Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data

We present a novel AI-based approach to the few-shot automated segmentation of mitochondria in large-scale electron microscopy images. Our framework leverages convolutional features from a pre-trained deep multilayer convolutional neural network, such as VGG-16. We then train a binary gradient boosting classifier on the resulting high-dimensional feature hypercolumns. We extract VGG-16 features from the first four convolutional blocks and apply bilinear upsampling to resize the obtained maps to the input image size. This procedure yields a 2688-dimensional feature hypercolumn for each pixel in a 224 x 224 input image. We then apply L1-regularized logistic regression for supervised active feature selection to reduce dependencies among the features, to reduce overfitting, as well as to speed-up gradient boosting-based training. During inference we block process 1728 x 2022 large microscopy images. Our experiments show that in such a formulation of transfer learning our processing pipeline is able to achieve high-accuracy results on very challenging datasets containing a large number of irregularly shaped mitochondria in cardiac and outer hair cells. Our proposed few-shot training approach gives competitive performance with the state-of-the-art using far less training data

Search for gravitational waves associated with the InterPlanetary Network short gamma ray bursts

We outline the scientific motivation behind a search for gravitational waves associated with short gamma ray bursts detected by the InterPlanetary Network (IPN) during LIGO's fifth science run and Virgo's first science run. The IPN localisation of short gamma ray bursts is limited to extended error boxes of different shapes and sizes and a search on these error boxes poses a series of challenges for data analysis. We will discuss these challenges and outline the methods to optimise the search over these error boxes.Comment: Methods paper; Proceedings for Eduardo Amaldi 9 Conference on Gravitational Waves, July 2011, Cardiff, U

Risk of chronic kidney disease after cancer nephrectomy.

The incidence of early stage renal cell carcinoma (RCC) is increasing and observational studies have shown equivalent oncological outcomes of partial versus radical nephrectomy for stage I tumours. Population studies suggest that compared with radical nephrectomy, partial nephrectomy is associated with decreased mortality and a lower rate of postoperative decline in kidney function. However, rates of chronic kidney disease (CKD) in patients who have undergone nephrectomy might be higher than in the general population. The risks of new-onset or accelerated CKD and worsened survival after nephrectomy might be linked, as kidney insufficiency is a risk factor for cardiovascular disease and mortality. Nephron-sparing approaches have, therefore, been proposed as the standard of care for patients with type 1a tumours and as a viable option for those with type 1b tumours. However, prospective data on the incidence of de novo and accelerated CKD after cancer nephrectomy is lacking, and the only randomized trial to date was closed prematurely. Intrinsic abnormalities in non-neoplastic kidney parenchyma and comorbid conditions (including diabetes mellitus and hypertension) might increase the risks of CKD and RCC. More research is needed to better understand the risk of CKD post-nephrectomy, to develop and validate predictive scores for risk-stratification, and to optimize patient management

The on-line determination of underground cable conductor temperatures

The criterion determining the maximum load able to be sustained by an underground cable is its maximum allowable conductor temperature. Above this value, degradation of insulation will commence and lead to ultimate failure of the cable. Methods using a digital computer program are available for calculating cable conductor temperature given the thermal characteristics of the cable and its environment and the loads at whlch the cable will be operated. Such methods invariably assume a 24 hourly load cycle to which the cable is subjected continuously and a maximum ground ambient temperature which conservatively occurs at the time of peak load. The thesis describes the development of an electronic device which can be installed in a substation, reading cable loading and ambient temperature in real time, and calculating in an on-line capacity, the cable conductor temperature. The device overcomes the limitations of the use of assumed variables. It calculates cable operating temperature which is continuously updated as loading and ambient conditions change. The algorithm used relies on a modification of the CIGRE Method (circa 1974) and a long term load test on a buried cable installation has confirmed its accuracy. All storage and calculation functions required are processed by a microcomputer developed specifically for the task using a proprietary line 16-bit processor. Software development was aided by the use of a high level language facilitated by the compatibility of the device processor and computer development systems already possessed by SEQEB. The device can be installed in a normal substation environment (5°c - 35°c ambient) without the need for a controlled atmosphere and will operate from normal 240V mains supply. Ten cable groups each consisting of one or two circuits may be processed from the one device and updated temperatures are calculated at hourlyIn the normal mode, continuous conductor temperature monitoring is provided which is able to accommodate any load or ground ambient temperature change. The SEQEB substation automated control system, a microprocessor based supervisory and control facility, can relay conductor temperature information from the device to remote system operators at VDU terminals via normal telecommunication lines. Alarm initiation is incorporated into software for operator attention in the case of conductor temperature exceeding allowable limits. Furthermore, the device may be used to predict conductor temperature response to a contingency situation known in advance. In the event of a power supply failure to the device and consequent memory loss, a cassette drive backup system has been employed. This system re-loads stored data and program instructions into memory upon power restoration and instructs the microcomputer to recommence operation. It is concluded that although devices of this type are new to the electricity supply industry in Australia, they can provide additional benefits for the planning and operation of a supply system. The added economic benefit to the supply authority, and ultimately the consumer, is evident in the more effective utilisation of the system with deferment of capital expenditure on new circuits while the existing system is operated nearer its full capacity. intervals

Fast synthesis of n-type half-heusler TiNiSn thermoelectric material

The n-type half-Heusler TiNiSn is very promising for thermoelectric applications in the medium temperature range. However, the synthesis of TiNiSn often involves long annealing times (up to several weeks) to obtain a single phase, which is a major barrier to scaling-up. In this work, TiNiSn was synthesized by a combination of arc-melting, ball-milling and spark plasma sintering. The obtained samples with diameters up to 30 mm had high-purity, high-density and fine-grains. Without the need for an annealing step, the total synthesis time was significantly shortened. Addition of Cu was used to optimize the thermoelectric properties of TiNiSn, and a maximum figure of merit of 0.6 was achieved at 773 K. The fast and scalable synthesis of TiNiSn with good thermoelectric performance presented in this work opens up the possibility of industrial scaling-up

Comparison of ERCC1/XPF genetic variation, mRNA and protein levels in women with advanced stage ovarian cancer treated with intraperitoneal platinum.

OBJECTIVE: Approximately 20% of patients receiving platinum-based chemotherapy for epithelial ovarian cancer (EOC) are refractory or develop early recurrence. Identifying these patients early could reduce treatment-associated morbidity and allow quicker transfer to more effective therapies. Much attention has focused on ERCC1 as a potential predictor of response to therapy because of its essential role in the repair of platinum-induced DNA damage. The purpose of this study was to accurately measure protein levels of ERCC1 and its essential binding partner XPF from patients with EOC treated with platinum-based therapy and determine if protein levels correlate with mRNA levels, patient genotypes or clinical outcomes. METHODS: ERCC1 and XPF mRNA and protein levels were measured in frozen EOC specimens from 41 patients receiving intraperitoneal platinum-based chemotherapy using reverse transcription polymerase chain reaction and western blots. Genotypes of common nucleotide polymorphisms were also analyzed. Patient outcomes included progression free (PFS) and overall survival (OS). RESULTS: Expression of ERCC1 and XPF were tightly correlated with one another at both the mRNA and protein level. However, the mRNA and protein levels of ERCC1 were not positively correlated. Likewise, none of the SNPs analyzed correlated with ERCC1 or XPF protein levels. There was an inverse correlation between mRNA levels and patient outcomes. CONCLUSION: Neither genotype nor mRNA levels are predictive of protein expression. Despite this, low ERCC1 mRNA significantly correlated with improved PFS and OS

Identification of an initiator-like element essential for the expression of the tissue inhibitor of metalloproteinases-4 (Timp-4) gene

We have used real-time quantitative reverse transcriptase PCR (TaqMan) to quantify the expression of the four tissue inhibitor of metalloproteinases (Timp) genes in mouse tissues during development and in the adult. Among the four Timp genes, Timp-4 shows the most restricted pattern of expression, with highest RNA levels in brain, heart and testes. These data indicate that in the brain, Timp-4 transcripts are temporally regulated during development, becoming more abundant than those of the other Timps after birth. Cloning of the Timp-4 gene confirmed a five-exon organization resembling that of Timp-2 and Timp-3, and like all Timps, Timp-4 is located within an intron of a synapsin gene. Ribonuclease protection analysis and 5'-rapid amplification of cDNA ends PCR identified multiple transcription starts for Timp-4 from brain and heart mRNA. The promoter region of Timp-4 was functional in transient transfection analysis in mouse C3H10T1/2 fibroblasts, where it directed basal expression that was non-inducible by serum. The TATA-less promoter contains consensus motifs for Sp1 and an inverted CCAAT box upstream of an initiator-like element that is in close proximity to a transcription start site. Mutation of the CCAAT box caused a 2-fold increase in reporter expression. More significantly, mutation of the Sp1 motif or initiator-like element almost completely abolished reporter expression. This first functional characterization of the Timp-4 promoter shows it to be distinct from other members of the Timp family and provides insights into potential mechanisms controlling the tight spatio-temporal expression pattern of the gene

Rapid Exclusion of Acute Myocardial Infarction in Patients With Undetectable Troponin Using a High-Sensitivity Assay

ObjectivesThis paper sought to evaluate whether high sensitivity troponin (hs-cTnT) can immediately exclude acute myocardial infarction (AMI) at a novel ‘rule out' cut-off.BackgroundSubgroup analysis of recent evidence suggests that undetectable hs-cTnT may exclude AMI at presentation.MethodsIn a cohort study, we prospectively enrolled patients with chest pain, evaluating them with standard troponin T and testing for hs-cTnT (Roche Diagnostics, Basel, Switzerland) at presentation. The primary outcome was a diagnosis of AMI. We also followed up patients for adverse events within 6 months. After subsequent clinical implementation of hs-cTnT, we again evaluated whether initially undetectable hs-cTnT ruled out a subsequent rise.ResultsOf 703 patients in the cohort study, 130 (18.5%) had AMI, none of whom initially had undetectable hs-cTnT (sensitivity: 100.0%, 95% confidence interval [CI]: 95.1% to 100.0%, negative predictive value: 100.0%, 95% CI: 98.1% to 100.0%). This strategy would rule out AMI in 27.7% of patients, 2 (1.0%) of whom died or had AMI within 6 months (1 periprocedural AMI, 1 noncardiac death). We evaluated this approach in an additional 915 patients in clinical practice. Only 1 patient (0.6%) with initially undetectable hs-cTnT had subsequent elevation (to 17 ng/l), giving a sensitivity of 99.8% (95% CI: 99.1% to 100.0%) and a negative predictive value of 99.4% (95% CI: 96.6% to 100.0%).ConclusionsUndetectable hs-cTnT at presentation has very high negative predictive value, which may be considered to rule out AMI, identifying patients at low risk of adverse events. Pending further validation, this strategy may reduce the need for serial testing and empirical treatment, enabling earlier reassurance for patients and fewer unnecessary evaluations and hospital admissions