Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of MALDI Biotyper Interpretation Criteria for Accurate Identification of Nontuberculous Mycobacteria

Identification of mycobacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) requires not only a good protein extraction protocol but also an adequate cutoff score in order to provide reliable results. The aim of this study was to assess the cutoff scores proposed by the MALDI-TOF MS system for mycobacterial identification. A total of 693 clinical isolates from a liquid medium and 760 from a solid medium were analyzed, encompassing 67 different species of nontuberculous mycobacteria (NTM). ABSTRACT Identification of mycobacteria by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) requires not only a good protein extraction protocol but also an adequate cutoff score in order to provide reliable results. The aim of this study was to assess the cutoff scores proposed by the MALDI-TOF MS system for mycobacterial identification. A total of 693 clinical isolates from a liquid medium and 760 from a solid medium were analyzed, encompassing 67 different species of nontuberculous mycobacteria (NTM). MALDI-TOF MS identified 558 (80.5%) isolates from the liquid medium and 712 (93.7%) isolates from the solid medium with scores of ≥1.60. Among these, four (0.7%) misidentifications were obtained from the liquid medium and four (0.5%) from the solid medium. With regard to species diversity, MALDI-TOF MS successfully identified 64 (95.5%) different species, while PCR-reverse hybridization (GenoType Mycobacterium CM and AS assays) identified 24 (35.8%) different species. With MALDI-TOF MS scores of ≥2, all isolates were correctly identified, and with scores in the range from 1.60 to 1.99, most isolates were correctly identified, except for Mycobacterium angelicum, M. parascrofulaceum, M. peregrinum, M. porcinum, and M. gastri. In conclusion, MALDI-TOF MS is a useful method for identifying a large diversity of NTM species. A score threshold of 1.60 proved useful for identifying almost all the isolates tested; only a few species required a higher score (≥2.00) to obtain a valid definitive identification.
Development of a Sensory Flavor Lexicon for Mushrooms and Subsequent Characterization of Fresh and Dried Mushrooms

Mushrooms are a nutritious versatile ingredient in many food products. They are low in calories and have various potential medicinal properties as well. Surprisingly, little research on their descriptive sensory properties has been conducted. The objectives of this study were to a) establish a descriptive sensory flavor lexicon for the evaluation of fresh, dried, and powdered mushrooms and 2) use that lexicon to compare a selection of different mushrooms of various species and in fresh dried and powdered forms. A lexicon for describing mushroom was developed using a consensus profile method. A highly trained, descriptive sensory panel identified, defined, and referenced 27 flavor attributes for commercially available mushroom samples prepared as “meat” and broth. Attributes could be grouped in categories such as musty (dusty/papery, earthy/humus, earthy/damp, earthy/potato, fermented, leather (new), leather (old), mold/cheesy, moldy/damp, mushroomy), and other attributes such as fishy, shell fish, woody, nutty, brown, green, cardboard, burnt/ashy, potato, umami, protein (vegetable), yeasty, bitter, salty, sweet aromatics, sour, and astringent. Samples were then tested in three replications and mean values were compared statistically. In addition, principal component analysis was used to understand the characteristics of mushrooms evaluated. Dried mushrooms showed bitter, burnt, musty/dusty, astringent, old leather, and fresh mushroom characteristics and fresh mushroom showed umami, sweet, earthy/potato, earthy/damp, yeasty, and fermented. Mushrooms were grouped and differentiated in similar ways regardless of whether they were tested as broth or “meat”. Mushroom growers, product developers, chefs and other culinary professionals, sensory scientists, researchers, the food industry, and ultimately consumers will benefit from this lexicon describing a wide variety of mushroom flavor properties.
OPTIMAL DEFENSE THEORY: ELASTICITY ANALYSIS AS A TOOL TO PREDICT INTRAPLANT VARIATION IN DEFENSES

Optimal defense theory (ODT) predicts that plants should have the highest defense levels in parts that have the highest value in terms of fitness. Assumptions about differences in fitness value among plant parts have previously been based on general reasoning, e.g., that reproductive tissue is more valuable than vegetative tissue since fitness ultimately depends on reproduction. Here we present a first example of how demographic elasticity (proportional sensitivity) analysis can be used as a tool to generate more objective and specific estimates of the fitness value of different plant parts, based on the entire life cycle. These estimates were further used to generate testable predictions about intraplant variation in defenses of the brown seaweed Ascophyllum nodosum (knotted wrack). The predictions were clearly supported by the results from both analyses of chemical defense levels (phlorotannins) and bioassays (feeding preference experiments), which showed that reproductive tissues had the lowest defense level of the three examined tissue types, in contrast to previous assumptions. We suggest that a stronger focus on variation in life history among species and populations, with demographic perturbation analysis as one important tool, could lead to a better understanding of intraplant variation in defense levels, in seaweeds as well as vascular plants and other modular organisms.
The Biological and Clinical Role of the Long Non-Coding RNA LOC642852 in Ovarian Carcinoma

The objective of the present study was to analyze the biological and clinical role of the long non-coding RNA LOC642852 in ovarian carcinoma (OC). LOC642852 expression was analyzed in seven OC cell lines (OVCAR-3, OVCAR-8, OVCA 433, OVCA 429, OC 238, DOV13, ES-2) and 139 high-grade serous carcinoma (HGSC) specimens (85 effusions, 54 surgical specimens). Following LOC642852 knockout (KO) using the CRISPR/Cas9 system, OVCAR-8 HGSC cells were analyzed for spheroid formation, migration, invasion, proliferation, matrix metalloproteinase (MMP) activity, and expression of cell signaling proteins. OVCAR-8 cells with LOC642852 KO were significantly less motile and less invasive compared to controls, with no differences in spheroid formation, proliferation, or matrix metalloproteinase (MMP) activity. Total Akt and Erk levels were comparable in controls and KO cells, but their phosphorylation was significantly increased in the latter. In clinical specimens, LOC642852 was overexpressed in ovarian tumors and omental/peritoneal metastases compared to effusion specimens (p = 0.013). A non-significant trend for shorter overall (p = 0.109) and progression-free (p = 0.056) survival was observed in patients with HGSC effusions with high LOC642852 levels. Bioinformatics analysis showed potential roles for LOC642852 as part of the TLE3/miR-221-3p ceRNA network and in relation to the FGFR3 protein. In conclusion, LOC642852 inactivation via CRISPR/Cas9 affects cell signaling, motility, and invasion in HGSC cells. LOC642852 is differentially expressed in HGSC cells at different anatomical sites. Its potential role in regulating the TLE3/miR-221-3p ceRNA network and FGFR3 merits further research.
A computationally efficient method for the attenuation of alternating current stimulation artifacts in electroencephalographic recordings

Objective. Recent studies suggest that the use of noninvasive closed-loop neuromodulation combining electroencephalography (EEG) and transcranial alternating current stimulation (tACS) may be a promising avenue for the treatment of neurological disorders. However, the attenuation of tACS artifacts in EEG data is particularly challenging, and computationally efficient methods are needed to enable closed-loop neuromodulation experiments. Here we introduce an original method to address this methodological issue. Approach. Our alternating current regression (AC-REG) method is an adaptive (time-varying) spatial filtering method. It relies on a data buffer of preset size, on which principal component analysis (PCA) is applied. The resulting components are used to build a spatial filter capable of regressing periodic signals in phase with the stimulation. PCA is performed each time that a new sample enters the buffer, such that the spatial filter can be continuously updated and applied to the EEG data. Main results. The AC-REG accuracy in terms of tACS artifact attenuation was assessed using simulated and real EEG data. Alternative offline processing techniques, such as the superimposition of moving averages (SMA) and the Helfrich method (HeM), were used as benchmark. Using simulations, we found that AC-REG can yield a more reliable reconstruction of the stimulation signal for any frequency between 1 and 80 Hz. Analysis of real EEG data of 18 healthy volunteers showed that AC-REG was able to better recover hidden neural activity as compared to SMA and HeM. Also, significantly higher correlations between power spectrum densities in tACS on and off conditions, respectively, were obtained using AC-REG (r = 0.90) than using SMA (r = 0.80) and HeM (r = 0.86). Significance. Thanks to its low computational complexity, the AC-REG method can be employed in noninvasive closed-loop neuromodulation experiments, with potential applications both in healthy individuals and in neurological patients.
The coordinate system of endogenous spatial attention during smooth pursuit

A central question in vision is whether spatial attention is represented in an eye-centered (retinotopic) or world-centered (spatiotopic) reference-frame. Most previous studies on this question focused on how coordinates are modulated across saccades. In the present study, we investigated the reference-frame of attention across smooth pursuit eye-movements using a goal-directed saccade task. In two experiments, participants were asked to pursue a moving target while attending to one or two grating stimuli. On each trial, one stimulus was constant in its retinal position and the other was constant in its spatial position. Upon detection of a slight change in stimulus orientation, participants were asked to stop pursuing and perform a fast saccade toward the modified stimulus. In the focused attention condition, they attended one, predefined, stimulus, and in the divided attention condition they attended both. In Experiment 1 the angle of the orientation change marking the target event was constant across participants and conditions. In Experiment 2, the angle was individually adapted to equate performance across participants and conditions. Findings of the two experiments were consistent and showed that the enhancement of mean visual sensitivity in the focused relative to the divided attention condition was similar in magnitude for both retinotopic and spatiotopic targets. This indicates that during smooth pursuit, endogenous attention was proportionally divided between targets in retinotopic and spatiotopic frames of reference.
Heart rate variability during sleep in children and adolescents with restless sleep disorder: a comparison with restless legs syndrome and normal controls.

STUDY OBJECTIVES Restless sleep disorder (RSD) has been recently characterized clinically and polysomnographically in children and differentiated from restless legs syndrome (RLS). Heart rate variability (HRV) is a reliable method to quantify autonomic changes during sleep. The aim of this study was to characterize HRV in children with RSD, RLS and normal controls, with the hypothesis that children with RSD have a shift toward sympathetic predominance during sleep. METHODS We analyzed polysomnographic recordings from thirty-two children who fulfilled RSD diagnostic criteria (19 boys and 13 girls), 32 children with RLS (20 boys and 12 girls) and 33 controls (17 boys and 16 girls) were included. Four ECG epochs were chosen, one for each stage, and were analyzed for automatic detection of R waves. Time domain and frequency domain HRV parameters were obtained and analyzed. RESULTS In terms of time domain only the standard deviation of the average RR interval during stage N3 was slightly but significantly higher in RSD than in RLS patients. In terms of frequency domain, in RSD the VLF and LF bands were increased (vs. RLS and controls, respectively), while LF/HF ratio tended to be increased in both RSD and RLS. In REM sleep, LF/HF ratio was increased in both RSD and RLS. The LF/HF ratio increased in RLS during stage W. CONCLUSIONS Children with RSD have increased sympathetic activation during sleep, particularly N3 and REM, compared to controls but, as expected, not during wakefulness. Differently, children with RLS have sympathetic activation during relaxed wakefulness preceding sleep and during sleep.
Day-neutral response of photoperiodic flowering in tomatoes: possible implications based on recent molecular genetics of Arabidopsis and rice

Photoperiodic flowering responses are classified into three major types: long day (LD), short day (SD), and day neutral (DN). Arabidopsis is one of the best-characterized LD plants and flowers much earlier under LD than SD conditions. In contrast, SD conditions promote flowering of SD plants such as rice and Pharbitis nil. Recently, molecular genetics of Arabidopsis (LD) and rice (SD) have identified genes that play key roles in the photoperiodic flowering of these plants. A common role of the GIGANTEA (GI)-CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway in Arabidopsis and rice, and a specific role of EARLY HEADING DATE 1 (EHD1) in rice, but not in Arabidopsis, have been demonstrated. The DN response is the most poorly characterized among the three types of photoperiodic flowering responses. In this short review, we discuss how the DN flowering response is achieved in tomato based on recent progress in the analysis of Arabidopsis mutations in the photoperiodic flowering pathway and circadian rhythms.
Reference Gene Validation in the Brain Regions of Young Rats after Pentylenetetrazole-Induced Seizures

Reverse transcription followed by quantitative polymerase chain reaction (qRT-PCR) is a powerful and commonly used tool for gene expression analysis. It requires the right choice of stably expressed reference genes for accurate normalization. In this work, we aimed to select the optimal reference genes for qRT-PCR normalization within different brain areas during the first week following pentylenetetrazole-induced seizures in immature (P20–22) Wistar rats. We have tested the expression stability of a panel of nine housekeeping genes: Actb, Gapdh, B2m, Rpl13a, Sdha, Ppia, Hprt1, Pgk1, and Ywhaz. Based on geometric averaging of ranks obtained by four common algorithms (geNorm, NormFinder, BestKeeper, Comparative Delta-Ct), we found that the stability of tested reference genes varied significantly between different brain regions. The expression of the tested panel of genes was very stable within the medial prefrontal and temporal cortex, and the dorsal hippocampus. However, within the ventral hippocampus, the entorhinal cortex and amygdala expression levels of most of the tested genes were not steady. The data revealed that in the pentylenetetrazole-induced seizure model in juvenile rats, Pgk1, Ppia, and B2m expression are the most stable within the medial prefrontal cortex; Ppia, Rpl13a, and Sdha within the temporal cortex; Pgk1, Ppia, and Rpl13a within the entorhinal cortex; Gapdh, Ppia, and Pgk1 within the dorsal hippocampus; Rpl13a, Sdha, and Ppia within the ventral hippocampus; and Sdha, Pgk1, and Ppia within the amygdala. Our data indicate the need for a differential selection of reference genes across brain regions, including the dorsal and ventral hippocampus.
General-Equilibrium Pricing of Stock Index Futures with Regular and Irregular Stochastic Volatilities

This study highlights the effects of regular and irregular volatilities on futures pricing and derives a general-equilibrium formula in its closed form. Our comparative static and simulation results show that disputed arguments in literature among economic variables can be explained by different dimensions of market volatility in the economy. For example, the relative size of speed of mean reversion parameters in the dynamics of growth and variability features dominates the relationship between futures price and market volatility.
Quadrocopter Control in Auto Tracking Mode

In this work the following has been done: ROS configuring, installing of catkin, exploring of Parrot AR.Drone 2.0 application programming interface (API), quadrocopter and computer data exchange through Wi-Fi. Result of work is a project with implemented different object tracking methods: Histogram Back Projection and Template Matching. Mouse listener function to capture the object for tracking has been implemented. Implemented mapping of unknown terrain through monocular vision of quadrocopter (PTAM). Methods of quadrocopter control for moving through optimal path considering vector of tracking object movement has been developed based on implemented video stream object tracking methods. Keywords—quadrocopter; ROS; catkin; AR.Drone; object tracking; OpenCV
TREATMENT OF MODEL UNCERTAINTY IN MODEL CALIBRATION

The problem of model calibration is often formulated as finding the parameters that minimize the squared difference between the model-computed data (the predicted data) and the actual experimental data. This approach does not allow for explicit treatment of uncertainty or error in the model itself: the model is considered the “true” deterministic representation of reality. While this approach does have utility, it is far from an accurate mathematical treatment of the true model calibration problem in which both the computed data and experimental data have error bars. Our proposed research focuses on methods to perform calibration accounting for the error in both the computer model and the data, as well as improving our understanding of its meaning for model predictability. We call this approach Calibration under Uncertainty (CUU). This talk presents our current thinking on CUU. We outline some current approaches in the literature, and discuss the Bayesian approach to CUU in detail.
Multidrug resistant protein-three gene regulation

This dissertation is presented in two sections. Section one recounts my investigations of modulating the multidrug-resistant protein-three (MRP3) levels, by either activating or silencing the transcription factor Nrf2, in normal lung cells and Keap1 wild-type and mutant non-small cell lung carcinoma cell lines (NSCLC). In section two direct interactions between Nrf2 and the MRP3 promoter were evaluated in NSCLC. Additionally, the relationships between MRP3 mRNA levels and Keap1, Nrf2, and p53 status were also investigated in cell lines and tumor specimens. Combined, these sections explore the complex regulation of the MRP3 gene.
A IMPORTâNCIA DOS BIOfILMES NAS INfEÇÕES NOSOCOMIAIS - O ESTADO DA ARTE

Nowadays nosocomial infections are a reality in all hospital environments. They are the cause of a high number of infections, morbidity and mortality, and are recognised as being notoriously difficult to eradicate. One of the reasons for the problems in the treatment of nosocomial infection is the fact that many of the pathogens involved in this infections form biofilms. Biofilms are normally defined as communities of microorganisms adhered to a surface and surrounded by a polymeric matrix of extracellular components, such as proteins, polysaccharides and eDNA. The growth of microorganisms in biofilms makes their eradica - tion difficult as this type of growth can be considered an adaptation of the pathogens in order to improve their persistence in the host. As such it is of special interest to account for the role of biofilms in nosocomial infections so that the appropriate approach can be taken in order to eradicate them. The aim of this article is to review the existing information on the prevalence of nosocomial infections potentially caused by biofilms.
Learning from Positive and Unlabeled Data with a Selection Bias

We consider the problem of learning a binary classifier only from positive data and unlabeled data (PU learning). Recent methods of PU learning commonly assume that the labeled positive data are identically distributed as the unlabeled positive data. However, this assumption is unrealistic in many instances of PU learning because it fails to capture the existence of a selection bias in the labeling process. When the data has selection bias, it is difficult to learn the Bayes optimal classifier by conventional methods of PU learning. In this paper, we propose a method to partially identify the classifier. The proposed algorithm learns a scoring function that preserves the order induced by the class posterior under mild assumptions, which can be used as a classifier by setting an appropriate threshold. Through experiments, we show that the method outperforms previous methods for PU learning on various real-world datasets.
Tratamiento de fracturas vertebrales por compresión con implante intramedular expandible SpineJack®: primera experiencia en Ecuador

espanolLas fracturas vertebrales por compresion han sido tratadas con cemento oseo en el interior de las mismas, con tecnicas como la cifoplastia y vertebroplastia; lo que afecta al paciente, pues hay una fuga del cemento a los tejidos aledanos; como consecuencia, una afeccion a la altura vertebral. Lo optimo es una adecuada reduccion de la fractura, ya que la altura vertebral influye directamente en la calidad de vida de los pacientes. La investigacion evalua la aplicacion del metodo implante intramedular expandible SpineJack® para este el tratamiento de este tipo de fracturas; la cual se efectuo por primera vez en Ecuador a una paciente de 65, en junio de 2016. El resultado dio valores similares a los reportados por otros investigadores, en otros paises, por lo tanto, el incremento de este uso no solo mejora la calidad de vida de los pacientes, sino, presentara un avance en lo anatomo-funcional de la vertebra fracturada. Con este estudio, se evidencia la necesidad del seguimiento de otras experiencias con este dispositivo en Ecuador, lo que permitiria evaluar de manera mas completa su aplicacion como tratamiento. EnglishVertebral compression fractures have been treated using bone cement inside them, with techniques such as kyphoplasty and vertebroplasty. However, the potential adverse effects are known, mainly the leakage of cement to the surrounding tissues, and in most cases the consequent affection at vertebral height. It is important that an adequate reduction of the fracture is achieved, since the vertebral height directly influences the quality of life of the patients. In this study, we report the application of SpineJack® expandable intramedullary implant method for the treatment of vertebral compression fractures for the first time in Ecuador. This interesting result is considered, not only for improving the quality of life of the patient, but also for the anatomo-functional point of view of the fractured vertebra. The follow-up of other experiences using this device in Ecuador will allow evaluate it in a more complete way.