gebhart/patrepeval huggingface dataset:
Expression of antioxidant enzymes in human prostatic adenocarcinoma (1997)

Cellular levels of CAT, MnSOD, and CuZnSOD in prostatic adenocarcinoma reveal that many tumors appear to have decreased levels of expression. The finding that malignant prostate epithelium may have lowered expression of AEs suggests that further study of the role of AEs in malignant transformation in the prostate is warranted.
Specific Catalysis of Asparaginyl Deamidation by Carboxylic Acids: Kinetic, Thermodynamic, and Quantitative Structure–Property Relationship Analyses (2014)

Asparaginyl (Asn) deamidation could lead to altered potency, safety, and/or pharmacokinetics of therapeutic protein drugs. In this study, we investigated the effects of several different carboxylic acids on Asn deamidation rates using an IgG1 monoclonal antibody (mAb1*) and a model hexapeptide (peptide1) with the sequence YGKNGG. Thermodynamic analyses of the kinetics data revealed that higher deamidation rates are associated with predominantly more negative ΔS and, to a lesser extent, more positive ΔH. The observed differences in deamidation rates were attributed to the unique ability of each type of carboxylic acid to stabilize the energetically unfavorable transition-state conformations required for imide formation. Quantitative structure property relationship (QSPR) analysis using kinetic data demonstrated that molecular descriptors encoding for the geometric spatial distribution of atomic properties on various carboxylic acids are effective determinants for the deamidation reaction. Specifically, the number of O–O and O–H atom pairs on carboxyl and hydroxyl groups with interatomic distances of 4–5 Å on a carboxylic acid buffer appears to determine the rate of deamidation. Collectively, the results from structural and thermodynamic analyses indicate that carboxylic acids presumably form multiple hydrogen bonds and charge–charge interactions with the relevant deamidation site and provide alignment between the reactive atoms on the side chain and backbone. We propose that carboxylic acids catalyze deamidation by stabilizing a specific, energetically unfavorable transition-state conformation of l-asparaginyl intermediate II that readily facilitates bond formation between the γ-carbonyl carbon and the deprotonated backbone nitrogen for cyclic imide formation.
Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer (2017)

We present an integrative genome-wide analysis that can be used to predict the risk of progression from leukoplakia to oral squamous cell carcinoma (OSCC) arising in the gingivobuccal complex (GBC). We find that the genomic and transcriptomic profiles of leukoplakia resemble those observed in later stages of OSCC and that several changes are associated with this progression, including amplification of 8q24.3, deletion of 8p23.2, and dysregulation of DERL3, EIF5A2, ECT2, HOXC9, HOXC13, MAL, MFAP5 and NELL2. Comparing copy number profiles of primary tumors with and without lymph-node metastasis, we identify alterations associated with metastasis, including amplifications of 3p26.3, 8q24.21, 11q22.1, 11q22.3 and deletion of 8p23.2. Integrative analysis reveals several biomarkers that have never or rarely been reported in previous OSCC studies, including amplifications of 1p36.33 (attributable to MXRA8), 3q26.31 (EIF5A2), 9p24.1 (CD274), and 12q13.2 (HOXC9 and HOXC13). Additionally, we find that amplifications of 1p36.33 and 11q22.1 are strongly correlated with poor clinical outcome. Overall, our findings delineate genomic changes that can be used in treatment management for patients with potentially malignant leukoplakia and OSCC patients with higher risk of lymph-node metastasis.
Structural differences in two biochemically defined populations of cardiac mitochondria (2005)

To determine whether there are structural differences in two topologically separated, biochemically defined mitochondrial populations in rat heart myocytes, the interior of these organelles was examined by high-resolution scanning electron microscopy. On the basis of a count of 159 in situ subsarcolemmal mitochondria (SSM, i.e., those that directly abut the sarcolemma), these organelles possess mainly lamelliform cristae (77%), whereas the cristae in in situ interfibrillar mitochondria (IFM, i.e., those situated between the myofibrils, n = 300) are mainly tubular (55%) or a mixture of tubular and lamelliform (24%). Isolated SSM (n = 374), similar to their in situ counterparts, have predominantly lamelliform cristae (75%). The proportions of crista types in isolated IFM (n = 337) have been altered, with only 20% of these organelles retaining exclusively tubular cristae, whereas 58% are mixed; of the latter, lamelliform cristae predominate. This finding suggests that, in contrast to SSM, the cristae in IFM are structurally plastic, changing during isolation. These observations on >1,000 organelles provide the first quantitative morphological evidence for definitive differences between the two populations of cardiac mitochondria.
Cytokines, stress and depressive illness: brain‐immune interactions (2003)

Cytokines, signaling molecules of the immune system, have been implicated as a contributing factor for mood disorders such as depression. Several lines of evidence supporting this contention are briefly reviewed and caveats are introduced. Essentially, a relationship between cytokines and depression is based on the findings that: 1) proinflammatory cytokines (interleukin-1, interleukin-6, tumor necrosis factor-alpha) and bacterial endotoxins elicit sickness behaviors (e.g., fatigue, soporific effects) and symptoms of anxiety/depression that may be attenuated by chronic antidepressant treatment, 2) cytokines induce neuroendocrine and central neurotransmitter changes reminiscent of those implicated in depression, and these effects are exacerbated by stressors, 3) severe depressive illness is accompanied by signs of immune activation and by elevations of cytokine production or levels, and 4) immunotherapy, using interleukin-2 or interferon-alpha, promotes depressive symptoms that are attenuated by antidepressant treatment. It is argued that cytokine synthesis and release, elicited upon activation of the inflammatory response system, provoke neuroendocrine and brain neurotransmitter changes that are interpreted by the brain as being stressors, and contribute to the development of depression. Furthermore, such effects are subject to a sensitization effect so that a history of stressful experiences or cytokine activation augment the response to later challenges and hence the evolution of depression
A Non-Local Algorithm for Image Denoising (2005)

We propose a new measure, the method noise, to evaluate and compare the performance of digital image denoising methods. We first compute and analyze this method noise for a wide class of denoising algorithms, namely the local smoothing filters. Second, we propose a new algorithm, the nonlocal means (NL-means), based on a nonlocal averaging of all pixels in the image. Finally, we present some experiments comparing the NL-means algorithm and the local smoothing filters.
Structure−Activity Relationships in 4-Aminoquinoline Antiplasmodials. The Role of the Group at the 7-Position (2002)

Antiplasmodial activities versus the chloroquine sensitive D10 strain of Plasmodium falciparum of a series of N(1),N(1)-diethyl-N(2)-(4-quinolinyl)-1,2-ethanediamines with 11 different substituents at the 7-position on the quinoline ring have been investigated in vitro. Electron-withdrawing groups at the 7-position have been shown to lower the pK(a) of both the quinoline ring nitrogen atom and the tertiary amino nitrogen in the alkyl side chain. The quinoline nitrogen pK(a) ranges from 6.28 in the nitro derivative to 8.36 in the amino derivative, while the tertiary amino nitrogen has a pK(a) ranging between 7.65 in the trifluoromethyl derivative and 10.02 in the amino derivative. Calculation suggests that the resulting pH trapping of these compounds in the parasite food vacuole ranges between about 7% of that observed in chloroquine for the NO(2) derivative and 97% in the amino derivative. A direct proportionality between antiplasmodial activity normalized for pH trapping and beta-hematin inhibitory activity was observed. Activity could not be correlated with any other observed physical parameter. The beta-hematin inhibitory activity of these derivatives appears to correlate with both the hematin-quinoline association constant and the electron-withdrawing capacity of the group at the 7-position (Hammett constant). For the compounds under investigation, the hematin association constant is in turn influenced by the lipophilicity of the group at the 7-position.
Nitric Oxide (1995)

Our results indicate that NO release from vascular endothelial cells appears to play an important physiological role in the regulation of tissue mitochondrial respiration in skeletal muscle and perhaps other organ systems.
Changing Concepts in Host-Pathogen Genetics (1981)

Since the rediscovery of Mendel's work at the tum of the century, there have been a number of changes in the concepts of genetics of host-parasite interactions. The kinds of data have not changed greatly but different interpretations have been given to the data. As expected, the changes in the interpretations have paralleled, to a certain degree, the progress made in genetics. In this paper I want to present my view of the principal concepts held during the past 75 years, and my reasons for deducing that these were the principal concepts. These views were deduced from an examination of the types of experiments performed. When concepts of host-parasite interac­ tions changed, there was a change in the types of experiments performed. In some instances it is possible to cite a single publication that illustrates a major change in these concepts. Other changes have obviously evolved quite gradually. For the latter, I have cited one or more papers that, in my judgment, best illustrate a concept, or the change in concepts. I restrict this discussion to genetic variability within a host species and within a pathogen species. No attempt is made to discuss, for example, why an oak tree is resistant to fuccinia graminis f. sp. tritici, normally a pathogen of wheat. The oak tree cannot be crossed with wheat to determine the number of gene differences related to resistance and susceptibility, or the kinds of gene actions, and therefore the differences cannot be manipu­ lated by present genetic procedures. (It might be possible in not too long a time to transfer a gene, by recombinant DNA techniques, from an oak tree to a wheat plant, and to experimentally analyze such differences.)
Relations of Serum Uric Acid to Longitudinal Blood Pressure Tracking and Hypertension Incidence (2004)

Serum uric acid (UA) has been implicated in the pathogenesis of hypertension. We investigated the relationship of serum UA to hypertension incidence and blood pressure (BP) progression in 3329 Framingham Study participants (mean age 48.7 years; 55.6% women) free of hypertension, myocardial infarction, heart failure, renal failure, or gout. At follow-up 4 years from baseline, 458 persons (13.8%) had developed hypertension, and 1201 persons (36.1%) had experienced progression to a higher BP stage. Age- and sex-adjusted rates of hypertension incidence increased progressively from 9.8% for the lowest quartile to 15.6% for the top quartile of serum UA; BP progression rates increased from 32.8% (lowest quartile) to 39.6% (top quartile). In multivariable analyses adjusting for age, sex, body mass index, diabetes, smoking, alcohol intake, serum creatinine, proteinuria, glomerular filtration rate, baseline BP, and interim weight change, a 1 SD higher serum UA was associated with an odds ratio (OR) of 1.17 (95% confidence interval [CI], 1.02 to 1.33) for developing hypertension, and an OR of 1.11 (95% CI, 1.01 to 1.23) for BP progression. In analyses of a subsample of 3157 individuals not on antihypertensive treatment at the follow-up examination, serum UA was positively associated with changes in systolic (P=0.02) and diastolic pressure 4 years later (P=0.04). In summary, serum UA level was an independent predictor of hypertension incidence and longitudinal BP progression at short-term follow-up in our community-based sample.
Fiber optic enzymatic biosensors and biosensor arrays for measurement of chlorinated ethenes (2007)

Chlorinated ethenes such as trichloroethylene (TCE), tetrachloroethylene (PCE), three isomers of dichloroethylene (DCEs) and vinyl chloride (VC) are used as solvents and cleaners in a variety of industrial and commercial areas. Chlorinated ethenes have become one of the most common environmental pollutants in groundwater contamination sites due to their widespread usage, moderate solubility compared with other organic pollutants and recalcitrance to natural attenuation. Fiber optic enzymatic biosensor was developed in this study as a continuous, real time and in situ measurement principle. TOM biosensor, first reported enzymatic biosensor, was initiated with toluene measurement in aqueous solution as proof-of-concept experiments. The subsequent success of TOM and TOM-Green in TCE analysis showed great potential of biosensor measurement for chlorinated ethenes, despite the ubiquitous problem for monooxygenase-based biosensor with NADH consumption overtime and after usage. In addition, epoxide toxicity also increased the difficulty of biosensor application for measurement of chlorinated ethenes, although several TOM-Green transformants could mitigate the toxicity with rapid epxoide degradation. Plasmid transformation with was introduced to manipulate the construction of new TOM and TOM-Green transformants with capability of intracellular NADH regeneration. FDH regeneration system was studied for both TOM and TOM-Green cells, while TOM+FDH showed great activity retention and regeneration ability and TOM-Green+FDH was able to retain activity over prolonged storage but failed on regeneration after repeated usage due to the toxicity of TCE epoxide. Biosensor array was built with pH-based biosensor to measure a group of haloalkanes. The design concept of biosensor array and detection instrumentation was successful. Linear approach in array data analysis was simple and fast but lacked of accuracy, while nonlinear approach increased the complexity of data analysis to a new level with precision in sacrifice of efficiency. Multivariable chemometric approach was also introduced in array data analysis, providing a high-throughput alternative and a means of quantitatively assessing matrix effects. This project demonstrates the potential of fiber optic enzymatic biosensor and biosensor array as measurements for different analyte are described. This is also one of the first comprehensive studies in oxygen-based biosensor and its application and great potential in food, clinical, and environmental monitoring, industrial process control and other related areas.
Liposome-mediated gene transfer into human vascular smooth muscle cells. (1994)

The efficiency of successful lipofection in human vascular smooth muscle cells in vitro is low. Transfection appears to be preferentially facilitated in cells derived from restenotic tissue, and specific properties of smooth muscle cells, including growth rates, appear to be critical for successful transfection. Further elucidation of cell properties that promote transfection is required to augment the efficiency of liposome-mediated gene transfer in human vascular cells.
Identification of a novel family of G protein‐coupled receptor associated sorting proteins (2004)

During the past few years several new interacting partners for G protein-coupled receptors (GPCRs) have been discovered, suggesting that the activity of these receptors is more complex than previously anticipated. Recently, candidate G protein-coupled receptor associated sorting protein (GASP-1) has been identified as a novel interacting partner for the delta opioid receptor and has been proposed to determine the degradative fate of this receptor. We show here that GASP-1 associates in vitro with other opioid receptors and that the interaction domain in these receptors is restricted to a small portion of the carboxyl-terminal tail, corresponding to helix 8 in the three-dimensional structure of rhodopsin. In addition, we show that GASP-1 interacts with COOH-terminus of several other GPCRs from subfamilies A and B and that two conserved residues within the putative helix 8 of these receptors are critical for the interaction with GASP-1. In situ hybridization and northern blot analysis indicate that GASP-1 mRNA is mainly distributed throughout the central nervous system, consistent with a potential interaction with numerous GPCRs in vivo. Finally, we show that GASP-1 is a member of a novel family comprising at least 10 members, whose genes are clustered on chromosome X. Another member of the family, GASP-2, also interacts with the carboxyl-terminal tail of several GPCRs. Therefore, GASP proteins may represent an important protein family regulating GPCR physiology.
Effect of prolonged nitrate therapy on left ventricular remodeling after canine acute myocardial infarction. (1994)

Prolonged nitrate therapy, in various regimens during healing after infarction, effectively reduced left ventricular loading and prevented infarct thinning, further infarct expansion, progressive ventricular dilation, and the increase in mass. These effects were associated with decreased asynergy and improved ejection fraction. The beneficial effects were greater with long-term therapy over 6 weeks than short-term therapy over the first 2 weeks.
Purification and Properties of Prostaglandin H‐E Isomerase from the Cytosol of Human Brain: Identification as Anionic Forms of Glutathione S‐Transferase (1987)

Prostaglandin H-E isomerase (EC 5.3.99.3) was purified from human brain cytosol. Purification was by ammonium sulfate fractionation, diethylaminoethyl-Sepharose chromatography, gel filtration on a BioGel P-100 column, GSH-agarose chromatography, and MonoQ chromatography. The activity was eluted in two peaks from the MonoQ column, which were designated peaks 1 and 2. The molecular weights of peaks 1 and 2, determined by gel filtration, were 42,000 and 44,000, respectively. On sodium dodecyl sulfate-polyacrylamide gel electrophoresis, peak 1 showed two bands at the molecular weights of 24,500 and 25,000, and peak 2 showed a single band at the molecular weight of 25,000, results suggesting that both were dimeric proteins. The pI values of both enzymes were approximately 5.4. The enzymes catalyzed selective conversion of prostaglandin H2 to prostaglandin E2. The Km values for prostaglandin H2 of peaks 1 and 2 were 147 and 308 microM, respectively, and the Vmax values were 380 and 720 nmol/min/mg of protein, respectively. GSH was required for the catalysis of both enzymes, and no other sulfhydryl compounds could support the reaction. A part of glutathione S-transferase (EC 2.5.1.18) was copurified with peaks 1 and 2 of prostaglandin H-E isomerase. Prostaglandin H-E isomerase activity of peak 2 enzyme was competitively inhibited by 1-chloro-2,4-dinitrobenzene, a substrate of glutathione S-transferase. These results suggested that prostaglandin H-E isomerases in human brain cytosol were identical with anionic forms of glutathione S-transferase.
Record Linkage: A Machine Learning Approach, A Toolbox, and a Digital Government Web Service (2003)

Data cleaning is a vital process that ensures the quality of data stored in real-world databases. Data cleaning problems are frequently encountered in many research areas, such as knowledge discovery in databases, data warehousing, system integration and eservices.
Measurements and modeling of ion energy distributions in high-density, radio-frequency biased CF4 discharges (2002)

Models of ion dynamics in radio-frequency (rf) biased, high-density plasma sheaths are needed to predict ion bombardment energies in plasma simulations. To test these models, we have measured ion energy distributions (IEDs) in pure CF4 discharges at 1.33 Pa (10 mTorr) in a high-density, inductively coupled plasma reactor, using a mass spectrometer equipped with an ion energy analyzer. IEDs of CF3+, CF2+, CF+, and F+ ions were measured as a function of bias frequency, bias amplitude, and inductive source power. Simultaneous measurements by a capacitive probe and a Faraday cup provide enough information to determine the input parameters of sheath models and allow direct comparison of calculated and measured IEDs. A rigorous and comprehensive test of one numerical sheath model was performed. The model, which includes a complete treatment of time-dependent ion dynamics in the sheath, was found to predict the behavior of measured IEDs to good accuracy over the entire range of bias frequency, including complicated effects that are observed when the ion transit time is comparable to the rf bias period.
Preservation of stem cells (2009)

Adult stem cells (hematopoietic and mesenchymal) have demonstrated tremendous human therapeutic potential. Currently, human embryonic stem cells are used principally for understanding development and disease progression but also hold tremendous therapeutic potential. The ability to preserve stem cells is critical for their use in clinical and research applications. Preservation of cells permits the transportation of cells between sites, as well as completion of safety and quality control testing. Preservation also permits the development of a 'manufacturing paradigm' for cell therapies, thereby maximizing the number of products that can be produced at a given facility. in this article, we will review modes of preservation and the current status of preservation of hematopoietic, mesenchymal and human embryonic stem cells. Current and emerging issues in the area of stem cell preservation will also be described.
Cross-scale electric manipulations of cells and droplets by frequency-modulated dielectrophoresis and electrowetting (2008)

Two important electric forces, dielectrophoresis (DEP) and electrowetting-on-dielectric (EWOD), are demonstrated by dielectric-coated electrodes on a single chip to manipulate objects on different scales, which results in a dielectrophoretic concentrator in an EWOD-actuated droplet. By applying appropriate electric signals with different frequencies on identical electrodes, EWOD and DEP can be selectively generated on the proposed chip. At low frequencies, the applied voltage is consumed mostly in the dielectric layer and causes EWOD to pump liquid droplets on the millimetre scale. However, high frequency signals establish electric fields in the liquid and generate DEP forces to actuate cells or particles on the micrometre scale inside the droplet. For better performance of EWOD and DEP, square and strip electrodes are designed, respectively. Mammalian cells (Neuro-2a) and polystyrene beads are successfully actuated by a 2 MHz signal in a droplet by positive DEP and negative DEP, respectively. Droplet splitting is achieved by EWOD with a 1 kHz signal after moving cells or beads to one side of the droplet. Cell concentration, measured by a cell count chamber before and after experiments, increases 1.6 times from 8.6 x 10(5) cells ml(-1) to 1.4 x 10(6) cells ml(-1) with a single cycle of positive DEP attraction. By comparing the cutoff frequency of the voltage drop in the dielectric layer and the cross-over frequency of Re(fCM) of the suspended particles, we can estimate the frequency-modulated behaviors between EWOD, positive DEP, and negative DEP. A proposed weighted Re(fCM) facilitates analysis of the DEP phenomenon on dielectric-coated electrodes.