gebhart/patrepeval huggingface dataset:
Biphasic aqueous/organic biotransformation of acetaldehyde and benzaldehyde by <i>Zymomonas mobilis</i> pyruvate decarboxylase (2004)

Zymomonas mobilis pyruvate decarboxylase (PDC) transformed acetaldehyde and benzaldehyde into (R)-phenylacetylcarbinol (PAC), the precursor for the synthesis of ephedrine and pseudoephedrine. Organic solvents were screened for a biphasic biotransformation with the enzyme in an aqueous phase and the toxic substrates delivered through the organic phase. In the absence of substrates a second phase of 1-pentanol, hexadecane or MTBE (methyl tertiary-butyl ether) stabilized the PDC activity in comparison to a control without added solvent. Organic phase solvents for optimal PAC production had partitioning coefficient (log P) values between 0.8 and 2.8 (production of more than 8 mg PAC/ U PDC), however there was no correlation between enzyme stability and log P. Best PAC formation was observed with the eight tested alcohols, which in contrast to the other solvents allowed lower initial concentrations of toxic acetaldehyde (54-81 mM) in the aqueous phase. 1-pentanol, 1-hexanol, and isobutanol resulted in the highest specific PAC production of 11 mg PAC /U PDC. Without the addition of an organic phase, only 1.2 mg/U was formed.
Policies and Procedures Related to Testing for Weak D Phenotypes and Administration of Rh Immune Globulin: Results and Recommendations Related to Supplemental Questions in the Comprehensive Transfusion Medicine Survey of the College of American Pathologists (2014)

Selective integration of RHD genotyping policies and practices could improve the accuracy of Rh typing results, reduce unnecessary administration of Rh immune globulin in women with a weak D, and decrease transfusion of Rh-negative red blood cells in most recipients with a serological weak D phenotype.
Parton construction of particle-hole-conjugate Read-Rezayi parafermion fractional quantum Hall states and beyond (2019)

The Read-Rezayi (RR) parafermion states form a series of exotic non-Abelian fractional quantum Hall (FQH) states at filling $\ensuremath{\nu}=k/(k+2)$. Computationally, the wave functions of these states are prohibitively expensive to generate for large systems. We introduce a series of parton states, denoted ${\overline{2}}^{k}{1}^{k+1}$, and show that they lie in the same universality classes as the particle-hole-conjugate RR (``anti-RR'') states. Our analytical results imply that a $[U{(1)}_{k+1}\ifmmode\times\else\texttimes\fi{}U{(2k)}_{\ensuremath{-}1}]/[SU{(k)}_{\ensuremath{-}2}\ifmmode\times\else\texttimes\fi{}U{(1)}_{\ensuremath{-}1}]$ coset conformal field theory describes the edge excitations of the ${\overline{2}}^{k}{1}^{k+1}$ state, suggesting nontrivial dualities with respect to previously known descriptions. The parton construction allows wave functions in anti-RR phases to be generated for hundreds of particles. We further propose the parton sequence $\overline{n}{\overline{2}}^{2}{1}^{4}$, with $n=1,2,3$, to describe the FQH states observed at $\ensuremath{\nu}=2+1/2$, $2+2/5$, and $2+3/8$.
ChemInform Abstract: Diversifying the Structural Architecture of Synthetic Oligomers: The Hetero Foldamer Approach (2011)

Abstract Review: 106 refs.
The histone acetyltransferase MOF activates hypothalamic polysialylation to prevent diet-induced obesity in mice (2014)

Overfeeding causes rapid synaptic remodeling in hypothalamus feeding circuits. Polysialylation of cell surface molecules is a key step in this neuronal rewiring and allows normalization of food intake. Here we examined the role of hypothalamic polysialylation in the long-term maintenance of body weight, and deciphered the molecular sequence underlying its nutritional regulation. We found that upon high fat diet (HFD), reduced hypothalamic polysialylation exacerbated the diet-induced obese phenotype in mice. Upon HFD, the histone acetyltransferase MOF was rapidly recruited on the St8sia4 polysialyltransferase-encoding gene. Mof silencing in the mediobasal hypothalamus of adult mice prevented activation of the St8sia4 gene transcription, reduced polysialylation, altered the acute homeostatic feeding response to HFD and increased the body weight gain. These findings indicate that impaired hypothalamic polysialylation contribute to the development of obesity, and establish a role for MOF in the brain control of energy balance.
Fabrication of Waveguide Laser Crystals by Laser Ablation Method. Toward the Fabrication of Laser Crystals on Si Substrates. (1998)

OEIC (Optoelectronic integrated circuit) which interconnects various optical and electronic elements on thesame substrate, is a promising device in near future. The fabrication method ofoptical waveguides is desirableto be a vapor phase epitaxy and suitable for in situ processing. LPE (Liquid Phase Epitaxy) methods arewidely used to fabricate thin films, but recently much attention has been paid to PLD (Pulsed Laser Deposition) methods in the fabrication of optical thin films with various advantages such as adaptability to in-situ, processing, simple arrangement, stoichiometry of the films, epitaxial quality of complicated compoundmaterials as good as those by MBE (Molecular Beam Epitaxy) and MOCVD (Metal-Organic Chemical Vapor Deposition). In the present paper, it is experimentally shown that this PLD method is very effective andaffordable as fabrication techniques of these optical thin films.
Viral vector mediated tolerance induction in experimental autoimmune encephalomyelitis by dendritic cell targeted expression of a self-antigen (115.2) (2011)

Abstract Multiple sclerosis (MS) is an autoimmune disease characterized by the presence of self-reactive T cells that target myelin components. Immunization of susceptible animals with myelin antigens induces experimental autoimmune encephalomyelitis (EAE), an animal model for MS. The aim of this project was to induce permanent, antigen-specific tolerance in EAE/MS and to address the mechanisms that would contribute to tolerance. The strategy includes the ex vivo modification of autologous hematopoietic stem cells (HSC) with lentiviral vectors that express myelin oligodendrocyte glycoprotein (MOG) under the control of a dendritic cell (DC) specific promoter. After re-infusion, the modified HSC will give rise to antigen expressing DCs. We demonstrated the effectiveness of this strategy for inducing MOG-specific tolerance in EAE, as 100% of the mice that received BM cells transduced with MOG-lentivector were protected. In addition, we show depletion of MOG specific T cells and generation of Foxp3+ regulatory T cells in chimeras that received HSC transduced with MOG-lentivector. As apposed to the protected animals, the diseased control mice showed high levels of IL-1, INF-γ and IL-17. The strategy presented here is particularly promising for clinical applications and important for addressing fundamental questions in immunity and tolerance.
Systematic investigation of the growth rate of β-Ga<sub>2</sub>O<sub>3</sub>(010) by plasma-assisted molecular beam epitaxy (2014)

β-Ga2O3(010) homo-epitaxial growth was performed by plasma-assisted molecular beam epitaxy. Under Ga-rich conditions and for growth temperatures above 650 °C, the growth rate was independent of the Ga/O ratio (>1). A high growth rate of 2.2 nm/min for β-Ga2O3(010) was achieved by optimizing the O flux between 650 and 750 °C. Under Ga-rich conditions between growth temperatures of 500–900 °C, smooth surfaces with rms roughness below 1 nm were realized. We found that the slightly Ga-rich conditions between 650 and 750 °C were optimal for β-Ga2O3(010) growth with a smooth surface and a high growth rate.
Situation Awareness and Cognitive Modeling (2012)

This paper discusses the basic concepts of computer support for situation awareness. The main idea is to share “situations” by computer and human agents. Two cases of situation awareness are discussed. Some of the future research topics are listed.
Probing the Dynamics of CO<sub>2</sub> and CH<sub>4</sub> within the Porous Zirconium Terephthalate UiO‐66(Zr): A Synergic Combination of Neutron Scattering Measurements and Molecular Simulations (2011)

Quasi-elastic neutron scattering (QENS) measurements combined with molecular dynamics (MD) simulations were conducted to deeply understand the concentration dependence of the self- and transport diffusivities of CH(4) and CO(2), respectively, in the humidity-resistant metal-organic framework UiO-66(Zr). The QENS measurements show that the self-diffusivity profile for CH(4) exhibits a maximum, while the transport diffusivity for CO(2) increases continuously at the loadings explored in this study. Our MD simulations can reproduce fairly well both the magnitude and the concentration dependence of each measured diffusivity. The flexibility of the framework implemented by deriving a new forcefield for UiO-66(Zr) has a significant impact on the diffusivity of the two species. Methane diffuses faster than CO(2) over a broad range of loading, and this is in contrast to zeolites with narrow windows, for which opposite trends were observed. Further analysis of the MD trajectories indicates that the global microscopic diffusion mechanism involves a combination of intracage motions and jump sequences between tetrahedral and octahedral cages.
Neutral-beam interactions with materials. Final report, 1 June 1984-31 October 1985 (1985)

The basic approach involves coupling a one-dimensional hydrodynamic code to an ionization dynamics and an energy-deposition model. Radiation emitted by the plasma is an important diagnostic tool; the ionization dynamics is accomplished by developing an ionization dynamics model which considers a large number of excited states and atomic processes. The atomic processes considered in the model are: 1) collisional ionization; 2) three-body recombination; 3) collisional excitation; 4) collisional de-excitation; 5) spontaneous emission; 6) radiative recombination; and 7) dielectric recombination. A model to calculate the stopping power for energetic, structured (those carrying electrons into the target) low-Z ions was developed. Low-Z ions are both energetic and structured at typical specific energies of a few hundred keV/amu (e.g. 1 MeV helium). The atomic structure is taken into account by describing the electron cloud of the projectile with elastic form factors in the first Born approximation. However, at these energies, the first Born approximation begins to break down. Hence, two corrections are included: the Bloch correction to account for the scattering of wave packets (instead of plane waves) for close collisions, and the Barkas effect which corrects for deviations from pure Rutherford scattering due to the displacement of an oscillating electron. Structure ismore » introduced more approximately in these two terms. An attempt was made to allow sufficient generality to describe ionized targets as well as neutral solids.« less
Bedaquiline resistance in drug-resistant tuberculosis HIV co-infected patients (2020)

<b>Genetic mutations linked to bedaquiline resistance were found before starting treatment and acquired during treatment in patients with drug-resistant TB and HIV in KwaZulu-Natal, South Africa. Routine bedaquiline resistance testing needs to be accelerated.</b>http://bit.ly/2vnL4VY
Time Weighted Average Concentration Monitoring Based on Thin Film Solid Phase Microextraction (2017)

Time weighted average (TWA) passive sampling with thin film solid phase microextraction (TF-SPME) and liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for collection, identification, and quantification of benzophenone-1, benzophenone-2, benzophenone-3, benzophenone-4, 2-phenylbenzimidazole-5-sulfonic acid, octocrylene, octylmethoxycinnamate, butylmethoxydibenzoylmethane, triclocarban and triclosan in the aquatic environment. Two types of TF-SPME passive samplers, including a retracted thin film device using a hydrophilic lipophilic balance (HLB) coating, and an open bed configuration with an octadecyl silica-based (C18)coating, were evaluated in an aqueous standard generation system. Laboratory calibration results indicated that the thin film retracted device using HLB coating is suitable to determine TWA concentrations of polar analytes in water, with an uptake that was linear up to 70 days. In open bed form, a one-calibrant kinetic calibration technique was accomplished by loading benzophenone3-d<sub>5</sub> as calibrant on the C18 coating to quantify all nonpolar compounds. The experimental results showed that the one-calibrant kinetic calibration technique can be used for determination of classes of compounds in cases where deuterated counterparts are either not available or expensive. The developed passive samplers were deployed in wastewater-dominated reaches of the Grand River (Kitchener, ON) to verify their feasibility for determination of TWA concentrations in on-site applications. Field trials results indicated that these devices are suitable for long-term and short-term monitoring of compounds varying in polarity, such as UV blockers and biocide compounds in water, and the data were in good agreement with literature data.
Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses (2017)

Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy. Here, we describe a novel application of UV laser-induced (L-) crosslinking and demonstrate that a combination of chemical and L-crosslinking is able to distinguish between direct and indirect DNA-protein interactions in a small number of living cells. The spatial and temporal dynamics of TF bindings to chromatin and their role in gene expression regulation may thus be assessed. The combination of chemical and L-crosslinking offers an exciting and unprecedented tool for biomedical applications.
Anatomic Anterior Cruciate Ligament Double-Bundle Reconstruction Using 2 Tibial and 2 Femoral Tunnels (2005)

Summary: Over the last decade, anterior cruciate ligament (ACL) reconstruction has been continuously improved. Although the current outcomes of the single-bundle ACL reconstruction are good, there remains significant room for improvement. A high percentage of patients do not return to their previous level of activity, and progressive cartilage degeneration continues to be a common problem after ACL injury. The evaluation of the 3-dimensional in vivo kinematics of the knee joint after single-bundle ACL reconstruction has demonstrated good restoration of the anteroposterior stability, whereas the rotational stability cannot be restored. Similarly, biomechanical studies in cadavers reveal that anatomic double-bundle ACL reconstruction restores the rotational knee stability more closely to normal than single-bundle ACL reconstruction. Based on these considerations, we suggest an anatomic double-bundle ACL reconstruction technique using 2 tibial and 2 femoral tunnels. This technique restores both the anteromedial and the posterolateral bundle of the ACL.
Performance of limited‐state sequence estimation under land mobile frequency‐selective fading channels (1996)

Abstract The frequency‐selective fading is one of the problems in the high‐speed transmission in land mobile communications. A solution is to use the Viterbi equalizer. When this method is applied to the highly efficient modulation system such as QPSK, however, the computational complexity increases rapidly with the increase of the delay time of the delayed wave to be compensated. This makes the instrumentation impractical. This paper proposes a method in which the computational complexity is reduced drastically by the limited‐state sequence estimation. In the proposed method, limited‐state sequence estimation (Viterbi algorithm) is applied where two waves with the largest powers are selected based on the estimated impulse response. Based on the tentative decision obtained beforehand by a simple method, the effects of other waves are eliminated. The number of states is estimated considering only the selected two waves. The performance of the proposed method is examined by a computer simulation. It is shown as a result that the range of compensation can be enlarged and the computational complexity can be reduced, compared to the conventional simplified method. In other words, the effectiveness of the proposed method is demonstrated.
Supplementary Methods, Figures 1-6 from Enhanced Efficacy of Therapeutic Cancer Vaccines Produced by Co-Treatment with &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; Heparin-Binding Hemagglutinin, a Novel TLR4 Agonist (2023)

Supplementary Methods, Figures 1-6 from Enhanced Efficacy of Therapeutic Cancer Vaccines Produced by Co-Treatment with &lt;i&gt;Mycobacterium tuberculosis&lt;/i&gt; Heparin-Binding Hemagglutinin, a Novel TLR4 Agonist
Novel pyrrolocycloalkylpyrazole analogues as CB<sub>1</sub> ligands (2017)

Novel 1,4-dihydropyrazolo[3,4-a]pyrrolizine-, 4,5-dihydro-1H-pyrazolo[4,3-g]indolizine- and 1,4,5,6-tetrahydropyrazolo[3,4-c]pyrrolo[1,2-a]azepine-3-carboxamide-based compounds were designed and synthesized for cannabinoid CB<sub>1</sub> and CB<sub>2</sub> receptor interactions. Any of the new synthesized compounds showed high affinity for CB<sub>2</sub> receptor with K<sub>i</sub> values superior to 314 nm, whereas some of them showed moderate affinity for CB<sub>1</sub> receptor with K<sub>i</sub> values inferior to 400 nm. 7-Chloro-1-(2,4-dichlorophenyl)-N-(homopiperidin-1-yl)-4,5-dihydro-1H-pyrazolo[4,3-g]indolizine-3-carboxamide (2j) exhibited good affinity for CB<sub>1</sub> receptor (K<sub>i</sub> CB<sub>1</sub> = 81 nm) and the highest CB<sub>2</sub> /CB<sub>1</sub> selectively ratio (>12). Docking studies carried out on such compounds were performed using the hCB<sub>1</sub> X-ray in complex with the close pyrazole analogue AM6538 and disclosed specific pattern of interactions related to the tricyclic pyrrolopyrazole scaffolds as CB<sub>1</sub> ligands.
Knowledge Transfer from Large-Scale Pretrained Language Models to End-To-End Speech Recognizers (2022)

End-to-end speech recognition is a promising technology for enabling compact automatic speech recognition (ASR) systems since it can unify the acoustic and language model into a single neural network. However, as a drawback, training of end-to-end speech recognizers always requires transcribed utterances. Since end-to-end models are also known to be severely data hungry, this constraint is crucial especially because obtaining transcribed utterances is costly and can possibly be impractical or impossible. This paper proposes a method for alleviating this issue by transferring knowledge from a language model neural network that can be pretrained with text-only data. Specifically, this paper attempts to transfer semantic knowledge acquired in embedding vectors of large-scale language models. Since embedding vectors can be assumed as implicit representations of linguistic information such as part-of-speech, intent, and so on, those are also expected to be useful modeling cues for ASR decoders. This paper extends two types of ASR decoders, attention-based decoders and neural transducers, by modifying training loss functions to include embedding prediction terms. The proposed systems were shown to be effective for error rate reduction without incurring extra computational costs in the decoding phase.
Conductively-cooled, high-energy, single-frequency diode pumped slab laser for space applications (2010)

A laser-diode-pumped high efficiency, high pulse energy and single-frequency oscillator and amplifier for potential space environment applications have been developed and demonstrated using conductively-cooled heat removal. A diode-pumped injection seeded single-frequency oscillator was achieved by using the resonance-detection technique in Q-Switching operation, and Nd: YAG zigzag slabs based on “pump on bounce” are used in power amplifier stage for high-efficiency pulse energy extraction. Output pulse energy of 800 mJ with 11 ns pulse duration is obtained at a repetition rate of 100 Hz, with a near 3× diffraction-limit beam and an optical-to-optical efficiency of 18%. The experimental result shows that the laser has compact structure, high efficiency, reliability, conductive cooling and can be used for space environments.
Acute compressive stress activates RHO/ROCK-mediated cellular processes (2018)

The ability to rapidly respond to applied force underpins cell/tissue homeostasis. This response is mediated by mechanotransduction pathways that regulate remodeling and tension of the actomyosin cytoskeleton to counterbalance external forces. Enhanced extracellular matrix tension hyper-activates mechanotransduction and characterizes diseased states such as cancer, but is also required for normal epidermal regeneration. While the impact of extracellular matrix tension on signaling and cell biology are well appreciated, that of acute compressive force is under-studied. We show here that acute compressive force applied to cells and tissues in a native 3-dimensional context elevates RHOA-GTP levels and increases regulatory myosin phosphorylation, actomyosin contractility and tension via ROCK. In consequence, cell proliferation was increased, as was the expression of regulators of epithelial-mesenchymal transition. Pharmacological inhibition of ROCK abrogated myosin phosphorylation, but not RHOA activation. Our results strongly suggest that acute compressive stress impairs cellular homeostasis in a RHO/ROCK-dependent manner, with implications for disease states such as cancer.
Effect of postoperative corticosteroids on surgical outcome and aqueous autotaxin following combined cataract and microhook ab interno trabeculotomy (2021)

To evaluate the effect of postoperative corticosteroids on surgical outcome and autotaxin (ATX) levels after microhook ab interno trabeculotomy combined with cataract surgery (μLOT-CS), prospective, consecutive non-randomized case series comparing outcomes of 30 eyes with primary open angle glaucoma was performed. The aqueous ATX, intraocular pressure (IOP) and glaucoma medications were monitored for 3 months postoperatively. An in-vivo mouse μLOT model was generated. In vitro, ATX and fibrotic changes induced by dexamethasone (Dex) treatment following scratch (S) in cultured human trabecular meshwork (hTM) cells were assessed by immunofluorescence, immunoenzymatic assay, and RT-qPCR. Postoperative ATX at 1 week and the number of antiglaucoma medications at 3 months were significantly lower in non-steroid group, and steroid use was the only variable significantly associated with postoperative medications at 3 months in multiregression analyses. In vitro, ATX activity was significantly upregulated in the Dex + S group, and αSMA was significantly upregulated in the Dex and Dex + S groups. Fibronectin and COL1A1 were significantly upregulated in the S group. μLOT-CS decreased IOP and medications in the overall cohort, and non-use of postoperative steroids resulted in a smaller number of postoperative medications. Limiting postoperative steroids in μLOT may minimize IOP elevation and postoperative fibrosis.