gebhart/patrepeval huggingface dataset:
Protein engineering of the high-alkaline serine protease PB92 from <i>Bacillus alcalophilus</i>: functional and structural consequences of mutation at the S4 substrate binding pocket (1992)

Serine endoproteases such as trypsins and subtilisins are known to have an extended substrate binding region that interacts with residues P6 to P3' of a substrate. In order to investigate the structural and functional effects of replacing residues at the S4 substrate binding pocket, the serine protease from the alkalophilic Bacillus strain PB92, which shows homology with the subtilisins, was mutated at positions 102 and 126-128. Substitution of Val102 by Trp results in a 12-fold increase in activity towards succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide (sAAPFpNA). An X-ray structure analysis of the V102W mutant shows that the Trp side chain occupies a hydrophobic pocket at the surface of the molecule leaving a narrow crevice for the P4 residue of a substrate. Better binding of sAAPFpNA by the mutant compared with the wild type protein as indicated by the kinetic data might be due to the hydrophobic interaction of Ala P4 of the substrate with the introduced Trp102 side chain. The observed difference in binding of sAAPFpNA by protease PB92 and thermitase, both of which possess a Trp at position 102, is probably related to the amino acid substitutions at positions 105 and 126 (in the protease PB92 numbering). Kinetic data for the variants obtained by random mutation of residues Ser126, Pro127 and Ser128 reveal that the activity towards sAAPFpNA increases when a hydrophobic residue is introduced at position 126.(ABSTRACT TRUNCATED AT 250 WORDS)
[Deletion of OPCML gene and promoter methylation in ovarian epithelial carcinoma]. (2006)

Deletion of OPCML gene exists in ovarian epithelial carcinoma cell. The gene promoter methylations, especially Hap II motif, may be one of pathways that contribute the inhibition of OPCML expression.
Heteromeric assembly of P2X subunits (2013)

Transcripts and/or proteins of P2X receptor (P2XR) subunits have been found in virtually all mammalian tissues. Generally more than one of the seven known P2X subunits have been identified in a given cell type. Six of the seven cloned P2X subunits can efficiently form functional homotrimeric ion channels in recombinant expression systems. This is in contrast to other ligand-gated ion channel families, such as the Cys-loop or glutamate receptors, where homomeric assemblies seem to represent the exception rather than the rule. P2XR mediated responses recorded from native tissues rarely match exactly the biophysical and pharmacological properties of heterologously expressed homomeric P2XRs. Heterotrimerization of P2X subunits is likely to account for this observed diversity. While the existence of heterotrimeric P2X2/3Rs and their role in physiological processes is well established, the composition of most other P2XR heteromers and/or the interplay between distinct trimeric receptor complexes in native tissues is not clear. After a description of P2XR assembly and the structure of the intersubunit ATP-binding site, this review summarizes the distribution of P2XR subunits in selected mammalian cell types and the biochemically and/or functionally characterized heteromeric P2XRs that have been observed upon heterologous co-expression of P2XR subunits. We further provide examples where the postulated heteromeric P2XRs have been suggested to occur in native tissues and an overview of the currently available pharmacological tools that have been used to discriminate between homo- and heteromeric P2XRs.
Autophagy-Lysosome Dysfunction in Amyotrophic Lateral Sclerosis and Frontotemporal Lobar Degeneration (2017)

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two devastating neurodegenerative diseases. Several lines of evidence suggest that these diseases are part of a continuum with common genetic factors. As researchers uncover more genes associated with ALS/FTLD, studies have shown that majority of these genes regulate lysosome‐related processes. Lysosomes play important roles in clearing damaged organelles and proteins through the autophagy‐lysosome pathway and clearing extracellular debris by the endolysosomal pathway. Disruption of both the autophagy and endolysosomal pathways has been implicated in ALS/FTLD pathogenesis.
[Effect of andrographolide on QS regulating virulence factors production in Pseudomonas aeruginosa]. (2006)

The inhibiting effect of andrographolide on virulence factors production in P. aeruginosa may play a role in its anti-infection activity.
Sparse representation of cast shadows via &#x2113;1-regularized least squares (2009)

Scenes with cast shadows can produce complex sets of images. These images cannot be well approximated by low-dimensional linear subspaces. However, in this paper we show that the set of images produced by a Lambertian scene with cast shadows can be efficiently represented by a sparse set of images generated by directional light sources. We first model an image with cast shadows as composed of a diffusive part (without cast shadows) and a residual part that captures cast shadows. Then, we express the problem in an ℓ1-regularized least squares formulation, with nonnegativity constraints. This sparse representation enjoys an effective and fast solution, thanks to recent advances in compressive sensing. In experiments on both synthetic and real data, our approach performs favorably in comparison to several previously proposed methods.
Position-effect Variegation in Drosophila: Recent Progress (1996)

Chromosomes of higher eukaryotes are cytologically differentiated into euchromatin, which decondenses at telophase, and heterochromatin, which remains visibly condensed (Heitz 1929). In Drosophila, heterochromatin forms at blocks of repetitive DNA, both simple sequence repeats (Mayfield and Ellison 1975; Lohe et al. 1993) and moderately repetitive sequences apparently derived from transposable elements (Carmena and Gonzalez 1995; Le et al. 1995; Pimpinelli et al. 1995). When euchromatin and heterochromatin are juxtaposed, mosaic gene silencing can occur, a phenomenon known as position-effect variegation (PEV). Although PEV has been familiar to geneticists for decades, mechanistic questions have only recently been addressed: What differences between euchromatin and heterochromatin are responsible for silencing? How do trans- acting factors participate in silencing? How are genes silenced from a distance? Do repeats play a direct role? Answering these questions is becoming increasingly important, given the mounting evidence that some of the same questions arise for PEV-like phenomena in a wide variety of systems. The focus of this brief critical review is recent work that seems most relevant to epigenetic phenomena, especially those involving repeats. Other aspects of PEV are discussed in excellent comprehensive reviews by Lewis (1950), Spofford (1976), and Weiler and Wakimoto (1995). DIFFERENT TYPES OF PEV Genes are subject to PEV in different situations that represent different vantage points from which interactions between euchromatin and heterochromatin can be observed. The most common situation is when a euchromatic gene is moved next to heterochromatin by chromosomal rearrangement, i.e., classic PEV. Figure 1a illustrates classic PEV on the famous...
Low Dose Radiation Epidemiology: What Can It Tell Us? (2009)

A small workshop entitled ‘‘Low Dose Radiation Epidemiology—What Can it Tell Us?’’ was held at the North Bethesda Marriott Hotel, December 10–11, 2008. The workshop was organized and funded by the Department of Energy’s Low Dose Radiation Research Program, and the Organizing Committee consisted of a member each from DOE, EPA and NCI, plus one member from an academic institution. Participants were chosen for their acknowledged expertise and included 29 epidemiologists, four dosimetrists, and five radiation biologists. The impetus for holding the workshop was the following: There is some suggestion from research in cellular and animal systems that the biological response may differ after highand low-dose/dose-rate radiation exposure. There is no consensus, however, as to whether these differences would result in higher or lower risks of cancer or other diseases than would be predicted from the linear extrapolation defined by current epidemiological data. The workshop participants discussed the value of current human epidemiological data at lower doses and the possibilities for improving and expanding lowdose data obtained from epidemiological studies. On the first day, the selected existing epidemiological studies of low-dose/low-dose-rate exposed populations were reviewed.
Detailed Examination of Relaxation Processes of Excitons in Photoluminescence Spectra of Cu<sub><b>2</b></sub>O (1997)

Variations of optical absorption and especially of photoluminescence spectra of Cu 2 O with photoexcitation wavelength and temperature have been for the first time investigated in details. We have newly observed that the relation of the increase and decrease with temperature in the integrated intensity is complementary with each other between the luminescence-band V Cu and the X O -Γ 12 - exciton luminescence over T =4.2–230 K, and the relative magnitudes of the intensity of the band V Cu and V O 2+ cross over each other at the vicinity of the energy level of exciton, λ∼610 nm. We recognize the evidences of the recombination processes of the excitons coupled with vacancies levels. These phenomena indicate universal natures even among the different quality of specimens. Thus, we request a consideration based on the many-body aspect.
Warpage Measurement on Dielectric Rough Surfaces of Microelectronics Devices by Far Infrared Fizeau Interferometry1 (1999)

Far infrared Fizeau interferometry is developed and it is proposed as a tool for warpage measurement of microelectronics devices. The method provides a whole-field map of surface topography with a basic measurement sensitivity of 5.31 μm per fringe contour. The method is implemented by a compact apparatus using a computer controlled environmental chamber for real-time measurement. The method retains the simplicity of classical interferometry while providing wide applicability to dielectric rough surfaces. Roughness tolerance is achieved by utilizing a far infrared light (λ=10.6 μm). The detailed optical and mechanical configuration is described and selected applications are presented to demonstrate the applicability. The unique advantages of the method are discussed. [S1043-7398(00)01303-7]
Two new sesquiterpenes from Atractylodes macrocehpala (1998)

Two new sesquiterpenes: beishulenolide A 1 and peroxiatractylenolide III 2 were isolated from Atractylodes macrocephala Koids (compositae). Their structures were elucidated on the basis of spectral evidence, especially 2D-NMR methods and chemical conversion.
Heparin Prevents Vascular Smooth Muscle Cell Progression through the G1 Phase of the Cell Cycle (1989)

To gain insight into the mechanism of the antiproliferative effects of heparin on vascular smooth muscle cells (SMC), the influence of this glycosaminoglycan on cell cycle progression and the expression of the c-fos, c-myc, and c-myb proto-oncogenes and two other growth-regulated genes was examined. SMC, synchronized by a serum-deprivation protocol, enter S phase 12-16 h after serum stimulation. Pretreatment with heparin for 48 h blocked the induction of histone H3 RNA, an S phase-expressed product, and prevented cell replication. Thus, heparin prevents entry of cells into S phase. Conversely, heparin had essentially no effect on changes in expression of the c-fos and c-myc proto-oncogenes during the G0 to G1 transition. Normal increases in c-fos and c-myc RNA were observed 30 min and 2 h following serum addition, respectively. However, the increase in expression of the mRNA of the c-myb proto-oncogene and the mitochondrial ATP/ADP carrier protein, 2F1, which begins to occur 8 h following serum addition to SMC, was completely inhibited by heparin. Two-dimensional polyacrylamide gel electrophoresis of the products of a rabbit reticulocyte cell-free translation of RNA isolated at various times confirmed this temporal assessment of the effects of heparin. These results suggest that heparin does not inhibit cell proliferation by blocking the G0 to G1 transition. Rather, heparin may affect a critical event in the mid-G1 phase of the cell cycle which is necessary for subsequent DNA synthesis.
SU-FF-I-09: Pediatric Patient Dose Management From a 64 Slice VCT (2007)

Purpose: As the clinical utilization of CT grows, it becomes more important to manage patient dose without compromising image quality, especially in children. A special effort should be made to reduce pediatric patient dose through age- and size-specific protocols. Methods & Materials: A pediatric 64 slice VCT scanner (GE Lightspeed) was tested with a group of cylindrical acrylic phantoms with diameters ranging from 6 – 32 cm. In addition, anthropomorphic phantoms (CIRS adult and pediatric dosimetry verification phantoms) were employed to correlate the CTDI values with the skin doses measured by a solid state dosimeter (Unfors PSD). The dose affecting factors included: kVp, mAs, beam filtration, beam collimation, pitch, patient size, detector configuration and dose reduction techniques such as mA modulation and post-processing. Various techniques and their combinations were included in this study. Finally, clinical protocols for pediatric applications were evaluated and adjusted based upon the measured patient dose and image quality. Results: The automated CTDI values displayed on the system agreed with our measurements when the standard phantom sizes were used, i.e., 16 cm in diameter for head, 32 cm for adult body and 16 cm for pediatric body. However, the measured dose differed from the automated CTDI by a factor of 1.72 for a reduced head phantom size of 6 cm in diameter and a factor of 3.2 for a reduced body phantom size of 10 cm in diameter. Patient age also played an important role in estimating effective dose. The changing beam filtration caused a variation of up to 42% in the in-air dose output. Concurrently, noise from the phantom images was evaluated. Conclusion: The clinical protocols were established based upon the dose level corresponding to the patient size and age as well as the tolerable noise level corresponding to the specific clinical applications.
DQA: Scalable, Automated and Interactive Data Quality Advisor (2019)

Fueled with growth in the fields of Internet of Things (IoT) and Big Data, data has become one of the most valuable assets in today's world. While we are leveraging this data for analyzing complex systems using machine learning and deep learning, a considerable amount of time and effort is spent on addressing data quality issues. If undetected, data quality issues can cause large deviations in the analysis, misleading data scientists. To ease the effort of identifying and addressing data quality challenges, we introduce DQA, a scalable, automated and interactive data quality advisor. In this paper, we describe the DQA framework, provide detailed description of its components and the benefits of integrating it in a data science process. We propose a programmatic approach for implementing the data quality framework which automatically generates dynamic executable graphs for performing data validations fine-tuned for a given dataset. We discuss the use of DQA to build a library of validation checks common to many applications. We provide insight into how DQA addresses many persistence and usability issues which currently make data cleaning a laborious task for data scientists. Finally, we provide a case study of how DQA is implemented in a realworld system and describe the benefits realized.
Real-time continuous collision detection for mobile manipulators - A general approach (2012)

We present a general real-time continuous collision detection algorithm for arbitrary systems of moving bodies connected to each other in a kinematic tree of joints. Here “joint” as a general term refers to the measured relative motion between two bodies, which may be physically connected or not. We provide a basic set of joints covering revolute and prismatic joints, vehicle motion, and 3d positioning which is sufficient for many applications in particular those involved with mobile manipulators, e.g. industrial and humanoid robots, intelligent transportation systems, or equipment at construction sites. Each joint implementation either operates on a motion bound (an interval covering the braking distance) or an uncertainty bound (measurement error) and computes a volume that spatially bounds the effect of that motion or uncertainty. Aggregating all joints in a kinematic tree then yields a conservative continuous collision detection for the complex and uncertain motion of the whole system. We further present an augmented reality visualization that overlays the collision volumes into the live image of a camera, which can be used to validate the collision model before bringing a system into service.
Solanum nigrum Linn. Water Extract Inhibits Metastasis in Mouse Melanoma Cells in Vitro and in Vivo (2010)

Metastatic melanoma is an aggressive skin cancer notoriously resistant to current cancer therapies. Thus, new treatment strategies are urgently needed. Solanum nigrum Linn., commonly used in Oriental medicine, has showed antineoplastic activity in human cancer cell lines. The aim of this study was to evaluate the inhibitive effect of S. nigrum Linn. water extract (SNWE) on melanoma metastasis and dissect the underlying mechanisms of SNWE actions. B16-F1 cells were analyzed for migrating and invasive abilities with SNWE treatment, and several putative targets involved in metastatic melanoma were examined. In parallel, primary mouse xenograft and lung metastasis of melanoma models were established to examine the therapeutic potential of SNWE. The results indicated SNWE significantly inhibited B16-F1 cell migration and invasion. Meanwhile, decreased Akt activity and PKCα, Ras, and NF-κB protein expressions were detected in dose-dependent manners. In line with this notion, >50% reduced tumor weight and lung metastatic nodules were observed in 1% SNWE fed mice. This was associated with reduced serum MMP-9 as well as Akt activity and PKCα, Ras, and NF-κB protein expressions. Thus, this work indicates SNWE has potential application for treating metastatic melanoma.
Topical honey application vs. acyclovir for the treatment of recurrent herpes simplex lesions. (2004)

Topical honey application is safe and effective in the management of the signs and symptoms of recurrent lesions from labial and genital herpes.
Multiscale real time and high sensitivity ion detection with complementary organic electrochemical transistors amplifier (2020)

Ions are ubiquitous biological regulators playing a key role for vital processes in animals and plants. The combined detection of ion concentration and real-time monitoring of small variations with respect to the resting conditions is a multiscale functionality providing important information on health states. This multiscale functionality is still an open challenge for current ion sensing approaches. Here we show multiscale real-time and high-sensitivity ion detection with complementary organic electrochemical transistors amplifiers. The ion-sensing amplifier integrates in the same device both selective ion-to-electron transduction and local signal amplification demonstrating a sensitivity larger than 2300 mV V<sup>-1</sup> dec<sup>-1</sup>, which overcomes the fundamental limit. It provides both ion detection over a range of five orders of magnitude and real-time monitoring of variations two orders of magnitude lower than the detected concentration, viz. multiscale ion detection. The approach is generally applicable to several transistor technologies and opens opportunities for multifunctional enhanced bioelectronics.
A linearizing predistorter with fast adaptation (2002)

An adaptive predistorter particularly suited to baseband implementation with digital signal-processing hardware is presented and analyzed. It is applicable to any modulation format and any AM/FM and FM/PM characteristic. With a table of well under 100 complex words, it reduces intermodulation products in a typical Class AB amplifier to levels suitable for the mobile environment. It adapts to a new amplifier in a few milliseconds, and its reconvergence time following a channel switch is virtually zero. Since it allows linearization of the power amplifier over 95% to 98% of the saturated output power, it provides power efficiency as well. In comparison with the most powerful predistorter previously reported, it requires four orders of magnitude less memory, reduces convergence time by over three orders of magnitude, eliminates reconvergence time following a channel switch, and eliminates the need for a phase shifter in the feedback path.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Surface molecule CD229 as a novel target for the diagnosis and treatment of multiple myeloma (2011)

Our results demonstrate that the immunoreceptor CD229 is specifically over-expressed on myeloma cells including their clonogenic precursors and contributes to their malignant phenotype. Monoclonal antibodies against this protein may represent a promising diagnostic and immunotherapeutic instrument in this disease.
Secondary electron emission and glow discharge properties of 12CaO·7Al<sub>2</sub>O<sub>3</sub>electride for fluorescent lamp applications (2011)

12CaO·7Al<sub>2</sub>O<sub>3</sub> electride, a sub-nanoporous compound having a work function of 2.4 eV, was examined as a candidate cathode material in fluorescent lamps. The electron emission yield was higher and the discharge voltage was lower for 12CaO·7Al<sub>2</sub>O<sub>3</sub> than for existing cathode materials such as Ni, Mo or W; therefore, the energy consumption of the fluorescent lamps can be improved using 12CaO·7Al<sub>2</sub>O<sub>3</sub> cathodes. Prototype glow-discharge lamps using 12CaO·7Al<sub>2</sub>O<sub>3</sub> were constructed and exhibited reasonable durability.
ENHANCEMENT OF STEREO IMAGERY BY ARTIFICIAL TEXTURE PROJECTION GENERATED USING A LIDAR (2016)

Passive stereo imaging is capable of producing dense 3D data, but image matching algorithms generally perform poorly on images with large regions of homogenous texture due to ambiguous match costs. Stereo systems can be augmented with an additional light source that can project some form of unique texture onto surfaces in the scene. Methods include structured light, laser projection through diffractive optical elements, data projectors and laser speckle. Pattern projection using lasers has the advantage of producing images with a high signal to noise ratio. We have investigated the use of a scanning visible-beam LIDAR to simultaneously provide enhanced texture within the scene and to provide additional opportunities for data fusion in unmatched regions. The use of a LIDAR rather than a laser alone allows us to generate highly accurate ground truth data sets by scanning the scene at high resolution. This is necessary for evaluating different pattern projection schemes. Results from LIDAR generated random dots are presented and compared to other texture projection techniques. Finally, we investigate the use of image texture analysis to intelligently project texture where it is required while exploiting the texture available in the ambient light image.