gebhart/patrepeval huggingface dataset:
Structure-Microbicidal Activity Relationship of Synthetic Fragments Derived from the Antibacterial α-Helix of Human Lactoferrin (2009)

There is a need for new microbicidal agents with therapeutic potential due to antibiotic resistance in bacteria and fungi. In this study, the structure-microbicidal activity relationship of amino acid residues 14 to 31 (sequence 14-31) from the N-terminal end, corresponding to the antibacterial alpha-helix of human lactoferrin (LF), was investigated by downsizing, alanine scanning, and substitution of amino acids. Microbicidal analysis (99% killing) was performed by a microplate assay using Escherichia coli, Staphylococcus aureus, and Candida albicans as test organisms. Starting from the N-terminal end, downsizing of peptide sequence 14-31 showed that the peptide sequence 19-31 (KCFQWQRNMRKVR, HL9) was the optimal length for antimicrobial activity. Furthermore, HL9 bound to lipid A/lipopolysaccharide, as shown by neutralizing endotoxic activity in a Limulus assay. Alanine scanning of peptide sequence 20-31 showed that Cys20, Trp23, Arg28, Lys29, or Arg31 was important for expressing full killing activity, particularly against C. albicans. Substituting the neutral hydrophilic amino acids Gln24 and Asn26 for Lys and Ala (HLopt2), respectively, enhanced microbicidal activity significantly against all test organisms compared to the amino acids natural counterpart, also, in comparison with HL9, HLopt2 had more than 10-fold-stronger fungicidal activity. Furthermore, HLopt2 was less affected by metallic salts than HL9. The microbicidal activity of HLopt2 was slightly reduced only at pH 7.0, as tested in the pH range of 4.5 to 7.5. The results showed that the microbicidal activity of synthetic peptide sequences, based on the antimicrobial alpha-helix region of LF, can be significantly enhanced by optimizing the length and substitution of neutral amino acids at specific positions, thus suggesting a sequence lead with therapeutic potential.
Modulation of Structure and Antibacterial and Hemolytic Activity by Ring Size in Cyclic Gramicidin S Analogs (1996)

We have evaluated the effect of ring size of gramicidin S analogs on secondary structure, lipid binding, lipid disruption, antibacterial and hemolytic activity. Cyclic analogs with ring sizes ranging from 4 to 14 residues were designed to maintain the amphipathic character as found in gramicidin S and synthesized by solid phase peptide synthesis. The secondary structure of these peptides showed a definite periodicity in beta-sheet content, with rings containing 6, 10, and 14 residues exhibiting beta-sheet structure, and rings containing 8 or 12 residues being largely disordered. Peptides containing 4 or 6 residues did not bind lipopolysaccharide, whereas longer peptides showed a trend of increasing binding affinity for lipopolysaccharide with increasing length. Destabilization of Escherichia coli outer membranes was only observed in peptides containing 10 or more residues. Peptides containing fewer than 10 residues were completely inactive and exhibited no hemolytic activity. The 10-residue peptide showed an activity profile similar to that of gramicidin S itself, with activity against Gram-positive and Gram-negative microorganisms as well as yeast, but also showed high hemolytic activity. Differential activities were obtained by increasing the size of the ring to either 12 or 14 residues. The 14-residue peptide showed no antibiotic activity but exhibited increased hemolytic activity. The 12-residue peptide lost activity against Gram-positive bacteria, retained activity against Gram-negative microorganisms and yeast, but displayed decreased hemolytic activity. Biological activities in the 12-residue peptide were optimized by a series of substitutions in residues comprising both hydrophobic and basic sites resulting in a peptide that exhibited activities comparable with gramicidin S against Gram-negative microorganisms and yeast but with substantially lower hemolytic activity. Compared with gramicidin S, the best analog showed a 10-fold improvement in antibiotic specificity for Gram-negative microorganisms and a 7-fold improvement in specificity for yeast over human erythrocytes as determined by a therapeutic index. These results indicate that it is possible to modulate structure and activities of cyclic gramicidin S analogs by varying ring sizes and further show the potential for developing clinically useful antibiotics based on gramicidin S.
ChemInform Abstract: Synthetic Studies on Cell‐Surface Glycans. Part 65. Highly Stereoselective Synthesis of Ganglioside GD3. (1990)

Abstract Gangliosides play a role in cellular recognition, differentiation and oncogenesis.
Microstructural Stability of a Single Crystal Superalloy DD8 during Thermal Exposure (2008)

Microstructural stability of a nickel base single crystal alloy DD8 has been investigated. Standard heat treated specimen showed good microstructural stability at 950 degrees C. While under the as-cast condition, a kind of rod-like phase precipitated in the interdendritic region of as-cast specimen during thermal exposure. The phase, which has bcc structure, was enriched with Cr. Thermo-calc also predicted precipitation of a bcc phase at around 950 degrees C. The Cr-rich bcc phase was considered as alpha-Cr and formed due to the segregation of Cr under the as-cast condition.
<title>Comparison of multiple compression cycle performance for JPEG and JPEG 2000</title> (2000)

Ideally, when the same set of compression parameters are used, it is desirable for a compression algorithm to be idempotent to multiple cycles of compression and decompression. However, this condition is generally not satisfied for most images and compression settings of interest. Furthermore, if the image undergoes cropping before recompression, there is a severe degradation in image quality. In this paper we compare the multiple compression cycle performance of JPEG and JPEG2000. The performance is compared for different quantization tables (shaped or flat) and a variety of bit rates, with or without cropping. It is shown that in the absence of clipping errors, it is possible to derive conditions on the quantization tables under which the image is idempotent to repeated compression cycles. Simulation results show that when images have the same mean squared error (MSE) after the first compression cycle, there are situations in which the images compressed with JPEG2000 can degrade more rapidly compared to JPEG in subsequent compression cycles. Also, the multiple compression cycle performance of JPEG2000 depends on the specific choice of wavelet filters. Finally, we observe that in the presence of cropping, JPEG2000 is clearly superior to JPEG. Also, when it is anticipated that the images will be cropped between compression cycles when using JPEG2000, it is recommended that the canvas system be used.
Renal Solute Transporters and Their Relevance to Serum Urate Disorder (2010)

Since uric acid (urate), the final product of purine metabolism, exhibits antioxidative activity, its protective role against oxidative stress becomes attractive. Low serum urate levels have been associated with multiple sclerosis, Parkinsons disease, and Alzheimers disease. Despite its beneficial role, hyperuricemia is associated with gout, hypertension, cardiovascular diseases such as myocardial infarction and stroke, and renal diseases such as acute urate nephropathy and nephrolithiasis. The urate transport system of the kidney is an important determinant of the serum urate level, but clarification of its molecular mechanism remains incomplete. In 2002, our group identified URAT1 (SLC22A12), a renal apical urate/anion exchanger, leading to the accumulation of information concerning individual molecules involved in urate transport in the kidney. In 2008, we functionally characterized facilitatory glucose transporter family member GLUT9 (SLC2A9) as a voltage-driven urate transporter URATv1 and analysis of a renal hypouricemia patient with a genetic defect in SLC2A9 have established the main route of the urate reabsorption pathway at the basolateral side of renal proximal tubules, where urate in the urinary lumen is taken up via apical URAT1 and intracellular urate exits from the cell to the interstitium/blood space via basolateral URATv1. In this review, recent findings concerning these molecules are presented. Keywords: Urate, transporter, hypouricemia, hyperuricemia, gout, PDZ
Time Reversal for 6G Spatiotemporal Focusing: Recent Experiments, Opportunities, and Challenges (2022)

Late visions and trends for the future 6G of wireless communications advocate, among other technologies, the deployment of network nodes with extreme numbers of antennas and up to terahertz frequencies as a means to enable various immersive applications. However, these technologies impose several challenges in the design of radio-frequency (RF) front ends and beamforming architectures as well as ultrawideband waveforms and computationally efficient transceiver signal processing. In this article, we revisit the time-reversal (TR) technique, which was initially experimented in acoustics, in the context of large-bandwidth 6G wireless communications, capitalizing on its high-resolution spatiotemporal focusing realized with low-complexity transceivers. We first overview the representative state of the art in TR-based wireless communications, identifying the key competencies and requirements of TR for efficient operation. Recent and novel experimental setups and results for the spatiotemporal-focusing capability of TR at the carrier frequencies 2.5, 36, and 273 GHz are then presented, demonstrating in quantitative ways the technique’s effectiveness in these very different frequency bands as well as the roles of the available bandwidth and the number of transmit antennas. We also showcase the TR potential for realizing low-complexity multiuser communications. The opportunities arising from TR-based wireless communications as well as the challenges for finding their place in 6G networks, also in conjunction with other complementary candidate technologies, are highlighted.
Electromagnetic Safety Assessment of a Cortical Implant for Vision Restoration (2018)

A cortical visual prosthetic system bypasses the components of the visual pathway, which may be damaged due to injury or disease, by directly stimulating the visual cortex; therefore, cortical visual prostheses promise the capability of restoring a form of vision to patients who cannot benefit from other types of visual neural stimulators. A high data rate, multielectrode, implantable device, such as that utilized for a cortical visual prosthesis, requires continuous power provided by an external telemetry unit, which is nonnegligible, given the number of stimulating electrodes and the stimulation rate necessary to avoid flickering visual percepts. This aspect motivates the need to develop models and methods that aid the development of such devices by assessing their compliance with electromagnetic safety standards. In this paper, the electromagnetic safety assessment of a cortical visual prosthetic system is considered, and the solutions employed to numerically treat the computational complexities associated with it are discussed. The specifics of the implementation of an actual visual cortical implant are discussed, and the parameters of such an implant are used as a test case to determine whether IEEE and ICNIRP electromagnetic standards are met in what can be considered a typical embodiment of the prosthesis. Results show that, for the considered implant, such a system meets IEEE and ICNIRP safety standards, thus enabling further development of similar neurorehabilitative devices.
Tumor Necrosis Factor Modulates Fibroblast Apoptosis, PMN Recruitment, and Osteoclast Formation in Response to P. gingivalis Infection (2001)

P. gingivalis is an important oral pathogen, which has been closely linked to periodontal disease as well as lesions of endodontic origin. Both infections are associated with a decrease in fibroblast numbers, formation of an inflammatory infiltrate, and bone resorption. The goal of this study was to investigate the role that the host response plays in the capacity of P. gingivalis to stimulate fibroblast apoptosis, PMN recruitment, and osteoclastogenesis. This was accomplished by the use of an in vivo calvarial model in mice with targeted deletion of TNF receptors p55 and p75 and matched wild-type mice. The results indicate that P. gingivalis induces fibroblast apoptosis in vivo and establish for the first time that this involves the stimulation of a host response. Moreover, bacteria-stimulated PMN recruitment and osteoclastogenesis were also dependent upon the host response. The results suggest that much of the damage caused by P. gingivalis infection, including fibroblast apoptosis, at least under some circumstances, results from stimulation of the host response rather than the direct effect of bacterial products. Furthermore, this may represent a more general mechanism by which bacterial challenge induces apoptosis of matrix-producing cells through the induction of TNF.
The Art of Lecturing: A Practical Guide to Successful University Lectures and Business Presentations (2011)

This simple and clear guide to lecturing is an example-based account of effective strategies for exciting and successful lectures for academic and business lecturers. From the lecturing mindset, combating fear and nervousness, to lecturing tricks and tactics, this book discusses a wide array of practical ideas that may surprise and help even the most experienced public speakers and lecturers. The author provides unique insights into lecturing for twenty-first century audiences, based on his academic and non-academic lecturing experiences at the University of Toronto and Stanford University; experiences which have resulted in numerous institutional, provincial, and international teaching and lecturing awards. Further resources for this title, including lecture slides and videos of presentations and lectures, are available online from www.cambridge.org/9780521876100
PhoneHome: Robust Extension of Cellular Coverage (2016)

Ubiquitous cellular coverage is often taken for granted, yet numerous people live outside, or at the fringes, of commercial cellular coverage. Further, natural disasters and human rights violations cause the displacement of millions of people annually worldwide, with many of these people relocating to shelters and camps in areas at or just beyond the margins of existing cellular infrastructure. In this work we design PhoneHome, a system prototype that extends existing cellular coverage to areas with no or damaged cellular infrastructure, or infrastructure that is otherwise poorly performing. We explore the feasibility of PhoneHome and address current limitations and future directions for independently operated, user-extensible cellular infrastructure.
Supplementary Data from The Proapoptotic Molecule BLID Interacts with Bcl-X<sub>L</sub> and Its Downregulation in Breast Cancer Correlates with Poor Disease-Free and Overall Survival (2023)

Supplementary Data from The Proapoptotic Molecule BLID Interacts with Bcl-X&lt;sub&gt;L&lt;/sub&gt; and Its Downregulation in Breast Cancer Correlates with Poor Disease-Free and Overall Survival
Subpectoral, Suprapectoral, and Top‐of‐Groove Biceps Tenodesis Procedures Lead to Similar Good Clinical Outcomes: Comparison of Biceps Tenodesis Procedures (2023)

Level III, retrospective comparative study.
Low-supply-noise Low-power Embedded Modular SRAM For Mixed Analog-digital ICs (1992)

A low-power, low-noise embedded modular SRAM has been designed that dissipates 0.22 mWA4Hz and generates 25 mAlns dVdt for a 512 x 15 configuration at 3.3 V. Results are achieved using a pulsed divided word line architecture, with internal cascaded clocks, weak static sensing, low-noise buffers and flip-flops and low-power decoding techniques.
OBJECT CLASSIFICATION VIA PLANAR ABSTRACTION (2016)

Abstract. We present a supervised machine learning approach for classification of objects from sampled point data. The main idea consists in first abstracting the input object into planar parts at several scales, then discriminate between the different classes of objects solely through features derived from these planar shapes. Abstracting into planar shapes provides a means to both reduce the computational complexity and improve robustness to defects inherent to the acquisition process. Measuring statistical properties and relationships between planar shapes offers invariance to scale and orientation. A random forest is then used for solving the multiclass classification problem. We demonstrate the potential of our approach on a set of indoor objects from the Princeton shape benchmark and on objects acquired from indoor scenes and compare the performance of our method with other point-based shape descriptors.
Enhanced Duplicate Address Detection (2015)

IPv6 Loopback Suppression and Duplicate Address Detection (DAD) are
discussed in Appendix A of RFC 4862. That specification mentions a
hardware-assisted mechanism to detect looped back DAD messages. If
hardware cannot suppress looped back DAD messages, a software solution
is required. Several service provider communities have expressed a
need for automated detection of looped back Neighbor Discovery (ND)
messages used by DAD. This document includes mitigation techniques and
outlines the Enhanced DAD algorithm to automate the detection of
looped back IPv6 ND messages used by DAD. For network loopback tests,
the Enhanced DAD algorithm allows IPv6 to self-heal after a loopback
is placed and removed. Further, for certain access networks, this
document automates resolving a specific duplicate address conflict.
This document updates RFCs 4429, 4861, and 4862.
Unexpected visible‐light‐induced free radical photopolymerization at low light intensity and high viscosity using a titanocene photoinitiator (2012)

Abstract Most visible‐light photoinitiators are based on electron transfer processes and are comprised of two or more components. These initiators can lose effectiveness in viscous systems because the underlying reactions are diffusion controlled. In this contribution, the visible‐light photoinitiator bis(cyclopentadienyl) bis[2,6‐difluoro‐3‐(1‐pyrryl)phenyl]titanium is characterized for polymerization of viscous systems and low light intensities. This compound absorbs visible light at wavelengths up to 550 nm, and does not rely on diffusion‐controlled electron transfer reactions because it undergoes unimolecular decomposition. In contrast to trends observed for other photoinitiators, the effectiveness of the compound is found to increase markedly with the addition of protonic acids and with increasing system viscosity. For a given concentration of initiator and acid, a remarkably low optimal light intensity for effective polymerization is observed. The origins of these surprising results are discussed in terms of the mechanism of decomposition of the photoinitiator. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Specific nonlipid agonists of the lysophosphatidic acid type 2 GPCR with subnanomolar potency mitigate radiation injury (998.2) (2014)

Previous studies have identified ligands of the LPA2 GPCR as mitigators of high‐dose radiation injury in vitro and in vivo. These early hit compounds originating from the hit scaffold GRI977143 had EC50 values in the hundred nanomolar range. Lead optimization guided by a validated computational model of the LPA2 GPCR led us to explore the structure‐activity relationship of a group of aromatic sulfonamides. The apparent EC50 value for oleoyl lysophosphatidic acid (LPA 18:1) at LPA2 is 1.4 nM. Synthetic modifications of the aromatic sulfonamide scaffold led to the synthesis of compounds RP 10‐73 and 10‐83, which have subnanomolar potency at LPA2. The EC50 value of ligand activated Ca2+ transient in LPA2 reconstituted mouse embryonic fibroblasts derived from LPA1&amp;amp;2 double knockout mice was 0.15 ± 0.02 nM and 6 ± 3.9 pM for RP 10‐73 and 10‐83, respectively. These two nonlipid compounds lack agonist or antagonist activity at other LPA GPCR up to 10 µM when tested for eliciting or inhibiting ligand‐activated Ca2+ responses. RP 10‐73 and 10‐83 rescued cells from apoptosis induced by ionizing radiation or by the radiomimetic chemotherapeutic agent Adriamycin. The protective effect was not detectable in cells lacking the LPA2 receptor subtype indicating that the antiapoptotic effect requires functional LPA2 receptors in the target cell. The pharmacological properties of RP 10‐73 and 10‐83 make them ideal drug candidates for the specific activation of LPA2 in various disease conditions. Grant Funding Source : Supported by NIAID AI‐107331
Novel Polymeric Resists Based on Vinyl Ether Functionality. Photochemistry and Evaluation as A Lithographic Resist for Synchrotron X-ray and Deep UV. (1996)

A new positive resist composed of a bifunctional vinyl ether monomer as crosslink-er and a photoacid generator and a protic base resin was investigated. This resist materials utilizes the unique reaction of vinyl ether monomer. The vinyl ether monomer forms crosslinks of base polymer by prebaking and the crosslinks are decoupled by acidolytic reaction via generation of acids upon exposure. The lithographic properties for x-ray lithography such as effects of crosslinker concentration and process conditions were evaluated. The resist has a high sensitivity of 35mJ/cm2 and a high gamma value of of 10. A good profile for 0.2μm lines and spaces patterns was obtained. Furthermore, it was found that the resist material has high thermal resistance up to 180°C against both pattern deformation and resist thickness loss.
Supplementary Figure Legends from MM-141, an IGF-IR– and ErbB3-Directed Bispecific Antibody, Overcomes Network Adaptations That Limit Activity of IGF-IR Inhibitors (2023)

&lt;p&gt;PDF - 91K, Supplementary Figure Legends.&lt;/p&gt;
Clostridium difficile Modulates Host Innate Immunity via Toxin-Independent and Dependent Mechanism(s) (2013)

Clostridium difficile infection (CDI) is the leading cause of hospital and community-acquired antibiotic-associated diarrhoea and currently represents a significant health burden. Although the role and contribution of C. difficile toxins to disease pathogenesis is being increasingly understood, at present other facets of C. difficile-host interactions, in particular, bacterial-driven effects on host immunity remain less studied. Using an ex-vivo model of infection, we report that the human gastrointestinal mucosa elicits a rapid and significant cytokine response to C. difficile. Marked increase in IFN-γ with modest increase in IL-22 and IL-17A was noted. Significant increase in IL-8 suggested potential for neutrophil influx while presence of IL-12, IL-23, IL-1β and IL-6 was indicative of a cytokine milieu that may modulate subsequent T cell immunity. Majority of C. difficile-driven effects on murine bone-marrow-derived dendritic cell (BMDC) activation were toxin-independent; the toxins were however responsible for BMDC inflammasome activation. In contrast, human monocyte-derived DCs (mDCs) released IL-1β even in the absence of toxins suggesting host-specific mediation. Infected DC-T cell crosstalk revealed the ability of R20291 and 630 WT strains to elicit a differential DC IL-12 family cytokine milieu which culminated in significantly greater Th1 immunity in response to R20291. Interestingly, both strains induced a similar Th17 response. Elicitation of mucosal IFN-γ/IL-17A and Th1/Th17 immunity to C. difficile indicates a central role for this dual cytokine axis in establishing antimicrobial immunity to CDI.