Articulated Multi-Instrument 2D Pose Estimation Using Fully Convolutional Networks

Instrument detection, pose estimation and tracking in surgical videos is an important vision component for computer assisted interventions. While significant advances have been made in recent years, articulation detection is still a major challenge. In this paper, we propose a deep neural network for articulated multi-instrument 2D pose estimation, which is trained on a detailed annotations of endoscopic and microscopic datasets. Our model is formed by a fully convolutional detection-regression network. Joints and associations between joint pairs in our instrument model are located by the detection subnetwork and are subsequently refined through a regression subnetwork. Based on the output from the model, the poses of the instruments are inferred using maximum bipartite graph matching. Our estimation framework is powered by deep learning techniques without any direct kinematic information from a robot. Our framework is tested on single-instrument RMIT data, and also on multi-instrument EndoVis and in vivo data with promising results. In addition, the dataset annotations are publicly released along with our code and model

Reconstructing Words from Right-Bounded-Block Words

A reconstruction problem of words from scattered factors asks for the minimal information, like multisets of scattered factors of a given length or the number of occurrences of scattered factors from a given set, necessary to uniquely determine a word. We show that a word $w \in \{a, b\}^{*}$ can be reconstructed from the number of occurrences of at most $\min(|w|_a, |w|_b)+ 1$ scattered factors of the form $a^{i} b$. Moreover, we generalize the result to alphabets of the form $\{1,\ldots,q\}$ by showing that at most $\sum^{q-1}_{i=1} |w|_i (q-i+1)$ scattered factors suffices to reconstruct $w$. Both results improve on the upper bounds known so far. Complexity time bounds on reconstruction algorithms are also considered here

Decline in Clostridium difficile-associated disease rates in Singapore public hospitals, 2006 to 2008

<p>Abstract</p> <p>Background</p> <p><it>Clostridium difficile </it>is the major cause of pseudomembranous colitis associated with antibiotic use, and the spread of the hypervirulent epidemic ribotype 027/NAP-1 strain across hospitals worldwide has re-focused attention on this nosocomial pathogen. The overall incidence and trend of <it>C. difficile</it>-associated disease (CDAD) in Singapore is unknown, and a surveillance program to determine these via formal laboratory-based reporting was established.</p> <p>Findings</p> <p>Laboratory and pharmacy data were collated from one tertiary and two secondary hospitals on a quarterly basis between 2006 and 2008. All hospitals tested for <it>C. difficile </it>using Immunocard Toxins A&B (Meridian Bioscience Inc., Cincinnati, OH) during this period. Duplicate positive <it>C. difficile </it>results within a 14-day period were removed. The CDAD results were compared with trends in hospital-based prescription of major classes of antibiotics.</p> <p>Overall CDAD incidence-density decreased from 5.16 (95%CI: 4.73 - 5.62) cases per 10,000 inpatient-days in 2006 to 2.99 (95%CI: 2.67 to 3.33) cases per 10,000 inpatient-days in 2008 (<it>p </it>< 0.001), while overall rates for <it>C. difficile </it>testing increased significantly (<it>p </it>< 0.001) within the same period. These trends were mirrored at the individual hospital level. Evaluation of antibiotic prescription data at all hospitals showed increasing use of carbapenems and fluoroquinolones, while cephalosporin and clindamycin prescription remained stable.</p> <p>Conclusions</p> <p>Our results demonstrate a real decline of CDAD rates in three large local hospitals. The cause is unclear and is not associated with improved infection control measures or reduction in antibiotic prescription. Lack of <it>C. difficile </it>stool cultures as part of routine testing precluded determination of the decline of a major clone as a potential explanation. For more accurate epidemiological trending of CDAD and early detection of epidemic clones, data collection will have to be expanded and resources set in place for reference laboratory culture and typing.</p

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution

It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing

Impact of optical coherence tomography on diagnostic decision-making by UK community optometrists: a clinical vignette study.

PURPOSE: In recent years, there has been widespread investment in imaging technologies by community optometrists in the UK, most notably optical coherence tomography (OCT). The aim of the current study was to determine the value of OCT in the diagnosis of posterior segment diseases in a representative sample of community optometrists using a clinical vignette methodology. METHODS: A group of community optometrists (n = 50) initially completed a standardised training package on OCT interpretation followed by a computer-based assessment featuring 52 clinical vignettes, containing images of healthy (n = 8) or glaucomatous (n = 18) discs or healthy (n = 8) or diseased (n = 18) fundi. Each vignette featured either a single fundus/disc photographic image, or a combination of a fundus/disc image with the corresponding OCT scan. An expert panel confirmed that the fundus images presented alone and those in combination with OCT data were of a similar level of difficulty and that the cases were typical of those seen in primary care. For each case, the optometrist selected their diagnosis from a pull-down list and reported their confidence in their decision using a 10-point Likert scale. Pairwise comparisons of the fundus image alone and fundus image/OCT combination were made for both diagnostic performance and confidence. RESULTS: The mean percentage of correct diagnoses using fundus imaging alone was 62% (95% CI 59-64%) and for the combination of fundus image/OCT was 80% (95% CI 77-82%). The mean false negative rate with fundus alone was 27% reducing to 13% with the OCT combination. Median confidence scores for fundus imaging alone was 8.0 (IQR 7.0-8.0) and 8.3 (IQR 8.0-9.0) for the combination. Improvements in performance and confidence were statistically significant (p < 0.001). CONCLUSION: The results from this vignette study suggests that OCT improves optometrists' diagnostic performance compared to fundus observation alone. These initial results suggest that OCT provides valuable additional data that could augment case-finding for glaucoma and retinal disease; however, further research is needed to assess its diagnostic performance in a routine clinical practice setting

Allele frequencies of hemojuvelin gene (HJV) I222N and G320V missense mutations in white and African American subjects from the general Alabama population

BACKGROUND: Homozygosity or compound heterozygosity for coding region mutations of the hemojuvelin gene (HJV) in whites is a cause of early age-of-onset iron overload (juvenile hemochromatosis), and of hemochromatosis phenotypes in some young or middle-aged adults. HJV coding region mutations have also been identified recently in African American primary iron overload and control subjects. Primary iron overload unexplained by typical hemochromatosis-associated HFE genotypes is common in white and black adults in Alabama, and HJV I222N and G320V were detected in a white Alabama juvenile hemochromatosis index patient. Thus, we estimated the frequency of the HJV missense mutations I222N and G320V in adult whites and African Americans from Alabama general population convenience samples. METHODS: We evaluated the genomic DNA of 241 Alabama white and 124 African American adults who reported no history of hemochromatosis or iron overload to detect HJV missense mutations I222N and G320V using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Analysis for HJV I222N was performed in 240 whites and 124 African Americans. Analysis for HJV G320V was performed in 241 whites and 118 African Americans. RESULTS: One of 240 white control subjects was heterozygous for HJV I222N; she was also heterozygous for HFE C282Y, but had normal serum iron measures and bone marrow iron stores. HJV I222N was not detected in 124 African American subjects. HJV G320V was not detected in 241 white or 118 African American subjects. CONCLUSIONS: HJV I222N and G320V are probably uncommon causes or modifiers of primary iron overload in adult whites and African Americans in Alabama. Double heterozygosity for HJV I222N and HFE C282Y may not promote increased iron absorption

Entomological Surveillance of Behavioural Resilience and Resistance in Residual Malaria Vector Populations.

The most potent malaria vectors rely heavily upon human blood so they are vulnerable to attack with insecticide-treated nets (ITNs) and indoor residual spraying (IRS) within houses. Mosquito taxa that can avoid feeding or resting indoors, or by obtaining blood from animals, mediate a growing proportion of the dwindling transmission that persists as ITNs and IRS are scaled up. Increasing frequency of behavioural evasion traits within persisting residual vector systems usually reflect the successful suppression of the most potent and vulnerable vector taxa by IRS or ITNs, rather than their failure. Many of the commonly observed changes in mosquito behavioural patterns following intervention scale-up may well be explained by modified taxonomic composition and expression of phenotypically plastic behavioural preferences, rather than altered innate preferences of individuals or populations. Detailed review of the contemporary evidence base does not yet provide any clear-cut example of true behavioural resistance and is, therefore, consistent with the hypothesis presented. Caution should be exercised before over-interpreting most existing reports of increased frequency of behavioural traits which enable mosquitoes to evade fatal contact with insecticides: this may simply be the result of suppressing the most behaviourally vulnerable of the vector taxa that constituted the original transmission system. Mosquito taxa which have always exhibited such evasive traits may be more accurately described as behaviourally resilient, rather than resistant. Ongoing national or regional entomological monitoring surveys of physiological susceptibility to insecticides should be supplemented with biologically and epidemiologically meaningfully estimates of malaria vector population dynamics and the behavioural phenotypes that determine intervention impact, in order to design, select, evaluate and optimize the implementation of vector control measures

Insights into udder health and intramammary antibiotic usage on Irish dairy farms during 2003-2010

By international standards, Ireland is a relatively small dairy producer. However, the industry plays a critical role to the national economy, accounting for approximately 3% of national gross domestic product. This paper presents insights into udder health and intramammary antibiotic usage on Irish dairy farms during 2003-2010, based on data from several sources. Three data sources were used, including data on milk recording data, intramammary antibiotic sales and animal health assessment. The milk recording data included a single unadjusted herd-level somatic cell count (SCC) value for each herd at each milk recording, being the arithmetic mean of cow-level SCC of each cow at that recording, weighted by cow-level yield. These data were used to calculate the percentage of herds each month where the unadjusted herd SCC exceeded 200,000 and 400,000 cells/mL. Two logistic generalised estimating-equations (GEE) models were developed, the outcome variable being either the probability that the monthly SCC of a herd was greater than 400,000 cells/mL or less than or equal to 200,000 cells/mL. Spring herds had a lower probability of a high SCC (> 400,000 cells/mL) during February to October compared to non-Spring herds but a higher probability between November to January. The odds of a high SCC were greater in 2005, 2006, 2009 and 2010 but less in 2007 and 2008 compared to 2004. Smaller herds had higher odds of having a high SCC compared to larger herds. We present the number of intramammary tubes and the quantity of active substance (kg) sold annually in Ireland during 2003-2010. We infer an incidence of clinical mastitis of 54.0 cases per 100 cow-years at risk, assuming 4 tubes per treatment regime, one affected quarter per cow, tubes restricted to clinical cases only and 100% of treated cases considered new cases, based on data collected on sales of in-lactation intra-mammary antibiotics. With differing assumptions, this estimate varied between 25.8 and 77.0 cases per 100 cow-years at risk. Using data on sales of dry cow therapy intra-mammary antibiotics, we also infer that most Irish dairy farmers use blanket dry cow therapy. It is important that Ireland has an objective understanding of current levels of udder health, to facilitate benchmarking and improvement into the future. Udder health is a concern on a number of Irish dairy farms. High SCC results were present throughout the year, but more marked towards the start and end of each milking season. Animal Health Ireland recently commenced a major national programme, CellCheck, in collaboration with a broad range of stakeholders, to support national SCC improvement. In this paper, relevant European and national legislation is also reviewed