Miracle-dz/UniFAR-FTUs huggingface dataset:
The Magnitude of Androgen Receptor Positivity in Breast Cancer Is Critical for Reliable Prediction of Disease Outcome

Purpose: Consensus is lacking regarding the androgen receptor (AR) as a prognostic marker in breast cancer. The objectives of this study were to comprehensively review the literature on AR prognostication and determine optimal criteria for AR as an independent predictor of breast cancer survival. Experimental Design: AR positivity was assessed by immunostaining in two clinically validated primary breast cancer cohorts [training cohort, n = 219; validation cohort, n = 418; 77% and 79% estrogen receptor alpha (ERα) positive, respectively]. The optimal AR cut-point was determined by ROC analysis in the training cohort and applied to both cohorts. Results: AR was an independent prognostic marker of breast cancer outcome in 22 of 46 (48%) previous studies that performed multivariate analyses. Most studies used cut-points of 1% or 10% nuclear positivity. Herein, neither 1% nor 10% cut-points were robustly prognostic. ROC analysis revealed that a higher AR cut-point (78% positivity) provided optimal sensitivity and specificity to predict breast cancer survival in the training (HR, 0.41; P = 0.015) and validation (HR, 0.50; P = 0.014) cohorts. Tenfold cross-validation confirmed the robustness of this AR cut-point. Patients with ERα-positive tumors and AR positivity ≥78% had the best survival in both cohorts (P < 0.0001). Among the combined ERα-positive cases, those with comparable or higher levels of AR (AR:ERα-positivity ratio >0.87) had the best outcomes (P < 0.0001). Conclusions: This study defines an optimal AR cut-point to reliably predict breast cancer survival. Testing this cut-point in prospective cohorts is warranted for implementation of AR as a prognostic factor in the clinical management of breast cancer. Clin Cancer Res; 24(10); 2328–41. ©2018 AACR.
Association of Beta-2 Microglobulin with Inflammation and Dislipidemia in High-Flux Membrane Hemodialysis Patients

Background: Higher than expected cardiovascular mortality in hemodialysis patients, has been attributed to dyslipidemia as well as inflammation. Beta2-Microglobulin (β2M) is an independent predictor of outcome for hemodialysis patients and a representative substance of middle molecules. Results: In 40 patients in high-flux membrane hemodialysis, we found negative correlation of β2M with high density lipoprotein (r=-0.73, p<0.001) and albumin (r= -0.53, p<0.001) and positive correlation with triglycerides (r=0.69, p<0.001), parathyroid hormone (r=0.58, p < 0.05) and phosphorus (r= 0.53, p<0.001). There was no correlation of β2M with C- reactive protein (CRP) and interleukin-6 (IL-6). During the follow-up period of three years, 6 out of 40 patients have died from cardiovascular events. Conclusion: In high-flux membrane hemodialysis patients, we observed a significant relationship of β2M with dyslipidemia and mineral bone disorders, but there was no correlation with inflammation.
In vitro heterogeneous degradation of alginate and its validation of different molecular weight on blood bio-compatibility

Abstract In the present work, sodium alginate (ALG) was degraded by heterogeneous phase acid degradation. The molecular weight distribution of ALG after degradation was close to homogenization. Then the blood bio-compatibility of ALG with different molecular weights (ALG-0h 50,075, ALG-0.5h 20,680, ALG-2h 13,170 and ALG-96h 1170 kDa) was evaluated in vitro and vivo. The human umbilical vein endothelial cells were used to assess the cytotoxicity of ALGs, ALG-0.5h and ALG-2h exhibited greater increment in percentage of cell viability comparing with ALG-0h and ALG-96h. With increasing of molecular weight of ALG, the blood clotting time was shortened and the hemolysis rate was slightly decreased. The different degree aggregation of red blood cells (RBCs) was observed in the ALG with different molecular groups and ALG-0h caused a severe aggregation of RBCs. Hematology analysis in vivo behavior after intraperitoneal (i.p.) injection indicated ALG-0h could cause blood solidification. Above results provided a reference for molecular weight selection in different applications.
A modified fast local region based method for image segmentation

Among many different methods of image segmentation, local region based algorithms received noticeable attention. In particular, these algorithms can be practically useful for images with intensity inhomogeneity like medical ultrasound images and tumor images. Although local based algorithms, unlike edge based methods, are insensitive to noise and weak edges, presence of severe noise in the images is still a problem. In this study, a modified local region based method is proposed for solving this problem, additionally the time consuming re-initialization process is removed by using the robust and fast Reaction Diffusion method. Conclusively, the final results reveal that the proposed modified algorithm can achieve more appropriate results in terms of accuracy and speed than five well-known local based methods.
A semisynthetic Streptococcus pneumoniae serotype 8 glycoconjugate vaccine

Automated glycan assembly enabled antibody reverse engineering to develop a semisynthetic carbohydrate–based vaccine against the highly virulent Streptococcus pneumoniae serotype 8. Pruning out nonprotective glycotopes Pediatric vaccines targeting bacterial capsular polysaccharides are more effective for certain types of bugs than others, and the manufacturing process as well as immunodominance of different glycan epitopes (glycotopes) can lead to a mixed immune response that does not protect against disease. To directly identify glycotopes that induce a protective response, Schumann et al. combined antibody reverse engineering with automated glycan assembly using Streptococcus pneumoniae serotype 8 as a proof of concept. Promising glycotopes conjugated to a carrier protein induced protective antibodies in mice and were also immunogenic in rabbits. When combined with a commercially available pneumococcal vaccine, these glycoconjugates were able to boost the opsonophagocytic bacterial killing ability of sera from immunized rabbits. This approach leveraging semisynthetic glycoconjugates could lead to the design of more effective bacterial vaccines. Glycoconjugate vaccines based on capsular polysaccharides (CPSs) of pathogenic bacteria such as Streptococcus pneumoniae successfully protect from disease but suffer from incomplete coverage, are troublesome to manufacture from isolated CPSs, and lack efficacy against certain serotypes. Defined, synthetic oligosaccharides are an attractive alternative to isolated CPSs but require the identification of immunogenic and protective oligosaccharide antigens. We describe a medicinal chemistry strategy based on a combination of automated glycan assembly (AGA), glycan microarray–based monoclonal antibody (mAb) reverse engineering, and immunological evaluation in vivo to uncover a protective glycan epitope (glycotope) for S. pneumoniae serotype 8 (ST8). All four tetrasaccharide frameshifts of ST8 CPS were prepared by AGA and used in glycan microarray experiments to identify the glycotopes recognized by antibodies against ST8. One tetrasaccharide frameshift that was preferentially recognized by a protective, CPS-directed mAb was conjugated to the carrier protein CRM197. Immunization of mice with this semisynthetic glycoconjugate followed by generation and characterization of a protective mAb identified protective and nonprotective glycotopes. Immunization of rabbits with semisynthetic ST8 glycoconjugates containing protective glycotopes induced an antibacterial immune response. Coformulation of ST8 glycoconjugates with the marketed 13-valent glycoconjugate vaccine Prevnar 13 yielded a potent 14-valent S. pneumoniae vaccine. Our strategy presents a facile approach to develop efficient semisynthetic glycoconjugate vaccines.
An evaluation of melodic similarity models

The advance of music information retrieval (MIR) has brought about a strong interest in melodic similarity models. In fact, the majority of these models derive their rational from the implementation within a MIR context. This is, so authors argue in general, a model is suitable if it retrieves the desired melody or a close variation of it. This post hoc method does not permit the evaluation and comparison of these models (although such a “comparison” competition has been proposed for ISMIR 2005). The author of this paper approaches the issue form a different angle; rather than testing models in an unsystematic fashion, the author will discuss the underlying cognitive principles of the similarity models. Here, it will be shown that four principle strategies exist: The contrast models, the distance models, dynamic programming and transition matrices. The author will then demonstrate that a variety of distance measures based upon a specific representation of melodies appears most promising while insisting that no single measurement can be seen as the answer to everything.
Caregiver Perceptions of a Telehealth Wellness Program

OBJECTIVE. We sought to understand caregivers’ experience of an education‐based wellness program delivered using telehealth. METHOD. In this qualitative pilot study, 4 caregivers participated in a focus group after completing a 6‐wk telehealth program. Data analysis involved open coding, thematic analysis, and coding triangulation. RESULTS. Two major themes emerged. The first, “I feel like I am now prepared,” included the subthemes of strategies for caregiver self‐maintenance, the understanding that caregiving is a normal process, and the value of a group experience. The second theme, “It was just a good interaction,” included the subthemes of benefits of telehealth, challenges of telehealth, and process of learning the technology. CONCLUSION. Participant discussion of the content learned and the value of group support indicated that telehealth was effective in both promoting learning and facilitating relationships. Even with challenges, participants reported an overall positive experience. Telehealth holds promise for increasing access to health promotion programs. Serwe, K. M. , Hersch, G. I. , Pickens, N. D. , & Pancheri, K. (2017). Brief Report—Caregiver perceptions of a telehealth wellness program.
Prolonging the Past Counteracts the Pull of the Present: Protracted Speciation Can Explain Observed Slowdowns in Diversification

Abstract Phylogenetic trees show a remarkable slowdown in the increase of number of lineages towards the present, a phenomenon which cannot be explained by the standard birth–death model of diversification with constant speciation and extinction rates. The birth–death model instead predicts a constant or accelerating increase in the number of lineages, which has been called the pull of the present. The observed slowdown has been attributed to nonconstancy of the speciation and extinction rates due to some form of diversity dependence (i.e., species-level density dependence), but the mechanisms underlying this are still unclear. Here, we propose an alternative explanation based on the simple concept that speciation takes time to complete. We show that this idea of “protracted” speciation can be incorporated in the standard birth–death model of diversification. The protracted birth–death model predicts a realistic slowdown in the rate of increase of number of lineages in the phylogeny and provides a compelling fit to four bird phylogenies with realistic parameter values. Thus, the effect of recognizing the generally accepted fact that speciation is not an instantaneous event is significant; even if it cannot account for all the observed patterns, it certainly contributes substantially and should therefore be incorporated into future studies.
Consistent Robustness Analysis (CRA) Identifies Biologically Relevant Properties of Regulatory Network Models

Background A number of studies have previously demonstrated that “goodness of fit” is insufficient in reliably classifying the credibility of a biological model. Robustness and/or sensitivity analysis is commonly employed as a secondary method for evaluating the suitability of a particular model. The results of such analyses invariably depend on the particular parameter set tested, yet many parameter values for biological models are uncertain. Results Here, we propose a novel robustness analysis that aims to determine the “common robustness” of the model with multiple, biologically plausible parameter sets, rather than the local robustness for a particular parameter set. Our method is applied to two published models of the Arabidopsis circadian clock (the one-loop [1] and two-loop [2] models). The results reinforce current findings suggesting the greater reliability of the two-loop model and pinpoint the crucial role of TOC1 in the circadian network. Conclusions Consistent Robustness Analysis can indicate both the relative plausibility of different models and also the critical components and processes controlling each model.
The Spliceosomal Phosphopeptide P140 Controls the Lupus Disease by Interacting with the HSC70 Protein and via a Mechanism Mediated by γδ T Cells

The phosphopeptide P140 issued from the spliceosomal U1-70K snRNP protein is recognized by lupus CD4+ T cells, transiently abolishes T cell reactivity to other spliceosomal peptides in P140-treated MRL/lpr mice, and ameliorates their clinical features. P140 modulates lupus patients' T cell response ex vivo and is currently included in phase IIb clinical trials. Its underlying mechanism of action remains elusive. Here we show that P140 peptide binds a unique cell-surface receptor, the constitutively-expressed chaperone HSC70 protein, known as a presenting-protein. P140 induces apoptosis of activated MRL/lpr CD4+ T cells. In P140-treated mice, it increases peripheral blood lymphocyte apoptosis and decreases B cell, activated T cell, and CD4−CD8−B220+ T cell counts via a specific mechanism strictly depending on γδ T cells. Expression of inflammation-linked genes is rapidly regulated in CD4+ T cells. This work led us to identify a powerful pathway taken by a newly-designed therapeutic peptide to immunomodulate lupus autoimmunity.
Bioengineering the Lung : Molecules , Materials , Matrix , Morphology , and Mechanics VEGF and endothelium-derived retinoic acid regulate lung vascular and alveolar development

Yun EJ, Lorizio W, Seedorf G, Abman SH, Vu TH. VEGF and endothelium-derived retinoic acid regulate lung vascular and alveolar development. Am J Physiol Lung Cell Mol Physiol 310: L287–L298, 2016. First published November 13, 2015; doi:10.1152/ajplung.00229. 2015. —Prevention or treatment of lung diseases caused by the failure to form, or destruction of, existing alveoli, as observed in infants with bronchopulmonary dysplasia and adults with emphysema, requires understanding of the molecular mechanisms of alveolar development. In addition to its critical role in gas exchange, the pulmonary circulation also contributes to alveolar morphogenesis and maintenance by the production of paracrine factors, termed “angiocrines,” that impact the development of surrounding tissue. To identify lung angiocrines that contribute to alveolar formation, we disrupted pulmonary vascular development by conditional inactivation of the Vegf-A gene during alveologenesis. This resulted in decreased pulmonary capillary and alveolar development and altered lung elastin and retinoic acid (RA) expression. We determined that RA is produced by pulmonary endothelial cells and regulates pulmonary angiogenesis and elastin synthesis by induction of VEGF-A and fibroblast growth factor (FGF)-18, respectively. Inhibition of RA synthesis in newborn mice decreased FGF-18 and elastin expression and impaired alveolarization. Treatment with RA and vitamin A partially reversed the impaired vascular and alveolar development induced by VEGF inhibition. Thus we identified RA as a lung angiocrine that regulates alveolarization through autocrine regulation of endothelial development and paracrine regulation of elastin synthesis via induction of FGF-18 in mesenchymal cells.
Electrode Coverage Optimization for Piezoelectric Energy Harvesting from Tip Excitation

Piezoelectric energy harvesting using cantilever-type structures has been extensively investigated due to its potential application in providing power supplies for wireless sensor networks, but the low output power has been a bottleneck for its further commercialization. To improve the power conversion capability, a piezoelectric beam with different electrode coverage ratios is studied theoretically and experimentally in this paper. A distributed-parameter theoretical model is established for a bimorph piezoelectric beam with the consideration of the electrode coverage area. The impact of the electrode coverage on the capacitance, the output power and the optimal load resistance are analyzed, showing that the piezoelectric beam has the best performance with an electrode coverage of 66.1%. An experimental study was then carried out to validate the theoretical results using a piezoelectric beam fabricated with segmented electrodes. The experimental results fit well with the theoretical model. A 12% improvement on the Root-Mean-Square (RMS) output power was achieved with the optimized electrode converge ratio (66.1%). This work provides a simple approach to utilizing piezoelectric beams in a more efficient way.
Pathogen-Specific Burden of Outpatient Diarrhea in Infants in Nepal: A Multisite Prospective Case-Control Study

Background Nonsevere diarrheal disease in Nepal represents a large burden of illness. Identification of the specific disease-causing pathogens will help target the appropriate control measures. Methods Infants aged 6 weeks to 12 months were recruited from 5 health facilities in eastern, central, and western Nepal between August 2012 and August 2013. The diarrhea arm included infants with mild or moderate diarrhea treatable in an outpatient setting; the nondiarrhea arm included healthy infants who presented for immunization visits or had a mild nondiarrheal illness. Stool samples were tested for 15 pathogens with a multiplex polymerase chain reaction (PCR) assay and real-time reverse-transcription (RT)-PCR assays for rotavirus and norovirus. Rotavirus- and norovirus-positive specimens were genotyped. We calculated attributable fractions (AFs) to estimate the pathogen-specific burden of diarrhea and adjusted for facility, age, stunting, wasting, and presence of other pathogens. Results We tested 307 diarrheal and 358 nondiarrheal specimens. Pathogens were detected more commonly in diarrheal specimens (164 of 307 [53.4%]) than in nondiarrheal specimens (113 of 358 [31.6%]) (P < .001). Rotavirus (AF, 23.9% [95% confidence interval (CI), 14.9%-32.8%]), Salmonella (AF, 12.4% [95% CI, 6.6%-17.8%]), and Campylobacter (AF, 5.6% [95% CI, 1.3%-9.8%]) contributed most to the burden of disease. In these diarrheal specimens, the most common genotypes for rotavirus were G12P[6] (27 of 82 [32.9%]) and G1P[8] (16 of 82 [19.5%]) and for norovirus were GII.4 Sydney (9 of 26 [34.6%]) and GII.7 (5 of 26 [19.2%]). Conclusions The results of this study indicate that the introduction of a rotavirus vaccine in Nepal will likely decrease outpatient diarrheal disease burden in infants younger than 1 year, but interventions to detect and target other pathogens, such as Salmonella and Campylobacter spp, should also be considered.
Sustained Antibody Responses 6 Years Following 1, 2, or 3 Doses of Quadrivalent Human Papillomavirus (HPV) Vaccine in Adolescent Fijian Girls, and Subsequent Responses to a Single Dose of Bivalent HPV Vaccine: A Prospective Cohort Study

Background The duration of antibody response following reduced human papillomavirus (HPV) vaccine doses has not been determined. We compared the antibody responses in girls previously vaccinated with zero, 1, 2, or 3 doses of quadrivalent HPV vaccine (4vHPV; Gardasil, Merck) 6 years previously. Methods A prospective cohort study was undertaken in 200 Fijian girls 15-19 years of age. Approximately equal numbers of girls from 2 main ethnic groups (Fijians of Indian descent [FID] and Indigenous Fijians [iTaukei]) in Fiji were recruited for each dosage groups. Blood was drawn before and 28 days following a single dose of bivalent HPV vaccine (2vHPV; Cervarix, GlaxoSmithKline). We measured neutralizing antibodies (NAb) against HPV-6, -11, -16, and -18 using the pseudovirion-based neutralization assay. Results After 6 years (before a dose of 2vHPV was given), the geometric mean NAb titers for all 4 HPV types were not statistically different between 2-dose (2D) and 3-dose (3D) recipients: HPV-6 (3D: 2216 [95% confidence interval {CI},1695-2896]; 2D: 1476 [95% CI, 1019-2137]; P = .07), HPV-11 (3D: 4431 [95% CI, 3396-5783]; 2D: 2951 [95% CI, 1984-4390]; P = .09), HPV-16 (3D: 3373 [95% CI, 2511-4530]; 2D: 3275 [95% CI, 2452-4373]; P = .89); HPV-18 (3D: 628 [95% CI: 445-888]; 2D: 606 [95% CI, 462-862]; P = .89), and were higher in FID than iTaukei girls. Although 1-dose recipients had significantly lower NAb titers than 2-/3-dose recipients, their NAb titers were 5- to 30-fold higher than unvaccinated girls. Post-2vHPV NAb titers against HPV-16 and -18 were not statistically different between girls who received 1, 2, or 3 doses of 4vHPV previously. Conclusions Two doses of 4vHPV provide similar NAb titers as 3 doses for 6 years, although the clinical significance is unknown. A single dose of 4vHPV elicits antibodies that persisted for at least 6 years, and induced immune memory, suggesting possible protection against HPV vaccine types after a single dose of 4vHPV.
node.dating: dating ancestors in phylogenetic trees in R

Summary Phylogenetic trees encode the evolutionary distances between species or populations. With sufficient information, these evolutionary distances can be rescaled over time to provide estimates of the dates of the most recent ancestors of the species. Here we present the R program node.dating, divergence-time analysis software, which uses a maximum-likelihood method to estimate the dates of the internal nodes of a phylogenetic tree. Availability and Implementation node.dating is available as a part of the R v3.30 package ape v4.0 (cran.r-project.org). node.dating is also available in the GitHub repository: https://github.com/brj1/node.dating , along with supplementary software and tests. Contact brj1@sfu.ca. Supplementary information Supplementary data are available at Bioinformatics online.
STING-associated vasculopathy develops independently of IRF3 in mice

Patients with stimulator of interferon genes (STING)–associated vasculopathy with onset in infancy (SAVI) develop systemic inflammation characterized by vasculopathy, interstitial lung disease, ulcerative skin lesions, and premature death. Autosomal dominant mutations in STING are thought to trigger activation of IRF3 and subsequent up-regulation of interferon (IFN)-stimulated genes (ISGs) in patients with SAVI. We generated heterozygous STING N153S knock-in mice as a model of SAVI. These mice spontaneously developed inflammation within the lung, hypercytokinemia, T cell cytopenia, skin ulcerations, and premature death. Cytometry by time-of-flight (CyTOF) analysis revealed that the STING N153S mutation caused myeloid cell expansion, T cell cytopenia, and dysregulation of immune cell signaling. Unexpectedly, we observed only mild up-regulation of ISGs in STING N153S fibroblasts and splenocytes and STING N154S SAVI patient fibroblasts. STING N153S mice lacking IRF3 also developed lung disease, myeloid cell expansion, and T cell cytopenia. Thus, the SAVI-associated STING N153S mutation triggers IRF3-independent immune cell dysregulation and lung disease in mice.