- ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files. [Journal Article]
- JCJ Cheminform 2016; 8:73
- Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular infor...
Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.
- Comparison of neoadjuvant vs concurrent/adjuvant androgen deprivation in men with high-risk prostate cancer receiving definitive radiation therapy. [Journal Article]
- TTumori 2017 Jan 12; :0
- CONCLUSIONS: External beam radiation therapy with N-HT was associated with improved overall survival compared to C-HT. This study is hypothesis-generating and further studies are needed to best qualify the sequencing of hormone therapy with the duration of treatment.
- Perioperative Search for Circulating Tumor Cells in Patients Undergoing Prostate Brachytherapy for Clinically Nonmetastatic Prostate Cancer. [Journal Article]
- IJInt J Mol Sci 2017 Jan 11; 18(1)
- Despite the absence of local prostate cancer recurrence, some patients develop distant metastases after prostate brachytherapy. We evaluate whether prostate brachytherapy procedures have a potential ...
Despite the absence of local prostate cancer recurrence, some patients develop distant metastases after prostate brachytherapy. We evaluate whether prostate brachytherapy procedures have a potential risk for hematogenous spillage of prostate cancer cells. Fifty-nine patients who were undergoing high-dose-rate (HDR) or low-dose-rate (LDR) brachytherapy participated in this prospective study. Thirty patients with high-risk or locally advanced cancer were treated with HDR brachytherapy after neoadjuvant androgen deprivation therapy (ADT). Twenty-nine patients with clinically localized cancer were treated with LDR brachytherapy without neoadjuvant ADT. Samples of peripheral blood were drawn in the operating room before insertion of needles (preoperative) and again immediately after the surgical manipulation (intraoperative). Blood samples of 7.5 mL were analyzed for circulating tumor cells (CTCs) using the CellSearch System. While no preoperative samples showed CTCs (0%), they were detected in intraoperative samples in 7 of the 59 patients (11.8%; preoperative vs. intraoperative, p = 0.012). Positive CTC status did not correlate with perioperative variables, including prostate-specific antigen (PSA) at diagnosis, use of neoadjuvant ADT, type of brachytherapy, Gleason score, and biopsy positive core rate. We detected CTCs from samples immediately after the surgical manipulation. Further study is needed to evaluate whether those CTCs actually can survive and proliferate at distant sites.
- LncRNAs and miRNAs: potential biomarkers and therapeutic targets for prostate cancer. [Review]
- AJAm J Transl Res 2016; 8(12):5141-5150
- Prostate cancer (PCa) is the second lethal disease for men in western countries. Although androgen receptor (AR) signaling has been widely investigated, noncoding RNAs (ncRNAs), deficient of open rea...
Prostate cancer (PCa) is the second lethal disease for men in western countries. Although androgen receptor (AR) signaling has been widely investigated, noncoding RNAs (ncRNAs), deficient of open reading frame, have also received considerable attention. Growing studies showed that the aberrant ncRNAs expression contributed to cell proliferation, metastasis and drug resistance in PCa. Therefore, therapeutically targeting ncRNAs may synergize androgen deprivation therapy (ADT) to have a better effect to fight against PCa, especially castration-resistant prostate cancer (CRPC). This review would systematically summarize the multicellular events controlled by ncRNAs and give a snapshot of future scientific activities and clinical applications.
- Inflammation, cardiometabolic markers and functional changes in a randomized controlled trial of a 12-month exercise program for prostate cancer men. [Journal Article]
- PAPol Arch Med Wewn 2017 Jan 10
- INTRODUCTION Previous studies have shown that physical exercise in cancer patients during radiotherapy (RT) and androgen deprivation therapy (ADT) improves cardiac fitness and quality of life (QoL...
INTRODUCTION Previous studies have shown that physical exercise in cancer patients during radiotherapy (RT) and androgen deprivation therapy (ADT) improves cardiac fitness and quality of life (QoL), and reduces fatigue but it is still not entirely known how it affects inflammation or metabolic factors and what its consequences are in prostate cancer (PCa) patients. OBJECTIVES Effect of a 12-month physical exercise program on inflammatory and cardiometabolic factors, and on functional status in PCa patients undergoing RT and ADT. PATIENTS AND METHODS Seventy-two high-risk and intermediate-risk PCa men were allocated to two groups before RT. This was a randomized controlled clinical trial. The physical exercise group (EG) trained 5 days/wk during RT and then 3 days/wk. Patients in control group performed usual care according to recommendations (UG). Measurements were performed at baseline, after RT (8 weeks), and after 10 months. The parameters assessed were pro-inflammatory cytokine levels (IL-1β, IL-6, TNF-α), lipid profile, aerobic capacity, BMI, WHR, and functional status (FACT-F and EORTC questionnaires). RESULTS There was a significant improvement in functional capacity, BMI, WHR (p<0.05), decrease in the levels of pro-inflammatory cytokines (p>0.05) and fatigue (p<0.05) in EG compared to UG after 12 months. The fatigue was significantly higher in UG (p<0.05) especially after RT. CONCLUSIONS Long-term supervised exercise training is more effective than physical activity educational materials as regards cardiovascular risk decrease and improvement of functional status in PCa patients during RT and ADT.
- Sentinel Lymph Node Dissection to Select Clinically Node-negative Prostate Cancer Patients for Pelvic Radiation Therapy: Effect on Biochemical Recurrence and Systemic Progression. [Journal Article]
- IJInt J Radiat Oncol Biol Phys 2017 Feb 01; 97(2):347-354
- CONCLUSIONS: For radioisotope-guided SLND, the high staging accuracy is accompanied by low morbidity. The better than expected outcomes observed in the lower quartiles of BCR prediction suggest a role for SLN biopsy as a potential selection tool for the addition of pelvic radiation therapy and ADT intensification in pN1 patients.
- Hormone therapy for prostate cancer increases the risk of Alzheimer's disease: a nationwide 4-year longitudinal cohort study. [Journal Article]
- AMAging Male 2017 Jan 09; :1-6
- CONCLUSIONS: The present results suggest that ADT use is associated with an increased risk of developing AD.
- The clinical importance of quantifying fat distribution during androgen deprivation. [Journal Article]
- EREndocr Relat Cancer 2017 Jan 06
- Androgen deprivation therapy (ADT) is now considered a mainstay in the treatment of metastatic and locally advanced prostate cancer (PCa). Despite well-established benefits of ADT in relation to over...
Androgen deprivation therapy (ADT) is now considered a mainstay in the treatment of metastatic and locally advanced prostate cancer (PCa). Despite well-established benefits of ADT in relation to overall survival, this treatment has been associated with a number of adverse effects, particularly with regard to key cardiometabolic risk factors including the development of insulin resistance, dyslipidaemia and increases in total and regional fat mass. In non-ADT populations, increased levels of visceral adipose tissue (VAT) are thought to be a key mediator of the increased cardiometabolic risk associated with weight gain, but this has received limited attention in men treated with ADT. VAT is best assessed using tools such as computed tomography or magnetic resonance imaging, however these tools are not readily accessible for the majority of researchers or clinicians. Recent advances allow for a method of estimating VAT using a whole-body dual-energy X-ray absorptiometry (DXA) scan that shows promise as a practical tool for researchers to evaluate changes in body fat distribution during ADT. The aim of this narrative review is to (1) review the available evidence with regard to the relationship between ADT and cardiometabolic risk; (2) discuss the role of body fat distribution on cardiometabolic risk in non-ADT populations, with a particular emphasis on the importance of visceral adiposity; (3) examine the potential influence of ADT on body fat distribution and visceral adiposity, and (4) provide an overview of current tools used to measure changes in body fat distribution in men treated with ADT, highlighting the potential utility of a recently developed DXA-derived measure of VAT.
- The RAS-Effector Interaction as a Drug Target. [Review]
- CRCancer Res 2017 Jan 06
- About a third of all human cancers harbor mutations in one of the K-, N-, or HRAS genes that encode an abnormal RAS protein locked in a constitutively activated state to drive malignant transformatio...
About a third of all human cancers harbor mutations in one of the K-, N-, or HRAS genes that encode an abnormal RAS protein locked in a constitutively activated state to drive malignant transformation and tumor growth. Despite more than three decades of intensive research aimed at the discovery of RAS-directed therapeutics, there are no FDA-approved drugs that are broadly effective against RAS-driven cancers. Although RAS proteins are often said to be "undruggable," there is mounting evidence suggesting it may be feasible to develop direct inhibitors of RAS proteins. Here, we review this evidence with a focus on compounds capable of inhibiting the interaction of RAS proteins with their effectors that transduce the signals of RAS and that drive and sustain malignant transformation and tumor growth. These reports of direct-acting RAS inhibitors provide valuable insight for further discovery and development of clinical candidates for RAS-driven cancers involving mutations in RAS genes or otherwise activated RAS proteins. Cancer Res; 77(2); 1-6. ©2017 AACR.
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- Classifying high-risk versus very high-risk prostate cancer: is it relevant to outcomes of conformal radiotherapy and androgen deprivation? [Journal Article]
- RORadiat Oncol 2017 Jan 06; 12(1):5
- CONCLUSIONS: Patients with HR and VHR disease treated with CRT and ADT had good outcomes. Stratification into HR and VHR sub-groups provided no predictive value. Only PSA ≥40 ng/ml predicted poor outcomes on MVA. Distant failure was dominant and local recurrence rare, suggesting that improved systemic treatment rather than intensification of local therapy is needed. Patients with high-risk prostate cancer are most often treated with conformal dose escalated radiation therapy with androgen deprivation. Stratification into high versus very high-risk subgroups using 2014 or revised 2015 National Comprehensive Cancer Network (NCCN) criteria did not impact treatment outcomes. Only Prostate Serum Antigen (PSA) ≥40 ng/ml was predictive of poor prognosis. Distant failure was dominant and local recurrence uncommon which challenges the notion that intensification of local therapy will further improve outcomes in patients with high-risk disease.