gebhart/patrepeval huggingface dataset:
Spin diffusion in a triblock thermoplastic elastomer (1994)

A triblock copolymer thermoplastic elastomer (SEBS) consisting of an ethylene–butylene random-copolymer rubbery domain flanked by rigid polystyrene short blocks has been analyzed using novel solid-state NMR techniques. 13 C NMR relaxation measurements suggest that at the T 1 (H) level (minimum observable phase size of about 18 nm) the material appears homogeneous, but at the T 1ρ (H) level (minimum observable phase size of about 3 nm) the expected two distinct phases are noted. Two-dimensional WISE spectra (high-resolution 13 C – broadline 1 H) show the different mobility in the two phases. A broad component associated with the highly mobile rubbery phase indicates the presence of an interface. The mobile phase is selected using a dipolar filter pulse sequence and the magnetization is allowed to transfer to the rigid polystyrene phase during a period called "mixing time." From the growth of the polystyrene magnetization during the mixing period, the size of the dispersed polystyrene phase can be calculated to be 16 ± 2 nm.
The Photoreactive Carbohydrate Probe, a Novel Method for Detection of Lectins (1995)

Article The Photoreactive Carbohydrate Probe, a Novel Method for Detection of Lectins was published on January 1, 1995 in the journal Clinical Chemistry and Laboratory Medicine (CCLM) (volume 33, issue 12).
CONCRETE MIX DESIGN AND OPTIMIZATION (1998)

SUMMARY Determination of ingredients of aggregate mixes is discussed as an important part of concrete mix design. Different types of “ideal” aggregate grading curves are presented in the work. Analytic and numerical methods of aggregate mix design are proposed. A concrete mix design method is used taking into account granulation parameters of aggregates. The task of concrete mix optimization implies selecting the most suitable concrete aggregates from the Data Base. The following properties are to be optimized: cost of raw materials, quality of aggregate packing, water and cement consumption. Computer programs for aggregate and concrete mix design as well as for concrete mix optimization have been worked out.
Peer-to-peer architecture case study: Gnutella network (2002)

Despite recent excitement generated by the P2P paradigm and despite surprisingly fast deployment of some P2P applications, there are few quantitative evaluations of P2P system behavior. Due to its open architecture and achieved scale, Gnutella is an interesting P2P architecture case study. Gnutella, like most other P2P applications, builds at the application level a virtual network with its own routing mechanisms. The topology of this overlay network and the routing mechanisms used have a significant influence on application properties such as performance, reliability, and scalability. We built a 'crawler' to extract the topology of Gnutella's application level network, we analyze the topology graph and evaluate generated network traffic. We find that although Gnutella is not a pure power-law network, its current configuration has the benefits and drawbacks of a power-law structure. These findings lead us to propose changes to the Gnutella protocol and implementations that bring significant performance and scalability improvements.
Identification and Evaluation of a New Tumor Cell-Binding Peptide, FROP-1 (2007)

The target of FROP-1 is most likely a molecule found generally in tumors, making this peptide highly attractive for diagnostic or therapeutic applications. However, modifications are needed to increase stability and affinity.
Differential activation of MAP kinase family members triggered by CD99 engagement (2000)

The molecular basis for the modulatory properties of CD99 is not well understood. Treatment of human Jurkat T lymphocytes with anti-CD99 antibody led to activation of three mitogen-activated protein kinase (MAPK) members, ERK, JNK, and p38 MAPK, along with homotypic aggregation. While phosphorylation of ERK and JNK was inhibited by the pretreatment of a PKC inhibitor, bisindolylmaleimide I, activation of p38 MAPK was upregulated by the same pretreatment. The signaling pathways to MAPKs by CD99 engagement were independent of PI-3 kinase, distinguishing from those by CD3 engagement. Among MAPKs, ERK pathway was essential for homotypic aggregation together with intracytoplasmic Ca(2+).
Monitoring ATPase induced pH changes in single proteoliposomes with the lipid-coupled fluorophore Oregon Green 488 (2017)

Monitoring the proton pumping activity of proteins such as ATPases in reconstituted single proteoliposomes is key to quantify the function of proteins as well as potential proton pump inhibitors. However, most pH-detecting assays available are either not quantitative, require well-adapted reconstitution protocols or are not appropriate for single vesicle studies. Here, we describe the quantitative and time-resolved detection of F-type ATPase-induced pH changes across vesicular membranes doped with the commercially available pH sensitive fluorophore Oregon Green 488 DHPE. This dye is shown to be well suited to monitor acidification of lipid vesicles not only in bulk but also at the single vesicle level. The pK<sub>a</sub> value of Oregon Green 488 DHPE embedded in a lipid environment was determined to be 6.1 making the fluorophore well suited for a variety of physiologically relevant proton pumps. The TF<sub>O</sub>F<sub>1</sub>-ATPase from a thermophilic bacterium was reconstituted into large unilamellar vesicles and the bulk acidification assay clearly reveals the overall activity of the F-type ATPase in the vesicle ensemble with an average pH change of 0.45. However, monitoring the pH changes in individual vesicles attached to a substrate demonstrates that the fraction of vesicles with a significant observable pH change is only about 5%, a number that cannot be gathered from bulk experiments and which is considerably lower than expected.
Scalable parallel data mining for association rules (1997)

One of the important problems in data mining is discovering association rules from databases of transactions where each transaction consists of a set of items. The most time consuming operation in this discovery process is the computation of the frequency of the occurrences of interesting subset of items (called candidates) in the database of transactions. To prune the exponentially large space of candidates, most existing algorithms, consider only those candidates that have a user defined minimum support. Even with the pruning, the task of finding all association rules requires a lot of computation power and time. Parallel computers offer a potential solution to the computation requirement of this task, provided efficient and scalable parallel algorithms can be designed. In this paper, we present two new parallel algorithms for mining association rules. The Intelligent Data Distribution algorithm efficiently uses aggregate memory of the parallel computer by employing intelligent candidate partitioning scheme and uses efficient communication mechanism to move data among the processors. The Hybrid Distribution algorithm further improves upon the Intelligent Data Distribution algorithm by dynamically partitioning the candidate set to maintain good load balance. The experimental results on a Cray T3D parallel computer show that the Hybrid Distribution algorithm scales linearly and exploits the aggregate memory better and can generate more association rules with a single scan of database per pass.
Therapeutic Effect of Dinitrochlorobenzene (DNCB) on Verruca Plana and Verruca Vulgaris (1984)

Fifty-nine patients with verrucae (45 with verrucae plana and 14 with verrucae vulgaris) were treated with dinitrochlorobenzene (DNCB) as a topical application on the normal uninvolved skin of the shoulder for sensitization and challenge. The patients were sensitized with 0.5 ml of 0.4% DNCB solution and then challenged with 0.1% DNCB ointment twice a week. Six cases of verrucae plana and 1 case of verrucae vulgaris were completely cured by sensitization only and 32 cases of verrucae plana and 7 cases of verrucae vulgaris were completely resolved by repeated challenges. The therapeutic effect was better in verrucae plana (84.4%) than in verrucae vulgaris (57.1%), and the verrucae were completely resolved within 10 weeks in more than 90% of the patients cured by challenge. The side effects of DNCB were mild allergic contact dermatitis and slight transitory hyperpigmentation at the site of application.
Efficacy of a new once-daily long-acting inhaled 2-agonist indacaterol versus twice-daily formoterol in COPD (2010)

NCT 00393458.
Radiation Performance of Highly Miniaturized Implantable Devices (2019)

Miniature wireless implantable bioelectronics provide powerful capabilities for biotelemetry, therapeutics, and neural interfacing. These technologies rely on antennas to communicate with external receivers, yet existing systems suffer from poor radiation performance. We address this issue by studying the through-tissue propagation, deriving the optimal frequency range, and obtaining the maximum achievable far-field radiation efficiency. Three problem formulations are considered with increasing complexity and anatomical realism. Polarization effects of TM and TE modes are investigated using an infinitesimal magnetic dipole and a magnetic current sources, respectively. The optimal operating frequency is found within the [10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> , 3 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> ]-Hz range and can be roughly approximated as f ≈ 2.2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> /d for deep implantation (i.e. d ≳ 2 cm). Considering the implantation depth, the operating frequency, the polarization, and the directivity, we show that about an order-of-magnitude efficiency improvement is achievable compared to existing devices.
Impact of periprocedural biomarker elevation on mortality in stable angina pectoris patients undergoing elective coronary intervention: a systematic review and meta-analysis including 24 666 patients (2019)

The occurrence of periprocedural myocardial infarction after an elective percutaneous coronary intervention in patients with stable angina pectoris is associated with a statistically significant increase in subsequent all-cause mortality and cardiac mortality.
Seamlessly interlinking TV and Web content to enable Linked Television (2014)

This paper explains Linked Television, a concept for interlinked TV and Web content within a shared digital ecosystem under the control of the content owner. An end to end platform is being developed to ingest, analyse and annotate TV programmes, and generate links to related Web content from the TV programme itself. We focus on a highly automated system available as a Web service to help lower the cost of enrichment of TV programming, and report on current demonstrators of the system's capabilities. While still the subject of research, we hope to provide wider access to this platform as a step towards making Linked Television a future reality. Author Keywords Linked Television; hypervideo; interactive TV; smart TV; second screen; annotation; enrichment
Video object cut and paste (2005)

In this paper, we present a system for cutting a moving object out from a video clip. The cutout object sequence can be pasted onto another video or a background image. To achieve this, we first apply a new 3D graph cut based segmentation approach on the spatial-temporal video volume. Our algorithm partitions watershed presegmentation regions into foreground and background while preserving temporal coherence. Then, the initial segmentation result is refined locally. Given two frames in the video sequence, we specify two respective windows of interest which are then tracked using a bi-directional feature tracking algorithm. For each frame in between these two given frames, the segmentation in each tracked window is refined using a 2D graph cut that utilizes a local color model. Moreover, we provide brush tools for the user to control the object boundary precisely wherever needed. Based on the accurate binary segmentation result, we apply coherent matting to extract the alpha mattes and foreground colors of the object.
Thiazole: A Versatile Standalone Moiety Contributing to the Development of Various Drugs and Biologically Active Agents (2022)

For many decades, the thiazole moiety has been an important heterocycle in the world of chemistry. The thiazole ring consists of sulfur and nitrogen in such a fashion that the pi (π) electrons are free to move from one bond to other bonds rendering aromatic ring properties. On account of its aromaticity, the ring has many reactive positions where donor-acceptor, nucleophilic, oxidation reactions, etc., may take place. Molecules containing a thiazole ring, when entering physiological systems, behave unpredictably and reset the system differently. These molecules may activate/stop the biochemical pathways and enzymes or stimulate/block the receptors in the biological systems. Therefore, medicinal chemists have been focusing their efforts on thiazole-bearing compounds in order to develop novel therapeutic agents for a variety of pathological conditions. This review attempts to inform the readers on three major classes of thiazole-bearing molecules: Thiazoles as treatment drugs, thiazoles in clinical trials, and thiazoles in preclinical and developmental stages. A compilation of preclinical and developmental thiazole-bearing molecules is presented, focusing on their brief synthetic description and preclinical studies relating to structure-based activity analysis. The authors expect that the current review may succeed in drawing the attention of medicinal chemists to finding new leads, which may later be translated into new drugs.
[Curative Surgery for Advanced Gastric Cancer with Extensive Lymph Node Metastasis after Long-Term Chemotherapy]. (2015)

A 65-year-old man was diagnosed with HER2-positive gastric cancer considered unresectable owing to multiple distant lymph node metastases. After long-term chemotherapy, the original lesion disappeared, while peri-gastric lymph node metastases remained. Therefore, we performed lower mediastinal lymph node dissection, total gastrectomy with regional lymph node dissection (D2) and cholecystectomy. Pathological evaluation indicated that the main gastric tumor showed complete response, while there was metastasis in the No.3 lymph nodes, which showed HER2 positivity (3+). At present, the patient has received Xeloda plus trastuzumab and remains relapse-free 5 months after conversion surgery.
Purification and characterization of an endo-1,3-β-glucanase from Arthrobacter sp. (2004)

An endo-1,3-β-glucanase from Arthrobacter sp. was purified by ammonium sulfate precipitation, anion-exchange and gel-filtration chromatographies. SDS/PAGE and gel-filtration chromatography suggested a monomer enzyme with molecular mass of 32,500. N-terminal sequence for 10 residues was APGDLLWSDE. Stable and optimum pHs were 5 to 8 and 6.5, respectively. Optimum temperature was 55°C , however, above 50°C its activity was lost rapidly. The Michaelis constant Km for laminaritetraose, laminaripentaose, laminarihexaose, laminariheptaose, and laminarin were 0.12, 0.11, 0.067, 0.066mM, and 0.16mg/ml, respectively. Curdlan and lichenan were also hydrolyzed. The purified enzyme did not give product by digestion with endoglycosidase H (Streptomyces griseus), indicating that the carbohydrate moiety was little consisted in the enzyme protein, if any, with N-linked chain or other type linkage. It was suggested that the enzyme belong to the family 16 of glucosyl hydrolase from the properties as above mentioned.
Stem cells do play with dice: A statistical physics view of transcription (2009)

Embryonic stem cells display wide-spread pervasive transcriptional output. Here, we propose that multiple simultaneous transcriptional states underlay pluripotency.
Abstract 4541: The design, synthesis and evaluation of selective FR α and β substrates with potent GARFTase inhibitory activity as antitumor agents (2010)

Abstract Glycinamide ribonucleotide formyl transferase (GARFTase) catalyzes the first of two formyl transfer steps in the de novo purine biosynthetic pathway. Potent inhibitors of GARFTase and de novo purine biosynthesis have shown promise as antitumor drugs. However, a lack of selectivity and toxicity has been a major hurdle for GARFTase inhibitors as cancer chemotherapeutic agents. We recently reported a series of thieno[2,3-d]pyrimidine classical antifolates that are specifically taken up by the folate receptor (FR) and inhibit FR expressing tumor cells at nanomolar IC50 values (IC50= 4.9 nM in human KB tumor cells, IC50= 5.9 nM in human IGROV1 tumor cells,). GARFTase was confirmed as the target. Notably, the thieno[2,3-d]pyrimidine antifolates are unique and distinct from all other classical antifolates evaluated, including pemetrexed (PMX), raltitrexed (RTX), and methotrexate (MTX) in that they are neither substrates for reduced folate carrier (RFC) nor for the proton-coupled folate transporter (PCFT). This characteristic results in selective targeting of FR-expressing cells, without toxicity to normal cells that express RFC. To further investigate the structural requirements of antifolates with respect to FR substrate activity, a series of four 2-amino-4-oxo-6-substituted thieno[2,3-d]pyrimidines with different aryl side chains were synthesized. This afforded potent antitumor agents with increased inhibitory activity against FRα expressing tumor cells (IC50= 2 nM in human KB tumor cells) 2.5- fold more potent than the lead benzoyl compound. In addition, these thieno[2,3-d]pyrimidines were specific for FRα and were not transported by RFC or PCFT and indicated that the nature of the bicyclic scaffold is an important structural determinant for transport specificity. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4541.
Quantitative phase microscopy of cells in flow using flipping interferometry (Conference Presentation) (2017)

Measurements of biological cells during flow are highly important for medical diagnosis based on cell sorting. In the case of cell imaging during flow, very rapid image acquisition capabilities are required to enable fast cell flow for analyzing a sufficient number of cells. We present a new flipping interferometry (FI) module for simplified off-axis close-to-common-path interferometric phase microscopy. This wide-field off-axis interferometric module provides rapid quantitative phase microscopy of biological cells during flow in a microfluidic channel, with potential of integration into cell sorting devices. Various experimental demonstrations are presented.
Mechanism for the Enzymatic Formation of 4-(β-d-Ribofuranosyl)aminobenzene 5‘-Phosphate during the Biosynthesis of Methanopterin (1998)

A central step in the biosynthesis of the modified folate methanopterin is the condensation of p-aminobenzoic acid (pAB) and 5-phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) which produce 4-(beta-D-ribofuranosyl)aminobenzene 5'-phosphate (beta-RFA-P) [White, R. H. (1996) Biochemistry 35, 3447-3456]. This reaction, catalyzed by the enzyme beta-RFA-P synthase, is unique among known phosphoribosyltransferases in that a decarboxylation of one of the substrates (pAB) occurs during the reaction and a C-riboside rather than an N-riboside is the product. In this work, the reaction catalyzed by the enzyme from Methanosarcina thermophila is shown to be analogous to other phosphoribosyltransferase reactions in that pyrophosphate is released as a product of the reaction, which is dependent upon magnesium ions. The molecular weight of the enzyme was estimated to be 65 000 using gel filtration chromatography, and the pH optimum was 4.8. Kinetic analysis indicated that the reaction involved a sequential pattern of substrate binding. Benzoic acid and several para-substituted benzoic acids inhibited beta-RFA-P synthase activity, while aniline, 4-aminobenzamide, and the methyl ester of pAB did not, indicating that an ionized carboxylic group plays a role in the binding of pAB. The observation that the enzyme was not inhibited by carbonyl reagents and that 4-hydroxybenzoic acid served as an alternate substrate, producing 4-(beta-D-ribofuranosyl)hydroxybenzene 5'-phosphate as the product, indicated that pyridoxal phosphate was not directly involved in the reaction mechanism. Incubation of the enzyme with PRPP and either pAB or 4-aminothiobenzoic acid in the presence of sodium cyanoborohydride led to the decreased production of beta-RFA-P and the accumulation of a reduced form of the proposed cyclohexadienimine reaction intermediates. These compounds were characterized by their acid-catalyzed decomposition which produces beta-D-ribofuranosylbenzene 5'-phosphate. On the basis of these results, a concerted mechanism is proposed for beta-RFA-P synthase in which an SN1-like reaction produces oxonium ion character at C-1 of PRPP which undergoes an ipso electrophilic aromatic substitution reaction at the carboxylic acid-bound carbon of pAB. Decarboxylation of the resulting cyclohexadienimine intermediate leads to the formation of beta-RFA-P.
A Novel 2-D Position Sensitive Silicon Detector With Micron Resolution for Heavy Ion Tracking (2006)

A new 2-D position sensitive silicon detector for tracking of energetic heavy ions is under development in a program to study the radiation effect within a single human cell. The detector is based on a concept of interleaved pixel electrodes arranged in a projective 2-D strip readout (stripixel). A fine position resolution in the sub-micron range can be achieved by determining the centroid of the charge collected on pixel electrodes with a granularity in the range of 10 mum. Beam test results with 1 GeV/n Fe ions have demonstrated an rms position resolution of about 0.5 mum with a 30 mum pixel pitch
Data from RIPK3-Induced Inflammation by I-MDSCs Promotes Intestinal Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;Myeloid-derived suppressor cells (MDSC) promote colorectal cancer by several mechanisms, including suppression of antitumor T cells and production of tumorigenic factors. We previously showed that an intermediate MDSC subset (I-MDSC) is expanded in an intestinal tumor model (Apc&lt;sup&gt;Min/+&lt;/sup&gt; mice), but the importance of this subset in promoting tumors is unclear. Here, we show that I-MDSCs are a distinct heterogeneous subset due to differential and reduced expression of the monocytic marker, Ly6C, and granulocytic marker, Ly6G. Besides causing necroptotic cell death, receptor-interacting protein kinase 3 (RIPK3) has an alternate function as a signaling component inducing cytokine synthesis. We evaluated whether RIPK3 regulates inflammatory cytokines in I-MDSCs to assess the nonimmunosuppressive function of I-MDSCs in promoting tumors. Inhibition of RIPK3 with the commercially available small-molecule inhibitor GSK 872 showed that RIPK3-mediated inflammation promoted intestinal tumors in two intestinal tumor models, Apc&lt;sup&gt;Min/+&lt;/sup&gt; mice and an MC38 transplantable tumor model. Mechanistically, RIPK3 signaling in I-MDSC increased tumor size by expanding IL17-producing T cells in MC38 tumors. Collectively, these data suggest RIPK3 signaling as a potential therapeutic target in colorectal cancer.&lt;/p&gt;Significance:&lt;p&gt;The specific role of RIPK3 in intestinal tumors and MDSC function sheds light on a key inflammatory mechanism driving tumorigenesis and allows for possible therapeutic intervention.&lt;/p&gt;&lt;/div&gt;