gebhart/patrepeval huggingface dataset:
Site‐specific recombination in the immune system 1 (1991)

Site-specific DNA recombination has been identified in a wide variety of biological systems. In vertebrates, however, the only identified use of this genetic device is in the immune system. Here it plays a critical role in generating a diverse repertoire of surface receptors to intercept invading microbes and parasites. The mechanism and orchestration of this reaction are intriguing and are relevant to a broad array of related biological and biomedical issues.
Targeted disruption of the class B scavenger receptor CD36 protects against atherosclerotic lesion development in mice (2000)

Macrophage scavenger receptors have been implicated as key players in the pathogenesis of atherosclerosis. To assess the role of the class B scavenger receptor CD36 in atherogenesis, we crossed a CD36-null strain with the atherogenic apo E-null strain and quantified lesion development. There was a 76.5% decrease in aortic tree lesion area (Western diet) and a 45% decrease in aortic sinus lesion area (normal chow) in the CD36-apo E double-null mice when compared with controls, despite alterations in lipoprotein profiles that often correlate with increased atherogenicity. Macrophages derived from CD36-apo E double-null mice bound and internalized more than 60% less copper-oxidized LDL and LDL modified by monocyte-generated reactive nitrogen species. A similar inhibition of in vitro lipid accumulation and foam cell formation after exposure to these ligands was seen. These results support a major role for CD36 in atherosclerotic lesion development in vivo and suggest that blockade of CD36 can be protective even in more extreme proatherogenic circumstances.
A Convenient Synthesis of Pyrrolo[3,4‐c]quinolines. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Protection of hDAF‐transgenic porcine endothelial cells against activation by human complement: role of the membrane attack complex (2002)

Xenograft rejection in the discordant pig-to-primate model is dependent on binding of natural antibodies to gal-alpha [1-3]-gal epitopes on the porcine endothelial cell (EC). This leads to complement activation and deposition of activation products onto the membrane and results in perturbation of EC function and thrombus formation. Here we investigated the ability of human complement activation products to directly induce activation of porcine EC, with subsequent upregulation of adhesion and pro-coagulant molecules. Porcine aortic EC were isolated from wild-type and hDAF-transgenic pigs and incubated with human serum, either in the presence or absence of the soluble complement inhibitor TP10 (sCR1). Recombinant C5a, C1q-IgG immune complexes, C6-deficient human serum and serum containing anti-C9 Ab were used to identify EC activating complement products. Heat-inactivated human serum was used as a negative control. Cells were stained with antibodies against human C3, the MAC or with antibodies cross-reactive for porcine E-Selectin, VCAM-1 or Tissue Factor, and analyzed by flow cytometry. We found upregulation of E-Selectin and Tissue Factor on wild-type EC after incubation with human serum. This effect coincided with the deposition of C3 and MAC on the membrane of these cells. The addition of TP10 inhibited EC activation by up to 95%. In contrast, greatly reduced C3 and MAC deposition was detected on hDAF transgenic cells, and no complement-mediated EC activation was seen. Experiments with C6-deficient serum and incubation with anti-C9 Ab indicate a major role of the MAC in serum-mediated EC activation, whereas neither C5a nor C1q-IgG caused activation of EC. These data provide further explanation of the protective role of human DAF in the pig-to-primate xenotransplantation model.
Low complexity adaptive beamforming and power allocation for OFDM over wireless networks (2003)

In this paper, the performance of a multiuser wireless network using OFDM, combined with power control and adaptive beamforming for uplink transmission is presented. An adaptive power control algorithm is exploited to achieve the desired signal to noise and interference ratio (SINR) at each subchannel and increase the power efficiency of the mobile transmitter. Therefore, we can achieve a better overall error probability with a fixed total power. A distributed iterative algorithm is used to jointly update the transmission power and the beamformer weights at each subchannel so that it can converge to the optimal solution for both power and beamforming vectors at each subchannel. Another algorithm has been proposed to decrease the complexity resulting from the number of beamformers and FFT blocks. The algorithms use only the interference measured locally by the transmitter. Unlike most of the loading algorithms which optimize the bit distribution and subchannel power allocation for a single transmitter, this approach tries to optimize the power allocation and decrease the interference for the whole network.
A Tridecamer DNA Sequence Supports Human Mitochondrial RNA 3′-End Formation In Vitro (1988)

Vertebrate mitochondrial genomes contain a putative transcription termination site at the boundary between the genes for 16S rRNA and leucyl-tRNA. We have described previously an in vitro transcription system from human cells with the capacity to generate RNA 3' ends with the same map positions as those synthesized in vivo. By assaying the ability of variously truncated templates to support 3'-end formation, we demonstrated that the tridecamer sequence 5'-TGGCAGAGCCCCGG-3', contained entirely within the gene for leucyl-tRNA, is necessary to direct accurate termination. When two tridecamer sequences and their immediate flanking regions were placed in tandem, termination occurred at both promoter-proximal and promoter-distal sites. Furthermore, termination was competitively inhibited, in a concentration-dependent manner, by DNA containing the tridecamer sequence. These results suggest a modest sequence requirement for transcription termination that is contingent on a factor capable of recognizing the presence of the tridecamer DNA sequence.
Why Atherosclerotic Vessels Narrow: The Fibrin Hypothesis (1999)

We have tried to offer a unifying hypothesis tying vessel wall narrowing in atherosclerotic plaques to plaque rupture and healing (Fig. 7). This hypothesis is supported by evidence that smooth muscle cells are capable of interacting with a fibrin clot, specifically contracting a fibrin clot, and that inhibition of coagulation prevents narrowing of injured vessels. This work also presents alpha 5 beta 1 and a bridge protein, fibronectin, as possible targets to be used in pharmaceutical intervention to inhibit atherosclerosis progression.
Discovery, Design, and Optimization of Isoxazole Azepine BET Inhibitors (2013)

The identification of a novel series of small molecule BET inhibitors is described. Using crystallographic binding modes of an amino-isoxazole fragment and known BET inhibitors, a structure-based drug design effort lead to a novel isoxazole azepine scaffold. This scaffold showed good potency in biochemical and cellular assays and oral activity in an in vivo model of BET inhibition.
Association Between an Aggrecan Gene Polymorphism and Lumbar Disc Degeneration (1999)

The current study showed that multilevel and severe disc degeneration was present in the participants with shorter variable numbers of tandem repeat length of the aggrecan gene. This suggests that subjects with shorter variable numbers of tandem repeat length of the aggrecan gene have a risk of having multilevel disc degeneration develop at an early age.
QRON: QoS-Aware Routing in Overlay Networks (2004)

Recently, many overlay applications have emerged in the Internet. Currently, each of these applications requires their proprietary functionality support. A general unified framework may be a desirable alternative to application-specific overlays. We introduce the concept of overlay brokers (OBs). We assume that each autonomous system in the Internet has one or more OBs. These OBs cooperate with each other to form an overlay service network (OSN) and provide overlay service support for overlay applications, such as resource allocation and negotiation, overlay routing, topology discovery, and other functionalities. The scope of our effort is the support of quality-of-service (QoS) in overlay networks. Our primary focus is on the design of QoS-aware routing protocols for overlay networks (QRONs). The goal of QRON is to find a QoS-satisfied overlay path, while trying to balance the overlay traffic among the OBs and the overlay links in the OSN. A subset of OBs, connected by the overlay paths, can form an application specific overlay network for an overlay application. The proposed QRON algorithm adopts a hierarchical methodology that enhances its scalability. We analyze two different types of path selection algorithms. We have simulated the protocols based on the transit-stub topologies produced by GT-ITM. Simulation results show that the proposed algorithms perform well in providing a QoS-aware overlay routing service.
Biochemical Applications of Differential Scanning Calorimetry (1987)

Differential scanning calorimetry (DSC) and the closely related differential thermal analysis (DTA) have been widely employed during the last several decades in the thermodynamic study of processes that are initiated by either an increase or a decrease in temperature. This review focuses on biochemical applications of DSC. Macromolecular and polymolecular structures stabilized by the cooperation of numerous weak forces are important to most biochemical processes. Since such highly cooperative structures undergo conformational or phase transitions upon being heated, significant information concerning these structures can be obtained by DSC. Small molecules cannot be studied by DSC unless they form aggregates showing intermolecular cooperation, as in crystals. This is illustrated in Table 1. Since the enthalpies of chemical processes rarely are as large as 20 cal g-l, it is evident that molecules having molecular weights, or molecular aggregates having aggregate weights, in the thousands of daltons are required to give transitions sufficiently sharp for useful DSC observation. In a scanning calorimeter, one measures the specific heat of a system as a function of the temperature. For a solution, the apparent specific heat of the solute, c2, is given by the expression
“Inclonals” (2009)

Full-length antibodies and antibodies that ferry a cargo to target cells are desired biopharmaceuticals. We describe the production of full-length IgGs and IgG-toxin fusion proteins in E. coli. In the presented examples of anti CD30 and anti EGF-receptor antibodies, the antibody heavy and light chains or toxin fusions thereof were expressed in separate bacterial cultures, where they accumulated as insoluble inclusion bodies. Following refolding and purification, high yields (up to 50 mg/L of shake flask culture) of highly purified (>90%) full-length antibodies and antibody-toxin fusions were obtained. The bacterially produced antibodies, named "Inclonals," equaled the performance of the same IgGs that were produced using conventional mammalian cell culture in binding properties as well as in cell killing potency. The rapid and cost effective IgG production process and the high quality of the resultant product may make the bacterial production of full-length IgG and IgG-drug fusion proteins an attractive option for antibody production and a significant contribution to recombinant antibody technology.
Temperature effects in hydrophobic interaction chromatography. (1996)

The effect of temperature from 5 degrees C to 50 degrees C on the retention of dansyl derivatives of amino acids in hydrophobic interaction chromatography (HIC) was investigated by HPLC on three stationary phases. Plots of the logarithmic retention factor against the reciprocal temperature in a wide range were nonlinear, indicative of a large negative heat capacity change associated with retention. By using Kirchoff's relations, the enthalpy, entropy, and heat capacity changes were evaluated from the logarithmic retention factor at various temperatures by fitting the data to a logarithmic equation and a quadratic equation that are based on the invariance and on an inverse square dependence of the heat capacity on temperature, respectively. In the experimental temperature interval, the heat capacity change was found to increase with temperature and could be approximated by the arithmetic average. For HIC retention of a set of dansylamino acids, both enthalpy and entropy changes were positive at low temperatures but negative at high temperatures as described in the literature for other processes based on the hydrophobic effect. The approach presented here shows that chromatographic measurements can be not only a useful adjunct to calorimetry but also an alternative means for the evaluation of thermodynamic parameters.
CAR-CRASH RECORDERS : BLACK BOXES ARE MOVING FROM AIRLINERS TO AUTOS (2002)

Most people know that electronic flight data recorders, also known as black boxes or event data recorders (EDR), are a critical source of information to aircraft crash investigators. Yet most motorists don't realize that if they're driving a newer model car, especially from General Motors or Ford, chances are good that their vehicle also has a device that can record accident data. Now, traffic safety experts and makers of these types of devices are pushing for more widespread use of this technology, which they say can lead to safer cars, better drivers, lower insurance rates and faster accident investigations. Includes interview with Ricardo Martinez, former head of the National Highway Traffic Safety Administration
Intraclonal homogeneity of clonotypic immunoglobulin M and diversity of nonclinical post-switch isotypes in multiple myeloma: insights into the evolution of the myeloma clone. (2002)

Detection of intraclonal diversity in the post-switch nonclinical isotype pool suggests that remnants of the parent B-cell clone coexist with malignant clonal precursors. The presence of intraclonal homogeneity in the pre-switch IgM pool supports the idea that pre-switch MM cells play a role in malignant events within the MM clone.
A Control System of the Nobeyama Millimeter Array (1991)

We have developed a control system of the Nobeyama Millimeter Array which is a radio interferometer for as­tronomical observations at millimeter wavelengths. The system consists of three sub-systems (MANAGER, EN­GINE, and STATUS CONTROLLER). Observers conduct their observations with MANAGER sub-system, which run on a UNIX workstation. ENGINE is a rigid system on an IBM compatible mainframe. It controls the accurate tracking of astronomical radio objects, and acquires a large amount of observed data from a receiver backend. STA­TUS CONTROLLER consists of several personal comput­ers which control and monitor the receiver system. These sub-systems are connected with an ethernet.
A performance analysis of the gamma database machine (1988)

This paper presents the results of an initial performance evaluation of the Gamma database machine. In our experiments we measured the effect of relation size and indices on response time for selection, join, and aggregation queries, and single-tuple updates. A Teradata DBC/1012 database machine of similar size is used as a basis for interpreting the results obtained. We also analyze the performance of Gemma relative to the number of processors employed and study the impact of varying the memory size and disk page size on the execution time of a variety of selection and join queries. We analyze and interpret the results of these experiments based on our understanding of the system hardware and software, and conclude with an assessment of the strengths and weaknesses of Gamma.
Electro-Magnetic Fields in the Home Environment (Color TV, Computer Monitor, Microwave Oven, Cellular Phone, ETC) as Potential Contributing Factors for the Induction of Oncogen C-fos Ab1, Oncogen C-fos Ab2, Integrin α 5 β 1 and Development of Cancer, as Well as Effects of Microwave on Amino Acid Composition of Food and Living Human Brain (1993)

The effects, on normal human subjects, of 3 minutes exposure to electro-magnetic fields (EMFs) emitted from: A) personal computers, B) color television sets, or C) microwave-ovens, or cellular phones were compared by placing the same large sheet of aluminum foil with a square hole or rectangular band-shaped hole at the chest level (or at the side of the head with the cellular phone), with or without grounding the aluminum foil, using the Bi-Digital O-Ring Test Dysfunction Localization and Molecular Identification Methods with cancer related substances (i.e., Oncogen C-fos Ab2 and mercury in the cell nucleus, Integrin alpha 5 beta 1 in the cell & nuclear membranes, and disappearance of Acetylcholine) as reference control substances. All the above sources of the EMFs not only induced the following various transitional abnormalities on the EMF entry area, but also induced similar abnormalities at the EMF exit area on the back (where the abnormality was found in the same shape as exposed EMF entry area, and the effect lasted for a shorter time than the entry point of the EMF): A) Exposure of the body at about 50 cm from the monitor of some of the typical personal computers resulted in: A1) decrease in Acetylcholine; A2) appearance of circulatory disturbance with the appearance of Thromboxane B2; A3) short-lasting appearance of Oncogen C-fos Ab2; A4) short-lasting appearance of Oncogen C-fos Ab1, though it lasted longer than C-fos Ab2; A5) no appearance of Integrin alpha 5 beta 1. B) part of the chest was exposed at a distance between 1 meter and up to 3 meters from a color television sized anywhere from 13'' to 21'', resulting in: B1) decrease in Acetylcholine; B2) appearance of circulatory disturbance with the appearance of Thromboxane B2; B3) short-lasting appearance of Oncogen C-fos Ab2; B4) short-lasting appearance of Oncogen C-fos Ab1, though it lasted longer than C-fos Ab2; B5) very short-lasting appearance of Integrin alpha 5 beta 1. C) When body was exposed, at a distance of 0.5m-2 meters, to microwaves emitted as leakage from a small microwave oven (about 2.45 GHz with 450 Watt output), the effects usually lasted about 2 to 3 times the exposure time at the exposed area and 1.6 to 2 times the exposure time at the back of the body at the EMF exit area.(ABSTRACT TRUNCATED AT 400 WORDS)
<title>Macroporous silicon formation for micromachining</title> (1997)

This paper presents a new technique of micromachining using macro porous silicon. Macro porous silicon is made by electrochemical etching in hydrofluoric acid. The etch rate and the morphology of the etched surface as a function of etch parameters, (current density, applied voltage and HF concentration) are investigated. Optimization of these parameters makes it possible to fabricate a micromechanical structures such as 45 micrometer deep, 3 micrometer wide and 8 micrometer pitch trenches. Furthermore the diameter of the pore is easy to control by adjusting the current density. During the pore formation an increase in the current density leads to an increase in the pore diameter. This does not effect the diameter of existing pores. This connection of the pores under the structure can be achieved. In this way, various kinds of single crystal silicon micromachined structures can be fabricated.
The genetics of age‐related macular degeneration (2001)

AIM: To review the genetics of age-related macular degeneration (AMD). The pathogenesis of AMD, the leading cause of severe visual disability and blindness in our community, remains unknown. However, AMD is regarded as a genetic disease where family history of AMD is a significant risk factor for the disease. Understanding the genetic factors associated with AMD offers the greatest chance for understanding the underlying disease processes. METHODS: Through a review of the literature and the use of original research findings, the current knowledge of the genetics of AMD is explored. CONCLUSION: AMD is increasing in prevalence and remains a major challenge for eye heath providers. Finding the genes that are associated with AMD offers the greatest chance for the development of preventative strategies and treatments.
Unusual Resistance of Peptidyl Transferase to Protein Extraction Procedures (1992)

Peptidyl transferase, the ribosomal activity responsible for catalysis of peptide bond formation, is resistant to vigorous procedures that are conventionally employed to remove proteins from protein-nucleic acid complexes. When the "fragment reaction" was used as a model assay for peptide bond formation, Escherichia coli ribosomes or 50S subunits retained 20 to 40 percent activity after extensive treatment with proteinase K and SDS, but lost activity after extraction with phenol or exposure to EDTA. Ribosomes from the thermophilic eubacterium Thermus aquaticus remained more than 80 percent active after treatment with proteinase K and SDS, which was followed by vigorous extraction with phenol. This activity is attributable to peptidyl transferase, as judged by specific inhibition by the peptidyl transferase-specific antibiotics chloramphenicol and carbomycin. In contrast, activity is abolished by treatment with ribonuclease T1. These findings support the possibility that 23S ribosomal RNA participates in the peptidyl transferase function.
Drug-induced pulmonary fibrosis. (2004)

Pulmonary fibrosis is characterized by the accumulation of excessive connective tissue in the lungs. Its causes include chronic administration of some drugs for example bleomycin, cyclophosphamide, amiodarone, procainamide, penicillamine, gold and nitrofurantoin; exposure to certain environmental factors such as gases, asbestos and silica and bacterial or fungal infections. Some systemic diseases also predispose to the disease for example rheumatoid arthritis and systemic lupus erythematosus. The disease is associated with release of oxygen radicals and some mediators such as tumor necrosis factor-alpha TNF-alpha, transforming growth factor-beta TGF-beta, PDGF, IGF-I, ET-I and interleukins 1, 4, 8 and 13. The symptoms of the disease include dyspnea, non-productive cough, fever and damage to the lung cells. It is diagnosed with the aid of chest radiography, high resolution computed tomographic scanning and the result of pulmonary function tests. Drug-induced pulmonary fibrosis may involve release of free oxygen radicals and various cytokines for example IL-Ibeta and TNF-alpha via activation of nuclear transcription factor NF-beta as in the case of bleomycin and mitomycin or via release of TGF-beta as in case of tamoxifen or via inhibition of macrophages' and lymphocytes' phospholipases as in the case of amiodarone with the resultant accumulation of phospholipids and reduction of the immune system.
Novel catalysts, catalysts support and catalysts coated membrane methods (2010)

Abstract This chapter introduces a new type of catalyst electrode for proton exchange membrane (PEM) fuel cells based on a nanostructured thin film catalyst support system. The nanostructured film consists of a single layer of a dense distribution of oriented crystalline whiskers of an organic pigment material. With areal number densities of 3–5 billion cm −2 and micrometer scale lengths, using dry processes, the whiskers are grown, coated uniformly with catalysts and transferred to the surface of a PEM to form an electrode. The physical and chemical properties of the nanostructured supports are reviewed first, followed by properties of the catalyst coatings and finally the electrode layer formation. Differences of these characteristics and properties from conventional carbon particle supported dispersed catalysts are widely made. Fuel cell performance examples and comparisons contrasting the mass and area cathode specific activities of the two types of catalyst electrode systems are demonstrated. The differences have implications for how membrane electrode assembly (MEA) are fabricated, ultimate catalyst loadings, system humidification requirements and durability.