Genetic background affects the strength of crossover interference in house mice.

Meiotic recombination is required for faithful chromosome segregation in most sexually reproducing organisms and shapes the distribution of genetic variation in populations. Both the overall rate and the spatial distribution of crossovers vary within and between species. Adjacent crossovers on the same chromosome tend to be spaced more evenly than expected at random, a phenomenon known as crossover interference. Although interference has been observed in many taxa, the factors that influence the strength of interference are not well understood. We used house mice (Mus musculus), a well-established model system for understanding recombination, to study the effects of genetics and age on recombination rate and interference in the male germline. We analyzed crossover positions in 503 progeny from reciprocal F1 hybrids between inbred strains representing the three major subspecies of house mice. Consistent with previous studies, autosomal alleles from M. m. musculus tend to increase recombination rate, while inheriting a M. m. musculus X chromosome decreases recombination rate. Old males transmit an average of 0.6 more crossovers per meiosis (5.0%) than young males, though the effect varies across genetic backgrounds. We show that the strength of crossover interference depends on genotype, providing a rare demonstration that interference evolves over short timescales. Differences between reciprocal F1s suggest that X-linked factors modulate the strength of interference. Our findings motivate additional comparisons of interference among recently diverged species and further examination of the role of paternal age in determining the number and positioning of crossovers.

The dynamics of competition and decision-making.

We examine the underlying cognitive mechanisms that govern how competitions play out over time. We used cognitive modeling to examine the dynamic effects of time remaining and relative performance (whether the person is winning or losing) on effort and strategy. In this experiment, participants completed a competitive decision-making task with varying time limits and starting scores, in a repeated-measures design. Participants were tasked with scoring more points than their computerized opponent during a certain time frame, gaining and losing points for correct and incorrect decisions, respectively. The results showed that as the competition deadline approached and as participants drew ahead of their opponent within a competition, they increased effort and became more cautious. Furthermore, the effect of relative score on effort and caution changed over the course of a competition as the deadline approached. These results highlight the importance of considering dynamics when working to understand how competitions unfold as well as the underlying cognitive mechanisms that give rise to the dynamic behavior.

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles.

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between 105 structural models and 106 XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the nonequilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable "shape envelope" among nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

A Longitudinal Pediatric Primary Care Residency Tailored to Meet Workforce Need: A 10-Year Evaluation.

Background We started a primary care residency program intended to prepare graduates for primary care and increase entry into primary care, using time-limited funds from the Health Resources and Services Administration (HRSA). Objective To compare the graduates of the primary care residency program to their categorical peers, and whether they remained in the state, began primary care careers, and whether they identified as underrepresented in medicine. Methods This is a retrospective study of a cohort of 39 residents who graduated from the University of North Carolina primary care residency program from 2014-2023. In 2016, HRSA grant funding expired and the program continued with ongoing financial support from the 2 institutions. Graduate demographics and career choices were compared to categorical residents (159 total) for graduate years 2014 to 2023. Results The primary care pediatrics residency has graduated 39 residents to date. Job placement data was obtained for all 39 graduates. Graduates of the program have 5.5-fold greater odds (95% CI, 2.5-12.5) of working in primary care roles following graduation than peer categorical residents. Most graduates (33 of 39, 85%) have taken jobs in general pediatrics (including primary care, urgent care, adolescent medicine, or hospital medicine). The program has recruited a large proportion of its residents (12 of 39, 31%) from groups historically underrepresented in medicine. Conclusions We developed an innovative primary care pediatric residency in collaboration with a community partner, spurred by HRSA funds, that has trained a diverse group of new primary care pediatricians.

Association Between In-Training Exam Scores and Clinical Exposure During the COVID-19 Pandemic.

BACKGROUND: We sought to evaluate changes in In-Training Examination (ITE) scores and associations with clinical work during the COVID-19 pandemic. We hypothesized that residents saw a decrease in clinical encounters during the pandemic and that this would be associated with smaller gains in ITE scores. METHODS: We compared ITE score changes with data on patient notes for three classes of pediatric residents at four residency programs: one not exposed to the pandemic during their intern year who entered residency in 2018, one partially exposed to COVID-19 in March of their intern year (2019-2020), and one that was fully exposed to the pandemic, starting residency in June of 2020. RESULTS: ITE scores on average improved from the PGY1 to PGY2 year in the "no covid" and "partial COVID" cohorts. The "full COVID" cohort had little to no improvement, on average. The total number of patient encounters was not associated with a change in ITE scores from PGY1 to PGY2. There was a small but statistically significant association between change in ITE score and number of inpatient H+P notes. CONCLUSIONS: A drop in ITE scores occurred in pediatric residents who entered residency during the COVID-19 pandemic. This change was largely unrelated to clinical encounter number changes.

Robust whole-hand spatial manipulation via energy maps with caging, rolling, and sliding.

Humans regularly use all inner surfaces of the hand during manipulation, whereas traditional formulations for robots tend to use only the tips of their fingers, limiting overall dexterity. In this paper, we explore the use of the whole hand during spatial robotic dexterous within-hand manipulation. We present a novel four-fingered robotic hand called the Model B, which is designed and controlled using a straight-forward potential energy-based motion model that is based on the hand configuration and applied actuator torques. In this way the hand-object system is driven to a new desired configuration, often through sliding and rolling between the object and hand, and with the fingers "caging" the object to prevent ejection. This paper presents the first ever application of the energy model in three dimensions, which was used to compare the theoretical manipulability of popular robotic hands, which then inspired the design of the Model B. We experimentally validate the hand's performance with extensive benchtop experimentation with test objects and real world objects, as well as on a robotic arm, and demonstrate complex spatial caging manipulation on a variety of objects in all six object dimensions (three translation and three rotation) using all inner surfaces of the fingers and the palm.

Identification of genomic loci regulating platelet plasminogen activator inhibitor-1 in mice.

BACKGROUND: Plasminogen activator inhibitor-1 (PAI-1, Serpine1) is an important circulating fibrinolysis inhibitor. PAI-1 exists in 2 pools, packaged within platelet α-granules and freely circulating in plasma. Elevated plasma PAI-1 levels are associated with cardiovascular disease. However, little is known about the regulation of platelet PAI-1 (pPAI-1). OBJECTIVES: We investigated the genetic control of pPAI-1 levels in mice and humans. METHODS: We measured pPAI-1 antigen levels via enzyme-linked immunosorbent assay in platelets isolated from 10 inbred mouse strains, including LEWES/EiJ (LEWES) and C57BL/6J (B6). LEWES and B6 were crossed to produce the F1 generation, B6LEWESF1. B6LEWESF1 mice were intercrossed to produce B6LEWESF2 mice. These mice were subjected to genome-wide genetic marker genotyping followed by quantitative trait locus analysis to identify pPAI-1 regulatory loci. RESULTS: We identified differences in pPAI-1 between several laboratory strains, with LEWES having pPAI-1 levels more than 10-fold higher than those in B6. Quantitative trait locus analysis of B6LEWESF2 offspring identified a major pPAI-1 regulatory locus on chromosome 5 from 136.1 to 137.6 Mb (logarithm of the odds score, 16.2). Significant pPAI-1 modifier loci on chromosomes 6 and 13 were also identified. CONCLUSION: Identification of pPAI-1 genomic regulatory elements provides insights into platelet/megakaryocyte-specific and cell type-specific gene expression. This information can be used to design more precise therapeutic targets for diseases where PAI-1 plays a role.

Multiple Schedules Facilitate Rapid Noncontingent Reinforcement Schedule Thinning.

We evaluated a noncontingent reinforcement treatment that included initial brief exposures to signaled alternation of availability and nonavailability of reinforcement, followed by rapid schedule thinning. Results confirmed findings from previous research (typically with differential reinforcement schedules) that establishing stimulus control across multiple treatment components facilitated schedule thinning. We discuss both the clinical utility of this procedure and the utility of stimulus control for making interventions more practical for clinicians.

Using cognitive modeling to examine the effects of competition on strategy and effort in races and tournaments.

We investigated the effects of two types of competition, races and tournaments (as well as an individual challenge and a do-your-best condition), on two different aspects of performance: effort and strategy. In our experiment, 100 undergraduate participants completed a simple cognitive task under four experimental conditions (in a repeated-measures design) based on different types of competitions and challenges. We used the Linear Ballistic Accumulator to quantify the effects of competition on strategy and effort. The results reveal that competition produced changes in strategy rather than effort, and that trait competitiveness had minimal impact on how people responded to competition. This suggests individuals are more likely to adjust their strategy in competitions, and the uncertainty created by different competition types influences the direction of these strategy adjustments.

Predictors of emotional distress in uveal melanoma survivors: a systematic review.

Uveal melanoma (UM) survivors can experience significant emotional distress, although the factors underpinning this are poorly understood. Systematic reviews of distress in UM only include cross-sectional studies, thereby limiting our understanding of causal factors. This review identified prospective clinical, demographic, social and psychological predictors of distress in UM survivors. A systematic search of the literature for English language prospective studies was conducted. Thirteen papers, reporting data from seven unique datasets were included in a narrative synthesis of the results. Younger age (3 studies from 3 datasets), physical health (including visual impairment, ocular symptoms, and other UM-related factors; 3 studies from 3 datasets), and psychological factors (mainly baseline distress; 3 studies from 3 datasets and worry about recurrence; 2 studies from 2 datasets), significantly predicted distress. There was no consistent evidence for other demographic, clinical or social variables (significant in <50% of datasets). Generally, the quality of the papers was adequate. However, attrition rates were high or not reported in over half of the included studies. The findings of this review emphasise the importance of attempts to prevent and recognise distress immediately post-diagnosis of UM. Particular focus should be given to younger patients, those with physical and psychological health difficulties at the time of diagnosis, and those who develop adverse treatment symptoms during survivorship. More research into potential social and psychological variables and their role in predicting distress in survivors is recommended.

Unusual Presentation of Hodgkin's Lymphoma in Pregnancy: A Case Report and Systematic Review of Literature.

Diseases occurring during pregnancy create a dilemma of managing the patient without causing harm to the unborn child. Three percent of the peak incidence of Hodgkin lymphoma (HL) is congruent with the reproductive period, particularly with pregnancy. Pregnant patients with HL always require a team of medical experts ranging from a medical oncologist, high-risk obstetrician, and neonatologist. Effective communication with both the patient and family is also necessary. The treatment goal for these patients should focus on achieving complete remission for the mother while permitting the delivery of a healthy child. Pregnant patients diagnosed with HL should undergo similar clinical investigations as other non-pregnant patients with accurate disease staging and appropriate non-radiation imaging such as ultrasound while avoiding invasive procedures.

Precise wavefront characterization of x-ray optical elements using a laboratory source.

Improvements in x-ray optics critically depend on the measurement of their optical performance. The knowledge of wavefront aberrations, for example, can be used to improve the fabrication of optical elements or to design phase correctors to compensate for these errors. At present, the characterization of such optics is made using intense x-ray sources, such as synchrotrons. However, the limited access to these facilities can substantially slow down the development process. Improvements in the brightness of lab-based x-ray micro-sources in combination with the development of new metrology methods, particularly ptychographic x-ray speckle tracking, enable characterization of x-ray optics in the lab with a precision and sensitivity not possible before. Here, we present a laboratory setup that utilizes a commercially available x-ray source and can be used to characterize different types of x-ray optics. The setup is used in our laboratory on a routine basis to characterize multilayer Laue lenses of high numerical aperture and other optical elements. This typically includes measurements of the wavefront distortions, optimum operating photon energy, and focal length of the lens. To check the sensitivity and accuracy of this laboratory setup, we compared the results to those obtained at the synchrotron and saw no significant difference. To illustrate the feedback of measurements on performance, we demonstrated the correction of the phase errors of a particular multilayer Laue lens using a 3D printed compound refractive phase plate.

Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers.

The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX.

Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales.

House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.

Observations of phase changes in monoolein during high viscous injection.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

'I Don't Like Uncertainty, I Like to Know': How and why uveal melanoma patients consent to life expectancy prognostication.

BACKGROUND: Technological advances have led to cancer prognostication that is increasingly accurate but often unalterable. However, a reliable prognosis of limited life expectancy can cause psychological distress. People should carefully consider offers of prognostication, but little is known about how and why they decide on prognostication. Using uveal melanoma (UM) patients, we aimed to identify (i) how and why do people with UM decide to accept prognostication and (ii) alignment and divergence of their decision-making from conceptualizations of a 'well-considered' decision. METHODS: UM provides a paradigm to elucidate clinical and ethical perspectives on prognostication, because prognostication is reliable but prognoses are largely nonameliorable. We used qualitative methods to examine how and why 20 UM people with UM chose prognostication. We compared findings to a template of 'well-considered' decision-making, where 'well-considered' decisions involve consideration of all likely outcomes. RESULTS: Participants wanted prognostication to reduce future worry about uncertain life expectancy. They spontaneously spoke of hoping for a good prognosis when making their decisions, but largely did not consider the 50% possibility of a poor prognosis. When pressed, they argued that a poor outcome at least brings certainty. CONCLUSIONS: While respecting decisions as valid expressions of participants' wishes, we are concerned that they did not explicitly consider the realistic possibility of a poor outcome and how this would affect them. Thus, it is difficult to see their decisions as 'well-considered'. We propose that nondirective preference exploration techniques could help people to consider the possibility of a poor outcome. PATIENT OR PUBLIC CONTRIBUTION: This paper is a direct response to a patient-identified and defined problem that arose in therapeutic and conversational discourse. The research was informed by the responses of patient participants, as we used the material from interviews to dynamically shape the interview guide. Thus, participants' ideas drove the analysis and shaped the interviews to come.

Unsupervised learning approaches to characterizing heterogeneous samples using X-ray single-particle imaging.

One of the outstanding analytical problems in X-ray single-particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and the fact that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. Proposed here are two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA), provides a rough classification which is essentially parameter free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs), can generate 3D structures of the objects at any point in the structural landscape. Both these methods are implemented in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and its utility is demonstrated by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern. Both discrete structural classes and continuous deformations are recovered. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility of moving beyond the study of homogeneous sample sets to addressing open questions on topics such as nanocrystal growth and dynamics, as well as phase transitions which have not been externally triggered.

Epigenetic drugs induce the potency of classic chemotherapy, suppress post-treatment re-growth of breast cancer, but preserve the wound healing ability of stem cells.

Epigenetic therapy augments neoadjuvant chemotherapy (NACT) in breast cancer and may aid post-surgical wound healing affected by NACT. Our study investigates: (1) The cytotoxicity of classic paclitaxel chemotherapy on triple negative breast cancer (TNBC) independently and in combination with epigenetic drugs. (2) The sustainable inhibition of breast cancer regrowth following paclitaxel and epigenetic therapies. (3) The effects of paclitaxel with and without epigenetic therapy on the post-treatment viability and wound healing potential of adipose stem cells (ASCs). Cytotoxicity assays were performed on TNBC and ASCs. Cells were treated and recovered in drug-free medium. Cell viability was measured via cell counts and MTT assays. W -ound healing was tested with scratch assays. The combination of epigenetic drugs shows increased toxicity against TNBC cells compared to standard chemotherapy alone. Moreover, the combination of paclitaxel with epigenetic treatments causes cancer toxicity that is sustainable to TNBC cells after the drugs' removal with minimal effect on ASCs wound healing ability. The use of epigenetic drugs in addition to standard chemotherapy is cytotoxic to TNBC cells and prevents post-treatment recovery of TNBC while maintaining ASC wound healing ability. This strategy may be useful in maximizing post-surgical wound healing following NACT in TNBC.

Investigating cell autonomy in microorganisms.

Cell-cell signaling in microorganisms is still poorly characterized. In this Methods paper, we describe a genetic procedure for detecting cell-nonautonomous genetic effects, and in particular cell-cell signaling, termed the chimeric colony assay (CCA). The CCA measures the effect of a gene on a biological response in a neighboring cell. This assay can measure cell autonomy for range of biological activities including transcript or protein accumulation, subcellular localization, and cell differentiation. To date, the CCA has been used exclusively to investigate colony patterning in the budding yeast Saccharomyces cerevisiae. To demonstrate the wider potential of the assay, we applied this assay to two other systems: the effect of Grr1 on glucose repression of GAL1 transcription in yeast and the effect of rpsL on stop-codon translational readthrough in Escherichia coli. We also describe variations of the standard CCA that address specific aspects of cell-cell signaling, and we delineate essential controls for this assay. Finally, we discuss complementary approaches to the CCA. Taken together, this Methods paper demonstrates how genetic assays can reveal and explore the roles of cell-cell signaling in microbial processes.