gebhart/patrepeval huggingface dataset:
Initial therapy for mild to moderate Crohn's disease: mesalamine or budesonide? (2002)

The initial choice of therapy for mild to moderately active Crohn's disease is controversial. Both the National Cooperative Crohn's Disease Study (NCCDS) and the European Cooperative Crohn's Disease Study (ECCDS) demonstrated that sulfasalazine is effective for the induction of remission. Subsequent studies of new mesalamine formulations showed inconsistent results; two trials, however, demonstrated a statistically significant improvement with Pentasa and Asacol treatment, and meta-analyses suggest a modest benefit of mesalamine maintenance therapy. The NCCDS and ECCDS trials found that corticosteroid therapy is much more effective than sulfasalazine for induction of remission, but corticosteroids did not show maintenance benefits. Corticosteroid use is frequently associated with adverse effects, and the majority of patients treated with prednisone become either steroid-refractory or steroid-dependent; many of these patients ultimately need treatment with immunosuppressives and/or surgery. Budesonide, a topical corticosteroid with high first-pass hepatic metabolism, is slightly less effective in inducing remission than conventional corticosteroids but is significantly less likely to cause side effects. Budesonide 9 mg/day was shown to be more effective than mesalamine (Pentasa 4 g/day) for induction therapy, but budesonide has been ineffective as a maintenance therapy. Mesalamine may be useful for patients with more extensive disease, those intolerant of sulfasalazine, or those with contraindications or intolerance to budesonide. Alternatively, sulfasalazine is effective in the presence of colonic disease. Clinicians must decide on the basis of the existing evidence whether budesonide or mesalamine is the preferred initial therapy for active Crohn's disease.
Phospholipase D1 Is Phosphorylated and Activated by Protein Kinase C in Caveolin-enriched Microdomains within the Plasma Membrane (2000)

Activities of phospholipase D (PLD) in diverse subcellular organelles have been identified but the details of regulatory mechanisms in such locations are unknown. Protein kinase C (PKC) is a major regulator of PLD. Serine 2, threonine 147, and serine 561 residues of phospholipase D1 (PLD1) were determined as sites of phosphorylation by PKC (Kim, Y., Han, J. M., Park, J. B., Lee, S. D., Oh, Y. S., Chung, C., Lee, T. G., Kim, J. H., Park, S. K., Yoo, J. S., Suh, P. G., Ryu, S. H. (1999) Biochemistry 38, 10344-10351). In our present study, a triple mutation of these phosphorylation sites diminished markedly phorbol 12-myristate 13-acetate (PMA)-induced PLD1 activity in COS-7 cells. We looked at the location of the PLD1 phosphorylation by PKC by observing PMA induced band shifts and by use of anti-phospho-PLD1 monoclonal antibody. The shifted PMA-induced proteins and the immunoreactivity of the anti-phospho-PLD1 antibody were mainly found in the caveolin-enriched membrane (CEM) fraction. Depletion of cellular cholesterol led to a loss of this compartmentalization of phosphorylated PLD1 in the CEM. Replacement of the cellular cholesterol led to the restoration of phosphorylated PLD1 in the CEM. Immunocytochemical studies of COS-7 cells revealed that PLD1 was localized in the plasma membrane as well as in the vesicular structures in the cytoplasm, but the phosphorylation of PLD1 occurred only in the plasma membrane. Our results, therefore, show that phosphorylation, and thereby activation, of PLD1 by PKC occurs in the caveolin and cholesterol-enriched low density domain of the plasma membrane in COS-7 cells.
Design and Synthesis of Tight Pitch FLCs for Analog Voltage-Limited Electro-Optic Modulators (1994)

The goal of this project was to make liquid crystal materials suitable for use a deformable-helix ferroelectric liquid crystal (DHFLC) device for analog light transmission. Towards this goal, 141 new compounds were synthesized with potential in DHF mixtures, including compounds with novel chiral tails and cores. one class achiral dopants was found to amplify the C* pitch induction abilities of chiral dopants. A subset of this family also helped decrease the crystallization point of mixtures. other compounds, showed tight C* pitch and high polarization. Still other compounds had C* pitch and N* pitch of opposite signs, making them useful for N* pitch compensation. Several compounds, which increase the birefringence of mixture while increasing solubility, are also reported. The newly synthesized compounds we extensively evaluated for relevant properties. Formulation efforts with these new materials resulted in new DHFLC mixtures with tight C* pitch (0.13 microns), long N* pitch, and very wide (&lt;-30 deg C to 73 deg C) C* phases. These could potentially be used in fast-switching analog display devices. The mixtures were evaluated in FLC cells. Further research is required to optimize the LC cells and driving electronics to take full advantage of the newly formulated DHF mixtures. Ferroelectric liquid crystals, Deformable helix ferroelectric liquid crystals, Display devices.
Structural analysis of both products of a reciprocal translocation between c-myc and immunoglobulin loci in Burkitt lymphoma (1985)

The balanced translocations that occur between the c-myc and immunoglobulin loci in Burkitt lymphoma provide an unusual opportunity to analyze both products of a reciprocal recombination. Accordingly, we have determined the structure of the two reciprocal products of a translocation that joins the 5' portion of the c-myc gene on chromosome 8 to the immunoglobulin mu switch recombination signal on chromosome 14. By determining the nucleotide sequences at the translocation crossover points of both product chromosomes, we precisely locate these points with respect to nearby genes. This determination allows us to conclude that translocation involves nonhomologous recombination, is highly conservative of c-myc sequences (deleting only 16 bp at the crossover point), but deletes over 2 Kb of immunoglobulin sequences from the mu switch signal. The mu constant and c-myc genes are joined head-to-head about 3 Kb apart, while the IgH enhancer and an aberrantly rearranged D/J region are linked to sequences 5' of c-myc on the reciprocal product.
Low temperature, low profile, ultra-fine pitch copper-to-copper chip-last embedded-active interconnection technology (2010)

In a continuous drive to achieve low form-factor packages, chip-to-package interconnections have evolved from the conventional solders to a more hybrid technology consisting of copper and solder. However, scaling down the bump pitch to increase the interconnect density poses serious reliability and yield issues. In the previous, a low-profile interconnect architecture, ~20μm total height, was demonstrated comprising of copper-to-copper interconnection and novel adhesive materials. This paper focuses on: (1) design and fabrication of test vehicles to assess the robustness of the interconnect architecture, (2) assembly process development for copper-to-copper interconnections, and (3) reliability and failure analysis of the interconnection. Excellent reliability results are demonstrated under thermal cycling test (TCT) using non-conductive films (NCF) as adhesive. This interconnect scheme is also shown to perform well with different die sizes, die thicknesses and with embedded dies thus offering a great potential for integration with flip chip packages as well as with chip-last embedded active chips in organic substrates. A simple and reliable low-cost and low-temperature direct Cu-Cu bonding is thus demonstrated for the first time.
Artificial Pancreas: In Silico Study Shows No Need of Meal Announcement and Improved Time in Range of Glucose With Intraperitoneal vs. Subcutaneous Insulin Delivery (2021)

Contemporary Artificial Pancreas (AP) consists of a subcutaneous (SC) glucose sensor, a SC insulin pump and a control algorithm. Even the most advanced systems are far from optimal, in particular due to the non-physiologic nature of SC route. While SC insulin delivery is convenient and minimally invasive, it introduces delays to insulin action that make tight control difficult, particularly during meals. In addition frequent patient interventions are needed, e.g., at mealtime. The intraperitoneal (IP) insulin delivery could address this major challenge since it exhibits a faster pharmacokinetics/pharmacodynamics, hence making easier to quickly respond to glycemic disturbances. A 1-day hospital closed-loop study has shown significant improvements of IP glucose control vs SC AP, and that meal announcement is not necessary. However, the IP AP has not been tested in more realistic everyday life conditions. In this work we have performed an in silico study of 14 days of an IP AP by using the UVA/Padova simulator which includes intra- and inter-day variability of insulin sensitivity and several real life scenarios. We show superiority of IP AP vs SC AP in terms of quality of glucose control (time in range 87% IP vs 80% SC) without the need of a meal announcement.
In-die overlay metrology method using SEM images (2018)

We present an overlay measurement method that is designed to use scanning electron microscope (SEM) images taken in the circuit pattern region. In the semiconductor manufacturing, the overlay is currently measured using target patterns fabricated in the scribe line region. However, there are residual errors between the measurement values in the scribe line region and the actual values in the circuit pattern region. Therefore, in-die overlay accuracy measurements using circuit patterns are required for precise overlay control. We have developed an in-die overlay accuracy measurement method based on SEM images. The overlay is directly measured by comparing a golden image and a test image captured in the circuit pattern region. Each layer is automatically recognized from the images by utilizing a “graph cut” technique, and the placement error between the two images is determined and used to calculate the overlay accuracy. This enables us to measure the overlay accuracy without specially designed target patterns or the setting up of measurement cursors. In the numerical experiments using pseudoimages, the proposed method has linearity and sensitivity for the subpixel-order overlay even if the patterns have size variations. The basic performance of this method was evaluated using real SEM images. A measurement repeatability of less than 1.35 nm (0.36 pixel) was achieved, and a reasonable wafer map of the overlay was obtained.
Pathway Analysis and Modeling of the Differentiation of Human Embryonic Stem Cells into Hepatocyte-like Cells (2011)

A more detailed understanding of the differentiation of human embryonic and induced pluripotent stem cells into hepatocyte‐like cells can help to improve therapies for liver diseases, like steatohepatitis. In this work we used microarray‐based expression data to analyze the in vitro differentiation of human embryonic stem cells into hepatocytes. Pathway analysis has been carried out on gene expression data of different stages of the differentiation process from embryonic stem cells into hepatocyte‐like cells via definitive endoderm and hepatic endoderm. Based on pathway analysis we identified signaling pathways, like the GPCR signaling pathway as well as FOXA2 regulatory networks. Based on these highly enriched pathways we constructed a model prototype to better understand and study the differentiation of stem cells into hepatocytes.
Internal photonic crystal lattice structures of planarized opal-patterned chips probed by laser scanning confocal fluorescence microscopy (2002)

Laser scanning confocal microscopy, advantageous as a non-destructive spatial imaging technique, has been used to probe the internal photonic crystal lattice structure of micron scale core–fluorescein-labeled shell–corona silica microspheres that had been crystallized within anisotropically etched relief patterns in the 100 surface of silicon wafers. Using this method it was possible to determine the three-dimensional positioning of individual microspheres that had been allowed to self-assemble within the confines of square and rectangular shaped pyramidal microwells with sub-micron lateral and vertical spatial resolution. This methodology confirmed that microspheres underwent vectorial crystal growth in the form of a face centered cubic lattice inside the pyramidal microwells in which the 100 face of the photonic crystal was oriented parallel to the 100 surface of the silicon wafer. Furthermore it was feasible to visualize both external and internal defects buried within photonic crystal lattices in the planarized opal-patterned chips.
Synthesis and structure of tetraols with convergent and divergent arrays of hydroxy groups (1999)

As hydrogen-bonding hosts with a partially flexible framework, two types of tetrahydroxy compounds with respectively convergent and divergent arrays of hydroxy groups were prepared. The structures of the tetraol with a diethyleneoxy bridge (1a), and that with a m-phenylenedioxy bridge (syn-13a and anti-13b) were determined by X-ray crystallographic studies. syn-13a forms an inclusion crystal with 1,4-dioxane, one molecule of which is bound in the cleft of syn-13a and the other in the intermolecular cavity.
A decision-making framework for acoustic echo cancelation (2006)

We present a decision-making framework for the problem of echo control. This framework enables a unified approach to detecting the changes in the echo path, adaptation, and double-talk detection. Using this framework, we provide new analytical results on consistency and convergence of the echo control algorithm. We also address a new approach, based on the generalized likelihood ratio test, toward joint detection of double-talk and echo path change.
Halichonadins A—D, New Sesquiterpenoids from a Sponge Halichondria sp. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Prosodic and other Long-Term Features for Speaker Diarization (2009)

Speaker diarization is defined as the task of determining ldquowho spoke whenrdquo given an audio track and no other prior knowledge of any kind. The following article shows how a state-of-the-art speaker diarization system can be improved by combining traditional short-term features (MFCCs) with prosodic and other long-term features. First, we present a framework to study the speaker discriminability of 70 different long-term features. Then, we show how the top-ranked long-term features can be combined with short-term features to increase the accuracy of speaker diarization. The results were measured on standardized datasets (NIST RT) and show a consistent improvement of about 30% relative in diarization error rate compared to the best system presented at the NIST evaluation in 2007.
Characterization of the murine IL-5 receptor complex with the use of a panel of monoclonal antibodies. Relationship to the murine IL-3 receptor (1991)

To obtain mAb against the murine IL-5R (mIL-5R), Wistar rats were immunized with B13 cells, a murine Ly-1+ (CD5+) pre-B cell line which is dependent on IL-3 or IL-5 for its growth. A first group of six mAb could immunoprecipitate, from detergent-lysed B13 cells, a 60-kDa polypeptide (p60) corresponding to the recently cloned mIL-5R alpha-chain. A second group of three mAb was able to immunoprecipitate a protein doublet of 130 to 140 kDa (p130 and p140) corresponding to the previously characterized mIL-3R and mIL-3R-like polypeptide, respectively. One mAb (25C9) specifically bound the p130 polypeptide only. Here we show that: 1) mAb directed against the mIL-5R p60 component completely block IL-5 binding; 2) mAb recognizing the p130-p140 doublet interfere with both IL-3 and IL-5 binding; 3) mAb recognizing p130-p140 block the high affinity binding of IL-5 and hence the high affinity mIL-5R consists of the association of the p60 and p130 and/or p140 component; 4) one particular mAb, 25C9, which binds only to the p130 polypeptide, interferes with only IL-3 binding, and has no effect on the binding of IL-5. These results on binding were corroborated by a biologic assay based on the cytokine-dependent proliferation of B13 cells. The results presented here support a model for the mIL-5R consisting of the alpha-chain (p60) associated with the p140 (IL-3R-like), whereas the p130 (IL-3R) is not involved in the IL-5R complex.
Prevention of Action Potentials During Extracellular Electrical Stimulation of Long Duration (1997)

Both depolarization and hyperpolarization caused by an electrical field can prevent action potentials.
Effects of HuIFN-α2 and HuIFN-α (Namalwa) on Breast Cancer Cells Grown in Culture and as Xenografts in the Nude Mouse (1982)

The activity of HuIFN-alpha 2 produced in bacteria has been compared with that of HuIFN-alpha from Namalwa cells (HuIFN-alpha N) as an antiviral (against EMC virus) and antiproliferative agent in normal and malignant cultured human breast cells. The IFN preparations show the same spectrum of antiviral and antiproliferative activity in the human cell strains and lines examined, and are equally effective, when comparable amounts of IFN protein are used. Both interferon preparations inhibit virus growth (EMC) in four types of bovine cells but neither inhibit the growth of these cells. HuIFN-alpha 2 and HuIFN-alpha N can also be shown to effectively inhibit the growth of a transplantable human breast cancer, grown as xenografts in the nude mouse, although the amounts of IFN protein required may not be the same for both preparations.
Femtosecond time-resolved spectroscopy of polarization dynamics in KNbO3 (1991)

Femtosecond time-resolved impulsive stimulated scattering experiments were conducted on KNbO3 at temperatures spanning the orthorhombic phase. A heavily damped soft optic phonon mode associated with the displacive character of the transition and relaxational modes associated with order-disorder character were examined. Previous frequency-domain light scattering experiments had yielded conflicting results for the dynamics of the soft mode and the symmetry of the order-disorder motions. We find the relaxational motion to be of A1 symmetry and the soft mode to be the only low-frequency exictation of B2 symmetry. The soft mode is well described by a damped polariton model without any coupling to a relaxational mode. These results are consistent with a previously proposed eight-site model for the phase transitions.
mTOR acts as a pivotal signaling hub for neural crest cells during craniofacial development (2018)

mTOR is a highly conserved serine/threonine protein kinase that is critical for diverse cellular processes in both developmental and physiological settings. mTOR interacts with a set of molecules including Raptor and Rictor to form two distinct functional complexes, namely the mTORC1 and mTORC2. Here, we used novel genetic models to investigate functions of the mTOR pathway for cranial neural crest cells (NCCs), which are a temporary type of cells arising from the ectoderm layer and migrate to the pharyngeal arches participating craniofacial development. mTOR deletion elicited a proliferation deficit and excessive apoptosis of post-migratory NCCs, leading to growth arrest of the facial primordia along with midline orofacial clefts. Furthermore, NCC differentiation was impaired. Thus, NCC derivatives, such as skeletons, vasculatures and neural tissues were either rudimentary or malformed. We further demonstrate that disruption of mTOR caused P53 hyperactivity and cell cycle arrest in cranial NCCs, and lowering P53 activity by one copy reduction attenuated the severity of craniofacial phenotype in NCC-mTOR knockout mice. Remarkably, NCC-Rptor disruption caused a spectrum of defects mirroring that of the NCC-mTOR deletion, whereas NCC-Rictor disruption only caused a mild craniofacial phenotype compared to the mTOR and Rptor conditional knockout models. Altogether, our data demonstrate that mTOR functions mediated by mTORC1 are indispensable for multiple processes of NCC development including proliferation, survival, and differentiation during craniofacial morphogenesis and organogenesis, and P53 hyperactivity in part accounts for the defective craniofacial development in NCC-mTOR knockout mice.
Synchronous RCC and TCC of the Kidney in a Patient With Multiple Recurrent Bladder Tumors. (1999)

Development of concomitant renal TCC and RCC is an uncommon occurrence, yet many interesting issues can be addressed with this model. The possibility of misdiagnosing a renal TCC for an RCC, the options and importance of treating a retained ureteral stump after performing a radical nephrectomy for a renal TCC, and the risk of developing lower tract TCC in patients with upper tract TCC are some of the issues raised in this case review.
Kinetic Evidence for π-Complex Formation Prior to Oxidative Addition of Propargyl Halides to Triphenylphosphine−Platinum(0) Complexes (2000)

The mechanism of oxidative addition of phenylpropargyl halides to Pt(PPh3)4 to give Pt(η1-CH2C⋮CPh)(X)(PPh3)2 has been investigated on the basis of the kinetics of the reaction and stereomeric analysis of the products. The kinetic results of the reaction showed the contributions of two pathways involving Pt(PPh3)3 and Pt(PPh3)2 complexes as active species. The second-order rate constants for both pathways were on the order of 103 larger than the corresponding rate constants of the oxidative addition reaction of CH3I. Moreover, both active species and the substrate halide gave, as the kinetic product, the isomer having two PPh3 groups located cis, which is also in sharp contrast to the case of the reaction of CH3I. It is proposed that the rate-determining step in the reaction involving Pt(PPh3)2 is the coordination of the C⋮C bond to Pt(PPh3)2 to form Pt(η2-PhC⋮CCH2X)(PPh3)2, which subsequently undergoes rapid collapse to the η3-propargyl complex [Pt(η3-CH2CCPh)(PPh3)2]X and eventually to cis-Pt(η1-CH2C⋮CPh)(X)(PPh3)2. The reaction of Pt(PPh3)3 may also involve a rate-determining C⋮C bond coordination step.
Controlled Sequence Photoresists from Polypeptoids (2022)

Low stochastics, high sensitivity photoresists remain a goal for lithography. Here we present a study of a polymer system, polypeptoids, using a synthetic strategy borrowed from the biomedical community to make improvements to these resist characteristics through control of polymer sequence. We describe peptoid polymers that possess identical molecular size, composition and sequence with higher molecular uniformity than possible by conventional synthetic techniques. We report the results of exposure of these materials to DUV radiation and the chemical changes that occur. In addition, we highlight unexpected observations of the role of sequence on lithographic performance.
Synthesis of 4-Amino-8-(2, 2-Difluoro-2-Deoxy-β-D-Ribo Furanosyl Amino)Pyrimido [5, 4-D]Pyrimidine (dFARPP). Stability and Cellular Cytotoxicity (1994)

Abstract The synthesis of β-dFARPP was accomplished by Mitsunobu coupling of 6-cyanopurine with 2-deoxy-2, 2-difluororibose followed by purine ring-expansion under the action of methanolic ammonia. The title compound inhibited the growth of proliferating human leukemic CCRF-CEM cells at 6.1μg/ml but had no effect on plaque formation by a variety of DNA and RNA viruses.
Volume Rendering FPGA Hardware (1999)

This paper discusses the implementation of volume rendering on FPGA hardware. The FPGA board is based on a 2x2 matrix of FPGA devices that are reprogrammed for different data processing tasks that occur during rendering. Moreover, it is shown how branch and data hazards are overcome in the pipelined system by multithreading.