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Introduction: Despite global surveillance efforts, antibiotic resistance (ABR) is difficult to address in low- and middle-income countries (LMICs). In the absence of country-wide ABR surveillance data, peer-reviewed literature is the next most significant source of publicly available ABR data. Médecins Sans Frontières conducted this review in hopes of using the pooled findings to inform treatment choices in the studied countries where sufficient local ABR data are unavailable., Methods: A systematic literature review reporting ABR rates for six infection sites in nine countries in the Middle East and Southern Asia was conducted. PubMed was used to identify literature published between January 2012 and August 2022. A meta-analysis of the included studies ( n  = 694) was conducted, of which 224 are reviewed in this paper. The JBI critical appraisal tool was used to evaluate risk of bias for included studies., Results: This paper focuses on sepsis, burns and wound infections, specifically, with the largest number of papers describing data from Iran, Türkiye and Pakistan. High (>30%) resistance to recommended first-line antibiotics was found. Gram-negative resistance to ceftriaxone, aminoglycosides and carbapenems was high in burn-related infections; colistin resistance among Klebsiella pneumoniae isolates in Pakistan was alarmingly high (81%)., Conclusions: High-quality data on ABR in LMIC settings remain difficult to obtain. While peer-reviewed literature is a source of publicly available ABR data, it is of inconsistent quality; the field also lacks agreed reporting standards, limiting the capacity to pool findings. Nonetheless, high resistance to first-line antibiotics underscores the need for improved localized surveillance and stewardship., (© The Author(s) 2025. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

Inherited glycosylphosphatidylinositol deficiency disorders (IGDs) are a group of rare multisystem disorders arising from pathogenic variants in glycosylphosphatidylinositol anchor pathway (GPI-AP) genes. Despite associating 24 of at least 31 GPI-AP genes with human neurogenetic disease, prior reports are limited to single genes without consideration of the GPI-AP as a whole and with limited natural history data. In this multinational retrospective observational study, we systematically analyse the molecular spectrum, phenotypic characteristics and natural history of 83 individuals from 75 unique families with IGDs, including 70 newly reported individuals; the largest single cohort to date. Core clinical features were developmental delay or intellectual disability (DD/ID, 90%), seizures (83%), hypotonia (72%) and motor symptoms (64%). Prognostic and biologically significant neuroimaging features included cerebral atrophy (75%), cerebellar atrophy (60%), callosal anomalies (57%) and symmetric restricted diffusion of the central tegmental tracts (60%). Sixty-one individuals had multisystem involvement including gastrointestinal (66%), cardiac (19%) and renal (14%) anomalies. Though dysmorphic features were appreciated in 82%, no single dysmorphic feature had a prevalence >30%, indicating substantial phenotypic heterogeneity. Follow-up data were available for all individuals, 15 of whom were deceased at the time of writing. Median age at seizure onset was 6 months. Individuals with variants in synthesis stage genes of the GPI-AP exhibited a significantly shorter time to seizure onset than individuals with variants in transamidase and remodelling stage genes of the GPI-AP (P = 0.046). Forty individuals had intractable epilepsy. The majority of individuals experienced delayed or absent speech (95%), motor delay with non-ambulance (64%), and severe-to-profound DD/ID (59%). Individuals with a developmental epileptic encephalopathy (51%) were at greater risk of intractable epilepsy (P = 0.003), non-ambulance (P = 0.035), ongoing enteral feeds (P < 0.001) and cortical visual impairment (P = 0.007). Serial neuroimaging showed progressive cerebral volume loss in 87.5% and progressive cerebellar atrophy in 70.8%, indicating a neurodegenerative process. Genetic analyses identified 93 unique variants (106 total), including 22 novel variants. Exploratory analyses of genotype-phenotype correlations using unsupervised hierarchical clustering identified novel genotypic predictors of clinical phenotype and long-term outcome with meaningful implications for management. In summary, we expand both the mild and severe phenotypic extremities of the IGDs, provide insights into their neurological basis, and vitally, enable meaningful genetic counselling for affected individuals and their families., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Background: Despite continuous advances in post-resuscitation management, outcome after out-of-hospital cardiac arrest (OHCA) is limited. To improve the outcome, interdisciplinary Cardiac Arrest Centers (CACs) have been established in recent years, but survival remains low and treatment strategies vary considerably in clinical and geographical aspects. Here we analyzed a strategy of in-hospital post-resuscitation management while evaluating the outcome., Methods: A broad spectrum of pre- and in-hospital parameters of 545 resuscitated patients, admitted to the Cardiac Arrest Center of the University Hospital of Marburg (MCAC) between 01/2018 and 12/2022 were retrospectively analyzed. Inclusion criteria were ≥ 18 years, resuscitation by emergency medical services, and non-traumatic cause of OHCA., Results: In the overall patient cohort, the survival rate to hospital discharge was 39.8% (n = 217/545), which is 50.7% higher than in the EuReCa-TWO registry. 77.2% of the survivors had CPC status 1 or 2 (favorable neurological outcome) before and after therapy. A standardized 'therapy bundle' for in-hospital post-resuscitation management was applied to 445 patients who survived the initial treatment in the emergency department. In addition to basic care (standardized antimicrobial therapy, adequate anticoagulation, targeted sedation, early enteral and parenteral nutrition), it includes early whole-body CT (n = 391; 87.9%), invasive coronary diagnostics (n = 322; 72.4%), targeted temperature management (n = 293; 65.8%) and if indicated, mechanical circulatory support (n = 145; 32.6%) and appropriate neurological diagnostics., Conclusions: Early goal-directed post-resuscitation management in a well-established and highly frequented CAC leads to significantly higher survival rates. However, our results underline the need for a broader standardization in post-resuscitation management to ultimately improve the outcome., (© The Author(s) 2024. Published by Oxford University Press on behalf of the European Society of Cardiology.)

Background: Antimicrobial resistance (AMR) is an urgent global health concern, especially in countries facing instability or conflicts, with compromised healthcare systems. Médecins Sans Frontières (MSF) established an acute trauma hospital in Aden, Yemen, treating mainly war-wounded civilians, and implemented an antimicrobial stewardship (AMS) programme. This study aimed to describe clinical characteristics and identify antibiotic susceptibility patterns representative of patients treated with antibiotics., Methods: Retrospective cross-sectional study using routinely collected data from all patients treated with antibiotics in the MSF-Aden Acute Trauma hospital between January 2018 and June 2021. Routine clinical data from patients' files was entered into an AMS electronic database and microbiological data were entered into WHONET. Both databases were imported and merged in REDCap and analysed using RStudio., Results: Three hundred and sixty-three of 481 (75%) included patients were injured by violence-related trauma. Most were men aged 19-45 years ( n  = 331; 68.8%). In total, 598 infections were diagnosed and treated. MDR organisms were identified in 362 (60.5%) infections in 311 (65%) patients. Skin and soft-tissue infections (SSTIs) ( n  = 143; 24%) were the most common, followed by osteomyelitis ( n  = 125; 21%) and intra-abdominal-infections (IAIs) ( n  = 116; 19%), and 111 (19%) secondary bloodstream infections were identified. Escherichia coli was the most frequently identified pathogen, causing IAI ( n  = 87; 28%) and SSTI ( n  = 43; 16%), while Staphylococcus aureus caused mainly osteomyelitis ( n  = 84; 19%). Most Gram-negatives were ESBL producers, including E. coli ( n  = 193; 81.4%), Klebsiella pneumoniae ( n  = 72; 77.4%) and Enterobacter cloacae ( n  = 39; 50%) while most S. aureus were methicillin resistant ( n  = 93; 72.6%)., Conclusions: High rates of MDR were found. This information will facilitate a comprehensive review of the empirical antibiotic treatment guidelines., (© The Author(s) 2024. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

There has been an increase in the number of women using marijuana whilst pregnant. Previous studies have shown that children with prenatal marijuana exposure have developmental deficits in memory and decreased attentiveness. In this study, we assess whether prenatal marijuana exposure is associated with alterations in brain regional morphometry and functional and structural connectivity in adolescents. We downloaded behavioural scores and subject image files from the Adolescent Brain Cognitive Development SM Study. A total of 178 anatomical and diffusion magnetic resonance imaging files (88 prenatal marijuana exposure and 90 age- and gender-matched controls) and 152 resting-state functional magnetic resonance imaging files (76 prenatal marijuana exposure and 76 controls) were obtained. Behavioural metrics based on the parent-reported child behavioural checklist were also obtained for each subject. The associations of prenatal marijuana exposure with 17 subscales of the child behavioural checklist were calculated. We assessed differences in brain morphometry based on voxel-based and surface-based morphometry in adolescents with prenatal marijuana exposure versus controls. We also evaluated group differences in structural and functional connectivity in adolescents for region-to-region connectivity and graph theoretical metrics. Interactions of prenatal marijuana exposure and graph networks were assessed for impact on behavioural scores. Multiple comparison correction was performed as appropriate. Adolescents with prenatal marijuana exposure had greater abnormal or borderline child behavioural checklist scores in 9 out of 17 subscales. There were no significant differences in voxel- or surface-based morphometry, structural connectivity or functional connectivity between prenatal marijuana exposure and controls. However, there were significant differences in prenatal marijuana exposure-graph network interactions with respect to behavioural scores. There were three structural prenatal marijuana exposure-graph network interactions and seven functional prenatal marijuana exposure-graph network interactions that were significantly associated with behavioural scores. Whilst this study was not able to confirm anatomical or functional differences between prenatal marijuana exposure and unexposed pre-adolescent children, there were prenatal marijuana exposure-brain structural and functional graph network interactions that were significantly associated with behavioural scores. This suggests that altered brain networks may underlie behavioural outcomes in adolescents with prenatal marijuana exposure. More work needs to be conducted to better understand the prognostic value of brain structural and functional network measures in prenatal marijuana exposure., Competing Interests: The authors have conducted this research in the absence of any commercial, financial or personal relationships that would be considered a conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Guarantors of Brain.)

Objective: The optimal approach to the surveillance of non-functioning pituitary microadenomas (micro-NFPAs) is not clearly established. Our aim was to generate evidence on the natural history of micro-NFPAs to support patient care., Design: Multi-centre, retrospective, cohort study involving 23 endocrine departments (UK NFPA consortium)., Methods: Clinical, imaging, and hormonal data of micro-NFPA cases between January, 1, 2008 and December, 21, 2021 were analysed., Results: Data for 459 patients were retrieved [median age at detection 44 years (IQR 31-57)-152 males/307 females]. Four hundred and nineteen patients had more than two magnetic resonance imagings (MRIs) [median imaging monitoring 3.5 years (IQR 1.71-6.1)]. One case developed apoplexy. Cumulative probability of micro-NFPA growth was 7.8% (95% CI, 4.9%-8.1%) and 14.5% (95% CI, 10.2%-18.8%) at 3 and 5 years, respectively, and of reduction 14.1% (95% CI, 10.4%-17.8%) and 21.3% (95% CI, 16.4%-26.2%) at 3 and 5 years, respectively. Median tumour enlargement was 2 mm (IQR 1-3) and 49% of micro-NFPAs that grew became macroadenomas (nearly all >5 mm at detection). Eight (1.9%) patients received surgery (only one had visual compromise with surgery required >3 years after micro-NFPA detection). Sex, age, and size at baseline were not predictors of enlargement/reduction. At the time of detection, 7.2%, 1.7%, and 1.5% patients had secondary hypogonadism, hypothyroidism, and hypoadrenalism, respectively. Two (0.6%) developed hypopituitarism during follow-up (after progression to macroadenoma)., Conclusions: Probability of micro-NFPA growth is low, and the development of new hypopituitarism is rare. Delaying the first follow-up MRI to 3 years and avoiding hormonal re-evaluation in the absence of tumour growth or clinical manifestations is a safe approach for micro-NFPA surveillance., Competing Interests: Conflicts of interest: None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of European Society of Endocrinology.)

Objectives: C-reactive protein (CRP) and procalcitonin (PCT) are widely used biomarkers in high-income countries. However, evidence for their use in low- and middle-income countries (LMICs) is scant. Because many factors, including rates of endemic disease, comorbidities and genetics, may influence biomarkers' behaviour, we aimed to review available evidence generated in LMICs., Methods: We searched the PubMed database for relevant studies within the last 20 years that originated in regions of interest (Africa, Latin America, Middle East, South Asia or South East Asia), and full-text articles involving diagnosis, prognostication and evaluation of therapeutic response with CRP and/or PCT in adults ( n  = 88) were reviewed and categorized in 12 predefined focus areas., Results: Overall, results were highly heterogeneous, at times conflicting, and often lacking clinically useful cut-off values. However, most studies demonstrated higher levels of CRP/PCT in patients with bacterial versus other infections. HIV and TB patients had consistently higher levels of CRP/PCT versus controls. In addition, higher CRP/PCT levels at baseline and follow-up in HIV, TB, sepsis and respiratory tract infections were associated with poorer prognosis., Conclusions: Evidence generated from LMIC cohorts suggests that CRP and PCT may have potential to become effective clinical guiding tools particularly in respiratory tract infections, sepsis and HIV/TB. However, more studies are needed to define potential scenarios for use and cost-effectiveness. Consensus across stakeholders regarding target conditions, laboratory standards and cut-off values would support the quality and applicability of future evidence., (© The Author(s) 2023. Published by Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.)

BCR-ABL1 kinase inhibitors have improved the prognosis of Philadelphia-chromosome-positive (Ph+)-acute lymphoblastic leukemia (ALL). Ph-like (or BCR-ABL1-like) ALL does not express BCR-ABL1 but commonly harbors other genomic alterations of signaling molecules that may be amenable to therapy. Here, we report a case with a NUP214-ABL1 fusion detected at relapse by multiplexed, targeted RNA sequencing. It had escaped conventional molecular work-up at diagnosis, including cytogenetic analysis and fluorescence in situ hybridization for ABL1 rearrangements. The patient had responded poorly to initial multi-agent chemotherapy and inotuzumab immunotherapy at relapse before the fusion was revealed. The addition of dasatinib targeting NUP214-ABL1 to inotuzumab resulted in complete molecular remission, but recurrence occurred rapidly with dasatinib alone. However, deep molecular remission was recaptured with a combination of blinatumomab and ponatinib, so he could proceed to allotransplantation. This case illustrates that next-generation sequencing approaches designed to discover cryptic gene fusions can benefit patients with Ph-like ALL., (© The Author(s) 2022. Published by Oxford University Press.)

Precision oncology emphasizes genotyping as one of the mainstays of oncological decision-making. The core information element exchanged between the laboratory and the oncologist is the precise mutation. Specifically, it is the written representation typically in the form of a variant description at the DNA or protein level. These annotations can be confusing, and many commercial laboratories have abandoned DNA-level annotations. Here we present a complex double-point mutation to illustrate a situation where a formally "correct" reporting nomenclature can obscure clinically relevant and potentially clinically actionable information. KEY POINTS: The Human Genome Variation Society (HGVS) currently recommends that "two variants separated by one or more nucleotides should be described individually and not as a combined 'delins' (deletion-inserion)." There remains confusion about the appropriate nomenclature to report variants and the significance of these variants among clinicians. It is the clinically integrated molecular-genetic interpretation that will help clinicians make informed decisions to improve patient care., (© 2021 AlphaMed Press.)

Objectives: Concern has been raised in the rheumatology community regarding recent regulatory warnings that HCQ used in the coronavirus disease 2019 pandemic could cause acute psychiatric events. We aimed to study whether there is risk of incident depression, suicidal ideation or psychosis associated with HCQ as used for RA., Methods: We performed a new-user cohort study using claims and electronic medical records from 10 sources and 3 countries (Germany, UK and USA). RA patients ≥18 years of age and initiating HCQ were compared with those initiating SSZ (active comparator) and followed up in the short (30 days) and long term (on treatment). Study outcomes included depression, suicide/suicidal ideation and hospitalization for psychosis. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate database-specific calibrated hazard ratios (HRs), with estimates pooled where I2 <40%., Results: A total of 918 144 and 290 383 users of HCQ and SSZ, respectively, were included. No consistent risk of psychiatric events was observed with short-term HCQ (compared with SSZ) use, with meta-analytic HRs of 0.96 (95% CI 0.79, 1.16) for depression, 0.94 (95% CI 0.49, 1.77) for suicide/suicidal ideation and 1.03 (95% CI 0.66, 1.60) for psychosis. No consistent long-term risk was seen, with meta-analytic HRs of 0.94 (95% CI 0.71, 1.26) for depression, 0.77 (95% CI 0.56, 1.07) for suicide/suicidal ideation and 0.99 (95% CI 0.72, 1.35) for psychosis., Conclusion: HCQ as used to treat RA does not appear to increase the risk of depression, suicide/suicidal ideation or psychosis compared with SSZ. No effects were seen in the short or long term. Use at a higher dose or for different indications needs further investigation., Trial Registration: Registered with EU PAS (reference no. EUPAS34497; http://www.encepp.eu/encepp/viewResource.htm? id=34498). The full study protocol and analysis source code can be found at https://github.com/ohdsi-studies/Covid19EstimationHydroxychloroquine2., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Rheumatology.)

Background and Aims: Persons with inflammatory bowel disease (IBD) may be particularly vulnerable to COVID-19 either because of their underlying disease or its management. Guidance has been presented on the management of persons with IBD in the time of this pandemic by different groups. We aimed to determine how gastroenterologists around the world were approaching the management of IBD., Methods: Members of the World Gastroenterology Organization (WGO) IBD Task Force contacted colleagues in countries largely beyond North America and Europe, inviting them to review the WGO website for IBD and COVID-19 introduction, with links to guideline documents, and then to respond to 9 ancillary open-ended management questions., Results: Fifty-two gastroenterologists from 33 countries across 6 continents completed the survey (April 14 to May 16, 2020). They were all adhering for the most part to published guidelines on IBD management in the COVID-19 era. Some differences and reductions in services related to access, and some related to approach within their communities in terms of limiting virus spread. In particular, most gastroenterologists reduced in-person clinics (43 of 52), limited steroid use (47 of 51), limited elective endoscopy (45 of 52), and limited elective surgeries (48 of 51). If a patient was diagnosed with COVID-19, immunomodulatory therapy was mostly held., Conclusions: In most countries, the COVID-19 pandemic significantly altered the approach to persons with IBD. The few exceptions were mostly based on low burden of COVID-19 in individual communities. Regardless of resources or health care systems, gastroenterologists around the world took a similar approach to the management of IBD., (© 2020 Crohn’s & Colitis Foundation. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented., Methods: We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences., Results: We found considerable improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome, compared to an average of 0.63% without enrichment. Consequently, an increase in genome coverage was obtained using substantially less sequencing data, enabling higher scalability and sizable cost reductions. We also demonstrated how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains., Conclusions: SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic., (© American Association for Clinical Chemistry 2020. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background and Aims: Poor knowledge of inflammatory bowel disease [IBD] in pregnancy underlies unwarranted voluntary childlessness [VC], and risks poorer obstetric outcomes and adverse fetal outcomes. IBD is increasing worldwide but education on IBD issues might be heterogeneous based on cultural differences and variations in models of care., Methods: Consecutive female IBD subjects aged 18-45 years were prospectively recruited from two dedicated IBD-pregnancy clinics, two multidisciplinary IBD clinics and nine general gastroenterology clinics. Subjects completed the validated CCPKnow [score 0-17] with questions on demographics, medical history and pregnancy knowledge. The primary outcome was knowledge per clinic-type and per geographical region., Results: Surveys were completed by 717 subjects from 13 hospitals across ten countries. Dedicated IBD-pregnancy clinics had the highest knowledge, followed by multidisciplinary IBD clinics then general IBD clinics (median CCPKnow 10.0 [IQR: 8.0-11.0], 8.0 [IQR: 5.0-10.5] and 4.0 [IQR:2.0-6.0]; p < 0.001). Median CCPKnow scores in Western, Asian and Middle Eastern clinics were 9.0, 5.0 and 3.0 respectively [p < 0.001]. Dedicated IBD-pregnancy clinics, IBD support organization membership, childbearing after IBD diagnosis and employment independently predicted greater knowledge. Patient perception of disease severity [r = -0.18, p < 0.01] and consideration of VC [r = -0.89, p = 0.031] negatively correlated with CCPKnow score. The overall VC rate was 15.0% [95% CI: 12.2-18.2]. VC subjects had significantly lower pregnancy-specific IBD knowledge than non-VC subjects (median CCPKnow 4.0 [IQR: 2.0-6.0] and 6.0 [IQR: 3.0-9.0] respectively; p < 0.001). Pregnancy-specific IBD knowledge and dedicated IBD-pregnancy clinic attendance were significant negative predictors of VC., Conclusions: In this large international study we identified predictors of pregnancy-specific IBD knowledge. Dedicated IBD-pregnancy clinics had the greatest IBD-related pregnancy knowledge and lowest VC rates, reflecting the benefits of pre-conception counselling., (© The Author(s) 2020. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Several Eastern Harris County communities lie near the now enclosed San Jacinto River (SJR) Waste Pit Superfund, a dumping ground for chlorinated dioxins and other paper mill waste products. Currently, no active monitoring of the SJR is conducted for these toxins with the exact concentration and health impact to the area unknown. As such, remediation and monitoring efforts outside of the Superfund itself could be necessary. To better understand the possible environmental fate of these aromatics, here we provide a shotgun metagenomic analysis of the structural and putative functional diversity of the SJR microbiome from two impacted Channelview, Texas communities bordering the Superfund. Results show that the underlying SJR microbiome possesses a core of metabolic enzymes related to the β-ketoadipate and benzoate degradation pathways. This suggests possible endpoints for many aromatics found deposited in the SJR including dioxin-like compounds. However, degradation biomarkers related to the priming and initial cleavage of chlorinated dioxin-like aromatics while present, are poorly concentrated across sampled sites. This may be due in part to decreased coverage of low abundance bacterial species, but also be a contributing factor leading to increased recalcitrance of these compounds in this environment compared to other aromatics., (© FEMS 2020.)

Context: Long-term outcomes of patients with Nelson's syndrome (NS) have been poorly explored, especially in the modern era., Objective: To elucidate tumor control rates, effectiveness of various treatments, and markers of prognostic relevance in patients with NS., Patients, Design, and Setting: Retrospective cohort study of 68 patients from 13 UK pituitary centers with median imaging follow-up of 13 years (range 1-45) since NS diagnosis., Results: Management of Cushing's disease (CD) prior to NS diagnosis included surgery+adrenalectomy (n = 30; eight patients had 2 and one had 3 pituitary operations), surgery+radiotherapy+adrenalectomy (n = 17; two received >1 courses of irradiation, two had ≥2 pituitary surgeries), radiotherapy+adrenalectomy (n = 2), and adrenalectomy (n = 19). Primary management of NS mainly included surgery, radiotherapy, surgery+radiotherapy, and observation; 10-year tumor progression-free survival was 62% (surgery 80%, radiotherapy 52%, surgery+radiotherapy 81%, observation 51%). Sex, age at CD or NS diagnosis, size of adenoma (micro-/macroadenoma) at CD diagnosis, presence of pituitary tumor on imaging prior adrenalectomy, and mode of NS primary management were not predictors of tumor progression. Mode of management of CD before NS diagnosis was a significant factor predicting progression, with the group treated by surgery+radiotherapy+adrenalectomy for their CD showing the highest risk (hazard ratio 4.6; 95% confidence interval, 1.6-13.5). During follow-up, 3% of patients had malignant transformation with spinal metastases and 4% died of aggressively enlarging tumor., Conclusions: At 10 years follow-up, 38% of the patients diagnosed with NS showed progression of their corticotroph tumor. Complexity of treatments for the CD prior to NS diagnosis, possibly reflecting corticotroph adenoma aggressiveness, predicts long-term tumor prognosis., (© Endocrine Society 2019. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Exposure to ambient fine particulate matter (particulate matter ≤2.5 μm in aerodynamic diameter (PM2.5)) during pregnancy is associated with preterm birth (PTB), a leading cause of infant morbidity and mortality. Results from studies attempting to identify etiologically relevant exposure periods of vulnerability have been inconsistent, possibly because of failure to consider the time-to-event nature of the outcome and lagged exposure effects of PM2.5. In this study, we aimed to identify critical exposure windows for weekly PM2.5 exposure and PTB in California using California birth cohort data from 2005-2010. Associations were assessed using distributed-lag Cox proportional hazards models. We assessed effect-measure modification by race/ethnicity by calculating the weekly relative excess risk due to interaction. For a 10-μg/m3 increase in PM2.5 exposure over the entire period of gestation, PTB risk increased by 11% (hazard ratio = 1.11, 95% confidence interval: 1.09, 1.14). Gestational weeks 17-24 and 36 were associated with increased vulnerability to PM2.5 exposure. We find that non-Hispanic black mothers may be more susceptible to effects of PM2.5 exposure than non-Hispanic white mothers, particularly at the end of pregnancy. These findings extend our knowledge about the existence of specific exposure periods during pregnancy that have the greatest impact on preterm birth., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objectives: The current study utilized mHealth technologies that were objective (e.g., sleep actigraphy and pulse oximetry) and time-sensitive (e.g., ecological momentary assessments [EMAs]) to characterize sleep in youth with sickle cell disease (SCD) and investigate the relationships between sleep variables and pain. It also investigated the influence of age on sleep and the sleep-pain relationship., Methods: Eighty-eight youth with SCD (aged 8-17 years) were recruited from three regional pediatric SCD clinics. Youth completed twice daily EMAs for up to 4 weeks to assess nighttime subjective sleep quality and daily pain. They also wore a sleep actigraph for 2 weeks to assess sleep duration, sleep efficiency, and sleep latency, and a wrist-worn pulse oximeter for two nights to assess whether they had sleep apnea. Multilevel models were calculated predicting daily SCD pain using the sleep variables, age, and the interaction between age and the sleep variables., Results: None of the sleep variables were related to one another. Poor subjective sleep quality during the night was related to high pain severity the next day, and high pain was related to poor subjective sleep quality that night. Older age was associated with poorer subjective sleep quality, shorter duration of nighttime sleep, and high sleep latency. Also, findings indicated that as age increased, the strength of the relationship between poor continuous subjective sleep quality and high pain severity increased., Conclusions: Future research is needed to examine possible mechanisms connecting subjective sleep quality to high pain., (Published by Oxford University Press on behalf of the Society of Pediatric Psychology 2019.)

Objective: Cohort definition is a bottleneck for conducting clinical research and depends on subjective decisions by domain experts. Data-driven cohort definition is appealing but requires substantial knowledge of terminologies and clinical data models. Criteria2Query is a natural language interface that facilitates human-computer collaboration for cohort definition and execution using clinical databases., Materials and Methods: Criteria2Query uses a hybrid information extraction pipeline combining machine learning and rule-based methods to systematically parse eligibility criteria text, transforms it first into a structured criteria representation and next into sharable and executable clinical data queries represented as SQL queries conforming to the OMOP Common Data Model. Users can interactively review, refine, and execute queries in the ATLAS web application. To test effectiveness, we evaluated 125 criteria across different disease domains from ClinicalTrials.gov and 52 user-entered criteria. We evaluated F1 score and accuracy against 2 domain experts and calculated the average computation time for fully automated query formulation. We conducted an anonymous survey evaluating usability., Results: Criteria2Query achieved 0.795 and 0.805 F1 score for entity recognition and relation extraction, respectively. Accuracies for negation detection, logic detection, entity normalization, and attribute normalization were 0.984, 0.864, 0.514 and 0.793, respectively. Fully automatic query formulation took 1.22 seconds/criterion. More than 80% (11+ of 13) of users would use Criteria2Query in their future cohort definition tasks., Conclusions: We contribute a novel natural language interface to clinical databases. It is open source and supports fully automated and interactive modes for autonomous data-driven cohort definition by researchers with minimal human effort. We demonstrate its promising user friendliness and usability., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

We piloted PrEP@Home, a preexposure prophylaxis system of remote laboratory and behavioral monitoring designed to replace routine quarterly follow-up visits with home care to reduce the patient and provider burden. The system was highly acceptable and in-demand for future use, and more than one-third of participants reported greater likelihood of persisting in care if available.

Few investigations have explored temperature and birth outcomes. In a retrospective cohort study, we examined apparent temperature, a combination of temperature and relative humidity, and term low birth weight (LBW) among 43,629 full-term LBW infants and 2,032,601 normal-weight infants in California (1999-2013). The California Department of Public Health provided birth certificate data, while meteorological data came from the California Irrigation Management Information System, US Environmental Protection Agency, and National Centers for Environmental Information. After considering several temperature metrics, we observed the best model fit for term LBW over the full gestation (per 10-degrees-Fahrenheit (°F) increase in apparent temperature, 13.0% change, 95% confidence interval: 4.1, 22.7) above 55°F, and the greatest association was for third-trimester exposure above 60°F (15.8%, 95% confidence interval: 5.0, 27.6). Apparent temperature during the first month of pregnancy exhibited no significant risk, while the first trimester had a significantly negative association, and second trimester, last month, and last 2 weeks had slightly increased risks. Mothers who were black or older, delivered male infants, or gave birth during the warm season had infants at the highest risks. This study provides further evidence for adverse birth outcomes from heat exposure for vulnerable subgroups of pregnant women.

The association between ambient temperature and morbidity has been explored previously. However, the association between temperature and mental health-related outcomes, including violence and self-harm, remains relatively unexamined. For the period 2005-2013, we obtained daily counts of mental health-related emergency room visits involving injuries with an external cause for 16 California climate zones from the California Office of Statewide Health Planning and Development and combined them with data on mean apparent temperature, a combination of temperature and humidity. Using Poisson regression models, we estimated climate zone-level associations and then used random-effects meta-analyses to produce overall estimates. Analyses were stratified by season (warm: May-October; cold: November-April), race/ethnicity, and age. During the warm season, a 10°F (5.6°C) increase in same-day mean apparent temperature was associated with 4.8% (95% confidence interval (CI): 3.6, 6.0), 5.8% (95% CI: 4.5, 7.1), and 7.9% (95% CI: 7.3, 8.4) increases in the risk of emergency room visits for mental health disorders, self-injury/suicide, and intentional injury/homicide, respectively. High temperatures during the cold season were also positively associated with these outcomes. Variations were observed by race/ethnicity, age group, and sex, with Hispanics, whites, persons aged 6-18 years, and females being at greatest risk for most outcomes. Increasing mean apparent temperature was found to have acute associations with mental health outcomes and intentional injuries, and these findings warrant further study in other locations.

Background and Aims: Success in delivering value-based healthcare involves measuring outcomes that matter most to patients. Our aim was to develop a minimum Standard Set of patient-centred outcome measures for inflammatory bowel disease [IBD], for use in different healthcare settings., Methods: An international working group [n = 25] representing patients, patient associations, gastroenterologists, surgeons, specialist nurses, IBD registries and patient-reported outcome measure [PROM] methodologists participated in a series of teleconferences incorporating a modified Delphi process. Systematic review of existing literature, registry data, patient focus groups and open review periods were used to reach consensus on a minimum set of standard outcome measures and risk adjustment variables. Similar methodology has been used in 21 other disease areas [www.ichom.org]., Results: A minimum Standard Set of outcomes was developed for patients [aged ≥16] with IBD. Outcome domains included survival and disease control [survival, disease activity/remission, colorectal cancer, anaemia], disutility of care [treatment-related complications], healthcare utilization [IBD-related admissions, emergency room visits] and patient-reported outcomes [including quality of life, nutritional status and impact of fistulae] measured at baseline and at 6 or 12 month intervals. A single PROM [IBD-Control questionnaire] was recommended in the Standard Set and minimum risk adjustment data collected at baseline and annually were included: demographics, basic clinical information and treatment factors., Conclusions: A Standard Set of outcome measures for IBD has been developed based on evidence, patient input and specialist consensus. It provides an international template for meaningful, comparable and easy-to-interpret measures as a step towards achieving value-based healthcare in IBD.

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB's chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC-MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Aims: Intraplaque haemorrhage is considered a major contributor to lesion progression. We assessed coronary lesions with intraplaque haemorrhage using intravascular ultrasound (IVUS) and near-infrared spectroscopy (NIRS)., Methods and Results: We evaluated coronary arteries from autopsy hearts using 40MHz IVUS and NIRS and compared the imaging findings to histopathology. A total of 2324 2-mm long histological segments from 101 coronary arteries from 56 autopsy hearts were included. Intraplaque haemorrhage was found pathologically in 0.8% (18/2324) of segments. Segments with intraplaque haemorrhage had more fibroatheromas (FAs) with a greater IVUS plaque burden, a greater prevalence of IVUS echolucent zones, and a higher NIRS-lipid core burden index (LCBI) compared to segments without intraplaque haemorrhage (FAs: 72.2% vs. 18.3%, P < 0.0001; plaque burden: 59.7% [95% confidence interval: 55.5, 64.0] vs. 48.6% [45.8, 51.3], P < 0.0001; echolucent zones: 88.9% vs. 2.8%, P < 0.0001; NIRS-LCBI: 176 [88, 264] vs. 72 [53, 91], P = 0.02). The 16 IVUS superficial echolucent zones with intraplaque haemorrhage had more late FAs but shorter echolucent zone lengths (0.9 mm [0.7, 1.1] vs. 1.7 mm [1.5, 1.9], P < 0.0001) compared to 65 IVUS superficial echolucent zones without intraplaque haemorrhage., Conclusions: Intracoronary imaging features consistent with intraplaque haemorrhage included a greater plaque burden, a higher NIRS-LCBI, and a greater prevalence of IVUS echolucent zones compared to lesions without intraplaque haemorrhage., (Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions, please email: journals.permissions@oup.com.)

Recent Zika virus (ZIKV) outbreaks have been associated with an increased incidence of neonatal microcephaly. Subsequently, tropism for the brain was established in human fetal brain tissue. We present the first congenital ZIKV infection in the United States, confirmed by high ZIKV immunoglobulin M antibody titers in serum and cerebrospinal fluid. The phenotypic characteristics of the patient fall within fetal brain disruption sequence, suggesting impaired brain development in the second half of gestation. Brain imaging revealed an almost agyric brain with diffuse parenchymal calcifications, hydrocephalus ex vacuo, and cerebellar hypoplasia. Ophthalmologic examination revealed macular pigment stippling and optic nerve atrophy. Liver, lungs, heart, and bone marrow were not affected. The patient had progressive neurologic deterioration in the first month of life. The discovery of ZIKV infection in human fetal brain tissue along with serologic confirmation proves the vertical transmission of ZIKV. Therefore, ZIKV has joined the group of congenital infections., (© The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.)

Recent studies have linked elevated apparent temperatures with adverse birth outcomes, such as preterm delivery, but other birth outcomes have not been well studied. We examined 8,510 fetal deaths (≥20 weeks' gestation) to estimate their association with mean apparent temperature, a combination of temperature and humidity, during the warm season in California (May-October) from 1999 to 2009. Mothers whose residential zip codes were within 10 km of a meteorological monitor were included. Meteorological data were provided by the California Irrigation Management Information System, the US Environmental Protection Agency, and the National Climatic Data Center, while the California Department of Public Health provided stillbirth data. Using a time-stratified case-crossover study design, we found a 10.4% change (95% confidence interval: 4.4, 16.8) in risk of stillbirth for every 10°F (5.6°C) increase in apparent temperature (cumulative average of lags 2-6 days). Risk varied by maternal race/ethnicity and was greater for younger mothers, less educated mothers, and male fetuses. The highest risks were observed during gestational weeks 20-25 and 31-33. No associations were found during the cold season (November-April), and the observed associations were independent of air pollutants. This study adds to the growing body of literature identifying pregnant women and their fetuses as subgroups vulnerable to heat exposure., (© The Author 2016. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for 'lab-on-a-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

A prospective observational study was conducted in a tertiary care hospital to study clinicoepidemiological profile of potentially rabid animal bite cases from rural India. Total of 308 children (median age 6 years) admitted to hospital, were recruited over 1 year and followed up till completion of antirabies vaccine course. Dog was the commonest (77.27%) offending animal. Of the exposures, 66.88% were scratches, 88.96% were unprovoked and 27.27% were categorized as Class III. The median times to wound toileting and reporting to health facility were 1 and 6 h, respectively. Majority received prompt PEP in hospital, and RIG was administered in 34.55% of Class II and 90.48% of Class III exposures. Compared with their older counterparts, children aged <5 years suffered more bites on face and trunk and more Class III exposures. The rabies prophylaxis scenario is encouraging, when compared with earlier studies, but there are gaps to be addressed., (© The Author [2015]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

NUCKS1 (nuclear casein kinase and cyclin-dependent kinase substrate 1) is a 27 kD chromosomal, vertebrate-specific protein, for which limited functional data exist. Here, we demonstrate that NUCKS1 shares extensive sequence homology with RAD51AP1 (RAD51 associated protein 1), suggesting that these two proteins are paralogs. Similar to the phenotypic effects of RAD51AP1 knockdown, we find that depletion of NUCKS1 in human cells impairs DNA repair by homologous recombination (HR) and chromosome stability. Depletion of NUCKS1 also results in greatly increased cellular sensitivity to mitomycin C (MMC), and in increased levels of spontaneous and MMC-induced chromatid breaks. NUCKS1 is critical to maintaining wild type HR capacity, and, as observed for a number of proteins involved in the HR pathway, functional loss of NUCKS1 leads to a slow down in DNA replication fork progression with a concomitant increase in the utilization of new replication origins. Interestingly, recombinant NUCKS1 shares the same DNA binding preference as RAD51AP1, but binds to DNA with reduced affinity when compared to RAD51AP1. Our results show that NUCKS1 is a chromatin-associated protein with a role in the DNA damage response and in HR, a DNA repair pathway critical for tumor suppression., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Long range regulatory interactions among distal enhancers and target genes are important for tissue-specific gene expression. Genome-scale identification of these interactions in a cell line-specific manner, especially using the fewest possible datasets, is a significant challenge. We develop a novel computational approach, Regulatory Interaction Prediction for Promoters and Long-range Enhancers (RIPPLE), that integrates published Chromosome Conformation Capture (3C) data sets with a minimal set of regulatory genomic data sets to predict enhancer-promoter interactions in a cell line-specific manner. Our results suggest that CTCF, RAD21, a general transcription factor (TBP) and activating chromatin marks are important determinants of enhancer-promoter interactions. To predict interactions in a new cell line and to generate genome-wide interaction maps, we develop an ensemble version of RIPPLE and apply it to generate interactions in five human cell lines. Computational validation of these predictions using existing ChIA-PET and Hi-C data sets showed that RIPPLE accurately predicts interactions among enhancers and promoters. Enhancer-promoter interactions tend to be organized into subnetworks representing coordinately regulated sets of genes that are enriched for specific biological processes and cis-regulatory elements. Overall, our work provides a systematic approach to predict and interpret enhancer-promoter interactions in a genome-wide cell-type specific manner using a few experimentally tractable measurements., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Recent studies have suggested an association between air pollution and stillbirth. In this California study, we examined the records of 13,999 stillbirths and 3,012,270 livebirths occurring between 1999 and 2009. Using a retrospective cohort design and logistic regression models, we calculated the odds of stillbirth associated with each pollutant exposure by trimester and throughout the entire pregnancy. Covariates considered in the model included infant sex, maternal demographic characteristics, season of last menstrual period, apparent temperature, air basin of mother's residence, and year of conception. In single-pollutant models, we found that a 10-µg/m(3) increase in particulate matter with an aerodynamic diameter less than or equal to 2.5 µm (odds ratio (OR) = 1.06, 95% confidence interval (CI): 0.99, 1.13) and a 10-ppb increase in nitrogen dioxide (OR = 1.08, 95% CI: 1.03, 1.13) during the entire pregnancy were associated with stillbirth. A 10-ppb increase in ozone exposure during the third trimester was also associated with a slightly elevated risk (OR = 1.03, 95% CI: 1.01, 1.05). These ozone and nitrogen dioxide findings were fairly stable after adjustment in 2-pollutant models. However, adjustment for nitrogen dioxide attenuated the full-pregnancy-particulate matter relationship. No significant associations were found for sulfur dioxide or carbon monoxide. These findings support growing evidence of an association between air pollution and adverse birth outcomes., (© The Author 2015. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objectives: To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research., Materials and Methods: Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results., Results: Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour., Discussion: The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases., Conclusion: Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases., (© The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.)

In alignment with a major shift toward patient-centered care as the model for improving care in our health system, informatics is transforming patient-provider relationships and overall care delivery. AMIA's 2013 Health Policy Invitational was focused on examining existing challenges surrounding full engagement of the patient and crafting a research agenda and policy framework encouraging the use of informatics solutions to achieve this goal. The group tackled this challenge from educational, technical, and research perspectives. Recommendations include the need for consumer education regarding rights to data access, the need for consumers to access their health information in real time, and further research on effective methods to engage patients. This paper summarizes the meeting as well as the research agenda and policy recommendations prioritized among the invited experts and stakeholders., (© The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Recent reports indicated high miltefosine treatment failure rates for visceral leishmaniasis (VL) on the Indian subcontinent. To further explore the pharmacological factors associated with these treatment failures, a population pharmacokinetic-pharmacodynamic study was performed to examine the relationship between miltefosine drug exposure and treatment failure in a cohort of Nepalese patients with VL., Methods: Miltefosine steady-state blood concentrations at the end of treatment were analyzed using liquid chromatography tandem mass spectrometry. A population pharmacokinetic-pharmacodynamic analysis was performed using nonlinear mixed-effects modeling and a logistic regression model. Individual estimates of miltefosine exposure were explored for their relationship with treatment failure., Results: The overall probability of treatment failure was 21%. The time that the blood concentration was >10 times the half maximal effective concentration of miltefosine (median, 30.2 days) was significantly associated with treatment failure: each 1-day decrease in miltefosine exposure was associated with a 1.08-fold (95% confidence interval, 1.01-1.17) increased odds of treatment failure., Conclusions: Achieving a sufficient exposure to miltefosine is a significant and critical factor for VL treatment success, suggesting an urgent need to evaluate the recently proposed optimal allometric miltefosine dosing regimen. This study establishes the first evidence for a drug exposure-effect relationship for miltefosine in the treatment of VL.

Objective: DNA sequencing tests are enabling physicians to interrogate the molecular profiles of patients' tumors, but most oncologists have not been trained in advanced genomics. We initiated a molecular tumor board to provide expert multidisciplinary input for these patients., Materials and Methods: A team that included clinicians, basic scientists, geneticists, and bioinformatics/pathway scientists with expertise in various cancer types attended. Molecular tests were performed in a Clinical Laboratory Improvement Amendments environment., Results: Patients (n = 34, since December 2012) had received a median of three prior therapies. The median time from physician order to receipt of molecular diagnostic test results was 27 days (range: 14-77 days). Patients had a median of 4 molecular abnormalities (range: 1-14 abnormalities) found by next-generation sequencing (182- or 236-gene panels). Seventy-four genes were involved, with 123 distinct abnormalities. Importantly, no two patients had the same aberrations, and 107 distinct abnormalities were seen only once. Among the 11 evaluable patients whose treatment had been informed by molecular diagnostics, 3 achieved partial responses (progression-free survival of 3.4 months, ≥6.5 months, and 7.6 months). The most common reasons for being unable to act on the molecular diagnostic results were that patients were ineligible for or could not travel to an appropriately targeted clinical trial and/or that insurance would not cover the cognate agents., Conclusion: Genomic sequencing is revealing complex molecular profiles that differ by patient. Multidisciplinary molecular tumor boards may help optimize management. Barriers to personalized therapy include access to appropriately targeted drugs., (©AlphaMed Press.)

Although respiratory disease has been strongly connected to fine particulate air pollution (particulate matter <2.5 μm in diameter (PM2.5)), evidence has been mixed regarding the effects of coarse particles (particulate matter from 2.5 to 10 μm in diameter), possibly because of the greater spatial heterogeneity of coarse particles. In this study, we evaluated the relationship between coarse particles and respiratory emergency department visits, including common subdiagnoses, from 2005 to 2008 in 35 California counties. A time-stratified case-crossover design was used to help control for time-invariant confounders and seasonal influences, and the study population was limited to those residing within 20 km of pollution monitors to mitigate the influence of spatial heterogeneity. Significant associations between respiratory emergency department visits and coarse particle levels were observed. Asthma visits showed associations (for 2-day lag, excess risk per 10 μg/m³ = 3.3%, 95% confidence interval: 2.0, 4.6) that were robust to adjustment by other common air pollutants (particles <2.5 μm in diameter, ozone, nitrogen dioxide, carbon monoxide, and sulfur dioxide). Pneumonia and acute respiratory infection visits were not associated, although some suggestion of a relationship with chronic obstructive pulmonary disease visits was present. Our results indicate that coarse particle exposure may trigger asthma exacerbations requiring emergency care, and reducing exposures among asthmatic persons may provide benefits.

Background: Miltefosine (MIL), the only oral drug for visceral leishmaniasis (VL), is currently the first-line therapy in the VL elimination program of the Indian subcontinent. Given the paucity of anti-VL drugs and the looming threat of resistance, there is an obvious need for close monitoring of clinical efficacy of MIL., Methods: In a cohort study of 120 VL patients treated with MIL in Nepal, we monitored the clinical outcomes up to 12 months after completion of therapy and explored the potential role of drug compliance, parasite drug resistance, and reinfection., Results: The initial cure rate was 95.8% (95% confidence interval [CI], 92.2-99.4) and the relapse rate at 6 and 12 months was 10.8% (95% CI, 5.2-16.4) and 20.0% (95% CI, 12.8-27.2) , respectively. No significant clinical risk factors of relapse apart from age <12 years were found. Parasite fingerprints of pretreatment and relapse bone marrow isolates within 8 patients were similar, suggesting that clinical relapses were not due to reinfection with a new strain. The mean promastigote MIL susceptibility (50% inhibitory concentration) of isolates from definite cures was similar to that of relapses. Although more tolerant strains were observed, parasite resistance, as currently measured, is thus not likely involved in MIL treatment failure. Moreover, MIL blood levels at the end of treatment were similar in cured and relapsed patients., Conclusions: Relapse in one-fifth of the MIL-treated patients observed in our study is an alarming signal for the VL elimination campaign, urging for further review and cohort monitoring.

Background: The objective of this study was to examine the predictive value of parameters of 3D (1)H magnetic resonance spectroscopic imaging (MRSI) prior to treatment with radiation/chemotherapy (baseline) and at a postradiation 2-month follow-up (F2mo) in relationship to 6-month progression-free survival (PFS6) and overall survival (OS)., Methods: Sixty-four patients with newly diagnosed glioblastoma multiforme (GBM) being treated with radiation and concurrent chemotherapy were involved in this study. Evaluated were metabolite indices and metabolite ratios. Logistic linear regression and Cox proportional hazards models were utilized to evaluate PFS6 and OS, respectively. These analyses were adjusted by age and MR scanner field strength (1.5 T or 3 T). Stepwise regression was performed to determine a subset of the most relevant variables., Results: Associated with shorter PFS6 were a decrease in the ratio of N-acetyl aspartate to choline-containing compounds (NAA/Cho) in the region with a Cho-to-NAA index (CNI) >3 at baseline and an increase of the CNI within elevated CNI regions (>2) at F2mo. Patients with higher normalized lipid and lactate at either time point had significantly worse OS. Patients who had larger volumes with abnormal CNI at F2mo had worse PFS6 and OS., Conclusions: Our study found more 3D MRSI parameters that predicted PFS6 and OS for patients with GBM than did anatomic, diffusion, or perfusion imaging, which were previously evaluated in the same population of patients.

Objective: To assess the inter-rater reliability of the BILAG2004-Pregnancy index for assessment of SLE disease activity in pregnancy., Methods: Pregnant SLE patients were recruited from four centres and assessed separately by two raters/physicians in routine clinical practice. Disease activity was determined using the BILAG2004-Pregnancy index. Reliability was assessed using level of agreement, κ-statistics and analysis of disagreement. Major disagreement was defined as a score difference of A and C/D/E or B and D/E between the two raters, and minor disagreement was a score difference of A and B or B and C between raters., Results: A total of 30 patients (63.3% Caucasian, 13.3% Afro-Caribbean, 16.7% South Asian) were recruited. The majority of patients had low-level disease activity according to the local rater's assessment, and there was no grade A activity, with grade B activity present in the following systems: mucocutaneous (nine patients), musculoskeletal (two patients), cardiorespiratory (one patient) and renal (one patient). The distribution of disease activity was similar to the external rater's assessment. Good levels of agreement (>70%) were achieved in all systems. κ-statistics were not appropriate for use in the gastrointestinal, ophthalmic, constitutional and neuropsychiatric systems, as there was minimal variation between patients but good levels of agreement otherwise. There were three major disagreements (0.1 per patient, all differences between B and D/E) and five minor disagreements (0.17 per patient)., Conclusion: The BILAG2004-Pregnancy index is reliable for assessment of disease activity in pregnant SLE patients.

Histopathologic evaluation of glioblastoma multiforme (GBM) at initial diagnosis is typically performed on tissue obtained from regions of contrast enhancement (CE) as depicted on gadolinium-enhanced, T1-weighted images. The non-enhancing (NE) portion of the lesion, which contains both reactive edema and infiltrative tumor, is only partially removed due to concerns about damaging functioning brain. The purpose of this study was to evaluate histopathologic and physiologic MRI features of image-guided tissue specimens from CE and NE regions to investigate correlations between imaging and histopathologic parameters. One hundred nineteen tissue specimens (93 CE and 26 NE regions) were acquired from 51 patients with newly diagnosed GBM by utilizing stereotactic image-guided sampling. Variables of anatomic, diffusion-weighted imaging (DWI), and dynamic susceptibility-weighted, contrast-enhanced perfusion imaging (DSC) from each tissue sample location were obtained and compared with histopathologic features such as tumor score, cell density, proliferation, architectural disruption, hypoxia, and microvascular hyperplasia. Tissue samples from CE regions had increased tumor score, cellular density, proliferation, and architectural disruption compared with NE regions. DSC variables such as relative cerebral blood volume, peak height, and recovery factor were significantly higher, and the percentage of signal intensity recovery was significantly lower in the CE compared with the NE regions. DWI variables were correlated with histopathologic features of GBM within NE regions. Image-guided tissue acquisition and assessment of residual tumor from treatment-naive GBM should be guided by DSC in CE regions and by DWI in NE regions.

This open-label, single-arm, phase II study combined enzastaurin with temozolomide plus radiation therapy (RT) to treat glioblastoma multiforme (GBM) and gliosarcoma. Adults with newly diagnosed disease and Karnofsky performance status (KPS) ≥ 60 were enrolled. Treatment was started within 5 weeks after surgical diagnosis. RT consisted of 60 Gy over 6 weeks. Temozolomide was given at 75 mg/m(2) daily during RT and then adjuvantly at 200 mg/m(2) daily for 5 days, followed by a 23-day break. Enzastaurin was given once daily during RT and in the adjuvant period at 250 mg/day. Cycles were 28 days. The primary end point was overall survival (OS). Progression-free survival (PFS), toxicity, and correlations between efficacy and molecular markers analyzed from tumor tissue samples were also evaluated. A prospectively planned analysis compared OS and PFS of the current trial with outcomes from 3 historical phase II trials that combined novel agents with temozolomide plus RT in patients with GBM or gliosarcoma. Sixty-six patients were enrolled. The treatment regimen was well tolerated. OS (median, 74 weeks) and PFS (median, 36 weeks) results from the current trial were comparable to those from a prior phase II study using erlotinib and were significantly better than those from 2 other previous studies that used thalidomide or cis-retinoic acid, all in combination with temozolomide plus RT. A positive correlation between O-6-methylguanine-DNA methyltransferase promoter methylation and OS was observed. Adjusting for age and KPS, no other biomarker was associated with survival outcome. Correlation of relevant biomarkers with OS may be useful in future trials.

We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation between the positions of css and introns, whereby css within the exons of one species frequently match the exact position of introns in equivalent genes from another species. These results strongly indicate that many introns were inserted into css during evolution and they also imply that the splicing information that lies outside some introns can be independently recognized by the splicing machinery and was in place prior to intron insertion. This indicates that non-intronic splicing information had a key role in shaping the split structure of eukaryote genes.