gebhart/patrepeval huggingface dataset:
Structure of Bcl-x L -Bak Peptide Complex: Recognition Between Regulators of Apoptosis (1997)

Heterodimerization between members of the Bcl-2 family of proteins is a key event in the regulation of programmed cell death. The molecular basis for heterodimer formation was investigated by determination of the solution structure of a complex between the survival protein Bcl-xL and the death-promoting region of the Bcl-2-related protein Bak. The structure and binding affinities of mutant Bak peptides indicate that the Bak peptide adopts an amphipathic alpha helix that interacts with Bcl-xL through hydrophobic and electrostatic interactions. Mutations in full-length Bak that disrupt either type of interaction inhibit the ability of Bak to heterodimerize with Bcl-xL.
Cholesteryl Ester Transfer Protein (2003)

Cholesteryl ester transfer protein (CETP) promotes the transfer of cholesteryl esters from antiatherogenic HDLs to proatherogenic apolipoprotein B (apoB)-containing lipoproteins, including VLDLs, VLDL remnants, IDLs, and LDLs. A deficiency of CETP is associated with increased HDL levels and decreased LDL levels, a profile that is typically antiatherogenic. Studies in rabbits, a species with naturally high levels of CETP, support the therapeutic potential of CETP inhibition as an approach to retarding atherogenesis. Studies in mice, a species that lacks CETP activity, have provided mixed results. Human subjects with heterozygous CETP deficiency and an HDL cholesterol level >60 mg/dL have a reduced risk of coronary heart disease. Evidence that atherosclerosis may be increased in CETP-deficient subjects whose HDL levels are not increased is difficult to interpret and may reflect confounding or bias. Small-molecule inhibitors of CETP have now been tested in human subjects and shown to increase the concentration of HDL cholesterol while decreasing that of LDL cholesterol and apoB. Thus, it seems important and timely to test the hypothesis in randomized trials of humans that pharmacological inhibition of CETP retards the development of atherosclerosis.
Ceruloplasmin gene variations and substantia nigra hyperechogenicity in Parkinson disease (2004)

Detection of sequence variations in a single Parkinson disease (PD) patient or associated with the ultrasound marker for increased substantia nigra iron levels and the presence of ceruloplasmin (Cp) immunoreactivity in Lewy bodies underline a suspected role for Cp in the pathogenesis of PD. Further functional analyses are warranted to investigate whether these variations are causally linked to the complex pathogenesis of PD in a subset of cases.
Model based concordance compression (2003)

The authors discuss concordance compression using the framework now customary in compression theory. They begin by creating a mathematical model of concordance generation, and then use optimal compression engines, such as Huffman or arithmetic coding, to do the actual compression. It should be noted that in the context of a static information retrieval system, compression and decompression are not symmetrical tasks. Compression is done only once, while building the system, whereas decompression is needed during the processing of every query and directly affects the response time. One may thus use extensive and costly preprocessing for compression, provided reasonably fast decompression methods are possible. Moreover, compression is applied to the full files (text, concordance, etc.), but decompression is needed only for (possibly many) short pieces, which may be accessed at random by means of pointers to their exact locations. Therefore the use of adaptive methods based on tables that systematically change from the beginning to the end of the file is ruled out. However, their concern is less the speed of encoding or decoding than relating concordance compression conceptually to the modern approach of data compression, and testing the effectiveness of their models.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9 (2014)

The CRISPR/Cas9 system has ushered in a new era of targeted genetic manipulations. Here, we report the use of CRISPR/Cas9 to induce double-stranded breaks in the genome of the sea squirt Ciona intestinalis. We use electroporation to deliver CRISPR/Cas9 components for tissue-specific disruption of the Ebf (Collier/Olf/EBF) gene in hundreds of synchronized Ciona embryos. Phenotyping of transfected embryos in the 'F0' generation revealed that endogenous Ebf function is required for specification of Islet-expressing motor ganglion neurons and atrial siphon muscles. We demonstrate that CRISPR/Cas9 is sufficiently effective and specific to generate large numbers of embryos carrying mutations in a targeted gene of interest, which should allow for rapid screening of gene function in Ciona.
Optimal Eavesdropping in Quantum Cryptography with Six States (1998)

A generalization of the quantum cryptographic protocol by Bennett and Brassard is discussed, using three conjugate bases, i.e., six states. By calculating the optimal mutual information between sender and eavesdropper it is shown that this scheme is safer against eavesdropping on single qubits than the one based on two conjugate bases. We also address the question for a connection between the maximal classical correlation in a generalized Bell inequality and the intersection of mutual informations between sender/receiver and sender/eavesdropper.
Study on Undulating Well in Anisotropic Reservoir by Semi-Analytical Method (2013)

Abstract To maximize the production rate and develop marginal/unconventional fields, all kinds of intelligent wells have been proposed and practiced in field, including multi-stage fractured horizontal well, multi-lateral or fishbone completions. Undulating horizontal well, also called snaky well, is one of the most common intelligent completions nowadays. This paper presents a semi-analytical model for undulating horizontal well, which predicts not only the inflow from reservoir and pressure drop inside the wellbore, but also takes into account the interference among well segments. As the undulation index and cycles increase, the undulating completion can result in a good effective vertical permeability and inflow. Although the advantage is marked, the related technical challenges and high cost are increased correspondently. Thus, an optimization of the undulation index and cycle is required to maximize the project Net-Present-Value (NPV). Along with appropriate economic analysis, the proposed semi-analytical model can suggest and evaluate the field development in a time manner. Further, the undulating well can be a substitute for multi-stage fractured horizontal well, especially for dual porosity shale gas/oil fields.
Array-Based ELISAs for High-Throughput Analysis of Human Cytokines (2001)

In this report, we describe the development of a mini-array system suitable for high-throughput quantification of proteins. This mini-array is a multiplexed, sandwich-type ELISA that measures the concentration of seven different human cytokines--TNF-alpha, IFN alpha, IFN gamma, IL-1 alpha, IL-1 beta, IL-6, and IL-10--from a single sample in each well of a 96-well plate. The mini-array is produced by spotting monoclonal antibodies (mAbs) in a 3 x 3 pattern in the bottom of the wells of 96-well polystyrene plates. Cytokines that are captured by the arrayed mAbs are detected by using biotinylated mAbs, followed by the addition of a streptavidin-horseradish peroxidase (HRP) conjugate and a chemiluminescent substrate. The light produced from the HRP-catalyzed oxidation of the substrate is measured at each spot in the array by imaging the entire plate with a commercially available CCD camera. Here, we demonstrate that these 96-well-plate format mini-arrays have performance characteristics that make them suitable for the high-throughput screening of anti-inflammatory compounds.
A Macrophage-Dominant PI3K Isoform Controls Hypoxia-Induced HIF1α and HIF2α Stability and Tumor Growth, Angiogenesis, and Metastasis (2014)

This study indicates that PI3K inhibitors are excellent candidates for the treatment of cancers where macrophages promote tumor progression.
Statistical analysis of the performance of PMD compensators using multiple importance sampling (2003)

In this letter, we evaluate the performance of fixed and variable differential group delay (DGD) polarization-mode dispersion (PMD) compensators as the first- and second-order PMD varies using multiple importance sampling. We show that importance sampling yields estimates of the average penalty with low variance over the entire region of interest of first- and second-order PMD. We also show that there is little advantage in using a compensator with a variable-DGD element and that the performance of a compensator that minimizes the residual DGD at the central frequency of the channel is considerably worse than a compensator that maximizes the eye opening.
Educación Legal en el Perú: ¿Estamos listos para la Globalización? (2013)

Examina la educación legal tradicional y moderna, el nuevo rol que el abogado debe asumir en esta nueva era globalizada y tecnológica y el impacto que este cambio ha tenido en la enseñanza del Derecho en el Perú.
Epitope Specificity of Anti-HIV Antibodies in Human and Murine Autoimmune Diseases (1996)

This article reports the HIV epitope specificity of antibodies present in the sera of HIV-negative patients with autoimmune diseases. Recombinant gp120 and a panel of synthetic peptides derived from the amino acid consensus sequences of either related (gp120, gp41, and p24) or unrelated (Mage-1, necdin, heat shock protein [65 kDa], and amyloid) HIV proteins were tested by a specific ELISA. The first set of experiments performed on four patients with Sjögren's syndrome (SjS) and four patients with systemic lupus erythematosus (SLE) revealed a significant anti-gp120 antibody reactivity in autoimmune patients when compared to healthy HIV-negative controls. Moreover, such binding could be almost completely inhibited by preincubation with free gp120. A significant anti-p24 reactivity was observed in 18 of 29 sera from SjS patients and in 13 of 25 sera from SLE patients, while anti-gp41 was observed only in 3 of 14 SjS and in 2 of 20 SLE-affected patients. Similar analyses were performed in the murine model of autoimmunity, showing that sera from MRL/lpr mice were able to bind all HIV-related peptides in an age-dependent manner. The analysis of a panel of HIV-unrelated peptides showed that SLE as well as MRL/lpr sera bind both HIV-related and unrelated peptides, while SjS sera failed to do so, revealing the polyclonal nature of the SLE and MRL/lpr repertoire and the oligoclonal reactivity of SjS sera. This is also supported by inhibition experiments, which showed that SLE, but not SjS, sera competitively inhibited the binding to HIV gp120 peptide of sera from autoimmune MRL/lpr mice. These results indicate that an overlapping polyclonal repertoire is present in both SLE and MRL/lpr sera, while the oligoclonal specificity of SjS antibodies may be related to a specific, nonpolyclonal, activation against putative retroviral antigens.
HIV-1 drug discovery: targeting folded RNA structures with branched peptides (2015)

Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
Microarrays Reveal that Each of the Ten Dominant Lineages ofStaphylococcus aureusHas a Unique Combination of Surface-Associated and Regulatory Genes (2005)

Staphylococcus aureus is the most common cause of hospital-acquired infection. In healthy hosts outside of the health care setting, S. aureus is a frequent colonizer of the human nose but rarely causes severe invasive infection such as bacteremia, endocarditis, or osteomyelitis. To identify genes associated with community-acquired invasive isolates, regions of genomic variability, and the S. aureus population structure, we compared 61 community-acquired invasive isolates of S. aureus and 100 nasal carriage isolates from healthy donors using a microarray spotted with PCR products representing every gene from the seven S. aureus sequencing projects. The core genes common to all strains were identified, and 10 dominant lineages of S. aureus were clearly discriminated. Each lineage carried a unique combination of hundreds of "core variable" (CV) genes scattered throughout the chromosome, suggesting a common ancestor but early evolutionary divergence. Many CV genes are regulators of virulence genes or known or predicted to be expressed on the bacterial surface and to interact with the host during nasal colonization and infection. Within each lineage, isolates showed substantial variation in the carriage of mobile genetic elements and their associated virulence and resistance genes, indicating frequent horizontal transfer. However, we were unable to identify any association between lineage or gene and invasive isolates. We suggest that the S. aureus gene combinations necessary for invasive disease may also be necessary for nasal colonization and that community-acquired invasive disease is strongly dependent on host factors.
Polyamines Are Essential for the Formation of Plague Biofilm (2006)

ABSTRACT We provide the first evidence for a link between polyamines and biofilm levels in Yersinia pestis , the causative agent of plague. Polyamine-deficient mutants of Y. pestis were generated with a single deletion in speA or speC and a double deletion mutant. The genes speA and speC code for the biosynthetic enzymes arginine decarboxylase and ornithine decarboxylase, respectively. The level of the polyamine putrescine compared to the parental speA + speC + strain (KIM6+) was depleted progressively, with the highest levels found in the Y. pestis Δ speC mutant (55% reduction), followed by the Δ speA mutant (95% reduction) and the Δ speA Δ speC mutant (&gt;99% reduction). Spermidine, on the other hand, remained constant in the single mutants but was undetected in the double mutant. The growth rates of mutants with single deletions were not altered, while the Δ speA Δ speC mutant grew at 65% of the exponential growth rate of the speA + speC + strain. Biofilm levels were assayed by three independent measures: Congo red binding, crystal violet staining, and confocal laser scanning microscopy. The level of biofilm correlated to the level of putrescine as measured by high-performance liquid chromatography-mass spectrometry and as observed in a chemical complementation curve. Complementation of the Δ speA Δ speC mutant with speA showed nearly full recovery of biofilm to levels observed in the speA + speC + strain. Chemical complementation of the double mutant and recovery of the biofilm defect were only observed with the polyamine putrescine.
Structural Studies of LNA:RNA Duplexes by NMR: Conformations and Implications for RNase H Activity (2000)

We have used NMR and CD spectroscopy to study the conformations of modified oligonucleotides (locked nucleic acid, LNA) containing a conformationally restricted nucleotide (T(L)) with a 2'-O,4'-C-methylene bridge. We have investigated two LNA:RNA duplexes, d(CTGAT(L)ATGC):r(GCAUAUCAG) and d(CT(L)GAT(L)AT(L)GC):r(GCAUAUCAG), along with the unmodified DNA:RNA reference duplex. Increases in the melting temperatures of +9.6 degrees C and +8.1 degrees C per modification relative to the unmodified duplex were observed for these two LNA:RNA sequences. The three duplexes all adopt right-handed helix conformations and form normal Watson-Crick base pairs with all the bases in the anti conformation. Sugar conformations were determined from measurements of scalar coupling constants in the sugar rings and distance information derived from 1H-1H NOE measurements; all the sugars in the RNA strands of the three duplexes adopt an N-type conformation (A-type structure), whereas the sugars in the DNA strands change from an equilibrium between S- and N-type conformations in the unmodified duplex towards more of the N-type conformation when modified nucleotides are introduced. The presence of three modified T(L) nucleotides induces drastic conformational shifts of the remaining unmodified nucleotides of the DNA strand, changing all the sugar conformations except those of the terminal sugars to the N type. The CD spectra of the three duplexes confirm the structural changes described above. On the basis of the results reported herein, we suggest that the observed conformational changes can be used to tune LNA:RNA duplexes into substrates for RNase H: Partly modified LNA:RNA duplexes may adopt a duplex structure between the standard A and B types, thereby making the RNA strand amenable to RNase H-mediated degradation.
Catheter Ablation of Long‐Lasting Persistent Atrial Fibrillation: Clinical Outcome and Mechanisms of Subsequent Arrhythmias (2005)

Catheter ablation of long-lasting persistent AF associated with acute AF termination achieves medium to long-term restoration and maintenance of sinus rhythm in 95% of patients. Arrhythmia recurrence in the majority of patients is AT.
Detection of hepatitis C virus RNA by a combined reverse transcription PCR assay: comparison with nested amplification and antibody testing (1995)

Many of the current reverse transcription (RT)-PCR assays for the detection of hepatitis C virus (HCV) RNA are multistep processes which use multiple enzymes and buffers. The assays are also often suboptimal, requiring nested amplification to achieve the desired levels of sensitivity. As a result, these assays are cumbersome and prone to false-positive results. The susceptibility to contamination is further aggravated by the lack of carryover controls. We have previously reported the development of a combined RT-PCR assay for HCV RNA detection which is sensitive and simple to perform. We have since successfully integrated dUTP-uracil-N-glycosylase carryover prevention into the combined assay. Restriction of as much as 0.5 microliter of deoxyuridine-containing amplification products has been achieved. The performance of the improved combined assay was compared directly with conventional nested RT-PCR and antibody detection. The combined assay was found to have sensitivity similar to that of nested RT-PCR in detecting HCV RNA from HCV antibody-positive specimens. In an analysis of hepatitis B virus antibody-positive specimens, nested amplification had false-positive rates ranging from 8 to 31%, while no false-positive results were seen with the combined assay. In comparison with serological methods, the combined assay had specificity and sensitivity of 100 and 95%, respectively.
Deep predictive policy training using reinforcement learning (2017)

Skilled robot task learning is best implemented by predictive action policies due to the inherent latency of sensorimotor processes. However, training such predictive policies is challenging as it involves finding a trajectory of motor activations for the full duration of the action. We propose a data-efficient deep predictive policy training (DPPT) framework with a deep neural network policy architecture which maps an image observation to a sequence of motor activations. The architecture consists of three sub-networks referred to as the perception, policy and behavior super-layers. The perception and behavior super-layers force an abstraction of visual and motor data trained with synthetic and simulated training samples, respectively. The policy super-layer is a small subnetwork with fewer parameters that maps data in-between the abstracted manifolds. It is trained for each task using methods for policy search reinforcement learning. We demonstrate the suitability of the proposed architecture and learning framework by training predictive policies for skilled object grasping and ball throwing on a PR2 robot. The effectiveness of the method is illustrated by the fact that these tasks are trained using only about 180 real robot attempts with qualitative terminal rewards.
Polymer Based Lanthanide Luminescent Sensors for the Detection of Nerve Agents (1997)

Several devices are being constructed to measure and detect the nerve agents Sarin and Soman. The devices function by selectively binding the phosphonate hydrolysis products to a luminescent functionality-imprinted copolymer. The copolymers possess a securely bound luminescent lanthanide ion, such as Eu 3 + , in a coordination complex that has been templated for the chemical functionality resulting from the hydrolysis of Sarin and Soman but has had a weakly bound anion substituted by mass action. The instrumental support for the device is being designed to monitor the change that occurs in the luminescence spectrum of the lanthanide when the analyte is coordinated. The ligand field shifted luminescence of the lanthanide is excited by a compact laser and monitored via optical fiber by either a filter photometer or a monochromator. Miniaturization will be applied to each of the lab bench components to produce a field portable device that will potentially be comparable in size to a pH meter. Initial results using an Ar ion laser excitation source providing 0.3 mW at 465.7 nm yield a limit of detection of 125 ppt. The chemical and spectroscopic selectivity of this device are being combined to reduce the likelihood of false positive analyses.
An ornithine decarboxylase-deficient mutant of Chinese hamster ovary cells. (1982)

We have selected a mutant of Chinese hamster ovary cells that is severely deficient in ornithine decarboxylase activity and is auxotrophic for putrescine. The mutant we obtained (C54) has only 3% of the maximum inducible ornithine decarboxylase activity of the parental Chinese hamster ovary cells and the rate of incorporation of [3H]ornithine into acid-soluble material is correspondingly reduced. The defect in the mutant was recessive in somatic cell hybrids. The mutant requires at least 10(-5) M putrescine in the medium to maintain a normal growth rate. Spermidine and spermine can also serve as a polyamine source, and very high (millimolar) concentrations of ornithine can support a normal growth rate. In the absence of polyamine supplementation the cells stop growing after about 3 population doublings and begin to die after 5 or 6 days. The intracellular concentrations of putrescine and spermidine are depleted after 24 and 48 h, respectively. Spermine levels remain essentially constant for 4 days. Unexpectedly, the Km for ornithine of the enzyme from mutant cells was consistently somewhat lower than the Km for the enzyme from wild type cells. It is possible but not yet certain that the mutant is the result of a mutation in the structural gene coding for ornithine decarboxylase.