gebhart/patrepeval huggingface dataset:
Complete cDNA Sequence of the Preproform of Human Pregnancy‐Associated Plasma Protein‐A (1996)

A cDNA that encodes the prepropeptide of pregnancy-associated plasma protein-A (preproPAPP-A), a putative metalloproteinase, has been cloned and sequenced. PAPP-A is synthesized in the placenta as a 1627-residue precursor preproprotein with a putative 22-residue signal peptide and a highly basic propeptide of 58 residues. The prepro-PAPP-A-encoding transcript contains a region with an extremely high G+C content and has an unusually long 5' untranslated region with several upstream short ORF. No alternatively spliced products could be identified by means of Northern blotting experiments or with rapid amplification of 5' cDNA ends experiments. A stretch within the 5' untranslated region shows sequence identities to a partial cDNA isolated from brain and a to cAMP-inducible sequence from a choriocarcinoma cell line.
Volumetric spectroscopic imaging with spiral‐based k‐space trajectories (1998)

Spiral-based k-space trajectories were applied in a spectroscopic imaging sequence with time-varying readout gradients to collect volumetric chemical shift information. In addition to spectroscopic imaging of low signal-to-noise ratio (SNR) brain metabolites, the spiral trajectories were used to rapidly collect reference signals from the high SNR water signal to automatically phase the spectra and to aid the reconstruction of metabolite maps. Spectral-spatial pulses were used for excitation and water suppression. The pulses were designed to achieve stable phase profiles in the presence of up to 20% variation in the radiofrequency field. A gridding algorithm was used to resample the data onto a rectilinear grid before fast Fourier transforms. This method was demonstrated by in vivo imaging of brain metabolites at 1.5 T with 10 slices of 18 x 18 pixels each. Nominal voxel size was 1.1 cc, spectral bandwidth was 400 Hz, scan time was 18 min for the metabolite scan and 3 min for the reference scan.
Differential Expression of CD66a (BGP), a Cell Adhesion Molecule of the Carcinoembryonic Antigen Family, in Benign, Premalignant, and Malignant Lesions of the Human Mammary Gland (1997)

CD66a, also known as biliary glycoprotein (BGP), is a member of the carcinoembryonic antigen (CEA) family and the human homologue of the rat cell-CAM. There is evidence that aberrant expression or loss of CD66a in tumor tissue is of biological significance. No data about its expression in breast carcinoma cells and only sparse information about the expression of CD66a in normal breast are available thus far. In this study we used monoclonal antibodies to analyze the expression of CD66a and CEA in normal tissue, benign lesions, and in noninvasive and invasive carcinomas of the mammary gland. In normal tissue and benign lesions, CD66a was consistently expressed at the apical sites of epithelial cells and in myoepithelia, whereas CEA was absent or was restricted only to some apical membranes within the ductal tree. The specific staining of myoepithelia was most evident in pseudoinfiltrative radial scars and sclerosing adenosis. However, the apical expression of CD66a disappeared with the development of the malignant phenotype in noninvasive and invasive carcinomas, and changed gradually from low- to high-grade noninvasive carcinomas into a predominant uniform membrane staining all around the atypical cells. CEA expression was irregular in intensity and distribution. The native apical CD66a staining was partially preserved in some highly differentiated invasive carcinomas with a better prognosis, such as tubular and papillary carcinomas. These findings indicate that loss of CD66a expression rather than a change in staining patterns coincides with the development of the malignant phenotype.
Modulation of Transforming Growth Factor-βProduction in Normal Human Osteoblast-Like Cells by 17β-Estradiol and Parathyroid Hormone (1991)

Although our laboratory has reported that normal human osteoblast-like (hOB) cells contain estrogen receptors, we have failed to find major effects of 17 beta-estradiol (E2) on modulation of proliferation of bone matrix protein production by hOB cells. Because the major effect of E2 in vivo is to decrease bone resorption and because transforming growth factor-beta (TGF-beta) has been reported to decrease osteoclast-mediated bone resorption, we have tested the hypothesis that the effect of E2 on osteoclast activity is, at least in part, indirectly mediated by enhancing production of TGF-beta by osteoblasts. We therefore have extended our studies to examine possible TGF-beta gene expression including the modulation of the release of TGF-beta by E2 in near homogenous populations of hOB cells. TGF-beta protein production was measured using growth inhibition of CCL-64 cells and verified by blocking effects with anti-TGF-beta antibodies. TGF-beta 1 messenger RNA (mRNA) steady state levels were assessed by northern blot analysis and quantitated by densitometric measurement using 18S ribosomal RNA as a reference. There was an E2 dose-dependent increase in TGF-beta protein production within 24 h of challenge with E2. Northern blots from these cells demonstrated a dose-dependent increase in steady state mRNA levels of TGF-beta 1 within 6 h of treatment. PTH was also a potent stimulator of TGF-beta protein and message levels in a dose-dependent manner. Interestingly, coincubation of equimolar concentrations of E2 and PTH (10(-8) M) abrogated the stimulation of TGF-beta 1 mRNA and protein. Decreasing the relative concentration of PTH in this coincubation with E2 increased TGF-beta 1 mRNA and protein levels. These data support the fact that E2 modulates TGF-beta production in osteoblasts. In this manner TGF-beta may mediate E2 inhibition of osteoclast activity.
Scalable robotic biofabrication of tissue spheroids (2011)

Development of methods for scalable biofabrication of uniformly sized tissue spheroids is essential for tissue spheroid-based bioprinting of large size tissue and organ constructs. The most recent scalable technique for tissue spheroid fabrication employs a micromolded recessed template prepared in a non-adhesive hydrogel, wherein the cells loaded into the template self-assemble into tissue spheroids due to gravitational force. In this study, we present an improved version of this technique. A new mold was designed to enable generation of 61 microrecessions in each well of a 96-well plate. The microrecessions were seeded with cells using an EpMotion 5070 automated pipetting machine. After 48 h of incubation, tissue spheroids formed at the bottom of each microrecession. To assess the quality of constructs generated using this technology, 600 tissue spheroids made by this method were compared with 600 spheroids generated by the conventional hanging drop method. These analyses showed that tissue spheroids fabricated by the micromolded method are more uniform in diameter. Thus, use of micromolded recessions in a non-adhesive hydrogel, combined with automated cell seeding, is a reliable method for scalable robotic fabrication of uniform-sized tissue spheroids.
Development of Multi-Dimensional Data-Modeling Software (2004)

近年のコンピュータの進歩にともない、化学の分野においては日々多くの数値データが蓄積されている。そして、これらのデータから効率的に意味のある知識を抽出するために、多くのケモメトリックス手法が開発、提案されている。通常これらのデータは多次元/多変量であり、従来の統計ソフトウェアでは扱うのが困難であった。そこで、本研究ではこれらのデータを直接扱うことを目的とした、多次元データモデリングソフトウェアの開発を行った。本ソフトウェアを用いることにより、多次元の数値データを用いた解析が可能となる。ユーザは散布図、棒グラフ、折れ線グラフなどの様々なグラフを描くことによって、データの構造を視覚的に捉えることができる。また、Multi-way PLS法やKohonenニューラルネットワークといったモデリング手法を用いて、より詳細な解析を行うことが可能である。
Epidemiology of liver cancer: an overview. (2004)

The incidence of liver cancer varies widely throughout the world, with high rates in sub - Saharan Africa, eastern and southeastern Asia, and Melanesia and a low incidence in Northern and Western Europe and the Americas. Primary cancers of the liver in adults are of two main histological types: hepatocellular carcinoma, which is derived from hepatocytes, and cholangiocarcinoma, which is derived from the epithelial lining of the intrahepatic bile ducts. Hepatocellular cancer is a frequently occurring tumor in individuals in many developing countries, where several important risk factors have been demonstrated, including chronic infection with hepatitis B and C viruses and other environmental factors, such as exposure to aflatoxin, consumption of alcohol, and cigarette smoking. By contrast, cholangiocarcinoma is less common, accounting for only 7.7% of malignant tumors of the liver in the United States. However, in parts of Southeast Asia, cholangiocarcinoma occurs more frequently; it is responsible for more than 60% of liver tumors in northeastern Thailand. The geographic distribution worldwide coincides with endemic areas of the liver flukes, Opisthorchis viverrini and Clonorchis sinensis. The interaction between genes and the environment and the interplay of environmental factors, which include diet and other lifestyle parameters, illustrate the complexity underlying susceptibility.
PEGylated Gold Nanoparticles Conjugated to Monoclonal F19 Antibodies as Targeted Labeling Agents for Human Pancreatic Carcinoma Tissue (2008)

In this study, we describe optical detection of antibody-conjugated nanoparticles bound to surgically resected human pancreatic cancer tissue. Gold nanoparticles stabilized by heterobifunctional polyethylene glycol (PEG) were prepared using approximately 15 nm spherical gold cores and covalently coupled to F19 monoclonal antibodies. The heterobifunctional PEG ligands contain a dithiol group for stable anchoring onto the gold surface and a terminal carboxy group for coupling of antibodies to the outside of the PEG shell. The nanoparticle-antibody bioconjugates form highly stable dispersions and exhibit long-term resistance to agglomeration. This has been demonstrated by dynamic light scattering, size exclusion chromatography, and transmission electron microscopy. The nanoparticle bioconjugates were used to label tumor stroma in approximately 5 mum thick sections of resected human pancreatic adenocarcinoma. After rinsing away nonbound nanoparticles and fixation, the tissue samples were imaged by darkfield microscopy near the nanoparticle resonance scattering maximum (approximately 560 nm). The images display pronounced tissue features and suggest that this novel labeling method could provide for facile identification of cancer tissue. Tumor samples treated with gold nanoparticles conjugated to nonspecific control antibodies and noncancerous pancreatic tissue treated with mAb-F19-conjugated gold nanoparticles both exhibited correctly negative results and showed no tissue staining.
Required presence of both estrogen and pituitary factors for the growth of human breast cancer cells in athymic nude mice. (1981)

Estrogen, prolactin, and other pituitary factors are implicated in the etiology of human breast cancer. In the present study, the effects of estrogen and factors from GH3 rat pituitary tumor cells on the growth of T-47D human breast cancer cells were tested in athymic nude mice. Four groups of nude mice were used: Group 1 (T) received s.c. injection of T-47D cells only; Group 2 (TE) mice were given injections of estradiol valerate and T-47D cells; Group 3 mice were given injections of T-47D and GH3 cells (TG), one cell type on each flank; and Group 4 received estradiol valerate and T-47D and GH3 cells (TEG). We found that the human breast cancer cells, T-47D, did not proliferate in Groups 1 and 3 despite the presence of high circulating levels of prolactin and growth hormone produced by the growing GH3 pituitary tumors in Group 3. This suggested that prolactin and growth hormone were not sufficient to stimulate the growth of human breast cancer cells. T-47D cells exhibited only moderate growth in Group 2 but proliferated rapidly in Group 4. The T-47D tumors of Group 4 were 8 times larger than those in Group 2 after 42 days of growth. These results demonstrate that the simultaneous presence of estrogen and pituitary growth factors are required for maximal growth of T-47D human breast cancer cells in nude mice. The identity of the pituitary-dependent growth factor(S) that stimulates the growth in vivo of human breast cancer cells remains to be elucidated.
Determination of the orientation of an integral membrane protein and sites of glycosylation by oligonucleotide-directed mutagenesis: influenza B virus NB glycoprotein lacks a cleavable signal sequence and has an extracellular NH2-terminal region. (1986)

The membrane orientation of the NB protein of influenza B virus, a small (Mr, approximately 18,000) glycoprotein with a single internal hydrophobic domain, was investigated by biochemical and genetic means. Cell fractionation and protein solubility studies indicate NB is an integral membrane protein, and NB has been shown to be a dimer under nonreducing conditions. Treatment of infected-cell surfaces with proteinase K and endoglycosidase F and immunoprecipitation with a site-specific antibody suggests that the 18-amino-acid NH2-terminal region of NB is exposed at the cell surface. Oligonucleotide-directed mutagenesis to eliminate each of the four potential sites of N-linked glycosylation and expression of the mutant NB proteins in eucaryotic cells suggest that the two sites adjacent to the NH2 terminus are glycosylated. This provides further evidence that NB, which lacks a cleavable NH2-terminal signal sequence, has an exposed NH2 terminus at the cell surface.
Inhibition of cellular proliferation after experimental balloon angioplasty by low-molecular-weight heparin. (1992)

Our data indicate that the proliferative response after balloon angioplasty can be reduced in vivo by early treatment with LMWH and thus encourage further clinical investigations.
Exploring the Structure of Complex Software Designs: An Empirical Study of Open Source and Proprietary Code (2006)

This paper reports data from a study that seeks to characterize the differences in design structure between complex software products. We use design structure matrices (DSMs) to map dependencies between the elements of a design and define metrics that allow us to compare the structures of different designs. We use these metrics to compare the architectures of two software products—the Linux operating system and the Mozilla Web browser—that were developed via contrasting modes of organization: specifically, open source versus proprietary development. We then track the evolution of Mozilla, paying attention to a purposeful “redesign” effort undertaken with the intention of making the product more “modular.” We find significant differences in structure between Linux and the first version of Mozilla, suggesting that Linux had a more modular architecture. Yet we also find that the redesign of Mozilla resulted in an architecture that was significantly more modular than that of its predecessor and, indeed, than that of Linux. Our results, while exploratory, are consistent with a view that different modes of organization are associated with designs that possess different structures. However, they also suggest that purposeful managerial actions can have a significant impact in adapting a design’s structure. This latter result is important given recent moves to release proprietary software into the public domain. These moves are likely to fail unless the product possesses an “architecture for participation.”
Efficient continuous-wave chromium-doped YAG laser (1995)

Continuous-wave power performance of a chromium-doped YAG laser pumped by a Nd:YAG laser is investigated as a function of crystal temperature, output coupling transmission, and emission wavelength. Using a 2%-transmitting output coupler, we obtained as much as 1.9 W of cw output power at 1.45 μm with an absorbed power slope efficiency of 42% when the gain medium was cooled at 3°C. Using the laser efficiency data, we estimated the emission and excited-state absorption cross sections at 1.45 μm and compared them with the previously reported values.
Waterborne Spray Can Coatings (1978)

In preparing to cover this subject for this Symposium, it was difficult to determine how broadly to define water borne coatings and the reasons for their increased interest in the industrial coatings field. Other presentations here have and will mention some of the areas I wish to review. However, for understanding of water borne spray can coatings, we will explain the purpose of spraying the interior of metal cans, review why the various legislative actions of recent years have stimulated development of water borne sprays, give a general insight into coating formulations, and relate field experience with coating handling and equipment operation. From this, we will be able to have some feeling for the future of water borne spray can coatings. The metal can industry supplies the major share of its production for the beer and soft drink markets. With calculations from various industry figures, this highly specialized business today
ChemInform Abstract: Solid‐Supported Reagent Strategies for Rapid Purification of Combinatorial Synthesis Products (1999)

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.
A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach (2008)

The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. A number of computational tools have been developed for this purpose, but there is a lack of large-scale systematic evaluation of their performance. Herein, we used a comprehensive dataset consisting of more than 10,000 previously unpublished MHC-peptide binding affinities, 29 peptide/MHC crystal structures, and 664 peptides experimentally tested for CD4+ T cell responses to systematically evaluate the performances of publicly available MHC class II binding prediction tools. While in selected instances the best tools were associated with AUC values up to 0.86, in general, class II predictions did not perform as well as historically noted for class I predictions. It appears that the ability of MHC class II molecules to bind variable length peptides, which requires the correct assignment of peptide binding cores, is a critical factor limiting the performance of existing prediction tools. To improve performance, we implemented a consensus prediction approach that combines methods with top performances. We show that this consensus approach achieved best overall performance. Finally, we make the large datasets used publicly available as a benchmark to facilitate further development of MHC class II binding peptide prediction methods.
An Economic Analysis of Optimum Population Size Achieved Through Boosting Total Fertility and Net Immigration (2012)

Without net immigration, the population size is projected to decline from 2025 on-ward. Does it matter? To answer this question, the paper proceeds in two main parts. In the first part, taking a citizen’s utility as a measure of welfare, we identify the channels through which a larger population size reduces welfare, on the one hand, and increases welfare on the other hand. The optimum population size is achieved when the net resul-tant effect of all these channels leaves citizens ’ welfare at the maximum. When current and projected total fertility rates without net immigration lead to a projected path of actual population size that glides below the path of optimum population size, the policy question is how best to boost population increase to reach the optimum. The second part of the paper analyzes the costs to Singapore society of reaching the optimum by
Isolation and characterization of a calendic acid producing (8,11)‐linoleoyl desaturase1 (1999)

For the biosynthesis of calendic acid a (8,11)-linoleoyl desaturase activity has been proposed. To isolate this desaturase, PCR-based cloning was used. The open reading frame of the isolated full-length cDNA is a 1131 bp sequence encoding a protein of 377 amino acids. For functional identification the cDNA was expressed in Saccharomyces cerevisiae, and formation of calendic acid was analyzed by RP-HPLC. The expression of the heterologous enzyme resulted in a significant amount of calendic acid presumably esterified within phospholipids. The results presented here identify a gene encoding a new type of (1,4)-acyl lipid desaturase.
Proton and electron radiation analysis of GaInP/sub 2//GaAs solar cells (2002)

Electron and proton radiation damage analysis of solar cells is extremely important for predicting the response of solar cells to radiation environments in space. Two different, compatible methods of analyzing ground based radiation data have been developed. The "displacement damage dose" method is of particular interest because less experimental testing is required to make accurate performance predictions for new photovoltaic devices. In this paper we present electron and proton radiation data for the dual junction GaInP/sub 2//GaAs cell as well as an analysis of the data using the displacement damage dose method.
‘Making up Your Mind’ and the Activity of Reason (2011)

A venerable philosophical tradition holds that we rational creatures are distinguished by our capacity for a special sort of mental agency or self--determination: we can "make up" our minds about what to believe.But what sort of activity is this?Many contemporary philosophers accept a Process Theory of this activity, according to which a rational subject exercises her capacity for doxastic self--determination only on certain discrete occasions, when she goes through a process of consciously deliberating about whether P and concludes by "making a judgment," thereby bringing about a change in what she believes.I argue that the Process Theory implies an unacceptable picture of the agency we exercise in judging, and of the relation of such agency to the condition of belief itself.I suggest that the beliefs of a rational creature are themselves "acts of reason," which reflect the capacity for doxastic self--determination in their very nature, not merely in certain facts about how they can originate.'Making up Your Mind' and the Activity of Reason
Macrophage Markers in Serum and Tumor Have Prognostic Impact in American Joint Committee on Cancer Stage I/II Melanoma (2009)

Both serum levels of sCD163 and the presence of CD68(+) macrophage infiltration at the tumor invasive front are independent predictors of survival in AJCC stage I/II melanoma. CD163(+) cell infiltration in tumor stroma may be predictive of survival.
2nd Order Distortion Cancellation in Photonic Time Stretch Analog-to-Digital Converter (2007)

We show that the symmetry properties of a dual output push-pull Mach-Zehnder modulator can be exploited for rejection of dispersion induced 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">nd</sup> order non-linearities in the time-stretch analog to digital converter. Using differential modulation, followed by signal processing in digital domain, we experimentally demonstrate rejection of harmonic and intermodulation distortions. Simulations predict that non-linear distortion limited dynamic range improves from 34 dB to 57 dB. The approach can also be used for obtaining ultra-wide-band (multi-octave) and high dynamic range analog fiber optic links.