gebhart/patrepeval huggingface dataset:
Characterization of the N-Acetyl-5-neuraminic Acid-binding Site of the Extracytoplasmic Solute Receptor (SiaP) of Nontypeable Haemophilus influenzae Strain 2019 (2007)

Nontypeable Haemophilus influenzae is an opportunistic human pathogen causing otitis media in children and chronic bronchitis and pneumonia in patients with chronic obstructive pulmonary disease. The outer membrane of nontypeable H. influenzae is dominated by lipooligosaccharides (LOS), many of which incorporate sialic acid as a terminal nonreducing sugar. Sialic acid has been demonstrated to be an important factor in the survival of the bacteria within the host environment. H. influenzae is incapable of synthesizing sialic acid and is dependent on scavenging free sialic acid from the host environment. To achieve this, H. influenzae utilizes a tripartite ATP-independent periplasmic transporter. In this study, we characterize the binding site of the extracytoplasmic solute receptor (SiaP) from nontypeable H. influenzae strain 2019. A crystal structure of N-acetyl-5-neuraminic acid (Neu5Ac)-bound SiaP was determined to 1.4A resolution. Thermodynamic characterization of Neu5Ac binding shows this interaction is enthalpically driven with a substantial unfavorable contribution from entropy. This is expected because the binding of SiaP to Neu5Ac is mediated by numerous hydrogen bonds and has several buried water molecules. Point mutations targeting specific amino acids were introduced in the putative binding site. Complementation with the mutated siaP constructs resulted either in full, partial, or no complementation, depending on the role of specific residues. Mass spectrometry analysis of the O-deacylated LOS of the R127K point mutation confirmed the observation of reduced incorporation of Neu5Ac into the LOS. The decreased ability of H. influenzae to import sialic acid had negative effects on resistance to complement-mediated killing and viability of biofilms in vitro, confirming the importance of sialic acid transport to the bacterium.
Survey of health care personnel's attitudes toward oral hygiene in long‐term care facilities in Finland (2019)

The health care personnel of long-term care facilities considered older adults' oral health important. Members of the health care personnel who showed a negative attitude with our scoring system toward older adults' daily oral hygiene indicated in their questionnaire responses the need for additional training and additional time for the task.
Antimicrobial and Efflux Pump Inhibitory Activity of Caffeoylquinic Acids from Artemisia absinthium against Gram-Positive Pathogenic Bacteria (2011)

These techniques facilitated the direct analysis of the active components from plant extracts, as well as dramatically reduced the time needed to analyze the compounds, without the need for prior isolation. The calculated energetics of the docking poses supported the biological information for the inhibitory capabilities of 4',5'-ODCQA and furthermore contributed evidence that CQAs show a preferential binding to Major Facilitator Super family efflux systems, a key multidrug resistance determinant in gram-positive bacteria.
Solid‐phase fluorescent labeling reaction of picomole amounts of insulin in very dilute solutions and their analysis by capillary electrophoresis (1995)

The fluorescent labeling of peptides at concentrations as low as 10(-8) M can be achieved by using a solid-phase reactor. Using oxidized insulin chain B as a test peptide, we demonstrate the use of an Immobilon CD membrane to capture and preconcentrate peptides. Insulin chain B can then be labeled with a fluorogenic reagent, 3-(2-furoyl)quinoline-2-carboxaldehyde, while it is still attached to the membrane. Unwanted fluorescent products (attributed to secondary reactions) can be washed away with methanol without significant removal of the labeled insulin chain B, which then can be extracted with a low pH buffer. The analysis by micellar electrokinetic capillary chromatography with post-column laser-induced fluorescence detection (mass limit of detection of 2.4 x 10(-21) moles insulin chain B) results in electropherograms that show great improvement in terms of unwanted peaks and high number of theoretical plates (up to 20 million). The use of the solid-phase reactor allows easy handling of as little as 5 picomoles of insulin chain B.
BIS-CHELATION AND ANION EFFECTS INVOLVING A MOLECULE CONSTRUCTED IN THE ORGANIC SOLID STATE USING MOLECULAR TEMPLATES (2005)

Transition-metal-ion complexes involving seven-membered chelation rings have emerged as important for applications in catalysis and biology. Specifically, N-C4-N bridged metallocycles [1] have found applications as catalysts [2] and models of biological compounds [3], as well as antibacterial [4] and antitumor [5] agents. In terms of catalysis, the application of chelating N-donor ligands as compared to analogous polyphosphines has begun to attract attention, especially for the activation of C-H bonds [6]. Thus, ligands that provide more than one pyridyl group in close proximity are being studied as preorganized metal chelation units [6b]. In addition, there is increasing interest in the development of novel non-metallocene catalysts for olefin polymerization for which complexes involving N-C4-N bridged chelate rings have been effective [2c]. Therefore, studies that involve N-C4-N ligands with a potential to offer seven-membered chelation are of much current interest.
Contour-Mode Aluminum Nitride Vibrating RF Microsystems (2007)

Contour-mode aluminum nitride vibrating micromechanical resonators are presented as a new class of RF microsystems capable of low-loss filtering and frequency synthesis for next generation wireless devices. Contour-mode piezoelectric resonators can span frequencies from 10 MHz up to few GHz on the same silicon chip offering high quality factors in air (1,000-4,000) and low motional resistance (25-500 Omega). Low loss electrically and mechanically coupled filters can be easily implemented using this resonator technology. A microsystems approach that takes advantage of massively arraying micromechanical vibrating resonators is presented as a solution for next generation cognitive radios based on low power transceivers that use frequency hopping, multi-band filtering and direct frequency synthesis.
PREDICTION OF ANTISENSE OLIGONUCLEOTIDE EFFICACY USING AGGREGATE MOTIFS (2008)

Antisense oligonucleotide technology allows the targeted reduction of mRNA expression through the in vitro application of short (approximately 20 nt) DNA molecules. Oligonucleotides are valuable both in the study of gene regulation and for having potential therapeutic effects. In theory, a base sequence complementary to a region of the transcript would hybridize to its mRNA target. Nevertheless, in practice some complementary antisense oligonucleotides are more active and more potent than others in suppressing specific gene expression. We present a novel computational approach to modeling oligonucleotide efficacy that uses aggregate motifs, which are flexible tetramotifs that expand the predictive ability of the data descriptors and the attribute space. We also demonstrate our findings on the largest dataset yet reported in the literature. It was shown that the prediction accuracy was significantly enhanced, offering more than eightfold improvement compared to the traditional methods.
Compte rendu de la session Ascomycota Zone Alpine 2019 (2020)

Report of the foray dedicated to the Alpine zone Ascomycota, in August 2019 in the massif of Oisans (France, Isère), including the inventory made in the reserve of Lauvitel, and listing of the taxa studied by the participants
Polymeric Antimicrobial N-Halamine-Surface Modification of Stainless Steel (2017)

The surfaces of materials fabricated from stainless steel are challenging to functionalize with antimicrobial moieties. This work demonstrates that stainless steel surfaces can be modified with an N-halamine-based copolymer in order to obtain antimicrobial activity. In this regard, a copolymer (HACM) of 2-acrylamido-2-methyl-1-(5-methylhydantoinyl)propane and 3-cloro-2-hydroxypropyl methacrylate was synthesized and grafted onto a stainless steel surface via covalent attachment. Synthesized monomers and copolymers were characterized by NMR, FTIR, and XPS spectral analyses. Upon treatment with dilute bleach, the stainless steel surfaces were rendered antimicrobial, possessing a sufficient amount of chlorine content and excellent stability and durability. The modified stainless steel samples inactivated 6 logs of Staphylococcus aureus and Escherichia coli O157:H7 bacteria within 15 min of contact time. Stabilities of the coatings toward washing and UVA exposure were also studied. The stainless steel samples showed superior washing stabilities and regenerabilities. After 5 cycles of washing, there was a very minimal change in the initial chlorine contents, and the chlorine content could be recharged to its initial number of Cl+ atoms/cm2. However, only a moderate stability of the coatings was observed after UVA irradiation. These results indicate that N-halamine precursor polymers can be facilely applied to stainless steel surfaces by covalent bonding and that robust, regenerable antimicrobial stainless steel surfaces could be prepared via the N-halamine technology. This technology exhibits potential for use in food processing, prevention of biofilm formation, and biomedical and health-care industries to support the prevention and reduction of cross-contamination and health-care related infections.
Using bus-based connections to improve field-programmable gate array density for implementing datapath circuits (2005)

As the logic capacity of Field-Programmable Gate Arrays (FPGAs) increases, they are being increasingly used to implement large arithmetic-intensive applications, which often contain a large proportion of datapath circuits. Since datapath circuits usually consist of regularly structured components (called bit-slices) which are connected together by regularly structured signals (called buses), it is possible to utilize datapath regularity in order to achieve significant area savings through FPGA architectural innovations. This paper describes such an FPGA routing architecture, called the multi-bit routing architecture, which employs bus-based connections in order to exploit datapath regularity. It is experimentally shown that, comparing to conventional FPGA routing architectures, the multi-bit routing architecture can achieve 14% routing area reduction for implementing datapath circuits, which represents an overall FPGA area savings of 10%. This paper also empirically determines the best values of several important architectural parameters for the new routing architecture including the most area efficient granularity values and the most area efficient proportion of bus-based connections.
Clustering Techniques forRuleExtraction from Unstructured TextFragments (2005)

Thispaper focuses ontechniques for clustering unstructured text fragments which are generated fromarule extraction agent. Thetext fragments represent paragraphs oftext containing potential rules. Thelatent semantic Indexing Method isapplied tomaptheunstructured text into alinear vector space. Similar text fragments areidentified based onthesimilarity between their vector representations. Theproblem ofclustering based on general similarity measures that aredifferent thanthe conventional distance based measures isdiscussed. A newversion oftheMountain Clustering Methodis developed toaddress theproblem ofidentifying groups ofsimilar vectors that correspond to documents withanalogous content. Several clustering algorithms arecompared intheir ability to satisfactorily cluster these textfragments into sets of related concepts. Anintelligent agent algorithm for extraction ofrules fromtext documents isproposed anddemonstrated.
Silicon photonic integrated devices for datacenter optical networks (2014)

The evolution of computing infrastructure and workloads has put an enormous pressure on datacenter networks. It is expected that bandwidth will scale without increases in the network power envelope and total cost of ownership. Networks based on silicon photonic devices promise to help alleviate these problems, but a viable development path for these technologies is not yet fully outlined. In this paper, we report our progress on developing components and strategies for datacenter silicon photonics networks. We will focus on recent progress on compact, low-threshold hybrid Si lasers and the CWDM transceivers based on these lasers as well as DWDM microring resonator-based transceivers.
Internal cooling of fiber and disc lasers by radiation balancing and other optical and phonon processes: radiation-balanced lasers: new vistas in optical gain and refrigeration materials (Conference Presentation) (2017)

A new AFOSR MURI program, devoted to the pursuit of cooling solid state lasers internally, is underway and will be described. Comprising research teams from four universities, this program will focus on fiber and disc lasers and the demonstration of optical and/or phonon-based processes capable of maintaining beam quality as power loading of the medium rises. Emphasis will be placed on leveraging novel resonator designs to enhance a targeted optical field-material interaction such that localized cooling occurs within the gain medium. Examples will be given of two systems that are being pursued initially.
Experiments on Laminar Flow about a Rotating Sphere in an Air Stream (1987)

Laminar flow about a rotating sphere which is subjected to a uniform stream of air in the direction of the axis of rotation is investigated experimentally. Measurements of the velocity components within the boundary layer and the separation angle were performed at a Reynolds number, Re, of 10 000 and Ta/Re 2 of 0, 1 and 5. These measurements are compared with the numerical solutions of the same problem where either theoretical potential or actual experimental boundary conditions are imposed on the governing equations.
Supplementary Methods from NMS-E973, a Novel Synthetic Inhibitor of Hsp90 with Activity against Multiple Models of Drug Resistance to Targeted Agents, Including Intracranial Metastases (2023)

&lt;p&gt;Supplementary Methods - PDF file 56K, Time-lapse imaging of A375 cells&lt;/p&gt;
Quantitative modeling of forces in electromagnetic tweezers (2010)

This paper discusses numerical simulations of the magnetic field produced by an electromagnet for generation of forces on superparamagnetic microspheres used in manipulation of single molecules or cells. Single molecule force spectroscopy based on magnetic tweezers can be used in applications that require parallel readout of biopolymer stretching or biomolecular binding. The magnetic tweezers exert forces on the surface-immobilized macromolecule by pulling a magnetic bead attached to the free end of the molecule in the direction of the field gradient. In a typical force spectroscopy experiment, the pulling forces can range between subpiconewton to tens of piconewtons. In order to effectively provide such forces, an understanding of the source of the magnetic field is required as the first step in the design of force spectroscopy systems. In this study, we use a numerical technique, the method of auxiliary sources, to investigate the influence of electromagnet geometry and material parameters of the magnetic core on the magnetic forces pulling the target beads in the area of interest. The close proximity of the area of interest to the magnet body results in deviations from intuitive relations between magnet size and pulling force, as well as in the force decay with distance. We discuss the benefits and drawbacks of various geometric modifications affecting the magnitude and spatial distribution of forces achievable with an electromagnet.
Monitoring Degree of Cure and Coating Thickness of Photocurable Resins Using Fluorescence Probe Techniques (1995)

In this paper, we report recent progress in developing fluorescence probe technology for photocurable coatings. Intramolecular charge transfer (ICT) fluorescence probes based on derivatives of dansyl amide were found to be useful for monitoring cure of various photocurable resins the polymerization of which was initiated with UV or visible initiators. Fluorescence emission spectra of chosen ICT probes exhibited spectral blue shifts due to the increases in microviscosity surrounding the probe molecules as the photocuring process proceeded. A fluorescence intensity ratio method was used to follow the probe spectral changes as a function of the degree of polymerization. Linear correlation plots between the intensity ratios as measured from the probe fluorescences and the degree of cure were obtained for varieties of photocurable resins with UV or visible initiators. In addition, a fluorescence probe technique for measuring coating thickness based on the nascent fluorescence from coating substrate is also described.
Local controlled release of 1-hydroxyethylidene diphosphonate using silicone-rubber matrices. Effects of sterilization on in vitro release and in vivo efficacy. (1989)

Calcification (CALC) is the most frequent cause of the clinical failure of bioprosthetic heart valves (BHVs). Controlled release of disodium ethanehydroxydiphosphonate (EHDP) has been demonstrated to inhibit subdermal BHV calcification at effective low local doses, avoiding adverse effects. However, the eventual circulatory use of controlled release EHDP necessitates addressing several critical issues that may affect efficacy. These include the effects of sterilization on EHDP release and the efficacy of sustained release matrices containing CaEHDP, which is less soluble than NaEHDP. The effects of CaEHDP-NaEHDP incorporation and steam sterilization on controlled release of EHDP from silicone-rubber matrices was studied both in vitro and in vivo using a rat subdermal model and sheep tricuspid valve replacements. Autoclaved EHDP matrices (20% wt/wt) released 88.9% +/- 7.84 of contained drug after 140 days in vitro, compared with control (87.6% +/- 10.3 cumulative release). Autoclaved EHDP matrices completely inhibited BHV CALC in 60 day rat subdermal implants (8.84 +/- 3.68 micrograms Ca++/mg tissue), comparable to nonsterilized EHDP-loaded matrices (7.06 +/- 2.00 micrograms Ca++/mg tissue). Nontreated CALC levels were 183 +/- 7.60 micrograms Ca++/mg tissue. Na-CaEHDP co-incorporation into silicone rubber matrices markedly prolonged controlled release with the 1:1 Na-CaEHDP mixture demonstrating an extrapolated release duration of approximately 20 years, assuming the total amount of dispersed drug was released. Data from tricuspid valve replacements in sheep demonstrate erratic control calcification (41.3 +/- 14.9 micrograms Ca++/mg tissue), but complete suppression of BHV calcification with Na2EHDP controlled release (5.74 +/- 1.35 micrograms Ca++/mg tissue) after 150 days.
Reconfigurable and Adaptive Radar Amplifiers for Spectrum Sharing in Cognitive Radar (2019)

The increased use of the wireless spectrum for broadband applications has necessitated a new approach to radar transmission. Future radar systems will be required to adjust operating frequency in real time to avoid interference from other wireless devices operating in the same band. This paper describes the use of a 90 W tunable power-amplifier matching circuit to reconfigure a power amplifier for high power-added efficiency and spectral compliance at multiple frequencies within the S-band. To reconfigure the amplifier in real-time spectrum sharing scenarios, a modified gradient search algorithm is employed to tune the amplifier based on measured data. A look-up table allows previous optimum tuner settings to be stored after the first reconfiguration at each operating frequency, allowing faster optimizations upon re-visits to each frequency. Next research steps are discussed; including the streamlining of system timing, operating the search algorithm under control of spectral prediction and decision-making processes and analyzing the effect of impedance tuning on range and Doppler detection.
Focus and dose deconvolution technique for improved CD control of immersion clusters (2010)

As critical dimension (CD) control requirements increase and process windows decrease, it is now of even higher importance to be able to determine and separate the sources of CD error in an immersion cluster, in order to correct for them. It has already been reported that the CD error contributors can be attributed to two primary lithographic parameters: effective dose and focus. In this paper, we demonstrate a method to extract effective dose and focus, based on diffraction based optical metrology (scatterometry). A physical model is used to describe the CD variations of a target with controlled focus and dose offsets. This calibrated model enables the extraction of effective dose and focus fingerprints across wafer and across scanner exposure field. We will show how to optimize the target design and the process conditions, in order to achieve an accurate and precise de-convolution over a larger range of focus and dose than the expected variation of the cluster. This technique is implemented on an ASML XT:1900Gi scanner interfaced with a Sokudo RF<sup>3S</sup> track. The systematic focus and dose fingerprints obtained by this de-convolution technique enable identification of the specific contributions of the track, scanner and reticle. Finally, specific corrections are applied to compensate for these systematic CD variations and a significant improvement in CD uniformity is demonstrated.
Field Evaluation of New Treating Technique To Recover Permeability Damaged by Polymeric Materials (1990)

ABSTRACT A recently developed treatment technique has significantly increased injectivity rates of injection wells which had been damaged by near-wellbore polymer blockage. Polymer blockage can be caused by incompletely dissolved solid polymer, improperly inverted emulsion polymer, and/or deposition and adsorption of the polymer on the rock. Strong oxidizers such as hydrogen peroxide or sodium hypochlorite are typically used to clean up polymer deposits left after polymer injection; however, both of these chemicals present significant handling hazards. The treatment technique presented in this paper utilizes a solid oxidizer which releases a peroxide to dissolve the polymer deposits. Field tests in Hockley County, TX, yielded injectivity rates more than double those recorded before treatment. The wells consisted of open-hole San Andres sections, at 4,850 to 5,050 ft (1,478.3 to 1,539.2 meters), with a bottom-hole temperature of 100°F (37.8°C). The polymer project was conducted from 1984 to 1986. This paper discusses the solid oxidizer treatment technique and presents case histories and laboratory results.
Comments on the origin of low-energy structure observed in the far-infrared cyclotron resonance of ultra-high mobility n-GaAs and n-InP (1992)

Recently optically detected cyclotron resonance spectra reported by Ahmed et al. in ultra-pure n-GaAs have revealed low-energy structure associated with the cyclotron resonance. The authors have investigated the far-infrared photoconductive response under conditions of cyclotron resonance in these n-GaAs ( mu approximately=400000 cm2 V-1 s-1) samples and also in n-InP ( mu approximately=170000 cm2 V-1 s-1) samples grown by MBE. The suggestion that the structure arises from transitions involving non-parabolicity and polaron coupling effects is discounted using a five-level P.p calculation as found in the literature. Other possible origins, supported by appropriate theory, are suggested for this structure.
Weak Measurements Compressed Sensing Quantum State Tomography (2016)

We show that prior knowledge that a quantum state is close to a pure state enables a direct and efficient measurement of the density matrix representing the state, using the weak measurements methodology.