gebhart/patrepeval huggingface dataset:
Functional Analysis of Developmentally Regulated Chromatin-Hypersensitive Domains Carrying the α 1 -Fetoprotein Gene Promoter and the Albumin/α 1 -Fetoprotein Intergenic Enhancer (1993)

During liver development, the tandem alpha 1-fetoprotein (AFP)/albumin locus is triggered at the AFP end and then asymmetrically enhanced; this is followed by autonomous repression of the AFP-encoding gene. To understand this regulation better, we characterized the two early developmental stage-specific DNase I-hypersensitive (DH) sites so far identified in rat liver AFP/albumin chromatin: an intergenic DH-enhancer site and the AFP DH-promoter site. Mutation-transfection analyses circumscribed the DH-enhancer domain to a 200-bp DNA segment stringently conserved among species. Targeted mutations, DNA-protein-binding assays, and coexpression experiments pinpointed C/EBP as the major activatory component of the intergenic enhancer. Structure-function relationships at the AFP DH-promoter site defined a discrete glucocorticoid-regulated domain activated cooperatively by HNF1 and a highly specific AFP transcription factor, FTF, which binds to a steroid receptor recognition motif. The HNF1/FTF/DNA complex is deactivated by glucocorticoid receptors or by the ubiquitous factor NF1, which eliminates HNF1 by competition at an overlapping, high-affinity binding site. We propose that the HNF1-NF1 site might serve as a developmental switch to direct autonomous AFP gene repression in late liver development. We also conclude that the intergenic enhancer is driven by C/EBP alpha primarily to fulfill albumin gene activation functions at early developmental stages. Factor FTF seems to be the key regulator of AFP gene-specific functions in carcinoembryonic states.
Monoclonal Antibodies against the Minimal DNA-Binding Domain in the Carboxyl-Terminal Region of Human Immunodeficiency Virus Type 1 Integrase (1999)

Integrase of human immunodeficiency virus type 1 (HIVIN) consists of 288 amino acids, and its minimum DNA-binding domain (MDBD) (amino acids [aa] 220 to 270) is required for the integration reaction. We produced and characterized four murine monoclonal antibodies (MAbs) to the MDBD of HIVIN (strain LAI). Immunoblot and enzyme-linked immunosorbent assays with truncated HIVINs showed that those MAbs recognized sequential epitopes within the MDBD (aa 228 to 236, 237 to 252, 253 to 261, and 262 to 270). Their binding to HIVIN inhibited terminal cleavage and strand transfer activities but not disintegration activity in vitro. This collection of MAbs is useful for studying the structure and function of the MDBD by complementing mutational analyses and other biochemical studies.
Preliminary investigation of KTP/532 laser light in the treatment of hemangiomas and tattoos (1986)

Preliminary investigation of a frequency-doubled YAG laser (KTP 532 nm) manufactured by Laserscope of Santa Clara was undertaken. Twenty-five patients with either port wine hemangiomas or decorative tattoos were treated with a 532-nm light and the results compared to argon laser at identical power settings. Clinical and histological results were identical between the two lasers.
CORM-3 Reactivity toward Proteins: The Crystal Structure of a Ru(II) Dicarbonyl−Lysozyme Complex (2011)

CORM-3, [fac-Ru(CO)(3)Cl(κ(2)-H(2)NCH(2)CO(2))], is a well-known carbon monoxide releasing molecule (CORM) capable of delivering CO in vivo. Herein we show for the first time that the interactions of CORM-3 with proteins result in the loss of a chloride ion, glycinate, and one CO ligand. The rapid formation of stable adducts between the protein and the remaining cis-Ru(II)(CO)(2) fragments was confirmed by Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), Liquid-Chromatography Mass Spectrometry (LC-MS), Infrared Spectroscopy (IR), and X-ray crystallography. Three Ru coordination sites are observed in the structure of hen egg white lysozyme crystals soaked with CORM-3. The site with highest Ru occupancy (80%) shows a fac-[(His15)Ru(CO)(2)(H(2)O)(3)] structure.
Biology of Intervertebral Disc Aging and Degeneration (2004)

Changes in intervertebral disc structure throughout life ultimately result in tissue degeneration and the need for medical intervention. Current research is aimed at trying to restore the integrity of the degenerate disc matrix by biologic means, although at present it is not clear what the structure of the most appropriate repair tissue should be or how it can be achieved.
동북아의 질서변화와 한국의 대응외교 (2016)

동북아시아 지역에서는 지역의 패권을 위한 미중의 경쟁 구도와 함께 중일 갈등, 한일 갈등, 남북한 갈등, 한미동맹 강화, 미일동맹 강화, 한중 협력, 한러 협력,중러 협력, 북러 협력 등 다양한 양자 간의 협력과 갈등관계들이 나타나고 있다. 한국은 동북아시아에서 벌어지고 있는 국제질서의 변화와 재편 동향을 정확히 파악함으로써 국가이익을 극대화시켜 국가를 발전시켜 나가야 한다. 이 글에서는 동북아질서의 변화를 미중의 협력과 경쟁, 일본과 러시아의 정책 변화, 북핵 갈등 등으로 구분하여 분석하였다. 이러한 동북아질서 변화에 대처하기 위한 한국의 대응외교를 미중과의 협력 및 균형외교, 대일 외교, 대러 외교, 다자안보 협력외교, 중견국 외교, 공공외교 등으로 구분하여 분석했다. 결론에서는 북한 핵 문제의 해결을 위한 몇 가지 방안을 제시했다
Retrovirus-Mediated Gene Expression in Hematopoietic Cells Correlates Inversely with Growth Factor Stimulation (1996)

Cells of the hematopoetic system, especially hematopoietic progenitor and stem cells, are perceived as ideal targets for human gene therapy. In this report, the stability of retrovirus-mediated gene expression driven by three different potent promoters has been examined in purified human CD34+ cells. The promoters, murine stem cell virus (MSCV) long terminal repeat (LTR) and pgk, show gene expression in 10 times more hematopoietic colonies derived from CD34+ cells than the commonly used Moloney murine leukemia virus (Mo-MLV) LTR. Quantitative reverse transcriptase polymerase chain reaction (RT-PCR) analysis, however, demonstrates that the levels of gene expression in retrovirus-transduced cells decrease with time in long-term bone marrow cultures and in suspension cultures containing hematopoietic growth factors. Removal of hematopoietic growth factors from the suspension culture medium was associated with a decrease in cell proliferation and differentiation, but with stable gene expression. Retrovirus-mediated gene expression is, therefore, inversely related to proliferation and differentiation of the transduced CD34+ cells. These observations may have implications in future design and implementation of human gene therapy protocols.
Pharmacodynamics of recombinant human DNase I in serum (1998)

Recombinant human deoxyribonuclease I (rhDNase) may be an effective therapeutic for the treatment of systemic lupus erythematosus (SLE). The pharmacodynamics of rhDNase in serum was investigated using two activity assays: one based on hydrolysis of a radiolabelled phage DNA and the other based on hydrolysis of human chromatin. The concentration of endogenous immunoreactive DNase in sera from 16 normal subjects was 3.2 +/- 1.4 ng/ml (mean +/- s.d.); however, low levels or no nuclease activity were detected in the same sera, suggesting the presence of DNase inhibitors. We assessed the ability of rhDNase to degrade DNA in undiluted serum, since the observed inhibition of endogenous DNase was reversed upon dilution. Addition of rhDNase to undiluted serum at a concentration of 50-100 ng/ml was necessary for degradation of radiolabelled phage DNA. The activity of rhDNase added to serum from normal subjects and SLE patients was similar. rhDNase degraded human chromatin and chromatin/anti-DNA immune complexes in serum with similar potency (EC50 approximately 100-200 ng/ml). A 500-fold variation in the chromatin/anti-DNA stoichiometry did not significantly affect the digestion of these immune complexes by rhDNase in buffer. These results indicate that a minimum rhDNase concentration of 50-100 ng/ml in serum was required to achieve detectable catalytic activity and that the presence of antibodies to DNA did not inhibit the degradation of DNA/anti-DNA immune complexes.
Morphogenesis of the Filamentous Single-stranded DNA Phages (1978)

One of the most fascinating aspects of the life cycle of the filamentous phages is their extraordinary morphogenesis. Whereas many other viruses, both enveloped and nonenveloped, are assembled in the cell and released by budding or lysis (Casjens and King 1975), the filamentous phages have evolved a different process for the release of their genetic material. They do not form intracellular phage particles; instead, in some way, they extrude their genomes through the bacterial membrane while assembling the capsid subunits around the genome to form the mature virion (for general reviews of the filamentous phage life cycle see Marvin and Hohn 1969; Denhardt 1975; Ray 1977). Approximately 200 phage particles are produced per cell generation without destruction of the host cell. The mature phage particle is about 6 nm in diameter by 1 μ m in length and is composed of the phage single-stranded (SS) DNA encapsulated by approximately 2800 molecules of the phage-specified B, or coat (gene-VIII), protein. Approximately four molecules of the A, or adsorption, protein are at one end of the filamentous particle (Rossomando and Zinder 1968; Marco 1975; Goldsmith and Konigsberg 1977; Woolford et al. 1977). There may also be a few copies of another protein in the phage particle, possibly phage-specified and located at the other end of the particle (Pratt et al. 1969; Beaudoin 1970; Kornberg 1974). The structure of these filamentous phage particles is discussed in this volume by Marvin, by Day and Wiseman, and by Makowski and Caspar. The membrane-associated process of phage...
Clostridium ljungdahlii represents a microbial production platform based on syngas (2010)

Clostridium ljungdahlii is an anaerobic homoacetogen, able to ferment sugars, other organic compounds, or CO(2)/H(2) and synthesis gas (CO/H(2)). The latter feature makes it an interesting microbe for the biotech industry, as important bulk chemicals and proteins can be produced at the expense of CO(2), thus combining industrial needs with sustained reduction of CO and CO(2) in the atmosphere. Sequencing the complete genome of C. ljungdahlii revealed that it comprises 4,630,065 bp and is one of the largest clostridial genomes known to date. Experimental data and in silico comparisons revealed a third mode of anaerobic homoacetogenic metabolism. Unlike other organisms such as Moorella thermoacetica or Acetobacterium woodii, neither cytochromes nor sodium ions are involved in energy generation. Instead, an Rnf system is present, by which proton translocation can be performed. An electroporation procedure has been developed to transform the organism with plasmids bearing heterologous genes for butanol production. Successful expression of these genes could be demonstrated, leading to formation of the biofuel. Thus, C. ljungdahlii can be used as a unique microbial production platform based on synthesis gas and carbon dioxide/hydrogen mixtures.
Amino-terminal mutation of the vesicular stomatitis virus glycoprotein does not affect its fusion activity (1986)

Earlier studies demonstrated that synthetic peptides corresponding to the amino terminus of the vesicular stomatitis virus glycoprotein (G protein) have a pH-dependent hemolytic activity that is thought to be related to the fusion activity of G protein (R. Schlegel and M. Wade, J. Biol. Chem. 259: 4691-4694, 1984; R. Schlegel and M. Wade, J. Virol. 53: 319-323, 1985). A single amino acid change (lysine to glutamic acid at the amino terminus) abolishes the hemolytic activity of the peptide. Here we used oligonucleotide-directed mutagenesis to create a DNA encoding G protein with this same amino acid change at its amino terminus. The mutant protein encoded by this gene was expressed transiently in a monkey fibroblast cell line (COS) and was found to have a pH-dependent fusion activity indistinguishable from wild-type G protein. This result indicates that the hemolytic activity of the synthetic peptides was not related to the fusion activity of the G protein.
Phage infection, transfection and transformation of Mycobacterium avium complex and Mycobacterium paratuberculosis (1995)

Mycobacterium avium complex strains and Mycobacterium paratuberculosis are closely related intracellular pathogens affecting humans and animals. M. avium complex infections are a leading cause of morbidity and mortality in AIDS patients, and M. paratuberculosis is the agent of Johne's disease in ruminants. Genetic manipulation of these micro-organisms would facilitate the understanding of their pathogenesis, the construction of attenuated vaccine strains and the development of new drugs and treatment methods. This paper describes the replication of mycobacterial shuttle phasmids and plasmids, and the expression of the firefly luciferase reporter gene in M. avium complex and M. paratuberculosis. The mycobacteriophage TM4 propagated on M. smegmatis or M. paratuberculosis plaqued at the same efficiency on these two mycobacterial hosts. Screening of M. avium complex and M. paratuberculosis clinical isolates with TM4-derived luciferase reporter phages demonstrated that the majority of these isolates were susceptible to TM4. Conditions for introduction of DNA were determined by transfection of M. paratuberculosis with TM4 DNA and applied to isolate kanamycin-resistant transformants of M. avium complex and M. paratuberculosis with Escherichia coli-Mycobacterium shuttle plasmids. Recombinant plasmids were recovered from transformants without apparent loss of DNA sequences. These results provide the basis for the genetic manipulation of these pathogenic mycobacterial species.
Zero-Configuration, Robust Indoor Localization: Theory and Experimentation (2006)

With the technical advances in ubiquitous comput- ing and wireless networking, there has been an increasing need to capture the context information (such as the location) and to figure it into applications. In this paper, we establish the theoreti- cal base and develop a localization algorithm for building a zero- configuration and robust indoor localization and tracking system to support location-based network services and management. The localization algorithm takes as input the on-line measurements of received signal strengths (RSSs) between 802.11 APs and between a client and its neighboring APs, and estimates the location of the client. The on-line RSS measurements among 802.11 APs are used to capture (in real-time) the effects of RF multi-path fading, temperature and humidity variations, opening and closing of doors, furniture relocation, and human mobility on the RSS measurements, and to create, based on the truncated singular value decomposition (SVD) technique, a mapping between the RSS measure and the actual geographical distance. The proposed system requires zero-configuration because the on-line calibration of the effect of wireless physical characteristics on RSS measurement is automated and no on-site survey or initial training is required to bootstrap the system. It is also quite responsive to environmental dynamics, as the impacts of physical characteristics changes have been explicitly figured in the mapping between the RSS measures and the actual geographical distances. We have implemented the proposed system with inexpensive off-the-shelf Wi-Fi hardware and sensory functions of IEEE 802.11, and carried out a detailed empirical study in our division building. The empirical results show the proposed system is quite robust and gives accurate localization results (i.e., with the localization error within 3 meters).
Tunable Photoluminescence of Monolayer MoS2 via Chemical Doping (2013)

We demonstrate the tunability of the photoluminescence (PL) properties of monolayer (1L)-MoS2 via chemical doping. The PL intensity of 1L-MoS2 was drastically enhanced by the adsorption of p-type dopants with high electron affinity but reduced by the adsorption of n-type dopants. This PL modulation results from switching between exciton PL and trion PL depending on carrier density in 1L-MoS2. Achievement of the extraction and injection of carriers in 1L-MoS2 by this solution-based chemical doping method enables convenient control of optical and electrical properties of atomically thin MoS2.
Increased survival after massive thermal injuries in adults (1989)

Survival of major burn injuries has improved markedly from an expected survival of 10% to 20% in both children and adults to an expected survival of 60% in children with burns greater than 70% BSA. Increased survival for adults after similar burn injuries has been less dramatic than in children because of the profound influences of advancing age and the coexistent processes of aging upon survival after a major injury. Consecutive admissions of patients with massive burn injuries (greater than or equal to 70% BSA) to the Massachusetts General Hospital Adult Burn Unit from 1974 to 1986 were analyzed statistically using univariate and multiple logistic regression analysis to identify factors associated with survival and to identify patient characteristics associated with increases in expected survival. Survival of adults with massive burn injuries has improved markedly, from 24% of adults admitted to the Adult Burn Center in 1974-75 to 48% of adults admitted in 1984-86. An increased likelihood of survival was shown to be associated with the use of artificial skin. Improved survival rates in these massive burn injuries were attributed to multiple factors including wound management of prompt eschar excision and immediate wound closure.
Amino acid sequence of rat liver cathepsin L (1988)

The complete amino acid sequences of the heavy and light chains of rat liver cathepsin L (EC 3.4.22.15) were determined at the protein level. The heavy and light chains consisted of 175 and 44 amino acid residues, respectively, and their Mr values without glycosyl groups calculated from these sequences were 18941 and 5056, respectively. The amino acid sequence was also determined from the N-terminal sequences of the heavy and light chains, and the sequences of cleavage fragments of the heavy chain with lysylendopeptidase and cyanogen bromide. The fragments were aligned by comparison with the amino acid sequence deduced from the sequence of cDNA of rat preprocathepsin L. The sequence of rat liver cathepsin L determined at the protein level was identical with that deduced from the cDNA sequence except that in the heavy chain, residues 176-177 (Asp-Ser) were not present at the C-terminus and alanine was replaced by proline at residue 125. Asn-108 in the heavy chain is modified with carbohydrate.
Is There a Seasonal Variation in the Incidence or Intensity of Allergic Eosinophilic Esophagitis in Newly Diagnosed Children? (2007)

A seasonal variation was noted with Winter, a season of low outdoor allergens, having the fewest number of newly diagnosed AEE patients.
Molecular regulation of human megakaryocyte development (1990)

Extracellular regulators of human megakaryocyte development are becoming better defined. How these regulators function at the subcellular and, in particular, the molecular levels remains almost completely unknown. The recent development of molecular micromethodologies such as in situ hybridization, the polymerase chain reaction, and the use of antisense oligodeoxynucleotides now make such studies possible in normal cells. We therefore examined the effect of several recombinant human hematopoietic growth factors and the maturation agonist phorbol myristate acetate on the expression of selected growth-regulated and maturation/function-related genes. We also examined the role of the c-myb proto-oncogene in regulating megakaryocyte proliferative activity and ploidy development. Our results demonstrate that growth factors have complex time and concentration effects on gene expression in morphologically recognizable human megakaryocytes. They also suggest that a more complete understanding of normal megakaryocyte development at the molecular level will soon be possible.
A region of antisense RNA from human p120 cDNA with high homology to mouse p120 cDNA inhibits NIH 3T3 proliferation. (1992)

The human nucleolar p120 protein is a proliferation-associated antigen which is expressed in G1 and peaks during the early S phase of the cell cycle. Overexpression of the human p120 protein caused the transformation of NIH 3T3 cells and expression of an antisense p120 construct inhibited the growth of NIH 3T3 cells (Perlaky et al., Cancer Res., 52:428-436, 1992). The middle region of the antisense p120 RNA was found to be almost as inhibitory as the full length antisense construct but the 5' and 3' antisense portions did not affect NIH 3T3 cell proliferation. After the mouse p120 complementary DNA was cloned and sequenced, comparison with the human p120 complementary DNA showed a striking conservation of 85% of the nucleotide sequence and 96% of the amino acid sequence. The two ends of the p120 molecule had less homology in their nucleotide and amino acid sequences. Based on this homology, the observed inhibitory effects of the middle portion of antisense human p120 RNA may be related to suppression of mouse p120 expression by RNA:RNA duplex formation. The high evolutionary conservation of the middle region suggests it has a critical role for the function of this protein.
Synthesis and conformational properties of 2′‐deoxy‐2′‐methylthio‐pyrimidine and ‐purine nucleosides: Potential antisense applications (1993)

Abstract A convenient and shorter synthesis of 2′‐deoxy‐2′‐methylthiouridine analogs 5 , −5‐methyluridine 6 , ‐cyti‐dine 15 , −5‐methylcytidine 16 , ‐adenosine 27 and ‐guanosine 34 was accomplished. Successful conversion of ribonucleosides (5‐methyl U, U, A, G) into the corresponding 2′‐substituted nucleosides involves nucleophilic displacement (S N 2) of an appropriate leaving group at the 2′‐position by methanethiol, a soft nucleophile. Reaction between 2,2′‐anhydrouridine and methanethiol in the presence of N 1 , N 1 , N 3 , N 3 ‐tetramethylguani‐dine in N , N ‐dimethylformamide gave 5 , in 75% yield. Preparation of 6 by a similar route was described. Acylated 5 and 6 were transformed into their triazole derivatives, which on ammonolysis furnished 15 and 16 , respectively in good yield. Similarly, tetraisopropyldisiloxanyl (TIPS) protected 2′‐ O ‐aratriflates‐ of‐adenosine and ‐guanosine reacted with methanethiol in the presence of 1,8‐diazabicyclo[5.4.0]undec‐7‐ene at ‐ 25°, followed by deblocking of the TIPS protecting group furnished 27 and 34 , respectively. The confor‐mational flexibility (N/S equilibrium) of the sugar moiety in nucleosides 5 , 15 , 27 and 34 was studied utilizing nmr spectroscopy, suggesting that the 2′‐methylthio group influenced the sugar conformation to adopt a rigid S‐pucker in all cases. The extra stiffness of the sugar moiety in these analogs is believed to be due to the electronegativity of the substituent and the steric bulk. The usefulness of these nucleosides to prepare uniformly modified 2′‐deoxy‐2′‐methylthio oligonucleotides for antisense therapeutics is proposed.
Middle Temporal Visual Area Microstimulation Influences Veridical Judgments of Motion Direction (2002)

Microstimulation of direction columns in the middle temporal visual area (MT, or V5) provides a powerful tool for probing the relationship between cortical physiology and visual motion perception. In the current study we obtained "veridical" reports of perceived motion from rhesus monkeys by permitting a continuous range of possible responses that mapped isomorphically onto a continuous range of possible motion directions. In contrast to previous studies, therefore, the animals were freed from experimenter-imposed "categories" that typify forced choice tasks. We report three new findings: (1) MT neurons with widely disparate preferred directions can cooperate to shape direction estimates, inconsistent with a pure "winner-take-all" read-out algorithm and consistent with a distributed coding scheme like vector averaging, whereas neurons with nearly opposite preferred directions seem to compete in a manner consistent with the winner-take-all hypothesis, (2) microstimulation can influence direction estimates even when paired with the most powerful motion stimuli available, and (3) microstimulation effects can be elicited when a manual response (instead of our standard oculomotor response) is used to communicate the perceptual report.