Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data

Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an opportunity to call variants directly from lrRNA-seq data. However, most state-of-the-art variant callers have been developed for genomic DNA. Here, there are two objectives: first, we perform a mini-benchmark on GATK, DeepVariant, Clair3, and NanoCaller primarily on PacBio Iso-Seq, data, but also on Nanopore and Illumina RNA-seq data; second, we propose a pipeline to process spliced-alignment files, making them suitable for variant calling with DNA-based callers. With such manipulations, high calling performance can be achieved using DeepVariant on Iso-seq data

Identification of Cell-Free Circulating MicroRNAs for the Detection of Early Breast Cancer and Molecular Subtyping

Early detection is crucial for achieving a reduction in breast cancer mortality. Analysis of circulating cell-free microRNAs present in the serum of cancer patients has emerged as a promising new noninvasive biomarker for early detection of tumors and for predicting their molecular classifications. The rationale for this study was to identify subtype-specific molecular profiles of cell-free microRNAs for early detection of breast cancer in serum. Fifty-four early-stage breast cancers with 27 age-matched controls were selected for circulating microRNAs evaluation in the serum. The 54 cases were molecularly classified (luminal A, luminal B, luminal B Her2 positive, Her-2, triple negative). NanoString platform was used for digital detection and quantitation of 800 tagged microRNA probes and comparing the overall differences in serum microRNA expression from breast cancer cases with controls. We identified the 42 most significant (P ≤ 0.05, 1.5-fold) differentially expressed circulating microRNAs in each molecular subtype for further study. Of these microRNAs, 19 were significantly differentially expressed in patients presenting with luminal A, eight in the luminal B, ten in luminal B HER 2 positive, and four in the HER2 enriched subtype. AUC is high with suitable sensitivity and specificity. For the triple negative subtype miR-25-3p had the best accuracy. Predictive analysis of the mRNA targets suggests they encode proteins involved in molecular pathways such as cell adhesion, migration, and proliferation. This study identified subtype-specific molecular profiles of cell-free microRNAs suitable for early detection of breast cancer selected by comparison to the microRNA profile in serum for female controls without apparent risk of breast cancer. This molecular profile should be validated using larger cohort studies to confirm the potential of these miRNA for future use as early detection biomarkers that could avoid unnecessary biopsy in patients with a suspicion of breast cancer.Foundation for Research Support of the State of São Paulo (FAPESP process 2015/21082-0) and Public Ministry of Labor Campinas (Research, Prevention, and Education of Occupational Cancer)

Introducing comics as an alternative scientific narrative in chemistry teaching

In this work we present an experience report involving the execution of a pedagogical workshop about comics with Chemistry teaching undergraduate students. The workshop had as main goal to promote a discussion on the potential of narratives as an alternative approach to teach Chemistry, focusing on the development of teachers' authorship of pedagogical material and at the same time on the integration of information and communication technologies (ICT) in the classroom. The report is divided in two segments: (i) the description of the workshop execution; (ii) a synthesis of the reflections collected from the participants by means of a questionnaire applied in the end of the workshop. The main results praise comics' playful character and their potential to stimulate creativity in students, as well as indicate the relevance of educational material authorship in the pedagogical practices of professors in training. Overall, the discussions performed point to the still incipient presence of ICT in the pedagogical training of Chemistry teaching degrees, which highlights the pressing need for incorporating these technologies on formative practices. Moreover, reflections on the pedagogical value of using comics as a narrative approach aiming at the development of scientific and media literacy were raised by the present wor

Home visit improves knowledge, self-care and adhesion in heart failure: randomized Clinical Trial HELEN-I

OBJECTIVE: To verify the effect of an educative nursing intervention composed of home visits and phone calls on patients' knowledge about the disease, self-care and adhesion to the treatment. METHODS: Randomized clinical trial with patients with recent hospitalization caused by decompensated heart failure. There were two groups: the intervention group, which has received four home visits and four phone calls to reinforce the guidelines during six months of follow up; and the control group, which has received conventional follow up with no visits or phone calls. RESULTS: Two hundred patients were randomized (101 in the intervention group and 99 in the control group). After six months, a significant improvement was observed in self-care and knowledge about the disease in the intervention group (P=0.001 and P<0.001), respectively; the adhesion to the treatment, measured and compared between the groups, was significantly higher in the intervention group (P=0.001). CONCLUSION: the strategy of home visits to patients who were recently hospitalized with decompensated heart failure was effective in improving the outcomes assessed and its implementation deserves to be considered in Brazil aiming at avoiding unplanned hospitalizations. NCT-0121386

Dendritic Cells Transfected with scFv from Mab 7.B12 Mimicking Original Antigen gp43 Induces Protection against Experimental Paracoccidioidomycosis

Paracoccidioidomycosis (PCM), endemic in Latin America, is a progressive systemic mycosis caused by Paracoccidioides brasiliensis (P. brasiliensis), which primarily attacks lung tissue. Dendritic cells (DCs) are able to initiate a response in naïve T cells, and they also participate in Th-cell education. Furthermore, these cells have been used for therapy in several disease models. Here we transfected DCs with a plasmid (pMAC/PS-scFv) encoding a single chain variable fragment (scFv) of an anti-Id antibody that is capable of mimicking gp43, the main antigenic component of P. brasiliensis. First, Balb/c mice were immunized subcutaneously with pMAC/PS-scFv and, after seven days, scFv protein was presented to the regional lymph nodes cells. Moreover, we showed that the DCs transfected with scFv were capable of efficiently activating proliferation of total lymph node cells and inducing a decrease in lung infection. Therefore, our results suggested that the use of scFv-transfected DCs may be a promising therapy in the paracoccidioidomycosis (PCM) model

The perception of disability by community groups: Stories of local understanding, beliefs and challenges in a rural part of Kenya

Cultural narratives on disability have received much attention over the past few decades. In contexts of poverty, limited information and everyday challenges associated with having, or caring for someone with a disability, different understandings have emerged. A project was set up to promote disability awareness in neighborhood communities in a rural part of Kenya, using a process of reflection and education. This paper reports on the first aspect–reflection. The aim was to investigate local understanding of disability as a co-constructed concept. The research questions were: 1. What cultural beliefs shape local understanding of disability? 2. What challenges are perceived to be associated with disability? A phenomenological approach was adopted. Focus group discussions were conducted with twenty-one community groups involving 263 participants and audio-recorded. The data were transcribed and thematic analysis was carried out. Visual maps were created to illustrate any interconnections, before establishing the final conclusions. Local beliefs attributed disability to: human transgression of social conventions, particularly concerning inappropriate family relations, which invoked a curse; supernatural forces affecting the child; the will of God; unexplained events; and biomedical factors. Challenges associated with disability related to the burden of caregiving and perceived barriers to inclusion, with stress as a shared bi-product. Local understanding of disability in this rural part of Kenya demonstrated overlapping explanations and plurality of beliefs. Two possible interpretations are offered. Firstly, oscillation between explanatory lines demonstrated instability, affecting broader acceptance of disability. Secondly, and more positively, in the face of challenges, the desire to make sense of the existing situation, reflected a healthy pluralism

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

The Prevalence of Adenoid Hypertrophy among Children with Zika Related Microcephaly.

Upper respiratory obstruction is a common sequela in children with Zika-related microcephaly (ZRM). As a cross-sectional analysis nested in a cohort study, this study aims to investigate the prevalence of adenoid hypertrophy (AH) in children with ZRM and symptoms of respiratory obstruction. The data were collected in the first three years of life from children with ZRM who were followed in two reference centers for otorhinolaryngological care of patients with congenital Zika syndrome. Out of 92 children with confirmed ZRM, 57 were evaluated by nasopharyngoscopy after presenting with upper respiratory obstruction symptoms. In this study, 31 of the 57 (54%) children with ZRM who were evaluated had obstructive AH. Thirteen children with obstructive AH were submitted to surgery, which resulted in the complete resolution of symptoms for 11, partial resolution in 1, and no improvement in 1. No evidence of direct involvement by Zika virus (ZIKV) infection in the adenoid tissues was demonstrated by histology or immunohistochemistry. Our results suggest that there is a high prevalence and early presentation of AH in children with ZRM, with consequent upper airway obstruction causing upper airway obstructive disorder, secretory otitis media, and dysphagia