Integrating Active Learning and Transfer Learning for Carotid Intima-Media Thickness Video Interpretation.

Cardiovascular disease (CVD) is the number one killer in the USA, yet it is largely preventable (World Health Organization 2011). To prevent CVD, carotid intima-media thickness (CIMT) imaging, a noninvasive ultrasonography method, has proven to be clinically valuable in identifying at-risk persons before adverse events. Researchers are developing systems to automate CIMT video interpretation based on deep learning, but such efforts are impeded by the lack of large annotated CIMT video datasets. CIMT video annotation is not only tedious, laborious, and time consuming, but also demanding of costly, specialty-oriented knowledge and skills, which are not easily accessible. To dramatically reduce the cost of CIMT video annotation, this paper makes three main contributions. Our first contribution is a new concept, called Annotation Unit (AU), which simplifies the entire CIMT video annotation process down to six simple mouse clicks. Our second contribution is a new algorithm, called AFT (active fine-tuning), which naturally integrates active learning and transfer learning (fine-tuning) into a single framework. AFT starts directly with a pre-trained convolutional neural network (CNN), focuses on selecting the most informative and representative AU s from the unannotated pool for annotation, and then fine-tunes the CNN by incorporating newly annotated AU s in each iteration to enhance the CNN's performance gradually. Our third contribution is a systematic evaluation, which shows that, in comparison with the state-of-the-art method (Tajbakhsh et al., IEEE Trans Med Imaging 35(5):1299-1312, 2016), our method can cut the annotation cost by >81% relative to their training from scratch and >50% relative to their random selection. This performance is attributed to the several advantages derived from the advanced active, continuous learning capability of our AFT method.

A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency.

BACKGROUND: Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. RESULTS: Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. CONCLUSIONS: Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.

Hyperacute Vasospasm After Aneurysmal Subarachnoid Hemorrhage.

BACKGROUND: Cerebral vasospasm after aneurysmal subarachnoid hemorrhage typically occurs 3-14 days after aneurysm rupture. We describe a series of patients who developed vasospasm within minutes of aneurysm rupture. This phenomenon, which we term, "hyperacute vasospasm," has been reported in animal models of SAH, but hitherto has been poorly described in humans. METHODS: Eleven patients were identified from an institutional registry who had aneurysmal rupture during catheter cerebral angiography between 1997 and 2009. We quantified the degree of vasoconstriction using vascular diameter index (VDI). The change in VDI (delta VDI or DVDI) was calculated by determining the difference in VDI before and after the procedure. We also examined the relationship between hyperacute vasospasm and delayed cerebral ischemia. RESULTS: Ten of eleven (91%) patients with intraoperative aneurysm rupture had cerebral vasoconstriction within minutes of intra-procedural aneurysmal rupture. Six of eleven patients (55%) with hyperacute vasospasm developed delayed cerebral infarction. CONCLUSIONS: Hyperacute vasospasm is likely common in patients with intraoperative aneurysm rupture and may be an unrecognized element of the natural history of aneurysmal subarachnoid hemorrhage. In this limited series, there was an association between hyperacute vasospasm and delayed cerebral infarction.

The retinoic acid-producing capacity of gut dendritic cells and macrophages is reduced during persistent T. muris infection.

Trichuris muris is an intestinal nematode that invades the colonic epithelium triggering a mucosal inflammation. Vitamin A and its active metabolite retinoic acid are strongly linked with the modulation of gut immune responses. Here, we describe the temporal changes in the expression of aldehyde dehydrogenase (ALDH) enzymes, responsible for converting dietary-absorbed vitamin A into the immuno-modulatory retinoic acid in lamina propria leucocytes post-infection. We show that ALDH enzymes are expressed by both colonic macrophages and dendritic cells. Further, during an on-going T. muris infection, ALDH expression is repressed from uninfected levels and only recovers to normal levels following expulsion of the parasite. These results suggest that local regulation of cellular levels of retinoic acid is an important component of infection-driven inflammation.

Retinoic acid signalling in gastrointestinal parasite infections: lessons from mouse models.

Retinoic acid or vitamin A is important for an extensive range of biological processes, including immunomodulatory functions, however, its role in gastrointestinal parasite infections is not yet clear. Despite this, parasite infected individuals are often supplemented with vitamin A, given the co-localised prevalence of parasitic infections and vitamin deficiencies. Therefore, it is important to understand the impact of this vitamin on the immune responses to gastrointestinal parasites. Here, we review data regarding the role of retinoic acid signalling in mouse models of intestinal nematode infection, with a view to understanding better the practice of giving vitamin A supplements to worm-infected people.

Cardiopulmonary exercise testing predicts postoperative outcome in patients undergoing gastric bypass surgery.

BACKGROUND: For several types of non-cardiac surgery, the cardiopulmonary exercise testing (CPET)-derived variables anaerobic threshold (AT), peak oxygen consumption (VO2 peak), and ventilatory equivalent for CO(2) (VE/VCO2 ) are predictive of increased postoperative risk: less physically fit patients having a greater risk of adverse outcome. We investigated this relationship in patients undergoing gastric bypass surgery. METHODS: All patients (<190 kg) who were referred for CPET and underwent elective gastric bypass surgery at the Whittington Hospital NHS Trust between September 1, 2009, and February 25, 2011, were included in the study (n=121). Fifteen patients did not complete CPET. CPET variables (VO2 peak, AT, and VE/VCO2 ) were derived for 106 patients. The primary outcome variables were day 5 morbidity and hospital length of stay (LOS). The independent t-test and Fisher's exact test were used to test for differences between surgical outcome groups. The predictive capacity of CPET markers was determined using receiver operating characteristic (ROC) curves. RESULTS: The AT was lower in patients with postoperative complications than in those without [9.9 (1.5) vs 11.1 (1.7) ml kg(-1) min(-1), P=0.049] and in patients with a LOS>3 days compared with LOS ≤ 3 days [10.4 (1.4) vs 11.3 (1.8) ml kg(-1) min(-1), P=0.023]. ROC curve analysis identified AT as a significant predictor of LOS>3 days (AUC 0.640, P=0.030). The VO2 peak and VE/VCO2 were not associated with postoperative outcome. CONCLUSIONS: AT, determined using CPET, predicts LOS after gastric bypass surgery.

Carotid intima-media thickness measurements are not affected by the ultrasound frequency.

OBJECTIVE: Carotid intima-media thickness (IMT) is a B-mode ultrasound measure of subclinical atherosclerosis predictive of future cardiovascular risk. Carotid IMT measurements were historically obtained at an ultrasound frequency of 8 MHz or lower, but it is unknown whether measurements obtained at higher frequencies using newer, more advanced ultrasound technology allow for valid comparison to the older general population databases that are commonly used for the interpretation of carotid IMT results. METHODS: Carotid IMT studies were conducted in 35 consecutive patients at standard (8 MHz) and high (14 MHz) frequencies and measurements were performed by two independent expert readers. Systematic bias was assessed by using the paired t-test and agreement was analyzed with the Bland-Altman method. RESULTS: The sample mean carotid IMT obtained at 14 MHz was 0.006 mm lower than that obtained at 8 MHz. The 95% confidence interval (CI) for the mean difference between frequencies indicated that the population mean for 14 MHz is unlikely to be more than 0.02 mm lower than for 8 MHz (95% CI -0.017 to 0.004). The 95% reference range for the difference between the two transducer frequencies indicated that the thickness obtained at 14 MHz was within 0.05 mm of that obtained at 8 MHz for 95% of subjects. CONCLUSIONS: Carotid IMT measurements obtained at higher transducer frequencies are similar to those obtained at standard frequency. This finding has important clinical implications because it validates comparison of carotid IMT measurements obtained with newer, more advanced ultrasound technology with the landmark reference carotid IMT studies commonly used for interpretation of carotid IMT results.

How to detect the Chandler and the annual wobble of the Earth with a large ring laser gyroscope.

We demonstrate a 16 m(2) helium-neon ring laser gyroscope with sufficient sensitivity and stability to directly detect the Chandler wobble of the rotating Earth. The successful detection of both the Chandler and the annual wobble is verified by comparing the time series of the ring laser measurements against the "C04 series" of Earth rotation data from the International Earth Rotation and Reference System Service.

Selenium concentration and speciation in biofortified flour and bread: Retention of selenium during grain biofortification, processing and production of Se-enriched food.

The retention and speciation of selenium in flour and bread was determined following experimental applications of selenium fertilisers to a high-yielding UK wheat crop. Flour and bread were produced using standard commercial practices. Total selenium was measured using inductively coupled plasma-mass spectrometry (ICP-MS) and the profile of selenium species in the flour and bread were determined using high performance liquid chromatography (HPLC) ICP-MS. The selenium concentration of flour ranged from 30ng/g in white flour and 35ng/g in wholemeal flour from untreated plots up to >1800ng/g in white and >2200ng/g in wholemeal flour processed from grain treated with selenium (as selenate) at the highest application rate of 100g/ha. The relationship between the amount of selenium applied to the crop and the amount of selenium in flour and bread was approximately linear, indicating minimal loss of Se during grain processing and bread production. On average, application of selenium at 10g/ha increased total selenium in white and wholemeal bread by 155 and 185ng/g, respectively, equivalent to 6.4 and 7.1µg selenium per average slice of white and wholemeal bread, respectively. Selenomethionine accounted for 65-87% of total extractable selenium species in Se-enriched flour and bread; selenocysteine, Se-methylselenocysteine selenite and selenate were also detected. Controlled agronomic biofortification of wheat crops for flour and bread production could provide an appropriate strategy to increase the intake of bioavailable selenium.

The effect of New Zealand blackcurrant on sport performance and related biomarkers: a systematic review and meta-analysis.

BACKGROUND: Blackcurrants have come to be regarded as a superfood because of their high polyphenol content, namely anthocyanins. While many berry types have been studied, blackcurrant-anthocyanins may be the superior berry when it comes to athletic performance. The purpose of the review was to evaluate the effects of blackcurrant supplementation on athletic performance, oxidative markers, cognition, and side effects. METHODS: Systematic review and meta-analysis. Review manager software (version 5.3) was used for the meta-analysis. The risks of bias was independently assessed using the guidelines and criteria outlined in the Cochrane Handbook for Systematic Reviews of Interventions. The data sources for the search included MEDLINE (Ovid), Google Scholar databases, additional references lists, conference proceedings and grey literature until August 2019. Eligibility Criteria included all blackcurrant (New Zealand derived) interventions, randomised control trials, human participants, placebo-controlled only. RESULTS: A total of 16 separate studies met the criteria for inclusion in the systematic review, with 9 studies contributing to this sport performance meta-analysis. There was an improvement in sport performance when supplementing with blackcurrant, 0.45 (95% CI 0.09-0.81, p = 0.01). The effective dose appears to be between 105 and 210 mg of total blackcurrant anthocyanins, prior to exercise. There were insufficient studies reporting oxidative markers, cognitive effects or biomarkers, and/or side effects to comment on the mechanism of action. CONCLUSION: Blackcurrant has a small, but significant, effect on sport performance, with no known detrimental side effects.

Short-term blackcurrant extract consumption modulates exercise-induced oxidative stress and lipopolysaccharide-stimulated inflammatory responses.

Exercise-induced oxidative stress is instrumental in achieving the health benefits from regular exercise. Therefore, inappropriate use of fruit-derived products (commonly applied as prophalytic antioxidants) may counteract the positive effects of exercise. Using human exercise and cellular models we found that 1) blackcurrant supplementation suppressed exercise-induced oxidative stress, e.g., plasma carbonyls (0.9 +/- 0.1 vs. 0.6 +/- 0.1 nmol/mg protein, placebo vs. blackcurrant), and 2) preincubation of THP-1 cells with an anthocyanin-rich blackcurrant extract inhibited LPS-stimulated cytokine secretion [TNF-alpha (16,453 +/- 322 vs. 10,941 +/- 82 pg/ml, control vs. extract, P < 0.05) and IL-6 (476 +/- 14 vs. 326 +/- 32 pg/ml, control vs. extract, P < 0.05)] and NF-kappaB activation. In addition to its antioxidant and anti-inflammatory properties, we found that postexercise plasma collected after blackcurrant supplementation enhanced the differential temporal LPS-stimulated inflammatory response in THP-1 cells, resulting in an early suppression of TNF-alpha (1,741 +/- 32 vs. 1,312 +/- 42 pg/ml, placebo vs. blackcurrant, P < 0.05) and IL-6 (44 +/- 5 vs. 36 +/- 3 pg/ml, placebo vs. blackcurrant, P < 0.05) secretion after 24 h. Furthermore, by using an oxidative stress cell model, we found that preincubation of THP-1 cells with hydrogen peroxide (H(2)O(2)) prior to extract exposure caused a greater suppression of LPS-stimulated cytokine secretion after 24 h, which was not evident when cells were simultaneously incubated with H(2)O(2) and the extract. In summary, our findings support the concept that consumption of blackcurrant anthocyanins alleviate oxidative stress, and may, if given at the appropriate amount and time, complement the ability of exercise to enhance immune responsiveness to potential pathogens.

Group B erythrocytes enzymatically converted to group O survive normally in A, B, and O individuals.

With an alpha-galactosidase, B erythrocytes can be converted to blood group O under conditions that neither impair their viability in vitro nor affect their ability to survive normally after transfusion to individuals of groups O, A, and B. Such an approach has the potential for producing enzymatically converted group O cells for use in transfusion therapy. It should also be possible to convert A cells to group O by using the appropriate alpha-N-acetylgalactosaminidase.

Fly ash-derived strontium as an index to monitor deposition from coal-fired power plants.

The combustion of western U.S. coals releases significant amounts of strontium, which is relatively enriched in the fine particles of fly ash. Fly ash-derived strontium is readily absorbed by agronomic and native plant species when incorporated in soil. The strontium-87 to strontium-86 ratios of fly ash and soils were significantly different, but similar ratios were found in fly ash and plants treated with fly ash. A technique for measuring and monitoring deposition from coal-fired power plants is inferred from the enhanced plant uptake of fly ash strontium and the similarity in the isotopic ratios of fly ash and treated plants.

Exercise-induced elevation in plasma oxidative generating capability augments the temporal inflammatory response stimulated by lipopolysaccharide.

Prolonged oxidative stress is detrimental to health; however, transient oxidative stress may improve immune capability. We examined whether exercise-induced increases in the plasma oxidative generating capability enhance immune responsiveness to potential pathogens. Twelve individuals underwent a 30-min row and pre and post-exercise bloods were collected for oxidative stress and immune assessment. We found that exercise induced a transient increase in plasma carbonyls (3.2-5.3 nmol/mg protein) and creatine kinase activity (0.5-1.2 absorbance/min/mg protein) and that lipopolysaccharide (LPS) stimulation (0.5-24 h) of pre- and post-exercise blood augmented temporal tumour necrosis factor-alpha (TNFalpha) secretion. Further characterisation of plasma using a modified dihydro-2',7'-dichlorohydrofluorescein (DCF) assay revealed that addition of a sub-threshold of hydrogen peroxide to post-exercise (and not pre-exercise) plasma caused a sixfold increase in the radical oxygen species (ROS) generating capability after 15 min (555 +/- 131 to 3607 +/- 488 change in fluorescent intensity [DeltaFI]), which was inhibited using 60 mM N-acetyl-L: -cysteine (920 +/- 154 DeltaFI). Furthermore, cell experiments revealed that LPS stimulation of either THP-1 cells pre-incubated with post-exercise plasma or peripheral blood mononuclear cells pre-treated with pro-oxidants, modulated the temporal secretion of key cytokines that regulate the initiation, progression and resolution of an inflammatory response. These results indicate that exercise-induced changes in plasma parameters (e.g. oxidative generating capability-dependent or independent of inflammatory mediators) augment the temporal LPS response and support the notion that repeated transient oxidative stress (such as that induced by regular exercise) is important for a "healthy" immune system.

Caveolin1 interacts with the glucocorticoid receptor in the lung but is dispensable for its anti-inflammatory actions in lung inflammation and Trichuris Muris infection.

Glucocorticoids (Gcs) are widely prescribed anti-inflammatory compounds, which act through the glucocorticoid receptor (GR). Using an unbiased proteomics screen in lung tissue, we identified the membrane protein caveolin -1 (Cav1) as a direct interaction partner of the GR. In Cav1 knockout mice GR transactivates anti-inflammatory genes, including Dusp1, more than in controls. We therefore determined the role of Cav1 in modulating Gc action in two models of pulmonary inflammation. We first tested innate responses in lung. Loss of Cav1 impaired the inflammatory response to nebulized LPS, increasing cytokine/chemokine secretion from lung, but impairing neutrophil infiltration. Despite these changes to the inflammatory response, there was no Cav1 effect on anti-inflammatory capacity of Gcs. We also tested GR/Cav1 crosstalk in a model of allergic airway inflammation. Cav1 had a very mild effect on the inflammatory response, but no effect on the Gc response - with comparable immune cell infiltrate (macrophage, eosinophils, neutrophils), pathological score and PAS positive cells observed between both genotypes. Pursuing the Th2 adaptive immune response further we demonstrate that Cav1 knockout mice retained their ability to expel the intestinal nematode parasite T.muris, which requires adaptive Th2 immune response for elimination. Therefore, Cav1 regulates innate immune responses in the lung, but does not have an effect on Th2-mediated adaptive immunity in lung or gut. Although we demonstrate that Cav1 regulates GR transactivation of anti-inflammatory genes, this does not translate to an effect on suppression of inflammation in vivo.

Multiple subunits of a voltage-dependent potassium channel contribute to the binding site for tetraethylammonium.

RNAs encoding a wild-type (RBK1) and a mutant (RBK1(Y379V,V381T); RBK1*) subunit of voltage-dependent potassium channels were injected into Xenopus oocytes. When expressed separately, they made homotetrameric channels that differed about 100-fold in sensitivity to tetraethylammonium (TEA). Mixtures of channels having one, two, or three low affinity subunits were expressed by injecting various proportions of RBK1 and RBK1* RNAs. The affinity for TEA of these three channel species was deduced by fitting concentration-response curves for the inhibition of potassium currents. DNAs were also concatenated to construct a sequence that encoded two connected subunits, and channels that contained four, two, or no TEA-sensitive subunits were expressed. The results suggest that bound TEA interacts simultaneously with all four subunits.

Preoperative dobutamine stress echocardiographic findings and subsequent short-term adverse cardiac events after orthotopic liver transplantation.

Cardiovascular (CV) complications are the leading cause of non-graft-related death in orthotopic liver transplant (OLT) patients. Pretransplant cardiac evaluation using dobutamine stress echocardiography (DSE) is commonly utilized for risk stratification of OLT candidates. To determine if clinical and echocardiographic variables identify patients with increased CV risk, we performed a retrospective chart review of all 284 patients that underwent OLT at our institution between June 1999 and August 2005. Of these patients, 157 had a DSE prior to their OLT. Serious adverse CV events occurring during surgery and up to 4 months post-transplantation were defined as cardiac-related death, myocardial infarction (MI), new heart failure, or asystole or unstable ventricular arrhythmia requiring acute treatment. Sixteen of 157 patients (10%) had an adverse CV event with 2 deaths. These included ventricular tachycardia (n = 8), asystole (n = 2), MI (n = 5), and new heart failure (n = 1). Nine of the 16 CV events occurred at the time of surgery (including both deaths), 5 occurred postoperatively, and 3 occurred after hospital discharge. Variables that correlated with increased CV events were inability during DSE to achieve >82% of the maximum predicted heart rate (22% versus 6%, P = 0.01), a peak rate pressure product during DSE of <16,333 (17% versus 5%, P = 0.02), and a Model for End-Stage Liver Disease (MELD) score of >24 at the time of OLT. A multivariate model calculated from the DSE maximum achieved heart rate (MAHR) and MELD score (result = 3.78 + 0.07 MELD - 0.05 MAHR) identified a 47% risk for a value > 0 versus a 6% risk for a value < 0 (P < 0.001). In conclusion, the maximum heart rate achieved during DSE together with the MELD score may be a predictor of adverse CV events up to 4 months post-OLT. A large prospective study is needed to more decisively support this conclusion.

Three methods for evaluation of left atrial volume.

AIM: To compare and contrast 3 different echocardiographic methods used to measure left atrial (LA) volume: biplane area length (AL), biplane modified Simpson (SIMP), and prolate ellipse (PE) methods. METHODS AND RESULTS: A review of consecutive patients who presented to our outpatient echocardiography laboratory for a resting transthoracic study between April 2006 and May 2006 was performed. Echocardiograms were reexamined and LA volume measured using the AL, SIMP, and PE methods. Of 102 consecutive patients evaluated, 97 had a measure of LA volume using all 3 methods. A significant difference in the measurement of mean +/- SD LA volume was noted among the 3 different methods: 37 +/- 16 mL/m(2) for AL, 34 +/- 14 mL/m(2) for SIMP, and 27 +/- 12 mL/m(2) for PE. The PE method yielded routinely smaller values compared with either the AL or SIMP method (P < 0.001). Differences increased with increased LA volume. The SIMP method derived consistently smaller (<5 mL/m(2)) values than those of the AL method, consistent across the full range of LA volumes. CONCLUSION: Significant differences exist among these 3 commonly used methods for measuring LA volume. Standardization of the measurement of LA volume is recommended.

Transcriptome profiling of bovine ovarian theca cells treated with fibroblast growth factor 9.

We reported previously that fibroblast growth factor 9 (FGF9) acts as an antidifferentiation factor, stimulating proliferation of granulosa cells (GCs) and theca cells (TCs) while suppressing hormone-induced steroidogenesis of these cells. How FGF9 acts to simultaneously suppress steroidogenesis and stimulate proliferation remains to be fully elucidated. Thus, this study was undertaken to clarify the effects of FGF9 on the TC transcriptome. Ovaries were obtained from beef heifers at a local abattoir, TCs were isolated from large antral follicles, and cultured with or without 30 ng/mL of FGF9 for 24 h in the presence of LH and IGF-1. After treatment, total RNA was extracted from TC and processed for microarray using Affymetrix GeneChip Bovine Genome Arrays (n = 4/group). Transcriptome analysis comparing FGF9-treated TC with control TC using 1.3-fold cutoff, and a P < 0.05 significance level identified 355 differentially expressed transcripts, with 164 elements upregulated and 191 elements downregulated by FGF9. The ingenuity pathway analysis (IPA) was used to investigate how FGF9 treatment affects molecular pathways, biological functions, and the connection between molecules in bovine TC. The IPA software identified 346 pathways in response to FGF9 in TC involved in several biological functions and unveiled interesting relationships among genes related to cell proliferation (eg, CCND1, FZD5, and MYB), antioxidation/cytoprotection (eg, HMOX1 and NQO1), and steroidogenesis (eg, CYP11A1 and STAR). Overall, genes, pathways, and networks identified in this study painted a picture of how FGF9 may regulate folliculogenesis, providing novel candidate genes for further investigation of FGF9 functions in ovarian follicular development.

Endovascular treatment for acute basilar thrombosis via a transradial approach: Initial experience and future considerations.

Acute basilar artery occlusion (BAO) secondary to emergent large vessel occlusion (ELVO) has an extremely poor natural history, with a reported mortality rate up to 95%. Mechanical thrombectomy in the setting of ELVO is generally performed via a transfemoral approach. However, radial access is increasingly being utilized as an alternative. We report our initial multi-institutional experience using primary radial access in the treatment of acute BAO in nine consecutive cases. Technical success defined as a TICI score of 2B or 3 was achieved in 89% of cases. Average puncture to revascularization time was 35.8 minutes. There were no complications related to radial artery catheterization. We contend radial access should potentially be considered as the first-line approach given inherent advantages over femoral access for mechanical thrombectomy for BAO.