Simplified Metrics Calculation for Soft Bit Detection in DVB-T2

The constellation rotation and cyclic quadrature component delay (RQD) technique has been adopted in the second generation terrestrial digital video broadcasting (DVB-T2) standard. It improves the system performance under severe propagation conditions, but introduces serious complexity problems in the hardware implementation of the detection process. In this paper, we present a simplified scheme that greatly reduces the complexity of the demapper by simplifying the soft bit metrics computation having a negligible overall system performance loss

Stable isotope compositions of fluid inclusions in biogenic carbonates

Measurements have been made of hydrogen, carbon, and oxygen isotope compositions of inclusion waters and CO2 extracted from eleven species of modern marine and freshwater skeletal carbonates. The samples were collected in environments of highly contrasting temperatures and isotopic compositions of ambient waters. Inclusion waters were extracted in vacuum by thermal decrepitation of samples that were previously treated with H2O2 to remove organic matter. Water extractions were quantitative above 200[deg]C for aragonite species and above 350-400[deg]C for calcite species. Amounts of water liberated ranged from 0.6% to 2.2% and were generally very reproducible within a species but varied strongly from one species to another. Except for red algae and corals, the [delta]18O values of the shells are in accord with crystallization of carbonate at or near equilibrium with marine water of [delta]18O near 0[per mille sign]. The inclusion waters, however, are not in oxygen isotope equilibrium with ambient water and have high [delta]18O values of +6 to +18[per mille sign]. These high [delta]18O values do not result from partial exchange between water and either the host carbonate or small amounts of CO2 released during decrepitation. [delta]D values of inclusion waters range from -80 to -10[per mille sign] and are sensitive to the presence of small amounts of organic matter. The data for each species define a distinct field in [delta]D-[delta]18O space that is controlled by a vital fractionation effect. Stable isotope compositions of inclusion waters can be explained by metabolic reactions that incorporate relatively 18O-rich O2 that is dissolved in the water and used by the organism in respiration. Thus, inclusion waters in shells probably represent remnants of metabolic fluids produced by the mantle epithelium. The stable isotope compositions of such waters most likely result from varying metabolic rates that are specific to each species, as well as to formation temperature and the isotopic composition of ambient waters.Inclusion fluids in biogenic carbonates constitute an isotopic reservoir that has heretofore been unrecognized. The [delta]18O and [delta]D values of the inclusion waters are very different from those of meteoric, magmatic, and seawaters. Because these trapped fluids are released by the shells during heating, they could play a role in burial diagenesis. Burial of significant amounts of biogenic carbonates could liberate enough water to control diagenetic or metamorphic reactions in some cases. In the absence of other types of fluids, the participation of inclusion waters in such reactions should be easily recognized by their distinctive isotopic compositions.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31923/1/0000876.pd

Joint stage recognition and anatomical annotation of drosophila gene expression patterns

Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms

Examining the Connections within the Startup Ecosystem: A Case Study of St. Louis

This paper documents the resurgence of entrepreneurial activity in St. Louis by reporting on the collaboration and local learning within the startup community. This activity is happening both between entrepreneurs and between organizations that provide support, such as mentoring and funding, to entrepreneurs. As these connections deepen, the strength of the entrepreneurial ecosystem grows. Another finding from the research is that activity-based events, where entrepreneurs have the chance to use and practice the skills needed to grow their businesses, are most useful. St. Louis provides a multitude of these activities, such as Startup Weekend, 1 Million Cups, Code Until Dawn, StartLouis, and GlobalHack. Some of these are St. Louis specific, but others have nationwide or global operations, providing important implications for other cities

Oxygen isotope composition of a section of lower oceanic crust, ODP Hole 735B

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95244/1/ggge964.pd

TeCNO: Surgical Phase Recognition with Multi-Stage Temporal Convolutional Networks

Automatic surgical phase recognition is a challenging and crucial task with the potential to improve patient safety and become an integral part of intra-operative decision-support systems. In this paper, we propose, for the first time in workflow analysis, a Multi-Stage Temporal Convolutional Network (MS-TCN) that performs hierarchical prediction refinement for surgical phase recognition. Causal, dilated convolutions allow for a large receptive field and online inference with smooth predictions even during ambiguous transitions. Our method is thoroughly evaluated on two datasets of laparoscopic cholecystectomy videos with and without the use of additional surgical tool information. Outperforming various state-of-the-art LSTM approaches, we verify the suitability of the proposed causal MS-TCN for surgical phase recognition.Comment: 10 pages, 2 figure

Minimizing off-target signals in RNA fluorescent in situ hybridization

Fluorescent in situ hybridization (FISH) techniques are becoming extremely sensitive, to the point where individual RNA or DNA molecules can be detected with small probes. At this level of sensitivity, the elimination of ‘off-target’ hybridization is of crucial importance, but typical probes used for RNA and DNA FISH contain sequences repeated elsewhere in the genome. We find that very short (e.g. 20 nt) perfect repeated sequences within much longer probes (e.g. 350–1500 nt) can produce significant off-target signals. The extent of noise is surprising given the long length of the probes and the short length of non-specific regions. When we removed the small regions of repeated sequence from either short or long probes, we find that the signal-to-noise ratio is increased by orders of magnitude, putting us in a regime where fluorescent signals can be considered to be a quantitative measure of target transcript numbers. As the majority of genes in complex organisms contain repeated k-mers, we provide genome-wide annotations of k-mer-uniqueness at http://cbio.mskcc.org/∼aarvey/repeatmap

Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element

RNA localization is emerging as a general principle of sub-cellular protein localization and cellular organization. However, the sequence and structural requirements in many RNA localization elements remain poorly understood. Whereas transcription factor-binding sites in DNA can be recognized as short degenerate motifs, and consensus binding sites readily inferred, protein-binding sites in RNA often contain structural features, and can be difficult to infer. We previously showed that zebrafish squint/nodal-related 1 (sqt/ndr1) RNA localizes to the future dorsal side of the embryo. Interestingly, mammalian nodal RNA can also localize to dorsal when injected into zebrafish embryos, suggesting that the sequence motif(s) may be conserved, even though the fish and mammal UTRs cannot be aligned. To define potential sequence and structural features, we obtained ndr1 3′-UTR sequences from approximately 50 fishes that are closely, or distantly, related to zebrafish, for high-resolution phylogenetic footprinting. We identify conserved sequence and structural motifs within the zebrafish/carp family and catfish. We find that two novel motifs, a single-stranded AGCAC motif and a small stem-loop, are required for efficient sqt RNA localization. These findings show that comparative sequencing in the zebrafish/carp family is an efficient approach for identifying weak consensus binding sites for RNA regulatory proteins

Bacterial infection profiles in lung cancer patients with febrile neutropenia

<p>Abstract</p> <p>Background</p> <p>The chemotherapy used to treat lung cancer causes febrile neutropenia in 10 to 40% of patients. Although most episodes are of undetermined origin, an infectious etiology can be suspected in 30% of cases. In view of the scarcity of data on lung cancer patients with febrile neutropenia, we performed a retrospective study of the microbiological characteristics of cases recorded in three medical centers in the Picardy region of northern France.</p> <p>Methods</p> <p>We analyzed the medical records of lung cancer patients with neutropenia (neutrophil count < 500/mm³) and fever (temperature > 38.3°C).</p> <p>Results</p> <p>The study included 87 lung cancer patients with febrile neutropenia (mean age: 64.2). Two thirds of the patients had metastases and half had poor performance status. Thirty-three of the 87 cases were microbiologically documented. Gram-negative bacteria (mainly enterobacteriaceae from the urinary and digestive tracts) were identified in 59% of these cases. <it>Staphylococcus </it>species (mainly <it>S. aureus</it>) accounted for a high proportion of the identified Gram-positive bacteria. Bacteremia accounted for 60% of the microbiologically documented cases of fever. 23% of the blood cultures were positive. 14% of the infections were probably hospital-acquired and 14% were caused by multidrug-resistant strains. The overall mortality rate at day 30 was 33% and the infection-related mortality rate was 16.1%. Treatment with antibiotics was successful in 82.8% of cases. In a multivariate analysis, predictive factors for treatment failure were age >60 and thrombocytopenia < 20000/mm³.</p> <p>Conclusion</p> <p>Gram-negative species were the most frequently identified bacteria in lung cancer patients with febrile neutropenia. Despite the success of antibiotic treatment and a low-risk neutropenic patient group, mortality is high in this particular population.</p