gebhart/patrepeval huggingface dataset:
Sites of Estrogen Uptake in Embryonic Trachemys Scripta, a Turtle with Temperature-Dependent Sex Determination1 (1992)

Female sex determination can be induced in embryonic red-eared slider turtles (Trachemys scripta) by exogenous estrogen, as well as by incubation at warm temperature. In the present study, estrogen target areas were identified in embryos before (stage 15), during (stage 18), and after (stage 22) the critical period for sex determination. Both hyperfilm and emulsion autoradiography were used to localize tritium accumulation after the injection of radiolabeled 17 beta-estradiol. Site-specific tritium-labelling was found at all stages, notably in the mesonephros at stage 15, in the mesonephros and oviduct at stage 18, and in the mesonephros, oviduct, and the interrenal gland at stage 22. Few if any cells in the gonad were tritium-labeled at any stage. The large number of estrogen-concentrating cells in the mesonephros and interrenal and the lack of binding to gonadal tissues indicates that estrogen action on gonadal differentiation during the period of sex determination may be indirect.
8-Aryl- and 8-cycloalkyl-1,3-dipropylxanthines: further potent and selective antagonists for A1-adenosine receptors (1988)

A series of 1,3-dipropylxanthines were prepared with a variety of substituents at the 8-position. These included 8-aryl and 8-cycloalkyl groups. Polar carboxylate and carboxamide moieties were introduced as aryl substituents to increase water solubility. 1,3-Dipropyl-8-[2-hydroxy-4-[(carboxymethyl)oxy]phenyl]xanthine provided a functionalized congener with high potency (Ki = 37 nM) and selectivity (54-fold) for A1-adenosine receptors. This congener was used for preparation of a series of other analogues, some with higher potency and some with higher selectivity. 8-Cyclopentyl- and 8-cyclohexyl-1,3-dipropylxanthines were both very potent (Ki = 1-1.5 nM) and selective for A1 receptors, while 8-cycloalkylmethyl analogues were 10-fold less potent, but still very selective for A1 receptors. 8-Piperidinyl and 8-pyrazinyl analogues had very low activities as adenosine receptor antagonists.
Combined time‐resolved and high‐spatial‐resolution 3D MRA using an extended adaptive acquisition (2002)

The advantages of time-resolved and high-spatial-resolution imaging were combined using an extended dual-phase acquisition. Some SNR and CNR gain was achieved by signal averaging. This process is facilitated by background and vein suppression.
Fatty acid production in <i>Schizochytrium</i> sp.: Involvement of a polyunsaturated fatty acid synthase and a type I fatty acid synthase (2006)

Schizochytrium sp. is a marine microalga that has been developed as a commercial source for docosahexaenoic acid (DHA, C22:6 (omega-3), enriched biomass, and oil. Previous work suggested that the DHA, as well as docosapentaenoic acid (DPA, C22:5 omega-6), that accumulate in Schizochytrium are products of a multi-subunit polyunsaturated fatty acid (PUFA) synthase (1). Here we show data to support this view and also provide information on other aspects of fatty acid synthesis in this organism. Three genes encoding subunits of the PUFA synthase were isolated from genomic DNA and expressed in E. coli along with an essential accessory gene encoding a phosphopantetheinyl transferase (PPTase). The resulting transformants accumulated both DHA and DPA. The ratio of DHA to DPA was approximately the same as that observed in Schizochytrium. Treatment of Schizochytrium cells with certain levels of cerulenin resulted in inhibition of 14C acetate incorporation into short chain fatty acids without affecting labeling of PUFAs, indicating distinct biosynthetic pathways. A single large gene encoding the presumed short chain fatty acid synthase (FAS) was cloned and sequenced. Based on sequence homology and domain organization, the Schizochytrium FAS resembles a fusion of fungal FAS beta and alpha subunits.
Virtual cursors for XML joins (2004)

Structural joins are a fundamental operation in XML query processing and a large body of work has focused on index-based algorithms for executing them. In this paper, we describe how two well-known index features -- path indices and ancestor information -- can be combined in a novel way to replace one or more of the physical index cursors in a structural join with <i>virtual cursors</i>. The position of a virtual cursor is derived from the path and ancestor information of a physical cursor. Implementation results are provided to show that, by eliminating index I/O, virtual cursors can improve the performance of structural joins by an order of magnitude or more.
Sensitive Immunoluminometric Assay for the Detection of Procalcitonin (2002)

to be no substantive objection to implementing the suggestion by Favus (11 ) with 45 Ca as the tracer.However, whether a stable or a radioactive tracer is used, there is now a suitable algorithm for both men and women, requiring only a single serum sample and providing results within 1 day.
Private information retrieval (2002)

We describe schemes that enable a user to access k replicated copies of a database (k/spl ges/2) and privately retrieve information stored in the database. This means that each individual database gets no information on the identity of the item retrieved by the user. For a single database, achieving this type of privacy requires communicating the whole database, or n bits (where n is the number of bits in the database). Our schemes use the replication to gain substantial saving. In particular, we have: A two database scheme with communication complexity of O(n/sup 1/3/). A scheme for a constant number, k, of databases with communication complexity O(n/sup 1/k/). A scheme for 1/3 log/sub 2/ n databases with polylogarithmic (in n) communication complexity.
A Statistical Robust Approach to Design Parallel Transmit Radiofrequency Excitations in MRI (2020)

In MRI, at ultrahigh field, the use of parallel transmit radiofrequency (RF) arrays is very beneficial to better control spin excitation spatially. In that framework, the so-called “universal pulse” technique, proposed recently for head imaging at 7 tesla, gives access to “plug-and-play” nonadiabatic solutions exhibiting good robustness against intersubject variations in the resonant transmit fields. This new type of solution has been defined so far as the result of numerical pulse optimizations performed across a collection of RF field maps acquired on a small population sample (pulse design database). In this work, we investigate an alternative universal pulse design approach in the linear small tip angle regime whereby the database of RF field maps is first transformed into a second-order statistical model and which then exploits a statistical robust design formalism for the optimization of the RF and magnetic field gradient waveforms. Experimental validation with an eightfold transmit RF coil for 7 tesla brain imaging shows that this new approach brings some benefit in terms of computational efficiency. Hence, for a design database composed of 35 maps, the computation time initially of 50 min could be reduced down to 3 min. The proposed statistical approach thus enables integration of large databases, presumably necessary to ensure robust solutions. Finally, it provides means to compute flip angle statistics and, along with it, simple performance metrics for quality assurance (RF pulse performance) or guidance in the optimization of TX array architectures.
Organization of the genes encoding the biosynthesis of actagardine and engineering of a variant generation system (2009)

The biosynthetic pathway of the type B lantibiotic actagardine (formerly gardimycin), produced by Actinoplanes garbadinensis ATCC31049, has been cloned, sequenced and annotated. The gene cluster contains the gene garA that encodes the actagardine prepropeptide, a modification gene garM, involved in the dehydration and cyclization of the prepeptide, several putative transporter and regulatory genes as well as a novel luciferase-like monooxygenase gene designated garO. Expression of these genes in Streptomyces lividans resulted in the production of ala(0)-actagardine while deletion of the garA gene from A. garbadinensis generated a strain incapable of producing actagardine. Actagardine production was successfully restored however, by the delivery of the plasmid pAGvarX. This plasmid contains an engineered cassette of the actagardine encoding gene garA and offers an alternative route to generating extensive libraries of actagardine variants. Using this plasmid, an alanine scanning library has been constructed and the mutants analysed. Further modifications include the removal of the novel garO gene from A. garbadinensis. Deletion of this gene resulted in the production of deoxy variants of actagardine, demonstrating that the formation of the sulfoxide group is enzyme catalysed and not a spontaneous chemical modification as previously believed.
Intercenter variance in clinical trials of head trauma—experience of the National Acute Brain Injury Study: Hypothermia (2001)

For Phase III clinical trials we recommend: 1) a detailed protocol specifying fluid and MABP, ICP, and CPP management: 2) continuous monitoring of protocol compliance; 3) a run-in period for new centers to test accrual and protocol adherence; and 4) inclusion of only centers in which patients are regularly randomized.
A Reconfigurable Direct RF Receiver With Jitter Analysis and Applications (2013)

In typical direct radio frequency (RF) sampling receivers, the sample clock jitter results in SNR degradation on received signals that increases log linearly with RF signal frequency. De-jittering received signals is computationally expensive, especially for wideband communications signals, because the induced jitter on received signals varies as a function of RF signal frequency. This paper considers a reconfigurable direct RF receiver (RDRFR) that has a stair-step jitter pattern as a function of RF signal frequency. The RDRFR uses a two-stage sampling circuit. In the first stage, the RF input is bandpass filtered and pulse sampled without quantizing the signal. The discrete-time analog signal is then interpolated with a continuous time low-pass filter, then sampled and quantized by a traditional analog-to-digital converter. With this two-stage sampling circuit, the induced signal jitter from the RF sampling is identical for all in-band signals and is the same to within an integer scale factor for all signals, in-band or out-of-band. This key circuit property means that it is possible to remove jitter with very low computational complexity in the RDRFR. Furthermore, this result can be exploited to improve system performance with non-ideal anti-alias filters by identifying non-desired signals caused by out-of-band leakage.
Slow-Release Sodium Fluoride in the Management of Postmenopausal Osteoporosis (1994)

Intermittent slow-release sodium fluoride plus continuous calcium citrate, administered for about 2.5 years, inhibits new vertebral fractures, increases the mean spinal bone mass without decreasing the radial shaft bone density, and is safe to use.
Interference cancellation in full-duplex multicell networks (2017)

The advent and advancement of full-duplex (FD) technology in radio transceivers is expected to lead to full-duplex enabled multi-cell (FD-MC) networks in next generation wireless communication systems. Additional interferences between FD nodes and devices are the main challenges for the deployment of such networks. As in an early deployment scenario where the base stations (BS) operate in FD mode while the user equipments (UE) remain in the half-duplex (HD) mode, the self-interference (SI) within the FD-BS, the mutual interference (MI) between the FD-BS's and between the HD-UE's paired for FD scheduling are the major issues that could jeopardize the capitalization of FD system gains if they are not well addressed. In this paper, we present a system architecture for multi-stage cancellation of SI and joint cancellation of MI and residual SI in an FD-MC network. Multiple orthogonal pilots and their derived forms are utilized for channel estimation during a common training period. System-level delay calibration necessary for SI and MI channel estimation and cancellation is also provided.
Characterization of CMOS position sensitive solid-state photomultipliers (2009)

We have designed position sensitive solid-state photomultipliers (PS-SSPM) using a complementary metal-oxide-semiconductor (CMOS) process. Four variations of the PS-SSPM design were fabricated, however, only three were characterized for their energy and coincidence timing resolution, spatial resolution, and scintillator array imaging. Each PS-SSPM is 1.5 × 1.5 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , however, each device has different micro-pixel geometries and different micro-pixel electrical readout for event position sensing. When coupled to 1 × 1 × 20 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> LYSO, the energy resolution at 511 keV was measured as a function of bias. The same LYSO scintillator was used to measure the coincidence timing resolution. Results varied from 2.1 ns to 1.0 ns (FWHM) at 511 keV. Spatial resolution studies were conducted using a focused (~15 ¿m beam spot diameter) pulsed 635 nm diode laser. For each PS-SSPM, the X and Y FWHM spatial resolution was measured between 70 and 75 ¿m (FWHM). Lastly, a scintillator array studies were conducted for each PS-SSPM using a CsI:Tl and LYSO array having 300 × 300 ¿m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and 500 × 500 ¿m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> pixels respectively.
Optimized Fresh and Hardened Properties of Strain-Hardening Cementitious Composites: Effect of Sand Size and Workability (2016)

The feasibility of the preparation of strain-hardening cementitious composites (SHCC) relies to a great extent on the properties of one of its main constituents, quartz sand. The particle size distribution (PSD) of such sand should satisfy certain criteria specifically for SHCC to deliver quasi-static responses under tensile stress. The successful use of naturally available sand helps preparation of a cost-effective SHCC. The aim of the current paper was to evaluate the potential use of white quartz sand that is naturally available in the Arabian Gulf with different PSDs to produce different mixtures of SHCC. These mixtures were prepared with different ranges of workability to obtain optimized fresh and hardened properties with improved strain-hardening response. The effect of workability on the compressive, flexural and tensile properties has shown that there is an optimal workability range among the defined ranges that provided improved strain-hardening responses under tensile stress. The mode of cracking propagation and fiber failure in tested SHCC mixtures was investigated using stereo-optical microscopy and SEM analyses to reveal different failure mechanisms of the mixtures.
<title>Fluorescence and absorbance analyte sensing in whole blood and plasma based on diffusion separation in silicon-microfabricated flow structures</title> (1997)

Based on the recently introduced T-Sensor method, we demonstrate the fluorescence-determination of various analytes directly in whole blood and in serum. The method relies on microfluidic flow in silicon structures, diffusion-based separation, and analyte determination using fluorescent and absorption indicator dyes. Due to extremely small inertial forces in such structures, practically all flow in microstructures is laminar. This allows the movement of different layers of fluid and particles next to each other in a channel without mixing other than by diffusion. A sample solution (e.g., blood), and a receptor solution containing the indicator dye are introduced in a common channel, and flow laminarly next to each other until they exit the structure. Small ions such as H<SUP>+</SUP>, and Na<SUP>+</SUP> diffuse rapidly across the channel, whereas larger molecules diffuse more slowly. Larger particles such as blood cells and polymer beads show no significant diffusion within the time the two flow streams are in contact. The fluorescence emission of indicator dyes is a function of the concentration of the analyte molecules and the dye concentration in the interaction zone between the two streams. This device allows continuous monitoring of the concentration of analytes in whole blood without the use of membranes or prior removal of blood cells. This principle is illustrated by the determination of human albumin, total calcium, and pH in whole blood and serum.
Comparison of Biophysical and Biologic Properties of <i>α</i>‐Helical Enantiomeric Antimicrobial Peptides (2006)

In our previous study (Chen et al. J Biol Chem 2005, 280:12316-12329), we utilized an alpha-helical antimicrobial peptide V(681) as the framework to study the effects of peptide hydrophobicity, amphipathicity, and helicity on biologic activities where we obtained several V(681) analogs with dramatic improvement in peptide therapeutic indices against gram-negative and gram-positive bacteria. In the present study, the D-enantiomers of three peptides--V(681), V13A(D) and V13K(L) were synthesized to compare biophysical and biologic properties with their enantiomeric isomers. Each D-enantiomer was shown by circular dichroism spectroscopy to be a mirror image of the corresponding L-isomer in benign conditions and in the presence of 50% trifluoroethanol. L- and D-enantiomers exhibited equivalent antimicrobial activities against a diverse group of Pseudomonas aeruginosa clinical isolates, various gram-negative and gram-positive bacteria and a fungus. In addition, L- and D-enantiomeric peptides were equally active in their ability to lyse human red blood cells. The similar activity of L- and D-enantiomeric peptides on prokaryotic or eukaryotic cell membranes suggests that there are no chiral receptors and the cell membrane is the sole target for these peptides. Peptide D-V13K(D) showed significant improvements in the therapeutic indices compared with the parent peptide V(681) by 53-fold against P. aeruginosa strains, 80-fold against gram-negative bacteria, 69-fold against gram-positive bacteria, and 33-fold against Candida albicans. The excellent stability of D-enantiomers to trypsin digestion (no proteolysis by trypsin) compared with the rapid breakdown of the L-enantiomers highlights the advantage of the D-enantiomers and their potential as clinical therapeutics.
Identification and Characterization of Novel Matrix-Derived Bioactive Peptides: A Role for Collagenase from Santyl® Ointment in Post-Debridement Wound Healing? (2016)

Debridement, the removal of diseased, nonviable tissue, is critical for clinicians to readily assess wound status and prepare the wound bed for advanced therapeutics or downstream active healing. Removing necrotic slough and eschar through surgical or mechanical methods is less specific and may be painful for patients. Enzymatic debridement agents, such as Clostridial collagenase, selectively and painlessly degrade devitalized tissue. In addition to its debriding activities, highly-purified Clostridial collagenase actively promotes healing, and our past studies reveal that extracellular matrices digested with this enzyme yield peptides that activate cellular migratory, proliferative and angiogenic responses to injury in vitro, and promote wound closure in vivo. Intriguingly, while collagenase Santyl® ointment, a sterile preparation containing Clostridial collagenases and other non-specific proteases, is a well-accepted enzymatic debridement agent, its role as an active healing entity has never been established. Based on our previous studies of pure Clostridial collagenase, we now ask whether the mixture of enzymes contained within Santyl® produces matrix-derived peptides that promote cellular injury responses in vitro and stimulate wound closure in vivo. Here, we identify novel collagen fragments, along with collagen-associated peptides derived from thrombospondin-1, multimerin-1, fibronectin, TGFβ-induced protein ig-h3 and tenascin-C, generated from Santyl® collagenase-digested human dermal capillary endothelial and fibroblastic matrices, which increase cell proliferation and angiogenic remodeling in vitro by 50-100% over controls. Using an established model of impaired healing, we further demonstrate a specific dose of collagenase from Santyl® ointment, as well as the newly-identified and chemically-synthesized ECM-derived peptides significantly increase wound re-epithelialization by 60-100% over saline-treated controls. These results not only confirm and extend our earlier studies using purified collagenase- and matrix-derived peptides to stimulate healing in vitro and in vivo, but these Santyl®-generated, matrix-derived peptides may also represent exciting new opportunities for creating advanced wound healing therapies that are enabled by enzymatic debridement and potentially go beyond debridement.
High‐Throughput Label‐Free Enzymatic Assays Using Desorption Electrospray‐Ionization Mass Spectrometry (2020)

High-throughput (HT) enzymatic assays, which typically rely on labeled compounds and plate readers, are important for drug discovery. Mass spectrometry (MS) provides an alternative method of performing HT label-free assays. Here we demonstrate the use of a HT platform based on desorption electrospray ionization (DESI) MS for the label-free study of enzymatic reactions directly from the bioassay matrix with an effective analysis time of 0.3 s per sample. This system allows for thorough analysis of the enzymatic process through monitoring of its substrate and product after an external calibration. We show the platform capabilities by an in-depth study of the acetylcholinesterase assay, including kinetic parameter determination, rapid inhibitor screening, and further characterization of positive hits (that is, IC<sub>50</sub> and K<sub>i</sub> ), as well as inhibition-reactivation assays. We anticipate that the expansion of this platform has high potential impact in label-free enzymology as well as in drug discovery.
Novel nanosensing technologies for exosome detection and profiling (2017)

Exosomes have recently emerged as highly promising cancer biomarkers because they are abundant in biofluids, carry proteins and RNA reflecting their originating cells and are stable over weeks. Beyond abundance and stability, detailed exosome analyses could be clinically useful for diagnosing and profiling cancers. Despite their clinical potential, simple, reliable and sensitive approaches for rapidly quantifying exosomes and their molecular information has been challenging. Therefore, there is a clear need to develop next-generation sensing technologies for exosome detection and analysis. In this critical review, we will describe three nanotechnology sensing platforms developed for analysis of exosomal proteins and RNAs directly from clinical specimens and discuss future development to facilitate their translation into routine clinical use.