Miracle-dz/UniFAR-FTUs huggingface dataset:
Alkbh5, a RNA Demethylase, Is Involved in Fine-tuning of Cell Differentiation (FS11-07-19).

Objectives N6-Methyladenosine (m6A) is the most prevalent mRNA modification, which modulates mRNA export, splicing, and stability. Recent studies showed that m6A is involved in cell differentiation such as spermatogenesis, but the underlying mechanism is still unclear. This study was aimed to investigate whether alkylation repair homolog 5 (ALKBH5)-dependent m6A demethylation plays a role in metabolic-related cell differentiation. Methods Expression analysis upon differentiation was done using R studio on publicly available data from two independent cell differentiation models, adipogenic 3T3-L1 and myogenic C2C12. M6A levels in mRNA were measured using dot blot. Knockdown of ALKBH5 was conducted by small interference RNA at two days prior to differentiation induction. For phenotypic measures upon differentiation, staining analysis by Giemsa and Oil Red-O was conducted for 3T3-L1 and C2C12 cells, respectively, followed by histogram analysis using ImageJ. Total RNA was isolated from cells and was reverse-transcribed to cDNA, followed by qRT-PCR for gene expression analysis. Results Comparative analysis of adipogenesis and myogenesis models revealed common pathways, including oxidative phosphorylation. Among a-ketoglutarate-dependent demethylases, Alkbh5 expression was substantial and its substrate, m6A level was changed upon induction of differentiation. Staining analysis showed that Alkbh5 knockdown using siRNA significantly increased production of triglycerides and myotubes in 3T3-L1 and C2C12, respectively, indicating promotion of cell differentiation. To identify putative targets, expression data using microarray and qRT-PCR were analyzed. Expression of CEBPb and myogenin among adipogenic and myogenic markers was significantly altered upon Alkbh5 knockdown in 3T3-L1 and C2C12, respectively. Conclusions The results together showed that ALKBH repression promoted cell differentiation in both adipogenic and myogenic models, possibly regulating early differentiating markers such as CEBPb and myogenin, respectively. Funding Sources NRF of Korea (2018R1D1A1B07051274 & 22A20130012143).
Engaging Children to Support Parental Weight Loss: A Randomized Trial

Background. Despite evidence that social network members influence the eating behaviors of adults, no study to date has had the primary aim of examining children as support partners for parents in a weight loss intervention. Aim. To evaluate parent adherence with eating/exercise goals and weight loss in a 6-month study engaging children as support partners. Method. Adults with obesity (body mass index ≥ 30 kg/m2, n = 102) and at least one child ≥12 years were randomized to a child support or control group. In the child support group, children enrolled with their parent and engaged in a supportive behavior 2 days/week. In the control group, there was no enrolled child support. Parents in both groups selected a healthy eating strategy and daily step goal. Results. There was no difference in weight loss between the child support and control groups (−5.97 vs. −5.42 lbs, p = .81). In the child support group, 30% of children did not engage in the study. The majority of parents whose children did not engage withdrew from the study. In secondary analyses, parent adherence with eating/exercise goals increased with the days of child support (p < .001). For all participants, low chaos in the home environment (p < .04) and increased parent adherence with follow-ups (p < .008) predicted weight loss. Conclusions. We found no treatment effect of child support on weight loss. Active child support of eating/exercise goals appeared to facilitate goal adherence, while anticipated but unrealized child support may have had iatrogenic consequences. Further investigation of family-focused weight loss interventions is warranted.
Neutrality in the Metaorganism

Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and which are therefore interesting candidates for further study. Moreover, using simulated communities we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.
The Impact of a Community Fruit and Vegetable Voucher Program (Vouchers 4 Veggies) on Improvements in Dietary Intake and Food Security (P04-013-19).

Objectives Vouchers 4 Veggies (V4V) is a transformative healthy food voucher program aimed at increasing access to and affordability of healthy food in the most vulnerable communities. Between 2015-2018, over 2600 ethnically diverse low-income individuals were enrolled in the program with the goal to increase their fruit and vegetable intake, improve food security status and change health perception. Methods V4V partners with local community-based organizations and clinics that serve as voucher distribution sites as well as neighborhoods stores, grocery stores, and famer's markets where participants can redeem their vouchers. Participants receive $20-$40 worth of vouchers per month for 6 months. Data for this evaluation were collected using pre- and post- surveys (at 0 and 4-6 months) that included a validated fruit and vegetable intake screener, the USDA 7-item food security screener, demographic questions and health perception questions. Results Data from 862 matched surveys indicate that mean fruit and vegetable intake increased from 2.49 to 3.52 servings daily, corresponding to a 1.03 servings increase after six months in the program (0.89,1.77; P < .001). In addition, V4V participants' food security scores improved, decreasing 0.88 points (-1.07, -0.71; P < 0.001) on a 6 point scale (0 being the most food secure and 6 being very food insecure), from a mean of 5.53 to 4.65 using the USDA validated 6-item scale. When stratified by race, food security improved significantly for all major racial groups except Black/African Americans. Finally, participants reported a statistically significant improvement in self-reported health status (P < 0.001), with a 14% change in status from poor/fair health to good/very good/excellent health. Conclusions This evaluation suggests that a modest supplement for fruits and vegetables may be able to improve dietary intake, support food security, and improve health perception among vulnerable residents of San Francisco. More research is needed to understand differences in maintaining long-term health and behavior changes among program participants. Funding Sources V4V received funding from the SF Department of Public Health, Hellman Foundation, AARP Foundation, and Kaiser Permanente Community Benefits Program.
ANALISIS SENTIMEN MENGGUNAKAN METODE NAÏVE BAYES CLASSIFIER DENGAN SELEKSI FITUR CHI SQUARE

Sentiment analysis is the computational study of opinions, sentiments, and emotions expressed in texts. The basic task of sentiment analysis is to classify the polarity of the existing texts in documents, sentences, or opinions. Polarity has meaning if there is text in the document, sentence, or the opinion has a positive or negative aspect. In this study, classification of the polarity in sentiment analysis using machine learning techniques, that is Naive Bayes classifier. Criteria for text classification decisions, learned automatically from learning the data. The need for manual classification is still required because training the data derived from manually labeling, the label (feature) refers to the process of adding a description of each data according to its category. In the process of labeling, feature selection is used and performed by chi-square feature selection, to reduce the disturbance (noise) in the classification. The results showed that the frequency of occurrences of the expected features in the true category and in the false category have an important role in the chi-square feature selection. Then classification breaking news by Naive Bayes classifier obtained an accuracy of 83% and a harmonic average of 90.713%.
Young sex chromosomes in plants and animals.

A major reason for studying plant sex chromosomes is that they may often be "young" systems. There is considerable evidence for the independent evolution of separate sexes within plant families or genera, in some cases showing that the maximum possible time during which their sex-determining genes have existed must be much shorter than those of several animal taxa. Consequently, their sex -linked regions could either have evolved soon after genetic sex determination arose, or considerably later. Plants therefore include species with both young and old systems. I review several questions about the evolution of sex-determining systems and sex chromosomes that require studies of young systems, including: the kinds of mutations involved in the transition to unisexual reproduction from hermaphroditism or monoecy (a form of functional hermaphroditism); the times when they arose; and the extent to which the properties of sex-linked regions of genomes reflect responses to new selective situations created by the presence of a sex-determining locus. I also evaluate which questions are best studied in plants, versus other suitable candidate organisms. Studies of young plant systems can help understand general evolutionary processes that are shared with the sex chromosomes of other organisms. This article is protected by copyright. All rights reserved.
A new approach to the classification of muscle health: preliminary investigations

Objective: Upper leg skeletal or lean tissue mass (LTM), strength and muscle quality have emerged as time-sensitive indices of muscular health. The aim of this study was to generate a comparative data set based on these indices, in healthy young (n = 30, 29.0 ± 3.0 y old) and older (n = 32, 58.7 ± 2.8 years old) adults, in order to evaluate their construct validity in establishing cut-points for muscle health. Approach: Whole body and upper leg LTM was obtained (iDXATM; GE Healthcare, Madison, WI) prior to the assessment of maximal voluntary isometric torque of the knee extensors and flexors (Cybex Isokinetic Dynamometer; Humac Norm, USA). Main results: Peak isometric upper leg torque showed the greatest age-related difference (−29.0%), followed by muscle quality (−19.1%) and upper leg LTM (–9.8%). Significance: Cut-points based on Z and T-scores generated from the young adult mean suggest muscle quality demonstrates the greatest construct validity toward the aim of classifying the muscular health of adults. Data generated from large, representative and sex-specific samples are required to adequately classify the muscular health of adults.
Phraseology in specialized language and its representation in environmental knowledge resources

Phraseology in Specialized Language and its Representation in Environmental Knowledge Resources This research presents the design of a template for encoding and describing phraseological information in the environmental knowledge base, EcoLexicon (ecolexicon.ugr.es). One of the objectives of this study was to formulate a methodology that could also be used to codify phraseological information in other specialized knowledge domains. The focus of our analysis was on verb collocations (verb+noun, noun+verb) because of the need to enrich specialized knowledge resources with information regarding predicates and their arguments. As is well known, verbs are an extremely important part of language since, in a manner of speaking, they set the scene or establish the structure for the rest of the sentence. However, very few specialized knowledge resources include them. The phraseological template proposed in this research takes its theoretical premises from cognitive approaches to Terminology, namely, Sociocognitive Terminology and Frame-based Terminology. In addition, assumptions from linguistic models that deal with predicate argument structure were also included, such as the Lexical Grammar Model, Lexical Constructional Model, Role and Reference Grammar, and FrameNet. The practical guidelines for the design of our template were based on a detailed analysis of the most representative lexicographic and terminographic resources that contain phraseological information. A set of the most important meaning-based resources for verb description was also analyzed. The underlying idea of our research is that verbs and their potential arguments can be classified and structured in a set of conceptual-semantic categories typical of a given specialized domain. In this context, when semantic roles and macroroles are specified as well as the resulting phrase structure, it is then possible to establish templates that represent this meaning for entire frames. In this regard, within the context of a specialized knowledge domain, the range of verbs generally associated with potential arguments can be predicted within the frame of a specialized event. This occurs, of course, because the nature of arguments is constrained by verb meaning. However, it is our assertion that this influence is reciprocal since in specialized language, verbs are also to some extent constrained by their arguments. In this regard, there is an interaction between the meaning components of the entities and processes activated in specialized knowledge event representations. Finally, the results of our analysis have been implemented in EcoLexicon. As shown, the methodology proposed in this thesis for encoding and describing verbal collocations in terminographic resources is useful both for text comprehension and text production.
Characterization of pathogenic monoclonal autoantibodies derived from muscle-specific kinase myasthenia gravis patients

Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by muscle weakness and caused by pathogenic autoantibodies that bind to membrane proteins at the neuromuscular junction. Most patients have autoantibodies against the acetylcholine receptor (AChR), but a subset of patients have autoantibodies against muscle-specific tyrosine kinase (MuSK) instead. MuSK is an essential component of the pathway responsible for synaptic differentiation, which is activated by nerve-released agrin. Through binding MuSK, serum-derived autoantibodies inhibit agrin-induced MuSK autophosphorylation, impair clustering of AChRs, and block neuromuscular transmission. We sought to establish individual MuSK autoantibody clones so that the autoimmune mechanisms could be better understood. We isolated MuSK autoantibody-expressing B cells from 6 MuSK MG patients using a fluorescently tagged MuSK antigen multimer, then generated a panel of human monoclonal autoantibodies (mAbs) from these cells. Here we focused on 3 highly specific mAbs that bound quantitatively to MuSK in solution, to MuSK-expressing HEK cells, and at mouse neuromuscular junctions, where they colocalized with AChRs. These 3 IgG isotype mAbs (2 IgG4 and 1 IgG3 subclass) recognized the Ig-like domain 2 of MuSK. The mAbs inhibited AChR clustering, but intriguingly, they enhanced rather than inhibited MuSK phosphorylation, which suggests an alternative mechanism for inhibiting AChR clustering.
To Explore the Potentials of Independent Component Analysis in Brain-Computer Interface of Motor Imagery

This paper is focused on the experimental approach to explore the potential of independent component analysis (ICA) in the context of motor imagery (MI)-based brain-computer interface (BCI). We presented a simple and efficient algorithmic framework of ICA-based MI BCI (ICA-MIBCI) for the evaluation of four classical ICA algorithms (Infomax, FastICA, Jade, and Sobi) as well as a simplified Infomax (sInfomax). Two novel performance indexes, self-test accuracy and the number of invalid ICA filters, were employed to assess the performance of MIBCI based on different ICA variants. As a reference method, common spatial pattern (CSP), a commonly-used spatial filtering method, was employed for the comparative study between ICA-MIBCI and CSP-MIBCI. The experimental results showed that sInfomax-based spatial filters exhibited significantly better transferability in session to session and subject to subject transfer as compared to CSP-based spatial filters. The online experiment was also introduced to demonstrate the practicability and feasibility of sInfomax-based MIBCI. However, four classical ICA variants, especially FastICA, Jade, and Sobi, performed much worse as compared to sInfomax and CSP in terms of classification accuracy and stability. We consider that conventional ICA-based spatial filtering methods tend to be overfitting while applied to real-life electroencephalogram data. Nevertheless, the sInfomax-based experimental results indicate that ICA methods have a great space for improvement in the application of MIBCI. We believe that this paper could bring forth new ideas for the practical implementation of ICA-MIBCI.
Action Graphs for Performing Goal Recognition Design on Human-Inhabited Environments †

Goal recognition is an important component of many context-aware and smart environment services; however, a person’s goal often cannot be determined until their plan nears completion. Therefore, by modifying the state of the environment, our work aims to reduce the number of observations required to recognise a human’s goal. These modifications result in either: Actions in the available plans being replaced with more distinctive actions; or removing the possibility of performing some actions, so humans are forced to take an alternative (more distinctive) plan. In our solution, a symbolic representation of actions and the world state is transformed into an Action Graph, which is then traversed to discover the non-distinctive plan prefixes. These prefixes are processed to determine which actions should be replaced or removed. For action replacement, we developed an exhaustive approach and an approach that shrinks the plans then reduces the non-distinctive plan prefixes, namely Shrink–Reduce. Exhaustive is guaranteed to find the minimal distinctiveness but is more computationally expensive than Shrink–Reduce. These approaches are compared using a test domain with varying amounts of goals, variables and values, and a realistic kitchen domain. Our action removal method is shown to increase the distinctiveness of various grid-based navigation problems, with a width/height ranging from 4 to 16 and between 2 and 14 randomly selected goals, by an average of 3.27 actions in an average time of 4.69 s, whereas a state-of-the-art approach often breaches a 10 min time limit.
Evaluation of the Accuracy of Four Digital Methods by Linear and Volumetric Analysis of Dental Impressions

The quality of dental arch impression has a substantial role in the precision of the intervention. It is traditionally acquired with resins that solidify when in contact with the air. Compared to that method, digital impression gives great advantages and, together with three-dimensional (3D) digitization devices, allows a simplification of the digital impression process. The growing adoption of such systems by a large number of dental clinics determines the need for an in-depth evaluation of the accuracy and the precision of the different systems. The aim of this work is to define a methodology for the evaluation of the accuracy and precision of 3D intraoral and desktop scanning systems, by using volumetric and linear methods. The replica of a tooth was realized with zirconium; afterward, high-accuracy point clouds of the master model were acquired by a coordinate measurement machine (CMM). In this way, the dimensions of the replica were accurately known. An intraoral scanner (I) and three desktops (D1, D2, D3) were then used to scan the replica. The geometry resulting from the CMM was compared with the ones derived from the scanners, using two different commercial programs (Geomagic and 3-Matic) and a custom-developed algorithm (MATLAB). Geomagic showed the mean values to be in a range from 0.0286 mm (D1) to 0.1654 mm (I), while 3-Matic showed mean values from −0.0396 mm (D1) to 0.1303 mm (I). MATLAB results ranged from 0.00014 mm (D1) to 0.00049 mm (D2). The probability distributions of the volumetric error of the measurements obtained with the different scanners allow a direct comparison of their performances. For the results given by our study, the volumetric approach that we adopted appears to be an excellent system of analysis.
Retrospective analysis of esophageal imaging features in brachycephalic versus non‐brachycephalic dogs based on videofluoroscopic swallowing studies

Abstract Background Idiopathic esophageal dysmotility (ED) is increasingly recognized in young dogs of brachycephalic breeds. Few studies have objectively associated specific videofluoroscopic swallowing study (VFSS) features with brachycephaly, leading to under‐recognition of ED in brachycephalic breeds. Hypothesis/objectives To describe and compare VFSS in brachycephalic dogs versus non‐brachycephalic dogs presented for dysphagia or regurgitation, and to investigate associations between these imaging findings and patient signalment. Methods Retrospective analysis of VFSS of dogs presented for dysphagia or regurgitation (not megaesophagus) from 2006 to 2017. Cases were divided into brachycephalic and mesaticephalic breeds. The VFSS were reviewed using a standardized protocol by 2 examiners. Esophageal motility was assessed using specific criteria, and particular imaging features were noted and graded. Fisher's exact test was used to determine associations among signalment (including brachycephaly), final diagnosis, outcomes, and ED features. Results Thirty‐six dogs were included (n = 10 normal, n = 26 presumed ED). Twenty dogs (77%) with presumed ED were brachycephalic with a median age of 1 year (range, 0.2‐10.5 years). Most common were prolonged esophageal transit time (ETT; n = 21/26), decreased propagation of secondary peristaltic waves (n = 20/26), and gastroesophageal reflux (GER; n = 18/28). Eight dogs (all brachycephalic) had hiatal herniation (HH). Morphological esophageal variations were only observed in brachycephalic dogs. Brachycephaly was significantly associated with ED (P = .005), prolonged ETT (P = .41), GER (P = .02), and HH (P = .03). Conclusions and Clinical Importance The majority of dogs with presumed ED was young and brachycephalic and had specific abnormalities that were less frequent in mesaticephalic dogs with regurgitation or dysphagia.