gebhart/patrepeval huggingface dataset:
Cloning of the major histocompatibility complex class II promoter binding protein affected in a hereditary defect in class II gene regulation. (1989)

The regulation of major histocompatibility complex class II gene expression is directly involved in the control of normal and abnormal immune responses. In humans, HLA-DR, -DQ, and -DP class II heterodimers are encoded by a family of alpha- and beta-chain genes clustered in the major histocompatibility complex. Their expression is developmentally controlled and normally restricted to certain cell types. This control is mediated by cis-acting sequences in class II promoters and by trans-acting regulatory factors. Several nuclear proteins bind to class II promoter sequences. In a form of hereditary immunodeficiency characterized by a defect in a trans-acting regulatory factor controlling class II gene transcription, we have observed that one of these nuclear factors (RF-X) does not bind to its target sequence (the class II X box). A cDNA encoding RF-X was isolated by screening a phage expression library with an X-box binding-site probe. The recombinant protein has the binding specificity of RF-X, including a characteristic gradient of affinity for the X boxes of HLA-DR, -DP, and -DQ promoters. RF-X mRNA is present in the regulatory mutants, indicating a defect in the synthesis of a functional form of the RF-X protein.
Rapid HPLC Screening of Jasmonate-Induced Increases in Tobacco Alkaloids, Phenolics, and Diterpene Glycosides in Nicotiana attenuata (2001)

A rapid, HPLC-based screening procedure for the main classes of secondary metabolites in Nicotiana attenuata leaves (alkaloids, phenolics, and diterpene glycosides) is reported. In a single step, leaves are extracted in aqueous acidified (0.5% acetic acid) methanol, and the extracted compounds are separated by reversed-phase HPLC with an acidic water/acetonitrile gradient in <30 min. The utility of the method in quantifying changes in the secondary metabolites after methyl jasmonate treatment of the plants, a treatment known to elicit resistance to herbivores in nature, is illustrated. Methyl jasmonate treatment elicited dramatic increases in some secondary metabolites (caffeoylputrescine, nicotine, and diterpene glycosides increased 12.5-, 1.4-, and 1.9-fold, respectively) but left others, such as rutin, unchanged. Such broad-based analytical screens will help characterize environmental and genetic changes in secondary metabolite profiles.
Identification of a novel partner gene, KIAA1217, fused to RET: Functional characterization and inhibitor sensitivity of two isoforms in lung adenocarcinoma (2016)

REarranged during Transfection (RET) fusion genes are detected in approximately 1% of lung adenocarcinomas and known primarily as oncogenic driver factors. Here, we found a novel RET fusion gene, KIAA1217-RET, and examined the functional differences of RET51 and RET9 protein, fused with KIAA1217 in cancer progression and drug response. KIAA1217-RET, resulting from the rearrangement of chromosome 10, was generated by the fusion of KIAA1217 exon 11 and RET exon 11 from a non-small cell lung cancer patient. Expression of this gene led to increased cell growth and invasive properties through activations of the PI3K/AKT and ERK signaling pathways and subsequently enabled oncogenic transformation of lung cells. We observed that cells expressing KIAA1217-RET9 fusion protein were more sensitive to vandetanib than those expressing KIAA1217-RET51 and both isoforms attenuated cellular growth via cell cycle arrest. These results demonstrated that KIAA1217-RET fusion represents a novel oncogenic driver gene, the products of which are sensitive to vandetanib treatment, and suggested that the KIAA1217-RET-fusion gene is a promising target for lung cancer treatment.
Relaxed Quantization for Discretized Neural Networks (2018)

Neural network quantization has become an important research area due to its great impact on deployment of large models on resource constrained devices. In order to train networks that can be effectively discretized without loss of performance, we introduce a differentiable quantization procedure. Differentiability can be achieved by transforming continuous distributions over the weights and activations of the network to categorical distributions over the quantization grid. These are subsequently relaxed to continuous surrogates that can allow for efficient gradient-based optimization. We further show that stochastic rounding can be seen as a special case of the proposed approach and that under this formulation the quantization grid itself can also be optimized with gradient descent. We experimentally validate the performance of our method on MNIST, CIFAR 10 and Imagenet classification.
Application of Data Mining and Evolutionary Optimization in Catalyst Discovery and High‐Throughput Experimentation – Techniques, Strategies, and Software (2005)

Abstract Data‐mining and evolutionary optimization techniques are powerful tools to improve the efficiency of high‐throughput experimentation (HTE) to discover new materials, drugs, or catalysts.
Gender differences in the patterns of coronary angiography and PTCA use in a university hospital in Taiwan. (2000)

We concluded that women had fewer CAG and PTCA procedures than men, and the influence of CAG on the PTCA series was significantly higher in men than in women.
Experimental Security Analysis of a Modern Automobile (2010)

Modern automobiles are no longer mere mechanical devices; they are pervasively monitored and controlled by dozens of digital computers coordinated via internal vehicular networks. While this transformation has driven major advancements in efficiency and safety, it has also introduced a range of new potential risks. In this paper we experimentally evaluate these issues on a modern automobile and demonstrate the fragility of the underlying system structure. We demonstrate that an attacker who is able to infiltrate virtually any Electronic Control Unit (ECU) can leverage this ability to completely circumvent a broad array of safety-critical systems. Over a range of experiments, both in the lab and in road tests, we demonstrate the ability to adversarially control a wide range of automotive functions and completely ignore driver input\dash including disabling the brakes, selectively braking individual wheels on demand, stopping the engine, and so on. We find that it is possible to bypass rudimentary network security protections within the car, such as maliciously bridging between our car's two internal subnets. We also present composite attacks that leverage individual weaknesses, including an attack that embeds malicious code in a car's telematics unit and that will completely erase any evidence of its presence after a crash. Looking forward, we discuss the complex challenges in addressing these vulnerabilities while considering the existing automotive ecosystem.
Cloning, sequence analysis, and expression of ligninolytic phenoloxidase genes of the white-rot basidiomycete Coriolus hirsutus. (1990)

Two cDNAs and two genomic DNAs coding for the allelic forms of the ligninolytic phenoloxidase were isolated from the white-rot fungus Coriolus hirsutus. The cloned genes were identified in genetic libraries by hybridization screening using four deoxyoligonucleotide probes which corresponded to the partial amino acid sequence of the purified enzyme. Each cDNA encoded the full-length of the phenoloxidase, a protein consisting of 499 amino acid residues, and its putative signal peptide of 21 amino acid residues. The nucleotide sequences of the two alleles differed by 18 single base changes within the open reading frames resulting in one amino acid substitution. Ten small introns interrupted both genomic DNAs as indicated by direct comparison with the corresponding cDNAs. Putative eukaryotic regulatory sequences, "CAAT" and "TATA," were observed in the 5'-flanking region of both genomic DNAs. Each of the phenoloxidase cDNAs was successfully expressed in an active form in Saccharomyces cerevisiae using the useful yeast expression vector YEp51.
Bmp4 and Fgf10 play opposing roles during lung bud morphogenesis (2000)

Morphogenesis of the mouse lung involves reciprocal interactions between the epithelial endoderm and the surrounding mesenchyme, leading to an invariant early pattern of branching that forms the basis of the respiratory tree. There is evidence that Fibroblast growth factor 10 (Fgf10) and Bone Morphogenetic Protein 4 (Bmp4), expressed in the distal mesenchyme and endoderm, respectively, play important roles in branching morphogenesis. To examine these roles in more detail, we have exploited an in vitro culture system in which isolated endoderm is incubated in Matrigel(TM) substratum with Fgf-loaded beads. In addition, we have used a Bmp4(lacZ) line of mice in which lacZ faithfully reports Bmp4 expression. Analysis of lung endoderm in vivo shows a dynamic pattern of Bmp4(lacZ) expression during bud outgrowth, extension and branching. In vitro, Fgf10 induces both proliferation and chemotaxis of isolated endoderm, whether it is derived from the distal or proximal lung. Moreover, after 48 hours, Bmp4(lacZ) expression is upregulated in the endoderm closest to the bead. Addition of 30-50 ng/ml of exogenous purified Bmp4 to the culture medium inhibits Fgf-induced budding or chemotaxis, and inhibits overall proliferation. By contrast, the Bmp-binding protein Noggin enhances Fgf-induced morphogenesis. Based on these and other results, we propose a model for the combinatorial roles of Fgf10 and Bmp4 in branching morphogenesis of the lung.
Art and accountability: the languages of design and managerial control (1996)

To hard‐pressed managements in competitive product markets, the aesthetic design of products appears to offer an attractive means of creating competitive advantage. In this situation, researchers on design management are beginning to construct forms of accountability for design so as to guarantee its impact on the market in advance. There are parallels between this initiative and the encroachment of audit controls in the public services. Drawing on theoretical resources developed in the body of research on this ‘audit explosion’, this paper argues that these attempts to subject the design process to audit involve a redefinition of the ‘language’ through which it communicates. Insofar as the result is to subordinate design’s languages of form texture and colour to audit’s languages of words and number, the result is likely to be a self‐defeating reduction of design to rehearsals of the banal, the clichéd and the bland.
Stem cell delivery vehicle. (1990)

Bone marrow contains a rare class of stem cells capable of developing into a number of mesenchymal tissues. The delivery of these cells to appropriate skeletal sites will require uniquely compatible biomaterials. Porous calcium phosphate ceramics may provide such a vehicle for the repair of bone. The experimental basis for this proposal is discussed.
Ribonucleotide reductase R2 component is a novel malignancy determinant that cooperates with activated oncogenes to determine transformation and malignant potential (1996)

Ribonucleotide reductase is a highly regulated cell cycle-controlled activity that is essential for DNA synthesis and repair. A retroviral vector for the R2 component of mammalian ribonucleotide reductase, the rate-limiting protein for enzyme activity and DNA synthesis in proliferating cells, was constructed and introduced into mammalian cells. Expression of Myc epitope-tagged R2 protein in benign BALB/c 3T3 and NIH 3T3 cells leads to a greatly increased frequency of focus formation in cooperation with H-ras transformation. Four lines of H-ras-transformed mouse 10T1/2 fibroblasts showed increased growth efficiency in soft agar after infection with the recombinant R2 expression virus vector. Furthermore, cells with altered R2 expression also exhibited significantly reduced subcutaneous tumor latency and increased tumor growth rates in syngeneic mice, and showed markedly elevated metastatic potential in lung metastasis assays. The results indicate that altered R2 gene expression cooperates with ras in mechanisms of malignant progression. A major Ras pathway involves the Raf-1 protein, which is recruited to the plasma membrane for activation. We show that recombinant R2 expression leads to significant increases in membrane-associated Raf-1 protein and mitogenactivating protein kinase-2 activity suggesting a mechanism for the observed Ras/R2 synergism. In support of this finding, we observed that activated Rac-1, which operates parallel to Raf-1 and cooperates with Raf-1 in Ras activated pathways, also cooperates with R2 in cellular transformation. These studies demonstrate that the R2 protein can participate in other critical cellular functions in addition to ribonucleotide reduction, and that deregulated R2 is a novel tumor progressor determinant that cooperates in oncogene-mediated mechanisms, which control malignant potential.
Technology for SiGe heterostructure-based CMOS devices (1999)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1999.
Characterization of soluble forms of NCAM (1987)

Neural cell adhesion molecule (NCAM) has been described as a family of membrane glycoproteins. However, soluble NCAM immunoreactivity has long been recognized. We here show that soluble NCAM is composed of two quantitatively major polypeptides of Mr 180,000 and 115,000 and two minor components of Mr 160,000 and 145,000. Soluble NCAM was immunochemically identical to membrane NCAM, was polysialylated and carried the HNK-1 epitope. It only constituted 0.8% of total NCAM in newborn rat brain. Soluble NCAM appeared in neuronal cell culture medium 15-30 min after the start of synthesis preceding accumulation of membrane-associated NCAM on the cell surface. This indicates that soluble NCAM contains a secreted component.
Nucleotide sequence and genome organization of human parvovirus B19 isolated from the serum of a child during aplastic crisis (1986)

The nucleotide sequence of an almost-full-length clone of human parvovirus B19 was determined. Whereas the extreme left and right ends of this genomic clone are incomplete, the sequence clearly indicates that the two ends of viral DNA are related by inverted terminal repeats similar to those of the Dependovirus genus. The coding regions are complete in the cloned DNA, and the two large open reading frames which span almost the entire genome are restricted to one strand, as has been found for all other parvoviruses characterized to date. From the DNA sequence we conclude that the organization of the B19 transcription units is similar although not identical to those of other parvoviruses. In particular, we predict that the B19 genome may utilize a fourth promoter to transcribe mRNA encoding the major structural polypeptide, VP2. Analysis of the putative polypeptides confirms that B19 is only distantly related to the other parvoviruses but reveals that there is a small region in the gene probably encoding the major nonstructural protein of B19, which is closely conserved between all of the parvovirus genomes for which sequence information is currently available.
In vivo and in vitro complexes of activated protein C with two inhibitors in baboons (1991)

Abstract In vivo complex formation of activated protein C with protein C inhibitor (APC-PCI) and with alpha 1-antitrypsin (APC-alpha 1AT) following infusion of 0.25 or 1.0 mg APC/kg in 1 hour into baboons was studied using immunoblotting and sandwich enzyme-linked immunosorbent assay (ELISA)s. Before APC infusion, detectable plasma levels (about 30 ng/mL) of APC-alpha 1AT complex were found in the baboon plasma. At the lower APC dose, APC-PCI and APC-alpha 1AT complex levels were 1.4 +/- 0.3 (mean +/- SD) and 0.8 +/- 0.1 microgram/mL after 1 hour of infusion. At the higher APC dose, the APC-PCI level was similar to the APC-alpha 1AT level during the first 30 minutes, but after 1 hour of infusion the APC-alpha 1AT level was higher than the APC-PCI level, reaching 4.1 +/- 1.2 and 2.9 +/- 1.2 microgram/mL, respectively. After 24 hours, complex levels had returned to basal conditions. During infusion of protein C (1.0 mg/kg in 1 hour), both complexes were detected in low concentrations. Following bolus injection of APC, half- lives (t1/2) for APC and APC-PCI and APC-alpha 1AT complexes of 10, 40, and 140 minutes, respectively, were observed. After 1-hour incubation with 2.5 micrograms/mL APC, baboon plasma contained 1.0 +/- 0.2 and 0.8 +/- 0.1 microgram/mL of APC-PCI and APC-alpha 1AT, respectively. Addition of 10 micrograms/mL APC to baboon plasma yielded 2.5 and 2.4 micrograms/mL APC-PCI and APC-alpha 1AT after 1 hour, respectively. Immunoblotting analysis also showed in vivo formation of complexes of APC with an auxilliary inhibitor but not in vitro in citrated plasma. These data show that both PCI and alpha 1AT are physiologic inhibitors of APC and suggest that when PCI is depleted by a high dose of APC, alpha 1AT becomes the major inhibitor of APC.
Expression of high-affinity interleukin 4 receptors on murine sarcoma cells and receptor-mediated cytotoxicity of tumor cells to chimeric protein between interleukin 4 and Pseudomonas exotoxin. (1991)

The presence of interleukin 4 receptor (IL-4R) on methylcholanthrene (MCA-106, MCA-102, and MC-38)- and viral DNA (G-2TS and 14-2TS)-induced murine sarcoma cells was demonstrated. MCA-106 tumor cells express about 500 to 1348 (median, 800) interleukin 4 (IL-4) binding sites/cell with a dissociation constant (Kd) of 115 +/- 26 pM (mean +/- SD, n = 4). By Northern blot analysis, tumor cells exhibited a single mRNA species of 3.9 kilobases. Other murine sarcoma (MCA-102), colon adenocarcinoma (MC-38), G-2TS, and 14-2TS tumor cells express low numbers of IL-4R. By immunoperoxidase staining, 81 to 92% of the cells from fresh MCA-106 tumors were positive for IL-4 receptors, while only 7 to 10% of tumor-infiltrating cells were Thy 1.2 and less than 1% Mac-1 positive. Using a chimeric protein composed of IL-4 and Pseudomonas exotoxin (IL-4-PE40), we observed that IL-4-PE40 was cytotoxic (determined by inhibition of protein synthesis by [3H]leucine uptake) to MCA-106 tumor cells in a dose-dependent manner. A nonchimeric protein (PE40) that cannot bind to the IL-4R did not inhibit protein synthesis in tumor cells. A chimeric mutant protein (IL4-PE40 asp553) that can bind to IL-4 receptors but does not have the capability to inhibit protein synthesis was not cytotoxic to tumor cells. These studies strongly suggest that IL-4R on murine MCA-106 sarcoma cells is internalized when occupied by IL-4 PE40. Furthermore, a neutralizing antibody (11B11) to IL-4 completely abolished the protein synthesis-inhibitory activity of IL-4-PE40. G-2TS tumor cells which expressed low numbers of IL-4 receptors were not vulnerable to cytotoxicity by IL-4-PE40. Taken together, these data suggest that IL-4 receptor may be a target for IL-4-toxin therapy.
Fair cryptosystems (1994)

There is a growing concern that the wide use of encryption may be more dangerous than helpful to society. In particular, good encryption schemes make court-authorized line-tapping, an effective tool for law enforcement, impossible. Addressing this concern, we show how to construct cryptosystems in a fair way, that is, so as to allow a democratic country to strike the desired balance between the needs of the Government and those of the Citizens. Fair cryptosystems enjoy the following properties: (1) they cannot be misused by criminal organizations and (2) they guarantee to the Citizens exactly the same rights to privacy they currently have under the law. We actually show how to transform any cryptosystem into a fair one. The transformed systems preserve the security and efficiency of the original ones. Thus one can still use whatever system he believes to be more secure, and enjoy the additional properties of fairness. Moreover, for today''s best known cryptosystems, our transformation is particularly efficient and convenient.
Barrier inhomogeneities at Schottky contacts (1991)

We present a new analytical potential fluctuations model for the interpretation of current/voltage and capacitance/voltage measurements on spatially inhomogeneous Schottky contacts. A new evaluation schema of current and capacitance barriers permits a quantitative analysis of spatially distributed Schottky barriers. In addition, our analysis shows also that the ideality coefficient n of abrupt Schottky contacts reflects the deformation of the barrier distribution under applied bias; a general temperature dependence for the ideality n is predicted. Our model offers a solution for the so-called T0 problem. Not only our own measurements on PtSi/Si diodes, but also previously published ideality data for Schottky diodes on Si, GaAs, and InP agree with our theory.
Keratinocyte Growth Factor Expression and Activity in Cancer: Implications for Use in Patients With Solid Tumors (2006)

Keratinocyte growth factor (KGF) is a locally acting epithelial mitogen that is produced by cells of mesenchymal origin and has an important role in protecting and repairing epithelial tissues. Use of recombinant human KGF (palifermin) in patients with hematologic malignancies reduces the incidence and duration of severe oral mucositis experienced after intensive chemoradiotherapy. These results suggest that KGF may be useful in the treatment of patients with other kinds of tumors, including those of epithelial origin. However, its application in this context raises issues that were not pertinent to its use in hematologic cancer because epithelial tumor cells, unlike blood cells, often express the KGF receptor (FGFR2b). Thus, it is important to examine whether KGF could promote the growth of epithelial tumors or protect such tumor cells from the effects of chemotherapy agents. Analyses of KGF and FGFR2b expression in tumor specimens and of KGF activity on transformed cells in vitro and in vivo do not indicate a definitive role for KGF in tumorigenesis. On the contrary, restoring FGFR2b expression to certain malignant cells can induce cell differentiation or apoptosis. However, other observations suggest that, in specific situations, KGF may contribute to epithelial tumorigenesis. Thus, further studies are warranted to examine the nature and extent of KGF involvement in these settings. In addition, clinical trials in patients with solid tumors are underway to assess the potential benefits of using KGF to protect normal tissue from the adverse effects of chemoradiotherapy and its possible impact on clinical outcome.