gebhart/patrepeval huggingface dataset:
Myelodysplastic Syndrome (2005)

During the past 15 years, important progress has been made in the understanding of the biology and prognosis of myelodysplastic syndrome (MDS). MDS is a clonal disorder characterized by ineffective hematopoiesis, which can lead to either fatal cytopenias or acute myelogenous leukemia (AML). Risk-adapted treatment strategies were established because of the high median age (60-75 years) of the MDS patients and the individual history of the disease (number of cytopenias, cytogenetic changes, transfusion requirements). Allogeneic bone marrow transplantation currently offers the only potentially curative treatment, but this form of therapy is not available for the typical MDS patient, who is >60 years of age. Therapy with erythropoietin and G-CSF has improved the quality of life of selected patients. The development of small molecules directed against specific molecular targets with minimal adverse effects is the hope for the future. Innovative uses of immunomodulatory agents and the optimizing of cytotoxic treatment should continue to help in the treatment of MDS.
FORMATION OF SULFOXIDE ‘DIMERS’ FROM HYDROGEN PEROXIDE OXIDATION OF 2-CHLOROETHYL METHYL SULFIDE AND 2-CHLOROETHYL ETHYL SULFIDE (1992)

Abstract The oxidation of 2-chioroethyl methyl sulfide and 2-chloroethyl ethyl sulfide (analogs of sulfur mustard) by hydrogen peroxide have resulted in the isolation of the oxidation products in crystalline form. The IR spectra of these products showed the typical sulfoxide absorption in the 1070–1030 cm−1 region. However, MS and NMR spectroscopy indicated that oxidation of 2-chloroethyl sulfides resulted in a dimerization and elimination reaction, leading to the formation of sulfoxides having the structure RSOCH2CH2SOCH2CH2Cl, where R = −CH3 or −CH2CH3. Similar dimers were not produced from thiodiglycol, which contains no beta chlorine. The structures of these dimeric sulfoxides were fully established by spectroscopic and elemental analyses. Key Words: Hydrogen peroxide oxidationformation of atypical sulfoxide “dimers”2-chioroethyl ethyl sulfide2-chloroethyl methyl sulfidethiodiglycol.
A Multiplex PCR-Ligase Detection Reaction Assay for Human Identity Testing (1996)

Current methods of forensic DNA identification at our facilities use PCR for typing single nucleotide and tandem repeat polymorphisms. Unfortunately, these PCR-based methods are relatively expensive and time consuming and are not well suited for total automation. The ligase detection reaction (LDR) when used in conjunction with PCR offers distinct advantages. In LDR, two adjacent primers hybridize to the target and are ligated only when there is perfect complementarity at the junction. Since Taq DNA ligase used in LDR is thermostable, several rounds of thermal cycling may be used to unambiguously distinguish any single nucleotide polymorphisms. We have developed a coupled multiplex PCR-LDR assay to type single base variations at 12 biallelic loci, giving a power of discrimination of 1.12 × 105. The 12 loci are PCR amplified in a single reaction using a unique two-step method that produces similar amounts of multiplexed products without the need to carefully adjust primer concentrations or PCR conditions. Following PCR, these products are used in a single LDR to generate products that are resolved and typed on an Applied Biosystems 373 DNA sequencer, creating an LDR profile. Our ability to easily generate similar amounts of product in a 12-locus multiplex PCR amplification is the basis for expanding the assay to type 30 biallelic loci to give a theoretical power to discriminate one individual in 1012.
Adjuncts to dopamine replacement: A pragmatic approach to reducing the problem of dyskinesia in Parkinson's disease (1998)

Dyskinesias following long-term dopamine replacement therapy are a major limitation of current treatments for Parkinson's disease. Recently, attention has been focused on the concept of using non-dopaminergic adjuncts to currently available therapies in an attempt to reduce the problem of dyskinesia. Thus, an enhanced understanding of the neural mechanisms underlying dyskinetic symptoms has led to the realization that it might be possible to manipulate non-dopaminergic systems and reduce dyskinesia without compromising the anti-parkinsonian efficacy of drugs such as L-dopa. This article discusses how non-dopaminergic manipulations could reverse the abnormalities in basal ganglia circuitry responsible for generating dyskinesia. It is proposed that potential anti-dyskinetic drugs might include glutamate (NMDA) receptor antagonists, opioid receptor antagonists, cannabinoid receptor agonists or antagonists, alpha2 adrenergic receptor antagonists, and 5-HT-enhancing agents.
STABILIZATION OF LIPID BILAYERS ON SURFACES THROUGH CHARGED POLYMERS (1999)

ABSTRACT It is our concept to use a polymer as a hydrophilic cushion to stabilize a lipid bilayer on a solid support. This can be accomplished by using polyacrylamides with disulfides and DMPE anchors as a hydrophilic cushion. These polymers have the additional functionalities to chemisorb on gold surfaces through the disulfides and to bind a lipid bilayer on it through the insertion of the lipid anchors into the lipid bilayer. This paper shows that a polymer with the additional functionality of charged groups increases the attraction of vesicles to form a tethered supported lipid bilayer. By varying the amount of charged groups in the polymer, we are able to control the hydrophilic behavior of the polymer and therefore are able to change the wetting on a surface. This was examined by measuring the contact angles. Using the technique of the surface plasmon spectroscopy, we are able to monitor the process of vesicle fusion on the polymer support.
Ionic Current Basis of Electrocardiographic Waveforms (2002)

Body surface electrocardiograms and electrograms recorded from the surfaces of the heart are the basis for diagnosis and treatment of cardiac electrophysiological disorders and arrhythmias. Given recent advances in understanding the molecular mechanisms of arrhythmia, it is important to relate these electrocardiographic waveforms to cellular electrophysiological processes. This modeling study establishes the following principles: (1) voltage gradients created by heterogeneities of the slow-delayed rectifier (I(Ks)) and transient outward (I(to)) potassium current inscribe the T wave and J wave, respectively; T-wave polarity and width are strongly influenced by the degree of intercellular coupling through gap-junctions. (2) Changes in [K+]o modulate the T wave through their effect on the rapid-delayed rectifier, I(Kr). (3) Alterations of I(Ks), I(Kr), and I(Na) (fast sodium current) in long-QT syndrome (LQT1, LQT2, and LQT3, respectively) are reflected in characteristic QT-interval and T-wave changes; LQT1 prolongs QT without widening the T wave. (4) Accelerated inactivation of I(Na) on the background of large epicardial I(to) results in ST elevation (Brugada phenotype) that reflects the degree of severity. (5) Activation of the ATP-sensitive potassium current, I(K(ATP)), is sufficient to cause ST elevation during acute ischemia. These principles provide a mechanistic cellular basis for interpretation of electrocardiographic waveforms.
Effects of carbon nanofibers on polystyrene nanocomposites and foams (2004)

With extraordinary mechanical properties, carbon nanofibers (CNF) are expected to serve as reinforcements for both lightweight and ultrastrong composite materials. In this study, we used CNF as the reinforcing nanoelements to synthesize polystyrene/CNF nanocomposites by the in-situ polymerization process. The obtained composites were further foamed using supercritical CO 2 as the foaming agent. A homogeneous dispersion of CNF was observed and the final PS/CNF nanocomposite foam showed microcellular foam morphology.
Localization of VEGF receptor-2 (KDR/Flk-1) and effects of blocking it in oxygen-induced retinopathy. (2002)

KDR/Flk-1 was only weakly associated with normal developing primary retinal vessels but was strongly expressed by proliferating endothelial cells in reforming retinal vessels and intravitreal neovascularization after hyperoxic insult. Anti-KDR antibody delivered by slow-release pellets had no effect on normal vasculogenesis, but it inhibited the formation of intravitreal neovascularization and retinal vessel development in OIR. The study suggests that blocking KDR may be beneficial for treating pathologic angiogenesis in adult tissue.
Alteration of apparent restriction endonuclease recognition specificities by DNA methylases (1984)

An in vitro method of altering the apparent cleavage specificities of restriction endonucleases was developed using DNA modification methylases. This method was used to reduce the number of cleavage sites for 34 restriction endonucleases. In particular, single-site cleavages were achieved for Nhe I in Adeno-2 DNA and for Acc I and Hinc II in pBR322 DNA by specifically methylating all but one recognition sequence.
In vitro assembly of intermediate filaments from baby hamster kidney (BHK-21) cells. (1979)

Intermediate filaments (IF) from baby hamster kidney (BHK-21) cells can be disassembled at low ionic strength and reassembled upon addition of salt. Turbidimetric analyses show that reassembled IF exhibit the light scattering properties of long rods under physiological conditions (5 mM Na+/K+ phosphate, pH 7.2/170 mM NaCl at 21 degrees C). IF weight concentration, determined by centrifugation, is directly proportional to the optical density at 3000 nm. Thus, turbidity can be used as a quantitative assay for IF assembly. Turbidimetric and centrifugation analyses both indicate that IF assembly exhibits a critical protein concentration of 0.05-0.15 mg/ml. Above the critical concentration, IF weight concentration at steady-state is a linear function of the total protein concentration. Negative stain observations at early stages of the assembly process suggest lateral association of protofilaments to form short IF. This lateral association is accompanied by a rapid turbidity increase which is then followed by IF elongation and a slower turbidity increase to plateau. Further purification of IF by low/high-NaCl-induced cycles of disassembly/reassembly results in retention of 54- and 55-kilodalton (decamin) polypeptides. These results constitute a quantitative description of in vitro reassembly of IF from homogeneous cultures of nonkeratinizing cells and establish conditions for further studies on the regulation of IF assembly.
A digitally controlled oscillator in a 90 nm digital CMOS process for mobile phones (2005)

We propose and demonstrate the first RF digitally controlled oscillator (DCO) for cellular mobile phones. The DCO is part of a single-chip quad-band fully compliant GSM transceiver realized in a 90 nm digital CMOS process. Wide and precise linear frequency tuning is achieved through digital control of a large array of standard n-poly/n-well MOSCAP devices that operate in flat regions of their C- V curves. The varactors are partitioned into binary-weighted and unit-weighted banks that are sequentially activated during frequency locking and tracking. The finest varactor step size is 12 kHz at the 1.6-2.0 GHz high-band output. To attenuate the quantization noise to below the natural oscillator phase noise, the varactors undergo high-speed second-order /spl Sigma//spl Delta/ dithering. We analyze the effect of the /spl Sigma//spl Delta/ dithering on the phase noise and show that it can be made sufficiently small. The measured phase noise at 20 MHz offset in the GSM900 band is -165 dBc/Hz and shows no degradation due to the /spl Sigma//spl Delta/ dithering. The 3.6 GHz DCO core consumes 18.0 mA from a 1.4 V supply and has a very wide tuning range of 900 MHz to support the quad-band operation.
High-performance timing simulation of embedded software (2008)

This paper presents an approach for cycle-accurate simulation of embedded software by integration in an abstract SystemC model. Compared to existing simulation-based approaches, we present a hybrid method that resolves performance issues by combining the advantages of simulation-based and analytical approaches. In a first step, cycle-accurate static execution time analysis is applied at each basic block of a cross-compiled binary program using static processor models. After that, the determined timing information is back-annotated into SystemC for fast simulation of all effects that can not be resolved statically. This allows the consideration of data dependencies during run-time and the incorporation of branch prediction and cache models by efficient source code instrumentation. The major benefit of our approach is that the generated code can be executed very efficiently on the simulation host with approximately 90% of the speed of the untimed software without any code instrumentation.
A Cmos 500 Mbps/pin Synchronous Point to Point Link Interface (2005)

This paper describes the design of a high speed interface for a multiprocessor interconnection network. To achieve higher transfer rates, the interface utilizes a voltage swing of 1 V, a Delay Line PLL and sampling of the data on both edges of the clock. Chips fabricated in a 0.8 pm CMOS technology achieve transfer rates of 700 Mbpdpin operating from a 3.3-V supply. Worst case measured peak-to-peak clock jitter is 260 ps (63 ps RMS). The layout area occupied by the DLL and the associated clock duty cycle adjuster is 460x800 pni2.
Power line enhanced cooperative wireless communications (2006)

In this paper, we investigate the use of power line communication (PLC) to assist cooperative wireless relaying. We consider a communication scheme that uses the power line to initialize and synchronize wireless amplify-and-forward relays and to broadcast information between the relays. Starting from an analysis of transfer functions and noise measurements of PLC channels in office and residential environments, we propose a power line transmission scheme for the inter-relay-communication and assess the influence of this scheme on wireless relaying. This scheme is based on linear precoded orthogonal frequency-division multiplexing; it is designed to optimally exploit the frequency diversity available on PLC channels. The use of PLC leads to a very flexible way of enhancing wireless communications by plugging in additional relays where they are needed-without additional wiring.
Improved matrix-assisted laser desorption/ionization mass spectrometric analysis of tryptic hydrolysates of proteins following guanidination of lysine-containing peptides (2000)

Analysis of tryptic digests of proteins using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry commonly results in superior detection of arginine-containing peptides compared with lysine-containing counterparts. The effect is attributable in part to the greater stability of the arginine-containing peptide ions associated with the sequestration of the single ionizing proton on the arginine side-chain. Reaction of peptides with O-methylisourea resulted in conversion of lysine to homoarginine residues with consequent improved detection during MALDI-MS. Analysis of the underivatized tryptic digest of the yeast protein, enolase, revealed peptides representing 20% of the protein; the corresponding figure after derivatization was 46%.
USE OF DONOR β2-MICROGLOBULIN-DEFICIENT TRANSGENIC MOUSE LIVER CELLS FOR ISOGRAFTS, ALLOGRAFTS, AND XENOGRAFTS (1993)

Donor graft major histocompatibility complex class I antigens are targets for both allogeneic and xenogeneic rejection. Mice homozygous for beta 2-microglobulin gene disruption express reduced amounts of surface MHC class I antigens. Liver cells from such mutant mice were transplanted into isogeneic, allogeneic, and xenogeneic recipients to evaluate the potential of these animals as transplant donors. The survival of allografts of transgenic 129 mouse liver cells in 15 immunocompetent and histoincompatible mouse recipients (BALB/c, D1.C) was only slightly improved 30 days after transplantation relative to normal 129 mouse allografts. These results could be attributable: (1) to host natural killer cell-mediated lysis of donor MHC class I antigen-deficient cells; (2) to donor liver cell MHC class I determinants that are reduced but not eliminated serving as rejection targets; (3) to the plentiful host supply of serum beta 2-microglobulin reconstituting the graft and restoring donor MHC class I. Culture studies confirmed the ability of exogenous human and bovine beta 2-microglobulin to restore rapidly MHC class I antigen expression on transgenic cells. Because cell surface exchange of beta 2-microglobulin is less efficient between species with divergent beta 2-microglobulin sequences, the survival of transgenic 129 mouse liver cells in guinea pig (60% beta 2-microglobulin identity) and Xenopus (34% beta 2-microglobulin identity) hosts was investigated. Significant prolongation of MHC class I antigen-deficient liver cell xenografts was apparently only in Xenopus hosts. Furthermore, transplants of transgenic 129 mouse liver cells into isogeneic normal 129 mouse recipients showed evidence of rejection in seven of nine recipients, suggesting that transgenic donor cells also may be susceptible to lysis by host natural killer cells.
Ly-49 mediates EL4 lymphoma adhesion to isolated class I major histocompatibility complex molecules. (1994)

Ly-49 is a recently identified cell surface molecule expressed on a subpopulation of natural killer (NK) cells and certain T lymphomas. It has been suggested, based on gene transfection and antibody blocking studies, that Ly-49 is a negative regulator of NK lytic activity, possibly through an interaction with target cell class I molecules. However, it has not been demonstrated that class I molecules indeed serve as ligands for Ly-49. We have found that T lymphomas expressing Ly-49 bind isolated class I major histocompatibility complex (MHC) molecules but not class II molecules immobilized on plastic. Adhesion to class I molecules was not found with T lymphomas lacking Ly-49 expression. The Ly-49 expressing EL4 lymphoma bound Dd, Dk, and Kb, but not Kd, Kk, or Db, thus demonstrating a restricted pattern of class I adhesion. The observed cell adhesion was class I density dependent, and binding to Dd and Dk was extensively inhibited by the A1 monoclonal antibody directed against Ly-49. These results provide direct evidence for Ly-49 serving as a receptor for a subset of class I MHC molecules.
Connexin43 Knockdown Accelerates Wound Healing but Inhibits Mesenchymal Transition after Corneal Endothelial Injury In Vivo (2008)

These results show that Cx43 knockdown induces corneal endothelium proliferation but inhibits endothelial-mesenchymal transition/transformation after injury, suggesting that Cx43 knockdown is a new therapeutic approach for acceleration of wound closure and for prevention of retrocorneal fibrous membrane formation.
Transcranial Doppler: Technique and Application to Headache (1992)

This article reviews the technique and physics relevant to a functional understanding of transcranial doppler. The frequently contradictory findings in migraine are reviewed. Several studies suggest increased flow velocities are common in the interictal period. There are disparate findings between studies of the ictal period. In cluster headache, there appear to be more easily reproduced changes between and during cluster attacks.
Homogeneous Immunosensor Based on Luminescence Resonance Energy Transfer for Glycated Hemoglobin Detection Using Upconversion Nanoparticles (2016)

We report an immunosensor based on luminescence resonance energy transfer (LRET) to detect homogeneous glycated hemoglobin (HbA1c). This system uses near-infrared (NIR)-to-visible rare-earth upconversion nanoparticles (UCNPs), such as NaYF4:Yb(3+), Er(3+), as the donor and HbA1c as the acceptor. The HbA1c used as target molecules showed absorption at 541 nm, which corresponded with the emission of the UCNPs. When HbA1c was added, LRET occurred between the donor and acceptor under laser irradiation of 980 nm because of the specific recognition between the anti-HbA1c monocolonal antibody-functionalized UCNPs and HbA1c. In the absence of HbA1c, there was strong upconversion luminescence intensity; however, in its presence, the distance between the donor and acceptor decreased to enable energy transfer, consequently quenching the luminescence of the UCNPs. The proposed method was successfully applied to HbA1c detection in blood samples. Our results indicate that the LRET-based immunosensor allows for specific and sensitive detection of HbA1c in a homogeneous manner.
No alloantibodies against mesenchymal stromal cells, but presence of anti-fetal calf serum antibodies, after transplantation in allogeneic hematopoietic stem cell recipients (2007)

We have shown that immunosuppressed patients can exhibit anti-FCS antibodies, but no alloantibodies, that may bind to MSC. These antibodies seem clinically insignificant.
A novel synthetic route to fused propenochlorin and benzochlorin photodynamic therapy probes (2002)

Reaction of meso-(2-formylvinyl)octaethylporphyrin with (CH3)3SiCN-Cu(OTf)2 produced unexpected 10(3)-trimethylsiloxyl and 10(3)-hydroxyl fused propenochlorins which, in H2SO4, underwent subsequent migration of the 8-ethyl group to the 10(3)-position of the exocyclic benzene ring to form a novel benzochlorin.
Suppression of MEK/ERK Signaling Pathway Enhances Cisplatin-induced NF-κB Activation by Protein Phosphatase 4-mediated NF-κB p65 Thr Dephosphorylation (2004)

We previously reported that suppression of the MEK/ERK pathway increases drug resistance of SiHa cells. In this study, we further characterized the underlying mechanism of this phenomenon. Pretreatment of SiHa cells with MEK/ERK inhibitor enhanced cisplatin-induced NF-kappaB activation. However, results of immunoblotting analysis showed that neither cisplatin nor MEK/ERK inhibitors induced marked IkappaBalpha degradation, suggesting that suppression of the MEK/ERK signaling pathway may enhance cisplatin-induced NF-kappaB activation via mechanisms other than the conventional pathway. Previous findings that protein phosphatase 4 (PP4), a nuclear serine/threonine phosphatase, directly interacts with and activates NF-kappaB led us to examine the phosphorylation status of NF-kappaB p65. Coincident with activation of NF-kappaB, cisplatin induced Ser phosphorylation but decreased Thr phosphorylation of NF-kappaB p65. Suppression of the MEK/ERK pathway further enhanced cisplatin-induced Thr dephosphorylation but did not affect cisplatin-induced Ser phosphorylation of NF-kappaB p65. Further, in parallel with Thr dephosphorylation, the protein level of nuclear PP4 was increased in cisplatin-treated cells and was further increased by suppression of the MEK/ERK pathway. SiHa cells were then transfected by a sense or an antisense PP4 gene. PP4-overexpressing cells showed a decrease in Thr phosphorylation of NF-kappaB p65 to nearly undetectable levels, and both basal and cisplatin-induced NF-kappaB activities were higher than those in parental cells. By contrast, cisplatin, either alone or with MEK/ERK inhibitors, induced little NF-kappaB activation in antisense PP4-transfected cells. Coprecipitated complex kinase assay revealed a fragment of NF-kappaB p65 (amino acids 279-444) to contain potential phosphorylation sites that directly interact with PP4. Further studies by site-directed mutagenesis suggested that Thr(435) was the major phosphorylation site.