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The serine-/arginine-rich splicing factor 2 (SRSF2) plays pivotal roles in pre-mRNA processing and gene transcription. Recurrent mutations, particularly a proline-to-histidine substitution at position 95 (P95H), are common in neoplastic diseases. Here, we assess SRSF2's diverse functions in squamous cell carcinoma. We show that SRSF2 deletion or homozygous P95H mutation both cause extensive DNA damage leading to cell-cycle arrest. Mechanistically, SRSF2 regulates efficient bi-directional transcription of DNA replication and repair genes, independent from its function in splicing. Further, SRSF2 haploinsufficiency induces DNA damage without halting the cell cycle. Exposing mouse skin to tumor-promoting carcinogens enhances the clonal expansion of heterozygous Srsf2 P95H epidermal cells but unexpectedly inhibits tumor formation. To survive carcinogen treatment, Srsf2 P95H +/- cells undergo substantial transcriptional rewiring and restore bi-directional gene expression. Thus, our study underscores SRSF2's importance in regulating transcription to orchestrate the cell cycle and the DNA damage response., Competing Interests: Declaration of interests The authors declare no competing interests., (Crown Copyright © 2024. Published by Elsevier Inc. All rights reserved.)

The epitaxial growth of complex oxides enables the production of high-quality films, yet substrate choice is restricted to certain symmetry and lattice parameters, thereby limiting the technological applications of epitaxial oxides. In comparison, the development of free-standing oxide membranes gives opportunities to create novel heterostructures by nonepitaxial stacking of membranes, opening new possibilities for materials design. Here, we introduce a method for writing, with atomic precision, ionically bonded crystalline materials across the gap between an oxide membrane and a carrier substrate. The process involves a thermal pretreatment, followed by localized exposure to the raster scan of a scanning transmission electron microscopy (STEM) beam. STEM imaging and electron energy-loss spectroscopy show that we achieve atomically sharp interface reconstructions between a 30-nm-thick SrTiO 3 membrane and a niobium-doped SrTiO 3 (001)-oriented carrier substrate. These findings indicate new strategies for fabricating synthetic heterostructures with novel structural and electronic properties.

Introduction: The neurobehavioral significance of white matter hyperintensities (WMHs) seen on magnetic resonance imaging after traumatic brain injury (TBI) remains unclear, especially in Veterans and Service Members with a history of mild TBI (mTBI). In this study, we investigate the relation between WMH, mTBI, age, and cognitive performance in a large multisite cohort from the Long-term Impact of Military-relevant Brain Injury Consortium-Chronic Effects of Neurotrauma Consortium., Materials and Methods: The neuroimaging and neurobehavioral assessments for 1,011 combat-exposed, post-9/11 Veterans and Service Members (age range 22-69 years), including those with a history of at least 1 mTBI (n = 813; median postinjury interval of 8 years) or negative mTBI history (n = 198), were examined., Results: White matter hyperintensities were present in both mTBI and comparison groups at similar rates (39% and 37%, respectively). There was an age-by-diagnostic group interaction, such that older Veterans and Service Members with a history of mTBI demonstrated a significant increase in the number of WMHs present compared to those without a history of mTBI. Additional associations between an increase in the number of WMHs and service-connected disability, insulin-like growth factor-1 levels, and worse performance on tests of episodic memory and executive functioning-processing speed were found., Conclusions: Subtle but important clinical relationships are identified when larger samples of mTBI participants are used to examine the relationship between history of head injury and radiological findings. Future studies should use follow-up magnetic resonance imaging and longitudinal neurobehavioral assessments to evaluate the long-term implications of WMHs following mTBI., (© Oxford University Press 2024.)

Background: Upper limb proprioceptive impairments are common after stroke and affect daily function. Recent work has shown that stroke survivors have difficulty using visual information to improve proprioception. It is unclear how eye movements are impacted to guide action of the arm after stroke. Here, we aimed to understand how upper limb proprioceptive impairments impact eye movements in individuals with stroke., Methods: Control (N = 20) and stroke participants (N = 20) performed a proprioceptive matching task with upper limb and eye movements. A KINARM exoskeleton with eye tracking was used to assess limb and eye kinematics. The upper limb was passively moved by the robot and participants matched the location with either an arm or eye movement. Accuracy was measured as the difference between passive robot movement location and active limb matching (Hand-End Point Error) or active eye movement matching (Eye-End Point Error)., Results: We found that individuals with stroke had significantly larger Hand (2.1×) and Eye-End Point (1.5×) Errors compared to controls. Further, we found that proprioceptive errors of the hand and eye were highly correlated in stroke participants ( r  = .67, P  = .001), a relationship not observed for controls., Conclusions: Eye movement accuracy declined as a function of proprioceptive impairment of the more-affected limb, which was used as a proprioceptive reference. The inability to use proprioceptive information of the arm to coordinate eye movements suggests that disordered proprioception impacts integration of sensory information across different modalities. These results have important implications for how vision is used to actively guide limb movement during rehabilitation., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

The Four Core Genotypes (FCG) is a mouse model system used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the Y Sry- chromosome and thus increased the expression of X-linked genes including the single-stranded RNA sensor and autoimmune disease mediator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on C57BL/6J FCG mice., (© 2024. The Author(s).)

Background: Whether or not to progress from a pilot study to a definitive trial is often guided by pre-specified quantitative progression criteria with three possible outcomes. Although the choice of these progression criteria will help to determine the statistical properties of the pilot trial, there is a lack of research examining how they, or the pilot sample size, should be determined., Methods: We review three-outcome trial designs originally proposed in the phase II oncology setting and extend these to the case of external pilots, proposing a unified framework based on univariate hypothesis tests and the control of frequentist error rates. We apply this framework to an example and compare against a simple two-outcome alternative., Results: We find that three-outcome designs can be used in the pilot setting, although they are not generally more efficient than simpler two-outcome alternatives. We show that three-outcome designs can help allow for other sources of information or other stakeholders to feed into progression decisions in the event of a borderline result, but this will come at the cost of a larger pilot sample size than the two-outcome case. We also show that three-outcome designs can be used to allow adjustments to be made to the intervention or trial design before commencing the definitive trial, providing the effect of the adjustment can be accurately predicted at the pilot design stage. An R package, tout, is provided to optimise progression criteria and pilot sample size., Conclusions: The proposed three-outcome framework provides a way to optimise pilot trial progression criteria and sample size in a way that leads to desired operating characteristics. It can be applied whether or not an adjustment following the pilot trial is anticipated, but will generally lead to larger sample size requirements than simpler two-outcome alternatives., (© 2024. The Author(s).)

Undescended testis (UDT, cryptorchidism) is the most frequent genital anomaly in boys. However, its treatment varies widely throughout the world. This second part of our roundtable discussion aims to continue to ask global experts to express their attitudes towards several case scenarios of UDT in order to explore the rationale for their clinical decisions. As the European Association of Urology - Young Academic Urologists Pediatric Urology Working Group, we believe that this roundtable series will facilitate colleagues all over the world to reflect and improve their practices regarding the treatment of UDT., Competing Interests: Conflict of interest None declared., (Copyright © 2024 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

Introduction: Endometriosis typically presents in postmenarchal patients with cyclic and acyclic pelvic pain. However, there are reports of endometriosis in premenarchal patients., Case: We report a 10-year-old individual with 46,XY difference of sex development who was found to have endometriosis at the time of laparoscopic gonadectomy for gonadoblastoma., Conclusions: Although rare, endometriosis can occur in 46,XY individuals prior to puberty, highlighting the complex origin of the disease., Competing Interests: Conflicts of Interest NJN is a consultant and PI for Neurocrine Biosciences, Inc., a consultant for Ionis Pharmaceuticals, and on an expert panel for World Athletics., (Copyright © 2024. Published by Elsevier Inc.)

Introduction: The opioid epidemic response led to increased use of postoperative, non-opioid analgesia. Some pediatric urologists do not routinely use non-steroidal anti-inflammatory drugs (NSAIDs) for fear of causing acute kidney injury (AKI). While previous studies have demonstrated the safety and efficacy of NSAIDs in children, safety after lower urinary tract reconstruction has not been well characterized., Objective: ptUsing the Kidney Disease: Improving Global Outcomes (KDIGO) criteria for AKI (increase in creatinine ≥0.3 mg/dL or increase in creatinine ≥1.5x baseline or urine output <0.5 mL/kg/hr for 6 h), we hypothesized there would be a difference in the incidence of postoperative AKI between patients who did and did not receive NSAIDs following surgery., Study Design: Patients 2-18 years old who underwent lower urinary tract reconstruction (i.e., bladder augmentation and/or creation of a catheterizable channel) from 2009 to 2021 and had documented urine output were retrospectively reviewed. Chronic kidney disease (CKD) stage was calculated from creatinine and cystatin C within 6 months of surgery using the CKiD U25 equations. Patients who received NSAIDs were propensity matched on 11 characteristics with patients undergoing similar surgeries who did not receive NSAIDs. The primary outcome was incidence of AKI within 48 h of surgery., Results: The unmatched cohorts included 243 patients. Propensity matching identified 166 patients in the NSAID arm and 41 in the no NSAID arm. 26 patients with CKD stage 2-3 were included. There was no significant difference in the incidence of postoperative AKI based on any KDIGO criteria (17.1% no NSAID versus 16.3% NSAID, p = 0.87). Median postoperative opioids fell from 0.88 mg/kg in the no NSAID arm to 0.37 mg/kg morphine equivalents in the NSAID arm, although this was not statistically significant. Log-rank testing by Kaplan-Meier analysis demonstrated no difference in time to incidence of low urine output between the groups (p = 0.32). In the whole population not stratified by NSAID use, no differences were seen in AKI between those with and without CKD (16.7% with versus 17.9% without CKD)., Discussion: There was no difference in the incidence of postoperative AKI among patients who did and did not receive NSAIDs after lower urinary tract reconstruction, excluding those with advanced CKD., Conclusion: These results support that postoperative NSAIDs were an unlikely source of AKI. However, AKI remained a risk following these surgeries, regardless of NSAID use, likely owing to underlying disease, longer operations, and fluid shifts., Competing Interests: Conflicts of interest No conflicts of interest to report., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

In the public imaginary, drinking is often thought of as a behaviour separate from individuals' formal labour practices, but studies increasingly highlight the complex ways alcohol is entwined with work. Building on recent conceptual developments in the sociological fields of youth, health and work, we illustrate how drinking can be productively understood as 'affective labour', and thus itself a form of work that generates valuable embodied states and atmospheres. To do so, we draw on data from six focus groups with men coworkers from three hospitality workplaces and three corporate workplaces in Victoria. For the corporate groups, work-related drinking was tied to an unravelling of certain professional affects and facilitated harmonious and productive workplace relationships, but also introduced risks ranging from embarrassment to sexual harassment. For hospitality workers, drinking was more deeply enmeshed in workplace relationships and, for one group, drinking on-shift was positively framed as creating an affect and atmosphere that appealed to clientele, despite taking a toll on workers' wellbeing. In both settings not drinking risked limiting one's ability to get on colleagues' affective 'level'. Our data deepens current understandings of how drinking cultures may be woven through occupational settings, produce value for organisations and introduce unique potential for exclusion., (© 2024 The Authors. Sociology of Health & Illness published by John Wiley & Sons Ltd on behalf of Foundation for the Sociology of Health & Illness.)

Energy-dispersive X-ray spectroscopy (EDXS) mapping with a scanning transmission electron microscope (STEM) is commonly used for chemical characterization of materials. However, STEM-EDXS quantification becomes challenging when the phases constituting the sample under investigation share common elements and overlap spatially. In this paper, we present a methodology to identify, segment, and unmix phases with a substantial spectral and spatial overlap in a semi-automated fashion through combining non-negative matrix factorization with a priori knowledge of the sample. We illustrate the methodology using a sample taken from an electron beam-sensitive mineral assemblage representing Earth's deep mantle. With it, we retrieve the true EDX spectra of the constituent phases and their corresponding phase abundance maps. It further enables us to achieve a reliable quantification for trace elements having concentration levels of ∼100 ppm. Our approach can be adapted to aid the analysis of many materials systems that produce STEM-EDXS datasets having phase overlap and/or limited signal-to-noise ratio (SNR) in spatially-integrated spectra., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Energy dispersive X-ray (EDX) spectroscopy in the transmission electron microscope is a key tool for nanomaterials analysis, providing a direct link between spatial and chemical information. However, using it for precisely determining chemical compositions presents challenges of noisy data from low X-ray yields and mixed signals from phases that overlap along the electron beam trajectory. Here, we introduce a novel method, non-negative matrix factorization based pan-sharpening (PSNMF), to address these limitations. Leveraging the Poisson nature of EDX spectral noise and binning operations, PSNMF retrieves high-quality phase spectral and spatial signatures via consecutive factorizations. After validating PSNMF with synthetic data sets of different noise levels, we illustrate its effectiveness on two distinct experimental cases: a nanomineralogical lamella, and supported catalytic nanoparticles. Not only does PSNMF obtain accurate phase signatures, but data sets reconstructed from the outputs have demonstrably lower noise and better fidelity than from the benchmark denoising method of principle component analysis.

Background & Aims: Polyploidy in hepatocytes has been proposed as a genetic mechanism to buffer against transcriptional dysregulation. Here, we aim to demonstrate the role of polyploidy in modulating gene regulatory networks in hepatocytes during ageing., Methods: We performed single-nucleus RNA sequencing in hepatocyte nuclei of different ploidy levels isolated from young and old wild-type mice. Changes in the gene expression and regulatory network were compared to three independent strains that were haploinsufficient for HNF4A, CEBPA or CTCF, representing non-deleterious perturbations. Phenotypic characteristics of the liver section were additionally evaluated histologically, whereas the genomic allele composition of hepatocytes was analysed by BaseScope., Results: We observed that ageing in wild-type mice results in nuclei polyploidy and a marked increase in steatosis. Haploinsufficiency of liver-specific master regulators (HFN4A or CEBPA) results in the enrichment of hepatocytes with tetraploid nuclei at a young age, affecting the genomic regulatory network, and dramatically suppressing ageing-related steatosis tissue wide. Notably, these phenotypes are not the result of subtle disruption to liver-specific transcriptional networks, since haploinsufficiency in the CTCF insulator protein resulted in the same phenotype. Further quantification of genotypes of tetraploid hepatocytes in young and old HFN4A-haploinsufficient mice revealed that during ageing, tetraploid hepatocytes lead to the selection of wild-type alleles, restoring non-deleterious genetic perturbations., Conclusions: Our results suggest a model whereby polyploidisation leads to fundamentally different cell states. Polyploid conversion enables pleiotropic buffering against age-related decline via non-random allelic segregation to restore a wild-type genome., Impact and Implications: The functional role of hepatocyte polyploidisation during ageing is poorly understood. Using single-nucleus RNA sequencing and BaseScope approaches, we have studied ploidy dynamics during ageing in murine livers with non-deleterious genetic perturbations. We have identified that hepatocytes present different cellular states and the ability to buffer ageing-associated dysfunctions. Tetraploid nuclei exhibit robust transcriptional networks and are better adapted to genomically overcome perturbations. Novel therapeutic interventions aimed at attenuating age-related changes in tissue function could be exploited by manipulation of ploidy dynamics during chronic liver conditions., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Huntingtin protein, mutated in Huntington's disease, is implicated in nucleic acid-mediated processes, yet the evidence for direct huntingtin-nucleic acid interaction is limited. Here, we show wild-type and mutant huntingtin copurify with nucleic acids, primarily RNA, and interact directly with G-rich RNAs in in vitro assays. Huntingtin RNA-immunoprecipitation sequencing from patient-derived fibroblasts and neuronal progenitor cells expressing wild-type and mutant huntingtin revealed long noncoding RNA NEAT1 as a significantly enriched transcript. Altered NEAT1 levels were evident in Huntington's disease cells and postmortem brain tissues, and huntingtin knockdown decreased NEAT1 levels. Huntingtin colocalized with NEAT1 in paraspeckles, and we identified a high-affinity RNA motif preferred by huntingtin. This study highlights NEAT1 as a huntingtin interactor, demonstrating huntingtin's involvement in RNA-mediated functions and paraspeckle regulation.

Introduction: Women born with anorectal malformation (ARM) or Hirschsprung disease (HD) may have impaired urologic function resulting in sequelae in adulthood. This study assessed and compared self-reported urinary outcomes in adult females born with ARM or HD to a reference population., Methods: This was an IRB approved, cross-sectional study of female-born patients with ARM or HD, who completed surveys between November 2021 and August 2022. Female patients between the ages of 18 and 80 years were included. Lower Urinary Tract Symptom Questionnaires were administered through REDCap and the responses were compared to a reference population using Chi-squared or Fisher's exact tests., Results: Sixty-six born female patients answered the questionnaires, two of them identified as non-binary. The response rate was 76%. Median age was 31.6 years. The majority were born with cloaca (56.3%), followed by other type of ARMs (28.1%), complex malformation (9.4%), and HD (6.3%). A history of bladder reconstruction was present for 26.6%. Catheterization through a channel or native urethra was present in 18.8%. Two had ureterostomies and were excluded from the analysis. Seven had chronic kidney disease or end-stage renal disease, three with a history of kidney transplantation. Patients with cloaca had significantly higher rates of urinary incontinence, urinary tract infection, and social problems due to impaired urological functioning, when compared to an age-matched reference population (Table 3)., Conclusion: This study emphasizes the need for a multi-disciplinary team that includes urology and nephrology following patients with ARM long term, especially within the subgroup of cloaca., Level of Evidence: III., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Vincristine (VCR) is one of the most widely used chemotherapy agents in treating pediatric cancer. Nonetheless, it is known to cause dose-dependent neurotoxicity which can impact virtually every organ system. Despite its widespread use, the precise impact of VCR on the lower urinary tract (LUT) remains inadequately elucidated. Our initial clinical and translational investigations suggest a sex-specific influence of childhood VCR exposure on LUT function. Thus, the current study aimed to investigate the late effects of systemic VCR exposure on LUT physiology and the underlying mechanisms, focusing on dosage and male-sex, employing juvenile CD-1 mice as a model. Male mice subjected to VCR exhibited augmented functional bladder capacity accompanied by frequent non-void contractions during awake cystometry, alongside mast cell accumulation within the bladder, compared to the saline-treated control group. Noteworthy functional changes were observed in bladder strips from the VCR group, including decreased nerve-mediated contraction, heightened contractile responses to cholinergic and purinergic agonists, enhanced responsiveness to histamine-primarily via histamine receptor 1 (Hrh1)-and an augmented relaxation effect with compound 48/80 (a mast cell degranulator), relative to the control group. Significant changes in gene expression levels associated with neuroinflammation and nociception were observed in both the bladder and lumbosacral dorsal root ganglia (Ls-DRG) of the VCR group. These findings suggest that VCR exposure during childhood, particularly in males, triggers neuroimmune responses in the bladder and Ls-DRG, amplifying responsiveness to neurotransmitters in the bladder, thereby contributing to LUT dysfunction characterized by a mixed bladder phenotype as a late effect during survivorship., (© 2024. The Author(s).)

Purpose: Urodynamic testing (UDS) is an important tool in the management of pediatric lower urinary tract conditions. There have been notable efforts to standardize pediatric UDS nomenclature and technique, but no formal guidelines exist on essential elements to include in a clinical report. We sought to identify ideal structure and elements of a pediatric UDS assessment based on expert consensus., Materials and Methods: Pediatric urologists regularly performing UDS were queried using a Delphi process. Participants were invited representing varied geographic, experience, and societal involvement. Participants underwent 3 rounds of questionnaires between November 2022 and August 2023 focusing on report organization, elements, definitions, and automated electronic health record clinical decision support. Professional billing requirements were also considered. Consensus was defined as 80% agreeing either in favor of or against a topic. Elements without consensus were discussed in subsequent rounds., Results: A diverse sample of 30 providers, representing 27 institutions across 21 US states; Washington, District of Columbia; and Canada completed the study. Participants reported interpreting an average number of 5 UDS reports per week (range 1-22). The finalized consensus report identifies 93 elements that should be included in a pediatric UDS report based on applicable study conditions and findings., Conclusions: This consensus report details the key elements and structure agreed upon by an expert panel of pediatric urologists. Further standardization of documentation should aid collaboration and research for patients undergoing UDS. Based on this information, development of a standardized UDS report template using electronic health record implementation principles is underway, which will be openly available for pediatric urologists.

Background: DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but low in transcription factor (TF) binding sites and active regulatory regions. However, the mechanisms establishing genome-wide and TF binding site methylation patterns are still unclear., Results: Here we use a comparative approach to investigate the association of DNA methylation to TF binding evolution in mammals. Specifically, we experimentally profile DNA methylation and combine this with published occupancy profiles of five distinct TFs (CTCF, CEBPA, HNF4A, ONECUT1, FOXA1) in the liver of five mammalian species (human, macaque, mouse, rat, dog). TF binding sites are lowly methylated, but they often also have intermediate methylation levels. Furthermore, biding sites are influenced by the methylation status of CpGs in their wider binding regions even when CpGs are absent from the core binding motif. Employing a classification and clustering approach, we extract distinct and species-conserved patterns of DNA methylation levels at TF binding regions. CEBPA, HNF4A, ONECUT1, and FOXA1 share the same methylation patterns, while CTCF's differ. These patterns characterize alternative functions and chromatin landscapes of TF-bound regions. Leveraging our phylogenetic framework, we find DNA methylation gain upon evolutionary loss of TF occupancy, indicating coordinated evolution. Furthermore, each methylation pattern has its own evolutionary trajectory reflecting its genomic contexts., Conclusions: Our epigenomic analyses indicate a role for DNA methylation in TF binding changes across species including that specific DNA methylation profiles characterize TF binding and are associated with their regulatory activity, chromatin contexts, and evolutionary trajectories., (© 2024. The Author(s).)

Melioidosis is a life-threatening, emerging infectious disease caused by the environmental bacterium Burkholderia pseudomallei. Melioidosis is hyperendemic in tropical Australia and southeast Asia, however the disease is increasingly encountered beyond these regions. Early diagnosis is essential as the infection has a case-fatality rate of up to 50 %. Melioidosis most commonly involves the lungs, although almost any organ can be affected. Most patients present acutely but an insidious presentation over weeks to months is also well described. We present a case series of 7 patients from tropical Australia whom local clinicians initially believed to have cancer ‒ most commonly lung cancer ‒ only for further investigation to establish a diagnosis of melioidosis. All 7 patients had comorbidities that predisposed them to developing melioidosis and all survived, but their delayed diagnosis resulted in 3 receiving anti-cancer therapies that resulted in significant morbidity. The study emphasises the importance of thorough diagnostic evaluation and repeated collection of microbiological samples. It is hoped that our experience will encourage other clinicians ‒ in the appropriate clinical context ‒ to consider melioidosis as a potential explanation for a patient's presentation, expediting its diagnosis and the initiation of potentially life-saving therapy., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

DNA base damage is a major source of oncogenic mutations 1 . Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation 2 . Here we exploited these properties to reveal how strand-asymmetric processes, such as replication and transcription, shape DNA damage and repair. Despite distinct mechanisms of leading and lagging strand replication 3,4 , we observe identical fidelity and damage tolerance for both strands. For small alkylation adducts of DNA, our results support a model in which the same translesion polymerase is recruited on-the-fly to both replication strands, starkly contrasting the strand asymmetric tolerance of bulky UV-induced adducts 5 . The accumulation of multiple distinct mutations at the site of persistent lesions provides the means to quantify the relative efficiency of repair processes genome wide and at single-base resolution. At multiple scales, we show DNA damage-induced mutations are largely shaped by the influence of DNA accessibility on repair efficiency, rather than gradients of DNA damage. Finally, we reveal specific genomic conditions that can actively drive oncogenic mutagenesis by corrupting the fidelity of nucleotide excision repair. These results provide insight into how strand-asymmetric mechanisms underlie the formation, tolerance and repair of DNA damage, thereby shaping cancer genome evolution., (© 2024. The Author(s).)

DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage., Competing Interests: Competing interests statement:The authors declare no competing interest.

Objective: This study aimed to compare the risks of adverse perinatal outcomes by body mass index (BMI) categories in healthy pregnant individuals delivered by term elective repeat cesarean (ERCD) to describe an optimal timing of delivery in otherwise healthy patients at the highest-risk BMI threshold., Study Design: A secondary analysis of a prospective cohort of pregnant individuals undergoing ERCD at 19 centers in the Maternal-Fetal Medicine Units Network from 1999 to 2002. Nonanomalous singletons undergoing prelabor ERCD at term were included. The primary outcome was composite neonatal morbidity; secondary outcomes included composite maternal morbidity and individual components of the composites. Patients were stratified by BMI classes and to identify a BMI threshold for which morbidity was the highest. Outcomes were then examined by completed week's gestation, between BMI classes. Multivariable logistic regression was used to calculate adjusted odds ratios (aOR) and 95% confidence intervals (CI)., Results: A total of 12,755 patients were included in analysis. Patient's with BMI ≥ 40 had the highest rates of newborn sepsis, neonatal intensive care unit admissions, and wound complications. While a weight-related response was observed between BMI class and neonatal composite morbidity ( p  < 0.001), only those with BMI ≥ 40 had significantly higher odds of composite neonatal morbidity (aOR: 1.4, 95% CI: 1.0-1.8). In analyses of patients with BMI ≥ 40 ( n  = 1,848), there was no difference in the incidence of composite neonatal or maternal morbidity across weeks' gestation at delivery; however, as gestational age approached 39 to 40 weeks, rates of adverse neonatal outcomes decreased, only to increase again at 41 weeks' gestation. Of note, the odds of the primary neonatal composite were the highest at 38 weeks compared with 39 weeks (aOR: 1.5, 95% CI: 1.1-2.0)., Conclusion: Neonatal morbidity is significantly higher in pregnant individuals with BMI ≥40 delivering by ERCD. Despite this increased perinatal morbidity, delivery prior to 39 and after 41 weeks in these patients is associated with increased neonatal risks., Key Points: · Obese patients without additional comorbidities have higher rates of neonatal morbidity.. · Patients with BMI ≥ 40 carry the highest odds of poor perinatal outcomes.. · Earlier timing of delivery does not appear to reduce this risk.., Competing Interests: None declared., (Thieme. All rights reserved.)

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, during single mitoses and at single-strand resolution. To distinguish between chronic (reactive oxygen species (ROS)) and acute (ultraviolet light (UV)) mutagenesis, we microfluidically separate pairs of sister cells from the first mitosis following burst UV damage. Strikingly, UV mutations manifest as sister-specific events, revealing mirror-image mutation phasing genome-wide. In contrast, ROS mutagenesis in transcribed regions is reduced strand agnostically. Successive rounds of genome replication over persisting UV damage drives multiallelic variation at CC dinucleotides. Finally, we show that mutation phasing can be resolved to single strands across the entire genome of liver tumors from F1 mice. This strategy can be broadly used to distinguish the contributions of overlapping cancer relevant mutational processes., (© 2024. The Author(s).)

Introduction/background: Enhanced Recovery After Surgery (ERAS) is a fundamental shift in perioperative care that has consistently demonstrated an improved outcome for a wide variety of surgeries in adults but has only limited evidence in the pediatric population., Objective: We aimed to assess the success with and barriers to implementation of ERAS in a prospective, multi-center study on patients undergoing complex lower urinary tract reconstruction., Study Design: Centers were directed to implement an ERAS protocol using a multidisciplinary team and quality improvement methodologies. Providers completed pre- and post-pilot surveys. An audit committee met after enrolling the first 5 patients at each center. Pilot-phase outcomes included enrollment of ≥2 patients in the first 6 months of enrollment, completion of 90 days of follow-up, identification of barriers to implementation, and protocol adherence., Results: A total of 40 patients were enrolled across 8 centers. The median age at surgery was 10.3 years (IQR 6.4-12.5). Sixty five percent had a diagnosis of myelomeningocele, and 33 % had a ventriculoperitoneal shunt. A bladder augmentation was performed in 70 %, Mitrofanoff appendicovesicostomy in 52 %, Monti ileovesicostomy in 15 %, and antegrade continence enema channel in 38 %. The most commonly perceived barriers to implementation on the pre-pilot survey were "difficulty initiating and maintaining compliance with care pathway" in 51 % followed by a "lack of time, money, or clinical resources" in 36 %. The pre-pilot study experience, implementation, and pilot-phase outcomes are provided in the Table. All primary and secondary outcomes were achieved., Discussion: The findings of the present study were similar to several small comparative studies with regard to the importance of a multidisciplinary team, strong leadership, and continuous audit for successful implementation of ERAS. Similar barriers were also encountered to other studies, which primarily related to a lack of administrative support, leadership, and buy-in from other services. The limitations of the present study included a relatively small heterogeneous cohort and absence of a comparative group, which will be addressed in the larger exploratory phase of the trial. The findings may also not be generaziable due to the need for sustainable processes that were unique to each center as well as an absence of adequate volume or resources at smaller centers., Conclusions: ERAS was successfully implemented for complex lower urinary tract reconstruction across 8 centers through a multidisciplinary team, structured approach based on the local context, and focus on a continuous audit., Competing Interests: Conflicts of interest None., (Copyright © 2024 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

Anorectal malformations (ARM) are rare congenital anomalies characterized by a spectrum of defects resulting in the absence of a normal anal opening with or without fistula. Urogenital involvement is common, and the fistulous tract may terminate in the genitourinary system in males or within gynecological structures in females. Surgical reconstruction occurs early in life and survival of these patients to adulthood is the norm. There has, therefore, been increased focus on their long-term outcomes to better anticipate and treat the sequelae that may impact their health and well-being as this population ages. For urologists, urinary health, sexual function, and fertility outcomes are of particular interest among this population. This article aims to provide a review of urological, sexual, and fertility outcomes for individuals born with ARM with a focus on key issues that may occur later in life to ensure adequate counseling, screening, and treatment., Competing Interests: Conflicts of interest The authors have no conflicts of interest, financial or otherwise, to disclose., (Copyright © 2023. Published by Elsevier Ltd.)

Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Objectives: To develop and validate a predictive model to predict the risk of postoperative mortality after emergency laparotomy taking into account the following variables: age, age ≥ 80, ASA status, clinical frailty score, sarcopenia, Hajibandeh Index (HI), bowel resection, and intraperitoneal contamination., Summary Background Data: The discriminative powers of the currently available predictive tools range between adequate and strong; none has demonstrated excellent discrimination yet., Methods: The TRIPOD and STROCSS statement standards were followed to protocol and conduct a retrospective cohort study of adult patients who underwent emergency laparotomy due to non-traumatic acute abdominal pathology between 2017 and 2022. Multivariable binary logistic regression analysis was used to develop and validate the model via two protocols (Protocol A and B). The model performance was evaluated in terms of discrimination (ROC curve analysis), calibration (calibration diagram and Hosmer-Lemeshow test), and classification (classification table)., Results: One thousand forty-three patients were included (statistical power = 94%). Multivariable analysis kept HI (Protocol-A: P =0.0004; Protocol-B: P =0.0017), ASA status (Protocol-A: P =0.0068; Protocol-B: P =0.0007), and sarcopenia (Protocol-A: P <0.0001; Protocol-B: P <0.0001) as final predictors of 30-day postoperative mortality in both protocols; hence the model was called HAS (HI, ASA status, sarcopenia). The HAS demonstrated excellent discrimination (AUC: 0.96, P <0.0001), excellent calibration ( P <0.0001), and excellent classification (95%) via both protocols., Conclusions: The HAS is the first model demonstrating excellent discrimination, calibration, and classification in predicting the risk of 30-day mortality following emergency laparotomy. The HAS model seems promising and is worth attention for external validation using the calculator provided. HAS mortality risk calculator https://app.airrange.io/#/element/xr3b&#95;E6yLor9R2c8KXViSAeOSK ., Competing Interests: The authors declare no conflict of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems., (© 2024. The Author(s).)

Undescended testis (UDT, cryptorchidism) is the most common congenital anomaly of the genital tract. Despite its high incidence, the management of UDT varies between specialties (urology, pediatric surgery, pediatric urology, pediatric endocrinology). Therefore, as the European Association of Urology - Young Academic Urologists Pediatric Urology Working Group, we requested experts around the world to express their own personal approaches against various case scenarios of UDT in order to explore their individual reasoning. We intended to broaden the perspectives of our colleagues who deal with the treatment of this frequent genital malformation., Competing Interests: Conflict of interest None declared., (Copyright © 2023 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

The objective of this scoping review is to provide a summary of the current literature regarding adolescents and young adults with histories of cloacal anomalies. Preferred Reporting Items for Systematic Reviews and Meta-analysis Extension for Scoping Reviews were used. Data were categorized into four domains-urologic, colorectal, gynecologic/obstetric, and sexual/psychosocial. The current literature has poor study quality and mostly consists of retrospective studies of small cohorts with varying definitions of outcomes. Women with cloacal anomalies are at high risk for urologic dysfunction but can maintain kidney health and achieve social continence with medical and surgical management. Sexual function and adult healthcare transition are areas ripe for improved future research., Competing Interests: Declaration of Competing Interest All authors declare no disclosure., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Patients with ovarian cancer (OC) often experience anxiety, depression and fear of progression (FOP); however, it is unclear whether surgical complexity has a role to play. We investigated the prevalence of anxiety, depression and FOP at 12 months post-cytoreductive surgery and investigated associations with surgical complexity, patient (age, ethnicity, performance status, BMI) and tumour (stage, disease load) factors. One hundred and forty-one patients with FIGO Stage III-IV OC, who did not have disease progression at 12 months post-surgery, completed the Hospital Anxiety and Depression Scale and FOP short-form questionnaire. Patients underwent surgery with low (40.4%), intermediate (31.2%) and high (28.4%) surgical complexity scores. At 12 months post-surgery, 99 of 141 (70%) patients with advanced OC undergoing surgery experienced clinically significant anxiety, 21 of 141 (14.9%) patients experienced moderate to severe depression and 37 of 140 (26.4%) experienced dysfunctional FOP. No associations were identified between the three different surgical complexity groups with regards to anxiety, depression or FOP scores. Unsurprisingly, given the natural history of the disease, most patients with OC suffer from anxiety, depression and fear of progression after completion of first-line cancer treatment. Surgical complexity at the time of surgery is not associated with a deleterious impact on anxiety, depression or FOP for patients with OC. Patients with OC experience a profound mental health impact and should be offered mental health support throughout their cancer journey.

Low-grade chronic inflammation is a hallmark of ageing, associated with impaired tissue function and disease development. However, how cell-intrinsic and -extrinsic factors collectively establish this phenotype, termed inflammaging, remains poorly understood. We addressed this question in the mouse intestinal epithelium, using mouse organoid cultures to dissect stem cell-intrinsic and -extrinsic sources of inflammaging. At the single-cell level, we found that inflammaging is established differently along the crypt-villus axis, with aged intestinal stem cells (ISCs) strongly upregulating major histocompatibility complex class II (MHC-II) genes. Importantly, the inflammaging phenotype was stably propagated by aged ISCs in organoid cultures and associated with increased chromatin accessibility at inflammation-associated loci in vivo and ex vivo, indicating cell-intrinsic inflammatory memory. Mechanistically, we show that the expression of inflammatory genes is dependent on STAT1 signaling. Together, our data identify that intestinal inflammaging in mice is promoted by a cell-intrinsic mechanism, stably propagated by ISCs, and associated with a disbalance in immune homeostasis., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Mutations in the PCDH15 gene, encoding protocadherin-15, are among the leading causes of Usher syndrome type 1 (USH1F), and account for up to 12% USH1 cases worldwide. A founder truncating variant of PCDH15 has a ∼2% carrier frequency in Ashkenazi Jews accounting for nearly 60% of their USH1 cases. Although cochlear implants can restore hearing perception in USH1 patients, presently there are no effective treatments for the vision loss due to retinitis pigmentosa. We established a founder allele-specific Pcdh15 knockin mouse model as a platform to ascertain therapeutic strategies. Using a dual-vector approach to circumvent the size limitation of adeno-associated virus, we observed robust expression of exogenous PCDH15 in the retinae of Pcdh15 KI mice, sustained recovery of electroretinogram amplitudes and key retinoid oxime, substantially improved light-dependent translocation of phototransduction proteins, and enhanced levels of retinal pigment epithelium-derived enzymes. Thus, our data raise hope and pave the way for future gene therapy trials in USH1F subjects., Competing Interests: Declaration of interests S.S., L.S.C., Saima Riazuddin, and Z.M.A. filed a patent application for the composition of a protocadherin-15 dual vector system., (Copyright © 2023. Published by Elsevier Inc.)

Expansions of repeat DNA tracts cause >70 diseases, and ongoing expansions in brains exacerbate disease. During expansion mutations, single-stranded DNAs (ssDNAs) form slipped-DNAs. We find the ssDNA-binding complexes canonical replication protein A (RPA1, RPA2, and RPA3) and Alternative-RPA (RPA1, RPA3, and primate-specific RPA4) are upregulated in Huntington disease and spinocerebellar ataxia type 1 (SCA1) patient brains. Protein interactomes of RPA and Alt-RPA reveal unique and shared partners, including modifiers of CAG instability and disease presentation. RPA enhances in vitro melting, FAN1 excision, and repair of slipped-CAGs and protects against CAG expansions in human cells. RPA overexpression in SCA1 mouse brains ablates expansions, coincident with decreased ATXN1 aggregation, reduced brain DNA damage, improved neuron morphology, and rescued motor phenotypes. In contrast, Alt-RPA inhibits melting, FAN1 excision, and repair of slipped-CAGs and promotes CAG expansions. These findings suggest a functional interplay between the two RPAs where Alt-RPA may antagonistically offset RPA's suppression of disease-associated repeat expansions, which may extend to other DNA processes., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Electrochemical reduction of CO 2 (CO 2 RR) is an attractive technology to reintegrate the anthropogenic CO 2 back into the carbon cycle driven by a suitable catalyst. This study employs highly efficient multi-carbon (C 2+ ) producing Cu 2 O nanocubes (NCs) decorated with CO-selective Au nanoparticles (NPs) to investigate the correlation between a high CO surface concentration microenvironment and the catalytic performance. Structure, morphology and near-surface composition are studied via operando X-ray absorption spectroscopy and surface-enhanced Raman spectroscopy, operando high-energy X-ray diffraction as well as quasi in situ X-ray photoelectron spectroscopy. These operando studies show the continuous evolution of the local structure and chemical environment of our catalysts during reaction conditions. Along with its alloy formation, a CO-rich microenvironment as well as weakened average CO binding on the catalyst surface during CO 2 RR is detected. Linking these findings to the catalytic function, a complex compositional interplay between Au and Cu is revealed in which higher Au loadings primarily facilitate CO formation. Nonetheless, the strongest improvement in C 2+ formation appears for the lowest Au loadings, suggesting a beneficial role of the Au-Cu atomic interaction for the catalytic function in CO 2 RR. This study highlights the importance of site engineering and operando investigations to unveil the electrocatalyst's adaptations to the reaction conditions, which is a prerequisite to understand its catalytic behavior., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures that form down each side of the neural tube. We have analyzed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during mouse embryonic development. We show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation program followed by all somites, but somites from more developed embryos concomitantly switch on differentiation programs from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities identified opposing regulatory modules controlling the onset of differentiation. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals., Competing Interests: Declaration of interests J.C.M. has been an employee of Genentech since September 2022., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background/aim: Emerging data suggest that addition of hyperthermic intraperitoneal chemotherapy (HIPEC) at the time of interval cytoreduction for patients with metastatic ovarian cancer is associated with a survival benefit. However, the implementation of this treatment is affected by concerns related to its potential morbidity. We present data from the first centre in the UK implementing HIPEC as part of treatment for patients with advanced ovarian cancer undergoing interval cytoreductive surgery., Patients and Methods: This is a prospective study of patients planned to undergo cytoreductive surgery and HIPEC for advanced ovarian cancer over a 30-month period. All patients had undergone neoadjuvant chemotherapy prior to surgery. Patients with stage III/IV ovarian cancer who underwent complete or near complete cytoreduction (<2.5 mm residual disease) received HIPEC using a closed technique., Results: A total of 31 patients were included in the study, of which 30 had complete cytoreduction and 1 patient had residual disease <2.5 mm. The mean age of the patients was 63.7±2.8 years. Median peritoneal cancer index score was 9 (range=3-31). The mean operating time was 515.4±55.1 min. The mean length of hospital stay was 7.6±0.8 days. In total, 24 complications were observed in 18 patients (58.1%), while 6.5% of the patients experienced grade 3/4 complications. There were no deaths within 30-days from the surgery. Age was found to be an independent predictor of both postoperative complications of any grade and prolonged hospital stay., Conclusion: Interval cytoreductive surgery and HIPEC for patients with advanced ovarian cancer is associated with low perioperative morbidity., (Copyright © 2023 International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Introduction: Outdoor activities have accelerated in the past several years. The authors were tasked with providing medical care for the Union Cycliste International (UCI) mountain biking World Cup in Snowshoe, West Virginia (USA) in September 2021. The Hartman and Arbon models were designed to predict patient presentation and hospital transport rates as well as needed medical resources at urban mass-gathering events. However, there is a lack of standardized methods to predict injury, illness, and insult severity at rural mass gatherings., Study Objective: This study aimed to determine whether the Arbon model would predict, within 10%, the number of patient presentations to be expected and to determine if the event classification provided by the Hartman model would adequately predict resources needed during the event., Methods: Race data were collected from UCI event officials and injury data were collected from participants at time of presentation for medical care. Predicted presentation and transport rates were calculated using the Arbon model, which was then compared to the actual observed presentation rates. Furthermore, the event classification provided by the Hartman model was compared to the resources utilized during the event., Results: During the event, 34 patients presented for medical care and eight patients required some level of transport to a medical facility. The Arbon predictive model for the 2021 event yielded 30.3 expected patient presentations. There were 34 total patient presentations during the 2021 race, approximately 11% more than predicted. The Hartman model yielded a score of four. Based on this score, this race would be classified as an "intermediate" event, requiring multiple Advanced Life Support (ALS) and Basic Life Support (BLS) personnel and transport units., Conclusion: The Arbon model provided a predicted patient presentation rate within reasonable error to allow for effective pre-event planning and resource allocation with only a four patient presentation difference from the actual data. While the Arbon model under-predicted patient presentations, the Hartman model under-estimated resources needed due to the high-risk nature of downhill cycling. The events staffed required physician skills and air medical services to safely care for patients. Further evaluation of rural events will be needed to determine if there is a generalized need for physician presence at smaller events with inherently risky activities, or if this recurring cycling event is an outlier.

One of the most widely used materials for bone graft substitution is β-Tricalcium phosphate (β-TCP; β-Ca 3 (PO 4 ) 2 ). β-TCP is typically produced by sintering in air or vacuum. During this process, evaporation of phosphorus (P) species occurs, leading to the formation of a calcium-rich alkaline layer. It was recently shown that the evaporation of P species could be prevented by co-sintering β-TCP with dicalcium phosphate (DCPA; CaHPO 4 ; mineral name: monetite). The aim of this study was to see how a change of sintering atmosphere could affect the physico-chemical and biological properties of β-TCP. For this purpose, three experimental groups were considered: β-TCP cylinders sintered in air and subsequently polished to remove the surface layer (control group); the same polished cylinders after subsequent annealing at 500 °C in air to generate a calcium-rich alkaline layer (annealed group); and finally, β-TCP cylinders sintered in a monetite-rich atmosphere and subsequently polished (monetite group). XPS analysis confirmed that cylinders from the annealed group had a significantly higher Ca/P molar ratio at their surface than that of the control group while this ratio was significantly lower for the cylinders from the monetite group. Sintering β-TCP in the monetite-rich atmosphere significantly reduced the grain size and increased the density. Changes of surface composition affected the activity of osteoclasts seeded onto the surfaces, since annealed β-TCP cylinders were significantly less resorbed than β-TCP cylinders sintered in the monetite-rich atmosphere. This suggests that an increase of the surface Ca/P molar ratio leads to a decrease of osteoclastic resorption. STATEMENT OF SIGNIFICANCE: Minimal changes of surface and bulk (< 1%) composition have major effects on the ability of osteoclasts to resorb β-tricalcium phosphate (β-TCP), one of the most widely used ceramics for bone substitution. The results presented in this study are thus important for the calcium phosphate community because (i) β-TCP may have up to 5% impurities according to ISO and ASTM standards and still be considered to be "pure β-TCP", (ii) β-TCP surface properties are generally not considered during biocompatibility assessment and (iii) a rationale can be proposed to explain the various inconsistencies reported in the literature on the biological properties of β-TCP., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

In this work, we report on the efficiency of single InGaN/GaN quantum wells (QWs) grown on thin (<1 µm) GaN buffer layers on silicon (111) substrates exhibiting very high threading dislocation (TD) densities. Despite this high defect density, we show that QW emission efficiency significantly increases upon the insertion of an In-containing underlayer, whose role is to prevent the introduction of point defects during the growth of InGaN QWs. Hence, we demonstrate that point defects play a key role in limiting InGaN QW efficiency, even in samples where their density (2-3 × 109 cm-2) is much lower than that of TD (2-3 × 1010 cm-2). Time-resolved photoluminescence and cathodoluminescence studies confirm the prevalence of point defects over TDs in QW efficiency. Interestingly, TD terminations lead to the formation of independent domains for carriers, thanks to V-pits and step bunching phenomena.

This publisher's note contains a correction to Appl. Opt.62, 3485 (2023)APOPAI0003-693510.1364/AO.487089.

Massive-scale SARS-CoV-2 testing using the SwabSeq diagnostic platform came with quality assurance challenges due to the novelty and scale of sequencing-based testing. The SwabSeq platform relies on accurate mapping between specimen identifiers and molecular barcodes to match a result back to a patient specimen. To identify and mitigate mapping errors, we instituted quality control using placement of negative controls within a rack of patient samples. We designed 2-dimensional paper templates to fit over a 96-position rack of specimens with holes to show the control tube placements. We designed and 3-dimensionally printed plastic templates that fit onto 4 racks of patient specimens and provide accurate indications of the correct control tube placements. The final plastic templates dramatically reduced plate mapping errors from 22.55% in January 2021 to less than 1% after implementation and training in January 2021. We show how 3D printing can be a cost-effective quality assurance tool to mitigate human error in the clinical laboratory., (© American Society for Clinical Pathology 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Using DNA methylation profiles ( n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.

Background: Little is known about fertility and pregnancy outcomes in patients with anorectal malformations (ARM), particularly those with long common channel cloaca and cloacal exstrophy who may have impaired fertility. The purpose of this study is to describe pregnancy and offspring data from a cohort of patients with ARM., Methods: A retrospective review of female patients with ARM from our database, which includes patients operated on since 1980, was performed as well as a review of the literature. Demographic, operative, and self-reported fertility, obstetric, and offspring data were collected., Results: There were 37 females identified in our database who reported any pregnancy or having children. There were 59 pregnancies, 48 (81.3%) of which resulted in live birth. The most common mode of delivery was cesarean delivery. There were five patients with long channel cloaca (>3 cm) and one with cloacal exstrophy that reported 11 total pregnancies, eight of which resulted in live birth. Four cloaca patients in which the native vagina was pulled through were able to conceive spontaneously. Three patients with cloacal anomalies required in vitro fertilization to conceive; one was unsuccessful. No patients who underwent bowel partial vaginal replacement became pregnant. Women with ARM face many unique challenges in assisted reproduction, pregnancy, and delivery owing to their anatomy and associated anomalies., Conclusions: Women with recto-perineal, recto-vestibular, and cloacas in which the native vagina was pulled through are capable of spontaneous pregnancy. Assisted reproduction, however, may be needed those with more complex anomalies and surgical repairs., Level of Evidence: IV., Competing Interests: Declaration of Competing Interest The authors have no conflicts of interest, financial or otherwise, to disclose., (Copyright © 2022 Elsevier Inc. All rights reserved.)

We present two open-source Python packages: "electron spectro-microscopy" (espm) and "electron microscopy tables" (emtables). The espm software enables the simulation of scanning transmission electron microscopy energy-dispersive X-ray spectroscopy datacubes, based on user-defined chemical compositions and spatial abundance maps of constituent phases. The simulation process uses X-ray emission cross-sections generated via state-of-the-art calculations made with emtables. These tables are designed to be easily modifiable, either manually or using espm. The simulation framework is designed to test the application of decomposition algorithms for the analysis of STEM-EDX spectrum images with access to a known ground truth. We validate our approach using the case of a complex geology-related sample, comparing raw simulated and experimental datasets and the outputs of their non-negative matrix factorization. In addition to testing machine learning algorithms, our packages will also help experimental design, for instance, predicting dataset characteristics or establishing minimum counts needed to measure nanoscale features., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)