gebhart/patrepeval huggingface dataset:
Quantifying Mixed Populations of Drug-Resistant Human Immunodeficiency Virus Type 1 (2005)

In order to survive prolonged treatment with antiretroviral nucleoside analogs, the human immunodeficiency virus type 1 (HIV-1) is selectively forced to acquire mutations in the reverse transcriptase (RT) gene. Some of these mutations are more common than others and have become markers for antiretroviral resistance. For the early detection of these markers, a novel MultiCode-RTx one-step testing system to rapidly and simultaneously characterize mixtures of HIV-1 targets was designed. For cDNA, nucleotide polymorphisms for codon M184V (ATG to GTG) and K65R (AAA to AGA) could be differentiated and quantified even when the population mixture varied as much as 1 to 10,000. Standard mixed-population curves using 1 to 100% of the mutant or wild type generated over 4 logs of total viral particle input did not affect the overall curves, making the method robust. The system was also applied to a small set of samples extracted from infected individuals on nucleoside reverse transcriptase inhibitor therapy. Of 13 samples tested, all were positive for HIV and 10 of the 13 genotypes determined were concordant with the line probe assay. MultiCode-RTx could be applied to other drug-selected mutations in the viral genome or for applications where single-base changes in DNA or RNA occur at frequencies reaching 0.01% to 1%, respectively.
Synthetic and Immunological Studies on Clustered Modes of Mucin-Related Tn and TF O-Linked Antigens:  The Preparation of a Glycopeptide-Based Vaccine for Clinical Trials against Prostate Cancer (1998)

The syntheses of two tumor-associated carbohydrate antigens, Tn and TF, have been achieved using glycal assembly and cassette methodologies. These synthetic antigens were subsequently clustered (c) and immunoconjugated to a carrier protein (KLH or BSA) or a synthetic lipopeptide (pam) for immunological study. Three Tn conjugates were used to vaccinate groups of mice, and all preparations proved to be immunogenic. The Tn(c) covalently linked to KLH (27−KLH) plus the adjuvant QS-21 was the optimal vaccine, inducing high median IgM and IgG titers against Tn(c) by ELISA. These antibodies were strongly reactive with the Tn(c) positive human colon cancer cell line LS-C but not the Tn(c) negative colon cancer cell line LS-B by FACS. The antibodies' reactivities with natural antigens were inhibited with synthetic Tn(c) but not with structurally unrelated compounds. On the basis of these results, vaccines containing 27−KLH and 30−pam plus QS-21 are being tested in patients with prostate cancer.
Male participation in safe motherhood in selected village development committee of Morang, Nepal, 2016 (2017)

Background and Objective: Men can affect pregnancy and childbirth. However, the role of husbands in maternal health is often overlooked and neglected. Thus the objective of this study is to assess the Male participation in Safe Motherhood. Methods: A descriptive cross sectional research study was conducted in community people of Bahuni Village Development Committee, Morang Ward no 8. Systemic sampling technique was used to select 87 participants. Similarly, semi-structured questionnaire with self-reported face to face interview technique was used for data collection. The obtained data were summarized using frequency and percentage for socio-demographic factors, knowledge and practice while one way ANOVA was used to assess the differences in knowledge and practice of the male participation in safe motherhood based on demographic characteristics. Besides these, Pearson's correlation coefficient was computed to describe the relationship between knowledge of safe motherhood and practice of participation among male. Results/Findings: Among 87 participants, all (100%) have inadequate knowledge in safe motherhood and almost all of them (96.6%) have a low participation. Despite inadequate knowledge and low practice in majority, comparison among socio-demographic variables showed Buddhist had comparatively higher knowledge (Mean 17.39, SD 6.14) and high participation (Mean 30.25, SD 13.33). Similarly, Brahmin and Chettri had more knowledge (Mean 21.49, SD 12.51) and high participation (Mean 33.16, SD 14.28), Graduate and above education had more knowledge (Mean 39.13, SD 6.23) and high participation (Mean 64.70, SD 8.5). Similarly, Government job holders had more knowledge (Mean 21.30, SD 10.93) and high participation (Mean 35.88, SD 14.79). Lastly, High income had more knowledge (Mean 22.65, SD 9.78) and high participation (Mean 24.13, SD 13.52) than low income. There is the significant association between the ethnicity, education, occupation, income with knowledge and practice (p-value <0.05). There is high positive (88.2%) correlation between knowledge and practice. Conclusion: All participants had inadequate knowledge, and also their participation in safe motherhood is very low. There is the significant association between the ethnicity, education, occupation, income with knowledge and practice (p-value <0.05). It clearly showed that the health professionals from each region of the country should make efforts to make the maximum participation of male in safe motherhood issues.
Simultaneous Detection of Staphylococcus aureus and Coagulase-Negative Staphylococci in Positive Blood Cultures by Real-Time PCR with Two Fluorescence Resonance Energy Transfer Probe Sets (2004)

A real-time PCR assay that uses two fluorescence resonance energy transfer probe sets and targets the tuf gene of staphylococci is described here. One probe set detects the Staphylococcus genus, whereas the other probe set is specific for Staphylococcus aureus. One hundred thirty-eight cultured isolates, which contained 41 isolates of staphylococci representing at least nine species, and 100 positive blood cultures that contained gram-positive cocci in clusters were tested. This assay was 100% sensitive and 100% specific for the detection of the Staphylococcus genus and of S. aureus.
Site of G Protein Binding to Rhodopsin Mapped with Synthetic Peptides from the α Subunit (1988)

The interaction between receptors and guanine nucleotide binding (G) proteins leads to G protein activation and subsequent regulation of effector enzymes. The molecular basis of receptor-G protein interaction has been examined by using the ability of the G protein from rods (transducin) to cause a conformational change in rhodopsin as an assay. Synthetic peptides corresponding to two regions near the carboxyl terminus of the G protein alpha subunit, Glu311-Val328 and Ile340-Phe350, compete with G protein for interaction with rhodopsin. Amino acid substitution studies show that Cys321 is required for this effect. Ile340-Phe350 and a modified peptide, acetyl-Glu311-Lys329-amide, mimic G protein effects on rhodopsin conformation, showing that these peptides bind to and stabilize the activated conformation of rhodopsin.
Flow-dependant photothermal modulation of the photoacoustic response (2012)

The temperature dependence of photoacoustic generation is utilized for monitoring the temperature in flowing blood. A phantom blood vessel is probed with photoacoustic (PA) excitation from a 830nm laser diode whose intensity is sinusoidally modulated at ultrasound frequencies. A second laser diode at the same wavelength is used to photothermally (PT) induce sinusoidal temperature fluctuations in the probed volume. The temperature oscillations lead to modulation sidebands in the PA response. Measurement of the sidebands amplitude as a function of the PT modulation frequency, for different flow rates, reveals a strong dependence of the PT modulation frequency response (MFR) on the flow rate. This is attributed to the thermal properties of the volume under test, and in particular to the heat clearance rate, which is strongly affected by the flow. A simplified lumped model based on the similarity between the system temporal behavior and that of an RC circuit is used to analyze the resulting MFR's. With the addition of an appropriate calibration protocol and by using multispectral PA and/or PT excitation the proposed approach can be used for simultaneous in-vivo measurement of both flow and oxygenation level.
Analytical capacitance model for high-speed interconnects with diagonal routing (2003)

We propose a novel quasi-3D capacitance model based on an "effective width" (W/sub eff/) concept. The model is derived from a new analytical 2D model combined with a 3D "wall-to-wall" approach. With W/sub eff/, complicated 3D structures are readily interpreted as a combination of consecutive 2D structures, leading to efficient capacitance extraction. The analytical 2D model is generated for easy application to recent technology, featuring multilayer dielectric and non-ideal vertical profile. Finally, our model is generalized to diagonal routing and confirmed by comparison with a field solver.
Monte Carlo modeling of light propagation in highly scattering tissues. I. Model predictions and comparison with diffusion theory (1989)

Using optical interaction coefficients typical of mammalian soft tissues in the red and near infrared regions of the spectrum, calculations of fluence-depth distributions, effective penetration depths and diffuse reflectance from two models of radiative transfer, diffusion theory, and Monte Carlo simulation are compared for a semi-infinite medium. The predictions from diffusion theory are shown to be increasingly inaccurate as the albedo tends to zero and/or the average cosine of scatter tends to unity.
Human CD4+CD25+ cells: a naturally occurring population of regulatory T cells (2001)

Despite thymic deletion of cells with specificity for self-antigens, autoreactive T cells are readily detectable in the normal T-cell repertoire. In recent years, a population of CD4(+) T cells that constitutively express the interleukin-2 receptor-alpha chain, CD25, has been shown to play a pivotal role in the maintenance of self-tolerance in rodent models. This study investigated whether such a regulatory population exists in humans. A population of CD4(+)CD25(+) T cells, taken from the peripheral blood of healthy individuals and phenotypically distinct from recently activated CD4(+) T cells, was characterized. These cells were hyporesponsive to conventional T-cell stimuli and capable of suppressing the responses of CD4(+)CD25(-) T cells in vitro. Addition of exogenous interleukin-2 abrogated the hyporesponsiveness and suppressive effects of CD4(+)CD25(+) cells. Suppression required cell-to-cell contact but did not appear to be via the inhibition of antigen-presenting cells. In addition, there were marked changes in the expression of Notch pathway molecules and their downstream signaling products at the transcriptional level, specifically in CD4(+)CD25(+) cells, suggesting that this family of molecules plays a role in the regulatory function of CD4(+)CD25(+) cells. Cells with similar phenotype and function were detected in umbilical venous blood from healthy newborn infants. These results suggest that CD4(+)CD25(+) cells represent a population of regulatory T cells that arise during fetal life. Comparison with rodent CD4(+)CD25(+) cells suggests that this population may play a key role in the prevention of autoimmune diseases in humans.
Abstract 10740: Bendavia, a Mitochondria-targeting Peptide, Reduces Reperfusion Injury and Reactive Oxygen Species Levels Through a Mechanism Independent of Direct Oxygen Radical Scavenging: A Multicenter Study (2012)

We recently showed that Bendavia, a novel mitochondria-targeting peptide, reduced infarction and no-reflow across several experimental models. The purpose of the present study was to determine the ...
The beta subunit of the Fc epsilon RI is associated with the Fc gamma RIII on mast cells. (1992)

Fc epsilon RI is a tetrameric receptor, composed of a ligand recognition subunit, alpha, a beta chain, and dimeric gamma chains. Previous studies have indicated that the dimeric gamma chain is associated with Fc gamma RIIIA (CD16) on natural killer cells and macrophages as well as the clonotypic T cell receptor. Here we show that in mast cells, in addition to the dimeric gamma chains, the beta subunit is associated not only with Fc epsilon RI, but also with Fc gamma RIIIA. Functional reconstitution studies with a mastocytoma cell line indicate that Fc gamma RIIIA composed of alpha, beta, and gamma subunits has the capacity for signal transduction. These studies suggest that through the association of alternative ligand recognition subunits (alpha epsilon, alpha gamma), a common signal transduction complex (beta gamma 2) mediates similar biochemical and effector functions in response to immunoglobulin G (IgG) and IgE.
Optimization of an Unnatural Base Pair toward Natural-Like Replication (2009)

Predominantly hydrophobic unnatural nucleotides that selectively pair within duplex DNA as well as during polymerase-mediated replication have recently received much attention as the cornerstone of efforts to expand the genetic alphabet. We recently reported the results of a screen and subsequent lead hit optimization that led to identification of the unnatural base pair formed between the nucleotides dMMO2 and d5SICS. This unnatural base pair is replicated by the Klenow fragment of Escherichia coli DNA polymerase I with better efficiency and fidelity than other candidates reported in the literature. However, its replication remains significantly less efficient than a natural base pair, and further optimization is necessary for its practical use. To better understand and optimize the slowest step of replication of the unnatural base pair, the insertion of dMMO2 opposite d5SICS, we synthesized two dMMO2 derivatives, d5FM and dNaM, which differ from the parent nucleobase in terms of shape, hydrophobicity, and polarizability. We find that both derivatives are inserted opposite d5SICS more efficiently than dMMO2 and that overall the corresponding unnatural base pairs are generally replicated with higher efficiency and fidelity than the pair between dMMO2 and d5SICS. In fact, in the case of the dNaM:d5SICS heteropair, the efficiency of each individual step of replication approaches that of a natural base pair, and the minimum overall fidelity ranges from 10(3) to 10(4). In addition, the data allow us to propose a generalized model of unnatural base pair replication, which should aid in further optimization of the unnatural base pair and possibly in the design of additional unnatural base pairs that are replicated with truly natural-like efficiency and fidelity.
Life in the Fast Lane: The Evolution of an Adaptive Vehicle Control System (1996)

Giving robots the ability to operate in the real world has been, and continues to be, one of the most difficult tasks in AI research. Since 1987, researchers at Carnegie Mellon University have been investigating one such task. Their research has been focused on using adaptive, vision-based systems to increase the driving performance of the Navlab line of on-road mobile robots. This research has led to the development of a neural network system that can learn to drive on many road types simply by watching a human teacher. This article describes the evolution of this system from a research project in machine learning to a robust driving system capable of executing tactical driving maneuvers such as lane changing and intersection navigation.
The dual PI3K/mTOR inhibitor BEZ235 is effective in lung cancer cell lines. (2011)

The dual PI3K/mTOR inhibitor BEZ235 is effective in lung cancer cell lines and a promising compound to be tested in clinical phase I studies.
Performance of reverse-link packet transmission in mobile cellular CDMA networks (2002)

Mobile CDMA cellular networks for tactical applications require base-station mobility in order to provide communications on the move. Because of the mobility of the base stations and the lack of a high-speed wire-line network between base stations, handoff of mobiles among base stations is more difficult than in a commercial CDMA cellular network. In this paper, we examine the performance of the reverse links in a tactical CDMA cellular network using continuous transmission for packet data communications. In particular, we consider the effect of limited handoff capability on the reverse-link capacity of the network.
Pulsed-spray pharmacomechanical thrombolysis: preliminary clinical results (1989)

Pulsed-spray pharmacomechanical thrombolysis was used to treat 41 patients with 47 complete thrombotic occlusions of hemodialysis grafts (n = 29), arterial bypass grafts (n = 10), or peripheral native arteries (n = 8). The procedure involves the use of small pulses of highly concentrated urokinase, which are forcefully sprayed throughout the thrombus during systemic heparinization. Virtually complete lysis was achieved in 46 of 47 occlusions. In the 46 thrombi that lysed, mean time for completion of lysis was 63 +/- 35 min and initial partial return of flow required 26 +/- 18 min. Complications included small peripheral emboli in one treated bypass graft (which cleared promptly after further pulse-spray therapy) and bleeding in three cases (one case of hematoma in the infused field at the site of recent surgery, one case of bilateral hematomas at the femoral puncture site, and one minor delayed self-limited gastrointestinal hemorrhage). Results to date suggest that the pulsed-spray pharmacomechanical method augments the speed, consistency, safety, and cost efficacy of clinical thrombolysis. Further study is warranted.
Interleukin-8 and SDF1-α mRNA expression in colonic biopsies from patients with inflammatory bowel disease (2000)

OBJECTIVES: Interleukin-8 (IL-8) as an α-chemokine recruits and activates neutrophils, which are abundant in the intestinal lesions of ulcerative colitis (UC) and Crohn’s disease (CD). Stromal cell-derived factor 1 (SDF1-α) is a new chemokine that is chemotactic to neutrophils. The aims of this study were to assess the relative expression of SDF1-α and IL-8 mRNA in different colonic regions and patients with inflammatory bowel disease with varied degrees of inflammation in the colon. METHODS: Colon biopsy samples were obtained from 19 patients with UC, 12 with CD, and 5 with irritable bowel syndrome (IBS) who underwent colonoscopy. Levels of IL-8 and SDF1-α mRNA expression were measured semiquantitatively by reverse-transcription and polymerase chain reaction amplification. The cytokine mRNA levels were corrected for glyceraldelyde-3-phosphate dehydrogenase mRNA expression. RESULTS: IL-8 mRNA expression was significantly correlated with SDF1-α expression in normal biopsies from IBS patients (r = 0.58, p < 0.01). There was no significant difference in cytokine mRNA expression (IL-8 or SDF1-α) across different regions of the colon or rectum in uninflamed normal biopsies. The IL-8 mRNA expression ratios in UC (mean ± SD, 1.03 ± 0.52) and CD (0.90 ± 0.38) patients were significantly higher than in IBS (0.52 ± 0.17) (p < 0.01, p < 0.05, respectively). The SDF1-α mRNA expression ratio in UC (0.30 ± 0.52) was higher than in both CD (0.21 ± 0.10) and IBS patients (0.22 ± 0.11) (p < 0.01, <0.05, respectively). A statistically significant correlation was found between the IL-8 mRNA expression and the colonic inflammation in UC patients (r = 0.44, p < 0.05) but not for SDF1-α expression in UC patients. CONCLUSIONS: IL-8 but not SDF1-α mRNA expression was associated with inflammation in UC. This suggests that IL-8 may play a more important role in inflammatory bowel disease than does SDF1-α.
Advances in optical security systems (2014)

Information security with optical means, such as double random phase encoding, has been investigated by various researchers. It has been demonstrated that optical technology possesses several unique characteristics for securing information compared with its electronic counterpart, such as many degrees of freedom. In this paper, we present a review of optical technologies for information security. Optical security systems are reviewed, and theoretical principles and implementation examples are presented to illustrate each optical security system. In addition, advantages and potential weaknesses of each optical security system are analyzed and discussed. It is expected that this review not only will provide a clear picture about current developments in optical security systems but also may shed some light on future developments.
Racing to Defuse a Bacterial Time Bomb (2007)

UBON RATCHATHANI, THAILAND-- Once ignored as an obscure disease, melioidosis and the frighteningly versatile bacterium that causes it are drawing attention as a bioterror threat.
RNAs from two independently isolated defective interfering particles of Sindbis virus contain a cellular tRNA sequence at their 5' ends. (1983)

Defective interfering (DI) particles are deletion mutants that interfere specifically with the replication of homologous standard virus. We have determined the 5'-terminal nucleotide sequences of two DI RNA populations by the following methods: (i) cloning of the cDNA from one of the DI RNA populations and sequencing a representative clone, and (ii) using both DI RNA populations as templates for preparing primer-directed cDNA transcripts and sequencing these transcripts. The 5' terminal sequences of the two DI RNA populations were not derived from standard Sindbis viral RNA but were almost identical to those of a cellular tRNAAsp.
Glycoxidation and lipid peroxidation of low-density lipoprotein can synergistically enhance atherogenesis (2001)

Our results suggest that glycoxidation and lipid peroxidation of LDL synergistically promote the development of atherosclerotic lesions through interaction with macrophage scavenger receptor-A.
In vivo imaging of lymphatic vessels in development, wound healing, inflammation, and tumor metastasis (2012)

Lymphatic vessel growth or lymphangiogenesis occurs during embryonic development and wound healing and plays an important role in tumor metastasis and inflammatory diseases. However, the possibility of noninvasive detection and quantification of lymphangiogenesis has been lacking. Here, we present the Vegfr3(EGFPLuc) mouse model, where an EGFP-luciferase fusion protein, expressed under the endogenous transcriptional control of the Vegfr3 gene, allows the monitoring of physiological and pathological lymphangiogenesis in vivo. We show tracking of lymphatic vessel development during embryogenesis as well as lymphangiogenesis induced by specific growth factors, during wound healing and in contact hypersensitivity (CHS)--induced inflammation where we also monitor down-regulation of lymphangiogenesis by the glucocorticoid dexamethasone. Importantly, the Vegfr3-reporter allowed us to tracking tumor-induced lymphangiogenesis at the tumor periphery and in lymph nodes in association with the metastatic process. This is the first reporter mouse model for luminescence imaging of lymphangiogenesis. It should provide an important tool for studying the involvement of lymphangiogenesis in pathological processes.