gebhart/patrepeval huggingface dataset:
Post‐transplant lymphoproliferative disorder subtypes correlate with different recurring chromosomal abnormalities (2005)

Although cytogenetic analysis advanced the understanding of the pathogenesis of primary non-Hodgkin lymphoma and led to improved clinical management, there have been no large cytogenetic studies of post-transplant lymphoproliferative disorder (PTLD). We examined the karyotypes of 36 PTLD cases and correlated them with clinical, laboratory, and pathologic findings. The cases included 2 early lesions, 13 polymorphic PTLDs, and 21 monomorphic PTLDs (18 B-cell and 3 T-cell proliferations). Cytogenetic abnormalities were identified in 72% of monomorphic B-cell PTLDs and in all T-cell PTLDs, but in only 15% of polymorphic PTLDs and in no early lesions. The most frequent clonal abnormalities in monomorphic PTLD were trisomies 9 and/or 11 (5 cases), followed by rearrangements of 8q24.1 (4 cases), 3q27 (2 cases), and 14q32 (2 cases). MYC rearrangement (8q24.1) and T-cell-associated chromosomal abnormalities correlated with poor outcome and short survival. PTLD with trisomy 9 and/or 11 developed early after transplant, presenting as Epstein-Barr virus-positive large B-cell lymphoma with prolonged survival.
Towards autonomous robotic butlers: Lessons learned with the PR2 (2011)

As autonomous personal robots come of age, we expect certain applications to be executed with a high degree of repeatability and robustness. In order to explore these applications and their challenges, we need tools and strategies that allow us to develop them rapidly. Serving drinks (i.e., locating, fetching, and delivering), is one such application with well-defined environments for operation, requirements for human interfacing, and metrics for successful completion. In this paper we present our experiences and results while building an autonomous robotic assistant using the PR2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> platform and ROS2. The system integrates several new components that are built on top of the PR2's current capabilities. Perception components include dynamic obstacle identification, mechanisms for identifying the refrigerator, types of drinks, and human faces. Planning components include navigation, arm motion planning with goal and path constraints, and grasping modules. One of the main contributions of this paper is a new task-level executive system, SMACH, based on hierarchical concurrent state machines, which controls the overall behavior of the system. We provide in-depth discussions on the solutions that we found in accomplishing our goal, and the implementation strategies that let us achieve them.
CT Image Fusion for 3D Depiction of Anatomic Abnormalities of the Hepatic Hilum (2007)

The purpose of this article is to show how CT image fusion with 3D reconstruction is used to depict in detail the anatomic structures of the hepatic hilum in the presence of hepatobiliary abnormalities.CT image fusion is a comprehensive imaging technique for preoperative evaluation of the blood vessels and bile ducts of the hepatic hilum.
DNA activates human immune cells through a CpG sequence‐dependent manner (1999)

While bacterial DNA and cytosine-guanosine-dinucleotide-containing oligonucleotides (CpG ODN) are well described activators of murine immune cells, their effect on human cells is inconclusive. We investigated their properties on human peripheral blood mononuclear cells (PBMC) and subsets thereof, such as purified monocytes, T and B cells. Here we demonstrate that bacterial DNA and CpG ODN induce proliferation of B cells, while other subpopulations, such as monocytes and T cells, did not proliferate. PBMC mixed cell cultures, as well as purified monocytes, produced interleukin-6 (IL-6), IL-12 and tumour necrosis factor-alpha upon stimulation with bacterial DNA; however, only IL-6 and IL-12 secretion became induced upon CpG ODN stimulation. We conclude that monocytes, but not B or T cells, represent the prime source of cytokines. Monocytes up-regulated expression of antigen-presenting, major histocompatibility complex class I and class II molecules in response to CpG DNA. In addition, both monocytes and B cells up-regulate costimulatory CD86 and CD40 molecules. The activation by CpG ODN depended on sequence motifs containing the core dinucleotide CG since destruction of the motif strongly reduced immunostimulatory potential.
The wavefront phenomenon of ischemic cell death. 1. Myocardial infarct size vs duration of coronary occlusion in dogs. (1977)

Irreversible ischemic myocardial cell injury developes in an increasing number of cells as the duration of coronary occlusion is prolonged. The present study quantitates myocardial necrosis produced by 40 minutes, 3 hours, or 6 hours of temporary circumflex coronary occlusion (CO) followed by 2 to 4 days of reperfusion, or by 24 or 96 hours of permanent circumflex ligation in pentobarbital anesthetized open chest dogs. After 40 minutes of ischemia, myocyte necrosis was subendocardial but with increasing duration of coronary occlusion, irreversible injury progressed as a wavefront toward the subepicardium. Transmural necrosis was 38 +/- 4% after 40 min, 57 +/- 7% after 3 hours, 71 +/- 7% after 6 hours and 85 +/- 2% after 24 hours of ischemic injury. These results document the presence of a subepicardial zone of ischemic but viable myocardium which is available for pharmacologic or surgical salvage for at least three and perhaps six hours following circumflex occlusion in the dog.
A reactively loaded aperture antenna array (1978)

The use of variable reactive loads to control the beam direction of an antenna array consisting of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</tex> closely spaced waveguide-backed dielectric-filled rectangular slots is considered. Only the center waveguide is driven (no complex feed network is required for the array), and the other waveguides are short circuited at specified distances to provide reactive loading. The solution uses the method of moments applied to the integral equation for the equivalent magnetic current in the aperture region. The initial, design of the array is obtained by resonating the complex excitation voltages required for maximum gain with all of the elements driven. This is then improved by an optimum seeking univariate search method. Computed results are given for seven- and fifteen-element aperture arrays.
XENOGENEIC TRANSPLANTATION (1998)

This review summarizes the clinical history and rationale for xenotransplantation; recent progress in understanding the physiologic, immunologic, and infectious obstacles to the procedure's success; and some of the strategies being pursued to overcome these obstacles. The problems of xenotransplantation are complex, and a combination of approaches is required. The earliest and most striking immunologic obstacle, that of hyperacute rejection, appears to be the closest to being solved. This phenomenon depends on the binding of natural antibody to the vascular endothelium, fixation of complement by that antibody, and finally, activation of the endothelium and initiation of coagulation. Therefore, these three pathways have been targeted as sites for intervention in the process. The mechanisms responsible for the next immunologic barrier, that of delayed xenograft/acute vascular rejection, remain to be fully elucidated. They probably also involve multiple pathways, including antibody and/or immune cell binding and endothelial cell activation. The final immunologic barrier, that of the cellular immune response, involves mechanisms that are similar to those involved in allograft rejection. However, the strength of the cellular immune response to xenografts is so great that it is unlikely to be controlled by the types of nonspecific immunosuppression used routinely to prevent allograft rejection. For this reason, it may be essential to induce specific immunologic unresponsiveness to at least some of the most antigenic xenogeneic molecules.
Allelic discrimination by nick-translation PCR with fluorgenic probes (1993)

Nick-translation PCR was performed with fluorogenic probes. Two probes were used: one complementary to a sequence containing the F508 codon of the normal human cystic fibrosis (CF) gene (wt DNA) and one complementary to a sequence containing the delta F508 three base pair deletion (mut DNA). Each probe contained a unique and spectrally resolvable fluorescent indicator dye at the 5' end and a common quencher dye attached to the seventh nucleotide from the 5' end. The F508/delta F508 site was located between the indicator and quencher. The probes were added at the start of a PCR containing mut DNA, wt DNA or heterozygous DNA and were degraded during thermal cycling. Although both probes were degraded, each probe generated fluorescence from its indicator dye only when the sequence between the indicator and quencher dyes was perfectly complementary to target. The identify of the target DNA could be determined from the post-PCR fluorescence emission spectrum.
Test results of a 130 W AC module; a modular solar AC power station (2002)

An AC module is a PV module with an integrated DC/AC power converter which generates grid conforming AC power. In this paper, the ideas behind this portable and expandable AC PV power system are highlighted. The block diagram, the principle of operation and test results of a 130 W inverter are shown. The measurements show a power factor exceeding 0.99 at full load, whilst at 12 W partial load the power factor is better than 0.89. The harmonic distortion decreases from 8% at 30 W to 5% at 50 W and slightly decreases further at higher power levels. Previous measurements showed that an efficiency over 90% over a wide operation range is obtained. It is estimated that the cost price of the "touch safe" inverter (dimensions 100*100*20 mm), when produced in large quantities is between 0.5 and 1 $/Wp. The price performance ratio is obtained by application of resonant switching techniques enabling low component size and costs.
Cloning and Expression of a Rat Brain GABA Transporter (1990)

A complementary DNA clone (designated GAT-1) encoding a transporter for the neurotransmitter gamma-aminobutyric acid (GABA) has been isolated from rat brain, and its functional properties have been examined in Xenopus oocytes. Oocytes injected with GAT-1 synthetic messenger RNA accumulated [3H]GABA to levels above control values. The transporter encoded by GAT-1 has a high affinity for GABA, is sodium-and chloride-dependent, and is pharmacologically similar to neuronal GABA transporters. The GAT-1 protein shares antigenic determinants with a native rat brain GABA transporter. The nucleotide sequence of GAT-1 predicts a protein of 599 amino acids with a molecular weight of 67 kilodaltons. Hydropathy analysis of the deduced protein suggests multiple transmembrane regions, a feature shared by several cloned transporters; however, database searches indicate that GAT-1 is not homologous to any previously identified proteins. Therefore, GAT-1 appears to be a member of a previously uncharacterized family of transport molecules.
Catalytic ability and stability of two recombinant mutants of D‐amino acid transaminase involved in coenzyme binding (1995)

Of the major amino acid side chains that anchor pyridoxal 5'-phosphate at the coenzyme binding site of bacterial D-amino acid transaminase, two have been substituted using site-directed mutagenesis. Thus, Ser-180 was changed to an Ala (S180A) with little effect on enzyme activity, but replacement of Tyr-31 by Gln (Y31Q) led to 99% loss of activity. Titration of SH groups of the native Y31Q enzyme with DTNB proceeded much faster and to a greater extent than the corresponding titration for the native wild-type and S180A mutant enzymes. The stability of each mutant to denaturing agents such as urea or guanidine was similar, i.e., in their PLP forms, S180A and Y31Q lost 50% of their activities at a 5-15% lower concentration of urea or guanidine than did the wild-type enzyme. Upon removal of denaturing agent, significant activity was restored in the absence of added pyridoxal 5'-phosphate, but addition of thiols was required. In spite of its low activity, Y31Q was able to form the PMP form of the enzyme just as readily as the wild-type and the S180A enzymes in the presence of normal D-amino acid substrates. However, beta-chloro-D-alanine was a much better substrate and inactivator of the Y31Q enzyme than it was for the wild-type or S180A enzymes, most likely because the Y31Q mutant formed the pyridoxamine 5-phosphate form more rapidly than the other two enzymes. The stereochemical fidelity of the Y31Q recombinant mutant enzyme was much less than that of the S180A and wild-type enzymes because racemase activity, i.e., conversion of L-alanine to D-alanine, was higher than for the wild-type or S180A mutant enzymes, perhaps because the coenzyme has more flexibility in this mutant enzyme.
Enzymatic Modification of Self-Assembled Peptide Structures with Tissue Transglutaminase (2003)

A de novo peptide that self-assembles into fibrillar structures and serves as a substrate for the cross-linking enzyme tissue transglutaminase was developed (Ac-QQKFQFQFEQQ-Am). Congo red staining, circular dichroism, and FTIR spectroscopy showed that this 11-amino acid peptide produced predominantly beta-sheet structures. TEM with negative staining and quick-freeze deep etch (QFDE) TEM showed that the peptide structures were composed of a highly entangled fibrillar network. These beta-sheet fibrillar nanostructures were then covalently coupled to pendant amine-containing biomolecules via tissue transglutaminase. MALDI-TOF mass spectrometry and HPLC were utilized to monitor the extent of the transglutaminase modification of the peptide, showing that as many as five glutamines in the peptide were reactive via transglutaminase for covalent conjugation. This strategy, based on the post-assembly modification of a self-assembling peptide, has potential applications for tailoring supramolecular structures for drug delivery, tissue engineering, or other biomedical applications.
Complex Patterning by Vertical Interchange Atom Manipulation Using Atomic Force Microscopy (2008)

The ability to incorporate individual atoms in a surface following predetermined arrangements may bring future atom-based technological enterprises closer to reality. Here, we report the assembling of complex atomic patterns at room temperature by the vertical interchange of atoms between the tip apex of an atomic force microscope and a semiconductor surface. At variance with previous methods, these manipulations were produced by exploring the repulsive part of the short-range chemical interaction between the closest tip-surface atoms. By using first-principles calculations, we clarified the basic mechanisms behind the vertical interchange of atoms, characterizing the key atomistic processes involved and estimating the magnitude of the energy barriers between the relevant atomic configurations that leads to these manipulations.
Renal Function in Adult Beta-Thalassemia/Hb E Disease (1998)

Beta-Thalassemia hemoglobin E (beta-thal/Hb E) is the commonest form of hemoglobinopathy in Thailand. Shortened red cell life span, rapid iron turnover and tissue deposition of excess iron are major factors responsible for functional and physiological abnormalities found in various forms of thalassemia. Increased deposition of iron had been found in renal parenchyma of thalassemic patients, but no systematic study of the effect of the deposits on renal functions has been available. The purpose of this study is to describe the functional abnormalities of the kidney in patients with beta-thal/Hb E and provide evidence that increased oxidative stress might be one of the factors responsible for the damage. Urine and serum samples from 95 patients with beta-thal/Hb E were studied comparing with 27 age-matched healthy controls. No difference in the creatinine clearance was observed. beta-thal/Hb E patients excreted significantly more urinary protein (0.8+/-0.5 vs. 0.3+/-0.1 g/day, p < 0.001). Aminoaciduria was found in 16 % of the patients. Analysis of urinary protein by SDS-PAGE electrophoresis and silver staining revealed abnormal pattern of protein with increased small molecular weight (<45 kD) bands. Morning urine analysis showed significant lower urine osmolality (578.3+/-164.6 vs. 762.4+/-169.9 mosm/kg, p < 0.001) in patients. Patients excreted more NAG (N-acetyl beta-D-glucosaminidase, 26.3+/-41.3 vs. 8.4+/-3.9 U/g Cr, p < 0.0001) and beta2-microglobulin, 124.3+/-167 vs. 71+/-65.5 microg/g Cr, p = 0.001. Plasma and urine MDA (malonyldialdehyde) levels were both raised (p < 0.0001). Nine patients were selected for renal acidification study. All were found to be normal, but showed poor response to DDAVP challenge (urine osmolality 533+/-71). This is the first report of renal tubular defects found associated with beta-thal/Hb E disease. The mechanism leading to the damage is not known but it might be related to increased oxidative stress secondary to tissue deposition of iron, as indicated by the raised levels of serum and urine MDA. It is not known whether these functional defects would have any long-term effects on the patients. Further studies are warranted and means of prevention of these defects should urgently be sought.
Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing (2014)

Targeted genome editing with engineered nucleases has transformed the ability to introduce precise sequence modifications at almost any site within the genome. A major obstacle to probing the efficiency and consequences of genome editing is that no existing method enables the frequency of different editing events to be simultaneously measured across a cell population at any endogenous genomic locus. We have developed a method for quantifying individual genome-editing outcomes at any site of interest with single-molecule real-time (SMRT) DNA sequencing. We show that this approach can be applied at various loci using multiple engineered nuclease platforms, including transcription-activator-like effector nucleases (TALENs), RNA-guided endonucleases (CRISPR/Cas9), and zinc finger nucleases (ZFNs), and in different cell lines to identify conditions and strategies in which the desired engineering outcome has occurred. This approach offers a technique for studying double-strand break repair, facilitates the evaluation of gene-editing technologies, and permits sensitive quantification of editing outcomes in almost every experimental system used.
Uniqueness, Advantages, Challenges, Solutions, and Perspectives in Therapeutics Applying RNA Nanotechnology (2012)

The field of RNA nanotechnology is rapidly emerging. RNA can be manipulated with the simplicity characteristic of DNA to produce nanoparticles with a diversity of quaternary structures by self-assembly. Additionally RNA is tremendously versatile in its function and some RNA molecules display catalytic activities much like proteins. Thus, RNA has the advantage of both worlds. However, the instability of RNA has made many scientists flinch away from RNA nanotechnology. Other concerns that have deterred the progress of RNA therapeutics include the induction of interferons, stimulation of cytokines, and activation of other immune systems, as well as short pharmacokinetic profiles in vivo. This review will provide some solutions and perspectives on the chemical and thermodynamic stability, in vivo half-life and biodistribution, yield and production cost, in vivo toxicity and side effect, specific delivery and targeting, as well as endosomal trapping and escape.
Performance issues on wireless 2.4 GHz ISM band in multisystem environment (2003)

Adoption of wireless systems in consumer electronics products is increasing rapidly. The 2.4 GHz industrial scientific and medical (ISM) band offers an attractive platform for the implementation of different mass products due to worldwide appearance and existing standards, like the most well-known, Bluetooth, wireless LAN and HomeRF. Popularity and multiple standards present also a threat to the usability of this popular band, and it is essential to understand how the different systems affect each other. This paper presents both the theoretical background of these systems and measured results.
Synthesis of Hierarchically Porous Carbon Monoliths with Highly Ordered Microstructure and Their Application in Rechargeable Lithium Batteries with High‐Rate Capability (2007)

Abstract In this paper, we report on Li storage in hierarchically porous carbon monoliths with a relatively higher graphite‐like ordered carbon structure. Macroscopic carbon monoliths with both mesopores and macropores were successfully prepared by using meso‐/macroporous silica as a template and using mesophase pitch as a precursor. Owing to the high porosity (providing ionic transport channels) and high electronic conductivity (ca. 0.1 S cm –1 ), this porous carbon monolith with a mixed conducting 3D network shows a superior high‐rate performance if used as anode material in electrochemical lithium cells. A challenge for future research as to its applicability in batteries is the lowering of the irreversible capacity.
Measuring quality of life of patients with different clinical types of psoriasis using the SF-36 (2006)

A generic quality of life instrument (e.g. the SF-36) provides information that is complementary to that derived from dermatological questionnaires, and may give further insight in the evaluation of the burden of psoriasis.
Expression Analyses of Epidermal Growth Factor Receptor and HER-2/neu: No Advantage of Prediction of Recurrence or Survival in Breast Cancer Patients (1996)

The overexpression of two members of the erbB oncogene family-the epidermal growth factor receptor protein (EGF-R) and the HER-2/neu protein-in breast cancer has been investigated by numerous authors. Their exact role in breast cancer is still not defined. The simultaneous investigation of EGF-R and HER-2/neu in the same study population has only rarely been performed in breast cancer. Therefore, we analyzed the EGF-R and the HER-2/neu protein expression in 142 breast cancer specimens and 12 benign breast samples by immunohistochemistry. Results of the different expression analyses were compared with established clinicopathological parameters including estrogen and progesterone receptor status. In our study group EGF-R expression correlated with advanced tumor stage, axillary lymph node status and histological grade. HER-2/neu expression correlated with larger tumor size. Neither the evaluation of a single parameter of the erbB family nor the combination of both parameters showed a significant correlation with the disease-free and the overall survival of the individual patient with breast cancer. Only the expression of the progesterone receptor correlated with a better overall survival. Steroid hormone receptor expression and the expression of EGF-R and HER-2/ neu seem to be two independent phenomena in our samples of breast cancer. The simultaneous evaluation of EGF-R and HER-2/neu expression did not lead to new information of prognostic relevance.