gebhart/patrepeval huggingface dataset:
Isolation and characterization of a cDNA clone from Catharanthus roseus encoding NADPH:cytochrome P‐450 reductase, an enzyme essential for reactions catalysed by cytochrome P‐450 mono‐oxygenases in plants (1993)

The membrane-bound flavoprotein NADPH:cytochrome P-450 (cytochrome c) reductase, that functions in electron transfer to cytochrome P-450 monooxygenases, was purified from a cell suspension culture of the higher plant Catharanthus roseus. Anti-serum raised against the purified protein was found to inhibit NADPH:cytochrome c reductase activity as well as the activities of the cytochrome P-450 enzymes geraniol 10-hydroxylase and trans-cinnamate 4-hydroxylase, which are involved in alkaloid biosynthesis and phenylpropanoid biosynthesis, respectively. Immunoscreening of a C. roseus cDNA expression library resulted in the isolation of a partial NADPH: cytochrome P-450 reductase cDNA clone, which was identified on the basis of sequence homology with NADPH:cytochrome P-450 reductases from yeast and animal species. The identify of the cDNA was confirmed by expression in Escherichia coli as a functional protein capable of NADPH-dependent reduction of cytochrome c and neotetrazolium, two in vitro substrates for the reductase. The N-terminal sequence of the reductase, which was not present in the cDNA clone, was determined from a genomic NADPH: cytochrome P-450 reductase clone. It was demonstrated that the reductase probably is encoded by a single copy gene. A sequence comparison of this plant NADPH:cytochrome P-450 reductase with the corresponding enzymes from yeast and animals species showed that functional domains involved in binding of the cofactors FMN, FAD and NADPH are highly conserved between all kingdoms. In C. roseus cell cultures a rapid increase of the reductase steady state mRNA level was observed after the addition of fungal elicitor preparations that are known to induce cytochrome P-450-dependent biosynthetic pathways.
Characterization of a Highly Pathogenic Molecular Clone of Feline Immunodeficiency Virus Clade C (2004)

We have derived and characterized a highly pathogenic molecular isolate of feline immunodeficiency virus subtype C (FIV-C) CABCpady00C. Clone FIV-C36 was obtained by lambda cloning from cats that developed severe immunodeficiency disease when infected with CABCpady00C (Abbotsford, British Columbia, Canada). Clone FIV-C36 Env is 96% identical to the noninfectious FIV-C isolate sequence deposited in GenBank (FIV-Cgb; GenBank accession number AF474246) (A. Harmache et al.) but is much more divergent in Env when compared to the subgroup A clones Petaluma (34TF10) and FIV-PPR (76 and 78% divergence, respectively). Clone FIV-C36 was able to infect freshly isolated feline peripheral blood mononuclear cells and primary T-cell lines but failed to productively infect CrFK cells, as is typical of FIV field isolates. Two-week-old specific-pathogen-free cats infected with FIV-C36 tissue culture supernatant became PCR positive and developed severe acute immunodeficiency disease similar to that caused by the uncloned CABCpady00C parent. At 4 to 5 weeks postinfection (PI), 3 of 4 animals developed CD4(+)-T-cell depletion, fever, weight loss, diarrhea, and opportunistic infections, including ulcerative stomatitis and tonsillitis associated with abundant bacterial growth, pneumonia, and pyelonephritis, requiring euthanasia. Histopathology confirmed severe thymic and systemic lymphoid depletion. Interestingly, the dam also became infected with a high viral load at 5 weeks PI of the kittens and developed a similar disease syndrome, requiring euthanasia at 11 weeks PI of the kittens. This constitutes the first report of a replication-competent, infectious, and pathogenic molecular clone of FIV-C. Clone FIV-C36 will facilitate dissection of the pathogenic determinants of FIV.
Patient selection and targeted treatment in the management of platinum-resistant ovarian cancer (2013)

Ovarian cancer (OC) has the highest mortality rate of any gynecologic cancer, and patients generally have a poor prognosis due to high chemotherapy resistance and late stage disease diagnosis. Platinum-resistant OC can be treated with cytotoxic chemotherapy such as paclitaxel, topotecan, pegylated liposomal doxorubicin, and gemcitabine, but many patients eventually relapse upon treatment. Fortunately, there are currently a number of targeted therapies in development for these patients who have shown promising results in recent clinical trials. These treatments often target the vascular endothelial growth factor pathway (eg, bevacizumab and aflibercept), DNA repair mechanisms (eg, iniparib and olaparib), or they are directed against folate related pathways (eg, pemetrexed, farletuzumab, and vintafolide). As many targeted therapies are only effective in a subset of patients, there is an increasing need for the identification of response predictive biomarkers. Selecting the right patients through biomarker screening will help tailor therapy to patients and decrease superfluous treatment to those who are biomarker negative; this approach should lead to improved clinical results and decreased toxicities. In this review the current targeted therapies used for treating platinum-resistant OC are discussed. Furthermore, use of prognostic and response predictive biomarkers to define OC patient populations that may benefit from specific targeted therapies is also highlighted.
Realtime analysis of the Haze environment trapped between the pellicle film and the mask surface (2006)

With the use of 193nm lithography, time-dependent haze problem has become a critical issue for semiconductor industry. The understanding of the conditions that create haze defects is very crucial for the future development of haze-free cleaning processes. The gaseous environment trapped between the pellicle film and the mask surface triggers photochemical reaction under laser exposure, which could result in the formation of killer (printable) defects on the mask surface. Therefore, the real time analysis of the haze environment in the trapped space could provide essential clues to the characterization of haze defect growth mechanism. This fundamental study can be applied to the invention of real-time monitoring tools for the defect growth progress on the mask surface as well as the development of haze-free cleaning processes. Here, we propose a method to analyze the gaseous space trapped between the pellicle film and the mask surface that creates a highly reactive environment.
Photooxidation: A Decolorization Procedure and a Pre-Treatment Step for Biodegradation of Reactive Azo Dye (2006)

In this study, by using a different variety of TiO 2 catalyst, photocatalytic oxidation of reactive azo dye used in textile industry and an improvement in the biodegradability of the dye by photocatalytic oxidation are investigated. It was found that the addition of TiO 2 in the photooxidation of dye increased color removal by 30.84 %, the addition of H
View Synthesis for Advanced 3D Video Systems (2008)

Interest in 3D video applications and systems is growing rapidly and technology is maturating. It is expected that multiview autostereoscopic displays will play an important role in home user environments, since they support multiuser 3D sensation and motion parallax impression. The tremendous data rate cannot be handled efficiently by representation and coding formats such as MVC or MPEG-C Part 3. Multiview video plus depth (MVD) is a new format that efficiently supports such advanced 3DV systems, but this requires high-quality intermediate view synthesis. For this, a new approach is presented that separates unreliable image regions along depth discontinuities from reliable image regions, which are treated separately and fused to the final interpolated view. In contrast to previous layered approaches, the algorithm uses two boundary layers and one reliable layer, performs image-based 3D warping only, and was generically implemented, that is, does not necessarily rely on 3D graphics support. Furthermore, different hole-filling and filtering methods are added to provide high-quality intermediate views. As a result, high-quality intermediate views for an existing 9-view auto-stereoscopic display as well as other stereo- and multiscopic displays are presented, which prove the suitability of the approach for advanced 3DV systems.
Distinct TLR- and NLR-Mediated Transcriptional Responses to an Intracellular Pathogen (2008)

How the innate immune system tailors specific responses to diverse microbial infections is not well understood. Cells use a limited number of host receptors and signaling pathways to both discriminate among extracellular and intracellular microbes, and also to generate responses commensurate to each threat. Here, we have addressed these questions by using DNA microarrays to monitor the macrophage transcriptional response to the intracellular bacterial pathogen Listeria monocytogenes. By utilizing combinations of host and bacterial mutants, we have defined the host transcriptional responses to vacuolar and cytosolic bacteria. These compartment-specific host responses induced significantly different sets of target genes, despite activating similar transcription factors. Vacuolar signaling was entirely MyD88-dependent, and induced the transcription of pro-inflammatory cytokines. The IRF3-dependent cytosolic response induced a distinct set of target genes, including IFNbeta. Many of these cytosolic response genes were induced by secreted cytokines, so we further identified those host genes induced independent of secondary signaling. The host response to cytosolic bacteria was reconstituted by the cytosolic delivery of L. monocytogenes genomic DNA, but we observed an amplification of this response by NOD2 signaling in response to MDP. Correspondingly, the induction of IFNbeta was reduced in nod2-/- macrophages during infection with either L. monocytogenes or Mycobacterium tuberculosis. Combinatorial control of IFNbeta induction by recognition of both DNA and MDP may highlight a mechanism by which the innate immune system integrates the responses to multiple ligands presented in the cytosol by intracellular pathogens.
Platelet-Derived Growth Factor Gene Delivery Stimulates ex Vivo Gingival Repair (2003)

Destruction of tooth support due to the chronic inflammatory disease periodontitis is a major cause of tooth loss. There are limitations with available treatment options to tissue engineer soft tissue periodontal defects. The exogenous application of growth factors (GFs) such as platelet-derived growth factor (PDGF) has shown promise to enhance oral and periodontal tissue regeneration. However, the topical administration of GFs has not led to clinically significant improvements in tissue regeneration because of problems in maintaining therapeutic protein levels at the defect site. The utilization of PDGF gene transfer may circumvent many of the limitations with protein delivery to soft tissue wounds. The objective of this study was to test the effect of PDGF-A and PDGF-B gene transfer to human gingival fibroblasts (HGFs) on ex vivo repair in three-dimensional collagen lattices. HGFs were transduced with adenovirus encoding PDGF-A and PDGF-B genes. Defect fill of bilayer collagen gels was measured by image analysis of cell repopulation into the gingival defects. The modulation of gene expression at the defect site and periphery was measured by RT-PCR during a 10-day time course after gene delivery. The results demonstrated that PDGF-B gene transfer stimulated potent (>4-fold) increases in cell repopulation and defect fill above that of PDGF-A and corresponding controls. PDGF-A and PDGF-B gene expression was maintained for at least 10 days. PDGF gene transfer upregulated the expression of phosphatidylinosital 3-kinase and integrin alpha5 subunit at 5 days after adenovirus transduction. These results suggest that PDGF gene transfer has potential for periodontal soft tissue-engineering applications.
Changing the Activity of Electrocatalysts for Oxygen Reduction by Tuning the Surface Electronic Structure (2006)

Going platinum: The theoretical description of electrocatalytic phenomena is extremely challenging. A simple, density functional theory based model has been developed that is able to give a semiquantitative description of the reaction kinetics for the electrocatalytic oxygen reduction on several platinum binary alloys, Pt3M (see graph).
Multicommodity max-flow min-cut theorems and their use in designing approximation algorithms (1999)

In this paper, we establish max-flow min-cut theorems for several important classes of multicommodity flow problems. In particular, we show that for any n-node multicommodity flow problem with uniform demands, the max-flow for the problem is within an O(log n) factor of the upper bound implied by the min-cut. The result (which is existentially optimal) establishes an important analogue of the famous 1-commodity max-flow min-cut theorem for problems with multiple commodities. The result also has substantial applications to the field of approximation algorithms. For example, we use the flow result to design the first polynomial-time (polylog n-times-optimal) approximation algorithms for well-known NP-hard optimization problems such as graph partitioning, min-cut linear arrangement, crossing number, VLSI layout, and minimum feedback arc set. Applications of the flow results to path routing problems, network reconfiguration, communication in distributed networks, scientific computing and rapidly mixing Markov chains are also described in the paper.
Dicyanomethylenated Acridone Based Crystals: Torsional Vibration Confinement Induced Emission with Supramolecular Structure Dependent and Stimuli Responsive Characteristics (2015)

A series of dicyanomethylenated acridone derivatives, DCNAC-Cn (n = 1, 4, 6) and DPA-DCNAC-C4, are designed and synthesized. They are highly luminescent in the crystalline state but nonemissive in the amorphous state. The interesting crystallization-induced-emission (CIE) behavior is attributed to the restricted torsional vibrations of the molecular skeletons in crystal lattices. DCNAC-Cn-based crystals display obvious molecular-packing-dependent emission properties. The molecular packing of DCNAC-Cn in crystals is easily regulated by modifying the length of alkyl chains, resulting in the tunable emission colors from green to red. A DPA-DCNAC-C4 molecule consisting of a DCNAC acceptor and two diphenylamino donors shows intramolecular charge-transfer (ICT) characteristic and strong near-infrared emission (λem = 707 nm, ΦF = 0.16) in the crystalline state. Mechanical, thermal, and organic-vapor stimuli can reversibly alter the aggregation phases between crystalline and amorphous states. Therefore, this study presents a stimuli-responsive emission on/off switching system with various emission colors (560 to 700 nm).
Dendrimers as scaffolds for multifunctional reversible addition–fragmentation chain transfer agents: Syntheses and polymerization (2004)

Abstract The synthesis and characterization of novel first‐ and second‐generation true dendritic reversible addition–fragmentation chain transfer (RAFT) agents carrying 6 or 12 pendant 3‐benzylsulfanylthiocarbonylsulfanylpropionic acid RAFT end groups with Z‐group architecture based on 1,1,1‐hydroxyphenyl ethane and trimethylolpropane cores are described in detail. The multifunctional dendritic RAFT agents have been used to prepare star polymers of poly(butyl acrylate) (PBA) and polystyrene (PS) of narrow polydispersities (1.4 &lt; polydispersity index &lt; 1.1 for PBA and 1.5 &lt; polydispersity index &lt; 1.3 for PS) via bulk free‐radical polymerization at 60 °C. The novel dendrimer‐based multifunctional RAFT agents effect an efficient living polymerization process, as evidenced by the linear evolution of the number‐average molecular weight ( M n ) with the monomer–polymer conversion, yielding star polymers with molecular weights of up to M n = 160,000 g mol −1 for PBA (based on a linear PBA calibration) and up to M n = 70,000 g mol −1 for PS (based on a linear PS calibration). A structural change in the chemical nature of the dendritic core (i.e., 1,1,1‐hydroxyphenyl ethane vs trimethylolpropane) has no influence on the observed molecular weight distributions. The star‐shaped structure of the generated polymers has been confirmed through the cleavage of the pendant arms off the core of the star‐shaped polymeric materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5877–5890, 2004
Matrix metalloproteinases 1 and 3, tissue inhibitor of metalloproteinase-1 and the complex of metalloproteinase-1/tissue inhibitor in plasma of patients with prostate cancer (1997)

We analyzed blood plasma concentrations of matrix metalloproteinase-1 and -3 (MMP-1; MMP-3), the tissue inhibitor of metalloproteinase-1 (TIMP-1) and the complex MMP-1/TIMP-1, and looked for any correlation with prostate cancer stage. These components were measured by ELISA tests specific for these proteins in healthy male controls (n = 35), and in patients with benign prostatic hyperplasia (BPH; n = 29), with prostate cancer (PCa) without metastasis (T2,3pN0M0; n = 29) and with PCa with metastatic disease (T2,3,4pN1,2M1; n = 18). Mean values of MMP-1 and of the complex MMP-1/TIMP-1 were not different among the 4 groups studied. The mean MMP-3 and especially TIMP-1 concentrations were significantly higher in PCa patients with metastases compared with controls, BPH and PCa patients without metastases. Ten of these 18 patients had TIMP-1 concentrations higher than the upper reference limit. TIMP-1 concentrations were correlated with staging but not with grading. Our results point towards plasma TIMP-1 concentration as a potential marker of malignant progression of PCa.
Vasopressin vs. norepinephrine in endotoxic shock: systemic, renal, and splanchnic hemodynamic and oxygen transport effects (2003)

The effects of intravenous norepinephrine (NE, group 1) and vasopressin (AVP, group 2) infusions on systemic, splanchnic, and renal circulations were studied in anesthetized dogs under basal conditions and during endotoxic shock. Under basal conditions, AVP infusion induced a 12 +/- 7% drop in left ventricular stroke work, a 45 +/- 5% fall in portal venous blood flow, and a 31 +/- 13% decrease in intestinal mucosal blood flow (P < 0.05). AVP also decreased splanchnic oxygen delivery (Do2) and increased splanchnic and renal oxygen extraction significantly during basal conditions. Except for more pronounced brady-cardia among animals in group 2, the systemic and splanchnic changes were comparable between study groups during endotoxic shock. AVP infusion restored renal blood flow and Do2 in endotoxic shock compared with animals resuscitated with NE, which had persistently low renal blood flow and Do2. Our data demonstrate that, in contrast to NE, administration of AVP effectively restores renal blood flow and Do2 with comparable systemic and splanchnic hemodynamic and metabolic effects in endotoxin-induced circulatory shock.
Leveraging latency-insensitivity to ease multiple FPGA design (2012)

Traditionally, hardware designs partitioned across multiple FPGAs have had low performance due to the inefficiency of maintaining cycle-by-cycle timing among discrete FPGAs. In this paper, we present a mechanism by which complex designs may be efficiently and automatically partitioned among multiple FPGAs using explicitly programmed latency-insensitive links. We describe the automatic synthesis of an area efficient, high performance network for routing these inter-FPGA links. By mapping a diverse set of large research prototypes onto a multiple FPGA platform, we demonstrate that our tool obtains significant gains in design feasibility, compilation time, and even wall-clock performance.
The effects of L‐dopa on excessive daytime sleepiness in narcolepsy (1991)

We examined the effects of L-dopa on the excessive daytime sleepiness of six narcoleptic patients while using a double-blind design and objective measurements of vigilance. The two treatment periods, L-dopa or placebo, lasted for 2 weeks each, separated by a 1-week washout period. In addition to the standard Multiple Sleep Latency Test (MSLT), two different tests assessed the daytime vigilance: the Analogue Vigilance Scale (AVS) and the Four Choice Reaction Time Test (FCRTT). L-dopa improved vigilance and performance as evaluated by the AVS and the FCRTT, while the capacity to fall asleep rapidly remained unchanged as evaluated by the MSLT. Results of the present study suggest that L-dopa is effective in improving the vigilance level of narcoleptic patients and raises the hypothesis that dopamine may play a role in the physiopathology of excessive daytime sleepiness of this condition.
Clinical assessment of early tooth demineralization using polarization sensitive optical coherence tomography (2010)

Our results indicate that PS-OCT can non-destructively measure early enamel demineralization on the buccal and occulsal surfaces in vivo.
Anaplerotic diet therapy in inherited metabolic disease: Therapeutic potential (2005)

Beginning with phenylketonuria, dietary therapy for inborn errors has focused primarily on the restriction of the precursor to an affected catabolic pathway in an attempt to limit the production of potential toxins. Anaplerotic therapy is based on the concept that there may exist an energy deficit in these diseases that might be improved by providing alternative substrate for both the citric acid cycle (CAC) and the electron transport chain for enhanced ATP production. This article focuses on this basic problem, as it may relate to most catabolic disorders, and provides our current experience involving inherited diseases of mitochondrial fat oxidation, glycogen storage, and pyruvate metabolism using the anaplerotic compound triheptanoin. The observations have led to a realization that 'inter-organ' signalling and 'nutrient sensors' such as adenylate monophosphate mediated-protein kinase (AMPK) and mTOR (mammalian target of rapamycin) appear to play a significant role in the intermediary metabolism of these diseases. Activated AMPK turns on catabolic pathways to augment ATP production while turning off synthetic pathways that consume ATP. Information is provided regarding the inter-organ requirements for more normal metabolic function during crisis and how anaplerotic therapy using triheptanoin, as a direct source of substrate to the CAC for energy production, appears to be a more successful approach to an improved quality of life for these patients.
Treatment With Adjuvant Endocrine Therapy for Early-Stage Breast Cancer: Is It Forever? (2015)

Article Tools ONCOLOGY GRAND ROUNDS Article Tools OPTIONS & TOOLS Export Citation Track Citation Add To Favorites Rights & Permissions COMPANION ARTICLES No companion articles ARTICLE CITATION DOI: 10.1200/JCO.2014.58.2361 Journal of Clinical Oncology - published online before print January 26, 2015 PMID: 25624431 Treatment With Adjuvant Endocrine Therapy for Early-Stage Breast Cancer: Is It Forever? Beth OvermoyerxBeth OvermoyerSearch for articles by this author Show More Dana-Farber Cancer Institute, Boston, MA https://doi.org/10.1200/JCO.2014.58.2361 First Page Full Text PDF Figures and Tables © 2015 by American Society of Clinical Oncology
Validation of a Multimarker Model for Assessing Risk of Type 2 Diabetes from a Five-Year Prospective Study of 6784 Danish People (Inter99) (2009)

The PreDx DRS provides the absolute risk of diabetes conversion in five years for subjects identified to be "at risk" using the clinical factors.
Effect of pre-storage gamma irradiation on red blood cells. (2005)

Our findings indicated that the gamma irradiation of blood resulted in increased plasma haemoglobin, potassium and LDH. These biochemical changes might not have clinical significance when irradiated blood is transfused to a select group of patients. There is a need for further in vivo studies to follow up the consequences of transfusion of irradiated blood in patients.