gebhart/patrepeval huggingface dataset:
Imaging the Lipidome: ω-Alkynyl Fatty Acids for Detection and Cellular Visualization of Lipid-Modified Proteins (2009)

Fatty acylation or lipid modification of proteins controls their cellular activation and diverse roles in physiology. It mediates protein-protein and protein-membrane interactions and plays an important role in regulating cellular signaling pathways. Currently, there is need for visualizing lipid modifications of proteins in cells. Herein we report novel chemical probes based on omega-alkynyl fatty acids for biochemical detection and cellular imaging of lipid-modified proteins. Our study shows that omega-alkynyl fatty acids of varying chain length are metabolically incorporated onto cellular proteins. Using fluorescence imaging, we describe the subcellular distribution of lipid-modified proteins across a panel of different mammalian cell lines and during cell division. Our results demonstrate that this methodology is a useful diagnostic tool for analyzing the lipid content of cellular proteins and for studying the dynamic behavior of lipid-modified proteins in various disease or physiological states.
Single-step electronic detection of femtomolar DNA by target-induced strand displacement in an electrode-bound duplex (2006)

We report a signal-on, electronic DNA (E-DNA) sensor that is label-free and achieves a subpicomolar detection limit. The sensor, which is based on a target-induced strand displacement mechanism, is composed of a "capture probe" attached by its 5' terminus to a gold electrode and a 5' methylene blue-modified "signaling probe" that is complementary at both its 3' and 5' termini to the capture probe. In the absence of target, hybridization between the capture and signaling probes minimizes contact between the methylene blue and electrode surface, limiting the observed redox current. Target hybridization displaces the 5' end of the signaling probe, generating a short, flexible single-stranded DNA element and producing up to a 7-fold increase in redox current. The observed signal gain is sufficient to achieve a demonstrated (not extrapolated) detection limit of 400 fM, which is among the best reported for single-step electronic DNA detection. Moreover, because sensor fabrication is straightforward, the approach appears to provide a ready alternative to the more cumbersome femtomolar electrochemical assays described to date.
Complex I deficiency: clinical features, biochemistry and molecular genetics (2012)

Complex I deficiency is the most frequent mitochondrial disorder presenting in childhood, accounting for up to 30% of cases. As with many mitochondrial disorders, complex I deficiency is characterised by marked clinical and genetic heterogeneity, leading to considerable diagnostic challenges for the clinician, not least because of the involvement of two genomes. The most prevalent clinical presentations include Leigh syndrome, leukoencephalopathy and other early-onset neurodegenerative disorders; fatal infantile lactic acidosis; hypertrophic cardiomyopathy; and exercise intolerance. Causative genetic defects may involve the seven mitochondrial-encoded or 38 nuclear-encoded subunits of the enzyme, or any of an increasing number of assembly factors implicated in the correct biosynthesis of complex I within the inner mitochondrial membrane. In this review, we discuss recent advances in knowledge of the structure, function and assembly of complex I and how these advances, together with new high-throughput genetic screening techniques, have translated into improved genetic diagnosis for affected patients and their families. Approximately 25% of cases have mitochondrial DNA mutations, while a further ∼25% have mutations in a nuclear subunit or in one of nine known assembly factors. We also present a systematic review of all published cases of nuclear-encoded complex I deficiency, including 117 cases with nuclear subunit mutations and 55 with assembly factor mutations, and highlight clinical, radiological and biochemical clues that may expedite genetic diagnosis.
Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III (2009)

Glutamate carboxypeptidase III (GCPIII) is a metalloenzyme that belongs to the transferrin receptor/glutamate carboxypeptidase II (GCPII; EC 3.4.17.21) superfamily. GCPIII has been studied mainly because of its evolutionary relationship to GCPII, an enzyme involved in a variety of neuropathologies and malignancies, such as glutamatergic neurotoxicity and prostate cancer. Given the potential functional and pharmacological overlap between GCPIII and GCPII, studies addressing the structural and physiological properties of GCPIII are crucial for obtaining a deeper understanding of the GCPII/GCPIII system. In the present study, we report high-resolution crystal structures of the human GCPIII ectodomain in a 'pseudo-unliganded' state and in a complex with: (a) L-glutamate (a product of hydrolysis); (b) a phosphapeptide transition state mimetic, namely (2S,3'S)-{[(3'-amino-3'-carboxy-propyl)-hydroxyphosphinoyl]methyl}-pentanedioic acid; and (c) quisqualic acid, a glutamate biostere. Our data reveal the overall fold and quaternary arrangement of the GCPIII molecule, define the architecture of the GCPIII substrate-binding cavity, and offer an experimental evidence for the presence of Zn(2+) ions in the bimetallic active site. Furthermore, the structures allow us to detail interactions between the enzyme and its ligands and to characterize the functional flexibility of GCPIII, which is essential for substrate recognition. A comparison of these GCPIII structures with the equivalent GCPII complexes reveals differences in the organization of specificity pockets, in surface charge distribution, and in the occupancy of the co-catalytic zinc sites. The data presented here provide information that should prove to be essential for the structurally-aided design of GCPIII-specific inhibitors and might comprise guidelines for future comparative GCPII/GCPIII studies.
Incremental Sampling-based Algorithms for Optimal Motion Planning (2010)

During the last decade, incremental sampling-based motion planning algorithms, such as the Rapidly-exploring Random Trees (RRTs), have been shown to work well in practice and to possess theoretical guarantees such as probabilistic completeness. However, no theoretical bounds on the quality of the solution obtained by these algorithms, e.g., in terms of a given cost function, have been established so far. The purpose of this paper is to fill this gap, by designing efficient incremental samplingbased algorithms with provable optimality properties. The first contribution of this paper is a negative result: it is proven that, under mild technical conditions, the cost of the best path returned by RRT converges almost surely to a non-optimal value, as the number of samples increases. Second, a new algorithm is considered, called the Rapidly-exploring Random Graph (RRG), and it is shown that the cost of the best path returned by RRG converges to the optimum almost surely. Third, a tree version of RRG is introduced, called RRT * , which preserves the asymptotic optimality of RRG while maintaining a tree structure like RRT. The analysis of the new algorithms hinges on novel connections between sampling-based motion planning algorithms and the theory of random geometric graphs. In terms of computational complexity, it is shown that the number of simple operations required by both the RRG and RRT * algorithms is asymptotically within a constant factor of that required by RRT.
Experience in using business scenarios to assess COTS components in integrated solutions (2005)

Constructing software by integrating commercial off-the-shelf (COTS) components is widely practised, particularly in the IT service industry. For vendors of COTS components, requirements engineering is particularly challenging. To continually improve their products, vendors must identify and analyze problems that occur when their components are used in a wide variety of integrated solutions, and they must anticipate new applications in which their components could be used. In this paper, we describe a scenario-based framework developed at the Software Group division of IBM Corporation (IBM SWG) The framework mimics the solution integration process for new business opportunities, allowing the development teams to evaluate their components, discover and re-solve integration issues, and to surface new requirements for future releases. This paper describes the framework, gives an example of its use in a business scenario, discusses the experience of using this framework at IBM SWG, and relates the lessons learned.
Potentiation of melphalan cytotoxicity in human ovarian cancer cell lines by glutathione depletion. (1984)

The effectiveness of alkylating agents in the treatment of ovarian cancer is limited by the frequent development of drug resistance. In order to examine the mechanisms of resistance and potential ways in which this resistance could be overcome, we have developed a human ovarian cancer cell line, 1847ME, resistant to the bifunctional amino acid nitrogen mustard, melphalan. A 4-fold higher concentration of melphalan was required to produce an equivalent reduction in tumor colony formation in 1847ME cells as compared to the parent melphalan-sensitive line A1847. The magnitude of resistance in 1847ME was similar to that observed in the cell lines NIH:OVCAR-2, NIH:OVCAR-3, and NIH:OVCAR-4 which were derived from ovarian cancer patients clinically resistant to alkylating agents. There was no detectable difference in melphalan uptake between A1847 and 1847ME. The cellular content of the inactive dihydroxy melphalan metabolite, however, was two times greater in 1847ME compared to A1847. Levels of the principal intracellular thiol, glutathione, were found to be 2-fold greater in 1847ME than in A1847, and to be similarly elevated in the OVCAR lines. Depletion of glutathione by incubation of the cells in cystine-free medium or in the presence of the specific inhibitor of glutathione synthesis, DL-buthionine-S,R-sulfoximine, was accompanied by a marked increase in melphalan cytotoxicity. Doses of DL-buthionine-S,R-sulfoximine which were only minimally cytotoxic were associated with complete reversal of the induced resistance to melphalan in 1847ME. Synergism between melphalan and DL-buthionine-S,R-sulfoximine was also demonstrated in the OVCAR cell lines derived from previously treated ovarian cancer patients. The reversal of induced resistance to melphalan by modulation of glutathione levels is of potential clinical relevance. In addition, these cell lines provide a useful model system in which to study further the mechanisms of alkylating agent resistance in human tumors.
Partial purification and properties of mevalonate kinase from neonatal chick liver. (1982)

Mevalonate kinase from neonatal chick liver has been partially purified by ammonium sulphate precipitation and Sephadex G100 and DEAE-cellulose fractionation. The kinetic characteristics agreed with the sequential mechanism suggested for the enzyme and provided apparent Km values of 0.01 mM for mevalonic acid and 0.25 mM for ATP. Partially purified mevalonate kinase from neonatal chick liver showed an absolute specificity for ATP. Mn2+ was a better activator than Mg2+ at low concentrations (0.1-1.0 mM). Higher Mn2+ concentrations produced a clear inhibition of mevalonate kinase. Likewise, addition of EDTA, with or without metal ions, clearly inhibited the enzymatic reaction.
The Human Polyomavirus, JCV, Uses Serotonin Receptors to Infect Cells (2004)

The human polyomavirus, JCV, causes the fatal demyelinating disease progressive multifocal leukoencephalopathy in immunocompromised patients. We found that the serotonergic receptor 5HT2AR could act as the cellular receptor for JCV on human glial cells. The 5HT2A receptor antagonists inhibited JCV infection, and monoclonal antibodies directed at 5HT2A receptors blocked infection of glial cells by JCV, but not by SV40. Transfection of 5HT2A receptor-negative HeLa cells with a 5HT2A receptor rescued virus infection, and this infection was blocked by antibody to the 5HT2A receptor. A tagged 5HT2A receptor colocalized with labeled JCV in an endosomal compartment following internalization. Serotonin receptor antagonists may thus be useful in the treatment of progressive multifocal leukoencephalopathy.
Novel Potential Therapeutics for Schizophrenia: Focus on the Modulation of Metabotropic Glutamate Receptor Function (2005)

Schizophrenia is the most disabling psychiatric disorder and one of the worlds top ten causes of long-term disability, affecting 1% of the population worldwide. The major symptoms of schizophrenia, psychosis (positive symptoms), apathy, social withdrawal (negative symptoms) and cognitive impairment, become manifest in late adolescence/early adulthood and persist thereafter, resulting in chronic disability. The pharmacotherapy of schizophrenia has evolved from typical antipsychotics (dopamine D2 receptor antagonists) to atypical antipsychotics (mixed D2 and serotonin 5-HT2A antagonists with activity at various other receptors) with improved efficacy and side effect profile. More recently, the glutamate/ N-methyl-Daspartate glutamate receptor (NMDAR) hypothesis of schizophrenia has been formulated. This hypothesis is supported by the observation that administration of NMDAR blockers to human volunteers is psychotomimetic and administration to schizophrenic patients exacerbates pre-existing symptoms. This has generated an interest to develop novel antipsychotics focused on the identification of novel molecular targets and susceptibility genes that result in deregulation of glutamatergic, GABAergic and dopaminergic neurotransmission. In particular, metabotropic glutamate (mGlu) receptors mGlu2/3 and mGlu5 are prominently expressed in relevant forebrain regions and their activation modulates glutamatergic transmission and NMDAR function in the mammalian brain. The activity of mGlu2/3 and mGlu5 receptor agonists and more recently, the activity shown by selective mGlu2 and mGlu5 receptor allosteric potentiators in preclinical models of psychosis are promising. Further evaluation of the efficacy and side effect profile of potent, selective and brain-penetrant mGlu receptor activators may provide novel therapeutic avenues for the treatment of schizophrenia.
Administration of N‐acetylcysteine after focal cerebral ischemia protects brain and reduces inflammation in a rat model of experimental stroke (2004)

Free radicals and inflammatory mediators are involved in transient focal cerebral ischemia (FCI). Preadministration of N-acetylcysteine (NAC) has been found to attenuate the cerebral ischemia-reperfusion injury in a rat model of experimental stroke. This study was undertaken to investigate the neuroprotective potential of NAC administered after ischemic events in experimental stroke. FCI was induced for 30 min by occluding the middle cerebral artery (MCA). NAC (150 mg/kg) was administered intraperitoneally at the time of reperfusion followed by another dose 6 hr later. Animals were sacrificed after 24 hr of reperfusion. The cerebral infarct consistently involved the cortex and striatum. Infarction was assessed by staining the brain sections with 2,3,5-triphenyltetrazolium chloride. Animals treated with NAC showed a significant reduction in infarct area and infarct volume and an improvement in neurologic scores and glutathione level. Reduction in infarction was significant even when a single dose of NAC was administered at 6 hr of reperfusion. Immunohistochemical and quantitative real-time PCR studies demonstrated a reduction in the expression of proinflammatory cytokines such as tumor necrosis factor alpha (TNFalpha) and interleukin 1beta (IL-1beta) and inducible nitric oxide synthase (iNOS) in NAC compared to that in vehicle-treated animals. The expression of activated macrophage/microglia (ED1) and apoptotic cell death in ischemic brain was also reduced by NAC treatment. These results indicate that in a rat model of experimental stroke, administration of NAC even after ischemia onset protected the brain from free radical injury, apoptosis, and inflammation, with a wide treatment window.
Alzheimer disease amyloid beta protein forms calcium channels in bilayer membranes: blockade by tromethamine and aluminum. (1993)

Amyloid beta protein (A beta P) is the 40- to 42-residue polypeptide implicated in the pathogenesis of Alzheimer disease. We have incorporated this peptide into phosphatidylserine liposomes and then fused the liposomes with a planar bilayer. When incorporated into bilayers the A beta P forms channels, which generate linear current-voltage relationships in symmetrical solutions. A permeability ratio, PK/PCl, of 11 for the open A beta P channel was estimated from the reversal potential of the channel current in asymmetrical KCl solutions. The permeability sequence for different cations, estimated from the reversal potential of the A beta P-channel current for each system of asymmetrical solutions, is Pcs > PLi > PCa > or = PK > PNa. A beta P-channel current (either CS+ or Ca2+ as charge carriers) is blocked reversibly by tromethamine (millimolar range) and irreversibly by Al3+ (micromolar range). The inhibition of the A beta P-channel current by these two substances depends on transmembrane potential, suggesting that the mechanism of blockade involves direct interaction between tromethamine (or Al3+) and sites within the A beta P channel. Hitherto, A beta P has been presumed to be neurotoxic. On the basis of the present data we suggest that the channel activity of the polypeptide may be responsible for some or all of its neurotoxic effects. We further propose that a useful strategy for drug discovery for treatment of Alzheimer disease may include screening compounds for their ability to block or otherwise modify A beta P channels.
Liquid chromatography tandem mass spectrometric quantitation of sulfamethazine and its metabolites: direct analysis of swine urine by triple quadrupole and by ion trap mass spectrometry (2000)

This work describes a new method for the quantitation of trace amounts of sulfamethazine (SMZ) and its main metabolite, N4-acetylsulfamethazine (Ac-SMZ), in swine urine, using high-performance liquid chromatography (HPLC) tandem mass spectrometric analysis of crude urine after addition of internal standard and simple dilution with water. The aim was to determine whether residues of this sulfamidic drug, normally administered to swine in order to prevent infectious diseases, were present in urine at levels lower than those permitted by regulatory authorities before human consumption (EU Project SMT, contract number CT 96-2092). A 10 µL volume of diluted urine was injected into a very short, narrow-bore chromatographic column (Zorbax SB-C18 2.1 i.d. ×30 mm length, 3.5 µm pore size). Elution of the analytes of interest was achieved in less than seven minutes using a rapid gradient (from 20 to 80% methanol in 3 minutes). Either a PE Sciex API 365 triple quadrupole (QqQ), operated in the selected reaction monitoring (SRM) mode, or a Finnigan LCQ ion trap (IT) mass spectrometer, operated in narrow-range product ion scan, was used as the final detector. Electrospray (ESI) was used as the ionization technique. A comparison of the two tandem mass spectrometers was performed by analyzing the same set of test samples, at three concentration levels, on three different days. Linearity of responses of the calibration standards, intra- and inter-assay precision of the samples, specificity and limits of detection were evaluated for both systems. Both the QqQ and the IT instrument was suitable for rapid, sensitive and specific determination of the analytes, although the overall performance of the QqQ was slightly superior in terms of linearity, precision and sensitivity. Copyright © 2000 John Wiley & Sons, Ltd.
Abstract 4830: Preclinical anti-tumor activity of nanoliposomal irinotecan (Nal-IRI, MM-398) + 5-FU + oxaliplatin in pancreatic cancer (2016)

Abstract Nanoliposomal irinotecan (Nal-IRI, MM-398) recently gained approval in combination with 5-fluorouracil/leucovorin (5-FU/LV) in post-gemcitabine metastatic pancreatic cancer based on results of the Phase 3 NAPOLI-1 trial. Nal-IRI, in combination with 5-FU/LV, improved overall survival in gemcitabine-refractory metastatic PDAC relative to 5-FU/LV alone with a well-defined and manageable toxicity profile in pretreated patients. FOLFIRINOX (5-FU/LV, irinotecan and oxaliplatin) is a chemotherapy regimen active in first-line metastatic PDAC. Herein, we evaluate the preclinical anti-tumor activity of a nal-IRI + 5-FU + oxaliplatin regimen relative to the FOLFIRINOX regimen. Using pancreatic cancer cell lines, we demonstrate enhanced cell death when nal-IRI treatment is simulated using prolonged exposure of SN-38 (the active metabolite of irinotecan) in combination with 5-FU and oxaliplatin. In cell line-derived and patient-derived xenograft models of pancreatic cancer we demonstrate improved anti-tumor activity of nal-IRI relative to exposure-matched doses of unencapsulated irinotecan. Further, nal-IRI consistently improved tumor growth inhibition and survival relative to unencapsulated irinotecan in preclinical models, both as a monotherapy and in combination with 5-FU and oxaliplatin. The addition of nal-IRI to 5-FU and/or oxaliplatin did not exacerbate the baseline toxicities of these agents, including weight loss and neutropenia, and tolerability could be further improved by delaying the administration of oxaliplatin to 1 day post-MM-398. These findings illustrate the therapeutic potential of nal-IRI in combination with 5-FU/LV and oxaliplatin and support an ongoing Phase 2 trial (NCT02551991) of this triplet regimen in first-line PDAC. Citation Format: Daniel F. Gaddy, Helen Lee, Nancy Paz, Shannon C. Leonard, Ashish Kalra, Ninfa L. Straubinger, Robert M. Straubinger, Bryan M. Gillard, Michael T. Moser, Daryl C. Drummond, Stephan G. Klinz, Bart S. Hendriks, Jonathan B. Fitzgerald. Preclinical anti-tumor activity of nanoliposomal irinotecan (Nal-IRI, MM-398) + 5-FU + oxaliplatin in pancreatic cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4830.
Combined ultrasonic and photoacoustic imaging to age deep vein thrombosis: preliminary studies (2006)

There is a need for a clinical imaging technique to reliably diagnose and adequately age deep vein thrombosis (DVT). Maturation of DVT is associated with the reorganization and possibly significant changes in the optical absorption of the blood clot. In this paper, we explore photoacoustic imaging to age DVT. Photoacoustic imaging is a technique capable of remote measurements of optical absorption of tissue. Theoretical and experimental studies were performed using DVT-mimicking phantoms. The results of our study suggest that combined ultrasound and photoacoustic imaging of thrombi can provide information about the structure and age of deep vein thrombosis.