gebhart/patrepeval huggingface dataset:
Simultaneous compression of multiple error-corrected short-read sets for faster data transmission and betterde novoassemblies (2022)

Next-Generation Sequencing has produced incredible amounts of short-reads sequence data for de novo genome assembly over the last decades. For efficient transmission of these huge datasets, high-performance compression algorithms have been intensively studied. As both the de novo assembly and error correction methods utilize the overlaps between reads data, a concern is that the will the sequencing errors bring up negative effects on genome assemblies also affect the compression of the NGS data. This work addresses two problems: how current error correction algorithms can enable the compression algorithms to make the sequence data much more compact, and whether the sequence-modified reads by the error-correction algorithms will lead to quality improvement for de novo contig assembly. As multiple sets of short reads are often produced by a single biomedical project in practice, we propose a graph-based method to reorder the files in the collection of multiple sets and then compress them simultaneously for a further compression improvement after error correction. We use examples to illustrate that accurate error correction algorithms can significantly reduce the number of mismatched nucleotides in the reference-free compression, hence can greatly improve the compression performance. Extensive test on practical collections of multiple short-read sets does confirm that the compression performance on the error-corrected data (with unchanged size) significantly outperforms that on the original data, and that the file reordering idea contributes furthermore. The error correction on the original reads has also resulted in quality improvements of the genome assemblies, sometimes remarkably. However, it is still an open question that how to combine appropriate error correction methods with an assembly algorithm so that the assembly performance can be always significantly improved.
Ba-Ni-Hexaaluminate as a New Catalyst in the Steam Reforming of 1-Methyl Naphthalene and Methane (2019)

Abstract This work investigates the long-term performance of Ba-Ni-hexaaluminate, BaNi x Al 12− x O 19 as a catalyst in reforming of 1-methyl naphthalene and/or methane in a model-gas simulating that from a circulating fluidized bed (CFB) gasifier during 23–29 h in a lab scale set-up, as well as the tendency for coke formation, sintering and sulphur poisoning. 1-Methyl naphthalene is used as a tar model substance. The Ba-Ni-hexaaluminate induces a high conversion of both compounds in the temperatures investigated (850 and 950 °C) under sulphur-free conditions. In sulphur-containing gas, the methane conversion stops at 20 ppm H 2 S and the reforming of 1-MNP at 850 °C is slightly reduced at 100 ppm. Graphic Abstract
Processor verification using efficient reductions of the logic of uninterpreted functions to propositional logic (2001)

The logic of Equality with Uninterpreted Functions (EUF) provides a means of abstracting the manipulation of data by a processor when verifying the correctness of its control logic. By reducing formulas in this logic to propositional formulas, we can apply Boolean methods such as ordered Binary Decision Diagrams (BDDs) and Boolean satisfiability checkers to perform the verification. We can exploit characteristics of the formulas describing the verification conditions to greatly simplfy the propostional formulas generated. We identify a class of terms we call “p-terms” for which equality comparisons can only be used in monotonically positive formulas. By applying suitable abstractions to the hardware model, we can express the functionality of data values and instruction addresses flowing through an instruction pipeline with p-terms. A decision procedure can exploit the restricted uses of p-terms by considering only “maximally diverse” interpretations of the associated function symbols, where every function application yields a different value execept when constrainted by functional consistency. We present two methods to translate formulas in EUF into propositional logic. The first interprets the formula over a domain of fixed-length bit vectors and uses vectors of propositional variables to encode domain variables. The second generates formulas encoding the conditions under which pairs of terms have equal valuations, introducing propostional variables to encode the equality relations between pairs of terms. Both of these approaches can exploit maximal diversity to greatly reduce the number of propositional variables that need to be introduced and to reduce the overall formula sizes. We present experimental results demonstrating the efficiency of this approach when verifying pipelined processors using the method proposed by Burch and Dill. Exploiting positive equality allows us to overcome the experimental blow-up experienced previously when verifying microprocessors with load, store, and branch instructions.
HCC: Wann Chirurgie? Wann RFA? Wann TACE? (2009)

Die Behandlung des HCC folgt einem Stufenplan, der Tumorstadium und Leberfunktion in die Therapieentscheidung einbezieht. Neuere Klassifikationssysteme wie CLIP, Okuda oder BCLC kombinieren daher beide Faktoren. Über die letzten Jahre deutet sich ein Paradigmenwechsel der Therapiestandards an. Unbestritten ist, dass nur eine Lebertransplantation eine Kuration ermöglicht. Resektionsraten sind häufig rückläufig. Grund ist die Verbreitung bildgeführter Techniken wie der Radiofrequenzablation, die sich in vergleichenden Studien der chirurgischen Resektion bei selektierten Patienten als ebenbürtig erwiesen hat und die Leberfunktion nicht kompromittiert. Für die transarterielle Chemoembolisation zeigen prospektiv randomisierte Studien gegen best care einen Überlebensvorteil. Für die Y90-Radioembolisation als alternative locoregionäre Maßnahme liegen günstige Phase II Ergebnisse vor, die auch Patienten mit Pfortaderthrombose einbeziehen. Sehr ausgedehnte lokale Tumorablationen ohne Größenlimitation sind mittels CT-Brachytherapie möglich und haben in Phase II Studien oder matched-pair Analysen ihren positiven Einfluss auf die Prognose bewiesen. Seit 2007 besteht die Option einer systemischen Therapie mittels Sorafenib. Die Sicherheit der Kombination lokaler oder locoregionärer Maßnahmen wie der Y90-Radioembolisation mit Sorafenib ist mittels PhaseI/II Studien belegt. Zusammenfassend ist die optimale Behandlung des HCC von gelebter Interdisziplinarität mit ebenbürtiger Positionierung der Radiologie abhängig.
Hypervelocity Impact of Radioactive Projectiles into Stainless Steel and Aluminum (1963)

Radioactive, cylindrical, steel projectiles were explosively accelerated into plates of stainless steel and aluminum. The amounts of radioisotopes Fe59 and Cr51 in the projectile prior to acceleration and in the crater in plate were measured in order to determine the fraction of the original projectile remaining in the crater. Impact experiments with steel plates showed that 3.4 to 7.8% of the original projectile remained in the crater of the steel plate; 3.6 to 7.5% of the original projectile remained in the crater of the aluminum plate. Data on any given crater, obtained by the measurement of both Fe59 and Cr51, are in good concordance. The fraction of the projectile remaining in the crater is independent of the impact velocity over the range of 12 000 to 14 900 ft/sec (3600 to 4540 m/sec).
Murine Features of Neurogenesis in the Human Hippocampus across the Lifespan from 0 to 100 Years (2010)

Our data suggest that in the adult human hippocampus neurogenesis-associated features that have been identified in rodents show patterns, as well as qualitative and quantitative age-related changes, that are similar to the course of adult hippocampal neurogenesis in rodents. Consequently, although further validation as well as the application of independent methodology (e.g. electron microscopy and cell culture work) is desirable, our data will help to devise the framework for specific research on cellular plasticity in the aging human hippocampus.
Wnt-5a mRNA translation is suppressed by the Elav-like protein HuR in human breast epithelial cells (2006)

Wnt-5a is a non-transforming Wnt protein. Since Wnt-5a mRNA and protein levels differ within and between tumours, the potential of Wnt-5a as a prognostic factor has been debated. We have previously shown that the lack of Wnt-5a protein is a predictor of shorter disease-free survival in human breast cancer. Recently, however, we also showed that the breast tumours lacking Wnt-5a protein had a high or normal level of Wnt-5a mRNA that might explain the discrepancies in previous studies. We here report that Wnt-5a is regulated at the post-transcriptional level. The regulation was mediated by the Embryonic Lethal Abnormal Vision (ELAV)-like protein HuR, which inhibited translation of Wnt-5a when bound to highly conserved AU-rich sequences in the 3'-untranslated region (3'-UTR) of the Wnt-5a mRNA molecule, as shown by both HA-tagged Wnt-5a- and Luciferase-Wnt-5a-3'-UTR reporter assays. The HuR-dependent inhibition of Wnt-5a was supported by the fact that active HuR is located in the cytoplasm in invasive human breast tumours and that hypoxia-induced activation of HuR inhibits translation of both Luciferase-Wnt-5a-3'-UTR and endogenous Wnt-5a protein. We propose that the lack of Wnt-5a protein expression in invasive human breast tumours is caused by a HuR-mediated suppression of Wnt-5a mRNA translation.
Grounded Adaptation for Zero-shot Executable Semantic Parsing (2020)

We propose Grounded Adaptation for Zeroshot Executable Semantic Parsing (GAZP) to adapt an existing semantic parser to new environments (e.g. new database schemas). GAZP combines a forward semantic parser with a backward utterance generator to synthesize data (e.g. utterances and SQL queries) in the new environment, then selects cycleconsistent examples to adapt the parser. Unlike data-augmentation, which typically synthesizes unverified examples in the training environment, GAZP synthesizes examples in the new environment whose inputoutput consistency are verified. On the Spider, Sparc, and CoSQL zero-shot semantic parsing tasks, GAZP improves logical form and execution accuracy of the baseline parser. Our analyses show that GAZP outperforms dataaugmentation in the training environment, performance increases with the amount of GAZPsynthesized data, and cycle-consistency is central to successful adaptation.
Robotic-assisted thoracoscopic surgery for lung resection: the first Canadian series (2017)

The results of this case series are comparable to those reported in the literature. A prospective study to examine the outcomes and cost of robotic pulmonary resection compared with video-assisted thoracoscopic surgery should be done in the context of the Canadian health care system. We have presented the first consecutive case series of robotic lobectomy in Canada. Outcomes compare favourably to other series in the literature.
Determination of the effect of the release of methotrexate from an in situ forming implant on colon carcinoma cells and in vivo studies in the rat model (2011)

Despite advances in cancer therapy, the successful treatment of solid tumours remains difficult, as there are numerous barriers to treatment that must be overcome. 1 Among these barriers are physiological barriers, such as diffusion of the drug from the bloodstream through the tumour, as well as patient tolerability to the typically high doses required for the treatment of solid tumours. One solution to this problem is the development of novel drugs for the treatment of cancer. However, the time taken for the launch of a novel compound, from development stage to the patient, is long, and the expense of such development is considerable. Another simpler solution to the treatment of solid tumours is to investigate approaches to deliver existing drugs, so that current problems faced are overcome. Hence the focus has shifted to targeted drug delivery systems. 2
Virulence-attenuated Salmonella engineered to secrete immunomodulators reduce tumour growth and increase survival in an autochthonous mouse model of breast cancer (2020)

The ultimate goal of bacterial based cancer therapy is to achieve non-toxic penetration and colonisation of the tumour microenvironment. To overcome this efficacy-limiting toxicity of anticancer immunotherapy, we have tested a therapy comprised of systemic delivery of a vascular disrupting agent to induce intratumoral necrotic space, cannabidiol to temporarily inhibit angiogenesis and acute inflammation, and a strain of <i>Salmonella</i> Typhimurium that was engineered for non-toxic colonisation and expression of immunomodulators within the tumour microenvironment. This combination treatment strategy was administered to transgenic mice burdened with autochthonous mammary gland tumours and demonstrated a statistically significant 64% slower tumour growth and a 25% increase in mean survival time compared to control animals without treatment. These experiments were accomplished with minimal toxicity as measured by less than 7% weight loss and a return to normal weight gain within three days following intravenous administration of the bacteria. Thus, non-toxic, robust colonisation of the microenvironment was achieved to produce a significant antitumor effect.
A multi-scale Gaussian beam parametrix for the wave equation: the Dirichlet boundary value problem (2017)

We present a construction of a multi-scale Gaussian beam parametrix for the Dirichlet boundary value problem associated with the wave equation, and study its convergence rate to the true solution in the highly oscillatory regime. The construction elaborates on the wave-atom parametrix of Bao, Qian, Ying, and Zhang and extends to a multi-scale setting the technique of Gaussian beam propagation from a boundary of Katchalov, Kurylev and Lassas.
A Thermoresponsive Hydrogel Formed from a Star–Star Supramolecular Architecture (2013)

Smart stars: A novel star–star supramolecular architecture was self-assembled from a star-shaped adamantyl-terminated 8-arm poly(ethylene glycol) and a star-shaped poly(N-isopropylacrylamide) with a β-cyclodextrin core through inclusion complexation. The star–star supramolecules further self-aggregated into a 3D network in response to temperature change, forming a thermoresponsive reversible “smart” hydrogel. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Speeding Multicast by Acknowledgment Reduction Technique (SMART) Enabling Robustness of QoE to the Number of Users (2012)

We introduce a novel feedback protocol, called SMART, for wireless broadcast networks that use linear network coding. We consider transmission of packets from a single source to many receivers over a single-hop broadcast erasure channel with heterogeneous links. We propose a predictive model to minimize feedback as well as extraneous data transmissions by the source. In addition, we use the method of types to provide a lower bound for the expected total transmission time, and use simulations to show that our protocol operates close to this lower bound. We show that with SMART, counter to conventional wisdom, the average user's QoE improves slightly as the number of users increases. We demonstrate that SMART's algorithmic simplicity enables multicast transmissions that on average take fewer than 2 feedback rounds to complete. We show the favorable scalability of our technique with the number of users, which enables reliable quality of experience. We also show the robustness of this scheme to uncertainty in the number of receiving nodes, and packet erasure probability, as well as to partial loss of the feedback. Furthermore, we show that SMART performs nearly as well as an omniscient transmitter that requires no feedback.
Interleaved converters operation based on CMC (1999)

A new family of low-ripple DC-to-DC switching converters based on a parallel connection of N-identical boost converters with current-mode control (CMC) is presented. The CMC strategy ensures that all the converters operate at the same duty cycle, sharing an equal amount of input current and forcing the output voltage to be an integer multiple (N) of the input voltage. As a result, the total input current and output voltage ripples are extremely low. The generation of control signals from inductor currents feedback without using external triangular or sawtooth signals is another characteristic of the new converter family.
Register liveness analysis for optimizing dynamic binary translation (2003)

Dynamic binary translators compile machine code from a source architecture to a target architecture at run time. Due to the hard time constraints of just-in-time compilation only highly efficient optimization algorithms can be employed. Common problems are an insufficient number of registers on the target architecture and the different handling of condition codes in source and target architecture. Without optimizations useless stores and computations are generated by the dynamic binary translator and cause significant performance losses. In order to eliminate these useless operations, a very fast liveness analysis is required. We present a dynamic liveness analysis algorithm that trades precision for fast execution and conducted experiments with the SpecInt95 benchmark suite using our PowerPC to Alpha translator. The optimizations reduced the number of stores by about 50 percent. This resulted in a speed-up of 10 to 30 percent depending on the target machine. The dynamic liveness analysis results are very close to the most precise solution.
On the complexity of frequency-domain adaptive filtering (1991)

In frequency-domain adaptive filtering (FDAF), the 'crossover point' where the frequency domain becomes more efficient than the time domain is asymptotically 1.5 times as high for a DSP software realization as for a VLSI hardware realization. However, actual software realizations of FDAF may require as much as twice the computation predicted by theory, depending on the processor chosen. The approach can be extended to analyze other FDAF structures, such as multirate filters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of Multidrug Resistance Proteins in Rat and Human Chronic Pancreatitis (2003)

The expression of P-gp and related transporters could have impact on the metabolism, distribution, and availability of various compounds, including drugs, in the pancreas. The results indicate that this could be more pronounced in chronic pancreatitis.
HUNK suppresses metastasis of basal type breast cancers by disrupting the interaction between PP2A and cofilin-1 (2010)

Metastasis leads to the death of most cancer patients, and basal breast cancer is the most aggressive breast tumor type. Metastasis involves a complex cell migration process dependent on cytoskeletal remodeling such that targeting such remodeling in tumor cells could be clinically beneficial. Here we show that Hormonally Up-regulated Neu-associated Kinase (HUNK) is dramatically down-regulated in tumor samples and cell lines derived from basal breast cancers. Reconstitution of HUNK expression in basal breast cancer cell lines blocked actin polymerization and reduced cell motility, resulting in decreased metastases in two in vivo murine cancer models. Mechanistically, HUNK overexpression sustained the constitutive phosphorylation and inactivation of cofilin-1 (CFL-1), thereby blocking the incorporation of new actin monomers into actin filaments. HUNK reconstitution in basal breast cancer cell lines prevented protein phosphatase 2-A (PP2A), a phosphatase putatively acting on CFL-1, from binding to CFL-1. Our investigation of HUNK suggests that the interaction between PP2A and CFL-1 may be a target for antimetastasis therapy, particularly for basal breast cancers.
Serotonergic Neurons Are Targets for Leptin in the Monkey1 (2001)

Leptin is a secretory product of adipocytes that has been shown to affect food intake, metabolism, and reproduction. One site of leptin's action is the central nervous system, where the leptin receptor (Ob-R) messenger ribonucleic acid (mRNA) and protein are expressed in discrete areas. In both the rat and monkey, Ob-R mRNA has been localized in the Raphe nuclei of the brainstem. Neurons in the Raphe nuclei are the primary source of serotonin in the brain. Serotonergic pathways influence both feeding and reproduction, and these cells are plausible direct targets for leptin's action. We used double label in situ hybridization and computerized image analysis to determine whether serotonergic neurons in the brainstem of the female pigtailed macaque (Macaca nemestrina) express Ob-R mRNA. We observed that many cells in the Raphe nuclei express serotonin transporter mRNA, a marker of serotonergic cells, and Ob-R mRNA. Based on quantitative analysis, the highest number of cells that express both serotonin transporter and Ob-R mRNAs were found in the caudal dorsal Raphe and median Raphe nuclei; fewer double labeled cells were situated in the caudal linear nucleus and rostral median Raphe, whereas double labeled cells occurred infrequently in the rostral dorsal Raphe. These observations suggest that leptin may act on serotonergic cells to mediate some of its effects on ingestive behavior, metabolism, and reproduction.
Chronic intake of a high-cholesterol diet resulted in hepatic steatosis, focal nodular hyperplasia and fibrosis in non-obese mice (2009)

We investigated the effects of a high-cholesterol (HC) diet administered long term (25 or 55 weeks) on metabolic disorders including hepatic damage in mice. The mice were fed the HC diet (15 % milk fat, 1.5 % cholesterol and 0.1 % cholic acid, w/w) for 25 or 55 weeks. Body and adipose tissue weights were similar to those of mice fed a control diet. Consumption of the HC diet long term resulted in hypercholesterolaemia, hepatic steatosis and gallstones. In addition, focal nodular hyperplasia (FNH) and mild fibrosis of the liver developed in all mice fed the HC diet for 55 weeks. Plasma levels of monocyte chemoattractant protein (MCP)-1 were elevated, and the level of hepatic platelet-derived growth factor (PDGF)-B protein was increased in mice fed the HC diet compared with those fed the control diet. Thus, it seems likely that the liver fibrosis and FNH caused by the long-term consumption of a HC diet may be partly due to an elevation of plasma MCP-1 and hepatic PDGF expression.