gebhart/patrepeval huggingface dataset:
Spread Transform Dither Modulation using a Perceptual Model (2006)

In previous work, we demonstrated how perceptual modeling can be applied to dither modulated quantization index modulation and rational dither modulation, to improve both robustness and fidelity. These algorithms were shown to be significantly more robust to valumetric scaling. However, they, and their predecessors, remain extremely sensitive to re-quantization which commonly occurs due to JPEG compression, numerical rounding and analog-to-digital conversion. It is well known that spread transform dither modulation (STDM) is more robust to re-quantization. In this paper we describe how to incorporate a perceptual model into this framework and present two algorithms based on Watson's perceptual model. Experimental results of robustness to JPEG compression are reported for 1000 images at embedding rates of 1/32 and 1/320. At the high embedding rate, the robustness of the two algorithms is the same as STDM but the perceptual distortion is reduced 23 to about 4, based on Watson's perceptual distance. At the lower embedding rate, we simultaneously observed superior robustness to STDM as well as improved fidelity. If the perceptual distance rather than the document-to-watermark ratio (DWR) is held fixed, then the two adaptive spread transform methods exhibit significant improvements in robustness to JPEG compression
Lidar Optical Architectures with Digital Micromirror Devices (2020)

Lidar optical architectures employing Digital Micromirror Devices provide unique features such as low mechanical inertia, a large aperture area, fast scanning speed, and a high efficiency in beam steering.
Clustering Billions of Reads for DNA Data Storage (2017)

Storing data in synthetic DNA offers the possibility of improving information density and durability by several orders of magnitude compared to current storage technologies. However, DNA data storage requires a computationally intensive process to retrieve the data. In particular, a crucial step in the data retrieval pipeline involves clustering billions of strings with respect to edit distance. Datasets in this domain have many notable properties, such as containing a very large number of small clusters that are well-separated in the edit distance metric space. In this regime, existing algorithms are unsuitable because of either their long running time or low accuracy. To address this issue, we present a novel distributed algorithm for approximately computing the underlying clusters. Our algorithm converges efficiently on any dataset that satisfies certain separability properties, such as those coming from DNA data storage systems. We also prove that, under these assumptions, our algorithm is robust to outliers and high levels of noise. We provide empirical justification of the accuracy, scalability, and convergence of our algorithm on real and synthetic data. Compared to the state-of-the-art algorithm for clustering DNA sequences, our algorithm simultaneously achieves higher accuracy and a 1000x speedup on three real datasets.
Interwoven Systems: Self-Improving Systems Integration (2014)

Current trends in information and communication technology show that systems are increasingly influencing each other -- which is seldom completely anticipated at design-time. As a result, mastering system integration with traditional methods becomes infeasible due to the resulting complexity. In this paper we argue that self-improving system integration is the most promising solution to counter the resulting challenges. Thereby, we highlight the different aspects of such a process with special attention to the optimisation question and discuss how approaches from the domain of self-organising systems -- in particular Organic and Autonomic Computing -- will be beneficial when researching possible solutions.
Conjugated gold nanoparticles as a tool for probing the bacterial cell envelope: The case of Shewanella oneidensis MR-1 (2016)

The bacterial cell envelope forms the interface between the interior of the cell and the outer world and is, thus, the means of communication with the environment. In particular, the outer cell surface mediates the adhesion of bacteria to the surface, the first step in biofilm formation. While a number of ligand-based interactions are known for the attachment process in commensal organisms and, as a result, opportunistic pathogens, the process of nonspecific attachment is thought to be mediated by colloidal, physiochemical, interactions. It is becoming clear, however, that colloidal models ignore the heterogeneity of the bacterial surface, and that the so-called nonspecific attachment may be mediated by specific regions of the cell surface, whether or not the relevant interaction is ligand-mediate. The authors introduce surface functionalized gold nanoparticles to probe the surface chemistry of Shewanella oneidensis MR-1 as it relates to surface attachment to ω-substituted alkanethiolates self-assembled monolayers (SAMs). A linear relationship between the attachment of S. oneidensis to SAM modified planar substrates and the number of similarly modified nanoparticles attached to the bacterial surfaces was demonstrated. In addition, the authors demonstrate that carboxylic acid-terminated nanoparticles attach preferentially to the subpolar region of the S. oneidensis and obliteration of that binding preference corresponds in loss of attachment to carboxylic acid terminated SAMs. Moreover, this region corresponds to suspected functional regions of the S. oneidensis surface. Because this method can be employed over large numbers of cells, this method is expected to be generally applicable for understanding cell surface organization across populations.
Enhancing Safety with an Improved Cervical Test Device (1997)

The cervical spine serves two primary functions: (1) as a mechanical linkage that allows a large controlled range of head motions and (2) as a protective structure for the spinal cord that passes through the spinal canals of the vertebrae. Cervical injuries involving fracture or dislocation of the vertebrae often involve the spinal cord, leading to paralysis or even death. Although serious neck injuries have become relatively rare in American football since the adoption of new spearing rules and tackling procedures, the development of cervical protective equipment should further reduce both the severity and the frequency of neck injuries. Many developers of cervical protective devices use anthropomorphic test devices, or ATDs, as physical surrogates for the athlete. Currently available ATDs are of limited biofidelity and ability to predict neck injuries under conditions involving head impact. This paper discusses the ongoing development of a new cervical test device with improved biofidelity in the frontal, lateral, and axial directions. A new transducer is proposed to measure dynamically the three dimensional curvature along the length of the neck.
Identification of ABR-215050 as lead second generation quinoline-3-carboxamide anti-angiogenic agent for the treatment of prostate cancer (2006)

Based upon its robust and consistent anti-angiogenic activity and thus tumor growth, ABR-215050 has entered clinical trials for the treatment of prostate cancer.
Longitudinal gut microbial signals are associated with weight loss: insights from a digital therapeutics program (2023)

Abstract Obesity is a significant health problem due to its profound health deteriorating effects and high costs for healthcare systems. There exist lifestyle and pharmacological interventions available to prevent and reverse obesity; however, at the population level, these have shown to be insufficient, and we continue to see a worldwide increase in obesity prevalence. The gut microbiome has been shown to influence the susceptibility to weight gain and difficulty in losing weight and to be associated with successful long-term weight loss. Therefore, multiple studies have suggested that obesity interventions should consider the gut microbiome as a primary target through an improved diet and a crucial endpoint to monitor. However, there is a paucity of evidence regarding how to tailor the diet for an individual’s microbiome and what changes are expected to occur due to successful weight management. Digital therapeutics solutions have emerged as an exciting alternative to increase population access, reduce costs, and have the potential to accompany individuals on their health-promoting journey closely. Digbi Health has developed a dietary and lifestyle program to achieve weight loss that effectively reduces weight and improves diverse health outcomes by prioritizing and personalizing food ingredients to match an individual’s genetic profile and nurture the gut microbiome. In this study, we analyze the weight loss pattern and microbiome profile of 103 individuals to identify the effects of the weight loss program on the gut microbiome between their baseline and follow-up samples. We found that 80% of individuals lost weight during the study. Analysis of their gut microbiome identified genera, functional pathways, and microbial communities associated with BMI changes and dietary and lifestyle program. The microbial genera and functional pathways associated with a reduction in BMI during the study include several previously reported in the literature, including Akkermansia, Christensenella , Oscillospiraceae, Alistipes , and Sutterella , short-chain fatty acid (SCFA) production and degradation of simple sugars like arabinose, sucrose, and melibiose. Network analysis identified two microbiome communities associated with BMI, one of which also significantly responded to the weight loss program, which includes multiple known associations with BMI and obesity. Our findings provide additional evidence for using the gut microbiome as an endpoint of weight loss program and highlight how it positively impacts the gut microbiome, with significant parallels in weight loss and health outcomes. These results provide additional evidence for known microbiome biomarkers of obesity and highlight new ones that warrant further research.
Controlled reduction of aromaticity of alkylated polyaromatic compounds by selective oxidation using H2WO4, H3PO4 and H2O2: a route for upgrading heavy oil fractions (2021)

Selectivity in the oxidation of alkylated polynuclear aromatic hydrocarbon can be specifically controlled by the choice solvent.
Synthesis and catalytic activity of fluorous chiral primary amine-thioureas (2013)

Three enantiopure fluorous thioureas featuring a free –NH2 group were synthesized by direct addition of aromatic isothiocyanates bearing a single n-C8F17 substituent in the ortho, meta and para position, respectively, to enantiopure (1R,2R)-1,2-diaminocyclohexane. The catalytic behavior of these bifunctional molecules was assessed in representative Michael-type reactions. The three fluorous thioureas performed similarly in all the reactions tested, thus showing that the position of the fluorous ponytail does not have a major influence on the catalytic behavior of this class of compounds. In particular, excellent enantioselectivities (up to 99% ee) and yields (up to 98%) were obtained for the addition of aliphatic aldehydes to maleimides to give α-substituted succinimides. Recyclability of these primary amine-based thioureas was found to be limited by the concurrent formation of imine-derivatives during the catalytic process, leading to a structural modification of the organic catalyst.
Metabolic Profiling and Biological Activities of Bioactive Compounds Produced by Pseudomonas sp. Strain ICTB-745 Isolated from Ladakh, India (2012)

In an ongoing survey of the bioactive potential of microorganisms from Ladakh, India, the culture medium of a bacterial strain of a new Pseudomonas sp., strain ICTB-745, isolated from an alkaline soil sample collected from Leh, Ladakh, India, was found to contain metabolites that exhibited broad-spectrum antimicrobial and biosurfactant activities. Bioactivity-guided purification resulted in the isolation of four bioactive compounds. Their chemical structures were elucidated by (1)H and (13)C NMR, 2D-NMR (HMBC, HSQC, (1)H,(1)H-COSY, and DEPT- 135), FT-IR, and mass spectroscopic methods, and were identified as 1-hydroxyphenazine, phenazine-1-carboxylic acid (PCA), rhamnolipid-1 (RL-1), and rhamnolipid-2 (RL-2). These metabolites exhibited various biological activities like antimicrobial and efficient cytotoxic potencies against different human tumor cell lines such as HeLa, HepG2, A549, and MDA MB 231. RL-1 and RL-2 exhibited a dose-dependent antifeedant activity against Spodoptera litura, producing about 82.06% and 73.66% antifeedant activity, whereas PCA showed a moderate antifeedant activity (63.67%) at 60 microgram/cm2 area of castor leaf. Furthermore, PCA, RL-1, and RL-2 exhibited about 65%, 52%, and 47% mortality, respectively, against Rhyzopertha dominica at 20 microgram/ml. This is the first report of rhamnolipids as antifeedant metabolites against Spodoptera litura and as insecticidal metabolites against Rhyzopertha dominica. The metabolites from Pseudomonas sp. strain ICTB-745 have interesting potential for use as a biopesticide in pest control programs.
Tyrosine phosphorylation of theHelicobacter pyloriCagA antigen aftercag-driven host cell translocation (2000)

Helicobacter pylori strains associated with severe tissue damage and inflammation possess a unique genetic locus, cag, containing 31 genes originating from a distant event of horizontal transfer and retained as a pathogenicity island. The cag system is an Helicobacter-specific type IV secretion engine involved in cellular responses like induction of pedestals, secretion of IL-8, and phosphorylation of proteic targets. It has previously been reported that cocultivation of epithelial cells with Helicobacter pylori triggers signal transduction and tyrosine phosphorylation of a 145-kDa putative host cell protein. Herein, we demonstrate that this protein is not derived from the host but rather is the bacterial immunodominant antigen CagA, a virulence factor commonly expressed in peptic ulcer disease and thought to be an orphan of a specific biological function. Thus, CagA is delivered into the epithelial cells by the cag type IV secretion system where it is phosphorylated on tyrosine residues by an as yet unidentified host cell kinase and wired to eukaryotic signal transduction pathways and cytoskeletal plasticity.
Analog Front End, Array Elements, and Receiver Electronics (2018)

Having discussed the basic theory and approaches to phased array receiver modeling, as well as figures of merit and system characterization, we now turn to specific details of the design and fabrication of the front end aperture itself. A wide variety of element types and configurations have been explored. Chief examples include the wideband sinuous element of the early explorations of PAFs at NRAO [1], dipole elements for PAFs [2], [3] as well as aperture arrays [4], tapered slot antennas or Vivaldi elements [5], [6], derivatives of the TSA element such as the egg-crate array, the checkerboard array [7]–[9] and other current-sheet implementations, horn elements [10], and of course the ubiquitous microstrip patch antenna [11] and the patch excited cup antenna designed by RUAG Space [12]. Many of these designs were surveyed in Chapter 1. In this chapter, we review considerations on selecting an appropriate element type, methods for design optimization, and fabrication issues. Receiver electronics is also discussed, with a specific focus on low noise amplifiers. Signal transport is also briefly addressed. The chapter concludes with an overview of downconversion and sampling, as well as the analog filters which these processes require.
Computational Methods for Intelligent Information Access (1995)

Currently, most approaches to retrieving textual materials from scientific databases depend on a lexical match between words in users' requests and those in or assigned to documents in a database. Because of the tremendous diversity in the words people use to describe the same document, lexical methods are necessarily incomplete and imprecise. Using the singular value decomposition (SVD), one can take advantage of the implicit higher-order structure in the association of terms with documents by determining the SVD of large sparse term by document matrices. Terms and documents represented by 200-300 of the largest singular vectors are then matched against user queries. We call this retrieval method Latent Semantic Indexing (LSI) because the subspace represents important associative relationships between terms and documents that are not evident in individual documents. LSI is a completely automatic yet intelligent indexing method, widely applicable, and a promising way to improve users' access to many kinds of textual materials, or to documents and services for which textual descriptions are available. A survey of the computational requirements for managing LSI-encoded databases as well as current and future applications of LSI is presented.
Controlling Inrush Currents in Inductively Coupled Power Systems (2018)

In an Inductively Coupled Power Transfer (ICPT) system, a multiplicity of (moving) loads take power from an elongated conductive loop (track) excited by a current in the range of 15-125A by magnetic induction at a VLF frequency of between 5-50kHz. In this application, the track performs the same function as a distribution line in a power system. However, frequency deviations cannot be tolerated in ICPT systems and therefore there are difficulties with inrush power surges as loads switch on. In severe cases, the inrush surge may compromise the security of the whole system.This paper proposes a solution to this problem using an ICPT pickup controller with input shaping where the poles that can cause an inrush are not excited. The paper is supported by theoretical analysis and experimental measurements and is applicable across a wide range of ICPT sizes and applications. The solution reduces the inrush effects to 10% of an uncontrolled system.
MOESM1 of Carcinoembryonic antigen-targeted photodynamic therapy in colorectal cancer models (2019)

Additional file 1: Figure S2. Ex vivo biodistribution of two mice with subcutaneous LoVo tumors, one day after 111In-labeled DTPA-hMN-14-IRDye700DX injection.
Synthesis of ZSM-20. Comparison of properties with zeolite Y (1990)

Highly crystalline samples of ZSM-20 have been prepared using a procedure similar to that reported in the literature. Some factors affecting the crystallisation of ZSM-20 are discussed. The products are extensively characterised using X-ray powder diffraction, scanning electron microscopy and solid-state MASNMR. A direct comparison between ZSM-20 and zeolite Y is drawn from nitrogen sorption studies and from Fourier-transform infrared studies of both the framework and hydroxyl spectra. Preliminary results for a comparison of HZSM20 and H-USY in catalytic cracking of gas oil are also presented.
Antigen spread and survival with sipuleucel-T in patients with advanced prostate cancer. (2014)

88 Background: Tumor cell death in response to an immunotherapy may lead to the release of secondary (i.e. non-targeted) tumor antigens that prime subsequent immune responses (antigen spread). This may contribute to tumor control and reveal post-treatment biomarkers of clinical outcome. Sipuleucel-T, approved in the U.S. for treatment of patients with asymptomatic or minimally symptomatic, metastatic castration-resistant prostate cancer (mCRPC), is designed to elicit an immune response to prostatic acid phosphatase. Here we show that sipuleucel-T also elicits humoral antigen spread that may be associated with clinical benefit. Methods: We used protein microarrays and Luminex xMAP to identify and validate post-treatment serum immunoglobulin G (IgG) responses against secondary antigens. Association between IgG responder status (≥ 2-fold IgG elevation post-treatment) and overall survival (OS) was assessed using a Cox regression model adjusted for baseline prognostic factors (prostate-specific antigen [PSA], lactate dehydrogenase [LDH], bone lesions, Gleason score) and prior bisphosphonate use. Results: In IMPACT (NCT00065442, the pivotal trial of sipuleucel-T), IgG responses against secondary antigens were consistently observed three to four months post-treatment in the sipuleucel-T arm but not in the control arm. In evaluable sera from IMPACT (sipuleucel-T n=93; control n=40), IgG responses against an array of secondary antigens, including an oncogene (K-RAS) and a prostate-specific antigen (KLK2/hK2), were confirmed by Luminex xMAP in sipuleucel-T-treated patients (Wilcoxon test, p≤10 -6 ); responses were not observed in control patients (p&gt;0.1). Antigen spread was also observed post-sipuleucel-T treatment in ProACT (Wilcoxon test, p≤0.01), an independent study in patients with mCRPC (NCT00715078, evaluable n=26). In IMPACT, OS was longer in sipuleucel-T-treatment patients with IgG response to greater than or equal to two secondary antigens than in those without such response (Cox model, p≤0.01, HR≤0.4). Conclusions: Sipuleucel-T treatment resulted in humoral antigen spread that was associated with improved OS in IMPACT. These results contribute to an understanding of sipuleucel-T’s mechanism of action, and may enable identification of post-treatment biomarkers of clinical outcome. Clinical trial information: NCT00065442.
Optical module fabrication using nanoimprint technology (2006)

UV-NanoImprint Lithography (NIL) is a fast and low cost method, which becomes an increasingly important instrument for fabrication of &mu;-TAS and telecommunication devices. The key elements of UV-NIL are transparent molds and low viscosity resists. Two different transparent mold materials, allowing UV curing through the stamp, were developed: rigid quartz or flexible PDMS. Typical resist viscosities are in a range of <100mPas, ensuring fast and successful filling of the stamp cavities. UV-curing is carried out at a wavelength of 350-450 nm.