gebhart/patrepeval huggingface dataset:
HSP90: The Rosetta stone for cellular protein dynamics? (2008)

The Hsp90 proteomic network is expansive and includes a variety of cell processes operating within the cytoplasm and nucleoplasm. Though the functional significance of the extensive interactions has not been defined, we suggest that the Hsp90 molecular chaperone machinery promotes dynamic behaviors for client proteins that is critical to achieve homeostasis. A general rapid action by cell factors would permit both proper assembly of biological complexes and efficient transitions between distinct structures. Here, we describe why the properties that are inherent to molecular chaperones place these proteins in a unique position to drive the dynamic cellular environment.
Dip Pen Nanolithography®: A “Desktop Nanofab™” Approach Using High‐Throughput Flexible Nanopatterning (2008)

The ability to perform controllable nanopatterning with a broad range of "inks" at ambient conditions is a key aspect of the dip pen nanolithography (DPN) technique. The traditional ink system to demonstrate DPN is n-alkanethiols on a gold substrate, but the DPN method has found numerous other applications since. This article is meant to outline recent advances in the DPN toolkit, both in terms of research and patterning technology, and to discuss applications of DPN as a viable nanofabrication method. We will summarize new DPN developments, and introduce our concept of the "Desktop Nanofab." In addition, we outline our efforts to commercialize DPN as a viable nanofabrication technique by demonstrating massively parallel nanopatterning with the 55,000 tip 2D nano PrintArray. This demonstrates our ability to overcome the serial nature of DPN patterning and enable high-throughput nanofabrication.
국어교육 : 국어과 교육과정의 통합적 내용 구성 방안 -2011 교육과정 "독서와 문법" 과목을 대상으로 (2011)

이 연구는 국어교육의 통합에 대한 개념 정립을 바탕으로 2011 교육과정의 ``독서와 문법`` 과목을 비판적으로 고찰하여 통합 가능한 방안을 모색하는 데 그 목적이 있다. 이는 과목 간 통합 양상에 대한 검토를 통해 교육과정 실행 방안을 마련하고, 더 나아가 통합 지향 교육과정 개발 담론을 형성하는 데 의의가 있다. 통합은 총체, 융합, 연계와는 다른 개념으로, 국어교육의 총체를 지향하는 관점에서 국어교육 영역 내, 영역 간, 과목 간 내용 요소 융합 수준에서의 수평적 관계 맺기를 말한다. 이 가운데 과목 간 통합은 반드시 내용 요소 간의 융합을 지향해야 하며, 이를 위해서는 각 과목의 특성을 고려하여 통합 가능한 접점을 찾는 것이 중요하다. 이에 독서와 문법은 각각 ``텍스트의 의미를 구성하는 행위``와 ``텍스트 의미 구성을 위한 기저``라는 점에서 ``텍스트``를 중심으로 통합 가능하다. 다만 반드시 텍스트를 전제로 해야 하며, 통합된 양상을 바탕으로 논의의 확장이 어렵다는 점에서 한계가 있다. 이러한 통합에 대한 이론적 탐색을 바탕으로, 2011 교육과정의 ``독서와 문법`` 과목의 통합 양상을 비판적으로 살펴보았다. 그 결과 ``독서와 문법`` 과목의 내용 체계와 세부 내용은 통합이 거의 이루어지지 않았음을 알 수 있었다. 이에 두 과목 간 통합 가능한 내용을 구성하여 효과적인 통합 방안을 논구하였다. 이를 바탕으로 ``독서와 문법`` 과목의 지향적인 내용 체계로서 ``언어와 독서의 본질``, ``독서의 이해와 국어의 탐구``, ``독서와 국어 생활``을 제안하고자 한다.
RNA Tertiary Structure Mediation by Adenosine Platforms (1996)

The crystal structure of a group I intron domain reveals an unexpected motif that mediates both intra- and intermolecular interactions. At three separate locations in the 160-nucleotide domain, adjacent adenosines in the sequence lie side-by-side and form a pseudo-base pair within a helix. This adenosine platform opens the minor groove for base stacking or base pairing with nucleotides from a noncontiguous RNA strand. The platform motif has a distinctive chemical modification signature that may enable its detection in other structured RNAs. The ability of this motif to facilitate higher order folding provides one explanation for the abundance of adenosine residues in internal loops of many RNAs.
Bimetallic Fluorine-Substituted Anilido−Aldimine Zinc Complexes for CO2/(Cyclohexene Oxide) Copolymerization (2006)

Regioselective nucleophilic aromatic substitution of an o-fluorine occurs to afford fluorine-substituted o-phenylene-bridged bis(anilido-aldimine) compounds o-C6H4[(C6H2R2)N=CH-C6F4-(H)N(C6H3R'2)]2 when Li(H)N-C6H3R'2 (R' = iPr, Et, Me) is reacted with o-C6H4[(C6H2R2)N=CH-C6F5]2 (R = iPr, Et, Me) in a nonpolar solvent such as diethyl ether or toluene. Successive additions of Me2Zn and SO2 gas to the bis(anilido-aldimine) compounds afford quantitatively dinuclear mu-methylsulfinato zinc complexes o-C6H4[[(C6H2R2)N=CH-C6F4-N(C6H3R'2)-kappa2N,N]Zn(mu-OS(O)Me)]2 (R = iPr, R' = iPr, 3a; R = iPr, R' = Me, 3c; R = Et, R' = (i)Pr, 3d; R = Et, R' = Et, 3e; R = Et, R' = Me, 3f; R = Me, R' = iPr, 3g; R = Me, R' = Et, 3h; R = Me, R' = Me, 3i). The molecular structure of 3c was confirmed by X-ray crystallography. Fluorine-substituted complexes 3a-i show significantly higher TOF (turnover frequencies) than the unfluorinated analogues for CO2/(cyclohexene oxide) copolymerization. The TOF is highly sensitive to the substituents R and R', and the highest TOF (2480 h(-1)) is obtained with 3g (R = Me, R' = iPr). Complex 3g is less sensitive to the residual protic impurities present in the monomers and shows activity at such a low catalyst concentration as [Zn]:[cyclohexene oxide] = 1:50,000, at which the unfluorinated analogue is completely inactive. By realizing the activity at such an extremely low [Zn]:[cyclohexene oxide] ratio, we achieve a high TON (turnover number) up to 10,100. High-molecular-weight polymers (M(n), 100,000-200,000) are obtained with a rather broad molecular-weight distribution (M(w)/M(n), 1.3-2.5). The obtained polymers are not perfectly alternating, and variable carbonate linkages (65-85%) are observed depending on the N-aryl ortho substituents R and R' and the polymerization conditions.
Effect of pH on the Anodic Behavior of Tungsten (2002)

Potentiodynamic and potentiostatic polarization, and the rotating disk electrode technique, were used to study the anodic behavior of tungsten (W) in a broad pH range (0.5-13.5) in buffered solution. Surface oxides were found to play a prominent role in the anodic oxidation and dissolution of tungsten. Five distinct pH regimes and the corresponding reaction mechanisms were identified. Below pH 1 (region A) -assisted dissolution was the main dissolution pathway. As the pH increased, the role of diminished and at pH 2.6 (region B), which was identified as the point of zero charge (pzc) of the surface tungsten oxide, dissolution was mainly -assisted. The dissolution was observed to be -assisted above the pzc. The reaction order for was one between pH 4.5 and 6.5 (region C). The reaction order became zero at pH 8 (region D). This observation was attributed to the pH-independent dissolution of the hydrated oxide phase. Above pH 10, dependence of the anodic current commenced and at around pH 12.5 (region E) the reaction order for became one. © 2002 The Electrochemical Society. All rights reserved.
Critical Components of a DNA Fusion Vaccine Able to Induce Protective Cytotoxic T Cells Against a Single Epitope of a Tumor Antigen (2002)

DNA vaccines can activate immunity against tumor Ags expressed as MHC class I-associated peptides. However, priming of CD8(+) CTL against weak tumor Ags may require adjuvant molecules. We have used a pathogen-derived sequence from tetanus toxin (fragment C (FrC)) fused to tumor Ag sequences to promote Ab and CD4(+) T cell responses. For induction of CD8(+) T cell responses, the FrC sequence has been engineered to remove potentially competitive MHC class I-binding epitopes and to improve presentation of tumor epitopes. The colon carcinoma CT26 expresses an endogenous retroviral gene product, gp70, containing a known H2-L(d)-restricted epitope (AH1). A DNA vaccine encoding gp70 alone was a poor inducer of CTL, and performance was not significantly improved by fusion of full-length FrC. However, use of a minimized domain of FrC, with the AH1 sequence fused to the 3' position, led to rapid induction of high levels of CTL. IFN-gamma-producing epitope-specific CTL were detectable ex vivo and these killed CT26 targets in vitro. The single epitope vaccine was more effective than GM-CSF-transfected CT26 tumor cells in inducing an AH1-specific CTL response and equally effective in providing protection against tumor challenge. Levels of AH1-specific CTL in vivo were increased following injection of tumor cells, and CTL expanded in vitro were able to kill CT26 cells in tumor bearers. Pre-existing immunity to tetanus toxoid had no effect on the induction of AH1-specific CTL. These data demonstrate the power of epitope-specific CTL against tumor cells and illustrate a strategy for priming immunity via a dual component DNA vaccine.
The Population Genetics of the Origin and Divergence of the Drosophila simulans Complex Species (2000)

The origins and divergence of Drosophila simulans and close relatives D. mauritiana and D. sechellia were examined using the patterns of DNA sequence variation found within and between species at 14 different genes. D. sechellia consistently revealed low levels of polymorphism, and genes from D. sechellia have accumulated mutations at a rate that is approximately 50% higher than the same genes from D. simulans. At synonymous sites, D. sechellia has experienced a significant excess of unpreferred codon substitutions. Together these observations suggest that D. sechellia has had a reduced effective population size for some time, and that it is accumulating slightly deleterious mutations as a result. D. simulans and D. mauritiana are both highly polymorphic and the two species share many polymorphisms, probably since the time of common ancestry. A simple isolation speciation model, with zero gene flow following incipient species separation, was fitted to both the simulans/mauritiana divergence and the simulans/sechellia divergence. In both cases the model fit the data quite well, and the analyses revealed little evidence of gene flow between the species. The exception is one gene copy at one locus in D. sechellia, which closely resembled other D. simulans sequences. The overall picture is of two allopatric speciation events that occurred quite near one another in time.
Protease-activated receptor-2 protects against pancreatitis by stimulating exocrine secretion (2006)

Trypsin released during the early stages of pancreatitis activates PAR-2 receptors on the acinar cells and stimulates secretion from these cells. Thus, PAR-2 activation may decrease pancreatic injury and limit the severity of pancreatitis by allowing extracellular trypsin to act as a secretagogue.
VEGF‐C and VEGF‐D expression in neuroendocrine cells and their receptor, VEGFR‐3, in fenestrated blood vessels in human tissues (2000)

Recently, vascular endothelial growth factor receptor 3 (VEGFR-3) has been shown to provide a specific marker for lymphatic endothelia in certain human tissues. In this study, we have investigated the expression of VEGFR-3 and its ligands VEGF-C and VEGF-D in fetal and adult tissues. VEGFR-3 was consistently detected in the endothelium of lymphatic vessels such as the thoracic duct, but fenestrated capillaries of several organs including the bone marrow, splenic and hepatic sinusoids, kidney glomeruli and endocrine glands also expressed this receptor. VEGF-C and VEGF-D, which bind both VEGFR-2 and VEGFR-3 were expressed in vascular smooth muscle cells. In addition, intense cytoplasmic staining for VEGF-C was observed in neuroendocrine cells such as the alpha cells of the islets of Langerhans, prolactin secreting cells of the anterior pituitary, adrenal medullary cells, and dispersed neuroendocrine cells of the gastrointestinal tract. VEGF-D was observed in the innermost zone of the adrenal cortex and in certain dispersed neuroendocrine cells. These results suggest that VEGF-C and VEGF-D have a paracrine function and perhaps a role in peptide release from secretory granules of certain neuroendocrine cells to surrounding capillaries.
Effects of Hydrogen Sulfide-releasing l-DOPA Derivatives on Glial Activation (2010)

The main lesion in Parkinson disease (PD) is loss of substantia nigra dopaminergic neurons. Levodopa (L-DOPA) is the most widely used therapy, but it does not arrest disease progression. Some possible contributing factors to the continuing neuronal loss are oxidative stress, including oxidation of L-DOPA, and neurotoxins generated by locally activated microglia and astrocytes. A possible method of reducing these factors is to produce L-DOPA hybrid compounds that have antioxidant and antiinflammatory properties. Here we demonstrate the properties of four such L-DOPA hybrids based on coupling L-DOPA to four different hydrogen sulfide-donating compounds. The donors themselves were shown to be capable of conversion by isolated mitochondria to H(2)S or equivalent SH(-) ions. This capability was confirmed by in vivo results, showing a large increase in intracerebral dopamine and glutathione after iv administration in rats. When human microglia, astrocytes, and SH-SY5Y neuroblastoma cells were treated with these donating agents, they all accumulated H(2)S intracellularly as did their derivatives coupled to L-DOPA. The donating agents and the L-DOPA hybrids reduced the release of tumor necrosis factor-alpha, interleukin-6, and nitric oxide from stimulated microglia, astrocytes as well as the THP-1 and U373 cell lines. They also demonstrated a neuroprotective effect by reducing the toxicity of supernatants from these stimulated cells to SH-SY5Y cells. L-DOPA itself was without effect in any of these assays. The H(2)S-releasing L-DOPA hybrid molecules also inhibited MAO B activity. They may be useful for the treatment of PD because of their significant antiinflammatory, antioxidant, and neuroprotective properties.
Recombinant human monoclonal antibodies against different conformational epitopes of the E2 envelope glycoprotein of hepatitis C virus that inhibit its interaction with CD81 (2000)

The antibody response to the envelope proteins of hepatitis C virus (HCV) may play an important role in controlling the infection. To allow molecular analyses of protective antibodies, we isolated human monoclonal antibodies to the E2 envelope glycoprotein of HCV from a combinatorial Fab library established from bone marrow of a chronically HCV-infected patient. Anti-E2 reactive clones were selected using recombinant E2 protein. The bone marrow donor carried HCV genotype 2b, and E2 used for selection was of genotype 1a. The antibody clones were expressed as Fab fragments in E. coli, and as Fab fragments and IgG1 in CHO cells. Seven different antibody clones were characterized, and shown to have high affinity for E2, genotype 1a. Three clones also had high affinity for E2 of genotype 1b. They all bind to conformation-dependent epitopes. Five clones compete for the same or overlapping binding sites, while two bind to one or two other epitopes of E2. Four clones corresponding to the different epitopes were tested as purified IgG1 for blocking the CD81-E2 interaction in vitro; all four were positive at 0.3-0.5 microg/ml. Thus, the present results suggest the existence of at least two conserved epitopes in E2 that mediate inhibition of the E2-CD81 interaction, of which one appeared immunodominant in this donor.
The Effect of Nitric Oxide on Bacteria (1962)

Nitric oxide, as well as several other oxides of nitrogen, were assayed for their antibacterial action. It is shown that nitric oxide has virtually no effect on bacteria, whereas both NaNO(3) and NaNO(2) appear to have either neutral or stimulatory effects. It is suggested that the formation of nitrous acid is mainly responsible for the quantitative as well as the qualitative changes that occur in the bacterial flora of cured meat. A pH-dependent "nitrite cycle" is presented to account for the production of nitrous acid in cured meat systems.
Next generation iterative LDPC solutions for magnetic recording storage (2008)

Low-density parity-check (LDPC) codes have received considerable attention as a next-generation coding technique for communication and storage channels. The developments in the hardware storage business include hard disk drives that support higher capacities and transfer rate credit to perpendicular recording. To meet the demanding error correction requirements at a lower silicon cost, most storage systems manufacturers have started adopting LDPC based error correction systems. This paper summarizes the research on low complexity LDPC decoder architecture with statistical buffer management for magnetic recoding channels that require data rates of over 5 Gbps, real time bit error rates in the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> , and quasi real time bit error rates in the order of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-15</sup> .
CD24 staining of mouse mammary gland cells defines luminal epithelial, myoepithelial/basal and non-epithelial cells (2005)

Differential staining of mammary epithelial cells for CD24 can be used to simultaneously isolate pure populations of non-epithelial, myoepithelial/basal and luminal epithelial cells. Furthermore, mammary fat pad repopulation capacity is enriched in the CD24Low population. As separation is achieved using a single marker, it will be possible to incorporate additional markers to further subdivide these populations. This will considerably facilitate the further analysis of mammary epithelial subpopulations, whilst ensuring high purity, which is key for understanding mammary epithelial stem cells in normal tissue biology and carcinogenesis.
The TRPV1 Receptor: Target of Toxicants and Therapeutics (2005)

Understanding the structural and functional complexities of the transient receptor potential vanilloid receptor (TRPV1) is essential to the therapeutic modulation of inflammation and pain. Because of its central role in initiating inflammatory processes and integrating painful stimuli, there is an understandable interest in its pharmacological manipulation (sensitization/desensitization). The present Highlight entitled "TRPV1 antagonists elevate cell surface populations of receptor protein and exacerbate TRPV1 mediated toxicities in human lung epithelial cells" describes how exposure to various antagonists produces TRPV1 sensitization and proposes a possible mechanistic explanation to that sensitization.
45° polymer-based total internal reflection coupling mirrors for fully embedded intraboard guided wave optical interconnects (2005)

An array of 50μm×50μm polymer waveguides with 45° total internal reflection (TIR) wideband coupling mirrors were fabricated by soft molding to achieve fully embedded boardlevel optoelectronic interconnects. The 45° TIR coupling mirrors were formed at the ends of the waveguides to provide surface normal light coupling between waveguides and optoelectronic devices. Three-dimensional optoelectronic interconnects were replicated in one-step transfer by the soft molding technique. The measured propagation loss of the multimode waveguide was 0.16dB∕cm at 850nm wavelength. The coupling efficiency of the silver-coated 45° micromirrors buried under the top cladding was 92% with low polarization sensitivity.
Interpixel capacitance in non-destructive focal plane arrays (2003)

Inter-pixel capacitive coupling can exist in a non-destructive detector array if the detector nodes change voltage as they integrate charge and the design of the device allows for an electric fleld to exist between adjacent collection nodes. Small amounts of inter-pixel capacitance can cause large errors in the measurement of poissonian noise versus signal, and all subsequently derived measurements such as nodal capacitance and quantum e‐ciency. Crosstalk and MTF can also be signiflcantly in∞uenced by interpixel capacitance. Two 1K £ 1K Raytheon SB226-based hybridized silicon P-I-N arrays were tested for nodal capacitance and MTF. Initial results indicated unexpected and unexplainably large nodal capacitance, poor MTF, and odd edge spread. It was hypothesized that inter-pixel capacitive coupling was responsible for these discrepancies. A stochastic method of measuring the coupling using 2D autocorrelation and Fourier Transform techniques was devised and implemented. Autocorrelation of the shot noise in the images revealed a correlation consistent with 3.2% interpixel capacitive coupling. When the efiects of the measured interpixel capacitance were taken into account, the initially measured nodal capacitance of 56 fF was found to be in error, 30% higher than the corrected nodal capacitance measurement of 43 fF. Large discrepancies between the theoretical and observed edge spread response were also greatly reduced. A simulation of the electric fleld in the pin detector intrinsic region predicted an interpixel coupling very close to the observed coupling. Interpixel capacitance was also observed in 2K £ 2k Raytheon SB304-based InSb detector arrays, but was not strongly evident in a bare SB226 multiplexer.
Rapid Detection of Methicillin-Resistant Staphylococci from Blood Culture Bottles by Using a Multiplex PCR Assay (2002)

Rapid detection and accurate identification of methicillin-resistant staphylococci are critical for the effective management of infections caused by these organisms. We describe a multiplex PCR-based assay for the direct detection of methicillin-resistant staphylococci from blood culture bottles (BacT/Alert; Organon-Teknika, Durham, N.C.). A simple lysis method followed by a multiplex PCR assay designed to detect the nuc, mecA, and bacterial 16S rRNA genes was performed. A total of 306 blood culture specimens were collected over a period of 10 months from June 1998 to April 1999, consisting of 236 blood cultures growing staphylococci (including 124 methicillin-resistant Staphylococcus spp.), 50 positive blood cultures which grew organisms other than staphylococci, and 20 blood cultures that were negative for bacterial and fungal pathogens after 5 days of incubation and terminal subculture. DNA extraction, PCR, and detection could be completed in 2.5 h. Of the positive blood cultures with staphylococci, the multiplex PCR assay had a sensitivity and specificity of 99.2% and 100%, respectively. Our results show that rapid, direct detection of methicillin-resistant staphylococci is possible, allowing clinicians to make prompt and effective decisions for the management of patients with staphylococcal bacteremia.
Angiotensin II‐induced vascular smooth muscle cell hypertrophy: PDGF A‐chain mediates the increase in cell size (1993)

We report here that angiotensin II-mediated hypertrophy of vascular smooth muscle cells (VSMC) exhibits PDGF A-chain-dependent and -independent pathways. Secretion of PDGF A-chain is required for the increase in cell size, but not for the increase in protein synthesis. Angiotensin II stimulates a hypertrophic growth response in VSMC characterized by increases in cell size and protein synthesis, but not cell number. Because angiotensin II-stimulated VSMC hypertrophy has been associated with increased PDGF A-chain expression, we studied its role in the hypertrophic response by inhibiting PDGF A-chain expression with hydrocortisone or anti-PDGF antibody. Hydrocortisone (1 microM for 48 h) inhibited basal protein synthesis by 47%, but angiotensin II-stimulated protein synthesis was enhanced (111% increase after hydrocortisone treatment vs. 25% increase in control). In contrast, hypertrophy, as measured by cell size, was completely inhibited. Although hydrocortisone had no effect on early growth signals stimulated by angiotensin II (e.g., activation of protein kinase C, stimulation of Na+/H+ exchange, and c-fos and c-myc expression), it significantly decreased angiotensin II-stimulated secretion of PDGF-like material into the medium from 0.4 to 0.1 ng/ml/24 h (p < 0.01). However, the time course for PDGF secretion (maximal at 16-24 h) was significantly slower than the time course for angiotensin II-stimulated protein synthesis (maximal at 4-12 h). To block the action of PDGF A-chain selectively, VSMC were treated with anti-PDGF A-chain antibody. The antibody completely inhibited the angiotensin II-stimulated increase in cell size, but it had no significant effect on protein synthesis at early times (< 8 h). These findings demonstrate two pathways involved in angiotensin II-stimulated VSMC hypertrophy: an increase in cell size dependent on PDGF A-chain and an increase in protein synthesis independent of PDGF A-chain.