Miracle-dz/UniFAR-FTUs huggingface dataset:
A Stiffness-Fault-Tolerant Control Strategy for an Elastically Actuated Powered Knee Orthosis

Elastic actuators can provide safe human-robot interaction and energy efficient mobility. For this purpose they are ideal for wearable robotic applications. However, such actuators are subject to stiffness faults. We present a stiffness-fault-tolerant control strategy for complex elastic actuators, capable of adapting to changes in output stiffness, and demonstrate it on a smart variable stiffness actuator based on the MACCEPA concept. We develop the dynamics of the actuator and a model-based impedance control scheme. Biomechanical data extracted from the flexion/extension of a real knee joint are used as trajectory reference for the evaluation of the control concept in simulation. Results show that the controlled actuator is capable of tracking a reference trajectory under fault conditions and interaction disturbance while maintaining physical human-robot characteristics.
Single‐cell transcriptomics uncover distinct innate and adaptive cell subsets during tissue homeostasis and regeneration

Recently, immune cell‐mediated tissue repair and regeneration has been an emerging paradigm of regenerative medicine. Immune cells form an essential part of the wound as induction of inflammation is a necessary step to elicit tissue healing. Rapid progress in transcriptomic analyses by high‐throughput next‐generation sequencing has been developed to study gene regulatory network and establish molecular signatures of immune cells that could potentially predict their functional roles in tissue repair and regeneration. However, the identification of cellular heterogeneity especially on the rare cell subsets has been limited in transcriptomic analyses of bulk cell populations. Therefore, genome‐wide, single‐cell RNA sequencing (scRNA‐Seq) has offered an unprecedented approach to unravel cellular diversity and to study novel immune cell populations involved in tissue repair and regeneration through unsupervised sampling of individual cells without the need to rely on prior knowledge about cell‐specific markers. The analysis of gene expression patterns at a single‐cell resolution also holds promises to uncover the mechanisms and therefore the development of therapeutic strategy promoting immunoregenerative medicine. In this review, we will discuss how scRNA‐Seq facilitates the characterization of immune cells, including macrophages, innate lymphoid cells and T and B lymphocytes, discovery of immune cell heterogeneity, identification of novel subsets, and tracking of developmental trajectories of distinct immune cells during tissue homeostasis, repair, and regeneration.
Effects of plant essential oils in reducing fungal contamination of organic dried figs during storage.

As in many other fig growing countries, aflatoxin contamination due to fungal agents is an important problem in fig production in Turkey, which is the world’s biggest dry fig exporter. Contamination of fungal agents starts when fruits are still on trees and continue to progress after harvest, especially under inappropriate processing as well as storage conditions. The aim of this study was to investigate the possibilities of using some natural essential oils in reducing the post-harvest (dried fig fruits) decays caused by microbial contamination. Sarilop dried fig fruits were dipped to solutions containing essential oils of laurel (Laurus nobilis L) and origanum (Origanum onites L) at different doses. Fruits were then stored in boxes indoor conditions during 3 months. Fruit sections (each 1 g) from outside of fruits were taken 2, 30, 60 and 90 days after treatments and given to petri dishes containing potato dextrose agar (PDA) with three replications. Petri dishes were then incubated at 25 C for 5 days. They were then evaluated for the occurrence of molds. Results showed that essential oils showed limited efficacy which can be attributed to the low doses used in the study. Also low temperature during storage caused a natural decline in microbial population, so that the effects of treatments could have been masked. Further studies are needed with higher doses of essential oils under climatic conditions favoring the growth of microorganisms.
Testing the Effects of Hookah Tobacco Social Media Risk Communication Messages Among Young Adults

Background Hookah tobacco is commonly used among young adults, and use is driven in part by widespread misperceptions about risks. Social media use, particularly Instagram, is prominent in this population and exposure to commercial and user-generated content promoting hookah commonly occurs. Aims This study tested the effects of hookah tobacco risk messaging for delivery via Instagram as a strategy to offset exposure to content promoting hookah use among young adults. Method Young adult hookah smokers were recruited online for a 2 × 3 between-subjects experiment (n = 601). Participants completed preexposure measures and were randomized to view hookah tobacco Instagram ads (commercial or user generated) with risk messages (none, risk education, or graphic risk). Stimuli were presented as a simulated Instagram feed. After viewing the stimuli, participants completed postexposure outcome measures. Results There was a statistically significant main effect of risk message type but no significant main effect of Instagram ad type or risk message type by ad type interactions. Exposure to the graphic risk and risk education messages were associated with lower intentions to engage with hookah tobacco ads on Instagram. Graphic risk and risk education messages produced greater negative emotional response and the graphic messages increased motivation to quit compared with Instagram ads alone. Discussion Findings provide preliminary evidence that hookah tobacco risk messages delivered via Instagram can offset the influence of content promoting the use of hookah tobacco. Conclusion This study represents an example of risk message testing and the results suggest the messages warrant further testing via social media delivery.
Comparative genomics of Listeria bacteriophages

The dsDNA of Listeria bacteriophages A006, A500, A511, B025, B054, and P35 were sequenced and analysed regarding G+C content, open reading frames, tRNA genes and sequence identities on nucleotide and protein level. Additionally, bacterial integration sites for the temperate phages were identified. Genes are arranged into functional, life-cycle specific modules. The mosaic nature of the genomes supports the modular evolution theory and provides insight into the phylogenetic relationship among the Listeria phages. Analysis of the structural proteins via peptide mass fingerprinting allowed a correlation between predicted gene products and protein bands from the profiles (SDS-Page) and indicated translational frameshifts during synthesis of the major capsid and major tail proteins in some phages.
Developmental stages of the fungus, Synaptomitus orchiphilus, in the germinating seed, Mycophoris elongatus (Orchidaceae), in Dominican amber

Abstract The present study reports developmental stages of Synaptomitus orchiphilus inside the germinating orchid seed, Mycophoris elongatus, in Dominican amber. Evidence is presented of fungal hyphae, monilioform cells and basidiocarps with basidia and basidiospores developing in cells of the seed. This is the first record of the teleomorphic stages of a basidiomycete developing in an angiosperm seed.
Diversity and Allelopathic Potential of Weeds among Panamanian Coffee Crops

Worldwide, coffee is one of the most highly consumed and produced crops. Coffee production is a significant activity in the Panamanian economy, mainly in rural communities and among indigenous groups in the Chiriqui province highlands. Weeds growing alongside coffee plants can provoke considerable economic losses for producers by interfering with the growth, development and yield of coffee crop in cultivated areas. Designing an effective program to control weeds depends on identifying the different species found in the coffee plantations. The objective of this study was to assess the biological diversity and negative allelopathic potential of weeds in a coffee field to generate enough information that would better allow farmers to control them. As a result, we identified forty-two different species of weeds in all sampling transects within the study area. Emilia sonchifolia and Impatiens walleriana were the most abundant. In respect to phytotoxic activity, Emilia sonchifolia and Hyptis capitata showed the highest activity against the seed germination of dicotyledonous species Amaranthus hypochondriacus, exhibiting IC50 values of 160 and 178 µg mL-1, respectively. Finally, we proceeded to evaluate the organic extracts of two coffee weeds in a panel of bioassays to demonstrate to the farmers that weeds may also have useful applications for human health. Borreria verticillata showed antimalaric activity while Blechum pyramidatum displayed inhibition of the α-glucosidase enzyme. These results allow us to propose a rational and systematic management of coffee weeds.
Leaky Gut and Gut-Liver Axis in Liver Cirrhosis: Clinical Studies Update

Portal blood flows into the liver containing the gut microbiome and its products such as endotoxin and bacterial DNA. The cirrhotic liver acts and detoxifies as the initial site of microbial products. In so-called “leaky gut,” the increased intestinal permeability for bacteria and their products constitutes an important pathogenetic factor for major complications in patients with liver cirrhosis. Prolonged gastric and small intestinal transit may induce intestinal bacterial overgrowth, a condition in which colonic bacteria translocate into the small gut. Cirrhotic patients further show gut dysbiosis characterized by an overgrowth of potentially pathogenic bacteria and a decrease in autochthonous nonpathogenic bacteria. Pathological bacterial translocation (BT) is a contributing factor in the development of various severe complications. Bile acids (BAs) undergo extensive enterohepatic circulation and play important roles in the gut-liver axis. BT-induced inflammation prevents synthesis of BAs in the liver through inhibition of BA-synthesizing enzyme CYP7A1. A lower abundance of 7α-dehydroxylating gut bacteria leads to decreased conversion of primary to secondary BAs. Decreases in total and secondary BAs may play an important role in the gut dysbiosis characterized by a proinflammatory and toxic gut microbiome inducing BT and endotoxemia, as addressed in my previous reviews. Selective intestinal decontamination by the use of various antimicrobial drugs for management of complications has a long history. Lactobacillus GG decreasing endotoxemia is reported to improve the microbiome with beneficial changes in amino acid, vitamin and secondary BA metabolism. Current approaches for hepatic encephalopathy are the use of nonabsorbable antibiotics and disaccharides. Probiotics may become an additional therapeutic option for advanced liver cirrhosis. (Gut Liver 2021;15:-676)
Application of Bayesian Active Learning to the Estimation of Auditory Filter Shapes Using the Notched-Noise Method

Time-efficient hearing tests are important in both clinical practice and research studies. This particularly applies to notched-noise tests, which are rarely done in clinical practice because of the time required. Auditory-filter shapes derived from notched-noise data may be useful for diagnosis of the cause of hearing loss and for fitting of hearing aids, especially if measured over a wide range of center frequencies. To reduce the testing time, we applied Bayesian active learning (BAL) to the notched-noise test, picking the most informative stimulus parameters for each trial based on nine Gaussian Processes. A total of 11 hearing-impaired subjects were tested. In 20 to 30 min, the test provided estimates of signal threshold as a continuous function of frequency from 500 to 4000 Hz for nine notch widths and for notches placed both symmetrically and asymmetrically around the signal frequency. The thresholds were found to be consistent with those obtained using a 2-up/1-down forced-choice procedure at a single center frequency. In particular, differences in threshold between the methods did not vary with notch width. An independent second run of the BAL test for one notch width showed that it is reliable. The data derived from the BAL test were used to estimate auditory-filter width and asymmetry and detection efficiency for center frequencies from 500 to 4000 Hz. The results agreed with expectations for cochlear hearing losses that were derived from the audiogram and a hearing model.
Appropriateness of diagnosis and antibiotic use in sepsis patients admitted to a tertiary hospital in Indonesia

ABSTRACT Objective To evaluate the diagnostic and antibiotic treatment strategies for patients suspected of sepsis, in a tertiary hospital in Indonesia. This can identify areas for improvement in care provided, and inform diagnostic and antimicrobial stewardship activities within the hospital. Methods Retrospective review of medical records with regards to the diagnosis and management of adult patients with sepsis admitted to a tertiary hospital in Indonesia. We assessed the diagnostic process, and whether or not the antibiotic treatment provided was appropriate for the diagnosis. Appropriateness of antibiotic treatment was classified as being definite appropriate, probable appropriate, inappropriate, or unknown. Results The study included 535 adult patients, of whom 295 (55%) were diagnosed with a community-acquired sepsis, and 240 (45%) with a hospital-acquired sepsis. A specimen for culture and antimicrobial susceptibility testing was collected from three out of four patients (392/535). All but 10 patients had information on antibiotic treatment at the time of sepsis diagnosis. Of those, nearly 50% (257/525) of the patients received antibiotic treatment with unknown appropriateness because no cultures were taken (n = 141) or all cultures were negative (n = 116). Just 3.4% and 9.1% of the patients received definite or probable appropriate antibiotic treatment, respectively. Conclusions There is a clear need in encouraging attending physicians to obtain the much-required blood cultures, or cultures from the suspected source of infection before empirical antibiotic treatment is started. This will improve the use of appropriate antibiotic treatment strategies, and contribute to antimicrobial stewardship.
Simultaneous Inference of Cell Types, Lineage Trees, and Regulatory Genes From Gene Expression Data

Important goals of developmental biology include identifying cell types, understanding the sequence of lineage choices made by multipotent cells and unconvering the molecular networks controlling these decisions. Achieving these goals through computational analysis of gene expression data has been difficult. In this dissertation supervised by Sharad Ramanathan, I develop a probabilistic framework to identify cell types, infer lineage relationships and discover core gene networks controlling lineage decisions. Working with Sandeep Choubey and Sumin Jang, we infer the gene expression dynamics of early differentiation of mouse embryonic stem cells, revealing discrete state transitions across nine cell states. Using a probabilistic model of the gene regulatory networks, we predict that these states are further defined by distinct responses to perturbations and experimentally verify three such examples of state-dependent behavior. Working with Vilas Menon and Sam Melton, we infer a lineage tree for early neural development and putative regulatory transcription factors from single-cell transcriptomic profiles. The lineage tree shows a prominent bifurcation between cortical and mid/hindbrain cell types, and the inferred lineage relationships were confirmed by clonal analysis experiments. In summary, this study provides a framework to infer predictive models of the gene regulatory networks that drive cell fate decisions.
Prolonged antithrombotic therapy in patients after acute coronary syndrome: A critical appraisal of current European Society of Cardiology guidelines.

The increased risk of non-cardiovascular death in patients receiving clopidogrel or prasugrel in comparison with the placebo group in the dual antiplatelet therapy (DAPT) trial in contrast to the decreased risk of cardiovascular death and all-cause death seen in patients treated with low-dose ticagrelor in the EU label population of the PEGASUS-TIMI 54 trial, resulted in inclusion in the 2020 ESC NSTE-ACS guidelines the recommendation for use of clopidogrel or prasugrel only if the patient is not eligible for treatment with ticagrelor. The prevalence of the primary outcome composed of cardiovascular death, stroke, or myocardial infarction was lower in the low-dose rivaroxaban and acetylsalicylic acid (ASA) group than in the ASA-alone group in the COMPASS trial. Moreover, all-cause mortality and cardiovascular mortality rates were lower in the rivaroxaban-plus-ASA group. Comparison of the PEGASUS-TIMI 54 and COMPASS trial patient characteristics clearly shows that each of these treatment strategies should be addressed at different groups of patients. A greater benefit in post-acute coronary syndrome (ACS) patients with a high risk of ischemic events and without high bleeding risk may be expected with ASA and ticagrelor 60 mg b.i. d. when the therapy is continued without interruption or with short interruption only after ACS. On the other hand, ASA and rivaroxaban 2.5 mg b.i. d. seems to be a better option when indications for dual antithrombotic treatment (DATT) appear after a longer time from ACS (more than two years) and/or from cessation of DAPT (more than one year) and in patients with multiple vascular bed atherosclerosis. Thus, both options of DATTs complement each other rather than compete, as can be presumed from the recommendations. However, a direct comparison between these strategies should be tested in future clinical trials.
The Intersection of Regional Anesthesia and Cancer Progression: A Theoretical Framework

The surgical stress and inflammatory response and volatile anesthetic agents have been shown to promote tumor metastasis in animal and in-vitro studies. Regional neuraxial anesthesia protects against these effects by decreasing the surgical stress and inflammatory response and associated changes in immune function in animals. However, evidence of a similar effect in humans remains equivocal due to the high variability and retrospective nature of clinical studies and difficulty in directly comparing regional versus general anesthesia in humans. We propose a theoretical framework to address the question of regional anesthesia as protective against metastasis. This theoretical construct views the immune system, circulating tumor cells, micrometastases, and inflammatory mediators as distinct populations in a highly connected system. In ecological theory, highly connected populations demonstrate more resilience to local perturbations but are prone to system-wide shifts compared with their poorly connected counterparts. Neuraxial anesthesia transforms the otherwise system-wide perturbations of the surgical stress and inflammatory response and volatile anesthesia into a comparatively local perturbation to which the system is more resilient. We propose this framework for experimental and mathematical models to help determine the impact of anesthetic choice on recurrence and metastasis and create therapeutic strategies to improve cancer outcomes after surgery.
Follicular lymphomatoid papulosis – not a simple folliculitis

mations and result in capillary malformation overexpression of growth factors and matrix metalloproteinases. As a site where gene mutations known to cause both BCC development and tissue growth upregulation are found, capillary malformations could be more predisposed to BCC development. They are in essence a locus minoris resistentiae for BCCs, with the potential for more rapid tumour growth. Minimising other BCC risk factors including UV radiation and regular capillary malformation monitoring for tumour development is therefore important in capillary malformation management, even where the capillary malformation is no longer visible.
Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions

The human cerebral cortex has undergone rapid expansion and increased complexity during recent evolution. Hominid-specific gene duplications represent a major driving force of evolution, but their impact on human brain evolution remains unclear. Using tailored RNA sequencing (RNAseq), we profiled the spatial and temporal expression of Hominid-specific duplicated (HS) genes in the human fetal cortex, leading to the identification of a repertoire of 36 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among these we focused on NOTCH2NL, previously uncharacterized HS paralogs of NOTCH2. NOTCH2NL promote the clonal expansion of human cortical progenitors by increasing self-renewal, ultimately leading to higher neuronal output. NOTCH2NL function by activating the Notch pathway, through inhibition of Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes linking genomic evolution to human brain development, and reveals how hominin-specific NOTCH paralogs may have contributed to the expansion of the human cortex.
Obtenção e utilização do vetor viral SFV expressando GFP.

PUGLIA, A. L. P. Production and utilization of an SFV vector expressing GFP. 2014.74 p. Masters thesis (Biotechnology)Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2014. The recombinant Semliki Forest Virus (rSFV) has been considered as one of the most promising viral vectors, both for the expression of proteins of biotechnological interest or as a vector for immunizations. In this study, an rSFV carrying the gene of the green fluorescent protein (GFP) was obtained (rSFV-GFP) and used for the standardization of rSFV production and of a novel titration methodology. Through the analysis of the amounts of GFP expressed in BHK-21 cells infected with virus stocks obtained by transfection with a lipid reagent or electroporation, we established the best conditions for rSFV production based on the production of this recombinant protein. In addition, a standardized method of absolute quantitative RT-PCR (qRT-PCR), based in a standard curve and applicable to virtually all rSFV particles, regardless of the heterologous gene cloned, was validated. The direct analysis of the quantity of infected cells, by flow cytometry and fluorescence microscopy, confirmed that the rSFV-GFP was an appropriated tool to support ours studies of viral titration by qRTPCR. It was demonstrated the association between the amount of copies of viral RNA used for culture infection and the amount of GFP expression. This approach led to the development of technical and technological competence (construction, evaluation and titration) in the laboratory, that shall help the establishment of other rSFV of interest. We concluded that electroporation is the best methodology to obtain rSFV particles and the viral titre, as determined by qRT-PCR, can be used to calculate the volume of an rSFV stock necessary to obtain the desired multiplicity of infection.