Miracle-dz/UniFAR-FTUs huggingface dataset:
Neonatal leukaemia

Neonatal leukaemia is defined as occurring within the first 28 days of life and most, if not all, cases are congenital. With the exception of Down syndrome‐associated transient abnormal myelopoiesis, which is not considered here, neonatal leukaemias are rare. In two‐thirds of patients the disease manifests as an acute myeloid leukaemia, frequently with monocytic/monoblastic characteristics. Most other cases are acute lymphoblastic leukaemia, particularly B lineage, but some are mixed phenotype or blastic plasmacytoid dendritic cell neoplasms. The most frequently observed cytogenetic/molecular abnormality is t(4;11)(q21.3;q23.3)/KMT2A‐AFF1 followed by t(1;22)(p13.3;q13.1)/RBM15‐MKL1 and t(8;16)(p11.2;p13.3)/KAT6A‐CREBBP. Common clinical features include prominent hepatosplenomegaly and a high incidence of skin involvement, sometimes in the absence of bone marrow disease. A distinctive feature is the occurrence of spontaneous remission in some cases, particularly in association with t(8;16). In this review, we summarise current knowledge of the clinical, cytogenetic and molecular features of neonatal leukaemia and discuss clinical management of these cases.
In vitro Study of Anti-Leukemic Potential of Ursolic Acid in Jurkat Cell Line

This study aims to assess the possible antitumor effects of the Ursolic Acid through cell death studies. Hence, Jurkat cell lines related to leukemia were subjected to treatment with different concentrations of the Ursolic Acid in order to identify their likely mechanism of death. After completion of cell viability tests, we suggest that this acid used in this study have antiproliferative/ cytotoxic activity in a dose-dependent manner. The results obtained indicate that the Ursolic Acid assessed in this study have cytotoxic activity with IC50% value of 10 μM. In addition, we observed that the IC50% value tested on the same cell line revealed a significant percentage of stagnant cells in cell cycle sub-G1 phase, a finding that allows us to infer the cytotoxic ability of the acid assessed.
Mental Disorders in Subjects with Diabetes: A Systematic Review

Depression has been a common comorbidity and reduces the quality of life, the poor glycemic control and consequently worsens the diabetes course. The goals of this systematic review are searching of a population who have higher mental disorders in type 1 and 2 patients with diabetes and if there is a direct relationship between glycemic control and psychiatric disorders in this population. A total of 2527 references, review and review articles were excluded, 19 scientific studies were selected: 9 cross-sectional studies, 6 prospective observational studies, 3 retrospective observational studies, and 1 case-control study. Depression and anxiety have a high prevalence in subjects with diabetes. Therefore, the relevance of this study is showing that those mental disorders have a direct correlation in both types of diabetes treatments and decrease the quality of life. Also, the rates of depression could be up to three times higher in patients with type 1diabetes and twice as high in individuals with type 2 diabetes compared with the general population. Patients live in fear of complications from diabetes over the long term and also have damage due to the high psychiatric comorbidity of these chronic patients.
Unraveling Gardnerella vaginalis Surface Proteins Using Cell Shaving Proteomics

Gardnerella vaginalis is one of the main etiologic agents of bacterial vaginosis (BV). This infection is responsible for a wide range of public health costs and is associated with several adverse outcomes during pregnancy. Improving our understanding of G. vaginalis protein cell surface will assist in BV diagnosis. This study represents the first proteomic approach that has analyzed the exposed proteins on G. vaginalis cell surface using a shaving approach. The 261 G. vaginalis proteins identified using this approach were analyzed with bioinformatic tools to detect characteristic motifs from surface-exposed proteins, such as signal peptides (36 proteins), lipobox domains (17 proteins), LPXTG motifs (5 proteins) and transmembrane alpha-helices (66 proteins). One third of the identified proteins were found to have at least one typical motif of surface-exposed proteins. Furthermore, the subcellular location was examined using two predictors (PSORT and Gpos-mPLoc). These bioinformatic tools classified 17% of the identified proteins as surface-associated proteins. Interestingly, we identified 13 members of the ATP-binding cassette (ABC) superfamily, which were mainly involved in the translocation of various substrates across membranes. To validate the location of the G. vaginalis surface-exposed proteins, an immunofluorescence assay with antibodies against Escherichia coli GroEL was performed to reveal the extracellular location of the moonlighting GroEL. In addition, monoclonal antibodies (mAb) against G. vaginalis Cna protein were produced and used to validate the location of Cna on the surface of the G. vaginalis. These high affinity anti-Cna mAb represent a useful tool for the study of this pathogenic microorganism and the BV.
Long Noncoding RNA Profiling from Fasciola Gigantica Excretory/Secretory Product-Induced M2 to M1 Macrophage Polarization

Background/Aims: Long noncoding RNAs (lncRNAs) are well known regulators of gene expression that play essential roles in macrophage activation and polarization. However, the role of lncRNA in Fasciola gigantica excretory/secretory products (ESP)-induced M2 polarization into M1 macrophages is unclear. Herein, we performed lncRNA profiling of lncRNAs and mRNAs during the ESP-induced macrophage polarization process. Methods: F. gigantica ESP was used to induce peritoneal cavity M2 macrophages in BALB/c mice (5-6 weeks old) in vivo, and these cells were subsequently isolated and stimulated with IFN-γ + LPS to induce M1 cells in vitro. LncRNA and mRNA profiling was performed via microarray at the end of both polarization stages. Results: In total, 2,844 lncRNAs (1,579 upregulated and 1,265 downregulated) and 1,782 mRNAs (789 upregulated and 993 downregulated) were differentially expressed in M2 macrophages compared to M1 macrophages, and six lncRNAs were identified during polarization. We selected 34 differentially expressed lncRNAs and mRNAs to validate the results of microarray analysis using quantitative real-time PCR (qPCR). Pathway and Gene Ontology (GO) analyses demonstrated that these altered transcripts were involved in multiple biological processes, particularly peptidase activity and carbohydrate metabolism. Furthermore, coding and non-coding gene (CNC) and mRNA-related ceRNA network analyses were conducted to predict lncRNA expression trends and the potential target genes of these lncRNAs and mRNAs. Moreover, we determined that four lncRNAs and four mRNAs might participate in F. gigantica ESP-induced M2 polarization into M1 macrophages. Conclusions: This study illustrates the basic profiling of lncRNAs and mRNAs during F. gigantica ESP-induced M2 polarization into M1 macrophages and deepens our understanding of the mechanism underlying this process.
Yes We CAN: A low-cost approach to simulate real-world automotive platforms in systems engineering education for non-computer science majors

In system engineering education, physical computing and problem-based learning are used successfully for some time. These concepts are especially suitable for programming novices and computer science non-major students. However, their broad adoption in universities requires access to affordable low-cost hardware. But for courses specific to the automotive domain, usually specific and expensive hardware and toolchains are required. Therefore, in this paper an approach is presented simulating real-world embedded systems by low-cost single-board computer hardware and allowing the students to focus on the essential elements of the system design. A customized teaching scenario including a laboratory vehicle based on low-cost hardware enables practical lessons in the area of "Connected Car Applications" (Car2x). The evaluation results demonstrate the practical feasibility and its strong acceptance and positive influence on the learning success.
Detecting emphysema with multiple instance learning

Emphysema is part of chronic obstructive pulmonary disease, a leading cause of mortality worldwide. Visual assessment of emphysema presence is useful for identifying subjects at risk and for research into disease development. We train a machine learning method to predict emphysema from visually assessed expert labels. We use a multiple instance learning approach to predict both scan-level and region-level emphysema presence. We evaluate performance on 600 low-dose CT scans from the Danish Lung Cancer Screening Study and achieve an AUC of 0.82 for scan-level prediction and AUCs between 0.76 and 0.88 for region-level prediction.
Academic reading format preferences and behaviors among university students worldwide: A comparative survey analysis

This study reports the descriptive and inferential statistical findings of a survey of academic reading format preferences and behaviors of 10,293 tertiary students worldwide. The study hypothesized that country-based differences in schooling systems, socioeconomic development, culture or other factors might have an influence on preferred formats, print or electronic, for academic reading, as well as the learning engagement behaviors of students. The main findings are that country of origin has little to no relationship with or effect on reading format preferences of university students, and that the broad majority of students worldwide prefer to read academic course materials in print. The majority of participants report better focus and retention of information presented in print formats, and more frequently prefer print for longer texts. Additional demographic and post-hoc analysis suggests that format preference has a small relationship with academic rank. The relationship between task demands, format preferences and reading comprehension are discussed. Additional outcomes and implications for the fields of education, psychology, computer science, information science and human-computer interaction are considered.
Convectively Driven Sinks and Magnetic Fields in the Quiet-Sun

We study the relation between mesogranular flows, convectively driven sinks and magnetic fields using high spatial resolution spectropolarimetric data acquired with the Imaging Magnetograph eXperiment on board Sunrise. We obtain the horizontal velocity flow fields of two quiet-Sun regions (31.2 × 31.2 Mm2) via local correlation tracking. Mesogranular lanes and the central position of sinks are identified using Lagrange tracers. We find sinks per Mm2 in the two observed regions. The sinks are located at the mesogranular vertices and turn out to be associated with (1) horizontal velocity flows converging to a central point and (2) long-lived downdrafts. The spatial distribution of magnetic fields in the quiet-Sun is also examined. The strongest magnetic fields are preferentially located at sinks. We find that 40% of the pixels with longitudinal components of the magnetic field stronger than 500 G are located in the close neighborhood of sinks. In contrast, the small-scale magnetic loops detected by Martínez González et al. in the same two observed areas do not show any preferential distribution at mesogranular scales. The study of individual examples reveals that sinks can play an important role in the evolution of quiet-Sun magnetic features.
Chemical and nutritional characteristics of high-fibre rye milling fractions.

BACKGROUND Many studies have demonstrated the potential health benefits of consuming more high-fibre cereal-based food products. Therefore, there is a need to discover new ways to improve the overall nutritional balance of refined cereal products and focus on increasing their dietary fibre content, at the expense of readily digestible carbohydrates. METHODS Lab-scale milling and sieving of whole rye grain was used to obtain two fractions rich in dietary fibre. The fractions were analysed and compared, in terms of microstructure, chemical com- position and nutritional quality. RESULTS The two fractions significantly obtained differed in their particle size and contents of minerals, available saccharides, and nutritional fractions of starch and dietary fibre and its major components. The total dietary fibre concentrations in the coarse and fine fractions were 50.0 and 36.0 g/100 g, respectively, i.e. three and 2.2 times higher than that of wholegrain rye flour. Both fractions also differed in their relative proportions of major fibre components. In the fine fraction, the levels of soluble fibre, as well as soluble arabinoxylans and fructans, were significantly higher than those in the coarse fraction. CONCLUSIONS It was shown that the application of a simple dry-fractionation method to wholemeal rye flour allows the preparation of two rye products which can serve as concentrated sources of dietary fibre low in available saccharides.
A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle

Muscles organise pseudo-crystalline arrays of actin, myosin and titin filaments to build force-producing sarcomeres. To study sarcomerogenesis, we have generated a transcriptomics resource of developing Drosophila flight muscles and identified 40 distinct expression profile clusters. Strikingly, most sarcomeric components group in two clusters, which are strongly induced after all myofibrils have been assembled, indicating a transcriptional transition during myofibrillogenesis. Following myofibril assembly, many short sarcomeres are added to each myofibril. Subsequently, all sarcomeres mature, reaching 1.5 µm diameter and 3.2 µm length and acquiring stretch-sensitivity. The efficient induction of the transcriptional transition during myofibrillogenesis, including the transcriptional boost of sarcomeric components, requires in part the transcriptional regulator Spalt major. As a consequence of Spalt knock-down, sarcomere maturation is defective and fibers fail to gain stretch-sensitivity. Together, this defines an ordered sarcomere morphogenesis process under precise transcriptional control – a concept that may also apply to vertebrate muscle or heart development.
Pacing of Paleozoic macroevolutionary rates by Milankovitch grand cycles

Significance There has been long-standing debate about the relative roles of intrinsic biotic interactions vs. extrinsic environmental factors as drivers of biodiversity change. Here, we show that, relatively early in the history of complex life, Milankovitch “grand cycles” associated with astronomical rhythms explain between 9 and 16% of variation in species turnover probability (extinction probability plus speciation probability) in a major Early Paleozoic zooplankton group, the graptoloids. These grand cycles would have modulated climate variability, alternating times of relative stability in the environment with times of maximum volatility, which influenced oceanic circulation and structure and thus, phytoplankton populations at the base of the marine food web. Periodic fluctuations in past biodiversity, speciation, and extinction have been proposed, with extremely long periods ranging from 26 to 62 million years, although forcing mechanisms remain speculative. In contrast, well-understood periodic Milankovitch climate forcing represents a viable driver for macroevolutionary fluctuations, although little evidence for such fluctuation exists except during the Late Cenozoic. The reality, magnitude, and drivers of periodic fluctuations in macroevolutionary rates are of interest given long-standing debate surrounding the relative roles of intrinsic biotic interactions vs. extrinsic environmental factors as drivers of biodiversity change. Here, we show that, over a time span of 60 million years, between 9 and 16% of the variance in biological turnover (i.e., speciation probability plus species extinction probability) in a major Early Paleozoic zooplankton group, the graptoloids, can be explained by long-period astronomical cycles (Milankovitch “grand cycles”) associated with Earth’s orbital eccentricity (2.6 million years) and obliquity (1.3 million years). These grand cycles modulate climate variability, alternating times of relative stability in the environment with times of maximum volatility. We infer that these cycles influenced graptolite speciation and extinction through climate-driven changes to oceanic circulation and structure. Our results confirm the existence of Milankovitch grand cycles in the Early Paleozoic Era and show that known processes related to the mechanics of the Solar System were shaping marine macroevolutionary rates comparatively early in the history of complex life. We present an application of hidden Markov models to macroevolutionary time series and protocols for the evaluation of statistical significance in spectral analysis.
Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit

DNA methylation is an essential feature of epigenetic regulation and plays a role in various physiological and biochemical processes at CG, CHG, and CHH sites in plants. LeERF1 is an ethylene response factor (ERF) found in tomatoes which plays an important role in ethylene signal transduction. To explore the characteristics of DNA methylation in the ethylene pathway, sense-/antisense-LeERF1 transgenic tomato fruit were chosen for deep sequencing and bioinformatics parsing. The methylation type with the greatest distribution was CG, (71.60–72.80%) and CHH was found least frequently (10.70–12.50%). The level of DNA methylation was different among different tomato genomic regions. The differentially methylated regions (DMRs) and the differentially expressed genes (DEGs) were conjointly analyzed and 3030 different expressed genes were found, of which several are involved in ethylene synthesis and signaling transduction (such as ACS, ACO, MADS-Box, ERFs, and F-box). Furthermore, the relationships between DNA methylation and microRNAs (miRNAs) were also deciphered, providing basic information for the further study of DNA methylation and small RNAs involved in the ethylene pathway.
Core morphology in child directed speech: Crosslinguistic corpus analyses of noun plurals

Learning inflectional systems is a crucial task taken up early on by toddlers. From a distributional point of view, inflection is characterized by high token frequency, and general and obligatory applicability (Bybee 1985). From a semantic point of view, inflection exhibits transparency, regularity and predictability. These aspects of inflection render it highly salient for young children and facilitate the initial mapping of meaning or function onto inflectional segments. At the same time, many inflectional systems are also fraught with morphological and morpho-phonological complexity, opacity, inconsistency, irregularity, and unpredictability. These structural aspects of inflection constitute a serious challenge to the successful launching of this central function of human language. Most studies of inflectional morphology start from an analysis of the adult system, and reason from that system the when and how of children’s acquisition. However, the discrepancy between the complexity of the mature system, on the one hand, and the need to facilitate acquisition, on the other, needs to be resolved. Child Directed Speech (CDS) – simply defined as input to children from caregivers and early peer-group – has been shown to account for emerging lexical and morpho-syntactic features in
HIV infection, high-risk behaviors and substance use in homeless men sheltered in therapeutic communities in Central Brazil

Homeless men present high vulnerability to HIV infection, mainly due to sexual risk behaviors and substance use. The objective was to estimate the prevalence of HIV infection, risk behaviors and substance use in homeless men. A cross-sectional study was conducted in 481 homeless men recruited in four therapeutic communities in the Goiás State, Central Brazil. All were interviewed about sociodemographic characteristics, substance use, and risk behaviors. Furthermore, all were tested for HIV. Poisson regression was used to verify factors associated with HIV infection. HIV prevalence was 1.24% (95.0% CI: 0.57 to 2.69%). Previous HIV testing (adjusted prevalence ratio [APR]: 10.0; 95.0% CI: 1.86–55.8) and years of education (APR: 0.76; 95.0% CI: 0.60–0.97) were factors associated with HIV infection. Participants had high rates of hazardous alcohol use and illicit drug use. The prevalence of HIV infection among homeless men was higher than that found in the Brazilian male population and we identified a high rate of risk behaviors for HIV among the homeless men investigated. Thus, it is necessary to expand HIV prevention measures in Brazil, such as health education, condom availability, regular HIV testing and increased testing coverage in this population, and treatment for alcohol and/or illicit drug dependence/abuse.
Assessing Generative Models via Precision and Recall

Recent advances in generative modeling have led to an increased interest in the study of statistical divergences as means of model comparison. Commonly used evaluation methods, such as the Frechet Inception Distance (FID), correlate well with the perceived quality of samples and are sensitive to mode dropping. However, these metrics are unable to distinguish between different failure cases since they only yield one-dimensional scores. We propose a novel definition of precision and recall for distributions which disentangles the divergence into two separate dimensions. The proposed notion is intuitive, retains desirable properties, and naturally leads to an efficient algorithm that can be used to evaluate generative models. We relate this notion to total variation as well as to recent evaluation metrics such as Inception Score and FID. To demonstrate the practical utility of the proposed approach we perform an empirical study on several variants of Generative Adversarial Networks and Variational Autoencoders. In an extensive set of experiments we show that the proposed metric is able to disentangle the quality of generated samples from the coverage of the target distribution.
Sexual selection on male body size, genital length and heterozygosity: Consistency across habitats and social settings

Spatial and temporal variation in environmental factors and the social setting can help to maintain genetic variation in sexually selected traits if it affects the strength of directional selection. A key social parameter which affects the intensity of, and sometimes predicts the response to, mating competition is the operational sex ratio (OSR; ratio of receptive males to females). How the OSR affects selection for specific male traits is poorly understood. It is also unclear how sexual selection is affected by interactions between the OSR and environmental factors, such as habitat complexity, that alter key male-female interactions such as mate encounter rates. Here, we experimentally manipulated the OSR and habitat complexity and quantified sexual selection on male mosquitofish (Gambusia holbrooki) by directly measuring male reproductive success (i.e. paternity). We show that despite a more equitable sharing of paternity (i.e. higher levels of multiple paternity) under a male-biased OSR, selection on focal male traits was unaffected by the OSR or habitat complexity. Instead, sexual selection consistently, and significantly, favoured smaller bodied males, males with higher genome wide heterozygosity (based on >3,000 SNP markers) and males with a relatively long gonopodium (intromittent organ). Our results show that sexual selection on male body size, relative genital size and heterozygosity in this system is consistent across environments that vary in ecological parameters that are expected to influence mate encounter rates.