gebhart/patrepeval huggingface dataset:
Analysis of near-infrared spectroscopy and indocyanine green dye dilution with Monte Carlo simulation of light propagation in the adult brain (2006)

Near-infrared spectroscopy (NIRS) combined with indocyanine green (ICG) dilution is applied externally on the head to determine the cerebral hemodynamics of neurointensive care patients. We applied Monte Carlo simulation for the analysis of a number of problems associated with this method. First, the contamination of the optical density (OD) signal due to the extracerebral tissue was assessed. Second, the measured OD signal depends essentially on the relative blood content (with respect to its absorption) in the various transilluminated tissues. To take this into account, we weighted the calculated densities of the photon distribution under baseline conditions within the different tissues with the changes and aberration of the relative blood volumes that are typically observed under healthy and pathologic conditions. Third, in case of NIRS ICG dye dilution, an ICG bolus replaces part of the blood such that a transient change of absorption in the brain tissues occurs that can be recorded in the OD signal. Our results indicate that for an exchange fraction of Delta=30% of the relative blood volume within the intracerebral tissue, the OD signal is determined from 64 to 74% by the gray matter and between 8 to 16% by the white matter maximally for a distance of d=4.5 cm.
Polyelectrolyte Multilayer Films as Substrates for Photoreceptor Cells (2005)

Reconstruction of extracellular matrix substrates for delivery of functional photoreceptors is crucial in pathologies such as retinal degeneration and age-related macular degeneration. In this study, we assembled polyelectrolyte films using the layer-by-layer deposition method. The buildup of three different films composed of poly(L-lysine)/chondroitin sulfate (PLL/CSA), poly(L-lysine)/poly(styrenesulfonate) (PLL/PSS), or poly(L-lysine)/hyaluronic acid (PLL/HA) was followed by means of quartz crystal microbalance measurements, optical waveguide light mode spectroscopy, confocal microscopy, and atomic force microscopy. The exponential growth regime and the diffusion of PLL chains from the bulk through the PLL/CSA, PLL/PSS, and PLL/HA films was examined. Evaluation of photoreceptor cell viability was optimal on one layer of PLL (PLL(1)), followed by 10 bilayers of PLL/HA [(PLL/HA)(10)] and 10 bilayers of PLL/CSA [(PLL/CSA)(10)]. The number of bilayers and the type of terminating layer also had a significant influence on the number of photoreceptor cells attached. Functionalized polyelectrolyte multilayer films were obtained by adsorbing basic fibroblastic factor (bFGF) or the insoluble fraction of interphotoreceptor matrix (IPM) on or within polyelectrolyte multilayers. bFGF and IPM adsorption on top of the (PLL/CSA)(10)/PLL polyelectrolyte films increased the number of photoreceptor cells attached and maintained the differentiation of rod and cone cells.
Mechanistic Studies of Azaphilic versus Carbophilic Activation by Gold(I) in the Gold/Palladium Dual-Catalyzed Rearrangement of Alkenyl Vinyl Aziridines (2012)

A vinyl aziridine activation strategy cocatalyzed by palladium(0) and a gold(I) Lewis acid has been developed. This rearrangement installs a C-C and a C-N bond in one synthetic step to form pyrrolizidine and indolizidine products. Two proposed mechanistic roles for the gold cocatalyst were considered: (1) carbophilic gold catalysis or (2) azaphilic gold catalysis. Mechanistic studies support an azaphilic Lewis acid activation of the aziridine over a carbophilic Lewis acid activation of the alkene.
Foligno all'incrocio delle strade (1999)

Sensi Mario. Foligno all'incrocio delle strade. In: Angèle de Foligno. Le dossier. Rome : École Française de Rome, 1999. pp. 267-292. (Publications de l'École française de Rome, 255)
ChemInform Abstract: Laser and Pulsed‐Laser NMR Spectroscopy (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
673. The chemotherapy of schistosomiasis. Part I. Derivatives and analogues of αω-di-(p-aminophenoxy)alkanes (1958)

J. N. Ashley, R. F. Collins, M. Davis and N. E. Sirett, J. Chem. Soc., 1958, 3298 DOI: 10.1039/JR9580003298
Enantioselective Synthesis of (−)‐Exiguolide by Iterative Stereoselective Dioxinone‐Directed Prins Cyclizations (2011)

Three become one: The title compound can be prepared in 26 steps by employing a unified Prins cyclization strategy to construct both tetrahydropyran rings (see scheme). The route combines two similar dioxinone fragments and one aldehyde component to generate the core structure. (−)-Exiguolide selectively inhibits the growth of A549 cancer cells at low concentrations; the triene side chain and the Z-enoate geometry are both necessary for this cytotoxicity. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Generation of Functional Blocking Monoclonal Antibodies Against Mouse Interleukin-12 p40 Homodimer and Monomer (2008)

The role of interleukin (IL)-12 (p40:p35) and IL-23 (p40:p19) is becoming clear in immune response and inflammation. However, biological functions of IL-12 p40 homodimer (p40(2)) and monomer (p40) remain poorly understood due to the lack of specific monoclonal antibodies (MAb). Earlier we have demonstrated that both p40(2) and p40 activate microglia and macrophages to induce the expression of iNOS and TNF-alpha. To facilitate the studies on p40(2) and p40 further, we here describe the production of neutralizing MAb against mouse p40(2) and p40 for the first time after immunization of Armenian hamsters with recombinant p40(2). Antibodies produced from clones a3-1d and d7-12c specifically recognized p40(2) but not p40, IL-12, and IL-23. These MAbs also inhibited p40(2)- but not p40-, IL-12-, and IL-23-induced production of inflammatory molecules and activation of NF-kappaB. On the other hand, antibodies produced from clones a3-3a and a3-7g specifically recognized p40 and inhibited p40- but not p40(2)-, IL-12-, and IL-23-induced production of inflammatory molecules and activation of NF-kappaB. While MAbs a3-1d and d7-12c were used to establish p40(2)-specific ELISA, we utilized MAbs a3-3a and a3-7g to develop p40-specific ELISA. Interestingly, the production of p40(2) and p40 but not IL-12 in mouse peritoneal macrophages and primary microglia was an immediate early response to bacterial lipopolysaccharides. Furthermore, double-stranded RNA, the active component of a viral infection, induced the production of p40(2) and p40 but not IL-12 in macrophages and microglia. These results indicate the presence of different regulatory mechanisms for the production of IL-12p40(2)/p40 and IL-12p70.
Combinatorial Heterogeneous Catalysis—A New Path in an Old Field (2001)

Combinatorial catalysis is the systematic preparation, processing, and testing of large diversities of chemically and physically different materials libraries in a high-throughput fashion. It also embodies microfabrication, robotics, automation, instrumentation, computational chemistry, and large-scale information management (informatics), and as such carries the promise of a renaissance in catalytic reaction engineering. Significant progress has already been made in demonstrating the speed and economic advantage of combinatorial approaches by the discovery of superior catalytic materials in a matter of hours and days, as opposed to the months and years required using traditional methods. Combinatorial methods can also significantly contribute to our understanding of catalytic function by increasing our chances of discovering totally new and unexpected catalytic materials, and by expediting the recognition of trends and patterns of structure-activity relations, from which new catalytic materials can be designed more efficiently. Combinatorial catalysis undoubtedly will be the new paradigm of catalysis research as the industry faces increasing global competition and pressure for the development of environmentally friendly processes at a time when resources for research are diminishing.
Molecular pathology of breast apocrine carcinomas: A protein expression signature specific for benign apocrine metaplasia (2006)

Breast cancer is a heterogeneous disease that encompasses a wide range of histopathological types including: invasive ductal carcinoma, lobular carcinoma, medullary carcinoma, mucinous carcinoma, tubular carcinoma, and apocrine carcinoma among others. Pure apocrine carcinomas represent about 0.5% of all invasive breast cancers according to the Danish Breast Cancer Cooperative Group Registry, and despite the fact that they are morphologically distinct from other breast lesions, there are at present no standard molecular criteria available for their diagnosis. In addition, the relationship between benign apocrine changes and breast carcinoma is unclear and has been a matter of discussion for many years. Recent proteome expression profiling studies of breast apocrine macrocysts, normal breast tissue, and breast tumours have identified specific apocrine biomarkers [15-hydroxyprostaglandin dehydrogenase (15-PGDH) and hydroxymethylglutaryl coenzyme A reductase (HMG-CoA reductase)] present in early and advanced apocrine lesions. These biomarkers in combination with proteins found to be characteristically upregulated in pure apocrine carcinomas (psoriasin, S100A9, and p53) provide a protein expression signature distinctive for benign apocrine metaplasias and apocrine cystic lesions. These studies have also presented compelling evidence for a direct link, through the expression of the prostaglandin degrading enzyme 15-PGDH, between early apocrine lesions and pure apocrine carcinomas. Moreover, specific antibodies against the components of the expression signature have identified precursor lesions in the linear histological progression to apocrine carcinoma. Finally, the identification of proteins that characterize the early stages of mammary apocrine differentiation such as 15-PGDH, HMG-CoA reductase, and cyclooxygenase 2 (COX-2) has opened a window of opportunity for pharmacological intervention, not only in a therapeutic manner but also in a chemopreventive setting. Here we review published and recent results in the context of the current state of research on breast apocrine cancer.
Anti-oncogene and tumor suppressor gene therapy--examples from a lung cancer animal model. (1995)

Rapid advances in cancer gene therapy are driven by an explosive development of gene transfer technology and a strong demand for effective alternatives to unsatisfactory conventional cancer therapies. Discovery of the genetic basis of cancer has indicated that cancer is a disease of genes. Among a variety of approaches to gene therapy of cancer, anti-oncogene and tumor suppressor gene therapy of cancer are the two strategies that aim at correcting genetic disorders of cancer. The potential effectiveness of these approaches is promised by their precise targeting at the mechanisms of the disease. Successful examples of human lung cancer animal models by applying anti-K-ras retrovirus and recombinant p53 adenovirus are reviewed. Future development of these approaches towards clinical application is also discussed.
Molecular Determinants of Cetuximab Efficacy (2005)

This pilot study suggests that gene expression levels of Cox-2, EGFR, IL-8, and VEGF in patients with metastatic CRC may be useful markers of clinical outcome in single-agent cetuximab treatment.
Protein kinase C-independent activation of nuclear factor kappa B by tumor necrosis factor. (1990)

Tumor necrosis factor (TNF) is one of the few physiological inducers of the pleiotropic transcription factor NF kappa B. NF kappa B may play a central role in mediating TNF's gene regulatory action; however, the molecular mechanisms of TNF-induced NF kappa B activation are poorly understood. In this study, we demonstrate with two human leukemic cell lines, K562 and Jurkat, that TNF induces rapid and transient activation and translocation of protein kinase C (PK-C) from the cytosol to the membranes, which is followed by the emergence of kappa B-binding activity. In order to investigate whether TNF-mediated PK-C activation can be linked to induction of NF kappa B, we tried to block TNF action by use of various protein kinase C inhibitors as well as down-regulation of PK-C. Preincubation of Jurkat cells with protein kinase inhibitor H7 or staurosporine blocked PK-C activation by either TNF or phorbol 12-myristate 12-acetate (PMA). This pretreatment regimen completely inhibited NF kappa B activation by PMA. In contrast, TNF's ability to induce NF kappa B remained unaffected. In addition, NF kappa B was TNF-inducible in Jurkat cells depleted for PK-C by long-term exposure to high dose phorbol ester. The data indicate that PK-C is not required for NF kappa B activation by TNF and imply a novel, PK-C-independent mechanism of physiological NF kappa B activation.
Covalent binding of electron relays to glucose oxidase (1987)

Modification of glucose oxidase by the covalent coupling of ferrocenecarboxylic acids gives mediator modified enzymes which undergo direct oxidation at an electrode; the use of ferroceneacetic acid instead of ferrocenecarboxylic acid is an improvement in terms of the overpotential for oxidation, the reactivity towards glucose, and the stability on storage.
Synthetic peptide‐containing surfactants (1998)

Pulmonary surfactant contains two hydrophobic proteins, SP-B and SP-C. With the aim of identifying synthetic SP-B and SP-C substitutes for replacement therapy of respiratory distress syndromes, we have studied two transmembrane peptides and two amphipathic peptides that are located in the plane of a phospholipid bilayer. One amphipathic peptide was designed by changing the amino acid sequence, but not the composition or size, of the 21-residue peptide KL4. This peptide, designated KL(2,3) from its spacing of nonpolar and polar residues, exhibited similar alpha-helical content as KL4 but was oriented along a phospholipid bilayer plane, in contrast to the transmembrane orientation of KL4 in the same environment. The second amphipathic peptide analyzed was succinyl-LLEKLLEWLK-amide (WMAP10). KL4 more efficiently accelerated the spreading of a mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (Pam2GroPCho)/phosphatidylglycerol (PtdGro)/palmitic acid (PamOH), 68:22:9 (by mass), at an air/water interface than did any of the amphipathic peptides. Similarly, KL4, but not KL(2,3), when present in an interfacial monolayer composed of Pam2GroPCho/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol, 7:3 (by mass), increased lipid insertion from subphase vesicles. An SP-C analogue, SP-C(Leu), with all helical valyl residues in native SP-C replaced with Leu and the palmitoylcysteines at positions 5 and 6 replaced with Ser, but otherwise with essentially the same primary structure as the native peptide, was analyzed. SP-C(Leu) exhibited similar alpha-helical content as native SP-C and a transmembrane orientation and, in contrast to poly-valyl-containing synthetic peptides, it folds into a helical conformation after acid-induced denaturation. SP-C(Leu) accelerated the spreading of Pam2GroPCho/PtdGro/PamOH, 68:22:9 (by mass), almost identically to native SP-C, and lowered the surface tension during rapid cyclic film compressions in a pulsating bubble surfactometer to near zero and 43 mN/m at minimum and maximum bubble size, respectively. Airway instillation of 2% (by mass) SP-C(Leu) combined with Pam2GroPCho/PtdGro/PamOH in preterm rabbit fetuses improved dynamic lung compliance by about 30% compared with untreated controls.
Regulation of Methionyl-Transfer Ribonucleic Acid Synthetase Formation in Escherichia coli and Salmonella typhimurium (1973)

The control of methionyl-transfer ribonucleic acid (tRNA) synthetase (l-methionine: soluble RNA ligase [adenosine monophosphate]) was studied in methionyl-tRNA synthetase mutants of Escherichia coli and Salmonella typhimurium. The results of activity determinations with crude extracts indicate that this enzyme of the E. coli mutant strain possessed a reduced affinity for methionine-tRNA, whereas this enzyme of the S. typhimurium mutant exhibited a decreased affinity for l-methionine. The differential rate of methionyl-tRNA synthetase formation in these two mutants was several-fold greater than that of the respective parental strains. On the other hand, the level of in vivo aminoacylation of methionine-tRNA was only about one-third that of the parent strains. These results suggest that aminoacylation of methionine-tRNA is a necessary step in repression control of methionyl-tRNA synthetase of both E. coli and S. typhimurium strains.
Research on Open Source Encoding Technology for MPEG Unified Speech and Audio Coding (2013)

통합 음성/오디오 부호화기 (Unified Speech and Audio Coding, USAC)는 2011년 MPEG에서 FDIS (Final Draft International Standard)를 승인받은 최고 성능의 통합 음성/오디오 부호화기이다. 전통적으로 MPEG에서는 복호화기 기술만 표준화하므로 인코더 기술에 대한 고찰이 쉽지 않을 뿐 아니라, 예제로 공개하는 인코더 (Reference Model, RM)의 경우에도 기본 아이디어만을 포함하고 있기 때문에 이를 사용할 경우 성능 저하가 매우 심각하다. 성능 열화는 매우 심각하다. 이러한 문제를 최소화하기 위해 오픈 소스 기반으로 진행되고 있는 프로젝트 JAME에서는 USAC에 적용된 핵심 인코더 기술의 성능을 최대화 할 수 있는 방법을 제안하고 있다. 본 논문에서는 입력 신호에 따라 두 코더가 선택적으로 동작되게 하는 신호 분류기와 심리 음향 모델을 기반으로 하는 주파수 부호화 기술, 그리고 전이 윈도우 기술 등의 주요 인코더 기술들에 대하여 소개한다. 또한 FDIS를 위한 verification test 결과와 Common Encoder의 성능 평가를 덧붙인다.
‘Sticky feet’-directed mutagenesis and its application to swapping antibody domains (1989)

We describe a novel technique for precisely cutting and pasting two DNA sequences without using restriction sites. The method is based on site-directed mutagenesis and uses a long primer, generated by the polymerase chain reaction (PCR), to transfer large segments of DNA into a single-stranded template. The primer anneals to the template by virtue of 'sticky feet' sequences (complementary to the template) which are introduced at the ends of the primer by the PCR. Yields of desired recombinants were high (approximately 36%) and the transplanted sequences (approximately 400bp) free of errors. We have used this technique to swap CH2 domains between two mouse antibodies, and find that this domain can carry features critical for triggering complement lysis, in addition to the C1q binding motif.
In vitro and in vivo evaluation of folate receptor-targeting amphiphilic copolymer-modified liposomes loaded with docetaxel (2011)

Liposomes modified by FA-PEG-PCHL could be one of the promising suspensions for the delivery of antitumor drugs in cancer.
Evolving Concept of Cancer Stem Cells: Role of Micro-RNAs and their Implications in Tumor Aggressiveness (2011)

Recent advances in cancer stem cell (CSC) research and the role of miroRNAs (miRNAs) provided renewed interest, as supported by some convincing data showing that deregulation of miRNAs are important molecular events in the maintenance of CSC niche, which contribute to therapeutic resistance, resulting in treatment failure. Therefore, we are succinctly providing state-of-the-art knowledge on miRNAs that are associated with CSCs in this article, and it is quite clear that CSCs and miRNAs are implicated in therapeutic resistance, suggesting that novel approaches must be devised to eliminate CSCs or drug resistant cells focusing on overcoming therapeutic resistance. This indeed could be achieved by targeted strategies either to re-express the lost miRNAs or inactivate over-expressed miRNAs in cancers in general and CSCs in particular. We sincerely hope that this article would be educational to attract innovative research in the field so that we can find specific novel approaches to eradicate cancer by overcoming therapeutic resistance by targeting miRNAs, which will be useful to eliminate tumor recurrence and metastasis.
αKlotho deficiency in acute kidney injury contributes to lung damage (2015)

αKlotho is a circulating protein that originates predominantly from the kidney and exerts cytoprotective effects in distant sites. We previously showed in rodents that the lung is particularly vulnerable to αKlotho deficiency. Because acute lung injury is a common and serious complication of acute kidney injury (AKI), we hypothesized that αKlotho deficiency in AKI contributes to lung injury. To test the hypothesis, we created AKI by renal artery ischemia-reperfusion in rats and observed the development of alveolar interstitial edema and increased pulmonary oxidative damage to DNA, protein, and lipids. Administration of αKlotho-containing conditioned media 6 h post-AKI did not alter plasma creatinine but improved recovery of endogenous αKlotho production 3 days post-AKI, reduced lung edema and oxidative damage, and increased endogenous antioxidative capacity in the lung. Intravenously injected αKlotho rapidly exits alveolar capillaries as a macromolecule, suggesting transcytosis and direct access to the epithelium. To explore the epithelial action of αKlotho, we simulated oxidative stress in vitro by adding hydrogen peroxide to cultured A549 lung epithelial cells. Purified recombinant αKlotho directly protected cells at 20 pM with half-maximal effects at 40-50 pM, which is compatible with circulating αKlotho levels. Addition of recombinant αKlotho activated an antioxidant response element reporter and increased the levels of target proteins of the nuclear factor erythroid-derived 2 related factor system. In summary, αKlotho deficiency in AKI contributes to acute lung injury by reducing endogenous antioxidative capacity and increasing oxidative damage in the lung. αKlotho replacement partially reversed these abnormalities and mitigated pulmonary complications in AKI.
Lightweight Distributed Execution Engine for Large-Scale Spatial Join Query Processing (2015)

Existing Big Data systems are mostly designed for relational data. They are either incapable or inefficient in processing large-scale semi-structured data efficiently due to the inherent limitations on data abstraction, indexing support and exposure to native parallel programming tools. In this study, we report our work in developing a lightweight distributed execution engine for spatial join query processing on large-scale geospatial data. By integrating data parallel designs for single computing nodes, our execution engine is able to automatically dispatch data partitions to distributed computing nodes for efficient local execution on multi-core CPUs and GPUs. The execution engine supports asynchronous data transfer over network, asynchronous disk I/O and asynchronous computing. It also directly accesses distributed file systems to support creating and using indices conveniently and efficiently. In addition to be lightweight by design, which has less than 1,000 Lines Of Code (LOC), experiments using a real world application have demonstrated significant efficiency improvement over our previous works on extending a leading in-memory Big Data system (Impala) for spatial join query processing.