gebhart/patrepeval huggingface dataset:
cycloSal Phosphates as Chemical Trojan Horses for Intracellular Nucleotide and Glycosylmonophosphate Delivery — Chemistry Meets Biology (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Quantitative reproducibility of measurements from Coomassie Blue‐stained two‐dimensional gels: Analysis of mouse liver protein patterns and a comparison of BALB/c and C57 strains (1985)

Abstract Using the ISO‐DALT system for two‐dimensional (2‐D) electrophoresis and the TYCHO system for computer analysis of the resulting protein maps, we obtained high quality quantitative protein abundance data from Coomassie Brilliant Bluestained gels of mouse liver samples. High resolution gels allow more than 100 proteins to be measured with coefficients of variation less than 15 %. A comparison of results from two mouse strains (C57BL/6 and BALB/c) and the cross between them (BCF 1 ) shows that a large number of qutive polymorphisms can be detected, and that, as expected, the amount of protein produced in the heterozygote is intermediate between the parental values. The system described is shown to be capable of reliably detecting decreases in protein abundance such as those expected to result from radiation‐induced deletion of one copy of a gene. The implications of these results for the study of gene regulation are discussed in relation to applications in genetics, toxicology, and differentiation.
An electronic windscreen for microphones (2006)

Wind-noise pickup in microphones can be highly disturbing, especially for directional microphones that attain their directivity by using velocity or spatial derivatives of the acoustic pressure. Since small directional microphones are common in audio communications systems, the problem of wind noise is well known and the typical solution is to use a windscreen. Conventional windscreens that block the wind but do not significantly alter the sound field can be very effective, but need to be relatively large to attain a good reduction in wind-noise pick-up. Small directional microphone arrays are more commonly used in hearing aids since they have been clinically shown to improve hearing in noise for hearing-impaired users. Since hearing aids are required to be compact, an effective conventional windscreen is not practical. This talk describes a novel multi-microphone wind-noise reduction algorithm that we refer to as an ‘‘electronic windscreen.’’ This new algorithm and its variants have low computational cost and are therefore applicable to commercial digital hearing aids that use multi-microphone arrays to attain directionality.
Design and implementation of a gated-laser entrance hole imaging diagnostic (G-LEH-1) at NIF (2015)

Gated x-ray images through the laser entrance hole (LEH) of a hohlraum can provide critical information for ICF experiments at the National Ignition Facility (NIF), such as the size of the LEH vs time, the growth of the gold bubble<sup>1</sup>, and the change in the brightness of inner beam spots due to time-varying cross beam energy transfer<sup>2</sup>. Incorporating a high-speed multi-frame CMOS x-ray imager developed by Sandia National Laboratories<sup>3,4</sup> into the existing Static X-ray Imager (SXI) diagnostic5 at NIF, the new Gated LEH Imager #1 (G-LEH-1) diagnostic is capable of capturing two to four LEH images per shot on its 1024x448 pixel photo detector array, with integration times as low as 2 ns per frame. The design of this diagnostic and its implementation on NIF will be presented.
Time Series Data Decomposition-Based Anomaly Detection and Evaluation Framework for Operational Management of Smart Water Grid (2021)

With the increasing adoption of advanced meter infrastructure (AMI), smarter sensors, and temporary and/or permanent data loggers, it is imperative to leverage data analytics methods with hydraulic modeling to improve the quality and efficiency of water service. One important task is to timely detect and evaluate anomaly events so that corresponding actions can be taken to prevent and mitigate the impact of possible water service disruption, which may be caused by the anomaly incidents including but not limited to pipe bursts and unauthorized water usages. In this paper, a comprehensive analysis framework is developed for anomaly event detection and evaluation by developing an integrated solution, which is implemented in multiple components including: (1) data-preprocess or cleansing to eliminate and correct error data records; (2) decomposition of time series data to ensure data stationarity; (3) outlier detection by statistical process control methods with stationary time series; (4) classification of system anomaly events by either correlation analysis of high-flow events with low-pressure events or high-flow outliers with low-pressure outliers; and (5) quantitative evaluation of the system anomaly events with field reported leak incidents. The solution framework has been applied to the water supply zone that is permanent monitored with the flow meter at the inlet and 12 pressure stations throughout the zone with more than 8,000 pipes. Analysis has been conducted with one-year monitoring data and 106 historical leak records, which are employed to validate 526 detected anomaly events. Among them, a 75% true positive rate has been achieved and 90% of 106 field events have been successfully detected with a lead time of more than 24 h. The results obtained indicate that the developed solution method is effective at facilitating the operational management of a smart water grid by maximizing the return of investment in continuously monitoring water distribution networks.
Antimicrobial Activity of Glass Ionomer Cement Incorporated with Chlorhexidine-Loaded Zeolite Nanoparticles (2015)

A functional dental restorative system with antimicrobial properties was developed using zeolite (ZE) nanoparticles (NPs) as a drug delivery carrier. ZE NPs loaded with chlorhexidine (CHX) were prepared using the ionic immobilization method. The resulting CHX-loaded ZE NPs were then incorporated into commercial dental glass ionomer cement (GIC). The average size of the CHX-loaded ZE NPs was about 100 to 200 nm, and the NPs were dispersed homogeneously in the GIC. The in vitro release profile of encapsulated GIC containing CHX showed an early release burst of approximately 30% of the total CHX by day 7, whereas GIC containing CHX-loaded ZE NPs showed a sustained release of CHX without the early release burst in a 4-week immersion study. The agar diffusion test results showed that the GIC incorporated with CHX-loaded ZE NPs showed a larger growth inhibition zone of Streptococcus mutans than GIC alone, indicating that this innovative delivery platform potently imparted antimicrobial activity to the GIC. Moreover, these findings suggest that a range of antimicrobial drugs that inhibit the growth of oral bacteria can be incorporated efficiently into dental GIC using CHX-loaded ZE NPs.
Long Term Inhibitory Effects of Pancreastatin and Diazepam Binding Inhibitor on Pancreatic β-Cell Deoxyribonucleic Acid Replication, Polyamine Content, and Insulin Secretion* (1991)

The two peptides pancreastatin and diazepam binding inhibitor (DBI) were recently demonstrated in pancreatic islets and were shown to inhibit insulin secretion in short term experiments. In the present study we investigated long term effects of pancreastatin and DBI on the DNA synthesis, polyamine content, and insulin secretion of pancreatic beta-cells in tissue culture. For this purpose fetal rat pancreatic islets enriched in beta-cells were isolated and cultured for 3 days at different concentrations of rat pancreastatin and porcine DBI. It was found that pancreastatin dose-dependently decreased beta-cell DNA synthesis, reaching maximal inhibition at 100 nM. In parallel with this, pancreastatin also decreased insulin secretion and the islet contents of insulin and the polyamines spermidine and spermine. These effects were abolished by a high glucose concentration or addition of GH. Also, DBI evoked a dose-dependent inhibition of beta-cell DNA synthesis but affected neither the islet contents of insulin or polyamines nor insulin secretion. Like pancreastatin, DBI was ineffective in preventing the increased beta-cell DNA synthesis, insulin content, or secretion in response to high glucose or GH. It is concluded that pancreastatin and DBI inhibit beta-cell DNA synthesis and function in vitro. In the case of pancreastatin these inhibitory effects may be mediated by a decrease in islet polyamine content. It is suggested that pancreastatin and DBI may influence beta-cell replication and function in vivo in an autocrine or paracrine fashion.
Combinatorial Selection Among Geometrical Isomers of Discrete Long-Carbon-Chain Naphthalenediimides Induces Local Order at the Liquid/Solid Interface (2020)

We report two families of naphthalenediimides (NDIs) symmetrically functionalized with discrete carbon chains comprising up to 55 carbon atoms (<b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub>, <i>n</i> = 39, 44, 50, and 55) and their self-assembly at the 1-phenyloctane/highly oriented pyrolytic graphite interface (1-PO/HOPG interface). The compounds differ by the presence or absence of two or three internal double bonds in the carbon chains (unsaturated and saturated <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub>, respectively). Combinatorial distributions of geometrical isomers displaying either the <i>E</i>- or <i>Z</i>-configuration at each double bond are obtained for the unsaturated compounds. Analysis of the self-assembled monolayers of equally long unsaturated and saturated <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub> by scanning tunneling microscopy (STM) reveal that all <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub> tend to form lamellar systems featuring alternating areas of aromatic cores and carbon chains. Extended chain lengths are found to significantly increase disorder in the self-assembled monolayers due to misalignments and enhanced strength of interchain interactions. This phenomenon is antagonized by the local order-inducing effect of the internal double bonds: unsaturated <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub> give qualitatively more ordered self-assembled monolayers compared to their saturated counterparts. The use of combinatorial distributions of unsaturated <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub> geometrical isomers does not represent a limitation to achieve local order in the self-assembled monolayers. The self-assembly process operates a combinatorial search and selects the geometrical isomer(s) affording the most thermodynamically stable pattern, highlighting the adaptive character of the system. Finally, the antagonistic interplay between the extended carbon chain lengths and the presence of internal double bonds brings to the discovery of the lamellar "phase C" morphology for unsaturated <b>C</b><sub><b><i>n</i></b></sub><b>-NDI-C</b><sub><b><i>n</i></b></sub> with <i>n</i> ≥ 50.
Sex steroid receptors and human parturition (1997)

These data suggest that, in the human, 1) oxytocin-resistant labor is associated with low levels of progesterone receptors, 2) estrogen receptors content in myometrium might have no or little relation to labor, and 3) functional labor seems not to be related to a decreased progesterone activity in the myometrium.
How to build a research system in your spare time (2010)

This paper is based on a talk that I gave at CoNEXT 2009. Inspired by Hal Varian's paper on building economic models, it describes are search method for building computer systems. I find this method useful in my work and hope that some readers will find it helpful as well.
The Integrity of the Intradimer Interface of the Hepatitis B Virus Capsid Protein Dimer Regulates Capsid Self-Assembly (2020)

During the hepatitis B virus lifecycle, 120 copies of homodimeric capsid protein assemble around a copy of reverse transcriptase and viral RNA and go on to produce an infectious virion. Assembly needs to be tightly regulated by protein conformational change to ensure symmetry, fidelity, and reproducibility. Here, we show that structures at the intradimer interface regulate conformational changes at the distal interdimer interface and so regulate assembly. A pair of interacting charged residues, D78 from each monomer, conspicuously located at the top of a four-helix bundle that forms the intradimer interface, were mutated to serine to disrupt communication between the two monomers. The mutation slowed assembly and destabilized the dimer to thermal and chemical denaturation. Mutant dimers showed evidence of transient partial unfolding based on the appearance of new proteolytically sensitive sites. Though the mutant dimer was less stable, the resulting capsids were as stable as the wildtype, based on assembly and thermal denaturation studies. Cryo-EM image reconstructions of capsid indicated that the subunits adopted an "open" state more usually associated with a free dimer and that the spike tips were either disordered or highly flexible. Molecular dynamics simulations provide mechanistic explanations for these results, suggesting that D78 stabilizes helix 4a, which forms part of the intradimer interface, by capping its N-terminus and hydrogen-bonding to nearby residues, whereas the D78S mutation disrupts these interactions, leading to partial unwinding of helix 4a. This in turn weakens the connection from helix 4 and the intradimer interface to helix 5, which forms the interdimer interface.
Empirical analysis of user data in game software development (2012)

For several years empirical studies have spanned the spectrum of research from software productivity, quality, reliability, performance to human computer interaction. Analyses have involved software systems ranging from desktop software to telecommunication switching systems. But surprising there has been little work done on the emerging digital game industry, one of the fastest growing domains today. To the best of our knowledge, our work is one of the first empirical analysis of a large commercially successful game system. In this paper, we introduce an analysis of the significant user data generated in the gaming industry by using a successful game: Project Gotham Racing 4.
Morphological Proxies for Taxonomic Decision in Turrids (Mollusca, Neogastropoda): a Test of the Value of Shell and Radula Characters Using Molecular Data (2008)

The state of the art of turrid (=Turridae s. l.) systematics is that shells - when they include the protoconch - are reliable species-level identifiers, but inadequate proxies for allocation to genera or subfamilies. Generally, the radula is used for allocation to a (sub)family, but the hypothesis that the radula is a more adequate proxy than the shell for relationships has not yet been tested by molecular data. Species of Xenuroturris may have drastically different radulae, with either "semi-enrolled" or "duplex" marginal teeth, although their shells are very similar or even almost indistinguishable. Molecular data confirm that specimens with different types of radulae constitute different species, but two species of a pair with respectively semi-enrolled and duplex teeth end up being not closely related. However, it is still unresolved whether species with semi-enrolled (= Iotyrris ) and duplex teeth (= Xenuroturris ) form two supported monophyletic clades. Iotyrris devoizei n.sp. and I. musivum n.sp. are described from Vanuatu, where they occur sympatrically with I. cingulifera and Xenuroturris legitima .
Altered Gene Expression of Caspase-10, Death Receptor-3 and IGFBP-3 in Preeclamptic Placentas (2006)

Enhanced apoptosis has been observed in the placentas of women with preeclampsia, but few studies have examined changes at the molecular level. This study was designed to detect genes specifically expressed in full-term preeclamptic placentas. Tissue samples were collected immediately after cesarean delivery from 11 normal and 8 preeclamptic placentas at 35-40 weeks of gestation. Total RNAs were extracted and hybridized to a cDNA microarray. Results were confirmed by reverse-transcription polymerase chain reaction (RT-PCR), Western blotting and immunohistochemistry. Hematoxylin and eosin and TUNEL staining were also performed to confirm apoptosis in preeclamptic placentas. Among 205 genes, three were up- or down-regulated in preeclamptic placentas. The expression of caspase-10 and death receptor 3 (DR-3) was significantly increased, whereas insulin-like growth factor binding protein-3 (IGFBP-3) was strongly down-regulated. RT-PCR analysis and Western blotting confirmed these effects. Immunohistochemical analysis showed that the DR-3, caspase-10 and IGFBP-3 proteins were localized in the syncytial membrane. Apoptosis in the trophoblast was also increased in term placentas from women with pregnancies complicated by preeclampsia. These results suggest that caspase-10, DR-3 and IGFBP-3 are involved in apoptosis in the preeclamptic placenta.
RF frequency down-conversion with quadratic electro-optic effect (2009)

The frequency down-converter is an essential element of a photonic radar frontend. In this paper we describe a new photonic frequency down-conversion approach employing a quadratic optical phase modulator. When paired with an OPLL linear phase demodulator, this approach can potentially achieve a large dynamic range and a low conversion loss. A preliminary experiment has been performed to verify frequency down-conversion with an InP MQW optical phase modulator. It has been found that the unwanted 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sup> order electro-optic effect that exists in phase modulator results in spurious distortion for the down-converted RF signal. The techniques for mitigation are discussed.
Molecular Dynamics Estimation of Shearing Deformation Properties of &alpha;-Silicon Nitride Single Crystal (1999)

Shear deformation properties of α-silicon nitride single crystal are investigated by molecular dynamics. Three cases of shearing directions are analyzed, two of which were reported to be slip system on the basis of experimental observations. The simulation results show that for the experimentally predicted slip system, shear strength is low and localized band-like shear deformation appears. Disordered atomic structure produced by shear deformation is regarded to be amorphous.
Modal system design of multi-robot systems by interaction mode control (2006)

Motion control technology in open environment will be more and more important. Motion systems should interact with other systems or environment. To adapt complicated environments and do tasks, a realization of multidegree-of-freedom motion is necessary for human cooperating motion. This paper proposes a unified control approach for multi-robot systems by interaction mode control. The proposed interaction mode control considers only the interactions between the systems. The interactions are abstracted by using the quarry matrix. Since the transformed modes are independent to each other, it is possible to design controller in the modal space. This paper also proposes a novel control index named "hybrid ratio". The hybrid ratio is defined as the transfer function from the external acceleration input to the acceleration response of the system. Since it is possible to realize the assigned hybrid ratio in each mode according to the task, the motion command with the hybrid ratio is represented as the task language. Thus, the interaction mode control is able to be treated as the task kinematics. The proposed interaction mode control is applied for grasping motion by multi-robot systems. The experimental results show viability of the proposed method
High-Q CMOS-integrated photonic crystal microcavity devices (2014)

Integrated optical resonators are necessary or beneficial in realizations of various functions in scaled photonic platforms, including filtering, modulation, and detection in classical communication systems, optical sensing, as well as addressing and control of solid state emitters for quantum technologies. Although photonic crystal (PhC) microresonators can be advantageous to the more commonly used microring devices due to the former's low mode volumes, fabrication of PhC cavities has typically relied on electron-beam lithography, which precludes integration with large-scale and reproducible CMOS fabrication. Here, we demonstrate wavelength-scale polycrystalline silicon (pSi) PhC microresonators with Qs up to 60,000 fabricated within a bulk CMOS process. Quasi-1D resonators in lateral p-i-n structures allow for resonant defect-state photodetection in all-silicon devices, exhibiting voltage-dependent quantum efficiencies in the range of a few 10 s of %, few-GHz bandwidths, and low dark currents, in devices with loaded Qs in the range of 4,300-9,300; one device, for example, exhibited a loaded Q of 4,300, 25% quantum efficiency (corresponding to a responsivity of 0.31 A/W), 3 GHz bandwidth, and 30 nA dark current at a reverse bias of 30 V. This work demonstrates the possibility for practical integration of PhC microresonators with active electro-optic capability into large-scale silicon photonic systems.
Activation of mitogen‐activated protein kinases (Erk1 and Erk2) cascade results in phosphorylation of NF‐M tail domains in transfected NIH 3T3 cells (1999)

Neurofilaments (NFs) are neuron-specific intermediate filaments, and are the major cytoskeletal component in large myelinated axons. Lysine-serine-proline (KSP) repeats in the tail domains of high molecular weight NF proteins (NF-M and NF-H) are extensively phosphorylated in vivo in the axon. This phosphorylation in the tail domain has been postulated to play an important role in mediating neuron-specific properties, including axonal caliber and conduction velocity. Recent studies have shown that the mitogen-activated protein kinases (extracellular signal-regulated kinases, Erk1 and Erk2) phosphorylate KSP motifs in peptide substrates derived from the NF-M and NF-H tail domains in vitro. However, it is not clear whether activation of the mitogen activated protein (MAP) kinase pathway is able to phosphorylate these domains in vivo. To answer this question, a constitutively active form of mitogen-activated Erk activating kinase (MEK1) was cotransfected with an NF-M expression construct into NIH 3T3 cells. The activated mutant, but not the dominant negative mutant, induced phosphorylation of NF-M. In addition, it was shown that epidermal growth factor, which induces the MAP kinase cascade in NIH 3T3 cells, also activated endogenous Erk1 and Erk2 and NF-M tail domain phosphorylation in the transfected cells. These results present direct evidence that in-vivo activation of Erk1 and Erk 2 is sufficient for NF-M tail domain phosphorylation in transfected cells.