gebhart/patrepeval huggingface dataset:
Informational Complexity and Functional Activity of RNA Structures (2004)

Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an approximately 1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers.
Major cereal crops benefit from biological nitrogen fixation when inoculated with the nitrogen‐fixing bacterium Pseudomonas protegens Pf‐5 X940 (2016)

A main goal of biological nitrogen fixation research has been to expand the nitrogen-fixing ability to major cereal crops. In this work, we demonstrate the use of the efficient nitrogen-fixing rhizobacterium Pseudomonas protegens Pf-5 X940 as a chassis to engineer the transfer of nitrogen fixed by BNF to maize and wheat under non-gnotobiotic conditions. Inoculation of maize and wheat with Pf-5 X940 largely improved nitrogen content and biomass accumulation in both vegetative and reproductive tissues, and this beneficial effect was positively associated with high nitrogen fixation rates in roots. <sup>15</sup> N isotope dilution analysis showed that maize and wheat plants obtained substantial amounts of fixed nitrogen from the atmosphere. Pf-5 X940-GFP-tagged cells were always reisolated from the maize and wheat root surface but never from the inner root tissues. Confocal laser scanning microscopy confirmed root surface colonization of Pf-5 X940-GFP in wheat plants, and microcolonies were mostly visualized at the junctions between epidermal root cells. Genetic analysis using biofilm formation-related Pseudomonas mutants confirmed the relevance of bacterial root adhesion in the increase in nitrogen content, biomass accumulation and nitrogen fixation rates in wheat roots. To our knowledge, this is the first report of robust BNF in major cereal crops.
Resistive Polymer Versus Forced-Air Warming: Comparable Heat Transfer and Core Rewarming Rates in Volunteers (2008)

Heating efficacy and core rewarming rates were similar with full-body forced-air and full-body resistive polymer heating in healthy volunteers.
Long-Range Electron Transfer in Heme Proteins (1986)

Kinetic experiments have conclusively shown that electron transfer can take place over large distances (greater than 10 angstroms) through protein interiors. Current research focuses on the elucidation of the factors that determine the rates of long-range electron-transfer reactions in modified proteins and protein complexes. Factors receiving experimental and theoretical attention include the donor-acceptor distance, changes in geometry of the donor and acceptor upon electron transfer, and the thermodynamic driving force. Recent experimental work on heme proteins indicates that the electron-transfer rate falls off exponentially with donor-acceptor distance at long range. The rate is greatly enhanced in proteins in which the structural changes accompanying electron transfer are very small.
Link-level connection control schemes in a high-speed satellite data network: a performance comparison (1992)

The author makes a performance comparison between a connection-oriented (CO) logical link control (LLC) protocol and a connectionless (CL) LLC protocol in a high-speed satellite packet network with the time-division-multiple-access (TDMA)-reservation multiple-access protocol. In particular, the way that the channel transmission rate affects the performance of the two LLC protocols is examined. The most suitable LLC protocol for any given system environment is determined. The comparison indicates that the CL-LLC protocol has more advantages over the CO-LLC protocol as the channel transmission rate increases and that the suitable region for the CL-LLC protocol becomes wider as the receiver-buffer capacity increases and as the network load decreases.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
<title>Preliminary lithographic characteristics of an all-organic chemically amplified resist formulation for single-layer deep-UV lithography</title> (1991)

When used in conjunction with a nitrobenzylester photoacid generator, poly(t-butoxycarbonyloxy-styrene-sulfone) deep-UV resist films exhibit high contrast, good resolution and linewidth stability. Use of overcoat materials dramatically reduce the surface inhibition problems, improve the latent image stability (time delay) and enhance the sensitivity by isolating the resist surface from environmental contaminants that react with the photogenerated acid. The photospeed of the all organic CAMP formulation is lower compared to the arsenate based system but can be improved by using more aggressive PEB conditions. Coded, 0.35 micrometers l/s pairs could be resolved in 1 micrometers thick resist films at a dose of 20-30 mJ/cm2. The exposure latitude is approximately equals 25% for 0.5 micrometers features, upon exposure with a GCA prototype deep-UV exposure tool with a NA equals 0.35 and 5x reduction optics. This paper will discuss the resolution, depth-of-focus, exposure latitude and processing characteristics obtained during the evaluation of this chemically amplified resist.
A conjugation-like mechanism for prespore chromosome partitioning during sporulation in Bacillus subtilis. (1995)

Spore formation in Bacillus subtilis begins with an asymmetric cell division that superficially resembles the division of vegetative cells. Mutations in the spoIIIE gene of B. subtilis partially block partitioning of one chromosome into the smaller (prespore) compartment of the sporulating cell. Point mutations that specifically block prespore chromosome partitioning affect a carboxy-terminal domain of SpoIIIE that shows significant sequence similarity to the DNA transfer (Tra) proteins of several conjugative plasmids of Streptomyces. In wild-type sporulating cells, the prespore chromosome passes through an intermediate stage resembling the state in which spoIIIE mutant cells are blocked. The prespore chromosome is then transferred progressively through the newly formed spore septum. We propose that translocation of the prespore chromosome occurs by a mechanism that is functionally related to the conjugative transfer of plasmid DNA.
ChemInform Abstract: Anomeric O‐Alkylation. Part 6. A Simple Synthesis of KDO α‐Glycosides by Anomerically Selective O‐Alkylation. (1988)

Abstract Treatment of the KDO (= 3‐deoxy‐D‐manno‐2‐octulosonic acid) derivative (I) with NaH followed by reaction with the D‐glucose derivative (II) gives selectively the α‐linked product (III).
Determination of neutralizing epitopes in variable domains I and IV of the major outer-membrane protein from Chlamydia trachomatis serovar K (1994)

Chlamydia trachomatis is a leading cause of sexually transmitted diseases and a number of strategies have been developed to produce vaccines to prevent its transmission. The purpose of this study was to map the neutralizing epitopes of C. trachomatis major outer-membrane protein (MOMP) serovar K by using anti-MOMP antibodies and synthetic peptides. Seven anti-MOMP monoclonal antibodies and three polyclonal antisera were produced and characterized. Their fine specificity was defined by direct binding assay on 15 peptides of 10 amino acid residues, overlapping by five residues, corresponding to the four variable domains (VDI-VDIV: residues 64-85, 139-160, 224-237 and 287-319) of MOMP serovar K. Our data confirmed that a neutralizing epitope is found in VDIV, defined by peptides K12 and K13. This epitope is 296TTLNPTIAG304, which has never been reported as a neutralizing epitope of serovar K. Another neutralizing epitope, defined by peptide K2, has been identified in VDI. This epitope is in the same position as 71VAGLEK76, a peptide with neutralizing activity found in serovar A, but they are not identical because antibodies against peptide K2 do not bind to this epitope. No neutralizing epitope was found in the two other variable domains (VDII and III). In summary, two neutralizing sites, one in variable domain I and one in variable domain IV, were identified in serovar K.
Coprecipitation and Characterization of Nickel-Cobalt- Manganese Hydroxides Precursor for Battery Cathode Materials (2013)

Abstract not Available.
Evaluation of the Audible Distortion and Noise Produced by Digital Audio Converters (1987)

Une methode de mesure revele les non-linearites du convertisseur numerique a faible niveau. Distorsion resultant de tels defauts
A Comparison of Sulfonate and Carboxylate Ionomers (1980)

A comparison of metal carboxylate and metal sulfonate ionomers based on identical polystyrene backbones was conducted, showing a substantial difference between these two ionomers. Sodium carboxylated and sodium sulfonated polystyrenes were synthesized containing 0.3-5.0 mol % ionic functionality. The softening behavior of the metal sulfonate ionomer suggests that strong ionic association persists to temperatures of 50°-100°C above that of the corresponding carboxylate ionomer. Similarly, the melt viscosities of the sulfonate ionomers at a given level of functionality are two to three orders of magnitude greater than those of the carboxylate analogues. Similar differences are observed in the solution behavior of these two ionomers. These results are attributable to greater polarization in the sulfonate ionomers, thereby providing stronger ionic association.
A flagella-less mutant of Borrelia burgdorferi. Structural, molecular, and in vitro functional characterization. (1991)

A nonmotile mutant of Borrelia burgdorferi, the etiologic agent of Lyme disease, was isolated and characterized. The mutant was compared with the wild-type predecessor as well as with a motile back-revertant of the same genetic background. The mutant lacked, by morphologic, biochemical, and immunologic criteria, the major structural protein of flagella, flagellin. This mutation was not associated with major DNA rearrangements or with failure of transcription. An apparent consequence of a loss of flagella was reduced ability to penetrate human endothelial cell layers in vitro. In another assessment of functional significance, the flagella-less mutant was equal if not superior to flagella-bearing, isogenic isolates when examined in an enzyme-linked immunosorbent assay for anti-B. burgdorferi antibodies in the sera of Lyme disease patients. These studies of a mutant, the first among pathogenic Borrelia spp. to be characterized, indicate that the flagellum and motility it confers play a role in B. burgdorferi's invasion of human tissues. A flagella-less B. burgdorferi may be useful as the basis of a more specific immunoassay and a vaccine for protection against Lyme disease.
A Multiple Testing Procedure for Clinical Trials (1979)

A multiple testing procedure is proposed for comparing two treatments when response to treatment is both dichotomous (i.e., success or failure) and immediate. The proposed test statistic for each test is the usual (Pearson) chi-square statistic based on all data collected to that point. The maximum number (N) of tests and the number (m1 + m2) of observations collected between successive tests is fixed in advance. The overall size of the procedure is shown to be controlled with virtually the same accuracy as the single sample chi-square test based on N(m1 + m2) observations. The power is also found to be virtually the same. However, by affording the opportunity to terminate early when one treatment performs markedly better than the other, the multiple testing procedure may eliminate the ethical dilemmas that often accompany clinical trials.
Signaling Events in Amyloid β-Peptide-induced Neuronal Death and Insulin-like Growth Factor I Protection (2002)

Amyloid -peptide (A) is implicated as the toxic agent in Alzheimer's disease and is the major component of brain amyloid plaques. In vitro, A causes cell death, but the molecular mechanisms are unclear. We analyzed the early signaling mechanisms involved in A toxicity using the SH-SY5Y neuroblastoma cell line. A caused cell death and induced a 2-to 3-fold activation of JNK. JNK activation and cell death were inhibited by overexpression of a dominant-negative SEK1 (SEK1-AL) construct. Butyrolactone I, a cdk5 inhibitor, had an additional protective effect against A toxicity in these SEK1-AL-expressing cells suggesting that cdk5 and JNK activation independently contributed to this toxicity. A also weakly activated ERK and Akt but had no effect on p38 kinase. Inhibitors of ERK and phosphoinositide 3-kinase (PI3K) pathways did not affect A-induced cell death, suggesting that these pathways were not important in A toxicity. Insulin-like growth factor I protected against A toxicity by strongly activating ERK and Akt and blocking JNK activation in a PI3K-dependent manner. Pertussis toxin also blocked A-induced cell death and JNK activation suggesting that G i/o proteins were upstream activators of JNK. The results suggest that activation of the JNK pathway and cdk5 may be initial signaling cascades in A-induced cell death.
Extracellular ATP causes apoptosis and necrosis of cultured mesangial cells via P2Z/P2X7receptors (1998)

Mesangial cells undergo cell death both by apoptosis and necrosis during glomerular disease. Since nucleotides are released from injured and destroyed cells in the glomerulus, we examined whether extracellular ATP and its receptors may regulate cell death of cultured mesangial cells. Addition of extracellular ATP (300 microM to 5 mM) to cultured rat mesangial cells for 90 min caused a 5. 8-fold increase in DNA fragmentation (terminal deoxynucleotidyl transferase assay) and a 4.2-fold increase in protein levels of the tumor suppressor p53, which is thought to regulate apoptosis. Apoptotic DNA fragmentation was confirmed by the diphenylamine assay and by staining with the DNA-specific fluorochrome Hoechst 33258. The necrotic markers, release of lactate dehydrogenase and uptake of trypan blue, were not positive before 3 h of ATP addition. The effects of ATP on DNA fragmentation and p53 expression were reproduced by the purinergic P2Z/P2X7 receptor agonist, 3'-O-(4-benzoylbenzoyl)-ATP, and inhibited by the P2Z/P2X7 receptor blocker, oxidized ATP. Transcripts encoding the P2Z/P2X7 receptor were expressed by cultured mesangial cells as determined by Northern blot analysis. P2Z/P2X7 receptor-associated pore formation in the plasma membrane was demonstrated by the Lucifer yellow assay. We conclude that activation of P2Z/P2X7 receptors by extracellular ATP causes apoptosis and necrosis of cultured mesangial cells. Activation of purinergic P2Z/P2X7 receptors may play a role in causing death of mesangial cells during glomerular disease.
Satellite DAB (1995)

Abstract Service requirements for digital audio broadcasting (DAB) from satellites are presented, and plans for implementing such systems in various countries are surveyed. Technical and economic constraints, including satellite transmitter power, frequencies of operation, transmission bandwidth, service interference and user receiver design are discussed particularly for DAB systems employing mobile receiving terminals where transmission outage from blockage and multipath fading must be addressed. Transmission performance improvement techniques such as spatial diversity, modulation, coding and interleaving are described. An illustration of a specific satellite DAB system design is presented to show the technical and economic feasibility of such new services.
Stimulation of endogenous adenosine release by oral administration of quercetin and resveratrol in man. (1999)

Epidemiological evidence indicates that moderate alcohol consumption is associated with a significant decrease in the incidence of certain cardiovascular disorders, which can lead to impaired quality of life and to death. However, there are no objective data suggesting a cause-effect relationship and detailed research based on definitive working hypotheses is needed. We tested two flavonoids in man and found that these substances can belong, at least in part, to a wine-dependent mechanism, which leads to increased adenosine plasma levels. If these results could be confirmed by analyzing all the possible influences leading to blood nucleoside increase, a hypothesis of diet-dependent cellular preconditioning could be discussed.
Treatment with GM-CSF Secreting Myeloid Leukemia Cell Vaccine Prior to Autologous-BMT Improves the Survival of Leukemia-Challenged Mice (2010)

Vaccination with irradiated autologous tumor cells, engineered to secrete granulocyte macrophage colony stimulating factor (GM-CSF) (GM-tumor), can generate potent anti-tumor effects when combined with autologous bone marrow transplantation (BMT). That notwithstanding, the post-BMT milieu, characterized by marked cytopenia, can pose a challenge to the implementation of vaccine immunotherapies. To bypass this problem, partial post-BMT immune reconstitution has been allowed to develop prior to vaccination. However, delaying vaccination can also potentially allow the expansion of residual tumor cells. Other approaches have used re-infusion of “primed” autologous lymphocytes and multiple administrations of GM-tumor cells, which required the processing of large amounts of tumor. Utilizing the MMB3.19 murine myeloid leukemia model, we tested whether a single dose of GM-tumor cells, 7 days prior to syngeneic BMT, could be a curative treatment in MMB3.19-challenged recipient mice. This vaccination protocol significantly improved survival of mice by eliciting long-lasting host immune responses that survived lethal irradiation, and were even protective against post-BMT tumor rechallenge. Furthermore, we demonstrated that mature donor lymphocytes can also play a limited role in mounting the anti-tumor response, but our pre-BMT vaccination strategy obviated the need for either established de novo immune reconstitution or the use of multiple post-BMT immunizations.
Effect of Bimatoprost on Intraocular Pressure in Prostaglandin FP Receptor Knockout Mice (2005)

An intact FP receptor gene is critical to the IOP response to bimatoprost in the mouse eye.
Crystal Structure of Human Plasma Platelet-activating Factor Acetylhydrolase (2008)

Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A2. The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5 angstroms. It has a classic lipase alpha/beta-hydrolase fold, and it contains a catalytic triad of Ser273, His351, and Asp296. Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser273. The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.
Diabetic Retinopathy and Diabetic Macular Edema (2003)

Diabetic retinopathy (DR) and diabetic macular edema (DME) are leading causes of blindness in the working-age population of most developed countries. The increasing number of individuals with diabetes worldwide suggests that DR and DME will continue to be major contributors to vision loss and associated functional impairment for years to come. Early detection of retinopathy in individuals with diabetes is critical in preventing visual loss, but current methods of screening fail to identify a sizable number of high-risk patients. The control of diabetes-associated metabolic abnormalities (i.e., hyperglycemia, hyperlipidemia, and hypertension) is also important in preserving visual function because these conditions have been identified as risk factors for both the development and progression of DR/DME. The currently available interventions for DR/DME, laser photocoagulation and vitrectomy, only target advanced stages of disease. Several biochemical mechanisms, including protein kinase C-beta activation, increased vascular endothelial growth factor production, oxidative stress, and accumulation of intracellular sorbitol and advanced glycosylation end products, may contribute to the vascular disruptions that characterize DR/DME. The inhibition of these pathways holds the promise of intervention for DR at earlier non-sight-threatening stages. To implement new therapies effectively, more individuals will need to be screened for DR/DME at earlier stages-a process requiring both improved technology and interdisciplinary cooperation among physicians caring for patients with diabetes.
Early experiences and integration in the persistence of first‐generation college students in STEM and non‐STEM majors (2015)

Abstract Representation of diverse groups in science, technology, engineering, and mathematics (STEM) fields is a persistent concern in the United States. Although there have been some strides toward more diverse representation, significant problems of underrepresentation remain in particular STEM fields: physical sciences, engineering, math, and computer sciences (PEMC). The purpose of this study is to understand the significance of pre‐college personal and academic factors along with early college experiences to explain persistence among first‐generation college students (FGCS) considering possible differences among PEMC‐STEM majors, other‐STEM majors, and non‐STEM majors. Using institutional and survey data from one 4‐year urban research institution in the Southeast, logistic regression models demonstrate the importance of early academic performance (first‐semester GPA) to increase odds of FGCS persistence across majors; and also reveal important differences. Besides early academic performance, the only other significant factor for persistence of PEMC‐STEM majors was perceived preparation in math. Perceived social fit was significant for persistence for the other‐STEM and non‐STEM majors, whereas perceived academic fit was only significant for non‐STEM majors. These results align generally with previous research, and also suggest that examining differences among STEM subgroups may help develop more nuanced understandings of the needs of different groups. © 2015 Wiley Periodicals, Inc. J Res Sci Teach 53: 368–383, 2016