Critical Appraisal Guidelines for Single Case Study Research

The use of critical appraisal guidelines to assess the validity of research findings has become an established technique in those disciplines, such as healthcare and medicine, that encourage the use of evidence-based practice. Critical appraisal guidelines provide a rigorous set of criteria, often in the form of a checklist, against which a piece of research can be assessed. Although well established criteria exist for many forms of quantitative research, such as clinical trials and cohort studies, qualitative research is less well served. Through a synthesis of existing best practices in interpretative research this paper provides comprehensive guidelines for the conduct of single case study research and extrapolates from them a set of critical appraisal guidelines to assist in the evaluation of such work

Multiple gene aberrations and breast cancer: lessons from super-responders.

BackgroundThe presence of multiple molecular aberrations in patients with breast cancer may correlate with worse outcomes.Case presentationsWe performed in-depth molecular analysis of patients with estrogen receptor-positive, HER2-negative, hormone therapy-refractory breast cancer, who achieved partial or complete responses when treated with anastrozole and everolimus. Tumors were analyzed using a targeted next generation sequencing (NGS) assay in a Clinical Laboratory Improvement Amendments laboratory. Genomic libraries were captured for 3,230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to high coverage. Patients received anastrozole (1 g PO daily) and everolimus (5 or 10 mg PO daily). Thirty-two patients with breast cancer were treated on study and 5 (16 %) achieved a partial or complete response. Primary breast tissue was available for NGS testing in three of the responders (partial response with progression free survival of 11 and 14 months, respectively; complete response with progression free survival of 9+ months). The following molecular aberrations were observed: PTEN loss by immunohistochemistry, CCDN1 and FGFR1 amplifications, and PRKDC re-arrangement (NGS) (patient #1); PIK3CA and PIK3R1 mutations, and CCDN1, FGFR1, MYC amplifications (patient #2); TP53 mutation, CCNE1, IRS2 and MCL1 amplifications (patient #3). Some (but not all) of these aberrations converge on the PI3K/AKT/mTOR pathway, perhaps accounting for response.ConclusionsPatients with estrogen receptor-positive breast cancer can achieve significant responses on a combination of anastrozole and everolimus, even in the presence of multiple molecular aberrations. Further study of next generation sequencing-profiled tumors for convergence and resistance pathways is warranted

A quantum mechanical model of the upper bounds of the cascading contribution to the second hyperpolarizability

Microscopic cascading of second-order nonlinearities between two molecules has been proposed to yield an enhanced third-order molecular nonlinear-optical response. In this contribution, we investigate the two-molecule cascaded second hyperpolarizability and show that it will never exceed the fundamental limit of a single molecule with the same number of electrons as the two-molecule system. We show the apparent divergence behavior of the cascading contribution to the second hyperpolarizability vanishes when properly taking into account the intermolecular interactions. Although cascading can never lead to a larger nonlinear-optical response than a single molecule, it provides alternative molecular design configurations for creating materials with large third-order susceptibilities that may be difficult to design into a single molecule.Comment: 13 pages, 9 figures, 1 tabl

Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies

The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD

Anastrozole and everolimus in advanced gynecologic and breast malignancies: activity and molecular alterations in the PI3K/AKT/mTOR pathway.

BackgroundSince PI3K/AKT/mTOR pathway activation diminishes the effects of hormone therapy, combining aromatase inhibitors (anatrozole) with mTOR inhibitors (everolimus) was investigated.Patients and methodsWe evaluated anastrozole and everolimus in 55 patients with metastatic estrogen (ER) and/or progesterone receptor (PR)-positive breast and gynecologic tumors. Endpoints were safety, antitumor activity and molecular correlates.ResultsFull doses of anastrozole (1 mg PO daily) and everolimus (10 mg PO daily) were well tolerated. Twelve of 50 evaluable patients (24%) (median = 3 prior therapies) achieved stable disease (SD) ≥ 6 months/partial response (PR)/complete response (CR) (n = 5 (10%) with PR/CR): 9 of 32 (28%) with breast cancer (n=5 (16%) with PR/CR); 2 of 10 (20%), ovarian cancer; and 1 of 6 (17%), endometrial cancer. Six of 22 patients (27%) with molecular alterations in the PI3K/AKT/mTOR pathway achieved SD ≥ 6 months/PR/CR. Six of 8 patients (75%) with SD ≥ 6 months/PR/CR with molecular testing demonstrated at least one alteration in the PI3K/AKT/mTOR pathway: mutations in PIK3CA (n=3) and AKT1 (n=1) or PTEN loss (n=3). All three responders (CR (n = 1); PR (n=2)) who had next generation sequencing demonstrated additional alterations: amplifications in CCNE1, IRS2, MCL1, CCND1, FGFR1 and MYC and a rearrangement in PRKDC.ConclusionsCombination anastrozole and everolimus is well tolerated at full approved doses, and is active in heavily-pretreated patients with ER and/or PR-positive breast, ovarian and endometrial cancers. Responses were observed in patients with multiple molecular aberrations. CLINICAL TRAILS INCLUDED: NCT01197170

The Grizzly, April 3, 1981

Board of Directors Elects Corey to Five Year Term • Fire Alarm and Damage Plague Beta Sig • Parents Day Packed With Fun • Resident Assistants Announced • Reagan\u27s Programs • Departmental Focus: Political Science • Music News • Transplanted Texan: Cult of Violence • Franken and Davis Bring Saturday Night to Bomberger • ProTheatre\u27s Dream Fresh and Funny • Pennsylvania Folk Art • Chamber Orchestra Salutes Bach • History Department Sponsors Phillies Contest • Men\u27s Lacrosse Off to Slow Start • Thinclads Just Off F&M\u27s Mark • Lacrosse 4th in Nation • Baseball Sweeps F&Mhttps://digitalcommons.ursinus.edu/grizzlynews/1057/thumbnail.jp

Could humans recognize odor by phonon assisted tunneling?

Our sense of smell relies on sensitive, selective atomic-scale processes that are initiated when a scent molecule meets specific receptors in the nose. However, the physical mechanisms of detection are not clear. While odorant shape and size are important, experiment indicates these are insufficient. One novel proposal suggests inelastic electron tunneling from a donor to an acceptor mediated by the odorant actuates a receptor, and provides critical discrimination. We test the physical viability of this mechanism using a simple but general model. Using values of key parameters in line with those for other biomolecular systems, we find the proposed mechanism is consistent both with the underlying physics and with observed features of smell, provided the receptor has certain general properties. This mechanism suggests a distinct paradigm for selective molecular interactions at receptors (the swipe card model): recognition and actuation involve size and shape, but also exploit other processes.Comment: 10 pages, 1 figur

The Grizzly, March 27, 1981

Parents Day Slated for Early April • Overwhelming Enthusiasm Welcomes Special Olympics • Bomberger Tower Under Construction • SPC Elects New Grizzly Editor-in-Chief • Shakespeare Opens • Departmental Focus: Math Department • Transplanted Texan: NY to Collegeville • Spectrum Tries New Ticket Sales • Values Next Forum Topic • TV Production in Communications • Language Clubs Host Dessert Festival • Final Exam Schedule • Baseball Team Carries Much Potential • Hoopsters Finish 3rd in Nation • Tennis Team Prepares for Tough Season • Women\u27s Lacrosse Start Season 1-1https://digitalcommons.ursinus.edu/grizzlynews/1056/thumbnail.jp