Parsing

Lipidomics generates large data that makes manual annotation and interpretation challenging. Lipid chemical and structural diversity with structural isomers further complicates annotation. Although, several commercial and open-source software for targeted lipid identification exists, it lacks automated method generation workflows and integration with statistical and bioinformatics tools. We have developed the Comprehensive Lipidomic Automated Workflow (CLAW) platform with integrated workflow for parsing, detailed statistical analysis and lipid annotations based on custom multiple reaction monitoring (MRM) precursor and product ion pair transitions...

BACKGROUND: Spinal cord and brain atrophy are common in neuromyelitis optica spectrum disorder (NMOSD) and relapsing-remitting multiple sclerosis (RRMS) but harbor distinct patterns accounting for disability and cognitive impairment. METHODS: This study included 209 NMOSD and 304 RRMS patients and 436 healthy controls. Non-negative matrix factorization was used to parse differences in spinal cord and brain atrophy at subject level into distinct patterns based on structural MRI...

Oil spilled into an aquatic environment produces oil droplet and dissolved component concentrations and compositions that are highly variable in space and time. Toxic effects on aquatic biota vary with sensitivity of the organism, concentration, composition, environmental conditions, and frequency and duration of exposure to the mixture of oil-derived dissolved compounds. For a range of spill (surface, subsea, blowout) and oil types under different environmental conditions, modeling of oil transport, fate, and organism behavior was used to quantify expected exposures over time for planktonic, motile, and stationary organisms...

Cropping-and-segmenting pattern parsers often combine diverse inner correlations into a single metric/scheme, resulting in over-generalizations and redundant representations. It is proposed to streamline pattern parsing by using presenting a redundant association elimination network (RAEN) with capsule attention twisters (CATs) and capsule-attention routing agreement (CARA). CATs trim delicate relationships between parts and wholes that are weak and interchangeable. Senior entities can only be updated by primary entities that meet the requirements of inter-part diversity and intra-object cohesiveness...

BACKGROUND: Interpersonal trauma is a risk factor for a wide array of adverse mental health outcomes, including substance use. Research has begun investigating the role of shame in the intersection between substance use and interpersonal trauma. The current systematic review summarizes the existing literature documenting the relation among shame, substance use, and interpersonal trauma. METHOD: Articles were collected using a Boolean search strategy of terms related to interpersonal trauma, substance use, and shame across six databases...

This paper describes the methodology used to create a fuel data library comprising safeguards-relevant quantities that may be useful for verification of spent nuclear fuel (SNF) produced by simulating a concept Molten Salt Reactor (MSR). The Monte-Carlo particle transport code, Serpent2 and the calculation code SOURCES 4C were used to compile this fuel data library. The data library is based on the Compact Molten Salt Reactor (CMSR) concept being developed by Seaborg Technologies (based in Copenhagen, Denmark)...

How do parenthood and publishing contribute to gender gaps in academic career advancement? While extensive research examines the causes of gender disparities in science, technology, engineering, and mathematics (STEM) careers, we know much less about the factors that constrain women's advancement in the social sciences. Combining detailed career- and administrative register data on 976 Danish social scientists in Business and Management, Economics, Political Science, Psychology, and Sociology (5703 person-years) that obtained a PhD degree between 2000 and 2015, we estimate gender differences in attainment of senior research positions and parse out how publication outputs, parenthood and parental leave contribute to these differences...

Psychological therapies are among the most effective treatments for common mental health problems-however, we still know relatively little about how exactly they improve symptoms. Here, we demonstrate the power of combining theory with computational methods to parse effects of different components of cognitive-behavioral therapies onto underlying mechanisms. Specifically, we present data from a series of randomized-controlled experiments testing the effects of brief components of behavioral and cognitive therapies on different cognitive processes, using well-validated behavioral measures and associated computational models...

The maxillary palp is an auxiliary olfactory organ in insects, which, different from the antennae, is equipped with only a few olfactory sensory neuron (OSN) types. We postulated that these derived mouthpart structures, positioned at the base of the proboscis, may be particularly important in mediating feeding behaviors. As feeding is spatio-temporally segregated from oviposition in most Tephritidae, this taxonomic group appears quite suitable to parse out sensory breadth and potential functional divergence of palps and antennae...

Existing human parsing frameworks commonly employ joint learning of semantic edge detection and human parsing to facilitate the localization around boundary regions. Nevertheless, the parsing prediction within the interior of the part contour may still exhibit inconsistencies due to the inherent ambiguity of fine-grained semantics. In contrast, binary edge detection does not suffer from such fine-grained semantic ambiguity, leading to a typical failure case where misclassification occurs inner the part contour while the semantic edge is accurately detected...

Computational models of infant word-finding typically operate over transcriptions of infant-directed speech corpora. It is now possible to test models of word segmentation on speech materials, rather than transcriptions of speech. We propose that such modeling efforts be conducted over the speech of the experimental stimuli used in studies measuring infants' capacity for learning from spoken sentences. Correspondence with infant outcomes in such experiments is an appropriate benchmark for models of infants...

Medical dramas offer unique insights into the way popular media makes sense of genetic technology and the ethics of its applications. In this paper we evaluate the contrasting depictions in television medical dramas of reproductive genetic screening and eugenics-two medical themes that some commentators see as closely related. By conducting a content analysis of 32 episodes of doctor shows featuring eugenic and/or genetic screening themes, we put the medical drama landscape in conversation with bioethics scholarship and mark a significant divergence between the two...

The way in which college students learn online has dramatically altered due to the COVID-19 pandemic. Using the triadic reciprocal determinism (TRD) theory, this study aimed to identify the key factors influencing college students' online learning experience through sentiment analysis, text mining, and social network analysis (SNA). Macro- and micro-level parsing was conducted on the SNA model, which was divided into core, mantle, and shell layers to determine the most influential factors in the core layer...

Feature selection is a critical component of machine learning and data mining to remove redundant and irrelevant features from a dataset. The Chimp Optimization Algorithm (CHoA) is widely applicable to various optimization problems due to its low number of parameters and fast convergence rate. However, CHoA has a weak exploration capability and tends to fall into local optimal solutions in solving the feature selection process, leading to ineffective removal of irrelevant and redundant features. To solve this problem, this paper proposes the Enhanced Chimp Hierarchy Optimization Algorithm for adaptive lens imaging (ALI-CHoASH) for searching the optimal classification problems for the optimal subset of features...

Phenotypic variation within species can affect the ecological dynamics of populations and communities. Characterizing the genetic variation underlying such effects can help parse the roles of genetic evolution and plasticity in 'eco-evolutionary dynamics' and inform how genetic variation may shape patterns of evolution. Here we employ genome-wide association (GWA) methods in Timema cristinae stick insects and their co-occurring arthropod communities to identify genetic variation associated with community-level traits...

BACKGROUND: Epigenetic changes are plausible molecular sources of clinical heterogeneity in schizophrenia. A subgroup of schizophrenia patients with elevated inflammatory or immune-dysregulation has been reported by previous studies. However, little is known about epigenetic changes in genes related to immune activation in never-treated first-episode patients with schizophrenia (FES) and its consistency with that in treated long-term ill (LTS) patients. METHODS: In this study, epigenome-wide profiling with a DNA methylation array was applied using blood samples of both FES and LTS patients, as well as their corresponding healthy controls...

Humans perceive and construct the world as an arrangement of simple parametric models. In particular, we can often describe man-made environments using volumetric primitives such as cuboids or cylinders. Inferring these primitives is important for attaining high-level, abstract scene descriptions. Previous approaches for primitive-based abstraction estimate shape parameters directly and are only able to reproduce simple objects. In contrast, we propose a robust estimator for primitive fitting, which meaningfully abstracts complex real-world environments using cuboids...

Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein...

Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides...

Neurodevelopmental disorders, such as Attention Deficit/Hyperactivity Disorder (ADHD) and Autism Spectrum Disorder (ASD), are characterized by comorbidity and heterogeneity. Identifying distinct subtypes within these disorders can illuminate the underlying neurobiological and clinical characteristics, paving the way for more tailored treatments. We adopted a novel transdiagnostic approach across ADHD and ASD, using cutting-edge contrastive graph machine learning to determine subtypes based on brain network connectivity as revealed by resting-state functional magnetic resonance imaging...