Smaller, smarter, faster: the development and application of microfluidic devices to the determination of phosphorus in natural waters

The development of a miniaturised microfluidic instrument for monitoring phosphorus in natural waters from the optimisation of the chemistry through to the fabrication of the microfluidic manifold in polymeric materials is presented. The research initially was concerned with optimising the yellow colorimetric method for a phosphate determination and its transferral to a Si-etched microfluidic chip configuration. Th is simple method employs one reagent mixed in a 1:1 ratio with an orthophosphate-containing sample to produce a yellow colour absorbing strongly below 400nm. A stopped flow approach is used which, together with the very rapid kinetics and simple reagent stream, enables a very uncomplicated microfluidic manifold design to be adopted. The working wavelength wa s 380nm, which coincided with the peak output of a recently developed U V -L E D narrow bandwidth light source. The limit of detection for the yellow method is 0.2 mgL'1 P O ^ - P with a linear range from 0 - 5 0 mgL*1 P O 43“ - P possible. T h e reaction time at room temperature is less than 3 minutes, which m ean s up to 20 sam ple s / hour can be analysed. The next stage in the research involved applying the results obtained in the Sietched microfluidic chips to the design and fabrication of a microfluidic manifold in polymer materials. Chips were made by a combination of microfabrication techniques including a C 0 2 laser ablation, hot embossing and micromilling. Transferring the technology to a polymeric platform required a whole new set of experiments to be undertaken. The key is su e s add ressed were multiple layer alignment, optical detection, bonding of polymeric materials; the provision of leakfree fluidic interconnects to external tubing and reproducible analytical measurements

AKT1[low] quiescent cancer cells persist after neoadjuvant chemotherapy in triple negative breast cancer

Background: Absence of pathologic complete response (pCR) to neoadjuvant chemotherapy (NACT) correlates with poor long-term survival in patients with triple negative breast cancer (TNBC). These incomplete treatment responses are likely determined by mechanisms that enable cancer cells to resist being killed. However, the detailed characterization of a drug-resistant cancer cell state in residual TNBC tissue after NACT has remained elusive. AKT1(low) quiescent cancer cells (QCCs) are a quiescent, epigenetically plastic, and chemotherapy-resistant subpopulation initially identified in experimental cancer models. Here, we asked whether QCCs exist in primary tumors from patients with TNBC and persist after treatment with NACT. Methods: We obtained pre-treatment biopsy, post-treatment mastectomy, and metastatic specimens from a retrospective cohort of TNBC patients treated with NACT at Massachusetts General Hospital (n = 25). Using quantitative automated immunofluorescence microscopy, QCCs were identified as AKT(low)/H3K9me2(low)/HES1(high) cancer cells using prespecified immunofluorescence intensity thresholds. QCCs were represented in 2D and 3D digital tumor maps and QCC percentage (QCC-P) and QCC cluster index (QCC-CI) were determined for each sample. Results: We showed that QCCs exist as non-random and heterogeneously distributed clusters within primary breast tumors. In addition, these QCC clusters persist after treatment with multi-agent, multi-cycle, neoadjuvant chemotherapy in both residual primary tumors and nodal and distant metastases in patients with triple negative breast cancer. Conclusions: These first-in-human data potentially qualify AKT1(low) quiescent cancer cells as a non-genetic cell state that persists after neoadjuvant chemotherapy in triple negative breast cancer patients and warrants further study

Development and psychometric validation of the mental health-related barriers and benefits to EXercise (MEX) scale in healthy adults

Background: Physical exercise has been shown to reduce anxiety and depression symptoms, the most common mental health disorders globally. Despite the benefits of exercise in anxiety and depression, the symptoms of these disorders may directly contribute to a lack of engagement with exercise. However, mental health-related barriers and benefits to exercise engagement have not been addressed in quantitative research. We introduce the development and psychometric validation of the Mental health-related barriers and benefits to EXercise (MEX) scale. Methods: Three samples were collected online prospectively (sample 1 n = 492; sample 2 n = 302; sample 3 n = 303) for scale refinement and validation with exploratory and confirmatory factor analysis. All participants were generally healthy adults, aged 18–45, and had no history of severe mental illness requiring hospitalization and no physical disability impacting over 50% of daily function. Results: We identified a 30-item, two-factor model comprising 15 barrier and 15 benefit items. Overall model fit was excellent for an item-level scale across the three samples (Comparative Fit Index = 0.935–0.951; Root-Mean-Square Error of Approximation = 0.037–0.039). Internal consistency was also excellent across the three samples (α = 0.900–0.951). The barriers subscale was positively correlated with symptoms of anxiety, depression and stress, and negatively correlated with measures of physical activity and exercise engagement. The benefits subscale was negatively correlated with symptoms of anxiety, depression and stress, and positively correlated with measures of physical activity and exercise engagement. Conclusion: The MEX is a novel, psychometrically robust scale, which is appropriate for research and for clinical use to ascertain individual and/or group level mental health-related barriers and benefits to exercise

TOP2A and EZH2 Provide Early Detection of an Aggressive Prostate Cancer Subgroup.

Purpose: Current clinical parameters do not stratify indolent from aggressive prostate cancer. Aggressive prostate cancer, defined by the progression from localized disease to metastasis, is responsible for the majority of prostate cancer–associated mortality. Recent gene expression profiling has proven successful in predicting the outcome of prostate cancer patients; however, they have yet to provide targeted therapy approaches that could inhibit a patient\u27s progression to metastatic disease. Experimental Design: We have interrogated a total of seven primary prostate cancer cohorts (n = 1,900), two metastatic castration-resistant prostate cancer datasets (n = 293), and one prospective cohort (n = 1,385) to assess the impact of TOP2A and EZH2 expression on prostate cancer cellular program and patient outcomes. We also performed IHC staining for TOP2A and EZH2 in a cohort of primary prostate cancer patients (n = 89) with known outcome. Finally, we explored the therapeutic potential of a combination therapy targeting both TOP2A and EZH2 using novel prostate cancer–derived murine cell lines. Results: We demonstrate by genome-wide analysis of independent primary and metastatic prostate cancer datasets that concurrent TOP2A and EZH2 mRNA and protein upregulation selected for a subgroup of primary and metastatic patients with more aggressive disease and notable overlap of genes involved in mitotic regulation. Importantly, TOP2A and EZH2 in prostate cancer cells act as key driving oncogenes, a fact highlighted by sensitivity to combination-targeted therapy. Conclusions: Overall, our data support further assessment of TOP2A and EZH2 as biomarkers for early identification of patients with increased metastatic potential that may benefit from adjuvant or neoadjuvant targeted therapy approaches. ©2017 AACR

Transcriptomic analysis of micropapillary high grade T1 urothelial bladder cancer

No consensus currently exist on the optimal treatment of patients with high-risk nonmuscle invasive (HGT1) micropapillary variant of bladder cancer (MPBC). Transcripsome analysis may allow stratification of MPBC-HGT1 enabling prediction of recurrence and guide therapeutic management for individual patients. Whole transcriptome RNA-Sequencing of tumors from 23 patients with MPBC-HGT1 and 64 conventional urothelial carcinomas (cUC) (reference set) was performed. Differentially expressed genes between MPBC-HGT1 and cUC-HGT1 were explored. Cox proportional hazard models and Kapplan-Meier methods were used to assess the relation between time to progression (TTP) and individual gene expression adjusting for clinical covariates. Over 3000 genes were differentially expressed in MPBC-HGT1 as compared with cUC-HGT1 and a 26-gene signature is characteristic of MPBC within HGT1. A set of three genes; CD36, FAPB3 and RAETE1 ; were significantly associated with TTP. High expression of FABP3 and CD36 were associated with shorter TTP (p = 0.045 and p = 0.08) as was low expression of RAET1E (p = 0.01). Our study suggest that a 26-gene signature can define MPBC-HGT1 within conventional urothelial carcinomas. A prognostic risk index of three genes (FABP3, CD36 and RAET1E) was found to be associated with shorter TTP and may help classify a group of patients with MPBC-HGT1 with high-risk of early progression. These observations might have implications in terms of radical cystectomy recommendation in MPBC patients

Association of tumour microRNA profiling with outcomes in patients with advanced urothelial carcinoma receiving first-line platinum-based chemotherapy

Background: Tumour expression of selected microRNAs (miRs) correlates with cisplatin efficacy in multiple cancers. We investigated the role of selected miRs in patients receiving cisplatin-based therapy for advanced urothelial carcinoma (UC). Methods: RNA was extracted from formalin-fixed paraffin-embedded tumour from 83 advanced UC patients who received cisplatin. A miR panel based on relevance for platinum sensitivity and UC was studied by quantitative reverse transcription quantitative PCR (RT–qPCR). Association of progression-free survival (PFS) with miR expression was analysed using cox regression. Selected TFs were chosen by association with the panel of miRs using the Transcription Regulation algorithm (GeneGo MetaCore+MetaDrug version 6.23 build 67496). Bladder cancer (BC) cell lines were used to investigate the previously described role of miR-21 mediating cisplatin sensitivity. Results: The 83 patients had a median PFS of 8 months. In multivariate analysis, higher levels of E2F1 (P=0.01, HR: 1.95 (1.14, 3.33)), miR-21 (P=0.01, HR: 2.01 (1.17, 3.45)) and miR-372 (P=0.05, HR: 1.70 (1.00, 2.89)) were associated with a shorter PFS. In the 8 BC cell lines, miR-21 was not shown to be necessary nor sufficient for modulating cisplatin sensitivity. Conclusions: In metastatic UC patients treated with cisplatin-based therapy, high primary tumour levels of E2F1, miR-21 and miR-372 are associated with poor PFS independent of clinical prognostic factors. The in vitro study could not confirm miR-21 levels role in modulating platinum sensitivity

The Second Monocular Depth Estimation Challenge

This paper discusses the results for the second edition of the Monocular Depth Estimation Challenge (MDEC). This edition was open to methods using any form of supervision, including fully-supervised, self-supervised, multi-task or proxy depth. The challenge was based around the SYNS-Patches dataset, which features a wide diversity of environments with high-quality dense ground-truth. This includes complex natural environments, e.g. forests or fields, which are greatly underrepresented in current benchmarks. The challenge received eight unique submissions that outperformed the provided SotA baseline on any of the pointcloud- or image-based metrics. The top supervised submission improved relative F-Score by 27.62%, while the top self-supervised improved it by 16.61%. Supervised submissions generally leveraged large collections of datasets to improve data diversity. Self-supervised submissions instead updated the network architecture and pretrained backbones. These results represent a significant progress in the field, while highlighting avenues for future research, such as reducing interpolation artifacts at depth boundaries, improving self-supervised indoor performance and overall natural image accuracy.Comment: Published at CVPRW202

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness