An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing.

BACKGROUND AND OBJECTIVES: Next generation sequencing (NGS) has promising applications in transfusion medicine. Exome sequencing (ES) is increasingly used in the clinical setting, and blood group interpretation is an additional value that could be extracted from existing data sets. We provide the first release of an open-source software tailored for this purpose and describe its validation with three blood group systems. MATERIALS AND METHODS: The DTM-Tools algorithm was designed and used to analyse 1018 ES NGS files from the ClinSeq® cohort. Predictions were correlated with serology for 5 antigens in a subset of 108 blood samples. Discrepancies were investigated with alternative phenotyping and genotyping methods, including a long-read NGS platform. RESULTS: Of 116 genomic variants queried, those corresponding to 18 known KEL, FY and JK alleles were identified in this cohort. 596 additional exonic variants were identified KEL, ACKR1 and SLC14A1, including 58 predicted frameshifts. Software predictions were validated by serology in 108 participants; one case in the FY blood group and three cases in the JK blood group were discrepant. Investigation revealed that these discrepancies resulted from (1) clerical error, (2) serologic failure to detect weak antigenic expression and (3) a frameshift variant absent in blood group databases. CONCLUSION: DTM-Tools can be employed for rapid Kell, Duffy and Kidd blood group antigen prediction from existing ES data sets; for discrepancies detected in the validation data set, software predictions proved accurate. DTM-Tools is open-source and in continuous development.

Improving teamwork and communication in trauma care through in situ simulations.

OBJECTIVES: Teamwork and communication often play a role in adverse clinical events. Due to the multidisciplinary and time-sensitive nature of trauma care, the effects of teamwork and communication can be especially pronounced in the treatment of the acutely injured patient. Our hypothesis was that an in situ trauma simulation (ISTS) program (simulating traumas in the trauma bay with all members of the trauma team) could be implemented in an emergency department (ED) and that this would improve teamwork and communication measured in the clinical setting. METHODS: This was an observational study of the effect of an ISTS program on teamwork and communication during trauma care. The authors observed a convenience sample of 39 trauma activations. Cases were selected by their presenting to the resuscitation bay of a Level I trauma center between 09:00 and 16:00, Monday through Thursday, during the study period. Teamwork and communication were measured using the previously validated Clinical Teamwork Scale (CTS). The observers were three Trauma Nursing Core Course certified RNs trained on the CTS by observing simulated and actual trauma cases and following each of these cases with a discussion of appropriate CTS scores with two certified Advanced Trauma Life Support instructors/emergency physicians. Cases observed for measurement were scored in four phases: 1) preintervention phase (baseline); 2) didactic-only intervention, the phase following a lecture series on teamwork and communication in trauma care; 3) ISTS phase, real trauma cases scored during period when weekly ISTSs were performed; and 4) potential decay phase, observations following the discontinuation of the ISTSs. Multirater agreement was assessed with Krippendorf's alpha coefficient; agreement was excellent (mean agreement = 0.92). Nonparametric procedures (Kruskal-Wallis) were used to test the hypothesis that the scores observed during the various phases were different and to compare each individual phase to baseline scores. RESULTS: The ISTS program was implemented and achieved regular participation of all components of our trauma team. Data were collected on 39 cases. The scores for 11 of 14 measures improved from the baseline to the didactic phase, and the mean and median scores of all CTS component measures were greatest during the ISTS phase. When each phase was compared to baseline scores, using the baseline as a control, there were no significant differences seen during the didactic or the decay phases, but 12 of the 14 measures showed significant improvements from the baseline to the simulation phase. However, when the Kruskal-Wallis test was used to test for differences across all phases, only overall communication showed a significant difference. During the potential decay phase, the scores for every measure returned to baseline phase values. CONCLUSIONS: This study shows that an ISTS program can be implemented with participation from all members of a multidisciplinary trauma team in the ED of a Level I trauma center. While teamwork and communication in the clinical setting were improved during the ISTS program, this effect was not sustained after ISTS were stopped.

Factors that influence medical student selection of an emergency medicine residency program: implications for training programs.

OBJECTIVES: An understanding of student decision-making when selecting an emergency medicine (EM) training program is essential for program directors as they enter interview season. To build upon preexisting knowledge, a survey was created to identify and prioritize the factors influencing candidate decision-making of U.S. medical graduates. METHODS: This was a cross-sectional, multi-institutional study that anonymously surveyed U.S. allopathic applicants to EM training programs. It took place in the 3-week period between the 2011 National Residency Matching Program (NRMP) rank list submission deadline and the announcement of match results. RESULTS: Of 1,525 invitations to participate, 870 candidates (57%) completed the survey. Overall, 96% of respondents stated that both geographic location and individual program characteristics were important to decision-making, with approximately equal numbers favoring location when compared to those who favored program characteristics. The most important factors in this regard were preference for a particular geographic location (74.9%, 95% confidence interval [CI] = 72% to 78%) and to be close to spouse, significant other, or family (59.7%, 95% CI = 56% to 63%). Factors pertaining to geographic location tend to be out of the control of the program leadership. The most important program factors include the interview experience (48.9%, 95% CI = 46% to 52%), personal experience with the residents (48.5%, 95% CI = 45% to 52%), and academic reputation (44.9%, 95% CI = 42% to 48%). Unlike location, individual program factors are often either directly or somewhat under the control of the program leadership. Several other factors were ranked as the most important factor a disproportionate number of times, including a rotation in that emergency department (ED), orientation (academic vs. community), and duration of training (3-year vs. 4-year programs). For a subset of applicants, these factors had particular importance in overall decision-making. CONCLUSIONS: The vast majority of applicants to EM residency programs employed a balance of geographic location factors with individual program factors in selecting a residency program. Specific program characteristics represent the greatest opportunity to maximize the success of the immediate interview experience/season, while others provide potential for strategic planning over time. A working knowledge of these results empowers program directors to make informed decisions while providing an appreciation for the limitations in attracting applicants.

2,3-Dihydrowithaferin A-3beta-O-sulfate, a new potential prodrug of withaferin A from aeroponically grown Withania somnifera.

Preparations of the roots of the medicinal plant Withania somnifera (L.) Dunal commonly called ashwagandha have been used for millennia in the Ayurvedic medical tradition of India as a general tonic to relieve stress and enhance health, especially in the elderly. In modern times, ashwagandha has been shown to possess intriguing antiangiogenic and anticancer activity, largely attributable to the presence of the steroidal lactone withaferin A as the major constituent. When cultured using the aeroponic technique, however, this plant was found to produce a new natural product, 2,3-dihydrowithaferin A-3beta-O-sulfate (1), as the predominant constituent of methanolic extracts prepared from aerial tissues. The characteristic bioactivities exhibited by 1 including inhibition of cancer cell proliferation/survival, disruption of cytoskeletal organization and induction of the cellular heat-shock response paralleled those displayed by withaferin A (2). The delayed onset of action and reduced potency of 1 in cell culture along with previous observations demonstrating the requirement of the 2(3)-double bond in withanolides for bioactivity suggested that 1 might be converted to 2 in cell culture media and this was confirmed by HPLC analysis. The abundant yield of 1 from aeroponically cultivated plants, its good aqueous solubility and spontaneous conversion to 2 under cell culture conditions, suggest that 1 could prove useful as a readily formulated prodrug of withaferin A that merits further evaluation in animal models.

Evaluation of denoising algorithms for biological electron tomography.

Tomograms of biological specimens derived using transmission electron microscopy can be intrinsically noisy due to the use of low electron doses, the presence of a "missing wedge" in most data collection schemes, and inaccuracies arising during 3D volume reconstruction. Before tomograms can be interpreted reliably, for example, by 3D segmentation, it is essential that the data be suitably denoised using procedures that can be individually optimized for specific data sets. Here, we implement a systematic procedure to compare various nonlinear denoising techniques on tomograms recorded at room temperature and at cryogenic temperatures, and establish quantitative criteria to select a denoising approach that is most relevant for a given tomogram. We demonstrate that using an appropriate denoising algorithm facilitates robust segmentation of tomograms of HIV-infected macrophages and Bdellovibrio bacteria obtained from specimens at room and cryogenic temperatures, respectively. We validate this strategy of automated segmentation of optimally denoised tomograms by comparing its performance with manual extraction of key features from the same tomograms.

Sorbifolivaltrates A-D, diene valepotriates from Valeriana sorbifolia(1).

Four new diene valepotriates, sorbifolivaltrates A-D ( 1- 4), and the known compounds isovaltrate ( 5), valtrate ( 6), seneciovaltrate ( 7), valtrate hydrine B3 ( 8), and valtrate hydrine B7 ( 9), have been isolated by bioassay-guided fractionation of the cytotoxic hexanes and methyl ethyl ketone crude extracts of the aerial parts of Valeriana sorbifolia occurring in the Sonoran desert. The structures of 1- 4 were determined on the basis of their high-resolution mass spectrometric and NMR spectroscopic data. All compounds exhibited weak to moderate cytotoxicity against the human metastatic prostate cancer cell line, PC-3M.

Frequency-coded quantum key distribution.

We report an intrinsically stable quantum key distribution scheme based on genuine frequency-coded quantum states. The qubits are efficiently processed without fiber interferometers by fully exploiting the nonlinear interaction occurring in electro-optic phase modulators. The system requires only integrated off-the-shelf devices and could be used with a true single-photon source. Preliminary experiments have been performed with weak laser pulses and have demonstrated the feasibility of this new setup.

Implementation and evaluation of a training program for the management of sexual assault in the emergency department.

STUDY OBJECTIVE: Sexual assault nurse examiner (SANE) programs have improved the quality of care for sexual assault victims. An adverse effect of these programs is reduced resident clinical exposure to victims of sexual assault. The objectives of this project are to determine the baseline level of resident competence in knowledge and management of sexual assault and to demonstrate the effectiveness of training in developing resident competence. METHODS: The study included 27 emergency medicine residents at an urban academic center with an active SANE program. The design included pretest, intervention, and retest at 6 months. The intervention included 8 hours of lecture, role play, and skills laboratories. Objectives were based on SANE standards. The 4 assessments were a written knowledge test, evidence collection on mannequin, standardized patient interviews, and a written emergency department note. Data were compared with paired t tests. RESULTS: Twenty-three (85%) residents completed the study. Preintervention, residents scored 56% on the written knowledge test, 63% on evidence collection, 71% on standardized patient interviews, and 66% on the written note. Residents showed significant postintervention improvements in written knowledge (improvement 24%; 95% confidence interval [CI] 20% to 27%) and evidence collection (improvement 18%; 95% CI 12% to 24%). Performance on standardized patient-based communication skills did not change after the intervention. Resident posttest scores were similar to those of SANE providers. CONCLUSION: Emergency medicine residents training in an urban center with an active SANE program had limited knowledge and skills in the treatment of victims of sexual assault. Our multimodal educational intervention increased residents' knowledge and evidence collection skills to levels equivalent to that of experienced providers in a SANE program.

Zinagrandinolides A-C, cytotoxic delta-elemanolide-type sesquiterpene lactones from Zinnia grandiflora.

Three new delta-elemanolide-type sesquiterpene lactones, zinagrandinolides A-C (1-3), and the known delta-elemanolide 4 have been isolated by a bioassay-guided fractionation of a cytotoxic hexane extract of the aerial parts of Zinnia grandiflora. The structures of 1-3 were determined on the basis of high-resolution mass and NMR data. All compounds exhibited strong cytotoxicity against the cancer cell lines NCI-H460, MCF-7, SF-268, and MIA Pa Ca-2 and the normal human fibroblast cell type WI-38, but none showed significant selectivity.

Metabolic profiling and phylogenetic analysis of medicinal Zingiber species: Tools for authentication of ginger (Zingiber officinale Rosc).

Phylogenetic analysis and metabolic profiling were used to investigate the diversity of plant material within the ginger species and between ginger and closely related species in the genus Zingiber (Zingiberaceae). In addition, anti-inflammatory data were obtained for the investigated species. Phylogenetic analysis demonstrated that all Zingiber officinale samples from different geographical origins were genetically indistinguishable. In contrast, other Zingiber species were significantly divergent, allowing all species to be clearly distinguished using this analysis. In the metabolic profiling analysis, the Z. officinale samples derived from different origins showed no qualitative differences in major volatile compounds, although they did show some significant quantitative differences in non-volatile composition, particularly regarding the content of [6]-, [8]-, and [10]-gingerols, the most active anti-inflammatory components in this species. The differences in gingerol content were verified by HPLC. The metabolic profiles of other Zingiber species were very different, both qualitatively and quantitatively, when compared to Z. officinale and to each other. Comparative DNA sequence/chemotaxonomic phylogenetic trees showed that the chemical characters of the investigated species were able to generate essentially the same phylogenetic relationships as the DNA sequences. This supports the contention that chemical characters can be used effectively to identify relationships between plant species. Anti-inflammatory in vitro assays to evaluate the ability of all extracts from the Zingiber species examined to inhibit LPS-induced PGE(2) and TNF-alpha production suggested that bioactivity may not be easily predicted by either phylogenetic analysis or gross metabolic profiling. Therefore, identification and quantification of the actual bioactive compounds are required to guarantee the bioactivity of a particular Zingiber sample even after performing authentication by molecular and/or chemical markers.

The status of human simulation training in emergency medicine residency programs.

INTRODUCTION: : The objective of this study was to describe the availability and current use of high-fidelity mannequin-based simulation (HFMB) in emergency medicine (EM) training programs. METHODS: : A 12-item survey instrument was used to collect data on the status of human simulation training at the 126 approved EM residencies and the 30 accredited osteopathic EM residencies. RESULTS: : In all, 114 out of 156 programs completed the survey for a response rate of 73%. There are 54 (47%) EM training programs with HFMB simulators at their institution, 38 (33%) EM training programs with access to these HFMB simulators, and 33 (29%) EM training programs that have EM residents use HFMB simulators. The Department of Anesthesia manages the HFMB simulator at 19 (17%) institutions. EM manages the HFMB simulator at nine (8%) institutions. EM residents are using HFMB simulation every 1-2 weeks at three (8%) programs, every 1-4 months at 16 (42%) programs, yearly at nine (24%) programs, and not regularly at 10 (26%) programs. The simulation curriculum is described as "no formal curriculum" or "initial development" in 60% of programs. CONCLUSION: : HFMB simulation technology has not been completely adopted by EM training programs even when it is available. Most EM training programs are using HFMB simulation less often than every month and curriculum development in EM training is still in the early phases.

Impact of the Liaison Committee on Medical Education requirements for emergency medicine education at U.S. schools of medicine.

The Liaison Committee on Medical Education (LCME) accredits complete and independent medical education programs leading to the MD degree. The LCME standards for accreditation are described in the online document "Functions and Structure of a Medical School." There are ongoing minor and major changes to these standards. This article examines how the newest LCME requirements may affect emergency medicine (EM) rotations. The descriptions focus on 1) how the LCME requirements affect EM educational activities and 2) how the department of EM can help the school of medicine meet the LCME requirements. The recommendations focus on the general areas of the instructional setting, components of the educational program, resources for medical students, and faculty development. The department of EM can provide the students at the school of medicine with a number of key experiences and opportunities through its educational offerings and graduate medical education programs that will help satisfy the LCME standards. The new LCME standards will also have a significant impact on the way EM educators/clerkship directors develop curricula, assess students, provide feedback, and develop their own faculty/residents as teachers. The leadership of EM should recognize their increasingly important role within the school of medicine and be sensitive to additional requirements for faculty development and scholarship.

Faculty development.

As emergency medicine faculty, we are called upon to be skilled in a great number of different areas. Residency training prepares us to be knowledgeable clinicians, skillful at procedures, good communicators, and effective at multitasking. Rarely, however, does it prepare us as educators or in the nuances of career advancement in an academic environment. Faculty development is a term used to describe both our growth as clinician-educators and navigation of the tenure and promotion process. An important role of medical student educators is to assist in preparing themselves and the faculty to be good teachers. In addition, we all hope to have successful careers as clinician-educators. The goal of this report is 2-fold: to provide a guide for faculty to advance their skills as educators and to help teaching faculty to advance their academic career. The first section of this report presents an approach to becoming a skilled educator, and the second section focuses on career development as an educator in an academic setting.

Frequency, severity, and costs of adverse reactions following mass treatment for lymphatic filariasis using diethylcarbamazine and albendazole in Leogane, Haiti, 2000.

In October 2000, 71,187 persons were treated for lymphatic filariasis using albendazole and diethylcarbamazine (DEC) or DEC alone in Leogane, Haiti. We documented the frequency of adverse reactions, severity and cost of treatment. Adverse reactions were classified as minor, moderate, or severe. Overall, 24% (17,421) of the treated persons reported one or more adverse reactions. There were 15,916 (91%) minor and 1502 (9%) moderate adverse reaction reports. Men outnumbered women 2:1 in reporting moderate problems. Three patients, representing roughly one in 25,000 persons treated, were hospitalized with severe adverse reactions judged to be treatment-associated by physician review. The cost per person treated for adverse reactions was more than twice the cost per person treated for lymphatic filariasis (dollar 1.60 versus dollar 0.71). Severe adverse reactions to lymphatic filariasis treatment using DEC with or without albendazole are uncommon. Minor and moderate reactions are more commonly reported and their management represents a challenge to lymphatic filariasis elimination programs.

Comparison of methods for estimating drug coverage for filariasis elimination, Leogane Commune, Haiti.

In the global effort to eliminate lymphatic filariasis, annual mass treatments are conducted with diethylcarbamazine (DEC) or ivermectin, combined with albendazole. The success of this strategy depends on achieving high levels of drug coverage, which reduces the number of persons with circulating microfilariae so that transmission of the parasite is interrupted. Because resources are often limited, a simple, inexpensive, and reliable method to estimate drug coverage is needed. During the period December 2000 to February 2001, three methods were used to assess drug coverage in Leogane Commune, Haiti: a probability survey using a cluster sample design (n = 1421 persons); a distribution-point survey based on a convenience sample of houses near the distribution points (n = 4341 persons); and a survey based on a convenience sample of primary schools (n = 5036 children). The coverage estimations were 71.3% (95% CI 66.7-75.9), 73.6% (95% CI 70.1-77.0), and 77.8% (95% CI 73.5-82.1), respectively. Survey costs for the probability, distribution point, and school surveys were US$2217, US$979, and US$312, respectively. The 2 convenience sampling methods provided point estimates of drug coverage that were similar to those of the probability survey. These methods may have a role for monitoring drug treatment coverage between less frequent, but more costly, probability sample surveys.

Human simulation in emergency medicine training: a model curriculum.

The authors propose a three-year curriculum for emergency medicine residents using human simulation both to teach and to assess the Accreditation Council for Graduate Medical Education (ACGME) core competencies. Human simulation refers to a variety of technologies that allow residents to work through realistic patient problems so as to allow them to make mistakes, learn, and be evaluated without exposing a real patient to risk. This curriculum incorporates 15 simulated patient encounters with gradually increasing difficulty, complexity, and realism into a three-year emergency medicine residency. The core competencies are incorporated into each case, focusing on the areas of patient care, interpersonal skills and communication, professionalism, and practice based learning and improvement. Because of the limitations of current assessment tools, the demonstration of resident competence is used only for formative evaluations. Limitations of this proposal and difficulties in implementation are discussed, along with a description of the organization and initiation of the simulation program.