gebhart/patrepeval huggingface dataset:
Poly(N-isopropylacrylamide)-Based Semi-interpenetrating Polymer Networks for Tissue Engineering Applications. 1. Effects of Linear Poly(acrylic acid) Chains on Phase Behavior (2002)

Poly(N-isopropylacrylamide)-based [P(NIPAAm)-based] semi-interpenetrating polymer networks (semi-IPNs), consisting of P(NIPAAm)-based hydrogels and linear poly(acrylic acid) [P(AAc)] chains, were synthesized, and the effects of the P(AAc) chains on semi-IPN injectability and phase behavior were analyzed. In P(NIPAAm)- and P(NIPAAm-co-AAc)-based semi-IPN studies, numerous reaction conditions were varied, and the effects of these factors on semi-IPN injectability, transparency, phase transition, lower critical solution temperature (LCST), and volume change were examined. The P(AAc) chains did not significantly affect the LCST or volume change of the semi-IPNs, compared to control hydrogels. However, the P(AAc) chains affected the injectability, transparency, and phase transition of the matrices, and these effects were dependent on chain amount and molecular weight (MW) and on interactions between the P(AAc) chains and the solvent and/or copolymer chains in P(NIPAAm-co-AAc) hydrogels. These results can be used to design "tailored" P(NIPAAm)-based semi-IPNs that have the potential to serve as functional scaffolds in tissue engineering applications.
Clinical Use of Anti‐Epidermal Growth Factor Receptor Monoclonal Antibodies in Metastatic Colorectal Cancer (2008)

Abstract Cetuximab and panitumumab, monoclonal antibodies used to target the epidermal growth factor receptor (EGFR), were recently approved by the United States Food and Drug Administration for use as single agents or in combination with other chemotherapy drugs in the treatment of metastatic colorectal cancer. The anti-EGFR monoclonal antibodies, either as single agents or in combination with chemotherapy, have demonstrated clinical activity in this setting. When combined with standard cytotoxic chemotherapy or other targeted agents (e.g., bevacizumab, an anti-vascular endothelial growth factor monoclonal antibody), anti-EGFR monoclonal antibodies have been well tolerated and produced minimal toxicities. However, cetuximab and panitumumab appear to benefit only select patients. Predictive markers of efficacy, including EGFR overexpression, development of skin rash, and the absence of a K-ras mutation, have been evaluated in clinical studies to identify patients likely to respond to anti-EGFR monoclonal antibody therapy. This review discusses recent clinical studies of anti-EGFR monoclonal antibodies in the treatment of metastatic colorectal cancer, predictive markers of their efficacy, and common toxicities associated with their use.
Poly(ADP-ribose) may signal changing metabolic conditions to the chromatin of mammalian cells. (1987)

In mammalian cells, NAD+ serves a dual role as a respiratory coenzyme and as a substrate for the posttranslational poly(ADP-ribose) modification of chromatin proteins, catalyzed by the nuclear enzyme poly(ADP-ribose) polymerase [NAD+ ADP-ribosyltransferase, EC 2.4.2.30]. Biological evidence strongly suggests that poly(ADP-ribosyl)ation modulates chromatin functions, although the precise molecular mechanisms involved have not yet been elucidated. Here we describe conditions for the rapid uptake of exogenously supplied NAD+ by living hepatocytes in primary monolayer culture. Raising the intracellular NAD+ concentration by 70% caused a 5-fold increase of chromatin-bound poly(ADP-ribose). We conclude that the constitutive level of posttranslational poly(ADP-ribose) modifications of chromatin proteins in mammalian cells is related to the availability of NAD+, which varies in different physiological and pathological states. We propose that poly-(ADP-ribose) may serve a hitherto unrecognized function by signaling altered metabolic conditions to the chromatin and thus modulate its functions in tune with changing metabolic states.
Vinyl Sulfide Cyclized Analogues of Angiotensin II with High Affinity and Full Agonist Activity at the AT1Receptor (2002)

Vinyl sulfide cyclized analogues of the octapeptide angiotensin II that are structurally related to the cyclic disulfide agonist c[Hcy3,5]Ang II have been prepared. The synthesis relies on the reaction of the mercapto group of a cysteine residue in position 3 with the formyl group of allysine incorporated in position 5 of angiotensin II. A mixture of the cis and the trans isomers was formed, and these were separated and isolated by RP-HPLC. Thus, the three-atom CH2−S−S element of the AT1 receptor agonist c[Hcy3,5]Ang II has been displaced by a bioisosteric three-atom S−CHCH element. A comparative conformational analysis of the 13-membered ring systems of c[Hcy3,5]Ang II and the 13-membered cyclic vinyl sulfides with cis and trans configuration, respectively, suggested that all three systems adopted very similar low-energy conformations. This similarity was also reflected in the bioactivity. Both of the compounds that contained the ring systems encompassing the cis or trans vinyl sulfide elements between positions 3 and 5 exhibited Ki values less than 2 nM and exerted full agonism at the AT1 receptor. In contrast, vinyl sulfide cyclization involving the amino acid residues 5 and 7 rendered inactive compounds. The cyclic vinyl sulfides that have agonist activity were both shown to possess low-energy conformers compatible with the previously proposed 3D model for the bioactive conformation of Ang II.
The Michael Addition of Mononitroparaffins to Nitrochalcones (1966)

Abstract Mononitroparaffins add, in the presence of piperidine, to 3‐nitro‐, 3′‐nitro‐, 3, 3′dinitro‐and 3,4′‐dinitrochalcones. The nitroparaffins also serve as solvents for these reactions. The infrared spectra of the addition products are discussed.
Integrating Big Data: A Semantic Extract-Transform-Load Framework (2015)

Current tools that facilitate the extract-transform-load (ETL) process focus on ETL workflow, not on generating meaningful semantic relationships to integrate data from multiple, heterogeneous sources. A proposed semantic ETL framework applies semantics to various data fields and so allows richer data integration.
Monocytes from patients with osteoarthritis display increased osteoclastogenesis and bone resorption: The In Vitro Osteoclast Differentiation in Arthritis study (2012)

During 3 weeks of culture under identical conditions, monocytes from patients with OA display enhanced capacity to generate osteoclasts compared to cells from controls. Enhanced osteoclastogenesis is accompanied by increased resorptive activity, reduced osteoclast apoptosis, and diminished IL-1RI expression. These findings support the possibility that generalized changes in bone metabolism affecting osteoclasts participate in the pathophysiology of OA.
Immunomodulation by cytokine antisense oligonucleotides. (1995)

The cytokine network is involved in normal immune reaction and in the progression of several pathologies. Antisense (AS) oligonucleotides, which allow specific inhibition of expression of proteins, offer a new methodology to investigate this complex network. This review focuses on the use of AS to modulate cytokine expression. AS may act in different ways such as blocking fixation or progression of the ribosome along the mRNA, mRNA cleavage by RNase H, or preventing normal RNA maturation. In order to improve AS efficiency, chemical modifications have been developed, and improvement of oligonucleotide uptake has been achieved with different systems of vectorization including liposomes (neutral, cationic, immunoliposome), nanoparticles, or covalent attachment of a carrier. In oncogenesis, intracellular or extracellular autocrine loops have been demonstrated by the use of cytokine AS. Involvement of cytokines in immunological reactions (TH1 and TH2 subset, IgE response, lymphokine activated killer, cytotoxic T lymphocyte...) and in hematopoiesis have also been studied with this approach. Therapeutic application of AS has been suggested by inhibition of inflammatory cytokines in vivo. Clinical trials using AS are under investigation in virological and in oncological diseases. At present, cytokine antisenses primarily represent a tool for dissecting the function of a cytokine in vitro, but they may offer in the future a new way for immunomodulation intervention.
Wyner-Ziv Video Coding using LDPC Codes (2006)

Wyner-Ziv video coding aims to design encoders based on the Slepian-Wolf and Wyner-Ziv distributed source coding theorems. In this coding scenario, source statistics are exploited at the decoder so that it is feasible to design simplified encoders. The shift of the computational complexity from the encoder to the decoder is suitable for emerging mobile multimedia applications. Many channel coding techniques are used for the construction of distributed video coding systems. In this paper we present a Wyner-Ziv video coding design using low-density parity-check (LDPC) codes. We also present a refined side estimator to further improve the decoded video quality. Experimental results are presented to demonstrate the rate-distortion performance of the method
The Refined Structure of the Selenoenzyme Glutathione Peroxidase at 0.2‐nm Resolution (1983)

The crystal structure of bovine erythrocyte glutathione peroxidase has been refined by a combined procedure of restrained crystallographic refinement and energy minimization at 0.20 nm resolution. The final R value at this resolution is 0.178. The r.m.s. deviation of main‐chain atoms of the two independently refined monomers is 0.019 nm. The structure at 0.28 nm resolution, which has been determined by multiple isomorphous replacement, served as a starting model. The refined model allowed a detailed survey of the hydrogen‐bonding pattern and of the subunit contact areas in the molecule. The model contains 165 solvent molecules per dimer, all taken as water molecules. The mobility of the structure was derived from the individual atomic temperature factors. The complete tetramer, including the active sites, seems to be rather rigid, except for narrow loops near to the N‐terminal ends and some β turns exposed to solvent. The active centres of glutathione peroxidase are found in flat depressions on the molecular surface. The catalytically active selenocysteine residues could be located at the N‐terminal ends of α helices forming βαβ substructures together with two adjacent parallel β strands. In the vicinity of the reactive group some aromatic amino acid side‐chains could be localized. Especially Trp‐148, which could be hydrogen bonded to SeCys‐35, may play a functional role during catalysis. The results of substrate and inhibitor binding studies in solution and in the crystalline state could be interpreted by an apparent half‐site reactivity of glutathione peroxidase. The enzyme seems to react in the sense of negative cooperativity with dimers being the functional units. Based on difference Fourier analyses of appropriate derivatives a reasonable model of glutathione binding is presented. Among the residues which could be of functional importance are Arg‐40, Gln‐130 and Arg‐167, presumably forming salt bridges and a hydrogen bond to the glutathione molecule. In conclusion, a general picture of a minimal reaction mechanism, which is in good agreement with functional and structural data, is proposed. The main reaction of the catalytic cycle presumably shuttles between the selenolate and the selenenic acid state of SeCys‐35.
Multidentate Polyethylene Glycol Modified Gold Nanorods for in Vivo Near-Infrared Photothermal Cancer Therapy (2014)

Gold nanorods (AuNRs), because of their strong absorption of near-infrared (NIR) light, are very suitable for in vivo photothermal therapy of cancer. However, appropriate surface modification must be performed on AuNRs before their in vivo application because of the high toxicity of their original stabilizer cetyltrimethylammonium bromide. Multidentate ligands have attracted a lot of attention for modification of inorganic nanoparticles (NPs) because of their high ligand affinity and multifunctionality, while the therapeutic effect of multidentate ligands modified NPs in vivo remains unexplored. Here, we modified AuNRs with a polythiol PEG-based copolymer. The multidentate PEG coated AuNRs (AuNR-PTPEGm950) showed good stabilities in high saline condition and wide pH range. And they had much stronger resistance to ligand competition of dithiothreitol (DTT) than AuNRs coated by monothiol-anchored PEG. The AuNR-PTPEGm950 had very low cytotoxicity and showed high efficacy for the ablation of cancer cells in vitro. Moreover, the AuNR-PTPEGm950 showed good stability in serum, and they had a long circulation time in blood that led to a high accumulation in tumors after intravenous injection. In vivo photothermal therapy showed that tumors were completely cured without reoccurrence by one-time irradiation of NIR laser after a single injection of these multidentate PEG modified AuNRs.
Synthesis and beta-adrenoreceptor blocking activity of [[3-(alkylamine)-2-hydroxypropyl]oximino]pyridines and O[3-(alkylamine)-2-hydroxypropyl]methylpyridine ketone oximes derivatives. (1997)

[[3-(alkylamine)-2-hydroxypropyl]-2-oximino]pyridines and O-[3-(alkylamine)-2-hydroxypropyl]methylpyridine ketone oximes 5a-o were synthesized by a solid-liquid phase-transfer reaction, and their beta-adrenoreceptor blocking activity was evaluated in vitro and in vivo. The replacement of the aryl linked to the oximic carbon of the (methylenaminoxy)methyl moiety with the bioisoster pyridine ring produced a decrease of the beta-adrenergic blocking activity. The polarization of the oximic group, derived from the electron-withdrawing action of the nitrogen atom, is more evident for the 2-oxyminopyridine derivative 5d. But also conformational parameters may play an important role in the variation of activity of the compounds 5d, 5l and 5n. The replacement of the hydrogen linked to the oximic carbon with a methyl group increased the activity of the compounds 5a, 5i, 5m and 5o. The methyl could allow a delocalization of the partial positive charge present on the oximic carbon, but also its lipophilicity contributed to the increment of binding to the receptor site. None of the compounds showed high beta 1 or beta 2 selectivity in vitro. The (R) and (S) isomers of the compound 5a were synthesized and obtained with enantiomeric ratio 7:3 and 6:4, respectively. The binding tests and the pharmacological in vivo results confirmed the in vitro data.
A Cryptic Site of Vulnerability on the Receptor Binding Domain of the SARS-CoV-2 Spike Glycoprotein (2020)

SUMMARY SARS-CoV-2 is a zoonotic virus that has caused a pandemic of severe respiratory disease—COVID-19— within several months of its initial identification. Comparable to the first SARS-CoV, this novel coronavirus’s surface Spike (S) glycoprotein mediates cell entry via the human ACE-2 receptor, and, thus, is the principal target for the development of vaccines and immunotherapeutics. Molecular information on the SARS-CoV-2 S glycoprotein remains limited. Here we report the crystal structure of the SARS-CoV-2 S receptor-binding-domain (RBD) at a the highest resolution to date, of 1.95 Å. We identified a set of SARS-reactive monoclonal antibodies with cross-reactivity to SARS-CoV-2 RBD and other betacoronavirus S glycoproteins. One of these antibodies, CR3022, was previously shown to synergize with antibodies that target the ACE-2 binding site on the SARS-CoV RBD and reduce viral escape capacity. We determined the structure of CR3022, in complex with the SARS-CoV-2 RBD, and defined a broadly reactive epitope that is highly conserved across betacoronaviruses. This epitope is inaccessible in the “closed” prefusion S structure, but is accessible in “open” conformations. This first-ever resolution of a human antibody in complex with SARS-CoV-2 and the broad reactivity of this set of antibodies to a conserved betacoronavirus epitope will allow antigenic assessment of vaccine candidates, and provide a framework for accelerated vaccine, immunotherapeutic and diagnostic strategies against SARS-CoV-2 and related betacoronaviruses. HIGHLIGHTS High resolution structure of the SARS-CoV-2 Receptor-Binding-Domain (RBD). Recognition of the SARS-CoV-2 RBD by SARS-CoV antibodies. Structure of the SARS-COV-2 RBD in complex with antibody CR3022. Identification of a cryptic site of vulnerability on the SARS-CoV-2 Spike.
Naked DNA Gene Transfer in Mammalian Cells (2004)

Gene therapy—the goal of which is to cure inheritable and acquired diseases by supplying genetic information to various tissues—is a promising therapy of the new millennium. To date, many strategies have been attempted to cure a disease by adding a foreign gene or correcting a mutation in the genes. The success of these gene-therapy strategies is largely dependent on the development of a vector that delivers and efficiently expresses a therapeutic gene in a specific cell population. Viral vectors are potentially efficient, although nonviral vectors have some advantages in that they are typically less immunogenic and easier to prepare. Direct, nonviral gene transfer into the whole organism remains a desirable goal for gene therapy because it avoids laborious and costly cell culture; the gene could be administered as easily as a drug.
Can the Clusters Zr6O4(OH)4(OOCR)12 and [Zr6O4(OH)4(OOCR)12]2 Be Converted into Each Other? (2006)

Abstract Upon reaction of zirconium alkoxides, Zr(OR) 4 , with carboxylic acids, the clusters Zr 6 O 4 (OH) 4 (OOCR) 12 ( Zr6 ) or [Zr 6 O 4 (OH) 4 (OOCR) 12 ] 2 ( Zr12 ) were obtained, depending on the employed carboxylic acid. The structures of Zr12 clusters with acetate, propionate, vinyl acetate or 3,3′‐dimethylacrylate ligands were determined by single‐crystal X‐ray diffraction, as well as that of methacrylate/acetate and methacrylate/propionate mixed‐ligand clusters. The structure of the hafnium cluster [Hf 6 O 4 (OH) 4 (acetate) 12 ] 2 is also reported for comparison. The Zr12 clusters are structurally related to the Zr6 clusters since they are composed of two Zr6 sub‐units which are bridged by four carboxylate ligands. In each compound, carboxylic acid molecules interact with the cluster by hydrogen bonding to part of the μ 3 ‐OH ligands. The clusters are highly dynamic in solution, due to site exchange of the carboxylate ligands; low‐temperature NMR spectra of the clusters correspond to the solid‐state structures. The Zr6 and Zr12 clusters can be clearly distinguished by their solution NMR spectra. Reactions between selected Zr12 clusters and carboxylic acids led to the conclusion, that only part of the ligands is accessible for ligand exchange reactions. In contrast, all ligands were exchanged when the Zr6 cluster Zr 6 O 4 (OH) 4 (methacrylate) 12 was treated with an excess of propionic acid, and Zr 6 O 4 (OH) 4 (propionate) 12 was formed. However, the Zr12 cluster [Zr 6 O 4 (OH) 4 (propionate) 12 ] 2 was obtained from the reaction of Zr(OBu) 4 with propionic acid. The Zr6 and Zr12 clusters thus do not interconvert at the given reaction conditions. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Finding the right facts in the crowd (2008)

Community Question Answering has emerged as a popular and effective paradigm for a wide range of information needs. For example, to find out an obscure piece of trivia, it is now possible and even very effective to post a question on a popular community QA site such as Yahoo! Answers, and to rely on other users to provide answers, often within minutes. The importance of such community QA sites is magnified as they create archives of millions of questions and hundreds of millions of answers, many of which are invaluable for the information needs of other searchers. However, to make this immense body of knowledge accessible, effective answer retrieval is required. In particular, as any user can contribute an answer to a question, the majority of the content reflects personal, often unsubstantiated opinions. A ranking that combines both relevance and quality is required to make such archives usable for factual information retrieval. This task is challenging, as the structure and the contents of community QA archives differ significantly from the web setting. To address this problem we present a general ranking framework for factual information retrieval from social media. Results of a large scale evaluation demonstrate that our method is highly effective at retrieving well-formed, factual answers to questions, as evaluated on a standard factoid QA benchmark. We also show that our learning framework can be tuned with the minimum of manual labeling. Finally, we provide result analysis to gain deeper understanding of which features are significant for social media search and retrieval. Our system can be used as a crucial building block for combining results from a variety of social media content with general web search results, and to better integrate social media content for effective information access.
Special Edition Using Java 2 Enterprise Edition (2001)

From the Publisher:
Java 2 Enterprise Edition is a combination of Java-related technologies including Java Server Pages, Servlets, and Enterprise Java Beans. Working together these pieces make Java a viable solution for enterprise-scale applications. SE Using starts with a section covering the core J2EE components and how they fit into the overall application architecture. The book then builds off this foundation to explore the practical applications of J2EE including incorporating XML into J2EE, creating wireless Web applications, network programming with J2EE, managing security and encryption, object programming with Serialization and Reflection, and programming Java applets in the enterprise. Later chapters discuss alternative approaches to solving problems in J2EE applications including debugging, decompiling and disassembly. The book finishes with a useful reference section discussing each of the core J2EE APIs.
논문 : 막분리를 이용한 수도원수의 고도처리에 관한 연구 (1993)

Constant rate permeat experiments using polyethylene hollow fiber membranes were conducted in order to treat dam water for potable purposes. The experiments consisted of two series. One series consisted of six bench scale apparatuses, each having a 0.4㎡ nominal permeat area, which were applied in determining the optimum operating conditions. The other series was comprised of two pilot scale plant, each having a 40㎡ nominal permeat area. Both series were operated for six months. Coagulant was not used in any of the experiments. To suppress an increase in differential pressure between the inlet and outlet of the membrane, a hydrophilic membrane was found to be better than a hydrophobic membrane. Also, permeat flux should not be more than 0.03m/h, and air bubbling-washing for 1 minute should be conducted at 180 minutes intervals or less.