gebhart/patrepeval huggingface dataset:
A Highly Efficient Cell‐Free Protein Synthesis System from Escherichia coli (1996)

We modified a cell-free coupled transcription/translation system from Escherichia coli with the T7 phage RNA polymerase, and achieved a productivity as high as 0.4 mg protein/ml reaction mixture. First, we found that the optimal concentrations of phosphoenolpyruvate and poly(ethylene glycol) are interdependent; higher concentrations of the former should be used at higher concentrations of the latter. Second, the use of a condensed 30000 x g cell extract, in place of the conventional one, significantly increased the initial rate of protein synthesis. This phenomenon was demonstrated to be due to a reason other than elimination of inhibitory molecule(s) from the extract. For this system with the condensed extract, the phosphoenolpyruvate and poly(ethylene glycol) concentrations were again co-optimized, resulting in production of chloramphenicol acetyltransferase at a productivity of 0.3 mg/ml. Finally, the productivity was further increased up to 0.4 mg/ml, by supplementation of the pool of amino acids. This improved cell-free protein synthesis system is superior in productivity to any other cell-free systems reported so far, including the continuous-flow cell-free system.
Pseudomonas aeruginosa Contains a Novel Type V Porphobilinogen Synthase with No Required Catalytic Metal Ions† (1999)

Porphobilinogen synthases (PBGS) are metalloenzymes that catalyze the first common step in tetrapyrrole biosynthesis. The PBGS enzymes have previously been categorized into four types (I-IV) by the number of Zn(2+) and/or Mg(2+) utilized at three different metal binding sites termed A, B, and C. In this study Pseudomonas aeruginosa PBGS is found to bind only four Mg(2+) per octamer as determined by atomic absorption spectroscopy, in the presence or absence of substrate/product. This is the lowest number of bound metal ions yet found for PBGS where other enzymes bind 8-16 divalent ions. These four Mg(2+) allosterically stimulate a metal ion independent catalytic activity, in a fashion dependent upon both pH and K(+). The allosteric Mg(2+) of PBGS is located in metal binding site C, which is outside the active site. No evidence is found for metal binding to the potential high-affinity active site metal binding sites A and/or B. P. aeruginosa PBGS was investigated using Mn(2+) as an EPR probe for Mg(2+), and the active site was investigated using [3,5-(13)C]porphobilinogen as an NMR probe. The magnetic resonance data exclude the direct involvement of Mg(2+) in substrate binding and product formation. The combined data suggest that P. aeruginosa PBGS represents a new type V enzyme. Type V PBGS has the remarkable ability to synthesize porphobilinogen in a metal ion independent fashion. The total metal ion stoichiometry of only 4 per octamer suggests half-sites reactivity.
Integrated optics components and devices using periodic structures (1986)

The selected research activities on integrated optics components and devices using periodic structures are reviewed, with emphasis on the authors' works employing the electron-beam writing technique. The periodic structures include static gratings and dynamic ones produced through acoustooptic (AO) and electrooptic (EO) effects. They provide a variety of passive functions and effective means for guided-wave control. The review is made from the integration point of view, including the most recent results. First, the theoretical fundamentals are outlined and the electron-beam writing techniques, including the writing system, are discussed. Next, passive components (grating deflectors, filters, lenses, couplers, etc.) and elements for guided-wave controlling and detecting (AO and EO grating elements and photodetectors) are described. Then, integrated optic devices, i.e., wavelength demultiplexers, RF spectrum analyzers, optical disk pickup, etc., are presented. Finally, the possibility of future applications is discussed.
Performance of a Simulated Adaptive BCI Based on Experimental Classification of Movement-Related and Error Potentials (2011)

New paradigms for brain–computer interfacing (BCI), such as based on imagination of task characteristics, require long training periods, have limited accuracy, and lack adaptation to the changes in the users' conditions. Error potentials generated in response to an error made by the translation algorithm can be used to improve the performance of a BCI, as a feedback extracted from the user and fed into the BCI system. The present study addresses the inclusion of error potentials in a BCI system based on the decoding of movement-related cortical potentials (MRCPs) associated to the speed of a task. First, we theoretically quantified the improvement in accuracy of a BCI system when using error potentials for correcting the output decision, in the general case of multiclass BCI. The derived theoretical expressions can be used during the design phase of any BCI system. They were applied to experimentally estimated accuracies in decoding MRCPs and error potentials. Second we studied in simulation the performance of the closed-loop system in order to evaluate its ability to adapt to the changes in the mental states of the user. By setting the parameters of the simulator to experimentally determined values, we showed that updating the learning set with the examples estimated as correct based on the decoding of error potentials leads to convergence to the optimal solution.
Isolation and Characterization of a Cyclic Hydroxamic Acid from a Pollen Extract, Which Inhibits Cancerous Cell Growth in Vitro (1995)

One fraction, designated FV-7, in the water soluble ingredient of the pollen extract Cernilton was found to be inhibitory to the growth of a prostate cancer cell line. Characterization of FV-7 by high-resolution mass spectrometry and nuclear magnetic resonance identified the fraction as hydroxamic acid, 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA). To confirm this further, we synthesized an authentic sample of DIBOA and found subsequently that the synthetic DIBOA was structurally indistinguishable from FV-7. Furthermore, in a separate experiment we compared the in vitro effects of FV-7 and DIBOA on the growth of a prostate cancer cell line and found that in both cases the effect was inhibitory and that the inhibition curves obtained for both compounds were virtually identical.
Realization of microwave amplification, attenuation, and frequency conversion using a single three-level superconducting quantum circuit (2017)

Using different configurations of applied strong driving and weak probe fields, we find that only a single three-level superconducting quantum circuit (SQC) is enough to realize amplification, attenuation, and frequency conversion of microwave fields. Such a three-level SQC has to possess $\mathrm{\ensuremath{\Delta}}$-type cyclic transitions. Different from the parametric amplification (attenuation) and frequency conversion in nonlinear optical media, the real energy levels of the three-level SQC are involved in the energy exchange when these processes are completed. We quantitatively discuss the effects of amplification (attenuation) and the frequency conversion for different types of driving fields. The values and conditions are obtained for the optimal gains for amplification (attenuation) and the optimal conversion efficiencies. Our study provides a method to amplify (attenuate) microwave, realize frequency conversion, and also lay a foundation for generating single or entangled microwave photon states using a single three-level SQC.
Astroglial and fibroblast growth factors have neurotrophic functions for cultured peripheral and central nervous system neurons. (1987)

Embryonic and neonatal neurons require specific trophic supplements for their survival and the induction of transmitter-synthesizing enzymes in vivo and in vitro. Acidic and basic fibroblast growth factor (aFGF, bFGF) and the closely related astroglial growth factors AGF-1 and AGF-2 were studied for putative neurotrophic functions using dissociated, highly neuron-enriched cultures from chick and rat peripheral ganglia and central nervous system tissues. Embryonic chick ciliary ganglion neurons were the only peripheral neurons that responded to bFGF and AGF-2 by enhanced survival equivalent to that obtained with ciliary neurotrophic factor. Half-maximal effects were achieved with bFGF at 360 pg/ml or AGF-2 at 3 ng/ml. Small effects seen with aFGF could be potentiated by adding heparin at 1 microgram/ml. bFGF, but not ciliary neurotropic factor, also promoted neuron survival after the factor was bound to polyornithine and laminin. Both AGF-2 and ciliary neurotropic factor induced choline acetyltransferase activity during 48 hr. AGFs and FGFs also enhanced the long-term survival of embryonic chick spinal cord neurons, including motoneurons that had been retrogradely labeled with rhodamine isothiocyanate. These results demonstrate the potency of a class of mitogenic growth factors as neurotrophic agents for embryonic ciliary ganglion and spinal cord neurons--adding to the emerging evidence that mitogenic and neuronal growth factors are not strictly separate entities.
Overexpression of the Zinc Finger Protein MZF1 Inhibits Hematopoietic Development from Embryonic Stem Cells: Correlation with Negative Regulation of CD34 and c-myb Promoter Activity (1995)

Zinc finger genes encode proteins that act as transcription factors. The myeloid zinc finger 1 (MZF1) gene encodes a zinc finger protein with two DNA-binding domains that recognize two distinct consensus sequences, is preferentially expressed in hematopoietic cells, and may be involved in the transcriptional regulation of hematopoiesis-specific genes. Reverse transcription-PCR analysis of human peripheral blood CD34+ cells cultured under lineage-restricted conditions demonstrated MZF1 expression during both myeloid and erythroid differentiation. Sequence analysis of the 5'-flanking region of the CD34 and c-myb genes, which are a marker of and a transcriptional factor required for hematopoietic proliferation and differentiation, respectively, revealed closely spaced MZF1 consensus binding sites found by electrophoretic mobility shift assays to interact with recombinant MZF1 protein. Transient or constitutive MZF1 expression in different cell types resulted in specific inhibition of chloramphenicol acetyltransferase activity driven by the CD34 or c-myb 5'-flanking region. To determine whether transcriptional modulation by MZF1 activity plays a role in hematopoietic differentiation, constructs containing the MZF1 cDNA under the control of different promoters were transfected into murine embryonic stem cells which, under defined in vitro culture conditions, generate colonies of multiple hematopoietic lineages. Constitutive MZF1 expression interfered with the ability of embryonic stem cells to undergo hematopoietic commitment and erythromyeloid colony formation and prevented the induced expression of CD34 and c-myb mRNAs during differentiation of these cells. These data indicate that MZF1 plays a critical role in hematopoiesis by modulating the expression of genes involved in this process.
Design of antisense oligonucleotides stabilized by locked nucleic acids (2002)

The design of antisense oligonucleotides containing locked nucleic acids (LNA) was optimized and compared to intensively studied DNA oligonucleotides, phosphorothioates and 2'-O-methyl gapmers. In contradiction to the literature, a stretch of seven or eight DNA monomers in the center of a chimeric DNA/LNA oligonucleotide is necessary for full activation of RNase H to cleave the target RNA. For 2'-O-methyl gapmers a stretch of six DNA monomers is sufficient to recruit RNase H. Compared to the 18mer DNA the oligonucleotides containing LNA have an increased melting temperature of 1.5-4 degrees C per LNA depending on the positions of the modified residues. 2'-O-methyl nucleotides increase the T(m) by only <1 degree C per modification and the T(m) of the phosphorothioate is reduced. The efficiency of an oligonucleotide in supporting RNase H cleavage correlates with its affinity for the target RNA, i.e. LNA > 2'-O-methyl > DNA > phosphorothioate. Three LNAs at each end of the oligonucleotide are sufficient to stabilize the oligonucleotide in human serum 10-fold compared to an unmodified oligodeoxynucleotide (from t(1/2) = approximately 1.5 h to t(1/2) = approximately 15 h). These chimeric LNA/DNA oligonucleotides are more stable than isosequential phosphorothioates and 2'-O-methyl gapmers, which have half-lives of 10 and 12 h, respectively.
Abstract 3400: Mitochondrial profiling in AML patients treated with an Alvocidib containing regimen reveals MCL1 dependency in responder bone marrow (2015)

Abstract Background. Molecular profiles may provide insights into the likelihood of responding to traditional cytotoxic chemotherapy as well as important clues to the success of novel targeted agents. The anti-apoptotic BCL-2 family proteins have previously been shown to facilitate pro-survival and resistance to chemotherapy in AML, multiple myeloma, as well as in other types of cancer. Measuring the function of these proteins using BH3 profiling has proven to provide useful information in predicting AML treatment response with traditional ara-c based treatment. Here, we sought to determine if such an approach might detect response with the addition of Alvocidib to ara-c-based chemotherapy. Mitochrondrial apoptosis signaling was assessed in AML patients treated with Alvocidib, ara-c and mitoxantrone (FLAM). Methods. Pretreatment peripheral blood mononuclear cell and bone marrow specimens from 63 patients treated with FLAM were measured for mitochondrial outer membrane permeabilization following incubation with BH3 peptides as a surrogate for BCL-2 protein family function. Results. Analysis of the priming states (mitochondrial depolarization) in the patients who underwent complete remission (CR), compared with those who did not (NR), revealed that NOXA priming was significantly higher in CR bone marrow samples (median 44.5%) compared with NR samples (median 5.2%, p = 0.006). NOXA is known to interact most directly with MCL1, suggesting that these cancer cells may be MCL1 dependent. An additional multi-peptide algorithm using three BH3 members was also identified (involving BAD, PUMA, and BIM), which may also indirectly support MCL1 dependency. These BH3 priming profiles were both additive to known risk factors associated with clinical response to chemotherapy, including cytogenetic risk factors. Receiver operating characteristic (ROC) curve analysis of NOXA priming plus cytogenetics and MDS history indicated that these variables were highly predictive of response to FLAM (AUC-0.92, p = 0.0002). This correlation is distinct from our previous work which showed that the priming due to the BIM peptide predicts response to traditional ara-c based treatment. This work provides a basis for further studies into the MCL1 dependent action of Alvocidib, as well as a potential biomarker for identification of patients likely to respond to FLAM. Citation Format: Elisha J. Dettman, Steven L. Warner, Camille Doykan, Melissa Arn, Noel Blake, David J. Bearss, Michael Cardone, Bruce D. Smith. Mitochondrial profiling in AML patients treated with an Alvocidib containing regimen reveals MCL1 dependency in responder bone marrow. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3400. doi:10.1158/1538-7445.AM2015-3400
Mesotherapy and Phosphatidylcholine Injections (2006)

BACKGROUND Mesotherapy was originally conceived in Europe as a method of utilizing cutaneous injections containing a mixture of compounds for the treatment of local medical and cosmetic conditions. Although mesotherapy was traditionally employed for pain relief, its cosmetic applications, particularly fat and cellulite removal, have recently received attention in the United States. Another treatment for localized fat reduction, which was popularized in Brazil and uses injections of phosphatidylcholine, has been erroneously considered synonymous with mesotherapy. Despite their attraction as purported “fat-dissolving” injections, the safety and efficacy of these novel cosmetic treatments remain ambiguous to most patients and physicians. OBJECTIVE To distinguish mesotherapy from phosphatidylcholine injections by reviewing their history and the relevant experimental or clinical findings. METHODS A comprehensive search of Medline indexed literature and conference proceedings. RESULTS All the published studies evaluating the clinical efficacy of traditional mesotherapy currently originate from Europe. These reports focus primarily on musculoskeletal pain and vascular disease, rather than cosmetic applications. Although experimental data suggest that a number of traditional mesotherapy ingredients may theoretically reduce fat, these effects have not been supported in peer-reviewed studies. An increasing number of reports demonstrate that subcutaneous injections of a formula containing phosphatidylcholine combined with its emulsifier, deoxycholate, are effective in removing small collections of adipose tissue. Cell lysis, resulting from the detergent action of deoxycholate, may account for this clinical effect. CONCLUSIONS Mesotherapy is distinct from a method of treating adipose tissue with subcutaneous injections of deoxycholate alone or in combination with phosphatidylcholine. Additional clinical and experimental studies are necessary to more definitively establish the safety and efficacy of these treatments.
The Treatment of Malaria with Hydroxychloroquine (1955)

SummaryTwo hundred and thirteen Hondurans were treated for acute malaria with hydroxychloroquine or Plaquenil® (7-chloro-4-[4-(N-ethyl-N-β-hydroxyethylamino)-1-methylbutyl-amino] quinoline diphosphate). Twenty-five of them received a single oral dose of 0.75 gram and 125 received 1.25 grams. Twenty-six others with P. falciparum infections were given an intravenous dose of 0.36 gram in 500 cc. of normal saline, and 37 with P. falciparum infections were given 0.36 gram intramuscularly in 9.0 cc. of saline. Except with the lower oral dose, both the immediate and late results were quite good—comparing favorably with the other 4-aminoquinolines in common use. Toxic side effects were not noted on any of the regimens.
The static water supply program: reducing the impact of urban/bushland interface fires through partnerships and the use of community resources and education (1999)

The program's two major aims were to find solutions to the problems of inadequate water supplies available to fight major interface fires and insufficient public awareness about how to react to the threat of bushfires. The factors that influenced the program's design were cost-effectiveness and easy implementation. The program formally recognises the billions of litres of water stored in suburban backyard swimming pools and other static water supplies as a strategic weapon against the impact of a bushfire. (extract from author abstract)
Alterations in the structure of new and old forms of simian virus 40 large T antigen (T) defined by age-dependent epitope changes: new T is the same as ATPase-active T (1989)

The reactivity of simian virus 40 large T antigen labeled under pulse-chase conditions towards 22 antibodies was measured. Changes in epitope reactivity occurred in several domains of T as it matured, defining major structural alterations that distinguished mature from new molecules. New T reacted best with the same antibodies that bind and inhibit ATPase-active T. These antibodies thus can distinguish new T as a distinct structural and functional form.
Reduced Anxiety, Conditioned Fear, and Hippocampal Long-Term Potentiation in Transient Receptor Potential Vanilloid Type 1 Receptor-Deficient Mice (2007)

The transient receptor potential vanilloid type 1 channel (TRPV1) (formerly called vanilloid receptor VR1) is known for its key role of functions in sensory nerves such as perception of inflammatory and thermal pain. Much less is known about the physiological significance of the TRPV1 expression in the brain. Here we demonstrate that TRPV1 knock-out mice (TRPV1-KO) show less anxiety-related behavior in the light-dark test and in the elevated plus maze than their wild-type littermates with no differences in locomotion. Furthermore, TRPV1-KO mice showed less freezing to a tone after auditory fear conditioning and stress sensitization. This reduction of conditioned and sensitized fear could not be explained by alterations in nociception. Also, tone perception per se was unaffected, as revealed by determination of auditory thresholds through auditory brainstem responses and distortion-product otoacoustic emissions. TRPV1-KO showed also less contextual fear if assessed 1 d or 1 month after strong conditioning protocols. These impairments in hippocampus-dependent learning were mirrored by a decrease in long-term potentiation in the Schaffer collateral-commissural pathway to CA1 hippocampal neurons. Our data provide first evidence for fear-promoting effects of TRPV1 with respect to both innate and conditioned fear and for a decisive role of this receptor in synaptic plasticity.
Least squares based cell-to-cell interference cancelation technique for multi-level cell nand flash memory (2012)

Cell-to-cell interference becomes a major source of bit errors in NAND flash memories as the semiconductor technology continuously shrinks down. Recently, signal processing approaches to mitigate the interference have been proposed, and the least mean square (LMS) adaptive filtering based method [1] offers a promising solution. In this research, we propose a least squares based cell-to-cell interference cancelation method, which is more suitable for NAND flash memory devices where one page of data is accessed at a time. With a simulation model, we show that this approach outperforms the LMS filtering based one whether the interference is severe or not. In order to simplify the algorithm, the input data to compute the channel characteristics is decimated, and as a result the arithmetic intensity of the proposed algorithm is comparable to the LMS based one.
Increased postprandial lipemia in Apo A-IMilano carriers. (1993)

Plasma lipid/lipoprotein changes were monitored after a fat load (65 g fat per square meter body surface area) in six carriers of the apolipoprotein A-IMilano (A-IM) variant and six age- and sex-matched control subjects. The magnitude of postprandial lipemia, calculated as the area under the curve (AUC) described by plasma triglyceride (TG) level versus time, was threefold higher in the A-IM carriers; however, after correction for the different baseline TG levels, it was similar to control subjects. Moreover, the magnitude of postprandial lipemia was positively correlated with baseline TG in both A-IM carriers (r = 0.77) and control subjects (r = 0.80), indicating that fasting TGs are a major determinant of postprandial response in all subjects. Postprandial lipemia was also inversely correlated with high density lipoprotein (HDL) and HDL2 cholesterol in both groups (A-IM, r = -0.81 and -0.79; control subjects, r = -0.87 and -0.94). Different from those in control subjects, the plasma apo A-I levels in the A-IM carriers decreased progressively while apo B increased up to 4 hours but decreased thereafter. Postprandial rises of low density lipoprotein TG but not of HDL-TG AUC were significantly higher in the A-IM carriers, even after normalization for the different fasting concentrations. These data show that the low plasma HDL levels of A-IM carriers, which are secondary to a primary structural alteration of the major HDL apolipoprotein, are associated with elevated fasting and postprandial TG levels and an anomalous postprandial redistribution of TG among lipoprotein classes.