Post-Darwinian fish classifications: theories and methodologies of Günther, Cope, and Gill.

We analyze the relationship between evolutionary theory and classification of higher taxa in the work of three ichthyologists: Albert C.L.G. Günther (1830-1914), Edward Drinker Cope (1840-1897), and Theodore Gill (1837-1914). The progress of ichthyology in the early years following the Origin has received little attention from historians, and offers an opportunity to further evaluate the extent to which evolutionary theorizing influenced published views on systematic methodology. These three ichthyologists held radically different theoretical views. The apparent commensurability of claims about relationships among groups of fishes belies differences in what the relationships actually were supposed to be. As well, interpreting classification as genealogical did not lead to agreement about taxonomic methodology; instead, applying evolutionary theory raised new axes of disagreement.

Round goby (Neogobius melanostomus) δ13C/δ15N discrimination values and comparisons of diets from gut content and stable isotopes in Oneida Lake.

Gut content analyses have found that round gobies (Neogobius melanostomus) are highly dependent on dreissenid mussels but stable isotope analysis has often suggested that the dreissenid contribution is lower. However, estimation of dietary contributions with stable isotopes relies on accurate discrimination factors (fractionation factors). To test if discrimination values commonly used in aquatic food web studies are suitable for round gobies, we collected round gobies from Oneida Lake, raised them for 63 days under four different diets (Chironomus plumosus, Mytilus chilensis, Dreissenia spp., Euphausia superba) and measured the change in white muscle δ13C and δ15N. Gobies were also collected throughout Oneida Lake for gut content and stable isotope analysis. Diets changed as round gobies grew, with small round gobies (17-42mm) feeding mostly on cladocera and chironomids, intermediate sized gobies (43-94mm) transitioning from chironomid to dreissenid consumption, and larger gobies (95-120mm) predominantly consuming dreissenids, similar to findings in other studies. Discrimination factors were obtained by fitting a commonly used asymptotic regression equation describing changes in fish δ13C and δ15N as a function of time and diet stable isotope ratios. The discrimination factor determined for δ13C (-0.4‰ ± 0.32, SE) was lower than the "standard" value of 0.4‰, while that of δ15N (4.0‰ ± 0.32, SE) was higher than the standard value of 3.4‰. Turnover rates for both δ13C and δ15N were estimated as 0.02 ‰*day-1. The use of experimentally determined discrimination factors rather than "standard" values resulted in model estimates that agree more closely with the observed increasing importance of dreissenids in gut content of larger gobies. Our results suggest that the importance of dreissenid mussels inferred from stable isotope studies may be underestimated when using standard isotopic discrimination values.

Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens).

Modern pyrosequencing has the potential to uncover many interesting aspects of genome evolution, even in lineages where genomic resources are scarce. In particular, 454 pyrosequencing of nonmodel species has been used to characterize expressed sequence tags, xenobiotics, gene ontologies, and relative levels of gene expression. Herein, we use pyrosequencing to study the evolution of genes expressed in the gonads of a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454 pyrosequencing of transcribed genes, we produced more than 125 MB of sequence data from 473,577 high-quality sequencing reads. Sequences that passed stringent quality control thresholds were assembled into 12,791 male contigs and 32,629 female contigs. Average depth of coverage was 4.2 x for the male assembly and 5.5x for the female assembly. Analytical rarefaction indicates that our assemblies include most of the genes expressed in lake sturgeon gonads. Over 86,700 sequencing reads were assigned gene ontologies, many to general housekeeping genes like protein, RNA, and ion binding genes. We searched specifically for sex determining genes and documented significant sex differences in the expression of two genes involved in animal sex determination, DMRT1 and TRA-1. DMRT1 is the master sex determining gene in birds and in medaka (Oryzias latipes) whereas TRA-1 helps direct sexual differentiation in nematodes. We also searched the lake sturgeon assembly for evidence of xenobiotic organisms that may exist as endosymbionts. Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome.

Effects of climate and land-use changes on fish catches across lakes at a global scale.

Globally, our knowledge on lake fisheries is still limited despite their importance to food security and livelihoods. Here we show that fish catches can respond either positively or negatively to climate and land-use changes, by analyzing time-series data (1970-2014) for 31 lakes across five continents. We find that effects of a climate or land-use driver (e.g., air temperature) on lake environment could be relatively consistent in directions, but consequential changes in a lake-environmental factor (e.g., water temperature) could result in either increases or decreases in fish catch in a given lake. A subsequent correlation analysis indicates that reductions in fish catch was less likely to occur in response to potential climate and land-use changes if a lake is located in a region with greater access to clean water. This finding suggests that adequate investments for water-quality protection and water-use efficiency can provide additional benefits to lake fisheries and food security.

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery.

BACKGROUND: Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads. RESULTS: Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (approximately 19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from > 50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type. CONCLUSION: Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.

The Explanatory Visualization Framework: An Active Learning Framework for Teaching Creative Computing Using Explanatory Visualizations.

Visualizations are nowadays appearing in popular media and are used everyday in the workplace. This democratisation of visualization challenges educators to develop effective learning strategies, in order to train the next generation of creative visualization specialists. There is high demand for skilled individuals who can analyse a problem, consider alternative designs, develop new visualizations, and be creative and innovative. Our three-stage framework, leads the learner through a series of tasks, each designed to develop different skills necessary for coming up with creative, innovative, effective, and purposeful visualizations. For that, we get the learners to create an explanatory visualization of an algorithm of their choice. By making an algorithm choice, and by following an active-learning and project-based strategy, the learners take ownership of a particular visualization challenge. They become enthusiastic to develop good results and learn different creative skills on their learning journey.

Educating Physicians for Rural America: Validating Successes and Identifying Remaining Challenges With the Rural Medical Scholars Program.

PURPOSE: To evaluate the Rural Medical Scholars (RMS) Program's effectiveness to produce rural physicians for Alabama. METHODS: A nonrandomized intervention study compared RMS (1997-2002) with control groups in usual medical education (1991-2002) at the University of Alabama School of Medicine's main and regional campuses. Participants were RMS and others admitted to regular medical education, and the intervention was the RMS Program. Measures assessed the percentage of graduates practicing in rural areas. Odds ratios compared effectiveness of producing rural Alabama physicians. FINDINGS: The RMS Program (N = 54), regional campuses (N = 182), and main campus (N = 649) produced 48.1% (odds ratio 6.4, P < .001), 23.8% (odds ratio 2.5, P < .001), and 11.2% (odds ratio 1.0) rural physicians, respectively. CONCLUSIONS: The RMS Program, contrasted to other local programs of medical education, was effective in producing rural physicians. These results were comparable to benchmark programs in the Northeast and Midwest USA on which the RMS Program was modeled, justifying the assumption that model programs can be replicated in different regions. However, this positive effect was not shared by a disparate rural minority population, suggesting that models for rural medical education must be adjusted to meet the challenge of such communities for physicians.

LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes.

Understanding the factors that affect water quality and the ecological services provided by freshwater ecosystems is an urgent global environmental issue. Predicting how water quality will respond to global changes not only requires water quality data, but also information about the ecological context of individual water bodies across broad spatial extents. Because lake water quality is usually sampled in limited geographic regions, often for limited time periods, assessing the environmental controls of water quality requires compilation of many data sets across broad regions and across time into an integrated database. LAGOS-NE accomplishes this goal for lakes in the northeastern-most 17 US states.LAGOS-NE contains data for 51 101 lakes and reservoirs larger than 4 ha in 17 lake-rich US states. The database includes 3 data modules for: lake location and physical characteristics for all lakes; ecological context (i.e., the land use, geologic, climatic, and hydrologic setting of lakes) for all lakes; and in situ measurements of lake water quality for a subset of the lakes from the past 3 decades for approximately 2600-12 000 lakes depending on the variable. The database contains approximately 150 000 measures of total phosphorus, 200 000 measures of chlorophyll, and 900 000 measures of Secchi depth. The water quality data were compiled from 87 lake water quality data sets from federal, state, tribal, and non-profit agencies, university researchers, and citizen scientists. This database is one of the largest and most comprehensive databases of its type because it includes both in situ measurements and ecological context data. Because ecological context can be used to study a variety of other questions about lakes, streams, and wetlands, this database can also be used as the foundation for other studies of freshwaters at broad spatial and ecological scales.

Saturated Branched Chain, Normal Odd-Carbon-Numbered, and n-3 (Omega-3) Polyunsaturated Fatty Acids in Freshwater Fish in the Northeastern United States.

The fatty acid profiles of wild freshwater fish are poorly characterized as a human food source for several classes of fatty acids, particularly for branched chain fatty acids (BCFA), a major bioactive dietary component known to enter the US food supply primarily via dairy and beef fat. We evaluated the fatty acid content of 27 freshwater fish species captured in the northeastern US with emphasis on the BCFA and bioactive polyunsaturated fatty acids (PUFA) most associated with fish, specifically n-3 (omega-3) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Mean BCFA content across all species was 1.0 ± 0.5% (mean ± SD) of total fatty acids in edible muscle, with rainbow smelt (Osmerus mordax) and pumpkinseed (Lepomis gibbosus) the highest at >2% BCFA. In comparison, EPA + DHA constituted 28% ± 7% of total fatty acids. Across all fish species, the major BCFA were iso-15:0, anteiso-15:0, iso-16:0, iso-17:0 and anteiso-17:0. Fish skin had significantly higher BCFA content than muscle tissues, at 1.8% ± 0.7%, but lower EPA and DHA. Total BCFA in fish skins was positively related with that in muscle (r2 = 0.6). The straight chain saturates n-15:0 and n-17:0 which have been identified previously as markers for dairy consumption were relatively high with means of 0.4% and 0.6%, respectively, and may be an underappreciated marker for seafood intake. Consuming a standardized portion, 70 g (2.5 oz), of wild freshwater fish contributes only small amounts of BCFA, 2.5-24.2 mg, to the American diet, while it adds surprisingly high amounts of EPA + DHA (107 mg to 558 mg).

Do factors that are important during obstetrics and gynecology residency program selection differ by applicant gender?

OBJECTIVE: The purpose of this study was to examine the relationship between applicant gender and factors that influence obstetrics and gynecology residency program selection. STUDY DESIGN: A national survey was conducted of graduates of US allopathic medical schools who were registered with the Electronic Residency Application Service for the year 2003 and who indicated that obstetrics and gynecology was their primary specialty choice. The selection prevalence of 20 possible influential factors was analyzed by gender. RESULTS: Our study cohort consisted of 450 eligible respondents, 80.4% of whom were female. There were no significant differences by gender in regards to applicant age, race, marital status, number of dependents, or geographic region of medical school. Overall, the 4 factors with the highest selection prevalence in both gender groups were all related to workplace environment. Compared with male respondents, female respondents were more likely to consider how well the current residents seemed to work together (99.2% vs 94.3%; P = .002) and the amount of conference/didactic teaching (80.4% vs 68.2%; P = .01). Male respondents were more likely to consider the quality of the hospital facility (92% vs 82%; P = .02), salary (28.4% vs 17.1%; P = .02), and supplemental income (moonlighting) opportunities (18.2% vs 8.6%; P = .008), as compared with female respondents. CONCLUSION: Significant differences in gender-associated preferences that are related to obstetrics and gynecology residency program selection exist and include both curricular and financial factors.

Integration of gross anatomy in an organ system-based medical curriculum: strategies and challenges.

The University of Alabama School of Medicine (UASOM) instituted a fully integrated, organ system-based preclinical curriculum in 2007. Gross anatomy and embryology were integrated with other basic science disciplines throughout the first two years of undergraduate medical education. Here we describe the methods of instruction and integration of gross anatomy and embryology in this curriculum as well as challenges faced along the way. Gross anatomy and embryology are taught through a combination of didactic lectures, team-based learning activities, and cadaveric dissection laboratories. Vertical integration occurs through third- and fourth-year anatomy and embryology elective courses. Radiology is integrated with anatomy instruction through self-study modules and hands-on ultrasound sessions. Our model of anatomy instruction is time efficient, clinically relevant, and effective as demonstrated by student performance on the United States Medical Licensing Examination(®) (USMLE(®) ) Step 1 examination. We recommend that medical schools considering full integration of gross anatomy and embryology (1) carefully consider the sequencing of organ system modules, (2) be willing to sacrifice anatomical detail for clinical application, (3) provide additional electives to third- and fourth-year students, and (4) integrate radiology with anatomical education.

The influence of quality-of-life, academic, and workplace factors on residency program selection.

PURPOSE: To examine the influence of quality-of-life, academic, and workplace factors on residency program selection and determine whether factors are valued differently by applicants choosing surgical (SP) versus nonsurgical (NSP) programs. METHOD: All 16,183 graduates of U.S. allopathic medical schools registered with the Electronic Residency Application Service were surveyed during the 2003 residency match. A total of 7,183 (44%) applicants responded. Selection prevalence from among 20 possible influential factors and the relative importance assigned to those chosen factors were analyzed. RESULTS: The most common factors influencing residency program selection were how much the residency program seemed to care about its trainees (98%), how satisfied the current residents are with their program (98%), how well the applicant thought he or she would fit into the program (97%), the geographic location of the residency (95%), and how well the current residents seem to work with each other (94%). Applicants to NSP were more likely to consider geographic location (p <.001), emphasis on interacting with medical students (p =.019), amount of clinical support services (p <.001), frequency of on-call duty (p =.047), types of benefits (p <.001), salary (p =.023), and supplemental income (moonlighting) opportunities (p <.001) than were applicants to SP. SP applicants were more likely to consider emphasis on research in the residency curriculum (p <.001) and how well the current residents worked together (p <.001) than were NSP applicants. CONCLUSIONS: Of factors that influence residency program selection, those related to the characteristics of the workplace environment and geography are the most important. Minimal differences exist between applicants selecting surgical and nonsurgical specialties regarding academic and quality-of-life issues.

Premedical education: the contribution of small local colleges.

CONTEXT: Small local colleges may be sources of medical students with the gender, ethnicity, and background that promote identity with and empathy for underserved populations. PURPOSE: This study examined the impact of attendance at these premedical colleges on outcomes of medical education. METHODS: Data for 2508 matriculates to the University of Alabama School of Medicine, a state-supported medical school, were examined according to premedical colleges attended. FINDINGS: Medical students who had graduated from small local colleges were more diverse in gender, race, and rural background than other students. They had slightly lower academic performance in medical school, were more likely to drop out (10.6% versus 5.3% overall), and were more likely to locate in rural areas of the host state. CONCLUSIONS: Small local colleges may be rich sources of student diversity and medical students who choose rural practice, outcomes that are gained at a cost in terms of drop-out rate. Compared with other students, minor differences in performance and larger differences in the drop-out rate raise the question of cultural context and social support during medical school as points for intervention.

The rural medical scholars program study: data to inform rural health policy.

INTRODUCTION: medical education to produce rural physicians hinges on the characteristics of students, educational programs, and rural experiences. Family physicians are key components of rural medicine. This study tested the effectiveness of multiple, combined strategies of the Rural Medical Scholars Program to produce family medicine residents. METHODS: we compared the relative effectiveness of the Rural Medical Scholars Program, family medicine-oriented branch campuses, and a traditional urban campus to produce family medicine residents using a prospective quasi-experimental design. Logistic regression was used to account for covariates. RESULTS: the relative effectiveness of 3 educational modalities to produce family medicine residents was examined: Rural Medical Scholars Program (44.0%; odds ratio [OR], 15.6), family medicine-oriented branch campuses (18.9%; OR, 5.8), and a traditional urban campus (3.9%; OR, 1). These differences were significant (P < .05) after controlling for sex, race, Medical College Admission Test scores, and graduation rate. CONCLUSIONS: the findings are consistent with the literature, which recommends multiple strategy interventions to produce rural physicians (e.g., admit rural students who have an interest in family medicine, use family medicine faculty, and provide rural experiences). Further study will determine whether rural practice follows training in family medicine among Rural Medical Scholars.

Rural health leaders pipeline, 1990-2005: case study of a second-generation rural medical education program.

A pipeline model has been suggested to increase the rural physician supply. This study is an institutional case report used to describe the context, development, and in-house evaluation of the University of Alabama Rural Health Leaders Pipeline, 1990-2005. This program was developed at a University of Alabama School of Medicine branch campus to target rural students at multiple levels, elementary schools through residency, and includes a minority focus. Requirements to enter the medical program include living 8 years in rural Alabama, meeting admission requirements, and affinity for rural lifestyles. Twenty-six percent of 316 high school participants, all 40 students in the minority-focused college program, and 3% of 90 medical program students were African American. The program includes (1) puppet shows in elementary schools depicting different health professions, (2) Rural Health Scholars Program for 11th-grade students, (3) Minority Rural Health Pipeline Program for college students, (4) Rural Medical Scholars Program, a 5-year track of study in rural community health and medicine, and (5) assured admission to family medicine residency. Outcomes studied in this case report included medical school performance, graduation rate, selection of family medicine specialty, and rural practice location. Medical scholars were anticipated to experience academic difficulty, select family medicine specialty, and locate in rural practice more often than peers. Compared to peers, medical scholars showed lower scores on preclinical courses and USMLE steps 1 and 2, reflective of their lower MCAT and GPA scores, but had (1) similar graduation rates (95% vs peers 84%), (2) higher family medicine selection rate (47% vs Huntsville 27% vs Tuscaloosa 12% vs Birmingham 4% [OR compared to Birmingham 22.7, 95% CI 10.5-49.4]), and (3) higher rural practice rate (67% vs peers 14% vs national group 9%) in the first RMSP classes. Based on these important outcomes being better than or equal to the traditional student cohorts, the institution concluded that the Rural Health Leaders Pipeline demonstrates successful use of the rural pipeline model.

Assessing the impact of a comprehensive sexually transmitted disease curriculum on learning outcomes.

OBJECTIVE: Our purpose was to assess the impact of a curriculum designed to improve third-year medical students' knowledge of sexually transmitted diseases, measured by sexually transmitted disease-related items from the National Board of Medical Examiners subject examination and by a locally developed sexually transmitted disease test. STUDY DESIGN: All students (n = 108) were exposed to a new sexually transmitted disease curriculum: a 2-hour laboratory module, lectures, syllabus, and locally developed pretest/posttest with review of the test prior to taking the National Board of Medical Examiners subject examination. Students were randomized to a attend sexually transmitted disease clinic (n = 47) versus no sexually transmitted disease clinic (n = 61). RESULTS: Students performed equal to or better than the national average on 85% of the National Board of Medical Examiners sexually transmitted disease-related items after curriculum institution, compared with 56% of the test items prior ( P < .001). Magnitude of improvement was dependent on clerkship timing, with greater improvement in students taking the obstetrics-gynecology clerkship earlier in the third year. Mean postcurriculum test scores of sexually transmitted disease improved significantly ( P < .001), independent of clinic site and clerkship timing. CONCLUSION: The curriculum for sexually transmitted disease produced significant improvement in third-year medical students' knowledge of sexually transmitted disease. This might have an impact on future prevention and control of sexually transmitted diseases in communities in which these students practice.

Low attendance by basic science educators at medical education meetings.

BACKGROUND: Recently, concern has been expressed about the perception that few basic science educators (BSE) attend national and regional medical education meetings. PURPOSE: This study was designed to analyze the issues affecting BSE decisions about whether to attend medical education meetings. METHOD: An online survey was created and submitted to basic science course directors at the 128 U.S. allopathic medical schools. RESULTS: Responses from 486 BSE suggest that because of the pressure to obtain research funding and achieve academic promotion, participation in medical education meetings is not a high priority with most BSE. CONCLUSIONS: BSE attendance at medical education meetings can be improved, but it will require joint efforts by the BSE home institution and medical education organizations.