gebhart/patrepeval huggingface dataset:
<i>In Silico</i> Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide (2009)

A new amino acid has been designed as a replacement for arginine (Arg, R) to protect the tumor-homing pentapeptide CREKA (Cys-Arg-Glu-Lys-Ala) from proteases. This amino acid, denoted (Pro)hArg, is characterized by a proline skeleton bearing a specifically oriented guanidinium side chain. This residue combines the ability of Pro to induce turn-like conformations with the Arg side-chain functionality. The conformational profile of the CREKA analogue incorporating this Arg substitute has been investigated by a combination of simulated annealing and molecular dynamics. Comparison of the results with those previously obtained for the natural CREKA shows that (Pro)hArg significantly reduces the conformational flexibility of the peptide. Although some changes are observed in the backbone...backbone and side-chain...side-chain interactions, the modified peptide exhibits a strong tendency to accommodate turn conformations centered at the (Pro)hArg residue and the overall shape of the molecule in the lowest energy conformations characterized for the natural and the modified peptides exhibit a high degree of similarity. In particular, the turn orients the backbone such that the Arg, Glu, and Lys side chains face the same side of the molecule, which is considered important for bioactivity. These results suggest that replacement of Arg by (Pro)hArg in CREKA may be useful in providing resistance against proteolytic enzymes while retaining conformational features which are essential for tumor-homing activity.
Holographic optics for thin and lightweight virtual reality (2020)

We present a class of display designs combining holographic optics, directional backlighting, laser illumination, and polarization-based optical folding to achieve thin, lightweight, and high performance near-eye displays for virtual reality. Several design alternatives are proposed, compared, and experimentally validated as prototypes. Using only thin, flat films as optical components, we demonstrate VR displays with thicknesses of less than 9 mm, fields of view of over 90° horizontally, and form factors approaching sunglasses. In a benchtop form factor, we also demonstrate a full color display using wavelength-multiplexed holographic lenses that uses laser illumination to provide a large gamut and highly saturated color. We show experimentally that our designs support resolutions expected of modern VR headsets and can scale to human visual acuity limits. Current limitations are identified, and we discuss challenges to obtain full practicality.
Anti-MUC1 Monoclonal Antibody (C595) and Docetaxel Markedly Reduce Tumor Burden and Ascites, and Prolong Survival in an in vivo Ovarian Cancer Model (2011)

MUC1 is associated with cellular transformation and tumorigenicity and is considered as an important tumor-associated antigen (TAA) for cancer therapy. We previously reported that anti-MUC1 monoclonal antibody C595 (MAb C595) plus docetaxel (DTX) increased efficacy of DTX alone and caused cultured human epithelial ovarian cancer (EOC) cells to undergo apoptosis. To further study the mechanisms of this combination-mediated apoptosis, we investigated the effectiveness of this combination therapy in vivo in an intraperitoneal (i.p.) EOC mouse model. OVCAR-3 cells were implanted intraperitoneally in female athymic nude mice and allowed to grow tumor and ascites. Mice were then treated with single MAb C595, DTX, combination test (MAb C595 and DTX), combination control (negative MAb IgG(3) and DTX) or vehicle control i.p. for 3 weeks. Treated mice were killed 4 weeks post-treatment. Ascites volume, tumor weight, CA125 levels from ascites and survival of animals were assessed. The expression of MUC1, CD31, Ki-67, TUNEL and apoptotic proteins in tumor xenografts was evaluated by immunohistochemistry. MAb C595 alone inhibited i.p. tumor growth and ascites production in a dose-dependent manner but did not obviously prevent tumor development. However, combination test significantly reduced ascites volume, tumor growth and metastases, CA125 levels in ascites and improved survival of treated mice compared with single agent-treated mice, combination control or vehicle control-treated mice (P<0.05). The data was in a good agreement with that from cultured cells in vitro. The mechanisms behind the observed effects could be through targeting MUC1 antigens, inhibition of tumor angiogenesis, and induction of apoptosis. Our results suggest that this combination approach can effectively reduce tumor burden and ascites, prolong survival of animals through induction of tumor apoptosis and necrosis, and may provide a potential therapy for advanced metastatic EOC.
Magnetoelastic-Harmonic Stress Sensors With Tunable Sensitivity (2011)

A wireless and passive stress sensor was developed by measuring changes in the induced magnetic field of a magnetoelastic strip under varying force loadings. The magnetoelastic strip was made of an amorphous ferromagnetic alloy and was attached to a solid body at its two longitudinal ends to form a bridge-like structure. When subjected to a lateral loading, the bridge-like structure allows the magnetoelastic strip to deflect, creating a longitudinal stress and changing its magnetic property. To remotely monitor the force loading, an AC magnetic field is applied and the magnetic fields induced by the magnetoelastic strip are recorded at multiple frequencies of the excitation frequency (higher-order harmonic fields). Experimental results showed that the second-order harmonic field (at twice the excitation frequency) amplitude produced by the sensor increased with applied compressive stress. It was also illustrated that sensor sensitivity with applied stress could be controlled by changing the length of the magnetoelastic strip. Good repeatability and stability were demonstrated with the highest signal drift of 9.45% occurring at a 9.7 kPa compressive load. Furthermore, a theoretical model was developed and evaluated to show the correlation between mechanical loading and second-order harmonic fields. Potential applications of this wireless and passive sensor technology include the monitoring of pressure in sphincter of Oddi, aortic aneurysms, and knee joint prostheses.
ChemInform Abstract: Total Synthesis of Balanol: A Potent Protein Kinase C Inhibitor of Fungal Origin. (1996)

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.
Semi-Supervised Learning of Bearing Anomaly Detection via Deep Variational Autoencoders (2019)

Most of the data-driven approaches applied to bearing fault diagnosis up to date are established in the supervised learning paradigm, which usually requires a large set of labeled data collected a priori. In practical applications, however, obtaining accurate labels based on real-time bearing conditions can be far more challenging than simply collecting a huge amount of unlabeled data using various sensors. In this paper, we thus propose a semi-supervised learning approach for bearing anomaly detection using variational autoencoder (VAE) based deep generative models, which allows for effective utilization of dataset when only a small subset of data have labels. Finally, a series of experiments is performed using both the Case Western Reserve University (CWRU) bearing dataset and the University of Cincinnati's Center for Intelligent Maintenance Systems (IMS) dataset. The experimental results demonstrate that the proposed semi-supervised learning scheme greatly outperforms two mainstream semi-supervised learning approaches and a baseline supervised convolutional neural network approach, with the overall accuracy improvement ranging between 3% to 30% using different proportions of labeled samples.
Conservative Management of Infections in Cochlear Implant Recipients (2001)

Postoperative cochlear implant infections can be effectively controlled with limited surgical and prolonged medical management. Chronic implant infections may be explained by a primary immunodeficiency. With appropriate treatment leading to infection control, a conservative management strategy is advocated before consideration of device explantation.
Tissue-specific Expression of the Human Gene for Lecithin: Cholesterol Acyltransferase in Transgenic Mice Alters Blood Lipids, Lipoproteins and Lipases towards a Less Atherogenic Profile (1995)

Lecithin:cholesterol acyltransferase (LCAT) is a key enzyme in the reverse cholesterol pathway but its role in lipid metabolism is still unclear. We have generated mice transgenic for a 7-kb genomic DNA fragment comprising the 6 exons and 5 introns of the LCAT gene with 1932 bp of 5' flanking and 908 bp of 3' flanking sequences. One line had integrated about 30 copies and expressed about 40-fold increased LCAT activity in a human test system. The expression showed correct tissue specificity of the human LCAT gene. Increased LCAT activity resulted in a decrease of plasma triacylglycerols below 50% of fasting controls. This reduction was seen in all lipoprotein fractions. Lipoprotein lipase activity did not change significantly, whereas hepatic triacylglycerol lipase increased markedly. Plasma total cholesterol was similar in fasting transgenic and control mice, but low-density lipoprotein and very low-density lipoprotein cholesterol were reduced to about 50%. High-density lipoprotein cholesterol increased about 20%, accompanied by a correspondingly increased size and a higher cholesterol efflux-stimulating activity of transgenic LCAT high-density lipoprotein. Both apolipoprotein A-I and A-II plasma concentrations increased in transgenic mice. Plasma triacylglycerol and cholesteryl ester fatty acid distribution showed an increased proportion of palmitic acid, whereas oleic, linoleic and arachidonic acid decreased, thus resembling more closely the human situation. Overexpression of the human LCAT gene provokes major changes in plasma lipoprotein and apolipoprotein concentrations, resulting in a less atherogenic plasma lipoprotein profile through a reduction in atherogenic and an increase in anti-atherogenic lipoproteins.
Improvement of a High-Current-Density Power Backplane Design With a PID Fan Control Cooling System on an Enterprise Server (2021)

Power consumption saving and direct airflow to enhance a system's cooling efficiency are important for the per watt index performance both of a server system and a data center's application. In this research project, we design the high-current-density power distribution printed circuit board (PCB) as an enterprise server power backplane board. This project also includes a design of both the vent hole size and the location to distribute the direct current path not only to attain a satisfactory loading balance but also to obtain the necessary direct airflow to improve cooling efficiency. In addition, we design the proportional-integral-derivative (PID) control module as a universal management control module for an enterprise server as a rack system assembly, in order to control the fan speed duty cycle more efficiently, all of which depends on a temperature that is different from the present error, the accumulation of past errors, and the prediction of future errors. We also consider the server system airflow impedance and fan speed duty and their dependence on other items, to ensure that the airflow is controllable and to prevent not only interference but also noise between enterprise server systems.
Self-monitoring of blood glucose: language and financial barriers in a managed care population with diabetes. (2000)

Considerable gaps persist between actual and recommended SMBG practices in this large managed care organization. A somewhat reduced SMBG frequency in subjects with linguistic barriers, some ethnic minorities, and subjects with lower education levels suggests the potential for targeted, culturally sensitive, multilingual health education. The somewhat lower frequency of SMBG among subjects paying higher out-of-pocket expenditures for strips suggests that removal of financial barriers by providing more comprehensive coverage for these costs may enhance adherence to recommendations for SMBG.
A Fast and Usually Linear Algorithm for Global Flow Analysis (1976)

A new algorithm for global flow analysis on reducible graphs is presented. The algorithm is shown to treat a very general class of function spaces. For a graph of e edges, the algorithm has a worst-case time bound of O ( e log e ) function operations. It is also shown that in programming terms, the number of operations is proportional to e plus the number of exits from program loops. Consequently a restriction to one-entry one-exit control structures guarantees linearity. The algorithm can be extended to yet larger classes of function spaces and graphs by relaxing the time bound. Examples are given of code improvement problems which can be solved using the algorithm.
Effect of Short-Term Supplementation of Potassium Chloride and Potassium Citrate on Blood Pressure in Hypertensives (2005)

Randomized trials have shown that increasing potassium intake lowers blood pressure. However, most previous trials used potassium chloride, whereas potassium in fruits and vegetables is not a chloride salt. It is unclear whether a nonchloride salt of potassium has a greater or lesser effect on blood pressure compared with potassium chloride. We performed a randomized crossover trial comparing potassium chloride with potassium citrate (96 mmol/d, each for 1 week) in 14 hypertensive individuals. At baseline, blood pressure was 151+/-16/93+/-7 mm Hg with a 24-hour urinary potassium of 81+/-24 mmol. During the randomized crossover part of the study, blood pressure was 140+/-12/88+/-7 mm Hg with potassium chloride (24-hour urinary potassium: 164+/-36 mmol) and 138+/-12/88+/-6 mm Hg with potassium citrate (24-hour urinary potassium: 160+/-33 mmol). These blood pressures were significantly lower compared with that at baseline; however, there was no significant difference in blood pressure between potassium chloride and potassium citrate, mean difference (95% confidence interval): 1.6 (-2.3 to 5.6) mm Hg for systolic and 0.6 (-2.4 to 3.7) mm Hg for diastolic. Our results, in conjunction with the evidence from many previous trials that potassium chloride has a significant blood pressure-lowering effect, suggest that potassium citrate has a similar effect on blood pressure as potassium chloride. These results support other evidence for an increase in potassium intake and indicate that potassium does not need to be given in the form of chloride to lower blood pressure. Increasing the consumption of foods high in potassium is likely to have the same effect on blood pressure as potassium chloride.
Cloning, sequencing and distribution of the <i>Salmonella typhimurlum</i> LT2 siaiidase gene, <i>nanH</i>, provides evidence for interspecies gene transfer (1992)

The Salmonella typhimurium LT2 sialidase (neuraminidase, EC 3.2.1.18) structural gene, nanH, has been cloned and sialidase overproduced from multicopy plasmids in Escherichia coli. Sialidase expression was regulated positively by cAMP. In contrast, certain Tn1000 insertions located upstream of nanH coding sequences reduced sialidase activity. A nanH chromosomal insertion mutation constructed by marker exchange demonstrated a single sialidase gene copy in S. typhimurium LT2. The complete nucleotide sequence of nanH, encoding a 41,300 dalton polypeptide, was determined and the derived primary structure was similar to sialidases from Clostridium perfringens, Clostridium sordellii, Bacteroides fragilis, and Trypanosoma cruzi. Comparative sequence analysis, including codon usage and secondary structure predictions, indicated that the S. typhimurium and clostridial sialidases are homologous, strongly suggestive of an interspecies gene transfer event. At least two primary sequence motifs of the bacterial enzymes were detected in influenza A virus sialidases. The predicted secondary structure of the bacterial enzymes was strikingly similar to viral sialidase. From the population distribution of nanH detected within a collection of salmonellae, it was apparent that S. typhimurium obtained its nanH copy most recently from Salmonella arizonae. S. typhimurium LT2 is thus a genetic mosaic that differs from other strains of even the same serotype by nanH plus potentially additional characters linked to nanH. These results have relevance to the evolution and function of sialidases in pathogenic microbes, and to the origin of the sialic acids.
Development of a hybrid emulation platform based on RTDS and reconfigurable power converter-based testbed (2016)

A real-time hardware testbed (HTB) has been constructed to emulate the power system by modular regenerative converters. This allows system realistic testing and demonstration with the true measurement, communication, and control. However, the size of the system that can be emulated by the HTB is limited, and certain phenomena are not easy or not needed to be modeled in the HTB. A hybrid emulation platform, which combines real time digital simulator (RTDS) and HTB, is developed in this paper to complement the advantages of RTDS and HTB. A power electronics converter is designed to act as the power interface between the RTDS and the HTB, and an integrated interface with two complementary algorithms is implemented to realize the hybrid emulation stably under different system conditions. At the same time, the closed loop control method under dq0 axis is implemented to realize faster response characteristics, and a time delay correction algorithm is integrated into the Park transformation. Experiment results demonstrate the performance and effectiveness of the hybrid emulation compared with the pure HTB emulation and digital simulation.
Amino acid management of Parkinson&rsquo;s disease: a case study (2011)

When 5-HTP and l-dopa are administered in proper balance along with l-tyrosine, l-cysteine, and cofactors under the guidance of OCT assay interpretation, the long list of problems that can interfere with optimum administration of l-dopa becomes controllable and manageable or does not occur at all. Patient treatment then becomes more effective by allowing the implementation of the optimal dosing levels of l-dopa needed for the relief of symptoms without the dosing value barriers imposed by side effects and adverse reactions seen in the past.
The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex–interactive agents (2008)

Previous studies on the functional analysis of the human vascular endothelial growth factor (VEGF) promoter using the full-length VEGF promoter reporter revealed that the proximal 36-bp region (-85 to -50 relative to transcription initiation site) is essential for basal or inducible VEGF promoter activity in several human cancer cells. This region consists of a polypurine (guanine) tract that contains four runs of at least three contiguous guanines separated by one or more bases, thus conforming to a general motif capable of forming an intramolecular G-quadruplex. Here, we show that the G-rich strand in this region is able to form an intramolecular propeller-type parallel-stranded G-quadruplex structure in vitro by using the electrophoretic mobility shift assay, dimethyl sulfate footprinting technique, the DNA polymerase stop assay, circular dichroism spectroscopy, and computer-aided molecular modeling. Two well-known G-quadruplex-interactive agents, TMPyP4 and Se2SAP, stabilize G-quadruplex structures formed by this sequence in the presence of a potassium ion, although Se2SAP is at least 10-fold more effective in binding to the G-quadruplex than TMPyP4. Between these two agents, Se2SAP better suppresses VEGF transcription in different cancer cell lines, including HEC1A and MDA-MB-231. Collectively, our results provide evidence that specific G-quadruplex structures can be formed in the VEGF promoter region, and that the transcription of this gene can be controlled by ligand-mediated G-quadruplex stabilization. Our results also provide further support for the idea that G-quadruplex structures may play structural roles in vivo and therefore might provide insight into novel methodologies for rational drug design.
Hyperbolic 0-1 Programming and Query Optimization in Information Retrieval (1990)

Unconstrained hyperbolic 0–1 programming can be solved in linear time when the numerator and the denominator are linear and the latter is always positive. It is NP-hard, and finding an approximate solution with a value equal to a positive multiple of the optimal one is also NP-hard, if this last hypothesis does not hold. Determining the optimal logical form of a query in information retrieval, given the attributes to be used, can be expressed as a parametric hyperbolic 0–1 program and solved in O(n logn) time, wheren is the number of elementary logical conjunctions of the attributes. This allows to characterize the optimal queries for the Van Rijsbergen synthetic criterion.
NodeRank: Observation-Point Insertion for Fault Localization in Monolithic 3D ICs (2020)

Monolithic 3D (M3D) ICs have emerged as a promising technology with significant improvement in power, performance, and area (PPA) over conventional 3D-stacked ICs. However, the sequential assembly of M3D tiers and immature fabrication process are prone to manufacturing defects and intertier process variations. Tier-level fault localization is therefore essential for yield ramp-up and diagnosis. Due to overhead concerns, only a limited number of observation points (OPs) can be inserted on the outgoing inter-layer vias (ILVs) of a tier to enable fault localization. We propose the computationally efficient NodeRank algorithm for observation-point insertion (OPI) on a small subset of outgoing ILVs. An ATPG-independent heuristic is presented, which is several orders-of-magnitude faster than ATPG fault simulation-based OPI. We introduce a metric called degree of fault localization to quantify the effectiveness of OPs. Evaluation results for two-tier M3D benchmark circuits show the effectiveness of the proposed method.
Nonlinear optics of Bessel beams (1993)

We investigated the frequency-doubling properties of light beams whose transverse profile is given by the zero-order Bessel function ${\mathit{J}}_{0}$(r), Bessel beams. Phase-matched second-harmonic generation in a KDP crystal was observed at angles usually not suited for phase matching. It is thereby demonstrated that under certain circumstances, Bessel beams can be viewed as light beams with tunable wavelength. A variety of applications in the field of nonlinear optics is expected.
One-Pot Synthesis of New 1,3-Imidazolidines Possessing Three Aryl Groups via a 1,3-Dipolar Cycloaddition Reaction (1994)

Tri-aryl-substituted imidazolidines (3) were readily synthesized by heating a mixture of arylaldehyde ( 7 ) , diethyl ketomalonate (8), and benzyl(or substituted benzyl)amine (6) in benzene in the presence of a catalytic amount of p-toluene-sulfonic acid.