bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissociating implicit and explicit ensemble representations reveals the limits of visual perception and the richness of behavior
Authors: Hansmann-Roth Sabrina , Kristjánsson Árni , Whitney David , Chetverikov Andrey 
Published: February 2021

AbstractOur senses provide us with a rich experience of a detailed visual world, yet the empirical results seem to suggest severe limitations on our ability to perceive and remember. In recent attempts to reconcile the contradiction between what is experienced and what can be reported, it has been argued that the visual world is condensed to a set of summary statistics, explaining both the rich experience and the sparse reports. Here, we show that explicit reports of summary statistics underestimate the richness of ensemble perception. Our observers searched for an odd-one-out target among heterogeneous distractors and their representation of distractor characteristics was tested explicitly or implicitly. Observers could explicitly distinguish distractor sets with different mean and variance, but not differently-shaped probability distributions. In contrast, the implicit assessment revealed that the visual system encodes the mean, the variance, and even the shape of feature distributions. Furthermore, explicit measures had common noise sources that distinguished them from implicit measures. This suggests that explicit judgments of stimulus ensembles underestimate the richness of visual representations. We conclude that feature distributions are encoded in rich detail and can guide behavior implicitly, even when the information available for explicit summary judgments is coarse and limited.
The relationship of indoxyl sulfate and p-cresyl sulfate with target cardiovascular proteins in hemodialysis patients
Authors: Wu Ping-Hsun , Lin Yi-Ting , Chiu Yi-Wen , Baldanzi Gabriel , Huang Jiun-Chi , Liang Shih-Shin , Lee Su-Chu , Chen Szu-Chia , Hsu Ya-Ling , Kuo Mei-Chuan , Hwang Shang-Jyh 
Published: February 2021

AbstractProtein-bound uremic toxins (Indoxyl sulfate [IS] and p-cresyl sulfate [PCS]) are both associated with cardiovascular (CV) and all-cause mortality in subjects with chronic kidney disease (CKD). Possible mechanisms have not been elucidated. In hemodialysis patients, we investigated the relationship between the free form of IS and PCS and 181 CV-related proteins. First, IS or PCS concentrations were checked, and high levels were associated with an increased risk of acute coronary syndrome (ACS) in 333 stable HD patients. CV proteins were further quantified by a proximity extension assay. We examined associations between the free form protein-bound uremic toxins and the quantified proteins with correction for multiple testing in the discovery process. In the second step, the independent association was evaluated by multivariable-adjusted models. We rank the CV proteins related to protein-bound uremic toxins by bootstrapped confidence intervals and ascending p-value. Six proteins (signaling lymphocytic activation molecule family member 5, complement component C1q receptor, C–C motif chemokine 15 [CCL15], bleomycin hydrolase, perlecan, and cluster of differentiation 166 antigen) were negatively associated with IS. Fibroblast growth factor 23 [FGF23] was the only CV protein positively associated with IS. Three proteins (complement component C1q receptor, CCL15, and interleukin-1 receptor-like 2) were negatively associated with PCS. Similar findings were obtained after adjusting for classical CV risk factors. However, only higher levels of FGF23 was related to increased risk of ACS. In conclusion, IS and PCS were associated with several CV-related proteins involved in endothelial barrier function, complement system, cell adhesion, phosphate homeostasis, and inflammation. Multiplex proteomics seems to be a promising way to discover novel pathophysiology of the uremic toxin.
Precision analysis model and experimentation of vision reconstruction with two cameras and 3D orientation reference
Authors: Chen Rong , Chen Fang , Xu Guan , Li Xiaotao , Shen Hui , Yuan Jing 
Published: February 2021

AbstractActive vision reconstruction is widely used in industrial manufacturing and three-dimensional inspection. The reconstruction accuracy is an important problem to be investigated for the inspection process. The paper conducts an analysis study of the reconstruction error for the vision reconstruction with a planar laser, two cameras and a 3D orientation board. The variation principles of the spatial coordinates caused by the variations of the extrinsic parameters of the cameras, intrinsic parameters of the internal camera, and image coordinate points of the internal camera, are modeled and analyzed in this paper. The analysis is also proved by the verification experiments, which provides the application potential for other active-vision-based reconstructions.
Pigeons show how meta-control enables decision-making in an ambiguous world
Authors: Manns Martina , Otto Tobias , Salm Laurenz 
Published: February 2021

AbstractIn situations where the left and right brain sides receive conflicting information that leads to incompatible response options, the brain requires efficient problem-solving mechanisms. This problem is particularly significant in lateralized brains, in which the hemispheres differ in encoding strategies or attention focus and hence, consider different information for decision-making. Meta-control, in which one hemisphere dominates ambiguous decisions, can be a mechanism that ensures fast behavioral reactions. We therefore confronted pigeons with a task in which two stimulus classes were brought into conflict. To this end, we trained pigeons simultaneously on two categories (cats or dogs) whereby each hemisphere learnt only one of the categories respectively. After learning, the birds were confronted with stimulus pairs that combined a picture with a cat (positive for one hemisphere) and a picture with a dog (positive for the other hemisphere). Pecking responses indicated the hemisphere dominating response selection. Pigeons displayed individual meta-control despite equal categorization performances of both brain hemispheres. This means that hemispheric dominance only emerged in interhemispheric conflict situations. The analysis of response latencies indicate that conflict decisions relied on intrahemispheric processes. Interhemispheric components played a role for more complex decisions. This flexibility could be a crucial building block for the evolutionary success of a lateralized brain.
Dicke and Fano-Andreev reflections in a triple quantum-dot system
Authors: González I. A. , Pacheco M. , Calle A. M. , Siqueira E. C. , Orellana P. A. 
Published: February 2021

AbstractThis article studies quantum interference effects and their influence on the electronic transport through a parallel triple quantum-dot system coupled to normal and superconducting leads in the linear response and non-equilibrium regime. We model the system by a triple impurity Anderson Hamiltonian including the Coulomb intra-dot correlations in all quantum-dots. Using the non-equilibrium Green’s function formalism, we calculate the Andreev conductance and the transmittance for energies within the superconductor gap. Our results show that the Andreev reflection spectra, both in the presence and absence of Coulomb interaction, reveal Fano and Dicke-like resonances in analogy to the Fano and Dicke effects in atomic physics. As one of the main results, we obtain that the charge shows abrupt changes due to the Dicke effect.
Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment
Authors: Ghezzi D. , Sauro F. , Columbu A. , Carbone C. , Hong P.-Y. , Vergara F. , De Waele J. , Cappelletti M. 
Published: February 2021

AbstractThe orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.
Exploring the predictive value of lesion topology on motor function outcomes in a porcine ischemic stroke model
Authors: Scheulin Kelly M. , Jurgielewicz Brian J. , Spellicy Samantha E. , Waters Elizabeth S. , Baker Emily W. , Kinder Holly A. , Simchick Gregory A. , Sneed Sydney E. , Grimes Janet A. , Zhao Qun , Stice Steven L. , West Franklin D. 
Published: February 2021

AbstractHarnessing the maximum diagnostic potential of magnetic resonance imaging (MRI) by including stroke lesion location in relation to specific structures that are associated with particular functions will likely increase the potential to predict functional deficit type, severity, and recovery in stroke patients. This exploratory study aims to identify key structures lesioned by a middle cerebral artery occlusion (MCAO) that impact stroke recovery and to strengthen the predictive capacity of neuroimaging techniques that characterize stroke outcomes in a translational porcine model. Clinically relevant MRI measures showed significant lesion volumes, midline shifts, and decreased white matter integrity post-MCAO. Using a pig brain atlas, damaged brain structures included the insular cortex, somatosensory cortices, temporal gyri, claustrum, and visual cortices, among others. MCAO resulted in severely impaired spatiotemporal gait parameters, decreased voluntary movement in open field testing, and higher modified Rankin Scale scores at acute timepoints. Pearson correlation analyses at acute timepoints between standard MRI metrics (e.g., lesion volume) and functional outcomes displayed moderate R values to functional gait outcomes. Moreover, Pearson correlation analyses showed higher R values between functional gait deficits and increased lesioning of structures associated with motor function, such as the putamen, globus pallidus, and primary somatosensory cortex. This correlation analysis approach helped identify neuroanatomical structures predictive of stroke outcomes and may lead to the translation of this topological analysis approach from preclinical stroke assessment to a clinical biomarker.
A two-herb formula inhibits hyperproliferation of rheumatoid arthritis fibroblast-like synoviocytes
Authors: Chen Ying-Jie , Liu Yu-Xi , Wu Jia-Ying , Li Chun-Yu , Tang Min-Min , Bai Lu , Fu Xiu-Qiong , Li Jun-Kui , Chou Ji-Yao , Yin Cheng-Le , Wang Ya-Ping , Bai Jing-Xuan , Wu Ying , Wang Xiao-Qi , Yu Zhi-Ling 
Published: February 2021

AbstractFibroblast-like synoviocytes (FLS) play a pathogenic role in rheumatoid arthritis (RA). STAT3 signaling is activated in FLS of RA patients (RA-FLS), which in turn causes RA-FLS hyperproliferation. RL is a traditional remedy for treating inflammatory diseases in China. It comprises Rosae Multiflorae Fructus and Lonicerae Japonicae Flos. A standardized ethanolic extract of RL (RLE) has been shown to exert anti-arthritic effects in collagen-induced arthritis (CIA) rats. Some constituents of RLE were reported to inhibit JAK2/STAT3 signaling in rat FLS. Here, we determined whether RLE inhibits FLS hyperproliferation, and explored the involvement of STAT3 signaling in this inhibition. In joints of CIA rats, RLE increased apoptotic FLS. In IL-6/sIL-6R-stimulated RA-FLS, RLE reduced cell viability and evoked cell apoptosis. In synovial tissues of CIA rats, RLE lowered the protein level of phospho-STAT3. In IL-6/sIL-6R-stimulated RA-FLS, RLE inhibited activation/phosphorylation of STAT3 and JAK2, decreased the nuclear localization of STAT3, and downregulated protein levels of Bcl-2 and Mcl-1. Over-activation of STAT3 diminished RLE’s anti-proliferative effects in IL-6/sIL-6R-stimulated RA-FLS. In summary, RLE inhibits hyperproliferation of FLS in rat and cell models, and suppression of STAT3 signaling contributes to the underlying mechanisms. This study provides further pharmacological groundwork for developing RLE as a modern anti-arthritic drug.
European cephalopods distribution under climate-change scenarios
Authors: Schickele Alexandre , Francour Patrice , Raybaud Virginie 
Published: February 2021

AbstractIn a context of increasing anthropogenic pressure, projecting species potential distributional shifts is of major importance for the sustainable exploitation of marine species. Despite their major economical (i.e. important fisheries) and ecological (i.e. central position in food-webs) importance, cephalopods literature rarely addresses an explicit understanding of their current distribution and the potential effect that climate change may induce in the following decades. In this study, we focus on three largely harvested and common cephalopod species in Europe:Octopus vulgaris,Sepia officinalisandLoligo vulgaris. Using a recently improved species ensemble modelling framework coupled with five atmosphere–ocean general circulation models, we modelled their contemporary and potential future distributional range over the twenty-first century. Independently of global warming scenarios, we observed a decreasing in the suitability of environmental conditions in the Mediterranean Sea and the Bay of Biscay. Conversely, we projected a rapidly increasing environmental suitability in the North, Norwegian and Baltic Seas for all species. This study is a first broad scale assessment and identification of the geographical areas, fisheries and ecosystems impacted by climate-induced changes in cephalopods distributional range.
Phosphorylation of the proline-rich domain of WAVE3 drives its oncogenic activity in breast cancer
Authors: Kansakar Urna , Wang Wei , Markovic Vesna , Sossey-Alaoui Khalid 
Published: February 2021

AbstractPost-translational modification of proteins, such as tyrosine phosphorylation, plays a major role in driving the oncogenic activity of oncogenes. WAVE3 (WASF3), an adaptor and actin cytoskeleton remodeling protein, contributes to cell migration, cancer cell invasion, and metastasis. WAVE3 plays a vital role in the progression and metastasis of triple negative breast cancer (TNBC), in part through the regulation of cancer stem cells (CSCs). Several studies have shown that WAVE3 tyrosine phosphorylation is required for its oncogenic activity. Moreover, our recent study showed that the proline rich domain (PRD) of WAVE3 is required for maintenance of the CSC niche in breast cancer by regulating the nuclear translocation of the CSC-specific nuclear transcription factor YB1. Here, we show that the PRD domain of WAVE3 and its phosphorylation are essential for driving the oncogenic activity of WAVE3. We show that phosphorylation of WAVE3 PRD is essential for migration and invasion of breast cancer cells in vitro, as well as tumor growth and metastasis in vivo. Mechanistically, we show that phosphorylation of the WAVE3 PRD is essential for interaction between WAVE3 and YB1. Loss of PRD phosphorylation inhibits such interaction and the YB1-mediated activation of expression of CSC markers, as well as the WAVE3 mediated activation of EMT. Together, our study identifies a novel role of WAVE3 and its PRD domain in the regulation of the invasion metastasis cascade in BC that is independent of the known function of WAVE3 as an actin cytoskeleton remodeling protein through the WAVE regulatory complex (WRC).
Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex
Authors: Nosaki Shohei , Terada Tohru , Nakamura Akira , Hirabayashi Kei , Xu Yuqun , Bui Thi Bao Chau , Nakano Takeshi , Tanokura Masaru , Miyakawa Takuya 
Published: February 2021

AbstractThe maltose-binding protein (MBP) fusion tag is one of the most commonly utilized crystallization chaperones for proteins of interest. Recently, this MBP-mediated crystallization technique was adapted to Arabidopsis thaliana (At) BRZ-INSENSITIVE-LONG (BIL1)/BRASSINAZOLE-RESISTANT (BZR1), a member of the plant-specific BZR TFs, and revealed the first structure of AtBIL1/BZR1 in complex with target DNA. However, it is unclear how the fused MBP affects the structural features of the AtBIL1/BZR1-DNA complex. In the present study, we highlight the potential utility of the MBP crystallization chaperone by comparing it with the crystallization of unfused AtBIL1/BZR1 in complex with DNA. Furthermore, we assessed the validity of the MBP-fused AtBIL1/BZR1-DNA structure by performing detailed dissection of crystal packings and molecular dynamics (MD) simulations with the removal of the MBP chaperone. Our MD simulations define the structural basis underlying the AtBIL1/BZR1-DNA assembly and DNA binding specificity by AtBIL1/BZR1. The methodology employed in this study, the combination of MBP-mediated crystallization and MD simulation, demonstrates promising capabilities in deciphering the protein-DNA recognition code.
Environmental enrichment influences novelty reactivity, novelty preference, and anxiety via distinct genetic mechanisms in C57BL/6J and DBA/2J mice
Authors: Dickson Price E. , Mittleman Guy 
Published: February 2021

AbstractEnvironmental factors such as stress drive the development of drug addiction in genetically vulnerable individuals; the genes underlying this vulnerability are unknown. One strategy for uncovering these genes is to study the impact of environmental manipulation on high-throughput phenotypes that predict drug use and addiction-like behaviors. In the present study, we assessed the viability of this approach by evaluating the relative effects of environmental enrichment and isolation housing on three high-throughput phenotypes known to predict variation on distinct aspects of intravenous drug self-administration. Prior to behavioral testing, male and female C57BL/6J and DBA/2J mice (BXD founders) were housed in enrichment or isolation for ten weeks beginning at weaning. Enrichment significantly reduced novelty reactivity; this effect was significantly more robust in C57BL/6J mice relative to DBA/2J mice. Enrichment significantly reduced novelty preference; this effect was significantly dependent on novel environment characteristics and was significantly more robust in DBA/2J mice relative to C57BL/6J mice. Enrichment significantly increased anxiety; this effect was not strain-dependent. Collectively, these data indicate that (1) environmental enrichment influences novelty reactivity, novelty preference, and anxiety via distinct genetic mechanisms in mice, and (2) the BXD panel can be used to discover the genetic and epigenetic mechanisms underlying this phenomenon.
A look-ahead Monte Carlo simulation method for improving parental selection in trait introgression
Authors: Moeinizade Saba , Han Ye , Pham Hieu , Hu Guiping , Wang Lizhi 
Published: February 2021

AbstractMultiple trait introgression is the process by which multiple desirable traits are converted from a donor to a recipient cultivar through backcrossing and selfing. The goal of this procedure is to recover all the attributes of the recipient cultivar, with the addition of the specified desirable traits. A crucial step in this process is the selection of parents to form new crosses. In this study, we propose a new selection approach that estimates the genetic distribution of the progeny of backcrosses after multiple generations using information of recombination events. Our objective is to select the most promising individuals for further backcrossing or selfing. To demonstrate the effectiveness of the proposed method, a case study has been conducted using maize data where our method is compared with state-of-the-art approaches. Simulation results suggest that the proposed method, look-ahead Monte Carlo, achieves higher probability of success than existing approaches. Our proposed selection method can assist breeders to efficiently design trait introgression projects.
Rare deleterious germline variants and risk of lung cancer
Authors: Liu Yanhong , Xia Jun , McKay James , Tsavachidis Spiridon , Xiao Xiangjun , Spitz Margaret R. , Cheng Chao , Byun Jinyoung , Hong Wei , Li Yafang , Zhu Dakai , Song Zhuoyi , Rosenberg Susan M. , Scheurer Michael E. , Kheradmand Farrah , Pikielny Claudio W. , Lusk Christine M. , Schwartz Ann G. , Wistuba Ignacio I. , Cho Michael H. , Silverman Edwin K. , Bailey-Wilson Joan , Pinney Susan M. , Anderson Marshall , Kupert Elena , Gaba Colette , Mandal Diptasri , You Ming , de Andrade Mariza , Yang Ping , Liloglou Triantafillos , Davies Michael P. A. , Lissowska Jolanta , Swiatkowska Beata , Zaridze David , Mukeria Anush , Janout Vladimir , Holcatova Ivana , Mates Dana , Stojsic Jelena , Scelo Ghislaine , Brennan Paul , Liu Geoffrey , Field John K. , Hung Rayjean J. , Christiani David C. , Amos Christopher I. 
Published: February 2021

AbstractRecent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04–75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71–8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3′ UTR (OR 4.33, 95%CI 2.03–9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73–11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33–5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.