gebhart/patrepeval huggingface dataset:
Purification and Characterization of 2-Hydroxybiphenyl 3-Monooxygenase, a Novel NADH-dependent, FAD-containing Aromatic Hydroxylase from Pseudomonas azelaica HBP1 (1997)

2-Hydroxybiphenyl 3-monooxygenase (HbpA), the first enzyme of 2-hydroxybiphenyl degradation in Pseudomonas azelaica HBP1, was purified 26-fold with a yield of 8% from strain HBP1 grown on 2-hydroxybiphenyl. The enzyme was also purified from a recombinant of Escherichia coli JM109, which efficiently expressed the hbpA gene. Computer densitometry of scanned slab gels revealed a purity of over 99% for both enzyme preparations. Gel filtration, subunit cross-linking, and SDS-polyacrylamide gel electrophoresis showed that the enzyme was a homotetramer with a molecular mass of 256 kDa. Each subunit had a molecular mass of 60 kDa containing one molecule of noncovalently bound FAD. The monooxygenase had a pI of 6.3. It catalyzed the NADH-dependent ortho-hydroxylation of 2-hydroxybiphenyl to 2,3-dihydroxybiphenyl. Molecular oxygen was the source of the additional oxygen of the product. The enzyme hydroxylated various phenols with a hydrophobic side chain adjacent to the hydroxy group. All substrates effected partial uncoupling of NADH oxidation from hydroxylation with the concomitant formation of hydrogen peroxide. 2,3-Dihydroxybiphenyl, the product of the reaction with 2-hydroxybiphenyl, was a non-substrate effector that strongly facilitated NADH oxidation and hydrogen peroxide formation without being hydroxylated and also was an inhibitor. The apparent Km values (30 degrees C, pH 7.5) were 2.8 microM for 2-hydroxybiphenyl, 26.8 microM for NADH, and 29.2 microM for oxygen. The enzyme was inactivated by p-hydroxymercuribenzoate, a cysteine-blocking reagent. In the presence of 2-hydroxybiphenyl, the enzyme was partly protected against the inactivation, which was reversed by the addition of an excess of dithiothreitol. The NH2-terminal amino acid sequence of the enzyme contained the consensus sequence GXGXXG, indicative of the betaalphabeta-fold of the flavin binding site and shared homologies with that of phenol 2-hydroxylase from Pseudomonas strain EST1001 as well as with that of 2,4-dichlorophenol 6-hydroxylase from Ralstonia eutropha.
Microinjection of Antibody to Mad2 Protein into Mammalian Cells in Mitosis Induces Premature Anaphase (1998)

In yeast, the Mad2 protein is required for the M phase arrest induced by microtubule inhibitors, but the protein is not essential under normal culture conditions. We tested whether the Mad2 protein participates in regulating the timing of anaphase onset in mammalian cells in the absence of microtubule drugs. When microinjected into living prophase or prometaphase PtK1 cells, anti-Mad2 antibody induced the onset of anaphase prematurely during prometaphase, before the chromosomes had assembled at the metaphase plate. Anti-Mad2 antibody-injected cells completed all aspects of anaphase including chromatid movement to the spindle poles and pole-pole separation. Identical results were obtained when primary human keratinocytes were injected with anti-Mad2 antibody. These studies suggest that Mad2 protein function is essential for the timing of anaphase onset in somatic cells at each mitosis. Thus, in mammalian somatic cells, the spindle checkpoint appears to be a component of the timing mechanism for normal mitosis, blocking anaphase onset until all chromosomes are aligned at the metaphase plate.
Automated testcase generation for data abstraction (2003)

The authors present a simple strategy for generating testcases for implementations of abstract data types, based on syntactic information about the operations on the type. The developed tool has been used on a number of different types including stacks, strings, etc. It is found that choosing depth 2 for generating the testcases results in an effective set of testcases for detecting errors and can provide 100% statement coverage if proper initial values are selected. There are no rules for selecting the initial values.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Peroxides with Anthelmintic, Antiprotozoal, Fungicidal and Antiviral Bioactivity: Properties, Synthesis and Reactions (2017)

The biological activity of organic peroxides is usually associated with the antimalarial properties of artemisinin and its derivatives. However, the analysis of published data indicates that organic peroxides exhibit a variety of biological activity, which is still being given insufficient attention. In the present review, we deal with natural, semi-synthetic and synthetic peroxides exhibiting anthelmintic, antiprotozoal, fungicidal, antiviral and other activities that have not been described in detail earlier. The review is mainly concerned with the development of methods for the synthesis of biologically active natural peroxides, as well as its isolation from natural sources and the modification of natural peroxides. In addition, much attention is paid to the substantially cheaper biologically active synthetic peroxides. The present review summarizes 217 publications mainly from 2000 onwards.
Acute myeloid leukemia with KMT2Ar and association with risk of bleeding and early mortality. (2022)

7026 Background: Acute myeloid leukemia (AML) with rearrangement of KMT2A is characterized by chemotherapy resistance and high rates of relapse. However, additional causes of treatment failure or early mortality have not been well-defined in this entity. Methods: In a retrospective analysis, we compared causes and rates of early mortality following induction treatment between a cohort of adults with KMT2Ar AML (N=172) and an age-matched cohort of patients (pts) with normal karyotype (NK) AML (N=522). Results: The 30 and 60-day (60d) mortality in pts with KMT2Ar AML were significantly higher compared to those with NK AML, with rates of 10% (17/172 pts) and 15% (26/172 pts) in KMT2Ar AML vs 4% (20/522 pts) and 7% (38/522 pts) in NK AML, respectively ( P=0.004). Among those who died within 60d, the most common contributing cause in KMT2Ar was respiratory failure without a clear infectious etiology in 38% (10/26 pts) vs 11% (4/38 pts) in NK AML ( P=0.01). We found 42% (11/26 pts) with KMT2Ar AML who died within 60d were either diagnosed with or had high clinical suspicion for diffuse alveolar hemorrhage (DAH) that warranted empiric therapy vs 18% (7/38 pts) with NK AML ( P=0.05). Given the high occurrence of DAH in KMT2Ar AML, we set out to quantify bleeding events and recorded major and minor bleeds as defined by the International Society of Thrombosis and Haemostasis. We found 65% (17/26 pts) with KMT2Ar AML had at least one bleeding event vs 32% (12/38 pts) with NK AML ( P=0.01). There was a significantly higher frequent occurrence of major bleeds (rate ratio=6.22; P=0.005) and total bleeding events (rate ratio=4.5; P=0.001) in KMT2Ar AML vs NK AML. KMT2Ar was associated with disseminated intravascular coagulopathy (DIC), as 93% of evaluable pts (14/15 pts) vs 54% (7/13 pts) in NK AML had overt DIC before death. Longitudinal trajectories of DIC parameters of pts who died within 60d showed significantly higher prothrombin time levels ( P=0.008) in KMT2Ar. In a multivariate analysis, KMT2Ar and a monocytic phenotypic were the only independent predictors of any bleeding event in pts who died within 60d (OR 3.5, 95% CI 1.4-10.4, P=0.03; OR 3.2, 95% CI 1.1-9.4, P=0.04). Conclusions: KMT2Ar AML is associated with higher early mortality and an increased risk of bleeding and coagulopathy compared with NK AML. Early recognition and aggressive management of DIC and coagulopathy are important considerations that could mitigate the risk of death during induction treatment.[Table: see text]
Transition from electrostatic-to-electromagnetic mode in a radio-frequency Ar inductively coupled plasma in atmospheric pressure (2003)

The dynamics of mode transition from the electrostatic (E) to electromagnetic (H) mode of a radio-frequency argon inductively coupled plasma (ICP) in atmospheric pressure is investigated, both experimentally and theoretically. High-speed (4500 f/s) camera imaging is performed to investigate the dynamics of E–H discharge mode transition. The temporal plasma loading impedance of Ar inductive discharges at the E–H transition stage is also observed to investigate the transition dynamics. The experimental observations reveal that the formation of the multiple streamerlike electrostatic discharge paths followed by the strong ring-shaped azimuthal discharges leads to ignite the high-pressure (around 1 atm or more) ICPs. The time scale of E–H discharge mode transition is estimated by using proposed models and the estimated results are compared with that of the experimental one. It is found that the estimated results agree well with that of the experimental one.
KernelNet: A Blind Super-Resolution Kernel Estimation Network (2021)

Recently developed deep neural network methods have achieved remarkable performance in the Super Resolution problem when applied to Low Resolution (LR) images that are obtained from High Resolution (HR) images with ideal and predefined downsampling processing, i.e., convolution with a known blurring kernel that is followed by subsampling (e.g., Bicubic). However, when these algorithms are applied to real-world images whose downsampling pattern is unknown, unlike synthetically generated LR-HR image pairs, their performance drops drastically. Blind SR problem can be defined as real-world image SR when the down-sampling blurring kernel (SR kernel) is unknown. The recent SR kernel estimation techniques like KernelGAN have shown promising results in this direction. However, their limited recovery performance and high computational complexity make them unsuitable for real-time usage, like for applications in mobile cameras. This paper proposes a modular and interpretable neural network structure, KernelNet, for the blind SR kernel estimation problem. The proposed model outperforms the state-of-the-art SR kernel estimator, KernelGAN, by a significant margin in SR kernel reconstruction accuracy. Moreover, to the best of our knowledge, the proposed algorithm is the first one that can estimate the SR kernel in real-time by performing O(1k) times faster than KernelGAN.
A Pattern-Based Layout Algorithm for Diagram Editors (2024)

The diagram editor generator framework DIAMETA utilizes meta-model-based language specifications and supports free-hand as well as structured editing. We presented a generic layout algorithm that meets the demands of this kind of editors. The algorithm combines two concepts, constraint satisfaction and attribute evaluation, to a powerful methodology for specifying the layout for a particular visual language. As the layout specification for this algorithm is rather complex, we encapsulated basic functionality into reusable patterns. This paper describes this pattern concept of the generic layout algorithm, and shows how they simplify the layout specification of a specific language.
Radial Immunodiffusion: a Simple and Rapid Method for Detection of Marek's Disease Antigen(s) (1972)

A qualitative radial immunodiffusion technique is described which detects antigen(s) in feathers from live or dead chickens infected with Marek's disease herpesvirus. Antiserum, which is incorporated into a support medium, reacts with antigen(s) in the feather tip producing a radial precipitin ring. Antigen(s) was detected in 93.3% of experimentally inoculated chickens 21 days postinoculation and in 100% of infected birds subsequently tested through 6 weeks. No antigen was detectable in the feathers of uninoculated control chickens. The technique is simple and rapid to perform. Positive tests could be detected after 1 to 2 hours of incubation. Antigen detection by the radial immunodiffusion test correlated well with other criteria of infection. This technique should have application as a laboratory research tool and as an adjunct for a rapid flock diagnosis of Marek's disease.
Temperature effects modelling and compensation analysis in analogue implementation of stochastic artificial neural networks (2002)

The implementation of Artificial Neural Networks (ANN) as CMOS analogue integrated circuits shows several attractive features. Numerous papers show that small size analogue networks operate correctly. However, real ANN applications will require large networks. On the other hand, all of the presented implementations of ANN have been supposed to be working in ideal conditions but real applications will be subject to some global perturbations. For the analogue and mixed digital/analogue implementation cases, the behaviour analysis of the neural network with perturbation conditions is thus inevitable. Unfortunately, very few papers analyse the behaviour of analogue neural network with global perturbations. In this paper we present the behaviour analysis of a CMOS analogue implementation of the synchronous Boltzmann machine model with physical temperature perturbations. The relation between the T parameter of the Boltzmann machine's model and the physical temperature of circuit has been established. Simulation results have been given, temperature effects compensation have been discussed and finally, experimental results have been presented.
Activity of Ampicillin/Sulbactam, Ticarcillin/Clavulanate, Clarithromycin, and Eleven Other Antimicrobial Agents Against Anaerobic Bacteria Isolated from Infections in Children (1995)

The activity of 14 antimicrobial agents against 253 clinical isolates of anaerobic bacteria from pediatric infections was assessed by the agar dilution method. Fifty-eight percent of the isolates were from intraabdominal sites. The drugs tested were ampicillin/sulbactam, ticarcillin/clavulanate, ampicillin, sulbactam, piperacillin, cefoxitin, cefotaxime, cefoperazone/sulbactam, clarithromycin, azithromycin, erythromycin, clindamycin, metronidazole, and chloramphenicol. Ticarcillin/clavulanate was active against all isolates. Clarithromycin was the most active macrolide; combination of this agent with its 14-hydroxy metabolite did not result in synergy. Sixty-two percent of Bacteroides fragilis group isolates, 13% of B. fragilis isolates, and 22% of peptostreptococcal isolates were resistant to clindamycin at a concentration of 4 micrograms/mL. The distribution of these strains in clinical specimens and the patterns of antimicrobial susceptibility documented were different from the findings for isolates from adults in the Los Angeles area.
Interactions of Nucleotide Release Factor Dss4p with Sec4p in the Post-Golgi Secretory Pathway of Yeast (1997)

SEC4 is an essential gene encoding a small GTPase that is involved in Golgi to cell surface transport in Saccharomyces cerevisiae and is a paradigm for studies on the mode of action of Rab proteins. We describe here the features of interaction of Sec4p with the accessory protein Dss4p. Dss4p is found both on membranes and in the cytosol; however, it is the membrane fraction that is complexed to Sec4p. Dss4p, like its mammalian counterpart, Mss4, binds zinc, and disruption of the zinc-binding site disrupts the ability of the protein to interact with Sec4p. DSS4 overexpression can rescue the lethal phenotype of two alleles of SEC4, corresponding to dominant mutations of Ras. We demonstrate that this suppression is due to the ability of Dss4p to form a tight complex with the mutant forms of Sec4p and hence sequester the mutant protein from its inhibitory effect. These results imply an in vivo role for Dss4p as a guanine nucleotide dissociation stimulator. In vitro the protein has the ability to stimulate the dissociation rate of both GDP and GTP from Sec4p. We examined the relationship of GDI1 and DSS4 with SEC4 both genetically and biochemically. These results exclude a role for DSS4 in the recruitment of Sec4p/GDI onto membranes.
Cisplatin-selected resistance is associated with increased motility and stem-like properties via activation of STAT3/Snail axis in atypical teratoid/rhabdoid tumor cells (2015)

Atypical teratoid/rhabdoid tumor (ATRT) is a malignant pediatric brain tumor with great recurrence after complete surgery and chemotherapy. Here, we demonstrate that cisplatin treatment selects not only for resistance but also for a more oncogenic phenotype characterized by high self-renewal and invasive capabilities. These phenomena are likely due to STAT3 upregulatoin which occurred simultaneously with higher expression of Snail, an activator of epithelial-mesenchymal transition (EMT), in ATRT-CisR cells. STAT3 knockdown effectively suppressed Snail expression and blocked motility and invasion in ATRT-CisR cells, while overexpressing Snail reversed these effects. Chromatin immunoprecipitation assay indicated that STAT3 directly bound to Snail promoter. Moreover, STAT3 knockdown effectively suppressed cancer stem-like properties, synergistically enhanced the chemotherapeutic effect, and significantly improved survival rate in ATRT-CisR-transplanted immunocompromised mice. Finally, immunohistochemistrical analysis showed that STAT3 and Snail were coexpressed at high levels in recurrent ATRT tissues. Thus, the STAT3/Snail pathway plays an important role in oncogenic resistance, rendering cells not only drug-resistant but also increasingly oncogenic (invasion, EMT and recurrence). Therefore, the STAT3/Snail could be a target for ATRT treatment.
Two isoforms of a nucleotide‐sugar pyrophosphatase/phosphodiesterase from barley leaves (Hordeum vulgare L.) are distinct oligomers of HvGLP1, a germin‐like protein (2001)

Two isoforms of ADPglucose pyrophosphatase/phosphodiesterase (AGPPase) have been characterized using barley leaves (Hordeum vulgare L.). Whilst one of the isoforms, designated as soluble AGPPase1 (SAGPPase1), is soluble in low ionic strength buffers, the other, SAGPPase2, is extractable using cell wall hydrolytic enzymes or high salt concentration solutions, thus indicating that it is adventitiously bound to the cell wall. Both AGPPase isoforms are highly resistant to SDS, this characteristic being utilized to purify them to homogeneity after zymographic detection of AGPPase activity in SDS-containing gels. N-terminal and internal amino acid sequencing analyses revealed that both SAGPPase1 and SAGPPase2 are distinct oligomers of the previously designated HvGLP1, which is a member of the ubiquitously distributed group of proteins of unknown function designated as germin-like proteins (GLPs).
In vitro effect of thymosin‐α1 and interferon‐α on Th1 and Th2 cytokine synthesis in patients with chronic hepatitis C (2001)

Current evidence suggests that increased expression of Th1-associated cytokines is important for immune-mediated eradication of hepatitis C infection, while an increase in Th2-associated cytokines is associated with persistence of infection. In this study we evaluated the effects of thymosin-alpha1 (TA1), a naturally occurring thymic peptide, and interferon-alpha (IFN-alpha) on cytokine production in peripheral blood mononuclear cells from untreated patients with chronic hepatitis C. We examined the effect of incubation with TA1, IFN-alpha, or both, on production of Th1-associated cytokines (IL-2, IFN-gamma), Th2-associated cytokines (IL-4, IL-10), and synthesis of the antiviral protein 2',5'-oligoadenylate synthetase. TA1 treatment induced a significant increase in production of IL-2 and 2',5'-oligoadenylate synthetase. Smaller increases were also seen after treatment with IFN-alpha, while incubation with TA1 and IFN-alpha together led to an additive or synergistic effect. Incubation with TA1 resulted in a decrease in IL-4 and IL-10, whereas IFN-alpha increased these cytokines. The addition of TA1 to IFN-alpha significantly reversed this IFN-alpha-induced increase. Hence, TA1 treatment could benefit patients with hepatitis C infection by increasing the Th1-type response, fundamental for sustained clearance of hepatitis C; and by decreasing the Th2-type response, associated with persistence of viraemia.
Photonics Research and Development Perspectives in Poland (2012)

Abstract Photonics is one of the most promising and fastest developing innovative technologies and a key‐enabling technology of Europe. Poland has a long tradition in optics and photonics research, especially in laser‐based and optical fiber technologies. This article will describe current research activities in the field of photonics as well as presenting selected development perspectives occurring in this area in recent years in Poland.
A Novel MnSOD Mimetic Targets Various Redox States to Selectively Treat Hematopoietic Malignancies via Control of AP-1 Signaling (2017)

Antioxidant compounds that can mimic the activity of endogenous enzymes via redox cycling offer a novel method of targeted cancer treatment. Here, we investigated the therapeutic effect of a mitochondrial- targeted, MnSOD mimetic, Mn(III) mesotetrakis (N-n-butoxyethylpyridinium-2yl) porphyrin, (MnTnBuOE) within sensitive and resistant myeloid lineage hematopoietic malignancies and utilize the hematopoietic disorder myelodysplastic syndrome (MDS) for the presentation of mechanistic insights to MnTnBuOE efficacy. MnTnBuOE treatment results in an increase in both CD34+CD38‒ and CD34+CD38+ normal stem/progenitor cell viability. Similar treatment shows significant cytotoxicity within AML and MDS models. Furthermore, manipulation of the cellular redox state via inhibition of glutathione synthesis, glutathione reductase activity, and treatment with glutathione disulfide sensitizes drug resistant CD34+ CML cells to MnTnBuOE treatment induced cytotoxicity. These results demonstrate glutathione metabolism and redox balance as a potential determinant of MnTnBuOE efficacy. Transcriptional analysis indicates that MnTnBuOE treatment initiates activator protein 1 (AP-1) activity in MDSL cells. DNA binding and immunoprecipitation identifies JunB as a transcriptional mediator of MnTnBuOE induced cytotoxicity. This is supported by siRNA knock down of JunB, resulting in protection against MnTnBuOE induced cytotoxicity. JunB precipitation via reaction with biotin-1,3-cyclopentadione demonstrates MnTnBuOE mediated oxidation of the JunB DNA binding region via hydrogen peroxide. This, in concert with co-immunoprecipitation of JunB, offers an alternative mechanism of JunB transcriptional activation through the identification of Ref-1; a protein specifically involved in the redox-modification of JunB. The finding that MnTnBuOE can target varying cellular redox states and exert selective cytotoxicity in malignant cells via differential activation of molecular pathways controlling lifespan and cell fate will significantly aid further development of safe, effective redox-active therapeutics for clinical applications.
Thermotropic liquid crystal behaviour of alkaline-earth-metal dihexadecyl phosphate salts (2000)

Abstract Alkaline-earth-metal dihexadecyl phosphate salts were synthesized, and their thermal stability was evaluated by thermogravimetry. Their thermotropic liquid crystal behaviour was investigated by differential scanning calorimetry, polarizing optical microscopy, dilatometry, and X-ray diffraction. On heating, the calcium, strontium, and barium salts exhibit columnar liquid crystal phases, whereas the less ionic beryllium and magnesium salts melt directly into isotropic liquids.