Antagonistic conflict between transposon-encoded introns and guide RNAs.

TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function as programmable RNA-guided homing endonucleases in bacteria, driving transposon maintenance through DNA double-strand break-stimulated homologous recombination. In this work, we uncovered molecular mechanisms of the transposition life cycle of IS607-family elements that, notably, also encode group I introns. We identified specific features for a candidate "IStron" from Clostridium botulinum that allow the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts evolved an ability to balance competing and mutually exclusive activities that promote selfish transposon spread while limiting adverse fitness costs on the host. Collectively, this work highlights molecular innovation in the multifunctional utility of transposon-encoded noncoding RNAs.

DOCSIC: A Mean-Field Method for Orbital-by-Orbital Self-Interaction Correction.

We introduce a new method to remove the one-electron self-interaction error in approximate density functional calculations on an orbital-by-orbital basis, as originally proposed by Perdew and Zunger [Phys. Rev. B 1981, 23, 5048]. This method is motivated by a recent proposal by Pederson et al. [J. Chem. Phys. 2014, 140, 121103] to remove self-interaction that employs orbitals derived from the real-space density matrix, known as FLOSIC (Fermi Löwdin orbitals self-interaction correction). However, instead of Fermi Löwdin orbitals, our scheme utilizes columns of the density matrix to determine localized orbitals, like the localization procedure proposed by Fuemmeler et al. [J. Chem. Theory Comput. 2023, 19, 8572]. The new method, dubbed DOCSIC for density matrix as orbital coefficients self-interaction correction, contrasts with traditional Perdew-Zunger or FLOSIC in that it does not incorporate additional optimization parameters, and, unlike the average density self-interaction correction of Ciofini et al. [Chem. Phys. Lett. 2003, 380, 12], it makes use of localized orbitals. Another advantage of DOCSIC is that it can be implemented as a mean-field formalism. We show details of the self-consistent generalized Kohn-Sham implementation, some illustrative results, and we finally highlight its advantages and limitations.

Symptom subtype progression in obstructive sleep apnea over 5 years.

STUDY OBJECTIVES: There is limited knowledge regarding the progression or consistency of symptoms in OSA over time. Our objective was to examine the changes in symptom subtypes and identify predictors over a span of 5 years. METHODS: Data of 2,643 participants of the Sleep Heart Health Study with complete baseline and 5-year follow-up visits were analyzed. Latent Class Analysis on 14 symptoms at baseline and follow-up determined symptom subtypes. Individuals without OSA (AHI<5) were incorporated as a known class at each time point. Multinomial logistic regression assessed the effect of age, sex, body mass index (BMI) and AHI on specific class transitions. RESULTS: The sample consisted of 1,408 women (53.8%) and mean (SD) age 62.4 (10.5) years. We identified four OSA symptom subtypes at both baseline and follow-up visits: minimally symptomatic, disturbed sleep, moderately sleepy, and excessively sleepy. Nearly half (44.2%) of the sample transitioned to a different subtype; transitions to moderately sleepy were the most common (77% of all transitions). A five-year older age was associated with a 50% increase in odds to transit from excessively sleepy to moderately sleepy [OR (95% CI: 1.52 (1.17, 1.97)]. Women had 1.97 times higher odds (95% CI: 1.21, 3.18) to transition from moderately sleepy to minimal symptoms. A 5-unit increase in BMI was associated with 2.39 greater odds (95% CI: 1.30, 4.40) to transition from minimal symptoms to excessively sleepy. Changes in AHI did not significantly predict any transitions. CONCLUSIONS: The symptoms of OSA may fluctuate or remain stable over time. Knowledge of symptom progression in OSA may support clinicians with treatment decisions.

Susceptibility evaluation of novel beta-lactam/beta-lactamase inhibitor combinations against carbapenem-resistant Klebsiella pneumoniae from bloodstream infections in hospitalized patients in Brazil.

Novel beta-lactams/beta-lactamase inhibitors (BIBLI) combinations are commercially available and they have been used for treating carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. Continuous surveillance of susceptibility profile and resistance mechanisms identification are necessary to monitor the evolution of resistance as these agents are used. The purpose of this study was to evaluate susceptibility rates to ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam in CRKP isolates from patients with bloodstream infection screened for a randomized clinical trial in Brazil. Minimum inhibitory concentration (MIC) was determined by gradient diffusion strip method for meropenem, ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam. Carbapenemase genes were detected by multiplex qPCR. KPC-producing isolates showing resistance to any BLBLI and NDM-producing isolates showing susceptibility to any BLBLI were further submitted to whole genome sequencing. From a total of 69 CRKP isolates, 39 were positive for blaKPC, 19 for blaNDM and 11 for blaKPC and blaNDM. KPC-producing isolates demonstrated susceptibility rates above 94% for all BLBLI. Two isolates with resistance to meropenem/vaborbactam showed a Gly and Asp duplication at OmpK36 protein and truncated ompK35 genes. All NDM-producing isolates, including KPC and NDM coproducers, demonstrated susceptibility rates for ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam of 0%, 9.1 to 21.1% and 9.1 to 26.3%, respectively. Five NDM-producing isolates that presented susceptibility to BLBLI also demonstrated alterations in porins. This study demonstrated that, although high susceptibility rates to the BLBLI were found, KPC-2 isolates can also demonstrate resistance due to porin mutations. Additionally, NDM-1 isolates can demonstrate susceptibility in vitro to the BLBLI.

Utilizing COVID-19 as a Model for Diagnostics Using an Electrochemical Sensor.

This paper reports a rapid and sensitive sensor for the detection and quantification of the COVID-19 N-protein (N-PROT) via an electrochemical mechanism. Single-frequency electrochemical impedance spectroscopy was used as a transduction method for real-time measurement of the N-PROT in an immunosensor system based on gold-conjugate-modified carbon screen-printed electrodes (Cov-Ag-SPE). The system presents high selectivity attained through an optimal stimulation signal composed of a 0.0 V DC potential and 10 mV RMS-1 AC signal at 100 Hz over 300 s. The Cov-Ag-SPE showed a log response toward N-PROT detection at concentrations from 1.0 ng mL-1 to 10.0 µg mL-1, with a 0.977 correlation coefficient for the phase (θ) variation. An ML-based approach could be created using some aspects observed from the positive and negative samples; hence, it was possible to classify 252 samples, reaching 83.0, 96.2 and 91.3% sensitivity, specificity, and accuracy, respectively, with confidence intervals (CI) ranging from 73.0 to 100.0%. Because impedance spectroscopy measurements can be performed with low-cost portable instruments, the immunosensor proposed here can be applied in point-of-care diagnostics for mass testing, even in places with limited resources, as an alternative to the common diagnostics methods.

Memory T-cell enriched haploidentical transplantation with NK cell addback results in promising long-term outcomes: a phase II trial.

BACKGROUND: Relapse remains a challenge after transplantation in pediatric patients with hematological malignancies. Myeloablative regimens used for disease control are associated with acute and long-term adverse effects. We used a CD45RA-depleted haploidentical graft for adoptive transfer of memory T cells combined with NK-cell addback and hypothesized that maximizing the graft-versus-leukemia (GVL) effect might allow for reduction in intensity of conditioning regimen. METHODS: In this phase II clinical trial (NCT01807611), 72 patients with hematological malignancies (complete remission (CR)1: 25, ≥ CR2: 28, refractory disease: 19) received haploidentical CD34 + enriched and CD45RA-depleted hematopoietic progenitor cell grafts followed by NK-cell infusion. Conditioning included fludarabine, thiotepa, melphalan, cyclophosphamide, total lymphoid irradiation, and graft-versus-host disease (GVHD) prophylaxis consisted of a short-course sirolimus or mycophenolate mofetil without serotherapy. RESULTS: The 3-year overall survival (OS) and event-free-survival (EFS) for patients in CR1 were 92% (95% CI:72-98) and 88% (95% CI: 67-96); ≥ CR2 were 81% (95% CI: 61-92) and 68% (95% CI: 47-82) and refractory disease were 32% (95% CI: 11-54) and 20% (95% CI: 6-40). The 3-year EFS for all patients in morphological CR was 77% (95% CI: 64-87) with no difference amongst recipients with or without minimal residual disease (P = 0.2992). Immune reconstitution was rapid, with mean CD3 and CD4 T-cell counts of 410/µL and 140/µL at day + 30. Cumulative incidence of acute GVHD and chronic GVHD was 36% and 26% but most patients with acute GVHD recovered rapidly with therapy. Lower rates of grade III-IV acute GVHD were observed with NK-cell alloreactive donors (P = 0.004), and higher rates of moderate/severe chronic GVHD occurred with maternal donors (P = 0.035). CONCLUSION: The combination of a CD45RA-depleted graft and NK-cell addback led to robust immune reconstitution maximizing the GVL effect and allowed for use of a submyeloablative, TBI-free conditioning regimen that was associated with excellent EFS resulting in promising long-term outcomes in this high-risk population. The trial is registered at ClinicalTrials.gov (NCT01807611).

Current status of robotic training during the urology residency: results from a national survey in Spain.

INTRODUCTION AND OBJECTIVES: The increasing number of robotic urological procedures observed in recent years highlights the need to expand training opportunities in robotic surgery. Our objective is to investigate the state of robotic training during urology residency in Spain in order to identify significant deficiencies. MATERIALS AND METHODS: A 20-item online survey was conducted among urology residents in Spain who were registered in the database of the Residents and Young Urologists Group of the Spanish Association of Urology. The survey assessed subjective opinions, institutional aspects, training resources, and experience regarding robotic surgery. A total of 455 email invitations were sent throughout the year 2021. Descriptive analysis of the responses was performed. RESULTS: The participation rate reached 30%, with a total of 135 residents. 52% of respondents lacked access to a robotic system in their institution, of which only 48% could compensate for this deficiency through external rotations. Among those with access to a robotic system, 25% and 23% reported having access to theoretical and practical training, respectively. The existence of a formal training program was low (13%). 85% of the respondents considered robotic surgery training in Spain to be deficient. CONCLUSIONS: Training for Spanish residents in robotic urological surgery is perceived as inadequate, emphasizing the crucial need for improvement in training programs in this field.

Synthesis and characterization of 64Cu-labeled Geldanamycin derivative for imaging HSP90 expression in breast cancer.

Heat shock protein 90 (HSP90) plays a crucial role in cancer cell growth and metastasis by stabilizing overexpressed signaling proteins. Inhibiting HSP90 has emerged as a promising anti-cancer strategy. In this study, we aimed to develop and characterize a HSP90-targeted molecular imaging probe, [64Cu]Cu-DOTA-BDA-GM, based on a specific HSP90 inhibitor, geldanamycin (GM), for PET imaging of cancers. GM is modified at the C-17 position with 1,4-butane-diamine (BDA) and linked to 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for 64Cu radiolabeling. We evaluated the probe's specific binding to HSP90-expressing cells using Chinese hamster ovary (CHO) cells and breast cancer cells including MDA-MB-231, MDA-MB-435S, MCF7, and KR-BR-3 cell lines. A competition study with non-radioactive GM-BDA yielded an IC50 value of 1.35 ± 0.14 nM, underscoring the probe's affinity for HSP90. In xenograft models of MDA-MB-231 breast cancer, [64Cu]Cu-DOTA-BDA-GM showcased targeted tumor localization, with significant radioactivity observed up to 18 h post-injection. Blocking studies using unlabeled GM-BDA and treatment with the anticancer drug Vorinostat (SAHA), which can affect the expression and activity of numerous proteins, such as HSPs, confirmed the specificity and sensitivity of the probe in cancer targeting. Additionally, PET/CT imaging in a lung metastasis mouse model revealed increased lung uptake of [64Cu]Cu-DOTA-BDA-GM in metastatic sites, significantly higher than in non-metastatic lungs, illustrating the probe's ability to detect metastatic breast cancer. In conclusion, [64Cu]Cu-DOTA-BDA-GM represents a sensitive and specific approach for identifying HSP90 expression in breast cancer and metastases, offering promising implications for clinical diagnosis and monitoring.

Seroprevalence of Measles (Rubeola) Antibodies in Childhood Cancer Survivors.

Background: Measles is reemerging as a public health threat, raising important questions about disease vulnerability among childhood cancer survivors. This secondary analysis assessed the seroprevalence of anti-measles immunoglobulin G (IgG) antibodies as a marker of immune status in survivors of childhood cancer and associated demographic/treatment variables. Method: Participants were childhood cancer survivors who were free of active disease, having routine blood studies drawn, and could provide documentation of having received two doses of measles, mumps, and rubella vaccine before their cancer diagnosis. Patient record review documented demographic and treatment variables. Antimeasles (rubeola) IgG antibody seroprevalence was assessed by enzyme immunoassay for vaccine-specific antibodies. Results: Of 270 survivors evaluated, 110 (42%) were female, 196 (75%) were White, and 159 (61%) were leukemia/lymphoma survivors. Of these 262, 110 (42%) had negative measles seroprevalence, suggesting loss of immunity. Conclusion: Measles antibody surveillance and the need for reimmunization for survivors of childhood cancer survivors outside the transplant setting remains controversial. Our analysis indicates that a substantial proportion of survivors lose vaccine-related immunity to measles. Pediatric oncology nurses play important roles in educating cancer survivors regarding their risk of measles infection, evaluating the need for reimmunization, correcting misinformation about vaccine safety and effectiveness, and working to optimize community herd-based immunity.

Pavement ant extract is a chemotaxis repellent for C. elegans.

Ant behavior relies on a collection of natural products, from following trail pheromones during foraging to warding off potential predators. How nervous systems sense these compounds to initiate a behavioral response remains unclear. Here, we used Caenorhabditis elegans chemotaxis assays to investigate how ant compounds are detected by heterospecific nervous systems. We found that C. elegans avoid extracts of the pavement ant ( Tetramorium immigrans ) and either osm-9 or tax-4 ion channels are required for this response. These experiments were conducted in an undergraduate laboratory course, demonstrating that new insights into interspecies interactions can be generated through genuine research experiences in a classroom setting.

A variance-based optimization for determining ground and excited N-electron wave functions within the doubly occupied configuration interaction scheme.

This work describes optimizations of N-electron system wave functions by means of the simulated annealing technique within the doubly occupied configuration interaction framework. Using that technique, we minimize the energy variance of a Hamiltonian, providing determinations of wave functions corresponding to ground or excited states in an identical manner. The procedure that allows us to determine electronic spectra can be performed using treatments of restricted or unrestricted types. The results found in selected systems, described in terms of energy, spin, and wave function, are analyzed, showing the performance of each method. We also compare these results with those arising from more traditional approaches that minimize the energy, in both restricted and unrestricted versions, and with those obtained from the full configuration interaction treatment.

Sex Differences in the Role of Sleep on Cognition in Older Adults.

Study Objectives: The study aimed to investigate sex differences in the relationship between sleep quality (self-report and objective) and cognitive function across three domains (executive function, verbal memory, and attention) in older adults. Methods: We analyzed cross-sectional data from 207 participants with normal cognition or mild cognitive impairment (89 males and 118 females) aged over 60. The relationship between sleep quality and cognitive performance was estimated using generalized additive models. Objective sleep was measured with the GT9X Link Actigraph, and self-reported sleep was measured with the Pittsburgh Sleep Quality Index. Results: We found that females exhibited stable performance of executive function with up to about 400 minutes of total sleep time, with significant declines in performance (p = 0.02) when total sleep time was longer. Additionally, a longer total sleep time contributed to lower verbal memory in a slightly non-linear manner (p = 0.03). Higher self-reported sleep complaints were associated with poorer executive function in females with normal cognition (p = 0.02). In males, a positive linear relationship emerged between sleep efficiency and executive function (p = 0.04), while self-reported sleep was not associated with cognitive performance in males with normal cognition. Conclusions: Our findings suggest that the relationships between sleep quality and cognition differ between older males and females, with executive function being the most influenced by objective and self-reported sleep. Interventions targeting sleep quality to mitigate cognitive decline in older adults may need to be tailored according to sex, with distinct approaches for males and females.

Intrapulmonary administration of recombinant activated factor VII in pediatric, adolescent, and young adult oncology and hematopoietic cell transplant patients with pulmonary hemorrhage.

Introduction: Diffuse alveolar hemorrhage (DAH) is a devastating disease process with 50-100% mortality in oncology and hematopoietic cell transplant (HCT) recipients. High concentrations of tissue factors have been demonstrated in the alveolar wall in acute respiratory distress syndrome and DAH, along with elevated levels of tissue factor pathway inhibitors. Activated recombinant factor VII (rFVIIa) activates the tissue factor pathway, successfully overcoming the tissue factor pathway inhibitor (TFPI) inhibition of activation of Factor X. Intrapulmonary administration (IP) of rFVIIa in DAH is described in small case series with successful hemostasis and minimal complications. Methods: We completed a single center retrospective descriptive study of treatment with rFVIIa and outcomes in pediatric oncology and HCT patients with pulmonary hemorrhage at a quaternary hematology/oncology hospital between 2011 and 2019. We aimed to assess the safety and survival of patients with pulmonary hemorrhage who received of IP rFVIIa. Results: We identified 31 patients with pulmonary hemorrhage requiring ICU care. Thirteen patients received intrapulmonary rFVIIa, while eighteen patients did not. Overall, 13 of 31 patients (41.9%) survived ICU discharge. ICU survival (n=6) amongst those in the IP rFVIIa group was 46.2% compared to 38.9% (n=7) in those who did not receive IP therapy (p=0.69). Hospital survival was 46.2% in the IP group and 27.8% in the non-IP group (p=0.45). There were no adverse events noted from use of IP FVIIa. Conclusions: Intrapulmonary rFVIIa can be safely administered in pediatric oncology patients with pulmonary hemorrhage and should be considered a viable treatment option for these patients.

Approach for defining human adenovirus infection and disease for central review adjudication in clinical studies.

BACKGROUND: Pediatric allogeneic hematopoietic cell transplant (allo-HCT) recipients are at risk for morbidity and mortality from human adenovirus (HAdV). HAdV can be detected in an asymptomatic state, referred to as infection or with signs or symptoms of illness, referred to as disease. Standardized case definitions are needed to distinguish infection from disease and allow for consistent reporting in both observational cohort studies and therapeutic clinical trials. METHODS: A working group of experts in virology, transplant infectious disease, and HCT was assembled to develop HAdV infection and disease definitions with the degree of certainty (i.e., possible, probable, and proven). Definitions were further refined through an iterative process and independently applied by two central review committees (CRCs) to 20 pediatric allo-HCT recipients with at least one HAdV-positive PCR. RESULTS: Initial HAdV infection and disease definitions were developed and updated through an iterative process after reviewing clinical and virological details for 81 subjects with at least one positive HAdV PCR detected in a clinical specimen. Independent application of final definitions to 20 HAdV positive allo-HCT recipients by two CRCs yielded similar number of HAdV infection or disease events but with variation of degree of certainty for some events. CONCLUSIONS: Application of definitions by a CRC for a study of HAdV infection and disease is feasible and can provide consistency in the assignment of outcomes. Definitions need further refinement to improve reproducibility and to provide guidance on determining clinical improvement or worsening after initial diagnosis of HAdV infection or disease.

Using full-text content to characterize and identify best seller books: A study of early 20th-century literature.

Artistic pieces can be studied from several perspectives, one example being their reception among readers over time. In the present work, we approach this interesting topic from the standpoint of literary works, particularly assessing the task of predicting whether a book will become a best seller. Unlike previous approaches, we focused on the full content of books and considered visualization and classification tasks. We employed visualization for the preliminary exploration of the data structure and properties, involving SemAxis and linear discriminant analyses. To obtain quantitative and more objective results, we employed various classifiers. Such approaches were used along with a dataset containing (i) books published from 1895 to 1923 and consecrated as best sellers by the Publishers Weekly Bestseller Lists and (ii) literary works published in the same period but not being mentioned in that list. Our comparison of methods revealed that the best-achieved result-combining a bag-of-words representation with a logistic regression classifier-led to an average accuracy of 0.75 both for the leave-one-out and 10-fold cross-validations. Such an outcome enhances the difficulty in predicting the success of books with high accuracy, even using the full content of the texts. Nevertheless, our findings provide insights into the factors leading to the relative success of a literary work.

Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance.

Chromatin structure is regulated through posttranslational modifications of histone variants that modulate transcription. Although highly homologous, histone variants display unique amino acid sequences associated with specific functions. Abnormal incorporation of histone variants contributes to cancer initiation, therapy resistance, and metastasis. This study reports that, among its biologic functions, histone H3.1 serves as a chromatin redox sensor that is engaged by mitochondrial H2O2. In breast cancer cells, the oxidation of H3.1Cys96 promotes its eviction and replacement by H3.3 in specific promoters. We also report that this process facilitates the opening of silenced chromatin domains and transcriptional activation of epithelial-to-mesenchymal genes associated with cell plasticity. Scavenging nuclear H2O2 or amino acid substitution of H3.1(C96S) suppresses plasticity, restores sensitivity to chemotherapy, and induces remission of metastatic lesions. Hence, it appears that increased levels of H2O2 produced by mitochondria of breast cancer cells directly promote redox-regulated H3.1-dependent chromatin remodeling involved in chemoresistance and metastasis.

Guidance for prevention and management of COVID-19 in children and adolescents: A consensus statement from the Pediatric Infectious Diseases Society Pediatric COVID-19 Therapies Taskforce.

BACKGROUND: Since November 2019, the SARS-CoV-2 pandemic has created challenges for preventing and managing COVID-19 in children and adolescents. Most research to develop new therapeutic interventions or to repurpose existing ones has been undertaken in adults, and although most cases of infection in pediatric populations are mild, there have been many cases of critical and fatal infection. Understanding the risk factors for severe illness and the evidence for safety, efficacy, and effectiveness of therapies for COVID-19 in children is necessary to optimize therapy. METHODS: A panel of experts in pediatric infectious diseases, pediatric infectious diseases pharmacology, and pediatric intensive care medicine from 21 geographically diverse North American institutions was re-convened. Through a series of teleconferences and web-based surveys and a systematic review with meta-analysis of data for risk factors, a guidance statement comprising a series of recommendations for risk stratification, treatment, and prevention of COVID-19 was developed and refined based on expert consensus. RESULTS: There are identifiable clinical characteristics that enable risk stratification for patients at risk for severe COVID-19. These risk factors can be used to guide the treatment of hospitalized and non-hospitalized children and adolescents with COVID-19 and to guide preventative therapy where options remain available.