The latent structure of the Delis-Kaplan system for autism.

A core feature of autism is deficits in executive functioning (EF), including difficulty with planning, cognitive flexibility, and working memory. Despite a growing need for evidence-based assessments of EF for autism populations, statistical models of many commonly used measures of EF, including the Delis-Kaplan Executive Function System (D-KEFS), have not been investigated for a sample of autistic participants. The purpose of this study was to address a gap in the literature regarding the latent structure of the D-KEFS in a sample of autistic individuals. The D-KEFS is one of the most widely used clinical assessments of executive function, but its factor structure has not been examined in a sample of autistic participants. Reliability analyses were performed for sample subgroups based on participants' clinical and demographic characteristics, including IQ, autism severity, age, and race/ethnicity. Verbal Fluency (VF) was found to consistently decrease or not affect the overall reliability score. Additionally, one- and two-factor structure models were tested for the D-KEFS with a sample of autistic participants. The one-factor model was not found to be a good fit for the data. However, the two-factor model, with Cognitive Flexibility and Abstraction latent factors, was found to fit the data relatively well. This two-factor model was reexamined excluding the VF observed variable, resulting in a better overall model fit. Communication deficits are a common feature of autism, which explains why the VF task, that requires participants to produce novel words, may not be an adequate measure of executive function for autism populations.

Survival outcomes in pediatric patients with metastatic Ewing sarcoma who achieve a rapid complete response of pulmonary metastases.

PURPOSE: Our objectives were to compare overall survival (OS) and pulmonary relapse between patients with metastatic Ewing sarcoma (EWS) at diagnosis who achieve rapid complete response (RCR) and those with residual pulmonary nodules after induction chemotherapy (non-RCR). PATIENTS AND METHODS: This retrospective cohort study included children under 20 years with metastatic EWS treated from 2007 to 2020 at 19 institutions in the Pediatric Surgical Oncology Research Collaborative. Chi-square tests were conducted for differences among groups. Kaplan-Meier curves were generated for OS and pulmonary relapse. RESULTS: Among 148 patients with metastatic EWS at diagnosis, 61 (41.2%) achieved RCR. Five-year OS was 71.2% for patients who achieved RCR, and 50.2% for those without RCR (p = .04), and in multivariable regression among patients with isolated pulmonary metastases, RCR (hazards ratio [HR] 0.42; 95% confidence interval [CI]: 0.17-0.99) and whole lung irradiation (WLI) (HR 0.35; 95% CI: 0.16-0.77) were associated with improved survival. Pulmonary relapse occurred in 57 (37%) patients, including 18 (29%) in the RCR and 36 (41%) in the non-RCR groups (p = .14). Five-year pulmonary relapse rates did not significantly differ based on RCR (33.0%) versus non-RCR (47.0%, p = .13), or WLI (38.8%) versus no WLI (46.0%, p = .32). DISCUSSION: Patients with EWS who had isolated pulmonary metastases at diagnosis had improved OS if they achieved RCR and received WLI, despite having no significant differences in rates of pulmonary relapse.

Campylobacter species abortion in sheep.

This focus article was prepared by Jasmine Smith of the APHA Small Ruminant Species Expert Group. Data extraction and analysis was done by Anna Brzozowska of the APHA Surveillance Intelligence Unit and Leanne Dempsey from APHA Thirsk.

Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda.

BACKGROUND: Paenibacillus thiaminolyticus may be an underdiagnosed cause of neonatal sepsis. METHODS: We prospectively enrolled a cohort of 800 full-term neonates presenting with a clinical diagnosis of sepsis at 2 Ugandan hospitals. Quantitative polymerase chain reaction specific to P. thiaminolyticus and to the Paenibacillus genus were performed on the blood and cerebrospinal fluid (CSF) of 631 neonates who had both specimen types available. Neonates with Paenibacillus genus or species detected in either specimen type were considered to potentially have paenibacilliosis, (37/631, 6%). We described antenatal, perinatal, and neonatal characteristics, presenting signs, and 12-month developmental outcomes for neonates with paenibacilliosis versus clinical sepsis due to other causes. RESULTS: Median age at presentation was 3 days (interquartile range 1, 7). Fever (92%), irritability (84%), and clinical signs of seizures (51%) were common. Eleven (30%) had an adverse outcome: 5 (14%) neonates died during the first year of life; 5 of 32 (16%) survivors developed postinfectious hydrocephalus (PIH) and 1 (3%) additional survivor had neurodevelopmental impairment without hydrocephalus. CONCLUSIONS: Paenibacillus species was identified in 6% of neonates with signs of sepsis who presented to 2 Ugandan referral hospitals; 70% were P. thiaminolyticus. Improved diagnostics for neonatal sepsis are urgently needed. Optimal antibiotic treatment for this infection is unknown but ampicillin and vancomycin will be ineffective in many cases. These results highlight the need to consider local pathogen prevalence and the possibility of unusual pathogens when determining antibiotic choice for neonatal sepsis.

Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study.

BACKGROUND: Paenibacillus thiaminolyticus is a cause of postinfectious hydrocephalus among Ugandan infants. To determine whether Paenibacillus spp is a pathogen in neonatal sepsis, meningitis, and postinfectious hydrocephalus, we aimed to complete three separate studies of Ugandan infants. The first study was on peripartum prevalence of Paenibacillus in mother-newborn pairs. The second study assessed Paenibacillus in blood and cerebrospinal fluid (CSF) from neonates with sepsis. The third study assessed Paenibacillus in CSF from infants with hydrocephalus. METHODS: In this observational study, we recruited mother-newborn pairs with and without maternal fever (mother-newborn cohort), neonates (aged ≤28 days) with sepsis (sepsis cohort), and infants (aged ≤90 days) with hydrocephalus with and without a history of neonatal sepsis and meningitis (hydrocephalus cohort) from three hospitals in Uganda between Jan 13, 2016 and Oct 2, 2019. We collected maternal blood, vaginal swabs, and placental samples and the cord from the mother-newborn pairs, and blood and CSF from neonates and infants. Bacterial content of infant CSF was characterised by 16S rDNA sequencing. We analysed all samples using quantitative PCR (qPCR) targeting either the Paenibacillus genus or Paenibacillus thiaminolyticus spp. We collected cranial ultrasound and computed tomography images in the subset of participants represented in more than one cohort. FINDINGS: No Paenibacillus spp were detected in vaginal, maternal blood, placental, or cord blood specimens from the mother-newborn cohort by qPCR. Paenibacillus spp was detected in 6% (37 of 631 neonates) in the sepsis cohort and, of these, 14% (5 of 37 neonates) developed postinfectious hydrocephalus. Paenibacillus was the most enriched bacterial genera in postinfectious hydrocephalus CSF (91 [44%] of 209 patients) from the hydrocephalus cohort, with 16S showing 94% accuracy when validated by qPCR. Imaging showed progression from Paenibacillus spp-related meningitis to postinfectious hydrocephalus over 1-3 months. Patients with postinfectious hydrocephalus with Paenibacillus spp infections were geographically clustered. INTERPRETATION: Paenibacillus spp causes neonatal sepsis and meningitis in Uganda and is the dominant cause of subsequent postinfectious hydrocephalus. There was no evidence of transplacental transmission, and geographical evidence was consistent with an environmental source of neonatal infection. Further work is needed to identify routes of infection and optimise treatment of neonatal Paenibacillus spp infection to lessen the burden of morbidity and mortality. FUNDING: National Institutes of Health and Boston Children's Hospital Office of Faculty Development.

Haemonchus contortus: an overview.

This focus article was prepared by Amanda Carson, Rudolf Reichel, Suzie Bell, Rachael Collins and Jasmine Smith of the APHA Small Ruminant Species Expert Group, and Dave Bartley from the Moredun Research Institute.

mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis.

We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized miRNA-mRNA relationships following target prediction.We present two use cases applying mirTarRnaSeq. First, to identify miRNA targets, we examined EBV miRNAs for interaction with human and virus transcriptomes of stomach adenocarcinoma. This revealed enrichment of mRNA targets highly expressed in CD105+ endothelial cells, monocytes, CD4+ T cells, NK cells, CD19+ B cells, and CD34 cells. Next, to investigate miRNA-mRNA relationships in SARS-CoV-2 (COVID-19) infection across time, we used paired miRNA and RNA sequenced datasets of SARS-CoV-2 infected lung epithelial cells across three time points (4, 12, and 24 hours post-infection). mirTarRnaSeq identified evidence for human miRNAs targeting cytokine signaling and neutrophil regulation immune pathways from 4 to 24 hours after SARS-CoV-2 infection. Confirming the clinical relevance of these predictions, three of the immune specific mRNA-miRNA relationships identified in human lung epithelial cells after SARS-CoV-2 infection were also observed to be differentially expressed in blood from patients with COVID-19. Overall, mirTarRnaSeq is a robust tool that can address a wide-range of biological questions providing improved prediction of miRNA-mRNA interactions.

Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus.

OBJECTIVES: To estimate the prevalence of cytomegalovirus (CMV) infections among newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus in Uganda. DESIGN AND METHODS: Three populations-newborn-mother pairs, neonates with sepsis, and infants (≤3 months) with nonpostinfectious (NPIH) or postinfectious (PIH) hydrocephalus-were evaluated for CMV infection at 3 medical centers in Uganda. Quantitative PCR (qPCR) was used to characterize the prevalence of CMV. RESULTS: The overall CMV prevalence in 2498 samples across all groups was 9%. In newborn-mother pairs, there was a 3% prevalence of cord blood CMV positivity and 33% prevalence of maternal vaginal shedding. In neonates with clinical sepsis, there was a 2% CMV prevalence. Maternal HIV seropositivity (adjusted odds ratio [aOR] 25.20; 95% confidence interval [CI] 4.43-134.26; p = 0.0001), residence in eastern Uganda (aOR 11.06; 95% CI 2.30-76.18; p = 0.003), maternal age <25 years (aOR 4.54; 95% CI 1.40-19.29; p = 0.02), and increasing neonatal age (aOR 1.08 for each day older; 95% CI 1.00-1.16; p = 0.05), were associated risk factors for CMV in neonates with clinical sepsis. We found a 2-fold higher maternal vaginal shedding in eastern (45%) vs western (22%) Uganda during parturition (n = 22/49 vs 11/50, the Fisher exact test; p = 0.02). In infants with PIH, the prevalence in blood was 24% and in infants with NPIH, it was 20%. CMV was present in the cerebrospinal fluid (CSF) of 13% of infants with PIH compared with 0.5% of infants with NPIH (n = 26/205 vs 1/194, p < 0.0001). CONCLUSIONS: Our findings highlight that congenital and postnatal CMV prevalence is substantial in this African setting, and the long-term consequences are uncharacterized.

Relative importance of clinical outcomes and safety risks of antiseizure medication monotherapy for patients and physicians: Discrete choice experiment eliciting preferences in real-world study "VOTE".

OBJECTIVE: This study was undertaken to elicit patients' preferences for attributes characterizing antiseizure medication (ASM) monotherapy options before treatment consultation, and to explore the trade-offs patients consider between treatment efficacy and risks of side effects. Further objectives were to explore how treatment consultation may affect patient preferences, to elicit physicians' preferences in selecting treatment, and to compare patient and physician preferences for treatment. METHODS: This prospective, observational study (EP0076; VOTE) included adults with focal seizures requiring a change in their ASM monotherapy. Patients completed a discrete choice experiment (DCE) survey before and after treatment consultation. Physicians completed a similar survey after the consultation. The DCE comprised 12 choices between two hypothetical treatments defined by seven attributes. The conditional relative importance of each attribute was calculated. RESULTS: Three hundred ten patients (mean [SD] age = 46.8 [18.3] years, 52.3% female) were enrolled from eight European countries, of whom 305 completed the survey before consultation and 273 completed the survey before and after consultation. Overall, this preference study in patients who intended to receive a new ASM monotherapy suggests that patient preferences were ordered as expected, with better outcomes being preferred to worse outcomes; patients preferred a higher chance of seizure freedom, lower risk of developing clinical depression, and fewer severe adverse events; avoiding moderate-to-severe "trouble thinking clearly" was more important than avoiding any other side effect. There were qualitative differences in what patients and physicians considered to be the most important aspects of treatment for patients; compared with patients, physicians had a qualitatively stronger preference for greater chance of seizure freedom and avoiding personality changes. Patients' preference weights were qualitatively similar before and after treatment consultation. SIGNIFICANCE: For patients, seizure freedom and avoiding trouble thinking clearly were the most important treatment attributes. Physicians and patients may differ in the emphasis they place on specific attributes.

Case Report: Haploidentical Bone Marrow Transplantation in Two Brothers With Wiskott-Aldrich Syndrome Using Their Father as the Donor.

Wiskott-Aldrich syndrome (WAS) is an X-linked genetic disorder with a variable phenotypic expression that includes thrombocytopenia, eczema, and immunodeficiency. Some patients may also exhibit autoimmune manifestations. Patients with WAS are at increased risk of developing malignancies such as lymphoma. Allogeneic hematopoietic cell transplantation remains the only curative treatment. Haploidentical bone marrow transplantation (haplo-BMT) with post-transplant cyclophosphamide (PT-CY) has more recently been applied in WAS. Here, we report two brothers who underwent successful T-cell replete haplo-BMT with PT-CY at ages 9 months and 4 years using their father as the donor. Our myeloablative regimen was well-tolerated with minimal organ toxicity and no acute or chronic graft vs. host disease (GvHD). Haplo-BMT may be considered as a safe and effective option for patients with WAS who do not have available human leukocyte antigen (HLA) matched donors.

Concurrent application of blinatumomab and haploidentical donor leukocyte infusions for refractory primary mediastinal large B-cell lymphoma.

Primary mediastinal large B-cell lymphoma (PMBCL) is a rare hematologic malignancy with distinct clinical and immunopathological features. We report a case of a young male with disease refractory to multiple lines of therapy, including chimeric antigen receptor-T cells, who achieved his first complete remission after haploidentical bone marrow transplantation (haplo-BMT), following donor leukocyte infusions (DLIs) given concurrently with blinatumomab. While DLI has been used after T-replete haplo-BMT with post-transplant cyclophosphamide, there are no reports on its use for PMBCL. Similarly, blinatumomab is active against B-cell lymphomas, but literature is lacking in patients with PMBCL. Our experience illustrates that blinatumomab can be used concurrently with DLI in a haploidentical setting to achieve disease response in PMBCL. Despite our encouraging experience with this case, we would not recommend this approach outside of a clinical trial as blinatumomab may exacerbate the graft versus host disease risks of DLI, especially in a haploidentical setting. Evaluating this treatment combination in high-risk patients in the setting of a clinical trial may be meaningful.

Effort-reward balance and work motivation in rats: Effects of context and order of experience.

Being motivated means exerting effort toward a goal. The 'law of least work' emphasizes a preference for exerting relatively less effort. The law crosses boundaries among species and between physical and mental work. Organisms should be highly sensitive to shifts in effort-reward balance (ERB) in order to make optimal choices. We used a free operant-foraging task to investigate changes in ERB on choice between options requiring more or less effort. Results showed a consistent preference for the option with less effort and insensitivity to shifts in ERB. A second aim explored the influence of order of experience on effort choice. Choice for the more effortful option significantly increased after experiencing an equal effort-reward relationship during the initial free operant-foraging session. This relative increase in choice for the effortful option persisted even after effort-reward imbalance. The findings highlight the importance of contextual factors such as order of experience when examining the impact of shifting effort-reward associations. Instead of ignoring or reducing order effects, the sequence of experience (e.g. for shifts in ERB) could be manipulated to enhance or reduce value of outcomes or effort itself.

Examination of a day programme for eating disorders: impact on 3-month follow-up by psychiatric comorbidity.

OBJECTIVE: The two aims of this preliminary investigation were to use a case series design to examine outcomes of a day programme (DP) for eating disorders and to investigate whether the presence of baseline psychiatric comorbidities moderated outcomes 3 months after discharge. METHOD: Linear mixed modelling was used to investigate changes over time in the 91 participants who had commenced the DP by April 2019; 87 (96%) female, 61 (67%) with a DSM-5 diagnosis of anorexia nervosa. RESULTS: Six of our seven outcome variables (dietary restraint; concern over weight, eating and shape; clinical impairment; and psychological distress) showed moderate to large effect size improvements from baseline to follow-up. Generally, improvement declined somewhat at follow-up from discharge, with a pattern of results suggesting this decline was less where there was comorbidity at baseline. CONCLUSIONS: These results suggest that a DP effectively reduces eating disorder psychopathology regardless of the presence of psychiatric comorbidity.

Spillover effects of an uninsured population.

A lack of health insurance has long been associated with negative effects on individual and family health due to access barriers. However, we know little about how a lack of health insurance affects wider communities beyond health care. Based on in-depth interviews in two Los Angeles communities, we report how a lack of health insurance affects the functioning of religious institutions and schools from kindergarten to 12th grade. We find a negative spillover effect at the individual and institutional levels for schools experiencing greater absenteeism due to health insurance problems of pupils. However, we find that religious organizations are little affected by a lack of health insurance of adherents. Instead, churches offer health programs as a means to engage their communities. Besides documenting a negative and a positive spillover effect, we offer a conceptual framework for the qualitative study of health spillover effects and examine the policy implications of our findings.

Chromosome segregation in Archaea mediated by a hybrid DNA partition machine.

Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea.

Systematic study on the effect of solvent removal rate on the morphology of solvent vapor annealed ABA triblock copolymer thin films.

Nanoscale self-assembly of block copolymer thin films has garnered significant research interest for nanotemplate design and membrane applications. To fulfill these roles, control of thin film morphology and orientation is critical. Solvent vapor annealing (SVA) treatments can be used to kinetically trap morphologies in thin films not achievable by traditional thermal treatments, but many variables affect the outcome of SVA, including solvent choice, total solvent concentration/swollen film thickness, and solvent removal rate. In this work, we systematically examined the effect of solvent removal rate on the final thin film morphology of a cylinder-forming ABA triblock copolymer. By kinetically trapping the film morphologies at key points during the solvent removal process and then using successive ultraviolet ozone (UVO) etching steps followed by atomic force microscopy (AFM) imaging to examine the through-film morphologies of the films, we determined that the mechanism for cylinder reorientation from substrate-parallel to substrate-perpendicular involved the propagation of changes at the free surface through the film toward the substrate as a front. The degree of reorientation increased with successively slower solvent removal rates. Furthermore, the AFM/UVO etching scheme permitted facile real-space analysis of the thin film internal structure in comparison to cross-sectional transmission electron microscopy.

Rudimentary G-quadruplex-based telomere capping in Saccharomyces cerevisiae.

Telomere capping conceals chromosome ends from exonucleases and checkpoints, but the full range of capping mechanisms is not well defined. Telomeres have the potential to form G-quadruplex (G4) DNA, although evidence for telomere G4 DNA function in vivo is limited. In budding yeast, capping requires the Cdc13 protein and is lost at nonpermissive temperatures in cdc13-1 mutants. Here, we use several independent G4 DNA-stabilizing treatments to suppress cdc13-1 capping defects. These include overexpression of three different G4 DNA binding proteins, loss of the G4 DNA unwinding helicase Sgs1, or treatment with small molecule G4 DNA ligands. In vitro, we show that protein-bound G4 DNA at a 3' overhang inhibits 5'→3' resection of a paired strand by exonuclease I. These findings demonstrate that, at least in the absence of full natural capping, G4 DNA can play a positive role at telomeres in vivo.

Cdc13 N-terminal dimerization, DNA binding, and telomere length regulation.

The essential yeast protein Cdc13 facilitates chromosome end replication by recruiting telomerase to telomeres, and together with its interacting partners Stn1 and Ten1, it protects chromosome ends from nucleolytic attack, thus contributing to genome integrity. Although Cdc13 has been studied extensively, the precise role of its N-terminal domain (Cdc13N) in telomere length regulation remains unclear. Here we present a structural, biochemical, and functional characterization of Cdc13N. The structure reveals that this domain comprises an oligonucleotide/oligosaccharide binding (OB) fold and is involved in Cdc13 dimerization. Biochemical data show that Cdc13N weakly binds long, single-stranded, telomeric DNA in a fashion that is directly dependent on domain oligomerization. When introduced into full-length Cdc13 in vivo, point mutations that prevented Cdc13N dimerization or DNA binding caused telomere shortening or lengthening, respectively. The multiple DNA binding domains and dimeric nature of Cdc13 offer unique insights into how it coordinates the recruitment and regulation of telomerase access to the telomeres.

Isolation of G-quadruplex DNA using NMM-sepharose affinity chromatography.

DNA can adopt a variety of non-standard conformations, including structures known as G-quadruplexes (G4-DNA), which consist of stacked tetrads of guanines. There are growing indications that G4-DNA is of biological importance, including evidence that it plays roles in telomere function, DNA recombination and the regulation of transcription and translation. However, it has been difficult to obtain direct, physical evidence for the presence of G-quadruplex DNA in vivo due, in part, to a lack of tools for G4-DNA identification. Here, we describe a method for coupling the G4-DNA binding ligand N-methyl mesoporphyrin IX (NMM) to a Sepharose resin, and demonstrate the ability of the resin to bind tightly and selectively to DNA oligonucleotides with the capacity to form G4-DNA. This technique might also be extended to examine genomic distributions of G4-DNA isolated from in vivo sources.

Significant correlation of species longevity with DNA double strand break recognition but not with telomere length.

The identification of the cellular mechanisms responsible for the wide differences in species lifespan remains one of the major unsolved problems of the biology of aging. We measured the capacity of nuclear protein to recognize DNA double strand breaks (DSBs) and telomere length of skin fibroblasts derived from mammalian species that exhibit wide differences in longevity. Our results indicate DNA DSB recognition increases exponentially with longevity. Further, an analysis of the level of Ku80 protein in human, cow, and mouse suggests that Ku levels vary dramatically between species and these levels are strongly correlated with longevity. In contrast mean telomere length appears to decrease with increasing longevity of the species, although not significantly. These findings suggest that an enhanced ability to bind to DNA ends may be important for longevity. A number of possible roles for increased levels of Ku and DNA-PKcs are discussed.