In mammals, seven proprotein convertases (PCs) cleave secretory proteins after basic residues, and four of them are called furin-like PCs: furin, PC5, PACE4, and PC7. In vitro, they share many substrates. However, furin is essential during development since deficient embryos die at embryonic day 11 and exhibit multiple developmental defects, particularly defects related to the function of endothelial cells. To define the role of furin in endothelial cells, an endothelial cell-specific knockout (ecKO) of the Furin gene was generated. Newborns die shortly after birth, indicating that furin is essential in these cells. Magnetic resonance imaging revealed that ecKO embryos exhibit ventricular septal defects (VSD) and/or valve malformations. In addition, primary cultures of wild-type and ecKO lung endothelial cells revealed that ecKO cells are unable to grow. Growth was efficiently rescued by extracellular soluble furin. Analysis of the processing of precursors of endothelin-1 (ET-1), adrenomedullin (Adm), transforming growth factor β1 (TGF-β1), and bone morphogenetic protein 4 (BMP4) confirmed that ET-1, Adm, and TGF-β1 are in vivo substrates of endothelial furin. Mature ET-1 and BMP4 forms were reduced by ∼90% in ecKO purified endothelial cells from lungs.
Imaging centers nationwide are seeking innovative means to record and monitor computed tomography (CT)-related radiation dose in light of multiple instances of patient overexposure to medical radiation. As a solution, we have developed RADIANCE, an automated pipeline for extraction, archival, and reporting of CT-related dose parameters. Estimation of whole-body effective dose from CT dose length product (DLP)—an indirect estimate of radiation dose—requires anatomy-specific conversion factors that cannot be applied to total DLP, but instead necessitate individual anatomy-based DLPs. A challenge exists because the total DLP reported on a dose sheet often includes multiple separate examinations (e.g., chest CT followed by abdominopelvic CT). Furthermore, the individual reported series DLPs may not be clearly or consistently labeled. For example, “arterial” could refer to the arterial phase of the triple liver CT or the arterial phase of a CT angiogram. To address this problem, we have designed an intelligent algorithm to parse dose sheets for multi-series CT examinations and correctly separate the total DLP into its anatomic components. The algorithm uses information from the departmental PACS to determine how many distinct CT examinations were concurrently performed. Then, it matches the number of distinct accession numbers to the series that were acquired and anatomically matches individual series DLPs to their appropriate CT examinations. This algorithm allows for more accurate dose analytics, but there remain instances where automatic sorting is not feasible. To ultimately improve radiology patient care, we must standardize series names and exam names to unequivocally sort exams by anatomy and correctly estimate whole-body effective dose.
RADIANCE; Computed tomography; Dose monitoring; CT series separation; Radiation dose; Data extraction; Databases
The goal of this study was to develop and validate text-mining algorithms to automatically identify radiology reports containing critical results including tension or increasing/new large pneumothorax, acute pulmonary embolism, acute cholecystitis, acute appendicitis, ectopic pregnancy, scrotal torsion, unexplained free intraperitoneal air, new or increasing intracranial hemorrhage, and malpositioned tubes and lines. The algorithms were developed using rule-based approaches and designed to search for common words and phrases in radiology reports that indicate critical results. Certain text-mining features were utilized such as wildcards, stemming, negation detection, proximity matching, and expanded searches with applicable synonyms. To further improve accuracy, the algorithms utilized modality and exam-specific queries, searched under the “Impression” field of the radiology report, and excluded reports with a low level of diagnostic certainty. Algorithm accuracy was determined using precision, recall, and F-measure using human review as the reference standard. The overall accuracy (F-measure) of the algorithms ranged from 81% to 100%, with a mean precision and recall of 96% and 91%, respectively. These algorithms can be applied to radiology report databases for quality assurance and accreditation, integrated with existing dashboards for display and monitoring, and ported to other institutions for their own use.
Algorithms; Communication; Critical Results Reporting; Data Mining; Natural Language Processing; Quality Assurance; Quality Control
The aim of this study was to determine the feasibility of automated detection of adrenal nodules, a common finding on CT, using a newly developed search engine that mines dictated radiology reports. To ensure Health Insurance Portability and Accountability Act compliance, we utilized a preexisting de-identified database of 32,974 CT reports from February 1, 2009 to February 28, 2010. Common adrenal descriptors from 29 staff radiologists were used to develop an automated rule-based algorithm targeting adrenal findings. Each sentence within the free text of reports was searched with an adapted NegEx negation algorithm. The algorithm was refined using a 2-week test period of reports and subsequently validated using a 6-week period. Manual review of the 3,693 CT reports in the validation period identified 222 positive reports while the algorithm detected 238 positive reports. The algorithm identified one true positive report missed on manual review for a total of 223 true positive reports. This resulted in a precision of 91% (217 of 238) and a recall of 97% (217 of 223). The sensitivity of the query was 97.3% (95% confidence interval (CI), 93.9–98.9%), and the specificity was 99.3% (95% CI, 99.1–99.6%). The positive predictive value of the algorithm was 91.0% (95% CI, 86.6–94.3%), and the negative predictive value was 99.8% (95% CI, 99.6–99.9%). The prevalence of true positive adrenal findings identified by the query (7.1%) was nearly identical to the true prevalence (7.2%). Automated detection of language describing common findings in imaging reports, such as adrenal nodules on CT, is feasible.
Data mining; Radiology information systems (RIS); Natural language; Processing; Computed tomography; Radiology reporting; Adrenal nodules; Negation algorithm; Unstructured radiology reports
Radiology residency and fellowship training provides a unique opportunity to evaluate trainee performance and determine the impact of various educational interventions. We have developed a simple software application (Orion) using open-source tools to facilitate the identification and monitoring of resident and fellow discrepancies in on-call preliminary reports. Over a 6-month period, 19,200 on-call studies were interpreted by 20 radiology residents, and 13,953 on-call studies were interpreted by 25 board-certified radiology fellows representing eight subspecialties. Using standard review macros during faculty interpretation, each of these reports was classified as “agreement”, “minor discrepancy”, and “major discrepancy” based on the potential to impact patient management or outcome. Major discrepancy rates were used to establish benchmarks for resident and fellow performance by year of training, modality, and subspecialty, and to identify residents and fellows demonstrating a significantly higher major discrepancy rate compared with their classmates. Trends in discrepancies were used to identify subspecialty-specific areas of increased major discrepancy rates in an effort to tailor the didactic and case-based curriculum. A series of missed-case conferences were developed based on trends in discrepancies, and the impact of these conferences is currently being evaluated. Orion is a powerful information technology tool that can be used by residency program directors, fellowship programs directors, residents, and fellows to improve radiology education and training.
Software design; Quality improvement; Residency; Medical informatics applications; Natural language processing; Performance measurement; Discrepancies; Performance; Web-based; Residents
ATP-binding cassette transporters of the subfamily A (ABCA) are responsible for the translocation of lipids including cholesterol, which is crucial for neurological function. Recent studies suggest that the ABC transporter ABCA7 may play a role in the development of brain disorders such as schizophrenia and Alzheimer’s disease. However, Abca7’s role in cognition and other behaviours has not been investigated. Therefore, we characterised homozygous Abca7 knockout mice in a battery of tests for baseline behaviours (i.e. physical exam, baseline locomotion and anxiety) and behaviours relevant to schizophrenia (i.e. prepulse inhibition and locomotor response to psychotropic drugs) and Alzheimer’s disease (i.e. cognitive domains). Knockout mice had normal motor functions and sensory abilities and performed the same as wild type-like animals in anxiety tasks. Short-term spatial memory and fear-associated learning was also intact in Abca7 knockout mice. However, male knockout mice exhibited significantly impaired novel object recognition memory. Task acquisition was unaffected in the cheeseboard task. Female mice exhibited impaired spatial reference memory. This phenomenon was more pronounced in female Abca7 null mice. Acoustic startle response, sensorimotor gating and baseline locomotion was unaltered in Abca7 knockout mice. Female knockouts showed a moderately increased motor response to MK-801 than control mice. In conclusion, Abca7 appears to play only a minor role in behavioural domains with a subtle sex-specific impact on particular cognitive domains.
Helicobacter pylori is the leading cause of gastritis, peptic ulcer disease and gastric adenocarcinoma and lymphoma in humans. Due to the decreasing efficacy of anti-H. pylori antibiotic therapy in clinical practice, there is renewed interest in the development of anti-H. pylori vaccines. In this study an in silico-based approach was utilized to develop a multi-epitope DNA-prime/peptide-boost immunization strategy using informatics tools. The efficacy of this construct was then assessed as a therapeutic vaccine in a mouse model of gastric cancer induced by chronic H. pylori infection. The multi-epitope vaccine administered intranasally induced a broad immune response as determined by interferon-gamma production in ELISpot assays. This was associated with a significant reduction in H. pylori colonization compared with mice immunized with the same vaccine intramuscularly, given an empty plasmid, or given a whole H. pylori lysate intranasally as the immunogen. Total scores of gastric histological changes were not significantly different among the 4 experimental groups. These results suggest that further development of an epitope-based mucosal vaccine may be beneficial in eradicating H. pylori and reducing the burden of the associated gastric diseases in humans.
Radiologists frequently search the Web to find information they need to improve their practice, and knowing the types of information they seek could be useful for evaluating Web resources. Our goal was to develop an automated method to categorize unstructured user queries using a controlled terminology and to infer the type of information users seek. We obtained the query logs from two commonly used Web resources for radiology. We created a computer algorithm to associate RadLex-controlled vocabulary terms with the user queries. Using the RadLex hierarchy, we determined the high-level category associated with each RadLex term to infer the type of information users were seeking. To test the hypothesis that the term category assignments to user queries are non-random, we compared the distributions of the term categories in RadLex with those in user queries using the chi square test. Of the 29,669 unique search terms found in user queries, 15,445 (52%) could be mapped to one or more RadLex terms by our algorithm. Each query contained an average of one to two RadLex terms, and the dominant categories of RadLex terms in user queries were diseases and anatomy. While the same types of RadLex terms were predominant in both RadLex itself and user queries, the distribution of types of terms in user queries and RadLex were significantly different (p < 0.0001). We conclude that RadLex can enable processing and categorization of user queries of Web resources and enable understanding the types of information users seek from radiology knowledge resources on the Web.
Ontologies; terminologies; vocabularies; RadLex; software tools; controlled vocabulary; natural language processing; web technology
The sexually transmitted insect virus Helicoverpa zea nudivirus 2 (HzNV-2) was determined to have a circular double-stranded DNA genome of 231,621 bp coding for an estimated 113 open reading frames (ORFs). HzNV-2 is most closely related to the nudiviruses, a sister group of the insect baculoviruses. Several putative ORFs that share homology with the baculovirus core genes were identified in the viral genome. However, HzNV-2 lacks several key genetic features of baculoviruses including the late transcriptional regulation factor, LEF-1 and the palindromic hrs, which serve as origins of replication. The HzNV-2 genome was found to code for three ORFs that had significant sequence homology to cellular genes which are not generally found in viral genomes. These included a presumed juvenile hormone esterase gene, a gene coding for a putative zinc-dependent matrix metalloprotease, and a major facilitator superfamily protein gene; all of which are believed to play a role in the cellular proliferation and the tissue hypertrophy observed in the malformation of reproductive organs observed in HzNV-2 infected corn earworm moths, Helicoverpa zea.
nudivirus; sterile insects; baculovirus; sexually transmitted virus; virus genome; juvenile hormone esterase; HzNV-2; HzNV-1; corn earworm; Helicoverpa zea
We present a lipidomics analysis of human Parkinson's disease tissues. We have focused on the primary visual cortex, a region that is devoid of pathological changes and Lewy bodies; and two additional regions, the amygdala and anterior cingulate cortex which contain Lewy bodies at different disease stages but do not have as severe degeneration as the substantia nigra.
Using liquid chromatography mass spectrometry lipidomics techniques for an initial screen of 200 lipid species, significant changes in 79 sphingolipid, glycerophospholipid and cholesterol species were detected in the visual cortex of Parkinson's disease patients (n = 10) compared to controls (n = 10) as assessed by two-sided unpaired t-test (p-value <0.05). False discovery rate analysis confirmed that 73 of these 79 lipid species were significantly changed in the visual cortex (q-value <0.05). By contrast, changes in 17 and 12 lipid species were identified in the Parkinson's disease amygdala and anterior cingulate cortex, respectively, compared to controls; none of which remained significant after false discovery rate analysis. Using gas chromatography mass spectrometry techniques, 6 out of 7 oxysterols analysed from both non-enzymatic and enzymatic pathways were also selectively increased in the Parkinson's disease visual cortex. Many of these changes in visual cortex lipids were correlated with relevant changes in the expression of genes involved in lipid metabolism and an oxidative stress response as determined by quantitative polymerase chain reaction techniques.
The data indicate that changes in lipid metabolism occur in the Parkinson's disease visual cortex in the absence of obvious pathology. This suggests that normalization of lipid metabolism and/or oxidative stress status in the visual cortex may represent a novel route for treatment of non-motor symptoms, such as visual hallucinations, that are experienced by a majority of Parkinson's disease patients.
Trimethylation on histone H3 lysine 27 (H3K27me3) by Polycomb repressive complex 2 (PRC2) regulates the balance between self-renewal and differentiation of embryonic stem cells (ESCs). The mechanisms by which the activity and recruitment of PRC2 are controlled are largely unknown. Here we demonstrate that the founding member of the Jumonji-family, JMJ (JUMONJI or JARID2), is tightly associated with PRC2, colocalizes with PRC2 and H3K27me3 on chromatin, and modulates PRC2 function. In vitro JMJ inhibits PRC2 methyltransferase activity, a finding consistent with increased H3K27me3 marks at PRC2 targets in Jmj−/− ESCs. Paradoxically, JMJ is required for efficient binding of PRC2, indicating that the interplay of PRC2 and JMJ fine-tunes deposition of the H3K27me3 mark. During differentiation, activation of genes marked by H3K27me3 and lineage commitments are delayed in Jmj−/− ESCs. Our results demonstrate that dynamic regulation of Polycomb complex activity orchestrated by JMJ balances self-renewal and differentiation, further highlighting the involvement of chromatin dynamics in cell-fate transitions.
Sphingolipids including sphingomyelin have been implicated as potential atherogenic lipids. Studies in apoE (apolipoprotein E)-null mice have revealed that the serine palmitoyltransferase inhibitor myriocin reduces plasma levels of sphingomyelin, ceramide, sphingosine-1-phosphate and glycosphingolipids and that this is associated with potent inhibition of atherosclerosis. Interestingly, hepatic apoA-I (apolipoprotein A-I) synthesis and plasma HDL (high-density lipoprotein)-cholesterol levels were also increased in apoE-null mice treated with myriocin. Since myriocin is a known inhibitor of ERK (extracellular-signal-related kinase) phosphorylation, we assessed the possibility that myriocin may be acting to increase hepatic apoA-I production via this pathway. To address this, HepG2 cells and primary mouse hepatocytes were treated with 200 μM myriocin for up to 48 h. Myriocin increased apoA-I mRNA and protein levels by approx. 3- and 2-fold respectively. Myriocin also increased apoA-I secretion up to 3.5-fold and decreased ERK phosphorylation by approx. 70%. Similar findings were obtained when primary hepatocytes were isolated from apoE-null mice that were treated with myriocin (intraperitoneal injection at a dose of 0.3 mg/kg body weight). Further experiments revealed that the MEK (mitogen-activated protein kinase/ERK kinase) inhibitor PD98059 potently inhibited ERK phosphorylation, as expected, and increased primary hepatocyte apoA-I production by 3-fold. These results indicate that ERK phosphorylation plays a role in regulating hepatic apoA-I expression and suggest that the anti-atherogenic mechanism of action for myriocin may be linked to this pathway.
apolipoprotein A-I (apoA-I); atherosclerosis; extracellular-signal regulated kinase (ERK); hepatocyte; myriocin; sphingolipid; 4-AAP, 4-aminoantipyrine; apoA-I, apolipoprotein A-I; apoE, apolipoprotein-E; DAOS, N-ethyl-N-(2-hydroxy-3-sulfopropyl)-3,5-dimethoxyaniline sodium salt; DMEM, Dulbecco's modified Eagle's medium; ERK, extracellular-signal-related kinase; FCS, fetal calf serum; GCS, glucosylceramide synthase; GSL, glycosphingolipid; HDL, high-density lipoprotein; HRP, horseradish peroxidase; i.p., intraperitoneal(ly); LDL, low-density lipoprotein; MAPK, mitogen-activated protein kinase; MEK, MAPK/ERK kinase; MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide; qPCR, quantitative PCR; S1P, sphingosine 1-phosphate; SM, sphingomyelin; SMase, sphingomyelinase; SPT, serine palmitoyltransferase
Aggregation of the amyloid β peptide (Aβ) plays a key role in the molecular etiology of Alzheimer’s disease. Despite the importance of this process, the relationship between the sequence of Aβ and the propensity of the peptide to aggregate has not been fully elucidated. The sequence determinants of aggregation can be revealed by probing the ability of amino acid substitutions (mutations) to increase or decrease aggregation. Numerous mutations that decrease aggregation have been isolated by laboratory-based studies. In contrast, very few mutations that increase aggregation have been reported, and most of these were isolated from rare individuals with early onset Familial Alzheimer’s disease. To augment the limited data set of clinically derived mutations, we developed an artificial genetic screen to isolate novel mutations that increase aggregation propensity. The screen relies on expression in E. coli of a fusion of Aβ to green fluorescent protein (GFP). In this fusion, the ability of the GFP reporter to fold and fluoresce is inversely correlated with the aggregation propensity of the Aβ sequence. Implementation of this screen enabled the isolation of 20 mutant versions of Aβ with amino acid substitutions at 17 positions in the 42-residue sequence of Aβ. Biophysical studies of synthetic peptides corresponding to sequences isolated by the screen confirm the increased aggregation propensity and amyloidogenic behavior of the mutants. The mutations were isolated using an unbiased screen that makes no assumptions about the sequence determinants of aggregation. Nonetheless, all 16 of the most aggregating mutants contain substitutions that reduce charge and/or increase hydrophobicity. These findings provide compelling evidence supporting the hypothesis that sequence hydrophobicity is a major determinant of Aβ aggregation.
Mild cognitive impairment (MCI) has been defined as a transitional state between normal aging and Alzheimer disease. Diffusion tensor imaging (DTI) can estimate the microstructural integrity of white matter tracts in MCI. We evaluated the microstructural changes in the white matter of MCI patients with DTI. We recruited 11 patients with MCI who met the working criteria of MCI and 11 elderly normal controls. The mean diffusivity (MD) and fractional anisotropy (FA) were measured in 26 regions of the brain with the regions of interest (ROIs) method. In the MCI patients, FA values were significantly decreased in the hippocampus, the posterior limb of the internal capsule, the splenium of corpus callosum, and in the superior and inferior longitudinal fasciculus compared to the control group. MD values were significantly increased in the hippocampus, the anterior and posterior limbs of the internal capsules, the splenium of the corpus callosum, the right frontal lobe, and in the superior and the inferior longitudinal fasciculus. Microstructural changes of several corticocortical tracts associated with cognition were identified in patients with MCI. FA and MD values of DTI may be used as novel biomarkers for the evaluation of neurodegenerative disorders.
Mild Cognitive Impairment; Alzheimer Disease; Diffusion Tensor Imaging; Mean Diffusivity; Fractional Anisotropy
The effect of Hz-2V virus infection on the reproductive physiology and behavior of infected Helicoverpa zea female moths was examined. In the absence of males, infected females exhibited calling behavior and called as often but for shorter periods on average than control females. As expected, control females mated with males for extend periods when they were present and did not call after mating, while virus-infected females made many frequent contacts with males and continued to call even after these contacts. Virus-infected females were found to produce five to seven times more pheromone than control females and attracted twice as many males as did control females in flight tunnel experiments. The ability of Hz-2V to alter the physiology and behavior of infected females observed here may serve to facilitate the transmission of virus in insect populations.
gonad specific virus
gonad specific virus; Helicoverpa zea; Hz-2V; insect virus; mating behavior; pheromone
This study reports on the identification and characterization of a novel abortive infection system, AbiU, from Lactococcus lactis. AbiU confers resistance to phages from the three main industrially relevant lactococcal phage species: c2, 936, and P335. The presence of AbiU reduced the efficiency of plaquing against specific phage from each species as follows: 3.7 × 10−1, 1.0 × 10−2, and 1.0 × 10−1, respectively. abiU involves two open reading frames, abiU1 (1,772 bp) and abiU2 (1,019 bp). Evidence indicates that AbiU1 is responsible for phage resistance and that AbiU2 may downregulate phage resistance against 936 and P335 type phages but not c2 type phage. AbiU appeared to delay transcription of both phage 712 and c2, with the effect being more marked on phage c2.
The survival response of Lactococcus lactis during long-term starvation was investigated. The cells were cultured with different levels of glucose (the sole energy source) and either were kept in the resultant spent medium or transferred to fresh medium (without glucose) for up to 2 years. The survival of the cells during starvation was not dependent on the nature of transition phase, as expected, but on the nature of medium in which the cells were kept. The proliferation of cells, despite the apparent lack of glucose, could have been due to some cells being able to utilize the small amounts of peptides still present in the spent medium or to use energy sources provided by the breakup of dead cells. The 1- and 2-year-old cultures contained cells with vastly changed morphotypes. When these isolates were examined, it was revealed that the original plasmids present in the parent were rearranged in a certain way, and an entirely new plasmid was generated. Changes were also evident in the chromosomal DNA and in gene expression. Furthermore, all of the isolates exhibited a growth advantage relative to the parent cells when grown in energy-limiting media. When they were tested against different types of stresses, they exhibited a higher resistance against the bile salt and hydrogen peroxide stresses compared to the parent. Because of the similar changes observed in the 2-year-old isolates, a similar survival strategy may be operational in those cells that survive for that length of time.