Interferon-γ induced expression of MHC antigens facilitates identification of donor cells in chimeric transplant recipients

After whole organ transplantation, donor bone marrow-derived cells migrate out of the graft into the recipient, leading to establishment of chimerism, which is the first step towards the subsequent induction of donor-specific tolerance. In routine immunohistochemical staining, monoclonal antibodies specific for heterotopic MHC alleles are used to identify donor and recipient cells. However, it is difficult to detect these cells using this technique in long-term allograft recipients who have a persistently low donor cell population (microchimerism). Because Interferon-gamma (IFN-γ) is known to induce expression of MHC class I and class II cell surface molecules, we used this cytokine 12-48 h before sacrifice, to facilitate the identification of donor and recipient cells in the tissues of animals transplanted with either liver (B10 → C3H) or bone marrow (LEW → BN). In long-term allograft recipients, the use of IFN-γ for as briefly as 12 h prior to sacrifice, results in marked upregulation of class I and class II antigens, leading to easy identification of ubiquitously distributed low numbers of donor cells. © 1994

Value of percutaneous transluminal coronary angioplasty after unsuccessful intravenous streptokinase therapy in acute myocardial infarction

The effect of sequential high-dose intravenous streptokinase (SK) (1.5 million units) followed by emergency percutaneous transluminal coronary angioplasty (PTCA) on preserving left ventricular function was assessed prospectively in 34 patients with acute myocardial infarction (AMI). Intravenous SK therapy was initiated 2.6 +/- 1.3 hours (mean +/- standard deviation) after the onset of chest pain. Urgent coronary angiography showed persistent total occlusion in 13 patients, significant diameter stenosis (70 to 99%) in 18 patients and a widely patent artery (less than 50% stenosis) in 3 patients. Emergency PTCA was performed in 29 patients 5.0 +/- 2.1 hours after symptom onset. Successful recanalization was achieved in 33 of the 34 patients (97%) treated with sequential therapy. Repeat contrast ventriculograms recorded 7 to 10 days after intervention in 23 patients showed that the left ventricular ejection fraction increased from 53 +/- 12% to 59 +/- 13% (area-length method, p < 0.002). Regional wall motion of the infarcted segments improved from - 2.7 +/- 1.1 to - 1.5 +/- 1.7 SD/chord (centerline method, p < 0.003). In the subgroup of patients with an occluded artery on initial angiography (group A, N = 10), both global left ventricular ejection fraction (49 +/- 12% vs 59 +/- 12%, p < 0.002) and regional wall motion (-3.2 +/- 1.0 vs -1.9 +/- 1.7 SD/chord, p < 0.002) improved significantly. In contrast, no significant improvement was seen in patients with a patent artery on initial angiography (n = 13). Thus, sequential intravenous SK and emergency PTCA is efficacious in achieving coronary reperfusion and in improving both global and regional left ventricular function. When thrombolytic therapy fails, successful recanalization can be achieved by emergency PTCA, resulting in significant myocardial salvage.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26031/1/0000104.pd

Early reperfusion therapy improves left ventricular function after acute inferior myocardial infarction associated with right coronary artery disease

Quantitative global and regional ventriculographic analysis was performed acutely and 1 week later in 46 patients undergoing reperfusion procedures within 6 hours of acute inferior myocardial infarction due to right coronary artery disease. While serial improvement in global left ventricular ejection fraction was not demonstrated for the group, infarct zone regional wall motion did improve (-2.7 +/- 0.9 vs -2.3 +/- 1.4 SD/chord, p p p p p < 0.0001). We conclude that significant improvement in global and reglonal left ventricular function in patients with inferior myocardial infarction is possible when reperfusion therapy is begun early or when arterial patency is achieved.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26625/1/0000166.pd

An Introspective Comparison of Random Forest-Based Classifiers for the Analysis of Cluster-Correlated Data by Way of RF++

Many mass spectrometry-based studies, as well as other biological experiments produce cluster-correlated data. Failure to account for correlation among observations may result in a classification algorithm overfitting the training data and producing overoptimistic estimated error rates and may make subsequent classifications unreliable. Current common practice for dealing with replicated data is to average each subject replicate sample set, reducing the dataset size and incurring loss of information. In this manuscript we compare three approaches to dealing with cluster-correlated data: unmodified Breiman's Random Forest (URF), forest grown using subject-level averages (SLA), and RF++ with subject-level bootstrapping (SLB). RF++, a novel Random Forest-based algorithm implemented in C++, handles cluster-correlated data through a modification of the original resampling algorithm and accommodates subject-level classification. Subject-level bootstrapping is an alternative sampling method that obviates the need to average or otherwise reduce each set of replicates to a single independent sample. Our experiments show nearly identical median classification and variable selection accuracy for SLB forests and URF forests when applied to both simulated and real datasets. However, the run-time estimated error rate was severely underestimated for URF forests. Predictably, SLA forests were found to be more severely affected by the reduction in sample size which led to poorer classification and variable selection accuracy. Perhaps most importantly our results suggest that it is reasonable to utilize URF for the analysis of cluster-correlated data. Two caveats should be noted: first, correct classification error rates must be obtained using a separate test dataset, and second, an additional post-processing step is required to obtain subject-level classifications. RF++ is shown to be an effective alternative for classifying both clustered and non-clustered data. Source code and stand-alone compiled versions of command-line and easy-to-use graphical user interface (GUI) versions of RF++ for Windows and Linux as well as a user manual (Supplementary File S2) are available for download at: http://sourceforge.org/projects/rfpp/ under the GNU public license

3D Morphometric and Posture Study of Felid Scapulae Using Statistical Shape Modelling

We present a three dimensional (3D) morphometric modelling study of the scapulae of Felidae, with a focus on the correlations between forelimb postures and extracted scapular shape variations. Our shape modelling results indicate that the scapular infraspinous fossa becomes larger and relatively broader along the craniocaudal axis in larger felids. We infer that this enlargement of the scapular fossa may be a size-related specialization for postural support of the shoulder joint

The Genomic and Evolutionary Landscapes of Anaplastic Thyroid Carcinoma

Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations

Clinical history and management recommendations of the smooth muscle dysfunction syndrome due to ACTA2 arginine 179 alterations

Smooth muscle dysfunction syndrome (SMDS) due to heterozygous ACTA2 arginine 179 alterations is characterized by patent ductus arteriosus, vasculopathy (aneurysm and occlusive lesions), pulmonary arterial hypertension, and other complications in smooth muscle-dependent organs. We sought to define the clinical history of SMDS to develop recommendations for evaluation and management. Medical records of 33 patients with SMDS (median age 12 years) were abstracted and analyzed. All patients had congenital mydriasis and related pupillary abnormalities at birth and presented in infancy with a patent ductus arteriosus or aortopulmonary window. Patients had cerebrovascular disease characterized by small vessel disease (hyperintense periventricular white matter lesions; 95%), intracranial artery stenosis (77%), ischemic strokes (27%), and seizures (18%). Twelve (36%) patients had thoracic aortic aneurysm repair or dissection at median age of 14 years and aortic disease was fully penetrant by the age of 25 years. Three (9%) patients had axillary artery aneurysms complicated by thromboembolic episodes. Nine patients died between the ages of 0.5 and 32 years due to aortic, pulmonary, or stroke complications, or unknown causes. Based on these data, recommendations are provided for the surveillance and management of SMDS to help prevent early-onset life-threatening complications

Synthetic Biology: Mapping the Scientific Landscape

This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves

Fine-Scale Mapping of the 4q24 Locus Identifies Two Independent Loci Associated with Breast Cancer Risk

Background: A recent association study identified a common variant (rs9790517) at 4q24 to be associated with breast cancer risk. Independent association signals and potential functional variants in this locus have not been explored. Methods: We conducted a fine-mapping analysis in 55,540 breast cancer cases and 51,168 controls from the Breast Cancer Association Consortium. Results: Conditional analyses identified two independent association signals among women of European ancestry, represented by rs9790517 [conditional P = 2.51 × 10−4; OR, 1.04; 95% confidence interval (CI), 1.02–1.07] and rs77928427 (P = 1.86 × 10−4; OR, 1.04; 95% CI, 1.02–1.07). Functional annotation using data from the Encyclopedia of DNA Elements (ENCODE) project revealed two putative functional variants, rs62331150 and rs73838678 in linkage disequilibrium (LD) with rs9790517 (r2 ≥ 0.90) residing in the active promoter or enhancer, respectively, of the nearest gene, TET2. Both variants are located in DNase I hypersensitivity and transcription factor–binding sites. Using data from both The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), we showed that rs62331150 was associated with level of expression of TET2 in breast normal and tumor tissue. Conclusion: Our study identified two independent association signals at 4q24 in relation to breast cancer risk and suggested that observed association in this locus may be mediated through the regulation of TET2. Impact: Fine-mapping study with large sample size warranted for identification of independent loci for breast cancer risk