gebhart/patrepeval huggingface dataset:
A Faster Approximation Algorithm for the Gibbs Partition Function. (2016)

We consider the problem of estimating the partition function $Z(\beta)=\sum_x \exp(-\beta(H(x))$ of a Gibbs distribution with a Hamilton $H(\cdot)$, or more precisely the logarithm of the ratio $q=\ln Z(0)/Z(\beta)$. It has been recently shown how to approximate $q$ with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in $[0,\beta]$. The current best known approach due to Huber [9] uses $O(q\ln n\cdot[\ln q + \ln \ln n+\varepsilon^{-2}])$ oracle calls on average where $\varepsilon$ is the desired accuracy of approximation and $H(\cdot)$ is assumed to lie in $\{0\}\cup[1,n]$. We improve the complexity to $O(q\ln n\cdot\varepsilon^{-2})$ oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within $O(\frac{\varepsilon^2}{q\ln n})$ variation distance from exact oracles. Finally, we prove a lower bound of $\Omega(q\cdot \varepsilon^{-2})$ oracle calls under a natural model of computation.
Condensation of Triethoxysilyl-Terminated Polystyrene with Acid Catalysts. (1994)

酸触媒によるトリエトキシシリル末端ポリスチレン (TESi-PS) の縮合反応を種々の条件で行った. ハロゲン化水素酸やスルホン酸は縮合反応の触媒として高活性を示した. これに対し, トリフルオロ酢酸は低活性であり, その場合, 溶媒の種類により反応速度の差が顕著にみられた. 例えば, テトラヒドロフラン (THF) を用いると反応は遅いが, ニトロベンゼンやジクロロエタンなどの溶媒では速やかに進行した. TESi-PSの縮合反応は, 末端エトキシ基の加水分解が律速段階で, 加水分解後は速やかにシラノール基の脱水縮合が起きていることが示唆された. 縮合生成物の重合度は, 用いた触媒や溶媒の種類によって異なり, 硝酸/THF系では2量体が生成し, 塩酸/THF系やメタンスルホン酸/THF系では3量体が, リン酸/THF系やメタンスルホン酸/ジクロロエタン系では4量体が生成した. これら縮合生成物はいずれも単分散性に優れていた (Mw/Mn&cong; 1.07).
Ferroelectricity in Gd-Doped HfO2Thin Films (2012)

The incorporation of Gd into HfO2 thin films is shown to induce ferroelectricity. A significant influence of electric field cycling on both polarization as well as small-signal capacitance-voltage measurements can be observed. X-ray diffraction measurements are supported by infrared absorption analysis and give further evidence of the previously proposed non-centrosymmetric transition phase of space group Pbc21.
Increased cathepsin D level in the serum of patients with metastatic breast carcinoma detected with a specific pro-cathepsin D immunoassay. (1997)

An increased level of cath-D in the serum of breast carcinoma patients is a late event observed only in patients with metastatic disease. This increased circulating level is more likely due to increased secretion of the proenzyme rather than to tumor cell lysis.
Expression Profiling Elucidates a Molecular Gene Signature for Pulmonary Hypertension in Sarcoidosis (2016)

Pulmonary hypertension (PH), when it complicates sarcoidosis, carries a poor prognosis, in part because it is difficult to detect early in patients with worsening respiratory symptoms. Pathogenesis of sarcoidosis occurs via incompletely characterized mechanisms that are distinct from the mechanisms of pulmonary vascular remodeling well known to occur in conjunction with other chronic lung diseases. To address the need for a biomarker to aid in early detection as well as the gap in knowledge regarding the mechanisms of PH in sarcoidosis, we used genome-wide peripheral blood gene expression analysis and identified an 18-gene signature capable of distinguishing sarcoidosis patients with PH (<i>n</i> = 8), sarcoidosis patients without PH (<i>n</i> = 17), and healthy controls (<i>n</i> = 45). The discriminative accuracy of this 18-gene signature was 100% in separating sarcoidosis patients with PH from those without it. If validated in a large replicate cohort, this signature could potentially be used as a diagnostic molecular biomarker for sarcoidosis-associated PH.
Atom‐Efficient Gold(I)‐Chloride‐Catalyzed Synthesis of α‐Sulfenylated Carbonyl Compounds from Propargylic Alcohols and Aryl Thiols: Substrate Scope and Experimental and Theoretical Mechanistic Investigation (2013)

Gold(I)-chloride-catalyzed synthesis of α-sulfenylated carbonyl compounds from propargylic alcohols and aryl thiols showed a wide substrate scope with respect to both propargylic alcohols and aryl thiols. Primary and secondary aromatic propargylic alcohols generated α-sulfenylated aldehydes and ketones in 60-97% yield. Secondary aliphatic propargylic alcohols generated α-sulfenylated ketones in yields of 47-71%. Different gold sources and ligand effects were studied, and it was shown that gold(I) chloride gave the highest product yields. Experimental and theoretical studies demonstrated that the reaction proceeds in two separate steps. A sulfenylated allylic alcohol, generated by initial regioselective attack of the aryl thiol on the triple bond of the propargylic alcohol, was isolated, evaluated, and found to be an intermediate in the reaction. Deuterium labeling experiments showed that the protons from the propargylic alcohol and aryl thiol were transferred to the 3-position, and that the hydride from the alcohol was transferred to the 2-position of the product. Density functional theory (DFT) calculations showed that the observed regioselectivity of the aryl thiol attack towards the 2-position of propargylic alcohol was determined by a low-energy, five-membered cyclic protodeauration transition state instead of the strained, four-membered cyclic transition state found for attack at the 3-position. Experimental data and DFT calculations supported that the second step of the reaction is initiated by protonation of the double bond of the sulfenylated allylic alcohol with a proton donor coordinated to gold(I) chloride. This in turn allows for a 1,2-hydride shift, generating the final product of the reaction.
Concentrations of canine prostate specific esterase, CPSE, at baseline are associated with the relative size of the prostate at three-year follow-up (2021)

The results support the use of CPSE for estimating present and future prostatic size in dogs ≥4 years, and the clinical usefulness of prostatic size for predicting development of clinical signs of prostatic disease in the dog. The association between corticosteroids and prostate growth warrants further investigation.
Erratum: “Practical guides for x-ray photoelectron spectroscopy: First steps in planning, conducting, and reporting XPS measurements” [J. Vac. Sci. Technol. A 37, 031401 (2019)] (2020)

First Page
Enhancing Feedback Control Scheduling Performance by On-line Quantification and Suppression of Measurement Disturbance (2005)

In the control of continuous and physical systems, the controlled system is sampled sufficiently fast to capture the system dynamics. In general, this property cannot be applied to the control of computer systems as the measured variables are often computed over a data set, e.g., deadline miss ratio. In this paper we quantize the disturbance present in the measured variable as a function of the sampling period and we propose a measurement disturbance suppressive control structure. The experiments we have carried out show that a controller using the proposed control structure outperforms a traditional control structure with regard to performance reliability and adaptation.
Biochemical Mechanisms for Disrupting the Proteinase-Proteinase Inhibitor Balance in Tissues (1993)

The regulation of proteolytic activity in tissues by members of the Serpin family of inhibitors is normally tightly controlled. However, numerous mechanisms are available for interrupting this process in pathological tissues by depleting functional inhibitory activity at inflammatory foci. These include a) saturation of inhibitory activity due to excessive proteinase release from inflammatory cells, b) oxidative inactivation of inhibitory activity, c) proteolytic inactivation of inhibitory activity by non-complexing proteinases. In an attempt to regain a normal inhibitor-proteinase balance, however, it is now known that both inhibitor: enzyme complexes and inactive forms of inhibitors can act as signalling agents for the resynthesis of functionally active proteins. Thus, during inflammatory episodes where the levels of functional inhibitors are continually being depleted, mechanisms are in place to signal either directly or indirectly for their resynthesis.
Array-Based Electrical Detection of DNA with Nanoparticle Probes* (2020)

A DNA array detection method is reported in which the binding of oligonucleotides functionalized with gold nanoparticles leads to conductivity changes associated with target-probe binding events. The binding events localize gold nanoparticles in an electrode gap; silver deposition facilitated by these nanoparticles bridges the gap and leads to readily measurable conductivity changes. An unusual salt concentration–dependent hybridization behavior associated 1458with these nanoparticle probes was exploited to achieve selectivity without a thermal-stringency wash. Using this method, we have detected target DNA at concentrations as low as 500 femtomolar with a point mutation selectivity factor of ~100,000:1.
PPARα siRNA–Treated Expression Profiles Uncover the Causal Sufficiency Network for Compound-Induced Liver Hypertrophy (2007)

Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi) phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs) against the gene for peroxisome proliferator-activated receptor alpha (Ppara), our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARalpha-induced liver hypertrophy is supported by their ability to predict non-PPARalpha-induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005). Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug-induced toxicity from siRNA-treated expression profiles. When combined with phenotypic evaluation, our approach should help to unleash the full potential of siRNAs in systematically unveiling the molecular mechanism of biological events.
Experimental techniques for the development of a uterus transplantation model in cynomolgus macaques (2020)

Uterus transplantation (UTx) is now a treatment for women with uterine factor infertility to have a child. However, UTx is still largely at the experimental stage, and many medical issues remain unsolved. Therefore, adequate studies in large animals including non-human primates are required for validation of these issues. UTx research, especially in non-human primates, can provide important information for its full establishment in humans due to the anatomical and physiological similarities between the two. We accumulated data from UTx studies using cynomolgus macaques since 2009 and established autologous and allogeneic UTx models which led to deliveries after performing the procedure. In this paper, we summarized key points to develop UTx models in cynomolgus macaques based on our experience. UTx models in non-human primates can surely contribute new and beneficial knowledge in this field and can be useful for the further development of UTx in humans.
A Method for Molecular Alignment of Ferroelectric Smectic Liquid Crystal: Combination of Metal Oxide Thin Film and Electric Field (1988)

A method for molecular alignment of a ferroelectric smectic liquid crystal is reported. Homeotropic alignment with a small angle of pretilt was obtained by surface treatment with oblique deposition of metal oxide, such as yttria and alumina. Furthermore, an electric field was applied during the cooling period from isotropic liquid to chiral smectic phase. Uniformly pretilted alignment could be obtained by using the oblique deposition and DC field application. On the other hand, a twisted alignment was obtained on the obliquely deposited metal oxide film when an AC electric field was applied instead of a DC field. Electrooptical characteristics of these cells are shown.
Straddling the Boundary between Contribution and Solution Driven Science (2020)

Advancing the state of the art in the context of products and services used by hundreds of millions of customers poses challenges that go beyond those associated with advancing the state of the art in customer-free settings. In this talk, I will highlight some of these challenges and discuss approaches to overcoming them in the context of two Amazon services: Amazon Translate and Alexa.
Sustainability of cellulose dissolution and regeneration in 1,5-diazabicyclo[4.3.0]non-5-enium acetate: a batch simulation of the IONCELL-F process (2015)

A laboratory batch simulation of the recovery and reuse of [DBNH][OAc] in the IONCELL-F process, yielding future directions for optimising the recycling process.
Front Cover: Direct coupling of size exclusion chromatography and mass spectrometry for the characterization of complex monoclonal antibody products (2022)

DOI: 10.1002/jssc.202200075 The SEC mobile phase was exclusively composed of 50 mM ammonium acetate in water, while a specially designed bioinert SEC column was employed, as highlighted in the central part of the picture. This column includes a novel hardware surface where column frits and metallic column walls were treated to have prototype hydrophilically modified hybrid organicinorganic silica surfaces. This new material instead of stainless steel strongly reduce non-desired hydrophobic and electrostatic interaction under SEC conditions with volatile mobile phase. Thus, an improvement of peak tailing, band broadening and above all recovery of mAb products was noticed with this new column hardware compared to regular SEC column, as illustrated in the left panel of the picture. Finally, the direct SEC-MS analysis was successfully applied to characterize low molecular weight species (fragments) and high molecular weight species (such as dimer) contained in complex bispecific mAb products with mass spectrometry, as shown in the right part of the picture.
Multi-level multi-thermal-electron FDTD simulation of plasmonic interaction with semiconducting gain media: applications to plasmonic amplifiers and nano-lasers (2010)

Interactions between a semiconducting gain medium and confined plasmon-polaritons are studied using a multilevel multi-thermal-electron finite-difference time-domain (MLMTE-FDTD) simulator. We investigated the amplification of wave propagating in a plasmonic metal-semiconductor-metal (MSM) waveguide filled with semiconductor gain medium and obtained the conditions required to achieve net optical gain. The MSM gain waveguide is used to form a plasmonic semiconductor nano-ring laser(PSNRL) with an effective mode volume of 0.0071 microm3, which is about an order of magnitude smaller than the smallest demonstrated integrated photonic crystal based laser cavities. The simulation shows a lasing threshold current density of 1kA/cm2 for a 300 nm outer diameter ring cavity with 80 nm-wide ring. This current density can be realistically achieved in typical III-V semiconductor, which shows the experimental feasibility of the proposed PSNRL structure.
Buckling of dielectric elastomeric plates for soft, electrically active microfluidic pumps (2014)

Elastic instabilities, when properly implemented within soft, mechanical structures, can generate advanced functionality. In this work, we use the voltage-induced buckling of thin, flexible plates to pump fluids within a microfluidic channel. The soft electrodes that enable electrical actuation are compatible with fluids, and undergo large, reversible deformations. We quantified the onset of voltage-induced buckling, and measured the flow rate within the microchannel. This embeddable, flexible microfluidic pump will aid in the generation of new stand-alone microfluidic devices that require a tunable flow rate.
Quantification of the Phase Transformation Kinetics in High Chromium Cast Irons Using Dilatometry and Metallographic Techniques (2020)

Abstract Further development of high chromium cast irons (HCCI) is based on tailoring the microstructure, necessitating an accurate control over the phase transformation and carbide precipitation temperatures and can be achieved by thermal treatments (TT). To understand the underlying mechanisms controlling the transformation kinetics during the different stages of the TT, it is imperative to adjust the TT parameters to have information of the transformations occurring during non-thermal and isothermal heating cycles, since proper selection of the TT parameters ensures the optimum use of the alloying elements. In this work, the boundaries of the phase transformations for a HCCI containing 26 wt pct Cr for different cooling rates (continuous cooling transformation, CCT, diagram) were established by applying dilatometric measurements. Based on the CCT diagram, a temperature-time-transformation (TTT) diagram was constructed by isothermally holding the samples until complete phase transformation. For determining the initiation and finishing of the transformation, the lever rule assisted by derivatives was applied. The phases present after transformation were determined by combining X-ray diffraction (XRD) and metallographic characterization using optical microscopy (OM) and scanning electron microscopy (SEM). Finally, the data obtained from the dilatometer was experimentally verified by isothermally heat treating some samples using laboratory furnaces. The transformed phase fraction from OM and SEM images was then correlated to the fraction obtained from the TTT diagram.
Reactions of H2 and R3SiH with Electrophilic Cobalt(III) Alkyl Complexes:  Spectroscopic Characterization, Dynamics, and Chemistry of [Cp*Co(L)(H)(η2-H2)][B(ArF)4] and [Cp*Co(L)(H)(η2-HSiR3)][B(ArF)4] (2007)

Co(III) agostic alkyl complexes [Cp*Co(L)(CH2CH2-μ-H)][B(ArF)4] (Cp* = C5(CH3)5, L = P(OCH3)3, 1a, or P(CH3)3, 1b; ArF = 3,5-(CF3)2C6H3) react with H2 to yield ethane and trihydride complexes characterized as η2-dihydrogen hydride species [Cp*Co(L)(H)(η2-H2)][B(ArF)], 2a and 2b, in which there is rapid scrambling between the η2-H2 ligand and the terminal Co−H. Complexes 2a and 2b react with a variety of neutral donor ligands (L‘ = RCN, PMe3, P(OMe)3, H2O, CH3OH) to yield [Cp*Co(L)(L‘)(H)][B(ArF)4] complexes. Reaction of silanes with either 1a,b in the presence of traces of water or 2a,b yields η2-silane hydrides, [Cp*Co(L)(H)(η2-HSiR3)][B(ArF)4]. Analysis of the dynamics of these species by NMR spectroscopy provides evidence for an extremely rapid process involving silyl migration between hydrogens and a slower process in which a cobalt-silyl η2-H2 complex is formed as an intermediate and results in hydrogen scrambling between the two diastereomers of [Cp*Co(L)(H)(η2-H-SiHMePh)][B(ArF)4]. The structures and dynamics of 2a,b and the η2-silane complexes imply that cleavage of the cobalt−alkyl bonds of 1a,b in hydrogenation and hydrosilation catalytic cycles occurs by the σ-CAM (σ-complex-assisted metathesis) process.
A Strategy for the Determination of Enzyme Kinetics Using Electrospray Ionization with an Ion Trap Mass Spectrometer (2001)

A simple and rapid means of enzyme kinetic analysis was achieved using electrospray ionization mass spectrometry and a one-point normalization factor. The model system used, glutathione S-transferase from porcine liver, is a two-substrate enzyme catalyzing the conjugation of glutathione with a variety of compounds containing an electrophilic center. An internal standard that is structurally similar to the product was added to the reaction quench solution, and a single-point normalization factor was used to determine the product concentration without the need of a calibration curve. Kinetic parameters, such as Km, Vmax and Ki (for thyroxine), obtained by electrospray mass spectrometry agreed with those obtained from traditional UV-vis spectroscopy, and competitive vs noncompetitive inhibition reactions could be delineated via mass spectrometry. These results suggest that our method can be applied to enzymatic processes in which spectrophotometric or spectrofluorometric assays are not feasible or when the relevant substrates do not incorporate chromophores or fluorophores. This new method is competitive with traditional UV assays in that it is facile and it involves very little analysis time.
Human monocytes educated with exosomes from TLR4 primed mesenchymal stem cells treat acute radiation syndrome by promoting hematopoietic recovery (2019)

Abstract Total body irradiation is often used as a conditioning regimen for bone marrow transplants but can cause life threatening damage to host tissues especially the bone marrow. Developing a cellular therapy that can protect the bone marrow from acute radiation syndrome and stimulate hematopoiesis is a priority for patients exposed to therapeutic or even accidental radiation injury. In this study, exosomes derived from MSCs stimulated with the TLR4 agonist lipopolysaccharide (LPS) were used to alternatively activate human monocytes, termed LPS EEMos, as a potential novel radioprotective cellular therapy. LPS EEMos expressed higher levels of PD-L1 (p&amp;lt;0.0001), and lower levels of CD16 (p&amp;lt;0.01), CD86 (p&amp;lt;0.01), and CD206 (p&amp;lt;0.0001) by flow cytometry compared to monocytes educated with exosomes from unstimulated MSCs (EEMos). Using qPCR, increased gene expression in LPS EEMos of IL-10 (p&amp;lt;0.05), IDO (p&amp;lt;0.001), FGF2 (p&amp;lt;0.05), IL-15 (p&amp;lt;0.05), and IL-6 (p&amp;lt;0.0001) were detected compared to EEMos. Using a xenogeneic radiation injury model, infusion of human LPS EEMos 4 hours after lethal radiation led to reduced clinical scores and an increased survival at 40 days post-infusion, as compared to infusions of PBS, EEMos, and monocytes alone, all of which led to worse clinical scores and 0% survival with uniform death by 20 days (p&amp;lt;0.05). Complete blood cell counts in LPS EEMo recipients showed leukocyte, erythrocyte and platelet counts equivalent to non-irradiated mice, demonstrating complete restoration of hematopoiesis. Infusion of LPS EEMos may be a useful strategy to protect the bone marrow from acute radiation syndrome by expression of anti-inflammatory molecules and cytokines that promote hematopoiesis/engraftment.
High resolution blue laser mastering with inorganic photoresist (2003)

An inexpensive and practical mastering technology was developed by using blue laser optics of 405 nm in wavelength /spl lambda/ and NA=0.95 with an inorganic photoresist. The resist system showed a higher resolution for successful 130 nm pit patterning than that of ordinary organic photoresist systems. Based on this technology, a ROM disc with a recording capacity of 25 GB on a 120 mm diameter surface was mastered at a fast recording speed of 4.92 m/s. The disc showed a reasonable jitter value of 9.3% and a push-pull signal by using conventional readout optics of /spl lambda/=405 nm and NA=0.85.