gebhart/patrepeval huggingface dataset:
Stat3 Mediates Expression of Autotaxin in Breast Cancer (2011)

We determined that signal transducer and activator of transcription 3 (Stat3) is tyrosine phosphorylated in 37% of primary breast tumors and 63% of paired metastatic axillary lymph nodes. Examination of the distribution of tyrosine phosphorylated (pStat3) in primary tumors revealed heterogenous expression within the tumor with the highest levels found in cells on the edge of tumors with relatively lower levels in the central portion of tumors. In order to determine Stat3 target genes that may be involved in migration and metastasis, we identified those genes that were differentially expressed in primary breast cancer samples as a function of pStat3 levels. In addition to known Stat3 transcriptional targets (Twist, Snail, Tenascin-C and IL-8), we identified ENPP2 as a novel Stat3 regulated gene, which encodes autotaxin (ATX), a secreted lysophospholipase which mediates mammary tumorigenesis and cancer cell migration. A positive correlation between nuclear pStat3 and ATX was determined by immunohistochemical analysis of primary breast cancer samples and matched axillary lymph nodes and in several breast cancer derived cell lines. Inhibition of pStat3 or reducing Stat3 expression led to a decrease in ATX levels and cell migration. An association between Stat3 and the ATX promoter, which contains a number of putative Stat3 binding sites, was determined by chromatin immunoprecipitation. These observations suggest that activated Stat3 may regulate the migration of breast cancer cells through the regulation of ATX.
Single-wall CNT spray for easy creation of DE electrodes (Conference Presentation) (2020)

The conductivity of DE can be further improved by using single-wall CNT (SWCNT), which has higher conductivity than carbon black. Electrodes using SWCNTs can be easily created by packing the CNTs in a spray can. This method was most recently developed by Zeon Corporation under the direction of Chiba et al. In the CNT dispersion, the CNT and 2% by weight sodium cholate were first added to the dispersion medium, and then dispersed using an ultrasonic homogenizer. When DE was produced using this CNT spray electrode on 3M acrylic, it was 2.2 times better than DE produced using the carbon.
Location Based Reliable Routing Protocol for Tactical Mobile Ad-Hoc Networks (2012)

최근 정보통신 산업 및 네트워크 분야의 기술발달로 국방 무기체계에 새로운 패러다임 변화가 형성되었고, 군에서도 이러한 전쟁양상에 변화에 맞추어 TICN(Tactical Information Communication Network)이라는 통신체계를 도입하여 구축 중에 있다. TICN체계가 그 기능을 갖추기 위해서는 전장의 소규모 전투로부터 신뢰성 있는 정보를 실시간으로 전송 받아야 하는데, 이러한 기능을 지원해 주는 기술의 핵심적인 요소가 바로 MANET(Mobile Ad-Hoc Network) 라우팅 프로토콜이다. 본 논문에서는 일반 MANET 라우팅 프로토콜에서 주로 사용되는 최단경로 설정 기법의 전술네트워크 적용에 따른 문제점을 식별하고, 소규모 전투부대의 전술환경을 바탕으로, 중계 노드들의 위치와 속도, 데이터 크기 등을 고려하여 경로의 신뢰성과 데이터 지연 시간을 계산함으로써, 신뢰성 있는 정보를 실시간으로 전송 받을 수 있는 효율적인 전술 MANET 라우팅 프로토콜을 제안해 보고자 한다. Recently, developments in the field of communication and network technologies induced new paradigm in the defense weapon system. As a consequence, military authorities develop the Tactical Information Communication Network(TICN) system to adapt to the changing paradigm. One of the most important functions of TICN is real-time communication. As a result, TICN system needs to receive real-time information from the battlefield, and the key technology to support these features is MANET(Mobile Ad-Hoc Network) routing protocol. In this paper, we analyze problems of the shortest path scheme in tactical Ad-Hoc networks, which is widely used in common Ad-Hoc networks. We propose efficient routing protocol for tactical MANET by considering the environment of small combat units, such as node position, speed and data size. The proposed algorithm shows reliable data transfer and low latency in battlefield.
Sporochartines A–E, A New Family of Natural Products from the Marine Fungus Hypoxylon monticulosum Isolated from a Sphaerocladina Sponge (2017)

Four new sporochartines B-E were isolated from the marine fungus Hypoxylon monticulosum CLL-205, isolated from a sponge belonging to the Sphaerocladina order and collected in Tahiti coast. Sporochartine A (1), the first representative of this family was previously isolated from the same fungus. The structures of sporochartines B-E were elucidated using 1D and 2D NMR, HRMS and IR data. Their configurations were established according to ROE correlations and comparison with the absolute configuration of sporochartine A (1) previously obtained from X-ray analysis. Sporochartines A-D (2-4) may be derived from endo Diels-Alderase type catalysis and sporochartine E (5) from an exo Diels-Alderase catalysis. The spatial conformation of sporochartines drastically influences the results of the cytotoxic bioassay against HCT-116, PC-3 and MCF-7 human cancer cell lines.
Nonparametric Combinatorial Regression for Shape Constrained Modeling (2009)

We introduce a unified approach for calculating nonparametric shape constrained regression. Enforcement of the shape constraint often accounts for the impact of a physical phenomenon or a specific property. It also improves the model's predicability and facilitates subsequent optimizations. The regression models are built by transforming the problem into the combinatorial domain where the shape constraints are imposed by bounding the combinatorial search space. We start by addressing isotonicity shape constraint using a dynamic programming algorithm and demonstrate how the problem can be mapped to the graph combinatorics domain. Next we show how a number of other important shape constraints including unimodality, convexity, limited level set, and limited slope can be addressed using the same framework. The flexibility of proposed framework enables solving the shape constrained regression problem with an arbitrary user-defined error metric. This flexibility is exploited to add robustness against outliers to the model. The algorithms are described in detail and their computational complexity is established. The performance and effectiveness of the shape constrained regression is evaluated on traces of temperature and humidity measurements from a deployed sensor network where a high degree of accuracy and robustness is demonstrated.
Synthesis of high molecular weight polyester carbonates via interfacial phosgenation of aromatic dicarboxylic acids and bisphenols (1984)

Abstract The synthesis of bisphenol A poly(carbonate–ester) copolymers was studied by phase‐transfer catalysis and modified interfacial polymerization. Only low molecular weight copolymers were prepared directly from dicarboxylic acids, phosgene, and bisphenol A by an interfacial process that involves the use of pyridine as catalyst, HCl acceptor, and weak base. To avoid the use of tertiary amines, which can be difficult to remove from the polymer products, and to produce higher molecular weight copolymers from the same dicarboxylic acid precursors another synthetic method was developed. This more effective method required careful pH control that was achieved by the selective use of the weak‐base potassium carbonate in the first stage of the process. Moreover, elevated reaction temperatures (∼65–70°C) and phase‐transfer catalysis were used. The carbonate–ester copolymers prepared by this technique had consistently high intrinisic viscosities, little or no anyhydride microstructure, and higher degrees of ester unit incorporation than those produced by the pyridine‐catalyzed method. These copolymers also had glass transition temperatures ( T g ) 20–30°C higher than bisphenol A polycarbonate homopolymer. An analytical method for determining quantitatively the amount of ester units in the bisphenol A poly(carbonate‐esters) was developed by using Fourier transform infrared spectroscopy (FT‐IR). Agreement between this FT‐IR method and a quantitative nuclear magnetic resonance (NMR) method was found to be reasonable, especially for copolymers with ester unit percentages lower than 40%.
Micromachined actuators/sensors for intratubular positioning/steering (2023)

Micromachined thin film cantilever actuators having means for individually controlling the deflection of the cantilevers, valve members, and rudders for steering same through blood vessels, or positioning same within a blood vessel, for example. Such cantilever actuators include tactile sensor arrays mounted on a catheter or guide wire tip for navigation and tissues identification, shape-memory alloy film based catheter/guide wire steering mechanisms, and rudder-based steering devices that allow the selective actuation of rudders that use the flowing blood itself to help direct the catheter direction through the blood vessel. While particularly adapted for medical applications, these cantilever actuators can be used for steering through piping and tubing systems.
Shape- and appearance-based segmentation of volumetric medical images (2002)

A novel approach to three-dimensional segmentation, parametric surface representation, and interactive surface modification is reported. The combination of shape-based and appearance-based volumetric segmentation, parametric representation of 3D surfaces, and their interactive modification and editing forms a very powerful paradigm for a variety of volumetric segmentation tasks. Performance assessment of the method for automated segmentation of diaphragm surfaces in volumetric 3D CT images is ongoing.
Contextual Advertising for IPTV Using Automated Metadata Generation (2009)

Current IPTV monetization focuses on mainstream programming that is well understood, with metadata that is stored in advance. Current contextual advertising is focused on web searches and static information. As the demand for online internet video grows into the IPTV market, the need to monetize it effectively becomes important. As the advertising market for IPTV expands into less mainstream video (e.g. YouTube and other user generated content) it becomes more important to automate the generation of metadata for the video The metadata associated with self-described YouTube videos are unreliable and can not be used as a basis for effective contextual advertising. Automatic generation, however, brings down the cost of creating metadata and gives advertisers a neutral party that evaluates the data. We propose a system in which a trusted intermediary automatically generates reliable metadata for multimedia.
Spatiotemporal dynamics of word processing in the human brain (2007)

We examined the spatiotemporal dynamics of word processing by recording the electrocorticogram (ECoG) from the lateral frontotemporal cortex of neurosurgical patients chronically implanted with subdural electrode grids. Subjects engaged in a target detection task where proper names served as infrequent targets embedded in a stream of task-irrelevant verbs and nonwords. Verbs described actions related to the hand (e.g, throw) or mouth (e.g., blow), while unintelligible nonwords were sounds which matched the verbs in duration, intensity, temporal modulation, and power spectrum. Complex oscillatory dynamics were observed in the delta, theta, alpha, beta, low, and high gamma (HG) bands in response to presentation of all stimulus types. HG activity (80-200 Hz) in the ECoG tracked the spatiotemporal dynamics of word processing and identified a network of cortical structures involved in early word processing. HG was used to determine the relative onset, peak, and offset times of local cortical activation during word processing. Listening to verbs compared to nonwords sequentially activates first the posterior superior temporal gyrus (post-STG), then the middle superior temporal gyrus (mid-STG), followed by the superior temporal sulcus (STS). We also observed strong phase-locking between pairs of electrodes in the theta band, with weaker phase-locking occurring in the delta, alpha, and beta frequency ranges. These results provide details on the first few hundred milliseconds of the spatiotemporal evolution of cortical activity during word processing and provide evidence consistent with the hypothesis that an oscillatory hierarchy coordinates the flow of information between distinct cortical regions during goal-directed behavior.
Non-Annealed Graphene Paper as a Binder-Free Anode for Lithium-Ion Batteries (2010)

Non-annealed graphene paper, prepared via reduction of prefabricated graphene oxide paper with hydrazine hydrate, was employed as the sole component of a binder-free lithium-ion battery anode, circumventing the polymer binders and other additives required for the fabrication of conventional electrodes. The binder-free anode fabricated from this non-annealed paper possessed excellent cyclability, while exhibiting a voltage versus capacity profile similar to that of a polymer-bound graphene powder anode. Kinetic barriers may exist for Li ion diffusion through the layered paper structure as decreasing the current rate from 50 to 10 mA·g−1 increased the reversible capacity by over 150%.
Rapid detection and profiling of cancer cells in fine-needle aspirates (2009)

There is a growing need for fast, highly sensitive and quantitative technologies to detect and profile unaltered cells in biological samples. Technologies in current clinical use are often time consuming, expensive, or require considerable sample sizes. Here, we report a diagnostic magnetic resonance (DMR) sensor that combines a miniaturized NMR probe with targeted magnetic nanoparticles for detection and molecular profiling of cancer cells. The sensor measures the transverse relaxation rate of water molecules in biological samples in which target cells of interest are labeled with magnetic nanoparticles. We achieved remarkable sensitivity improvements over our prior DMR prototypes by synthesizing new nanoparticles with higher transverse relaxivity and by optimizing assay protocols. We detected as few as 2 cancer cells in 1-microL sample volumes of unprocessed fine-needle aspirates of tumors and profiled the expression of several cellular markers in <15 min.
PERIOPERATIVE VARIABLES ASSOCIATED WITH POSTOPERATIVE AGITATION IN PATIENTS UNDERGOING NON-CARDIAC THORACIC SURGERY. (2005)

Cardiothoracic Anesthesiology, Cleveland Clinic Foundation, Cleveland, OH; (Diaz, Noguera, Bashour) Biostatistics and Epidemiology, Cleveland Clinic Foundation, Cleveland, OH (Xu)
Initial Two-Dimensional Laser Induced Fluorescence Measurements of OH Radicals in an Internal Combustion Engine (1988)

&lt;div class="htmlview paragraph"&gt;The imaging of two–dimensional laser–induced fluorescence is used for simultaneous, multiple point visualization of OH radical concentration in the combustion chamber of a single cylinder internal combustion engine. Sheet illumination from the frequency doubled output of a Nd:YAG pumped dye laser is used to excite the fluorescence which is detected using an image–intensified Reticon diode array camera. The camera is interfaced to an IBM–PC AT microcomputer for data acquisition and processing. The laser and camera are synchronized with the crankshaft of the engine so that 2–D images of the OH fluorescence can be obtained at different times through the engine cycle. The OH fluorescence was measured over a 3 cm × 3 cm field of view with 0.3 mm spatial resolution and temporal resolution of &amp;lt; 10 ns. The measurements were made with propane/air mixtures at equivalence ratios of 0.8, 0.9, 1.0 and 1.1 at an engine speed of 600 rpm and at a chamber pressure of 1.34 ± .03 MPa. The OH fluorescence rises sharply through the flame front to a peak value and then decreases gradually in the post–flame gases.&lt;/div&gt;
Promoter‐specific regulation of gene expression by an exogenously added homeodomain that promotes neurite growth (1995)

pAntp, a 60 amino acid long peptide corresponding to the homeodomain of the Drosophila Antennapedia protein, translocates through neuronal membranes when added exogenously to neurons in culture, where it accumulates in the nucleus and promotes neurite outgrowth. We proposed that the peptide, once internalized, may compete for homeoprotein DNA binding sites. To investigate this point, we have produced a permanent fibroblast cell line which carries a luciferase reporter gene under the control of a 93 bp genomic region of the HOXD9 promoter with binding sites for homeoproteins. Externally added pAntp specifically down-regulates the expression of the reporter gene, suggesting that the neurotrophic effects observed previously are mediated by direct binding of pAntp to homeoprotein target sites.
The Inductive Bias of In-Context Learning: Rethinking Pretraining\n Example Design (2021)

Pretraining Neural Language Models (NLMs) over a large corpus involves\nchunking the text into training examples, which are contiguous text segments of\nsizes processable by the neural architecture. We highlight a bias introduced by\nthis common practice: we prove that the pretrained NLM can model much stronger\ndependencies between text segments that appeared in the same training example,\nthan it can between text segments that appeared in different training examples.\nThis intuitive result has a twofold role. First, it formalizes the motivation\nbehind a broad line of recent successful NLM training heuristics, proposed for\nthe pretraining and fine-tuning stages, which do not necessarily appear related\nat first glance. Second, our result clearly indicates further improvements to\nbe made in NLM pretraining for the benefit of Natural Language Understanding\ntasks. As an example, we propose "kNN-Pretraining": we show that including\nsemantically related non-neighboring sentences in the same pretraining example\nyields improved sentence representations and open domain question answering\nabilities. This theoretically motivated degree of freedom for pretraining\nexample design indicates new training schemes for self-improving\nrepresentations.\n
The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus (2017)

Adaptation of influenza A viruses to new hosts are rare events but are the basis for emergence of new influenza pandemics in the human population. Thus, understanding the processes involved in such events is critical for anticipating potential pandemic threats. In 2013, the first case of human infection by an avian H10N8 virus was reported, yet the H10 hemagglutinin (HA) maintains avian receptor specificity. However, the 150-loop of H10 HA, as well as related H7 and H15 subtypes, contains a two-residue insert that can potentially block human receptor binding. Mutation of the 150-loop on the background of Q226L and G228S mutations, which arose in the receptor-binding site of human pandemic H2 and H3 viruses, resulted in acquisition of human-type receptor specificity. Crystal structures of H10 HA mutants with human and avian receptor analogs, receptor-binding studies, and tissue staining experiments illustrate the important role of the 150-loop in H10 receptor specificity.
Heat Shock Protein 27 modulate mesothelial and epithelial to mesenchymal transition (EMT) (2011)

Introduction: Pulmonary fibrosis (PF) has currently no treatment. We have shown that adenoviral gene transfer of TGF-β1 (AdTGF-β1) to the pleura induces a severe pleural fibrosis that invades the parenchyma. In this process, mesothelial cells differentiate into myofibroblastes (α-SMA positive cells) through an EMT-like process suggesting a key role of mesothelial cells in PF. Heat Shock Protein 27 (HSP27), is a chaperon for actin. Its role in fibrogenesis is unknown. Methods: Sprague Dawley rats received intrapleural injection of AdTGF-β1 or AdDL (empty vector). Mesothelial Met-5A and A549 cells were treated with rTGF-β1. Results: in vitro: 1) mesothelial cells are susceptible to rTGF-β1 induced EMT 2) HSP27 is strongly linked to α-SMA during EMT (colocalisation and co-immunoprecipitation). 3) HSP27 overexpression induces an EMT and siRNA mediated HSP27 inhibition blocks TGF-β1 induced EMT and mesothelial cell migration 4) HSP27 modulates the TGF-β1/SMAD pathway. Data were reproduced in A549 epithelial cells. In vivo: 7 days after AdTGF-β1 injection, HSP27 and α-SMA are overexpressed and colocalize in fibrotic sub-pleura areas. AdTGF-β1 rats treated by intrapleural injections of OGX427 (AntiSens Oligonucleotide, ASO, directed against HSP27) have a strong decrease in HPS27, α-SMA expression, mesothelial cells migration into the parenchyma and fibrosis compare to AdTGF-β1 rats treated with control ASO. Conclusion: HSP27 plays a major role in EMT and could be a key target to inhibit EMT in PF and others diseases involving EMT. This work is supported by: – the EU, 7th FP, HEALTH-F2-2007-202224 eurIPFnet – La “Recherche en santé Respiratoire” et la Société de Pneumologie de Langue Française
Corticosteroids and Local Anesthetics Decrease Positive Effects of Platelet‐Rich Plasma: An In Vitro Study on Human Tendon Cells (2012)

Anesthetics or corticosteroids either alone or in combination should be used carefully to preserve the proposed positive effects of PRP in the treatment of tendon injury.
Lignin depolymerization to monophenolic compounds in a flow-through system (2017)

A reductive lignocellulose fractionation in a flow-through system in which pulping and transfer hydrogenolysis steps were separated in time and space has been developed.
ChemInform Abstract: Practical, Stereoselective Synthesis of Palinavir, a Potent HIV Protease Inhibitor. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Minireview: The New Eukaryotic Precursor Processing Proteinases (1991)

One of the most exciting developments in the field of neuroendocrinology was the discovery last year that mammalian cells contain specialized proteinases homologous to the bacterial subtilisins. In contrast to the bacterial subtilisins, which show little sequence specificity, these new mammalian proteinases are remarkably specific and cleave exclusively at certain sets of basic residues. It now appears likely that this family of proteinases is responsible for the proteolytic activation of prohormones, neuropeptide precursors, and in all likelihood a wide variety of other protein precursors. The fact that yeasts use a proteinase known as Kex2 to process the precursor to the α-factor pheromone has been accepted since the mid-80s (see review, Ref. 1). Since this yeast precursor is cleaved at pairs of basic residues, similar to the sites at which proinsulin as well as many other mammalian hormone and neuropeptide precursors are cleaved, it was long hypothesized that mammalian cells contain a homologous proteinase which is responsible for the paired basic cleavage event. Many laboratories tried without success to clone such mammalian enzymes from cDNA libraries using Kex2-based probes.
Supplementary Materials and Methods, Figures 1 - 6, Tables 1 - 4 from High-Throughput Detection of Clinically Relevant Mutations in Archived Tumor Samples by Multiplexed PCR and Next-Generation Sequencing (2023)

&lt;p&gt;PDF file - 731KB, Supplementary Figure 1. Schematic workflow of MMP-seq. Supplementary Figure 2. Examples of tiling and hotspot amplicon designs. Supplementary Figure 3. Consistent target enrichment and variant allele quantification in FF biological replicates. Supplementary Figure 4. Correlation between called variant frequencies in paired FF and FFPE samples. Supplementary Figure 5. UDG treatment improves sequencing specificity but has no impact on sensitivity. Supplementary Figure 6. PIK3R1 mutation profiles from TCGA endometrial cancer study. Supplementary Table 1. MMP-seq target genes. Supplementary Table 2. Latin Square Design. Supplementary Table 3. Latin square mutation read frequency detected when sequencing input cell lines for Latin square cross-dilutions. Supplementary Table 4. Pretreatment of FFPE DNA samples with uracil-DNA glycosylase (UDG) resulted in markedly reduction of false positives.&lt;/p&gt;