PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases

Searching PubMed for citations related to a specific cancer center or group of authors can be labor-intensive. We have created a tool, PubMed QUEST, to aid in the rapid searching of PubMed for publications of interest. It was designed by taking into account the needs of entire cancer centers as well as individual investigators. The experience of using the tool by our institution’s cancer center administration and investigators has been favorable and we believe it could easily be adapted to other institutions. Use of the tool has identified limitations of automated searches for publications based on an author’s name, especially for common names. These limitations could likely be solved if the PubMed database assigned a unique identifier to each author

Computerized Automated Reminder Diabetes System (CARDS): E-Mail and SMS Cell Phone Text Messaging Reminders to Support Diabetes Management

Abstract Background: Cell phone text messaging, via the Short Messaging Service (SMS), offers the promise of a highly portable, well-accepted, and inexpensive modality for engaging youth and young adults in the management of their diabetes. This pilot and feasibility study compared two-way SMS cell phone messaging with e-mail reminders that were directed at encouraging blood glucose (BG) monitoring. Methods: Forty insulin-treated adolescents and young adults with diabetes were randomized to receive electronic reminders to check their BG levels via cell phone text messaging or e-mail reminders for a 3-month pilot study. Electronic messages were automatically generated, and participant replies with BG results were processed by the locally developed Computerized Automated Reminder Diabetes System (CARDS). Participants set their schedule for reminders on the secure CARDS website where they could also enter and review BG data. Results: Of the 40 participants, 22 were randomized to receive cell phone text message reminders and 18 to receive e-mail reminders; 18 in the cell phone group and 11 in the e-mail group used the system. Compared to the e-mail group, users in the cell phone group received more reminders (180.4 vs. 106.6 per user) and responded with BG results significantly more often (30.0 vs. 6.9 per user, P = 0.04). During the first month cell phone users submitted twice as many BGs as e-mail users (27.2 vs. 13.8 per user); by month 3, usage waned. Conclusions: Cell phone text messaging to promote BG monitoring is a viable and acceptable option in adolescents and young adults with diabetes. However, maintaining interest levels for prolonged intervals remains a challenge.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78128/1/dia.2008.0022.pd

Extracting information from the text of electronic medical records to improve case detection: a systematic review

Background: Electronic medical records (EMRs) are revolutionizing health-related research. One key issue for study quality is the accurate identification of patients with the condition of interest. Information in EMRs can be entered as structured codes or unstructured free text. The majority of research studies have used only coded parts of EMRs for case-detection, which may bias findings, miss cases, and reduce study quality. This review examines whether incorporating information from text into case-detection algorithms can improve research quality. Methods: A systematic search returned 9659 papers, 67 of which reported on the extraction of information from free text of EMRs with the stated purpose of detecting cases of a named clinical condition. Methods for extracting information from text and the technical accuracy of case-detection algorithms were reviewed. Results: Studies mainly used US hospital-based EMRs, and extracted information from text for 41 conditions using keyword searches, rule-based algorithms, and machine learning methods. There was no clear difference in case-detection algorithm accuracy between rule-based and machine learning methods of extraction. Inclusion of information from text resulted in a significant improvement in algorithm sensitivity and area under the receiver operating characteristic in comparison to codes alone (median sensitivity 78% (codes + text) vs 62% (codes), P = .03; median area under the receiver operating characteristic 95% (codes + text) vs 88% (codes), P = .025). Conclusions: Text in EMRs is accessible, especially with open source information extraction algorithms, and significantly improves case detection when combined with codes. More harmonization of reporting within EMR studies is needed, particularly standardized reporting of algorithm accuracy metrics like positive predictive value (precision) and sensitivity (recall)

Impacts of forests on children’s diet in rural areas across 27 developing countries

Micronutrient deficiency affects about a third of the world’s population. Children in developing countries are particularly vulnerable. Consequences include impaired cognitive and physical development and increased childhood morbidity and mortality. Recent studies suggest that forests help alleviate micronutrient deficiency by increasing dietary diversity. However, evidence is mostly based on weakly designed local case studies of limited relevance to global policies. Furthermore, impacts of forests on diet vary among communities, and understanding this variation can help target actions to enhance impact. We compile data on children’s diets in over 43,000 households across 27 developing countries to examine the impacts of forests on dietary diversity. We use empirical designs that are attentive to assumptions necessary for causal interpretations and that adequately account for confounding factors that could mask or mimic the impact. We find that high exposure to forests causes children to have at least 25% greater dietary diversity compared to lack of exposure, a result comparable to the impacts of some nutrition-sensitive agricultural programs. A closer look at a subset of African countries indicates that impacts are generally higher for less developed communities, but highest with certain access to markets, roads, and education. Our results also indicate that forests could help reduce vitamin A and iron deficiencies. Our study establishes the causal relationship between forests and diet and thus strengthens the evidence for integrating forest conservation and management into nutrition interventions. Our results also suggest that providing households some access to capital can increase the impact of forest-related interventions on nutrition

Deletion of the Coffin-Lowry Syndrome Gene Rsk2 in Mice is Associated With Impaired Spatial Learning and Reduced Control of Exploratory Behavior

Coffin-Lowry Syndrome (CLS) is an X-linked syndromic form of mental retardation associated with skeletal abnormalities. It is caused by mutations of the Rsk2 gene, which encodes a growth factor regulated kinase. Gene deletion studies in mice have shown an essential role for the Rsk2 gene in osteoblast differentiation and function, establishing a causal link between Rsk2 deficiency and skeletal abnormalities of CLS. Although analyses in mice have revealed prominent expression of Rsk2 in brain structures that are essential for learning and memory, evidence at the behavioral level for an involvement of Rsk2 in cognitive function is still lacking. Here, we have examined Rsk2-deficient mice in two extensive batteries of behavioral tests, which were conducted independently in two laboratories in Zurich (Switzerland) and Orsay (France). Despite the known reduction of bone mass, all parameters of motor function were normal, confirming the suitability of Rsk2-deficient mice for behavioral testing. Rsk2-deficient mice showed a mild impairment of spatial working memory, delayed acquisition of a spatial reference memory task and long-term spatial memory deficits. In contrast, associative and recognition memory, as well as the habituation of exploratory activity were normal. Our studies also revealed mild signs of disinhibition in exploratory activity, as well as a difficulty to adapt to new test environments, which likely contributed to the learning impairments displayed by Rsk2-deficient mice. The observed behavioral changes are in line with observations made in other mouse models of human mental retardation and support a role of Rsk2 in cognitive function

Baseline body mass index among children and adults undergoing allogeneic hematopoietic cell transplantation: clinical characteristics and outcomes

Obesity is an important public health problem that may influence the outcomes of hematopoietic cell transplantation (HCT). We studied 898 children and adults receiving first-time allogeneic hematopoietic stem cell transplants between 2004 and 2012. Pre-transplant body mass index (BMI) was classified as underweight, normal weight, overweight, or obese using the WHO classification, or age-adjusted BMI percentiles for children. The study population was predominantly Caucasian, and the median age was 51 years (5 months – 73 years). The cumulative 3-year incidence of non-relapse mortality (NRM) in underweight, normal weight, overweight, and obese patients was 20%, 19%, 20%, and 33%, respectively. Major causes of NRM were acute and chronic graft-versus-host disease (GVHD). The corresponding incidence of relapse was 30%, 41%, 37%, and 30%, respectively. Three-year overall survival was 59%, 48%, 47%, and 43%, respectively. Multivariate analysis showed that obesity was associated with higher NRM (HR 1.43, p=0.04), and lower relapse (HR 0.65, p=0.002). Pre-transplant plasma levels of ST2 and TNFR1 biomarkers were significantly higher in obese compared with normal weight patients (p=0.04 and p=0.05, respectively). The increase in NRM observed in obese patients was partially offset by lower incidence of relapse with no difference in overall survival

Rapid reduction of central line infections in hospitalized pediatric oncology patients through simple quality improvement methods

Background Pediatric hematology–oncology (PHO) patients are at significant risk for developing central line‐associated bloodstream infections (CLA‐BSIs) due to their prolonged dependence on such catheters. Effective strategies to eliminate these preventable infections are urgently needed. In this study, we investigated the implementation of bundled central line maintenance practices and their effect on hospital‐acquired CLA‐BSIs. Materials and Methods CLA‐BSI rates were analyzed within a single‐institution's PHO unit between January 2005 and June 2011. In May 2008, a multidisciplinary quality improvement team developed techniques to improve the PHO unit's safety culture and implemented the use of catheter maintenance practices tailored to PHO patients. Data analysis was performed using time‐series methods to evaluate the pre‐ and post‐intervention effect of the practice changes. Results The pre‐intervention CLA‐BSI incidence was 2.92 per 1,000‐patient days (PD) and coagulase‐negative Staphylococcus was the most prevalent pathogen (29%). In the post‐intervention period, the CLA‐BSI rate decreased substantially (45%) to 1.61 per 1,000‐PD ( P  < 0.004). Early on, blood and marrow transplant (BMT) patients had a threefold higher CLA‐BSI rate compared to non‐BMT patients ( P  < 0.033). With additional infection control countermeasures added to the bundled practices, BMT patients experienced a larger CLA‐BSI rate reduction such that BMT and non‐BMT CLA‐BSI rates were not significantly different post‐intervention. Conclusions By adopting and effectively implementing uniform maintenance catheter care practices, learning multidisciplinary teamwork, and promoting a culture of patient safety, the CLA‐BSI incidence in our study population was significantly reduced and maintained. Pediatr Blood Cancer 2013;60:262–269. © 2012 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95163/1/24187_ftp.pd

Correct quantum chemistry in a minimal basis from effective Hamiltonians

We describe how to create ab-initio effective Hamiltonians that qualitatively describe correct chemistry even when used with a minimal basis. The Hamiltonians are obtained by folding correlation down from a large parent basis into a small, or minimal, target basis, using the machinery of canonical transformations. We demonstrate the quality of these effective Hamiltonians to correctly capture a wide range of excited states in water, nitrogen, and ethylene, and to describe ground and excited state bond-breaking in nitrogen and the chromium dimer, all in small or minimal basis sets