gebhart/patrepeval huggingface dataset:
Quantifying Protein-Ligand Binding Constants using Electrospray Ionization Mass Spectrometry: A Systematic Binding Affinity Study of a Series of Hydrophobically Modified Trypsin Inhibitors (2012)

NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (K(D)) for high affinity ligands investigated by nanoESI-MS ranges from 15 nM to 450 nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in K(D) and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the K(D) values ranging from 2.9 to 17.6 μM, some 1-2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (K(D)) measured via nanoESI-MS were compared with kinetic inhibition constants (K(i)) in solution.
Renin angiotensin system inhibition prevents naturally advanced left ventricular hypertrophy via oxidized stress suppression (2005)

We designed in vivo study using high aged spontaneously hypertensive rats (SHR) treated with angiotensin converting enzyme inhibitor (ACEI), angiotensin receptor blocker (ARB) or their combined therapy to clarify the role of reactive oxygen species (ROS) for preventing left ventricular hypertrophy (LVH) and heart failure. We used 30 male SHR aged 50 weeks (6 rats in each group). Each group was treated for 4 weeks using osmotic mini-pump with ACEI (temocaprilat 1mg/kg/day), ARB (olmesartan 0.2mg/kg/day), combined therapy (CT; temocaprilat 0.5mg/kg/day and olmesartan 0.1mg/kg/day) or hydralazine (H; 15mg/kg/day) to reduce equivalently blood pressure (BP) and with saline as control (C). We measured Heart/body weight (Heart Weight Index), BP by tail cuff method and plasma BNP. We measured histologically myocytes size by hematoxylin eosin stain and myocardial fibrotic area by Azan stain using computerized morphometry system (MacSCOPE ver2.2). We also measured p22phox, p47phox, gp91phox, TGFβ1 and FGF2 mRNA levels by real-time PCR and serum NOx by ELISA. Heart/body weight (Heart Weight Index) treated with ARB (p<0.05) or CT (p<0.1) was reduced. Histological myocyte size in ACEI (p<0.05), ARB (p<0.01) or CT (p<0.001) and myocardial fibrosis in ACEI (p<0.05) or CT (p<0.01) was significantly reduced. Plasma BNP and NOx level in ACEI, ARB or CT was reduced (P<0.05). By real-time PCR, TGFβ1 mRNA in ACEI (p<0.05), ARB (p<0.05) or CT (p<0.01) or FGF2 mRNA in ACEI, ARB or CT (p<0.01) were significantly suppressed. The p22phox in ACEI (p<0.05), ARB (p<0.05) or CT (p<0.01), p47phox in ACEI (p<0.01 vs. C, p<0.05 vs. H), ARB (p<0.05 vs. C) or CT (p<0.01 vs. C, p<0.05 vs. H) or gp91phox in ACEI (p<0.01), ARB (p<0.01) or CT (p<0.005) were also significantly suppressed compared those in H or C. We conclude that the dual inhibition of RAS showed additional beneficial effects on improvement of cardiac hypertrophy via ROS suppression even in naturally advanced LVH.
Reduction of fructose-induced hypertriglyceridemia and fatty liver in rats by 4-(4'-chlorobenzyloxy)benzyl nicotinate (KCD-232). (1984)

The effect of KCD-232, a new compound with a structure of 4-(4'-chlorobenzyloxy)benzyl nicotinate, on fructose-induced hypertriglyceridemia and fatty liver was studied in rats refed experimental diets for 3 days after having been starved for 2 days. In younger or older rats refed 7% corn oil-containing diets, both the serum and livertriglyceride (TG) levels were higher in the fructose (F) group than in the glucose (G) group, and those of the F group were higher in the older rats than the younger rats. KCD-232effectively inhibited fructose-induced hypertriglyceridemia and fatty liver in both the younger and older rats. In older rats refed 7% corn oil diets, an increase in hepatic fatty acid (FA) synthesis and decreases in the activities of hepatic TG lipase (HTGL) and adipose tissue lipoprotein lipase (LPL) were found in the F group, while the serum free FA level and hepatic FA oxidative activity of the F group were equal to those of the G group. KCD-232 strongly inhibited the fructose-enhanced FA synthesis, slightly repressed the fructose-suppressed HTGLactivity and had no effect on LPL activity and FA oxidation. These results suggest that fructose-induced hypertriglyceridemia and fatty liver are due to an enhanced hepatic FA synthesis and decreased hydrolytic activities required for TG clearance from the circulation system and that KCD-232 prevents them by inhibiting enhanced FA synthesis.
Real-time surface light-field capture for augmentation of planar specular surfaces (2012)

A single hand-held camera provides an easily accessible but potentially extremely powerful setup for augmented reality. Capabilities which previously required expensive and complicated infrastructure have gradually become possible from a live monocular video feed, such as accurate camera tracking and, most recently, dense 3D scene reconstruction. A new frontier is to work towards recovering the reflectance properties of general surfaces and the lighting configuration in a scene without the need for probes, omni-directional cameras or specialised light-field cameras. Specular lighting phenomena cause effects in a video stream which can lead current tracking and reconstruction algorithms to fail. However, the potential exists to measure and use these effects to estimate deeper physical details about an environment, enabling advanced scene understanding and more convincing AR. In this paper we present an algorithm for real-time surface light-field capture from a single hand-held camera, which is able to capture dense illumination information for general specular surfaces. Our system incorporates a guidance mechanism to help the user interactively during capture. We then split the light-field into its diffuse and specular components, and show that the specular component can be used for estimation of an environment map. This enables the convincing placement of an augmentation on a specular surface such as a shiny book, with realistic synthesized shadow, reflection and occlusion of specularities as the viewpoint changes. Our method currently works for planar scenes, but the surface light-field representation makes it ideal for future combination with dense 3D reconstruction methods.
A Reflection on Reflection. (2002)

Reflects on the articles in this themed issue on reflective practice. Notes that these teacher/authors have been influenced by prior learning, past experience, feelings, attitudes, values, the school constraints on the learning environment, and their own assumptions about teaching. Describes how teachers have formed a learning community to increase awareness of reflective teaching.
One theorem of Zil′ber's on strongly minimal sets (1985)

Abstract Suppose D ⊂ M is a strongly minimal set definable in M with parameters from C . We say D is locally modular if for all X, Y ⊂ D , with X = acl( X ∪ C )∩ D , Y = acl( Y ∪ C ) ∩ D and X ∩ Y ≠ ∅, We prove the following theorems. Theorem 1. Suppose M is stable and D ⊂ M is strongly minimal. If D is not locally modular then in M eq there is a definable pseudoplane . (For a discussion of M eq see [M, §A].) This is the main part of Theorem 1 of [Z2] and the trichotomy theorem of [Z3]. Theorem 2. Suppose M is stable and D , D ′ ⊂ M are strongly minimal and nonorthogonal. Then D is locally modular if and only if D′ is locally modular .
A digital video system for multi-program broadcasting (2002)

We developed an efficient digital video broadcasting system suitable for multi-program applications. This system uses a joint bit-rate approach to significantly increase the number of compressed video streams transmitted in one channel. Compared to CBR implementations, our approach improves the bandwidth allocation by an average of 112%. As a result, for the same picture quality, our system can free a large number of transponders, which in turn can be used to carry real-time broadcasting.
Understanding the functions of acrylic processing aids in rigid PVC injection molding (1993)

Abstract Poly(vinyl chloride) (PVC) compound use is growing in specialty injection molding applications such as appliances, business equipment, and electrical enclosures. A key factor in determining the appearance and physical properties of the molded parts is the processability of the PVC compounds, which can be improved through the use of acrylic processing aids. Processing aids promote PVC fusion, modify the melt rheology, and/or provide lubrication. Some processing aid products are designed to serve one of these functions while others provide a combination of functions. Each of these functions and its major benefits in rigid PVC injection molding are described. Some guidelines for selecting appropriate processing aid products for applications are provided.
Compressive Light Field Sensing (2012)

We propose a novel design for light field image acquisition based on compressive sensing principles. By placing a randomly coded mask at the aperture of a camera, incoherent measurements of the light passing through different parts of the lens are encoded in the captured images. Each captured image is a random linear combination of different angular views of a scene. The encoded images are then used to recover the original light field image via a novel Bayesian reconstruction algorithm. Using the principles of compressive sensing, we show that light field images with a large number of angular views can be recovered from only a few acquisitions. Moreover, the proposed acquisition and recovery method provides light field images with high spatial resolution and signal-to-noise-ratio, and therefore is not affected by limitations common to existing light field camera designs. We present a prototype camera design based on the proposed framework by modifying a regular digital camera. Finally, we demonstrate the effectiveness of the proposed system using experimental results with both synthetic and real images.
Thermohydrological conditions and silica redistribution near high‐level nuclear wastes emplaced in saturated geological formations (1988)

Evaluation of the thermohydrological conditions near high‐level nuclear waste packages is needed for the design of the waste canister and for overall repository design and performance assessment. Most available studies in this area have assumed that the hydrologic properties of the host rock are not changed in response to the thermal, mechanical, or chemical effects caused by waste emplacement. However, the ramifications of this simplifying assumption have not been substantiated. We have studied dissolution and precipitation of silica in liquid‐saturated hydrothermal flow systems, including changes in formation porosity and permeability. Using numerical simulation, we compare predictions of thermohydrological conditions with and without inclusion of silica redistribution effects. Two cases were studied, namely, a canister‐scale problem, and a repository‐wide thermal convection problem and different pore models were employed for the permeable medium (fractures with uniform or nonuniform cross sections). We find that silica redistribution in water‐saturated conditions does not have a sizeable effect on host rock and canister temperatures, pore pressures, or flow velocities.
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks (2008)

Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose repression and human diabetes data brings hints towards the understanding of the principles of transcriptional regulation controlling these two important and potentially closely related systems.
Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development (2015)

Transcriptional program that drives human preimplantation development is largely unknown. Here, by using single-cell RNA sequencing of 348 oocytes, zygotes and single blastomeres from 2- to 3-day-old embryos, we provide a detailed analysis of the human preimplantation transcriptome. By quantifying transcript far 5'-ends (TFEs), we include in our analysis transcripts that derive from alternative promoters. We show that 32 and 129 genes are transcribed during the transition from oocyte to four-cell stage and from four- to eight-cell stage, respectively. A number of identified transcripts originates from previously unannotated genes that include the PRD-like homeobox genes ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB and LEUTX. Employing de novo promoter motif extraction on sequences surrounding TFEs, we identify significantly enriched gene regulatory motifs that often overlap with Alu elements. Our high-resolution analysis of the human transcriptome during preimplantation development may have important implications on future studies of human pluripotent stem cells and cell reprograming.
Influence of electric field distribution on laser induced damage threshold and morphology of high reflectance optical coatings (2007)

Various investigations show that damage threshold of optical coatings by intense ultrashort laser pulses is closely related to the intensity of electric field at layer interfaces. LIDT measurements of high reflectance optical coatings using femtosecond pulses at 800 nm wavelength are presented. ZrO<sub>2</sub>, HfO<sub>2</sub> and Ta<sub>2</sub>O<sub>5</sub> as high refractive index materials for two sets of experiments were chosen. Two different coating designs were investigated: standard quarter-wavelength design with SiO<sub>2</sub> overcoat and modified "E-field" non quarter-wavelength design with suppressed electric field. Damage sites were studied using optical and AFM microscopes. Relation between electric field distribution and damage morphology was observed. The results demonstrate, that suppressing electric field at layer interfaces enables to increase LIDT for high reflectance coatings almost twice if compared to standard quarter-wavelength design when using ultrashort laser pulses. However electric field distribution is sensitive to variations in thicknesses of outer layers, so deposition process should be precisely controlled to get improvement in LIDT of coatings.
CBN-TiN Composite Coating Using a Novel Combinatorial Method—Structure and Performance in Metal Cutting (2003)

Cubic boron nitride coatings are under development for a variety of applications but stabilization of the pure CBN form and adhesion of films deposited by PVD and ion-based methods have been difficult. An alternate two-stage process comprising of ESC (electrostatic spray coating) and CVI (chemical vapor infiltration) has been developed for depositing CBN-TiN composite coatings for wear related applications. The process optimization yields fully dense films of CBN particles evenly dispersed in a continuous TiN matrix. Metal cutting tests (turning–4340 steel), using CBN-TiN composite coating thus developed, have shown an increase in tool life of three to seven times, depending on machining parameters, in comparison with CVD deposited TiN films.
Response of human natural killer (NK) cells to NK cell stimulatory factor (NKSF): cytolytic activity and proliferation of NK cells are differentially regulated by NKSF. (1992)

Natural killer cell stimulatory factor (NKSF) is a 70-kD heterodimeric cytokine that was initially isolated from conditioned medium of human B lymphoblastoid cell lines. The effects of recombinant NKSF on the function of human peripheral blood NK cells were examined. NKSF directly augmented the cytolytic activity of freshly isolated NK cells. Both CD56dim and CD56bright NK cells demonstrated enhanced cytotoxicity after brief exposure to NKSF. In contrast, highly purified T lymphocytes did not exhibit major histocompatibility complex-unrestricted cytotoxicity after short-term culture with NKSF. Like interleukin 2 (IL-2), NKSF augmented the lysis of NK-sensitive, NK-resistant, and antibody-coated targets. Both NKSF and IL-2 induced marked upregulation of several NK cell adhesion molecules known to participate in cytolysis, including CD2, CD11a, and CD54. However, NKSF activates NK cells through a pathway distinct from that of IL-2, since the presence of anti-IL-2 receptor (anti-IL-2R) antibodies or IL-4 did not inhibit the effects of NKSF. NKSF by itself induced very little proliferation of resting NK cells. NK cells preactivated in vitro with IL-2 demonstrated enhanced proliferation to NKSF, but the degree of proliferation was always inferior to that induced by IL-2 alone. Moreover, NKSF strongly inhibited IL-2-induced proliferation of either resting or preactivated NK cells. This inhibition was not the result of decreased IL-2R expression, because NKSF-activated NK cells expressed higher levels of both IL-2Rs p75 and p55. Furthermore, NKSF did not inhibit the proliferation of mitogen-activated T cells, indicating a selective effect on NK cell proliferation. Human NK cells expanded in vivo by prolonged continuous infusions of IL-2 remained fully responsive to NKSF. Picomolar concentrations of NKSF were as effective as nanomolar concentrations of IL-2 in augmenting the cytolytic activity of NK cells expanded in vivo by IL-2. NKSF may play an important role in the regulation of human NK cell function, and its possible use as a therapeutic cytokine deserves further investigation.
Correlating mRUST scoring with fracture healing in the mouse model (2020)

Background/Objective: Long bone fractures are an expensive and frequent cause of disability in humans. Research seeking to accelerate and improve the healing process is more essential than ever. Animal models, mice especially, provide an inexpensive and reproducible model of in vivo fracture healing. However, many measures of murine fracture healing outcomes are either expensive or destructive, limiting their ability to be translated to clinical studies. We seek to determine how these measures such as biomechanics, µCT, and histology correlate to the relatively new, inexpensive, and non-destructive method of mRUST scoring in a mouse model. Methods: One hundred and thirty-five, 12-week old male C57BL6/J mice were divided into nine groups of 15 mice. Mice underwent a surgically created, femoral fracture. At biweekly timepoints, anteroposterior and lateral radiographs were taken, and 15 mice were sacrificed at each time point (7, 10, 14, 17, 21, 24, 28, 35, and 42 days post-surgery) for biomechanical, µCT, and histological analyses. The modified Radiographic Union Scale for Tibial fractures (mRUST scoring) provides a score based on the visualization of a callus and fracture line in four cortices on the radiographs. Data analysis will be performed to determine the degree of correlation between mRUST scoring and other fracture healing outcomes. Results/Conclusion: Data collection in this experiment is still forthcoming. Upon successful completion of this project, we will have established numerical correlations between mRUST scoring and other fracture healing outcomes, such as biomechanics, µCT microarchitecture, and histology. These correlations will provide a powerful tool in future mouse fracture healing studies, as data on the state and strength of fracture repair could be determined by simple radiograph. Scientific/Clinical Policy Impact and Implications: This study will both provide future murine fracture studies with an inexpensive and non-destructive method of assessment that is more directly translatable to human fracture studies.
Crystal Growth of Ternary Alloy Semiconductor and Preliminary Study for Microgravity Experiment at the International Space Station (2014)

Crystal growth of alloy semiconductor has been under investigation at the International Space Station (ISS) to investigate growth kinetics at the solid-liquid interface, because microgravity can suppress the natural convection. In this study, we focused on InGaSb which is one of the promising ternary alloy semiconductors. As a preliminary experiment, wetting angle between the InGaSb and the materials of the ampoule and cartridge, such as quartz, carbon sheet, BN, and C-103 alloy, were measured to check their affinity of the configuration. The InGaSb exhibited much higher wetting ability on the C-103 substrate than that on the other substrates (quartz, BN, and graphite), and this result suggested C-103 can prevent leakage of the InGaSb samples in case the ampoule collapses in the cartridge. On the other hand, BN and graphite exhibited low wetting abilities with InGaSb; therefore, they are suitable materials for the ampoule because they do not significantly affect the InGaSb crystal growth. In another preliminary experiment, concentration of Te dopant, which was added to make striation in the grown crystal, was measured using inductively coupled plasma mass spectrometry (ICP-MS). It is confirmed that Te concentrations were relatively higher at the striation area.
[Catalog] / (1907)

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