Citations

Abstract Motivation: Modern techniques have produced many sequence annotation databases and protein structure portals, but these Web resources are rarely integrated in ways that permit straightforward exploration of protein functional residues and their co-localization. Results: We have created the AMASS database, which maps 1D sequence annotation databases to 3D protein structures with an intuitive visualization interface. Our platform also provides an analysis service that screens mass spectrometry sequence data for post-translational modifications that reside in functionally relevant locations within protein structures. The system is built on the premise that functional residues such as active sites, cancer mutations and post-translational modifications within proteins may co-localize and share common functions. Availability and implementation: AMASS database is implemented with Biopython and Apache as a freely available Web server at amass-db.org. Contact: clinton.mielke@gmail.com

Key Points Alternatively polarized macrophages are abundant constituents of the tumor microenvironment in T-cell lymphoproliferative disorders. GATA-3 expression identifies a subset of PTCL, NOS with a distinct cytokine profile and inferior survival.

Reducing the incidence and mortality rates for clear cell renal cell carcinoma (ccRCC) remains a significant clinical challenge with poor 5‐year survival rates. A unique tissue cohort was assembled of matched ccRCC and distal nontumor tissues (n = 20) associated with moderate risk of disease progression, half of these from individuals who progressed to metastatic disease and the other half who remained disease free. These tissues were used for MALDI imaging MS profiling of proteins in the 2–20 kDa range, resulting in a panel of 108 proteins that had potential disease‐specific expression patterns. Protein lysates from the same tissues were analyzed by MS/MS, resulting in identification of 56 proteins of less than 20 kDa molecular weight. The same tissues were also used for global lipid profiling analysis by MALDI‐FT‐ICR MS. From the cumulative protein and lipid expression profile data, a refined panel of 26 proteins and 39 lipid species was identified that could either distinguish tumor from nontumor tissues, or tissues from recurrent disease progressors from nonrecurrent disease individuals. This approach has the potential to not only improve prognostic assessment and enhance postoperative surveillance, but also to inform on the underlying biology of ccRCC progression.

Depression symptoms contribute to significant morbidity and health care utilization. The aim of this study was to determine the impact of symptom improvement (to remission) on outpatient clinical visits by depressed primary care patients. This study was a retrospective chart review analysis of 1733 primary care patients enrolled into collaborative care management (CCM) or usual care (UC) with 6-month follow-up data. Baseline data (including demographic information, clinical diagnosis, and depression severity) and 6-month follow-up data (Patient Health Questionnaire scores and the number of outpatient visits utilized) were included in the data set. To control for individual patient complexity and pattern of usage, the number of outpatient visits for 6 months prior to enrollment also was measured as was the presence of medical comorbidities. Multiple logistic regression analysis demonstrated that clinical remission at 6 months was an independent predictor of outpatient visit outlier status (>8 visits) (odds ratio [OR] 0.609, confidence interval (CI) 0.460–0.805, P <0.01) when controlling for all other independent variables including enrollment into CCM or UC. The OR of those patients not in remission at 6 months having outpatient visit outlier status was the inverse of this at 1.643 (CI 1.243–2.173). The most predictive variable for determining increased outpatient visit counts after diagnosis of depression was increased outpatient visits prior to diagnosis (OR 4.892, CI 3.655–6.548, P <0.01). In primary care patients treated for depression, successful treatment to remission at 6 months decreased the likelihood of the patient having more than 8 visits during the 6 months after diagnosis. ( Population Health Management 2014;17:180–184)

Purpose High-quality supportive care is an essential component of comprehensive cancer care. We implemented a patient-centered quality of cancer care survey to examine and identify predictors of quality of supportive care for bowel problems, pain, fatigue, depression, and other symptoms among 1,109 patients with colorectal cancer. Patients and Methods Patients with new diagnosis of colorectal cancer at any Veterans Health Administration medical center nationwide in 2008 were ascertained through the Veterans Affairs Central Cancer Registry and sent questionnaires assessing a variety of aspects of patient-centered cancer care. We received questionnaires from 63% of eligible patients (N = 1,109). Descriptive analyses characterizing patient experiences with supportive care and binary logistic regression models were used to examine predictors of receipt of help wanted for each of the five symptom categories. Results There were significant gaps in patient-centered quality of supportive care, beginning with symptom assessment. In multivariable modeling, the impact of clinical factors and patient race on odds of receiving wanted help varied by symptom. Coordination of care quality predicted receipt of wanted help for all symptoms, independent of patient demographic or clinical characteristics. Conclusion This study revealed substantial gaps in patient-centered quality of care, difficult to characterize through quality measurement relying on medical record review alone. It established the feasibility of collecting patient-reported quality measures. Improving quality measurement of supportive care and implementing patient-reported outcomes in quality-measurement systems are high priorities for improving the processes and outcomes of care for patients with cancer.

AbstractPurposeCurrently, there is a paucity of literature regarding outcomes after isolated labral debridement. The purpose of this study was to (1) report the reoperation rate following isolated labral debridement, (2) report clinical and functional outcomes after labral debridement with a minimum 2‐year follow‐up and (3) identify risk factors for worse clinical and functional outcomes. It was hypothesized that inferior outcomes are associated with an increasing Tönnis grade and those with untreated femoral acetabular impingement (FAI).MethodsThe records of patients undergoing hip arthroscopy between 1998 and 2005 were reviewed. Patients with labral tears who underwent isolated arthroscopic labral debridement were identified. Kaplan–Meier estimate of failure (defined as subsequent surgery) was performed for all patients. Patients with minimum 2‐year follow‐up were assessed with Modified Harris Hip Score (MHHS) and Hip Outcome Score (HOS). Univariate analysis was then performed to assess which factors were associated with worse clinical and functional outcomes.ResultsFifty‐nine hips in 57 patients met our inclusion criteria (39 females, 18 males) with a mean age of 46 ± 14 years and mean follow‐up of 5 (range 2–14) years. Overall, 45 % of the hips failed for repeat surgery (20 %) or rating for hip function as abnormal or severely abnormal (25 %). Twelve hips (20 %) required subsequent surgical intervention at a mean 23 (range 6–60) months (7 total hip arthroplasties, 2 open revisions, 3 arthroscopic revisions). Of the remaining hips, mean MHHS was 83.4 ± 19.7, mean HOS ADL score was 83.8 ± 21.3 and mean HOS sport score was 70.6 ± 32.9, with 33 of 41 (75 %) reporting normal or nearly normal current level of function. Univariate analysis revealed that hips with untreated bony impingement (p = 0.01) or requiring concomitant chondroplasty (p = 0.03) had inferior clinical outcome scores.ConclusionsIsolated arthroscopic labral debridement for hip labral tears had 45 % combined poor results when strictly defining failure as repeat surgery or abnormal hip rating. Untreated FAI and concomitant chondroplasty were risk factors for inferior outcome. We recommend concomitant treatment for bony impingement lesions and preservation of the labrum whenever possible.Level of evidenceRetrospective case series, Level IV.