Famotidine increases cellular phospho-tyrosine levels.

While vaccines were being developed, the SARS-CoV-2 pandemic triggered a race to find known drugs that could be quickly repurposed to treat patients. One such candidate was famotidine, which retrospective cohort studies had shown increased survival in hospitalized patients. Computational studies had suggested that famotidine may target early viral proteases; however, ultimately, famotidine was shown not to function as a viral inhibitor. In contrast, we have observed a change in the cellular levels of phospho-tyrosine in A549 lung epithelial cells following treatment with famotidine. This quick change in phosphorylation was due mainly to a dose-dependent increase in cellular production of H2O2. Notably, these changes in phospho-tyrosine levels were able to affect cell signaling; we detected an increased short- and long-term response to IFNα stimulation. Our results suggest that famotidine can increase the anti-viral state of non-infected cells thereby potentially increasing viral resistance.

Laue-DIALS: Open-source software for polychromatic x-ray diffraction data.

Most x-ray sources are inherently polychromatic. Polychromatic ("pink") x-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure-ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most x-ray facilities to discard >99% of x-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

Gene expansions contributing to human brain evolution.

Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increased complexity of synaptic connections between neurons and the dramatic expansion of the neocortex. Discovering duplicate genes is challenging because the similarity of paralogs makes them prone to sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere human genome sequence (T2T-CHM13) and identified 213 duplicated gene families likely containing human-specific paralogs (>98% identity). Positing that genes important in universal human brain features should exist with at least one copy in all modern humans and exhibit expression in the brain, we narrowed in on 362 paralogs with at least one copy across thousands of ancestrally diverse genomes and present in human brain transcriptomes. Of these, 38 paralogs co-express in gene modules enriched for autism-associated genes and potentially contribute to human language and cognition. We narrowed in on 13 duplicate gene families with human-specific paralogs that are fixed among modern humans and show convincing brain expression patterns. Using long-read DNA sequencing revealed hidden variation across 200 modern humans of diverse ancestries, uncovering signatures of selection not previously identified, including possible balancing selection of CD8B . To understand the roles of duplicated genes in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and transiently introduced mRNA-encoding paralogs, effectively "humanizing" the larvae. Morphometric, behavioral, and single-cell RNA-seq screening highlighted, for the first time, a possible role for GPR89B in dosage-mediated brain expansion and FRMPD2B function in altered synaptic signaling, both hallmark features of the human brain. Our holistic approach provides important insights into human brain evolution as well as a resource to the community for studying additional gene expansion drivers of human brain evolution. Abstract short: Duplicated genes expanded in the human lineage likely contributed to brain evolution, yet challenges exist in their discovery due to sequence-assembly errors. We used a complete telomere-to-telomere genome sequence to identify 213 human-specific gene families. From these, 362 paralogs were found in all modern human genomes tested and brain transcriptomes, making them top candidates contributing to human-universal brain features. Choosing a subset of paralogs, we used long-read DNA sequencing of hundreds of modern humans to reveal previously hidden signatures of selection. To understand their roles in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and introduced mRNA-encoding paralogs, effectively "humanizing" larvae. Our findings implicate two new genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage-mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides new insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.

Disparities in contemporary human papilloma virus vaccination uptake among adult women living in the United States: An All of Us Research Program study.

OBJECTIVE: Age-adjusted rates of new cervical cancer diagnoses in the United States have remained stable despite increasing availability of Human Papilloma Virus (HPV) vaccination. As it is well established that sociodemographic factors drive cervical cancer care inequity, we aimed to evaluate their impact on catch-up HPV vaccination rates in adults. METHODS: The All of Us (AoU) Research Program is a longitudinal cohort study sponsored by the National Institutes of Health. All participants ages 18-47 assigned female sex at birth enrolled between May 2018 and April 2023 were included in this analysis. Primary outcome was receipt of HPV vaccination. Bivariable and multivariable tests were used to examine associations. RESULTS: A total of 113,344 participants were identified in the AoU program, with 53 % (n = 60,594) self-identifying as a racial or ethnic minority. Only 3575 participants (3.2 %) were documented as having received HPV vaccination. Median age of vaccination was 26 and participants ages 18-27 were more likely to be vaccinated. Participants without health insurance (OR = 0.32, 95 % CI 0.26-0.40), stable employment (OR = 0.85, 95 % CI 0.79-0.91), and those who reported lower income (OR = 0.87, 95 % CI 0.79-0.97) were significantly less likely to have received HPV vaccination. Participants who described cost as a barrier to healthcare were also less likely to have received HPV vaccination (OR = 0.82, 95 % CI 0.73-0.93). CONCLUSION: Sociodemographic factors including low income, lack of health insurance, and lack of stable employment were all associated with lower likelihood of catch-up HPV vaccination among adult women living in the United States.

Effect of mediolateral leg perturbations on walking balance in people with chronic stroke: A randomized controlled trial.

Many people with chronic stroke (PwCS) exhibit deficits in step width modulation, an important strategy for walking balance. A single exposure to swing leg perturbations can temporarily strengthen this modulation. The objective of this parallel, double-blinded, randomized controlled trial was to investigate whether repeated perturbations cause sustained increases in step modulation (NCT02964039; funded by the VA). 54 PwCS at the Medical University of South Carolina were randomly assigned to one of three intervention groups: Control (n = 18), with minimal forces; Assistive (n = 18), pushing the swing leg toward a mechanically appropriate location; Perturbing (n = 18), pushing the swing leg away from a mechanically appropriate location. All intervention groups included 24 training sessions over 12-weeks with up to 30-minutes of treadmill walking while interfaced with a novel force-field and a 12-week follow-up period, with five interspersed assessment sessions. Our primary outcome measure was paretic step width modulation, the partial correlation between step width and pelvis displacement (ρSW). Secondarily, we quantified swing and stance leg contributions to step modulation, clinical assessments of walking balance and confidence, and real-world falls. Outcomes were analyzed for participants who completed all assessment sessions (n = 44). Only the Perturbing group exhibited significant increases in paretic ρSW, which were present after 4-weeks of training and sustained through follow-up (t = 2.42-3.17). These changes were due to improved control of paretic swing leg positioning. However, perturbation-induced changes in step modulation were not always significantly greater than those in the Control group, and clinical assessments were similar across intervention groups. Participants in the Perturbing group experienced a lower fall rate than those in the Control group (incidence rate ratio = 0.53), although our small sample size warrants caution. The present results indicate that perturbations can cause sustained modifications of targeted biomechanical characteristics of post-stroke gait, although such changes alone may be insufficient to change more complex clinical assessments.

Exploring the Congruence of actigraphy and the Pediatric Autism Insomnia rating Scale.

OBJECTIVE/BACKGROUND: Insomnia is common in children with autism spectrum disorder (ASD). We recently developed and validated the 21-item Pediatric Autism Insomnia Rating Scale (PAIRS). This report explores the associations and agreements between actigraphy and PAIRS. PARTICIPANTS METHODS: Children with ASD, with and without sleep problems, were assessed with a battery of parent-rated and clinician measures (N = 134). In a subset (n = 70), a wrist-worn actigraph measured sleep for five consecutive nights. Parents completed logs for scoring sleep intervals. Spearman correlations evaluated associations with the PAIRS and actigraphy indices (sleep onset latency = SOL, wake after sleep onset = WASO, total sleep time = TST, sleep efficiency = SE%). Agreements on "poor sleepers" based on PAIRS total score (≥33) and conventional thresholds for TST and SE% were evaluated with Cohen's Kappa and McNemar's test. RESULTS: Actigraphy data were averaged over 4.64 ± 0.68 nights in 70 children (mean age = 7.3 ± 2.9, 74.3 % male). There were no significant correlations between PAIRS and any actigraphy indices. On TST, 48.6 % (n = 34) and on SE% 52.9 % (n = 37) were classified as "poor sleepers" compared to 32.9 % (n = 23) on PAIRS (kappa = 0.11 for TST and 0.27 for SE%). P-values on McNemar's Chi square test for PAIRS with TST and with SE% were 0.072 and 0.011, respectfully. CONCLUSIONS: These results suggest that actigraphy and PAIRS do not agree. Actigraphy TST captures movement and an estimate of specific sleep parameters. PAIRS is a broader measure that incorporates sleep disturbance and sleep-related impairment.

Germline Variants in Patients Affected by Both Uveal and Cutaneous Melanoma.

Uveal melanoma (UM) and nonacral cutaneous melanoma (CM) are distinct entities with varied genetic landscapes despite both arising from melanocytes. There are, however, similarities in that they most frequently affect people of European ancestry, and high penetrance germline variants in BAP1, POT1 and CDKN2A have been shown to predispose to both UM and CM. This study aims to further explore germline variants in patients affected by both UM and CM, shedding light on the underlying genetic mechanism causing these diseases. Using exome sequencing we analysed germline DNA samples from a cohort of 83 Australian patients diagnosed with both UM and CM. Eight (10%) patients were identified that carried pathogenic mutations in known melanoma predisposition genes POT1, MITF, OCA2, SLC45A2 and TYR. Three (4%) patients carried pathogenic variants in genes previously linked with other cancer syndromes (ATR, BRIP1 and MSH6) and another three cases carried monoallelic pathogenic variants in recessive cancer genes (xeroderma pigmentosum and Fanconi anaemia), indicating that reduced penetrance of phenotype in these individuals may contribute to the development of both UM and CM. These findings highlight the need for further studies characterising the role of these genes in melanoma susceptibility.

Incident Epilepsy Among US Medicare Beneficiaries, 2019: Differences by Age, Sex, and Race/Ethnicity.

BACKGROUND AND OBJECTIVES: Epilepsy is common among older adults, but previous incident studies have had limited ability to make comparisons across key subgroups. We aimed to provide updated epilepsy incidence estimates among older adults, comparing across age, sex, and race/ethnicity. METHODS: Using a random sample of 4,999,999 US Medicare beneficiaries older than 65 years, we conducted a retrospective cohort study of epilepsy incidence using administrative claims for 2016-2019. Sampled beneficiaries were enrolled in the Fee-for-Service (FFS) program in each of 2016-2018 and had no epilepsy claims in those years. Non-Hispanic Black and Hispanic beneficiaries were oversampled to ensure adequate cases for detailed comparisons. Incidence in 2019 was identified in the Master Beneficiary Summary File as ≥1 inpatient claim or ≥2 outpatient nondrug claims occurring at least 1 day apart (ICD-10 G40.x). Incidence models were estimated by age, sex, race/ethnicity, and combinations thereof, with adjustment for the racial/ethnic oversampling. RESULTS: We identified 20,545 incident epilepsy cases. The overall epilepsy incidence rate (IR) was 393 per 100,000 (99% CI 385-400). Incidence peaked at ages 85-89 (504 [481-529]) and was higher for men (396 [385-407]) than women (376 [366-385]). The sex difference in IRs was constant with age. Incidence was higher for non-Hispanic Black (678 [653-702]) and Hispanic (405 [384-426]), and lower for non-Hispanic Asian/Pacific Islander (272 [239-305]) beneficiaries, compared with non-Hispanic White beneficiaries (354 [299-408]). The age-specific IRs significantly differed by race/ethnicity and sex, but only among non-Hispanic Black beneficiaries-where men had higher rates at younger ages and women at older ages. DISCUSSION: We found higher epilepsy IRs among those enrolled in the Medicare FFS system 2016-2019 than previous studies using Medicare claims data from at least a decade ago. The risk of epilepsy onset is higher for those in their late 80s, men, and non-Hispanic Black and Hispanic older adults. There is also evidence that these age-graded risks operate differently for Black men and Black women. Efforts to provide care and services that improve quality of life for older adults living with epilepsy should consider differences by multiple social characteristics simultaneously: age, sex, and race/ethnicity.

Overfishing and climate change elevate extinction risk of endemic sharks and rays in the southwest Indian Ocean hotspot.

Here, we summarise the extinction risk of the sharks and rays endemic to coastal, shelf, and slope waters of the southwest Indian Ocean and adjacent waters (SWIO+, Namibia to Kenya, including SWIO islands). This region is a hotspot of endemic and evolutionarily distinct sharks and rays. Nearly one-fifth (n = 13 of 70, 18.6%) of endemic sharks and rays are threatened, of these: one is Critically Endangered, five are Endangered, and seven are Vulnerable. A further seven (10.0%) are Near Threatened, 33 (47.1%) are Least Concern, and 17 (24.3%) are Data Deficient. While the primary threat is overfishing, there are the first signs that climate change is contributing to elevated extinction risk through habitat reduction and inshore distributional shifts. By backcasting their status, few endemic species were threatened in 1980, but this changed soon after the emergence of targeted shark and ray fisheries. South Africa has the highest national conservation responsibility, followed by Mozambique and Madagascar. Yet, while fisheries management and enforcement have improved in South Africa over recent decades, substantial improvements are urgently needed elsewhere. To avoid extinction and ensure robust populations of the region's endemic sharks and rays and maintain ecosystem functionality, there is an urgent need for the strict protection of Critically Endangered and Endangered species and sustainable management of Vulnerable, Near Threatened, and Least Concern species, underpinned by species-level data collection and reduction of incidental catch.

Short CDRL1 in intermediate VRC01-like mAbs is not sufficient to overcome key glycan barriers on HIV-1 Env.

VRC01-class broadly neutralizing antibodies (bnAbs) have been isolated from people with HIV-1, but they have not yet been elicited by vaccination. They are extensively somatically mutated and sometimes accumulate CDRL1 deletions. Such indels may allow VRC01-class antibodies to accommodate the glycans expressed on a conserved N276 N-linked glycosylation site in loop D of the gp120 subunit. These glycans constitute a major obstacle in the development of VRC01-class antibodies, as unmutated antibody forms are unable to accommodate them. Although immunizations of knock-in mice expressing human VRC01-class B-cell receptors (BCRs) with specifically designed Env-derived immunogens lead to the accumulation of somatic mutations in VRC01-class BCRs, CDRL1 deletions are rarely observed, and the elicited antibodies display narrow neutralizing activities. The lack of broad neutralizing potential could be due to the absence of deletions, the lack of appropriate somatic mutations, or both. To address this point, we modified our previously determined prime-boost immunization with a germline-targeting immunogen nanoparticle (426c.Mod.Core), followed by a heterologous core nanoparticle (HxB2.WT.Core), by adding a final boost with a cocktail of various stabilized soluble Env trimers. We isolated VRC01-like antibodies with extensive somatic mutations and, in one case, a seven-amino acid CDRL1 deletion. We generated chimeric antibodies that combine the vaccine-elicited somatic mutations with CDRL1 deletions present in human mature VRC01 bnAbs. We observed that CDRL1 indels did not improve the neutralizing antibody activities. Our study indicates that CDRL1 length by itself is not sufficient for the broadly neutralizing phenotype of this class of antibodies. IMPORTANCE: HIV-1 broadly neutralizing antibodies will be a key component of an effective HIV-1 vaccine, as they prevent viral acquisition. Over the past decade, numerous broadly neutralizing antibodies (bnAbs) have been isolated from people with HIV. Despite an in-depth knowledge of their structures, epitopes, ontogenies, and, in a few rare cases, their maturation pathways during infection, bnAbs have, so far, not been elicited by vaccination. This necessitates the identification of key obstacles that prevent their elicitation by immunization and overcoming them. Here we examined whether CDRL1 shortening is a prerequisite for the broadly neutralizing potential of VRC01-class bnAbs, which bind within the CD4 receptor binding site of Env. Our findings indicate that CDRL1 shortening by itself is important but not sufficient for the acquisition of neutralization breadth, and suggest that particular combinations of amino acid mutations, not elicited so far by vaccination, are most likely required for the development of such a feature.

Molecular Hallmarks of Prostate-specific Membrane Antigen in Treatment-naïve Prostate Cancer.

BACKGROUND AND OBJECTIVE: We characterized tumor prostate-specific membrane antigen (PSMA) levels as a reflection of cancer biology and treatment sensitivities for treatment-naïve prostate cancer. METHODS: We first correlated PSMA positron emission tomography (PET) maximum standardized uptake values (SUVmax) in primary prostate cancer with tumor FOLH1 (PSMA RNA abundance) to establish RNA as a proxy (n = 55). We then discovered and validated molecular pathways associated with PSMA RNA levels in two large primary tumor cohorts. We validated those associations in independent cohorts (18 total; 5684 tumor samples) to characterize the pathways and treatment responses associated with PSMA. KEY FINDINGS AND LIMITATIONS: PSMA RNA abundance correlates moderately with SUVmax (ρ = 0.41). In independent cohorts, androgen receptor signaling is more active in tumors with high PSMA. Accordingly, patients with high PSMA tumors experienced longer cancer-specific survival when managed with androgen deprivation therapy for biochemical recurrence (adjusted hazard ratio [AHR] 0.54 [0.34-0.87]; n = 174). PSMA low tumors possess molecular markers of resistance to radiotherapy. Consistent with this, patients with high PSMA tumors experience longer time to recurrence following primary radiotherapy (AHR 0.50 [0.28-0.90]; n = 248). In the SAKK09/10 trial (n = 224), patients with high PSMA tumors who were managed with salvage radiotherapy experienced longer time to progression in the 64-Gy arm (restricted mean survival time [RMST] +7.60 [0.05-15.16]), but this effect was mitigated in the 70-Gy arm (RMST 3.52 [-3.30 to 10.33]). Limitations include using PSMA RNA as a surrogate for PET SUVmax. CONCLUSIONS AND CLINICAL IMPLICATIONS: PSMA levels in treatment-naïve prostate cancer differentiate tumor biology and treatment susceptibilities. These results warrant validation using PET metrics to substantiate management decisions based on imaging.

Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development.

The expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C, likely contributed to altered evolutionary brain features. The introduction of SRGAP2C in mouse models is associated with changes in cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring and that these larvae phenocopy "humanized" SRGAP2C larvae, including altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axonogenesis-, and vision-related genes. Through single-cell transcriptome analysis, we demonstrate a skewed balance of excitatory and inhibitory neurons that likely contribute to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also shows strong endogenous expression of srgap2 in microglia with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. Microglia cells expressing srgap2 were also detected in the developing eye together with altered expression of genes related to axonogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+SRGAP2C) and non-human primates (-SRGAP2C) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays a similar role altering microglia and the visual system in modern humans. Together, our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline.

Summary: DNA sequencing is becoming more affordable and faster through advances in high-throughput technologies. This rise in data availability has contributed to the development of novel algorithms to elucidate previously obscure features and led to an increased reliance on complex workflows to integrate such tools into analyses pipelines. To facilitate the analysis of DNA sequencing data, we created metapipeline-DNA, a highly configurable and extensible pipeline. It encompasses a broad range of processing including raw sequencing read alignment and recalibration, variant calling, quality control and subclonal reconstruction. Metapipeline-DNA also contains configuration options to select and tune analyses while being robust to failures. This standardizes and simplifies the ability to analyze large DNA sequencing in both clinical and research settings. Availability: Metapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is freely available at https://github.com/uclahs-cds/metapipeline-DNA.

Capturing the care of complex community-based health center patients: A comparison of multimorbidity indices and clinical classification software.

OBJECTIVE: To compare morbidity burden captured from multimorbidity indices and aggregated measures of clinically meaningful categories captured in primary care community-based health center (CBHC) patients. DATA SOURCES AND STUDY SETTING: Electronic health records of patients seen in 2019 in OCHIN's national network of CBHCs serving patients in rural and underserved communities. STUDY DESIGN: Age-stratified analyses comparing the most common conditions captured by the Charlson, Elixhauser, and Multimorbidity Weighted (MWI) indices, and Classification Software Refined (CCSR) and Chronic Condition Indicator (CCI) algorithms. DATA COLLECTION/EXTRACTION METHODS: Active ICD-10 conditions on patients' problem list in 2019. PRINCIPAL FINDINGS: Approximately 35%-56% of patients with at least one condition are not captured by the Charlson, Elixhauser, and MWI indices. When stratified by age, this range broadens to 9%-90% with higher percentages in younger patients. The CCSR and CCI reflect a broader range of acute and chronic conditions prevalent among CBHC patients. CONCLUSION: Three commonly used indices to capture morbidity burden reflect conditions most prevalent among older adults, but do not capture those on problem lists for younger CBHC patients. An index with an expanded range of care conditions is needed to understand the complex care provided to primary care populations across the lifespan.

Perspectives of Caregivers on Children Boarding With Mental Health Conditions.

OBJECTIVE: Addressing the acute mental healthcare needs of children is a national crisis. Despite the ongoing crisis, there are limited prior studies that capture caregiver perspectives on acute pediatric mental healthcare, notably in a general emergency department (ED) in a rural state. Based on these knowledge gaps, our objective was to assess caregiver opinions and perspectives of acute management for children boarding with mental health conditions. METHODS: Semistructured interviews were conducted with caregivers of patients (under 18 years old) with a primary mental health condition boarding in a general ED (length of stay ≥24 hours) within a qualitative grounded theory approach. An interview guide was developed a priori and reviewed among key stakeholders. A trained study team performed the interviews. A coding tree was developed through an iterative process that included double-coding transcripts and monitoring of interrater reliability to perform thematic analysis. RESULTS: Fourteen interviews were conducted to reach thematic saturation. Key themes elicited from caregivers included mental healthcare delivery, access to mental healthcare services, care setting, and level of support for families and caregivers. Most caregivers focused on the following challenges and suggestions: access to appropriate, evidence-based mental healthcare, improved communication between all stakeholders involved, and staff education on mental healthcare for children. CONCLUSIONS: Caregivers face considerable challenges in attaining timely and appropriate acute mental health care for their children. Immediate and innovative resource allocation is needed across the healthcare continuum to bolster the acute mental healthcare services currently offered to children and families, especially in the general ED setting.

Identifying the multiple drivers of cactus diversification.

Our understanding of the complexity of forces at play in the rise of major angiosperm lineages remains incomplete. The diversity and heterogeneous distribution of most angiosperm lineages is so extraordinary that it confounds our ability to identify simple drivers of diversification. Using machine learning in combination with phylogenetic modelling, we show that five separate abiotic and biotic variables significantly contribute to the diversification of Cactaceae. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance, while accounting for potential interactions between those variables. We use state-dependent diversification models to confirm that five abiotic and biotic variables shape diversification in the cactus family. Of highest importance are diurnal air temperature range, soil sand content and plant size, with lesser importance identified in isothermality and geographic range size. Interestingly, each of the estimated optimal conditions for abiotic variables were intermediate, indicating that cactus diversification is promoted by moderate, not extreme, climates. Our results reveal the potential primary drivers of cactus diversification, and the need to account for the complexity underlying the evolution of angiosperm lineages.

Ecological roles and importance of sharks in the Anthropocene Ocean.

In ecosystems, sharks can be predators, competitors, facilitators, nutrient transporters, and food. However, overfishing and other threats have greatly reduced shark populations, altering their roles and effects on ecosystems. We review these changes and implications for ecosystem function and management. Macropredatory sharks are often disproportionately affected by humans but can influence prey and coastal ecosystems, including facilitating carbon sequestration. Like terrestrial predators, sharks may be crucial to ecosystem functioning under climate change. However, large ecosystem effects of sharks are not ubiquitous. Increasing human uses of oceans are changing shark roles, necessitating management consideration. Rebuilding key populations and incorporating shark ecological roles, including less obvious ones, into management efforts are critical for retaining sharks' functional value. Coupled social-ecological frameworks can facilitate these efforts.

Laue-DIALS: open-source software for polychromatic X-ray diffraction data.

Most X-ray sources are inherently polychromatic. Polychromatic ("pink") X-rays provide an efficient way to conduct diffraction experiments as many more photons can be used and large regions of reciprocal space can be probed without sample rotation during exposure-ideal conditions for time-resolved applications. Analysis of such data is complicated, however, causing most X-ray facilities to discard >99% of X-ray photons to obtain monochromatic data. Key challenges in analyzing polychromatic diffraction data include lattice searching, indexing and wavelength assignment, correction of measured intensities for wavelength-dependent effects, and deconvolution of harmonics. We recently described an algorithm, Careless, that can perform harmonic deconvolution and correct measured intensities for variation in wavelength when presented with integrated diffraction intensities and assigned wavelengths. Here, we present Laue-DIALS, an open-source software pipeline that indexes and integrates polychromatic diffraction data. Laue-DIALS is based on the dxtbx toolbox, which supports the DIALS software commonly used to process monochromatic data. As such, Laue-DIALS provides many of the same advantages: an open-source, modular, and extensible architecture, providing a robust basis for future development. We present benchmark results showing that Laue-DIALS, together with Careless, provides a suitable approach to the analysis of polychromatic diffraction data, including for time-resolved applications.

BRCA Status Dictates Wnt Responsiveness in Epithelial Ovarian Cancer.

The association of BRCA1 and BRCA2 mutations with increased risk for developing epithelial ovarian cancer is well established. However, the observed clinical differences, particularly the improved therapy response and patient survival in BRCA2-mutant patients, are unexplained. Our objective is to identify molecular pathways that are differentially regulated upon the loss of BRCA1 and BRCA2 functions in ovarian cancer. Transcriptomic and pathway analyses comparing BRCA1-mutant, BRCA2-mutant, and homologous recombination wild-type ovarian tumors showed differential regulation of the Wnt/ß-catenin pathway. Using Wnt3A-treated BRCA1/2 wild-type, BRCA1-null, and BRCA2-null mouse ovarian cancer cells, we observed preferential activation of canonical Wnt/ß-catenin signaling in BRCA1/2 wild-type ovarian cancer cells, whereas noncanonical Wnt/ß-catenin signaling was preferentially activated in the BRCA1-null ovarian cancer cells. Interestingly, BRCA2-null mouse ovarian cancer cells demonstrated a unique response to Wnt3A with the preferential upregulation of the Wnt signaling inhibitor Axin2. In addition, decreased phosphorylation and enhanced stability of ß-catenin were observed in BRCA2-null mouse ovarian cancer cells, which correlated with increased inhibitory phosphorylation on GSK3ß. These findings open venues for the translation of these molecular observations into modalities that can impact patient survival. SIGNIFICANCE: We show that BRCA1 and BRCA2 mutation statuses differentially impact the regulation of the Wnt/ß-catenin signaling pathway, a major effector of cancer initiation and progression. Our findings provide a better understanding of molecular mechanisms that promote the known differential clinical profile in these patient populations.