gebhart/patrepeval huggingface dataset:
Bioactive Surface Modification of Metal Oxides via Catechol-Bearing Modular Peptides: Multivalent-Binding, Surface Retention, and Peptide Bioactivity (2014)

A series of multivalent dendrons containing a bioactive osteogenic growth peptide (OGP) domain and surface-binding catechol domains were obtained through solid phase synthesis, and their binding affinity to hydroxyapatite, TiO2, ZrO2, CeO2, Fe3O4 and gold was characterized using a quartz crystal microbalance with dissipation (QCM-d). Using the distinct difference in binding affinity of the bioconjugate to the metal oxides, TiO2-coated glass slides were selectively patterned with bioactive peptides. Cell culture studies demonstrated the bioavailability of the OGP and that OGP remained on the surface for at least 2 weeks under in vitro cell culture conditions. Bone sialoprotein (BSP) and osteocalcein (OCN) markers were upregulated 3-fold and 60-fold, respectively, relative to controls at 21 days. Similarly, 3-fold more calcium was deposited using the OGP tethered dendron compared to TiO2. These catechol-bearing dendrons provide a fast and efficient method to functionalize a wide range of inorganic materials with bioactive peptides and have the potential to be used in coating orthopaedic implants and fixation devices.
Explosive Crystallization in Atomic Layer Deposited Mixed Titanium Oxides (2009)

Anatase crystals with lateral sizes of tens of micrometers are impossible to prepare as thin films on amorphous substrates by normal thin film deposition techniques. When deposited on amorphous substrates, polycrystalline anatase titanium dioxide (TiO2) thin films have typically grain and crystal sizes comparable to the film thickness. We show that when a suitable amount of Nb2O5 or Ta2O5 is mixed with TiO2 using atomic layer deposition (ALD), upon postdeposition annealing large ∼10−100 μm sized anatase monocrystals are formed in films thinner than 100 nm on amorphous substrates. Such an exceptionally extensive lateral grain growth appears to be a result of explosive crystallization when amorphous Ti−Nb−O and Ti−Ta−O thin films are heated, a phenomenon that has not been reported before for TiO2 thin films. The prepared films will likely have a number of useful applications where well-ordered anatase surfaces are required, such as photocatalysis, and they also can be used as a transparent conducting oxide.
Fluorescent N<sup>2</sup>,N3‐ε‐Adenine Nucleoside and Nucleotide Probes: Synthesis, Spectroscopic Properties, and Biochemical Evaluation (2006)

N1,N(6)-ethenoadenine, epsilon-A, nucleos(t)ides have been previously applied as fluorescent probes in numerous biochemical systems. However, these epsilon-A analogues lack the H-bonding capability of adenine. To improve the fluorescence characteristics while preserving the H-bonding pattern required for molecular recognition, we designed a novel probe: N(2),N3-etheno-adenosine, (N(2),N3-epsilon-A). Here, we describe four novel syntheses of the target epsilon-nucleoside and related analogues. These methods are short, facile, and provide the product regiospecifically. In addition, we report the absorption and emission spectra of N(2),N3-epsilon-A and the dependence of the spectral features on the pH and polarity of the medium. Specifically, maximum emission of N(2),N3-epsilon-A in water is observed at 420 nm (phi=0.03, excitation at 290 nm). The biochemical relevance of the new probe was evaluated with respect to the P2Y(1) receptor and NTPDases 1 and 2. N(2),N3-epsilon-ATP was found to be almost equipotent with ATP at the P2Y(1) receptor and was hydrolyzed by NTPDases 1 and 2 at about 80 % of the rate of ATP. Furthermore, protein binding does not seem to shift the fluorescence of N(2),N3-epsilon-ATP. Based on the fluorescence and full recognition by ATP-binding proteins, we propose N(2),N3-epsilon-ATP and related nucleo(s)tides as unique probes for the investigation of adenine nucleo(s)tide-binding proteins as well as for other biochemical applications.
Electrochemiluminescence-Based Detection of β-Lactam Antibiotics and β-Lactamases (1996)

Bacterial resistance to clinically administered beta-lactam antibiotics is usually caused by beta-lactamases, enzymes that hydrolytically inactivate the antibiotics. This paper describes the use of electrogenerated chemiluminescence (ECL) to detect beta-lactam antibiotics and their hydrolysis by beta-lactamases. All 10 tested antibiotics were detected on the basis of their ability to participate in an ECL reaction with ruthenium(II) tris(bipyridine). In every case, antibiotic-promoted ECL changed when the antibiotic was hydrolyzed by beta-lactamases or NaOH. Standard curves of antibiotic concentration versus ECL intensity showed that antibiotics could be quantitated to low micromolar concentrations. Substrate profiles were generated for four beta-lactamases using six structurally diverse beta-lactam antibiotics. ECL-based antibiotic detection was accomplished in untreated whole milk, and beta-lactamases were detected in crude bacterial broth culture. Because several structurally diverse antibiotics were detectable by ECL, this method may become valuable for the detection of many or all beta-lactam antibiotics and their inactivation by beta-lactamases.
Cellular telephony and the question of privacy (2011)

A private overlay may ease concerns over surveillance tools supported by cellular networks.
(Collection of high quality acoustical records for honeybees) (1987)

High quality acoustical data records were collected for both European and Africanized honeybees under various field conditions. This data base was needed for more rigorous evaluation of a honeybee identification technique previously developed by the travelers from preliminary data sets. Laboratory-grade recording equipment was used to record sounds made by honeybees in and near their nests and during foraging flights. Recordings were obtained from European and Africanized honeybees in the same general environment. Preliminary analyses of the acoustical data base clearly support the general identification algorithm: Africanized honeybee noise has significantly higher frequency content than does European honeybee noise. As this algorithm is refined, it may result in the development of a simple field-portable device for identifying subspecies of honeybees. Further, the honeybee's acoustical signals appear to be correlated with specific colony conditions. Understanding these variations may have enormous benefit for entomologists and for the beekeeping industry.
A novel minimal Arabic script for preparing databases and benchmarks for Arabic text recognition research (2009)

This work presents a minimal Arabic script that may be used in training and testing of Arabic text recognition systems. Collecting handwritten samples from different writers to build handwritten text databases which may be used for benchmarking Arabic text recognition systems is another application. The suggested Arabic script covers the different shapes of Arabic alphabet in all positions (viz. standalone, initial, medial, and terminal). The frequency of each shape in the minimal text is designed to be the minimal possible. The suggested script is novel from different perspectives. A writer may participate with only three lines of meaningful Arabic text to cover all possible alphabet shapes, a total of 125 shapes. Collecting scripts from different writers provide evenly distributed letter frequencies that assure enough samples for all character shapes. This enables proper training resulting in more accuracy in the recognition phase. The same can be stated for printed Arabic text. This is especially useful when using large number of features with classifiers that require large number of samples for each category. Hidden Markov Models and Neural networks are two examples of these classifiers. In addition, the paper presents statistical analysis of Arabic corpora for estimating the number of occurrences of different shapes of Arabic alphabets in large corpora. The frequency of Arabic alphabet usage was utilized in enhancing the search for the minimal Arabic text.
Selecting Soybean Cultivars for Dual Resistance to Soybean Cyst Nematode and Sudden Death Syndrome Using Two DNA Markers (1999)

DNA markers for genes conditioning resistance to soybean [ Glycine max (L.) Merr.] root infection by [ Fusarium solani (Mart.) Sacc. f. sp. glycine (Burk.)] ( Rfs1 ), sudden death syndrome (SDS), and soybean cyst nematode (SCN; Heterodera glycines Ichinohe; Rhg4 and rhg1 ) were previously identified in ‘Essex’ × ‘Forrest’. This study tests the effectiveness of those markers in selecting for disease resistance among recombinant inbred lines from ‘Flyer’ × ‘Hartwig’. A total of 535 among 739 lines were scored by two markers, providing four genotypes. A stratified random sample of 50 lines was evaluated for SDS by F. solani root infection severity at two locations and SCN race 3 index of parasitism in the greenhouse. Selection with BLT65 identified 281 among 671 lines with the genomic region that underlies Rhg4 ‐derived SCN resistance. Selection with Satt038 identified 230 among 613 lines containing the genomic region that underlies resistance to SDS ( rfs1 ) and rhg1 ‐derived SCN resistance. A total of 93 out of 535 lines had genomic regions that underlie resistance to both SDS and SCN in Essex × Forrest. Segregation of both markers was not random ( P ≤ 0.05). Infection severity means for genotypes with the Hartwig allele at Satt038 (28–29%) were lower ( P = 0.0001, R 2 = 28%) than with the Flyer allele (31–42%); irrespective of maturity group. BLT65 was not associated with infection severity. Mean SCN index of parasitism was lower ( P ≤ 0.05) only for genotypes carrying the Hartwig allele at both Satt038 and BLT65. Therefore, alleles conferring resistance to SDS and SCN in Essex × Forrest are transferable to other populations.
Decorrelation of user defined function invocations in queries (2014)

Queries containing user-defined functions (UDFs) are widely used, since they allow queries to be written using a mix of imperative language constructs and SQL, thereby increasing the expressive power of SQL; further, they encourage modularity, and make queries easier to understand. However, not much attention has been paid to their optimization, except for simple UDFs without imperative constructs. Queries invoking UDFs with imperative constructs are executed using iterative invocation of the UDFs, leading to poor performance, especially if the UDF contains queries. Such poor execution has been a major deterrent to the wider usage of complex UDFs. In this paper we present a novel technique to decorrelate UDFs containing imperative constructs, allowing set-oriented execution of queries that invoke UDFs. Our technique allows imperative execution to be modeled using the Apply construct used earlier to model correlated subqueries, and enables transformation rules to be applied subsequently to decorrelate (or inline) UDF bodies. Subquery decorrelation was critical to the wide use of subqueries; our work brings the same benefits to queries that invoke complex UDFs. We have applied our techniques to UDFs running on two commercial database systems, and present results showing up to orders of magnitude improvement.
Non-Invasive Monitoring of Intracranial Pulse Wave During Body Tilting Test (2008)

This study was supported by UAB “Vittamed technologijos ” and EU Structural Funds Project “Technological development and applied research of complex equipment and innovative non-invasive methods of human brain physiological monitoring ” BPD04-ERPF-3.1.7-03-05/0020
<i>Sse</i>8387I, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5′-CCTGCAGG-3′ (1990)

A type II restriction endonuclease designated Sse8387I was partially purified from Streptomyces sp. 8387. This enzyme cleaved adenovirus 2 DNA at three sites, lambda phage DNA at five sites, and pUC18 and M13mp18 RF DNA at one site each, but did not cleave the DNAs from pBR322, SV40, or phi X174. Sse8387I recognized the octanucleotide sequence 5'-CCTGCA decreases GG-3', cleaving where shown by the arrow. Sse8387I is the first restriction endonuclease to be reported that recognizes an octanucleotide sequence consisting of all four nucleotides, G, A, T, and C. The frequency of occurrence of Sse8387I sites within sequenced regions of primate genomes was 2.4 times that of NotI sites.
Arterial compliance probe for cuffless evaluation of carotid pulse pressure (2018)

This technique could provide a direct measurement of local PWV, arterial dimensions, and a calibration-free estimate of beat-by-beat local ΔP. It can be potentially extended for calibration-free cuffless BP measurement and non-invasive characterization of central arteries with locally estimated biomechanical properties.
Laboratory Confirmation of Lyme Disease (1991)

Lyme disease can be confirmed in the laboratory by isolation or detection of its causative agent, a tick-borne spirochete Borrelia burgdorferi, or by a diagnostic change in the titre of antibodies specific to the agent. B burgdorferi can be isolated and cultivated in Barbour-Stoenner-Kelly II medium. It can be detected by light microscopy in tissue sections or, rarely, in blood smears using various staining methods. There is interest in the development of alternative detection methods, including identification of specific antigens of B burgdorferi in the urine of suspected cases and demonstration of the presence of species-specific DNA using polymerase chain reaction assays. Currently, serological tests (indirect immunofluorescence assay, enzyme-linked immunosorbent assay and Western immunoblot) are the most practical and available methods for confirming Lyme disease. The quest to improve the specificity and sensitivity of serological tests - for example, through the use of specific recombinant antigens - continues.
Cell labeling approaches for fluorescence‐based in vivo flow cytometry (2011)

We provide an overview of the methods used to label circulating cells for fluorescence detection by in vivo flow cytometry. These methods are useful for cell tracking in small animals without the need to draw blood samples and are particularly useful for the detection of circulating cancer cells and quantification of circulating immune cells.
High-performance autofocus circuit for biological microscopy (1998)

An autofocus circuit, based on measurement of the high spatial frequency image components, was designed for automated microscopic scanning of biological specimens. By careful consideration of the system transfer function, elimination of video end-of-line filter artifacts, correction for illumination instability, and incorporation of autogain, the focus measurement circuit attained the sensitivity and dynamic range necessary for robust operation even at the extremes of biological specimen detail encountered in exhaustive raster scans of thousands of fields. This new circuit exhibited a 25-fold improvement in dynamic range over a previous analog implementation, matched real-time digital performance at an order of magnitude lower cost, resulted in autofocus precision of 56 nm (or 10-fold better than the depth of field of the objective) in scanning experiments comprising over 10 000 microscope fields, and tracked focus at scanning speeds of up to 3.45 fields/s. Focus was correctly maintained in these scanning experiments without additional compensation for low-detail images. This circuit makes possible the widespread inclusion of high-performance autofocus as a low cost option in video microscopy systems.
Towards single molecule manipulation with dielectrophoresis using nanoelectrodes (2004)

We present measurements of the scaling of the dielectrophoresis force with electrode size and particle size, in order to determine the ultimate size limits for dielectrophoresis at the nanoscale. To demonstrate the feasibility of nano-manipulation we present studies on the dielectrophoretic manipulation of DNA with microfabricated electrodes using RF electric fields. We find that DNA undergoes positive dielectrophoresis (i.e. the DNA is attracted to high electric field regions) at frequencies between 500 kHz and 1 MHz. We present a nano-manipulation array platform which demonstrates the scalability of these concepts for massively parallel, economic manipulation at the molecular scale. Finally, based on these measurements, we present a concept for a nanomotor using nanotube electrodes. Applications in molecular electronics and molecular manufacturing are discussed.
PUBLIC: A Decision Tree Classifier that Integrates Building and Pruning (1998)

Abstract. Classification is an important problem in data mining. Given a database of records, each with a class label, a classifier generates a concise and meaningful description for each class that can be used to classify subsequent records. A number of popular classifiers construct decision trees to generate class models. These classifiers first build a decision tree and then prune subtrees from the decision tree in a subsequent pruning phase to improve accuracy and prevent “overfitting”. Generating the decision tree in two distinct phases could result in a substantial amount of wasted effort since an entire subtree constructed in the first phase may later be pruned in the next phase. In this paper, we propose PUBLIC, an improved decision tree classifier that integrates the second “pruning ” phase with the initial “building” phase. In PUBLIC, a node is not expanded during the building phase, if it is determined that it will be pruned during the subsequent pruning phase. In order to make this determination for a node, before it is expanded, PUBLIC computes a lower bound on the minimum cost subtree rooted at the node. This estimate is then used by PUBLIC to identify the nodes that are certain to be pruned, and for such nodes, not expend effort on splitting them. Experimental results with real-life as well as synthetic data sets demonstrate the effectiveness of PUBLIC’s integrated approach which has the ability to deliver substantial performance improvements. Keywords: data mining, classification, decision tree
Development of an Alarm Algorithm, With Nanotechnology Multimodal Sensor, to Predict Impending Infusion Failure and Improve Safety of Peripheral Intravenous Catheters in Neonates (2019)

After regulatory approval, a randomized controlled trial may be performed to investigate whether interventions at the time of an alarm would result in fewer adverse outcomes and improve safety.
Physisorbed buffer layer as a template for pulsed laser patterning of metallic thin films: an alternative approach for photolithography (2004)

Buffer Layer Assisted Laser Patterning (BLALP) method is presented, for patterning metallic layers on surfaces, using laser desorption of a physisorbed buffer layer, e.g. Xe, CO<sub>2</sub> or H<sub>2</sub>O. This technique is based on the utilization of a low power laser pulse used as the photolithographic printer of a metallic thin film. Using a weakly bound buffer material as the template for laser patterning, led to the development of two complementary procedures, 'positive' and 'negative' BLALP. It is discussed as a potential alternative for standard photo-lithography, promising a cleaner, more cost effective, better resolution and more environmentally friendly procedure.
Volume Sensor Development Test Series 2 - Lighting Conditions, Camera Settings, and Spectral and Acoustic Signatures (2004)

Real-scale fire tests in mock ship compartments were conducted to collect data of acoustic and spectral sensors and to experimentally evaluate the fire detection performance of three commercially available video image fire detection systems under various lighting and camera setting configurations. One goal was to establish an understanding of the performance sensitivity and limitations of the VID systems to various setup and environmental conditions that may occur onboard ship. The performance of the detections systems was compared to the response of multiple state-of-the-art smoke detection technologies for a range of fire and nuisance source exposures. Additionally, these tests provide a large database of information to evaluate the spectral and acoustic signatures of the various fire and nuisance sources. Toward this end, microphones, long wave-length video imaging and a test bed of single and multiple element sensors were included in the tests.
Microfluidic On-demand Engineering of Exosomes towards Cancer Immunotherapy (2018)

Extracellular Vesicles (EVs), particularly exosomes (30-150 nm), are an emerging delivery system in mediating cellular communications, which have been observed for priming immune responses by presenting parent cell signaling proteins or tumor antigens to immune cells. Therefore, preparation of antigenic exosomes that can play therapeutic roles, particularly in cancer immunotherapy, is emerging. However, standard benchtop methods (e.g., ultracentrifugation and filtration) lack the ability to purify antigenic exosomes specifically among other microvesicle subtypes, due to the non-selective and time-consuming (>10 h) isolation protocols. Exosome engineering approaches, such as the transfection of parent cells, also suffer from poor yield, low purity, and time-consuming operations. In this paper, we introduce a streamlined microfluidic cell culture platform for integration of harvesting, antigenic modification, and photo-release of surface engineered exosomes in one workflow, which enables the production of intact, MHC peptide surface engineered exosomes for cytolysis activation. The PDMS microfluidic cell culture chip is simply cast from a 3D-printed mold. The proof-of-concept study demonstrated the enhanced ability of harvested exosomes in antigen presentation and T cell activation, by decorating melanoma tumor peptides on the exosome surface (e.g., gp-100, MART-1, MAGE-A3). Such surface engineered antigenic exosomes were harvested in real-time from the on-chip culture of leukocytes isolated from human blood, leading to much faster cellular uptake. The activation of gp100-specific CD8 T cells which were purified from the spleen of 2 Pmel1 transgenic mice was evaluated using surface engineered exosomes prepared from muring antigen presenting cells. Antigen-specific CD8 T cell proliferation was significantly induced by the engineered exosomes compared to native, non-engineered exosomes. This microfluidic platform serves as an automated and highly integrated cell culture device for rapid, and real-time production of therapeutic exosomes that could advance cancer immunotherapy.