gebhart/patrepeval huggingface dataset:
Self-assembled bifunctional surface mimics an enzymatic and templating protein for the synthesis of a metal oxide semiconductor (2006)

The recent discovery and characterization of silicatein, a mineral-synthesizing enzyme that assembles to form the filamentous organic core of the glassy skeletal elements (spicules) of a marine sponge, has led to the development of new low-temperature synthetic routes to metastable semiconducting metal oxides. These protein filaments were shown in vitro to catalyze the hydrolysis and structurally direct the polycondensation of metal oxides at neutral pH and low temperature. Based on the confirmation of the catalytic mechanism and the essential participation of specific serine and histidine residues (presenting a nucleophilic hydroxyl and a nucleophilicity-enhancing hydrogen-bonding imidazole nitrogen) in silicatein's catalytic active site, we therefore sought to develop a synthetic mimic that provides both catalysis and the surface determinants necessary to template and structurally direct heterogeneous nucleation through condensation. Using lithographically patterned poly(dimethylsiloxane) stamps, bifunctional self-assembled monolayer surfaces containing the essential catalytic and templating elements were fabricated by using alkane thiols microcontact-printed on gold substrates. The interface between chemically distinct self-assembled monolayer domains provided the necessary juxtaposition of nucleophilic (hydroxyl) and hydrogen-bonding (imidazole) agents to catalyze the hydrolysis of a gallium oxide precursor and template the condensed product to form gallium oxohydroxide (GaOOH) and the defect spinel, gamma-gallium oxide (gamma-Ga(2)O(3)). Using this approach, the production of patterned substrates for catalytic synthesis and templating of semiconductors for device applications can be envisioned.
Low Power Depth Estimation of Rigid Objects for Time-of-Flight Imaging (2019)

Depth sensing is useful in a variety of applications that range from augmented reality to robotics. Time-of-flight (TOF) cameras are appealing because they obtain dense depth measurements with minimal latency. However, for many battery-powered devices, the illumination source of a TOF camera is power hungry and can limit the battery life of the device. To address this issue, we present an algorithm that lowers the power for depth sensing by reducing the usage of the TOF camera and estimating depth maps using concurrently collected images. Our technique also adaptively controls the TOF camera and enables it when an accurate depth map cannot be estimated. To ensure that the overall system power for depth sensing is reduced, we design our algorithm to run on a low power embedded platform, where it outputs 640 × 480 depth maps at 30 frames per second. We evaluate our approach on several RGB-D datasets, where it produces depth maps with an overall mean relative error of 0.96% and reduces the usage of the TOF camera by 85%. When used with commercial TOF cameras, we estimate that our algorithm can lower the total power for depth sensing by up to 73%.
Gene Structure, Expression Pattern, and Biological Activity of Mouse Killer Cell Activating Receptor-associated Protein (KARAP)/DAP-12 (1998)

Natural killer cell and T cell subsets express at their cell surface a repertoire of receptors for MHC class I molecules, the natural killer cell receptors (NKRs). NKRs are characterized by the existence of inhibitory and activating isoforms, which are encoded by highly homologous but separate genes present in the same locus. Inhibitory isoforms express an intracytoplasmic immunoreceptor tyrosine-based inhibition motif, whereas activating isoforms lack any immunoreceptor tyrosine-based inhibition motif but harbor a charged amino acid residue in their transmembrane domain. We previously characterized KARAP (killer cell activating receptor-associated protein), a novel disulfide-linked tyrosine-phosphorylated dimer that selectively associates with the activating NKR isoforms. We report here the identification of the mouse KARAP gene, its localization on chromosome 7 and its genomic organization in five exons. Point mutation and transfection studies revealed that KARAP is a novel signaling transmembrane subunit whose transduction function depends on the integrity of an intracytoplasmic immunoreceptor tyrosine-based activation motif. In contrast to previous members of the immunoreceptor tyrosine-based activation motif polypeptide family, KARAP is ubiquitously expressed on hematopoietic and nonhematopoietic cells, suggesting its association with a broad range of activating receptors in a variety of tissues.
Enhanced Flame Retardancy of Polylactic Acid with Aluminum Tri-Hydroxide and Phenolic Resins (2009)

ポリ乳酸を電子機器の外装材などに適用するためには高度な難燃性が要求されるので，安全性の高い水酸化アルミニウムとフェノール樹脂類の併用によるポリ乳酸の難燃化を検討した．アルカリ成分量を低減した水酸化アルミニウムを約 50 wt%添加することで，ポリ乳酸を UL94 規格の V-1 レベル(1.6 mm 厚)以上まで難燃化できたが，曲げ強度，曲げ破断ひずみ，耐衝撃性，および流動性が低下した．これに対して，フェノール樹脂類として，着火時のチャーの生成量が多く，しかもポリ乳酸中での分散性の良好な，フェノールノボラック樹脂やトリフェノールメタン樹脂を水酸化アルミニウムと併用した場合，難燃性の改良効果が高いことがわかった．これらのフェノール樹脂類は，着火時のチャーの生成量が多く，しかもポリ乳酸中での分散性が良好であるため，着火の際に均質なチャー層を表面で形成したために難燃効果が高かったものと考える．この難燃性の改善により，水酸化アルミニウムを削減でき，さらに，これらのフェノール樹脂類自体の効果によって，曲げ強度と流動性を向上できた．また，可とう性付与剤としてポリ乳酸-ポリエステル共重合体を添加することによって，曲げ破断ひずみと耐衝撃性を改善でき，流動性を一層向上できた．
New Treatment of Periodontal Diseases by Using NF-κB Decoy Oligodeoxynucleotides via Prevention of Bone Resorption and Promotion of Wound Healing (2009)

Nuclear factor-kappa B (NF-kappaB) is involved in osteoclast differentiation and activation. Thus, the blockade of the NF-kappaB pathway might be a novel therapeutic strategy for treating bone metabolic diseases. Periodontitis is subgingival inflammation caused by bacterial infection; this disease also is thought to be a chronic focal point responsible for systemic diseases. In this study, NF-kappaB decoy oligodeoxynucleotides (ODNs) were topically applied for experimental periodontitis in a debris-accumulation model and wound healing in a bone-defect model of beagle dogs to investigate the effect of decoy ODN on bone metabolism. Application of NF-kappaB decoy ODN significantly reduced interleukin-6 activity in crevicular fluid and improved alveolar bone loss in the analysis of dental radiographs and DEXA. Direct measurement of exposed root that lost alveolar bone support revealed that NF-kappaB decoy treatment dramatically protected bone from loss. In a bone-defect model, NF-kappaB decoy ODN promoted the healing process as compared with control scrambled decoy in micro-CT analysis. Overall, inhibition of NF-kappaB by decoy strategy prevented the progression of bone loss in periodontitis and promoted the wound healing in bone defects through the inhibition of osteoclastic bone resorption. Targeting of NF-kappaB might be a potential therapy in various bone metabolic diseases.
Sterilization of Mycobacterium tuberculosis Erdman Samples by Antimicrobial Fixation in a Biosafety Level 3 Laboratory (2001)

Incomplete sterilization of Mycobacterium tuberculosis Erdman cultures followed 1 h of incubation in low concentrations of glutaraldehyde (0.5 and 1.0%) or azide. In contrast, 2.5% glutaraldehyde, paraformaldehyde (2 or 4%), Vesphine IIse or 5% formalin sterilized these samples after 1 h. These results suggest caution in removing fixed M. tuberculosis samples from biosafety level 3.
Nanostructured Organic—Inorganic Hybrid Materials Synthesized Through Simultaneous Processes (1995)

The sol-gel process, with its associated mild conditions, offers a new approach to the synthesis of composite materials with domain sizes approaching the molecular level. Both the organic and inorganic phases can be simultaneously formed through the synchronous polymerization of the organic monomer and the sol-gel precursors. Depending upon such factors as the structures of the organic and inorganic components, the phase morphology, the degree of interpenetration, and the presence of covalent bonds between the phases, the properties of these composites can vary greatly and range from elastomeric rubbers to high modulus materials. In an attempt to solve the truculent shrinkage problem historically associated with sol-gel derived glasses, we have synthesized tetraalkoxy orthosilicates possessing polymerizable alkoxide groups. The resultant alcohols, which are liberated during the hydrolysis and condensation steps associated with the formation of the inorganic component, are polymerized in-situ to form the organic phase of the composite material. The synthesis and mechanical properties of these nonshrinking hybrid materials will be discussed.
Differential involvement of caspases in apoptosis of myeloid leukemic cells induced by chemotherapy versus growth factor withdrawal (1997)

To assess the potential involvement of the caspase family in the IL-3-dependent murine myeloid leukemic cell line 32D, we studied the effect of bcl-2, crmA and three synthetic caspase inhibitors on apoptosis induced by chemotherapy or IL-3 withdrawal. Apoptosis induced by IL-3 deprivation or by ActD appears to be mediated by a crmA-insensitive pathway. Cell death by IL-3 withdrawal is inhibited by the caspase-inhibitor ZVAD-fmk, but not DEVD-fmk or YVAD-cmk. In contrast, DEVD-fmk as well as ZVAD-fmk protect 32D cells from ActD-induced apoptosis. These results indicate that different caspases are involved in apoptosis induced by growth factor withdrawal and by chemotherapy.
Seal spot welding of steel and aluminum alloy by resistance spot welding (2014)

This research concerns a dissimilar metals joining of steel and aluminum (Al) alloys by means of zinc (Zn) insertion. The authors proposed a joining concept for achieving strong bonded joints between Zn coated steel and Al alloys. A eutectic reaction between Zn in the Zn coating and Al in Al alloy is used to remove the dense, strong oxide film on Al alloy surface at low temperature, thereby resulting in the formation of a thin, uniform Al-Fe intermetallic compound (IMC) layer at the joint interface, leading to a strong bonded joint. The ultimate aim of this research is to apply this joining concept in the resistance spot welding process for manufacturing vehicle bodies.As a practical issue characteristic to dissimilar metals joints, anticorrosion measures against electrochemical corrosion must be undertaken. If there is moisture near a dissimilar metals joint interface, electrochemical corrosion would progress. Therefore, a sealing function that could prevent moisture intrusion is required. By applying above mentioned welding process to a set of metals with thermosetting resin spread in between, we realized seal spot welding which would not only prevent moisture intrusion, but also retain high tensile strength.In this research, first, a cyclic corrosion test was performed on the seal spot welded joint of galvanized (GI) steel and Al alloy, and the anticorrosion measures were found to retain tensile strength and also secure sufficient corrosion resistance. Then galvannealed (GA) steel, a steel grade widely distributed in Japan, and Al alloy was bonded by seal spot welding, and following topics have been discussed. Complete removal of sealant from the joint interface is the key to realize high tensile strength joint, because remaining sealant would lead to reduction of tensile strength. Therefore, heat generation at the interface was monitored by measuring electrical current and potential difference between the two electrodes, and a precise temperature control was performed. Moreover, the bonding process was clarified by stepwise analysis of the joint interface using optical microscopy, and a guideline for producing strong joints was proposed. And finally, a TEM observation also confirmed that the interface structure of seal spot welded joint was the same as joints without the resin; a thin and uniform Al-Fe IMC layer was formed and a strong metallurgical bonding was achieved.
Joint Waveform and Beamforming Optimization for MIMO Wireless Power Transfer (2021)

In this paper, we study a multi-sine multiple-input multiple-output (MIMO) wireless power transfer (WPT) system with the objective to increase the output DC power. We jointly optimize the multi-sine waveform and beamforming accounting for the rectenna nonlinearity, and consider two combining schemes for the rectennas at the receiver, namely DC and RF combinings. For DC combining, the waveform and transmit beamforming are optimized, as a function of the channel state information (CSI). For RF combining, the optimal transmit and receive beamformings are provided in closed form and the waveform is optimized. We also consider a practical RF combining circuit using phase shifter and RF power combiner and optimize the waveform, transmit beamforming, and analog receive beamforming adaptive to the CSI. Two types of performance evaluations, based on the nonlinear rectenna model and accurate and realistic circuit simulations, are provided. The evaluations demonstrate that the joint waveform and beamforming design can increase the output DC power by leveraging the beamforming gain, the frequency diversity gain, and the rectenna nonlinearity. It also shows that the joint waveform and beamforming design provides a higher output DC power than the beamforming-only design with a relative gain of 180% in a two-transmit antenna sixteen-sinewave two-receive antenna setup.
Adaptive Computing as the Enabling Technology for SDR (2003)

This chapter contains sections titled: Introduction Algorithmic Evaluations in Communications Solving P3 – Performance, Power Consumption and Price Design Advantages ACM Benchmarks Marketplace Benefits Technology Status References
Sliding-frequency soliton laser (1995)

Sliding-frequency systems have been shown to be advantageous for soliton transmission1 and, more recently, for soliton generation.2,3 In the latter application, sliding-frequency lasers have a number of advantages over other optical-fiber short-pulse sources, including a significantly lower self-starting threshold and suppression of linear modes and noise. In this paper we demonstrate an optical-fiber sliding-frequency laser with a linear cavity geometry and an erbium-doped fiber as the gain medium. In-fiber Bragg gratings were used as end reflectors for the cavity.
Measurement Error in Nonlinear Models: A Modern Perspective, Second Edition (2006)

It's been over a decade since the first edition of Measurement Error in Nonlinear Models splashed onto the scene, and research in the field has certainly not cooled in the interim. In fact, quite the opposite has occurred. As a result, Measurement Error in Nonlinear Models: A Modern Perspective, Second Edition has been revamped and ex
Surface modifications of polypropylene with nonylphenol ethoxylates melt additives (2012)

Abstract Nonylphenol ethoxylated (NPE) additives were melt blended in polypropylene (PP) films and characteristics of the modified films were investigated. It was found that melt blending of NPE additives improved hydrophilicity of PP films through additive surface segregation. Surface specific techniques, such as X‐ray photoelectron spectroscopy (XPS) and Time‐of‐Flight Secondary Ion Mass Spectrometry (ToF‐SIMS) were used to study surface compositions of samples modified with NPE additives at different aging time after extrusion. We found that surface enrichment of additives lead to hydrophilic surfaces. Hydrophilic chain length in NPE affected surface composition and hydrophilicity of NPE containing PP polymer. The effect of water immersion and aging were also reported. POLYM. ENG. SCI., 52:1920–1927, 2012. © 2012 Society of Plastics Engineers
Nanoparticle-Mediated Cavitation via CO2 Laser Impacting on Water: Concentration Effect, Temperature Visualization, and Core-Shell Structures (2019)

By taking advantage of seeded polymer nanoparticles and strong photo energy absorption, we report CO<sub>2</sub> laser impacting on water to produce cavitation at the air/water interface. Using a high-speed camera, three regimes (no cavitation, cavitation, and pseudo-cavitation) are identified within a broad range of nanoparticles concentration and size. The underlying correlation among cavitation, nanoparticles and temperature is revealed by the direct observation of spatiotemporal evolution of temperature using a thermal cameral. These findings indicate that nanoparticles not only act as preexisted nuclei to promote nucleation for cavitation, but also likely affect temperature to change the nucleation rate as well. Moreover, by exploiting a compound hexane/water interface, a novel core-shell cavitation is demonstrated. This approach might be utilized to attain and control cavitations by choosing nanoparticles and designing interfaces while operating at a lower laser intensity, for versatile technological applications in material science and medical surgery.
Compositional Analysis for: Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment (2022)

This repository hosts the code for the statistical compositional analysis performed for the paper: "Stepwise-edited, human melanoma models reveal mutations’ effect on tumor and microenvironment".
Improvements to the InfiniBand Congestion Control Mechanism (2016)

The InfiniBand Congestion Control mechanism (IB CC) is able to reduce the negative consequences of congestion in many situations. However, its effectiveness depends on a set of parameters that must be set by administrators. If the parameters are not appropriately configured, IB CC could negatively impact network performance. Additionally, no one has been able to find a universal parameter setting that can fit all situations. These difficulties prevent IB CC from being widely used. In this paper we propose several enhancements to the existing IB CC. First, our improved IB CC significantly reduces parameter configuration. Second, the congestion will be removed quickly. Third, a new utilization-driven approach and a new Link Bandwidth Availability Report (LBAR) approach are implemented to guide sending interfaces on how and when to adjust their injection rates. These adjustments are aware of the actual network condition, rather than relying on preconfigured parameters, as in the existing IB CC. Simulation results have demonstrated that our improved IB CC is able to reduce the congestion consequences efficiently and can adapt to various network topologies and traffic patterns.
3D reconstruction of mirror-type objects using efficient ray coding (2016)

Mirror-type specular objects are difficult to reconstruct: they do not possess their own appearance and the reflections from environment are view-dependent. In this paper, we present a novel computational imaging solution for reconstructing the mirror-type specular objects. Specifically, we adopt a two-layer liquid crystal display (LCD) setup to encode the illumination directions. We devise an efficient ray coding scheme by only considering the useful rays. To recover the mirror-type surface, we derive a normal integration scheme under the perspective camera model. Since the resulting surface is determined up to a scale, we develop a single view approach to resolve the scale ambiguity. To acquire the object surface as completely as possible, we further develop a multiple-surface fusion algorithm to combine the surfaces recovered from different viewpoints. Both synthetic and real experiments demonstrate that our approach is reliable on recovering small to medium scale mirror-type objects.
A Strategy for Probing the Autonomy of Cross-Domain Stereochemical Communication in Glycoconjugates (2001)

Glycoproteins contain carbohydrate and peptide sectors. As a model for studying whether there exists stereochemical "communication" between the two domains, we prepared two glycopeptides differing only in the absolute stereochemistry of the peptide domain (L-peptide vs D-peptide). High-field NMR spectroscopy revealed that there are distinct and measurable differences, indicating that the two domains are at some level interactive.
Repolarization studies using human stem cell-derived cardiomyocytes: Validation studies and best practice recommendations (2020)

Human stem cell-derived cardiomyocytes (hSC-CMs) hold great promise as in vitro models to study the electrophysiological effects of novel drug candidates on human ventricular repolarization. Two recent large validation studies have demonstrated the ability of hSC-CMs to detect drug-induced delayed repolarization and "cellrhythmias" (interrupted repolarization or irregular spontaneous beating of myocytes) linked to Torsade-de-Pointes proarrhythmic risk. These (and other) studies have also revealed variability of electrophysiological responses attributable to differences in experimental approaches and experimenter, protocols, technology platforms used, and pharmacologic sensitivity of different human-derived models. Thus, when evaluating drug-induced repolarization effects, there is a need to consider 1) the advantages and disadvantages of different approaches, 2) the need for robust functional characterization of hSC-CM preparations to define "fit for purpose" applications, and 3) adopting standardized best practices to guide future studies with evolving hSC-CM preparations. Examples provided and suggested best practices are instructional in defining consistent, reproducible, and interpretable "fit for purpose" hSC-CM-based applications. Implementation of best practices should enhance the clinical translation of hSC-CM-based cell and tissue preparations in drug safety evaluations and support their growing role in regulatory filings.
Neoadjuvant Immunotherapy for Solid Tumors (2020)

Xing Hong, Wan MD; Sagiv-Barfi, Idit PhD; Czerwinski, Debra BS; Levy, Ronald MD Author Information
Striking a Balance: Reader Takeaways and Preferences when Integrating Text and Charts (2022)

While visualizations are an effective way to represent insights about information, they rarely stand alone. When designing a visualization, text is often added to provide additional context and guidance for the reader. However, there is little experimental evidence to guide designers as to what is the right amount of text to show within a chart, what its qualitative properties should be, and where it should be placed. Prior work also shows variation in personal preferences for charts versus textual representations. In this paper, we explore several research questions about the relative value of textual components of visualizations. 302 participants ranked univariate line charts containing varying amounts of text, ranging from no text (except for the axes) to a written paragraph with no visuals. Participants also described what information they could take away from line charts containing text with varying semantic content. We find that heavily annotated charts were not penalized. In fact, participants preferred the charts with the largest number of textual annotations over charts with fewer annotations or text alone. We also find effects of semantic content. For instance, the text that describes statistical or relational components of a chart leads to more takeaways referring to statistics or relational comparisons than text describing elemental or encoded components. Finally, we find different effects for the semantic levels based on the placement of the text on the chart; some kinds of information are best placed in the title, while others should be placed closer to the data. We compile these results into four chart design guidelines and discuss future implications for the combination of text and charts.
Impact of material homogeneity assumption on cortical stiffness estimates by MR elastography (2022)

This study suggests that inhomogeneous inversions provide small but significant benefits even when large stiffness gradients are absent.