gebhart/patrepeval huggingface dataset:
Mucins and associated O-glycans based immunoprofile for stratification of colorectal polyps: clinical implication for improved colon surveillance (2016)

Sessile serrated adenoma/polyps (SSA/P) are premalignant lesions of colorectal cancer that are difficult to distinguish histologically from hyperplastic polyps (HP) of minimal to no malignant potential. Specific markers for differentiating SSA/P from HP can aid clinicians for optimizing colon surveillance intervals. The present study investigates the potential of mucins and associated O-glycans to distinguish SSA/P from HP. Expression of colonic mucins (MUC1, MUC4, MUC17, MUC2, and MUC5AC) and O-glycans [Sialyl LewisA (CA19-9) and Tn/Sialyl-Tn on MUC1] were analyzed in HP (n=33), SSA/P (n=39), and tubular adenoma (TA) (n=36) samples by immunohistochemistry. A significantly reduced expression of MUC4 (p=0.0066), elevated expression of MUC17 (p=0.0002), and MUC5AC (p<0.0001) was observed in SSA/P cases in comparison to HP cases. Interestingly, significantly higher number of SSA/P cases (p<0.0001) exhibited MUC5AC expression in the goblet cells as well as filled the crypt lumen compared to only goblet cells in majority of the HP cases. Improved diagnostic potential was revealed by multivariate logistic regression analysis where combinatorial panel of MUC5AC/MUC17 discriminated SSA/P from HP (SN/SP=85/82%). Finally, the decision tree model based marker panel (CA19-9/MUC17/MUC5AC) predicted HP, SSA/P and TA with SN/SP of 58%/95%, 79%/90% and 97%/83%, respectively. Overall, the mucin and associated O-glycan based panel defined in the present study could aid in discriminating SSA/P from HP to devise better colon surveillance strategies.
The Drug Quality and Security Act — Mind the Gaps (2013)

The Drug Quality and Security Act aims to regulate compounding pharmacies and establish a track-and-trace pedigree system for drugs, but it falls short on both counts. Public health requires new state legislation, robust FDA enforcement, and greater vigilance.
Stretchable and bendable carbon nanotube on PDMS super-lyophobic sheet for liquid metal manipulation (2014)

We report a vertically-aligned carbon nanotube (CNT) forest on polydimethylsiloxane (PDMS) sheet as a novel widely stretchable and bendable anti-wetting super-lyophobic surface for naturally oxidized gallium-based liquid metals. The vertically-aligned CNT has inherent chemical inertness and a hierarchical texture combining micro/nanoscale roughness; these two characters render the developed sheet as a super-lyophobic substrate against gallium-based liquid metals. The vertically-aligned CNT forest was first grown on Si substrate and then transferred onto a PDMS sheet by imprinting. It was found that the transferred CNT on the PDMS sheet maintained its vertically-aligned nature as well as hierarchical micro/nano surface morphology. It was found that the static contact angles of the gallium-based liquid metal droplet on the CNT on Si and on the CNT on PDMS were both greater than 155° and the contact angle hysteresis on the CNT on Si was 4° and that on the transferred CNT on PDMS was 19°. These measurement results showed that the surface retains a super-lyophobic property before and after the CNT transfer onto PDMS. We tested the CNT on PDMS sheet for its mechanical flexibility using stretching (50% and 100%) and bending (curvature of 0.1 and 0.4 mm−1). We carried out a bouncing test and a rolling test on the stretched/bent CNT on the PDMS sheet and the results confirmed that the flexible sheet maintains anti-wetting characteristics under bending or stretching conditions.
Unspecific binding of group B streptococcal cocytolysin (CAMP factor) to immunoglobulins and its possible role in pathogenicity. (1987)

The protein B of group B streptococci can bind in a nonimmune reaction to Ig of the IgG and IgM classes of various mammalian species (i.e., human, mouse, rabbit, and bovine). Protein B binding involves the Fc parts of both IgG and IgM molecules. Monoclonal or polyclonal IgG or IgM and the IgM-FC5 mu fragment of human myeloma protein combined with the protein B thereby inhibiting protein B-induced hemolysis in the CAMP reaction. The protein B/Ig complex can be dissociated with 1% Triton or guanidine-HCl (6 M). Mice infected intraperitoneally with sublethal doses of group B streptococci (GBS) and that received seven repeated intravenous injections of highly purified protein B during the first 9 h of infection developed fatal septicemia within 24 h with colony counts of up to 10(8) CFU/ml in the blood. Animals treated in the same way with either PBS or trypsinized protein B recovered. The protein B itself was not pathogenic when injected into healthy mice. Tissue sections of liver or spleen from mice infected with a lethal dose of GBS revealed the presence of protein B together with large numbers of cocci when stained by the peroxidase method using specific antibodies raised against purified protein B in the rabbit.
The immunogenicity of chimeric antibodies. (1989)

Mice were immunized with model xenogeneic (both the VH frameworks and the CH domains of human origin), chimeric (just VH frameworks human), or self antibodies, and the antiantibody responses were dissected. Only the self antibody did not elicit a response. A strong response was elicited by the most xenogeneic antibody with approximately 90% against the C and approximately 10% against the V. The anti-V response was not attenuated in the chimeric antibody, demonstrating that foreign VH frameworks can be sufficient to lead to a strong antiantibody response. The magnitude of this xenogeneic anti-VH response was similar to that of the allotypic response elicited by immunizing mice of the Igha allotype with an Ighb antibody. Thus, although chimerization can diminish antiantibody responses, attention should be paid both to V region immunogenicity and to polymorphism.
Integration of a double polysilicon, fully self-aligned bipolar transistor into a 0.5 mu m BiCMOS technology for fast 4 MBit SRAMs (2002)

The single polysilicon, non-self-aligned bipolar transistor in a 0.5- mu m BiCMOS technology has been converted to a double polysilicon, fully self-aligned bipolar device with little increase in process complexity. Improved bipolar performance in the form of smaller base resistance, larger knee current, higher peak cutoff frequency, and shorter ECL gate delay has been demonstrated. This technology will prove useful in meeting the requirements for higher performance in fast, high-density SRAM circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Journal of Lipid Research: The New Era in Lipid Science and Medicine (2003)

At the end of the twentieth century, we saw a revolution in “genomics” that is having profound effects on basic science and clinical medicine today. Currently we are in the middle of another revolution, namely “proteomics”—the extension of genomics to attempt to identify, characterize, and quantitate the primary products of the genes (identified in the human genome project) and understand their interactions. We predict that the next revolution in biomedical science will be in “metabolomics”—the extension of proteomics to identify, characterize, and quantitate all of the metabolic products of the protein synthetic machinery in our cells.
Importance of the Pulse Oximeter Averaging Time When Measuring Oxygen Desaturation in Sleep Apnea (1998)

The accuracy of pulse oximeters in measuring transient changes in oxygen saturation (SaO2) may be affected by the oximeter time response. The aim of this study was to assess the effect of modifying the pulse oximeter averaging time (T) on the measurement of SaO2 in patients with the sleep apnea-hypopnea syndrome (SAHS). Twelve patients with severe SAHS were studied during a nap with conventional oximeters: Ohmeda 3740 and Criticare 501. We compared the readings of each patient's oxygen desaturation measured simultaneously with two identical pulse oximeters. One oximeter was the control (T = 3 seconds), and in the other T was set from 3 seconds to 21 seconds. No significant differences in SaO2 were found when both oximeters were set to the same T (3 seconds). In contrast, increasing T to 12 seconds and 21 seconds in one of the oximeters resulted in considerable and significant differences in the measured SaO2: oxygen desaturation was underestimated by up to 60% when compared with the control. The misestimation of SaO2 induced by settings of T which are within the range selectable in conventional oximeters may be of epidemiological significance when pulse oximetry is used as a complementary diagnostic tool to classify sleep events in SAHS.
Identification of electrophysiologically‐active compounds for the malaria mosquito, Anopheles gambiae , in human sweat extracts (1996)

Human sweat samples were chemically fractionated into acid and non-acid components. The most abundant volatile compounds present in the fractions were identified by linked gas chromatography mass spectrometry. The acid fractions were found to be composed of a range of twenty aliphatic and three aromatic carboxylic acids ranging, on average, from 0.02 to 20 micrograms per ml of sweat sampled. Non-acid fractions were found to contain: 6-methyl-5-hepten-2-one, 1-octen-3-ol, decanal, benzyl alcohol, dimethylsulphone, phenylethanol, phenol and 4-methylphenol, collectively amounting to 0.1 and 3 micrograms per ml of sweat. The major component of sweat was found to be L-lactic acid which constituted from 1 to 5 mg/ml. Using the intact antennae of the anthropophilic malaria vector mosquito Anopheles gambiae Giles, the peripheral olfactory activities of compounds identified in the sweat fractions were investigated by electroantennography (EAG). Short-chain saturated carboxylic acids, methanoic, ethanoic, propanoic, butanoic, pentanoic and hexanoic acids were found to elicit significantly larger EAG responses than longer chain saturated carboxylic acids from female An.gambiae. For a given dose the largest amplitude EAG response was elicited by methanoic acid. Pentanoic acid elicited larger EAG responses than either butanoic or hexanoic acids. Two non-acidic compounds, 1-octen-3-ol and 4-methylphenol, were found to elicit significant dose-dependent EAG responses from female An.gambiae. 1-Octen-3-ol elicited larger EAG responses than 4-methylphenol for a given dose, but both compounds elicited smaller EAG responses than the same dose of C1-C6 straight-chain aliphatic carboxylic acids. The possible behavioural significance of the EAG-active compounds identified in human sweat samples is discussed.
Combretastatin Analogs via Hydration of Stilbene Derivatives (1993)

Abstract Hydration of the double bond of some stilbene congeners of Picea abies bark by TiCl 4 ·NaBH 4 reagent is described. Five racemic 1,2‐diphenylethanol derivatives ( 9 – 13 ), structurally related to ( R )‐(·)‐combretastatin [( R )‐ 1 ], have been obtained and characterized mainly by 13 C‐ and 1 H‐NMR as well as mass spectrometry. The antileukemic activity of each compound has preliminarily been tested by the mouse leukemia L1210 system. Compound 10 has been synthesized by Friedel‐Crafts acylation.
Gene gun‐based nucleic acid immunization alone or in combination with recombinant vaccinia vectors suppresses virus burden in rhesus macaques challenged with a heterologous SIV (1997)

Gene gun-based DNA immunization alone or in combination with recombinant vaccinia vectors was evaluated for the ability to elicit protective immune responses in rhesus macaques challenged with a pathogenic, heterologous simian immunodeficiency virus (SIV). Six monkeys primed with seven consecutive doses of DNA encoding SIVmac239 gp120 and gp160 (DNA + DNA) were divided into two groups. Three of these animals received another DNA booster immunization and the remaining three received a booster immunization containing a homologous, live recombinant vaccinia virus expressing SIVmac251 gp160 (DNA + VAC). In addition, a group of 15 animals primed with recombinant vaccinia vectors were divided into two groups. One group of six monkeys received another immunization of vaccinia (VAC + VAC) and the other nine animals received a DNA (mac239) booster immunization (VAC + DNA). Geometric mean end-point IgG titres in the DNA + VAC and VAC + DNA groups were substantially higher than the responses seen in the VAC + VAC and DNA + DNA groups, demonstrating a synergistic relationship between DNA-based vaccines and recombinant vaccinia virus-based vaccines. All vaccinates and five naive controls were challenged 19 weeks after the final booster immunization with 10 animal infectious doses of SIVDelta/B670. The vaccines did not prevent infection. However, all vaccine groups showed significant virus load reductions from seven to 56 days post challenge when compared to controls. Although the DNA + DNA group developed the lowest prechallenge antibody responses, the most significant reduction (200-fold) in virus load was associated with this group. In addition, a significant delay in CD4+ T cell loss relative to controls was observed in the DNA + DNA group. These results demonstrate that a gene gun-based DNA vaccine provided some attenuation of infection and CD4+ T cell loss after a heterologous challenge.
Sensitivity of Metal Nanoparticle Surface Plasmon Resonance to the Dielectric Environment (2005)

Electrodynamic simulations of gold nanoparticle spectra were used to investigate the sensitivity of localized surface plasmon band position to the refractive index, n, of the medium for nanoparticles of various shapes and nanoshells of various structures. Among single-component nanoparticles less than 130 nm in size, sensitivities of dipole resonance positions to bulk refractive index are found to depend only upon the wavelength of the resonance and the dielectric properties of the metal and the medium. Among particle plasmons that peak in the frequency range where the real part of the metal dielectric function varies linearly with wavelength and the imaginary part is small and slowly varying, the sensitivity of the peak wavelength, lambda, to refractive index, n, is found to be a linearly increasing function of lambda, regardless of the structural features of the particle that determine lambda. Quasistatic theory is used to derive an analytical expression for the refractive index sensitivity of small particle plasmon peaks. Through this analysis, the dependence of sensitivity on band position is found to be determined by the wavelength dependence of the real part, epsilon', of the particle dielectric function, and the sensitivity results are found to extend to all particles with resonance conditions of the form, epsilon' = -2chin(2), where chi is a function of geometric parameters and other constants. The sensitivity results observed using accurate computational methods for dipolar plasmon bands of gold nanodisks, nanorods, and hollow nanoshells extend, therefore, to particles of other shapes (such as hexagonal and chopped tetrahedral), composed of other metals, and to higher-order modes. The bulk refractive index sensitivity yielded by the theory serves as an upper bound to sensitivities of nanoparticles on dielectric substrates and sensitivities of nanoparticles to local refractive index changes, such as those associated with biomolecule sensing.
Expression and Characterization of a Divalent Chimeric Anti‐Human CD3 Single Chain Antibody (1996)

Murine anti-CD3 monoclonal antibodies (MoAbs) are used in clinical practice for immunosuppression. However, there are two major drawbacks to this treatment: the associated cytokine release syndrome and human anti-mouse antibody response. To overcome these side-effects, the authors generated a chimeric anti-human CD3 single chain antibody, scUCHT1. It is an IgM variant of UCHT1, a mouse IgG1 MoAb directed against human CD3. scUCHT1 consists of the light and heavy variable chain binding domains of UCHT1 and a human IgM Fc region (CH2 to CH4). scUCHT1 was produced by COS-7 and SP2/0 transfectants, and mainly assembled in a dimeric form. It retained the binding specificity and affinity of the parental MoAb UCHT1. In contrast to UCHT1, scUCHT1 did not induce T-cell proliferation and cytokine release (TNF-alpha and IFN-gamma) in in vitro assays. These results suggest that the engineered chimeric anti-CD3 single chain antibody (scUCHT1) may be useful in clinical immunosuppressive treatment.
Effects of Aspirin on Platelet-Neutrophil Interactions (1995)

Our results show that a significant part of the effect of aspirin on platelet activation involves a neutrophil-mediated, NO/cGMP-dependent mechanism. The presence of ET-1 counterbalances these effects of neutrophils on platelet activation, therefore acting as an indirect proactivating agent. These results add new elements for interpreting the effects of aspirin on the interactions between blood cells, with special reference to high endothelin states (for example, ischemia/reperfusion processes).
Contribution of Cysteine 158, the Glycosylation Site Theonine 194, the Amino- and Carboxy-Terminal Domains of Apolipoprotein E in the Binding to Amyloid Peptide β (1−40) (1999)

Recent studies have shown that at physiological conditions (pH 7.6, 37 degrees C), the reactivity of recombinant apoE isoforms secreted by mammalian cells toward amyloid peptide beta (Abeta40) follows the order apoE2 > apoE3 > apoE4 for the apoE monomer and apoE2 > apoE3 for apoE dimer that is formed via that intramolecular disulfide bridges. Different Abeta binding properties have been reported for the plasma-derived apoE and commercially available apoE preparations that differ from the native apoE forms in the degree of their O-glycosylation. To define structural elements of apoE involved in the interaction with Abeta, we have introduced point mutations as well as amino- and carboxy-terminal deletions in the apoE structure. The mutant apoE forms were expressed transiently using the Semliki Forest Virus system, and the culture medium was utilized to study the reactivity of the mutated proteins with Abeta 40. This analysis showed that a mutation in the O-glycosylation site of apoE2 (Thr194-Ala) did not affect the SDS-stable binding of apoE to Abeta. In contrast, introduction of cysteine at position 158 of apoE4 (Arg112, Cys158) increased the SDS-stable binding of apoE to Abeta to the levels similar to those observed in apoE2. Similar analysis showed that apoE truncated at residues 259, 249, 239, and 229 retains the SDS-stable binding to Abeta40, whereas apoE truncated at residues 185 and 165 does not bind to Abeta. The deletion of aminoterminal residues 2-19 reduced the SDS-stable binding of apoE2 to Abeta and deletion of residues 2-81 abolished binding to Abeta. It is also noteworthy that the (Delta2-81) apoE mutant exists predominantly as a dimer, suggesting that removal of residues 2-81 promoted dimerization of apoE. These findings suggest that the amino- and carboxy-terminal residues of apoE are required for SDS-stable binding of apoE to Abeta and that the presence of at least one cysteine contributes to the efficient Abeta binding.
Privacy, accuracy, and consistency too (2007)

The contingency table is a work horse of official statistics, the format of reported data for the US Census, Bureau of Labor Statistics, and the Internal Revenue Service. In many settings such as these privacy is not only ethically mandated, but frequently legally as well. Consequently there is an extensive and diverse literature dedicated to the problems of statistical disclosure control in contingency table release. However, all current techniques for reporting contingency tables fall short on at leas one of privacy, accuracy, and consistency (among multiple released tables). We propose a solution that provides strong guarantees for all three desiderata simultaneously.
Lateral Position Decreases Collapsibility of the Passive Pharynx in Patients with Obstructive Sleep Apnea (2002)

Lateral position structurally improves maintenance of the passive pharyngeal airway in patients with obstructive sleep apnea.
Rapid Visualization of Human Tumor Xenografts through Optical Imaging with a Near-Infrared Fluorescent Anti–Epidermal Growth Factor Receptor Nanobody (2012)

Given that overexpression of the epidermal growth factor receptor (EGFR) is found in many types of human epithelial cancers, noninvasive molecular imaging of this receptor is of great interest. A number of studies have employed monoclonal antibodies as probes; however, their characteristic long half-life in the bloodstream has encouraged the development of smaller probes. In this study, an anti-EGFR nanobody-based probe was developed and tested in comparison with cetuximab for application in optical molecular imaging. To this aim, the anti-EGFR nanobody 7D12 and cetuximab were conjugated to the near-infrared fluorophore IRDye800CW. 7D12-IR allowed the visualization of tumors as early as 30 minutes postinjection, whereas with cetuximab-IR, no signal above background was observed at the tumor site. Quantification of the IR-conjugated proteins in the tumors revealed ≈ 17% of injected dose per gram 2 hours after injection of 7D12-IR, which was significantly higher than the tumor uptake obtained 24 hours after injection of cetuximab-IR. This difference is associated with the superior penetration and distribution of 7D12-IR within the tumor. These results demonstrate that this anti-EGFR nanobody conjugated to the NIR fluorophore has excellent properties for rapid preclinical optical imaging, which holds promise for its future use as a complementary diagnostic tool in humans.