A thorough evaluation of the Language Environment Analysis (LENA) system.
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ABSTRACT:
SUBMITTER: Cristia A
PROVIDER: S-EPMC7855224 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Phelan-McDermid syndrome (PMS) is a single-locus cause of developmental delay, autism spectrum disorder, and minimal verbal abilities. There is an urgent need to identify objective outcome measures of expressive language for use in this and other minimally verbal populations. One potential tool is an automated language processor called Language ENvironment Analysis (LENA). LENA was used to obtain over 542 h of audio in 18 children with PMS. LENA performance was adequate in a subset of children with PMS, specifically younger children and those with fewer stereotypic vocalizations. One LENA-derived language measure, Vocalization Ratio, had improved accuracy in this sample and may represent a novel expressive language measure for use in severely affected populations.
| S-EPMC6196360 | biostudies-literature
Project description:Early language environment plays a critical role in child language development. The Language ENvironment Analysis (LENA™) system allows researchers and clinicians to collect daylong recordings and obtain automated measures to characterize a child's language environment. This meta-analysis evaluates the predictability of LENA's automated measures for language skills in young children. We systematically searched reports for associations between LENA's automated measures, specifically, adult word count (AWC), conversational turn count (CTC), and child vocalization count (CVC), and language skills in children younger than 48 months. Using robust variance estimation, we calculated weighted mean effect sizes and conducted moderator analyses exploring the factors that might affect this relationship. The results revealed an overall medium effect size for the correlation between LENA's automated measures and language skills. This relationship was largely consistent regardless of child developmental status, publication status, language assessment modality and method, or the age at which the LENA recording was taken; however, the effect was weakly moderated by the gap between LENA recordings and language measures taken. Among the three measures, there were medium associations between CTC and CVC and language, whereas there was a small-to-medium association between AWC and language. These findings extend beyond validation work conducted by the LENA Research Foundation and suggest certain predictive strength of LENA's automated measures for child language. We discussed possible mechanisms underlying the observed associations, as well as the theoretical, methodological, and clinical implications of these findings.
| S-EPMC7337141 | biostudies-literature
Project description:Purpose The Language Environment Analysis (LENA) system provides automated measures facilitating clinical and nonclinical research and interventions on language development, but there are only a few, scattered independent reports of these measures' validity. The objectives of the current systematic review were to (a) discover studies comparing LENA output with manual annotation, namely, accuracy of talker labels, as well as involving adult word counts (AWCs), conversational turn counts (CTCs), and child vocalization counts (CVCs); (b) describe them qualitatively; (c) quantitatively integrate them to assess central tendencies; and (d) quantitatively integrate them to assess potential moderators. Method Searches on Google Scholar, PubMed, Scopus, and PsycInfo were combined with expert knowledge, and interarticle citations resulting in 238 records screened and 73 records whose full text was inspected. To be included, studies must target children under the age of 18 years and report on accuracy of LENA labels (e.g., precision and/or recall) and/or AWC, CTC, or CVC (correlations and/or error metrics). Results A total of 33 studies, in 28 articles, were discovered. A qualitative review revealed most validation studies had not been peer reviewed as such and failed to report key methodology and results. Quantitative integration of the results was possible for a broad definition of recall and precision (M = 59% and 68%, respectively; N = 12-13), for AWC (mean r = .79, N = 13), CVC (mean r = .77, N = 5), and CTC (mean r = .36, N = 6). Publication bias and moderators could not be assessed meta-analytically. Conclusion Further research and improved reporting are needed in studies evaluating LENA segmentation and quantification accuracy, with work investigating CTC being particularly urgent. Supplemental Material https://osf.io/4nhms/.
| S-EPMC7242991 | biostudies-literature
Project description:This paper proposes a fast methodology to synthesize hybrid lenalidomide gold nanoparticles. Gold (HAuCl4) is chelated with an antiangiogenic compound (lenalidomide (LENA)) and diacid poly(ethylene glycol) (PEG) as capping agent and reagent. The suggested synthesis is rapid and results in gold nanoparticles (AuNPs) with enhanced drug solubility. The binding between LENA, PEG, and Au(III) ions forms hybrid nanovectors named LENA IN PEG-AuNPs, which were characterized by different spectroscopic techniques (Raman and UV-vis), transmission electron microscopy (TEM), and compared with LENA ON PEG-AuNPs, in which the drug was grafted onto gold surface by carbodiimide chemistry (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide, EDC/NHS). The effective drug delivery under pH conditions was also reached, combined with doxorubicin (DOX) to improve the synergic chemotherapy and stability under experimental conditions. For biomedical purposes, hybrid gold nanocarriers were conjugated with folic acid (FA), which is specifically overexpressed in cancer cells. This paper will be very important in the domain of therapeutic gold complex, paving the way for reaching progress of novel drug carrier synthesis in nanomedicine.
| S-EPMC7658941 | biostudies-literature
Project description:PurposeTo characterize, by specific biomarkers and nucleic acid sequencing, the structural and genomic sperm characteristics of partial (PG) and complete globozoospermic (CG) men in order to identify the best reproductive treatment.MethodsWe assessed spermatozoa from 14 consenting men ultrastructurally, as well as for histone content, sperm chromatin integrity, and sperm aneuploidy. Additional genomic, transcriptomic, and proteomic evaluations were carried out to further characterize the CG cohort. The presence of oocyte-activating sperm cytosolic factor (OASCF) was measured by a phospholipase C zeta (PLCζ) immunofluorescence assay. Couples were treated in subsequent cycles either by conventional ICSI or by ICSI with assisted gamete treatment (AGT) using calcium ionophore (Ionomycin, 19657, Sigma-Aldrich, Saint Louis, MO, USA).ResultsUltrastructural assessment confirmed complete acrosome deficiency in all spermatozoa from CG men. Histone content, sperm chromatin integrity, and sperm aneuploidy did not differ significantly between the PG (n = 4) and CG (n = 10) cohorts. PLCζ assessment indicated a positive presence of OASCF in 4 PG couples, who underwent subsequent ICSI cycles that yielded a 36.1% (43/119) fertilization with a 50% (2/4) clinical pregnancy and delivery rate. PLCζ assessment failed to detect OASCF for 8 CG patients who underwent 9 subsequent ICSI cycles with AGT, yielding a remarkable improvement of fertilization (39/97; 40.2%) (P = 0.00001). Embryo implantation (6/21; 28.6%) and clinical pregnancies (5/7; 71.4%) were also enhanced, resulting in 4 deliveries. Gene mutations (DPY19L2, SPATA16, PICK1) were identified in spermatozoa from CG patients. Additionally, CG patients unable to sustain a term pregnancy had gene mutations involved in zygote development (NLRP5) and postnatal development (BSX). CG patients who successfully sustained a pregnancy had a mutation (PIWIL1) related to sperm phenotype. PLCZ1 was both mutated and underexpressed in these CG patients, regardless of reproductive outcome.ConclusionsSperm bioassays and genomic studies can be used to characterize this gamete's capacity to support embryonic development and to tailor treatments maximizing reproductive outcome.
| S-EPMC8417186 | biostudies-literature
Project description:G-language genome analysis environment (G-language GAE) contains more than 100 programs that focus on the analysis of bacterial genomes, including programs for the identification of binding sites by means of information theory, analysis of nucleotide composition bias and the distribution of particular oligonucleotides, calculation of codon bias and prediction of expression levels, and visualization of genomic information. We have provided a collection of web services for these programs by utilizing REST and SOAP technologies. The REST interface, available at http://rest.g-language.org/, provides access to all 145 functions of the G-language GAE. These functions can be accessed from other online resources. All analysis functions are represented by unique universal resource identifiers. Users can access the functions directly via the corresponding universe resource locators (URLs), and biological web sites can readily embed the functions by simply linking to these URLs. The SOAP services, available at http://www.g-language.org/wiki/soap/, provide language-independent programmatic access to 77 analysis programs. The SOAP service Web Services Definition Language file can be readily loaded into graphical clients such as the Taverna workbench to integrate the programs with other services and workflows.
| S-EPMC2896103 | biostudies-literature
Project description:Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.
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Project description:With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have "crib-sheets," user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer's Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its "modes of use" with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans. Electronic Supplementary Material:The online version of this article (10.1007/s11214-018-0576-4) contains supplementary material, which is available to authorized users.
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Project description:Membrane proteins (MPs) are key players in a variety of different cellular processes and constitute the target of around 60% of all Food and Drug Administration-approved drugs. Despite their importance, there is still a massive lack of relevant structural, biochemical and mechanistic information mainly due to their localization within the lipid bilayer. To help fulfil this gap, we developed the MEmbrane protein dimer Novel Structure Analyser database (MENSAdb). This interactive web application summarizes the evolutionary and physicochemical properties of dimeric MPs to expand the available knowledge on the fundamental principles underlying their formation. Currently, MENSAdb contains features of 167 unique MPs (63% homo- and 37% heterodimers) and brings insights into the conservation of residues, accessible solvent area descriptors, average B-factors, intermolecular contacts at 2.5 Å and 4.0 Å distance cut-offs, hydrophobic contacts, hydrogen bonds, salt bridges, π-π stacking, T-stacking and cation-π interactions. The regular update and organization of all these data into a unique platform will allow a broad community of researchers to collect and analyse a large number of features efficiently, thus facilitating their use in the development of prediction models associated with MPs. Database URL: http://www.moreiralab.com/resources/mensadb.
| S-EPMC8023553 | biostudies-literature
Project description:To evaluate the equivalence of the PROMIS(®) physical functioning item bank by language of administration (English versus Spanish).The PROMIS(®) wave 1 English-language physical functioning bank consists of 124 items, and 114 of these were translated into Spanish.Item frequencies, means and standard deviations, item-scale correlations, and internal consistency reliability were calculated. The IRT assumption of unidimensionality was evaluated by fitting a single-factor confirmatory factor analytic model. IRT threshold and discrimination parameters were estimated using Samejima's Graded Response Model. DIF by language of administration was evaluated.Item means ranged from 2.53 (SD = 1.36) to 4.62 (SD = 0.82). Coefficient alpha was 0.99, and item-rest correlations ranged from 0.41 to 0.89. A one-factor model fits the data well (CFI = 0.971, TLI = 0.970, and RMSEA = 0.052). The slope parameters ranged from 0.45 ("Are you able to run 10 miles?") to 4.50 ("Are you able to put on a shirt or blouse?"). The threshold parameters ranged from -1.92 ("How much do physical health problems now limit your usual physical activities (such as walking or climbing stairs)?") to 6.06 ("Are you able to run 10 miles?"). Fifty of the 114 items were flagged for DIF based on an R(2) of 0.02 or above criterion. The expected total score was higher for Spanish- than English-language respondents.English- and Spanish-speaking subjects with the same level of underlying physical function responded differently to 50 of 114 items. This study has important implications in the study of physical functioning among diverse populations.
| S-EPMC3683100 | biostudies-literature