gebhart/patrepeval huggingface dataset:
Abbreviated text input (2003)

We address the problem of improving the efficiency of natural language text input under degraded conditions (for instance, on PDAs or cell phones or by disabled users) by taking advantage of the informational redundacy in natural language. Previous approaches to this problem have been based on the idea of prediction of the text, but these require the user to take overt action to verify or select the system's predictions. We propose taking advantage of the duality between prediction and compression. We allow the user to enter text in compressed form, in particular, using a simple stipulated abbreviation method that reduces characters by about 30% yet is simple enough that it can be learned easily and generated relatively fluently. Using statistical language processing techniques, we can decode the abbreviated text with a residual word error rate of about 3%, and we expect that simple adaptive methods can improve this to about 1.5%. Because the system's operation is completely independent from the user's, the overhead from cognitive task switching and attending to the system's actions online is eliminated, opening up the possibility that the compression-based method can achieve text input efficiency improvements where the prediction-based methods have not
Two-pass alignment improves novel splice junction quantification (2015)

Supplementary data are available at Bioinformatics online.
Synthesis of verdinochlorins: a new class of long-wavelength absorbing photosensitizers (1998)

Reaction of 132-oxopyropheophorbide a with CH2N2 produced three isomeric methoxyverdinochlorins via expansion of the cyclopentanedione ring E; these long-wavelength absorbing verdinochlorins represent the first example of verdins with a reduced pyrrolic ring system, and their structural assignments have been made on the basis of 1H NMR studies; a mechanism of verdinochlorin formation is discussed.
Energy Detection of Unknown Signals in Fading and Diversity Reception (2011)

A comprehensive performance analysis of the energy detector over fading channels with single antenna reception or with antenna diversity reception is developed. For the no-diversity case and for the maximal ratio combining (MRC) diversity case, with either Nakagami-m or Rician fading, expressions for the probability of detection are derived by using the moment generating function (MGF) method and probability density function (PDF) method. The former, which avoids some difficulties of the latter, uses a contour integral representation of the Marcum-Q function. For the equal gain combining (EGC) diversity case, with Nakagami-m fading, expressions for the probability of detection are derived for the cases L =2,3,4 and L >; 4, where L is the number of diversity branches. For the selection combining (SC) diversity, with Nakagami-m fading, expressions for the probability of detection are derived for the cases L =2 and L >; 2. A discussion on the comparison between MGF and PDF methods is presented. We also derive several series truncation error bounds that allow series termination with a finite number of terms for a given figure of accuracy. These results help quantify and understand the achievable improvement in the energy detector's performance with diversity reception. Numerical and simulation results are also provided.
Two Cases of Pelvic Actinomycosis associated with Intrauterine Contraceptive Device (IUD) (2002)

Pelvic actinomycosis is a rare chronic anaerobic infectious disease, which occurs most commonly in association with an IUD. It is difficult to diagnose the disease initially. In most cases, the diagnosis is made postoperatively because of its diverse clinical manifestations and courses. Besides it is frequently misdiagnosed as pelvic malignancy or endometriosis. If physician has a full understand to these characteristics of pelvic actinomycosis, the use of preoperative antibiotics can reduce the risk of pelvic structure injuries and then a patient can be saved from an extensive surgical procedure. We experienced four cases of pelvic actinomycosis complicated by tubo-ovarian abscess in women wearing IUD and report it with a brief review. In three cases, it was helpful that preoperative intravenous antibiotics therapy.
21.1: Invited Paper : FullColor Quantum Dot Display (2010)

Abstract Colloidal quantumdot lightemitting diodes QDLED have recently received considerable attention due to their ease of color tunability, high brightness and narrow spectral bandwidth. In this paper, the progress of QDLED toward display system and possibility of QDs for the application to fullcolor display will be presented.
In vivo oligomerization and raft localization of Ebola virus protein VP40 during vesicular budding (2003)

The matrix protein VP40 plays a critical role in Ebola virus assembly and budding, a process that utilizes specialized membrane domains known as lipid rafts. Previous studies with purified protein suggest a role for oligomerization of VP40 in this process. Here, we demonstrate VP40 oligomers in lipid rafts of mammalian cells, virus-like particles, and in the authentic Ebola virus. By mutagenesis, we identify several critical C-terminal sequences that regulate oligomerization at the plasma membrane, association with detergent-resistant membranes, and vesicular release of VP40, directly linking these phenomena. Furthermore, we demonstrate the active recruitment of TSG101 into lipid rafts by VP40. We also report the successful application of the biarsenic fluorophore, FlAsH, combined with a tetracysteine tag for imaging of Ebola VP40 in live cells.
Sparsity-based recovery of three-photon quantum states from two-fold correlations (2016)

Recovery of quantum states from measurements is an essential component in quantum information processing. In quantum optical systems, which naturally offer low decoherence and easy manipulation, quantum states are characterized by correlation measurements. When the states comprise more photons so as to encode more qubits, high-order correlation measurements are required. However, high-order correlations are hard to measure in experiments, as the rate of high-order coincidences decreases very fast when increasing the correlation order. This results in a poor signal-to-noise ratio. Likewise, the number of measurements required to characterize a quantum state increases exponentially with the increase in the number of qubits. Here, we use structure, present in most quantum states of interest (for quantum computing, cryptography, boson sampling, etc.), to recover the full quantum state of three photons from two-fold correlations in a single experimental setup.
Synthesis of Highly Coherent SiGe and Si4Ge Nanostructures by Molecular Beam Epitaxy of H3SiGeH3 and Ge(SiH3)4 (2003)

Stoichiometric SiGe and Si4Ge epitaxial films and coherent islands are created on Si(100) via thermal dehydrogenation of H3SiGeH3 and Ge(SiH3)4, respectively. The control of morphology and composition x of Si1-xGex nanostructures at the atomic level is achieved for the first time via CVD growth of single-source precursors containing precise atomic arrangements with direct Si−Ge bonds.
Second-harmonic generation in sodium and niobium borophosphate glasses after poling under field-assisted silver ions anodic injection (2008)

Monovalent silver ions, resulting from a thin silver layer initially deposited at the anode surface, have been introduced using the field-assisted ion-exchange technique in sodium niobium borophosphate glasses. A reproducible susceptibility χ(2) could be gained after this poling treatment, although a drop in the nonlinearity is observed due to the introduction of silver ions. From energy dispersive x-ray spectroscopy, it has been found that the nonlinear layer is characterized by a strong migration of sodium ions 4 μm deep inside the anode side, which have been partially replaced by silver ions. These results indicate a complex space-charge-migration process during the poling treatment, which is involved in the decrease in the mean second-harmonic generation signal.
ChemInform Abstract: Peptide Chemistry: Designing Peptides, Pseudopeptides, and Peptidomimetics for Biological Receptors (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
KBase: The United States Department of Energy Systems Biology Knowledgebase (2018)

Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Olson, Dan; Chan, Stephen Y; Kamimura, Roy T; Kumari, Sunita; Drake, Meghan M; Brettin, Thomas S; Glass, Elizabeth M; Chivian, Dylan; Gunter, Dan; Weston, David J; Allen, Benjamin H; Baumohl, Jason; Best, Aaron A; Bowen, Ben; Brenner, Steven E; Bun, Christopher C; Chandonia, John-Marc; Chia, Jer-Ming; Colasanti, Ric; Conrad, Neal; Davis, James J; Davison, Brian H; DeJongh, Matthew; Devoid, Scott; Dietrich, Emily; Dubchak, Inna; Edirisinghe, Janaka N; Fang, Gang; Faria, José P; Frybarger, Paul M; Gerlach, Wolfgang; Gerstein, Mark; Greiner, Annette; Gurtowski, James; Haun, Holly L; He, Fei; Jain, Rashmi; Joachimiak, Marcin P; Keegan, Kevin P; Kondo, Shinnosuke; Kumar, Vivek; Land, Miriam L; Meyer, Folker; Mills, Marissa; Novichkov, Pavel S; Oh, Taeyun; Olsen, Gary J; Olson, Robert; Parrello, Bruce; Pasternak, Shiran; Pearson, Erik; Poon, Sarah S; Price, Gavin A; Ramakrishnan, Srividya; Ranjan, Priya; Ronald, Pamela C; Schatz, Michael C; Seaver, Samuel MD; Shukla, Maulik; Sutormin, Roman A; Syed, Mustafa H; Thomason, James; Tintle, Nathan L; Wang, Daifeng; Xia, Fangfang; Yoo, Hyunseung; Yoo, Shinjae; Yu, Dantong
Supplementary Tables from Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer (2023)

&lt;p&gt;Supplementary Tables S1-S7&lt;/p&gt;
Safety of adalimumab in global clinical trials of patients with Crohn's disease. (2011)

RESULTS: 10 patients ages 9-17 (mean: 14.6 6 2.7 years; 30% male, 70% female), were enrolled. Caregivers reported a mean frequency of abdominal pain in the last two weeks of 3-6 days. The mean frequency of disease related problems effecting quality of life in the past 7 days was ' 'almost never' ' and mean disease -related functional disability was ' 'little to none' ' . One patient finished the complete treatment and 4 patients completed part of the treatment; in addition, 2 patients discontinued treatment due to IBD exacerbation, and 3 patients were lost to follow-up. Of those enrolled, 2/3 of all patients had a diagnosed psychiatric illness CONCLUSION: In this pilot study, home-based guided imagery therapy was not feasible in pediatric IBD patients with quiescent disease who had abdominal discomfort due to IBS. There may be various explanations for this. Treatment material was considered not age appropriate for older adolescents; thus, they may benefit more from adult-based treatments. In addition, functional abdominal pain was high in this patient population, but decreased quality of life and functional disability were almost non-existent. Lack of perceived significant impairment differentiates these patients from pediatric patients with functional abdominal pain and likely reduces willingness to comply with guided imagery exercises daily. Finally, most IBD patients suffered from significant anxiety which is associated with poor treatment outcomes in behavioral trials. Of note, all medical providers reported that they liked guided imagery programs since it decreased parental/ patient reluctance to seek psychological treatment for patient anxiety. Further efforts to address the need for treatment of functional gastrointestinal symptoms, with or without associated psychological co-morbidity, may benefit children with IBD.
Pharmacokinetics, drug metabolism, and tissue distribution of CPX-351 in animals (2020)

CPX-351, a liposomal encapsulation of cytarabine and daunorubicin at a synergistic 5:1 molar ratio, is indicated for adults with newly diagnosed, therapy-related acute myeloid leukemia or acute myeloid leukemia with myelodysplasia-related changes. In preclinical species, this article demonstrated (1) similar release of cytarabine and daunorubicin by CPX-351 in plasma; (2) similar patterns of metabolism of cytarabine and daunorubicin following administration of CPX-351 versus non-liposomal cytarabine/daunorubicin combination; (3) prolonged tissue exposure to CPX-351; (4) dramatically different tissue distribution of cytarabine and daunorubicin following administration of CPX-351 versus non-liposomal combination (tissue:plasma ratios generally <1 versus >1, respectively); and (5) dramatically lower unbound plasma and tissue concentrations of cytarabine and daunorubicin following administration of CPX-351 versus non-liposomal combination. Together, these results provide insight into the safety profile of CPX-351, as well as mechanisms that drive the improved efficacy observed for CPX-351 versus the conventional 7 + 3 cytarabine/daunorubicin regimen in clinical studies.
MOCVD growth of AlGaN films for solar blind photodetectors (2004)

AlGaN based ultraviolet solar blind photodiodes, operating at a peak wavelength of 274 nm with external quantum efficiencies of up to 46% at zero bias, were grown by low pressure MOCVD. The photodiodes operate via backside illumination, allowing the use of Mg doped GaN instead of a high Al mole fraction p-AlGaN layer. The effects of: the individual layer thicknesses, the Al composition difference between the n-type layer and intrinsic layer, the use of an AlGaN composition grade at the i-n interface, and the inclusion of an electron blocking layer at the p-i interface on the device performance were investigated. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Valproate-Selective Membrane Electrode Based on Gallium(III) Tetraphenylporphyrin (2000)

Gallium(III) tetraphenylporphyrin (GaTPP) was found to act as an ionophore for valproate, an agent widely used for anti-epileptic therapy. An electrode constructed using GaTPP and bis(1-butylpentyl)decane-1,10-diyl diglutarate (ETH 469) as a membrane solvent in a poly(vinyl chloride) membrane matrix exhibited a near-Nernstian response to valproate in the concentration range 5×10–5–1×10–2 M with a slope of –55 mV per concentration decade in a buffer solution containing 0.1 M 2-morpholinoethanesulfonic acid (MES)-NaOH (pH 5.5). The lower limit of detection was 20 µM. The electrode displayed the following selectivity sequence: valproate>salicylate> SCN–>benzoate>ClO4–≈F–>NO2–>CH3COO–≈I–>Cl–>NO3–. This electrode was applied to the determination of valproate levels in deproteinized serum samples.
Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19 (2020)

SARS-CoV-2 is responsible for the current COVID-19 pandemic. On the basis of our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues (the triphosphates of Sofosbuvir, Alovudine, and AZT) inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). We also demonstrated that a library of additional nucleotide analogues terminate RNA synthesis catalyzed by the SARS-CoV-2 RdRp, a well-established drug target for COVID-19. Here, we used polymerase extension experiments to demonstrate that the active triphosphate form of Sofosbuvir (an FDA-approved hepatitis C drug) is incorporated by SARS-CoV-2 RdRp and blocks further incorporation. Using the molecular insight gained from the previous studies, we selected the active triphosphate forms of six other antiviral agents, Alovudine, Tenofovir alafenamide, AZT, Abacavir, Lamivudine, and Emtricitabine, for evaluation as inhibitors of the SARS-CoV-2 RdRp and demonstrated the ability of these viral polymerase inhibitors to be incorporated by SARS-CoV-2 RdRp, where they terminate further polymerase extension with varying efficiency. These results provide a molecular basis for inhibition of the SARS-CoV-2 RdRp by these nucleotide analogues. If sufficient efficacy of some of these FDA-approved drugs in inhibiting viral replication in cell culture is established, they may be explored as potential COVID-19 therapeutics.
Graded dielectric lens to match 100 ps pulses into biological targets (2010)

Results from analytical calculations, numerical simulations and experiments for a radially inhomogeneous hemispherical dielectric lens are compared in this paper. Such a lens is used at the second focal point of a prolate-spheroidal impulse radiating antenna to match 100 ps pulses in to biological targets.
Synthesis and structure-activity relationship of novel indolizinoindolones with&lt;em&gt; in vitro&lt;/em&gt; antimalarial activity (2021)

Malaria is a vector-borne parasitic disease that continues to pose a serious public health challenge worldwide, despite all effort made towards prevention and control. The etiological agent is parasites of the species Plasmodium. that are transmitted to humans by the bite of infected Anopheles mosquitoes. The emergence of drug-resistant parasites has challenged the goal of eradicating malaria in the near future. In addition, current malaria therapeutics needs to address problems such as relapse and recrudescence events due to persistence of exo-erythrocytic forms in hepatocytes, and erythrocytic forms. Thus, it is still necessary to develop drugs that are effective against drug-resistant strains and active against all stages of the parasite life cycle. Recently, our group has reported the dual-stage antimalarial activity of a series of benzoindolizinoindolones. As part of our continuous effort to identify more potent antiplasmodial compounds, we synthetized 26 novel indolizinoindolones, through stereoselective cyclocondensation of a racemic keto-acid with enantiopure S- or R-tryptophanol, followed by stereocontrolled cyclization on the aromatic ring. Subsequently, we performed structure-activity studies and identified compounds with improved (nanomolar) activity, compared to our previous hit compound, against cultured malaria parasites.Together, this study corroborates our previous results that that identified indolizinoindolones as a promising scaffold for antimalarial drug discovery.
Superconducting and Insulating Behavior in One-Dimensional Josephson Junction Arrays (2000)

Experiments on one-dimensional small capacitance Josephson Junction arrays are described. The arrays have a junction capacitance that is much larger than the stray capacitance of the electrodes, which we argue is important for observation of Coulomb blockade. The Josephson energy can be tuned in situ and an evolution from Josephson-like to Coulomb blockade behavior is observed. This evolution can be described as a superconducting to insulating, quantum phase transition. In the Coulomb blockade state, hysteretic current-voltage characteristics are described by a dynamic model which is dual to the resistively shunted junction model of classical Josephson junctions.
Scheduling Support for Mixed VoIP and Web Traffic over HSDPA (2007)

HSDPA (high-speed downlink packet access), introduced in WCDMA release 5, provides a high-bandwidth shared channel with short transmission time interval (TTI). The short TTI together with appropriate scheduling enable HSDPA to support efficient multiplexing of traffic. We explain the performance of four scheduling algorithms when transmitting a traffic mix consisting of both conversational (VoIP) traffic and background (Web) traffic over the high-speed downlink shared channel (HS-DSCH) of HSDPA. We consider both cell throughput and user satisfaction. The proportional fair (PF), the maximum rate (MR) scheduler and two extended versions of MR, are tested for different VoIP scheduling delay budgets and varying load. To understand the behaviour of the schedulers, we use the ns-2 simulator extended with a model of HS-DSCH to simulate a mixed traffic scenario. Our results show that a scheduler that gradually increases the VoIP priority and considers the user's current possible rate, performs well. A more drastic increase in VoIP priority is however needed when the delay budget is short. Furthermore, attempting to uphold quality for both VoIP and Web traffic makes the system sensitive to overload situations.
Benzo[c][2,7]naphthyridin-5-yl-amine und Benzo[h][1,6]naphthyridin-5-yl-amine - Potenzielle Antimalariamittel (2006)

The chloroimine 1a reacted with the novaldiamine-base to yield the 5-(2-methylpyrrolidinyl)-derivative 3. The 5-chloro-benzonaphthyridines 1 and 9 reacted with secondary aliphatic amines to give the amidines 5-8 and 10, while the aromatic amidines 11-14 were obtained with primary aromatic amines. Mixtures of the phenol Mannich bases 15 and 16 of the isoquine type were isolated from the aminomethylation of 13b. The amodiaquine analogues 19 and 20 were obtained from the reaction of 1b and 9a with 4-amino-2-piperidinomethyl-phenol dihydrochloride. The structure of the compounds 5a (potassium salt), 6b, 10a, 11e and 18 was proven by X-ray crystal analysis. Compounds 3, 6a-e, 7, 10a, 11a, 16, 19 and 20 were tested for in vitro antimalarial activity using a chloroquine-sensitive and -resistant Plasmodium falciparum strain. The highest activity against the sensitive strain was shown by the amodiaquine analogoue 20 with an IC 50 value of 160 nM. The mixture of the isoquine derivatives 15a and 16a possessed the highest activity against the resistant strain with an IC 50 value of 1100 nM.
Random benchmark application generation for evaluating program analysis and testing tools (2012)

No abstract available.
Bit error rate calculation for a single sideband OFDM signal with direct detection optically pre-amplified receivers (2008)

We provide a fast and accurate BER calculation for a SSB-OFDM signal by considering the SNR of each subcarrier separately. The numerical results show that our scheme can accurately evaluate the BER for different QAM formats even under a strong optical filtering.
<i>In vivo</i> Gene Transfer for the Therapy of Vascular Diseases (1995)

We have developed an efficient vector system for the delivery of genes into various organ cells. The vector, HVJ-liposome, consists of DNA-nuclear ptotein loaded liposomes and UV-inactivated HVJ (Sendai virus). We found that the HVJ-liposome was very effective for in vivo delivery of oligonucleotides. When FITC-labeled oligonucleotides were introduced into vascular smooth muscle cells in vitro and in vivo, fluorescence was accumulated in the nucleus in 5 min after the transfer and existed there for 3 days in cultured cells in vitro and for 2-3 weeks in vascular walls in vivo. Antisense oligonucleotides against basic fibroblast growth factor introduced into primary vascular smooth muscle cells by HVJ-liposomes reduced DNA synthesis of the cells responded to angiotensin II treatment to 40%, compared to the introdcution of sense oligonucleotides. Next, we attempted to prevent the neointima formation of vascular walls after balloon injury by the introduction of antisense oligonucleotides against cell-cycle regulatory genes. Cotransfection of antisense cdc2 kinase and proliferating-cell nuclear antigen, or antisense cdc2 kinase and cyclin Bl, or cdc2 kinase and cdk2 kinase oligonucleotides inhibited completely neointima formation at 2 weeks after angioplasty by a single intraluminal transfer of oligonucleotides.