Implementing differentially pigmented skin models for predicting drug response variability across human ancestries.

Persistent racial disparities in health outcomes have catalyzed legislative reforms and heightened scientific focus recently. However, despite the well-documented properties of skin pigments in binding drug compounds, their impact on therapeutic efficacy and adverse drug responses remains insufficiently explored. This perspective examines the intricate relationships between variation in melanin-based skin pigmentation and pharmacokinetics and -dynamics, highlighting the need for considering diversity in skin pigmentation as a variable to advance the equitability of pharmacological interventions. The article provides guidelines on the selection of New Approach Methods (NAMs) to foster inclusive study designs in preclinical drug development pipelines, leading to an improved level of translatability to the clinic.

Simultaneous Periprosthetic Joint Infection and Infective Endocarditis: Prevalence, Risk Factors, and Clinical Presentation.

BACKGROUND: Infective endocarditis (IE) and periprosthetic joint infections (PJI) occur due to hematogenous bacterial spread, theoretically increasing the risk for concurrent infections. There is a scarcity of literature investigating this specific association. We aimed to assess the prevalence, comorbidities, and clinical presentation of patients who have simultaneous PJI and IE. METHODS: We retrospectively identified 655 patients (321 men, 334 women; 382 total hip arthroplasty, 273 total knee arthroplasty) who developed a PJI from July 1, 2015, to December 31, 2020, at one institution. There were two groups created: patients diagnosed with PJI with IE (PJI + IE) and PJI patients who did not have IE (PJI). We analyzed clinical outcomes and comorbidities. RESULTS: There were nine patients who had PJI with IE (1.4% of PJI patients). The C-reactive protein (170.9 versus 78, P = 0.026), Elixhauser comorbidity score (P = 0.002), length of hospital stay (LOS) (10.9 versus 5.7 days, P = 0.043), and the two-year post-discharge mortality rate (55.6 versus 9.0%, P = 0.0007) were significantly greater in the PJI+IE group. Comorbidities such as iron deficiency anemia (P = 0.03), coagulopathy (P = 0.02), complicated diabetes mellitus (P = 0.02), electrolyte disorders (P = 0.01), neurological disease (P = 0.004), paralysis (P = 0.04), renal failure (P = 0.0001), and valvular disease (P = 0.0008) occurred more frequently in the PJI + IE group. Modified Duke's criteria were met for possible or definite IE in 8 of the 9 patients (88.9%). CONCLUSION: Concurrent PJIs and IE, although rare, are a potentially devastating disease state with increased LOS and two-year mortality rates. This emphasizes the need for appropriate IE workups in patients who have a PJI. The modified Duke's criteria is effective in establishing a diagnosis for IE in this scenario.

Diverse RNA viruses of parasitic nematodes can elicit antibody responses in vertebrate hosts.

Parasitic nematodes have an intimate, chronic and lifelong exposure to vertebrate tissues. Here we mined 41 published parasitic nematode transcriptomes from vertebrate hosts and identified 91 RNA viruses across 13 virus orders from 24 families in ~70% (28 out of 41) of parasitic nematode species, which include only 5 previously reported viruses. We observe widespread distribution of virus-nematode associations across multiple continents, suggesting an ancestral acquisition event and host-virus co-evolution. Characterization of viruses of Brugia malayi (BMRV1) and Onchocerca volvulus (OVRV1) shows that these viruses are abundant in reproductive tissues of adult parasites. Importantly, the presence of BMRV1 RNA in B. malayi parasites mounts an RNA interference response against BMRV1 suggesting active viral replication. Finally, BMRV1 and OVRV1 were found to elicit antibody responses in serum samples from infected jirds and infected or exposed humans, indicating direct exposure to the immune system.

Whole-exome sequencing uncovers the genetic complexity of bicuspid aortic valve in families with early-onset complications.

Bicuspid aortic valve (BAV) is the most common congenital heart lesion with an estimated population prevalence of 1%. We hypothesize that specific gene variants predispose to early-onset complications of BAV (EBAV). We analyzed whole-exome sequences (WESs) to identify rare coding variants that contribute to BAV disease in 215 EBAV-affected families. Predicted damaging variants in candidate genes with moderate or strong supportive evidence to cause developmental cardiac phenotypes were present in 107 EBAV-affected families (50% of total), including genes that cause BAV (9%) or heritable thoracic aortic disease (HTAD, 19%). After appropriate filtration, we also identified 129 variants in 54 candidate genes that are associated with autosomal-dominant congenital heart phenotypes, including recurrent deleterious variation of FBN2, MYH6, channelopathy genes, and type 1 and 5 collagen genes. These findings confirm our hypothesis that unique rare genetic variants drive early-onset presentations of BAV disease.

Early Improvement in Postoperative Clinical Outcomes without Patellar Resurfacing in Patella-friendly Design of Medial Pivot TKA.

INTRODUCTION: There is continued debate about the efficacy and indications for patellar resurfacing in total knee arthroplasty (TKA), especially with the emergence of patella-friendly designs. This study aimed to compare the postoperative outcomes in patients undergoing TKA with or without patellar resurfacing using the same implant design. METHOD: This is a retrospective cohort study of patients who underwent TKA including those with patellar resurfacing (PR group) and those without (NPR group). Demographic data included age, gender, side of surgery, operative time, and BMI. Outcomes included preoperative, 2-week, 6-week, and 1-year postoperative Knee Injury and Osteoarthritis Outcome Score and Joint Replacement (KOOS, JR) values along with knee range of motion (ROM). Postoperative complications were recorded. The power analysis with a large effect size indicated that a minimum sample size of 54 was required for the student t-test and 34 for the paired t-test. RESULT: A total of 90 medial pivot (MP) TKA were included in this study. There were 30 knees in the PR group and 60 in the NPR group. There was no significant difference between the groups for all demographic data, preoperative and postoperative ROM, and KOOS, JR values at all time points (p>0.05 for all variables). The KOOS, JR significantly improved in the NPR groups at 2-week, 6-week, and 1-year postoperatively when compared to the preoperative score and at 6-week and 1-year postoperatively in the PR group (p<0.01). No revisions related to the patellofemoral joint were observed in patients initially undergoing patellar resurfacing. One patient in the NPR group required secondary patellar resurfacing. CONCLUSION: The patella-friendly MP TKA yielded favorable postoperative outcomes, with or without patellar resurfacing. Improvements in KOOS, JR were observed earlier in the NPR group when compared to the PR group, suggesting that patellar resurfacing may not always be necessary for modern TKA designs.

An estimate of the impact rate on Mars from statistics of very-high-frequency marsquakes.

The number density of impact craters on a planetary surface is used to determine its age, which requires a model for the production rate of craters of different sizes. On Mars, however, estimates of the production rate of small craters (<60 m) from orbital imagery and from extrapolation of lunar impact data do not match. Here we provide a new independent estimate of the impact rate by analysing the seismic events recorded by the seismometer onboard NASA's InSight lander. Some previously confirmed seismically detected impacts are part of a larger class of marsquakes (very high frequency, VF). Although a non-impact origin cannot be definitively excluded for each VF event, we show that the VF class as a whole is plausibly caused by meteorite impacts. We use an empirical scaling relationship to convert between seismic moment and crater diameter. Applying area and time corrections to derive a global impact rate, we find that 280-360 craters >8 m diameter are formed globally per year, consistent with previously published chronology model rates and above the rates derived from freshly imaged craters. Our work shows that seismology is an effective tool for determining meteoroid impact rates and complements other methods such as orbital imaging.

Conservation of mutation and recombination parameters between mammals and zebra finch.

Most of our understanding of the fundamental processes of mutation and recombination stems from a handful of disparate model organisms and pedigree studies of mammals, with little known about other vertebrates. To gain a broader comparative perspective, we focused on the zebra finch (Taeniopygia castanotis), which, like other birds, differs from mammals in its karyotype (which includes many micro-chromosomes), in the mechanism by which recombination is directed to the genome, and in aspects of ontogenesis. We collected genome sequences from three generation pedigrees that provide information about 80 meioses, inferring 202 single-point de novo mutations, 1,174 crossovers, and 275 non-crossovers. On that basis, we estimated a sex-averaged mutation rate of 5.0 × 10-9 per base pair per generation, on par with mammals that have a similar generation time. Also as in mammals, we found a paternal germline mutation bias at later stages of gametogenesis (of 1.7 to 1) but no discernible difference between sexes in early development. We also examined recombination patterns, and found that the sex-averaged crossover rate on macro-chromosomes (1.05 cM/Mb) is again similar to values observed in mammals, as is the spatial distribution of crossovers, with a pronounced enrichment near telomeres. In contrast, non-crossover rates are more uniformly distributed. On micro-chromosomes, sex-averaged crossover rates are substantially higher (4.21 cM/Mb), as expected from crossover homeostasis, and both crossover and non-crossover events are more uniformly distributed. At a finer scale, recombination events overlap CpG islands more often than expected by chance, as expected in the absence of PRDM9. Despite differences in the mechanism by which recombination events are specified and the presence of many micro-chromosomes, estimates of the degree of GC-biased gene conversion (59%), the mean non-crossover conversion tract length (~23 bp), and the non-crossover to crossover ratio (6.7:1) are all comparable to those reported in primates and mice. The conservation of mutation and recombination properties from zebra finch to mammals suggest that these processes have evolved under stabilizing selection.

The ATOM-Seq sequence capture panel can accurately predict microsatellite instability status in formalin-fixed tumour samples, alongside routine gene mutation testing.

Microsatellite instability (MSI) occurs across a number of cancers and is associated with different clinical characteristics when compared to microsatellite stable (MSS) cancers. As MSI cancers have different characteristics, routine MSI testing is now recommended for a number of cancer types including colorectal cancer (CRC). Using gene panels for sequencing of known cancer mutations is routinely performed to guide treatment decisions. By adding a number of MSI regions to a small gene panel, the efficacy of simultaneous MSI detection in a series of CRCs was tested. Tumour DNA from formalin-fixed, paraffin-embedded (FFPE) tumours was sequenced using a 23-gene panel kit (ATOM-Seq) provided by GeneFirst. The mismatch repair (MMR) status was obtained for each patient from their routine pathology reports, and compared to MSI predictions from the sequencing data. By testing 29 microsatellite regions in 335 samples the MSI status was correctly classified in 314/319 samples (98.4% concordance), with sixteen failures. By reducing the number of regions in silico, comparable performance could be reached with as few as eight MSI marker positions. This test represents a quick, and accurate means of determining MSI status in FFPE CRC samples, as part of a routine gene mutation assay, and can easily be incorporated into a research or diagnostic setting. This could replace separate mutation and MSI tests with no loss of accuracy, thus improving testing efficiency.

16S rRNA gene amplicon sequencing data from the gut microbiota of adolescent Afghan refugees.

The gut microbiota residing in the distal ileum and colon is the most complex, diverse, and densest microbial ecosystem in the human body. Despite its known role in human health and disease, gut microbiome diversity and function are rarely explored in vulnerable populations such as refugees. The current study aimed to explore gut microbiota diversity and sources of variation among adolescent Afghan refugees residing in Peshawar, Pakistan. Stool samples were collected from 10 - 18 years old, healthy adolescents (n=205) for 16S rRNA gene sequence (V4-V5 hypervariable region) analysis on isolated faecal DNA. Bioinformatics analyses were performed using Kraken2, Bracken and Phyloseq. The data presented here will allow researchers to profile the gut microbiota of this rarely explored, vulnerable population who are at high risk of food insecurity and malnutrition. The data can be used to provide insight on the impact of demographic characteristics, dietary intake, nutritional status, and health on gut microbiome diversity, and enables a comparative analysis with similar data sets from other population groups of relevance. The amplicon sequencing data are deposited in the NCBI Sequence Read Archive as BioProject PRJNA1105775.

Who Is Treating Periprosthetic Femur Fractures? An Analysis of the Periprosthetic Research Consortium.

Background: Periprosthetic femur fractures (PPFFs) following total hip arthroplasty (THA) have increased in the past decade as the demand for primary surgery continues to grow. Although there is now more evidence to describe the treatment of Vancouver B fractures, there is still limited knowledge regarding factors that cause surgeons to perform either an open reduction and internal fixation (ORIF) or revision THA (rTHA). The purpose of this study was to determine what type of surgeons treat Vancouver B PPFFs at 11 major academic institutions and if there are trends in treatment decision-making regarding the use of ORIF or rTHA based on surgical training or patient factors. Methods: This multicenter retrospective study evaluated patients surgically treated for Vancouver B PPFF after THA between 2014 and 2019. Patients from 11 academic centers located in the United States were included in this study. Surgical outcomes and patient demographics were evaluated based on surgeon training, surgical treatment type, and institution. Results: Presence of Vancouver B2 (odds ratio [OR]: 0.02, P < .001) or B3 (OR: 0.04, P < .001) fractures were independent risk factors for treatment with rTHA. Treatment by a trauma (OR: 12.49, P < .001) or other-specified surgeon (OR: 13.63, P < .001) were independent risk factors for ORIF repair of Vancouver B fractures. There were no differences in outcomes based on surgeon subspecialty training. Conclusions: This study showed the trends in surgeons who surgically manage Vancouver B fractures at 11 major academic institutions and highlighted that regardless of surgical training or surgical treatment type, postoperative outcomes following management of PPFF were similar.

Rare genomic copy number variants implicate new candidate genes for bicuspid aortic valve.

Bicuspid aortic valve (BAV), the most common congenital heart defect, is a major cause of aortic valve disease requiring valve interventions and thoracic aortic aneurysms predisposing to acute aortic dissections. The spectrum of BAV ranges from early onset valve and aortic complications (EBAV) to sporadic late onset disease. Rare genomic copy number variants (CNVs) have previously been implicated in the development of BAV and thoracic aortic aneurysms. We determined the frequency and gene content of rare CNVs in EBAV probands (n = 272) using genome-wide SNP microarray analysis and three complementary CNV detection algorithms (cnvPartition, PennCNV, and QuantiSNP). Unselected control genotypes from the Database of Genotypes and Phenotypes were analyzed using identical methods. We filtered the data to select large genic CNVs that were detected by multiple algorithms. Findings were replicated in a BAV cohort with late onset sporadic disease (n = 5040). We identified 3 large and rare (< 1,1000 in controls) CNVs in EBAV probands. The burden of CNVs intersecting with genes known to cause BAV when mutated was increased in case-control analysis. CNVs intersecting with GATA4 and DSCAM were enriched in cases, recurrent in other datasets, and segregated with disease in families. In total, we identified potentially pathogenic CNVs in 9% of EBAV cases, implicating alterations of candidate genes at these loci in the pathogenesis of BAV.

Development of Fluoride-Ion Primary Batteries: The Electrochemical Defluorination of CF x.

The lithium-carbon monofluoride (Li-CF x ) couple has the highest specific energy of any practical battery chemistry. However, the large polarization associated with the CF x electrode (>1.5 V loss) limits it from achieving its full discharge energy, motivating the search for new CF x reaction mechanisms with reduced overpotential. Here, using a liquid fluoride (F)-ion conducting electrolyte at room temperature, we demonstrate for the first time the electrochemical defluorination of CF x cathodes, where metal fluorides form at a metal anode instead of the CF x cathode. F-ion primary cells were developed by pairing CF x cathodes with either lead (Pb) or tin (Sn) metal anodes, which achieved specific capacities of over 700 mAh g-1 and over 400 mAh g-1, respectively. Solid-state 19F and 119Sn{19F} nuclear magnetic resonance (NMR), X-ray diffraction (XRD), Raman, inductively coupled plasma (ICP), and X-ray fluorescence (XRF) measurements establish that upon discharge, the CF x cathode defluorinates while Pb forms PbF2 and Sn forms both SnF4 and SnF2. Technological development of F-ion metal-CF x cells based on this concept represents a promising avenue for realizing primary batteries with high specific energy.

An Examination of Hate-Motivated Behavior Among Adults in Scotland and Associations with Risk Factors for Self-Directed Violence.

Hate-motivated behavior (HMB) ranges from microaggressions to criminal acts and is a public health concern with consequences for the physical and mental well-being of individuals, families, and communities. The Hate-Motivated Behavior Checklist (HMBC) was developed with the goal of advancing the measurement of HMB perpetration. To provide insights into perpetration and victimization across the HMB continuum in Scotland, the present study sought to examine the factor structure of both the original HMBC and our adapted victimization version in a sample of adults currently living in Scotland. It also aimed to test associations between HMB and cognitions, which are related to self-directed violence (defeat and entrapment). Participants (n = 447) completed an online cross-sectional survey assessing demographic factors, HMB (perpetration and victimization), and perceptions of defeat and entrapment. Confirmatory factor analysis was used to examine the factor structure of the HMBC and the adapted victimization version of this checklist and path analyses were implemented to provide insights into potential links between HMB, defeat, and entrapment. In line with previous work, results provided support for interpreting the HMB Checklist as a single-factor total score. This was also true for the victimization version of the checklist. Results indicated that HMB victimization (but not perpetration) was associated with increased perceptions of defeat and entrapment. These findings suggest that the HMBC (for assessing both perpetration and victimization) represents potentially useful tools for HMB research and supports their applicability outside of an American context. Furthermore, by examining HMB through the lens of a contemporary model of suicidal behavior, our findings also provide insights into potential psychological mechanisms linking interpersonal and self-directed violence. Future research should implement prospective research designs and integrate measures of self-directed violence outcomes alongside HMB, defeat, and entrapment, to further advance understanding of this association.

Sialic acid and PirB are not required for targeting of neural circuits by neurotropic mammalian orthoreovirus.

Serotype 3 (T3) strains of mammalian orthoreovirus (reovirus) spread to the central nervous system to infect the brain and cause lethal encephalitis in newborn mice. Although reovirus targets several regions in the brain, susceptibility to infection is not uniformly distributed. The neuronal subtypes and anatomic sites targeted throughout the brain are not precisely known. Reovirus binds several attachment factors and entry receptors, including sialic acid (SA)-containing glycans and paired immunoglobulin-like receptor B (PirB). While these receptors are not required for infection of some types of neurons, reovirus engagement of these receptors can influence neuronal infection in certain contexts. To identify patterns of T3 neurotropism, we used microbial identification after passive tissue clearance and hybridization chain reaction to stain reovirus-infected cells throughout intact, optically transparent brains of newborn mice. Three-dimensional reconstructions revealed in detail the sites targeted by reovirus throughout the brain volume, including dense infection of the midbrain and hindbrain. Using reovirus mutants incapable of binding SA and mice lacking PirB expression, we found that neither SA nor PirB is required for the infection of various brain regions. However, SA may confer minor differences in infection that vary by region. Collectively, these studies indicate that many regions in the brain of newborn mice are susceptible to reovirus and that patterns of reovirus infection are not dependent on reovirus receptors SA and PirB.IMPORTANCENeurotropic viruses invade the central nervous system (CNS) and target various cell types to cause disease manifestations, such as meningitis, myelitis, or encephalitis. Infections of the CNS are often difficult to treat and can lead to lasting sequelae or death. Mammalian orthoreovirus (reovirus) causes age-dependent lethal encephalitis in many young mammals. Reovirus infects neurons in several different regions of the brain. However, the complete pattern of CNS infection is not understood. We found that reovirus targets almost all regions of the brain and that patterns of tropism are not dependent on receptors sialic acid and paired immunoglobulin-like receptor B. These studies confirm that two known reovirus receptors do not completely explain the cell types infected in brain tissue and establish strategies that can be used to understand complete patterns of viral tropism in an intact brain.

Evolutionary Systems Biology Identifies Genetic Trade-offs In Rice Defense Against Above- and Belowground Attackers.

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, and O. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different above- and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), respectively, and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at the KSL8 and MG1 loci on chromosome 11. KSL8 encodes the first committed step towards biosynthesis of either stemarane- or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking out KSL8-jap and CPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance to S. frugiperda and decreased resistance to M. incognita. Furthermore, MG1 resides in a haplotype that provided resistance to M. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungus Magnaporthe oryzae and other pests and pathogens. Finally, KSL8 and MG1 alleles are located within trans-species haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms at KSL8 and MG1 may be maintained through complex and diffuse community interactions.

CD91 and its ligand gp96 confer cross-priming capabilities to multiple APCs during immune responses to nascent, emerging tumors.

During cancer immunosurveillance, dendritic cells (DCs) play a central role in orchestrating T-cell responses against emerging tumors. Capture of miniscule amounts of antigen along with tumor-initiated costimulatory signals can drive maturation of DCs. Expression of CD91 on DCs is essential in cross-priming of T-cell responses in the context of nascent tumors. Multiple DC and macrophage subsets express CD91 and engage tumor-derived gp96 to initiate antitumor immune responses, yet the specific CD91+ antigen-presenting cells (APCs) that are required for T-cell cross-priming during cancer immunosurveillance are unknown. In this study, we determined that CD91 expression on type 1 conventional DCs (cDC1) is necessary for cancer immunosurveillance. Specifically, CD91-expressing cDC1 were found to capture the CD91 ligand gp96 from tumors and, upon migration to the lymph nodes, distribute gp96 among lymph-node resident APCs. However, cDC1 that captured tumor-derived gp96 only provided early tumor control, while sustained and long-term tumor rejection was bestowed to the host by other gp96+ cross-priming DCs. We further found that the CD91-induced transcriptome in APCs promoted cross-priming of T-cell responses while downregulating immune regulatory pathways. Our results show an elaborate and synchronized division of labor of APCs in the successful elimination of cancer cells via CD91. We predict that the specialized functions of APC subsets can be harnessed for immunotherapy of disease.

Structure-Based Optimization of a Series of Covalent, Cell Active Bfl-1 Inhibitors.

Bfl-1, a member of the Bcl-2 family of proteins, plays a crucial role in apoptosis regulation and has been implicated in cancer cell survival and resistance to venetoclax therapy. Due to the unique cysteine residue in the BH3 binding site, the development of covalent inhibitors targeting Bfl-1 represents a promising strategy for cancer treatment. Herein, the optimization of a covalent cellular tool from a lead-like hit using structure based design is described. Informed by a reversible X-ray fragment screen, the strategy to establish interactions with a key glutamic acid residue (Glu78) and optimize binding in a cryptic pocket led to a 1000-fold improvement in biochemical potency without increasing reactivity of the warhead. Compound (R,R,S)-26 has a kinact/KI of 4600 M-1 s-1, shows <1 µM caspase activation in a cellular assay and cellular target engagement, and has good physicochemical properties and a promising in vivo profile.

Drp1 splice variants regulate ovarian cancer mitochondrial dynamics and tumor progression.

Aberrant mitochondrial fission/fusion dynamics are frequently associated with pathologies, including cancer. We show that alternative splice variants of the fission protein Drp1 (DNM1L) contribute to the complexity of mitochondrial fission/fusion regulation in tumor cells. High tumor expression of the Drp1 alternative splice variant lacking exon 16 relative to other transcripts is associated with poor outcome in ovarian cancer patients. Lack of exon 16 results in Drp1 localization to microtubules and decreased association with mitochondrial fission sites, culminating in fused mitochondrial networks, enhanced respiration, changes in metabolism, and enhanced pro-tumorigenic phenotypes in vitro and in vivo. These effects are inhibited by siRNAs designed to specifically target the endogenously expressed transcript lacking exon 16. Moreover, lack of exon 16 abrogates mitochondrial fission in response to pro-apoptotic stimuli and leads to decreased sensitivity to chemotherapeutics. These data emphasize the pathophysiological importance of Drp1 alternative splicing, highlight the divergent functions and consequences of changing the relative expression of Drp1 splice variants in tumor cells, and strongly warrant consideration of alternative splicing in future studies focused on Drp1.