gebhart/patrepeval huggingface dataset:
Mouse Hippocampal Organotypic Tissue Cultures Exposed to <i>In Vitro</i> “Ischemia” Show Selective and Delayed CA1 Damage that is Aggravated by Glucose (2003)

Oxygen and glucose deprivation (OGD) in cell cultures is generally studied in a medium, such as artificial cerebrospinal fluid (CSF), with an ion composition similar to that of the extracellular fluid of the normal brain (2 to 4 mmol/L K+, 2 to 3 mmol/L Ca2+; pH 7.4). Because the distribution of ions across cell membranes dramatically shifts during ischemia, the authors exposed mouse organotypic hippocampal tissue cultures to OGD in a medium, an ischemic cerebrospinal fluid, with an ion composition similar to the extracellular fluid of the brain during ischemia (70 mmol/L K+, 0.3 mmol/L Ca2+; pH 6.8). In ischemic CSF, OGD induced a selective and delayed cell death in the CA1 region, as assessed by propidium iodide uptake. Cell death was glutamate receptor dependent since blockade of the N-methyl-D-aspartate and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors mitigated cell damage. Hyperglycemia aggravates ischemic brain damage whereas glucose in artificial CSF prevents oxygen deprivation-induced damage. The authors demonstrate that glucose in ischemic CSF significantly exacerbates cell damage after oxygen deprivation. This new model of "ischemia" can be useful in future studies of the mechanisms and treatment of ischemic cell death, including studies using genetically modified mice.
Exploration of the Amine Terminus in a Novel Series of 1,2,4-Triazolo-3-yl-azabicyclo[3.1.0]hexanes as Selective Dopamine D<sub>3</sub>Receptor Antagonists (2010)

A novel series of 1,2,4-triazol-3-yl-azabicyclo[3.1.0]hexanes with high affinity and selectivity for the DA D(3) receptor and excellent pharmacokinetic profiles was recently reported. We also recently discussed the role of the linker associated with the triazole moiety. In this manuscript, we are reporting a detailed exploration of the region of the receptor interacting with the amine terminus of the scaffold wherein SAR and developability data associated with these novel templates was undertaken.
Health benefits of Il-10 egg yolk antibodies administered to milk-fed dairy calves (2015)

Cryptosporidium parvum infection in calves causes villous atrophy, resulting in reduced surface area and absorptive capacity of the small intestine. Prevention and treatment of C. parvum infections are hindered by a lack of approved, efficacious products and inadequate colostral immunity. An integral component of infection is the dampening of the cell-mediated response by inducing anti-inflammatory cytokines. In calves, ileal intraepithelial lymphocytes express interleukin-10 (Il-10) when infected with C. parvum. Interleukin-10 decreases production of interferon-gamma, which is a vital Thl-associated cytokine. Studies have shown that Il-10 knockout mice are resistant to C. parvum infection. Oral administration of chicken egg yolk antibodies as a means of controlling enteric disease in calves is of interest to the dairy industry. Egg yolk Il-10 antibodies have been shown to survive gastrointestinal transit, are accessible in the intestinal lumen, and remain locally active, without persistence of systemic residues. Therefore, the objective of this trial was to investigate the effect of feeding Il-10 antibodies on calf health and performance after natural C. parvum infection in pre-weaned Holstein dairy calves.
Preparation of 2-aminomuconate from 2-aminophenol by coupled enzymatic dioxygenation and dehydrogenation reactions (1999)

2-Aminomuconate is an intermediate in the oxidative metabolism of tryptophan in mammals. The compound is not commercially available, and studies of its metabolism have been prevented by the lack of a chemical synthesis and the instability of the molecule. We report here the formation of 2-aminomuconate from 2-aminophenol by the coupled action of 2-aminophenol 1,6-dioxygenase and 2-aminomuconic semialdehyde dehydrogenase from Pseudomonas pseudoalcaligenes JS45, and isolation of the product by anion exchange chromatography. The overall procedure was completed within 3 h with a yield of 62%. The availability of the dicarboxyl alpha-amino acid provides the basis for investigation of the physiological function of 2-aminomuconate in the neuropathologically significant oxidative metabolism of tryptophan.
Site-specific cleavage of DNA at 8- and 10-base-pair sequences. (1984)

A method is described for cutting DNA at specific sites that are 8 and 10 base pairs long. The DNA is first treated with a specific methylase, either the restriction-modification enzyme M. Taq I, which converts the 4-base sequence T-C-G-A to T-C-G-mA, or the similar enzyme M. Cla I, which converts the 6-base sequence A-T-C-G-A-T to A-T-C-G-mA-T. The DNA is then cleaved with Dpn I, a restriction endonuclease that recognizes the sequence G-mA-T-C. Dpn I is unique in that it cuts only DNA that is methylated at adenine in both strands of its recognition sequence. In DNAs that are not otherwise methylated at adenine in both strands of the sequence G-A-T-C, cleavage by Dpn I occurs only at the following sequences: in the case of M. Taq I methylation, 5' T-C-G-mA - T-C-G-mA 3' 3' mA-G-C - T-mA-G-C - T 5'; in the case of M. Cla I methylation, 5' A - T-C-G-mA - T-C-G-mA-T 3' 3' T-mA-G-C - T-mA-G-C - T-A 5'. Specific cutting and cloning at these methylase/Dpn I-generated sites is shown experimentally. Further, we describe how the above technique can be extended to generate Dpn I cleavage sites of up to 12 base pairs. In DNA that contains equal amounts of each base distributed at random, 8- and 10-base-pair recognition sequences occur, on the average, approximately once every 65,000 and 1,000,000 base pairs, respectively. Potential applications, including the development of cloning vectors and a rapid method for chromosome walking, are discussed.
Breast cancer cell line proliferation blocked by the Src‐related Rak tyrosine kinase (2003)

Rak is a 54 kDa protein tyrosine kinase originally isolated from breast cancer cells and expressed in epithelial cells. It resembles the protooncogene Src structurally but lacks an amino-terminal myristylation site and localizes to the nuclear and perinuclear regions of the cell. We report here that expression of Rak in 2 different breast cancer cell lines inhibits growth and causes G(1) arrest of the cell cycle. This growth inhibition is kinase-dependent but does not require the Rak SH2 or SH3 domain. Rak also binds to the pRb tumor-suppressor protein but inhibits growth even in cells that lack pRb. These results suggest that Rak regulates cell growth by phosphorylating perinuclear proteins and has a function that is distinct from the Src-related kinase family.
Generic Efficient Dynamic Proofs of Retrievability. (2015)

Together with its great advantages, cloud storage brought many interesting security issues to our attention. Since 2007, with the first efficient storage integrity protocols Proofs of Retrievability (PoR) of Juels and Kaliski, and Provable Data Possession (PDP) of Ateniese et al., many researchers worked on such protocols. The first proposals worked for static or limited dynamic data, whereas later proposals enabled fully dynamic data integrity and retrievability. Since the beginning, the difference between PDP and PoR models were greatly debated. Most notably, it was thought that dynamic PoR (DPoR) was harder than dynamic PDP (DPDP). Historically this was true: The first DPDP scheme was shown by Erway et al. in 2009, whereas the first DPoR scheme was created by Cash et al. in 2013. We show how to obtain DPoR from DPDP and PDP, together with erasure codes, making us realize that even though we did not know it, in 2009 we already could have had a DPoR solution. We propose a general framework for constructing DPoR schemes. Our framework encapsulates all known DPoR schemes as its special cases. We further show practical and interesting optimizations that enable even better performance than Chandran et al. and Shi et al. constructions. For the first time, we show how to obtain audit bandwidth for DPoR that is independent of the data size, and how the client can greatly speed up updates with O(λ n) local storage (where n is the number of blocks, and λ is the security parameter), which corresponds to less than 3 MB for 10 GB outsourced data, and can easily be obtained in today’s smart phones, let alone computers.
Controlling Crystal Polymorphism in Organic-Free Synthesis of Na-Zeolites (2012)

Controlling polymorphism is critical in areas such as pharmaceuticals, biomineralization, and catalysis. Notably, the formation of unwanted polymorphs is a ubiquitous problem in zeolite synthesis. In this study, we propose a new platform for controlling polymorphism in organic-free Na-zeolite synthesis that enables crystal composition and properties to be tailored without sacrificing crystal phase purity. Through systematic adjustment of multiple synthesis parameters, we identified ternary (kinetic) phase diagrams at specific compositions (i.e., Si, Al, and NaOH mole fractions) using colloidal silica and sodium aluminate. Our studies identify multiple stages of zeolite phase transformations involving the framework types FAU, LTA, EMT, GIS, SOD, ANA, CAN, and JBW. We report an initial amorphous-to-crystalline transition of core-shell particles (silica core and alumina shell) to low-density framework types and their subsequent transformation to more dense structures with increasing temperature and/or time. We show that reduced water content facilitates the formation of structures such as EMT that are challenging to synthesize in organic-free media and reduces the synthesis temperature required to achieve higher-density framework types. A hypothesis is proposed for the sequence of phase transformations that is consistent with the Ostwald rule of stages, wherein metastable structures dissolve and recrystallize into more thermodynamically stable structures. The ternary diagrams developed here are a broadly applicable platform for rational design that offers an alternative to time- and cost-intensive methods of ad hoc parameter selection without a priori knowledge of crystal phase behavior.
Parameter Analysis for the Generalized LZ Compression of Audio (2005)

Summary form only given. We introduced (Kirovski and Landau (2004)) a memory-based model of the source signal, which explores multimedia repetitiveness to improve upon compression rates achieved by classic memoryless or simple prediction-based audio compression algorithms such as MP3. The representation error is masked using a psycho-acoustic filter. The goal of the masking function is to set the error such that reconstruction of audible samples is exact whereas the reconstruction of inaudible samples is such that the absolute magnitude of the error is minimized. We compute the entropy of the quantized pointers to all blocks, the quantized pointers to the applied transforms, the quantized scalars used to create the linear combination of transformed blocks, and the error vector returned.
Some Complexes of Cobalt(III) and Iron(III) Are Radiosensitizers of Hypoxic EMT6 Cells (1987)

The radiosensitizing potential in hypoxic EMT6 cells of several complexes of Co(III) and Fe(III) has been examined. The cytotoxicity of each of the agents toward oxygenated and hypoxic EMT6 cells was tested over the concentration range of 1 to 500 micron for 1-h drug exposure. There was no statistically significant difference between the cytotoxicity of these complexes toward oxygenated and hypoxic cells. Based on these findings, 100 micron was selected as the drug concentration for the initial assessment of radiosensitizing potential. The radiation survival of EMT6 cells in the presence of 100 microM drug for a series of Co(III) complexes in which the number of nitro ligands was varied showed that the hexanitro and the triamine-trinitro complexes are very effective radiosensitizers. The trans-tetrammine dinitro complex was a more effective radiosensitizer than the corresponding cis-dinitro complex. The diethylenetriamine and 1,10-phenanthroline complexes were very effective radiosensitizers, producing dose-modifying factors of 2.4. The trans-tetrammine dichloro complex was moderately effective, giving a dose-modifying factor of 1.9. On the other hand, the hexammine and triammine tricyano complexes and the trans-dinitro complex with negatively charged acetylacetonate ligands were ineffective as radiosensitizers in this system. Finally, three complexes with cyclopentadienyl ligands were examined. The ferricenium salt itself was a moderately effective radiosensitizer, giving a dose-modifying factor of 2.0. However, both the dimethylferricenium salt and the analogous cobalt complex were ineffective. The FSaIIC fibrosarcoma was used to study radiosensitizing potential in vivo. The trans-tetramminedinitro complex was administered at doses of 100, 200, or 300 mg/kg as a single ip injection 1 h prior to irradiation or as three daily ip injections. There was increasing dose modification with increasing drug dosage. With a fractionated radiation protocol in which five daily fractions of 2, 3, or 4 Gy were administered to the tumor-bearing limb with ip drug injections of 100 or 200 mg/kg given 1 h prior to irradiation, a dose-modifying effect of 1.6 was observed with 5 X 200 mg/kg of the drug.
Photoreactive Carboxybetaine Copolymers Impart Biocompatibility and Inhibit Plasticizer Leaching on Polyvinyl Chloride (2020)

Protein and cell interactions on implanted, blood-contacting medical device surfaces can lead to adverse biological reactions. Medical-grade poly(vinyl chloride) (PVC) materials have been used for decades, particularly as blood-contacting tubes and containers. However, there are numerous concerns with their performance including platelet activation, complement activation, and thrombin generation and also leaching of plasticizers, particularly in clinical applications. Here, we report a surface modification method that can dramatically prevent blood protein adsorption, human platelet activation, and complement activation on commercial medical-grade PVC materials under various test conditions. The surface modification can be accomplished through simple dip-coating followed by light illumination utilizing biocompatible polymers comprising zwitterionic carboxybetaine (CB) moieties and photosensitive cross-linking moieties. This surface treatment can be manufactured routinely at small or large scales and can impart to commercial PVC materials superhydrophilicity and nonfouling capability. Furthermore, the polymer effectively prevented leaching of plasticizers out from commercial medical-grade PVC materials. This coating technique is readily applicable to many other polymers and medical devices requiring surfaces that will enhance performance in clinical settings.
Stereo 3D Crop Maps from Aerial Images (2003)

Geographical Information Systems are moving from 2D to 3D. A three dimensionalrepresentation of a field scene can be employed for crop perception and monitoring as well as forautonomous operations inside the field. A compact stereo camera was mounted in both a groundvehicle and an unmanned helicopter to acquire stereo images of a cornfield. Individual images werefused in a global map by transforming local coordinates from the image into global coordinates.Position and orientation for every single image were recorded by a GPS receiver and an inertialsensor respectively. A stereo 3D crop map was generated from aerial images captured from ahelicopter. This map showed that three-dimensional maps can be created from the data gatheredwith a stereoscopic camera, an inertial sensor, and a GPS receiver.
Quantitative viral load monitoring and cidofovir therapy for the management of BK virus-associated nephropathy in children and adults1 (2003)

Quantitative PCR for BKV is a sensitive and reliable method for following the course of the infection in renal transplant patients. In addition, cidofovir therapy may be useful in the treatment of some of these patients, and its role needs to be investigated further.
Protein Identification by Spectral Networks Analysis (2010)

While advances in tandem mass spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra, standard algorithmic approaches for peptide identification recently seemed to be reaching the limit on the amount of information that could be extracted from MS/MS spectra. However, a closer look reveals that a common limiting procedure is to analyze each spectrum in isolation, even though high throughput mass spectrometry regularly generates many spectra from related peptides. By capitalizing on this redundancy we show that, similarly to the alignment of protein sequences, unidentified MS/MS spectra can also be aligned for the identification of modified and unmodified variants of the same peptide. Moreover, this alignment procedure can be iterated for the accurate grouping of multiple modification variants of the same peptides. Furthermore, the combination of shotgun proteomics with the alignment of spectra from overlapping peptides led to the development of Shotgun Protein Sequencing - similarly to the assembly of DNA reads into whole genomic sequences, we show that assembly of MS/MS spectra enables the highest ever de novo sequencing accuracy, while recovering nearly complete protein sequences. We further show that shotgun protein sequencing has the potential to overcome the limitations of -current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins.
The prevalence of bovine viral diarrhea virus infection in a population of feedlot calves in western Canada. (1995)

The prevalence of bovine viral diarrhea virus (BVDV) infection was examined in a population of 5129 recently weaned steer calves entering a large feedlot in central Saskatchewan from September to December 1991. Serum samples were collected within 24 h of arrival at the feedlot from every fifth calf processed and again 96 d postarrival. A microtiter virus isolation test was used to determine the prevalence of calves viremic with BVDV on entry to the feedlot. An enzyme-linked immunosorbent assay (ELISA) which detects antibody against glycoprotein 53 of the BVDV was used on paired sera to determine the seroconversion risk during the first 96 d in the feedlot. A virus neutralization (VN) test for BVDV was conducted on a sub-sample of paired sera to measure agreement in determination of seroconversion risk with the ELISA. A polymerase chain reaction (PCR) test which detects BVDV was used to determine if cattle were acutely viremic when treated for disease. The estimated prevalence of persistently infected calves in this population was < 0.1%. The seroconversion risk for BVDV was 27% (236/864) according to the ELISA and it varied from 0 to 63% among the 20 pens sampled. According to the VN test, the seroconversion risk for BVDV was 40% (132/327) and it varied from 0 to 100% among the 11 pens tested. The agreement between the ELISA and VN tests in seroconversion risk to BVDV was very poor (kappa = 0.15 +/- 0.039 SE). The prevalence of acute viremia in calves treated at the feedlot hospital was low at 4% (6/149).(ABSTRACT TRUNCATED AT 250 WORDS)
Mitigating the Risk of Cloud Services Downtime Using Live Migration and High Availability-Aware Placement (2016)

The growing dependency of users on social media, telecommunication services, mobile applications, banking amenities, and other cloud services requires a plan that mitigates inevitable failures and ensures the always-on access to these services. This emanates high availability (HA) concerns regarding the adoption of cloud. To maintain HA, the cloud provider and/or user should design a system that is immune to both application and infrastructure failures. This paper proposes live migration approach to maintain service delivery upon a sudden failure, a virtual machine (VM)/infrastructure overload, or maintenance. It develops a mixed integer linear programming model that minimizes the migration downtime based on the VM memory pages and the optimal HA-aware placement of the VM. It also provides different design considerations to achieve HA-aware applications placement. The proposed placement is used in the migration approach to find new hosts for the VMs. It considers VMs/applications deployments in geographically distributed data centers and satisfies redundancy, applications interdependency, and other HA and performance requirements. Then the deployments are assessed using a formal Petri Net model to improve them in terms of HA. The HA-aware placement and migration approaches are evaluated on 3-tier Web applications.
Low-impedance cable for parallel-connected surge protective devices (1995)

A coaxial low-impedance cable is described for power system surge protective device (SPD) wiring applications, The cable is designed to replace conventional wiring when parallel connecting any SPD which depends on the applied transient voltage to function. The cable is designed to minimize the transmission loss (voltage drop) of lightning and switching transients from the point of protection to the SPD components. This is accomplished primarily by minimizing the cable inductance through a reduced coaxial aspect ratio (major to minor diameter). The resultant cable has a very low characteristic impedance (2-15 /spl Omega/). The suppression performance of an SPD installed with 10 AWG coaxial cables provides an improvement of a factor of 2-4 over that using conventional wiring. The cable design details are discussed along with surge suppression performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>