gebhart/patrepeval huggingface dataset:
NRPS-Derived Isoquinolines and Lipopetides Mediate Antagonism between Plant Pathogenic Fungi and Bacteria (2017)

Bacterial-fungal interactions are presumed to be mediated chiefly by small-molecule signals; however, little is known about the signaling networks that regulate antagonistic relationships between pathogens. Here, we show that the ralstonins, lipopeptides produced by the plant pathogenic bacteria Ralstonia solanacearum, interfere with germination of the plant-pathogenic fungus Aspergillus flavus by down-regulating expression of a cryptic biosynthetic gene cluster (BGC), named imq. Comparative metabolomic analysis of overexpression strains of the transcription factor ImqK revealed imq-dependent production of a family of tripeptide-derived alkaloids, the imizoquins. These alkaloids are produced via a nonribosomal peptide synthetase- (NRPS-)derived tripeptide and contain an unprecedented tricyclic imidazo[2,1-a]isoquinoline ring system. We show that the imizoquins serve a protective role against oxidative stress that is essential for normal A. flavus germination. Supplementation of purified imizoquins restored wildtype germination to a ΔimqK A. flavus strain and protected the fungus from ROS damage. Whereas the bacterial ralstonins retarded A. flavus germination and suppressed expression of the imq cluster, the fungal imizoquins in turn suppressed growth of R. solanacearum. We suggest such reciprocal small-molecule-mediated antagonism is a common feature in microbial encounters affecting pathogenicity and survival of the involved species.
Non-audiofacial morbidity after Gamma Knife surgery for vestibular schwannoma (2009)

The results of our review of the literature provide a systematic summary of the published rates of nonaudiofacial morbidity following radiosurgery for vestibular schwannoma.
Chios Mastic Gum Consumption Has a Protective Effect on Ovariectomy-Induced Bone Loss in Rats (2021)

The purpose of this study was to examine the potential effect of Chios Mastic Gum (CMG) consumption on bone mineral density (BMD) and strength of ovariectomized rats. CMG is a known resin used from ancient times for its beneficial biological properties. Thirty mature female Wistar rats were randomized into three equal groups: sham-operated (control), ovariectomized (OVX), and ovariectomized and administered CMG <i>per os</i> (OVX+CMG). BMD of the total tibia, proximal tibia, and the 6th lumbar vertebra were measured at baseline and at 3 and 6 months post ovariectomy. Bone strength was assessed with three-point-bending (3pb) of the right femur. At 3 and 6 months, BMD values of the OVX+CMG group were significantly higher for the anatomical cites evaluated than those of the OVX group. Femoral thickness assessed via 3pb had intermediate values in the treated group compared to the other groups. Cytology of vaginal smears and uterine weight of the OVX+CMG group were consistent with estrogen depletion. Gastrocnemius muscle and intraperitoneal fat ratios to body weight (BW) of the OVX+CMG group did not significantly differ from the control group. Daily consumption CMG had a protective effect on BMD of the total and proximal tibia and the 6th lumbar vertebra of the rats, without causing undesirable effects on the vaginal epithelium and uterus. The 3pb results also demonstrated a favorable effect on the thickness of rat femurs. In addition, CMG was beneficial for both the muscular system and the intraperitoneal fat/BW ratio of the rats.
Enhancing FPGAs with Magnetic Tunnel Junction-Based Block RAMs (2018)

While plentiful on-chip memory is necessary for many designs to fully utilize an FPGA’s computational capacity, SRAM scaling is becoming more difficult because of increasing device variation. An alternative is to build FPGA block RAM (BRAM) from magnetic tunnel junctions (MTJ), as this emerging embedded memory has a small cell size, low energy usage, and good scalability. We conduct a detailed comparison study of SRAM and MTJ BRAMs that includes cell designs that are robust with device variation, transistor-level design and optimization of all the required BRAM-specific circuits, and variation-aware simulation at the 22nm node. At a 256Kb block size, MTJ-BRAM is 3.06× denser and 55% more energy efficient and its F max is 274MHz, which is adequate for most FPGA system clock domains. We also detail further enhancements that allow these 256 Kb MTJ BRAMs to operate at a higher speed of 353MHz for the streaming FIFOs, which are very common in FPGA designs and describe how the non-volatility of MTJ BRAM enables novel on-chip configuration and power-down modes. For a RAM architecture similar to the latest commercial FPGAs, MTJ-BRAMs could expand FPGA memory capacity by 2.95× with no die size increase.
Characterization of a Helicobacter pylori neutrophil-activating protein (1995)

Helicobacter pylori-associated gastritis is mainly an inflammatory cell response. In earlier work we showed that activation of human neutrophils by a cell-free water extract of H. pylori is characterized by increased expression of neutrophil CD11b/CD18 and increased adhesiveness to endothelial cells. The work reported here indicates that the neutrophil-activating factor is a 150,000-molecular-weight protein (150K protein). Neutrophil proadhesive activity copurified with this protein, which is a polymer of identical 15K subunits. Specific antibody, prepared against the purified 15K subunit, neutralized the proadhesive activity of the pure protein and of water extracts obtained from different strains of H. pylori. The gene (napA) for this protein (termed HP-NAP, for H. pylori neutrophil-activating protein) was detected, by PCR amplification, in all of the H. pylori isolates tested; however, there was considerable strain variation in the level of expression of HP-NAP activity in vitro. HP-NAP could play an important role in the gastric inflammatory response to H. pylori infection.
MBA-VO: Motion Blur Aware Visual Odometry (2021)

Motion blur is one of the major challenges remaining for visual odometry methods. In low-light conditions where longer exposure times are necessary, motion blur can appear even for relatively slow camera motions. In this paper we present a novel hybrid visual odometry pipeline with direct approach that explicitly models and estimates the camera’s local trajectory within the exposure time. This allows us to actively compensate for any motion blur that occurs due to the camera motion. In addition, we also contribute a novel benchmarking dataset for motion blur aware visual odometry. In experiments we show that by directly modeling the image formation process, we are able to improve robustness of the visual odometry, while keeping comparable accuracy as that for images without motion blur. Both the code and the datasets can be found from https://github.com/ethliup/MBA-VO.
Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer (2017)

Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA. WGS resulted in a read coverage of 23× per cell and an ensemble call rate of >95%. These barcoded reads enabled accurate detection of somatic mutations present in as few as 12% of CTCs. We found in CTCs a total of 2,766 somatic single-nucleotide variants and 543 indels and multi-base substitutions, 23 of which altered amino acid sequences. Another 16,961 somatic single nucleotide variant and 8,408 indels and multi-base substitutions, 77 of which were nonsynonymous, were detected with varying degrees of prevalence across the 34 CTCs. On the basis of our whole genome data of mutations found in all CTCs, we identified driver mutations and the tissue of origin of these cells, suggesting personalized combination therapies beyond the scope of most gene panels. Taken together, our results show how advanced WGS of CTCs can lead to high-resolution analyses of cancers that can reliably guide personalized therapy. <i>Cancer Res; 77(16); 4530-41. ©2017 AACR</i>.
Efficient Solar-to-Chemical Conversion by One Chip of n-Type Silicon with Surface Asymmetry (1999)

The surface band energy of an n‐type silicon chip in aqueous solution has been modulated by formation of silicon‐halogen termination bonds on a limited area of the surface. Such surface asymmetry produces efficient solar‐to‐chemical conversion owing to the presence of band bending within the chip in a photostationary state, leading to efficient electron‐hole separation, in contrast to homogeneous semiconductor surfaces. The principle can be applied to minute photochemical energy conversion systems made of nanometer‐sized semiconductor particles, organic thin films, and membranes. ©1998 The Electrochemical Society
Figure S5 from A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy (2023)

&lt;p&gt;Supplementary Figure 5: Overall tumor mutation burden and frequency of mutations in cancer-associated genes in UC tumors.&lt;/p&gt;
Influence of DNA Structure on Adjacent Site Cooperative Binding (2008)

Previous NMR studies of Hoechst 33258 with the d(CTTTTGCAAAAG)2 sequence have shown very strong (K2 >> K1) cooperativity between two adjacent binding sites (Searle, M. S.; Embrey, K. J. Nucleic Acids Res. 1990, 18 (13), 3753- 3762). In contrast, surface plasmon resonance (SPR) results with the hairpin analog of the same sequence show significantly reduced cooperativity. In an effort to explain the difference, two-dimensional (2-D) NMR experiments were done on both duplex and hairpin. Hoechst 33258 and an amidine analog, DB183, show very strong cooperativity with the duplex DNA but much weaker cooperativity with the hairpin. The significantly lower thermal melting temperature (Tm) of the duplex (34.8 degrees C) in comparison to its hairpin analog (62.3 degrees C) supports the idea of a dynamic difference between the two DNA structures that can influence cooperativity in binding. These results confirm the role of conformational entropy in positive cooperativity in some DNA interactions.
A cycle-accurate synthesizable MIPS simulator in Simulink (2014)

We introduce a novel methodology for creating a synthesizable, cycle-accurate simulator of the MIPS32 processor with concise, high-level programming expressions using Simulink and other matlab tools. The simulator, named SimuMIPS, is capable of running binaries generated by the GNU gcc compiler and associated binutils. It can be easily configured, modified and extended not only for academic instruction but also to be included in commercial SOC products. Synthesizable instantiations of SimuMIPS in Verilog and VHDL may be generated by Simulink HDL Coder for FPGA programming and system-on-chip prototyping. In addition, the SimuMIPS simulator can run on embedded processors, rapid prototyping boards, and off-the-shelf microprocessors via the Embedded Coder generated C and C++ implementations.
Kirk, David, "Temporal Dimensions of an Innovative Idea: A Case Study of Teacher-Initiated Innovation," Journal of Curriculum Studies, 18(July-September, 1986), 311-330. (1986)

Describes all facets of a teacher-initiated innovation in an Australian school (see related article in JCS, 20 (5).
Oriented Z-Type Langmuir−Blodgett Films from a Soluble Asymmetrically Substituted Polydiacetylene (1996)

A soluble, asymmetric polydiacetylene has been shown to form stable monolayers at the air−water interface of a Langmuir trough. The monolayers of this unconventional amphiphilic polymer could be repeatedly deposited onto hydrophobic substrates during every upstroke cycle of the vertical dipping method to form uniform Z-type multilayers. Characterization of the precise orientation of the polymer main chain has been carried out to determine the spatial correlation between the nonlinear optical chromophore responsible for second-order nonlinear optical properties and the backbone. Polarized UV/vis and IR spectroscopic studies indicate a preferential orientation of the main chain along the dipping direction with a mean fluctuation of ±30° between director axis and chain trajectories. Polarization-dependent second-harmonic generation (SHG) in multilayers indicates a high degree of orientational anisotropy of the backbone. As expected, SHG intensities increase with the number of layers due to the noncentrosymmetric Z-type structure. The second-order nonlinear coefficient (d33) was estimated to be 1.52 pm/V at 1064 nm of Nd:YAG laser after correcting for absorption. Surface characterization and alignment of the extended chain backbones is further established using atomic force microscopy (AFM).
An Electrically Actuated Microbeam-Based MEMS Device: Experimental and Theoretical Investigation (2017)

The present paper deals with the dynamic behavior of a microelectromechanical systems (MEMS). The device consists of a clamped-clamped microbeam electrostatically and electrodynamically actuated. Our objective is to develop a theoretical analysis, which is able to describe and predict all the main relevant aspects of the experimental response. In the first part of the paper an extensive experimental investigation is conducted. The microbeam is perfectly straight. The first three experimental natural frequencies are identified and the nonlinear dynamics are explored at increasing values of electrodynamic excitation. Several backward and forward frequency sweeps are acquired. The nonlinear behavior is highlighted. The experimental data show the coexistence of the nonresonant and the resonant branch, which perform a bending toward higher frequencies values before undergoing jump or pull-in dynamics. This kind of bending is not particularly common in MEMS. In the second part of the paper, a theoretical single degree-of-freedom model is derived. The unknown parameters are extracted and settled via parametric identification. A single mode reduced-order model is considered, which is obtained via the Galerkin technique. To enhance the computational efficiency, the contribution of the electric force term is computed in advance and stored in a table. Extensive numerical simulations are performed at increasing values of electrodynamic excitation. They are observed to properly predict all the main nonlinear features arising in the device response. This occurs not only at low values of electrodynamic excitation, but also at higher ones.
A FAST WAVELET-BASED VIDEO CODEC AND ITS APPLICATION IN AN IP VERSION 6-READY SERVERLESS VIDEOCONFERENCING SYSTEM (2004)

The purpose of this paper is twofold: On the one hand, we propose a fast wavelet-based video codec which is implemented into a real-time video conferencing tool. The proposed codec uses temporal frame difference coding, a computationally low-complex 5/3 tap wavelet transform, and a fast entropy coding scheme based on Golomb–Rice codes. On the other hand, we present an application of the video conferencing tool in a serverless peer-to-peer IP-based communication framework. For mobile communication we propose a simple, ready-to-use location scheme for video conference users in a global network.
Variable tapered pareto buffer design and implementation allowing run-time configuration for low-power embedded SRAMs (2005)

This paper presents a novel formalized technique for variable tapered buffer design achieving Pareto optimal energy-delay tradeoffs. Our main focus lies on the drivers typically found in embedded SRAMs. Much work has been done for variable tapered buffer design explicitly targeting energy (and/or area) tradeoffs for a given target delay. In contrast, the formalized techniques presented here are capable of providing all existing Pareto configurations achieving optimal energy/delay tradeoffs, and this is applicable for the full range of all possible delay constraints. Based on such techniques, a transistor-level implementation is also presented to allow a discrete set of Pareto configurations (from high-speed to low-energy) to be selected at run-time. This implementation has been validated via SPICE simulations for a 65-nm CMOS technology, confirming that a very wide range in delay (more than a factor 2) and energy consumption (up to 40%) can be achieved at the SRAM level, including process variability impact effects present in CMOS nanometer technologies.
Resistance to Leishmania major Induced by Tolerance to a Single Antigen (1996)

In mice, susceptibility to Leishmania major is associated with the early expansion of T helper 2 cells (TH2) cells, but nothing is known of the specificity of these cells. A previously identified antigen, Leishmania homolog of receptors for activated C kinase (LACK), was found to be the focus of this initial response. Mice made tolerant to LACK by the transgenic expression of the antigen in the thymus exhibited both a diminished TH2 response and a healing phenotype. Thus, T cells that are activated early and are reactive to a single antigen play a pivotal role in directing the immune response to the entire parasite.
Wood Carbon Based Single-Atom Catalyst for Rechargeable Zn–Air Batteries (2021)

Low-cost and efficient oxygen reduction reaction (ORR)/oxygen evolution reaction (OER) bifunctional electrocatalysts are vital for the applications of rechargeable Zn–air batteries (ZABs). Given the high catalytic activity of single-atom catalysts (SACs), preparing SACs on a large scale for ZABs is desirable but remains challenging. Herein, in situ formation of single-atom Fe–N–C catalysts on plate wood-based porous carbon is achieved via a facile Lewis acid pretreatment and carbonization process. Lewis acid FeCl3 pretreatment on the cell wall of wood not only produces abundant microchannels but also successfully introduces atomically dispersed Fe–N active species into the hierarchical structure. Such uniformly dispersive SACs on the hierarchical structure enhance the ORR/OER performance and durability. A ZAB using the catalyst in the cathode shows a high power density (70.2 mW cm–2, at quasi solid state) and long-term stability. This work provides a new path for the large-scale preparation of high-performance SACs.
Erratum: “Fabricating a n+-Ge contact with ultralow specific contact resistivity by introducing a PtGe alloy as a contact metal” [Appl. Phys. Lett. 107, 113503 (2015)] (2015)

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Electrokinetic pixels with biprimary inks for color displays and color-temperature-tunable smart windows (2015)

We report on the advanced implementation of the biprimary color system in applications where subtractive color is performed inside a single pixel to alter the magnitude and color of reflection (electronic paper displays) or the optical transmission and color temperature (smart windows). A novel device structure can switch between four states: clear, black, either of two complementary colors from RGB and CMY sets, and also mixed states between one of these four states. The device structure utilizes an electrokinetic pixel structure, which combines the spectral performance of in-plane electrophoretic devices with the improved switching speeds of vertical electrophoresis. The electrophoretic dispersions are dual-particle dual-colored and are controlled using two traditional planar electrokinetic electrodes on the front and back substrates, along with a third electrode conveniently located at the perimeter of each unit cell. Demonstrated performance includes contrast ratios reaching &#x223C;10&#x2236;1, reflectance of &#x223C;62%, and transparency of &#x223C;75%. For electronic paper displays, these results provide a pathway to double the reflective performance compared to the traditional RGBW color-filter approach. For smart windows, the technology provides not only control of shade (transmission) but also provides complete control over color temperature. Furthermore, this three-electrode device can be roll-to-roll fabricated without need for any alignment steps, requiring only a single micro-replication step followed by self-aligned contact printing of the third electrode.
Elevating the Discussion on Security Management: The Data Centric Paradigm (2007)

Corporate decision makers have normally been disconnected from the details of the security management infrastructures of their organizations. The management of security resources has traditionally been the domain of a small group of skilled and technically savvy professionals, who report to the executive team. As threats become more prevalent, attackers get smarter and the infrastructure required to secure corporate assets become more complex, the communication gap between the decision makers and the implementers has widened. The risk of misinterpretation of corporate strategy into technical safe controls also increases with the above-mentioned trends. In this paper, we articulate a paradigm for managing enterprise security called the data centric security model (DCSM), which puts IT policy making in the hands of the corporate executives, so that security decisions can be directly executed without the diluting effect of interpretation at different levels of the Infrastructure and with the benefit of seeing direct correlation between business objective and security mechanism. Our articulation of the DCSM vision is a starting point for discussion and provides a rich platform for research into business-driven security management.
Digital identity guidelines: enrollment and identity proofing (2017)

Certain commercial entities, equipment, or materials may be identified in this document in order to describe an experimental procedure or concept adequately.
ChemInform Abstract: Regio‐ and Stereoselective Control in the Alkylation of 1‐Alkoxy‐1,4‐cyclohexadienes by the Chiral Auxiliary Approach. Enantioselective Synthesis of Precursors for cis‐Hydrindans. (1990)

Abstract An enantioselective variant of the title reaction is developed, based on a number of preliminary experiments ‐ e.g. a study of the effect of substituents in substrates (I) and alkylating agents such as (II), as well as a comparison of various chiral auxiliaries.
Trends in regionalization of adrenalectomy to higher volume surgical centers (2011)

Simhan, Jay MD; Smaldone, Marc C. MD; Canter, Daniel J. MD; Zhu, Fang PhD; Starkey, Russell B. MBA; Stitzenberg, Karyn B. MD, MPH; Uzzo, Robert G. MD, FACS; Kutikov, Alexander MD Author Information