Semi-automated Protocol Research Articles

Thrombus volume is similar in patients with ruptured and intact abdominal aortic aneurysms

Most abdominal aortic aneurysms (AAAs) contain intraluminal thrombus (ILT), which has been demonstrated to contain proteolytic enzymes and proinflammatory cytokines implicated in AAA progression and rupture. In animal models, anticoagulants have been shown to limit AAA progression. Whether ILT plays a role in AAA rupture is unknown. The aim of this study was to compare the volume of ILT in patients with ruptured and intact AAAs. We matched by maximum axial diameter alone, on a 1:2 basis, 28 patients with ruptured AAAs and 56 patients with intact AAAs. Total infrarenal aortic volume and ILT volume were measured from computed tomography angiograms using a previously validated and reproducible semiautomated workstation protocol. Clinical risk factors were also recorded. The Mann-Whitney U test was used to compare ILT volumes between patients with ruptured and intact AAAs. Median (interquartile range [IQR]) maximum AAA diameter (84.0 [77.5-93.9] mm vs 82.6 [77.1-93.3] mm; P = .769) and median (IQR) total AAA volume (372.8 [277.4-486.1] cm(3) vs 358.4 [289.1-563.4] cm(3); P = .977) were similar in patients with ruptured and intact AAAs. Median (IQR) AAA ILT volume was similar in patients with ruptured (152.7 [84.8-252.4] cm(3)) and intact (180.1 [89.9-254.8] cm(3); P = .414) AAAs. This study suggests that ILT volume is not different in ruptured and intact AAAs.

256 : MAPPIT and Co: The importance of system artifacts

MAPPIT (Mammalian Protein–Protein Interaction Trap) is a cytokine receptor-based two-hybrid method that operates in intact mammalian cells ( www.mappit.be ). The bait is linked to a signaling-deficient receptor, allowing complementation assays upon interaction with a prey. Protein–protein interactions (PPIs) can thus be studied in their close-to-normal physiological habitat. MAPPIT can be used for detailed analysis of selected PPIs, but also for large-scale interactomics, e.g. for mapping the human interactome. Interactor hunts for novel human protein–protein interactions can be performed using either a FACS-based format for cDNA library screening or using a semi-automated protocol to interrogate proteome-wide ORF arrays. Over the past years, we have observed two types of technical “false positives” intrinsic to the MAPPIT system. Type 1 artifacts represent bait-independent PPIs with the cytokine receptor complex. These are useful as they provide novel insights into receptor functioning. As an example, we will discuss the role of the ring finger protein RNF41 in the regulation of receptor turn-over and shedding. Type 2 artifacts are autonomously signaling preys that operate completely independent of the cytokine receptor. One such case led to the development of a novel mammalian two-hybrid method that we termed KISS (KInase/Substrate Sensor). This alternative strategy accommodates PPI analysis of integral membrane and nuclear proteins and considerably expands the PPI repertoire seen by MAPPIT. As KISS uses the same read-out as MAPPIT, we expect that a combination of both methods will yield high coverage combined with the high sensitivity of the MAPPIT system. We will demonstrate KISS applications in the context of ER stress.

A semi-automated protocol for Archaea DNA extraction from stools

BackgroundThe PCR-based detection of archaea DNA in human specimens relies on efficient DNA extraction. We previously designed one such protocol involving only manual steps. In an effort to reduce the workload involved, we compared this manual protocol to semi-automated and automated protocols for archaea DNA extraction from human specimens.FindingsWe tested 110 human stool specimens using each protocol. An automated protocol using the EZ1 Advanced XL extractor with the V 1.066069118 Qiagen DNA bacteria card and the EZ1® DNA Tissue Kit (Qiagen, Courtaboeuf, France) yielded 35/110 (32%) positives for the real-time PCR detection of the Methanobrevibacter smithii 16S rRNA gene, with average Ct values of 36.1. A semi-automated protocol combining glass-powder crushing, overnight proteinase K digestion and lysis in the buffer from the EZ1 kit yielded 90/110 (82%) positive specimens (P = 0.001) with an average Ct value of 27.4 (P = 0.001). The manual protocol yielded 100/110 (91%) positive specimens (P = 0.001) with an average Ct value of 30.33 (P = 0.001). However, neither the number of positive specimens nor the Ct values were significantly different between the manual protocol and the semi-automated protocol (P > 0.1 and P > 0.1).ConclusionProteinase K digestion and glass powder crushing dramatically increase the extraction yield of archaea DNA from human stools. The semi-automated protocol described here was more rapid than the manual protocol and yielded significantly more archaeal DNA. It could be applied for extracting total stool DNA for further PCR amplification.

Imaging Interactions Between Transferrin‐containing Endosomes and Mitochondria

Iron transport occurs via iron binding to transferrin (Tfn), which is then taken up by the Tfn‐receptor (TFR) at the plasma membrane and delivered to endosomes, where upon acidification Tfn undergoes iron release. Iron is then transported to the mitochondria via a yet unknown mechanism; in the mitochondria, iron is incorporated into the heme groups of proteins involved in cellular respiration. The “kiss and run” hypothesis states that iron is transported into the mitochondria via a direct interaction between endosomes and mitochondria. To test the “kiss and run” hypothesis in epithelial cells, we will use time‐lapse live‐cell fluorescence TIRF microscopy to assay the colocalization of endosomes and mitochondria under various conditions that affect pH and Tfn‐iron binding capacity. Our goal is to develop a semi‐automated image analysis protocol based on the Imaris software to characterize putative “kiss and run” events. Our analysis shows that endosomal speed increases before the “kiss” as well as before the “run” of each “kiss and run” event. During the attachment period the endosome reduces its motility. We have developed an image analysis protocol that provides both qualitative and quantitative information on putative kiss and run events between endosomes and mitochondria, allowing us in the future to assay them functionally and ascertain their dependency on Tfn's iron binding ability as well as endocytic pH.

Assessment of a semi-automated protocol for multiplex analysis of sepsis-causing bacteria with spiked whole blood samples.

Sepsis is associated with high morbidity and mortality rates worldwide. Rapid and reliable diagnostic methods are needed for efficient and evidence-based treatment of septic patients. Recently, new molecular tools have emerged to complement the conventional culture-based diagnostic methods. In this study, we used spiked whole blood samples to evaluate together two ready-to-use molecular solutions for the detection of sepsis-causing bacteria. We spiked whole blood with bacterial species relevant in sepsis and extracted bacterial DNA with the NorDiag Arrow device, using the SelectNA Blood pathogen DNA isolation kit. DNA extracts were analyzed by the polymerase chain reaction (PCR)- and microarray-based Prove-it™ Bone and Joint assay, resulting in correctly identified bacterial species with detection limits of 11–600 colony-forming unit/mL (CFU/mL). To understand the recovery losses of bacterial DNA during the sample preparation step and the capability of the PCR- and microarray-based platform to respond to the sensitivity requirements, we also determined the analytical sensitivity of the PCR and microarray platform to be 1–21 genome equivalents for the tested bacterial species. In addition, the inclusivity of the Prove-it™ Bone and Joint assay was demonstrated with methicillin-resistant Staphylococcus aureus (MRSA) clones carrying SCCmec types I, II, IV, or V and a nontypable SCCmec type. The proof-of-concept for accurate multiplex pathogen and antibacterial resistance marker detection from spiked whole blood samples was demonstrated by the selective bacterial DNA extraction method combined with the high-throughput PCR- and microarray-based platform. Further investigations are needed to study the promising potential of the concept for sensitive, semi-automated identification of sepsis-causing pathogens directly from whole blood.

Optimized microbial DNA extraction from diarrheic stools

BackgroundThe detection of enteropathogens in stool specimens increasingly relies on the detection of specific nucleic acid sequences. We observed that such detection was hampered in diarrheic stool specimens and we set-up an improved protocol combining lyophilization of stools prior to a semi-automated DNA extraction.FindingsA total of 41 human diarrheic stool specimens comprising of 35 specimens negative for enteropathogens and six specimens positive for Salmonella enterica in culture, were prospectively studied. One 1-mL aliquot of each specimen was lyophilised and total DNA was extracted from lyophilised and non-lyophilised aliquots by combining automatic and phenol-chloroform DNA extraction. DNA was incorporated into real-time PCRs targeting the 16S rRNA gene of Bacteria and the archaea Methanobrevibacter smithii and the chorismate synthase gene of S. enterica. Whereas negative controls consisting in DNA-free water remained negative, M. smithii was detected in 26/41 (63.4%) non-lyophilised (Ct value 28.78 ± 9.1) versus 39/41 (95.1%) lyophilised aliquots (Ct value 22.04 ± 5.5); bacterial 16S rRNA was detected in 33/41 (80.5%) non-lyophilised (Ct value 28.11 ± 5.9) versus 40/41 (97.6%) lyophilised aliquots (Ct value 24.94 ± 6.6); and S. enterica was detected in 6/6 (100%) non-lyophilized and lyophilized aliquots (Ct value 26.98 ± 4.55 and 26.16 ± 4.97, respectively). S. enterica was not detected in the 35 remaining diarrheal-stool specimens. The proportion of positive specimens was significantly higher after lyophilization for the detection of M. smithii (p = 0.00043) and Bacteria (p = 0.015).ConclusionLyophilization of diarrheic stool specimens significantly increases the PCR-based detection of microorganisms. The semi-automated protocol described here could be routinely used for the molecular diagnosis of infectious diarrhea.

G03 Corpus callosal atrophy in Huntington's disease

<h3>Background</h3> Research into Huntington9s disease (HD) has revealed white-matter loss in individuals more than 10 years prior to predicted disease onset, focused around the striatum, corpus callosum (CC) and posterior white-matter tracts. Degeneration of the CC is of interest since it provides interhemispheric connections to cortical areas known to be affected in HD. <h3>Aims</h3> This study aims to investigate the utility of volumetric measurements of the CC in HD using a novel segmentation technique, multiple time-points and a large well-characterised cohort. Structure-function relationship in the CC will also be explored. <h3>Methods</h3> Volumetric 3T MRI from controls, premanifest gene carriers and early HD subjects enrolled in the TRACK-HD study will be analysed at baseline and 24 months. The CC will be delineated using a semi-automated segmentation protocol. Differences in baseline volumes and atrophy rates between groups will be examined, as well as correlations between volume loss and clinical impairment. <h3>Results</h3> Preliminary analysis of a subset of subjects indicates that early HD subjects have reduced CC volume compared with controls and premanifest subjects (p&lt;0.001). Increased longitudinal CC volume change was found in early HD subjects, compared with controls (p&lt;0.001). Interestingly there was significant difference in longitudinal change between controls and premanifest subjects close to disease onset (p&lt;0.05). This work will be extended to include multi-site data and correlations between atrophy and clinical and cognitive decline. <h3>Conclusions</h3> Measurement of CC atrophy may have potential as an imaging biomarker for HD and may prove useful for exploring interhemispheric structure-function relationships. <h3>Funding</h3> Helen Crawford is supported by the CHDI Foundation, a not for profit organisation dedicated to finding treatments for HD.

Investigation of pulmonary contusion extent and its correlation to crash, occupant, and injury characteristics in motor vehicle crashes

BackgroundPulmonary contusion (PC) is a leading injury in blunt chest trauma and is most commonly caused by motor vehicle crashes (MVC). To improve understanding of the relationship between insult and outcome, this study relates PC severity to crash, occupant, and injury parameters in MVCs. MethodsTwenty-nine subjects with PC were selected from the Crash Injury Research and Engineering Network (CIREN) database, which contains detailed crash and medical information on MVC occupants. Computed tomography scans of these subjects were segmented using a semi-automated protocol to quantify the volumetric percentage of injured tissue in each lung. Techniques were used to quantify the geometry and location of PC, as well as the location of rib fractures. Injury extent including percent PC volume and the number of rib fractures was analyzed and its relation to crash and occupant characteristics was explored. ResultsFrontal and near-side crashes composed 72% of the dataset and the near-side door was the component most often associated with PC causation. The number of rib fractures increased with age and fracture patterns varied with crash type. In near-side crashes, occupant weight and BMI were positively correlated with percent PC volume and the number of rib fractures, and the impact severity was positively correlated with percent PC volume in the lung nearest the impact. ConclusionsThis study quantified PC morphology in 29 MVC occupants and examined the relationship between injury severity and crash and occupant parameters to better characterize the mechanism of injury. The results of this study may contribute to the prevention, mitigation, and treatment of PC.

Severity of Leukoaraiosis in Large Vessel Atherosclerotic Disease

The severity of white matter hyperintensity, or leukoaraiosis, is a marker of cerebrovascular disease. In stroke, WMH burden is strongly linked to lacunar infarction; however, impaired cerebral perfusion due to extracranial or intracranial atherosclerosis may also contribute to WMH burden. We sought to determine whether WMH burden is associated with extracranial or intracranial stenosis in patients with AIS. Patients with AIS with admission head/neck CTA and brain MR imaging were included in this analysis. "Extracranial stenosis" was defined as >50% stenosis in the extracranial ICA, and "intracranial," as >50% stenosis in either the middle, anterior, or posterior cerebral arteries on CTA, on either side. WMHV was determined by using a validated semiautomated protocol. Multiple regression was used to assess the relationship between WMHV and extracranial/intracranial atherosclerosis. Of 201 subjects, 51 (25.4%) had extracranial and 63 (31.5%) had intracranial stenosis. Mean age was 62 ± 15 years; 36% were women. Mean WMHV was 12.87 cm(3) in the extracranial and 8.59 cm(3) in the intracranial stenosis groups. In univariate analysis, age (P < .0001), SBP and DBP (P = .004), and HTN (P = .0003) were associated with WMHV. Extracranial stenosis was associated with greater WMHV after adjustment for intracranial stenosis (P = .04). In multivariate analysis including extracranial stenosis, only age (P < .0001) and HTN (P = .03) demonstrated independent effects on WMHV. In our cohort of patients with AIS, age and HTN were the strongest determinants of the WMHV severity. Future studies are warranted to unravel further association between WMHV and cerebral vessel atherosclerosis.

Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking

A significant number of macromolecular structures solved by electron cryo-microscopy and X-ray crystallography obtain resolutions of 3.5-6Å, at which direct atomistic interpretation is difficult. To address this, we developed pathwalking, a semi-automated protocol to enumerate reasonable Cα models from near-atomic resolution density maps without a structural template or sequence-structure correspondence. Pathwalking uses an approach derived from the Traveling Salesman Problem to rapidly generate an ensemble of initial models for individual proteins, which can later be optimized to produce full atomic models. Pathwalking can also be used to validate and identify potential structural ambiguities in models generated from near-atomic resolution density maps. In this work, examples from the EMDB and PDB are used to assess the broad applicability and accuracy of our method. With the growing number of near-atomic resolution density maps from cryo-EM and X-ray crystallography, pathwalking can become an important tool in modeling protein structures.

Establishment of a semi-automated pathogen DNA isolation from whole blood and comparison with commercially available kits

Molecular methods for bacterial pathogen identification are gaining increased importance in routine clinical diagnostic laboratories. Achieving reliable results using DNA based technologies is strongly dependent on pre-analytical processes including isolation of target cells and their DNA of high quality and purity. In this study a fast and semi-automated method was established for bacterial DNA isolation from whole blood samples and compared to different commercially available kits: Looxster, MolYsis kit, SeptiFast DNA isolation method and standard EasyMAG protocol. The newly established, semi-automated method utilises the EasyMAG device combined with pre-processing steps comprising human cell lysis, centrifugation and bacterial pellet resuspension. Quality of DNA was assessed by a universal PCR targeting the 16S rRNA gene and subsequent microarray hybridisation. The DNA extractions were amplified using two different PCR-mastermixes, to allow comparison of a commercial mastermix with a guaranteed bacterial DNA free PCR mastermix. The modified semi-automated EasyMAG protocol and the Looxster kit gave the most sensitive results. After hybridisation a detection limit of 10 1 to 10 2 bacterial cells per mL whole blood was achieved depending on the isolation method and microbial species lysed. Human DNA present in the isolated DNA suspension did not interfere with PCR and did not lead to non-specific hybridisation events.

Measuring disease progression in frontotemporal lobar degeneration

There is currently much interest in biomarkers of disease activity in frontotemporal lobar degeneration (FTLD). We assessed MRI and behavioral measures of progression in a longitudinal FTLD cohort. Thirty-two patients with FTLD (11 behavioral variant frontotemporal dementia [bvFTD], 11 semantic dementia [SemD], 10 progressive nonfluent aphasia [PNFA]) and 24 age-matched healthy controls were assessed using volumetric brain MRI and standard behavioral measures (Mini-Mental State Examination, Frontal Assessment Battery, Clinical Dementia Rating Scale, Neuropsychiatric Inventory with Caregiver Distress scale) at baseline and 1 year later. A semi-automated image registration protocol was used to calculate annualized rates of brain atrophy (brain boundary shift integral [BBSI]) and ventricular expansion (ventricular boundary shift integral [VBSI]). Associations between these rates and changes in behavioral indices were investigated. Rates of whole brain atrophy were greater in the entire FTLD cohort and in each subgroup compared with controls (all p < or = 0.004). Rates of ventricular expansion were greater in the entire cohort (p < 0.001) and the SemD (p = 0.002) and PNFA (p = 0.05) subgroups compared with controls. Changes in Mini-Mental State Examination, Frontal Assessment Battery, and Clinical Dementia Rating Scale scores were associated with MRI measures of progression, though not uniformly across FTLD subgroups. Both BBSI and VBSI yielded feasible sample size estimates for detecting meaningful treatment effects in SemD and PNFA language subgroups. Sample sizes were substantially larger using MRI biomarkers for the bvFTD subgroup, and using behavioral biomarkers in general. Semi-automated MRI atrophy measures are potentially useful objective biomarkers of progression in frontotemporal lobar degeneration (FTLD); however, careful stratification of FTLD subtypes will be important in future clinical trials of disease-modifying therapies.

Rapid, robotic, small‐scale protein production for NMR screening and structure determination

Three-dimensional protein structure determination is a costly process due in part to the low success rate within groups of potential targets. Conventional validation methods eliminate the vast majority of proteins from further consideration through a time-consuming succession of screens for expression, solubility, purification, and folding. False negatives at each stage incur unwarranted reductions in the overall success rate. We developed a semi-automated protocol for isotopically-labeled protein production using the Maxwell-16, a commercially available bench top robot, that allows for single-step target screening by 2D NMR. In the span of a week, one person can express, purify, and screen 48 different (15)N-labeled proteins, accelerating the validation process by more than 10-fold. The yield from a single channel of the Maxwell-16 is sufficient for acquisition of a high-quality 2D (1)H-(15)N-HSQC spectrum using a 3-mm sample cell and 5-mm cryogenic NMR probe. Maxwell-16 screening of a control group of proteins reproduced previous validation results from conventional small-scale expression screening and large-scale production approaches currently employed by our structural genomics pipeline. Analysis of 18 new protein constructs identified two potential structure targets that included the second PDZ domain of human Par-3. To further demonstrate the broad utility of this production strategy, we solved the PDZ2 NMR structure using [U-(15)N,(13)C] protein prepared using the Maxwell-16. This novel semi-automated protein production protocol reduces the time and cost associated with NMR structure determination by eliminating unnecessary screening and scale-up steps.

Comparison of volume and diameter measurement in assessing small abdominal aortic aneurysm expansion examined using computed tomographic angiography

Aim First we aimed to assess the reproducibility of a computer tomography angiography (CTA) based technique for measuring infra-renal aortic volume and diameter. Second we sought to investigate whether changes in aortic volume and diameter were similar during follow-up. Materials and methods A prospective series of 57 patients, with aortic diameter initially measuring between 25 and 55 mm, were assessed with 2 CTAs a median of 14 months apart. Aortic volume and maximum diameter (both axial and orthogonal) were measured by a semi-automated workstation protocol based on previously defined techniques. Intra- and inter-observer reproducibility were assessed by repeat assessment of the initial CTA images of the first 33 patients included in the study, in order to estimate the 95% limits of agreements. Changes in aortic dimensions between the first and follow-up CTA, were defined for volume and diameter separately as changes greater than their respective 95% limits of agreement. Results Reproducibility of aortic volume and diameter was excellent with an average coefficient of variation <4%. The median (inter-quartile range) increases in total volume, orthogonal and axial diameters were 4.9 cm 3 (0.01–14.18), 1.2 mm (0.40–3.50) and 1.4 mm (−0.15 to 3.55) respectively. Forty-two percent of patients who had increased aortic volume above the 95% limit of agreement did not display corresponding axial or orthogonal diameter changes. Conclusions Infra-renal total aortic volume, axial and orthogonal diameter can all be measured reproducibly from CTA. Aortic volume changes are not always reflected by similar changes in diameter and therefore provide complementary information when assessing AAA expansion over time.

Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms

Next-generation sequencing platforms are powerful technologies, providing gigabases of genetic information in a single run. An important prerequisite for high-throughput DNA sequencing is the development of robust and cost-effective preprocessing protocols for DNA sample library construction. Here we report the development of a semi-automated sample preparation protocol to produce adaptor-ligated fragment libraries. Using a liquid-handling robot in conjunction with Carboxy Terminated Magnetic Beads, we labeled each library sample using a unique 6 bp DNA barcode, which allowed multiplex sample processing and sequencing of 32 libraries in a single run using Applied Biosystems' SOLiD sequencer. We applied our semi-automated pipeline to targeted medical resequencing of nuclear candidate genes in individuals affected by mitochondrial disorders. This novel method is capable of preparing as much as 32 DNA libraries in 2.01 days (8-hour workday) for emulsion PCR/high throughput DNA sequencing, increasing sample preparation production by 8-fold.

A collaborative decision support framework for managing the evolution of virtual enterprises

During the operation phase of a virtual enterprise (VE) different kinds of unexpected problems usually take place and they should be properly handled in order to keep the VE goals. However, the nature of a VE imposes new requirements as decisions should be taken in a distributed and decentralised manner due to members’ autonomy and independence. Besides quality, agility in the decision-making is a must to guarantee success. For that, this paper presents a framework that provides a supporting methodology for guiding VE members along the diverse steps in the problem resolution, including assistance in their discussion. The framework relies on Business Process Management (BPM) and Service Oriented Architecture (SOA) approaches, and the methodology on project management reference models (focused on changes management). A discussion about the problem is driven by a semi-automated protocol conducted by a Distributed Collaborative Decision Support System for the Management of VE Evolution (DSS-VE). The protocol delineates a sequence of steps to be taken but is flexible to cope with partners’ heterogeneity and VE uniqueness. The impact of decisions can be evaluated via a distributed toolbox, containing a set of techniques for performance measurement and evaluation analysis.

Appearance and incomplete label matching for diffeomorphic template based hippocampus segmentation

We present a robust, high-throughput, semiautomated template-based protocol for segmenting the hippocampus in temporal lobe epilepsy. The semiautomated component of this approach, which minimizes user effort while maximizing the benefit of human input to the algorithm, relies on "incomplete labeling." Incomplete labeling requires the user to quickly and approximately segment a few key regions of the hippocampus through a user-interface. Subsequently, this partial labeling of the hippocampus is combined with image similarity terms to guide volumetric diffeomorphic normalization between an individual brain and an unbiased disease-specific template, with fully labeled hippocampi. We solve this many-to-few and few-to-many matching problem, and gain robustness to inter and intrarater variability and small errors in user labeling, by embedding the template-based normalization within a probabilistic framework that examines both label geometry and appearance data at each label. We evaluate the reliability of this framework with respect to manual labeling and show that it increases minimum performance levels relative to fully automated approaches and provides high inter-rater reliability. Thus, this approach does not require expert neuroanatomical training and is viable for high-throughput studies of both the normal and the highly atrophic hippocampus.

Measurement and determinants of infrarenal aortic thrombus volume

Intra-luminal thrombus has been suggested to play a role in the progression of abdominal aortic aneurysm (AAA). The aims of this study were twofold. Firstly, to assess the reproducibility of a computer tomography (CT)-based technique for measurement of aortic thrombus volume. Secondly, to examine the determinants of infrarenal aortic thrombus volume in a cohort of patients with aortic dilatation. A consecutive series of 75 patients assessed by CT angiography with maximum aortic diameter > or = 25 mm were recruited. Intra-luminal thrombus volume was measured by a semi-automated workstation protocol based on a previously defined technique to quantitate aortic calcification. Intra- and inter-observer reproducibility were assessed using correlation coefficients, coefficient of variation and Bland-Altman plots. Infrarenal aortic thrombus volume percentage was related to clinical, anatomical and blood characteristics of the patients using univariate and multivariate tests. Infrarenal aortic thrombus volume was related to the severity of aortic dilatation assessed by total aortic volume (r = 0.87, P < 0.0001) or maximum aortic diameter (r = 0.74, P < 0.0001). We therefore examined the clinical determinates of aortic thrombus expressed as a percentage of total aortic volume. Aortic thrombus percentage was negatively correlated with serum high density lipoprotein (HDL, r = -0.31). By ordinal multiple logistic regression analysis serum HDL below median (< or = 1.2 mM: ) was associated with aortic thrombus percentage in the upper quartile adjusting for other risk factors (odds ratio 5.3, 95% CI 1.1-25.0). Infrarenal aortic thrombus volume can be measured reproducibly on CT. Serum HDL, which can be therapeutically raised, may play a role in discouraging aortic thrombus accumulation with implications in terms of delaying progression of AAA.

Differential effects of aging and Alzheimer's disease on medial temporal lobe cortical thickness and surface area

The volume of parcellated cortical regions is a composite measure related to both thickness and surface area. It is not clear whether volumetric decreases in medial temporal lobe (MTL) cortical regions in aging and Alzheimer's disease (AD) are due to thinning, loss of surface area, or both, nor is it clear whether aging and AD differ in their effects on these properties. Participants included 28 Younger Normals, 47 Older Normals, and 29 patients with mild AD. T1-weighted MRI data were analyzed using a novel semi-automated protocol (presented in a companion article) to delineate the boundaries of entorhinal (ERC), perirhinal (PRC), and posterior parahippocampal (PPHC) cortical regions and calculate their mean thickness, surface area, and volume. Compared to Younger Normals, Older Normals demonstrated moderately reduced ERC and PPHC volumes, which were due primarily to reduced surface area. In contrast, the expected AD-related reduction in ERC volume was produced by a large reduction in thickness with minimal additional effect (beyond that of aging) on surface area. PRC and PPHC also showed large AD-related reductions in thickness. Of all these MTL morphometric measures, ERC and PRC thinning were the best predictors of poorer episodic memory performance in AD. Although the volumes of MTL cortical regions may decrease with both aging and AD, thickness is relatively preserved in normal aging, while even in its mild clinical stage, AD is associated with a large degree of thinning of MTL cortex. These differential morphometric effects of aging and AD may reflect distinct biologic processes and ultimately may provide insights into the anatomic substrates of change in memory-related functions of MTL cortex.

BioGeomancer: Automated Georeferencing to Map the World's Biodiversity Data

BioGeomancer: Automated Georeferencing to Map the World's Biodiversity Data