gebhart/patrepeval huggingface dataset:
Presence of two distinct regions in the coiled-coil structure of the streptococcal Pep M5 protein: relationship to mammalian coiled-coil proteins and implications to its biological properties. (1985)

The complete amino acid sequence of Pep M5, a biologically active 197-residue fragment comprising nearly half of the group A streptococcal M5 protein, has structural features characteristic of an alpha-helical coiled-coil protein. Fourier analyses of the nonpolar residues show strong periodicities based on repeats of 7 residues (7/2 and 7/3). Except for the nonhelical NH2-terminal 12-residue segment, the 7-residue periodicity in the distribution of nonpolar residues extends through the remainder of the Pep M5 molecule, with some discontinuities and irregularities. The molecule contains two distinct regions that differ in the pattern of distribution of the nonpolar and charged residues. The 7-residue pattern "a, b, c, d, e, f, g" in region 13-121 is atypical in that position "a" is predominantly occupied by asparagine, rather than nonpolar residues. On the other hand, the periodicity in region 122-196 is more typical of that found in other coiled-coil proteins, such as the myosin rod region, keratin, desmin, and vimentin, rather than tropomyosin. Although the periodicity in nonpolar residues is not highly regular, the predominance of basic and acidic residues in the inner "e" and "g" positions, respectively, suggests that ionic interactions between chains may contribute significantly to the stability of the coiled-coil. The distribution of charged residues in the outer positions within the two regions of the molecule is also distinct. The NH2-terminal region carries a significantly higher net negative charge than the COOH-terminal region, suggesting that the former region may play an important role in some of the biological functions of the Pep M5 molecule.
Modeling and Control for Cooling Management of Data Centers With Hot Aisle Containment (2011)

In traditional raised-floor data center design with hot aisle and cold aisle separation, the cooling efficiency suffers from recirculation resulting from the mixing of cool air from the Computer Room Air Conditioning (CRAC) units and the hot exhaust air exiting from the back of the server racks. To minimize recirculation and hence increase cooling efficiency, hot aisle containment has been employed in an increasing number of data centers. Based on the underlying heat transfer principles, we present in this paper a dynamic model for cooling management in both open and contained environment, and propose decentralized model predictive controllers (MPC) for control of the CRAC units. One approach to partition a data center into overlapping CRAC zones of influence is discussed. Within each zone, the CRAC unit blower speed and supply air temperature are adjusted by a MPC controller to regulate the rack inlet temperatures, while minimizing the cooling power consumption. The proposed decentralized cooling control approach is validated in a production data center with hot aisles contained by plastic strips. Experimental results demonstrate both its stability and ability to reject various disturbances.
Micro-beam shaping to generate various non-diffracting modes (2004)

In this paper we report the dynamic generation of various non-diffracting modes and complete set of its interference pattern. We also present a review of our recent work on the novel optical beams by micro-beam shaping.
Outlook for New Experimental Programon Multiple-Mirror Confinement in GOL-3 with NBI-Heated Plasma (2015)

New plans for next-step experiments on a multiple-mirror confinement in GOL-3 are discussed. The proposed changes in the hardware configuration include separation of the existing GOL-3 device into two independent plasma facilities. The first device will continue research on physics of highly turbulent electron-beam-heated plasma. It will use the existing generator of the electron beam and a shortened part of the existing solenoid. The second device will be devoted to a new experimental program on studies of efficiency of multiple-mirror end sections that should decrease power and particle losses from the trap. Details of the physics and upgrade plans for the new device, tentatively named GOL-NB, are discussed.
Tip-induced modifications in scanning tunneling microscopy and atomic force microscopy (1995)

Tip-induced modifications of microscopic processes in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) of the Si(l00) surface are investigated with ab initio total energy pseudopotential calculations. The results of the calculations lead to a new understanding of the microscopic STM measurement process and the micro-mechanical changes (hysteresis and plastic deformation) in the AFM process. In particular, in the latter case, the results predict that the tip can be used to flip dimers on the surface, from one buckled configuration to the other, reversibly, and without inducing damage to either the intrinsic surface or the tip.
Population Pharmacokinetics of Fludarabine in Children and Adults during Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation (2018)

BW and eGFR are important predictors of fludarabine PK. Therefore, current linear BSA-based dosing leads to highly variable exposure, which may lead to variable treatment outcome.
Comparative Immunogenicity of HIV-1 Clade C Envelope Proteins for Prime/Boost Studies (2010)

While all of the clade C antigens tested were immunogenic, some were more effective than others in eliciting virus neutralizing antibodies. Neutralization titers did not correlate with rgp120 binding, V3 peptide binding, or CD4 blocking activity. CN97001 rgp120 elicited the highest level of neutralizing antibodies, and should be considered for further HIV vaccine development studies.
Katana (2012)

The mechanics of hot patching (the process of upgrading a program while it executes) remain understudied, even though it offers capabilities that act as practical benefits for both consumer and mission-critical systems. A reliable hot patching procedure would serve particularly well by reducing the downtime necessary for critical functionality or security upgrades. However, hot patching also carries the risk—real or perceived—of leaving the system in an inconsistent state, which leads many owners to forgo its benefits as too risky; for systems where availability is critical, this decision may result in leaving systems un-patched and vulnerable. In this paper, the authors present a novel method for hot patching ELF binaries that supports synchronized global data and code updates, and reasoning about the results of applying the hot patch. In this regard, the Patch Object format was developed to encode patches as a special type of ELF re-locatable object file. The authors then built a tool, Katana, which automatically creates these patch objects as a by-product of the standard source build process. Katana also allows an end-user to apply the Patch Objects to a running process.
Catalase as a regulator of reactive sulfur metabolism; a new interpretation beyond hydrogen peroxide✩ (2017)

Catalase regulation of RSS bioavailability- Under normoxic conditions, catalase can oxidize SO(2), H(2)S, and H(2)Sn species to as yet unidentified H(2)SnOy species. Conversely, catalase reduces sulfane sulfur species to H(2)S under hypoxic conditions. [Figure: see text]
Thermally Stable Blue-Light-Emitting Copolymers of Poly(alkylfluorene) (1998)

We have prepared a variety of high molecular weight, thermally stable, blue-light-emitting random copolymers of 9,9-di-n-hexylfluorene by nickel(0)-mediated polymerization. The copolymers are readily soluble and easily processable from organic solvents. Both the polymer and electronic properties may be tuned by selection of comonomer structure. The electronic properties also vary with composition and film morphology. A blue-light-emitting device has been prepared using ionic salts for electrochemical doping.
Stereoscopic Camera-Sensor Model for the Development of Highly Automated Driving Functions within a Virtual Test Environment (2023)

The need for efficient and reproducible development processes for sensor and perception systems is growing with their increased use in modern vehicles. Such processes can be achieved by using virtual test environments and virtual sensor models. In the context of this, the present paper documents the development of a sensor model for depth estimation of virtual three-dimensional scenarios. For this purpose, the geometric and algorithmic principles of stereoscopic camera systems are recreated in a virtual form. The model is implemented as a subroutine in the Epic Games Unreal Engine, which is one of the most common Game Engines. Its architecture consists of several independent procedures that enable a local depth estimation, but also a reconstruction of a whole three-dimensional scenery. In addition, a separate programme for calibrating the model is presented. In addition to the basic principles, the architecture and the implementation, this work also documents the evaluation of the model created. It is shown that the model meets specifically defined requirements for real-time capability and the accuracy of the evaluation. Thus, it is suitable for the virtual testing of common algorithms and highly automated driving functions.
Effect of the Dimensions of a Stepped-Pole Writer on Side Erasure and Recording Performance (2013)

Micromagnetic simulations are used to investigate side erasure as a function of write transducer geometry for shingled recording on a non-oriented barium-ferrite particulate tape media without a soft-underlayer. A ring-type writer with a short stepped pole is shown to produce very little transition curvature compared to conventional writers and to almost eliminate the erase band at the shingled track edge. In addition, the effect of the stepped pole on side erasure is found to be essentially independent of the writer gap size. However, the dimensions of the stepped pole do affect the system recording performance and should not be selected arbitrarily. We find that intermediate stepped-pole lengths produce smaller broad-band signal-to-noise ratio (BB-SNR) than a conventional writer, or require much larger deep-gap fields, whereas writers with short stepped poles (typically below 100 nm) provide more than 1 dB BB-SNR uplift at 200 kfci for only a moderate increase of writer deep-gap field. Finally, we find that the effect of the stepped pole on write performance also depends on the writer gap size.
Oxygen barrier, free volume, and blending properties of fully bio‐based polyamide 11/poly(vinyl alcohol) blends (2019)

ABSTRACT Fully bio‐based polyamide 11 (PA11) was melt‐blended with poly(vinyl alcohol) (PVA) with varying degrees of polymerization (DP) to prepare PA11 x PVA z y . The PA11 x PVA z y films demonstrated the lowest oxygen transmission rates (OTR) and free volume characteristics, when PVA contents of each PA11 x PVA z y series reached a corresponding critical concentration. The minimum OTR and free volume characteristics obtained for the optimal PA11 x PVA z y films reduced significantly with decreasing PVA DPs. The OTR of the optimal PA11 x PVA z y blown film was 1.07 cm 3 m −2 day −1 atm −1 , which is near to that of the ethylene‐vinyl alcohol copolymer high‐barrier polymer. The results of dynamical, mechanical, and other experimental characterizations demonstrated that PA11 and PVA are compatible to some extent when PVA concentrations are less‐than or equal to the respective critical values. The enhanced oxygen permeation resistance and free volume characteristics for optimal PA11 x PVA z y films are at least partly ascribed to the improved hydrogen‐bonded molecular interactions between PA11 CO groups and PVA O─H groups. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137 , 48562.
Abstract 2852: Torin2 suppresses ionizing radiation induced DNA damage repair (2015)

Abstract The phosphatidylinositol 3- kinase like kinase (PIKK) family of signaling proteins play a central role in stress response, DNA damage signaling, and sensing growth factor and nutrient levels to regulate cellular metabolism. In tumor cells, the PIKK signaling is often hyperactivated making it an attractive therapeutic target. In this study, we have focused our efforts on an ATP-competitive mTOR/PIKK inhibitor ‘Torin2′ which has been previously reported to exhibit potent activity against the DNA repair-associated proteins ATM, ATR and DNA-PK in addition to mTOR in biochemical profiling studies. Based on this profiling data, we hypothesized that Torin2 would have synergistic effects with agents or biological processes that cause DNA damage, especially in cases where high levels of replicative stress and non-oncogenic addiction to DNA repair factors are present. In order to understand the practical clinical implications, we evaluated how Torin2 modulates the effects of ionizing radiation (IR) induced DNA damage responses. With a defined set of biochemical and cytogenetic studies along with DNA repair reporter system, we established the role for Torin2 in double strand break repair responses in human tumor cell lines. Torin2 enhances ionizing radiation-induced cell killing in cancer cell lines independent of ATM status, suggesting that Torin2 simultaneously influences multiple PIKK targets. Moreover, Torin2 pre-treatment did not alter the appearance of γH2AX foci post irradiation but significantly delayed the disappearance of IR-induced γH2AX foci indicating a defective DNA repair processes. Pre-treatment of this drug decreased the number of IR-induced G2/S-phase specific chromosomal aberrations, and also reduces the frequency of the foci formation of IR-induced homologous recombination (HR) repair proteins, such as CtIP and Rad51, suggesting that the drug works by blocking HR, a repair process that predominantly works in S/G2 phase of the cell cycle. Consistent with these results, a HR reporter assay showed that Torin2 treatment reduces repair of I-SceI restriction enzyme induced DNA damage. Torin2 also influences DNA replicative stress through inhibition of ATR-Chk1 activation, and contributes to fork stalling during replication. With the above set of studies, we have identified key DNA damage signaling events by which Torin2 affects HR mediated double strand break repair after ionizing radiation treatment. This enhanced radiosensitizing effect of Torin2 merits further pre-clinical evaluation in combination with various radiotherapy modalities. Citation Format: Durga Udayakumar, Raj K. Pandita, Nobuo Horikoshi, Clayton R. Hunt, Qingsong Liu, Kwok-Kin Wong, Nathanael S. Gray, Tej K. Pandita, Kenneth D. Westover. Torin2 suppresses ionizing radiation induced DNA damage repair. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2852. doi:10.1158/1538-7445.AM2015-2852
Thromboxane generation by human monocytes enhances platelet function. (1986)

Human monocytes potentiate the ADP-stimulated aggregation of autologous platelets through a fourfold increased binding of 125I-fibrinogen to the platelet surface. The enhancement of platelet function is rapid, relatively transient and is due to thromboxane (Tx) synthesized by monocytes under these conditions. Tx generation by monocytes is triggered by the interaction between fibrinogen and the specific monocyte membrane receptor. These data suggest that the monocyte enhancement of platelet function combined with the clot-promoting activity of these cells might unbalance normal hemostasis.
Novel Aerodynamic Designs of a Hypersonic Warfighter (2006)

Boeing Integrated Defense Systems has performed exploratory studies of novel aerodynamic designs for future hypersonic air vehicles. These airframes feature concepts of a unique Arch wing and use conformal forward steering devices. An inflatable conical boattail to be deployed at lower flight speeds is also included for achieving base drag reduction to the afterbody of an Arch winged reusable launch vehicle (RLV). Potential applications of these designs include advanced RLVs that loft many similarly configured 'Bus-like' hypersonic glide vehicles. These latter vehicles are warfighters that stage from their boosters and can subsequently deliver tube-launched submunitions. These are to be base-released from the warfighter vehicles while along their flight paths and target against various enemy airborne and ground stations positioned at nominally distant and global locations. Preliminary wind tunnel tests of these innovative aerodynamic design concepts were compared to a typical planar wing (matched in planform) at low and hypersonic speeds with focus on the flight qualities that might be gained by the use of an Arch wing (Figure 1) and these results show potential benefits that may be realized in the successful performance of their military missions. Compared to typical RLVs equipped with planar wings, our novel concepts feature a uniquely configured Arch wing that can provide increased lift, reduced drag-due-to-lift, extended ranges, enhanced flight endurance, greater maneuverability and higher aerodynamic stability. In addition, our innovative conformal forward steering devices are designed to provide controllability in pitch as well as yaw. As envisioned in its role as a warfighter, multiple 'Bus-like' hypersonic gliders are likely capable of delivering scores of submunitions needed for defeating above and underground enemy stations. These 'Bus-like' vehicles are to be GPS/radar guided and have similar advanced Arch wing designs. The Busses are to be weaponized and staged from their boosters upon reaching high altitudes and hypersonic speeds. Subsequently, these warfighters are designed to carry and deliver multiple, aft- released weapons from their base regions and then be guided via GPS to attack and defeat a string of enemy ground targets (Figure 2). Compared to conventional high-speed air vehicles, our advanced warfighters are likely to be more cost effective and with greater success in the performance of their missions.
Optimized shape semantic graph representation for object understanding and recognition in point clouds (2016)

To understand and recognize the three-dimensional (3-D) objects represented as point cloud data, we use an optimized shape semantic graph (SSG) to describe 3-D objects. Based on the decomposed components of an object, the boundary surface of different components and the topology of components, the SSG gives a semantic description that is consistent with human vision perception. The similarity measurement of the SSG for different objects is effective for distinguishing the type of object and finding the most similar one. Experiments using a shape database show that the SSG is valuable for capturing the components of the objects and the corresponding relations between them. The SSG is not only suitable for an object without any loops but also appropriate for an object with loops to represent the shape and the topology. Moreover, a two-step progressive similarity measurement strategy is proposed to effectively improve the recognition rate in the shape database containing point-sample data.
Analysis of 1/f noise in CMOS APS (2000)

As CMOS technology scales, the effect of 1/f noise on low frequency analog circuits such as CMOS image sensors becomes more pronounced, and therefore must be more accurately estimated. analysis of 1/f noise is typically performed in the frequency domain even though the process is nonstationary. To find out if the frequency domain analysis produces acceptable results, the paper introduces a time domain method based on a nonstationary extension of a recently developed, and generally agreed upon physical model for 1/f noise in MOS transistors. The time domain method is used to analyze the effect of 1/f noise due to pixel level transistors in a CMOS APS. The results show that the frequency domain results can be quite inaccurate especially in estimating the 1/f noise effect of the reset transistor. It is also shown that CDS does not in general reduce the effect of the 1/f noise.
A Security Credential Management System for V2X Communications (2018)

The US Department of Transportation (USDOT) issued a proposed rule on January 12th, 2017 to mandate vehicle-to-vehicle (V2V) safety communications in light vehicles in the US. Cybersecurity and privacy are major challenges for such a deployment. The authors present a Security Credential Management System (SCMS) for vehicle-to-everything (V2X) communications in this paper, which has been developed by the Crash Avoidance Metrics Partners LLC (CAMP) under a Cooperative Agreement with the USDOT. This system design is currently transitioning from research to Proof-of-Concept, and is a leading candidate to support the establishment of a nationwide Public Key Infrastructure (PKI) for V2X security. It issues digital certificates to participating vehicles and infrastructure nodes for trustworthy communications among them, which is necessary for safety and mobility applications that are based on V2X communications. The main design goal is to provide both security and privacy to the largest extent reasonable and possible. To achieve a reasonable level of privacy in this context, vehicles are issued pseudonym certificates, and the generation and provisioning of those certificates are divided among multiple organizations. Given the large number of pseudonym certificates per vehicle, one of the main challenges is to facilitate efficient revocation of misbehaving or malfunctioning vehicles, while preserving privacy against attacks from insiders. The proposed SCMS supports all identified V2X use-cases and certificate types necessary for V2X communication security. This paper is based upon work supported by the USDOT. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the Authors ("we") and do not necessarily reflect the view of the USDOT.
Dual catalysis for the copolymerisation of epoxides and lactones (2019)

A dual catalysis system was developed to synthesize hydrolyzable polyether-polyester copolymers from propylene oxide and cyclic esters such as γ-butyrolactone, δ-valerolactone, and ε-caprolactone. A bimetallic chromium catalyst active for the enantioselective polymerisation of propylene oxide and an organocatalyst active for the ring-opening polymerisation of lactones were used in conjunction with an alcohol chain shuttling agent to create new copolymers. The monomer and alcohol ratios were varied to yield a wide range of copolymers with varying monomer ratios, molecular weights, and crystallinities.