julilili42/papers huggingface dataset:
The keys to the future? An examination of associative versus discriminative accounts of Serial Pattern Learning
2022-07-08

Sequence learning is fundamental to a wide range of cognitive functions, and explaining how sequences --- and the relations between the elements they comprise --- are learned is a fundamental challenge to cognitive science. However, although hundreds of articles addressing this question are published each year, the actual learning mechanisms involved in the learning of sequences are rarely investigated. We present three experiments that seek to examine this question during a typing task. Experiments 1 and 2 tested learning during typing single letters on each trial. Experiment 3 tested for `chunking' of these letters into `words'. The results of these experiments were used to examine the mechanisms that could best account for them, with a focus on two particular proposals: associative transitional probability learning and discriminative error-driven learning. Experiments 1 and 2 showed that error-driven learning was a better predictor of response latencies than either n-gram frequencies or transitional probabilities.No evidence for chunking was found in Experiment 3, probably due to interspersing visual cues with the motor response.In addition, learning occurred across a greater distance in Experiment 1 than Experiment 2, suggesting that the greater predictability that comes with increased structure leads to greater learnability. These results shed new light on the mechanism responsible for sequence learning. Despite the widely held assumption that transitional probability learning is essential to this process, the present results suggest instead that the sequences are learned through a process of discriminative learning, involving prediction and feedback from prediction error.
Sex-related differences in postoperative complications following elective craniotomy for intracranial lesions: An observational study
2022-07-08

Introduction: The integration of sex-related differences in neurosurgery is crucial for new, possible sex-specific, therapeutic approaches. In neurosurgical emergencies, such as traumatic brain injury and aneurysmal subarachnoid hemorrhage, these differences have been investigated. So far, little is known concerning the impact of sex on frequency of postoperative complications after elective craniotomy. This study investigates whether sex-related differences exist in frequency of postoperative complications in patients who underwent elective craniotomy for intracranial lesion. Material and Methods: All consecutive patients who underwent an elective intracranial procedure over a 2-year period at our center were eligible for inclusion in this retrospective study. Demographic data, comorbidities, frequency of postoperative complications at 24 hours following surgery and at discharge, and hospital length of stay were compared among females and males. Results: Overall, 664 patients were considered for the analysis. Of those, 339 (50.2%) were females. Demographic data were comparable among females and males. More females than males suffered from allergic, muscular, and rheumatic disorders. No differences in frequency of postoperative complications at 24 hours after surgery and at discharge were observed among females and males. Similarly, the hospital length of stay was comparable. Conclusions: In the present study, no sex-related differences in frequency of early postoperative complications and at discharge following elective craniotomy for intracranial lesions were observed.
Upscaling Reputation Communication Simulations
2022-07-08

Social communication is omnipresent and a fundamental basis of our daily lives. Especially, due to the increasing popularity of social media, communication flows are becoming more complex, faster and more influential. It is therefore not surprising that in these highly dynamic communication structures, strategies are also developed to spread certain opinions, to deliberately steer discussions or to inject misinformation. The reputation game is an agent-based simulation that uses information theoretical principles to model the effect of such malicious behavior taking reputation dynamics as an example. So far, only small groups of 3 to 5 agents have been studied whereas now we extend the reputation game to larger groups of up to 50 agents also including one-to-many conversations. In this setup, the resulting group dynamics are examined, with particular emphasis on the emerging network topology and the influence of agents' personal characteristics thereon. In the long term the reputation game should thus help to determine relations between the arising communication network structure, the used communication strategies and the recipients' behavior, allowing to identify potentially harmful communication patterns, e.g. in social media.
Extraction from Present Participle Adjuncts: The Relevance of the Corresponding Declaratives
2022-07-08

In this article, I will argue that many of the theoretical approaches to extraction from participle adjunct islands suffer from the fact that the focus of investigation lies on perceived grammaticality differences in interrogative structures. Following approaches which make an explicit connection between extraction asymmetries and properties of the underlying proposition, I will argue that there is good evidence for the existence of similar differences in declarative adjunct constructions which can explain most of the grammaticality patterns observed for interrogatives. A crucial distinction to the majority of previous theories is the focus on acceptability rather than grammaticality, and the assumption that acceptability in declaratives is determined by a variety of semantic and syntactic complexity factors which do not influence how strongly extraction degrades the structure. This line of argumentation is more compatible with approaches to island phenomena that explain the low acceptability of some extractions by independent effects such as processing complexity and discourse function instead of syntactic principles blocking the extraction. I will also discuss a partially weighted, multifactorial model for the acceptability of declarative and interrogative participle adjunct constructions, which explains the judgment patterns in the literature without the need for additional, complex licensing conditions for extraction.
Refining data-data and data-model biome comparisons using the Earth Movers' Distance (EMD)
2022-07-08

Abstract. Biome reconstructions are commonly used in data-data and data-model comparison studies to understand past vegetation dynamics. However, most of these assessments are based on the direct comparison of dominant biomes inferred from pollen samples or vegetation simulations. Dominant biomes are deduced from pollen samples using biome affinity scores, which aggregate pollen percentages of taxa assigned to the different biomes. While this approach generates good results over a large range of temporal and spatial scales, reducing pollen assemblages to a single dominant biome can substantially simplify the vegetation signal preserved in pollen samples and even bias conclusions when, for instance, minimal changes in pollen percentages can change the inferred dominant biome. To resolve these issues, we propose to use the Earth Movers’ distance (EMD) as a new metric to compare distributions of biome scores. The EMD has two main advantages: 1) the distributions of biome scores do not need to be reduced to their dominant biome, and the full breadth of the data is taken into account, and 2) different weights can be given to different types of disagreements to account for the ecological distance (e.g. reconstructing a temperate forest instead of a boreal forest is ecologically less wrong than reconstructing the temperate forest instead of a desert). We also introduce EMD-based statistical tests that determine if the similarity of two samples is significantly better than a random association. This paper illustrates the use of the EMD across a series of palaeoecological data-data and data-model case studies based on published data and simulations. These applications highlight the diverse types of analysis where the EMD adds value compared to analyses of the dominant biomes only. The EMD and the statistical tests are included in the paleotools R package (https://github.com/mchevalier2/paleotools).
On supercritical branching processes with emigration
2022-07-08

Abstract We study supercritical branching processes under the influence of an independent and identically distributed (i.i.d.) emigration component. We provide conditions under which the lifetime of the process is finite or has a finite expectation. A theorem of Kesten–Stigum type is obtained, and the extinction probability for a large initial population size is related to the tail behaviour of the emigration.
Additional file 1 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis
2022-07-08

Additional file 1: Table S1. Plant material for RNA samples for Iso-Seq. Table S2. Read statistics for Iso-seq libraries. Table S3A and B. Number and percentage of splice junctions with sequencing mismatches in positions L1 to L30 for A) upstream (left) and B) downstream (right) of splice junctions. Table S4. Position Weight Matrix scores for consensus splice site sequences of introns. Table S5A and B. Filtering of SJs on basis of mismatches in each position. Table S6. Sequence motifs for validation of TSS and TES sites. Table S7. Number of genes and transcripts contributed to AtIso from each Iso-seq library. Table S8. Saturation curve of the number of unique genes and transcripts added to AtIso with the addition of each library. Table S9. AtRTD3 - Transcript characteristics and translations from TransFeat. Table S10A. TranSuite output of AtRTD3 for mono-exonic/multi-exonic genes with single or multiple transcript isoforms; B Comparison of TranSuite output of AtRTD3 gene and transcript characterisation. Table S11. AtRTD3 - novel genes. Table S12. Functional analysis of transcripts from novel genes in AtRTD3 with TRAPID 2.0. Table S13. AtRTD3 - Chimeric Genes and transcripts. Table S14. Frequency of AS event type among AtRTD3, AtIso and Araport11. Table S15A. Frequency of AS event type among AtRTD3, AtIso and Araport11. Table S15B. Gene descriptions of genes containing non-stop RNAs.
A Draft Human Pangenome Reference
2022-07-09

Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence and are more than 99% accurate at the structural and base-pair levels. Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes, reveals novel alleles at structurally complex loci, and adds 119 million base pairs of euchromatic polymorphic sequence and 1,529 gene duplications relative to the existing reference, GRCh38. Roughly 90 million of the additional base pairs derive from structural variation. Using our draft pangenome to analyze short-read data reduces errors when discovering small variants by 34% and boosts the detected structural variants per haplotype by 104% compared to GRCh38-based workflows, and by 34% compared to using previous diversity sets of genome assemblies.
Using preregistration as a tool for transparent fNIRS study design
2022-07-09

Significance: The expansion of fNIRS methodology and analysis tools give rise to various design and analytical decisions researchers have to make. Several recent efforts have developed guidelines for preprocessing, analyzing, and reporting practices. For the planning stage of fNIRS studies, similar guidance would be desirable. Study preregistration helps researchers to transparently document study protocols before conducting the study - including materials, methods and analyses - and thus others to verify, understand, and reproduce a study. Preregistration can thus serve as a useful tool for transparent, careful and comprehensive fNIRS study design. Aim: We aim to create a guide about the design and analysis steps involved in fNIRS studies and provide a preregistration template specified for fNIRS studies.Approach: The presented preregistration guide has a strong focus on fNIRS specific requirements, and the associated template provides examples based on continuous-wave fNIRS studies conducted in humans. These can, however, be extended to other types of fNIRS studies. Results: On a step-by-step basis, we walk the fNIRS user through key methodological and analysis-related aspects central to a comprehensive fNIRS study design. These include items specific to the design of continuous-wave, task-based fNIRS studies, but also sections that are of general importance, including an in-depth elaboration on sample size planning. Conclusions: Our guide introduces these open science tools to the fNIRS community, providing researchers with an overview of key design aspects and specification recommendations for comprehensive study planning. As such it can be used as a template to preregister fNIRS studies or merely as a tool for transparent fNIRS study design.
Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers
2022-07-09

Abstract Today, one of the biggest challenges in antibiotic research is a targeted prioritization of natural compound producer strains and an efficient dereplication process to avoid undesired rediscovery of already known substances. Thereby, genome sequence-driven mining strategies are often superior to wet-lab experiments because they are generally faster and less resource-intensive. In the current study, we report on the development of a novel in silico screening approach to evaluate the genetic potential of bacterial strains to produce protein synthesis inhibitors (PSI), which was termed the protein synthesis inhibitor ('psi’) target gene footprinting approach = Ψ-footprinting. The strategy is based on the occurrence of protein synthesis associated self-resistance genes in genome sequences of natural compound producers. The screening approach was applied to 406 genome sequences of actinomycetes strains from the DSMZ strain collection, resulting in the prioritization of 15 potential PSI producer strains. For twelve of them, extract samples showed protein synthesis inhibitory properties in in vitro transcription/translation assays. For four strains, namely Saccharopolyspora flava DSM 44771, Micromonospora aurantiaca DSM 43813, Nocardioides albertanoniae DSM 25218, and Geodermatophilus nigrescens DSM 45408, the protein synthesis inhibitory substance amicoumacin was identified by HPLC-MS analysis, which proved the functionality of the in silico screening approach.
Uncertainty in equation learning
2022-07-09

Equation learning is a deep learning framework for explainable machine learning in regression settings, with applications in engineering and the natural sciences. Equation learners typically do not capture uncertainty about the model or its predictions, although uncertainty is often highly structured and particularly relevant for these kinds of applications. We show how simple, yet effective forms of Bayesian deep learning can be used to build structure and explainable uncertainty over a set of found equations. Specifically, we use a mixture of Laplace approximations, where each mixture component captures a different equation structure, and the local Laplace approximations capture parametric uncertainty within one family of equations. We present results on both synthetic and real world examples.
How to deal with toxic amino acids: the bipartite AzlCD complex exports histidine in Bacillus subtilis
2022-07-09

ABSTRACT In the Gram-positive model bacterium Bacillus subtilis , the presence of the amino acid glutamate triggers potassium uptake due to the glutamate-mediated activation of the potassium channel KtrCD. As a result, the intracellular accumulation of glutamate is toxic in strains lacking the second messenger cyclic di-AMP since these cells are unable to limit potassium uptake. We observed that the presence of histidine, which is degraded to glutamate, is also toxic for a B. subtilis strain that lacks all three c-di-AMP synthesizing enzymes. However, suppressor mutants emerged, and whole genome sequencing revealed mutations in the azlB gene encoding the repressor of the azl operon. This operon encodes an exporter and an importer for branched-chain amino acids. The suppressor mutations result in overexpression of the azl operon. Deletion of the azlCD genes encoding the branched-chain amino acid exporter restored the toxicity of histidine indicating that this exporter is required for histidine export and resistance to otherwise toxic levels of the amino acid. The higher abundance of the amino acid exporter AzlCD increased the extracellular concentration of histidine, thus confirming the new function of AzlCD as a histidine exporter. Unexpectedly, AzlB-mediated repression of the operon remains active even in the presence of amino acids suggesting that expression of the azl operon requires mutational inactivation of AzlB. IMPORTANCE Amino acids are building blocks for protein biosynthesis in each living cell. However, due to their reactivity as well as the similarity between several amino amino acids, they may also be involved in harmful reactions or in non-cognate interactions and thus be toxic. Bacillus subtilis can deal with otherwise toxic histidine by overexpressing a bipartite amino acid exporter AzlCD. Although encoded in an operon that also contains a gene for an amino acid importer, the corresponding genes are not expressed, irrespective of the availability or not of amino acids in the medium. This suggests that the azl operon is a last resort to deal with histidine stress that can be expressed due to mutational inactivation of the cognate repressor, AzlB.
Report on scipost_202205_00027v1
2022-07-09

We derive the quasiparticle picture for the fermionic logarithmic negativity in a tight-binding chain subject to gain and loss dissipation.We focus on the dynamics after the quantum quench from the fermionic Néel state.We consider the negativity between both adjacent and disjoint intervals embedded in an infinite chain.Our result holds in the standard hydrodynamic limit of large subsystems and long times, with their ratio fixed.Additionally, we consider the weakly-dissipative limit, in which the dissipation rates are inversely proportional to the size of the intervals.We show that the negativity is proportional to the number of entangled pairs of quasiparticles that are shared between the two intervals, as is the case for the mutual information.Crucially, in contrast with the unitary case, the negativity content of quasiparticles is not given by the Rényi entropy with Rényi index 1/2, and it is in general not easily related to thermodynamic quantities.
Virus exposure and neurodegenerative disease risk across national biobanks
2022-07-10

ABSTRACT BACKGROUND With recent findings connecting Epstein-Barr virus to increased risk of multiple sclerosis and growing concerns regarding the potential neurological impact of the coronavirus pandemic, we surveyed biobank scale real-world data to identify potential links between viral exposures and neurodegenerative disease risks. METHODS To assess the potential increased risk of neurodegenerative diseases due to viral exposures, we mined time series data from FinnGen as a discovery dataset and cross-sectional data from the UK Biobank as a replication dataset for 73 pairs of common viral exposures and neurodegenerative disease outcomes. We investigated the impact of time span between viral exposure and disease risk using time series data from FinnGen at 1, 5, and 15 year intervals between exposure and disease onset. This analysis helped us to avoid the potential confounding of concurrent diagnosis due to hospitalization with viral infection. Further, to address the possible bias of reverse causality we examined risk for severe viral infections after NDD diagnosis. RESULTS We identified 45 viral exposures significantly associated with increased risk of post-exposure neurodegenerative disease onset after multiple test correction in the discovery phase using longitudinal data. 22 of these associations were replicated in cross sectional data from the UK Biobank. The largest effect association we saw replicated was between viral encephalitis exposure and Alzheimer’s disease, with discovery hazard estimates of ∼30 and a replication odds ratio of ∼22. We also replicated the association between Epstein-Barr virus exposure and multiple sclerosis 5-15 years before diagnosis of multiple sclerosis. In total, 17 virus/neurodegeneration pairs were significant with 5-15 years between viral exposure and NDD diagnosis. In an investigation of potential confounding and reverse causality, we generally see larger hazard ratios associated with viruses preceding NDD diagnosis than viruses post NDD diagnosis. CONCLUSIONS Viral exposures contribute to later in life risk of neurodegenerative disease with increased risk of neurodegeneration still significant at up to 15 years between some events in this report.
The Interaction between HLA‐DRB1 and Smoking in Parkinson's Disease Revisited
2022-07-10

Abstract Background Two studies that examined the interaction between HLA‐DRB1 and smoking in Parkinson's disease (PD) yielded findings in opposite directions. Objective To perform a large‐scale independent replication of the HLA‐DRB1 × smoking interaction. Methods We genotyped 182 single nucleotide polymorphism (SNPs) associated with smoking initiation in 12 424 cases and 9480 controls to perform a Mendelian randomization (MR) analysis in strata defined by HLA‐DRB1 . Results At the amino acid level, a valine at position 11 (V11) in HLA‐DRB1 displayed the strongest association with PD. MR showed an inverse association between genetically predicted smoking initiation and PD only in absence of V11 (odds ratio, 0.74, 95% confidence interval, 0.59–0.93, P Interaction = 0.028). In silico predictions of the influence of V11 and smoking‐induced modifications of α‐synuclein on binding affinity showed findings consistent with this interaction pattern. Conclusions Despite being one of the most robust findings in PD research, the mechanisms underlying the inverse association between smoking and PD remain unknown. Our findings may help better understand this association. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society