Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron.

Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing-5' and 3' splice sites and a branchpoint-are especially well-characterized in Saccharomyces cerevisiae, but our understanding of additional intron features that impact splicing in this organism is incomplete, due largely to its small number of introns. To overcome this limitation, we constructed a library in S. cerevisiae of random 50-nt (N50) elements individually inserted into the intron of a reporter gene and quantified canonical splicing and the use of cryptic splice sites by sequencing analysis. More than 70% of approximately 140,000 N50 elements reduced splicing by at least 20%. N50 features, including higher GC content, presence of GU repeats, and stronger predicted secondary structure of its pre-mRNA, correlated with reduced splicing efficiency. A likely basis for the reduced splicing of such a large proportion of variants is the formation of RNA structures that pair N50 bases-such as the GU repeats-with other bases specifically within the reporter pre-mRNA analyzed. However, multiple models were unable to explain more than a small fraction of the variance in splicing efficiency across the library, suggesting that complex nonlinear interactions in RNA structures are not accurately captured by RNA structure prediction methods. Our results imply that the specific context of a pre-mRNA may determine the bases allowable in an intron to prevent secondary structures that reduce splicing. This large data set can serve as a resource for further exploration of splicing mechanisms.

Improving the Prescribing Gap For Guideline Recommended Medications Post Myocardial Infarction.

BACKGROUND: We assessed the effect of a pre-discharge medication checklist on discharge prescription rates of guideline recommended medications following myocardial infarction. In addition, we assessed what proportion of the residual prescribing gap following implementation of the checklist was due to the presence of contraindications. METHODS: We examined baseline prescription rates of guideline recommended medications in 100 patients discharged from our institution following acute myocardial infarction. We then introduced a pre-discharge checklist and reassessed discharge medications and reasons for non-prescription of guideline recommended medications in 447 patients with acute myocardial infarction. RESULTS: We demonstrated a significant gap in the prescription of guideline recommended secondary prevention medications at the time of discharge in our pre-intervention cohort. Introduction of a pre-discharge checklist resulted in a significant improvement in the prescription rates of all guideline recommended secondary prevention medications, with aspirin increasing from 90% to 97% (p=0.004), Adenosine diphosphate (ADP) receptor antagonist from 84% to 96% (p=0.0001), B-blocker from 79% to 87% (p=0.03), statin from 88% to 96% (p=0.002) and angiotensin converting enzyme (ACE) inhibitor from 58% to 70% (p=0.03). The residual gap in prescribing was largely explained by the presence of contraindications or absence of an indication in the case of ACE-inhibitors. Once these were taken into account there was a residual gap of 0-4% which represents genuine non-adherence to the guidelines. CONCLUSIONS: Introduction of a pre-discharge checklist led to significant improvement in prescription rates of all five guideline recommended secondary prevention medications. The residual gap in medication prescription following introduction of the checklist was largely due to the presence of contraindications rather than non-adherence.

Correlation between vectorcardiographic measures and cardiac magnetic resonance imaging of the left ventricle in an implantable cardioverter defibrillator population.

BACKGROUND: Measures of vectorcardiographic changes and LV remodelling have been associated with arrhythmic risk. However the correlation between the two modalities is not well characterised. METHODS: We correlated spatial QRS-T angle and ventricular gradient with cardiac MRI derived LV global measures and scar pattern in 66 ICD recipients. RESULTS: Spatial QRS-T angle was significantly larger in patients with ischaemic scar than those without scar (150°±22° vs. 119°±46°, p=0.01). Larger spatial QRS-T angle was also correlated with more depressed LV function, more dilated LV and larger LV mass. Ventricular gradient azimuth was significantly different between patients with no scar, non-ischaemic scar and ischaemic scar (20°±49° vs. 38°±62° vs. 65°±48°, p=0.009), but independent of spatial QRS-T angle and LV structure. CONCLUSIONS: Spatial QRS-T angle and ventricular gradient are partially related to LV structural properties. Further investigation is warranted to examine their comparative and combined prognostic value in risk stratification of ventricular arrhythmias.

Dose-Volume Predictors of Radiation Pneumonitis After Thoracic Hypofractionated Radiation Therapy.

PURPOSE: Hypofractionated radiation therapy (HFRT) is a common treatment for thoracic tumors, typically delivered as 60 Gy in 15 fractions. We aimed to identify dosimetric risk factors associated with radiation pneumonitis in patients receiving HFRT at 4 Gy per fraction, focusing on lung V20, mean lung dose (MLD), and lung V5 as potential predictors of grade ≥2 pneumonitis. METHODS AND MATERIALS: All patients were treated with thoracic HFRT to 60 Gy in 15 fractions or 72 Gy in 18 fractions at a single health care system from 2013 to 2020. Tumors near critical structures (trachea, proximal tracheobronchial tree, esophagus, spinal cord, or heart) were considered central (within 2 cm), and those closer were classified as ultracentral (within 1 cm). The primary endpoint was grade ≥2 pneumonitis. Logistic regression analyses, adjusting for target size and dosimetric variables, were used to establish a dose threshold associated with <20% risk of grade ≥2 pneumonitis. RESULTS: During a median 24.3-month follow-up, 18 patients (16.8%) developed grade ≥2 radiation pneumonitis, with no significant difference between the 2 dose regimens (17.3% vs 16.3%, P = .88). Four patients (3.7%) experienced grade ≥3 pneumonitis, including 2 grade 5 cases. Patients with grade ≥2 pneumonitis had significantly higher lung V20 (mean 23.4% vs 14.5%, P < .001), MLD (mean 13.0 Gy vs 9.5 Gy, P < .001), and lung V5 (mean 49.6% vs 40.6%, P = .01). Dose thresholds for a 20% risk of grade ≥2 pneumonitis were lung V20 <17.7%, MLD <10.6 Gy, and V5 <41.3%. Multivariable analysis revealed a significant association between lung V20 and grade ≥2 pneumonitis (adjusted odds ratio, 1.48, P = .03). CONCLUSIONS: To minimize the risk of grade ≥2 radiation pneumonitis when delivering 4 Gy per fraction at either 60 Gy or 72 Gy, it is advisable to maintain lung V20<17.7%. MLD <10.6 Gy and V5<41.3% can also be considered as lower-priority constraints. However, additional validation is necessary before incorporating these constraints into clinical practice or trial planning guidelines.

Dabigatran for anticoagulation in atrial fibrillation - early clinical experience in a hospital population and comparison to trial data.

BACKGROUND: Dabigatran is a recently introduced direct thrombin inhibitor licensed for use as an oral anticoagulant for stroke prevention in non-valvular atrial fibrillation. Our prospective observational study aimed to assess the adverse effects, tolerability and patient satisfaction of dabigatran therapy in a hospital-practice population. METHODS: Patients starting dabigatran, after its release in June 2011, were identified from clinical practice at two Wellington hospitals, New Zealand. Baseline characteristics were recorded from the clinical record and a telephone interview was performed in January 2012. Primary outcomes included adverse events, adherence, and satisfaction with treatment. RESULTS: Data were available for 70 patients: median age 71.9 years (IQR 62.7-79.0), weight 80 kg (IQR 71-95), CHA(2)DS(2)-VASc score 3 (IQR 2-4). Seventy-one percent of patients reported adverse events although the majority were minor. Twenty-four percent (16/70) had discontinued treatment with dabigatran; four due to predominantly gastrointestinal side effects, three due to bleeding (one severe), one as a result of adverse media coverage with the remainder comprising planned treatment discontinuation and undetermined. In total, 29% reported bleeding events, predominantly minor bleeding and bruising. There were no cerebrovascular events. Nineteen percent reported some difficulty with twice daily dosing adherence with 13 of 70 reporting missed doses. Seventy-seven percent reported treatment satisfaction and 79% of those previously treated with warfarin preferred dabigatran. CONCLUSION: In this population our study demonstrates a discontinuation rate of 10% due to side effects of dabigatran, similar to the rate reported in RE-LY. The majority of patients are satisfied with their treatment and preferred dabigatran to warfarin, mainly due to the reduced requirement for blood testing.

Complex transradial percutaneous coronary intervention using a sheathless guide catheter.

BACKGROUND: Radial access for percutaneous coronary intervention (PCI) has been shown to reduce access site complications, improve patient comfort and reduce mortality. Use of a sheathless guiding catheter for transradial PCI has the potential reduce trauma to the radial artery and to further expand the type of cases where this approach can be utilised. We report our initial experience with the recently developed Sheathless Eaucath. METHODS: We retrospectively evaluated outcomes in consecutive patients who underwent PCI using the Sheathless Eaucath at our institution between February 2009 and November 2011. All procedures were performed via radial access. There were no exclusion criteria. RESULTS: The study included 120 patients. Of these 87 (72.5%) presented with acute coronary syndromes. Primary PCI was performed in nine and rescue PCI in seven patients. Interventions were performed on a total of 147 lesions. The majority of lesions were complex (68% classified as type B2 or C). Bifurcation lesions were treated in 42.5% and chronic total occlusions in 5% of patients. Adjunctive devices including rotablation, IVUS and 6 or 7 Fr thrombus aspiration catheters were used in 30% of patients. Angiographic success was achieved in 97.5%. Five patients suffered peri-procedural non-ST-elevation myocardial infarctions. There was no in-hospital target vessel revascularisation or death. Peri-procedural radial artery occlusion was infrequent (2.3%). Haematomas larger than 5cm occurred in two patients. No other vascular complications occurred. CONCLUSION: Use of the Sheathless Eaucath is safe and allows complex interventions to be undertaken transradially with a high success rate.

A multimodality approach to a rare case of ruptured sinus of Valsalva aneurysm with tricuspid valve involvement: a case report.

Background: Ruptured sinus of Valsalva aneurysm is a rare disease entity that is potentially life-threatening if left untreated. While imaging is the mainstay of diagnosis, resultant tricuspid valve involvement may mask typical findings providing a diagnostic challenge. Disruption of the tricuspid valve during ruptured sinus of Valsalva aneurysm with consequent tricuspid regurgitation is rare and infrequently described in the literature. Description of the utility and limitations of multimodality imaging in this scenario is equally scarce. Case summary: We review the case of a young patient presenting with acute ruptured sinus of Valsalva aneurysm and involvement of the tricuspid valve on a background of severe aortic regurgitation requiring multimodality imaging for diagnostic and pre-surgical assessment. Discussion: In young patients presenting with acute decompensation and pre-existing bicuspid aortic valve regurgitation, an increased clinical suspicion of a sinus of Valsalva aneurysm rupture is imperative. Doppler and 3D transoesophageal echocardiographic assessment should be pursued to characterize abnormal flows and clarify aetiology in the context of tricuspid involvement and resultant tricuspid regurgitation. A large-volume left-right shunt in proximity to the tricuspid annulus may result in disproportionately severe tricuspid regurgitation in the absence of annular disruption due to forced systolic opening of the leaflets by shunt flow and 'windsock' prolapse. Multimodality imaging can be essential in these cases to adequately assess the extent of the ruptured sinus of Valsalva aneurysm and overcome limitations of single modality imaging.

Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings.

Deep learning methods have recently become the state-of-the-art in a variety of regulatory genomic tasks1-6 including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the full spectrum of genetic variation observed in personal genomes. Previous evaluation strategies have assessed their predictions of gene expression across genomic regions, however, systematic benchmarking is lacking to assess their predictions across individuals, which would directly evaluates their utility as personal DNA interpreters. We used paired Whole Genome Sequencing and gene expression from 839 individuals in the ROSMAP study7 to evaluate the ability of current methods to predict gene expression variation across individuals at varied loci. Our approach identifies a limitation of current methods to correctly predict the direction of variant effects. We show that this limitation stems from insufficiently learnt sequence motif grammar, and suggest new model training strategies to improve performance.

Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings.

Deep learning methods have recently become the state of the art in a variety of regulatory genomic tasks1-6, including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the full spectrum of genetic variation observed in personal genomes. Previous evaluation strategies have assessed their predictions of gene expression across genomic regions; however, systematic benchmarking is lacking to assess their predictions across individuals, which would directly evaluate their utility as personal DNA interpreters. We used paired whole genome sequencing and gene expression from 839 individuals in the ROSMAP study7 to evaluate the ability of current methods to predict gene expression variation across individuals at varied loci. Our approach identifies a limitation of current methods to correctly predict the direction of variant effects. We show that this limitation stems from insufficiently learned sequence motif grammar and suggest new model training strategies to improve performance.

The interweaved signatures of common-gamma-chain cytokines across immunologic lineages.

"γc" cytokines are a family whose receptors share a "common-gamma-chain" signaling moiety, and play central roles in differentiation, homeostasis, and communications of all immunocyte lineages. As a resource to better understand their range and specificity of action, we profiled by RNAseq the immediate-early responses to the main γc cytokines across all immunocyte lineages. The results reveal an unprecedented landscape: broader, with extensive overlap between cytokines (one cytokine doing in one cell what another does elsewhere) and essentially no effects unique to any one cytokine. Responses include a major downregulation component and a broad Myc-controlled resetting of biosynthetic and metabolic pathways. Various mechanisms appear involved: fast transcriptional activation, chromatin remodeling, and mRNA destabilization. Other surprises were uncovered: IL2 effects in mast cells, shifts between follicular and marginal zone B cells, paradoxical and cell-specific cross-talk between interferon and γc signatures, or an NKT-like program induced by IL21 in CD8+ T cells.

Repetitive transplantation of different cell types sequentially improves heart function after infarction.

Cell-based therapy is considered a novel and potentially new strategy in regenerative medicine. But the efficacy of cell-based therapy has been limited by the poor survival of the transplanted cells in an ischaemic environment. The goal of the present study is to present a possibility to increase survival of the transplanted cardiomyocytes, by increasing the vascularization of the infarcted area. First, we injected endothelial progenitor cells (EPCs) to augment the vascular density in infarcted areas and to improve the benefit of a subsequent Tx of foetal cardiomyocytes. Serial echocardiography indeed showed significant improvement of the left ventricular function after application of EPC and a significant additive improvement after Tx of foetal cardiomyocytes. In contrast, repetitive EPC transplantation as a control group did not show an additional improvement after the second transplantation. Histologically, cells could be readily detected after Tx by BrdU-staining for EPC and by carboxy-fluorescein diacetate succinimidyl ester (CFSE)-staining for foetal cardiomyocytes. Staining for CD31 revealed a significant increase in vessel density in the infarction area compared with medium controls, possibly contributing to the benefit of transplanted foetal cardiomyocytes. Notably, a significant increase in the number of apoptotic cells was observed in cell-transplanted hearts accompanied by an increase in proliferation, collagen content and neutrophil infiltration, suggesting an active remodelling concomitant with sustained inflammatory processes. In conclusion, repetitive Tx of different cell types after myocardial infarction in rat hearts significantly improved left ventricular function and could represent a feasible option to enhance the benefit of cell therapy.

Myocardial regeneration by transplantation of modified endothelial progenitor cells expressing SDF-1 in a rat model.

Cell based therapy has been shown to attenuate myocardial dysfunction after myocardial infarction (MI) in different acute and chronic animal models. It has been further shown that stromal-cell derived factor-1α (SDF-1α) facilitates proliferation and migration of endogenous progenitor cells into injured tissue. The aim of the present study was to investigate the role of exogenously applied and endogenously mobilized cells in a regenerative strategy for MI therapy. Lentivirally SDF-1α-infected endothelial progenitor cells (EPCs) were injected after 90 min. of ligation and reperfusion of the left anterior descending artery (LAD) intramyocardial and intracoronary using a new rodent catheter system. Eight weeks after transplantation, echocardiography and isolated heart studies revealed a significant improvement of LV function after intramyocardial application of lentiviral with SDF-1 infected EPCs compared to medium control. Intracoronary application of cells did not lead to significant differences compared to medium injected control hearts. Histology showed a significantly elevated rate of apoptotic cells and augmented proliferation after transplantation of EPCs and EPCs + SDF-1α in infarcted myocardium. In addition, a significant increased density of CD31(+) vessel structures, a lower collagen content and higher numbers of inflammatory cells after transplantation of SDF-1 transgenic cells were detectable. Intramyocardial application of lentiviral-infected EPCs is associated with a significant improvement of myocardial function after infarction, in contrast to an intracoronary application. Histological results revealed a significant augmentation of neovascularization, lower collagen content, higher numbers of inflammatory cells and remarkable alterations of apoptotic/proliferative processes in infarcted areas after cell transplantation.

Cholesterol treatment in patients with acute coronary syndromes: does stating a target improve management?

AIM: Previous research in New Zealand has demonstrated high rates of statin prescription in patients with acute coronary syndromes (ACS), but how widely a treat to target approach is adopted is unclear. METHODS: We retrospectively examined cholesterol management in 100 consecutive patients admitted with confirmed ACS. The primary end point was reaching low-density lipoprotein-cholesterol (LDL-C) target of <1.8 mmol/L within six months. Following this a change in practice was implemented, documenting patients' current LDL-C and the LDL-C target of <1.8mmol/L in the discharge summary. A prompt to arrange a follow-up lipid test was also added to the discharge process. A second cohort of 100 patients with confirmed ACS was prospectively examined and the same endpoints reassessed. RESULTS: Lipid testing increased post intervention, both in-hospital (70% vs 98%, P<0.001) and during outpatient follow-up (60% vs 82%, P=0.01). In the intervention group, the primary outcome was achieved in more frequently (47% vs. 64% P=0.02) and follow-up LDL-C was lower (2.01.1 mmol/L vs 1.730.77 mmol/L, P=0.002). Non-statin cholesterol medication was rarely used. CONCLUSION: At baseline a treat to target approach was infrequent. Stating a target in discharge documentation was associated with significant improvements in lipid testing and patients achieving LDL-C targets.

Hypofractionated vs. standard radiotherapy for locally advanced limited-stage small cell lung cancer.

Background: Hypofractionated radiotherapy in locally advanced limited-stage small cell lung cancer is preferred in many Western countries but not used regularly in the United States. We examined practice patterns and overall survival with definitive hypofractionated radiotherapy and chemotherapy vs. standard radiotherapy in this setting. Methods: We included patients in the National Cancer Database with unresected primary stage II-III small cell lung cancer in 2008-2016 who underwent chemotherapy within six months of either hypofractionated radiotherapy (40-45 Gy/15 fractions) or standard radiotherapy (45 Gy/30 fractions or 60-70 Gy/30-35 fractions) in this retrospective cohort study. Patient characteristics were assessed with univariable and multivariable logistic regression. Kaplan-Meier estimator, log-rank test, and multivariable Cox regression were used to evaluate overall survival. Propensity score matching (PSM) was performed as a sensitivity analysis. Early concurrent chemotherapy consisted of radiotherapy and chemotherapy initiated within 30 days of each other. Results: Seven thousand and one hundred forty-three patients were included: 97.9% received standard radiotherapy and 2.1% hypofractionated radiotherapy. Multivariable analysis on the whole cohort yielded comparable overall survival (HR for hypofractionated radiotherapy 1.09, CI: 0.90-1.32, P=0.37). On PSM (N=292), median overall survival was similar between standard radiotherapy [22.9 months (95% CI: 18.2-30.4 months)] vs. hypofractionated radiotherapy [21.2 months (CI: 16.3-24.7 months); P=0.13]. Overall survival was shorter with hypofractionated radiotherapy in the early concurrent chemotherapy subset (15.8 vs. 22.1 months, P=0.007) and longer with hypofractionated radiotherapy in the non-early concurrent chemotherapy subset (29.5 vs. 18.5 months, P=0.027). Conclusions: Overall survival with hypofractionated radiotherapy appears similar to standard radiotherapy in locally advanced limited-stage small cell lung cancer. Chemotherapy timing may modify the effect of fractionation on overall survival, though larger numbers must confirm. Hypofractionated radiotherapy may be considered in those unable to receive early concurrent chemotherapy.

Interactions between heart rate variability and pulmonary gas exchange efficiency in humans.

The respiratory component of heart rate variability (respiratory sinus arrhythmia, RSA) has been associated with improved pulmonary gas exchange efficiency in humans via the apparent clustering and scattering of heart beats in time with the inspiratory and expiratory phases of alveolar ventilation, respectively. However, since human RSA causes only marginal redistribution of heart beats to inspiration, we tested the hypothesis that any association between RSA amplitude and pulmonary gas exchange efficiency may be indirect. In 11 patients with fixed-rate cardiac pacemakers and 10 healthy control subjects, we recorded R-R intervals, respiratory flow, end-tidal gas tension and the ventilatory equivalents for carbon dioxide and oxygen during 'fast' (0.25 Hz) and 'slow' paced breathing (0.10 Hz). Mean heart rate, mean arterial blood pressure, mean arterial pressure fluctuations, tidal volume, end-tidal CO(2), and were similar between pacemaker and control groups in both the fast and slow breathing conditions. Although pacemaker patients had no RSA and slow breathing was associated with a 2.5-fold RSA amplitude increase in control subjects (39 +/- 21 versus 97 +/- 45 ms, P < 0.001), comparable (main effect for breathing frequency, F(1,19) = 76.54, P < 0.001) and reductions (main effect for breathing frequency, F(1,19) = 23.90, P < 0.001) were observed for both cohorts during slow breathing. In addition, the degree of (r = 0.36, P = 0.32) and reductions (r = 0.29, P = 0.43) from fast to slow breathing were not correlated to the degree of associated RSA amplitude enhancements in control subjects. These findings suggest that the association between RSA amplitude and pulmonary gas exchange efficiency during variable-frequency paced breathing observed in prior human work is not contingent on RSA being present. Therefore, whether RSA serves an intrinsic physiological function in optimizing pulmonary gas exchange efficiency in humans requires further experimental validation.

Noninvasive Myocardial Work Index: Characterizing the Normal and Ischemic Response to Exercise.

BACKGROUND: Myocardial work index (MWI) and work efficiency are new parameters for assessing left ventricular function. We aim to characterize the normal response to exercise in a mixed population and determine whether MWI can identify patients with inducible ischemia. METHODS: Patients were retrospectively enrolled from an existing database of exercise stress echocardiography. Inclusion criteria were a clinical indication of possible ischemia and technical suitability to calculate MWI. Exclusion criteria were abnormal baseline left ventricular function or inadequate image quality. Echocardiograms positive for ischemia were defined by independent visual assessment and compared with angiographic findings where available. Myocardial work index was determined using a proprietary algorithm and efficiency calculated as constructive work divided by the sum of constructive and wasted work. RESULTS: A total of 177 patients met inclusion criteria; 117 were excluded, leaving 40 normal and 20 positive tests. During normal exercise, global MWI increased 54% (from 2,296 to 3,523 mm Hg%) and efficiency remained at 96%. However, in patients with inducible ischemia, MWI decreased in affected segments, global MWI did not increase (2,069-2,070 mm Hg%), and global efficiency fell from 93% to 87%. The receiver operating characteristic curve for MWI had an area under the curve of 0.94. CONCLUSIONS: During normal exercise, MWI increases and efficiency remains unchanged. However, during exercise-induced ischemia, MWI paradoxically decreases in affected segments, while globally MWI fails to increase and efficiency decreases. We have demonstrated that MWI can be applied to stress echocardiography to identify ischemia, but its utility remains uncertain. Further research that makes comparisons with an objective measure of functional ischemia is needed.

Improved left ventricular function after transplantation of microspheres and fibroblasts in a rat model of myocardial infarction.

As a novel and promising therapeutic strategy for heart failure, the application of different cell types is the subject of increasing research interest. In this study we investigated the effect of several cell types and microspheres (uniform polystyrene microspheres, 10 microm diameter) transplanted 4 weeks after induction of myocardial infarction in a rat model. Eight weeks after intramyocardial application of fibroblasts and microspheres, left ventricular function was significantly improved as demonstrated by isolated heart studies (Langendorff) and echocardiographic findings (LVDP fibroblasts 129 +/- 32.9 mmHg, LVDP microspheres 119.2 +/- 24.1 mmHg, fractional shortening (FS) microspheres 38.9 +/- 4.6%, FS fibroblasts 36.84 +/- 6.05%) in contrast to injection of macrophages or medium alone (LVDP medium 67 +/- 22.6 mmHg, LVDP macrophages 75.9 +/- 24.8 mmHg, FS macrophages 29.16 +/- 8.7%, FS medium 27.2 +/- 7.2%, P < 0.05). Signals of Bromodesoxy-Uridine (BrdU) labeled transplanted fibroblasts were detected in infarcted areas. Microspheres were recorded abundantly by autofluorescence. Significantly more apoptotic cells were observed in infarcted areas of macrophage (328.6 +/- 37.4 cells/mm(2)) and medium (338.7 +/- 16.5 cells/mm(2); P < 0.05) treated hearts compared to microsphere (233.2 +/- 16.8 cells/mm(2)) and fibroblast (232.2 +/- 19.1 cells/mm(2)) injected hearts. Neovascularization, as reflected by the density of CD 31 positive vessels in the infracted area, did not differ between the four groups studied. The increased number of macrophages in infarcted areas after fibroblast and microsphere injection (fibroblasts 94.7 +/- 7.1 cells/mm(2), microspheres 82.2 +/- 3.0 cells/mm(2), macrophages 56.02 +/- 9.93 cells/mm(2), medium 46.35 +/- 9.03 cells/mm(2), P < 0.05) suggests that the underlying mechanism of augmented left ventricular function might be based on inflammatory processes.

Similarity regression predicts evolution of transcription factor sequence specificity.

Transcription factor (TF) binding specificities (motifs) are essential for the analysis of gene regulation. Accurate prediction of TF motifs is critical, because it is infeasible to assay all TFs in all sequenced eukaryotic genomes. There is ongoing controversy regarding the degree of motif diversification among related species that is, in part, because of uncertainty in motif prediction methods. Here we describe similarity regression, a significantly improved method for predicting motifs, which we use to update and expand the Cis-BP database. Similarity regression inherently quantifies TF motif evolution, and shows that previous claims of near-complete conservation of motifs between human and Drosophila are inflated, with nearly half of the motifs in each species absent from the other, largely due to extensive divergence in C2H2 zinc finger proteins. We conclude that diversification in DNA-binding motifs is pervasive, and present a new tool and updated resource to study TF diversity and gene regulation across eukaryotes.

Motif models for RNA-binding proteins.

Identifying the binding preferences of RNA-binding proteins (RBPs) is important in understanding their contribution to post-transcriptional regulation. Here, we review the current state-of-the art of RNA motif identification tools for RBPs. New in vivo and in vitro data sets provide sufficient statistical power to enable detection of relatively long and complex sequence and sequence-structure binding preferences, and recent computational methods are geared towards quantitative identification of these patterns. We classify methods by their motif model's representational power and describe the underlying considerations for RNA-protein interactions. All classical motif identification algorithms apply physically motivated architectures, consisting of a motif and an occupancy model, we call these explicit motif models. Recent methods, such as convolutional neural networks and support vector machines, abandon the classical architecture and implicitly model RNA binding without defining a motif model. Although they achieve high accuracy on held-out data they may be unsuitable to solve the ultimate goal of the field, using motifs trained on in vitro data to predict in vivo binding sites. For this task methods need to separate intrinsic binding preferences from cellular effects from protein and RNA concentrations, cooperativity, and competition. To tackle this problem, we advocate for the use of a `three-layer' architecture, consisting of motif model, occupancy model, and extrinsic factor model, which enables separation and adjustment to cellular conditions.