Miracle-dz/UniFAR-FTUs huggingface dataset:
Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta)

Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
A Restricted-Domain Dual Formulation for Two-Phase Image Segmentation

In two-phase image segmentation, convex relaxation has allowed global minimisers to be computed for a variety of data fitting terms. Many efficient approaches exist to compute a solution quickly. However, we consider whether the nature of the data fitting in this formulation allows for reasonable assumptions to be made about the solution that can improve the computational performance further. In particular, we employ a well known dual formulation of this problem and solve the corresponding equations in a restricted domain. We present experimental results that explore the dependence of the solution on this restriction and quantify imrovements in the computational performance. This approach can be extended to analogous methods simply and could provide an efficient alternative for problems of this type.
Cereblon gene expression and correlation with clinical outcomes in patients with relapsed/refractory multiple myeloma treated with pomalidomide: an analysis of STRATUS

Abstract We analyzed gene expression levels of CRBN, cMYC, IRF4, BLIMP1, and XBP1 in 224 patients with multiple myeloma treated with pomalidomide and low-dose dexamethasone in the STRATUS study (ClinicalTrials.gov: NCT01712789; EudraCT number: 2012-001888-78). Clinical responses were observed at all CRBN expression levels. A trend in progression-free survival (PFS; p = .038) and a potential trend in overall survival (OS; p = .059) favoring high CRBN expressers were observed; however, no notable difference in overall response rate (ORR) was observed. ORR (30%), median PFS (17.7 weeks), and median OS (52.3 weeks) in low-CRBN expressers were comparable to those in the STRATUS intent-to-treat population (ORR, 33%; median PFS, 20.0 weeks; median OS, 51.7 weeks). A trend in ORR (p = .050) favoring higher cMYC expressers was observed with no notable difference in PFS or OS. This analysis does not support exploring CRBN as a biomarker for selecting patients for pomalidomide therapy. Trial registration: ClinicalTrials.gov identifier: NCT01712789.
Biceps Femoris Long-Head Architecture Assessed Using Different Sonographic Techniques

Purpose To assess the repeatability of, and measurement agreement between, four sonographic techniques used to quantify biceps femoris long head (BFlh) architecture: (i) static-image with linear extrapolation; extended field-of-view (EFOV) with linear ultrasound probe path (linear-EFOV), using either (ii) straight or (iii) segmented analyses; and (iv) EFOV with nonlinear probe path and segmented analysis (nonlinear-EFOV) to follow the complex fascicle trajectories. Methods Twenty individuals (24.4 ± 5.7 yr; 175 ± 0.8 cm; 73 ± 9.0 kg) without history of hamstrings strain injury were tested in two sessions separated by 1 h. An ultrasound scanner coupled with 6-cm linear probe was used to assess BFlh architecture in B-mode. Results The ultrasound probe was positioned at 52.0% ± 5.0% of femur length and 57.0% ± 6.0% of BFlh length. We found an acceptable repeatability when assessing BFlh fascicle length (ICC3,k = 0.86–0.95; SEM = 1.9–3.2 mm) and angle (ICC3,k = 0.86–0.97; SEM = 0.8°–1.1o) using all sonographic techniques. However, the nonlinear-EFOV technique showed the highest repeatability (fascicle length ICC3,k = 0.95; fascicle angle, ICC3,k = 0.97). The static-image technique, which estimated 35.4% ± 7.0% of the fascicle length, overestimated fascicle length (8%–11%) and underestimated fascicle angle (8%–9%) compared with EFOV techniques. Also, the rank order of individuals varied by approximately 15% between static-image and nonlinear-EFOV (segmented) when assessing the fascicle length. Conclusions Although all techniques showed good repeatability, absolute errors were observed using static-image (7.9 ± 6.1 mm for fascicle length) and linear-EFOV (between 3.7 ± 3.0 and 4.2 ± 3.7 mm), probably because the complex fascicle trajectories were not followed. The rank order of individuals for fascicle length and angle were also different between static-image and nonlinear-EFOV, so different muscle function and injury risk estimates could likely be made when using this technique.
PET Imaging of Receptor Tyrosine Kinases in Cancer

Overexpression and/or mutations of the receptor tyrosine kinase (RTK) subfamilies, such as epidermal growth factor receptors (EGFR) and vascular endothelial growth factor receptors (VEGFR), are closely associated with tumor cell growth, differentiation, proliferation, apoptosis, and cellular invasiveness. Monoclonal antibodies (mAb) and tyrosine kinase inhibitors (TKI) specifically inhibiting these RTKs have shown remarkable success in improving patient survival in many cancer types. However, poor response and even drug resistance inevitably occur. In this setting, the ability to detect and visualize RTKs with noninvasive diagnostic tools will greatly refine clinical treatment strategies for cancer patients, facilitate precise response prediction, and improve drug development. Positron emission tomography (PET) agents using targeted radioactively labeled antibodies have been developed to visualize tumor RTKs and are changing clinical decisions for certain cancer types. In the present review, we primarily focus on PET imaging of RTKs using radiolabeled antibodies with an emphasis on the clinical applications of these immunoPET probes. Mol Cancer Ther; 17(8); 1625–36. ©2018 AACR.
Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System

Use of the Carba-R assay for detection of carbapenem-resistant Gram-negative organisms (CROs) can provide data for implementation of a rapid infection control response to minimize the spread of CROs in the health care setting. ABSTRACT In this pilot study, traditional culture and PCR methods were compared to the Cepheid GeneXpert IV molecular diagnostic system with the Xpert Carba-R assay (Carba-R assay) for detection of carbapenem resistance genes in primary environmental samples collected during a health care-related outbreak. Overall, traditional culture-dependent PCR and the Carba-R assay demonstrated 75% agreement. The Carba-R assay detected carbapenemase genes in five additional samples and in two samples that had additional genes when compared to culture-dependent PCR. The Carba-R assay could be useful for prioritizing further testing of environmental samples during health care-related outbreaks. IMPORTANCE Use of the Carba-R assay for detection of carbapenem-resistant Gram-negative organisms (CROs) can provide data for implementation of a rapid infection control response to minimize the spread of CROs in the health care setting.
Availability of food and beverage items on school canteen menus and association with items purchased by children of primary-school age

Abstract Objective To (i) describe the proportion of foods and beverages available on school canteen menus classified as having high (‘green’), moderate (‘amber’) or low (‘red’) nutritional value; (ii) describe the proportion of these items purchased by students; and (iii) examine the association between food and beverage availability on school canteen menus and food and beverage purchasing by students. Design A cross-sectional study was conducted as part of a larger randomised controlled trial (RCT). Setting A nested sample of fifty randomly selected government schools from the Hunter New England region of New South Wales, Australia, who had participated in an RCT of an intervention to improve the availability of healthy foods sold from school canteens, was approached to participate. Subjects School principals, canteen managers and students. Results The average proportion of green, amber and red items available on menus was 47·9, 47·4 and 4·7 %, respectively. The average proportion of green, amber and red items purchased by students was 30·1, 61·8 and 8·1 %, respectively. There was a significant positive relationship between the availability and purchasing of green (R 2=0·66), amber (R 2=0·57) and red menu items (R 2=0·61). In each case, a 1 % increase in the availability of items in these categories was associated with a 1·21, 1·35 and 1·67 % increase in purchasing of items of high, moderate and low nutritional value, respectively. Conclusions The findings provide support for school-based policies to improve the relative availability of healthy foods for sale in these settings.
Molecular Characterization Based on 16S rDNA Phylogeny of Some Ixodid Ticks in Turkey.

OBJECTIVE The genetic data related to Turkish ticks is limited. Therefore, this study was aimed to perform of the molecular characterization based on 16S rDNA gene region of some ixodid tick species in Turkey. METHODS The molecular characterizations of partial 16S rDNA gene region belonging to 17 individual ixodid tick species in Turkey have been made and their phylogenetic relationships based on the relevant gene region have been analysed. RESULTS The 16S rDNA phylogenetic relationships between the isolates obtained from this study and the homolog isolates have been revealed. The 16S rDNA data belonging to Ixodes laguri has been obtained for the first time and its phylogenetic location has been demonstrated. Original genetic data related to Haemaphysalis inermis, Ha. parva and Ha. sulcata, which have a limited number of genetic information, has been obtained. Besides, the new genetic data belonging to Dermacentor marginatus, D. reticulatus, Hyalomma anatolicum, H. detritum, Ha. inermis, Ha. parva, Ha. punctata, Ha. sulcata and I. laguri has been recorded for the first time from Turkey. CONCLUSION The molecular phylogenetic characterization based on 16S rDNA gene region of 17 ixodid tick species in Turkey has been performed. The obtained data has made a significant contribution to the genetic knowledge of the mentioned ticks species.
Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function

The levels of telomeric proteins, such as telomerase, can have profound effects on telomere function, cell division and human disease. Here we demonstrate how levels of Stn1, a component of the conserved telomere capping CST (Cdc13, Stn1, Ten1) complex, are tightly regulated by an upstream overlapping open reading frame (oORF). In budding yeast inactivation of the STN1 oORF leads to a 10-fold increase in Stn1 levels, reduced telomere length, suppression of cdc13-1 and enhancement of yku70Δ growth defects. The STN1 oORF impedes translation of the main ORF and reduces STN1 mRNA via the nonsense mediated mRNA decay (NMD) pathway. Interestingly, the homologs of the translation re-initiation factors, MCT-1Tma20/DENRTma22 also reduce Stn1 levels via the oORF. Human STN1 also contains oORFs, which reduce expression, demonstrating that oORFs are a conserved mechanism for reducing Stn1 levels. Bioinformatic analyses of the yeast and human transcriptomes show that oORFs are more underrepresented than upstream ORFs (uORFs) and associated with lower protein abundance. We propose that oORFs are an important mechanism to control expression of a subset of the proteome.
Management of behavioral and psychological symptoms in people with Alzheimer's disease: an international Delphi consensus

ABSTRACT Objectives: Behavioral and psychological symptoms of dementia (BPSD) are nearly universal in dementia, a condition occurring in more than 40 million people worldwide. BPSD present a considerable treatment challenge for prescribers and healthcare professionals. Our purpose was to prioritize existing and emerging treatments for BPSD in Alzheimer's disease (AD) overall, as well as specifically for agitation and psychosis. Design: International Delphi consensus process. Two rounds of feedback were conducted, followed by an in-person meeting to ratify the outcome of the electronic process. Settings: 2015 International Psychogeriatric Association meeting. Participants: Expert panel comprised of 11 international members with clinical and research expertise in BPSD management. Results: Consensus outcomes showed a clear preference for an escalating approach to the management of BPSD in AD commencing with the identification of underlying causes. For BPSD overall and for agitation, caregiver training, environmental adaptations, person-centered care, and tailored activities were identified as first-line approaches prior to any pharmacologic approaches. If pharmacologic strategies were needed, citalopram and analgesia were prioritized ahead of antipsychotics. In contrast, for psychosis, pharmacologic options, and in particular, risperidone, were prioritized following the assessment of underlying causes. Two tailored non-drug approaches (DICE and music therapy) were agreed upon as the most promising non-pharmacologic treatment approaches for BPSD overall and agitation, with dextromethorphan/quinidine as a promising potential pharmacologic candidate for agitation. Regarding future treatments for psychosis, the greatest priority was placed on pimavanserin. Conclusions: This international consensus panel provided clear suggestions for potential refinement of current treatment criteria and prioritization of emerging therapies.
Evaluation of Artesunate and Praziquantel Combination Therapy in Murine Schistosomiasis mansoni

Background: Despite the global efforts to control schistosomiasis, still prevalence in endemic regions unchanged. The present study was conducted to investigate the possible role of artesunate (AS) and praziquantel (PZQ) combination in enhancing cure in pre-patent and patent Schistosoma mansoni infection, and study the role of apoptosis in evaluation of the drugs efficacy. Methods: Eighty laboratory-bred Swiss albino male mice were classified into four groups (20 mice each); control, PZQ treated (500 mg/kg), AS treated (400 mg/kg) and combined AS (400 mg/kg) + PZQ (500 mg/g) groups. Efficacy of the drugs was assessed by parasitological (egg count/gram stool, worm burden, tissue egg load, oogram pattern), histopathological (haematoxylin and eosin –for detection of type of hepatic granulomas, number & diameter) and immunohistochemical studies (P53 and Bcl-2 markers for determination of inflammatory cells and the degree of apoptosis). Results: Significant reduction was recorded in stool egg count, tissue egg count (liver and intestine), worm burden, granuloma number and size and changed oogram patterns in artesunate -praziquantel combined group followed by artesunate monotherapy group. There was a significant increase in the apoptotic proteins P53 and slight increase in anti-apoptotic proteins Bcl-2 in the infected group compared to the control healthy group. A significant decrease and increase in P53 & Bcl-2 expressions respectively were observed in artesunate – praziquantel combined group compared to control infected group. Conclusion: artesunate-praziquantel combination is a potential upcoming chemotherapy for schistosomiasis mansoni. Both Bcl-2 and P53 are good markers assessing S. mansoni apoptosis, morbidity and chemotherapy efficacy.
Anaplastic lymphoma kinase rearrangement in surgically resected stage IA lung adenocarcinoma.

Background It has not been determined if adjuvant chemotherapy would be helpful for completely resected early-stage lung adenocarcinoma even with unfavorable genetic markers. As the positive anaplastic lymphoma kinase (ALK) rearrangement is associated with aggressive clinical feature in lung adenocarcinoma, we evaluated the treatment outcomes of completely resected stage IA lung adenocarcinoma according to initial ALK status. Methods This is a retrospective cohort study including 309 patients with surgically resected stage IA lung adenocarcinoma from February 2010 to December 2013. Patients were screened for ALK rearrangement using immunohistochemistry. A positive ALK status was defined as an immunohistochemistry score of 2+ or more. Both disease-free survival (DFS) and the initial recurrence pattern were analyzed according to ALK status. Results Twenty-three (7.4%) patients had ALK-positive adenocarcinoma. During the median follow-up of 35.8 months, recurrence developed in 34 (11.0%) patients. The patients with ALK-positive tumor had significantly lower 5-year DFS rate (62.4%) compared to those with ALK-negative tumor (86.5%; P=0.038). The multivariable analysis showed that ALK rearrangement was associated with a higher risk of disease recurrence (adjusted hazard ratio =2.64; 95% confidence interval, 1.08-6.44). In addition, patient with ALK-positive tumor showed more frequent recurrence in regional lymph nodes compared with those with ALK-negative tumor (83.3% vs. 28.6%; P=0.031). Conclusions In patients with completely resected stage IA lung adenocarcinoma, ALK rearrangement was associated with unfavorable DFS and more frequent regional lymph node metastasis. Therefore, careful surveillance for recurrence should be performed in this subset of patients.
ArsRS-Dependent Regulation of homB Contributes to Helicobacter pylori Biofilm Formation

One elusive area in the Helicobacter pylori field is an understanding of why some infections result in gastric cancer, yet others persist asymptomatically for the life-span of the individual. Even before the genomic era, the high level of intraspecies diversity of H. pylori was well recognized and became an intriguing area of investigation with respect to disease progression. Of interest in this regard is the unique repertoire of over 60 outer membrane proteins (OMPs), several of which have been associated with disease outcome. Of these OMPs, the association between HomB and disease outcome varies based on the population being studied. While the molecular roles for some of the disease-associated OMPs have been evaluated, little is known about the role that HomB plays in the H. pylori lifecycle. Thus, herein we investigated homB expression, regulation, and contribution to biofilm formation. We found that in H. pylori strain G27, homB was expressed at a relatively low level until stationary phase. Furthermore, homB expression was suppressed at low pH in an ArsRS-dependent manner; mutation of arsRS resulted in increased homB transcript at all tested time-points. ArsRS regulation of homB appeared to be direct as purified ArsR was able to specifically bind to the homB promoter. This regulation, combined with our previous finding that ArsRS mutations lead to enhanced biofilm formation, led us to test the hypothesis that homB contributes to biofilm formation by H. pylori. Indeed, subsequent biofilm analysis using a crystal-violet quantification assay and scanning electron microscopy (SEM) revealed that loss of homB from hyper-biofilm forming strains resulted in reversion to a biofilm phenotype that mimicked wild-type. Furthermore, expression of homB in trans from a promoter that negated ArsRS regulation led to enhanced biofilm formation even in strains in which the chromosomal copy of homB had been deleted. Thus, homB is necessary for hyper-biofilm formation of ArsRS mutant strains and aberrant regulation of this gene is sufficient to induce a hyper-biofilm phenotype. In summary, these data suggest that the ArsRS-dependent regulation of OMPs such as HomB may be one mechanism by which ArsRS dictates biofilm development in a pH responsive manner.
Trajetória profissional de doutores: a inserção de engenheiros na indústria brasileira

Resumo O projeto busca discutir a empregabilidade de doutores egressos em áreas relacionadas à ciência e tecnologia na indústria brasileira, analisando suas motivações e expectativas, bem como as expectativas e motivações da indústria, para a construção de um panorama que explique as preferências por esta carreira em detrimento de outras carreiras que são tradicionalmente seguidas por doutores, especialmente a carreira acadêmica.
Quantification of NGAL in Urine of Endurance Cycling Athletes.

BACKGROUND Neutrophil gelatinase-associated lipocalin (NGAL) is a glycoprotein released during early phases of a postischemic kidney in response to kidney injury, inflammation, and oxidative stress. It can be detected in urine after 2 hours of an ischemic event. The aim was to measure and to correlate the level of urine NGAL (uNGAL) with urea, creatinine, and glomerular filtration rate (GFR) of endurance cycling athletes (n = 19) and physically active individuals (control, n = 17). METHODS Quantification of urea and creatinine were performed by dry chemical method, and GFR was calculated using the modification of diet in renal disease formula, according to Brazilian Society of Nephrology. uNGAL analyses were performed by enzyme linked immunoabsorbent assay. Analyses were performed 48 hours after exercises. RESULTS uNGAL (in ng/mL) levels, expressed as median, minimum, and maximum, in cyclist group, 387.7 (109.7-1691.0), was significantly higher than that observed in control (physically active) group, 141.5 (4.8-657.0), (P < .05). No significant correlations were observed between uNGAL and creatinine, urea, or GFR (P > .05). CONCLUSIONS Results have pointed to increased uNGAL levels in endurance cycling athletes. Increase of uNGAL in absence of clinical signs or alterations in creatinine, urea, or GFR might suggest that there is metabolic adaptation to endurance exercise, or possibly predisposition to acute kidney injury over time.