gebhart/patrepeval huggingface dataset:
Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties (2009)

A new monotonicity-constrained maximum likelihood approach, called Partial Order Optimum Likelihood (POOL), is presented and applied to the problem of functional site prediction in protein 3D structures, an important current challenge in genomics. The input consists of electrostatic and geometric properties derived from the 3D structure of the query protein alone. Sequence-based conservation information, where available, may also be incorporated. Electrostatics features from THEMATICS are combined with multidimensional isotonic regression to form maximum likelihood estimates of probabilities that specific residues belong to an active site. This allows likelihood ranking of all ionizable residues in a given protein based on THEMATICS features. The corresponding ROC curves and statistical significance tests demonstrate that this method outperforms prior THEMATICS-based methods, which in turn have been shown previously to outperform other 3D-structure-based methods for identifying active site residues. Then it is shown that the addition of one simple geometric property, the size rank of the cleft in which a given residue is contained, yields improved performance. Extension of the method to include predictions of non-ionizable residues is achieved through the introduction of environment variables. This extension results in even better performance than THEMATICS alone and constitutes to date the best functional site predictor based on 3D structure only, achieving nearly the same level of performance as methods that use both 3D structure and sequence alignment data. Finally, the method also easily incorporates such sequence alignment data, and when this information is included, the resulting method is shown to outperform the best current methods using any combination of sequence alignments and 3D structures. Included is an analysis demonstrating that when THEMATICS features, cleft size rank, and alignment-based conservation scores are used individually or in combination THEMATICS features represent the single most important component of such classifiers.
Improving Efficiency and Quality in a Computerized ICU (1988)

We developed and validated a relatively easy-to-administer survey that was able to detect substantial variability in organizational culture across different hospitals and may be useful in measuring hospital culture and evaluating changes in culture over time as part performance improvement efforts.
When the Circadian Clock Becomes a Ticking Time Bomb (2012)

"When the Circadian Clock Becomes a Ticking Time Bomb." Chronobiology International, 29(9), pp. 1286–1287
An ethylene-linked catechol/8-hydroxyquinoline derivative and its dinuclear gallium(III) complex (2000)

The ethylene-linked catechol/8-hydroxyquinoline derivative 7-H3 is prepared in a three step procedure by Sonogashira–Hagihara coupling of (2,3-dimethoxyphenyl)acetylene (1) and 7-bromo-8-methoxyquinoline (2), followed by reduction of the alkyne and final ether cleavage. The unsymmetric type II triple-stranded dinuclear helicate M3[Ga2(7)3] (M=Na, K) is obtained with gallium(III) ions in the presence of potassium or sodium carbonate.
Crystal structure of poly(ω‐pentadecalactone) (2003)

Abstract The crystal structure of poly(ω‐pentadecalactone) (PPDL) synthesized by enzyme‐catalyzed polymerization was determined by full‐profile refinement. A pseudo‐orthorombic monoclinic unit cell with dimensions a = 7.49(1), b = 5.034(9), and c = 20.00(4)Å (fiber axis), and α = 90.06(4)° hosts two monomeric units belonging to polymer chains with opposite orientation, according to the P2 1 space‐group symmetry. A close similarity to the crystal structure of poly(ϵ‐caprolactone) was evident. However, the even number of backbone atoms in the monomer unit of PPDL leads to a lower crystal symmetry. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1009–1013, 2003
Investigation of the Lean Stable Limit of a Barrier Discharge Igniter and of a Streamer-Type Corona Igniter at Different Engine Loads in a Single-Cylinder Research Engine (2020)

Currently, the Radio-Frequency Corona Ignition systems represent an important solution for reducing pollutant emissions and fuel consumption related to Internal Combustion Engines, while at the same time ensuring high performance. These igniters are able to extend the lean stable limit by increasing the early flame growth speed. Kinetic, thermal, and ionic effects, together with the peculiar configuration of the devices, allow the combustion process to start in a wider region than the one involved with the traditional spark. In this work two corona igniters, namely a Barrier Discharge Igniter and a Corona Streamer Igniter, were tested in a single-cylinder research engine fueled with gasoline at different engine loads in order to investigate the igniters’ performance through indicated analysis and pollutant emissions analysis. For each operating point, the devices’ control parameters were set to ensure maximum energy releasement into the medium with the aim of investigating, at the extreme operating conditions, the capability of the devices to extend the lean stable limit of the engine. The corona igniters were tested on a constant volume calorimeter as well, reproducing the engine pressure conditions at the corresponding ignition timing. The target was to give an estimation of the thermal energy released during the discharge and then to compare their capability to provide high-stability energy.
Abstract B207: Prostate specific membrane antigen is a diagnostic marker of response to allosteric androgen receptor inhibition (2009)

Abstract Molecular imaging in oncology aims to complement the growing repertoire of chemotherapies with noninvasive diagnostic tools to measure pharmacodynamics and improve predictions of disease response. In prostate cancer, several chemotherapeutic strategies have been developed to inhibit androgen receptor (AR) function, and currently show promise in treating advanced, castration resistant disease. Among these, competitive inhibitors of steroid agonist/receptor interactions have been effectively staged with fluorine-18-fluoro-5α-dihydrotestosterone, an AR agonist compatible with quantitative PET imaging. However, some allosteric inhibitors of AR do not impact agonist/receptor interaction (or AR stability) and currently cannot be evaluated with a quantitative imaging technology. We address this problem here by presenting evidence that prostate specific membrane antigen is a diagnostic marker of allosteric AR inhibition. In culture or in xenograft models of LNCaP, 22Rv1, LAPC4, and VCaP, PSMA is repressed by androgen treatment. Ablation of AR with siRNA inhibits the hormone-mediated suppression of PSMA, directly implicating AR in the mechanism. We further show that PSMA suppression is antagonized by several competitive and allosteric AR inhibitors. Finally, we conducted a pilot study with 22Rv1 xenografts to demonstrate that 64Cu-DOTA-J591, a monoclonal antibody designed for clinical PET imaging of PSMA, quantitatively detects hormone-mediated PSMA suppression. Collectively, these results promote the use of PSMA imaging reagents in the clinic to stage allosteric AR inhibitors. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B207.
Fabrication of Graphene-Metal Transparent Conductive Nanocomposite Layers for Photoluminescence Enhancement (2019)

In this work, the synthesis and characterization ofgraphene-metal nanocomposite, a transparent conductive layer, is examined. This transparent conductive layer is named graphene-Ag-graphene (GAG), which makes full use of the high electron mobility and high conductivity characteristics of graphene, while electromagnetically induced transparency (EIT) is induced by Ag nanoparticles (NPs). The nanocomposite preparation technique delivers three key parts including the transfer of the first layer graphene, spin coating of Ag NPs and transfer of the second layer of graphene. The GAG transparent conductive nanocomposite layer possess a sheet resistance of 16.3 ohm/sq and electron mobility of 14,729 cm<sup>2</sup>/(v s), which are superior to single-layer graphene or other transparent conductive layers. Moreover, the significant enhancement of photoluminescence can be ascribed to the coupling of the light emitters in multiple quantum wells with the surface plasmon Ag NPs and the EIT effect.
Dual-Mobility Implants and Constrained Liners in Revision Total Hip Arthroplasty (2021)

Both CL and DM bearings have high aseptic failure rates at intermediate term follow-up after revision THA. CL did show a higher risk of failure than DM bearings, but it was not statistically significant with the numbers available for this study. Further prospective studies are needed to determine the optimal treatment for recurrent instability.
Alterations of BRMS1-ARID4A Interaction Modify Gene Expression but Still Suppress Metastasis in Human Breast Cancer Cells (2008)

The BRMS1 metastasis suppressor interacts with the protein AT-rich interactive domain 4A (ARID4A, RBBP1) as part of SIN3.histone deacetylase chromatin remodeling complexes. These transcriptional co-repressors regulate diverse cell phenotypes depending upon complex composition. To define BRMS1 complexes and their roles in metastasis suppression, we generated BRMS1 mutants (BRMS1(mut)) and mapped ARID4A interactions. BRMS1(L174D) disrupted direct interaction with ARID4A in yeast two-hybrid genetic screens but retained an indirect association with ARID4A in MDA-MB-231 and -435 human breast cancer cell lines by co-immunoprecipitation. Deletion of the first coiled-coil domain (BRMS1(DeltaCC1)) did not disrupt direct interaction in yeast two-hybrid screens but did prevent association by co-immunoprecipitation. These results suggest altered complex composition with BRMS1(mut). Although basal transcription repression was impaired and the pro-metastatic protein osteopontin was differentially down-regulated by BRMS1(L174D) and BRMS1(DeltaCC1), both down-regulated the epidermal growth factor receptor and suppressed metastasis in MDA-MB-231 and -435 breast cancer xenograft models. We conclude that BRMS1(mut), which modifies the composition of a SIN3.histone deacetylase chromatin remodeling complex, leads to altered gene expression profiles. Because metastasis requires the coordinate expression of multiple genes, down-regulation of at least one important gene, such as the epidermal growth factor receptor, had the ability to suppress metastasis. Understanding which interactions are necessary for particular biochemical/cellular functions may prove important for future strategies targeting metastasis.
Reactions of sulfides with S‐330, a potential decontaminant of sulfur mustard in formulations (1999)

Because the vesicant sulfur mustard (HD) remains a major chemical threat from either domestic terrorists or countries in conflict, topical preparations are being evaluated as protectants from HD exposure. The objective of this study was to evaluate the effectiveness of chloroamide S-330 as a potential reactive component in topical formulations. Therefore, the rate, mechanism and by-products of the oxidation reactions of sulfides by S-330 in solvent media or specific formulation vehicles were investigated. Using NMR, LC, LC-MS and GC-MS, the reactions of S-330 with HD, dibutyl sulfide (DBS) and methyl phenyl sulfide (MPS) were studied in acetonitrile, chloroform and perfluoropolyether (PFPE) oil. The oxidation of the three sulfides with S-330 was very rapid and completed in <4 min in acetonitrile-water or PFPE oil, but the rates of reaction in chloroform were significantly slower. In a large excess of S-330, the major products resulted from chlorination of the side chains. At a high HD/S-330 ratio, the major product was HD sulfoxide. Under both conditions, only a trace of HD sulfone, also a blistering agent, was observed. Reactions with DBS and MPS primarily gave sulfoxides and sulfones, with less side-chain chlorination. The chloroamide S-330 appeared to be a rapid and effective decontaminant of HD in either polar media or in a PFPE oil. The two alkyl and aryl sulfides are suitable simulants of HD for the initial screening and evaluation of S-330 or other similar oxidizing agents.
Influence of Surface Characteristics of TiO2 Coatings on the Response of Gingival Cells: A Systematic Review of In Vitro Studies (2023)

The soft tissue-implant interface requires the formation of epithelium and connective tissue seal to hinder microbial infiltration and prevent epithelial down growth. Nanoporous titanium dioxide (TiO<sub>2</sub>) surface coatings have shown good potential for promoting soft tissue attachment to implant surfaces. However, the impact of their surface properties on the biological response of gingival cells needs further investigation. This systematic review aimed to investigate the cellular behavior of gingival cells on TiO<sub>2</sub>-implant abutment coatings based on in vitro studies. The review was performed to answer the question: "How does the surface characteristic of TiO<sub>2</sub> coatings influence the gingival cell response in in vitro studies?". A search in MEDLINE/PubMed and the web of science databases from 1990 to 2022 was performed using keywords. A quality assessment of the studies selected was performed using the SciRAP method. A total of 11 publications were selected from the 289 studies that fulfilled the inclusion criteria. The mean reporting and methodologic quality SciRAP scores were 82.7 ± 6.4/100 and 87 ± 4.2/100, respectively. Within the limitations of this in vitro systematic review, it can be concluded that the TiO<sub>2</sub> coatings with smooth nano-structured surface topography and good wettability improve gingival cell response compared to non-coated surfaces.
Scheduling of Operations in Quantum Compiler (2020)

When scheduling quantum operations, a shorter overall execution time of the resulting schedule yields a better throughput and higher fidelity output. In this paper, we demonstrate that quantum operation scheduling can be interpreted as a special type of job-shop problem. On this basis, we provide its formulation as Constraint Programming while taking into account commutation between quantum operations. We show that this formulation improves the overall execution time of the resulting schedules in practice through experiments with a real quantum compiler and quantum circuits from two common benchmark sets.
Surface PD evolution of conventional and nanocomposite enamels (2016)

The stator motor windings of low voltage rotating electrical machines are usually insulated by organic enamel. When the motors are supplied by power electronic converters, the stator insulation system is subjected to pulsed voltage waveform and a fast degradation of the insulating system could occur. In fact, it is possible that partial discharge (PD) activity incepts leading to the deterioration of the insulating system. In this work the evolution of partial discharges is monitored when twisted pairs of copper enameled wires are subjected to sinusoidal and pulsed PWM-like voltage waveform. Conventional and nanocomposite enamels have been considered monitoring the behavior during the degradation processes evidencing the main peculiarities of each enamel when subjected to the PD action.
Real-Time Distributed Sensor-Assisted mHealth Applications on the Internet-of-Things (2012)

Existing sensor-assisted mHealth applications would benefit from large-scale sharing of sensor information in real-time. Existing communication solutions are however limited in this respect, because of centralized application-level communication. In response to this, we presents a distributed communication solution for mHealth applications which circumvents these limitations. Our Internet-of-Things architecture enables mHealth applications to utilize information from sensors and wireless sensor networks via a peer-to-peer overlay, where sensor information is organized in an information model which is stored in the overlay itself. We present a proof-of-concept application and evaluation results regarding the architecture's real-time capabilities. The results indicate that a fully distributed architecture can support real-time sensing in mHealth applications and the support is available as an open source platform, MediaSense. Current work is focused on evaluating scalability in very large scale scenarios using field trials.
Joint migration inversion: Simultaneous determination of velocity fields and depth images using all orders of scattering (2016)

The future in seismic exploration and seismic monitoring is the inclusion of all orders of scattering in the imaging and inversion algorithms. Using the full wavefield in an inversion process allows us to surpass imprints provided by incomplete acquisition and provide more accurate information on the subsurface, as noise becomes signal. We describe an inversion process that does not use the standard parameters from finite-difference-type modeling (being local velocity and density) but that describes the seismic data in terms of elastic reflectivity operators and propagation operators. With these operators, our full-wavefield modeling process builds the complete two-way seismic response. A major advantage of our alternative to the traditional full-waveform inversion methodology is that reflectivity operators are traveltime-free and propagation operators are scattering-free, making the inversion problem significantly more linear. A major advantage of our algorithm is (1) that multiples are utilized to improve both image and velocity accuracy, and (2) that both image and velocities are utilized to make a contribution in the nonlinear migration process. Hence, in joint migration inversion, multiples have a twofold active role.
Non-contact microdrilling of mouse zona pellucida with an objective-delivered 1.48-μm diode laser (1996)

The microdrilling procedure can generate standardized holes in mouse ZP, without any visible side effects. The hole formation can be explained by a local photothermolysis of the protein matrix.
Structure–Activity Relationship in the Leucettine Family of Kinase Inhibitors (2021)

The protein kinase DYRK1A is involved in Alzheimer's disease, Down syndrome, diabetes, viral infections, and leukemia. Leucettines, a family of 2-aminoimidazolin-4-ones derived from the marine sponge alkaloid Leucettamine B, have been developed as pharmacological inhibitors of DYRKs (dual specificity, tyrosine phosphorylation regulated kinases) and CLKs (cdc2-like kinases). We report here on the synthesis and structure-activity relationship (SAR) of 68 Leucettines. Leucettines were tested on 11 purified kinases and in 5 cellular assays: (1) CLK1 pre-mRNA splicing, (2) Threonine-212-Tau phosphorylation, (3) glutamate-induced cell death, (4) autophagy and (5) antagonism of ligand-activated cannabinoid receptor CB1. The Leucettine SAR observed for DYRK1A is essentially identical for CLK1, CLK4, DYRK1B, and DYRK2. DYRK3 and CLK3 are less sensitive to Leucettines. In contrast, the cellular SAR highlights correlations between inhibition of specific kinase targets and some but not all cellular effects. Leucettines deserve further development as potential therapeutics against various diseases on the basis of their molecular targets and cellular effects.
Omega-9 Modifies Viscoelasticity and Augments Bone Strength and Architecture in a High-Fat Diet-Fed Murine Model (2022)

The influence of diet on the development of osteoporosis is significant and not fully understood. This study investigated the effect of diets of varying lipid profiles and ω-3, ω-6 and ω-9 composition on the structural and mechanical properties of bone. The hypothesis studied was that a diet high in saturated fat would induce osteoporosis and produce an overall increased detrimental bony response when compared with a diet high in unsaturated ω-6, or ω-9. Male C57BL/6J mice were fed either a control diet, 50:50 mix (saturated:unsaturated) high in ω-9 (HFD50:50), a diet high in saturated fat (HSF) or a polyunsaturated fat diet high in ω-6 (PUFA) over an 8-week duration. Tibiae were retrieved and evaluated using DMA, 3-point-bending, histomorphometry, and microCT. Mice fed a HSF diet displayed key features characteristic of osteoporosis. The loss tangent was significantly increased in the HFD50:50 diet group compared with control (p = 0.016) and PUFA-fed animals (p = 0.049). HFD50:50-fed mice presented with an increased viscous component, longer tibiae, increased loss modulus (p = 0.009), and ultimate stress, smaller microcracks (p < 0.001), and increased trabecular width (p = 0.002) compared with control animals. A diet high in ω-9 resulted in an overall superior bone response and further analysis of its role in bone health is warranted.
Tremor suppression by FES using closed-loop control (2012)

In this work tremor suppression by functional electrical stimulation is described, using\nrepetitive and iterative learning control algorithm. Multibody and muscle dynamics are\nexploited to obtain models of the human arm. Furthermore, for first evidence and realistic\nfeasibility the wrist joint is chosen for tremor suppression. System parameters are obtained\nby measurements and frequency decomposition. For simulations robust high order repetitive\ncontrol, optimality-based repetitive control and norm-based iterative learning control are\napplied. For experiments optimality-based repetitive control is applied, using a wrist setup\nfor signal processing. The simulations and experiments are executed for tremor stabilization\nand reference tracking.
Fabrication on GaAs optoelectronic integration of a surface-emitting laser and a MESFET (1993)

Optoelectronic-integrated-circuit (OEIC) transmitters,1 which integrate laser diodes and driving circuits on a single chip, have great potential advantages over hybrid circuits in terms of speed, functionality, reliability, scalability, and cost. The major difficulties involved in OEIC transmitter fabrication lie not only in the incompatibility of material parameters and device structures, but also in the requirement of having a very low threshold current for minimizing heat dissipation on the chip and the necessity of facet formation by a cleaving or etching process, which limits the layout freedom and scalability of the entire circuit. The vertical-cavity surface-emitting laser (SEL) developed in recent years2 has many advantageous features, such as a very low threshold current (&lt;2 mA),3 single-mode operation,4 a small device area, and, in particular, no need for mirror formation and a two-dimensional (2-D) integration capability. Thus it is the best light source for 2-D OEIC transmitter arrays. In this paper we present the first demonstration, to our knowledge, of the monolithic integration of a SEL and a MESFET.