gebhart/patrepeval huggingface dataset:
Multiplexed volumetric bar-chart chip for point-of-care diagnostics (2012)

Microfluidics have become an enabling technology for point-of-care and personalized diagnostics. Desirable capabilities of microfluidics-based diagnostic devices include simplicity, portability, low cost and the performance of multiplexed and quantitative measurements, ideally in a high-throughput format. Here we present the multiplexed volumetric bar-chart chip (V-Chip), which integrates all these capabilities in one device. A key feature of the V-Chip is that quantitative results are displayed as bar charts directly on the device-without the need for optical instruments or any data processing or plotting steps. This is achieved by directly linking oxygen production by catalase, which is proportional to the concentration of the analyte, with the displacement of ink along channels on the device. We demonstrate the rapid quantification of protein biomarkers in diverse clinical samples with the V-Chip. The development of the V-Chip thus opens up the possibility of greatly simplified point-of-care and personalized diagnostics.
Discovery and Optimization of Two Eis Inhibitor Families as Kanamycin Adjuvants against Drug-Resistant <i>M. tuberculosis</i> (2016)

Drug-resistant tuberculosis (TB) is a global threat and innovative approaches such as using adjuvants of anti-TB therapeutics are required to combat it. High-throughput screening yielded two lead scaffolds of inhibitors of <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) acetyltransferase Eis, whose upregulation causes resistance to the anti-TB drug kanamycin (KAN). Chemical optimization on these scaffolds resulted in potent Eis inhibitors. One compound restored the activity of KAN in a KAN-resistant <i>Mtb</i> strain. Model structures of Eis-inhibitor complexes explain the structure-activity relationship.
Integrated Terahertz Communication With Reflectors for 5G Small-Cell Networks (2016)

As the cellular networks continue to progress between generations, the expectations of 5G systems are planned toward high-capacity communication links that can provide users access to numerous types of applications (e.g., augmented reality and holographic multimedia streaming). The demand for higher bandwidth has led the research community to investigate unexplored frequency spectrums, such as the terahertz band for 5G. However, this particular spectrum is strived with numerous challenges, which includes the need for line-of-sight (LoS) links as reflections will deflect the waves as well as molecular absorption that can affect the signal strength. This is further amplified when a high quality of service has to be maintained over infrastructure that supports mobility, as users (or groups of users) migrate between locations, requiring frequent handover for roaming. In this paper, the concept of mirror-assisted wireless coverage is introduced, where smart antennas are utilized with dielectric mirrors that act as reflectors for the terahertz waves. The objective is to utilize information such as the user's location and to direct the reflective beam toward the highest concentration of users. A multiray model is presented in order to develop the propagation models for both indoor and outdoor scenarios in order to validate the proposed use of the reflectors. An office and a pedestrian-walking scenarios are used for indoor and outdoor scenarios, respectively. The results from the simulation work show an improvement with the usage of mirror-assisted wireless coverage, improving the overall capacity, the received power, the path loss, and the probability of LoS.
Mixture autoregressive hidden Markov models for speech signals (1985)

In this paper a signal modeling technique based upon finite mixture autoregressive probabilistic functions of Markov chains is developed and applied to the problem of speech recognition, particularly speaker-independent recognition of isolated digits. Two types of mixture probability densities are investigated: finite mixtures of Gaussian autoregressive densities (GAM) and nearest-neighbor partitioned finite mixtures of Gaussian autoregressive densities (PGAM). In the former (GAM), the observation density in each Markov state is simply a (stochastically constrained) weighted sum of Gaussian autoregressive densities, while in the latter (PGAM) it involves nearest-neighbor decoding which in effect, defines a set of partitions on the observation space. In this paper we discuss the signal modeling methodology and give experimental results on speaker independent recognition of isolated digits. We also discuss the potential use of the modeling technique for other applications.
User intention modeling for interactive image retrieval (2010)

We propose three innovative interactive methods to let computer better understand user intention in content-based image retrieval: 1. Smart intention list induces user intention, thereby improves search results by intention-specific search schema; 2. Reference strokes interaction allows user to specify in detail about the intention by pointing out interested regions; 3. Natural user feedback easily collects data of user relevance feedbacks to boost the performance of the system. Systematic user study shows that the proposed interactive mechanism improves search efficiency, reduces user workload, and enhances user experience.
Coded aperture structured illumination digital holographic microscopy for superresolution imaging (2018)

This paper proposes a coded aperture structured illumination (CASI) technique in digital holographic microscopy (DHM). A CASI wave is generated using two binary phase codes (0° and 120°) for spatial phase shifting. The generated CASI wave then interferes with a reference wave to form a coded Fresnel hologram at a single exposure with compressive sensing (CS) to avoid the temporal phase-shifting process of the structured illumination (SI). The CS algorithm is applied to retrieve the missing data of decoded phase-shifted SI-modulated waves, which are used to separate overlapped spatial frequencies for obtaining a larger spatial frequency coverage to provide superresolution imaging. Two phase-only spatial light modulators are applied to generate a directional SI pattern for obtaining a coded aperture with a suitable size to perform one-shot acquisition in the DHM system.
Patterning of superhydrophobic paper to control the mobility of micro-liter drops for two-dimensional lab-on-paper applications (2009)

Superhydrophobic paper substrates were patterned with high surface energy black ink using commercially available desktop printing technology. The shape and size of the ink islands were designed to control the adhesion forces on water drops in two directions, parallel ('drag-adhesion') and perpendicular ('extensional-adhesion') to the substrate. Experimental data on the adhesion forces shows good agreement with classical models for 'drag' (Furmidge equation) and 'extensional' adhesion (modified Dupré equation). The tunability of the two adhesion forces was used to implement four basic unit operations for the manipulation of liquid drops on the paper substrates: storage, transfer, mixing and sampling. By combining these basic functionalities it is possible to design simple two-dimensional lab-on-paper (LOP) devices. In our 2D LOP prototype, liquid droplets adhere to the porous substrate, rather than absorbing into the paper; as a result, liquid droplets remain accessible for further quantitative testing and analysis, after performing simple qualitative on-chip testing. In addition, the use of commercially available desktop printers and word processing software to generate ink patterns enable end users to design LOP devices for specific applications.
Molecular co‐evolution of Gonadotropin‐releasing hormones and their receptors (2007)

Abstract Gonadotropin‐releasing hormone (GnRH), synthesized in the hypothalamus, plays a pivotal role in the regulation of vertebrate reproduction. Since molecular isoforms of GnRH and their receptors (GnRHR) have been isolated in a broad range of vertebrate species, GnRH and GnRHR provide an excellent model for understanding the molecular co‐evolution of a peptide ligand‐receptor pair. Vertebrate species possess multiple forms of GnRH, which have been created through evolutionary mechanisms such as gene/chromosome duplication, gene deletion and modification. Similar to GnRHs, GnRH receptors (GnRHR) have also been diversified evolutionarily. Comparative ligand‐receptor interaction studies for non‐mammalian and mammalian GnRHRs combined with mutational mapping studies of GnRHRs have aided the identification of domains or motifs responsible for ligand binding and receptor activation. Here we discuss the molecular basis of GnRH‐GnRHR co‐evolution, particularly the structure‐function relationship regarding ligand selectivity and signal transduction of mammalian and non‐mammalian GnRHRs.
Suppressed RNA-Polymerase 1 Pathway Is Associated with Benign Multiple Sclerosis (2012)

Benign multiple sclerosis (BMS) occurs in about 15% of patients with relapsing-remitting multiple sclerosis (RRMS) that over time do not develop significant neurological disability. The molecular events associated with BMS are not clearly understood. This study sought to underlie the biological mechanisms associated with BMS. Blood samples obtained from a cohort of 31 patients with BMS and 36 patients with RRMS were applied for gene expression microarray analysis using HG-U133A-2 array (Affymetrix). Data were analyzed by Partek and pathway reconstruction was performed by Ingenuity for the most informative genes (MIGs). We identified a differing gene expression signature of 406 MIGs between BMS patients, mean±SE age 44.5±1.5 years, 24 females, 7 males, EDSS 1.9±0.2, disease duration 17.0±1.3 years, and RRMS patients, age 40.3±1.8 years, 24 females, 12 males, EDSS 3.5±0.2, disease duration 10.9±1.4 years. The signature was enriched by genes related RNA polymerase I (POL-1) transcription, general inflammatory response and activation of cell death. The most significant under-expressed pathway operating in BMS was the POL-1 pathway (p = 4.0*10(-5)) known while suppressed to activate P53 dependent apoptosis and to suppress NFκB induced inflammation. In accordance, of the 30 P53 target genes presented within the BMS signature, 19 had expression direction consistent with P53 activation. The transcripts within the pathway include POL-1 transcription factor 3 (RRN3, p = 4.8*10(-5)), POL-1 polypeptide D (POLR1D, p = 2.2*10(-4)), leucine-rich PPR-motif containing protein (LRPPRC p = 2.3*10(-5)), followed by suppression of the downstream family of ribosomal genes like RPL3, 6,13,22 and RPS6. In accordance POL-1 transcript and release factor PTRF that terminates POL-1 transcription, was over-expressed (p = 4.4*10(-3)). Verification of POL-1 pathway key genes was confirmed by qRT-PCR, and RRN3 silencing resulted in significant increase in the apoptosis level of PBMC sub-populations in RRMS patients. Our findings demonstrate that suppression of POL-1 pathway induce the low disease activity of BMS.
An infectious and selectable full‐length replicon system with hepatitis C virus JFH‐1 strain (2007)

Selectable infection was established using HCV replicon containing full-length genotype 2a JFH-1 cDNA. This system might be useful for HCV research.
On Shared Situation Awareness for Supporting Human Decision-Making Teams. (2005)

One of the challenging issues in homeland security area is the early detection and successful processing of potential terrorist threats, which demands effective team collaboration. In this research, we investigate the way of incorporating naturalistic decision making models for supporting distributed team decision making. By extending Klein’s Recognition-Primed Decision model, we propose a Collaborative RPD model (C 2 RPD), which encourages proactive information seeking, linking, and sharing in distributed teamwork settings. This model establishes a basis for developing agent architectures that support both agent-agent and agent-human collaborations in developing shared situation awareness and in making decisions based on progressively refined recognitions.
All-Optical Wavelength Conversion Using Absorption Modulation of an Injection-Locked Fabry–PÉrot Laser Diode (2004)

A novel all-optical wavelength converter based on the transverse-magnetic (TM)-mode absorption modulation of a Fabry-Perot laser diode (FP-LD) is proposed and demonstrated. An FP-LD shows absorption nulls for TM mode probe beam, which are red-shifted by an additional optical pump injection. Using this, the transmission of the continuous-wave probe beam can be optically controlled and wavelength conversion is, thus, achieved. The proposed scheme is simple and cost-effective, and can be used for very wide-range wavelength conversion. Bit-error-rate measurements at 2.5 Gb/s were performed, and the power penalties of 2 and 6 dB were observed, respectively, for noninverted and inverted wavelength conversion.
Positive Resists Based on Non-polymeric Macromolecules (2005)

Derivatives of Polyhedral Oligomeric Silsesquioxanes (POSS) and Oligosaccharides have been investigated as potential candidates for high resolution resists. POSS materials are cage compounds with defined mono-disperse molecular weights. Oligosaccharides are carbohydrates with defined number of monosaccharide units (2 to10) and may be cyclic or linear. These materials are attractive candidates for molecular resist development because of their commercial availability and the ease with which they can be derivatized. We have developed high resolution positive resists suitable for 193-nm and other emerging lithographic applications based on these materials.
One-Step Cleaning Solution to Replace the Conventional RCA Two-Step Cleaning Recipe for Pregate Oxide Cleaning (2001)

This work proposes an advanced wet chemical one-step cleaning process which omits the hydrochloric acid/hydrogen peroxide/water mixture (HPM) step in RCA. A novel one-step cleaning solution had been developed for pregate oxide cleaning to replace the conventional RCA two-step cleaning recipe, which used ammonia/hydrogen peroxide (or SC-1) and HPM (or SC-2) step. Tetramethylammonium hydroxide (TMAH) and ethylenediaminetetraacetic acid (EDTA) were added into the RCA SC-1 cleaning solution to enhance cleaning efficiency. From the experimental results, the particles and metallic contamination on the bare Si wafer surface could be removed significantly by applying this one-step cleaning solution. The effectiveness of various cleaning recipes and their interaction mechanism with silicon surfaces were studied. The surface adsorption and double layer models could explain the surface behavior of TMAH solutions. Based on the model, the particle, surface roughness and metallic contaminants can be realized. It was observed that the electrical properties of metal oxide semiconductor capacitors after cleaning with this novel solution were better than those after the conventional RCA cleaning. Besides, the cleaning method combining tetramethylammonium hydroxide, ethylenediaminetetraacetic acid, and at 80°C for 3 min showed high performance on particle removal, metal cleaning, surface smoothness, and electrical properties. Hence, this one-step cleaning process is very promising for future large sized silicon wafer cleaning due to the advantages of time-saving, low cost, and high performance. © 2001 The Electrochemical Society. All rights reserved.
2‐substituted 2,3‐dihydro‐5<i>H</i>‐thiazolo[2,3‐<i>b</i>]quinazoline derivatives (1986)

Abstract The synthesis of a series of 2‐substituted 2,3‐dihydro‐5 H ‐thiazolo[2,3‐ b ]quinazoline derivatives is described. Some of the title compounds exerted antiinflammatory and immunomodulating activities in laboratory animal models.
Learning from structure-based drug design and new antivirals targeting the ribonucleoprotein complex for the treatment of influenza (2015)

To date, the antivirals targeting neuraminidase are by far the most developed and potent. Antiviral candidates targeting the NP and polymerase domains are in the pipeline but their pharmacokinetics needs further studies. The recently published structures of the polymerase expand the possibilities for development of new antivirals. Combination therapies targeting conserved viral targets and new cellular proteins or exploiting drug promiscuity hold promises to fight against the emergence of resistance.
Single-walled carbon nanotubes as a multimodal-thermoacoustic and photoacoustic-contrast agent (2009)

We have developed a novel carbon nanotube-based contrast agent for both thermoacoustic and photoacoustic tomography. In comparison to deionized water, single-walled carbon nanotubes exhibited more than twofold signal enhancement for thermoacoustic tomography at 3 GHz. In comparison to blood, they exhibited more than sixfold signal enhancement for photoacoustic tomography at 1064 nm wavelength. The large contrast enhancement of single-walled carbon nanotubes was further corroborated by tissue phantom imaging studies.
Effect of Material Stiffness on Intermodulation Response in Dynamic Atomic Force Microscopy (2010)

We perform simulations and experiments on an oscillating atomic force microscope cantilever approaching a surface, where the intermodulation response of the cantilever driven with two pure harmonic tones is investigated. In the simulations, the tip and surface interact with a conservative nonlinear force, and the parameter space of approach distance and surface stiffness is explored. Approach experiments are carried out on three surfaces with widely varying stiffness. Qualitative similarities between simulations and experiment can be seen, but quantitative comparison is difficult due to the overly idealized tip-surface force model used in the simulation.
Query by example in large-scale code repositories (2015)

Searching code samples in a code repository is an important part of program comprehension. Most of the existing tools for code search support syntactic element search and regular expression pattern search. However, they are text-based and hence cannot handle queries which are syntactic patterns. The proposed solutions for querying syntactic patterns using specialized query languages present a steep learning curve for users. The querying would be more user-friendly if the syntactic pattern can be formulated in the underlying programming language (as a sample code snippet) instead of a specialized query language. In this paper, we propose a solution for the query by example problem using Abstract Syntax Tree (AST) structural similarity match. The query snippet is converted to an AST, then its subtrees are compared against AST subtrees of source files in the repository and the similarity values of matching subtrees are aggregated to arrive at a relevance score for each of the source files. To scale this approach to large code repositories, we use locality-sensitive hash functions and numerical vector approximation of trees. Our experimental evaluation involves running control queries against a real project. The results show that our algorithm can achieve high precision (0.73) and recall (0.81) and scale to large code repositories without compromising quality.
Design of Diffractive Optics for Concentration of Light From Diode Laser Arrays (1992)

Diode-laser arrays are becoming increasingly popular as illumination sources because of their high efficiency, reliability, and ability to produce large amounts of optical power from a small package. In addition, their relatively narrow spectral bandwidth makes them ideal pump sources for solid-state lasers. This paper describes an optical technique to concentrate light from a linear diode-laser array into a small spot with a minimum divergence. Such optics are ideally suited to coupling into multimode optical fibers and longitudinal pumping of solid-state lasers.
Recombinant human ACE2 as a novel biotherapeutic for the treatment of patients with cancer. (2010)

e13653 Background: Angiotensin Converting Enzyme 2 (ACE2) is the key counterbalancing enzyme of the Renin Angiotensin System (RAS) and is expressed in most tissues. ACE2 degrades Angiotensin II (Ang II) to yield Angiotensin (1–7) (Ang(1–7)). Ang II increases blood pressure and is pro-inflammatory, angiogenic, a potent mitogen and increases vascular permeability. In contrast, Ang(1–7) has vasodilatory, anti-inflammatory, anti-angiogenic and antiproliferative properties. There is evidence that an activated RAS and elevated Ang II levels support tumor growth. A novel biological approach for cancer treatment thus is based on the utilization of ACE2 to degrade elevated Ang II to generate Ang(1–7). In this regard we are developing recombinant soluble ACE2 (rhACE2) for biologic therapy of diseases with an imbalanced RAS. rhACE2 was investigated in a phase I study in healthy volunteers and no side effects or toxicities were found. Methods: In order to explore the role of elevated Ang II on formation of malignant effusions, we have assessed Ang II levels in plasma and malignant effusions of patients with various solid cancers, using a commercially available Enzyme Immunoassay. Furthermore, the potential of rhACE2 was explored to degrade elevated Ang II in plasma of cancer patients ex-vivo. Results: In 15/24 patients (63%) plasma Ang II was elevated (> 16 pg/ml). Median plasma Ang II was 75 pg/ml (19-496 pg/ml). Six patients also presented with elevated Ang II in malignant effusions. A significant correlation between volume of effusions and Ang II levels in plasma was seen, suggesting that elevated Ang II contributes to formation of effusions. Ex-vivo treatment with 5μg/ml rhACE2 of undiluted heparinized plasma samples or effusions of cancer patients led to a rapid degradation of elevated Ang II. Conclusions: Treatment with rhACE2 of cancer patients with malignant effusions may cause reduction of elevated Ang II and increase production of Ang(1-7). This may lead to beneficial effects such as decreased formation of effusions, retarded proliferation of malignant cells, reduced angiogenesis and local inflammation. We have applied for a clinical study with rhACE2 in advanced cancer patients with elevated Ang II levels to test these hypotheses. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Apeiron Apeiron Apeiron
Guidelines for selecting iron stabilizers for use in acidizing treatments (1980)

During an acidizing treatment, some iron is dissolved by action of the acid upon treating lines, equipment, down-hole tubular goods, and iron minerals in the formation. Upon spending of the acid, this iron may precipitate as insoluble gelatinous ferric hydroxide, an effective plugging agent which damages permeability and restricts oil and gas production. To prevent iron precipitation, stabilizers are routinely added to the treating acid, which form soluble chelates or complexes with iron and prevent precipitation of ferric hydroxide. The advantages and limitations of the various commonly used iron stabilizing agents are described and guidelines presented for selecting the proper additive and determining the concentration needed for iron stabilizing agents, also are discussed.