Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold.

Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.

Medical education for African American communities in the rural South: A focus group approach to identify fundamental considerations.

PURPOSE: We sought to understand concerns fundamental to planning medical education specific to rural southern African Americans who are virtually nonexistent in American medical schools. METHODS: A diverse multidisciplinary research team conducted this qualitative study with 3 focus groups, including 17 rural medical educators recruited nationwide, 10 African American alumni of a rural medical education pipeline in Alabama, and 5 community and institutional associates of this pipeline. Analysis of recorded transcripts generated themes fitting an ecological model suggesting concerns and intervention foci at individual, community, and institutional levels. FINDINGS: Three major themes operating at all ecological levels were: (1) How "rural minority student" is defined, with "rural" often supplanting race to indicate minority status; (2) Multiple factors relate to rural racial minority student recruitment and success, including personal relationships with peers, mentors, and role models and supportive institutional policies and culturally competent faculty; and (3) Challenges to recruitment and retention of rural minority students, especially financial concerns and preparation for medical education. CONCLUSIONS: Our findings suggest that individuals, communities, and institutions provide intervention points for planning medical education specific to southern rural African Americans. These spheres of influence project a need for partnership among communities and rural medical educators to affect broad programmatic and policy changes that address the dire shortage of rural African American health professionals to help ameliorate health inequities experienced in their home communities. It is likely that linear thinking and programming will be replaced by integrated, intertwined conceptualizations to reach this goal.

Salivary and Serum Concentrations of Cortisol and Testosterone at Rest and in Response to Intense Exercise in Boys Versus Men.

This study compared salivary and serum concentrations of testosterone and cortisol at rest and in response to intense multitask exercise in boys and men. Early morning saliva and venous blood samples were obtained before and 15 minutes after exercise from 30 competitive swimmers (15 boys, age 14.3 [1.9] y; 15 men, age 21.7 [3.1] y). Exercise included a swim-bench maximal strength task and an all-out 200-m swim, followed by a high-intensity interval swimming protocol (5 × 100 m, 5 × 50 m, and 5 × 25 m). At baseline, fasting testosterone (but not cortisol) concentration was higher in men than boys in serum and saliva (P < .05). Salivary and serum cortisol increased postexercise, with a greater increase in men compared with boys (men: 226% and 242%; boys: 78% and 64%, respectively; group by time interaction, P < .05). Testosterone was reduced postexercise in serum but not in saliva (men: -14.7% and 0.1%; boys: -33.9% and -4.5%, respectively, fluid by time interaction, P < .01). Serum and salivary cortisol (but not testosterone), preexercise and postexercise values were strongly correlated in both men and boys (r = .79 and .82, respectively; P < .01). In summary, early morning high-intensity exercise results in a decrease in testosterone in serum, but not saliva, and an increase in cortisol irrespective of the fluid used, in both boys and men. When examining immediate postexercise changes, the lack of correlation in testosterone between saliva and serum suggests that saliva may not be an appropriate fluid to examine changes in testosterone. The high correlation observed between serum and saliva for cortisol indicates that, in both boys and men, saliva may be used to monitor the immediate cortisol response to exercise.

Teaching Medical Students in the Rural Setting Long Term: Physicians' Attitudes and Perceptions.

OBJECTIVES: The University of Alabama School of Medicine Tuscaloosa Regional Campus conducted a 2-month block in rural family practice, but committed to expanding to an 8-month longitudinal rural curriculum. We wanted to explore how rural physicians feel about teaching students in a prolonged rural preceptorship. METHODS: We brainstormed with colleagues, reviewed the literature, and conducted two focus groups supplemented by five interviews with rural physicians. The focus groups explored satisfaction and dissatisfaction in teaching, medical school and community support, evaluation of preceptors, and the sharing of information between students and preceptors. The analysis sought common themes among study participants and colleagues. RESULTS: Twenty-one study participants included 19 family physicians, 15 in private practice. Eleven had taught medical students. Our key finding, combining four themes, was that a satisfactory context within which to teach medical students long term in rural sites depends on the optimization of the roles of preceptors, students, communities, and educational institutions. There were comments addressing each of these roles. This finding cannot be generalized beyond the study group because of the qualitative methodology using a convenience sample. CONCLUSIONS: These physicians' concerns foment hypotheses about engaging rural physicians in their own unique local networks involving preceptors, students, community, and educational institutions to conduct satisfactory long-term medical education in rural sites. We recommend investigations to substantiate a prevalence among rural physicians of concern about the four roles and to describe various contexts in which these roles produce satisfactory long-term preceptorships, perhaps as best practices in different settings.

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.

Integration of Recurrent Somatic Mutations with Clinical Outcomes: A Pooled Analysis of 1049 Patients with Clear Cell Renal Cell Carcinoma.

BACKGROUND: Analyses of associations between clinicopathologic outcomes and recurrent somatic mutations in clear cell renal cell carcinoma (ccRCC) have been limited to individual cohorts. OBJECTIVE: To define clinicopathologic associations between specific mutations and ccRCC disease characteristics. DESIGN, SETTING, AND PARTICIPANTS: DNA sequencing data were pooled from three collaborative genomic cohorts (n=754) and our institutional database (n=295). All patients had clinical data and identification of somatic mutations from their primary tumors. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Analysis of gene mutations for associations with maximal tumor size (linear regression) and pathologic stage (logistic regression). Cancer-specific survival (CSS) and recurrence-free survival (RFS) were calculated using competing risks methods. Analyses were adjusted for cohort site, and results were adjusted for multiple testing (q value). Relevant genes were used in multivariable models that included confounding variables and the validated Mayo Clinic Stage, Size, Grade, and Necrosis (SSIGN) score. RESULTS AND LIMITATIONS: Association with tumor size was found for mutations in BAP1 (q=0.013). No mutations were found to be associated with stage after adjusted analysis. Mutations in BAP1 (q=0.004) and TP53 (q=0.001) were associated with decreased CSS in a multivariable model; only TP53 (q=0.005) remained significant when SSIGN score was included. SETD2 mutations (q=0.047) were associated with decreased RFS in multivariable models, including models with SSIGN score. CONCLUSIONS: In >1000 patients with ccRCC, pooled analysis and multivariable modeling demonstrated that three mutated genes have statistically significant associations with poor clinical outcomes. This included the more commonly mutated BAP1 and SETD2 and the less frequently mutated TP53. After adjustment for clinical confounders, mutations of TP53 and SETD2 were associated with decreased CSS and RFS, respectively. PATIENT SUMMARY: Using rigorous statistical methods, this study affirmed that certain mutations in clear cell renal cell carcinoma may portend inferior survival and an increased risk of recurrence.

Isometric and dynamic strength and neuromuscular attributes as predictors of vertical jump performance in 11- to 13-year-old male athletes.

In explosive contractions, neural activation is a major factor in determining the rate of torque development, while the latter is an important determinant of jump performance. However, the contribution of neuromuscular activation and rate of torque development to jump performance in children and youth is unclear. The purpose of this study was to examine the relationships between the rate of neuromuscular activation, peak torque, rate of torque development, and jump performance in young male athletes. Forty-one 12.5 ± 0.5-year-old male soccer players completed explosive, unilateral isometric and dynamic (240°/s) knee extensions (Biodex System III), as well as countermovement-, squat-, and drop-jumps. Peak torque (pT), peak rate of torque development (pRTD), and rate of vastus lateralis activation (Q30) during the isometric and dynamic contractions were examined in relation to attained jump heights. Isometric pT and pRTD were strongly correlated (r = 0.71) but not related to jump performance. Dynamic pT and pRTD, normalized to body mass, were significantly related to jump height in all 3 jumps (r = 0.38-0.66, p < 0.05). Dynamic normalized, but not absolute pRTD, was significantly related to Q30 (r = 0.35, p < 0.05). In young soccer players, neuromuscular activation and rate of torque development in dynamic contractions are related to jump performance, while isometric contractions are not. These findings have implications in the choice of training and assessment methods for young athletes.

Fumarate Mediates a Chronic Proliferative Signal in Fumarate Hydratase-Inactivated Cancer Cells by Increasing Transcription and Translation of Ferritin Genes.

Germ line mutations of the gene encoding the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) cause a hereditary cancer syndrome known as hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC-associated tumors harbor biallelic FH inactivation that results in the accumulation of the TCA cycle metabolite fumarate. Although it is known that fumarate accumulation can alter cellular signaling, if and how fumarate confers a growth advantage remain unclear. Here we show that fumarate accumulation confers a chronic proliferative signal by disrupting cellular iron signaling. Specifically, fumarate covalently modifies cysteine residues on iron regulatory protein 2 (IRP2), rendering it unable to repress ferritin mRNA translation. Simultaneously, fumarate increases ferritin gene transcription by activating the NRF2 (nuclear factor [erythroid-derived 2]-like 2) transcription factor. In turn, increased ferritin protein levels promote the expression of the promitotic transcription factor FOXM1 (Forkhead box protein M1). Consistently, clinical HLRCC tissues showed increased expression levels of both FOXM1 and its proliferation-associated target genes. This finding demonstrates how FH inactivation can endow cells with a growth advantage.

Testing children's ability to correctly use the "Shadow Rule" for sun protection.

INTRODUCTION: The "Shadow Rule" (SR) is a useful, immediate indicator of sunburn risk following the mnemonic "Short shadow? Seek shade!" However, some question people's ability to discern when their shadows are shorter or longer than them. METHODS: N = 76 10-year-old children were taught the SR and then asked to estimate their sun-cast shadow length relative to their height and whether this meant they should seek shade. Children were then asked to estimate a doll's shadow length at 10 systematically randomised angles. RESULTS: Children experienced greatest difficulty judging their shadows' lengths when they were equal to their height. At all other angles, they demonstrated high accuracy and 92 % of the time on average could correctly interpret the SR. CONCLUSIONS: Ten-year-old children appear capable, and by extension adults too, of applying the SR. Future research is now required to establish if education about the SR will translate into sun protection behaviour change.

Commissioning of intensity modulated neutron radiotherapy (IMNRT).

PURPOSE: Intensity modulated neutron radiotherapy (IMNRT) has been developed using inhouse treatment planning and delivery systems at the Karmanos Cancer Center∕Wayne State University Fast Neutron Therapy facility. The process of commissioning IMNRT for clinical use is presented here. Results of commissioning tests are provided including validation measurements using representative patient plans as well as those from the TG-119 test suite. METHODS: IMNRT plans were created using the Varian Eclipse optimization algorithm and an inhouse planning system for calculation of neutron dose distributions. Tissue equivalent ionization chambers and an ionization chamber array were used for point dose and planar dose distribution comparisons with calculated values. Validation plans were delivered to water and virtual water phantoms using TG-119 measurement points and evaluation techniques. Photon and neutron doses were evaluated both inside and outside the target volume for a typical IMNRT plan to determine effects of intensity modulation on the photon dose component. Monitor unit linearity and effects of beam current and gantry angle on output were investigated, and an independent validation of neutron dosimetry was obtained. RESULTS: While IMNRT plan quality is superior to conventional fast neutron therapy plans for clinical sites such as prostate and head and neck, it is inferior to photon IMRT for most TG-119 planning goals, particularly for complex cases. This results significantly from current limitations on the number of segments. Measured and calculated doses for 11 representative plans (six prostate∕five head and neck) agreed to within -0.8 ± 1.4% and 5.0 ± 6.0% within and outside the target, respectively. Nearly all (22∕24) ion chamber point measurements in the two phantom arrangements were within the respective confidence intervals for the quantity [(measured-planned)∕prescription dose] derived in TG-119. Mean differences for all measurements were 0.5% (max = 7.0%) and 1.4% (max = 4.1%) in water and virtual water, respectively. The mean gamma pass rate for all cases was 92.8% (min = 88.6%). These pass rates are lower than typically achieved with photon IMRT, warranting development of a planar dosimetry system designed specifically for IMNRT and∕or the improvement of neutron beam modeling in the penumbral region. The fractional photon dose component did not change significantly in a typical IMNRT plan versus a conventional fast neutron therapy plan, and IMNRT delivery is not expected to significantly alter the RBE. All other commissioning results were considered satisfactory for clinical implementation of IMNRT, including the external neutron dose validation, which agreed with the predicted neutron dose to within 1%. CONCLUSIONS: IMNRT has been successfully commissioned for clinical use. While current plan quality is inferior to photon IMRT, it is superior to conventional fast neutron therapy. Ion chamber validation results for IMNRT commissioning are also comparable to those typically achieved with photon IMRT. Gamma pass rates for planar dose distributions are lower than typically observed for photon IMRT but may be improved with improved planar dosimetry equipment and beam modeling techniques. In the meantime, patient-specific quality assurance measurements should rely more heavily on point dose measurements with tissue equivalent ionization chambers. No significant technical impediments are anticipated in the clinical implementation of IMNRT as described here.

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.

First human-caused extinction of a cetacean species?

The Yangtze River dolphin or baiji (Lipotes vexillifer), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November-December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis).

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.

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.