challenges remain due to the lack of effective low-cost electrocatalysts and insufficient understanding about sluggish reaction kinetics. Distinguish from complex nano-structuring, this work focuses on the spin-related charge transfer and orbital interaction between catalysts and intermediates to accelerate catalytic reaction kinetics. Herein, we propose a simple magnetic-stimulation approach to rearrange spin electron occupation in noble-metal-free metal-organic frameworks (MOFs) with a feature of thermal-differentiated superlattice, in which the localized magnetic heating in periodic spatial distribution makes the spin flip occur at particular active sites, demonstrating a spin-dependent reaction pathway. As a result, the spin-rearranged Co0.8Mn0.2 MOF displays mass activities of 3514.7 A gmetal−1 with an overpotential of ~0.27 V, which is 21.1 times that of pristine MOF. Our findings provide a new paradigm for designing spin electrocatalysis and steering reaction kinetics.
Giant anisotropic photonics in the 1D van der Waals semiconductor fibrous red phosphorus
Authors: Du Luojun , Zhao Yanchong , Wu Linlu , Hu Xuerong , Yao Lide , Wang Yadong , Bai Xueyin , Dai Yunyun , Qiao Jingsi , Uddin Md Gius , Li Xiaomei , Lahtinen Jouko , Bai Xuedong , Zhang Guangyu , Ji Wei , Sun Zhipei 
Published: August 2021

AbstractA confined electronic system can host a wide variety of fascinating electronic, magnetic, valleytronic and photonic phenomena due to its reduced symmetry and quantum confinement effect. For the recently emerging one-dimensional van der Waals (1D vdW) materials with electrons confined in 1D sub-units, an enormous variety of intriguing physical properties and functionalities can be expected. Here, we demonstrate the coexistence of giant linear/nonlinear optical anisotropy and high emission yield in fibrous red phosphorus (FRP), an exotic 1D vdW semiconductor with quasi-flat bands and a sizeable bandgap in the visible spectral range. The degree of photoluminescence (third-order nonlinear) anisotropy can reach 90% (86%), comparable to the best performance achieved so far. Meanwhile, the photoluminescence (third-harmonic generation) intensity in 1D vdW FRP is strong, with quantum efficiency (third-order susceptibility) four (three) times larger than that in the most well-known 2D vdW materials (e.g., MoS2). The concurrent realization of large linear/nonlinear optical anisotropy and emission intensity in 1D vdW FRP paves the way towards transforming the landscape of technological innovations in photonics and optoelectronics.
Zn-Nx sites on N-doped carbon for aerobic oxidative cleavage and esterification of C(CO)-C bonds
Authors: Xie Chao , Lin Longfei , Huang Liang , Wang Zixin , Jiang Zhiwei , Zhang Zehui , Han Buxing 
Published: August 2021

AbstractSelective cleavage of C-C bonds is very important in organic chemistry, but remains challenging because of their inert chemical nature. Herein, we report that Zn/NC-X catalysts, in which Zn2+ coordinate with N species on microporous N-doped carbon (NC) and X denotes the pyrolysis temperature, can effectively catalyze aerobic oxidative cleavage of C(CO)-C bonds and quantitatively convert acetophenone to methyl benzoate with a yield of 99% at 100 °C. The Zn/NC-950 can be applied for a wide scope of acetophenone derivatives as well as more challenging alkyl ketones. Detail mechanistic investigations reveal that the catalytic performance of Zn/NC-950 can be attributed to the coordination between Zn2+ and N species to change the electronic state of the metal, synergetic effect of the Zn single sites with their surrounding N atoms, as well as the microporous structure with the high surface area and structural defects of the NC.
Automatic detection of 39 fundus diseases and conditions in retinal photographs using deep neural networks
Authors: Cen Ling-Ping , Ji Jie , Lin Jian-Wei , Ju Si-Tong , Lin Hong-Jie , Li Tai-Ping , Wang Yun , Yang Jian-Feng , Liu Yu-Fen , Tan Shaoying , Tan Li , Li Dongjie , Wang Yifan , Zheng Dezhi , Xiong Yongqun , Wu Hanfu , Jiang Jingjing , Wu Zhenggen , Huang Dingguo , Shi Tingkun , Chen Binyao , Yang Jianling , Zhang Xiaoling , Luo Li , Huang Chukai , Zhang Guihua , Huang Yuqiang , Ng Tsz Kin , Chen Haoyu , Chen Weiqi , Pang Chi Pui , Zhang Mingzhi 
Published: August 2021

AbstractRetinal fundus diseases can lead to irreversible visual impairment without timely diagnoses and appropriate treatments. Single disease-based deep learning algorithms had been developed for the detection of diabetic retinopathy, age-related macular degeneration, and glaucoma. Here, we developed a deep learning platform (DLP) capable of detecting multiple common referable fundus diseases and conditions (39 classes) by using 249,620 fundus images marked with 275,543 labels from heterogenous sources. Our DLP achieved a frequency-weighted average F1 score of 0.923, sensitivity of 0.978, specificity of 0.996 and area under the receiver operating characteristic curve (AUC) of 0.9984 for multi-label classification in the primary test dataset and reached the average level of retina specialists. External multihospital test, public data test and tele-reading application also showed high efficiency for multiple retinal diseases and conditions detection. These results indicate that our DLP can be applied for retinal fundus disease triage, especially in remote areas around the world.
The sugar-responsive enteroendocrine neuropeptide F regulates lipid metabolism through glucagon-like and insulin-like hormones in Drosophila melanogaster
Authors: Yoshinari Yuto , Kosakamoto Hina , Kamiyama Takumi , Hoshino Ryo , Matsuoka Rena , Kondo Shu , Tanimoto Hiromu , Nakamura Akira , Obata Fumiaki , Niwa Ryusuke 
Published: August 2021

AbstractThe enteroendocrine cell (EEC)-derived incretins play a pivotal role in regulating the secretion of glucagon and insulins in mammals. Although glucagon-like and insulin-like hormones have been found across animal phyla, incretin-like EEC-derived hormones have not yet been characterised in invertebrates. Here, we show that the midgut-derived hormone, neuropeptide F (NPF), acts as the sugar-responsive, incretin-like hormone in the fruit fly,Drosophila melanogaster. Secreted NPF is received by NPF receptor in the corpora cardiaca and in insulin-producing cells. NPF-NPFR signalling resulted in the suppression of the glucagon-like hormone production and the enhancement of the insulin-like peptide secretion, eventually promoting lipid anabolism. Similar to the loss of incretin function in mammals, loss of midgut NPF led to significant metabolic dysfunction, accompanied by lipodystrophy, hyperphagia, and hypoglycaemia. These results suggest that enteroendocrine hormones regulate sugar-dependent metabolism through glucagon-like and insulin-like hormones not only in mammals but also in insects.
Tailoring atomic diffusion for in situ fabrication of different heterostructures
Authors: Zhang Hui , Xu Tao , Yu Kaihao , Wang Wen , He Longbing , Sun Litao 
Published: August 2021

AbstractAtomic diffusion has been recognized as a particularly powerful tool in the synthesis of heterostructures. However, controlled atomic diffusion is very difficult to achieve in the fabrication of individual nanostructures. Here, an electrically driven in situ solid-solid diffusion reaction inside a TEM is reported for the controlled fabrication of two different hetero-nanostructures in the Ag-Te system. Remarkably, the morphology and structure of the as-formed heterostructures are strongly dependent on the path of atomic diffusion. Our experiments revealed that the surface diffusion of Te atoms to Ag nanowires leads to a core-shell structure, while the bulk diffusion of Ag atoms give rise to a Ag2Te-Te segmented heterostructure. Heat released by Joule heating caused the surface diffusion process to be replaced by bulk diffusion and thereby determined the structure of the final product. Our experimental results provide an insight into solid-state diffusion reactions under an electric field and also propose a new process for the fabrication of complex nanostructures.
Choice-relevant information transformation along a ventrodorsal axis in the medial prefrontal cortex
Authors: Maisson David J.-N. , Cash-Padgett Tyler V. , Wang Maya Z. , Hayden Benjamin Y. , Heilbronner Sarah R. , Zimmermann Jan 
Published: August 2021

AbstractChoice-relevant brain regions in prefrontal cortex may progressively transform information about options into choices. Here, we examine responses of neurons in four regions of the medial prefrontal cortex as macaques performed two-option risky choices. All four regions encode economic variables in similar proportions and show similar putative signatures of key choice-related computations. We provide evidence to support a gradient of function that proceeds from areas 14 to 25 to 32 to 24. Specifically, we show that decodability of twelve distinct task variables increases along that path, consistent with the idea that regions that are higher in the anatomical hierarchy make choice-relevant variables more separable. We also show progressively longer intrinsic timescales in the same series. Together these results highlight the importance of the medial wall in choice, endorse a specific gradient-based organization, and argue against a modular functional neuroanatomy of choice.
The bright side of fibroblasts: molecular signature and regenerative cues in major organs
Authors: Gomes Rita N. , Manuel Filipa , Nascimento Diana S. 
Published: August 2021

AbstractFibrosis is a pathologic process characterized by the replacement of parenchymal tissue by large amounts of extracellular matrix, which may lead to organ dysfunction and even death. Fibroblasts are classically associated to fibrosis and tissue repair, and seldom to regeneration. However, accumulating evidence supports a pro-regenerative role of fibroblasts in different organs. While some organs rely on fibroblasts for maintaining stem cell niches, others depend on fibroblast activity, particularly on secreted molecules that promote cell adhesion, migration, and proliferation, to guide the regenerative process. Herein we provide an up-to-date overview of fibroblast-derived regenerative signaling across different organs and discuss how this capacity may become compromised with aging. We further introduce a new paradigm for regenerative therapies based on reverting adult fibroblasts to a fetal/neonatal-like phenotype.
3D brain tumor segmentation using a two-stage optimal mass transport algorithm
Authors: Lin Wen-Wei , Juang Cheng , Yueh Mei-Heng , Huang Tsung-Ming , Li Tiexiang , Wang Sheng , Yau Shing-Tung 
Published: August 2021

AbstractOptimal mass transport (OMT) theory, the goal of which is to move any irregular 3D object (i.e., the brain) without causing significant distortion, is used to preprocess brain tumor datasets for the first time in this paper. The first stage of a two-stage OMT (TSOMT) procedure transforms the brain into a unit solid ball. The second stage transforms the unit ball into a cube, as it is easier to apply a 3D convolutional neural network to rectangular coordinates. Small variations in the local mass-measure stretch ratio among all the brain tumor datasets confirm the robustness of the transform. Additionally, the distortion is kept at a minimum with a reasonable transport cost. The original $$240 \times 240 \times 155 \times 4$$

240
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240
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155
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dataset is thus reduced to a cube of $$128 \times 128 \times 128 \times 4$$

128
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128
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128
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, which is a 76.6% reduction in the total number of voxels, without losing much detail. Three typical U-Nets are trained separately to predict the whole tumor (WT), tumor core (TC), and enhanced tumor (ET) from the cube. An impressive training accuracy of 0.9822 in the WT cube is achieved at 400 epochs. An inverse TSOMT method is applied to the predicted cube to obtain the brain results. The conversion loss from the TSOMT method to the inverse TSOMT method is found to be less than one percent. For training, good Dice scores (0.9781 for the WT, 0.9637 for the TC, and 0.9305 for the ET) can be obtained. Significant improvements in brain tumor detection and the segmentation accuracy are achieved. For testing, postprocessing (rotation) is added to the TSOMT, U-Net prediction, and inverse TSOMT methods for an accuracy improvement of one to two percent. It takes 200 seconds to complete the whole segmentation process on each new brain tumor dataset.
Persistence and adherence to biologic therapies in juvenile idiopathic arthritis
Authors: Nieto-González Juan Carlos , Trives-Folguera Laura , Melgarejo-Ortuño Alejandra , Ais Aranzazu , Serrano-Benavente Belén , Sanjurjo María , Álvaro-Gracia José María , Sáez Indalecio Monteagudo 
Published: August 2021

AbstractJuvenile idiopathic arthritis (JIA) is a chronic inflammatory disease that often requires biological therapy to control its activity. Medication persistence and adherence are important aspects on which we have scarce information. We performed a longitudinal, retrospective, and observational study based on data from the daily clinical management of JIA patients. We recorded clinical remission at 6 and 12 months. Persistence of biological therapy was evaluated using Kaplan–Meier curves, and adherence was assessed using the medication possession ratio (MPR). We included 68 patients who received biological therapy. Of these, 11 (16.2%) and 5 (7.4%) required a second and third drug, respectively. The persistence rate for biological therapy at 5 years was 64%, with no differences between the first and second lines. Adherence was high during the first year of treatment (MPR80: 96.3%) and also in the second and third years (MPR80: 85.2% and 91.8%, respectively). Persistence and adherence to biological therapy were remarkably high in our JIA cohort. Adherence to biological treatments could be related to a higher probability of fulfilling the Wallace remission criteria at 6 months, although this was not confirmed at 12 months.
Contextual perception under active inference
Authors: Mirza M. Berk , Cullen Maell , Parr Thomas , Shergill Sukhi , Moran Rosalyn J. 
Published: August 2021

AbstractHuman social interactions depend on the ability to resolve uncertainty about the mental states of others. The context in which social interactions take place is crucial for mental state attribution as sensory inputs may be perceived differently depending on the context. In this paper, we introduce a mental state attribution task where a target-face with either an ambiguous or an unambiguous emotion is embedded in different social contexts. The social context is determined by the emotions conveyed by other faces in the scene. This task involves mental state attribution to a target-face (either happy or sad) depending on the social context. Using active inference models, we provide a proof of concept that an agent’s perception of sensory stimuli may be altered by social context. We show with simulations that context congruency and facial expression coherency improve behavioural performance in terms of decision times. Furthermore, we show through simulations that the abnormal viewing strategies employed by patients with schizophrenia may be due to (i) an imbalance between the precisions of local and global features in the scene and (ii) a failure to modulate the sensory precision to contextualise emotions.
Supercapacitance and superinductance of TiN and NbTiN films in the vicinity of superconductor-to-insulator transition
Authors: Mironov A. Yu. , Silevitch D. M. , Postolova S. V. , Burdastyh M. V. , Proslier T. , Baturina T. I. , Rosenbaum T. F. , Vinokur V. M. 
Published: August 2021

AbstractWe investigate the low-temperature complex impedance of disordered insulating thin TiN and NbTiN films in the frequency region 400 Hz–1 MHz in close proximity to the superconductor–insulator transition (SIT). The frequency, temperature, and magnetic field dependencies of the real and imaginary parts of the impedance indicate that in full accord with the theoretical predictions and earlier observations, the films acquire self-induced electronic granularity and become effectively random arrays of superconducting granules coupled via Josephson links. Accordingly, the inductive component of the response is due to superconducting droplets, while the capacitive component results from the effective Josephson junctions capacitances. The impedance crosses over from capacitive to inductive behavior as films go across the transition.
Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution
Authors: Imaizumi Toshiyuki , Ebana Kaworu , Kawahara Yoshihiro , Muto Chiaki , Kobayashi Hiroyuki , Koarai Akira , Olsen Kenneth M. 
Published: August 2021

AbstractAgricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin fromtropical japonicacrop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolvedtemperate japonica- andtropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.