gebhart/patrepeval huggingface dataset:
Mass Selection of Ions from Beams Using Waveform Isolation in Radiofrequency Quadrupoles (2009)

A waveform isolation method is described for the mass-selective transmission of ions through quadrupole mass filters, and it is implemented on a new tandem mass analyzer instrument. The method features the application of broad-band waveforms comprising appropriate frequencies to cause mass-selective instability in ions of particular mass-to-charge (m/z) and to transmit all others. The experiment is implemented in a tandem quadrupole system in which the first mass filter is a rectilinear ion trap (RIT) operated in a continuous mass-selective mode to transmit ions of ions of one or more arbitrarily selected m/z value(s). The second analyzer was used to verify the quality of the mass selection achieved using the first analyzer via conventional quadrupole ion trap mass-selective instability scanning. A new subtype of product ion tandem mass spectrometry (MS/MS) scan, termed the summed product ion scan, is demonstrated with a mixture of biological compounds. It is used to characterize product ions arising after simultaneous isolation and collisional activation of multiple precursor species, in this case ions of the same analyte generated in different charge states. The summed product ion scan can be useful for enhancing sensitivity for the analyte of interest or for providing more comprehensive information about an analyte than is available by monitoring a single ionized form of the analyte. The analytical performance of the waveform isolation method is tested using simple drug mixtures, and its potential for increasing overall yields in preparative mass spectrometry is explored briefly. It is shown that efficiencies of ca. 70% of ion transfer to a surface for ion soft landing surface can be achieved. The upper mass range is limited by axial acceleration arising from the stretched geometry, and one solution to this problem is provided.
Abstract 1677: Expression of lysophosphatidic acid acyltransferase-beta in human pancreatic ductal adenocarcinoma (2011)

Abstract Lysophosphatidic acid acyltransferase beta (LPAAT-β) is a new therapeutic target and prognostic marker in human cancer. The enzymatic function of LPAAT- β is to convert Lysophosphatidic Acid (LPA) to Phosphatidic Acid (PA), a lipid second messenger that functions to regulate the proliferation, adhesion, migration and survival of cancer cells. PA is an essential cofactor needed by the oncogenes c-Raf, BRAF, PKC-ζ and mTOR for their enzymatic and growth promoting activities in cancer. LPAAT-β protein over expression has been detected in tumors compared to normal tissue in ovarian, endometrial, breast and lung cancers. The over expression of LPAAT-β in ovarian tumors is associated with poor clinical outcome. Methods: In this study we determined LPAAT-β expression in paired specimens of pancreatic ductal adenocarcinoma and adjacent non-malignant pancreas obtained from 102 patients who underwent pancreatectomy with curative intent (stage IA-IIB). Formalin-fixed, paraffin-embedded core sections in a tissue microarray were immunostained using the avidin-biotin-peroxidase method with rabbit anti- LPAAT-β antibody. A semi-quantitative measure of LPAAT-β expression was determined as the product of immunostain intensity and percentage of cells stained, where intensity and percentage were each scored on a scale of 0 to 3, with 3 being maximal. Results: LPAAT-β expression (product score) in 57% (58/102) of pancreatic cancers was lower than in paired non-malignant pancreas, equal in 20% (20/102) of cancers, and greater in 23% (24/102) of cancers as compared to non-malignant pancreas. LPAAT-β expression in cancer (median product score = 3) was less than in non-malignant pancreas (median score = 4) (Wilcoxon signed-rank test, p &lt; 0.0001). Conclusions: Low LPAAT-β expression in pancreatic cancer as compared to non-malignant pancreas stands in contrast to previous studies showing increased LPAAT-β expression in several other cancers. This finding indicates that there may be tissue-specific differences in the biologic activity of LPAAT-β. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1677. doi:10.1158/1538-7445.AM2011-1677
Frequency-domain method for measuring spectral properties in multiple-scattering media: methemoglobin absorption spectrum in a tissuelike phantom (1995)

We have measured the optical absorption and scattering coefficient spectra of a multiple-scattering medium (i.e., a biological tissue-simulating phantom comprising a lipid colloid) containing methemoglobin by using frequency-domain techniques. The methemoglobin absorption spectrum determined in the multiple-scattering medium is in excellent agreement with a corrected methemoglobin absorption spectrum obtained from a steady-state spectrophotometer measurement of the optical density of a minimally scattering medium. The determination of the corrected methemoglobin absorption spectrum takes into account the scattering from impurities in the methemoglobin solution containing no lipid colloid. Frequency-domain techniques allow for the separation of the absorbing from the scattering properties of multiple-scattering media, and these techniques thus provide an absolute measurement of the optical absorption spectra of the methemoglobin/lipid colloid suspension. One accurately determines the absolute methemoglob in absorption spectrum in the frequency domain by extracting the scattering and absorption coefficients from the phase shift Φ and average light intensity DC (or Φ and the amplitude of the light-intensity oscillations AC) data with relationships provided by diffusion theory, but one determines it less accurately by using the Φ and modulation M (M ≡ AC/DC) data and the diffusion theory relationships. In addition to the greater uncertainty in the absorption and scattering coefficients extracted from the Φ and M data, the optical parameters extracted from the Φ and M data exhibit systematically inaccurate behavior that cannot be explained by random noise in the system. Possible reasons for the systematically lower accuracy of the methemoglobin absorption spectrum obtained from Φ and M data are discussed.
An Efficient, Regio- and Stereoselective Palladium-Catalyzed Route to Tetrasubstituted Olefins (2003)

An efficient, regio- and stereoselective palladium-catalyzed route to tetrasubstituted olefins has been developed, which involves the intermolecular coupling of an aryl iodide, an internal alkyne, and an arylboronic acid. The reaction involves cis-addition of the aryl group from the aryl halide to the less hindered or less electron-poor end of the alkyne, while the aryl group from the arylboronic acid adds to the other end. [reaction: see text]
A new MOS transistor design with self-registering source-drain and gate contacts (1980)

This paper describes a new method for fabricating MOSFETs with self-registering contacts to the source-drain and polysilicon gate regions. Contacts to the source-drain and gate regions are made through a second level of polysilicon which is directly deposited in contact with the doped source-drain and gate regions. Isolations are obtained by selectively oxidizing the entire layer of the second level polysilicon using a thin layer of silicon nitride as an oxidation mask. Metal is only needed in the areas where interconnects cross over the source-drain or gate regions. For an MOS circuit with buried contacts, this approach requires one less mask than the conventional approach since no buried contact masking is needed. Metal silicide can be incorporated into the second level of polysilicon to reduce the lire resistance of this interconnecting layer. Refractory metal or refractory metal silicide can also be used as the gate material. Some experimental results on devices fabricated using the new process will be presented.
Grouping and Optimization of XPath Expressions in System RX (2008)

Several XML DBMS support XQuery and/or SQL/XML languages, which are based on navigational primitives in the form of XPath expressions. Typically, these systems either model each XPath step as a separate query plan operator, or employ holistic approaches that can evaluate multiple steps of a single XPath expression. There have also been proposals to execute as many XPath expressions as possible within a single FLWOR block simultaneously in a data streaming context. We observe in our System-RX prototype that blindly combining all possible XPath expressions for concurrent execution can result in significant performance degradation. We identify two main problems. First, the simple strategy of grouping all XPath expressions on a single document does not always work if the query involves more than one data source or has nested query blocks. Second, merging XPath expressions may result in unnecessary execution of branches that can be filtered by predicates in other branches or elsewhere in the query. To rectify these problems, we develop a combination of heuristic-based rewrite transformations, to decide which XPath expressions should be grouped for concurrent evaluation, and cost-based optimization to globally order the groups within the query execution plan, and locally order the branches within individual groups. Experimental evaluation confirms that selectively grouping multiple XPath expressions allows for better query evaluation performance and reduces the query optimization complexity.
Alignment scheme for through-the-lens alignment (1995)

A real-time through-the-lens alignment system that locks the mask and wafer together via a feedback system on a deep ultraviolet (DUV) camera is described. The mask can be moved to actively track wafer motions even when the resist is being exposed. In support of this, we have devised a novel, high sample rate alignment system. Bench top experiments have verified the basic principles behind the design, emphasizing the ‘‘active’’ alignment mode. A one-dimensional aligner will be installed on a stepper to test the concept with exposures on silicon wafers. The goal is to produce an alignment system that improves both overlay accuracy and throughput on DUV steppers.
GaAs quantum cascade lasers (2003)

GaAs based quantum cascade lasers have been demonstrated and show promising potential with high pulsed output power of 1 W at 77 K and maximum operating temperature up to 200 K. These results have been partly accomplished through the low waveguide losses of 21 cm/sup -1/, in an Al free plasmon-enhanced waveguide.
Abstract 3896: New heat shock protein 90 inhibitors based on the 1,2,3-triazole structure (2012)

Abstract Hsp90 (heat shock protein 90) is a component of a molecular chaperone complex, involved in the folding, maturation and stabilisation of key signalling proteins which control cell proliferation, survival and transformation. It works by modulating a set of cancer-associated proteins, that are often over-expressed and/or mutated in tumor cells, collectively referred as ‘‘clients’’. Inhibition of Hsp90 causes destabilization and eventual degradation of client proteins involved in cell cycle, tumor growth, angiogenesis and apoptosis. Therefore, their modulation results in suppression of tumor growth by multiple parallel mechanisms. Consequently, inhibition of Hsp90 is believed to be a potential target for cancer therapy, also supported by a number of molecules currently under investigation in different phase of clinical trials. We recently synthesized 1,4,5-trisubstituted-1,2,3-triazole derivatives and surprisingly found that these new molecules demonstrated to be extremely active both on the biological target and on human tumor cell lines, even at nanomolar concentration. 3D QSAR analysis was also performed in order to rationalize HSP90 binding data. The overall profile of this new class of 1,2,3-triazoles, including stereoselective synthesis and a comprehensive pharmacological in vitro characterization, will be presented. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3896. doi:1538-7445.AM2012-3896
DJ‐1‐binding compounds prevent oxidative stress‐induced cell death and movement defect in Parkinson’s disease model rats (2008)

Parkinson's disease (PD) is caused by neuronal cell death. Although a precursor of dopamine and inhibitors of dopamine degradation have been used for PD therapy, cell death progresses during treatment. DJ-1, a causative gene product of a familial form of PD, PARK7, plays roles in transcriptional regulation and anti-oxidative stress, and loss of its function is thought to result in the onset of PD. Superfluous oxidation of cysteine at amino acid 106 (C106) of DJ-1 renders DJ-1 inactive, and such oxidized DJ-1 has been observed in patients with the sporadic form of PD. In this study, we isolated compounds that bind to the region at C106 by a virtual screening. These compounds prevented oxidative stress-induced death of SH-SY5Y cells, embryonic stem cell-derived dopaminergic cells and primary neuronal cells of the ventral mesencephalon, but not that of DJ-1-knockdown cells of SH-SY5Y and NIH3T3 cells, indicating that the effect of the compounds is specific to DJ-1. These compounds inhibited production of reactive oxygen species and restored activities of mitochondrial complex I and tyrosine hydroxylase that had been compromised by oxidative stress. These compounds prevented dopaminergic cell death in the substantia nigra and restored movement abnormality in 6-hydroxyldopamine-injected PD model rats. One mechanism of action of these compounds is prevention of superfluous oxidation of DJ-1, and the compounds passed through the blood-brain barrier in vitro. Taken together, the results indicate that these compounds should become fundamental drugs for PD therapy.
Molecular Optimization of Multiply-Functionalized Mesoporous Films with Ion Conduction Properties (2011)

Sequential processing of multiply functionalized mesoporous films is shown to yield materials that are compositionally and structurally heterogeneous on mesoscopic and molecular length scales, both of which must be controlled to optimize macroscopic ion-conduction properties. Cubic mesoporous silica films prepared from strongly acidic solutions were subsequently functionalized under highly alkaline conditions to incorporate hydrophilic aluminosilica surface moieties, followed by nonaqueous conditions to introduce perfluorosulfonic-acid surface groups. Such sequential combination of individually incompatible steps yielded stable mesoporous films with high surface hydrophilicities and strong acid functionalities that exhibited high proton conductivities (ca. 9 × 10(-2) S/cm) at elevated temperatures (120 °C). Molecular, mesoscopic, and macroscopic properties of the multiply functionalized films were monitored and correlated at each stage of the syntheses by nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), elemental analysis, adsorption, and ion conductivity measurements. In particular, variable-temperature solid-state two-dimensional (2D) (27)Al{(1)H}, (29)Si{(1)H}, (27)Al{(19)F}, and (29)Si{(19)F} HETeronuclear chemical-shift CORrelation (HETCOR) NMR spectra reveal separate surface adsorption and grafting sites for the different functional surface species within the mesopore channels. The hydrophilic aluminosilica and acidic fluoro-group loadings and interaction sites are demonstrated to be strongly affected by the different synthesis and functionalization treatments, which must be separately and collectively optimized to maximize the proton conductivities.
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification (2023)

Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads. GAMBIT incorporates this algorithm with a highly curated searchable database of 48,224 genomes. Herein, we describe validation of the scoring methodology, parameter robustness, establishment of confidence thresholds and the curation of the reference database. We assessed GAMBIT by way of validation studies when it was deployed as a laboratory-developed test in two public health laboratories. This method greatly reduces or eliminates false identifications which are often detrimental in a clinical setting.
Tissue‐mimicking gelatin–agar gels for use in magnetic resonance imaging phantoms (1988)

A new variety of tissue-mimicking materials for use in 1H nuclear magnetic resonance (NMR) phantoms has been developed and extensively tested, principally at 10 MHz and at room temperature. The materials can be formed with a broad range of T1's and T2's representative of soft tissues. They are mixtures of various percentages of agar, animal hide gelatin, water, and glycerol. Small concentrations of formaldehyde and n-propanol prevent melting through 100 degrees C and prevent bacterial invasion. The materials are easily produced. A thorough description of compositions and production procedures is given. T1's exhibit about a 5%/degrees C rise in temperature. T2's exhibit less than a 1% rise/degrees C. Long-term (12 months) stability is exhibited both for NMR properties and for absence of fluid extrusion. Preliminary results indicate that T1's depend on the Larmor frequency in a similar way to that observed in soft tissues.
Extraction of BoNT/A, /B, /E, and /F with a Single, High Affinity Monoclonal Antibody for Detection of Botulinum Neurotoxin by Endopep-MS (2010)

Botulinum neurotoxins (BoNTs) are extremely potent toxins that are capable of causing respiratory failure leading to long-term intensive care or death. The best treatment for botulism includes serotype-specific antitoxins, which are most effective when administered early in the course of the intoxication. Early confirmation of human exposure to any serotype of BoNT is an important public health goal. In previous work, we focused on developing Endopep-MS, a mass spectrometry-based endopeptidase method for detecting and differentiating the seven serotypes (BoNT/A-G) in buffer and BoNT/A, /B, /E, and /F (the four serotypes that commonly affect humans) in clinical samples. We have previously reported the success of antibody-capture to purify and concentrate BoNTs from complex matrices, such as clinical samples. However, to check for any one of the four serotypes of BoNT/A, /B, /E, or /F, each sample is split into 4 aliquots, and tested for the specific serotypes separately. The discovery of a unique monoclonal antibody that recognizes all four serotypes of BoNT/A, /B, /E and /F allows us to perform simultaneous detection of all of them. When applied in conjunction with the Endopep-MS assay, the detection limit for each serotype of BoNT with this multi-specific monoclonal antibody is similar to that obtained when using other serotype-specific antibodies.
Stem Cells for Retinal Repair (2014)

Remarkable progress over the past decade has led to the first clinical studies of stem cell therapy for retinal disease. The unique access retina offers for implantation, monitoring, and ablation is well suited for stem cell trials, and retinal applications have now moved to the forefront of the field of regenerative medicine. Retinal progeny derived from either pluripotent stem cells or tissue-specific retinal and retinal pigment epithelium (RPE) stem cells have the capacity both to replace damaged retina and to provide trophic support that slows disease progression. In contrast, bone marrow and neural stem cells produce nonretinal progeny that provide trophic support but with limited integration and capacity to differentiate into retinal progeny that can replace damaged retinal tissue. Embryonic and induced pluripotent stem cells differentiated into neural retinal and RPE progeny provide an unlimited supply of human cells for transplantation and disease modeling but raise the risks of aberrant differentiation and over proliferation. Tissue-specific stem cells isolated from neural retina or RPE that are naturally committed to retinal fates have a restricted lineage potential that improves the margin of safety. This improved safety of retina and RPE stem cells is balanced, however, by a restricted proliferative potential, which limits the quantity of progeny produced. In this chapter, we review the types of stem cells under development for retinal therapy.
Synthesis and Structure−Activity Relationship of (Lactamylvinyl)cephalosporins Exhibiting Activity against Staphylococci, Pneumococci, and Enterococci (1996)

The synthesis and structure-activity relationships of a new class of vinylcephalosporins substituted with a lactamyl residue are described. These compounds show excellent activity against enterococci and retain the broad spectrum activity of third-generation cephalosporins such as ceftriaxone.
Initiation and modulation of locomotor circuitry output with multisite transcutaneous electrical stimulation of the spinal cord in noninjured humans (2014)

The mammalian lumbar spinal cord has the capability to generate locomotor activity in the absence of input from the brain. Previously, we reported that transcutaneous electrical stimulation of the spinal cord at vertebral level T11 can activate the locomotor circuitry in noninjured subjects when their legs are placed in a gravity-neutral position (Gorodnichev RM, Pivovarova EA, Pukhov A, Moiseev SA, Savokhin AA, Moshonkina TR, Shcherbakova NA, Kilimnik VA, Selionov VA, Kozlovskaia IB, Edgerton VR, Gerasimenko IU. Fiziol Cheloveka 38: 46-56, 2012). In the present study we hypothesized that stimulating multiple spinal sites and therefore unique combinations of networks converging on postural and locomotor lumbosacral networks would be more effective in inducing more robust locomotor behavior and more selective control than stimulation of more restricted networks. We demonstrate that simultaneous stimulation at the cervical, thoracic, and lumbar levels induced coordinated stepping movements with a greater range of motion at multiple joints in five of six noninjured subjects. We show that the addition of stimulation at L1 and/or at C5 to stimulation at T11 immediately resulted in enhancing the kinematics and interlimb coordination as well as the EMG patterns in proximal and distal leg muscles. Sequential cessation of stimulation at C5 and then at L1 resulted in a progressive degradation of the stepping pattern. The synergistic and interactive effects of transcutaneous stimulation suggest a multisegmental convergence of descending and ascending, and most likely propriospinal, influences on the spinal neuronal circuitries associated with locomotor activity. The potential impact of using multisite spinal cord stimulation as a strategy to neuromodulate the spinal circuitry has significant implications in furthering our understanding of the mechanisms controlling posture and locomotion and for regaining significant sensorimotor function even after a severe spinal cord injury.