gebhart/patrepeval huggingface dataset:
Antagonist effects on human P2X7 receptor‐mediated cellular accumulation of YO‐PRO‐1 (2000)

We have examined the interaction of P2 antagonists with the human P2X(7) receptor by studying their effect on 2' and 3'-O-benzoyl-benzoyl-ATP (DbATP) stimulated cellular accumulation of the fluorescent, DNA binding dye, YO-PRO-1 (MW=375Da). In suspensions of HEK293 cells expressing human recombinant P2X(7) receptors, DbATP produced time and concentration-dependent increases in YO-PRO-1 fluorescence. This response presumably reflects YO-PRO-1 entry through P2X(7) receptor channels and binding to nucleic acids. When studies were performed in a NaCl-free, sucrose-containing buffer, full concentration-effect curves to DbATP could be constructed. The P2 antagonists, pyridoxalphosphate-6-azophenyl-2', 4'-disulphonic acid (PPADS) and periodate oxidized ATP (oATP), reduced the potency of DbATP and decreased its maximum response. 1-[N,O-bis(1, 5-isoquinolinesulphonyl)-N-methyl-L-tyrosyl]-4-phenylpiperazine (KN62) and its analogue, KN04, reduced the potency of DbATP. Schild slopes for KN62 and KN04 were shallow and exhibited a plateau at concentrations of compound greater than 1 microM, indicating that these compounds were not competitive antagonists. Calmidazolium and a monoclonal antibody to human P2X(7) receptors attenuated DbATP-stimulated YO-PRO-1 accumulation but they were not competitive antagonists and only produced 2 - 3 fold decreases in the potency of DbATP. The effects of PPADS and KN62 were partially reversible whereas those of oATP were not. PPADS protected cells against the irreversible antagonist effects of oATP suggesting a common site of action. In contrast KN62 was not effective suggesting that it may bind at a different site to oATP and PPADS. This study has demonstrated that P2X(7) receptor function can be quantified by measuring DbATP stimulated YO-PRO-1 accumulation and has provided additional information about the interaction of P2 receptor antagonists with the human P2X(7) receptor.
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures (2008)

Optical nanostructures have enabled the creation of subdiffraction detection volumes for single-molecule fluorescence microscopy. Their applicability is extended by the ability to place molecules in the confined observation volume without interfering with their biological function. Here, we demonstrate that processive DNA synthesis thousands of bases in length was carried out by individual DNA polymerase molecules immobilized in the observation volumes of zero-mode waveguides (ZMWs) in high-density arrays. Selective immobilization of polymerase to the fused silica floor of the ZMW was achieved by passivation of the metal cladding surface using polyphosphonate chemistry, producing enzyme density contrasts of glass over aluminum in excess of 400:1. Yields of single-molecule occupancies of approximately 30% were obtained for a range of ZMW diameters (70-100 nm). Results presented here support the application of immobilized single DNA polymerases in ZMW arrays for long-read-length DNA sequencing.
Transcriptional Regulation by Foxp3 Is Associated with Direct Promoter Occupancy and Modulation of Histone Acetylation (2006)

Regulatory T cells (T(reg)) express Foxp3, a forkhead family member that is necessary and sufficient for T(reg) lineage choice and function. Ectopic expression of Foxp3 in non-T(reg) leads to repression of the interleukin 2 (IL-2) and interferon gamma (IFNgamma) genes, gain of suppressor function, and induction of genes such as CD25, GITR, and CTLA-4, but the mode by which Foxp3 enforces this program is unclear. Using chromatin immunoprecipitation, we have demonstrated that Foxp3 binds to the endogenous IL-2 and IFNgamma loci in T cells, but only after T cell receptor stimulation. This activation-induced Foxp3 binding was abrogated by cyclosporin A, suggesting a role for the phosphatase calcineurin in Foxp3 function. We have also shown that binding of Foxp3 to the IL-2 and IFNgamma genes induces active deacetylation of histone H3, a process that inhibits chromatin remodeling and opposes gene transcription. Conversely, binding of Foxp3 to the GITR, CD25, and CTLA-4 genes results in increased histone acetylation. These data indicate that Foxp3 may regulate transcription through direct chromatin remodeling and show that Foxp3 function is influenced by signals from the TCR.
Wide bandwidth transimpedance preamplifier for a scanning tunneling microscope (1998)

A new two-stage transimpedance preamplifier in feedback picoammeter setup for use in scanning tunneling microscopy is represented. The first stage consisting of a wide band field effect transistor input operational amplifier with resistive feedback has a transimpedance of 20 kΩ and a 3 dB bandwidth of 35 MHz. This setup is built to investigate sub μs fluctuations in the tunneling current.
Biologic Markers as Predictors of Clinical Outcome From Systemic Therapy for Primary Operable Breast Cancer (1999)

Molecular markers may be used to predict the likelihood of achieving GCR, which seems to be a valid surrogate marker for survival.
Advantage of silicon nitride gate insulator transistor by using microwave excited high-density plasma for applying 100nm technology node (2005)

We have succeeded to prepare a hgh quality silicon nitride gate insulator with lower gate leakage current in three orders of magnitude compared to that of conventional thermal oxide film, by using a Kr/NH3 mixed gas microwave-excited highdensity plasma with metal (TaN/Ta/TaN) gate. Moreover, we have evaluated the current drive capability dependence on the silicon surface orientation and found that the channel hole mobility on (110) surface at the channel-width direction of 13 5 degree from the (111) cut plane was 2.4 times hlgher than that of (100) surface. The CMOS transistor with the silicon nitride gate insulator formed by the microwave-excited plasma and TaN/Ta/TaN metal gate on (110) surface orientation silicon having a higher current drive capability and high integration density is the most practical candidate for lOOnm technology node and beyond.
Good vibrations: a vibration damping setpoint controller for continuum robots (2002)

We focus on a class of robotic manipulators that utilize continuous backbone structures. Such manipulators, known as "continuum" robots, exhibit behavior similar to tentacles, trunks, and snakes. Specifically, we have previously discussed some of the mechanical and kinematic details of the Clemson -Tentacle Manipulator." This work examines the dynamic characteristics of this manipulator, proposing a vibration damping control strategy for configurations with the worst vibration characteristics. We begin by formulating the dynamics for one section of the Tentacle Manipulator. We then proceed to develop a vibration control strategy which incorporates a setpoint regulator. We supplement the theoretical developments with experimental results.
“Specificity Determinants” Improve Therapeutic Indices of Two Antimicrobial Peptides Piscidin 1 and Dermaseptin S4 Against the Gram-negative Pathogens Acinetobacter baumannii and Pseudomonas aeruginosa (2014)

A new class of antimicrobial agents with lower rates of resistance and different targets is urgently needed because of the rapidly increasing resistance to classical antibiotics. Amphipathic cationic α-helical antimicrobial peptides (AMPs) represent such a class of compounds. In our previous studies, using a 26-residue de novo designed antimicrobial peptide, we proposed the concept of "specificity determinant(s)": positively charged residue(s) in the center of the non-polar face of AMPs that could decrease hemolytic activity/toxicity but increase or maintain the same level of antimicrobial activity to increase dramatically the therapeutic index. In the current study, we used d-enantiomers of two AMPs, Piscidin 1 isolated from fish and dermaseptin S4 isolated from frog. We substituted different positions in the center of the hydrophobic face with one or two lysine residue(s) (one or two "specificity determinant(s)"). This simple modification not only maintained or improved antimicrobial activity against Gram-negative pathogens Acinetobacter baumannii (11 strains) and Pseudomonas aeruginosa (6 strains), but also dramatically decreased hemolytic activity of human red blood cells, as predicted. Therapeutic indices improved by 55-fold and 730-fold for piscidin 1 (I9K) and dermaseptin S4 (L7K, A14K), respectively, against A. baumannii. Similarly, the therapeutic indices improved 32-fold and 980-fold for piscidin 1 (I9K) and dermaseptin S4 (L7K, A14K), respectively, against P. aeruginosa.
The regulation of Rubisco by Rubisco activase (1995)

Abstract The activity of Rubisco depends on the conversion of the inactive form (E) to the active form (ECM); the binding of the inhibitors CA1P and RuBP to ECM and E, respectively; and the catalytic formation of inhibitory sugar bisphosphates from the enediol intermediate that precedes carboxylation/oxygenation. The regulatory protein, Rubisco activase, modulates the activity of Rubisco by kinetically increasing the dissociation rate of these sugar bisphosphates from their respective enzyme forms in a process that requires ATP hydrolysis. The activity of Rubisco activase is determined by the ATP:ADP ratio. The activity also appears to be influenced by thylakoid membranes in a light-dependent manner, but only a few details of this effect are currently understood. A species dependence in the interaction between heterologous Rubisco and Rubisco activase proteins has been observed. Whether the regulation of Rubisco is a constraint to crop productivity is debatable and will only be decided by detailed study of plants transformed with appropriately modified Rubisco activase and/or Rubisco proteins.
Properties of Known Drugs. 2. Side Chains (1999)

We continue our study of the common features present in drug molecules by looking in detail at drug side chains. Using shape description methods, we divide a database of commercially available drugs into a list of common drug side chains. On the basis of the atom pair shape descriptor (taking into account atom type, hybridization, and bond order), there are 1,246 different side chains among the 5,090 compounds analyzed. The average number of side chains per molecule is 4, and the average number of heavy atoms per side chain is 2. If we ignore the carbonyl side chain, then there are approximately 15,000 occurrences of side chains. Of these 15,000 approximately 11,000 are from the "top 20" group of side chains. This suggests that the diversity that side chains provide to drug molecules is quite low. We discuss ways that this work could be used to provide guidance for molecular design efforts.
Base-Promoted Silicon−Hydrogen Bond Activation of Silanes by Iridium(III) Porphyrin Complexes (2008)

Iridium(III) porphyrin silyls were synthesized in moderate to high yields conveniently from the reactions of iridium(III) porphyrin carbonyl chloride and methyl with silanes, via silicon−hydrogen bond activation (SiHA) in solvent-free conditions and nonpolar solvents. Base was found to promote the SiHA reactions. Specifically, K3PO4 accelerated the SiHA with iridium porphyrin carbonyl chloride, while KOAc promoted the SiHA by iridium porphyrin methyl. Mechanistic experiments suggested that iridium(III) porphyrin carbonyl chloride initially formed iridium porphyin cation, which then reacted with silanes likely via heterolysis to give iridium porphyrin hydride. Iridium porphyrin hydride further reacted with silanes to yield iridium porphyrin silyls. On the other hand, iridium(III) porphyrin methyl and silyls underwent either oxidative addition or σ-bond metathesis to form the products. In the presence of base, a pentacoordinated silicon hydride species likely formed and reacted with iridium porphyrin methyl to form iridium porphyrin anion, which could further react with silanes to yield iridium porphyrin hydride after protonation. Ir(ttp)H finally reacted with excess silanes to give iridium porphyrin silyl complexes.
Ultraviolet (UV-C) inactivation of Enterococcus faecium, Salmonella choleraesuis and Salmonella typhimurium in porcine plasma (2017)

The objective of this study was to assess the effectiveness of an ultraviolet (UV-C, 254 nm) irradiation system on reducing the load of Salmonella typhimurium (S. typhimurium), Salmonella choleraesuis (S. choleraesuis) resistant to streptomycin and Enterococcus faecium (E. faecium) inoculated in sterile porcine plasma and then subjected to different UV-C irradiation doses (750, 1500, 3000, 6000 and 9000 J/L) using a pilot plant UV-C device working under turbulent flow. Results indicated that UV-C treatment induced a viability reduction of 0.38, 1.18, 3.59, 4.72 and 5.06 log10 S. typhimurium when irradiated at 750, 1500, 3000, 6000 and 9000 J/L, respectively. The observed log10 reduction of S. choleraesuis was 1.44, 2.68, 5.55, 7.07 and 7.97 at 750, 1500, 3000, 6000 and 9000 J/L, respectively. The best-fit inactivation for S. choleraesuis was the Weibull distribution curve, while the best-fit curve for S. typhimurium was the Weibull plus tail model, indicating that around 102 cfu/mL resistant S. typhimurium was detected when the liquid plasma was UV-C irradiated at doses up to 9000 J/L. Viability reduction for E. faecium was 0.44, 1.01, 3.70, 5.61 and 6.22 log10 when irradiated at 750, 1500, 3000, 6000 and 9000 J/L, respectively, with no bacterial resistance observed with UV-C doses of 6000 J/L or higher. The biphasic model was the best fit model for the inactivation curve for E. faecium. For the three microorganisms tested, about a 4 log-unit reduction was achieved when the liquid plasma was irradiated at 3000J/L. Overall results demonstrate the usefulness of the UV-C system to inactivate bacteria in liquid plasma before spray-drying. We conclude that the UV-C system can provide an additional biosafety feature that can be incorporated into the manufacturing process for spray-dried animal plasma.
Electronic Control of DNA Polymerase Binding and Unbinding to Single DNA Molecules (2009)

DNA polymerases catalyze template-dependent genome replication. The assembly of a high affinity ternary complex between these enzymes, the double strand-single strand junction of their DNA substrate, and the deoxynucleoside triphosphate (dNTP) complementary to the first template base in the polymerase active site is essential to this process. We present a single molecule method for iterative measurements of DNA-polymerase complex assembly with high temporal resolution, using active voltage control of individual DNA substrate molecules tethered noncovalently in an alpha-hemolysin nanopore. DNA binding states of the Klenow fragment of Escherichia coli DNA polymerase I (KF) were diagnosed based upon their ionic current signature, and reacted to with submillisecond precision to execute voltage changes that controlled exposure of the DNA substrate to KF and dNTP. Precise control of exposure times allowed measurements of DNA-KF complex assembly on a time scale that superimposed with the rate of KF binding. Hundreds of measurements were made with a single tethered DNA molecule within seconds, and dozens of molecules can be tethered within a single experiment. This approach allows statistically robust analysis of the assembly of complexes between DNA and RNA processing enzymes and their substrates at the single molecule level.
Bleomycin-mediated electrochemotherapy of basal cell carcinoma (1996)

To our knowledge, this is the first study that documents the effects of bleomycin-mediated electrochemotherapy on BCC. Studies are ongoing with intralesional bleomycin during electrochemotherapy to see whether additional antitumour effects can be produced in patients with BCC by this route of administration.
One-step coating of fluoro-containing silicananoparticles for universal generation of surface superhydrophobicity (2007)

Stable superhydrophobic surfaces with water contact angles over 170 degrees and sliding angles below 7 degrees were produced by simply coating a particulate silica sol solution of co-hydrolysed TEOS/fluorinated alkyl silane with NH(3).H(2)O on various substrates, including textile fabrics (e.g. polyester, wool and cotton), electrospun nanofibre mats, filter papers, glass slides, and silicon wafers.
Efficient reactivation of Xenopus erythrocyte nuclei in Xenopus egg extracts (1995)

Rapid genome replication is one of the hallmarks of the frog embryonic cell cycle. We report here that complete reactivation of quiescent somatic cell nuclei in Xenopus egg extracts depends on prior restructuring of the nuclear substrate and prior preparation of cytoplasmic extract with the highest capacity to initiate and sustain DNA synthesis. Nuclei from mature erythrocytes swell, replicate their DNA efficiently, and enter mitosis in frozen/thawed extracts prepared from activated Xenopus eggs, provided the nuclei are first treated with trypsin, heparin, and an extract prepared from unactivated, meiotically arrested, eggs. Optimal replicating extracts are prepared from large batches of unfertilized eggs that are synchronously activated into the cell cycle for 28 minutes (at 20 degrees C). Because the Xenopus cell cycle progresses so rapidly, extracts prepared just a few minutes before or after this time have substantially lower DNA synthetic capacities. At the optimal time and temperature, eggs have just reached the G1/S boundary of the first cell cycle. This fact was revealed by injecting and replicating an SV40 plasmid in intact unfertilized eggs as described previously. We estimate that under optimal conditions approximately 6.14 x 10(9) base pairs of DNA/per nucleus are synthesized in 30-40 minutes, a rate that rivals that observed in the zygotic nucleus. The findings reported here are one step in our long term effort to develop a new in vitro/in vivo approach to nuclear transplantation. Nuclear transplantation in amphibian embryos has been used to establish that the genomes of many types of differentiated somatic cells are pluripotent. But very few such nuclei have ever developed into advanced tadpoles or adult frogs, probably because somatic nuclei injected directly into activated eggs fail to reactivate quickly enough to avoid being damaged during first mitosis. We have already shown that unfertilized eggs can be injected prior to activation of the first cell cycle. Future experiments will reveal whether in vitro reactivated somatic cell nuclei transplanted into such eggs reliably reach advanced stages of development.
Computational aspects of optical lithography extension by directed self-assembly (2013)

EUV insertion timing for High Volume Manufacturing is still an uncertainty due to source power and EUV mask infrastructure limitations. Directed Self Assembly (DSA) processes offer the promise of providing alternative ways to extend optical lithography cost-effectively for use in the 10nm node and beyond. The goal of this paper is to look into the technical prospect of DSA technology, particularly in the computational and DFM area. We have developed a prototype computational patterning toolset in-house to enable an early Design –Technology Co-Optimization to study the feasibility of using DSA in patterning semiconductor devices and circuits. From this toolset we can identify the set of DSA specific design restrictions specific to a DSA process and plan to develop a novel full chip capable computational patterning solution with DSA. We discuss the DSA Computational Lithography (CL) infrastructure using the via and fin layers as examples. Early wafer data is collected from the DSA testmask that was built using these new toolsets. Finally we discuss the DSA ecosystem requirements for enabling DSA lithography and propose how EDA vendors can play a role in making DSA Lithography (DSAL) a full-chip viable technology for multiple process layers.
Feasibility of Vagus Nerve Stimulation–Synchronized Blood Oxygenation Level–Dependent Functional MRI (2001)

Vagus nerve stimulation pulses from an NCP system can be detected externally to determine its firing pattern, thus allowing VNS-fMRI studies of VNS-induced brain activity.
Toward a Rapid, Integrated, and Fully Automated DNA Diagnostic Assay for Chlamydia trachomatis and Neisseria gonorrhoeae (2000)

Molecular testing for the diagnosis of bacterial or viral infections in raw clinical specimens requires complex, multistep procedures to release and isolate nucleic acid before PCR amplification (1)(2). Laboratory bench-top sample preparation procedures are very labor- and equipment-intensive, which reflects on total assay cost and increased susceptibility to sample and reagent carryover (3)(4). The need for automation has led to the development and introduction of robotics-based laboratory instruments with discrete operations that simulate the basic functions of a laboratory technician. These systems are typically developed for high-throughput applications and usually require intermittent operator involvement. In addition, because they directly emulate the operator’s manual functions for processing boluses of sample and reagents, the issue of sample or reagent carryover and carryin remains unresolved, and the complexity of the robotic mechanisms themselves contributes to high capital costs and poor reliability.

Several factors currently contribute to and facilitate the development of the next generation of automated and integrated diagnostics instruments. One factor includes the recent advances in the microfluidics field of miniaturized integrated platforms and supporting technologies, which potentially enable the seamless execution of a sequence of protocols (5). Miniaturized processor-controlled microfluidic platforms contain chambers and valves, and encapsulate entities such as filter membranes or solid-phase particles. They are able to execute important processes such as cell capture, lysis, and fluid mixing, which currently require discrete laboratory instruments (6). Another factor is the development of a miniature, rapid PCR thermocycler device with real-time optical detection capable of multiplex analysis (7)(8)(9). Its modularity and adaptability allows for easy integration into an instrument platform downstream of a sample preparation module. It is possible to envision a one-step operation covering sample preparation and analysis, from raw sample to results reporting. Finally, the utilization of …
SmI2-Promoted Radical Addition Reactions with N-(2-Indolylacyl)oxazolidinones:  Synthesis of Bisindole Compounds (2007)

The treatment of N-acyl oxazolidinones of N-benzyl 2-indolecarboxylic acids varying in the substitution pattern of the indole ring with samarium diiodide at -78 degrees C led to the formation of two indole dimer products. The major product isolated in yields from 55 to 59% represents an unsymmetrical dimer arising from 1,4-addition to the 2-indolecarboxylic acid derivative of a possible ketyl-type radical anion intermediate originating from the reduction of the exocyclic carbonyl group of the N-acyl oxazolidinone. The minor dimer, represented by a symmetrical diketone, was produced in yields ranging from 11 to 23%. Even in the presence of an alpha,beta-unsaturated amide, dimerization was the preferred pathway rather than the formation of a gamma-keto amide. Upon treatment with acid, the unsymmetrical indole dimer cyclized to form a diindolequinone. Finally, the N-acyl oxazolidinones of pyrrole-2-carboxylic acid and 3-indolecarboxylic acid preferred in both cases to undergo C-C bond formation with an acrylamide in the presence of SmI2 rather than dimerization.