Miracle-dz/UniFAR-FTUs huggingface dataset:
The Wnt Antagonist sFRP1 in Colorectal Tumorigenesis

Regions of the short arm of chromosome 8 are deleted frequently in a range of solid tumors, indicating that tumor suppressor genes reside at these loci. In this study, we have examined the properties of the Wnt signaling antagonist secreted frizzled-related protein (sFRP) 1 as a candidate for this role at c8p11.2. An initial survey of 10 colorectal tumors, selected by the presence of isolated short deletions of the 8p11.2 region, identified three chain-terminating mutations, all within the first exon, which encodes the cysteine-rich domain. None of these tumors exhibited microsatellite instability, indicating intact mismatch repair gene function. The preserved sFRP1 alleles in the remaining seven tumors each contained a polymorphic three-base insertion in the signal sequence, but in a broader study, no association was found between this and the development of colorectal cancer. Epigenetic inhibition of sFRP1 transcription was investigated, and increased methylation of the promotor region was demonstrated in an additional cohort of 51 locally advanced colorectal cancers. Hypermethylation was identified in 40 of 49 (82%) cancers and in only 11 of 36 (30%) matched normal mucosal samples (P < 0.001). Semiquantitative analysis, by real-time PCR, of mRNA expression in 37 of the same cohort of 51 cancers revealed that sFRP1 mRNA expression was down-regulated in 28 (76%) cases compared with matched normal large bowel mucosa. The 3′ end of the sFRP1 mRNA also was found to be alternatively spliced, compared with the prototype liver and lung forms, in the colon and a number of other tissues, yielding an extended COOH terminus, which may influence its activity in a tissue-specific manner. The inactivation and down-regulation of sFRP1 observed are consistent with it acting as a tumor suppressor gene in colorectal carcinogenesis. Because β-catenin is constitutively active in the majority of colorectal tumors, it is unlikely that sFRP1 can act in the canonical Wnt response pathway. Therefore, we propose that the reduced activity or absence of sFRP1 allows the transduction of noncanonical Wnt signals, which contribute to tumor progression.
Centromeres Cluster De Novo at the Beginning of Meiosis in Brachypodium distachyon

In most eukaryotes that have been studied, the telomeres cluster into a bouquet early in meiosis, and in wheat and its relatives and in Arabidopsis the centromeres pair at the same time. In Arabidopsis, the telomeres do not cluster as a typical telomere bouquet on the nuclear membrane but are associated with the nucleolus both somatically and at the onset of meiosis. We therefore assessed whether Brachypodium distachyon, a monocot species related to cereals and whose genome is approximately twice the size of Arabidopsis thaliana, also exhibited an atypical telomere bouquet and centromere pairing. In order to investigate the occurrence of a bouquet and centromere pairing in B distachyon, we first had to establish protocols for studying meiosis in this species. This enabled us to visualize chromosome behaviour in meiocytes derived from young B distachyon spikelets in three-dimensions by fluorescent in situ hybridization (FISH), and accurately to stage meiosis based on chromatin morphology in relation to spikelet size and the timing of sample collection. Surprisingly, this study revealed that the centromeres clustered as a single site at the same time as the telomeres also formed a bouquet or single cluster.
Deploying Safe User-Level Network Services with icTCP

We present icTCP, an "information and control" TCP implementation that exposes key pieces of internal TCP state and allows certain TCP variables to be set in a safe fashion. The primary benefit of icTCP is that it enables a variety of TCP extensions to be implemented at user-level while ensuring that extensions are TCP-friendly. We demonstrate the utility of icTCP through a collection of case studies. We show that by exposing information and safe control of the TCP congestion window, we can readily implement user-level versions of TCP Vegas, TCP Nice, and the Congestion Manager; we show how user-level libraries can safely control the duplicate acknowledgment threshold to make TCP more robust to packet reordering or more appropriate for wireless LANs; we also show how the retransmission timeout value can be adjusted dynamically. Finally, we find that converting a stock TCP implementation into icTCP is relatively straightforward; our prototype requires approximately 300 lines of new kernel code.
A new approach to the orientation of random hypergraphs

A h-uniform hypergraph H = (V, E) is called (l, k)-orientable if there exists an assignment of each hyper-edge e e to exactly l of its vertices v e e such that no vertex is assigned more than k hyperedges. Let Hn,m,h be a hypergraph, drawn uniformly at random from the set of all h-uniform hypergraphs with n vertices and m edges. In this paper, we determine the threshold of the existence of a (l, k)-orientation of Hn,m,h for k ≥ 1 and h > l ≥ 1, extending recent results motivated by applications such as cuckoo hashing or load balancing with guaranteed maximum load. Our proof combines the local weak convergence of sparse graphs and a careful analysis of a Gibbs measure on spanning subgraphs with degree constraints. It allows us to deal with a much broader class than the uniform hypergraphs.
Description of the content of geographic datasets

Customers for geographic data need metadata in order to decide whether the data is suitable for the intended use. The current metadata standards concentrate on technical and administrative aspects of datasets. However, the customers have to understand the data content before all else. This paper surveys different means of describing content of geographic data. Product information in marketing management promotes or describes products with the aim of managing expectations of customers. A conceptual model provides a formal structural description of data elements in a database design process. Human communication in a natural language is a powerful mean in building up the knowledge of the semantics of a dataset and the vagueness of many phenomena represented by geographic data. The paper concludes that users of metadata should be segmented on the basis of their varying needs and competence, and different description methods should be provided for different user segments.
A thermal characteristic study of extruded-type heat sinks in considering air flow bypass phenomenon

An experimental investigation carried out to study the forced air cooling heat sinks used in electronic packaging is discussed. The parameters include clearance between the heat sink and adjacent PCB (printed circuit board), lateral space between heat sinks, and height and width of heat sink. A fin efficiency model is used to calculate the convective coefficient and fin efficiency. The results show that the air flow bypass effect on thermal performance, due to top clearance or lateral space, is significant, more than 20%. Thermal performance can be improved by either increasing height or decreasing width of the heat sinks. The convective coefficient, however, may not increase monotonically with thermal performance. The results indicate that, generally the Nusselt number can be expressed as an exponential form of the Reynolds number and the exponent is about 0.6. <<ETX>>
Mitochondria Control Functional CaV1.2 Expression in Smooth Muscle Cells of Cerebral Arteries

Rationale: Physiological functions of mitochondria in contractile arterial myocytes are poorly understood. Mitochondria can uptake calcium (Ca2+), but intracellular Ca2+ signals that regulate mitochondrial Ca2+ concentration ([Ca2+]mito) and physiological functions of changes in [Ca2+]mito in arterial myocytes are unclear. Objective: To identify Ca2+ signals that regulate [Ca2+]mito, examine the significance of changes in [Ca2+]mito, and test the hypothesis that [Ca2+]mito controls functional ion channel transcription in myocytes of resistance-size cerebral arteries. Methods and Results: Endothelin (ET)-1 activated Ca2+ waves and elevated global Ca2+ concentration ([Ca2+]i) via inositol 1,4,5-trisphosphate receptor (IP3R) activation. IP3R-mediated sarcoplasmic reticulum (SR) Ca2+ release increased [Ca2+]mito and induced mitochondrial depolarization, which stimulated mitochondrial reactive oxygen species (mitoROS) generation that elevated cytosolic ROS. In contrast, a global [Ca2+]i elevation did not alter [Ca2+]mito, mitochondrial potential, or mitoROS generation. ET-1 stimulated nuclear translocation of nuclear factor (NF)-&kgr;B p50 subunit and ET-1–induced IP3R-mediated mitoROS elevated NF-&kgr;B–dependent transcriptional activity. ET-1 elevated voltage-dependent Ca2+ (CaV1.2) channel expression, leading to an increase in both pressure (myogenic tone)– and depolarization-induced vasoconstriction. Baseline CaV1.2 expression and the ET-1–induced elevation in CaV1.2 expression were both reduced by IP3R inhibition, mitochondrial electron transport chain block, antioxidant treatment, and NF-&kgr;B subunit knockdown, leading to vasodilation. Conclusions: IP3R-mediated SR Ca2+ release elevates [Ca2+]mito, which induces mitoROS generation. MitoROS activate NF-&kgr;B, which stimulates CaV1.2 channel transcription. Thus, mitochondria sense IP3R-mediated SR Ca2+ release to control NF-&kgr;B–dependent CaV1.2 channel expression in arterial myocytes, thereby modulating arterial contractility.
Optimal distributed scheduling for single-hop wireless networks

We consider the problem of optimal distributed scheduling for delay minimization in single-hop wireless networks. We focus on static scheduling policies, where the CSMA channel access rates are determined by the long-run traffic statistics, but not the instantaneous queue states. Such static scheduling is preferable over dynamic scheduling policies like max-weight when the traffic flows are heterogeneous. In this paper, we formulate the problem of optimizing the channel access rates of different links subject to an upper bound on the access rate of each link. This is a hard non-convex optimization. We propose an approximate solution that is asymptotically optimal in the limit as the maximum permissible channel access rate grows to infinity. We also study the role of the intra-queue scheduling policy. Specifically, we consider two policies: first come first served (FCFS) and pre-emptive last come first served (PLCFS). Analogous to the case of an M/G/1 queue, we show that PLCFS is preferable to FCFS for highly variable flows.
Metrics for evaluation of metaprogram complexity

The concept of complexity is used in many areas of computer science and software engineering. Software complexity metrics can be used to evaluate and compare quality of software development and maintenance processes and their products. Complexity management and measurement is especially important in novel programming technologies and paradigms, such as aspect-oriented programming, generative programming, and metaprogramming, where complex multilanguage and multi-aspect program specifications are developed and used. This paper analyzes complexity management and measurement techniques, and proposes five complexity metrics (Relative Kolmogorov Complexity, Metalanguage Richness, Cyclomatic Complexity, Normalized Difficulty, Cognitive Difficulty) for measuring complexity of metaprograms at information, metalanguage, graph, algorithm, and cognitive dimensions.
Head Kidney-Derived Macrophages of Common Carp (Cyprinus carpio L.) Show Plasticity and Functional Polarization upon Differential Stimulation1

Cells from the myeloid lineage are pluripotent. To investigate the potential of myeloid cell polarization in a primitive vertebrate species, we phenotypically and functionally characterized myeloid cells of common carp (Cyprinus carpio L.) during culture. Flow cytometric analysis, Ab labeling of cell surface markers, and light microscopy showed the presence of a major population of heterogeneous macrophages after culture. These head kidney-derived macrophages can be considered the fish equivalent of bone marrow-derived macrophages and show the ability to phagocytose, produce radicals, and polarize into innate activated or alternatively activated macrophages. Macrophage polarization was based on differential activity of inducible NO synthase and arginase for innate and alternative activation, respectively. Correspondingly, gene expression profiling after stimulation with LPS or cAMP showed differential expression for most of the immune genes presently described for carp. The recently described novel Ig-like transcript 1 (NILT1) and the CXCR1 and CXCR2 chemokine receptors were up-regulated after stimulation with cAMP, an inducer of alternative activation in carp macrophages. Up-regulation of NILT1 was also seen during the later phase of a Trypanosoma carassii infection, where macrophages are primarily alternatively activated. However, NILT1 could not be up-regulated during a Trypanoplasma borreli infection, a model for innate activation. Our data suggest that NILT1, CXCR1, and CXCR2 could be considered markers for alternatively activated macrophages in fish.
Determination of Key Residues for Catalysis and RNA Cleavage Specificity

RNase II is the prototype of a ubiquitous family of enzymes that are crucial for RNA metabolism. In Escherichia coli this protein is a single-stranded-specific 3′-exoribonuclease with a modular organization of four functional domains. In eukaryotes, the RNase II homologue Rrp44 (also known as Dis3) is the catalytic subunit of the exosome, an exoribonuclease complex essential for RNA processing and decay. In this work we have performed a functional characterization of several highly conserved residues located in the RNase II catalytic domain to address their precise role in the RNase II activity. We have constructed a number of RNase II mutants and compared their activity and RNA binding to the wild type using different single- or double-stranded substrates. The results presented in this study substantially improve the RNase II model for RNA degradation. We have identified the residues that are responsible for the discrimination of cleavage of RNA versus DNA. We also show that the Arg-500 residue present in the RNase II active site is crucial for activity but not for RNA binding. The most prominent finding presented is the extraordinary catalysis observed in the E542A mutant that turns RNase II into a “super-enzyme. ”
Development and implement of the IP camera based on DM6437

An IP camera based on TI's DaVinci DSP-TMS320DM6437 is developed in this paper. An intelligent video surveillance system is established using the designed IP camera. The real-time capture of the video is implemented in the system as well as the compression coding of the video using H.264 and the transmission of the encoded video through network. In the section of network communication, the performance of DSP processor in three scenes is tested, which is convenient for developers to optimize.
Dual-waveband optics for the visible and midwaveband infrared

The requirement for multi-sensor systems continues to expand in many areas of electro-optics. For defence applications, an increasing need to combine visual and infrared (IR) imagery in compact configurations drives advances in material processing and coating technology. This paper reviews the materials required for such systems, highlights the importance of optical coatings, and describes coating developments at Pilkington Optronics St. Asaph site.
Real-Time PCR Quantification and Diversity Analysis of the Functional Genes aprA and dsrA of Sulfate-Reducing Prokaryotes in Marine Sediments of the Peru Continental Margin and the Black Sea

Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5′-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 108/g sediment close to the sediment surface to less than 105/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5–1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40–121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 104/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere.
Effects of the H2‐receptor antagonist ranitidine on gastric motor function after a liquid meal in healthy humans

Objective. Studies on animals have shown that histamine may be involved in the regulation of gastrointestinal smooth muscle tone. However, the role of histamine in the regulation of human gastric motor function is not clear. This study examined the effect of ranitidine, an H2‐receptor antagonist, on gastric volume and gastric emptying after a liquid meal in healthy humans. Material and methods. Twelve healthy volunteers participated in a randomized crossover study with 50 mg ranitidine as a bolus intravenously versus no medication. Gastric volume at baseline was determined with single photon emission computed tomography (SPECT) after intravenous injection of 99mTc‐pertechnetate. After ingestion of a 600‐mL liquid meal radiolabelled with 111In‐diethylenetriaminepentaacetic acid, dual‐isotope technique with SPECT and planar imaging assessed gastric volume as well as gastric emptying. Results. Ranitidine did not change gastric volume before the meal, nor at 0 h or 1 h after it. Furthermore, ranitidine did not influence gastric retention of meal components after 0.5 h and 1 h. Conclusions. Intravenous bolus injection of 50 mg ranitidine does not modify gastric volume or gastric emptying after a 600 mL liquid meal in healthy humans.
Resource Sharing via Planed Relay for

We present an improved version of adaptive distributed cross-layer routing algorithm (ADCR) for hybrid wireless network with dedicated relay stations () in this paper. A mobile terminal (MT) may borrow radio resources that are available thousands mile away via secure multihop RNs, where RNs are placed at pre-engineered locations in the network. In rural places such as mountain areas, an MT may also communicate with the core network, when intermediate MTs act as relay node with mobility. To address cross-layer network layers routing issues, the cascaded ADCR establishes routing paths across MTs, RNs, and cellular base stations (BSs) and provides appropriate quality of service (QoS). We verify the routing performance benefits of over other networks by intensive simulation.
Mastering Security Anomalies in Virtualized Computing Environments via Complex Event Processing

—To protect computer systems and their users against security attacks, all potential security related incidents should be detected by monitoring system behavior. In this paper, a novel approach to detect, analyze and handle security anomalies in virtualized computing systems is presented. Adequate sensors on different virtualization layers monitor relevant events, a Complex Event Processing engine is used to aggregate and correlate events on the same or different layers to ﬁnd genuine attacks and eliminate false positives, and corresponding actions are performed if a security anomaly is detected. To enhance the quality of the results, machine learning techniques are used to analyze a historical database of recorded events ofﬂine to generate new or modify existing queries on the monitored event stream automatically. Furthermore, sensors can be activated and deactivated during runtime to gather interesting events, reduce the false alarm rate and ensure the system’s responsiveness when a sudden increase of monitored event data occurs. In this way, a ﬂexible, minimally-invasive approach for detecting, analyzing and reacting to a broad variety of security anomalies in a virtualized environment is provided.
Respiratory gas-exchange ratios during graded exercise in fed and fasted trained and untrained men.

We evaluated the hypotheses that endurance training increases relative lipid oxidation over a wide range of relative exercise intensities in fed and fasted states and that carbohydrate nutrition causes carbohydrate-derived fuels to predominate as energy sources during exercise. Pulmonary respiratory gas-exchange ratios [(RER) = CO2 production/O2 consumption (VO2)] were determined during four relative, graded exercise intensities in both fed and fasted states. Seven untrained (UT) men and seven category 2 and 3 US Cycling Federation cyclists (T) exercised in the morning in random order, with target power outputs of 20 and 40% peak VO2 (VO2 peak) for 2 h, 60% VO2 peak for 1.5 h, and 80% VO2 peak for a minimum of 30 min after either a 12-h overnight fast or 3 h after a standardized breakfast. Actual metabolic responses were 22 +/- 0.33, 40 +/- 0.31, 59 +/- 0.32, and 75 +/- 0.39% VO2 peak. T subjects showed significantly (P < 0.05) decreased RER compared with UT subjects at absolute workloads when fed and fasted. Fasting significantly decreased RER values compared with the fed state at 22, 40, and 59% VO2 peak in T and at 40 and 59% VO2 peak in UT subjects. Training decreased (P < 0.05) mean RER values compared with UT subjects at 22% VO2 peak when they fasted, and at 40% VO2 peak when fed or fasted, but not at higher relative exercise intensities in either nutritional state. Our results support the hypothesis that endurance training enhances lipid oxidation in men after a 12-h overnight fast at low relative exercise intensities (22 and 40% VO2 peak). However, a training effect on RER was not apparent at high relative exercise intensities (59 and 75% VO2 peak). Because most athletes train and compete at exercise intensities >40% maximal VO2, they will not oxidize a greater proportion of lipids compared with untrained subjects, regardless of nutritional state.