gebhart/patrepeval huggingface dataset:
Isolation of novel microbial 3 alpha-, 3 beta-, and 17 beta-hydroxysteroid dehydrogenases. Purification, characterization, and analytical applications of a 17 beta-hydroxysteroid dehydrogenase from an Alcaligenes sp. (1985)

By selecting for growth on testosterone or estradiol-17 beta as the only source of organic carbon, we have isolated a number of soil microorganisms which contain highly active and novel, inducible, NAD-linked 3 alpha-, 3 beta-, and 17 beta-hydroxysteroid dehydrogenases. Such enzymes are suitable for the microanalysis of steroids and of steroid-transforming enzymes, as well as for performing stereoselective oxidations and reductions of steroids. Of particular interest among these organisms is a new species of Alcaligenes containing 17 beta-hydroxysteroid dehydrogenase, easily separable from 3 beta-hydroxysteroid dehydrogenase. Unlike any of the other isolated organisms, this Alcaligenes sp. contained no 3 alpha-hydroxysteroid dehydrogenase activity. A large-scale purification (763-fold) to homogeneity of the major induced 17 beta-hydroxysteroid dehydrogenase was achieved by ion-exchange, hydrophobic, and affinity chromatographies. The enzyme has high specific activity for the oxidation of testosterone (Vmax = 303 mumol/min/mg of protein; Km = 3.6 microM) and reacts almost equally well with estradiol-17 beta (Vmax = 356 mumol/min/mg; Km = 6.4 microM). It consists of apparently identical subunits (Mr = 32,000) and exists in polymeric form under nondenaturing conditions (Mr = 68,000 by gel filtration and 86,000 by polyacrylamide gel electrophoresis). The isoelectric point is pH 5.1. The enzyme is almost completely specific for 17 beta-hydroxysteroids which may be delta 5-olefins or ring A phenols or have cis or trans A/B ring fusions. Substituents at other positions are tolerated, although the presence of a 16 alpha- or 16 beta-hydroxyl group blocks the oxidation of the 17 beta-hydroxyl function. 3 beta-Hydroxysteroids (A/B ring fusion trans, but not cis, or delta 5-olefins) are very poor substrates. The application of this highly active, specific, and stable 17 beta-hydroxysteroid dehydrogenase to the microestimation of steroids by enzymatic cycling of nicotinamide nucleotides and for the stereospecific oxidation of steroids is demonstrated.
New microRNA biotechnology as an in vivo therapeutic molecule to inhibit cancer (2018)

MicroRNAs (miRs) are biomarkers of cancer development and progression, they regulate cell fate, stemness and embryonic development. It is well-known that miRs play a role in cancer and are associated with numerous types of cancer as either oncogenes or tumor-suppressor genes. We developed the Plasmid-based microRNA Inhibitor System (PMIS), and it is the only miR inhibitor that can be used to generate transgenic mice to study the role of miRs during embryonic development and as disease models. The PMIS is very stable, efficient, has high specificity and affinity for specific miRs and is not toxic to cells or animals. We focused on miR-210 as it is increased in human colon cancer. The PMIS-miR-210 lentivirus construct and plasmid both express GFP. We made PMIS-miR-210 and PMIS-vector only stably transduced human SW620 colon cancer cell lines to determine the effect of inhibiting miR-210 on cell growth and phenotypes. The cells were transduced with the lentivirus and GFP expressing cells were FACS sorted and analyzed for growth. The PMIS-miR-210 cells proliferated very slowly (25% of the rate of PMIS-vector only cells). RNA-sequencing experiments and bioinformatics analyses revealed several new genes targeted by miR-210 and new pathways in colon tumor progression. We have identified a miR regulatory loop controlling the expression of other miRs. Nude mice were injected with PMIS-miR-210 or PMIS-vector stably expressing human colon cancer cells and 5 out of 8 mice with colon cancer cells expressing PMIS-miR-210 did not form tumors compared to the controls (PMIS-vector, 8 of 8 had tumors). To demonstrate the effectiveness of PMIS-miR-210 as a therapeutic, nude mice were injected with colon cancer cells and tumors were allowed to form (3 weeks), mice were then injected with naked plasmid DNA PMIS-miR-210 or vector control into and surrounding the solid tumor mass at several concentrations. No tumors were observed in 6 of the 10 mice injected with PMIS-miR-210 and the other 4 mice had small tumors compared to controls after 2 weeks of further growth (PMIS-vector, 10 of 10 had no effect on tumor growth). This is the first time that direct injection of a naked plasmid DNA expressing the PMIS microRNA inhibitor reduced or completely inhibited tumor growth, without using toxic delivery systems. The PMIS has great potential as a new therapeutic biological drug for cancer treatments. Support or Funding Information This work was supported by National Institutes of Health grant DE026433. A) Transduced colon cancer cells with either PMIS empty vector or PMIS-miR-210 were injected into nude mice and after 4 weeks the tumors were analyzed. B,C) Untreated colon cancer cells were put into nude mice and after 3 weeks, tumors were injected with PMIS empty vector or PMIS-miR-210, 2 weeks later the tumors were harvested and analyzed. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Endochin Optimization: Structure−Activity and Structure−Property Relationship Studies of 3-Substituted 2-Methyl-4(1<i>H</i>)-quinolones with Antimalarial Activity (2010)

Since the 1940s endochin and analogues thereof were known to be causal prophylactic and potent erythrocytic stage agents in avian models. Preliminary screening in a current in vitro assay identified several 4(1H)-quinolones with nanomolar EC(50) against erythrocytic stages of multidrug resistant W2 and TM90-C2B isolates of Plasmodium falciparum. Follow-up structure-activity relationship (SAR) studies on 4(1H)-quinolone analogues identified several key features for biological activity. Nevertheless, structure-property relationship (SPR) studies conducted in parallel revealed that 4(1H)-quinolone analogues are limited by poor solubilities and rapid microsomal degradations. To improve the overall efficacy, multiple 4(1H)-quinolone series with varying substituents on the benzenoid quinolone ring and/or the 3-position were synthesized and tested for in vitro antimalarial activity. Several structurally diverse 6-chloro-2-methyl-7-methoxy-4(1H)-quinolones with EC(50) in the low nanomolar range against the clinically relevant isolates W2 and TM90-C2B were identified with improved physicochemical properties while maintaining little to no cross-resistance with atovaquone.
InGaAsN solar cells with 1.0 eV band gap, lattice matched to GaAs (1999)

The design, growth by metalorganic chemical vapor deposition, and processing of an In0.07Ga0.93As0.98N0.02 solar cell, with 1.0 eV band gap, lattice matched to GaAs is described. The hole diffusion length in annealed, n-type InGaAsN is 0.6–0.8 μm, and solar cell internal quantum efficiencies &gt;70% are obtained. Optical studies indicate that defects or impurities, from InGaAsN doping and nitrogen incorporation, limit solar cell performance.
High temperature ultrahigh vacuum infrared window seal (1981)

An alkali halide-to-metal high vacuum window sealing method is described which is usable to 275 °C with a combined leak plus outgas rate of &lt;3×10−10 atm-cm3/s. This seal is usable for static laser photolysis of low pressure, reactive gaseous samples, since the only materials to come into sample contact are stainless steel, lead, and the alkali halide window. This method has also been successfully used to seal stainless steel to stainless steel.
Optimization problem in quantum cryptography (2003)

A complete optimization was recently performed, yielding the maximum information gain by a general unitary entangling probe in the four-state protocol of quantum cryptography. A larger set of optimum probe parameters was found than was known previously from an incomplete optimization. In the present work, a detailed comparison is made between the complete and incomplete optimizations. Also, a new set of optimum probe parameters is identified for the four-state protocol.
<sup>18</sup>F-Trifluoroborate Derivatives of [Des-Arg<sup>10</sup>]Kallidin for Imaging Bradykinin B1 Receptor Expression with Positron Emission Tomography (2015)

Bradykinin B1 receptor (B1R) is involved in pain and inflammation pathways and is upregulated in inflamed tissues and cancer. Due to its minimal expression in healthy tissues, B1R is an attractive target for the development of therapeutic agents to treat inflammation, chronic pain, and cancer. The goal of this study is to synthesize and compare two (18)F-labeled peptides derived from potent B1R antagonists B9858 and B9958 for imaging B1R expression with positron emission tomography (PET). Azidoacetyl-B9858 2 and azidoacetyl-B9958 3 were synthesized by a solid-phase approach and subsequently clicked to ammoniomethyl-trifluoroborate (AmBF3)-conjugated alkyne 1 to obtain AmBF3-B9858 and AmBF3-B9958, respectively. AmBF3-B9858 and AmBF3-B9958 bound B1R with high affinity, with Ki values at 0.09 ± 0.08 and 0.46 ± 0.03 nM, respectively, as measured by in vitro competition binding assays. (18)F labeling was performed via an (18)F-(19)F isotope exchange reaction. The radiofluorinated tracers were obtained within a synthesis time of 30 min and with 23-32% non-decay-corrected radiochemical yield, >99% radiochemical purity, and 43-87 GBq/μmol specific activity at the end of the synthesis. PET imaging and biodistribution studies were carried out in mice bearing both B1R-positive (B1R(+)) HEK293T::hB1R and B1R-negative (B1R(-)) HEK293T tumors. Both tracers cleared rapidly from most organs/tissues, mainly through the renal pathway. High uptake in B1R(+) tumors ((18)F-AmBF3-B9858: 3.94 ± 1.24% ID/g, tumor-to-muscle ratio 21.3 ± 4.33; (18)F-AmBF3-B9958: 4.20 ± 0.98% ID/g, tumor-to-muscle ratio 48.6 ± 10.7) was observed at 1 h postinjection. These results indicate that (18)F-AmBF3-B9858 and (18)F-AmBF3-B9958 are promising agents for the in vivo imaging of B1R expression with PET.
Multimode Imaging in the Thermal Infrared for Chemical Contrast Enhancement. Part 2: Simulation Driven Design (2010)

We present a simulation-driven process to design an infrared camera system that is tuned to specific analytes of interest based on "molecular factor computing". There are many factors involved in optimizing discrimination using optical filtering aids, including, but not limited to, the detector response, optical throughput of the system, optical properties of the samples, and optical properties of the materials for sensitizing films/filters. There are nearly infinite possible setups for the system, which means it is neither cost nor time efficient to physically test each one. In lieu of this, we developed routines in MATLAB (The Mathworks, Natick, MA) that simulate the camera output, per pixel, given specific conditions. Beginning with measured spectra of calibration samples or standards and using an objective function or figure of merit (FOM) to measure simulated performance, these routines evaluate large numbers of combinations of chemical films as filters for discrimination based on linear discriminant analysis (LDA). In this study, the FOM was the Fisher ratio between a neat fabric and one stained with either a polymer film or blood.
Noniterative method for two-lead fetal ECG extraction (2005)

We propose a novel noniterative technique for fetal electrocardiogram extraction. The polynomial networks technique is used to nonlinearly map the MECG signal recorded at the thorax area to the ECG signals recorded at the abdomen. The FECG component is then extracted by subtracting the nonlinearly mapped MECG component from the abdominal ECG signal. Visual test results obtained from real ECG signals show that the proposed algorithm is capable of reliably extracting the FECG from two leads only. The visual quality of the FECG extracted by the proposed technique is found to meet or exceed that of published results using other techniques.
A recommender system for efficient discovery of new anomalies in large-scale access logs (2016)

We present a novel, non-standard recommender system for large-scale security policy management(SPM). Our system Helios discovers and recommends unknown and unseen anomalies in large-scale access logs with minimal supervision and no starting information on users and items. Typical recommender systems assume availability of user- and item-related information, but such information is not usually available in access logs. To resolve this problem, we first use discrete categorical labels to construct categorical combinations from access logs in a bootstrapping manner. Then, we utilize rank statistics of entity rank and order categorical combinations for recommendation. From a double-sided cold start, with minimal supervision, Helios learns to recommend most salient anomalies at large-scale, and provides visualizations to security experts to explain rationale behind the recommendations. Our experiments show Helios to be suitable for large-scale applications: from cold starts, in less than 60 minutes, Helios can analyze roughly 4.6 billion records in logs of 400GB with about 300 million potential categorical combinations, then generate ranked categorical combinations as recommended discoveries. We also show that, even with limited computing resources, Helios accelerates unknown and unseen anomaly discovery process for SPM by 1 to 3 orders of magnitude, depending on use cases. In addition, Helios' design is flexible with metrics and measurement fields used for discoveries and recommendations. Overall, our system leads to more efficient and customizable SPM processes with faster discoveries of unseen and unknown anomalies.
Systemic delivery of therapeutics to neuronal tissues: a barrier modulation approach (2010)

The purpose of this review is to describe a new therapeutic strategy for systemic delivery of low-molecular-mass therapeutics to neuronal tissues.
Pattern based mask process correction: impact on data quality and mask writing time (2005)

The continuous drive of the semiconductor industry towards smaller features sizes requires mask manufacturers to achieve ever tighter tolerances for the most critical dimensions on the mask. CD uniformity requires particularly tight control. Equipment manufacturers and process engineers target their development to support these requirements. But as numerous publications indicate, more sophisticated data correction methods are still employed to compensate for shortcomings in equipment and process or to account for the boundary conditions in some layouts that contribute to process deviations. Among the corrected effects are proximity and linearity effects, fogging and etch effects, and pattern fidelity. Different designs vary by pattern size distribution as well as by pattern density distribution. As the implementation of corrections for optical proximity effects in wafer lithography has shown, breaking up the original polygons in the design layout for selective and environment-aware correction yields increased data volumes and can have an impact on the data quality of the mask writing data. The paper investigates the effect of various correction algorithms specifically deployed for mask process effects on top of wafer process related corrections. The impact of MPC flows such as rule-based linearity and proximity correction and density-based long range effect correction on the metrics for data preparation and mask making is analyzed. Experimental data on file size, shot count and data quality indicators including small figure counts are presented for different correction approaches and a variety of correction parameters.
SUMO4 and its role in type 1 diabetes pathogenesis (2007)

Susceptibility to type 1 diabetes (T1D) is determined by interactions of multiple genes with unknown environmental factors. Despite the characterization of over 20 susceptibility regions for T1D, identification of specific genes in these regions is still a formidable challenge. In 2004, we first reported the cloning of a novel, small ubiquitin-like modifier (SUMO) gene, SUMO4, in the IDDM5 interval on chromosome 6q25, and presented strong genetic and functional evidence suggesting that SUMO4 is a T1D susceptibility gene. Subsequent studies have consistently confirmed this association in multiple Asian populations despite controversial observations in Caucasians. In this review, we will update the genetic evidence supporting SUMO4 as a T1D susceptibility gene and discuss the possible explanations for the discrepant associations observed in Caucasians. We will then discuss the mechanisms through which SUMO4 contributes to the pathogenesis of T1D.
Follistatin like protein (FSTL-1) levels are elevated in acute Kawasaki Disease and may differentiate between patients with and without aneurysm formation (2012)

Kawasaki Disease is the most common vasculitis of childhood, and carries considerable morbidity with risk of development of coronary artery aneurysms. Serological predictors of the development of coronary artery aneurysms have not yet been found. FSTL-1 is a proinflammatory protein which is produced by mesenchymal tissue, including cardiac myocytes, and has been found to be elevated in inflammatory disorders such as Juvenile Idiopathic Arthritis. The current study was designed to determine if plasma levels of FSTL-1 correlate with the development of Kawasaki Disease and development of coronary artery aneurysms.
Optical frequency combs from high-order sideband generation (2018)

We report on the generation of frequency combs from the recently-discovered phenomenon of high-order sideband generation (HSG). A near-band gap continuous-wave (cw) laser with frequency f<sub>NIR</sub> was transmitted through an epitaxial layer containing GaAs/AlGaAs quantum wells that were driven by quasi-cw in-plane electric fields F<sub>THz</sub> between 4 and 50 kV/cm oscillating at frequencies f<sub>THz</sub> between 240 and 640 GHz. Frequency combs with teeth at f<sub>sideband</sub> = f<sub>NIR</sub> + nf<sub>THz</sub> (n even) were produced, with maximum reported n > 120, corresponding to a maximum comb span > 80 THz. Comb spectra with the identical product f<sub>THz</sub> × F<sub>THz</sub> were found to have similar spans and shapes in most cases, as expected from the picture of HSG as a scattering-limited electron-hole recollision phenomenon. The HSG combs were used to measure the frequency and linewidth of our THz source as a demonstration of potential applications.
Multi-Echo Quantitative Susceptibility Mapping for Strategically Acquired Gradient Echo (STAGE) Imaging (2020)

This study shows that using a data fidelity term and structural constraints results in reduced noise and streaking artifacts while preserving structural details. Furthermore, the use of STAGE imaging with multi-echo and multi-flip data helps to improve the signal-to-noise ratio in QSM data and yields less artifacts.
Variable duty cycle experiments in pulsed-impingement heat transfer (1996)

An experimental study was conducted to determine the effect of pulsation duty cycle on the heat transfer rates between an axisymmetric jet of air and a flat impingement surface. In all experiments the jet was heated and a pulsed flow field was generated using a high-speed solenoid valve. The duty cycle of the valve (on time divided by total cycle time) was adjusted using a repeat cycle timer and results are presented for duty cycles ranging from 0.20 to 0.73. Heat transfer rates to a finite area disk have been found to vary by up to 25% depending upon the duty cycle of the flow and the jet to plate spacing. The highest heat transfer rates are associated with the pulsed case with a large duty cycle. Numerical simulations of this experiment are being developed concurrently. This dual-mode approach, allows experimental validation of the numerical model followed by numerical experimentation in regimes not attainable with the experiment.
Improved spoken query transcription using co-occurrence information (2011)

Spoken queries are a natural medium for searching the Mobile Web. Language modeling for voice search recognition offers different challenges compared to more conventional speech applications. The challenges arise from the fact that spoken queries are usually a set of keywords and do not have a syntactic and grammatical structure. This paper describes a cooccurrence based approach to improve the accuracy of voice queries automatic transcription. With the right choice of scoring function and co-occurrence level, we show that co-occurrence information gives a 2% relative accuracy improvement over a state of the art system.
Cloning in Saccharomyces cerevisiae of a cycloheximide resistance gene from the Candida maltosa genome which modifies ribosomes (1986)

We have previously shown that cycloheximide resistance can be induced in a strain of Candida maltosa by modifying ribosomes (M. Takagi, S. Kawai, Y. Takata, N. Tanaka, M. Sunairi, M. Miyazaki, and K. Yano, J. Gen. Appl. Microbiol. 31:267-275, 1985). The present paper describes the cloning of the gene involved in this resistance (designated RIM-C for ribosome modification by cycloheximide) by using a host-vector system of Saccharomyces cerevisiae.
An <i>Arabidopsis thaliana</i> high-affinity molybdate transporter required for efficient uptake of molybdate from soil (2007)

Molybdenum (Mo) is a trace element essential for living organisms, however no molybdate transporter has been identified in eukaryotes. Here, we report the identification of a molybdate transporter, MOT1, from Arabidopsis thaliana. MOT1 is expressed in both roots and shoots, and the MOT1 protein is localized, in part, to plasma membranes and to vesicles. MOT1 is required for efficient uptake and translocation of molybdate and for normal growth under conditions of limited molybdate supply. Kinetics studies in yeast revealed that the K(m) value of MOT1 for molybdate is approximately 20 nM. Furthermore, Mo uptake by MOT1 in yeast was not affected by coexistent sulfate, and MOT1 did not complement a sulfate transporter-deficient yeast mutant strain. These data confirmed that MOT1 is specific for molybdate and that the high affinity of MOT1 allows plants to obtain scarce Mo from soil.
Development of Blending Chart for Different Degrees of Blending for Reclaimed Asphalt Pavements in HMA (2011)

The demand to utilize higher percentages of reclaimed asphalt pavement (RAP) in the construction of hot mix asphalt (HMA) pavements continues to rise. Utilization of RAP in HMA is an environmentally friendly and cost effective method of recycling. At high percentage of RAP properties of RAP binder and its interaction with virgin binder plays critical role. Researchers have consistently shown that when RAP is mixed with virgin binder and aggregates, partial blending occurs, that is, something between 100% blending and the "black rock" effect occurs. Impact of partial blending on new virgin binder content is apparent which may cause under-asphalted mixture, resulting in poor pavement performance. Also influence of partial blending on final grade of RAP mix and allowable percentage of RAP has not been evaluated. The purpose of this paper is to develop the blending chart for different degree of blending to study the impact of partial blending on final grade of blended binder. To achieve the objective, blending chart for 100%, 70% and 50% RAP has been developed for PG 70-28 and PG 58-28 binder by carrying out binder study.
Xenograft of Microencapsulated Sertoli Cells Reverses T1DM in NOD Mice by Inducing Neogenesis of Beta-Cells (2010)

SCs, enveloped in barium alginate-based microcapsules, showed no long-term loss of their functional and morphological properties in vitro or in vivo. Xenograft of microencapsulated-SC-induced reversal of spontaneous diabetes in the majority of the treated NOD mice, based on SC-related powerful immunomodulatory and pro-β-cell regeneration properties.
Light-induced self-assembly of nanofibers inside liposomes (2008)

Spatially confined self-assembly of peptide amphiphile nanofibers inside liposomes is triggered by light.