gebhart/patrepeval huggingface dataset:
Hairless Pigmented Guinea Pigs: A New Model for the Study of Mammalian Pigmentation (1990)

A stock of hairless pigmented guinea pigs was developed to facilitate studies of mammalian pigmentation. This stock combines the convenience of a hairless animal with a pigmentary system that is similar to human skin. In both human and guinea pig skin, active melanocytes are located in the basal layer of the interfollicular epidermis. Hairless albino guinea pigs on an outbred Hartley background (CrI:IAF/HA(hr/hr)BR; designated hr/hr) were mated with red-haired guinea pigs (designated Hr/Hr). Red-haired heterozygotes from the F1 generation (Hr/hr) were then mated with each other or with hairless albino guinea pigs. The F2 generation included hairless pigmented guinea pigs that retained their interfollicular epidermal melanocytes and whose skin was red-brown in color. Following UV irradiation, there was an increase in cutaneous pigmentation as well as an increase in the number of active epidermal melanocytes. An additional strain of black hairless guinea pigs was developed using black Hr/Hr animals and a similar breeding scheme. These two strains should serve as useful models for studies of the mammalian pigment system.
LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced Infection (2003)

The rhizobial infection of legumes has the most stringent demand toward Nod factor structure of all host responses, and therefore a specific Nod factor entry receptor has been proposed. The SYM2 gene identified in certain ecotypes of pea (Pisum sativum) is a good candidate for such an entry receptor. We exploited the close phylogenetic relationship of pea and the model legume Medicago truncatula to identify genes specifically involved in rhizobial infection. The SYM2 orthologous region of M. truncatula contains 15 putative receptor-like genes, of which 7 are LysM domain-containing receptor-like kinases (LYKs). Using reverse genetics in M. truncatula, we show that two LYK genes are specifically involved in infection thread formation. This, as well as the properties of the LysM domains, strongly suggests that they are Nod factor entry receptors.
Design and Synthesis of Non-proteinogenic Amino Acids and Secondary Structures of Their Peptides (2006)

Replacement of the alpha-hydrogen atom of L-alpha-amino acids with an alkyl substituent results in alpha,alpha-disubstituted amino acids. The modification changes the properties of the amino acids. Incorporation of alpha,alpha-disubstituted amino acids into oligopeptides restricts the conformational freedom of their peptides. The author developed a synthetic route for optically active alpha-ethylated alpha,alpha-disubstituted amino acids using chiral cyclic 1,2-diol, and disclosed that the preferred conformation of peptides composed of chiral alpha-ethylated disubstituted amino acids is a fully planar conformation, whereas that of chiral alpha-methylated disubstituted amino acids is a 3(10)-helical structure. Furthermore, the author designed and synthesized two chiral cyclic alpha,alpha-disubstituted amino acids, i.e., (3S,4S)-1-amino-3,4-di(methoxy)cyclopentanecarboxylic acid {(S,S)-Ac5cdOM}, and (1R,6R)-8-aminobicyclo-[4.3.0]non-3-ene-8-carboxylic acid {(R,R)-Ab5,6=c}. They do not have a chiral center at the alpha-position, but do have chiral centers on the side-chain cyclopentane or the bicyclic skeleton. The preferred secondary structure of the (S,S)-Ac5cdOM homopeptides was the left-handed (M) 3(10)-helical structure (hexapeptide) and the left-handed (M) alpha-helical structure (octa- and decapeptides), while that of the (R,R)-Ab5,6=c hexapeptide was both the right-handed (P) and left-handed (M) 3(10)-helices. These results indicate that the side-chain chiral centers affect the secondary structure of their peptides, and the side-chain chiral environment is important for the control of the helical-screw direction of peptides.
Environmental signal integration by a modular AND gate (2007)

Microorganisms use genetic circuits to integrate environmental information. We have constructed a synthetic AND gate in the bacterium Escherichia coli that integrates information from two promoters as inputs and activates a promoter output only when both input promoters are transcriptionally active. The integration occurs via an interaction between an mRNA and tRNA. The first promoter controls the transcription of a T7 RNA polymerase gene with two internal amber stop codons blocking translation. The second promoter controls the amber suppressor tRNA supD. When both components are transcribed, T7 RNA polymerase is synthesized and this in turn activates a T7 promoter. Because inputs and outputs are promoters, the design is modular; that is, it can be reconnected to integrate different input signals and the output can be used to drive different cellular responses. We demonstrate this modularity by wiring the gate to integrate natural promoters (responding to Mg(2+) and AI-1) and using it to implement a phenotypic output (invasion of mammalian cells). A mathematical model of the transfer function is derived and parameterized using experimental data.
Malonyl-Coenzyme A Reductase from Chloroflexus aurantiacus , a Key Enzyme of the 3-Hydroxypropionate Cycle for Autotrophic CO 2 Fixation (2002)

The 3-hydroxypropionate cycle is a new autotrophic CO(2) fixation pathway in Chloroflexus aurantiacus and some archaebacteria. The initial step is acetyl-coenzyme A (CoA) carboxylation to malonyl-CoA by acetyl-CoA carboxylase, followed by NADPH-dependent reduction of malonyl-CoA to 3-hydroxypropionate. This reduction step was studied in Chloroflexus aurantiacus. A new enzyme was purified, malonyl-CoA reductase, which catalyzed the two-step reduction malonyl-CoA + NADPH + H(+) --> malonate semialdehyde + NADP(+) + CoA and malonate semialdehyde + NADPH + H(+) --> 3-hydroxypropionate + NADP(+). The bifunctional enzyme (aldehyde dehydrogenase and alcohol dehydrogenase) had a native molecular mass of 300 kDa and consisted of a single large subunit of 145 kDa, suggesting an alpha(2) composition. The N-terminal amino acid sequence was determined, and the incomplete gene was identified in the genome database. Obviously, the enzyme consists of an N-terminal short-chain alcohol dehydrogenase domain and a C-terminal aldehyde dehydrogenase domain. No indication of the presence of a prosthetic group was obtained; Mg(2+) and Fe(2+) stimulated and EDTA inhibited activity. The enzyme was highly specific for its substrates, with apparent K(m) values of 30 microM malonyl-CoA and 25 microM NADPH and a turnover number of 25 s(-1) subunit(-1). The specific activity in autotrophically grown cells was 0.08 micromol of malonyl-CoA reduced min(-1) (mg of protein)(-1), compared to 0.03 micromol min(-1) (mg of protein)(-1) in heterotrophically grown cells, indicating downregulation under heterotrophic conditions. Malonyl-CoA reductase is not required in any other known pathway and therefore can be taken as a characteristic enzyme of the 3-hydroxypropionate cycle. Furthermore, the enzyme may be useful for production of 3-hydroxypropionate and for a coupled spectrophotometric assay for activity screening of acetyl-CoA carboxylase, a target enzyme of potent herbicides.
Identification and immunolocalisation of annexins V and VI, the major cardiac annexins, in rat heart (1993)

Annexins V and VI are the major cardiac annexins. The localisation of these annexins to different components of cardiac myocytes will serve to direct the search for their functions in the heart. The striking immunoreactivity for annexins, particularly annexin V, in the coronary vessels indicates that the functions of cardiac annexins include a role in the coronary circulatory system.
Antirhinovirus activity of 6-anilino-9-benzyl-2-chloro-9H-purines (1990)

A series of 6-anilino-9-benzyl-2-chloropurines was synthesized and tested for antirhinovirus activity. Most of the compounds were prepared by reaction of the appropriate aniline with 9-benzyl-2,6-dichloro-9H-purine. Structure-activity relationship studies revealed that compounds with small, lipophilic para substituents were good inhibitors of serotype 1B. Several compounds had good activity against four representative serotypes.
Full-phase photon-counting double-random-phase encryption (2014)

We investigate a full-phase-based photon-counting double-random-phase encryption (PC-DRPE) method. A PC technique is applied during the encryption process, creating sparse images. The statistical distribution of the PC decrypted data for full-phase encoding and amplitude-phase encoding are derived, and their statistical parameters are used for authentication. The performance of the full-phase PC-DRPE is compared with the amplitude-based PC-DRPE method. The PC decrypted images make it difficult to visually authenticate the input image; however, advanced correlation filters can be used to authenticate the decrypted images given the correct keys. Initial computational simulations show that the full-phase PC-DRPE has the potential to require fewer photons for authentication than the amplitude-based PC-DRPE.
Structure and expression of the gene locus encoding the phosphatidylglycerophosphate synthase of Escherichia coli. (1986)

This paper presents definitive results which establishes a direct gene-protein product relationship between the pgsA gene and the phosphatidylglycerophosphate synthase of Escherichia coli. The predicted protein sequence derived from the determined DNA sequence of pgsA is in close agreement with the amino acid composition and partially determined amino acid sequence of the purified enzyme. The purified synthase has the same apparent molecular mass as the gene product made by a plasmid-directed transcription-translation system. The plasmid-borne copy of the pgsA gene is also capable of expressing enzymatically active synthase in vitro. The DNA sequence analysis has established the exact linear relationship between the uvrC, pgsA, and glyW loci and revealed that these three genes are transcribed in the same direction. The terminal coding regions of these three genes also share common sequences with transcriptional regulatory elements for the adjacent genes.
Receiver structures for multiple access OFDM (2003)

Orthogonal frequency division multiplexing (OFDM) is an attractive technique for future wireless access. A major benefit of OFDM is its ability to support high-speed transmission in highly dispersive fading environments. Multiple access OFDM is based on organizing a wideband OFDM signal into clusters of tones in frequency, as well as a number of time-slots in time, that can be accessed by different users communicating with a base station. One of the main challenges associated with multiple access OFDM is how to effectively separate signals in both the base station and terminal receivers. In this paper, we examine receiver structures for both the downlink and uplink. We show that a single long discrete Fourier transform (DFT) with receiver windowing is attractive for terminals, but a filter-and-decimate structure with multiple short DFTs is more appropriate for base stations.
Teaching Machines to Read and Comprehend (2015)

Teaching machines to read natural language documents remains an elusive challenge. Machine reading systems can be tested on their ability to answer questions posed on the contents of documents that they have seen, but until now large scale training and test datasets have been missing for this type of evaluation. In this work we define a new methodology that resolves this bottleneck and provides large scale supervised reading comprehension data. This allows us to develop a class of attention based deep neural networks that learn to read real documents and answer complex questions with minimal prior knowledge of language structure.
Inhibition of Intimal Hyperplasia After Balloon Injury by Antibodies to Intercellular Adhesion Molecule-1 and Lymphocyte Function–Associated Antigen-1 (1997)

Balloon injury induced or upregulated the ICAM-1 expression on vascular SMC and on regenerating endothelial cells. MAb against ICAM-1 or ICAM-1/LFA-1 attenuated IH. These results suggest that ICAM-1 may play a role in the progression of IH after injury in rats.
Fabrication and Characterization of Thin Films of Single-Walled Carbon Nanotube Bundles on Flexible Plastic Substrates (2004)

A convenient method to obtain patterns of films of single-walled carbon nanotubes (SWNT) bundles on flexible plastic is described. Using the Line Patterning method SWNT films of thickness ranging from approximately 300-1500 nm can be obtained from aqueous surfactant-supported dispersions of chemically purified SWNT bundles synthesized by the pulsed-laser ablation method. These films are strongly adherent and are competitive in performance with commercially available films of indium-tin-oxide (ITO) on plastics. For example, an approximately 1500 thick film of SWNT on poly(ethylene terephthalate) (PET) shows a surface resisitvity of approximately 80 Omega/sq, optical transparency >80%, and robust flexibility. Unlike ITO/PET, films of SWNT/PET can be folded and bent to a crease without cracking. The simple techniques involoved in obtaining these films (i.e., those without requiring lithography or ink-jet printing) could help facilitate the rapid fabrication of transparent, flexible electronic devices, heralding what promises to be a new approach towards the development of next-generation optoelectronic devices.
CUL3 and NRF2 Mutations Confer an NRF2 Activation Phenotype in a Sporadic Form of Papillary Renal Cell Carcinoma (2013)

Sustained activation of the stress-regulated transcription factor NRF2 (NFE2L2) is a prominent feature of many types of cancer, implying that mutations driving NRF2 may be important to tumor progression. In hereditary type 2 papillary renal cell carcinoma (PRCC2, also known as hereditary leiomyomatosis and renal cell cancer), NRF2 activation is a direct consequence of the accumulation of intracellular fumarate, a result of fumarate hydratase (FH) inactivation, but it is not clear how NRF2 may be activated in sporadic forms of PRCC2. Here we show that somatic mutations in NRF2, CUL3, and SIRT1 are responsible for driving the NRF2 activation phenotype in sporadic PRCC2. Transcriptome sequencing revealed the expression pattern of mutant alleles of NRF2, CUL3, and SIRT1 and also confirmed NRF2 activation in clinical specimens. Our results show a convergence in somatic mutations in sporadic PRCC2 with FH mutation in hereditary PRCC2.
Interactive advertising (1998)

The number of people exploring the World Wrde Web is growing dramatically. Many companies are interested in the potential of advertising on the web, but there is little research to guide their decision. The present study demonstrates the concept of a corporate sponsored website as a promising direction for web advertisers. Advertisements for products targetiug lo-14 year-o& were presented as web games and inserted into a prototype website. For example, in one ad, players scored points by actively steering toward the advertised product with their web video-game car, while dodging undesirable obstacles on the road (sound effects included). For comparison, subjects also watched a TV ad for the same product embedded in a TV program. One day later, tests showed that web ads positively influenced how easily the advertised brand came to mind compared to TV ads and compared to no-ad controls. The effectiveness of interactive web ads for influencing consumers' memory in this preliiinaty study suggests that it merits more attention as a potentially viable medium for advertismg. Factors that could contribute to the advantage for web ads are ,discussed.
Monolithic transformers for silicon RF IC design (2002)

The construction and electrical characteristics of two-port transformers (1:1 and 1:n turns ratio) and multi-port transformer baluns fabricated in a production silicon technology are presented. A high-linearity 5 GHz mixer design illustrates the advantages of the trifilar transformer in an RF IC application.
Defect of human growth hormone receptors in the liver of two patients with Laron-type dwarfism. (1984)

Liver microsome pellets prepared from tissue obtained by elective open biopsy from two patients (aged 4 and 26 years) with Laron-type dwarfism (LTD) showed no specific binding of 125I-hGH (human growth hormone). In contrast, 31 assays of liver microsomes obtained immediately after clinical death from 6 healthy subjects (kidney transplantation donors with a mean age of 24 years) showed a mean specific binding of 14% (range 7.9 to 24%). We interpreted these findings as evidence that in patients with LTD there is a defect in the hGH receptors of the liver and a consequent lack of somatomedin generation. The fact that the liver microsomes from the two LTD patients showed active specific binding of 125I-insulin suggest that, in this syndrome, it is only the receptors for hGH that are defective.
A Novel Conditionally Replicative Adenovirus Vector Targeting Telomerase-Positive Tumor Cells (2004)

The telomerase-targeted adenovirus vector has significant potential as an oncolytic virus as well as a tumor-specific therapeutic gene delivery vehicle.
Importance of amine pKa and distribution coefficient in the metabolism of fluorinated propranolol derivatives. Preparation, identification of metabolite regioisomers, and metabolism by CYP2D6. (2001)

A series of 1"-mono-, di-, and trifluorinated analogs of propranolol and related steric congeners was prepared, and their metabolism was examined in recombinant-expressed CYP2D6. The structural changes in this series of compounds, principally added fluorines and methyl groups in the 1"-position of the N-isopropyl group, provided compounds that varied in pK(a) by more than 5 log units and also varied in lipophilicity and in steric size. Products of both aromatic hydroxylation and N-dealkylation were observed in the metabolic experiments. The regiochemistry of aromatic hydroxylation at the 4'- and 5'-positions was assigned based on high-pressure liquid chromatography, fluorescence, and mass spectral characteristics of the products and standards. Correlations of the metabolic kinetic parameters K(m) and catalytic efficiency (k(cat)/K(m)) with substituent parameters of the added groups showed that increased basicity (higher pK(a) values) was associated with increased enzyme affinity (low K(m) values) and increased catalytic efficiency. More basic methyl-substituted compounds showed higher affinities for CYP2D6 than the structurally analogous less basic fluorinated congeners, indicating the decrease in affinity of the fluorinated compounds was not due to the size of the N-alkyl substituent. Correlations with log D reflected the degree of ionization and showed that the less lipophilic substrates (more basic compounds) had higher affinity for CYP2D6. These results are consistent with the proposal in the literature that ion pairing of the protonated amine of the substrate with Asp301 in the active site of CYP2D6 is very important to substrate affinity.
Plasma Measurement of D-Dimer as Diagnostic Aid in Suspected Venous Thromboembolism: An Overview (1994)

This paper reviews the published experience with plasma measurement of D-dimer (DD), a specific degradation product of crosslinked fibrin, in the diagnostic approach of venous thromboembolism (VTE). Pooling 11 studies (with weighting of the figures according to sample size) with a total of 1337 patients clinically suspected of deep venous thrombosis (DVT) (prevalence of DVT 35%) disclosed an average weighted sensitivity of 96.8% (95% CI: 95.2-98.4) and specificity of 35.2% (95% CI: 32.0-38.4) for the presence of DVT when the ELISA technique was used. In 908 patients suspected of pulmonary embolism (PE) from 9 trials (prevalence of PE 38%), the ELISA technique was associated with a weighted sensitivity of 96.8% (95% CI: 95.0-98.6) and specificity of 45.1% (95% CI: 40.8-49.4) for the disease. Figures obtained with latex assays were definitely lower, precluding their use in the diagnostic approach of VTE. These results show that a low concentration of plasma DD measured by the ELISA technique (usually less than 500 micrograms/l) might be used to rule out VTE in clinically suspected patients. Increased plasma concentrations are of no utility because of the low specificity of this test result. The clinical usefulness of the DD ELISA test should now be assessed in management trials under routine conditions, in the frame of clinical decision-making diagnostic processes. Lastly, the promising data obtained in a small number of asymptomatic, postoperative patients at risk of VTE deserve confirmation before the test can be recommended for initial screening in thrombo-prophylactic trials.
Physical Realization of Generic-Element Parameters in Model Updating (2002)

The selection of parameters is most important to successful updating of finite element models. When the parameters are chosen on the basis of engineering understanding the model predictions are brought into agreement with experimental observations, and the behavior of the structure, even when differently configured, can be determined with confidence. Physical phenomena may be misrepresented in the original model, or may be absent altogether. In any case the updated model should represent an improved physical understanding of the structure and not simply consist of unrepresentative numbers which happen to cause the results of the model to agree with particular test data. The present paper introduces a systematic approach for the selection and physical realization of updated terms. In the realization process, the discrete equilibrium equation formed by mass, and stiffness matrices is converted to a continuous form at each node. By comparing the resulting differential equation with governing equations known to represent physical phenomena, the updated terms and their physical effects can be recognized. The approach is demonstrated by an experimental example.
The role of the ubiquitination-proteasome pathway in breast cancer: Use of mouse models for analyzing ubiquitination processes (2002)

Turnover of several regulatory proteins results from targeted destruction via ubiquitination and subsequent degradation through the proteosome. The timely and irreversible degradation of critical regulators is essential for normal cellular function. The precise biochemical mechanisms that are involved in protein turnover by ubiquitin-mediated degradation have been elucidated using in vitro assays and cell culture systems. However, pathways that lead to ubiquitination of critical regulatory proteins in vivo are more complex, and have both temporal and tissue-specific differences. In vivo models will allow identification of substrates and enzymes of the ubiquitin-proteosome pathway that play important roles in selected tissues and diseases. In addition, assessment of the therapeutic efficacy of drugs designed to inhibit or enhance protein turnover by ubiquitination requires in vivo models. In the present review we describe selected examples of transgenic and knockout models of proteins that are known either to be regulated by ubiquitin-mediated degradation or to have a catalytic function in this process, and to play an important role in breast cancer. We outline the functions of these proteins in vivo and focus on knowledge gained in the comparison of in vivo behavior predicted from cell-free in vitro data or from experiments conducted in cell culture systems.