Dispensed prescription medications and short-term risk of pulmonary embolism in Norway and Sweden.

Scandinavian electronic health-care registers provide a unique setting to investigate potential unidentified side effects of drugs. We analysed the association between prescription drugs dispensed in Norway and Sweden and the short-term risk of developing pulmonary embolism. A total of 12,104 pulmonary embolism cases were identified from patient- and cause-of-death registries in Norway (2004-2014) and 36,088 in Sweden (2005-2014).

Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer.

Purpose: Human papillomavirus (HPV) is the cause of the majority of cervical cancer cases and has been showed to be released as cell-free tumor DNA (ctHPV DNA) into the circulation. Here, we analyze if ctHPV DNA could be used as a prognostic biomarker and/or to detect relapse earlier than traditional methods in locally advanced cervical cancer (LACC).

Experimental Design: A total of 74 patients with LACC were included; 66of 74 were positive for 13 high-risk HPV types on a bead-based assay of tumor biopsy samples.

A systematic review of artificial intelligence impact assessments.

Artificial intelligence (AI) is producing highly beneficial impacts in many domains, from transport to healthcare, from energy distribution to marketing, but it also raises concerns about undesirable ethical and social consequences. AI impact assessments (AI-IAs) are a way of identifying positive and negative impacts early on to safeguard AI's benefits and avoid its downsides. This article describes the first systematic review of these AI-IAs.

T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin.

The reservoir of latently HIV-1 infected cells is heterogeneous. To achieve an HIV-1 cure, the reservoir of activatable proviruses must be eliminated while permanently silenced proviruses may be tolerated. We have developed a method to assess the proviral nuclear microenvironment in single cells.

Phase-type models for competing risks, with emphasis on identifiability issues.

We first review some main results for phase-type distributions, including a discussion of Coxian distributions and their canonical representations. We then consider the extension of phase-type modeling to cover competing risks. This extension involves the consideration of finite state Markov chains with more than one absorbing state, letting each absorbing state correspond to a particular risk.

Assessing short-term risk of ischemic stroke in relation to all prescribed medications.

We examined the short-term risk of stroke associated with drugs prescribed in Norway or Sweden in a comprehensive, hypothesis-free manner using comprehensive nation-wide data. We identified 27,680 and 92,561 cases with a first ischemic stroke via the patient- and the cause-of-death registers in Norway (2004-2014) and Sweden (2005-2014), respectively, and linked these data to prescription databases. A case-crossover design was used that compares the drugs dispensed within 1 to 14 days before the date of ischemic stroke occurrence with those dispensed 29 to 42 days before the index event.

Author Correction: Systematic assessment of prescribed medications and short-term risk of myocardial infarction - a pharmacopeia-wide association study from Norway and Sweden.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Chromatin maturation of the HIV-1 provirus in primary resting CD4+ T cells.

Human immunodeficiency virus type 1 (HIV-1) infection is a chronic condition, where viral DNA integrates into the genome. Latently infected cells form a persistent, heterogeneous reservoir that at any time can reactivate the integrated HIV-1. Here we confirmed that latently infected cells from HIV-1 positive study participants exhibited active HIV-1 transcription but without production of mature spliced mRNAs.

Age, SAPS 3 and female sex are associated with decisions to withdraw or withhold intensive care.

Background: Intensive care treat critically ill patients. When intensive care is not considered beneficial for the patient, decisions to withdraw or withhold treatments are made. We aimed to identify independent patient variables that increase the odds for receiving a decision to withdraw or withhold intensive care.

Systematic assessment of prescribed medications and short-term risk of myocardial infarction - a pharmacopeia-wide association study from Norway and Sweden.

Wholesale, unbiased assessment of Scandinavian electronic health-care databases offer a unique opportunity to reveal potentially important undiscovered drug side effects. We examined the short-term risk of acute myocardial infarction (AMI) associated with drugs prescribed in Norway or Sweden. We identified 24,584 and 97,068 AMI patients via the patient- and the cause-of-death registers and linked to prescription databases in Norway (2004-2014) and Sweden (2005-2014), respectively.

MACPET: model-based analysis for ChIA-PET.

We present model-based analysis for ChIA-PET (MACPET), which analyzes paired-end read sequences provided by ChIA-PET for finding binding sites of a protein of interest. MACPET uses information from both tags of each PET and searches for binding sites in a two-dimensional space, while taking into account different noise levels in different genomic regions. MACPET shows favorable results compared with MACS in terms of motif occurrence and spatial resolution.

Modeling of semi-competing risks by means of first passage times of a stochastic process.

In semi-competing risks one considers a terminal event, such as death of a person, and a non-terminal event, such as disease recurrence. We present a model where the time to the terminal event is the first passage time to a fixed level c in a stochastic process, while the time to the non-terminal event is represented by the first passage time of the same process to a stochastic threshold S, assumed to be independent of the stochastic process. In order to be explicit, we let the stochastic process be a gamma process, but other processes with independent increments may alternatively be used.

Sequential activation of the three protomers in the Moloney murine leukemia virus Env.

Viral membrane fusion proteins of class I are trimers in which the protomeric unit is a complex of a surface subunit (SU) and a fusion active transmembrane subunit (TM). Here we have studied how the protomeric units of Moloney murine leukemia virus envelope protein (Env) are activated in relation to each other, sequentially or simultaneously. We followed the isomerization of the SU-TM disulfide and subsequent SU release from Env with biochemical methods and found that this early activation step occurred sequentially in the three protomers, generating two asymmetric oligomer intermediates according to the scheme (SU-TM) → (SU-TM)TM → (SU-TM)TM → TM This was the case both when activation was triggered in vitro by depleting stabilizing Ca from solubilized Env and when viral Env was receptor triggered on rat XC cells.

Uncertainty of decibel levels.

The mean sound exposure level from a source is routinely estimated by the mean of the observed sound exposures from repeated measurements. A formula for the standard uncertainty based on the Guide to the expression of Uncertainty in Measurement (GUM) is derived. An alternative formula is derived for the case where the GUM method fails.

Residual plots to reveal the functional form for covariates in parametric accelerated failure time models.

We study residual plots for parametric accelerated failure time (AFT) models, using both standardized residuals and Cox-Snell residuals. Two different approaches are discussed in the case of censored data; adjusting censored residuals by adding a residual time, and using nonparametric exponential regression of non-adjusted censored Cox-Snell residuals. The main object of the paper is to show how residuals can be used to infer the correct functional form for possibly misspecified covariates.

Whole genome DNA methylation signature of HER2-positive breast cancer.

In order to obtain a comprehensive DNA methylation signature of HER2-positive breast cancer (HER2+ breast cancer), we performed a genome-wide methylation analysis on 17 HER2+ breast cancer and compared with ten normal breast tissue samples using the Illumina Infinium HumanMethylation450 BeadChip (450K). In HER2+ breast cancer, we found altered DNA methylation in genes involved in multicellular development, differentiation and transcription. Within these genes, we observed an overrepresentation of homeobox family genes, including several genes that have not been previously reported in relation to cancer (DBX1, NKX2-6, SIX6).

Furin cleavage of the Moloney murine leukemia virus Env precursor reorganizes the spike structure.

The trimeric Moloney murine leukemia virus Env protein matures by two proteolytic cleavages. First, furin cleaves the Env precursor into the surface (SU) and transmembrane (TM) subunits in the cell and then the viral protease cleaves the R-peptide from TM in new virus. Here we analyzed the structure of the furin precursor, by cryoelectron microscopy.

Variability in the precore and core promoter region of the hepatitis B virus genome.

There is increasing evidence that hepatitis B virus (HBV) infections with different genotypes and subgenotypes differ in response to treatment and long-term prognosis. The differences emerge from variability within the genomes that leads to structural deviations at the pregenomic level and to changes at the translational level. Naturally occurring HBV strains covering the four major genotypes A-D were obtained from 393 patients and part of the genome was amplified using polymerase chain reaction (PCR), sequenced, and analyzed for mutational differences in the precore and core promoter regions.

Bayesian estimation of HIV-1 dynamics in vivo.

Statistical analysis of viral dynamics in HIV-1 infected patients undergoing structured treatment interruptions were performed using a novel model that accounts for treatment efficiency as well as total CD8+ T cell counts. A brief review of parameter estimates obtained in other studies is given, pointing to a considerable variation in the estimated values. A Bayesian approach to parameter estimation was used with longitudinal measurements of CD4+ and CD8+ T cell counts and HIV RNA.

The mitochondrial transporter SLC25A43 is frequently deleted and may influence cell proliferation in HER2-positive breast tumors.

Background: Overexpression of the human epidermal growth factor receptor (HER) 2 is associated with poor prognosis and shortened survival in breast cancer patients. HER2 is a potent activator of several signaling pathways that support cell survival, proliferation and metabolism. In HER2-positive breast cancer there are most likely unexplored proteins that act directly or indirectly downstream of well established pathways and take part in tumor development and treatment response.