gebhart/patrepeval huggingface dataset:
Antimicrobial efficacy of cyclic α- and β-peptides incorporated in polyurethane coatings (2023)

Microbial growth on surfaces poses health concerns and can accelerate the biodegradation of engineered materials and coatings. Cyclic peptides are promising agents to combat biofouling because they are more resistant to enzymatic degradation than their linear counterparts. They can also be designed to interact with extracellular targets and intracellular targets and/or self-assemble into transmembrane pores. Here, we determine the antimicrobial efficacy of two pore-forming cyclic peptides, α-K3W3 and β-K3W3, against bacterial and fungal liquid cultures and their capacity to inhibit biofilm formation on coated surfaces. These peptides display identical sequences, but the additional methylene group in the peptide backbone of β-amino acids results in a larger diameter and an enhancement in the dipole moment. In liquid cultures, β-K3W3 exhibited lower minimum inhibitory concentration values and greater microbicidal power in reducing the number of colony forming units (CFUs) when exposed to a gram-positive bacterium, Staphylococcus aureus, and two fungal strains, Naganishia albida and Papiliotrema laurentii. To evaluate the efficacy against the formation of fungal biofilms on painted surfaces, cyclic peptides were incorporated into polyester-based thermoplastic polyurethane. The formation of N. albida and P. laurentii microcolonies (105 per inoculation) for cells extracted from coatings containing either peptide could not be detected after a 7-day exposure. Moreover, very few CFUs (∼5) formed after 35 days of repeated depositions of freshly cultured P. laurentii every 7 days. In contrast, the number of CFUs for cells extracted from the coating without cyclic peptides was >8 log CFU.
TH‐C‐137‐04: Separating the Dosimetric Consequences of Changing Tumor Anatomy Vs. Positional Uncertainty for Conventionally Fractionated Lung Cancer Patients (2013)

Purpose: To differentiate between the dosimetric consequences of positional uncertainty and changing tumor anatomy for conventionally fractionated lung cancer treatment plans. Methods: Modified IMRT photon treatment plans were retrospectively generated for 12 lung cancer patients (prescription range = 45–66 Gy). 10 of 12 patients had centrally located tumors, and the average internal target volume (ITV) was 119.5 cc (standard deviation = 133.3 cc). To simulate a large and immediate tumor response, all voxels corresponding to tumor within the ITV were reassigned an electron density equivalent to lung. The original, unchanged treatment plan was then calculated on this modified image set. To simulate positional uncertainty, isocenters in each plan were shifted by 2 mm and 5 mm in each of 6 directions: superior/inferior, left/right, anterior/posterior. Shifted plans were calculated for both the original and modified ITV. Paired t‐tests were used to compare the original and modified plans, both with and without simulated positional uncertainty. For the purposes of this abstract, changes to the volume of the PTV receiving 95% of prescription dose (PTV V95%), mean lung dose, the percent volume of lung receiving 20 Gy (Lung V20%), the volume in ccs of esophagus receiving 55 Gy (V55Gy(cc)), and the volume in ccs of spinal cord receiving 45 Gy (V45Gy(cc)) are reported. Results: Reduced tumor volumes alone resulted in minimal dosimetric impact. Shifts of 2 and 5 mm reduced PTV coverage by 0.54% and 3.3% respectively when compared to the original (unshifted) plan. When comparing modified and original plans which are both shifted in the same direction, small increases in dose were seen. Conclusion: The dosimetric consequences of positional uncertainty are larger than volumetric tumor reduction. Adaptive replanning techniques based solely on the perceived dosimetric consequences of shrinking tumor anatomy are unwarranted for conventionally fractionated lung cancer patients.
Neuromorphic binocular vision system for real-time disparity estimation (2007)

We describe a binocular vision system that emulates disparity computation in the neuronal circuit of the primary visual cortex (V1). The system consists of two sets of silicon retinas and simple cell chips that correspond to the binocular vision and field programmable gate array (FPGA) circuit. This arrangement mimics the hierarchical architecture of the visual system of the brain. The silicon retina is an analog very large scale integrated (aVLSI) circuit and possesses a Laplacian-Gaussian-like spatial filter similar to the receptive field of the vertebrate retina. The simple cell chip generates a Gabor-like spatial filter similar to the orientation-selective receptive field of the simple cell in V1 by aggregating several pixels of the silicon retina. The FPGA receives the outputs from the two simple cell chips corresponding to binocular inputs from the left and right eyes and calculates the binocular disparity in real-time based on the disparity energy model. The system provides output images tuned to five different disparities in parallel. The disparity map is obtained by comparing these disparity energy outputs. Due to the combination of the parallel and analog computation of the aVLSIs and the pixel-wise computation with hard-wired digital circuits, the present system can efficiently compute the binocular disparity using compact hardware and low power dissipation in real-time.
Heterogeneous vasomotor responses of anatomically distinct feline cerebral arteries (1988)

1. The vasomotor reactivity to a number of neurotransmitters and blood-borne substances was evaluated in several anatomically distinct arteries of the cat cerebral circulation. Few regional differences were observed in their vasoconstrictor responses to noradrenaline, dopamine, 5-hydroxytryptamine and prostaglandin F2 alpha. Only the anterior cerebral artery reacted strongly to all vasoconstrictor agents. 2. Adenosine, acetylcholine and histamine induced pronounced relaxation in the vast majority of the major cerebral arteries. The relaxation elicited by adenosine showed a slight degree of heterogeneity between the arteries and the overall response accounted for 81 +/- 6% of the pharmacologically-induced tone. On the other hand, the dilatation induced by acetylcholine and histamine varied as a function of the anatomical localization of the cerebral arteries. The acetylcholine-induced vasodilatation was significantly more pronounced in the middle cerebral, anterior communicating and anterior cerebellar arteries, with respective responses of 72, 66 and 83% of the induced tone as compared to 43% in the other vessels. However, all arteries were equally sensitive to acetylcholine with an overall mean pD2 value of 7.47 +/- 0.06. The most heterogeneous results were obtained with histamine and applied both to the magnitude of the maximal response and the sensitivity of the various arteries to this amine. The intensity of the relaxation varied from 20% (anterior communicating artery) to 118% (posterior cerebellar artery). 3. Among the neuropeptides studied, substance P and bradykinin were considerably less potent than vasoactive intestinal peptide on all the cerebral arteries. The least responsive vessel to bradykinin was the anterior cerebral artery with a maximal response of 22 +/- 5% of the induced-tone and a pD2 value of 7.56 +/- 0.24. All vessels responded weakly to substance P and those from the vertebrobasilar circulation were significantly less sensitive to this neuropeptide with pD2 values around 8.07 as compared to 9.82 in the more rostral arteries. Although all vessels were equally sensitive to vasoactive intestinal peptide, the dilator responses were significantly less pronounced in the middle cerebral and basilar arteries (maximal response of 86 +/- 5% and 69 +/- 6% of the induced-tone, respectively, as compared to 110 +/- 9% in the other vessels). 4. The vertebrobasilar arteries were as reactive, if not more reactive, to vasoconstrictors than the vessels originating from the carotid circulation. In contrast, the dilator responses were less marked in most caudal arteries. Such dichotomies may be important in the regulation of local cerebral blood flow. 5. The results emphasize the considerable heterogeneity in the vasomotor responses to a given substance among the various cerebral arteries. Further, they suggest the presence of multiple receptor populations which mediate opposite effects and which are distributed in different proportions among the cephalic arteries.
Transition Metal Catalyzed Carbon—Carbon Bond Activation (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
한국과 미국 무용학회지의 질적 연구와 학문적 글쓰기 동향 : 나와 본 연구자 사이 (2014)

This study investigates the current state of qualitative research and academic writing from articles in The Korean Journal of Dance Studies, Dance Research Journal of Korea, Korea Journal of Dance Documentation, Research of Dance Education, Dance Research Journal (DRJ), Dance Chronicle: Studies of Dance and Related Arts (DC), Journal of Dance Education (JODE) from 2009 to 2013. Of 873 research articles, 70 qualitative studies articulate research methods, data collection methods, data analysis methods, reflection on research process, methods of validation, and methods of ethical issue treatment. In addition, I examine the academic writing styles, focusing on research title, expressions referring to the researcher(s), and reflections on researchers themselves. The analysis of qualitative study methods suggests that Korean and American dance scholarships are more or less similar. The analysis of academic writing styles suggests that American dance scholarship shows relatively higher percentage of qualitative writing characteristics in the all three areas.
Efficient Microwave-Assisted Synthesis of 1,2,4-Triazole-Based Peptidomimetics Using Benzotriazole Methodology (2011)

A microwave-assisted three-step protocol allowed the rapid and convenient construction of a series of 1,2,4-triazole substituted amino acids and dipeptides as potential building blocks for peptidomimetics.
Margatoxin‐bound quantum dots as a novel inhibitor of the voltage‐gated ion channel Kv1.3 (2016)

Venom-derived ion channel inhibitors have strong channel selectivity, potency, and stability; however, tracking delivery to their target can be challenging. Herein, we utilized luminescent quantum dots (QDs) conjugated to margatoxin (MgTx) as a traceable vehicle to target a voltage-dependent potassium channel, Kv1.3, which has a select distribution and well-characterized role in immunity, glucose metabolism, and sensory ability. We screened both unconjugated (MgTx) and conjugated MgTx (QD-MgTx) for their ability to inhibit Shaker channels Kv1.1 to Kv1.7 using patch-clamp electrophysiology in HEK293 cells. Our data indicate that MgTx inhibits 79% of the outward current in Kv1.3-transfected cells and that the QD-MgTx conjugate is able to achieve a similar level of block, albeit a slightly reduced efficacy (66%) and at a slower time course (50% block by 10.9 ± 1.1 min, MgTx; vs. 15.3 ± 1.2 min, QD-MgTx). Like the unbound peptide, the QD-MgTx conjugate inhibits both Kv1.3 and Kv1.2 at a 1 nM concentration, whereas it does not inhibit other screened Shaker channels. We tested the ability of QD-MgTx to inhibit native Kv1.3 expressed in the mouse olfactory bulb (OB). In brain slices of the OB, the conjugate acted similarly to MgTx to inhibit Kv1.3, causing an increased action potential firing frequency attributed to decreased intraburst duration rather than interspike interval. Our data demonstrate a retention of known biophysical properties associated with block of the vestibule of Kv1.3 by QD-MgTx conjugate compared to that of MgTx, inferring QDs could provide a useful tool to deliver ion channel inhibitors to targeted tissues in vivo.
Utilization of sialic acid-binding synthetic peptide sequences derived from pertussis toxin as novel anti-inflammatory agents (1995)

Pertussis toxin, a virulence factor produced by the organism Bordetella pertussis, has been shown to have functional similarities with selectins and to bind to similar sialic acid-containing oligosaccharides structures. Previously, we demonstrated that the amino-terminal region of the S2 subunit of pertussis toxin contained a short six amino acid sequence (SPYGRC) which displayed reasonable homology to a sequence that constitutes a portion of the sialic acid binding site in wheat germ agglutinin. Synthetic peptides containing this hexapeptide motif had the ability to bind to sialic acid-containing glycoconjugates including the putative oligosaccharide receptors (sialyl Lewis X and sialyl Lewis A) for selectins. Control peptides containing randomized sequences were inactive at inhibiting binding, indicating that the hexapeptide motif is important for interacting with sialic acid. Since pertussis toxin-derived peptides demonstrated the ability to interact with selectin receptors, we speculated that they should antagonize selectin-mediated inflammatory activity. To test this hypothesis, we evaluated the peptides for the ability to reduce neutrophil binding to activated endothelial cells as well as the anti-inflammatory activity in the mouse footpad swelling assay. Both S2 peptides were active at reducing neutrophil binding and footpad swelling, while the randomized control peptides were inactive.
Optical and IR absorption as probe of dynamics of heme proteins (2002)

The spectroscopy of horseradish peroxidase with and without the substrate analogue benzohydroxamic acid (BHA) was monitored in different solvents as a function of the temperature in the interval from 10 to 300 K. Thermal broadening of the Q(0,0) optical absorption band arises mainly from interaction of the electronic pi --> pi transition with the heme vibrations. In contrast, the width of the IR absorption band of CO bound to heme is controlled by the coupling of the CO transition moment to the electric field of the protein matrix. The IR bandwidth of the substrate free enzyme in the glycerol/H2O solvent hardly changes in the glassy matrix and strongly increases upon heating above the glass transition. Heating of the same enzyme in the trehalose/H2O glass considerably broadens the band. The binding of the substrate strongly diminishes the temperature broadening of the CO band. This result is consistent with the view that the BHA strongly reduces the amplitude of vibrations of the heme pocket environment. Unusually strong thermal broadening of the CO band above the glass transition is interpreted to be caused by thermal population of a very flexible excited conformational substate. The thermal broadening of the same band in the trehalose glass is caused by an increase of the protein vibrational amplitude in each of the conformational substates, their population being independent of the temperature in the glassy matrix.
Modernizing Legacy Systems (2003)

Carnegie Mellon University does not discriminate and Carnegie Mellon University is required not to discriminate in admission, employment, or administra-tion of its programs or activities on the basis of race, color, national origin, sex or handicap in violation of Title VI of the Civil Rights Act of 1964, Title IX of the Educational Amendments of 1972 and Section 504 of the Rehabilitation Act of 1973 or other federal, state, or local laws or executive orders. In addition, Carnegie Mellon University does not discriminate in admission, employment or administration of its programs on the basis of religion, creed, ancestry, belief, age, veteran status, sexual orientation or in violation of federal, state, or local laws or executive orders. However, in the judgment of the Carnegie Mellon Human Relations Commission, the Department of Defense policy of &amp;quot;Don&amp;apos;t ask, don&amp;apos;t tell, don&amp;apos;t pursue &amp;quot; excludes openly gay, lesbian and bisexual students from receiving ROTC scholarships or serving in the military. Nevertheless, all ROTC classes at Carnegie Mellon University are available to all students.
Data from Enzalutamide, an Androgen Receptor Antagonist, Enhances Myeloid Cell–Mediated Immune Suppression and Tumor Progression (2023)

&lt;div&gt;Abstract&lt;p&gt;Androgen receptor (AR) antagonism increases overall survival in prostate cancer; however, treatment failure leads to tumor progression and patient mortality. The effect of AR modulation on AR&lt;sup&gt;+&lt;/sup&gt; nontumor cells that participate in the resistance to AR antagonism is poorly understood. Tumor-infiltrating myeloid cells, including macrophages and myeloid-derived suppressor cells (MDSC), express AR and promote prostate cancer progression. We investigated how AR antagonism affects myeloid cell function and metabolism in an AR-independent murine colon tumor model. Systemic blockade of AR with enzalutamide resulted in increased MC-38 tumor growth &lt;i&gt;in vivo&lt;/i&gt; even when AR was knocked out of MC-38 tumor cells. MC-38 tumor growth was also increased when immunocompetent, but not immunodeficient, mice were coinjected with tumor cells and MDSCs treated with enzalutamide or lacking AR, suggesting that AR regulated the ability of MDSCs to suppress adaptive immunity. Myeloid AR-knockout male mice also displayed increased growth of TRAMP C2 prostate tumors when compared with wild type. Inhibition of AR signaling suppressed mitochondrial respiration in myeloid cells via MPC/AMPK signaling pathways; suppression of mitochondrial respiration increased MDSC tumor–promoting functions. Our work showed that AR regulates a tumor-promoting myeloid cell phenotype and influences myeloid cell metabolism. These findings suggest that tumor resistance to AR antagonism is due, in part, to changes in myeloid cell function and metabolism.&lt;/p&gt;&lt;/div&gt;
A novel bio-inspired static image compression scheme for noisy data transmission over low-bandwidth channels (2010)

We present a novel bio-inspired static image compression scheme. Our model is a combination of a simplified spiking retina model and well known data compression techniques. The fundamental hypothesis behind this work is that the mammalian retina generates an efficient neural code associated to the visual flux. The main novelty of this work is to show how this neural code can be exploited in the context of still image compression. Our model has three main stages. The first stage is the bio-inspired retina model proposed by Thorpe et al, which transforms an image into a wave of spikes. This transform is based on the so-called rank order coding. In the second stage, we show how this wave of spikes can be expressed using a 4-ary dictionary alphabet, through a stack run coder. The third stage consists of applying a first order arithmetic coder to the stack run coded signal. We compare our results to JPEG standards and we show that our model has comparable performance for lower computational cost under strong bit rate restrictions when data is highly contaminated with noise. In addition, our model offers scalability for monitoring data transmission flow. The subject matter presented highlights a variety of important issues in the conception of novel bio-inspired compression schemes and additionally presents many potential avenues for future research efforts.
How to Assure Fracture-Propagation Control for Seamless Gas Pipelines? (2014)

Fracture propagation control in gas transmission gas pipelines belongs to the major design requirements for safe operation at high internal pressures. However, the current tests such as Drop-Weight-Tear Test (DWTT) and full-scale West-Jefferson (WJ) test reach the limits of their applicability with respect to transition temperature evaluation for seamless quenched and tempered small diameter pipes reflecting nowadays alloying concepts related to mechanical properties. Hereby, different geometry and material effects are evident which might lead to misinterpretation and unreliability of testing results. This paper aims to discuss open issues addressed in the literature and in own experimental findings with respect to reliability and transferability of testing methods, fracture parameters and their representativeness of seamless quenched and tempered pipeline behavior. By applying damage mechanics approach, it is possible to quantify the prevailing stress state and thus to understand the mechanisms controlling specific fracture appearance (ductile or brittle). Furthermore, studies were performed with objective to quantify the effect of different parameters (geometry, material and loading) on the fracture performance of the pipeline. The results from these investigations will serve as a basis for a safe pipeline design against propagating fracture.
Identification of three isozyme proteins of the catalytic subunit of the Na,K-ATPase in rat brain (1989)

Molecular genetic evidence indicates that there should be three different (Na+ + K+)-stimulated ATPase (Na,K-ATPase) alpha subunit isozymes in the brain where previously only two ("alpha" and "alpha(+)") were resolved as proteins. To detect and identify alpha 1, alpha 2, and alpha 3 isozymes, polypeptides made by cell-free translation (Schneider, J.W., Mercer, R.W., Gilmore-Hebert, M., Utset, M.F., Lai, C., Greene, A., and Benz, E.J., Jr. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 284-288) were analyzed by gel electrophoresis and proteolytic fingerprinting. Synthetic alpha 1 comigrated with tissue alpha 1, while alpha 2 and alpha 3 comigrated with the leading and trailing edges, respectively, of tissue "alpha(+)." Proteolytic fingerprints of newborn rat brain Na,K-ATPase labeled in vivo with L-[35S]methionine indicated the presence of alpha 1 and alpha 3, and a low level of alpha 2. Monoclonal antibodies were characterized by the electrophoretic mobility of their antigens and by their ability to recognize the Na,K-ATPases of kidney, brain, and skeletal muscle. The antibodies were used to assess isozyme expression in the brain. All three isozymes increased in abundance during development from the 18-day fetus to the adult. Small changes were seen in the relative level of expression of alpha 1 and alpha 3 at different developmental ages, while alpha 2 expression increased markedly between the neonate and adult. In adult brain, all three isozymes were found in all brain regions examined. We conclude that all three isozymes are expressed as proteins and that their expression and distribution must be under complex control. No single developmental age or macroscopic brain region provides an exclusive source of any of the isozymes.
Standoff acoustic-to-seismic landmine detection (2004)

This paper addresses a potential method to advance acoustic landmine detection by increasing operator and equipment standoff range from the minefield and developing a lightweight system that is potentially more practical than many currently researched systems. In this study, a parametric array acoustic source is evaluated to understand its potential for landmine detection. The array can transmit audible signals over 100 meters in air and has a weight of just four pounds. A proof-of-concept system was built at M.I.T. Lincoln Laboratory that uses a commercial parametric source to insonify the ground and excite buried mines. A commercial laser vibrometer was then used to measure the displacement velocity at the ground surface on and off the mine. This system has been demonstrated at an outdoor landmine facility and has measured signatures from buried anti-personnel mines. The overall concept shows promise; however, the parametric source used in this preliminary test was developed for home entertainment and will require substantial modification to be practical for landmine detection.