gebhart/patrepeval huggingface dataset:
BCR first exon sequences specifically activate the BCR/ABL tyrosine kinase oncogene of Philadelphia chromosome-positive human leukemias. (1991)

The c-abl proto-oncogene encodes a cytoplasmic tyrosine kinase which is homologous to the src gene product in its kinase domain and in the upstream kinase regulatory domains SH2 (src homology region 2) and SH3 (src homology region 3). The murine v-abl oncogene product has lost the SH3 domain as a consequence of N-terminal fusion of gag sequences. Deletion of the SH3 domain is sufficient to render the murine c-abl proto-oncogene product transforming when myristylated N-terminal membrane localization sequences are also present. In contrast, the human BCR/ABL oncogene of the Philadelphia chromosome translocation has an intact SH3 domain and its product is not myristylated at the N terminus. To analyze the contribution of BCR-encoded sequences to BCR/ABL-mediated transformation, the effects of a series of deletions and substitutions were assessed in fibroblast and hematopoietic-cell transformation assays. BCR first-exon sequences specifically potentiate transformation and tyrosine kinase activation when they are fused to the second exon of otherwise intact c-ABL. This suggests that BCR-encoded sequences specifically interfere with negative regulation of the ABL-encoded tyrosine kinase, which would represent a novel mechanism for the activation of nonreceptor tyrosine kinase-encoding proto-oncogenes.
Fabrication of 0.1-um T-shaped gates by phase-shifting optical lithography (1993)

We have developed a method for patterning sub-micrometer gates with T-shaped cross sections, which may be applied to manufacture high performance field effect transistors (FETs). The technique employs two exposures at the KrF excimer laser wavelength (248 nm). The first exposure uses a phase-shifting mask to pattern 0.1 micrometers isolated spaces. The resist used for the second exposure absorbs the 248 nm radiation strongly enough to produce a profile suitable for lift-off patterning.
Synthesis of extended polycyclic aromatic hydrocarbons by oxidative tandem spirocyclization and 1,2-aryl migration (2017)

The extended polycyclic aromatic hydrocarbons (PAHs) have received significant interdisciplinary attention due to their semiconducting applications in diverse organic electronics as well as intriguing structural interests of well-defined graphene segments. Herein, a highly efficient oxidative spirocyclization and 1,2-aryl migration tandem synthetic method for the construction of extended polyaromatic hydrocarbons (PAHs) has been developed. The CuCl-catalyst/PhCO<sub>3</sub><sup>t</sup>Bu or DDQ oxidation system in the presence of trifluoroacetic acid enables the selective single-electron oxidation to take place preferentially at the more electron-rich alkene moiety of o-biphenylyl-substituted methylenefluorenes, giving rise to the subsequent tandem process. A variety of structurally diverse extended PAHs including functionalized dibenzo[g,p]chrysenes, benzo[f]naphtho[1,2-s]picene, hexabenzo[a,c,fg,j,l,op]tetracene, tetrabenzo[a,c,f,m]phenanthro[9,10-k]tetraphene, tetrabenzo[a,c,f,k]phenanthro[9,10-m]tetraphene, tetrabenzo[a,c,f,o]phenanthro[9,10-m]picene and S-type helicene have been readily synthesized.
POTENT ABILITY OF ANTI-LFA-1 MONOCLONAL ANTIBODY TO PROLONG ALLOGRAFT SURVIVAL1 (1984)

Department of Microbiology University of Massachusetts Amherst MA 01003 Department of Microbiology-Immunology Northwestern University Medical School Chicago IL 60611
FOAD: Fast Optimization-based Autonomous Driving Motion Planner (2018)

Motion planning is one of the core modules for autonomous driving. Among the current motion planning techniques, optimization-based methods have unique advantages since they allow planning in continuous space and they can evaluate multiple objectives (such as hard constraints) in one formulation. However, it is hard to implement optimization-based methods in real-time in complicated environments due to 1) high computational complexity as the optimization problems are usually non-convex; and 2) difficulty to guarantee closed-loop performance because the low level trajectory tracking controller cannot perform perfect tracking. To solve the first challenge, convex feasible set algorithm (CFS) has been proposed for real time non-convex optimization. To solve the second challenge, a fast optimization-based autonomous driving motion planner (FOAD) is proposed in this paper which implements a soft constrained convex feasible set algorithm (SCCFS) as an enhanced version of CFS. The concept of closed-loop smoothness is defined and analyzed in this paper. Simulations and real vehicle experiments verify the efficiency and capability of the planner.
NKG2A Complexed with CD94 Defines a Novel Inhibitory Natural Killer Cell Receptor (1997)

CD94 is a C-type lectin expressed by natural killer (NK) cells and a subset of T cells. Blocking studies using anti-CD94 mAbs have suggested that it is a receptor for human leukocyte antigen class I molecules. CD94 has recently been shown to be a 26-kD protein covalently associated with an unidentified 43-kD protein(s). This report shows that NKG2A, a 43-kD protein, is covalently associated with CD94 on the surface of NK cells. Cell surface expression of NKG2A is dependent on the association with CD94 as glycosylation patterns characteristic of mature proteins are found only in NKG2A that is associated with CD94. Analysis of NK cell clones showed that NKG2A was expressed in all NK cell clones whose CD16-dependent killing was inhibited by cross-linking CD94. The induction of an inhibitory signal is consistent with the presence of two immunoreceptor tyrosine-based inhibitory motifs (V/LXYXXL) on the cytoplasmic domain of NKG2A. Similar motifs are found on Ly49 and killer cell inhibitory receptors, which also transmit negative signals to NK cells.
Construction of a lactococcal expression vector: expression of hen egg white lysozyme in Lactococcus lactis subsp. lactis (1989)

A pair of vectors for expression of heterologous genes in Lactococcus lactis was constructed. In addition to an origin of replication that has a broad host range, these vectors contain a multiple cloning site flanked by gene expression signals originating from L. lactis subsp. cremoris Wg2. The two vectors, about 3.7 kilobase pairs in size, differ only in the type of antibiotic resistance they confer to their hosts. pMG36 carries a kanamycin resistance marker, which was replaced by an erythromycin resistance marker in pMG36e. As an example of the use of these vectors, the hen egg white lysozyme-coding sequence was inserted. A fusion protein of the expected size was detected in a transformed L. lactis subsp. lactis strain by using Western blotting (immunoblotting).
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement (2004)

Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.
Nucleophosmin: from structure and function to disease development (2016)

Nucleophosmin (NPM1) is a critical cellular protein that has been implicated in a number of pathways including mRNA transport, chromatin remodeling, apoptosis and genome stability. NPM1 function is a critical requirement for normal cellular biology as is underlined in cancer where NPM1 is commonly overexpressed, mutated, rearranged and sporadically deleted. Consistent with a multifunctional role within the cell, NPM1 can function not only as a proto-oncogene but also as a tumor suppressor. The aim of this review is to look at the less well-described role of NPM1 in the DNA repair pathways as well as the role of NPM1 in the regulation of apoptosis and its mutation in cancers.
Vascular endothelial growth factor promotes cardiomyocyte differentiation of embryonic stem cells (2006)

Embryonic stem cells (ESCs) overexpressing the vascular endothelial growth factor (VEGF) improve cardiac function in mouse models of myocardial ischemia and infarction by mechanisms that are poorly understood. Here we studied the effects of VEGF on cardiomyocyte differentiation of mouse ESCs in vitro. We used flow cytometry to determine the expression of alpha-myosin heavy chain (alpha-MHC), cardiac troponin I (cTn-I), and Nkx2.5 in differentiated ESCs. VEGF (20 ng/ml) significantly enhanced alpha-MHC, cTn-I, and Nkx2.5 expression in differentiated ESCs. Western blot analysis confirmed these findings. We found that VEGF receptor FMS-like tyrosine kinase-1 (Flt-1) and fetal liver kinase-1 (Flk-1) expression increased during ESC differentiation. Antibodies against Flk-1 totally blocked and against Flt-1 partially blocked VEGF-induced NKx2.5-positive-stained cells. The ERK inhibitor PD-098059 abolished VEGF-induced cardiomyocyte differentiation of ESCs. Our results suggest that VEGF promotes cardiomyocyte differentiation predominantly by ERK-mediated Flk-1 activation and, to a lesser extent, by Flt-1 activation. These findings may be of significance for stem cell and growth factor therapies to regenerate failing cardiomyocytes.
The Role of Therapeutic Angiogenesis in Tissue Repair and Regeneration (2005)

After reading the article and taking the test, the participant should be able to:
Thinking Critically about Science and Religion (2005)

While his research primarily explores the ecological and evolutionary genetics of plants, he has also earned a doctorate in Philosophy and writes regularly on the philosophy of science.In addition to his substantial academic work, he lectures nationally to student and skeptical groups on issues related to science and science education, particularly those surrounding evolution and the battles over its place in the science classroom
Progressive Multifocal Leukoencephalopathy Complicating Treatment with Natalizumab and Interferon Beta-1a for Multiple Sclerosis (2005)

A 46-year-old woman with relapsing-remitting multiple sclerosis died from progressive multifocal leukoencephalopathy (PML) after having received 37 doses of natalizumab (300 mg every four weeks) as part of a clinical trial of natalizumab and interferon beta-1a. PML was diagnosed on the basis of the finding of JC viral DNA in cerebrospinal fluid on polymerase-chain-reaction assay and was confirmed at autopsy. Nearly every tissue section from bilateral cerebral hemispheres contained either macroscopic or microscopic PML lesions. There was extensive tissue destruction and cavitation in the left frontoparietal area, large numbers of bizarre astrocytes, and inclusion-bearing oligodendrocytes, which were positive for JC virus DNA on in situ hybridization.
Utilizing OODB schema modeling for vocabulary management. (1996)

Comprehension of complex controlled vocabularies is often difficult. We present a method, facilitated by an object-oriented database, for depicting such a vocabulary (the Medical Entities Dictionary (MED) from the Columbia-Presbyterian Medical Center) in a schematic way which uses a sparse inheritance network of area classes. The resulting Object Oriented Health Vocabulary repository (OOHVR) allows visualization of the 43,000 MED concepts as 90 area classes. This view has provided valuable information to those responsible with maintaining the MED. As a result, the MED organization has been improved and some previously-unrecognized errors and inconsistencies have been removed. We believe that this schematic approach allows improved comprehension of the gestalt of large controlled medical vocabulary.
The adenovirus tripartite leader may eliminate the requirement for cap-binding protein complex during translation initiation (1988)

The adenovirus tripartite leader is a 200-nucleotide 5' noncoding region that is found on all late viral mRNAs. This segment is required for preferential translation of viral mRNAs at late times during infection. Most tripartite leader-containing mRNAs appear to exhibit little if any requirement for intact cap-binding protein complex, a property previously established only for uncapped poliovirus mRNAs and capped mRNAs with minimal secondary structure. The tripartite leader also permits the translation of mRNAs in poliovirus-infected cells in the apparent absence of active cap-binding protein complex and does not require any adenovirus gene products for this activity. The preferential translation of viral late mRNAs may involve this unusual property.
Antisense properties of tricyclo-DNA (2002)

Tricyclo (tc)-DNA belongs to the class of conformationally constrained DNA analogs that show enhanced binding properties to DNA and RNA. We prepared tc-oligonucleotides up to 17 nt in length, and evaluated their binding efficiency and selectivity towards complementary RNA, their biological stability in serum, their RNase H inducing potential and their antisense activity in a cellular assay. Relative to RNA or 2'-O-Me-phosphorothioate (PS)-RNA, fully modified tc-oligodeoxynucleotides, 10-17 nt in length, show enhanced selectivity and enhanced thermal stability by approximately 1 degrees C/modification in binding to RNA targets. Tricyclodeoxyoligonucleotides are completely stable in heat-deactivated fetal calf serum at 37 degree C. Moreover, tc-DNA-RNA duplexes are not substrates for RNase H. To test for antisense effects in vivo, we used HeLa cell lines stably expressing the human beta-globin gene with two different point mutations in the second intron. These mutations lead to the inclusion of an aberrant exon in beta-globin mRNA. Lipofectamine-mediated delivery of a 17mer tc-oligodeoxynucleotide complementary to the 3'-cryptic splice site results in correction of aberrant splicing already at nanomolar concentrations with up to 100-fold enhanced efficiency relative to a 2'-O-Me-PS-RNA oligonucleotide of the same length and sequence. In contrast to 2'-O-Me-PS-RNA, tc-DNA shows antisense activity even in the absence of lipofectamine, albeit only at much higher oligonucleotide concentrations.
Poly(vinyl ester) Star Polymers via Xanthate-Mediated Living Radical Polymerization:  From Poly(vinyl alcohol) to Glycopolymer Stars (2005)

Poly(vinyl ester) stars have been synthesized via different macromolecular design via interchange of xanthate (MADIX)/reversible addition−fragmentation chain transfer (RAFT) polymerization methodologies. Two approaches were investigated. The first method involved attaching the xanthate functionality to the core via a nonfragmenting covalent bond (Z-group approach). The second approach involved attaching the xanthate functionality to the core via a fragmenting covalent bond (R-group approach). The R-group approach yielded well-defined poly(vinyl acetate), poly(vinyl pivalate), and poly(vinyl neodecanoate) stars with narrow polydispersities (PDI ≤ 1.4). In contrast, the molecular weight distributions of poly(vinyl acetate) stars prepared using the Z-approach tended to broaden at moderate to high conversions. We attribute this broadening to steric congestion around the xanthate functionality, restricting the access of monomer to the CS bonds. The R-group approach was also found to be superior for preparing precursor stars suitable for hydrolysis to poly(vinyl alcohol). Hydrolysis of stars generated by the Z-group approach resulted in destruction of the architecture, as the process also cleaved the xanthate linkage at the nexus of the arms and core. Preliminary experiments on using the R-group approach to mediate the star-polymerization of vinyl-functional glycomonomers demonstrated the possibility of generating complex glycopolymer architectures. However, some significant problems were observed, and this synthetic approach requires further optimization.
A new and facile stereocontrolled synthesis of conjugated dienyl trifluoromethyl ketones† (2000)

The stereocontrolled synthesis of conjugated dienyl trifluoromethyl ketones has been achieved by a Horner–Wadsworth–Emmons reaction starting from the key trifluoromethylated building block N-(4-methylphenyl)trifluoroacetimidoyl iodide.
Mutational analysis of two conserved sequence motifs in HIV‐1 reverse transcriptase (1991)

Two conserved sequence motifs, occurring in HIV-1 reverse transcriptase at residues 110-116 and 183-190, have been studied using site-directed mutagenesis of the cloned gene. In particular, aspartates at positions 185 and 186 have each been mutated to either asparagine or glutamate. The resulting mutant proteins were catalytically inactive but still able to bind the template-primer complex, poly rA-oligo dT. Other mutations in these regions resulted in reduced reverse trascriptase activity but the mutation of tyrosine-183 to serine caused a significant increase in the Km for dTTP and the Ki for inhibition by 3'-azidothymidine-triphosphate, 2',3'-dideoxythymidine-triphosphate and phosphonoformic acid.
Characterization of constitutive HSF2 DNA-binding activity in mouse embryonal carcinoma cells. (1994)

Two distinct murine heat shock transcription factors, HSF1 and HSF2, have been identified. HSF1 mediates the transcriptional activation of heat shock genes in response to environmental stress, while the function of HSF2 is not understood. Both factors can bind to heat shock elements (HSEs) but are maintained in a non-DNA-binding state under normal growth conditions. Mouse embryonal carcinoma (EC) cells are the only mammalian cells known to exhibit HSE-binding activity, as determined by gel shift assays, even when maintained at normal physiological temperatures. We demonstrate here that the constitutive HSE-binding activity present in F9 and PCC4.aza.R1 EC cells, as well as a similar activity found to be present in mouse embryonic stem cells, is composed predominantly of HSF2. HSF2 in F9 EC cells is trimerized and is present at higher levels than in a variety of nonembryonal cell lines, suggesting a correlation of these properties with constitutive HSE-binding activity. Surprisingly, transcription run-on assays suggest that HSF2 in unstressed EC cells does not stimulate transcription of two putative target genes, hsp70 and hsp86. Genomic footprinting analysis indicates that HSF2 is not bound in vivo to the HSE of the hsp70 promoter in unstressed F9 EC cells, although HSF2 is present in the nucleus and the promoter is accessible to other transcription factors and to HSF1 following heat shock. Thus trimerization and nuclear localization of HSF2 do not appear to be sufficient for in vivo binding of HSF2 to the HSE of the hsp70 promoter in unstressed F9 EC cells.
Defeasible logic programming: DeLP-servers, contextual queries, and explanations for answers (2014)

Argumentation represents a way of reasoning over a knowledge base containing possibly incomplete and/or inconsistent information, to obtain useful conclusions. As a reasoning mechanism, the way an argumentation reasoning engine reaches these conclusions resembles the cognitive process that humans follow to analyse their beliefs; thus, unlike other computationally reasoning systems, argumentation offers an intellectually friendly alternative to other defeasible reasoning systems. Logic Programming is a computational paradigm that has produced computationally attractive systems with remarkable success in many applications. Merging ideas from both areas, Defeasible Logic Programming offers a computational reasoning system that uses an argumentation engine to obtain answers from a knowledge base represented using a logic programming language extended with defeasible rules. This combination of ideas brings about a computationally effective system together with a human-like reasoning model facilitating its use in applications.
The kinemage: A tool for scientific communication (1992)

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared and specified by the author(s) of a journal article, in order to better communicate ideas that depend on three-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program, such as the one described here (called MAGE), which presently runs on Macintosh computers. A utility (called PREKIN) helps authors prepare the kinemages. Kinemages are being implemented under the auspices of the Innovative Technology Fund.
Nondestructive photolithography of conducting polymer structures (2006)

We have demonstrated a nondestructive method using ultraviolet (UV) photolithography to fabricate micrometer-sized conducting polymer structures. By coating a polymer film on patterned photoresist and then performing liftoff, UV exposure to the conducting polymer film was prevented throughout the lithography processes. We created features down to 1μm with high yield. Such complementary metal-oxide-semiconductor-compatible microfabrication can be applied generally to various organic films, and may allow the speed of organic electronics to be improved. Organic thin-film transistors (OTFTs) were fabricated using poly(3-hexylthiophene) as the active material, and typical OTFT characteristics were obtained.
Tissue Imaging at Atmospheric Pressure Using Desorption Electrospray Ionization (DESI) Mass Spectrometry (2006)

Images of the masses: Two-dimensional molecular imaging of intact rat brain tissue under ambient conditions was achieved by using the mass spectrometric technique of desorption electrospray ionization (DESI). The distributions of specific lipids, such as sulfatide 24:1, reveal distinctive subanatomical features of the rat brain (cc=corpus callosum; aca=anterior part of anterior commissure) with spatial resolution of less than 500 μm.