gebhart/patrepeval huggingface dataset:
Landscape of gene fusions in epithelial cancers: seq and ye shall find (2015)

Enabled by high-throughput sequencing approaches, epithelial cancers across a range of tissue types are seen to harbor gene fusions as integral to their landscape of somatic aberrations. Although many gene fusions are found at high frequency in several rare solid cancers, apart from fusions involving the ETS family of transcription factors which have been seen in approximately 50% of prostate cancers, several other common solid cancers have been shown to harbor recurrent gene fusions at low frequencies. On the other hand, many gene fusions involving oncogenes, such as those encoding ALK, RAF or FGFR kinase families, have been detected across multiple different epithelial carcinomas. Tumor-specific gene fusions can serve as diagnostic biomarkers or help define molecular subtypes of tumors; for example, gene fusions involving oncogenes such as ERG, ETV1, TFE3, NUT, POU5F1, NFIB, PLAG1, and PAX8 are diagnostically useful. Tumors with fusions involving therapeutically targetable genes such as ALK, RET, BRAF, RAF1, FGFR1-4, and NOTCH1-3 have immediate implications for precision medicine across tissue types. Thus, ongoing cancer genomic and transcriptomic analyses for clinical sequencing need to delineate the landscape of gene fusions. Prioritization of potential oncogenic "drivers" from "passenger" fusions, and functional characterization of potentially actionable gene fusions across diverse tissue types, will help translate these findings into clinical applications. Here, we review recent advances in gene fusion discovery and the prospects for medicine.
Recent developments in sonar for EOD applications (2005)

There are a number of sonar technology development efforts ongoing to support the explosive ordinance disposal (EOD) community with direct applicability to homeland security needs as well. These efforts seek to develop enabling technologies to detect, reacquire, classify and identify moored, bottom and limpet mines. This paper will discuss the motivation for these efforts, present a description of the technology approaches, and describe initial trial results of two test bed systems developed under the Office of Naval Research (ONR) sponsored EOD applied research program. The first system is a diver-held multi-beam sonar based on charge domain processing technology. The low power electronic beamforming (LPEB) sonar was developed to enable reacquisition of previously marked contacts for the purpose of identification. It also has applications to marine searches. A key system constraint was to maximize performance within a 20W, 440 cubic inch design space. The second system is intended for inspection of ship hulls from a UUV (unmanned undersea vehicle) platform and is based on blazed array technology. The blazed array implementation creates a frequency dispersed set of subdegree conical beams in response to a broadband input signal. The set of conical beams is scanned across the hull by the UUVs forward motion. Again power and size limitations were key drivers in the development of this sonar.
Cyclotrimerization versus cyclotetramerization in the electrophilic oligomerization of 3,4-bis(methyloxy)benzyl derivatives (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclotrimerization versus cyclotetramerization in the electrophilic oligomerization of 3,4-bis(methyloxy)benzyl derivativesVirgil Percec, Chang G. Cho, and Coleen PughCite this: Macromolecules 1991, 24, 11, 3227–3234Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ma00011a029https://doi.org/10.1021/ma00011a029research-articleACS PublicationsRequest reuse permissionsArticle Views224Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Do Low-density Cerebral Oximetry Measures Accurately Detect Variability of Cerebral Perfusion During Cardiac Surgery? (2010)

Neurocognitive deficits due to inadequate cerebral perfusion are prevalent sequelae of cardiac surgery. FDA-approved non-invasive cerebral oximetry devices, based on low-density arrays, are unlikely to yield accurate representation of complex heterogeneous cerebral perfusion.
Boundary Aware Networks for Medical Image Segmentation. (2019)

Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. We validate their effectiveness on the task of brain tumor segmentation using the BraTS 2018 dataset. Our experiments reveal that our approach yields more accurate segmentation results, which makes it promising for more extensive application to medical image segmentation.
Codificação de Redes Neurais sem Retreino (2021)

Resumo-Aprendizado de mquinas utilizado em vrias reas de atuao
ProgeniDB: A Novel Cell Lineage Database for Generation Associated Phenotypic Behavior in Cell-based Assays (2007)

ProgeniDB is a web-accessible cell lineage database, which comprises data derived from time-lapse microscopy image sequences, using our novel encoding software tool called ProgeniTRAK. This database provides information on qualitative and quantitative changes in cellular dynamics in response to anti-cancer drugs variation, which is critical for pharmacodynamic modeling and validation. The lineage data for each progenitor cell centers around the construction of a bifurcation map, locating in both space and time critical cellular events such as cell division and cell death. This database provides the opportunity to select a set of lineages based on different experimental constraints and observe the associated phenotypic behavior of progenitor cells. The output generated from this database depicts the cellular dynamic of selected population which can be downloaded to explore and exploit in relation to hypothesis-driven drug discovery. A case study is presented where we interrogate drug-induced perturbations on ensuing cell lineages. The database is available at http://biodiversity.cs.cf.ac.uk/cymart/progenidb.html.
Biomimetic Synthesis and Biological Evaluation of Aplidiopsamine A (2012)

The first total synthesis of Aplidiopsamine A, a rare 3H-pyrrolo[2,3-c]quinoline alkaloid from the Aplidiopsis confluata, has been achieved following the proposed biosynthesis. This biomimetic synthesis requires only five steps and proceeds in 20.8% overall yield. Biological evaluation across large panels of discrete molecular targets identified that Aplidiopsamine A is a highly selective PDE4 inhibitor, a target for numerous CNS disorders.
Multi-party human-robot interaction with distant-talking speech recognition (2012)

Speech is one of the most natural medium for human communication, which makes it vital to human-robot interaction. In real environments where robots are deployed, distant-talking speech recognition is difficult to realize due to the effects of reverberation. This leads to the degradation of speech recognition and understanding, and hinders a seamless human-robot interaction. To minimize this problem, traditional speech enhancement techniques optimized for human perception are adopted to achieve robustness in human-robot interaction. However, human and machine perceive speech differently: an improvement in speech recognition performance may not automatically translate to an improvement in human-robot interaction experience (as perceived by the users). In this paper, we propose a method in optimizing speech enhancement techniques specifically to improve automatic speech recognition (ASR) with emphasis on the human-robot interaction experience. Experimental results using real reverberant data in a multi-party conversation, show that the proposed method improved human-robot interaction experience in severe reverberant conditions compared to the traditional techniques.
The Kerf toolkit for intrusion analysis (2004)

We consider the problem of intrusion analysis and present the Kerf toolkit, whose purpose is to provide an efficient and flexible infrastructure for the analysis of attacks. The Kerf toolkit includes a mechanism for securely recording host and network logging information for a network of workstations, a domain-specific language for querying this stored data, and an interface for viewing the results of such a query, providing feedback on these results, and generating new queries in an iterative fashion. We describe the architecture of Kerf in detail, present examples to demonstrate the power of our query language, and discuss the performance of our implementation of this system.
Remdesivir (GS-5734) Is Efficacious in Cynomolgus Macaques Infected With Marburg Virus (2020)

Marburg virus (MARV) is a filovirus with documented human case-fatality rates of up to 90%. Here, we evaluated the therapeutic efficacy of remdesivir (GS-5734) in nonhuman primates experimentally infected with MARV. Beginning 4 or 5 days post inoculation, cynomolgus macaques were treated once daily for 12 days with vehicle, 5 mg/kg remdesivir, or a 10-mg/kg loading dose followed by 5 mg/kg remdesivir. All vehicle-control animals died, whereas 83% of animals receiving a 10-mg/kg loading dose of remdesivir survived, as did 50% of animals receiving a 5-mg/kg remdesivir regimen. Remdesivir-treated animals exhibited improved clinical scores, lower plasma viral RNA, and improved markers of kidney function, liver function, and coagulopathy versus vehicle-control animals. The small molecule remdesivir showed therapeutic efficacy in this Marburg virus disease model with treatment initiation 5 days post inoculation, supporting further assessment of remdesivir for the treatment of Marburg virus disease in humans.
Indirect passivation design for a diesel engine model (2002)

Unstable (nonminimum) zero dynamics are an obstacle to direct feedback passivation. In multivariable (MIMO) systems, the zero dynamics of a particular input-output pair may be stabilizable by another input, making indirect single-input single-output (SISO) passivation feasible. This indirect passivation methodology is illustrated by a design for a simplified model of turbocharged diesel engine and tested by simulation on a higher-order model.
Core-Shell Polymer-Based Nanoparticles Deliver miR-155-5p to Endothelial Cells (2019)

Heart failure occurs in over 30% of the worldwide population and most commonly originates from cardiovascular diseases such as myocardial infarction. microRNAs (miRNAs) target and silence specific mRNAs, thereby regulating gene expression. Because the endogenous miR-155-5p has been ascribed to vasculoprotection, loading it onto positively charged, core-shell poly(isobutylcyanoacrylate) (PIBCA)-polysaccharide nanoparticles (NPs) was attempted. NPs showed a decrease (p < 0.0001) in surface electrical charge (ζ potential), with negligible changes in size or shape when loaded with the anionic miR-155-5p. Presence of miR-155-5p in loaded NPs was further quantified. Cytocompatibility up to 100 μg/mL of NPs for 2 days with human coronary artery endothelial cells (hCAECs) was documented. NPs were able to enter hCAECs and were localized in the endoplasmic reticulum (ER). Expression of miR-155-5p was increased within the cells by 75-fold after 4 hours of incubation (p < 0.05) and was still noticeable at day 2. Differences between loaded NP-cultured cells and free miRNA, at days 1 (p < 0.05) and 2 (p < 0.001) suggest the ability of prolonged load release in physiological conditions. Expression of miR-155-5p downstream target BACH1 was decreased in the cells by 4-fold after 1 day of incubation (p < 0.05). This study is a first proof of concept that miR-155-5p can be loaded onto NPs and remain intact and biologically active in endothelial cells (ECs). These nanosystems could potentially increase an endogenous cytoprotective response and decrease damage within infarcted hearts.
A Maximum Likelihood Approach to Unsupervised Online Adaptation of Stochastic Vector Mapping Function for Robust Speech Recognition (2007)

In the past several years, we've been studying feature transformation approaches for robust automatic speech recognition (ASR) based on the concept of stochastic vector mapping (SVM) to compensating for possible "distortions" caused by factors irrelevant to phonetic classification in both training and recognition stages. Although we have demonstrated the usefulness of the SVM-based approaches for several robust ASR applications where diversified yet representative training data are available, the performance improvement of SVM-based approaches is less significant when there is a severe mismatch between training and testing conditions. In this paper, we present a maximum likelihood approach to unsupervised online adaptation (OLA) of SVM function parameters on an utterance-by-utterance basis for achieving further performance improvement. Its effectiveness is confirmed by evaluation experiments on Finnish AuroraS database.
The BayREN Integrated Commercial Retrofits (BRICR) Project: An Introduction and Preliminary Results (2018)

BayREN Integrated Commercial Retrofits (BRICR) is a DOE-funded project which aims to enhance the capacity of energy efficiency programs to recruit participants, develop retrofits, and measure outcomes in small and medium-sized commercial buildings, a sector notoriously hard to reach and expensive to serve, that accounts for 2/3 of US commercial floor space. To address these barriers, BRICR leverages existing incentives, financing, data, and open source software to facilitate two paths for comprehensive improvements: a deep energy retrofit, or serial upgrades integrated into capital improvement and maintenance cycles. BRICR is developing an integrated workflow for iterative energy modeling of commercial buildings for city energy program managers and auditors - starting with mass building-scale simulation based on public records and proceeding through audit, retrofit, and measurement and verification stages. BRICR builds on existing tools including LBNL’s CBES, NREL’s OpenStudio, PNNL’s Audit Template, and DOE’s BuildingSync and SEED PlatformTM. At each stage, BRICR uses available information to inform simulations (starting with public records but iteratively augmented with observations from energy program staff) to improve the quality of the models that inform decision making. This paper presents initial results from energy models of 1699 office and retail buildings in San Francisco. Building stock data from public records were translated to create a BuildingSync file for each building which was stored in SEED. Each BuildingSync file was then translated to multiple OpenStudio Workflow files for EnergyPlus simulation to estimate energy savings of energy conservation measures (ECM). Energy savings predictions for each ECM were written back to an updated BuildingSync file for each building and re-uploaded to SEED. The distribution of baseline energy simulations was calibrated against the publicly disclosed distribution of energy benchmarking data to increase confidence in results.
Identification of a Novel Calcium Binding Motif Based on the Detection of Sequence Insertions in the Animal Peroxidase Domain of Bacterial Proteins (2012)

Proteins of the animal heme peroxidase (ANP) superfamily differ greatly in size since they have either one or two catalytic domains that match profile PS50292. The orf PP_2561 of Pseudomonas putida KT2440 that we have called PepA encodes a two-domain ANP. The alignment of these domains with those of PepA homologues revealed a variable number of insertions with the consensus G-x-D-G-x-x-[GN]-[TN]-x-D-D. This motif has also been detected in the structure of pseudopilin (pdb 3G20), where it was found to be involved in Ca(2+) coordination although a sequence analysis did not reveal the presence of any known calcium binding motifs in this protein. Isothermal titration calorimetry revealed that a peptide containing this consensus motif bound specifically calcium ions with affinities ranging between 33-79 µM depending on the pH. Microcalorimetric titrations of the purified N-terminal ANP-like domain of PepA revealed Ca(2+) binding with a K(D) of 12 µM and stoichiometry of 1.25 calcium ions per protein monomer. This domain exhibited peroxidase activity after its reconstitution with heme. These data led to the definition of a novel calcium binding motif that we have termed PERCAL and which was abundantly present in animal peroxidase-like domains of bacterial proteins. Bacterial heme peroxidases thus possess two different types of calcium binding motifs, namely PERCAL and the related hemolysin type calcium binding motif, with the latter being located outside the catalytic domains and in their C-terminal end. A phylogenetic tree of ANP-like catalytic domains of bacterial proteins with PERCAL motifs, including single domain peroxidases, was divided into two major clusters, representing domains with and without PERCAL motif containing insertions. We have verified that the recently reported classification of bacterial heme peroxidases in two families (cd09819 and cd09821) is unrelated to these insertions. Sequences matching PERCAL were detected in all kingdoms of life.
Repeated Administrations of Human Umbilical Cord Blood Cells Improve Disease Outcomes in a Mouse Model of Sanfilippo Syndrome Type III B (2014)

Sanfilippo syndrome type III B (MPS III B) is an inherited disorder characterized by a deficiency of α-N-acetylglucosaminidase (Naglu) enzyme leading to accumulation of heparan sulfate in lysosomes and severe neurological deficits. We have previously shown that a single administration of human umbilical cord mononuclear cells (hUCB MNCs) into Naglu knockout mice decreased behavioral abnormalities and tissue pathology. In this study, we tested whether repeated doses of hUCB MNCs would be more beneficial than a single dose of cells. Naglu mice at 3 months of age were randomly assigned to either a Media-only group or one of three hUCB MNC treatment groups--single low dose (3 × 10(6) cells), single high dose (1.8 × 10(7) cells), or multiple doses (3 × 10(6) cells monthly for 6 months) delivered intravenously; cyclosporine was injected intraperitoneally to immune suppress the mice for the duration of the study. An additional control group of wild-type mice was also used. We measured anxiety in an open field test and cognition in an active avoidance test prior to treatment and then at monthly intervals for 6 months. hUCB MNCs restored normal anxiety-like behavior in these mice (p < 0.001). The repeated cell administrations also restored hippocampal cytoarchitecture, protected the dendritic tree, decreased GM3 ganglioside accumulation, and decreased microglial activation, particularly in the hippocampus and cortex. These data suggest that the neuroprotective effect of hUCB MNCs can be enhanced by repeated cell administrations.
Synthesis of Four-Disulfide Insulin Analogs via Sequential Disulfide Bond Formation (2017)

Naturally occurring, multiple cysteine-containing peptides are a structurally unique class of compounds with a wide range of therapeutic and diagnostic applications. The development of reliable, precise chemical methods for their preparation is of paramount importance to facilitate exploration of their utility. We report here a straightforward and effective approach based on stepwise, sequentially directed disulfide bond formation, exemplified by the synthesis of four-disulfide bond-containing insulin analogs. Cysteine protection consisted of tert-butylthiol (StBu), thiol-trimethoxyphenyl (STmp), trityl (Trt), 4-methoxytrityl (Mmt), S-acetamidomethyl (Acm), and tert-butyl (tBu). This report describes chemistry that is broadly applicable to cysteine-rich peptides and the influence of a fourth disulfide bond on insulin bioactivity.
Development and structure evaluation of small sensor element for distributed-type tri-axial force sensor of robot finger (2007)

For the purpose of the development of a distributed-type tactile sensor for a robot finger, a small sensor element is developed, and an evaluation of its structure is carried out. In this paper, a small sensor element is presented the dimensions of which are 5mm in length, 5mm in width, and 1mm in thickness. The sensor’ s structure was evaluated by simulation and experiment from the viewpoints of strain gauge sensitivity, force sensitivity, conditional number, and rigidity. As a result, it was proven that the proposed sensor element could be miniaturized, and could measure tri-axial force.
Improving the Synthesis Gas Quality in Catalytic Gasification of Rice Straw by an Integrated Hot-Gas Cleaning System (2014)

This research investigates an enhanced removal rate of tar and trace pollutants (e.g. hydrogen chloride and hydrogen sulfide, H2S) in the gasification of rice straw, using an integrated in situ tar reduction and hot-gas cleaning technique. The gasification temperature was set at 900°C and equilibrium ratio (ER) was 0.30 in the gasifier. In the in situ tar reduction method, the catalyst, dolomite with an amended ratio of 0–15% was introduced to the gasifier. The integrated hot-gas cleaning system applied a multi-packed tower to remove the tar, sulfur and/or chlorine byproduct in syngas at 250°C. The packed materials composed of zeolite, calcined dolomite and activated carbon. The experimental results indicated that the tar concentration of syngas was approximately 20 g/kg. However, in catalytic gasification with 5% dolomite addition, the tar concentration reduced to 17 g/kg. The tar reduction efficiency was approximately 15% by an in situ dolomite addition. When applying the integrated hot-gas cleanup system, the tar was virtually eliminated. The total tar elimination rate was almost 100% and the cleaned syngas could be applied in other energy utilization equipment. On the other hand, the H2S and HCl concentration were 101 ppmv and 991 ppmv, respectively. After the integrated syngas cleaning system, the H2S and HCl were decreased to 7.9 ppmv and 410 ppmv with a removal efficiency of 92.1% and 58.6%, respectively. It can be concluded that combining the in situ method with the integrated syngas cleaning system can effectively reduce the amount of byproduct and enhance the syngas quality in the gasification of rice straw.