gebhart/patrepeval huggingface dataset:
Triggered Real-Time Databases with Consistency Constraints (1990)

Abstract Real-time database systems incorporate the notion of a deadline into the database system model. USU- ally, deadlines are associated with transactions, and the system attempts to execute a given set of trans- actions so as to both meet the deadlines and ensure the database consistency. This paper presents an al- ternative model of real-time database processing in which deadlines are associated with consistency con- straints rather than directly with transactions. This model leads to a predicate-baaed approach to transac- tion management that allows greater concurrency and more flexibility in modeling real-world systems. 1 Introduction Real-time database systems (RTDBs) incorporate tim- ing considerations into a database system. Not only must the transactions execute correctly, but also, they must complete execution within some time limit called a deadline. Systems that incorporate strict deadlines are called
Thyristor controlled series compensation: some aspects of different circuit parameters and voltage stability margin (2002)

Variable series compensation allows power transfers to be increased and controlled in the UHV transmission lines. Much attention has been focused on using power electronics to improve the speed control of variable series compensation. Several devices have been presented. The main circuit studied is the thyristor controlled series compensator (TCSC). This paper presents a time domain simulation of the TCSC circuit. The analysis is performed by a simulation program based on Bergeron's method. The study of the TCSC module operation in an electric line shows that TCSC modules enable the transmission line performance to be improved (variable compensation), without introducing too many harmonics to the system.
Selenium Enhances the Anti-Angiogenic Effects of Bevacuzimab (Anti-VEGF Antibody) in Human Acute Myeloid Leukemia Xenograft Models. (2007)

Abstract Selenium, a known antioxidant used in chemoprevention, has recently been shown to improve the efficacy of chemotherapy agents and mediate anti-angiogenic effects in preclinical solid tumor models. Prior data has also shown that sodium selenite can induce apoptosis of human acute myeloid leukemia (AML) cells in vitro. While the use of high non-toxic doses of selenium has been demonstrated to effectively enhance the therapeutic efficacy and selectivity of various anti-cancer drugs in multiple solid tumor xenograft models (Cao et al, Clin Canc Res10: 2561–2569, 2004), the in vivo effects of selenium compounds in hematological malignancies have not been extensively explored. Our laboratory has previously demonstrated the preclinical efficacy of VEGF inhibitors in human leukemia xenograft models. Here we investigated the in vitro and in vivo effects of seleno-L-methionine (SLM), alone and in combination with chemotherapy and anti-VEGF antibody, in human AML. The mechanism of action, dosage, and time course of SLM effects on AML cells (ML-2 and HL60) in vitro were determined using colorimetric (CCK-8) viability, tritiated thymidine proliferation, and Annexin-V flow cytometric assays. SLM therapy resulted in dose dependent inhibition of AML proliferation with marked induction of apoptosis and a 67–92% reduction in viable cells at 400–500 μM. Ten million AML cells (ML-2 and HL60-luciferase) were then subcutaneously engrafted into immunodeficient (SCID/SCID) mice. ML-2 tumor bearing mice were treated with PBS (vehicle), SLM (200 mcg p.o. daily), cytarabine (Ara-C 2 mg i.p. for 3 days), or combination SLM + Ara-C therapy for over two weeks. SLM showed no effective modulation of therapeutic efficacy and toxicity in AML tumor models, when combined with Ara-C. Neither SLM nor Ara-C alone or in combination resulted in significant reduction of AML growth. ML-2 and HL60-luciferase tumor bearing mice were then treated with PBS, SLM (200 mcg p.o. daily), anti-VEGF antibody bevacuzimab (BV 100mcg i.p. twice weekly), or SLM + BV for three weeks. Disease progression was monitored by tumor volume, end tumor weight, and bioluminescent imaging. Although SLM alone was ineffective in reducing HL60 leukemia growth, SLM + BV combination therapy effectively induced a 75% reduction in mean tumor volume after 21 days of treatment which was statistically greater than BV therapy alone (62% reduction). Synergistic effects of SLM+BV therapy was also confirmed by differences in mean tumor weights and bioluminescent imaging as compared with single agent BV and SLM treated mice. Similar results were seen in the ML-2 AML xenograft model. Conclusions: SLM improved the anti-angiogenic and anti-tumor effects of anti-VEGF therapy with bevacizumab in human AML xenograft models. Additional studies investigating the mechanisms of action of these synergistic effects will be presented.
Assessing and enhancing foldability in designed proteins (2021)

Abstract Recent advances in protein-design methodology have led to a dramatic increase in reliability and scale. With these advances, dozens and even thousands of designed proteins are automatically generated and screened. Nevertheless, the success rate, particularly in design of functional proteins, is low and fundamental goals such as reliable de novo design of efficient enzymes remain beyond reach. Experimental analyses have consistently indicated that a major reason for design failure is inaccuracy and misfolding relative to the design model. To address this challenge, we describe complementary methods to diagnose and ameliorate suboptimal regions in designed proteins: first, we develop a Rosetta atomistic computational mutation scanning approach to detect energetically suboptimal positions in designs (available on a web server https://pSUFER.weizmann.ac.il ); second, we demonstrate that AlphaFold2 ab initio structure prediction flags regions that may misfold in designed enzymes and binders; and third, we focus FuncLib design calculations on suboptimal positions in a previously designed low-efficiency enzyme improving its catalytic efficiency by 330 fold. Furthermore, applied to a de novo designed protein that exhibited limited stability, the same approach markedly improved stability and expressibility. Thus, foldability analysis and enhancement may dramatically increase the success rate in design of functional proteins.
Towards Propagation of Changes by Model Approximations (2006)

A number of model transformation approaches have been proposed both from academia and industry since automated manipulation of models plays a central role in model driven development. Ideally, a model transformation technique should also be compatible with manual changes that might be performed by designers on the generated models in order to resolve unforeseen requirements or limited expressiveness of the involved metamodels. This paper proposes an approach to model transformation based on answer set programming. Starting from target models that have been manually modified (and possibly not belong to the co-domain of the transformation being used), the approach is able to deduce a collection of models that approximate the ideal one from which it is possible to generate the previously modified target.
The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa (2023)

The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and <i>Polaromonas</i> exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.
Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics (2017)

Abstract For many bacteria with sequenced genomes, we do not understand how they synthesize some amino acids. This makes it challenging to reconstruct their metabolism, and has led to speculation that bacteria might be cross-feeding amino acids. We studied heterotrophic bacteria from 10 different genera that grow without added amino acids even though an automated tool predicts that the bacteria have gaps in their amino acid synthesis pathways. Across these bacteria, there were 11 gaps in their amino acid biosynthesis pathways that we could not fill using current knowledge. Using genome-wide mutant fitness data, we identified novel enzymes that fill 9 of the 11 gaps and hence explain the biosynthesis of methionine, threonine, serine, or histidine by bacteria from six genera. We also found that the sulfate-reducing bacterium Desulfovibrio vulgaris synthesizes homocysteine (which is a precursor to methionine) by using DUF39, NIL/ferredoxin, and COG2122 proteins, and that homoserine is not an intermediate in this pathway. Our results suggest that most free-living bacteria can likely make all 20 amino acids and illustrate how high-throughput genetics can uncover previously-unknown amino acid biosynthesis genes.
Purification and Characterization of a New Anti-Nucleating Protein Isolated from <I>Acinetobacter calcoaceticus</I> KINI-1 (1996)

Strain KINI-1 capable of producing an anti-nucleating agent was isolated from a camphor leaf. Strain KINI-1 was identified as Acinetobacter calcoaceticus from its characteristics and taxonomics; the optimum temperature and pH for the production of the anti-nucleating agent were 30°C and 7.0, respectively. As the activity of this agent disappeared with the application of protease treatment, this agent, which was an anti-nucleating protein (ANP) was partially purified from the culture to an electrophoretically main band state by ultrafiltration, acetone precipitate, QA-52 column chromatography and Toyopearl HW 55S and Superose 12 gel filtration chromatography. The molecular weight of the ANP estimated by sodium dodecylsulfatepolyacrylamide gel electrophoresis was 55 kDa. The ANP had various substrate specificities for ice nuclei from various ice-nucleating bacteria and AgI. It was demonstrated that the antinucleating activity of ANP increased in proportion to the protein concentration and the antinucleating activity of ANP against ice nucleus from the cells of Erwinia uredovora KUIN-3 was 2.2°C at a concentration of 12.5μg/ml. Furthermore, we found that this ANP was bound to the surface of the ice nuclei, thereby causing anti-nucleating activity. The surface hydrophobicities of the ice nuclei were increased after binding with ANP, whereas the surface charge was changed from 6.6 to 6.1. Also, we confirmed that this action by ANP could give rise to a supercooling point at -5.0°C in the cell suspension of Erwinia uredovora KUIN-3.
IMC based set-point weighted PID tuning for first order delay unstable process (FODUP) (2011)

Present work provides a discussion for synthesizing PID from IMC controller for first order delay unstable process. Recently, Lee, et al. [1] has shown the effectiveness of using MacLaurin series for synthesizing PID controller tuning relation from IMC framework. In this paper, the desired closed loop response based on optimal performance for unit set point input and input disturbance are provided. We also develop the IMC-set point weighting tuning formulation.
CREATIN AS A SUPPLEMENT IN NUTRITION AND EFFECTS ON SWIMMING (2019)

The subject of the study is the effect of creatine on swimming speed. In previous studies, creatine monohydrate was thought to be an effective nutritional supplement currently available related to improving exercise results. Almost 70% of these studies report a significant improvement in exercise capacity, while in the other studies, no significant improvement in results was generally observed.The test was performed on a sample of 60 swimmers, members of the Academic Swimming Club "April 22" divided into three groups and ages from 21-25. All examinees are male and in good health. Examinees belonging to this population are at the zenith of their morphological and motor development and are well motivated to advance in swimming. The subjects were divided into three groups and engaged in recreational swimming until the application of this research.All three groups of swimmers performed a specific amount of swimming, which was accompanied by the plan for the development of swimming in recreation, with the first group of swimmers taking creatine in addition to swimming, the second group of swimmers doing fitness in addition to swimming, and the third group only swimming. The measurement was carried out at the end of May and half of June 2008 at the premises of the Recreation Center SrpskeToplice (water temperature 28 degrees C).Variablessemple referred to swimming speed at 50 m freestyle technique (both measurements and time differences) were used. Descriptive statistics indicators were used. The main objective of the study is to determine whether, with creatine ingestion, with a duration of three weeks, there are significant differences in the increase in swimming speeds compared to the training of strength and swimming training models. The results of the study, analyzed by t-test, show that the difference in swimming time of 50 m freestyle technique is statistically significant.
Miniaturized-Element Frequency-Selective Surfaces Based on the Transparent Element to a Specific Polarization (2016)

In this study, a novel technique has been introduced for the first time, which is based on the transparent element to a specific polarization in order to realize bandpass frequency selective surfaces. It is shown that the proposed technique is more successful than preceding miniaturized structures presented in a variety of literature with respect to reducing the unit cell size. The element sizes of the structures are about 0.017λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> to 0.053λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> . Furthermore, frequency response of the structures demonstrates perfect stability against the variations of the incident angle of the electromagnetic (EM) wave.
Acidity effect in the regiochemical control of the alkylation of phenol with alkenes (1997)

Treatment of 1∶1 mixtures of phenol and linear alkenes in the presence of an acidic promoter in CHCl3 at room temperature results in ortho-regioselective monoalkylation producing sec-alkylphenols in 48–60% yield. In similar reactions, branched alkenes lead exclusively to the corresponding para-tert-alkylphenols in 80–85% yield. Addition of increasing amounts of potassium phenolate to the reacting system reduces the protic acidity and promotes ortho-regioselective tert-alkylation. These results are tentatively explained in terms of competition of ‘H-bond-template’ and ‘charge-controlled’ mechanisms.
Pulsed laser deposited epitaxial Sm–Co thin films with uniaxial magnetic texture (2006)

Sm–Co thin films have been grown epitaxially with pulsed laser deposition on Cr buffered MgO(110) substrates. The buffer microstructure plays a significant role in controlling the growth and hence the magnetic properties of the Sm–Co film. High deposition temperatures of the Cr buffer result in a rough and discontinuous microstructure, thereby resulting in an x-ray amorphous or nanocrystalline Sm–Co layer, as has been confirmed by transmission electron microscopy studies. By lowering the buffer deposition temperature from 700to300°C, the roughness decreases from 5to0.6nm. Sm–Co films grow epitaxially on these low temperature buffers with the epitaxial relation MgO(110)[001]∥Cr(211)011∥SmCo(100)[001] which implies a single in-plane orientation of the c axis along the MgO[001] direction. The strong in-plane crystallographic texture seen in the pole figure measurements leads to a very pronounced magnetic texture, quantified by a remanence ratio JrMgO[110]∕JrMgO[001] as low as 0.08 and a high remanence of 0.84T along with a high coercivity of 3T when measured along the easy axis.
Enzymology of Bacterial Lysine Biosynthesis (1998)

Bacteria have evolved three strategies for the synthesis of lysine from aspartate via formation of the intermediate diaminopimelate (DAP), a metabolite that is also involved in peptidoglycan formation. The objectives of this chapter are descriptions of mechanistic studies on the reactions catalyzed by dihydrodipicolinate synthase, dihydrodopicolinate reductase, tetrahydrodipicolinate N-succinyl-transferase, N-succinyl-L,L-DAP aminotransferase, N-succinyl-L,L-DAP desuccinylase, L,L-DAP epimerase, L,L-DAP decarboxylase, and DAP dehydrogenase. These enzymes are discussed in terms of kinetic, isotopic, and X-ray crystallographic data that allow one to infer the nature of interactions of each of these enzymes with its substrate(s), coenzymes, and inhibitors.
The specific delivery of proteins to human liver cells by engineered bio‐nanocapsules (2005)

A bio-nanocapsule (BNC), composed of the surface antigen (sAg) of the hepatitis B virus, is an efficient nanomachine with which to accomplish the liver-specific delivery of genes and drugs. Approximately 110 molecules of sAg are associated to form a BNC particle with an average diameter of 130 nm. The L protein is an sAg peptide composed mainly of preS and S regions. The preS region, with specific affinity for human hepatocytes, is localized in the N-terminus. The S region following the preS has two transmembrane regions responsible for the formation of particles. In this study, the fusion of emerald green fluorescent protein (EGFP) at the C-terminus of the S region was designed to deliver proteins to human hepatocytes. Truncation of the C-terminus of the S region was required to obtain sufficient expression levels in Cos7 cells. The nanoparticles that were produced delivered EGFP to human hepatoma cells, displaying the EGFP moiety outside, or enclosing it inside. However, only a single orientation characterizes the particle, so that either type of L fusion particle could be effectively and independently separated by an antibody affinity column. The dual C-terminal topologies of the L fusion particles designed in this study could be applied to various proteins for the C-terminal moiety of the L fusion proteins, depending on the character of the proteins, such as cytoplasmic proteins, as well as cytokines or ligands to cell surface receptors. We suggest that this fusion design is the most efficient way to prepare a BNC that delivers proteins to specific cells or tissues.
Figure S1 from JAK1/STAT3 Activation through a Proinflammatory Cytokine Pathway Leads to Resistance to Molecularly Targeted Therapy in Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Figure S1. Phase-contrast images of parental and acquired-resistance cells. Three acquired-resistance cells showed morphological changes to spindle shapes compared to parental cells.&lt;/p&gt;
Raman scattering in pure and carbon-dopedMgB2films (2005)

We have studied Raman scattering in $\mathrm{Mg}{\mathrm{B}}_{2}$ thin films grown by hybrid physical-chemical vapor deposition on SiC and ${\mathrm{Al}}_{2}{\mathrm{O}}_{3}$ substrates. The Cooper-pair-breaking peak corresponding to the larger gap was observed and its position correlates with the value of ${T}_{c}$, which varies with film strain. The temperature dependence of the ${E}_{2g}$ phonon frequency and linewidth was studied. Carbon doping of $\mathrm{Mg}{\mathrm{B}}_{2}$ films suppresses ${T}_{c}$, and leads to a hardening of the ${E}_{2g}$ phonon mode, an increased luminescence background in the spectra, and a stronger contribution of disorder-activated phonons to Raman spectra.
Positive correlation between single or combined genotypes of CYP1A1 and GSTM1 in relation to prostate cancer in Chilean people (2003)

Taken together, these findings suggest that Chilean people carrying single or combined GSTM1 and CYP1A1 polymorphisms are more susceptible to prostate cancer.
Interplay between Akt and p38 MAPK pathways in the regulation of renal tubular cell apoptosis associated with diabetic nephropathy (2009)

Hyperglycemia induces p38 MAPK-mediated renal proximal tubular cell (RPTC) apoptosis. The current study hypothesized that alteration of the Akt signaling pathway by hyperglycemia may contribute to p38 MAPK activation and development of diabetic nephropathy. Immunoblot analysis demonstrated a hyperglycemia-induced increase in Akt phosphorylation in diabetic kidneys at 1 mo, peaking at 3 mo, and dropping back to baseline by 6 mo. Immunohistochemical staining with anti-pAkt antisera localized Akt phosphorylation to renal tubules. Maximal p38 MAPK phosphorylation was detected concomitant with increase in terminal uridine deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL)-positive cells and caspase-3 activity in 6-mo diabetic kidneys. Exposure of cultured RPTCs to high glucose (HG; 22.5 mM) significantly increased Akt phosphorylation at 3, 6, and 9 h, and decreased thereafter. In contrast, p38 MAPK phosphorylation was detected between 9 and 48 h of HG treatment. Increased p38 MAPK activation at 24 and 48 h coincided with increased apoptosis, demonstrated by increased caspase-3 activity at 24 h and increased TUNEL-positive cells at 48 h of HG exposure. Blockade of p38 cascade with SB203850 inhibited HG-induced caspase-3 activation and TUNEL-positive cells. Overexpression of constitutively active Akt abrogated HG-induced p38 MAPK phosphorylation and RPTC apoptosis. In addition, blockade of the phosphatidylinositol-3 kinase/Akt pathway with LY294002 and silencing of Akt expression with Akt small interfering RNA induced p38 MAPK phosphorylation in the absence of HG. These results collectively suggest that downregulation of Akt activation during long-term hyperglycemia contributes to enhanced p38 MAPK activation and RPTC apoptosis. Mechanism of downregulation of Akt activation in 6-mo streptozotocin diabetic kidneys was attributed to decreased Akt-heat shock protein (Hsp) 25, Akt-p38 interaction, and decreased PTEN activity. Thus PTEN or Hsp25 could serve as potential therapeutic targets to modulate Akt activation and control p38 MAPK-mediated diabetic complications.
Cellular Wave Computing the Multi-channel Mammalian Retina Model by the Bi-I Camera-computer (2006)

This demo displays a retina exploration system. The system is designed to explore and understand the essence of the retina channels and offers a potential input transformation for retinal implants [1] The primary motivation was to deduce a simple algorithmic skeleton from neurobiological measurements [2]. The model is tuned for several different retina channels with less than one-half percent spatial-temporal error The implementation platform of our novel neuromorphic retina model is the Bi-I [3] The Bi-I computer, containing the ACE16k CNN-UM [4] and DSP chips computes our parallel multi-channel model in video real-time. The on-line control is provided by external controllers to enable changing parameters on-line. The system will be available to experimentation.