gebhart/patrepeval huggingface dataset:
Diazo Reagents with Small Steric Footprints for Simultaneous Arming/SAR Studies of Alcohol-Containing Natural Products via O–H Insertion (2011)

Natural products are essential tools for basic cellular studies leading to the identification of medically relevant protein targets and the discovery of potential therapeutic leads. The development of methods that enable mild and selective derivatization of natural products continues to be of significant interest for mining their information-rich content. Herein, we describe novel diazo reagents for simultaneous arming and structure-activity relationship (SAR) studies of alcohol-containing natural products with a small steric footprint, namely, an α-trifluoroethyl (HTFB) substituted reagent. The Rh(II)-catalyzed O-H insertion reaction of several natural products, including the potent translation inhibitor lactimidomycin, was investigated, and useful reactivity and both chemo- and site (chemosite) selectivities were observed. Differential binding to the known protein targets of both FK506 and fumagillol was demonstrated, validating the advantage of the smaller steric footprint of α-trifluoroethyl derivatives. A p-azidophenyl diazo reagent is also described that will prove useful for photoaffinity labeling of low affinity small molecule protein receptors.
The science of literacy: From the laboratory to the classroom (2000)

Finding out “why Johnny can't read,” in addition to being of increasing social concern, has become a focus of scientific research. Although initially the domain of educational research, more recently a growing interest in the neurobiological basis of higher cortical functions, especially language and reading (and the sensory, perceptual, and cognitive systems that subserve these functions), has captured the attention of neuroscientists.
Coherence Disparity in Broadcast and Multiple Access Channels (2016)

Individual links in a wireless network may experience unequal fading coherence times due to differences in mobility or scattering environment, a practical scenario where the fundamental limits of communication have been mostly unknown. This paper studies broadcast and multiple access channels where multiple receivers experience unequal fading block lengths, and channel state information (CSI) is not available at the transmitter(s), or for free at any receiver. In other words, the cost of acquiring CSI at the receiver is fully accounted for in the degrees of freedom. In the broadcast channel, the method of product superposition is employed to find the achievable degrees of freedom. We start with unequal coherence intervals with integer ratios. As long as the coherence time is at least twice the number of transmit and receive antennas, these degrees of freedom meet the upper bound in four cases: when the transmitter has fewer antennas than the receivers, when all receivers have the same number of antennas, when the coherence time of one receiver is much shorter than all others, or when all receivers have identical block fading intervals. The degrees of freedom region of the broadcast under identical coherence times was also previously unknown and is settled by the results of this paper. The disparity of coherence times leads to gains that are distinct from those arising from other techniques such as spatial multiplexing or multi-user diversity; this class of gains is denoted coherence diversity. The inner bounds are further extended to the case of multiple receivers experiencing fading block lengths of arbitrary ratio or alignment. Also, in the multiple access channel with unequal coherence times, achievable and outer bounds on the degrees of freedom are obtained.
Multi-Surrogate Modeling for Computational Cost Reduction (2012)

To utilize high-fidelity simulation for computationally intensive engineering applications such as sensitivity analysis and uncertainty quantification, the surrogate modeling techniques have become an indispensable tool and have been widely used. However, for reactor physics problems that can be characterized as very large number of input parameters (i.e. reaction cross sections), the required computational cost to build a surrogate model itself would be impractical with the sole conventional surrogate modeling techniques. We have been exploring the efficient way of reducing the computational cost in surrogate modeling and contributed the surrogate approach incorporated with reduced order modeling techniques. Basic approach summarized in Ref. is to transform the input parameters into low dimension by hybridizing two prominent methods - variational methods and sampling methods. As a preprocessing for the surrogate modeling, the influential subspace of the input parameters with respect to response change is extracted by range finding algorithm and the input parameters are projected onto that subspace. Because the number of subspace basis vectors are much smaller than the number of input parameters, reduced order form of the surrogate model can be constructed, which means that the number of unknowns to be determined in the surrogate modeling is reduced and, opposed to the curse of dimensionality, one can save significant computational cost to generate the training sample set. This study is the extension of the previous method for further cost reduction. In Ref., the input parameter transformation and the surrogate modeling are conducted independently. By doing that, one can estimate the error due to input parameter transformation and the surrogate modeling, separately and theoretically one can eliminate the error due to input parameter transformation within the machine precision. However, in practice, the input parameter variations, which may be considered significant in view of the input parameter transformation, may not be influential on the actual response change. By properly filtering those components, we expect that more reduction would be achieved. The basic idea and the preliminary test results are presented
Supplementary Video 6 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by <i>In Vivo</i> Microscopy and Single-Cell Pharmacodynamics (2023)

Supplementary Video 6 from Analysis of Mitosis and Antimitotic Drug Responses in Tumors by &lt;i&gt;In Vivo&lt;/i&gt; Microscopy and Single-Cell Pharmacodynamics
Reductive Trimerization of the Trioxo Half‐Sandwich Complex [(η5‐C5Me5)ReO3] with Deoxygenation: The Electron‐Deficient Cluster Ion [(η5‐C5Me5)3Re3(μ‐O)6]2+ (1985)

A novel M3O6 skeletal geometry is shown by the cluster cation of the perrhenate 1. The six oxygen atoms form a trigonal prism whose three rectangular faces are each symmetrically bridged by a rhenium atom. The cluster cation is, with only 46 valence electrons, an electron-deficient species.
Modeling and Controls of a Fuel Delivery System With Dual Recirculation Lines for a PEM Fuel Cell System (2008)

A fuel delivery system with dual recirculation lines is investigated in this paper, which can reuse the exhausted gas from the outlet of anode flow channel. In the automotive application, the fuel delivery system regulates the hydrogen pressure and flow rate from the tank to the anode flow channel that change dynamically with load. The control objectives of fuel cell stack require that a slight pressure difference between the anode and cathode be maintained to prevent the damage of the membrane. In addition, the unconsumed hydrogen is circulated to a supply line by the recirculation lines. The fuel delivery system analyzed in this paper consists of two supply lines and two recirculation lines. The supply line with a low pressure regulator accounts for the supply of fuel at relatively low load demands. The other supply line with a flow controller starts to provide additional fuel with controllable flow rate at high load demands. The recirculation line with an ejector allows for mixing the unconsumed hydrogen with the supplied fuel. The other recirculation line with a blower is used to improve the controllability of the recirculation flow rate. Analysis of the fuel delivery system with dual recirculation lines is carried out by modeling and simulating an integrated system, where the components are modeled involving the dynamic characteristics. The major components of fuel delivery and recirculation system are an ejector, a blower, and a pressure regulator. In addition, the linearization of the integrated system is expressed in the approach of state equations to form the control problem of the system. Then the linear controllers are designed based on the decentralized proportional and integral control, and the state feed-back control. The systems with the different controllers are simulated at different operating points to evaluate their tracking performance by comparing the dynamic response curves.
Environment, Stability and Acidity of External Surface Sites of Silicalite-1 and ZSM-5 Micro and Nano Slabs, Sheets, and Crystals (2020)

Zeolites are nanoporous aluminosilicate crystals of prominent fundamental and industrial importance. Among these, ZSM-5 is the most investigated solid that can be obtained in various forms, with some of these (hierarchical forms, nanoslabs, nanosheets, and nanocrystals) exhibiting a very high external surface to volume ratio. Whereas most knowledge obtained so far at the atomic level concerns the internal nanopores, we here propose a density functional theory (DFT) study to establish the relative stability of relevant surface orientations for silicalite and ZSM-5 crystals ((100), (010), and (101)) at different hydration levels to identify the equilibrium morphology of the particles and the major sites present on their surfaces. Several kinds of surface sites have been identified. Bridging Al–OH–Si groups are present at the pore mouth with stability similar to or higher than those in bulk sites. Yet, these groups are not stable at the outermost surface, where the following groups prevail: Si–OH, Al–OH groups, and most importantly water adsorbed on aluminum, Al–(H2O)(OH) n . Water desorption reactions occur at temperatures that strongly depend on the local topology of the surface site and on the surface orientation: when a siloxane bridge is present below the surface Al atom, water desorption is promoted by the formation of an additional Al–O bond with the oxygen of the siloxane bridge. However, if such a bridge is not present below the surface aluminum atom, desorption leads to a less stable surface AlIII atom. The desorption temperature is influenced by this feature, as well as by the stabilization of the water molecule by hydrogen bonds, depending on the silanol content of the surface. This has in turn direct consequences on the Brønsted and Lewis acid properties, as probed by pyridine. Strong Lewis acid sites can easily be formed on the (010) orientation (relevant for nanosheets), whereas they are unlikely to occur at the (101) surface (tips of coffin-shaped particles), which promotes the mild Brønsted acid sites Al–(H2O) instead.
Abstract 3799: The PAK4 allosteric modulator (KPT-9274) attenuates the growth of renal cell carcinoma (2016)

Abstract Renal cell carcinoma (RCC) is an increasingly prevalent cancer type that is frequently asymptomatic on presentation and is associated with poor responses and resistance even to the current targeted therapies. Thus, novel therapeutic approaches to treat this disease are urgently needed. P21-activated kinase 4 (PAK4) is a mediator of filopodia formation and stabilizes β-catenin transcriptional activity, both of which are integral to nephrogenesis and cancer. We hypothesized that inhibitors of the PAK4 signaling pathway would result in salutary effects on RCC. To test this, we evaluated the in vitro response of several human RCC cells and normal kidney proximal epithelial cells (NHKs) to the specific PAK4 Allosteric Modulators (PAMs; KPT-8752 and KPT-9274). 786-O (VHL-mutant RCC) and caki-1 (VHL-wt RCC) cells showed decreases in cell viability (MTT), induction of apoptosis and arrest in G2/M phase when incubated with these inhibitors. These responses were diminished in NHK cells which served as a “normal” control cell line. Target and specific pathway proteins (phospho-PAK4, Phospho-β-catenin, c-Myc and cyclin D1) were reduced after RCC, but not NHK, were incubated with KPT-8752 and KPT-9274. To confirm specificity of the inhibitor to PAK4, all these responses were reproduced in RCC cells using specific PAK4 siRNA. Since ∼85% of RCC cases are associated with mutation in vhl we used 786-0 xenograft mouse model to evaluate the clinical candidate KPT-9274. KPT-9274 was orally administered at 100 and 200 mg/kg BIDX5 for 4 weeks, resulting in clear attenuation of tumor growth at both doses. There was no obvious change in the health or weight of any of the animals when compared to vehicle group suggesting manageable tolerability. We are currently evaluating combination therapy and plan to test this inhibitor on a metastatic RCC model. In summary, PAK4 inhibitors show considerable promise as novel treatments of RCC as a single agent and warrants further investigation. Citation Format: Robert H. Weiss, Omran Abu Aboud, Erkan Baloglu, William Senapedis, Sharon Shacham. The PAK4 allosteric modulator (KPT-9274) attenuates the growth of renal cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3799.
Supplementary Figure S3 from Augmentation of the Enhanced Permeability and Retention Effect with Nitric Oxide–Generating Agents Improves the Therapeutic Effects of Nanomedicines (2023)

&lt;p&gt;Supplementary Figure S3 shows potentiation of antitumor effect by treatment of various NO donors.&lt;/p&gt;
Gas sensing properties of $In_{2}O_{3}$ thin film prepared by spin-coating method (1998)

The thin films were fabricated on a alumina substrate by spin-coating method and the gas sensing properties were tested. The coating solution was synthesized by the mixing of aqueous solution of and acetic acid, and ammonium carboxymethyl cellulose as a binder. The thin films between 71 and 210nm thick were obtained by spin-coating between 1 and 7 times followed by drying at and calcining at . The films consisted of a dense stack of tiny particles between 23 and 27nm in diameter and covered well large grains of the alumina substrate. Then film thickness was well controlled by the number of spin-coating. The fabricated films showed high sensitivity and very fast response property to CO and .
Yule-Nielsen based multi-angle reflectance prediction of metallic halftones (2015)

Spectral prediction models are widely used for characterizing classical, almost transparent ink halftones printed on a diffuse substrate. Metallic-ink prints however reflect a significant portion of light in the specular direction. Due to their opaque nature, multi-color metallic halftones require juxtaposed halftoning methods where halftone dots of different colors are laid out side-by-side. In this work, we study the application of the Yule-Nielsen spectral Neugebauer (YNSN) model on metallic halftones in order to predict their reflectances. The model is calibrated separately at each considered illumination and observation angle. For each measuring geometry, there is a different Yule-Nielsen <i>n</i>-value. For traditional prints on paper, the <i>n</i>-value expresses the amount of optical dot gain. In the case of the metallic prints, the optical dot gain is much smaller than in paper prints. With the fitted n-values, we try to better understand the interaction of light and metallic halftones.
Acceleration-based Activity Recognition of Repetitive Works with Lightweight Ordered-work Segmentation Network (2022)

This study presents a new neural network model for recognizing manual works using body-worn accelerometers in industrial settings, named Lightweight Ordered-work Segmentation Network (LOS-Net). In industrial domains, a human worker typically repetitively performs a set of predefined processes, with each process consisting of a sequence of activities in a predefined order. State-of-the-art activity recognition models, such as encoder-decoder models, have numerous trainable parameters, making their training difficult in industrial domains because of the consequent substantial cost for preparing a large amount of labeled data. In contrast, the LOS-Net is designed to be trained on a limited amount of training data. Specifically, the decoder in the LOS-Net has few trainable parameters and is designed to capture only the necessary information for precise recognition of ordered works. These are (i) the boundary information between consecutive activities, because a transition in the performed activities is generally associated with the trend change of the sensor data collected during the manual works and (ii) long-term context regarding the ordered works, e.g., information about the previous and next activity, which is useful for recognizing the current activity. This information is obtained by introducing a module that can collect it at distant time steps using few trainable parameters. Moreover, the LOS-Net can refine the activity estimation by the decoder by incorporating prior knowledge regarding the order of activities. We demonstrate the effectiveness of the LOS-Net using sensor data collected from workers in actual factories and a logistics center, and show that it can achieve state-of-the-art performance.
Endometritis After Cesarean: The Effect of Age (1994)

In this study, we compared the rate of endometritis after cesarean section in two age groups. The first group consisted of patients who were 17 years old or younger (teenage group) and the second group of patients were 35 years of age or older (advanced maternal age group). Patients in each group were matched for length of labor, length of rupture of membranes, and the use of prophylactic antibiotics. In the teenage group, 18 of 41 (43.9%) developed endometritis compared with 6 of 41 (14.6%) in the advanced maternal age group (P < 0.003). This study supports the concept that young age is a risk factor for endometritis after cesarean section.
Effect of Complex Curatives on the Properties for Ethylene Propylene Diene Rubber/Polypropylene Blends (2009)

This study investigates the effects of different types of curatives at polypropylene (PP) and ethylene propylene diene monomer (EPDM) blend ratios (100 : 40 phr) in dynamically vulcanized products. The thermoplastic vulcanizates are prepared by batch melt mixing of PP with EPDM, using pheolic resin, dicumyl peroxide, hydrosilyation, and complex systems as curatives. Observed changes in curing characteristics and mechanical properties of blends have been correlated with phase morphology, as attested by scanning electron micrographs. On the basis of the obtained results, different curative systems control final vulcanizing characteristics, mechanical properties, morphology, intermolecular interaction, and thermal properties of EPDM/PP blends.
Detection of gp43 and ITS1-5.8S-ITS2 Ribosomal RNA Genes of Paracoccidioides brasiliensis in Paraffin-embedded Tissue. (2001)

Paracoccidioidomycosis (PCM) is a deep mycosis caused by the thermo-dependent dimorphic fungus Paracoccidioides brasiliensis and is prevalent in Latin American countries. An increase in PCM has been reported in recent years and the disease is now recognized as one of the imported fungal infections in Japan. To date, more than 15 cases of PCM have been reported in our country, and five of them were diagnosed by clinical and histopathological findings without mycological study. We applied 2 nested polymerase chain reaction (PCR) amplification methods for detecting P. brasiliensis genes from paraffin-embedded tissue specimens. Successfully amplified were: a 473 base pairs fragment of gp43 gene of P. brasiliensis (located from 741st to 1,213rd base), and a 418 base pairs fragment of 5.8S ribosomal RNA gene of P. brasilienisis which included internal transcribed spacers (ITS) 1 and 2 (located from 131st at ITS1 to 195th at ITS2) in paraffin-embedded murine tissues infected with P. brasiliensis yeast cells. The authenticity of the PCR products was confirmed by nucleotide sequence analysis. These results indicate that the two nested PCR methods may be useful for diagnosis of PCM.
Characterization of the murine macrophage response to infection with virulent and avirulent Burkholderia species (2015)

These results characterize the phenotypic and immunological differences in the host innate response to pathogenic and avirulent Burkholderia strains and provide insight into the phenotypic alterations and molecular targets underlying host-Burkholderia interactions.
Evidence for Coordinated Induction and Repression of Ecto-5'-Nucleotidase (CD73) and the A2a Adenosine Receptor in a Human B Cell Line (2003)

In the human B cell line P493-6 two mitogenic signals, the Epstein-Barr virus nuclear antigen 2 (EBNA2) and myc, can be independently regulated by means of an estrogen receptor fusion construct or an inducible expression vector, respectively. Shut off of EBNA2, either in the presence or absence of myc, leads to a significant increase in enzymatic activity and surface expression of ecto-5'-nucleotidase (CD73) as well as an increased adenosine receptor response in cyclic AMP formation. Shut off of myc expression has a small additional positive effect on CD73 activity. Among the four different subtypes of adenosine receptors, the A2a receptor exclusively is subject to regulation in this system, which is substantiated by pharmacologic data (specific agonists and inhibitors), as well as on the mRNA level. With up-regulated CD73 and A2a, cells also respond to 5'-AMP with increased cyclic AMP formation. Turn on of EBNA2 has the reverse effect of repression of CD73 and A2a expression. The time course of both induction and repression of CD73 and A2a is rather slow.
4D Semantic Cardiac Magnetic Resonance Image Synthesis on XCAT\n Anatomical Model (2020)

We propose a hybrid controllable image generation method to synthesize\nanatomically meaningful 3D+t labeled Cardiac Magnetic Resonance (CMR) images.\nOur hybrid method takes the mechanistic 4D eXtended CArdiac Torso (XCAT) heart\nmodel as the anatomical ground truth and synthesizes CMR images via a\ndata-driven Generative Adversarial Network (GAN). We employ the\nstate-of-the-art SPatially Adaptive De-normalization (SPADE) technique for\nconditional image synthesis to preserve the semantic spatial information of\nground truth anatomy. Using the parameterized motion model of the XCAT heart,\nwe generate labels for 25 time frames of the heart for one cardiac cycle at 18\nlocations for the short axis view. Subsequently, realistic images are generated\nfrom these labels, with modality-specific features that are learned from real\nCMR image data. We demonstrate that style transfer from another cardiac image\ncan be accomplished by using a style encoder network. Due to the flexibility of\nXCAT in creating new heart models, this approach can result in a realistic\nvirtual population to address different challenges the medical image analysis\nresearch community is facing such as expensive data collection. Our proposed\nmethod has a great potential to synthesize 4D controllable CMR images with\nannotations and adaptable styles to be used in various supervised multi-site,\nmulti-vendor applications in medical image analysis.\n