gebhart/patrepeval huggingface dataset:
Isolation, characterization and cDNA cloning of nicotianamine synthase from barley (1999)

Basic cellular processes such as electron transport in photosynthesis and respiration require the precise control of iron homeostasis. To mobilize iron, plants have evolved at least two different strategies. The nonproteinogenous amino acid nicotianamine which is synthesized from three molecules of S-adenosyl-L-methionine, is an essential component of both pathways. This compound is missing in the tomato mutant chloronerva, which exhibits severe defects in the regulation of iron metabolism. We report the purification and partial characterization of the nicotianamine synthase from barley roots as well as the cloning of two corresponding gene sequences. The function of the gene sequence has been verified by overexpression in Escherichia coli. Further confirmation comes from reduction of the nicotianamine content and the exhibition of a chloronerva-like phenotype due to the expression of heterologous antisense constructs in transgenic tobacco plants. The native enzyme with an apparent Mr of approximately 105 000 probably represents a trimer of S-adenosyl-L-methionine-binding subunits. A comparison with the recently cloned chloronerva gene of tomato reveals striking sequence homology, providing support for the suggestion that the destruction of the nicotianamine synthase encoding gene is the molecular basis of the tomato mutation.
Identifying Rate‐Controlling Enzymes in Metabolic Pathways without Kinetic Parameters (1991)

Abstract The flux control coefficients, originally defined by Kacser and Burns, provide a sound theoretical basis for identifying rate‐controlling enzymes in metabolic pathways. However, the calculation of these quantities requires kinetic parameters, which are usually unavailable in practical systems. This article presents a method for evaluating the flux control coefficients by using measurements of metabolite concentrations in a transient state. The basis of this approach is the relationship identified here between transient fluxes and the flux control coefficients. Principal component analysis in the form of singular value decomposition is used to identify such relationships and evaluate the flux control coefficients. The approach does not require kinetic parameters and depends only on the knowledge of pathway stoichiometry, which is generally available.
Mechanism of Substrate Recognition by Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variants Revealed by a Novel Structural Intermediate (2006)

Human immunodeficiency virus type 1 (HIV-1) protease processes and cleaves the Gag and Gag-Pol polyproteins, allowing viral maturation, and therefore is an important target for antiviral therapy. Ligand binding occurs when the flaps open, allowing access to the active site. This flexibility in flap geometry makes trapping and crystallizing structural intermediates in substrate binding challenging. In this study, we report two crystal structures of two HIV-1 protease variants bound with their corresponding nucleocapsid-p1 variant. One of the flaps in each of these structures exhibits an unusual "intermediate" conformation. Analysis of the flap-intermediate and flap-closed crystal structures reveals that the intermonomer flap movements may be asynchronous and that the flap which wraps over the P3 to P1 (P3-P1) residues of the substrate might close first. This is consistent with our hypothesis that the P3-P1 region is crucial for substrate recognition. The intermediate conformation is conserved in both the wild-type and drug-resistant variants. The structural differences between the variants are evident only when the flaps are closed. Thus, a plausible structural model for the adaptability of HIV-1 protease to recognize substrates in the presence of drug-resistant mutations has been proposed.
IL-21 is the primary common γ chain-binding cytokine required for human B-cell differentiation in vivo (2011)

SCID resulting from mutations in IL2RG or JAK3 is characterized by lack of T and natural killer cells; B cells are present in normal number, but antibody responses are defective. Hematopoietic cell transplantation (HCT) is curative for SCID. However, B-cell dysfunction persists in a substantial proportion of patients. We hypothesized that impaired B-cell responses after HCT in IL2RG/JAK3 deficiency results from poor donor B-cell engraftment and defective γc-dependent cytokine signaling in host B cells. To test this, and to identify which γc cytokine(s) is critical for humoral immunity, we studied 28 transplanted patients with IL2RG/JAK3 deficiency. Lack of donor B-cell engraftment associated with persistent humoral dysfunction and significantly reduced memory B cells. B-cell proliferation induced by CD40L alone or together with CpG, anti-Ig, IL-4, IL-10, or IL-13 was comparable in healthy controls and in post-HCT SCID patients, irrespective of their chimerism status. However, in vitro stimulation with CD40L/IL-21 induced B-cell proliferation, plasmablast differentiation, and antibody secretion in patients with donor B cells, but not in patients with autologous B cells. These data imply that IL-21-mediated signaling is critical for long-lived humoral immunity and to restore antibody responses in IL2RG/JAK3-deficient patients after HCT. Furthermore, in vitro stimulation with CD40L/IL-21 can predict in vivo B-cell immunity in IL2RG/JAK3 SCID after transplantation.
A functional folate receptor is induced during macrophage activation and can be used to target drugs to activated macrophages (2008)

Previous work has demonstrated that a subset of macrophages expresses a folate receptor (FR) that can mediate internalization of folate-linked molecules, including imaging and therapeutic agents. To characterize this subset, macrophages were collected from peritoneal cavities of mice injected with saline, thioglycolate, zymosan, heat-killed or live bacteria, and cell-surface markers that coexpress with FR were identified. Virtually no F4/80(+) peritoneal macrophages from saline-injected mice expressed FR, whereas numerous macrophages from mice injected with each inflammatory stimulus expressed FR. Examination of cell differentiation antigens that are up-regulated in FR(+) macrophages revealed markers characteristic of an activated state (CD80, CD86, Ly-6C/G), whereas macrophages lacking these activation markers expressed few or no FR. FR(+) macrophages also produced tumor necrosis factor-alpha (TNF-alpha) and reactive oxygen species, and production of reactive oxygen species correlated linearly with expression of FR. Synovial macrophages collected from arthritic patients were found to bind and internalize folate-linked dyes. Moreover, a folate-linked radioimaging agent was shown to image inflamed joints of rheumatoid arthritic patients. These results suggest that FR constitutes a marker for macrophage activation and that FR(+) macrophages can be targeted with folate-linked drugs without promoting drug uptake by nonactivated macrophages. This trial was registered at www.clinicaltrials.gov as #NCT00588393.
Removing weather effects from monochrome images (2005)

Images of outdoor scenes captured in bad weather suffer from poor contrast. Under bad weather conditions, the light reaching a camera is severely scattered by the atmosphere. The resulting decay in contrast varies across the scene and is exponential in the depths of scene points. Therefore, traditional space invariant image processing techniques are not sufficient to remove weather effects from images. In this paper, we present a fast physics-based method to compute scene structure and hence restore contrast of the scene from two or more images taken in bad weather In contrast to previous techniques, our method does not require any a priori weather-specific or scene information, and is effective under a wide range of weather conditions including haze, mist, fog and other aerosols. Further, our method can be applied to gray-scale, RGB color, multi-spectral and even IR images. We also extend the technique to restore contrast of scenes with moving objects, captured using a video camera.
Nanoscale CMOS spacer FinFET for the terabit era (2002)

A spacer lithography process technology, which uses a sacrificial layer and spacer layer formed by chemical vapor deposition (CVD), has been developed. It has been applied to make a sub-40-nm Si-fin structure for a double-gate FinFET with conventional dry etching for the first time. The minimum-sized features are defined not by the photolithography but by the CVD film thickness. Therefore, this spacer lithography technology yields better critical dimension uniformity than conventional optical or e-beam lithography and defines smaller features beyond the limit of current lithography technology. It also provides a doubling of feature density for a given lithography pitch, which increases current by a factor of two. To demonstrate this spacer lithography technology, Si-fin structures have been patterned for planar double-gate CMOS FinFET devices.
A CONVENIENT SYNTHESIS OF GLYCOSYLATED HYDANTOINS AS POTENTIAL ANTIVIRAL AGENTS (1997)

Abstract Reaction of 5-arylidene-2-thiohydantoins 3a-d with glycosyl halides 4a,b under alkaline conditions gave the respective bisglycosylated derivatives 5a-h. Deacetylation with ammonia in methanol caused a change of the S-glycosyl residue and gave the N-3 glycosylated analogues 7a-h. S-Glycosylation also occured when N-3 substituted hydantoins 9a-h were reacted. Key Words: 2-Thiohydantoins2,3,4,6-tetra-O-acetyl-α-D-glycopyranosyl bromidesmonoglycosylated hydantoinsbisglycosylated hydantoins
Visual overviews for discovering key papers and influences across research fronts (2009)

Abstract Gaining a rapid overview of an emerging scientific topic, sometimes called research fronts , is an increasingly common task due to the growing amount of interdisciplinary collaboration. Visual overviews that show temporal patterns of paper publication and citation links among papers can help researchers and analysts to see the rate of growth of topics, identify key papers, and understand influences across subdisciplines. This article applies a novel network‐visualization tool based on meaningful layouts of nodes to present research fronts and show citation links that indicate influences across research fronts. To demonstrate the value of two‐dimensional layouts with multiple regions and user control of link visibility, we conducted a design‐oriented, preliminary case study with 6 domain experts over a 4‐month period. The main benefits were being able (a) to easily identify key papers and see the increasing number of papers within a research front, and (b) to quickly see the strength and direction of influence across related research fronts.
Arterial smooth muscle cells in primary culture produce a platelet-derived growth factor-like protein. (1985)

Adult rat arterial smooth muscle cells (SMC) in primary culture modulate from contractile to synthetic phenotype. This process includes partial loss of myofilaments and formation of an extensive rough endoplasmic reticulum and a large Golgi complex. It gives the cells the ability to initiate DNA synthesis and actively proliferate when stimulated with serum or isolated growth factors. After a few divisions, growth becomes partly independent of exogenous mitogens and does not cease until multiple cell layers have been formed. Here, it is demonstrated that serum-free conditioned medium from primary cultures of adult rat arterial SMC contains a factor that initiates DNA synthesis in growth-arrested secondary cultures of SMC. The mitogenic activity was neutralized by antibodies to platelet-derived growth factor (PDGF), and no mitogenic activity occurred in conditioned medium from cultures pretreated with actinomycin D, excluding release into the medium of PDGF adsorbed to the plastic vessels during the initial culture in serum-containing medium. Exposure of human fibroblasts to samples of the conditioned medium at 4 degrees C inhibited subsequent binding of 125I-labeled PDGF. It was further shown that the SMC of the primary cultures were able to initiate DNA synthesis in a chemically defined medium lacking PDGF and other growth factors. During the early, most active, and partly autonomous growth phase, the SMC had a low binding capacity for 125I-labeled PDGF and responded but little to stimulation with exogenous PDGF. Later on, with increasing cell density and decreasing growth rate, the ability to bind and respond to exogenous PDGF increased. Taken together, the observations suggest that modulation of SMC from contractile to synthetic phenotype is accompanied by production of a PDGF-like protein and autocrine or possibly by mitogen-independent initiation of DNA synthesis. Functionally, this may be important during wound healing and in the development of atherosclerotic lesions.
Controlled trial of azathioprine in chronic ulcerative colitis. (1982)

A double-blind controlled trial of azathioprine in a dose of 2-2.5 mg/kg body weight over six months was conducted among 44 patients with active chronic ulcerative colitis. Three patients treated with placebo did not complete the trial because their disease became so severe that colectomy was performed. Among patients who completed the trial the mean dose of prednisolone necessary to control the disease decreased in those treated with azathioprine and those treated with placebo; the reduction was greater among those who took azathioprine (p less than 0.001). Activity of the disease apparently improved in both treatment groups but a significant (p less than 0.001) trend was observed only in those patients treated with azathioprine. No serious side effects from azathioprine occurred during the trial but seven of 24 patients had to stop the drug because of nausea. Azathioprine may have a role in the treatment of a few patients wih troublesome chronic colitis for whom conventional drug treatment is ineffectual, or for whom continuous systemic corticosteroid treatment is needed to control symptoms, and for whom surgical treatment is inappropriate.
A New Synthesis of 1,2,3,4-Tetrahydro-2-methyl-4-phenylisoquinolines (1990)

1,2,3,4-Tetrahyro-2-methyl-4-phenylisoquinolines 6 are obtained from aromatic aldehydes 1, methyl amine and α-haloacetophenones 2 in the presence of sodium borohydride followed by cyclization with sulfuric acid and zinc in methanol.
Glucose in Vaginal Secretions Before and After Oral Glucose Tolerance Testing in Women With and Without Recurrent Vulvovaginal Candidiasis (2006)

II-2.
Section IV.D.3 for DOE 2013 Annual Report: Novel Phosphazene-based Compounds to Enhance Safety and Stability of Cell Chemistries for High Voltage Applications (INL) (2013)

Electrolytes play a central role in performance and aging in most electrochemical systems. As automotive and grid applications place a higher reliance on electrochemical stored energy, it becomes more urgent to have electrolyte components that enable optimal battery performance while promoting battery safety and longevity. Safety remains a foremost concern for widespread utilization of Li-ion technology in electric-drive vehicles, especially as the focus turns to higher voltage systems (5V). This work capitalizes on the long established INL expertise regarding phosphazene chemistry, aimed at battery-viable compounds for electrolytes and electrodes that are highly tolerant to abusive conditions. This report showcases our 2013 work for the DOE applied battery research (ABR) program, wherein testing results are summarized for INL electrolytes and alternative anode materials.
Muscle contraction increases lactate transport while reducing sarcolemmal MCT4, but not MCT1 (2002)

Rates of lactate uptake into giant sarcolemmal vesicles were determined in vesicles collected from rat muscles at rest and immediately after 10 min of intense muscle contraction. This contraction period reduced muscle glycogen rapidly by 37-82% in all muscles examined (P < 0.05) except the soleus muscle (no change P > 0.05). At an external lactate concentration of 1 mM lactate, uptake into giant sarcolemmal vesicles was not altered (P > 0.05), whereas at an external lactate concentration of 20 mM, the rate of lactate uptake was increased by 64% (P < 0.05). Concomitantly, the plasma membrane content of monocarboxylate transporter (MCT)1 was reduced slightly (-10%, P < 0.05), and the plasma membrane content of MCT4 was reduced further (-25%, P < 0.05). In additional studies, the 10-min contraction period increased the plasma membrane GLUT4 (P < 0.05) while again reducing MCT4 (-20%, P < 0.05) but not MCT1 (P > 0.05). These studies have shown that intense muscle contraction can increase the initial rates of lactate uptake, but only when the external lactate concentrations are high (20 mM). We speculate that muscle contraction increases the intrinsic activity of the plasma membrane MCTs, because the increase in lactate uptake occurred while plasma membrane MCT4 was decreased and plasma membrane MCT1 was reduced only minimally, or not at all.
Genetic Variability of Seed Sugar Content in Worldwide Soybean Germplasm Collections (2009)

Soluble sugar is an important quality trait in food‐grade soybeans [ Glycine max (L.) Merr.]. Desirable sugars such as sucrose, glucose, and fructose can help improve the taste and flavor of soyfood including tofu, soymilk, and natto; whereas oligosaccharides including raffinose and stachyose are indigestible by humans and animals and often cause flatulence or diarrhea. In this study, 241 plant introductions (PIs) of three maturity groups (MGs) from 28 origins were investigated for seed sugar content including glucose, fructose, sucrose, raffinose, and stachyose. Variation was detected in individual and total sugars in soybean PIs from different origins and MGs. Sucrose and stachyose are the major sugars in soybean seed. The sucrose content ranged from 1.6 to 95.4 mg g −1 with 13 PIs containing greater than 70 mg g −1 and 14 PIs having less than 10 mg g −1 The stachyose content ranged from 0.2 to 69.6 mg g −1 with 14 PIs containing less than 10 mg g −1 stachyose. The high sucrose and low stachyose types are the most valuable for breeding specialty soybeans for soyfood and animal feed. In addition, 30 PIs were identified as having high concentrations of glucose or fructose as major sugars. This new class of high glucose or fructose has not been reported before. While soybean germplasm with unique sugar profiles may be useful for future breeding and genetic research, environmental effects on sugar stability will need to be further investigated.
Colloidal Carbon as a Combined Ophthalmoscopic and Microscopic Probe of Retinal and Choroidal Vascular Integrity (With 1 color plate) (1985)

While studying an experimental retinal immunopathy, we searched for a vascular tracer that would permit us to test the anatomical and functional status of retinal and choroidal vessels by ophthalmoscopy, light microscopy, and electron microscopy in the same eye. We found that colloidal carbon, administered intravenously, can be seen ophthalmoscopically in the choroidal and retinal circulations, and abnormal deposits of it can be visualized in vivo. The ophthalmoscopic findings can be corroborated and extended by stereomicroscopy, and later the same specimens can be used for light and transmission electron microscopical studies. This tracer, thus, would allow the correlation of the ophthalmoscopic appearance of a clinical lesion with its histological and ultrastructural substrata.
Numerical Computation of Fluid Flow and Aerosol Transport in a Long Electrical Mobility Spectrometer (2010)

Size distribution of submicron airborne particles can be effectively determined using electrical mobility technique. In this study, a numerical computation model for prediction of fluid flow and aerosol transport in a long column, electrical mobility spectrometer (EMS) has been developed. The internal 3D structure of an EMS [Intra and Tippayawong (2009), Korean J. Chem. Eng., 26(1), 269] was employed to simulate the complex flow patterns and aerosol particle trajectories in the EMS, including the swirling flow developed near the sheath air inlet slit. The incompressible Navier-Stokes equations were numerically calculated for the gas flow and particle trajectories, with a commercial computational fluid dynamics software package, FLUENT 6.3. The calculated results were found to agree well with previously published results in the literature. Prediction of fluid flow and aerosol transport was particularly useful in the EMS design and development
The cytomegalovirus enhancer: a pan-active control element in transgenic mice. (1990)

In an effort to identify widely active positive regulatory elements, we have examined the action of the cytomegalovirus enhancer-promoter in transgenic mice. These elements activated expression in 24 of 28 tissues tested. The greatest expression was observed in the heart, kidney, brain, and testis. Maximum expression further localized to specific cells within the heart and kidney.
Gain equalization of EDFA cascades (1997)

Investigates the impact of wavelength-dependent erbium-doped fiber amplifier (EDFA) gain spectrum on multichannel direct-detection lightwave transmission systems employing multiple amplifiers. An analysis is presented which quantifies the constraints imposed by received power imbalance, signal-to-noise ratio (SNR), and receiver sensitivity on an EDFA cascade. Expressions are derived which relate the system constraints to the EDFA gain imbalance, bit rate, number of channels, and receiver dynamic range. Results demonstrate that when four-wave mixing (FWM) is compensated in an 11-channel system, received power imbalance can impose a significant constraint on transmission distance when the EDFA gain imbalance is greater than 1 dB or when bit rate is less than 1.8 Gb/s. In addition, performance of the preemphasis gain equalization technique is studied for multichannel systems employing APD or p-i-n/FET direct-detection optical receivers. Simple expressions are derived which can be used to quantify the increase in transmission distance obtained when employing preemphasis equalization. Results indicate that equalization of the received power spectrum can provide a two- to four-fold increase in the transmission distance when using APD receivers, compared to a one- to two-fold improvement with p-i-n/FET receivers. Analytic results are compared with results obtained by proven simulation methods and found to be in good agreement.
Three band-gap QW intermixing in InP/InGaAs/InGaAsP system for monolithically integrated optical switch (2002)

We have demonstrated that independent control of three band-gaps across an InP-InGaAs-InGaAsP QW wafer can be achieved by a two-stage sputtered silica intermixing processes. This will be used for optimisation of the performance of optical switches which consist of passive components, modulators and amplifiers.