gebhart/patrepeval huggingface dataset:
Data from Organic Cation Transporters Are Determinants of Oxaliplatin Cytotoxicity (2023)

&lt;div&gt;Abstract&lt;p&gt;Although the platinum-based anticancer drugs cisplatin, carboplatin, and oxaliplatin have similar DNA-binding properties, only oxaliplatin is active against colorectal tumors. The mechanisms for this tumor specificity of platinum-based compounds are poorly understood but could be related to differences in uptake. This study shows that the human organic cation transporters (OCT) 1 and 2 (&lt;i&gt;SLC22A1&lt;/i&gt; and &lt;i&gt;SLC22A2&lt;/i&gt;) markedly increase oxaliplatin, but not cisplatin or carboplatin, accumulation and cytotoxicity in transfected cells, indicating that oxaliplatin is an excellent substrate of these transporters. The cytotoxicity of oxaliplatin was greater than that of cisplatin in six colon cancer cell lines [mean ± SE of IC&lt;sub&gt;50&lt;/sub&gt; in the six cell lines, 3.9 ± 1.4 μmol/L (oxaliplatin) versus 11 ± 2.0 μmol/L (cisplatin)] but was reduced by an OCT inhibitor, cimetidine, to a level similar to, or even lower than that of, cisplatin (29 ± 11 μmol/L for oxaliplatin versus 19 ± 4.3 μmol/L for cisplatin). Structure-activity studies indicated that organic functionalities on nonleaving groups coordinated to platinum are critical for selective uptake by OCTs. These results indicate that OCT1 and OCT2 are major determinants of the anticancer activity of oxaliplatin and may contribute to its antitumor specificity. They also strongly suggest that expression of OCTs in tumors should be investigated as markers for selecting specific platinum-based therapies in individual patients. The development of new anticancer drugs, specifically targeted to OCTs, represents a novel strategy for targeted drug therapy. The results of the present structure-activity studies indicate specific tactics for realizing this goal. (Cancer Res 2006; 66(17): 8847-57)&lt;/p&gt;&lt;/div&gt;
Reliable Determination of Site-Specific In Vivo Protein N-Glycosylation Based on Collision-Induced MS/MS and Chromatographic Retention Time (2014)

Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures.
Iron‐loaded PLLA nanoparticles as highly efficient intracellular markers for visualization of mesenchymal stromal cells by MRI (2014)

Monitoring of the fate of cells after injection appears paramount for the further development of cell therapies. In this context magnetic resonance imaging (MRI) is increasing in relevance owing to its unique tissue visualization properties. For assessment of cell trafficking and homing, the cells have to be labeled to become MR visible. The rather low sensitivity of MRI demands dedicated intracellular markers with high payloads of MR contrast agents for ensuring sensitive detection of local cell aggregations. In the presented work the application of custom-designed nanometer-sized iron oxide loaded poly-(l-lactide) (iPLLA) nanoparticles was investigated. The particles were synthesized by the mini-emulsion process and evaluated for labeling of mesenchymal stromal cells (MSCs). The efficient cellular uptake and long intracellular retention times of the particles as well as their nontoxicity are demonstrated. The average cellular iron content was 55 pg iron per cell. Further incorporation of, for example, fluorescent dye enables the generation of multireporter particles, providing the great potential for multimodal imaging. The efficiency of these nanoparticles as MRI contrast agent was evaluated in vitro using relaxation rate mapping, yielding relaxivities r2 = 273.3, r2 (*) = 545.1 mm(-1) s(-1) at 3 T and r2 = 415.7, r2 (*) = 872.3 mm(-1) s(-1) at 11.7 T. The high r2 (*) relaxivity of the iPLLA nanoparticles enabled visualization of a single labeled cell in vitro at 50-µm spatial resolution. In vivo evaluation in a rat injury model revealed the potential of the iPLLA particles to efficiently label MSCs for MRI monitoring of ~20 000-40 000 injected cells at 11.7 T. In conclusion the presented work demonstrates the applicability of iPLLA particles as efficient intracellular marker for MSC labeling for monitoring the fate of the cells by MRI.
A Learned Approach to Design Compressed Rank/Select Data Structures (2022)

We address the problem of designing, implementing, and experimenting with compressed data structures that support rank and select queries over a dictionary of integers. We shine a new light on this classical problem by showing a connection between the input integers and the geometry of a set of points in a Cartesian plane suitably derived from them. We then build upon some results in computational geometry to introduce the first compressed rank/select dictionary based on the idea of “learning” the distribution of such points via proper linear approximations (LA). We therefore call this novel data structure the la_vector . We prove time and space complexities of the la_vector in several scenarios: in the worst case, in the case of input distributions with finite mean and variance, and taking into account the k th order entropy of some of its building blocks. We also discuss improved hybrid data structures, namely, ones that suitably orchestrate known compressed rank/select dictionaries with the la_vector . We corroborate our theoretical results with a large set of experiments over datasets originating from a variety of applications (Web search, DNA sequencing, information retrieval, and natural language processing) and show that our approach provides new interesting space-time tradeoffs with respect to many well-established compressed rank/select dictionary implementations. In particular, we show that our select is the fastest, and our rank is on the space-time Pareto frontier.
A Dual-Microphone Algorithm That Can Cope With Competing-Talker Scenarios (2012)

This paper introduces a novel technique for signal-to-noise ratio (SNR) estimation for scenarios where two closely-spaced microphones are available. The proposed technique utilizes the real and imaginary parts of the coherence function between the input signals to estimate the SNR without assuming prior knowledge of the noise statistics. The corresponding dual-microphone speech enhancement algorithm utilizes a Wiener filter as a gain function constructed using the SNR values computed by the coherence function. Since the proposed SNR estimation technique does not require access to noise statistics, it can be applied in situations where interfering speakers are present. An adaptive speech reception threshold (SRT) test was used to assess the intelligibility of speech processed by the proposed algorithm in scenarios where one or two interfering talkers were present in anechoic and reverberant conditions. Intelligibility listening tests were conducted with both normal-hearing (NH) and cochlear implant (CI) listeners. Results revealed significant improvements in intelligibility and quality over a (baseline) fixed directional algorithm and a well-established beamformer algorithm. In a nearly anechoic room with competing talkers, the improvement in SRT obtained relative to the directional microphone ranged from 5-10 dB, while the improvement obtained by the beamformer was about 2 dB. In reverberant environments, the improvement in SRT remained high (4-7 dB) at <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> = 220 ms, and decreased to 1-2 dB at <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">60</sub> = 465 ms. Overall, the proposed algorithm provided significant benefits in intelligibility in anechoic and mildly reverberant environments making it suitable for hearing aid and cochlear implant applications.
Electrical Readouts of Single and Few Molecule Systems in Metal-Molecule-Metal Device Structures (2007)

Electrical conduction through molecular junctions are measured in different local environments through two test beds that are ideal for single/few molecule and molecular monolayer systems. A technique has been developed to realize Au films with approximately 1.5 A surface roughness comparable to the best available techniques and suitable for formation of patterned device structures. The technique utilizes room temperature e-beam evaporated Au films over oxidized Si substrates silanized with (3-mercaptopropyl)trimethoxysilane (MPTMS). The lateral (single/few molecule) and vertical (many molecules) device structures are both enabled by the process for realizing ultraflat Au layer. Lateral metal-molecule-metal (M-M-M) device structures are fabricated by forming pairs of Au electrodes with nanometer separation (nano-gap) through an electromigration-induced break-junction (EIBJ) technique at room temperature and conductivity measurements are carried out for dithiol functionalized single molecules. We have used the flat Au layer (using the current technique) as the bottom contact in vertical M-M-M device structures. Here, molecular self-assembly are formed on the Au surface, and patterned (20 x 20 microm2) top Au contacts were successfully transferred on to the device using a stamping technique (where the Au is deposited on a polydimethylsiloxane (PDMS) pad and following a physical contact on the thiolated Au layer). The single molecular property of XYL, a highly conductive molecule and many molecular property of HS-C9-SH, an insulating molecule in its molecular monolayer form are measured. Observation of enhanced conduction following molecular deposition, and comparison of conductance-voltage characteristics to those predicted theoretically, confirms the success of trapping single/few molecules in the nano-gap. The observed approximately 10(2) less conductance through the molecular monolayer of HS-C9-SH compared to the estimation of a linear sum of single molecule conductances over large area indicate that either all the molecules are not in physical contact with the top stamping electrode or electrode-molecule coupling has a less broadening in presence of it own environment or both.
A Simple, Inexpensive, Wearable Glove with Hybrid Resistive‐Pressure Sensors for Computational Sensing, Proprioception, and Task Identification (2020)

Wearable Gloves Using fluidic and resistive sensor inputs, MemGlove collects data which is then routed through MLP and LSTM neural networks to produce outputs reflecting the state of the user and the environment. In article number 2000002, Andrew Spielberg and co-workers show object, stiffness, and handwritten letter classification, as well as temperature, force, hand pose, and heart rate estimation.
Das "Landding" im mitteldeutschen Osten (1977)

Die Ausbildung des wettinischen Landesstaates in institutionell vollendeter Form geschah im 15. Jahrhundert. Ihre Vorgänge können zwar nicht ohne die politisch geschichtliche Betrachtung über die Territorialbildung des Landesherrn erklärt werden, aber können verfassungsgeschichtlich als der Veränderungsprozeß der Gerichtsverfassung erfaßt werden. Denn im deutschen Mittelalter wurden—das ist im allgemeinen gesagt—alle politische oder herrschaftliche Ordnungen in den Gerichten gestaltet, and sie konnten gar nicht die genossenschaftliche Mitwirkung der Gerichtsgemeinde entbehren, um sich wirklichmachen and bewahren zu lassen.Die Entstehung des Landesstaates war die Reorganisierung solch mittelalterlicher Ordnungen. Zugleich war sie auch ein Ansatz zu einem ihnen fremden Ordnungsprinzip, wie man den Landesstaat als die geschichtliche Grundlage für den modernen Verwaltungsstaat betrachtet.Das "Landding" im mitteldeutschen Osten war die große Gerichtsversammlung, die sich aus Markgrafen von Wettin als Vorsitzendern and Landadel als Gerichtsgenossen zusammensetzte. Quellenmäßig begegnet es uns in der Zeit, wo der wettinische Landesstaat auf dem Wege zur Ausbildung war, nämlich vom Ende des 12. Jahrhunderts bis zur Mitte des 14. Jahrhunderts.So wollen wir die folgenden Fragen untersuchen, 1) die Entstehung des „Landdings", 2) seine Zusammensetzung, and seine Wirkungen and Funktionen, 3) die wettinische Territorialpolitik and die Veränderung des "Landdings". Damit sollte ein Bild über die, Landesstaatsbildung durch Wettiner gewonnen werden.
Damage-free contact etching using balanced electron drift magnetron etcher (2002)

A new plasma source called balanced electron drift (BED) magnetron plasma has been developed for SiO/sub 2/ contact/via hole etching. E/spl times/B drift of electrons, which is notorious for degrading the uniformity of magnetron plasmas, has been completely balanced by applying appropriate 100 MHz rf power to the upper ring electrode. As a result, charge-up damage free and highly uniform etch rate of /spl plusmn/2.72% profiles were obtained on 200 mm wafer. Micro-loading effect free etching was also achieved by suppressing excess dissociation of C/sub 4/F/sub 8/. The BED magnetron etcher has an additional benefit of reducing dopant deactivation in the Si substrate because carbon-rich fluorocarbon film can protect the Si surface from high-energy ion bombardment during the over-etch period. Also, the addition of Xe has been confirmed to exhibit drastic suppression of the dopant deactivation even at p/sup +/Si surface, which results in low contact resistance without additional ion implantation after the contact etch. The BED magnetron etcher using Xe gas can reduce a few tens of process steps after the contact etch.
Techniques of Linear Lesion for Atrial Fibrillation Ablation (2008)

This chapter contains sections titled: Introduction Pulmonary vein ablation Indications for linear lesion Technical approach to linear ablation Post-ablation management Left atrial linear ablation for substrate modification Conclusion References
Characterization of Novel 18F-Labeled Phenoxymethylpyridine Derivatives as Amylin Imaging Probes (2018)

Deposition of islet amyloid consisting of amylin constitutes one of pathological hallmarks of type 2 diabetes mellitus (T2DM), and it may be involved in the development and progression of T2DM. However, the details about the relationship between the deposition of islet amyloid and the pathology of T2DM remain unclear, since no useful imaging tracer enabling the visualization of pancreatic amylin is available. In the present study, we synthesized and evaluated six novel <sup>18</sup>F-labeled phenoxymethylpyridine (PMP) derivatives as amylin imaging probes. All <sup>18</sup>F-labeled PMP derivatives showed not only affinity for islet amyloid in the post-mortem T2DM pancreatic sections but also excellent pharmacokinetics in normal mice. Furthermore, ex vivo autoradiographic studies demonstrated that [<sup>18</sup>F]FPMP-5 showed intense labeling of islet amyloids in the diabetes model mouse pancreas in vivo. The preclinical studies suggested that [<sup>18</sup>F]FPMP-5 may have potential as an imaging probe that targets amylin aggregates in the T2DM pancreas.
Blocking Notch3 Signaling Abolishes MUC5AC Production in Airway Epithelial Cells from Individuals with Asthma (2020)

In asthma, goblet cell numbers are increased within the airway epithelium, perpetuating the production of mucus that is more difficult to clear and results in airway mucus plugging. Notch1, Notch2, or Notch3, or a combination of these has been shown to influence the differentiation of airway epithelial cells. How the expression of specific Notch isoforms differs in fully differentiated adult asthmatic epithelium and whether Notch influences mucin production after differentiation is currently unknown. We aimed to quantify different Notch isoforms in the airway epithelium of individuals with severe asthma and to examine the impact of Notch signaling on mucin MUC5AC. Human lung sections and primary bronchial epithelial cells from individuals with and without asthma were used in this study. Primary bronchial epithelial cells were differentiated at the air-liquid interface for 28 days. Notch isoform expression was analyzed by Taqman quantitative PCR. Immunohistochemistry was used to localize and quantify Notch isoforms in human airway sections. Notch signaling was inhibited <i>in vitro</i> using dibenzazepine or Notch3-specific siRNA, followed by analysis of MUC5AC. NOTCH3 was highly expressed in asthmatic airway epithelium compared with nonasthmatic epithelium. Dibenzazepine significantly reduced MUC5AC production in air-liquid interface cultures of primary bronchial epithelial cells concomitantly with suppression of NOTCH3 intracellular domain protein. Specific knockdown using <i>NOTCH3</i> siRNA recapitulated the dibenzazepine-induced reduction in MUC5AC. We demonstrate that NOTCH3 is a regulator of MUC5AC production. Increased NOTCH3 signaling in the asthmatic airway epithelium may therefore be an underlying driver of excess MUC5AC production.
Theoretical and experimental studies of water interaction in acetate based ionic liquids (2012)

Water interactions in 1-ethyl-3-methylimidazolium acetate ([emim][CH(3)COO]) were studied utilizing classical and ab initio simulation methods. The self-diffusivities for water and the ionic liquid (IL) were studied experimentally using pulse field gradient NMR spectroscopy and correlated with computational results. Water forms hydrogen bonding networks with the ionic liquid, and depending on the concentration of water, there are profound effects on the self-diffusivities of the various species. Both simulation and experiments show that the self-diffusivities for species in the water-[emim][CH(3)COO] system exhibit minima at 40-50 mol% water. Water interaction with the [CH(3)COO](-) anion predominates over the water-water and water-cation interactions at most water concentrations. Simulations further indicate that decreasing water-[CH(3)COO](-) interaction will increase the IL and water self-diffusivities. Self-diffusivities in the water-IL systems are dependent upon the cation in a complex way. Water interactions with [P(4444)][CH(3)COO] are reduced compared to [emim][CH(3)COO]. The [P(4444)](+) cation is bulkier than the [emim](+) cation and has a smaller self-diffusivity, but when water was introduced to [P(4444)] [CH(3)COO], the water-[CH(3)COO](-) hydrogen bonding network in the [P(4444)][CH(3)COO] was much smaller than the one observed in [emim][CH(3)COO].
Management traumatischer Pankreasverletzungen: Unterschiedliche Manifestationen – interdisziplinäre Therapie (2017)

Traumatische Pankreasverletzung sind insgesamt selten, variieren jedoch stark in ihrer klinischen Manifestation und Therapienotwendigkeit. Das Therapiespektrum reicht von der konservativer Therapie, über radiologisch, bzw. endoskopisch interventionelle Verfahren bis hin zu komplexen chirurgischen Eingriffen. Einheitliche Therapieempfehlung gibt es nicht, was die individuelle Therapieentscheidungen erschwert.
Broadbanding of a Microstrip Antenna Using a Stub Excitation Under the Patch (2018)

A microstrip antenna using a stub excitation under the patch is investigated to obtain broadband characteristics. A stub with a line composed of three kinds of characteristic impedance is employed for broadbanding. We design a broadband microstrip antenna using the stub and evaluate bandwidth - efficiency product (Bη) of a prototype antenna compared with the theoretical limitation.
Aeration effect on the efficiency of swine manure treatment in a trickling filter packed with organic materials (2007)

Effect of aeration rate on the removal of organic matter and nitrogen and on the formation of NH3, N2O and N2 was studied for an extensive biofiltration system packed with an organic media, which was used to treat pig manure. The results show high removal of BOD5 and TSS (99 and > or = 98%), independently of the four aeration rate tested (3.4-34 m3/m2 x h). Aeration rate > or = 4.4 m/h resulted in high ammonia stripping during start-up (> or = 1.0 kg NH3-N/m3 of swine manure treated), while using 3.4 m/h only 0.3 kg NH3-N/m3 were stripped. Complete nitrification was achieved after day 100 of operation, except in the biofilter with the lowest aeration rate. Simultaneous denitrification established in all the biofilters. Applying an aeration rate of 9.4 m/h up to 1.2 kg nitrogen was removed in the form of N2 for each m3 of swine manure treated. Contrary to the expectations, N2 formation and release increased with the aeration rate. This particular behaviour seems to be related to the punctual accumulation of water layers inside the biofilters, caused by the air force flowing in the opposite direction to the water flux. N2O production was quite similar in all biofilters (between 0.25-0.36 kg N2O-N/m3 of swine manure treated).
Flexible framework for commodity FPGA cluster computing (2009)

With falling costs and successful demonstrations of performance, FPGAs have become a prime candidate for use in high performance computing. However, the use of FPGA technology in clustered environments has largely been limited to commercial and/or proprietary designs that require developers to learn new programming models and software tools. In this paper, a framework is presented which enables development of parallel programs across application-specific reconfigurable hardware using simple hardware interface abstractions and standard MPI application structure. This approach leverages commodity technologies including embedded Linux running on hardwired PowerPC processors to manage communication such that each hardware acceleration unit can function as a fully MPI-2 compatible node. The implied hardware/software design and programming model are discussed and an application case study is presented to demonstrate functionality and elucidate platform benefits through performance analysis.
Cutting Edge: IL-23 Receptor Deficiency Prevents the Development of Lupus Nephritis in C57BL/6– lpr/lpr Mice (2010)

IL-17-producing T cells infiltrate kidneys of patients with lupus nephritis, and IL-23-treated lymph node cells from lupus-prone mice may transfer disease to Rag1-deficient mice. In this study, we show that IL-23R-deficient lupus-prone C57BL/6-lpr/lpr mice display decreased numbers of CD3(+)CD4(-)CD8(-) cells and IL-17A-producing cells in the lymph nodes and produce less anti-DNA Abs. In addition, clinical and pathology measures of lupus nephritis are abrogated. The presented experiments document the importance of IL-23R-mediated signaling in the development of lupus nephritis and urge the consideration of proper biologics for the treatment of the disease.