Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors.

Mitotic errors generate micronuclei entrapping mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates diverse genomic rearrangements associated with human diseases. How specific repair pathways recognize and process these lesions remains poorly understood. Here we use CRISPR/Cas9 to systematically inactivate distinct DSB repair pathways and interrogate the rearrangement landscape of fragmented chromosomes. Deletion of canonical non-homologous end joining (NHEJ) components substantially reduces complex rearrangements and shifts the rearrangement landscape toward simple alterations without the characteristic patterns of chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within sub-nuclear micronuclei bodies (MN bodies) and undergo ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments are rarely engaged by alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics, persistent 53BP1-labeled MN bodies, and cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements from mitotic errors.

Understanding Species Boundaries that Arise from Complex Histories: Gene Flow Across the Speciation Continuum in the Spotted Whiptail Lizards.

Gene flow between diverging lineages challenges the resolution of species boundaries and the understanding of evolutionary history in recent radiations. Here, we integrate phylogenetic and coalescent tools to resolve reticulate patterns of diversification and use a perspective focused on evolutionary mechanisms to distinguish interspecific and intraspecific taxonomic variation. We use this approach to resolve the systematics for one of the most intensively studied but difficult to understand groups of reptiles: the spotted whiptail lizards of the genus Aspidoscelis (A. gularis complex). Whiptails contain the largest number of unisexual species known within any vertebrate group and the spotted whiptail complex has played a key role in the generation of this diversity through hybrid speciation. Understanding lineage boundaries and the evolutionary history of divergence and reticulation within this group is therefore key to understanding the generation of unisexual diversity in whiptails. Despite this importance, long-standing confusion about their systematics has impeded understanding of which gonochoristic species have contributed to the formation of unisexual lineages. Using reduced representation genomic data, we resolve patterns of divergence and gene flow within the spotted whiptails and clarify patterns of hybrid speciation. We find evidence that biogeographically structured ecological and environmental variation has been important in morphological and genetic diversification, as well as the maintenance of species boundaries in this system. Our study elucidates how gene flow among lineages and the continuous nature of speciation can bias the practice of species delimitation and lead taxonomists operating under different frameworks to different conclusions (here we propose that a two species arrangement best reflects our current understanding). In doing so, this study provides conceptual and methodological insights into approaches to resolving diversification patterns and species boundaries in rapid radiations with complex histories, as well as long-standing taxonomic challenges in the field of systematic biology.

Biomarkers of immunotherapy in glioblastoma.

Glioblastoma (GBM) is the most common primary brain cancer, comprising half of all malignant brain tumors. Patients with GBM have a poor prognosis, with a median survival of 14-15 months. Current therapies for GBM, including chemotherapy, radiotherapy, and surgical resection, remain inadequate. Novel therapies are required to extend patient survival. Although immunotherapy has shown promise in other cancers, including melanoma and non-small lung cancer, its efficacy in GBM has been limited to subsets of patients. Identifying biomarkers of immunotherapy response in GBM could help stratify patients, identify new therapeutic targets, and develop more effective treatments. This article reviews existing and emerging biomarkers of clinical response to immunotherapy in GBM. The scope of this review includes immune checkpoint inhibitor and antitumoral vaccination approaches, summarizing the variety of molecular, cellular, and computational methodologies that have been explored in the setting of anti-GBM immunotherapies.

Deep Learning Enabled Universal Multiplexed Fluorescence Detection for Point-of-Care Applications.

There is a significant demand for multiplexed fluorescence sensing and detection across a range of applications. Yet, the development of portable and compact multiplexable systems remains a substantial challenge. This difficulty largely stems from the inherent need for spectrum separation, which typically requires sophisticated and expensive optical components. Here, we demonstrate a compact, lens-free, and cost-effective fluorescence sensing setup that incorporates machine learning for scalable multiplexed fluorescence detection. This method utilizes low-cost optical components and a pretrained machine learning (ML) model to enable multiplexed fluorescence sensing without optical adjustments. Its multiplexing capability can be easily scaled up through updates to the machine learning model without altering the hardware. We demonstrate its real-world application in a probe-based multiplexed Loop-Mediated Isothermal Amplification (LAMP) assay designed to simultaneously detect three common respiratory viruses within a single reaction. The effectiveness of this approach highlights the system's potential for point-of-care applications that require cost-effective and scalable solutions. The machine learning-enabled multiplexed fluorescence sensing demonstrated in this work would pave the way for widespread adoption in diverse settings, from clinical laboratories to field diagnostics.

Medullary Thyroid Cancer: Molecular Drivers and Immune Cellular Milieu of the Tumour Microenvironment-Implications for Systemic Treatment.

In this review, we explore the underlying molecular biology of medullary thyroid carcinoma (MTC) and its interplay with the host immune system. MTC is consistently driven by a small number of specific pathogenic variants, beyond which few additional genetic events are required for tumorigenesis. This explains the exceedingly low tumour mutational burden seen in most MTC, in contrast to other cancers. However, because of the low tumour mutational burden (TMB), there is a correspondingly low level of tumour-associated neoantigens that are presented to the host immune system. This reduces tumour visibility and vigour of the anti-tumour immune response and suggests the efficacy of immunotherapy in MTC is likely to be poor, acknowledging this inference is largely based on the extrapolation of data from other tumour types. The dominance of specific RET (REarranged during Transfection) pathogenic variants in MTC tumorigenesis rationalizes the observed efficacy of the targeted RET-specific tyrosine kinase inhibitors (TKIs) in comparison to multi-kinase inhibitors (MKIs). Therapeutic durability of pathway inhibitors is an ongoing research focus. It may be limited by the selection pressure TKI treatment creates, promoting survival of resistant tumour cell clones that can escape pathway inhibition through binding-site mutations, activation of alternate pathways, and modulation of the cellular and cytokine milieu of the tumour microenvironment (TME).

Eight-Fold Increased COVID-19 Mortality in Autosomal Dominant Tubulointerstitial Kidney Disease due to MUC1 Mutations: An Observational Study.

Background: MUC1 and UMOD pathogenic variants cause autosomal dominant tubulointerstitial kidney disease (ADTKD). MUC1 is expressed in kidney, nasal mucosa and respiratory tract, while UMOD is expressed only in kidney. Due to haplo-insufficiency ADTKD- MUC1 patients produce approximately 50% of normal mucin-1. Methods: To determine whether decreased mucin-1 production was associated with an increased COVID-19 risk, we sent a survey to members of an ADTKD registry in September 2021, after the initial, severe wave of COVID-19. We linked results to previously obtained ADTKD genotype and plasma CA15-3 (mucin-1) levels and created a longitudinal registry of COVID-19 related deaths. Results: Surveys were emailed to 637 individuals, with responses from 89 ADTKD- MUC1 and 132 ADTKD- UMOD individuals. 19/83 (23%) ADTKD- MUC1 survey respondents reported a prior COVID-19 infection vs. 14/125 (11%) ADTKD- UMOD respondents (odds ratio (OR) 2.35 (95%CI 1.60-3.11, P = 0.0260). Including additional familial cases reported from survey respondents, 10/41 (24%) ADTKD- MUC1 individuals died of COVID-19 vs. 1/30 (3%) with ADTKD- UMOD , with OR 9.21 (95%CI 1.22-69.32), P = 0.03. The mean plasma mucin-1 level prior to infection in 14 infected and 27 uninfected ADTKD- MUC1 individuals was 7.06±4.12 vs. 10.21±4.02 U/mL ( P = 0.035). Over three years duration, our longitudinal registry identified 19 COVID-19 deaths in 360 ADTKD- MUC1 individuals (5%) vs. 3 deaths in 478 ADTKD- UMOD individuals (0.6%) ( P = 0.0007). Multivariate logistic regression revealed the following odds ratios (95% confidence interval) for COVID-19 deaths: ADTKD- MUC1 8.4 (2.9-29.5), kidney transplant 5.5 (1.6-9.1), body mass index (kg/m 2 ) 1.1 (1.0-1.2), age (y) 1.04 (1.0-1.1). Conclusions: Individuals with ADTKD- MUC1 are at an eight-fold increased risk of COVID-19 mortality vs. ADTKD- UMOD individuals. Haplo-insufficient production of mucin-1 may be responsible.

Virtual Reality for Preoperative Surgical Planning in Complex Pediatric Oncology.

Background: Virtual reality modeling (VRM) is a 3-dimensional simulation created from patient-specific 2-dimensional (2D) imaging. VRM creates a more accurate representation of the patient anatomy and can improve anatomical perception. We surveyed surgeons on their operative plan in complex pediatric oncology cases based on review of 2D imaging and subsequently after review of VRM. We hypothesized that the confidence level would increase with the use of virtual reality and that VRM may change the operative plan. Methods: Patients were selected and enrolled based on age (<18) and oncological diagnosis. VRM was created based on the 2D imaging. Surgeons identified surgical plans based on 2D imaging and again after VRM. A blinded surgeon not involved with the case also gave opinions on surgical plans after viewing both the 2D and the VRM imaging. These assessments were compared with the actual operation. Results: A total of 12 patients were enrolled. Diagnoses included six neuroblastomas, two Wilms tumors, one Ewing's sarcoma, one pseudopapillary tumor of the pancreas, one rhabdomyosarcoma, and one mediastinal germ cell tumor. VRM increased the operating surgeon's confidence 63% of the time. The operative plan changed 8.3% of the time after VRM. Conclusion: VRM is useful to help clarify operative plans for more complex pediatric cases.

Prognostic Implications of Quantifying Vasoactive Medications in Cardiogenic Shock.

None.

Use of Impedance Cardiography to Guide Blood Pressure Lowering Medication Selection: Systematic Review of Randomized Controlled Trials.

BACKGROUND: Blood pressure (BP) control can be difficult to attain due to multiple factors, including choosing and titrating antihypertensive medications. Measurement of hemodynamic parameters using impedance cardiography (ICG) at the point of care may allow better alignment of medication with the mechanism(s) underlying an individual's hypertension. We conducted a systematic review of randomized controlled trials of ICG compared to usual care for attainment of BP control. METHODS: We searched Medline inclusive of year 1946 to January 31, 2024 using a combination of MeSH terms and key words. English-language articles were eligible for inclusion if they described results of a randomized controlled trial designed to compare ICG-guided BP medication selection to usual care (i.e., clinician judgment/guidelines-based alone) among a sample of hypertensive patients. RESULTS: Of 1952 titles screened, six trials met inclusion criteria. The first was published in 2002 from a specialty clinic in the United States, and the most recent in 2021 from a specialty clinic in China. One trial was conducted in a primary care setting. Sample sizes ranged from 102 to 164. Participants randomized to ICG-guided antihypertensive medication had reduced BP in the short-term to a greater extent than those randomized to usual care, with odds ratios for BP control (<140/90 mmHg) at three months ranging from 1.87 to 2.92. This effect was seen in both specialty clinics and in a primary care setting. CONCLUSIONS: Incorporation of ICG in the clinical setting may facilitate medication selection that leads to a greater proportion of patients obtaining BP control in the short-term.

Initial surgery for spontaneous intestinal perforation in extremely low birth weight infants is not associated with mortality or in-hospital morbidities.

OBJECTIVE: Determine short-term outcomes following peritoneal drain (PD), laparotomy (LAP) after PD (PD-LAP), and LAP in extremely low birth weight (ELBW) infants with spontaneous intestinal perforation (SIP). STUDY DESIGN: ELBW infants with SIP were identified using the Children's Hospitals Neonatal Database. Mortality and length of stay (LOS) were compared among groups. RESULTS: Of 729 SIP infants from 6/2010-12/2016, 383(53%) received PD, 61(8%) PD-LAP, and 285(39%) LAP. PD infants had lower GA at birth, at SIP diagnosis and upon admission than PD-LAP or LAP; and higher sepsis rates than LAP. Bivariate analysis and Kaplan-Meier survival estimates suggested PD had increased mortality vs. PD-LAP and LAP (27%, 11.5%, and 15.8% respectively, p < 0.001). However, surgical approach was not significantly associated with mortality in multivariable analysis accounting for GA and illness severity. LOS did not differ by surgical approach. CONCLUSIONS: In ELBW infants with SIP, mortality, and LOS are independent of the initial surgical approach.

Pulmonary Embolism Presenting as ST-Elevation Myocardial Infarction: A Report of Two Cases.

Pulmonary embolism (PE) is often underrecognized due to its ability to mimic other conditions; however, ultrasound can provide diagnostic clues to aid in the diagnosis of PE. We describe two patients who presented with symptoms suggestive of cardiac ischemia and had electrocardiograms (EKGs) indicative of anteroseptal myocardial infarction. In both cases, cardiac point-of-care ultrasonography showed signs of large pulmonary emboli, which were then confirmed on computed tomography angiography of the chest. Both patients underwent successful aspiration thrombectomy with rapid resolution of cardiac dysfunction. Point-of-care ultrasonography should be used as an adjunct in patients presenting with anterior ischemia on EKG to evaluate for signs of PE.

Wartime penetrating skull base trauma with unpredictable internal fragment ricochet and migration: illustrative case.

BACKGROUND: Transnasal transsphenoidal penetrating craniocerebral injury is very rare even in wartime. Cases with good outcomes are even less common. OBSERVATIONS: A 20-year-old male sustained multiple fragment wounds to his head and face from a landmine explosion. One metal fragment entered his right nostril, traversed the nasal septum and anterior sphenoid sinus, and ricocheted superiorly off the clivus. The fragment then traveled almost to the surface of the left parietal lobe. Subsequently, under its own weight, it migrated back down its original track. The patient suffered cerebrospinal fluid rhinorrhea, pneumocephalus, and right-sided hemiparesis. Digital subtraction angiography was followed by microscopic transnasal skull base reconstruction supplemented by external lumbar drainage. Follow-up brain computed tomogrpahy showed further metallic fragment migration through the ventricular system. The fragment was removed through a transcortical approach. The patient's neurological examination and brain magnetic resonance imaging results demonstrated good recovery. LESSONS: The absence of external signs of deep injuries does not exclude the presence of a penetrating craniocerebral injury. Metal fragments may undergo ricochet and internal migration in both the brain parenchyma and the ventricular system. Timely diagnosis including three-dimensional reconstruction of a projectile's trajectory may facilitate appropriate surgical planning in complex cases. Intraventricular fragment migration may necessitate microsurgical removal. https://thejns.org/doi/10.3171/CASE24128.

Overcoming Challenges in O-Nitration: Selective Alcohol Nitration Deploying N,6-Dinitrosaccharin and Lewis Acid Catalysis.

Nitrate esters hold pivotal roles in pharmaceuticals, energetic materials, and atmospheric processes, motivating the development of efficient synthesis routes. Here, we present a novel catalytic method for the synthesis of nitrates via the direct O-nitration of alcohols, addressing limitations of current traditional methods. Leveraging bench-stable and recoverable N,6-dinitrosaccharin reagent, our catalytic strategy employs magnesium triflate to achieve mild and selective O-nitration of alcohols, offering broad substrate scope and unprecedented large functional group tolerance (e.g. alkenes, alkynes, carbonyls). DFT mechanistic studies reveal a dual role of the magnesium catalyst in the activation of both the nitrating reagent and the alcohol substrate. They also unveil a barrierless proton transfer upon formation of a widely-accepted - yet elusive in solution - nitrooxonium ion intermediate. Overall, our work contributes to the development of mild, selective, and sustainable approaches to nitrates synthesis, with potential applications in drug discovery, materials science, and environmental chemistry.

Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles.

Hereditary SDHB-mutant pheochromocytomas (PC) and paragangliomas (PG) are rare tumours with a high propensity to metastasize although their clinical behaviour is unpredictable. To characterize the genomic landscape of these tumours and identify metastasis biomarkers, we performed multi-omic analysis on 94 tumours from 79 patients using seven molecular methods. Sympathetic (chromaffin cell) and parasympathetic (non-chromaffin cell) PCPG had distinct molecular profiles reflecting their cell-of-origin and biochemical profile. TERT and ATRX-alterations were associated with metastatic PCPG and these tumours had an increased mutation load, and distinct transcriptional and telomeric features. Most PCPG had quiet genomes with some rare co-operative driver events observed, including EPAS1/HIF-2α mutations. Two mechanisms of acquired resistance to DNA alkylating chemotherapies were also detected - MGMT overexpression and mismatch repair-deficiency causing hypermutation. Our comprehensive multi-omic analysis of SDHB-mutant PCPG therefore identified features of metastatic disease and treatment response, expanding our understanding of these rare neuroendocrine tumours.

Synthesis and Properties of the Helium Clathrate and Defect Perovskite [He2-x □ x ][CaNb]F6.

The defect double perovskite [He2-x □ x ][CaNb]F6, with helium on its A-site, can be prepared by the insertion of helium into ReO3-type CaNbF6 at high pressure. Upon cooling from 300 to 100 K under 0.4 GPa helium, ∼60% of the A-sites become occupied. Helium uptake was quantified by both neutron powder diffraction and gas insertion and release measurements. After the conversion of gauge pressure to fugacity, the uptake of helium by CaNbF6 can be described by a Langmuir isotherm. The enthalpy of absorption for helium in [He2-x □ x ][CaNb]F6 is estimated to be ∼+3(1) kJ mol-1, implying that its formation is entropically favored. Helium is able to diffuse through the material on a time scale of minutes at temperatures down to ∼150 K but is trapped at 100 K and below. The insertion of helium into CaNbF6 reduces the magnitude of its negative thermal expansion, increases the bulk modulus, and modifies its phase behavior. On compressing pristine CaNbF6, at 50 and 100 K, a cubic (Fm3̅m) to rhombohedral (R3̅) phase transition was observed at <0.20 GPa. However, a helium-containing sample remained cubic at 0.4 GPa and 50 K. CaNbF6, compressed in helium at room temperature, remained cubic to >3.7 GPa, the limit of our X-ray diffraction measurements, in contrast to prior reports that upon compression in a nonpenetrating medium, a phase transition is detected at ∼0.4 GPa.

Lysophosphatidic acid receptor 1 inhibition: a potential treatment target for pulmonary fibrosis.

Lysophosphatidic acid (LPA)-mediated activation of LPA receptor 1 (LPAR1) contributes to the pathophysiology of fibrotic diseases such as idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc). These diseases are associated with high morbidity and mortality despite current treatment options. The LPA-producing enzyme autotaxin (ATX) and LPAR1 activation contribute to inflammation and mechanisms underlying fibrosis in preclinical fibrotic models. Additionally, elevated levels of LPA have been detected in bronchoalveolar lavage fluid from patients with IPF and in serum from patients with SSc. Thus, ATX and LPAR1 have gained considerable interest as pharmaceutical targets to combat fibrotic disease and inhibitors of these targets have been investigated in clinical trials for IPF and SSc. The goals of this review are to summarise the current literature on ATX and LPAR1 signalling in pulmonary fibrosis and to help differentiate the novel inhibitors in development. The mechanisms of action of ATX and LPAR1 inhibitors are described and preclinical studies and clinical trials of these agents are outlined. Because of their contribution to numerous physiologic events underlying fibrotic disease, ATX and LPAR1 inhibition presents a promising therapeutic strategy for IPF, SSc and other fibrotic diseases that may fulfil unmet needs of the current standard of care.

Engineering a "muco-trapping" ACE2-immunoglobulin hybrid with picomolar affinity as an inhaled, pan-variant immunotherapy for COVID-19.

Soluble angiotensin-converting enzyme 2 (ACE2) can act as a decoy molecule that neutralizes severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by blocking spike (S) proteins on virions from binding ACE2 on host cells. Based on structural insights of ACE2 and S proteins, we designed a "muco-trapping" ACE2-Fc conjugate, termed ACE2-(G4S)6-Fc, comprised of the extracellular segment of ACE2 (lacking the C-terminal collectrin domain) that is linked to mucin-binding IgG1-Fc via an extended glycine-serine flexible linker. ACE2-(G4S)6-Fc exhibits substantially greater binding affinity and neutralization potency than conventional full length ACE2-Fc decoys or similar truncated ACE2-Fc decoys without flexible linkers, possessing picomolar binding affinity and strong neutralization potency against pseudovirus and live virus. ACE2-(G4S)6-Fc effectively trapped fluorescent SARS-CoV-2 virus like particles in fresh human airway mucus and was stably nebulized using a commercial vibrating mesh nebulizer. Intranasal dosing of ACE2-(G4S)6-Fc in hamsters as late as 2 days postinfection provided a 10-fold reduction in viral load in the nasal turbinate tissues by Day 4. These results strongly support further development of ACE2-(G4S)6-Fc as an inhaled immunotherapy for COVID-19, as well as other emerging viruses that bind ACE2 for cellular entry.

Inadequate Performance of ChatGPT on Orthopedic Board-Style Written Exams.

BACKGROUND: Chat Generative Pre-Trained Transformer (ChatGPT) is an artificial intelligence (AI) chatbot capable of delivering human-like responses to a seemingly infinite number of inquiries. For the technology to perform certain healthcare-related tasks or act as a study aid, the technology should have up-to-date knowledge and the ability to reason through medical information. The purpose of this study was to assess the orthopedic knowledge and reasoning ability of ChatGPT by querying it with orthopedic board-style questions. METHODOLOGY: We queried ChatGPT (GPT-3.5) with a total of 472 questions from the Orthobullets dataset (n = 239), the 2022 Orthopaedic In-Training Examination (OITE) (n = 124), and the 2021 OITE (n = 109). The importance, difficulty, and category were recorded for questions from the Orthobullets question bank. Responses were assessed for answer choice correctness if the explanation given matched that of the dataset, answer integrity, and reason for incorrectness. RESULTS: ChatGPT correctly answered 55.9% (264/472) of questions and, of those answered correctly, gave an explanation that matched that of the dataset for 92.8% (245/264) of the questions. The chatbot used information internal to the question in all responses (100%) and used information external to the question (98.3%) as well as logical reasoning (96.4%) in most responses. There was no significant difference in the proportion of questions answered correctly between the datasets (P = 0.62). There was no significant difference in the proportion of questions answered correctly by question category (P = 0.67), importance (P = 0.95), or difficulty (P = 0.87) within the Orthobullets dataset questions. ChatGPT mostly got questions incorrect due to information error (i.e., failure to identify the information required to answer the question) (81.7% of incorrect responses). CONCLUSIONS: ChatGPT performs below a threshold likely to pass the American Board of Orthopedic Surgery (ABOS) Part I written exam. The chatbot's performance on the 2022 and 2021 OITEs was between the average performance of an intern and to second-year resident. A major limitation of the current model is the failure to identify the information required to correctly answer the questions.