gebhart/patrepeval huggingface dataset:
Enzyme-Responsive Nanoparticles for the Targeted Delivery of an MMP Inhibitor to the Heart post Myocardial Infarction (2022)

Abstract In this paper, we describe block copolymer amphiphiles consisting of a hydrophilic matrix metalloproteinase (MMP) peptide substrate, and a hydrophobic small molecule MMP inhibitor PD166793 for the treatment of acute myocardial infarction. These resulting drug loaded peptide-polymer amphiphiles (PPAs) assemble in aqueous solution to yield drug loaded micellar nanoparticles. Following minimally invasive intravenous injection, these nanoparticles preferentially exit the vasculature and are physically trapped at the infarcted region of the heart due to MMP-induced peptide cleavage and aggregation. This MMP directed active assembly prevents the material from leaking out into the blood stream, enabling long-term retention. Further, we show that the conjugated MMP inhibitor (PD166793) is inactivated in the core of the micelles and can be released upon the action of proteases and esterases, leading to MMP inhibition. This work establishes a promising targeted nanoparticle platform for delivering small molecule therapeutics to the heart.
ChemInform Abstract: Piperidine Carboxylic Acid Derivatives as Sialyl Lewis X Mimetics. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Electrophilic Additions to Dienes and Polyenes (2009)

Abstract Introduction Electrophilic Hydrogen Electrophilic Carbenium Ions Electrophilic Halogens and Positive Halogen Donors Electrophilic Sulfur and Selenium Electrophilic Mercury Conclusions Acknowledgements
Mutational Analysis of Conserved Residues in the GCN5 Family of Histone Acetyltransferases (2001)

GCN5 is a critical transcriptional co-activator and is the defining member of a large superfamily of N-acetyltransferases. GCN5 catalyzes the transfer of an acetyl group from acetyl-CoA to the epsilon-amino of lysine 14 within the core H3 histone protein. Previous biochemical analyses have indicated a fully ordered kinetic mechanism. Recent structural studies have implicated several conserved residues in catalysis and substrate binding. Here the roles of Glu-173, His-145, and Asp-214 in yeast GCN5 have been evaluated using site-directed mutagenesis, steady state and pre-steady state kinetics, pH analysis, isotope partitioning, and equilibrium binding studies. The results with wild type and E173Q, H145A, and D214A mutants are consistent with chemical catalysis being rate-determining in turnover. All mutants exhibited K(d) values (3.5-8.5 microm) for AcCoA that were similar to wild type enzyme, indicating no functional role for these residues in AcCoA binding. The E173Q mutant demonstrated a approximately 500-600-fold decreases in k(cat) and k(cat)/K(m),(H3), consistent with Glu-173 acting as the general base catalyst as proposed previously. No significant effect was observed on substrate binding steps. His-145 was identified as a residue in the peptide binding cleft that must be unprotonated (pK(a) = 5.8) for peptide binding and likely hydrogen-bonds to the Ser-10 hydroxyl of histone H3. His-145 also contributes to lowering the pK(a) value (by 0.8 units) of general base Glu-173 through a water-mediated hydrogen bond to the carboxylate side chain. Analysis of D214A revealed an obligate protein isomerization step that occurs after AcCoA binding and permits efficient peptide binding. Asp-214 is part of a conformationally flexible loop that mediates the isomerization by stabilizing distinct conformers of the protein.
cGAN Based Facial Expression Recognition for Human-Robot Interaction (2019)

As an emerging research topic for proximity service (ProSe), automatic emotion recognition enables the machines to understand the emotional changes of human beings which can not only facilitate natural, effective, seamless, and advanced human–robot interaction or human–computer interface but also promote emotional health. Facial expression recognition (FER) is a vital task for emotion recognition. However, significant gap between human and machine exists in FER task. In this paper, we present a conditional generative adversarial network-based approach to alleviate the intra-class variations by individually controlling the facial expressions and learning the generative and discriminative representations simultaneously. The proposed framework consists of a generator G and three discriminators ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Di</i> , <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Da</i> , and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Dexp</i> ). The generator G transforms any query face image into another prototypic facial expression image with other factors preserved. Armed with action units condition, the generator G pays more attention to information relevant to facial expression. Three loss functions ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$L_{I}$ </tex-math></inline-formula> , <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">La</i> , and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Lexp</i> ) corresponding to the three discriminators ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Di</i> , <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Da</i> , and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Dexp</i> ) were designed to learn generative and discriminative representations. Moreover, after rendering the generated expression back to its original facial expression, cycle consistency loss is also applied to guarantee the identity and produce more constrained visual representations. Optimized by combining both synthesis and classification loss functions, the learnt representation is explicitly disentangled from other variations such as identity, head pose, and illumination. Qualitative and quantitative experimental results demonstrate the proposed FER system is effective for expression recognition.
Reducing Emboli in Cardiac Surgery: Does It Make a Difference? (2008)

Particulate embolization remains a serious complication of cardiac surgery. Adverse events associated with particulate embolization affect patient morbidity and long-term survival, and increase the length of hospital stay and the cost of health care. Today, atherosclerosis plays a role in at least two-thirds of all adverse events after coronary artery revascularization, and postoperative stroke is the second most common cause of operative mortality. Because many lower-risk patients now undergo interventional revascularization, higher-risk patients are now typically referred for surgical revascularization. These patients are older and sicker, and have multiple comorbidities, making them more susceptible to adverse events. For these high-risk patients, surgeons should be proactive in attempting to reduce the possibility of emboli. Patients must be carefully assessed before surgery to determine their risk, and if the risk is high, surgeons should consider using newer, innovative devices, and techniques in their operative strategy that have proven to be effective in mitigating some of the potential embolic adverse events. A multifaceted, preventive strategy can make a difference, not only in reducing particulate emboli, but also in reducing morbidity and in lowering the economic burden on the health-care system. This brief review will address three areas of focus that are important for the prevention of particulate embolization: (i) prevalence and morbidity of atherosclerotic disease; (ii) risk factors for adverse neurologic events; and (iii) prevention/mitigation of adverse events for patients undergoing cardiac surgery.
Restriction Enzyme Kinetics Monitored by UV Linear Dichroism (2006)

The use of linear dichroism (LD) spectroscopy for biological applications has been brought to the forefront recently by our development of thermostated microvolume Couette cells. We present a method for following the digestion of DNA by restriction endonucleases in real time without the use of any extrinsic dyes or labels. This is accomplished using linear dichroism spectroscopy (the differential absorbance of light polarized parallel and perpendicular to the sample orientation axis). The differential absorbance signal depends on the degree of alignment of the molecules. In this case the DNA is aligned by Couette flow (flowing the solution in the annular gap between two concentric cylinders), and we monitor the increase in alignment upon linearization of a circular DNA molecule. In addition, we observe a decrease in alignment upon further digestion and subsequent shortening of the DNA. Ten enzymes were investigated: seven enzymes with a single cut site (EcoRI, KpnI, NdeI, NotI, NruI, SmaI, XbaI), two enzymes with two cut sites (BstZ17I, EagI), and one enzyme with no cut site (ClaI). LD, as implemented in this new assay, is broadly applicable across a wide range of DNA-modifying enzymes and compounds and, as such, is a useful addition to the toolbox of biological characterization.
Shape imprinting due to variable disulfide bonds in polyacrylamide gels (2001)

Through the use of variable disulfide crosslinkers, we have created polyacrylamide gels whose shape can be altered after polymerization. N,N′-bisacryloylcystamine is incorporated as a crosslinker, along with a smaller amount of a permanent crosslinker. After polymerization, the disulfide bonds are cleaved into thiols through reduction. By reoxidizing the thiols with the gel held in a new macroscopic shape, a new set of disulfide bonds is formed, and the gel is forced to adopt the new shape. Retension of the new shape improves with greater distortion from the original shape, as well as with increased concentration of variable disulfide bonds. A simple theoretical model has been developed to explain these data, although the enigmatic kinetics of relaxation remain unexplained.
Total Synthesis of (+)-Saponaceolide B (1999)

Coupling of three fragments results in the first total synthesis of a saponaceolide (see scheme). The first fragment, the spiroketal portion, is formed from two moieties, one derived from geraniol and the other from allyl malonate. A sulfone alkylation–desulfonylation sequence joins the spiroketal portion to the methylene-3,3-dimethylcyclohexane unit. The subsequent stereoselective Wittig reaction attaches the final piece to complete the synthesis of saponaceolide B (1), one of the most biologically active members of this family.
Electrochemical Stability of Carbon Fibers Compared to Aluminum as Current Collectors for Lithium-Ion Batteries (2012)

The electrochemical behaviors of highly conductive, fully-graphitic, semi-graphitic and non-graphitic carbon fibers were studied as the cathode current collectors of lithium batteries in standard electrolyte (alkyl carbonate/LiPF6) solutions and compared to bare aluminum (Al). All of these current collectors demonstrate a stable electrochemical behavior within the potential range of 2.5 to 5 V, due to passivation by surface films. Carbon fibers have comparable electrochemical stability of Al and may be used in place Al foil. While the carbon fibers do not contribute any irreversible or extra capacity when they are cycled below 4.5 V, for fully-graphitic and semi-graphitic fibers PF−6 intercalation and deintercalation into the carbon fiber may occur when they are cycled at high potentials >4.5 V.
Immunoassay Interference by a Commonly Used Blood Collection Tube Additive, the Organosilicone Surfactant Silwet L-720 (2005)

The Silwet L-720 surfactant, which is used to coat the inner surfaces of tubes, appears to account for previously reported immunoassay interference by BD Vacutainer SST blood collection tubes. One of the mechanisms for the interference is the desorption of antibodies from the solid phase by the surfactant. The results identify an important factor in the selection of suitable blood collection tube surfactants and provide an approach for solving similar tube-assay interference problems in the future.
A runlength limited low-density parity-check coding scheme (2004)

In this paper, we propose a novel approach to modulation and error control coding. The idea is to completely eliminate a constrained code and, instead, impose the constraint by the deliberate introduction of bit errors before transmission. The redundancy that would have been used for imposing the constraint is used in our scheme to strengthen the error control code (ECC), in such a way that the ECC becomes capable of correcting both deliberate errors as well as channel errors that occurs during the detection. The proposed ECC-modulation scheme is based on iterative decoding of low-density parity-check codes (LDPC) and a runlength constraint.
A pH‐Responsive Cleavage Route Based on a Metal–Organic Coordination Bond (2011)

The physical or chemical event that generally causes stimuli responses is limited to the formation or destruction of secondary forces, such as hydrogen bonding, hydrophobic effects, electrostatic interactions, and simple reactions. Here, pH-responsive behavior of metal-organic coordination bonding, which is intrinsic to natural systems (e.g., transferrin recycling in cells), is becoming a strong candidate for a new stimulus-responsive route. We have designed a simple pH-responsive release system by integrating a metal ion and ligand or self-assembling these species with biodegradable host molecules to form nanoparticles with "metal-ligand" or "host-metal-ligand" architectures. The cleavage of either or both the "metal-ligand" or the "host-metal" coordination bond in response to pH variations causes significant damage to the nanoparticles and the subsequent release of ligand molecules under designated pH conditions.
Expression of FcRn receptor in placental tissue and its relationship with IgG levels in term and preterm newborns (2018)

Our results obtained from clinical samples, were in line with previous descriptions in model systems and confirmed that the IgG transfer from maternal serum to the fetus is positively correlated with FcRn expression in placental tissue throughout gestation.
New insights into the mechanisms of carbon dioxide mineralization by portlandite (2021)

Abstract Portlandite (Ca(OH) 2 ; also known as calcium hydroxide or hydrated lime), an archetypal alkaline solid, interacts with carbon dioxide (CO 2 ) via a classic acid–base “carbonation” reaction to produce a salt (calcium carbonate: CaCO 3 ) that functions as a low‐carbon cementation agent, and water. Herein, we revisit the effects of reaction temperature, relative humidity (RH), and CO 2 concentration on the carbonation of portlandite in the form of finely divided particulates and compacted monoliths. Special focus is paid to uncover the influences of the moisture state (i.e., the presence of adsorbed and/or liquid water), moisture content and the surface area‐to‐volume ratio ( s a / v , mm −1 ) of reactants on the extent of carbonation. In general, increasing RH more significantly impacts the rate and thermodynamics of carbonation reactions, leading to high(er) conversion regardless of prior exposure history. This mitigated the effects (if any) of allegedly denser, less porous carbonate surface layers formed at lower RH. In monolithic compacts, microstructural (i.e., mass‐transfer) constraints particularly hindered the progress of carbonation due to pore blocking by liquid water in compacts with limited surface area to volume ratios. These mechanistic insights into portlandite's carbonation inform processing routes for the production of cementation agents that seek to utilize CO 2 borne in dilute (≤30 mol%) post‐combustion flue gas streams.
On the performance of chaos shift keying in MIMO communications systems (2011)

This paper carries out the first-ever study of the feasibility of using chaos shift keying (CSK) in a Multiple-Input, Multiple-Output (MIMO) channel. To that end, an Alamouti space time code scheme is combined with the CSK system for 2 transmit and 2 receiver antennas. Once the design of CSK-MIMO system is presented, the performance of the proposed system is analyzed in a mono-user case. An exact computation approach of the BER expression based on the probability density function of the bit energy of the chaotic sequence is presented. Simulation results prove the accuracy of our BER computation methodology.
Dietary Energy and Amino Acid Enhancement From a Multi-enzyme Preparation (2018)

This study investigated the effect of Rovabio® Advance (Enz), containing high levels of endo-xylanase (Xyl) and arabinofuranosidase (Abf) activities, on energy and ileal amino acid (AA) digestibility of a complete wheat/soybean-based diet in broilers. The commercial control diet was compared with a 3% nutrient-diluted version using silica as inert diluent. Digestibility of dry matter, AA, and gross energy were determined by analysis of feed, excreta, and digesta. Ross PM3 broiler chicks were studied during the grower period, and diet dilution did not cause feed intake to increase. Fecal energy digestibility was similar (approximating 73%) for diets without Enz (P = 0.99). However, apparent metabolizable energy (AME) content was significantly lower in the diluted vs. control diet. Enz improved energy utilization (P < 0.001), leading to an increase of AME content of the diluted and standard diets. AME content of the diluted diet with Enz was similar to that of the standard diet without Enz (P = 0.98), demonstrating the ability of Enz to fully compensate the 3% nutrient dilution. At ileal level, AA digestibility was around 75% across all treatments. The addition of Enz increased AA digestibility by an average of 4.4% (P < 0.001).
Genetically Modified Autoactivated Cells Expressing Intracellular Forms of GM‐CSF as a Model for Regulated Administration of Cytokines (2005)

The application of cytokines for immunotherapy is frequently hampered by undesirable side effects. To avoid systemic effects, cytokines can be directly expressed in the target cells by using gene transfer. However, the uncontrolled cellular secretion of cytokines could still exert some undesirable bystander effects. Therefore, it is important to develop additional methods for a more restricted administration of cytokines. Recently, using the murine granulocyte-macrophage colony-stimulating factor (mGM-CSF), we have demonstrated that cytokines can be targeted to different subcellular compartments as stable and biologically active proteins. This model could be used as a method of highly restricted administration of cytokines. Here, as model for the proof of principle, we have used a cell line (DA-3) strictly dependent on mGM-CSF for growth and demonstrated that these cells acquired autonomous growth after gene modification with plasmids encoding either extracellular or intracellular forms of mGM-CSF. Cell lines expressing secreted forms of mGM-CSF displayed the highest rates of autonomous growth and released substantial amounts of mGM-CSF. However, cell lines expressing intracellular forms of mGM-CSF also acquired autonomous growth induced by a mechanism of restricted autocrine stimulation and did not release detectable mGM-CSF to the extracellular medium. Cocultivation experiments of DA-3 cell lines expressing intracellular mGM-CSF with unmodified cells showed that there was no activation of the bystander cells. Taken together, these results support the concept that genes encoding intracellular cytokines may be used to provide the desired effect of cytokines on the target cells while avoiding the side effects of their uncontrolled secretion.
Analytic reconstruction for helical-orbit cone-beam SPECT (2005)

Helical-orbit cone-beam (CB) single-photon emission computed tomography (SPECT) provides improved sensitivity and also acquires a complete data set for the reconstruction of a three-dimensional (3D) source distribution. The authors have developed an analytic helical-orbit CB SPECT reconstruction algorithm that can be decomposed into three steps. The algorithm first rebins helical-orbit CB SPECT data into plane-integral space, then multiplies the rebinned data with normalization factors that compensate for the non-uniform sampling of CB SPECT systems, and finally uses a direct Fourier inversion method for the 3D reconstruction from the normalized plane integrals. The authors have also developed a method to speed up the rebinning procedure. After testing the algorithm with simulated mathematical Defrise phantoms, the authors found that helical-orbit CB SPECT produces fewer image artifacts than does a circular-orbit CB SPECT, and they also found that using a triple-camera helical-orbit CB SPECT system, which results in more uniform sampling, can further suppress the artifacts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prediction of DNA Integrity from Morphological Parameters Using a Single‐Sperm DNA Fragmentation Index Assay (2019)

Intracytoplasmic sperm injection is a popular form of in vitro fertilization, where single sperm are selected by a clinician and injected into an egg. Whereas clinicians employ general morphology-based guidelines to select the healthiest-looking sperm, it remains unclear to what extent an individual sperm's physical parameters correlate with the quality of internal DNA cargo-a measurement that cannot be obtained without first damaging the sperm. Herein, a single-cell DNA fragmentation index (DFI) assay is demonstrated, which combines the single-cell nature of the acridine orange test with the quantitative aspect of the sperm chromatin structure assay, to create a database of DFI-scored brightfield images. Two regression predictive models, linear and nonlinear regression, are used to quantify the correlations between individual sperm morphological parameters and DFI score (with model test <i>r</i> at 0.558 and 0.620 for linear and nonlinear regression models, respectively). The sample is also split into two categories of either relatively good or bad DFIs and a classification predictive model based on logistic regression is used to categorize sperm, resulting in a test accuracy of 0.827. Here, the first systematic study is presented on the correlation and prediction of sperm DNA integrity from morphological parameters at the single-cell level.
Novel ATPG algorithms for transition faults (2003)

This paper proposes novel algorithms for computing test patterns for transition faults in combinational circuits and fully scanned sequential circuits. The algorithms are based on the principle that s@ vectors can be effectively used to construct good quality transition test sets. Several algorithms are discussed. Experimental results obtained using the new algorithms show that there is a 20% reduction in test set size, test data volume and test application time compared to a state-of-the-art native transition test ATPG tool, without any reduction in fault coverage. Other benefits of our approach, viz. productivity improvement, constraint handling and design data compression are highlighted.
Effect of Alloying Elements (Magnesium and Copper) on Hot Cracking Susceptibility of AlSi<sub>7</sub>MgCu Alloys (2011)

This chapter contains sections titled: Introduction Theoretical Background Experimental Results Discussion Acknowledgement