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

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

The Need to Be Sure About CUREs: Discovery and Relevance as Critical Elements of CUREs for Nonmajors.

To the Editor, We read with interest the recently published paper from Ballen and colleagues (1), who indicated that discovery and relevance may be insignificant components of course-based undergraduate research experiences (CUREs) for nonbi-ology majors. We appreciate the authors for addressing this important topic because there is a need for empirical evidence to shed light on design features that are hypoth-esized to make CUREs distinctive as learning experiences (2). We write this letter in this spirit of collegial exchange and with the aim of promoting further investigation on how CURE instruction influences the learning and development of diverse students. In doing so, we also respectfully submit our opinion that the claims made by Ballen and colleagues overstate the evidence they present and potentially mislead readers in judging the importance of discovery and relevance to CUREs

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

Transition and Reflection in the Use of Health Information: The Case of Pediatric Bone Marrow Transplant Caregivers

ABSTRACT The impact of health information on caregivers is of increasing interest to HCI/CSCW in designing systems to support the social and emotional dimensions of managing health. Drawing on an interview study, as well as corroborating data including a multi-year ethnography, we detail the practices of caregivers (particularly parents) in a bone marrow transplant (BMT) center. We examine the interconnections between information and emotion work performed by caregivers through a liminal lens, highlighting the BMT experience as a time of transition and reflection in which caregivers must quickly adapt to the new social world of the hospital and learn to manage a wide range of patient needs. The transition from parent to &apos;caregiver&apos; is challenging, placing additional emotional burdens on the intensive information work for managing BMT. As a time of reflection, the BMT experience also provides an occasion for generative thinking and alternative approaches to health management. Our study findings call for health systems that reflect a design paradigm focused on &apos;transforming lives&apos; rather than &apos;transferring information.&apos; Autho

Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification

Abstract Background Numbers and numerical concepts appear frequently in free text clinical notes from electronic health records. Knowledge of the frequent lexical variations of these numerical concepts, and their accurate identification, is important for many information extraction tasks. This paper describes an analysis of the variation in how numbers and numerical concepts are represented in clinical notes. Methods We used an inverted index of approximately 100 million notes to obtain the frequency of various permutations of numbers and numerical concepts, including the use of Roman numerals, numbers spelled as English words, and invalid dates, among others. Overall, twelve types of lexical variants were analyzed. Results We found substantial variation in how these concepts were represented in the notes, including multiple data quality issues. We also demonstrate that not considering these variations could have substantial real-world implications for cohort identification tasks, with one case missing > 80% of potential patients. Conclusions Numbering within clinical notes can be variable, and not taking these variations into account could result in missing or inaccurate information for natural language processing and information retrieval tasks.https://deepblue.lib.umich.edu/bitstream/2027.42/148519/1/12911_2019_Article_784.pd

Complexities, variations, and errors of numbering within clinical notes: the potential impact on information extraction and cohort-identification

Background Numbers and numerical concepts appear frequently in free text clinical notes from electronic health records. Knowledge of the frequent lexical variations of these numerical concepts, and their accurate identification, is important for many information extraction tasks. This paper describes an analysis of the variation in how numbers and numerical concepts are represented in clinical notes. Methods We used an inverted index of approximately 100 million notes to obtain the frequency of various permutations of numbers and numerical concepts, including the use of Roman numerals, numbers spelled as English words, and invalid dates, among others. Overall, twelve types of lexical variants were analyzed. Results We found substantial variation in how these concepts were represented in the notes, including multiple data quality issues. We also demonstrate that not considering these variations could have substantial real-world implications for cohort identification tasks, with one case missing > 80% of potential patients. Conclusions Numbering within clinical notes can be variable, and not taking these variations into account could result in missing or inaccurate information for natural language processing and information retrieval tasks

The actin-bundling protein Fascin is overexpressed in inflammatory bowel disease and may be important in tissue repair

&lt;b&gt;Background&lt;/b&gt; Fascin is associated with increased cell motility in colorectal tumours but is absent from the normal colonic epithelium. We examined the expression of fascin in inflammatory bowel disease (IBD) and its location at regions undergoing restitution and regeneration. Tissue repair is essential for disease remission and we sought to determine the effects of therapeutic modalities on fascin expression and function using an in vitro model.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methods&lt;/b&gt; Immunohistochemistry was performed on colonic tissue from IBD patients to determine changes in fascin expression and distribution. A human colorectal epithelial cell line was treated with 5-aminosalicylate (a common treatment for IBD), or sodium butyrate to determine the effect on fascin expression and cell motility.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt; Fascin overexpression was observed in both ulcerative colitis and Crohn's colitis and expression correlated with disease severity. Immunoreactivity was more intense and widespread in Crohn's compared to ulcerative colitis. Interestingly, highly expressing foci were consistently observed at the edges of ulcers where flattened, motile epithelial cells are actively involved in restitution, and also in areas of mucosal regeneration. 5-aminosalicylate reduced fascin expression in colorectal epithelial cells and inhibited their motility. Conversely, sodium butyrate increased fascin expression and stimulated cell motility in the same cells.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt; Our data shows that fascin is overexpressed in inflammatory bowel disease and its location is indicative of a role in tissue repair. Our in vitro studies show that different therapeutic modalities may have converse effects on fascin expression and may have significant consequences for disease remission and the clinical management of IBD

Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching