Miracle-dz/UniFAR-FTUs huggingface dataset:
The Apolipoprotein E Antagonistic Pleiotropy Hypothesis: Review and Recommendations

Research on apolipoprotein E (APOE) has consistently revealed a relationship between the gene's ε4 allele and risk for development of Alzheimer's disease (AD). However, research with younger populations of ε4 carriers has suggested that the APOE ε4 allele may in fact be beneficial in earlier ages and may only confer risk of cognitive decline later in life. Accordingly, we and others have proposed that APOE may represent an example of antagonistic pleiotropy. Antagonistic pleiotropy is an evolutionary biology concept that proposes certain genes or alleles that may differentially impact fitness during different life stages. We critically review this hypothesis in light of new research of the impact of APOE on cognition and neural integrity across the lifespan. We provide recommendations for the revision of the antagonistic pleiotropy hypothesis of APOE and suggest important avenues for future research in this area.
Between Instruction and Reward: Human-Prompted Switching

Intelligent systems promise to amplify, augment, and extend innate human abilities. A principal example is that of assistive rehabilitation robots—artiﬁcial intelligence and machine learning enable new electrome-chanical systems that restore biological functions lost through injury or illness. In order for an intelligent machine to assist a human user, it must be possible for a human to communicate their intentions and preferences to their non-human counterpart. While there are a number of techniques that a human can use to direct a machine learning system, most research to date has focused on the contrasting strategies of instruction and reward. The primary contribution of our work is to demonstrate that the middle ground between instruction and reward is a fertile space for research and immediate technological progress. To support this idea, we introduce the setting of human-prompted switching, and illustrate the successful combination of switching with interactive learning using a concrete real-world example: human control of a multi-joint robot arm. We believe techniques that fall between the domains of instruction and reward are complementary to existing approaches, and will open up new lines of rapid progress for interactive human training of machine learning systems.
Incomplete Attribute Learning with auxiliary labels

Visual attribute learning is a fundamental and challenging problem for image understanding. Considering the huge semantic space of attributes, it is economically impossible to annotate all their presence or absence for a natural image via crowd-sourcing. In this paper, we tackle the incompleteness nature of visual attributes by introducing auxiliary labels into a novel transductive learning framework. By jointly predicting the attributes from the input images and modeling the relationship of attributes and auxiliary labels, the missing attributes can be recovered effectively. In addition, the proposed model can be solved efﬁciently in an alternative way by optimizing quadratic programming problems and updating parameters in closed-form solutions. Moreover, we propose and investigate different methods for acquiring auxiliary labels. We conduct experiments on three widely used attribute prediction datasets. The experimental re-sults show that our proposed method can achieve the state-of-the-art performance with access to partially observed attribute annotations.
RDF Knowledge Graph Visualization From a Knowledge Extraction System

In this paper, we present a system to visualize RDF knowledge graphs. These graphs are obtained from a knowledge extraction system designed by GEOLSemantics. This extraction is performed using natural language processing and trigger detection. The user can visualize subgraphs by selecting some ontology features like concepts or individuals. The system is also multilingual, with the use of the annotated ontology in English, French, Arabic and Chinese.
Unlexicalised Hidden Variable Models of Split Dependency Grammars

This paper investigates transforms of split dependency grammars into unlexicalised context-free grammars annotated with hidden symbols. Our best unlexicalised grammar achieves an accuracy of 88% on the Penn Treebank data set, that represents a 50% reduction in error over previously published results on unlexicalised dependency parsing.
The precision of temporal judgement: milliseconds, many minutes, and beyond

The principle that the standard deviation of estimates scales with the mean estimate, commonly known as the scalar property, is one of the most broadly accepted fundamentals of interval timing. This property is measured using the coefficient of variation (CV) calculated as the ratio between the standard deviation and the mean. In 1997, John Gibbon suggested that different time measurement mechanisms may have different levels of absolute precision, and would therefore be associated with different CVs. Here, we test this proposal by examining the CVs produced by human subjects timing a broad range of intervals (68 ms to 16.7 min). Our data reveal no evidence for multiple mechanisms, but instead show a continuous logarithmic decrease in CV as timed intervals increase. This finding joins other recent reports in demonstrating a systematic violation of the scalar property in timing data. Interestingly, the estimated CV of circadian judgements fits onto the regression of decreasing CV, suggesting a link between short interval and circadian timing mechanisms.
AGeS: A Software System for Microbial Genome Sequence Annotation

Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. Methodology The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions.
Gibberellic Acid-Induced Aleurone Layers Responding to Heat Shock or Tunicamycin Provide Insight into the N-Glycoproteome, Protein Secretion, and Endoplasmic Reticulum Stress1[W]

Overlapping responses of the aleurone layer proteome to tunicamycin and heat shock identify components of the plant protein secretory machinery. The growing relevance of plants for the production of recombinant proteins makes understanding the secretory machinery, including the identification of glycosylation sites in secreted proteins, an important goal of plant proteomics. Barley (Hordeum vulgare) aleurone layers maintained in vitro respond to gibberellic acid by secreting an array of proteins and provide a unique system for the analysis of plant protein secretion. Perturbation of protein secretion in gibberellic acid-induced aleurone layers by two independent mechanisms, heat shock and tunicamycin treatment, demonstrated overlapping effects on both the intracellular and secreted proteomes. Proteins in a total of 22 and 178 two-dimensional gel spots changing in intensity in extracellular and intracellular fractions, respectively, were identified by mass spectrometry. Among these are proteins with key roles in protein processing and secretion, such as calreticulin, protein disulfide isomerase, proteasome subunits, and isopentenyl diphosphate isomerase. Sixteen heat shock proteins in 29 spots showed diverse responses to the treatments, with only a minority increasing in response to heat shock. The majority, all of which were small heat shock proteins, decreased in heat-shocked aleurone layers. Additionally, glycopeptide enrichment and N-glycosylation analysis identified 73 glycosylation sites in 65 aleurone layer proteins, with 53 of the glycoproteins found in extracellular fractions and 36 found in intracellular fractions. This represents major progress in characterization of the barley N-glycoproteome, since only four of these sites were previously described. Overall, these findings considerably advance knowledge of the plant protein secretion system in general and emphasize the versatility of the aleurone layer as a model system for studying plant protein secretion.
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output.
The Admixture Structure and Genetic Variation of the Archipelago of Cape Verde and Its Implications for Admixture Mapping Studies

Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.
Segmentation methods for detection of stationary vehicles in combined elevation and optical data

Detection of vehicles in remote sensing data represents a captivating and challenging task that has been studied during many years. The state-of-the-art detection tools can be subdivided into implicit and explicit methods; the latter ones provide detection results by means of some explicitly characterizing features. Mostly, these methods rely on optical aerial images in which vehicles appear distorted. However, 3D elevation data and orthophotos are increasingly available and typically used to perform a full context-based scene analysis of which vehicles are an indispensable part. In this paper, we propose to combine elevation and optical data for segmentation of vehicle-like objects. To do this, several strategies, their advantages and disadvantages, will be discussed. Since any segmentation method also produces numerous false alarms, we will briefly describe the complete vehicle detection pipeline. The results indicate that sensor data fusion is crucial for obtaining the most accurate results in a reasonable time. For example, using trapezoids or stripes formed in optical and elevation data allows one to detect almost all targets with a very high accuracy exceeding the results obtained from single sensor data. We perform an extensive evaluation of all presented methods and outline the main ideas for correction of the existing shortcomings and for a closer embedding of vehicle detection into the process of urban terrain reconstruction from sensor data.
What’s for Dinner?: Entner-Doudoroff Metabolism inEscherichia coli

The Entner-Doudoroff (ED) pathway was first discovered in 1952 in Pseudomonas saccharophila (21) and several years later was shown to be present in Escherichia coli (23). Although generally considered to be restricted to gram-negative bacteria, the ED pathway is present in all three phylogenetic domains, including the most deeply rooted Archaea (18). The ubiquity of the ED pathway suggests that it is of far greater importance in nature than was previously recognized. In fact, a recent essay on the evolution of glycolytic pathways suggested that the ED pathway predates the Embden-Meyerhof-Parnas pathway (60). E. coli is generally recognized as a member of the normal gastrointestinal microbiota and is extremely versatile, with the ability to grow on many of the nutrients that can be found there (45). But what exactly are the nutrients preferred by E. coli to support its growth in the intestine? And what about growth of E. coli outside of the intestine? Certainly E. coli spends periods of time in aquatic, aerobic habitats when it is in between host intestinal tracts. Mounting evidence suggests that sugar acid metabolism via the ED pathway is important for growth of E. coli in both intestinal and aquatic habitats. The role of the ED pathway, especially with regard to colonization of the mammalian large intestine, will be discussed below. The biochemistry and physiology of sugar acid metabolism in E. coli are very well understood, and several newly discovered genes encoding sugar acid transporters, associated regulatory proteins, and a novel pathway for sugar acid catabolism have been identified as a result of the E. coli genome project (12). Homology searches reveal that the genes of the ED pathway are present on several other genomes (Table 1), and it is becoming clear that there will be additional, perhaps even novel, sugar acid catabolic pathways revealed by analysis of these genomes. OVERVIEW OF THE ED PATHWAY The ED pathway can be properly considered as one of three pathways found in nature, in addition to the Embden-Meyerhof-Parnas and pentose phosphate pathways, that feed into the “bottom half” of glycolysis, which is central to all of intermediary metabolism (18, 28). The overall schemes of the ED and Embden-Meyerhof-Parnas pathways are quite similar: 6-carbon sugars are primed by phosphorylation and subsequently cleaved by aldolase enzymes into two 3-carbon intermediates (Fig. 1). The primary distinction between the two pathways lies in the nature of the 6-carbon metabolites that serve as substrates for aldol cleavage: for the ED pathway this intermediate is 2-keto-3-deoxy-6-phosphogluconate (KDPG). The first of the two key enzymes is unique to the ED pathway, 6-phosphogluconate dehydratase (Edd), which catalyzes a dehydration of 6-phosphogluconate to form KDPG. The second enzyme of the ED pathway, KDPG aldolase (Eda), catalyzes an aldol cleavage of KDPG to form pyruvate and glyceraldehyde3-phosphate. The triose phosphate intermediate is further metabolized by the glycolytic pathway and provides energy via substrate-level phosphorylation.
On the consistency of the two-step estimates of the MS-DFM: a Monte Carlo study

The Markov-Switching Dynamic Factor Model (MS-DFM) has been used in different applications, notably in the business cycle analysis. When the cross-sectional dimension of data is high, the Maximum Likelihood estimation becomes unfeasible due to the excessive number of parameters. In this case, the MS-DFM can be estimated in two steps, which means that in the first step the common factor is extracted from a database of indicators, and in the second step the Markov-Switching autoregressive model is fit to this extracted factor. The validity of the two-step method is conventionally accepted, although the asymptotic properties of the two-step estimates have not been studied yet. In this paper we examine their consistency as well as the small-sample behavior with the help of Monte Carlo simulations. Our results indicate that the two-step estimates are consistent when the number of cross-section series and time observations is large, however, as expected, the estimates and their standard errors tend to be biased in small samples.
Mesoscale Convective Systems in the Asian Monsoon Region From Advanced Himawari Imager: Algorithms and Preliminary Results

The knowledge of mesoscale convective system (MCS) in the Asian monsoon region remains still deficient due to the limited available data and less powerful algorithms. Here, using the data from Advanced Himawari Imager onboard Himawari‐8 (HW8), an improved algorithm combining the area overlapping with the Kalman filter is developed, which captures much smaller MCSs that are unavailable otherwise. Several influential factors like the overlapping rate and splitting/merging in the area overlapping method, and the initial state variable in the Kalman filter method, all of which were less appreciated, are handled explicitly. The occurrence frequency, and moving trajectory of two types of MCS, including the ordinary MCS and superconvective system, has been comprehensively examined in the Asian monsoon region for the warm season (April to September) of 2016. Comparison analyses with ground precipitation and radar measurements confirm the good performance of our algorithm. In particular, the moving direction of MCS strongly depends on latitudes, so does the horizontal velocity. Compared with over ocean, the frequency of MCSs dominates over land or along coasts in the tropics, where strong moisture flux convergence is frequently observed in the low troposphere. In addition, the MCSs detected in eastern China can roughly capture the meridional propagation over time, which corresponds well to the precipitation belts linked to Meiyu front systems. The superconvective systems dominate over the Bay of Bengal and South China Sea due to the large‐scale circulation. Our findings provide new insights to spatiotemporal patterns of MCSs during warm season in the Asian monsoon region.
Falls reported among elderly Norwegians living at home.

BACKGROUND AND PURPOSE Norway has the highest reported incidence of hip fractures in western Europe. Little is known about the epidemiology of falls in Norway where the winter season is long and dark. The objective of this work was to study reported falls and their consequences among elderly Norwegians living at home. METHODS A cross-sectional design was used for the study. Interviews were performed in the homes of 431 subjects, aged 67-97 years, living at home. Information on falling was gathered through six questions: whether the subject had fallen during the last six months, and if so, how many falls they had, where the last fall occurred, its perceived reason, the activity the subject had been engaged in when the fall occurred, and the resulting injury. RESULTS In all, 24.1% of subjects reported falling during the last six months, and 9.5% had suffered more than one fall. Falls were most frequently linked to external events (63.1%). Outdoor falls were more frequent (59.0%; 95% CI = 51.2-82.0) than indoor falls. Older subjects were associated with more frequent indoor falls (p < 0.05), but gender was not significant. Fifty-one per cent of subjects had fallen while walking and 53% had suffered an injury from the last fall. In 13.4% of the women and 16.2% of the men, the last fall had resulted in a fracture. CONCLUSIONS Compared to the results of other studies from industrialized Western countries, a similar crude fall rate, similar frequency and similar type of injury were found. However, in contrast to other studies, no gender difference was observed with regard to falling, place of falling and fracture rate.
Quasigroups, isotopisms and authentication schemes

In 1992 Denes and Keedwell proposed an authentication scheme in which a message is divided into blocks of length t and a set of signature characters is obtained by taking the product of the elements of each block. An analysis of the security of Denes and Keedwell's scheme will be presented in this paper. It will be shown that the method used to divide the message into the blocks impacts on the security of the scheme. Also it will be shown that under certain circumstances the t-ary product is not unique, and so there are classes of binary operations all of which produce the same signature or authentication tag.