gebhart/patrepeval huggingface dataset:
Photoinitiated degradation of poly(diacetylene)s in solution by random chain scission (1984)

Abstract Poly(diacetylene)s dissolved in common organic solvents undergo random chain scission, if irradiated by UV‐light. The pure polymers and their solutions are, however, stable, if they are photoirradiated within the main‐absorption band of the polymer backbone. The usual triplet sensitizers, especially in the presence of oxygen, and radical donors such as 2,2′‐azoisobutyronitrile (AIBN) enhance the rate of photodegradation. Suitable dyes are able to sensitize the chain‐scission in the visible regions as well. Random chain scission occurs also in the dark, but only at temperatures above room temperature and is enhanced by the addition of radical‐donors, e.g. AIBN. A mechanism of chain scission, induced by the attack of a radical to a multiple bond of the polyconjugated backbone of the polymer is proposed.
Simultaneous Symbol Timing and Frame Synchronization for Phase Shift Keying (2014)

We develop an estimator of time offset (or time-of-arrival) of a transmitted communications signal that contains both pilot symbols, known to the receiver, and data symbols, unknown to the receiver. We focus on signalling constellations that have symbols lying on the complex unit circle, such as M-ary phase shift keying (M-PSK). We describe an algorithm for computing the estimator that requires O(L log L) operations in the worst case, where L is the number of transmitted symbols. Our estimator integrates information from the pilot symbols more effectively than popular estimators from the literature that usually split estimation into two subproblems called symbol timing and frame synchronisation. Our estimator combines these subproblems into a single operation, that of estimating time offset. We hypothesise that our estimator will be statistically more accurate. Monte-Carlo simulations support this hypothesis.
AMC - A framework for modelling and comparing matching systems as matching processes (2011)

We present the Auto Mapping Core (AMC), a new framework that supports fast construction and tuning of schema matching approaches for specific domains such as ontology alignment, model matching or database-schema matching. Distinctive features of our framework are new visualisation techniques for modelling matching processes, stepwise tuning of parameters, intermediate result analysis and performance-oriented rewrites. Furthermore, existing matchers can be plugged into the framework to comparatively evaluate them in a common environment. This allows deeper analysis of behaviour and shortcomings in existing complex matching systems.
User driven audio content navigation for spoken web (2010)

It is a common practice for us to skim textual content on a web page. While skimming, we usually skip words or phrases that are not of interest to us and we slow down our speed when the content seems to be of relevance to us. But when we listen to audio content, which is not persistent and is sequential, such skimming is not possible. In developing countries, cell-phone penetration is much higher than Internet penetration. Moreover, due to low literacy, voice is a convenient modality to access information. The skimming techniques are therefore more critical in the audio domain. In this paper, we describe the technique for navigating audio content while interacting with information systems in a client server environment, where a dumb phone is the client device. The paper presents techniques for skimming audio content and for placing markers in audio. The user studies conducted with 18 users for more than 1 month, in a live setting substantiates the usability and usefulness of the navigation techniques.
Design of an On-Board ESD Protection for USB3 Applications (2016)

This paper describes the development of an on-board system level protection for high-speed cable connections (e.g., USB3) with 15 kV robustness and a signal transfer rate of up to 10 Gb/s. A dedicated bipolar process is developed, on a high-resistive substrate with optimized diffusion profiles and a special via-on-via metallization to meet the capacitance target of 0.25 pF. The protection is shown to work well with several popular USB3 chipsets.
Laser-Induced Acoustic Desorption/Atmospheric Pressure Chemical Ionization Mass Spectrometry (2011)

Laser-induced acoustic desorption (LIAD) was successfully coupled to a conventional atmospheric pressure chemical ionization (APCI) source in a commercial linear quadrupole ion trap mass spectrometer (LQIT). Model compounds representing a wide variety of different types, including basic nitrogen and oxygen compounds, aromatic and aliphatic compounds, as well as unsaturated and saturated hydrocarbons, were tested separately and as a mixture. These model compounds were successfully evaporated into the gas phase by using LIAD and then ionized by using APCI with different reagents. From the four APCI reagent systems tested, neat carbon disulfide provided the best results. The mixture of methanol and water produced primarily protonated molecules, as expected. However, only the most basic compounds yielded ions under these conditions. In sharp contrast, using APCI with either neat benzene or neat carbon disulfide as the reagent resulted in the ionization of all the analytes studied to predominantly yield stable molecular ions. Benzene yielded a larger fraction of protonated molecules than carbon disulfide, which is a disadvantage. A similar but minor amount of fragmentation was observed for these two reagents. When the experiment was performed without a liquid reagent (nitrogen gas was the reagent), more fragmentation was observed. Analysis of a known mixture as well as a petroleum cut was also carried out. In summary, the new experiment presented here allows the evaporation of thermally labile compounds, both polar and nonpolar, without dissociation or aggregation, and their ionization to predominantly form stable molecular ions.
Reply to Liu et al.: <i>HNF4A</i> and <i>PTBP1</i> expression in the brain of neurodegenerative disease patients (2015)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Efficient production of indigoidine in <i>Escherichia coli</i> (2015)

Indigoidine is a bacterial natural product with antioxidant and antimicrobial activities. Its bright blue color resembles the industrial dye indigo, thus representing a new natural blue dye that may find uses in industry. In our previous study, an indigoidine synthetase Sc-IndC and an associated helper protein Sc-IndB were identified from Streptomyces chromofuscus ATCC 49982 and successfully expressed in Escherichia coli BAP1 to produce the blue pigment at 3.93 g/l. To further improve the production of indigoidine, in this work, the direct biosynthetic precursor L-glutamine was fed into the fermentation broth of the engineered E. coli strain harboring Sc-IndC and Sc-IndB. The highest titer of indigoidine reached 8.81 ± 0.21 g/l at 1.46 g/l L-glutamine. Given the relatively high price of L-glutamine, a metabolic engineering technique was used to directly enhance the in situ supply of this precursor. A glutamine synthetase gene (glnA) was amplified from E. coli and co-expressed with Sc-indC and Sc-indB in E. coli BAP1, leading to the production of indigoidine at 5.75 ± 0.09 g/l. Because a nitrogen source is required for amino acid biosynthesis, we then tested the effect of different nitrogen-containing salts on the supply of L-glutamine and subsequent indigoidine production. Among the four tested salts including (NH4)2SO4, NH4Cl, (NH4)2HPO4 and KNO3, (NH4)2HPO4 showed the best effect on improving the titer of indigoidine. Different concentrations of (NH4)2HPO4 were added to the fermentation broths of E. coli BAP1/Sc-IndC+Sc-IndB+GlnA, and the titer reached the highest (7.08 ± 0.11 g/l) at 2.5 mM (NH4)2HPO4. This work provides two efficient methods for the production of this promising blue pigment in E. coli.
Glutamatergic dysfunction in obsessive-compulsive disorder and the potential clinical utility of glutamate-modulating agents (2006)

Obsessive-compulsive disorder (OCD) is a common psychiatric disorder and the tenth leading cause of disability in the world. The introduction of serotonin reuptake inhibitors (SRIs) in the 1980s represented an important advance in the treatment of OCD. However, most patients show only a partial response to existing treatments and a full remission of OCD symptoms is not frequently observed. Clinical experience and research has highlighted the role of serotonin and dopamine in OCD. The clinical observation that SRIs and aug- mentation with dopamine antagonists only yields a partial treatment response in most patients suggests that other neurotransmitters contribute to the neurobiology of the illness. Recent research find- ings raise the possibility that agents that directly reduce glutamate hyperactivity or its consequences in the central nervous system are efficacious as novel therapeutic interventions. This article reviews current treatment strategies for OCD and summarizes the growing body of research implicating glutamatergic dysfunction in OCD.
A Generative Model of Terrain for Autonomous Navigation in Vegetation (2006)

Current approaches to off-road autonomous navigation are often limited by their ability to build a terrain model from sensor data. Available sensors make very indirect measurements of quantities of interest such as the supporting ground height and the location of obstacles, especially in domains where vegetation may hide the ground surface or partially obscure obstacles. A generative, probabilistic terrain model is introduced that exploits natural structure found in off-road environments to constrain the problem and use ambiguous sensor data more effectively. The model includes two Markov random fields that encode the assumptions that ground heights smoothly vary and terrain classes tend to cluster. The model also includes a latent variable that encodes the assumption that vegetation of a single type has a similar height. The model parameters can be trained by simply driving through representative terrain. Results from a number of challenging test scenarios in an agricultural domain reveal that exploiting the 3D structure inherent in outdoor domains significantly improves ground estimates and obstacle detection accuracy, and allows the system to infer the supporting ground surface even when it is hidden under dense vegetation.
Cloning and Characterization of MicroRNAs from Rice (2005)

MicroRNAs (miRNAs) are a growing family of small noncoding RNAs that downregulate gene expression in a sequence-specific manner. The identification of the entire set of miRNAs from a model organism is a critical step toward understanding miRNA-guided gene regulation. Rice (Oryza sativa) and Arabidopsis thaliana, two plant model species with fully sequenced genomes, are representatives of monocotyledonous and dicotyledonous flowering plants, respectively. Thus far, experimental identification of miRNAs in plants has been confined to Arabidopsis. Computational analysis based on conservation with known miRNAs from Arabidopsis has predicted 20 families of miRNAs in rice. To identify miRNAs that are difficult to predict in silico or not conserved in Arabidopsis, we generated three cDNA libraries of small RNAs from rice shoot, root, and inflorescence tissues. We identified 35 miRNAs, of which 14 are new, and these define 13 new families. Thirteen of the new miRNAs are not conserved in Arabidopsis. Four of the new miRNAs are conserved in related monocot species but not in Arabidopsis, which suggests that these may have evolved after the divergence of monocots and dicots. The remaining nine new miRNAs appear to be absent in the known sequences of other plant species. Most of the rice miRNAs are expressed ubiquitously in all tissues examined, whereas a few display tissue-specific expression. We predicted 46 genes as targets of the new rice miRNAs: 16 of these predicted targets encode transcription factors, and other target genes appear to play roles in diverse physiological processes. Four target genes have been experimentally verified by detection of miRNA-mediated mRNA cleavage. Our identification of new miRNAs in rice suggests that these miRNAs may have evolved independently in rice or been lost in other species.
Fluorescence Dilution Technique for Measurement of Cardiac Output and Circulating Blood Volume in Healthy Human Subjects (2007)

The study demonstrates that intense and reproducible fluorescence dilution signals can be measured transcutaneously in healthy humans and could potentially be used to measure cardiac output and circulating blood volume minimally invasively.
Insecticidal Activity of <i>Chromobacterium vaccinii</i><sup>1</sup> (2018)

New Chromobacterium sp. strains were isolated from water collected from several localities in the eastern United States and were subsequently identified as the species Chromobacterium vaccinii Soby et al. Bacteria were cultured in a liquid medium and applied to artificial insect diets in the laboratory. All of the recently discovered C. vaccinii isolates tested were toxic to larvae of the seedcorn maggot, Delia platura (Meigen), but had little activity against larvae of the diamondback moth, Plutella xylostella (L.). None of the new isolates of C. vaccinii were toxic to adults of the red flour beetle, Tribolium castaneum (Herbst).
Geopolymer concretes: a green construction technology rising from the ash (2009)

Researchers at Louisiana Tech University have embarked on a multi-year research initiative to develop applications for inorganic polymer concrete, or geopolymer concrete, in the area of civil construction, and to bring solve of these applications to market. One objective was to produce a spray-on coating for use in the harsh environment of wastewater conveyance and treatment facilities. Another project is to establish relationships between fly ash composition and particle size distribution and the mechanical attributes and workability of the resulting geopolymer concrete. A third project is to develop a 'smart' geopolymer concrete whose response to a given electric current can be correlated to the stress level to which the structure is subjected. 1 fig., 6 photos.
Multicarrier Underwater Acoustic Communications over Fast-Varying Channels (2007)

Multicarrier modulation in the form of orthogonal frequency division multiplexing (OFDM) has prevailed in recent broadband wireless radio applications due to the low complexity of receivers required to deal with highly dispersive channels. This fact motivates the use of OFDM in underwater environments. However, underwater acoustic (UWA) channels are far more challenging than their radio counterparts. Although with limited bandwidth, UWA channels are wideband in nature due to the small ratio of the carrier frequency to the signal bandwidth, which introduces frequency-dependent Doppler drifts that destroy the orthogonality among OFDM subcarriers. In this paper, a two-step approach is proposed to mitigate the frequency-dependent Doppler drifts in zero-padded OFDM transmissions over fast-varying underwater acoustic channels: (1) non-uniform Doppler compensation via resampling that converts a “wideband” problem into a “narrowband” problem; and (2) high-resolution uniform compensation of the residual Doppler. Null subcarriers are used to facilitate Doppler compensation, and pilot subcarriers are used for channel estimation. The receiver is based on block-by-block processing, and does not rely on channel dependence across OFDM blocks; thus, it is suitable for fast-varying UWA channels. The data from two shallow water experiments near Woods Hole, MA, are used to demonstrate the receiver performance. Excellent results are obtained even when the transmitter and the receiver are moving at a relative speed of up to 10 knots, at which the Doppler drifts are greater than the OFDM subcarrier spacing. These results support our belief that OFDM is a viable option for high-rate communications over fast-varying underwater acoustic channels.
Abstract DDT02-03: Discovery of GDC-0994, a potent and selective ERK1/2 inhibitor in early clinical development (2014)

Abstract The extracellular-signal-regulated kinases (ERK1 and ERK2) represent an essential node within the RAS/RAF/MEK/ERK signaling cascade that commonly is activated by oncogenic mutations in BRAF or RAS or by upstream oncogenic signaling, such as receptor tyrosine kinase (RTK) activation. While targeting upstream nodes with RAF and MEK inhibitors has proven effective clinically, resistance frequently develops through reactivation of the pathway. Simultaneous targeting of multiple nodes in the pathway, such as MEK and ERK, offers the prospect of enhanced efficacy as well as reduced potential for acquired resistance. Here, we present the discovery and characterization of GDC-0994, an orally bioavailable, small molecule inhibitor of ERK kinase activity. GDC-0994 is highly selective for ERK1 and ERK2, with biochemical potency of 1.1 nM and 0.3 nM, respectively. Daily, oral dosing of GDC-0994 results in significant single-agent activity in multiple in vivo cancer models, including KRAS-mutant and BRAF-mutant human xenograft tumors in mice. PD biomarker inhibition of phospho-p90RSK in these tumors correlates with potency in vitro and in vivo. In contrast to other published ERK inhibitors, GDC-0994 neither increases nor decreases phospho-ERK, suggesting that different ERK inhibitors have alternative mechanisms of action with respect to feedback signaling. Furthermore, we demonstrate a novel approach for targeting the oncogenic signaling through the RAS pathway by combining ERK and MEK inhibitors. GDC-0994 is currently in Phase I clinical development. Citation Format: Kirk Robarge, Jacob Schwarz, Jim Blake, Michael Burkard, Jocelyn Chan, Huifen Chen, Kang-Jye Chou, Dolores Diaz, John Gaudino, Stephen Gould, Jonas Grina, Xin Linghu, Lichuan Liu, Matthew Martinson, David A. Moreno, Christine Orr, Patricia Pacheco, Ann Qin, Kevin Rasor, Li Ren, Sheerin Shahidi-Latham, Jeffrey Stults, Francis Sullivan, Weiru Wang, Peter Yin, Aihe Zhou, Marcia Belvin, Mark Merchant, John G. Moffat. Discovery of GDC-0994, a potent and selective ERK1/2 inhibitor in early clinical development. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr DDT02-03. doi:10.1158/1538-7445.AM2014-DDT02-03
Liposome-encapsulated curcumin: <i>in vitro</i> and <i>in vivo</i> effects on proliferation, apoptosis, signaling, and angiogenesis (2005)

4091 Background: Because a role for nuclear factor-κB (NF-κB) has been implicated in the pathogenesis of pancreatic cancer, this transcription factor is a potential target for treatment of this devastating disease. Curcumin (diferuloylmethane) is a phytochemical with potent NF-κB-inhibitory activity. It is pharmacologically safe, but its bioavailability is poor after oral administration. Methods: We encapsulated curcumin in a liposomal delivery system that would allow intravenous administration. We studied the in vitro and in vivo effects of this compound on proliferation, apoptosis, signaling and angiogenesis using human pancreatic cancer cells. Results: NF-κB was constitutively active in all human pancreatic cancer cell lines examined and liposomal curcumin consistently suppressed NF-κB binding (electrophoretic mobility gel shift assay (EMSA)) and decreased the expression of NF-κB-regulated gene products, including cyclo-oxygenase-2 (COX-2) (immunoblots) and interleukin-8 (IL-8) (enzyme linked immunoassay), both of which have been implicated in tumor growth/invasiveness. These in vitro changes were associated with concentration- and time-dependent antiproliferative activity (MTT assay) and pro-apoptotic effects (annexin-V/propidium iodide staining (FACS) and polyadenosine-5’-diphosphate-ribose-polymerase (PARP) cleavage). The activity of liposomal curcumin was equal to or better than that of free curcumin at equimolar concentrations. In vivo, curcumin suppressed pancreatic cancer growth in murine xenograft models and inhibited tumor angiogenesis. Conclusions: Liposomal curcumin downregulates the NF-κB machinery, suppresses growth, and induces apoptosis of human pancreatic cells, in vitro. Antitumor and anti-angiogenesis effects are observed in vivo. Our experiments provide a biologic rationale for treatment of patients suffering from pancreatic cancer with this nontoxic phytochemical encapsulated in liposomes for systemic delivery. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Plantacor
Substrate Specificity of Glutaminyl Cyclases from Plants and Animals (2003)

Glutaminyl cyclases (QC) catalyze the intramolecular cyclization of N-terminal glutamine residues of peptides and proteins. For a comparison of the substrate specificity of human and papaya QC enzymes, a novel continuous assay was established by adapting an existing discontinuous method. Specificity constants (kcat/Km) of dipeptides and dipeptide surrogates were higher for plant QC, whereas the selectivity for oligopeptides was similar for both enzymes. However, only the specificity constants of mammalian QC were dependent on size and composition of the substrates. Specificity constants of both enzymes were equally pH-dependent in the acidic pH-region, revealing a pKa value identical to the pKa of the substrate, suggesting similarities in the substrate conversion mode. Accordingly, both QCs converted the L-beta homoglutaminyl residue in the peptide H-beta homoGln-Phe-Lys-Arg-Leu-Ala-NH2 and the glutaminyl residues of the branched peptide H-Gln-Lys(Gln)-Arg-Leu-Ala-NH2 as well as the partially cyclized peptide H-Gln-cyclo(N epsilon-Lys-Arg-Pro-Ala-Gly-Phe). In contrast, only QC from C. papaya was able to cyclize a methylated glutamine residue, while this compound did not even inhibit human QC-catalysis, suggesting distinct substrate recognition pattern. The conversion of the potential physiological substrates [Gln1]-gastrin, [Gln1]-neurotensin and [Gln1]-fertilization promoting peptide indicates that human QC may play a key role in posttranslational modification of most if not all pGlu-containing hormones.
A Novel Update Algorithm in Stokes Space for Adaptive Equalization in Coherent Receivers (2014)

We propose a novel update algorithm based on error signals evaluated in Stokes space, independent of both phase-noise and frequency-offset. We compare its performance to standard CMA for PM-16QAM modulation, showing 0.5-dB gain at BER=10−2.
Electrical Probing of Submicroliter Liquid Using Graphene Strip Transistors Built on a Nanopipette (2011)

Graphene sheets made by chemical vapor deposition are transferred onto a glass nanopipette to form graphene strips. Two strips are connected at the nanopipette tip end to form a transistor channel. This graphene-based transistor can be operated in a liquid-gating condition, thereby allowing the electrical detection of the pH value of a droplet with submicroliter volume.