julilili42/papers huggingface dataset:
Sensory Processing and Categorization in Cortical and Deep Neural Networks
2019-05-24

Abstract Many recent advances in artificial intelligence (AI) are rooted in visual neuroscience. However, ideas from more complicated paradigms like decision-making are less used. Although automated decision-making systems are ubiquitous (driverless cars, pilot support systems, medical diagnosis algorithms etc.), achieving human-level performance in decision making tasks is still a challenge. At the same time, these tasks that are hard for AI are easy for humans. Thus, understanding human brain dynamics during these decision-making tasks and modeling them using deep neural networks could improve AI performance. Here we modelled some of the complex neural interactions during a sensorimotor decision making task. We investigated how brain dynamics flexibly represented and distinguished between sensory processing and categorization in two sensory domains: motion direction and color. We used two different approaches for understanding neural representations. We compared brain responses to 1) the geometry of a sensory or category domain (domain selectivity) and 2) predictions from deep neural networks (computation selectivity). Both approaches gave us similar results. This confirmed the validity of our analyses. Using the first approach, we found that neural representations changed depending on context. We then trained deep recurrent neural networks to perform the same tasks as the animals. Using the second approach, we found that computations in different brain areas also changed flexibly depending on context. Color computations appeared to rely more on sensory processing, while motion computations more on abstract categories. Overall, our results shed light to the biological basis of categorization and differences in selectivity and computations in different brain areas. They also suggest a way for studying sensory and categorical representations in the brain: compare brain responses to both a behavioral model and a deep neural network and test if they give similar results.
RETRACTED ARTICLE: Long noncoding RNA MAGI1-IT1 promoted invasion and metastasis of epithelial ovarian cancer via the miR-200a/ZEB axis
2019-05-24

We, the Editors and Publisher of the journal <i>Cell Cycle</i>, have retracted the following article: Hao Gao, Xiaofeng Li, Guangxi Zhan, Yong Zhu, Jing Yu, Jiapo Wang, Li Li, Weimin Wu, Na Liu and Xiaoqing Guo. Long noncoding RNA MAGI1-IT1 promoted invasion and metastasis of epithelial ovarian cancer via the miR-200a/ZEB axis. Cell Cycle. 2019;18(12):1393-1406. doi: 10.1080/15384101.2019.1618121 Since publication, concerns have been raised about the integrity of the data in the article. When approached for an explanation, the authors have been unable to fully address the concerns raised and have not been able to provide their original data in the appropriate format. As verifying the validity of published work is core to the integrity of the scholarly record, we are therefore retracting the article. The corresponding author listed in this publication has been informed. The authors do not agree with the retraction. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as ‘Retracted’.
Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification
2019-05-27

This is a version of the Likelihood Ratio calculator tool created, adapted and/or used by ENIGMA analytical working group members, primarily David Goldgar, Kyriaki Michailidou, Paul James and Amanda Spurdle for use in calibrating data types for ENIGMA research and ENIGMA contributions to Variant Curation Expert Panel activities. Components of this excel spreadsheet based calculator have been developed from the activities and manuscripts produced by ENIGMA members, and have been informed by input from Michael Parsons, Maria Zanti and Sean Tavtigian.
Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation
2019-05-27

We have found that mtKRAS cells are substantially rewired at the transcriptional, translational and metabolic levels and that this rewiring may reveal new vulnerabilities in oncogenic KRAS CRC cells that could be exploited in future.
Evaluating Complexity of Fetal MEG Signals: A Comparison of Different Metrics and Their Applicability
2019-05-27

In this work, we aim to investigate whether information based metrics of neural activity are a useful tool for the quantification of consciousness before and shortly after birth. Neural activity is measured using fetal magnetoencephalography (fMEG) in human fetuses and neonates. Based on recent theories on consciousness, information-based metrics are established to measure brain complexity and to assess different levels of consciousness. Different metrics (measures of entropy, compressibility and fractality) are, thus, explored in a reference population and their usability is evaluated. For comparative analysis, two fMEG channels were selected: one where brain activity was previously detected and one at least 15 cm away, that represented a control channel. The usability of each metric was evaluated and results from the brain and control channel were compared. Concerning the ease of use with fMEG data, Lempel-Ziv-Complexity (LZC) was evaluated as best, as it is unequivocal and needs low computational effort. The fractality measures have a high number of parameters that need to be adjusted prior to analysis and therefore forfeit comparability, while entropy measures require a higher computational effort and more parameters to adjust compared to LZC. Comparison of a channel with brain activity and a control channel in neonatal recordings showed significant differences in most complexity metrics. This clear difference can be seen as proof of concept for the usability of complexity metrics in fMEG. For fetal data, this comparison produced less clear results which can be related to leftover maternal signals included in the control channel. Further work is necessary to conclusively interpret results from the analysis of fetal recordings. Yet this study shows that complexity metrics can be used for fMEG data on early consciousness and the evaluation gives a guidance for future work. The inconsistency of results from different metrics highlights the challenges of working with complexity metrics as neural correlates of consciousness, as well as the caution one should apply to interpret them.
Single-dose diclofenac in healthy volunteers can cause decrease in renal perfusion measured by functional magnetic resonance imaging
2019-05-27

Abstract Objectives We investigated changes of renal perfusion after topical and oral diclofenac administration in healthy volunteers using functional magnetic resonance imaging (MRI) with arterial spin labelling (ASL). Methods Twenty-four healthy human participants (21–51 years) underwent 1.5T MRI before and 1 h after a single oral dose of diclofenac (50 mg). Twelve of 24 participants underwent an additional MRI examination following 3-day topical diclofenac administration. For renal perfusion imaging, a flow-sensitive alternating inversion-recovery TrueFISP ASL sequence was applied. Plasma concentrations of diclofenac and serum concentrations of thromboxane were determined. Key findings After oral diclofenac application, large interindividual differences in plasma concentrations were observed (range &amp;lt;3–4604 nm). Topical diclofenac application did not result in relevant systemic diclofenac levels (range 5–75 nm). MRI showed a significant reduction of renal perfusion in individuals with diclofenac levels ≥225 nm (baseline: 347 ± 7 vs diclofenac: 323 ± 8 ml/min/100 g, P &amp;lt; 0.01); no significant differences were observed in participants with diclofenac levels &amp;lt;225 nm. Diclofenac levels correlated negatively with thromboxane B2 levels pointing towards target engagement. Conclusions Single-dose diclofenac caused a decrease in renal perfusion in participants with diclofenac levels ≥225 nm. We demonstrated that even a single dose of diclofenac can impair renal perfusion, which could be detrimental in patients with underlying chronic kidney disease or acute kidney injury.
Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
2019-05-27

Abstract We report an improved assembly and scaffolding of the European pear ( Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.
Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)
2019-05-27

Abstract We report an improved assembly and scaffolding of the European pear ( Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.
Digital Mapping of Soil Classes Using Ensemble of Models in Isfahan Region, Iran
2019-05-28

Digital soil maps can be used to depict the ability of soil to fulfill certain functions. Digital maps offer reliable information that can be used in spatial planning programs. Several broad types of data mining approaches through Digital Soil Mapping (DSM) have been tested. The usual approach is to select a model that produces the best validation statistics. However, instead of choosing the best model, it is possible to combine all models realizing their strengths and weaknesses. We applied seven different techniques for the prediction of soil classes based on 194 sites located in Isfahan region. The mapping exercise aims to produce a soil class map that can be used for better understanding and management of soil resources. The models used in this study include Multinomial Logistic Regression (MnLR), Artificial Neural Networks (ANN), Support Vector Machine (SVM), Decision Tree (DT), Random Forest (RF), Bayesian Networks (BN), and Sparse Multinomial Logistic Regression (SMnLR). Two ensemble models based on majority votes (Ensemble.1) and MnLR (Ensemble.2) were implemented for integrating the optimal aspects of the individual techniques. The overall accuracy (OA), Cohen's kappa coefficient index (κ) and the area under the curve (AUC) were calculated based on 10-fold-cross validation with 100 repeats at four soil taxonomic levels. The Ensemble.2 model was able to achieve larger OA, κ coefficient and AUC compared to the best performing individual model (i.e., RF). Results of the ensemble model showed a decreasing trend in OA from Order (0.90) to Subgroup (0.53). This was also the case for the κ statistic, which was the largest for the Order (0.66) and smallest for the Subgroup (0.43). Same decrease was observed for AUC from Order (0.81) to Subgroup (0.67). The improvement in κ was substantial (43 to 60%) at all soil taxonomic levels, except the Order level. We conclude that the application of the ensemble model using the MnLR was optimal, as it provided a highly accurate prediction for all soil taxonomic levels over and above the individual models. It also used information from all models, and thus this method can be recommended for improved soil class modelling. Soil maps created by this DSM approach showed soils that are prone to degradation and need to be carefully managed and conserved to avoid further land degradation.
Transformation Products of Fluoxetine Formed by Photodegradation in Water and Biodegradation in Zebrafish Embryos (Danio rerio)
2019-05-28

The present study investigates the transformation of the antidepressant fluoxetine (FLX) by photo- and biodegradation and shows similarities and differences in transformation products (TPs). TPs were identified using LC-high-resolution mass spectrometry with positive and negative electrospray ionization. In a sunlight simulator, photodegradation was carried out using ultrapure water (pH 6, 8, and 10) and surface water (pH 8) to study the effect of direct and indirect photolysis, respectively. The well-known metabolite norfluoxetine (NFLX) proved to be a minor TP in photolysis (≤2% of degraded FLX). In addition, 26 TPs were detected, which were formed by cleavage of the phenolether bond ( O-dealkylation) which primarily formed 3-(methylamino)-1-phenyl-1-propanol (TP 166) and 4-(trifluoromethyl)phenol, by hydroxylation of the benzyl moiety, by CF<sub>3</sub> substitution to benzoic aldehyde/acid, and by adduct formation at the amine group ( N-acylation with aldehydes and carboxylic acids). Higher pH favors the neutral species of FLX and the neutral/anionic species of primary TPs and, therefore, photodegradation. In zebrafish embryos, the bioconcentration factor of FLX was found to be 110, and about 1% of FLX taken up by the embryos was transformed to NFLX. Seven metabolites known from photodegradation and formed by hydrolysis, hydroxylation, and N-acylation as well as three new metabolites formed by N-hydroxylation, N-methylation, and attachment of an amine group were identified in zebrafish embryos. The study highlights the importance of considering a broad range of TPs of FLX in fresh water systems and in ecotoxicity tests and to include TP formation in both environmental processes and metabolism in organisms.
Risk factors for and management of anterior chamber intravitreal dexamethasone implant migration
2019-05-28

The anterior chamber migration of an intravitreal dexamethasone implant is a serious complication. To minimize the risk of permanent corneal edema, immediate removal of the implant with a 20-gauge alligator forceps over a 2.75-mm long clear corneal tunnel is important. Those patients with insufficient zonular support, defects, or missing posterior capsular membranes and vitrectomy histories present a high risk of anterior chamber dexamethasone implant migration.
Inactivation of farR Causes High Rhodomyrtone Resistance and Increased Pathogenicity in Staphylococcus aureus
2019-05-28

Rhodomyrtone (Rom) is an acylphloroglucinol antibiotic originally isolated from leaves of <i>Rhodomyrtus tomentosa</i>. Rom targets the bacterial membrane and is active against a wide range of Gram-positive bacteria but the exact mode of action remains obscure. Here we isolated and characterized a spontaneous Rom-resistant mutant from the model strain <i>Staphylococcus aureus</i> HG001 (Rom<sup>R</sup>) to learn more about the resistance mechanism. We showed that Rom-resistance is based on a single point mutation in the coding region of <i>farR</i> [regulator of fatty acid (FA) resistance] that causes an amino acid change from Cys to Arg at position 116 in FarR, that affects FarR activity. Comparative transcriptome analysis revealed that mutated <i>farR</i> affects transcription of many genes in distinct pathways. FarR represses for example the expression of its own gene (<i>farR</i>), its flanking gene <i>farE</i> (effector of FA resistance), and other global regulators such as <i>agr</i> and <i>sarA</i>. All these genes were consequently upregulated in the Rom<sup>R</sup> clone. Particularly the upregulation of <i>agr</i> and <i>sarA</i> leads to increased expression of virulence genes rendering the Rom<sup>R</sup> clone more cytotoxic and more pathogenic in a mouse infection model. The Rom-resistance is largely due to the de-repression of <i>farE</i>. FarE is described as an efflux pump for linoleic and arachidonic acids. We observed an increased release of lipids in the Rom<sup>R</sup> clone compared to its parental strain HG001. If <i>farE</i> is deleted in the Rom<sup>R</sup> clone, or, if native <i>farR</i> is expressed in the Rom<sup>R</sup> strain, the corresponding strains become hypersensitive to Rom. Overall, we show here that the high Rom-resistance is mediated by overexpression of <i>farE</i> in the Rom<sup>R</sup> clone, that FarR is an important regulator, and that the point mutation in <i>farR</i> (Rom<sup>R</sup> clone) makes the clone hyper-virulent.
Regulating Clinical Innovation: Trachea Transplants and Tissue Engineering
2019-05-28

Earl (2019) proposes permissive oversight for innovation in clinical practice, based on prospective review that requires justifications not only for deviating from standard clinical practice but al...
A new framework for understanding vision from the perspective of the primary visual cortex
2019-05-28

Visual attention selects only a tiny fraction of visual input informationfor further processing. Selection starts in the primary visual cortex (V1), which creates abottom-up saliency map to guide the fovea to selected visual locations via gaze shifts.This motivates a new framework that views visionas consisting of encoding, selection, and decoding stages, placingselection on center stage. It suggests a massive loss of non-selectedinformation from V1 downstream along the visual pathway.Hence, feedback from downstream visual cortical areas to V1 for better decoding (recognition),through analysis-by-synthesis, should query for additional information and be mainly directed atthe foveal region. Accordingly, non-foveal vision is not only poorer in spatial resolution,but also more susceptible to many illusions.
3D Exoscope System in Neurosurgery—Comparison of a Standard Operating Microscope With a New 3D Exoscope in the Cadaver Lab
2019-05-29

Abstract BACKGROUND For decades, the operating microscope has been the “gold standard” visualization device in neurosurgery. The development of endoscopy revolutionized different surgical disciplines, whereas in neurosurgery, the endoscope is commonly used as an additional device more than as single visualization tool. Invention of a 3D exoscope system opens new possibilities in visualization and ergonomics in neurosurgery. OBJECTIVE To assess the prototype of a 3D exoscope (3D exoscope, year of manufacture 2015, FA Aesculap, Tüttlingen, Germany) as neurosurgical visualization device in comparison to a standard operating microscope. METHODS A pterional approach was performed in 3 ETOH-fixed specimens (6 sides). A standard operating microscope was compared to a 3D exoscope prototype. Dimensions like visual field, magnification, illumination, ergonomics, depth effect, and 3D impression were compared. RESULTS In all approaches, the structures of interest could be clearly visualized with both devices. Magnification showed similar results. The exoscope had more magnification potential, whereas the visual quality got worse in higher magnification levels. The illumination showed better results in the microscope. Surgeons felt more comfortable with the 3D exoscope, concerning ergonomic considerations. Depth effect and 3D impression showed similar results. None of the surgeons felt uncomfortable using the exoscope. CONCLUSION The operating microscope is the gold standard visualization tool in neurosurgery because of its illumination, stereoscopy, and magnification. Nevertheless, it causes ergonomic problems. The prototype of a 3D exoscope showed comparable features in visual field, stereoscopic impression, and magnification, with a clear benefit concerning the ergonomic possibilities.
The Nature of Interests
2019-05-29

This chapter begins to establish a theoretical framework of what interests are, how interests are represented and organized in the human mind, and where interests are positioned in the nomological network. It reviews that research from educational psychology and vocational psychology, in which interests are conceptualized as states and traits, respectively. The chapter discusses incorporate insights from other fields—notably, behavioral genetics, cognitive psychology, and developmental psychology—to bridge the state and trait perspectives on interests and to develop theoretical propositions that establish an integrative framework. The chapter addresses some of the fundamental issues and presents an overview of new conceptualizations of interests, followed by a discussion of our proposed theoretical framework and a series of specific propositions. Studies on trait complexes and integrative frameworks of individual differences provide a new approach to understanding the nature of interests. Interests and values are similar in that they are both contextualized and involve external objects.
d‐Fructose Based Spiro‐Fused PHOX Ligands: Palladium Complexes and Application in Catalysis
2019-05-29

Phosphinooxazoline (PHOX) ligands are an important class of ligands in asymmetric catalysis. Recently we reported on the synthesis of d ‐fructose based spiro‐fused PHOX ligands. Here, we now present the application of these ligands in asymmetric alkylation. In addition, we prepared palladium complexes of our previous spiro‐PHOX ligands and characterized them by X‐ray crystallography. With the knowledge of the molecular structure of these spiro‐PHOX palladium complexes we prepared two “improved” d ‐fructose based spiro‐fused PHOX ligands the application of which in asymmetric alkylation resulted in high enantioselectivities ( er up to 93:7) in a broad substrate range.
The Costs of Economic Nationalism: Evidence from the Brexit Experiment*
2019-05-30

Abstract Economic nationalism is on the rise, but at what cost? We study this question using the unexpected outcome of the Brexit referendum vote as a natural macroeconomic experiment. Employing synthetic control methods, we first show that the Brexit vote has caused a UK output loss of 1.7% to 2.5% by year-end 2018. An expectations-augmented VAR suggests that these costs are, to a large extent, driven by a downward revision of growth expectations in response to the vote. Linking quasi-experimental identification to structural time-series estimation allows us not only to quantify the aggregate costs but also to understand the channels through which expected economic disintegration impacts the macroeconomy.
Gluon fusion into Higgs pairs at NLO QCD and the top mass scheme
2019-05-30

We present the calculation of the full next-to-leading order (NLO) QCD corrections to Higgs boson pair production via gluon fusion at the LHC, including the exact top-mass dependence in the two-loop virtual and one-loop real corrections. This is the first independent cross-check of the NLO QCD corrections presented in the literature before. Our calculation relies on numerical integrations of Feynman integrals, stabilised with integration-by-parts and a Richardson extrapolation to the narrow width approximation. We present results for the total cross section as well as for the invariant Higgs-pair-mass distribution at the LHC, including for the first time a study of the uncertainty due to the scheme and scale choice for the top mass in the loops.