Miracle-dz/UniFAR-FTUs huggingface dataset:
Promises and pitfalls of using high‐throughput sequencing for diet analysis

The application of high‐throughput sequencing‐based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic composition and diversity. Here, we review these studies in the light of high‐throughput sequencing‐based assessment of trophic interactions. We address how the study design can account for distortion factors, and how acknowledging limitations and biases inherent to sequencing‐based diet analyses are essential for obtaining reliable results, thus drawing appropriate conclusions. Furthermore, we suggest strategies to minimize the effect of distortion factors, measures to increase reproducibility, replicability and comparability of studies, and options to scale up DNA sequencing‐based diet analyses. In doing so, we aim to aid end‐users in designing reliable diet studies by informing them about the complexity and limitations of DNA sequencing‐based diet analyses, and encourage researchers to create and improve tools that will eventually drive this field to its maturity.
Arabidopsis ACC Oxidase 1 Coordinated by Multiple Signals Mediates Ethylene Biosynthesis and Is Involved in Root Development

Ethylene regulates numerous aspects of plant growth and development. Multiple external and internal factors coordinate ethylene production in plant tissues. Transcriptional and post-translational regulations of ACC synthases (ACSs), which are key enzymes mediating a rate-limiting step in ethylene biosynthesis have been well characterized. However, the regulation and physiological roles of ACC oxidases (ACOs) that catalyze the final step of ethylene biosynthesis are largely unknown in Arabidopsis. Here, we show that Arabidopsis ACO1 exhibits a tissue-specific expression pattern that is regulated by multiple signals, and plays roles in the lateral root development in Arabidopsis. Histochemical analysis of the ACO1 promoter indicated that ACO1 expression was largely modulated by light and plant hormones in a tissue-specific manner. We demonstrated that point mutations in two E-box motifs on the ACO1 promoter reduce the light-regulated expression patterns of ACO1. The aco1-1 mutant showed reduced ethylene production in root tips compared to wild-type. In addition, aco1-1 displayed altered lateral root formation. Our results suggest that Arabidopsis ACO1 integrates various signals into the ethylene biosynthesis that is required for ACO1’s intrinsic roles in root physiology.
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins

Abstract The EncoMPASS online database (http://encompass.ninds.nih.gov) collects, organizes, and presents information about membrane proteins of known structure, emphasizing their structural similarities as well as their quaternary and internal symmetries. Unlike, e.g. SCOP, the EncoMPASS database does not aim for a strict classification of membrane proteins, but instead is organized as a protein chain-centric network of sequence and structural homologues. The online server for the EncoMPASS database provides tools for comparing the structural features of its entries, making it a useful resource for homology modeling and active site identification studies. The database can also be used for inferring functionality, which for membrane proteins often involves symmetry-related mechanisms. To this end, the online database also provides a comprehensive description of both the quaternary and internal symmetries in known membrane protein structures, with a particular focus on their orientation relative to the membrane.
LIDAR Based Altitude Estimation for Autonomous Vehicles using Elevation Maps

This paper presents a strategy to estimate the vehicle altitude using predefined elevation maps. The map images in multilayers roads must be distinguished and separated with respect to the driving segments during the autonomous driving. This can be achieved by continuously estimating the altitude value and retiring the map images accordingly. The main influence is to increase the lateral and longitudinal Iocalization based on matching the LIDAR and retrieving map images. Accordingly, a framework is designed and evaluated in complicated environments of common driving areas between bridges, tunnels and ground roads. The experimental results have verified that the proposed strategy is very reliable and provides precise altitude estimation with averaged accuracy of 10cm.
Effect of Docosahexaenoic Acid Supplementation vs Placebo on Developmental Outcomes of Toddlers Born Preterm: A Randomized Clinical Trial

Importance Intake of dietary docosahexaenoic acid (DHA) among toddlers is low. Supplementation may benefit developmental outcomes of toddlers who were born preterm. Objective To determine whether 6 months of daily DHA supplementation improves developmental outcomes of toddlers who were born preterm. Design, Setting, and Participants A randomized, fully masked, placebo-controlled trial was conducted from April 26, 2012, to March 24, 2017, at a large US pediatric academic center with 9 neonatal intensive care units. Children born at less than 35 weeks’ gestation who were 10 to 16 months corrected age underwent 6 months of intervention. Of 2363 children assessed, 982 were eligible, 605 declined, and 377 enrolled and were randomized. Analyses were according to intent to treat. Interventions One-to-one allocation to receive daily microencapsulated DHA, 200 mg, and arachidonic acid (AA), 200 mg (DHA+AA), or microencapsulated corn oil (placebo). Main Outcomes and Measures The primary outcome specified a priori was Bayley Scales of Infant and Toddler Development, third edition (Bayley-III), cognitive composite score at 16 to 22 months corrected age. Secondary outcomes were Bayley-III language and motor composite scores and Infant Behavior Questionnaire–Revised and Early Childhood Behavior Questionnaire effortful control and activity level scores. Subgroup analyses defined a priori were by income, sex, and birth weight. Results Among 377 children randomized and included in the analysis (182 girls and 195 boys; median corrected age, 15.7 months), 338 children (89.7%) had complete data on the primary outcome. Bayley-III cognitive scores did not differ between the DHA+AA and placebo groups (difference in change, 0.5 [95% CI, –1.8 to 2.8]; effect size, 0.05; P = .66). Assignment to the DHA+AA group had a small to medium negative effect on Bayley-III language scores among children with lower birth weights (eg, a child with a birth weight of 1000 g assigned to receive DHA+AA experienced a 4.1-point relative decrease, while a child assigned to placebo did not; P = .03 for interaction). Supplementation had a similar negative effect on effortful control scores among children with annual household incomes greater than $35 000 (difference in change, –0.3 [95% CI, –0.4 to –0.1]; effect size, –0.37; P = .01). Bayley-III motor scores and activity level scores were unaffected. Conclusions and Relevance Daily supplementation with 200 mg of DHA and 200 mg of AA for 6 months resulted in no improvement in cognitive development and early measures of executive function vs placebo, and may have resulted in negative effects on language development and effortful control in certain subgroups of children. These findings do not support DHA supplementation in the second year of life for children who are born preterm. Trial Registration ClinicalTrials.gov Identifier: NCT01576783
Effectiveness of 13-Valent Pneumococcal Conjugate Vaccine Against Invasive Disease Caused by Serotype 3 in Children: A Systematic Review and Meta-analysis of Observational Studies

Abstract The 13-valent pneumococcal conjugate vaccine (PCV13) is the only licensed PCV with serotype 3 polysaccharide in its formulation. Postlicensure PCV13 effectiveness studies against serotype 3 invasive pneumococcal disease (IPD) in children have shown inconsistent results. We performed a systematic review and meta-analysis of observational studies to assess PCV13 vaccine effectiveness (VE) for serotype 3 IPD in children. We systematically searched PubMed, Embase, and the Cochrane library for studies published before 14 August 2017. We identified 4 published studies and 2 conference posters that provided PCV13 VE estimates stratified by serotype. The pooled PCV13 VE against serotype 3 IPD from the random-effects meta-analysis was 63.5% (95% confidence interval [CI], 37.3%–89.7%). A sensitivity analysis including conference posters gave a pooled VE estimate of 72.4% (95% CI, 56.7%–88.0%). The pooled data from case-control studies with similar methodologies and high quality support direct PCV13 protection against serotype 3 IPD in children.
Efficacy of Traditional Chinese Medicine Regimen Jian Pi Qu Shi Formula for Refractory Patients with Idiopathic Membranous Nephropathy: A Retrospective Case-Series Study

Background The treatment of adult refractory idiopathic membranous nephropathy with steroid and other immunosuppressant-resistant nephrotic syndromes can be a significant challenge. We evaluated the efficacy and safety of the traditional Chinese medicine Jian Pi Qu Shi Formula (JPQSF) as a promising regimen. Methods We analyzed 15 consecutive patients with biopsy-proven idiopathic membranous nephropathy who failed immunosuppressive therapy from October 2013 to January 2017. JPQSF was administered orally two times per day, respectively, in the morning and at night for 6 months. All patients had at least 1 year of follow-up. The primary endpoints included complete or partial remission. Secondary endpoints included change of clinical parameters and adverse events after 12 months of treatment. Results After 12 months, complete remission was achieved in 13.3% of patients and partial remission in 66.7%, yielding a response rate of 80%. Proteinuria, serum albumin, and cholesterol were improved significantly (P<0.001, P<0.001, and P<0.05, respectively). After 1 year of treatment, proteinuria (mean ± SD) decreased from 5.93 ± 2.54 g per 24 h to 1.99 ± 1.17 g per 24 h (P<0.001). No serious adverse events occurred during the observation. Conclusions JPQSF may be an alternative therapeutic option for steroid and general immunosuppressant-resistant membranous nephrotic syndrome patients, with a favorable safety profile. Larger and longer follow-up studies evaluating this regimen are warranted.
Applying the unified protocol to a single case of major depression with schizoid and depressive personality traits

Background: The study presents the use of the Unified Protocol (UP) in a case of a male diagnosed with major depressive disorder and schizoid and depressive personality traits. The therapeutic focus of UP is to identify maladaptive behaviors of emotion regulation and to train new regulation strategies such as cognitive re‐appraisal or emotional exposure exercises. Method: This is a single‐case research study. The intervention was carried out in twenty 1‐hour sessions for 6 months. After treatment completion, follow‐ups were conducted at three, six, and twelve months. Results: The results of the 12‐month follow‐up revealed a clinically significant change in depressive symptomatology (RCIBDI‐II = ‐5.51), negative affect (RCINEGATIVE PANAS = ‐3.61), quality of life (RCIICV‐Sp = 4.61) and schizoid (RCIMCMIIII‐Schizoid = ‐4.36) and depressive (RCIMCMI‐III‐Depressive = ‐5.24) personality traits. Schizoid and depressive personality traits did not interfere with the application, course, and compliance with treatment. These results are discussed with regard to similar studies, also based on the use of the UP to work on emotion regulation in the treatment of emotional disorders with clinical comorbidity. Conclusions: The training of emotion regulation strategies through UP could be an effective proposal to treat emotional disorders with pathological personality traits comorbidity. &NA; Aplicando el protocolo unificado en un caso de depresión mayor y rasgos de personalidad depresivos y esquizoides. Antecedentes: presentamos la utilización del Protocolo Unificado (PU) en un caso de un hombre diagnosticado con Trastorno Depresivo Mayor y rasgos de personalidad Esquizoides y Depresivos. El PU se centra en identificar las conductas de regulación emocional desadaptativas y entrenar en nuevas estrategias de regulación como la re‐evaluación cognitiva o la exposición emocional. Método: estudio de investigación de caso único. La intervención se desarrolló en 20 sesiones de 1 hora de duración durante 6 meses. Se realizaron seguimientos a los 3, 6 y 12 meses. Resultados: a los 12 meses de seguimiento se produjo un cambio clínico significativo en la sintomatología depresiva (RCIBDI‐II = ‐5.51), afecto negativo (RCINEGATIVE PANAS = ‐3.61), calidad de vida (RCIICV‐Sp = 4.61) y rasgos de personalidad esquizoides (RCIMCMI‐III‐Esquizoide = ‐4.36) y Depresivos (RCIMCMIIII‐Depresivos = ‐5.24). Los rasgos de personalidad no interfirieron en la implementación, curso y adherencia al tratamiento. Los resultados se discuten con respecto a estudios similares basados en la utilización del PU para el entrenamiento en regulación emocional en casos con comorbilidad clínica. Conclusiones: el entrenamiento en estrategias de regulación emocional a través del PU puede ser una propuesta efectiva para el tratamiento de trastornos emocionales con rasgos de personalidad patológicos comórbidos.
University of Melbourne: combining practice with innovation in the latest completely online Masters of Sports Medicine (continuing professional development series)

Faculty of Medicine, Dentistry & Health Sciences, The University of Melbourne, Melbourne, Australia. Masters of Sports Medicine. Delivered 100% online, the newly released Masters of Sports Medicine at the University of Melbourne targets clinicians looking to develop a successful sports and exercise medicine (SEM) career. Such postgraduate qualifications open doors as an SEM professional with recognised expertise, as well as providing stepping stones towards final-stage specialty training.1–4 Launched in 2018, this is Australia’s latest postgraduate SEM programme. It is designed for medical doctors, physiotherapists and podiatrists worldwide with ≥3 years of sports-relevant clinical experience (table 1), seeking to extend expertise in all areas of SEM including physical activity, community participation and high-performance sport. The programme is directed by Sonya …
Learning from the Syndrome

In this paper, we introduce the syndrome loss, an alternative loss function for neural error-correcting decoders based on a relaxation of the syndrome. The syndrome loss penalizes the decoder for producing outputs that do not correspond to valid codewords. We show that training with the syndrome loss yields decoders with consistently lower frame error rate for a number of short block codes, at little additional cost during training and no additional cost during inference. The proposed method does not depend on knowledge of the transmitted codeword, making it a promising tool for online adaptation to changing channel conditions.
Fully automatic segmentation of 4D MRI for cardiac functional measurements

PURPOSE Segmentation of cardiac medical images, an important step in measuring cardiac function, is usually performed either manually or semiautomatically. Fully automatic segmentation of the left ventricle (LV), the right ventricle (RV) as well as the myocardium of three-dimensional (3D) magnetic resonance (MR) images throughout the entire cardiac cycle (four-dimensional, 4D), remains challenging. This study proposes a deformable-based segmentation methodology for efficiently segmenting 4D (3D + t) cardiac MR images. METHODS The proposed methodology first used the Hough transform and the local Gaussian distribution method (LGD) to segment the LV endocardial contours from cardiac MR images. Following this, a novel level set-based shape prior method was applied to generate the LV epicardial contours and the RV boundary. RESULTS This automatic image segmentation approach has been applied to studies on 17 subjects. The results demonstrated that the proposed method was efficient compared to manual segmentation, achieving a segmentation accuracy with average Dice values of 88.62 ± 5.47%, 87.35 ± 7.26%, and 82.63 ± 6.22% for the LV endocardial, LV epicardial, and RV contours, respectively. CONCLUSIONS We have presented a method for accurate LV and RV segmentation. Compared to three existing methods, the proposed method can successfully segment the LV and yield the highest Dice value. This makes it an option for clinical assessment of the volume, size, and thickness of the ventricles.
Evolution of semantic networks in biomedical texts

Language is hierarchically organized: words are built into phrases, sentences, and paragraphs to represent complex ideas. Here we ask whether the organization of language in written text displays the fractal hierarchical architecture common in systems optimized for efficient information transmission. We test the hypothesis that the expositional structure of scientific research articles displays Rentian scaling, and that the exponent of the scaling law changes as the article's information transmission capacity changes. Using 32 scientific manuscripts - each containing between three and 26 iterations of revision - we construct semantic networks in which nodes represented unique words in each manuscript, and edges connect nodes if two words appeared within the same 5-word window. We show that these semantic networks display clear Rentian scaling, and that the Rent exponent varies over the publication life cycle, from the first draft to the final revision. Furthermore, we observe that manuscripts fell into three clusters in terms of how the scaling exponents changed across drafts: exponents rising over time, falling over time, and remaining relatively stable over time. This change in exponent reflects the evolution in semantic network structure over the manuscript revision process, highlighting a balance between network complexity, which increases the exponent, and network efficiency, which decreases the exponent. Lastly, the final value of the Rent exponent is negatively correlated with the number of authors. Taken together, our results suggest that semantic networks reflecting the structure of exposition in scientific research articles display striking hierarchical architecture that arbitrates tradeoffs between competing constraints on network organization, and that this arbitration is navigated differently depending on the social environment characteristic of the collaboration.
Circulating Plasma Extracellular Vesicles from Septic Mice Induce Inflammation via MicroRNA- and TLR7-Dependent Mechanisms

We have previously reported that a group of host cellular microRNAs (miRNAs; miR-34a-5p, miR-122-5p, miR-145-5p, miR-146a-5p, miR-210-3p) are released into the blood during sepsis, some of which are capable of inducing complement activation, cytokine production, and leukocyte migration. Extracellular vesicles (EVs) have been proposed as vehicles for extracellular miRNA-mediated intercellular communication. However, the biological function of plasma EVs and the associated miRNAs in sepsis are largely unknown. In this study, we tested the hypothesis that plasma EVs in sepsis are proinflammatory and EV-associated miRNAs are responsible for EV-induced cytokine production. Compared with those of sham mice, the plasma EVs from septic mice were slightly smaller (157 ± 2 versus 191 ± 6 nm, p < 0.0001), but more abundant [(1.6 ± 0.14) × 1010 versus (0.93 ± 0.14) × 1010/ml plasma, p < 0.003]. miRNA array revealed that among 65 miRNAs, 8 miRNAs exhibited >1.5-fold increase in septic EVs compared with sham EVs, including miR-126-3p, miR-122-5p, miR-146a-5p, miR-145-5p, miR-26a-5p, miR-150-5p, miR-222-3p, and miR-181a-5p. Septic but not sham EVs were proinflammatory, promoting IL-6, TNF-α, IL-1β, and MIP-2 production. The effects of EVs were resistant to polymyxin B (an endotoxin inhibitor) but significantly inhibited by anti-miR inhibitors against miR-34a, miR-122, and miR-146a. Moreover, the septic EV-induced cytokine production was attenuated in TLR7−/− or MyD88−/− cells but remained the same in TLR3−/− or Trif−/− cells. In vivo, mice i.p. injected with septic EVs had marked peritoneal neutrophil migration, which was significantly attenuated in MyD88−/− mice. Taken together, these data demonstrate that plasma EVs of septic animals play an important role in inflammation, and EV-associated miRNAs likely mediate the cytokine production via TLR7-MyD88 signaling.
DNA Sequencing of Small Bowel Adenocarcinomas Identifies Targetable Recurrent Mutations in the ERBB2 Signaling Pathway

Purpose: Little is known about the genetic alterations characteristic of small bowel adenocarcinoma (SBA). Our purpose was to identify targetable alterations and develop experimental models of this disease. Experimental Design: Whole-exome sequencing (WES) was completed on 17 SBA patient samples and targeted-exome sequencing (TES) on 27 samples to confirm relevant driver mutations. Two SBA models with ERBB2 kinase activating mutations were tested for sensitivity to anti-ERBB2 agents in vivo and in vitro. Biochemical changes were measured by reverse-phase protein arrays. Results: WES identified somatic mutations in 4 canonical pathways (WNT, ERBB2, STAT3, and chromatin remodeling), which were validated in the TES cohort. Although APC mutations were present in only 23% of samples, additional WNT-related alterations were seen in 12%. ERBB2 mutations and amplifications were present in 23% of samples. Patients with alterations in the ERBB2 signaling cascade (64%) demonstrated worse clinical outcomes (median survival 70.3 months vs. 109 months; log-rank HR = 2.4, P = 0.03). Two ERBB2-mutated (V842I and Y803H) cell lines were generated from SBA patient samples. Both demonstrated high sensitivity to ERBB2 inhibitor dacomitinib (IC50 < 2.5 nmol/L). In xenografts derived from these samples, treatment with dacomitinib reduced tumor growth by 39% and 59%, respectively, whereas it had no effect in an SBA wild-type ERBB2 model. Conclusions: The in vitro and in vivo models of SBA developed here provide a valuable resource for understanding targetable mutations in this disease. Our findings support clinical efforts to target activating ERBB2 mutations in patients with SBA that harbor these alterations.
In Vitro Effect of Bromelain on the Regenerative Properties of Mesenchymal Stem Cells.

BACKGROUND Bromelain belongs to a group of protein-digesting enzymes obtained commercially from the fruit or stem of pineapple. Several studies demonstrated that bromelain exhibits various fibrinolytic, anti-edematous, antithrombotic, and anti-inflammatory activities supporting its application for many therapeutic benefits. The aim of this study was to analyze the effects of bromelain on the pro-wound healing activities and the regenerative properties of mesenchymal stem cells. METHODS Mesenchymal stem cells were treated in vitro with bromelain alone or combined with dexamethasone sodium phosphate. Real-time polymerase chain reaction was performed to profile the expression of extracellular matrix components and remodeling enzymes, and cytokines. RESULTS The combination of bromelain and dexamethasone sodium phosphate induced a great activation of mesenchymal stem cells with an increase in hyaluronan and collagen production and anti-inflammatory cytokines release. CONCLUSION Based on the results of this in vitro study, the combined use of bromelain and dexamethasone sodium phosphate stimulated the pro-wound healing activities and the regenerative properties of mesenchymal stem cells better than bromelain and dexamethasone alone.