gebhart/patrepeval huggingface dataset:
An integrated cell‐free metabolic platform for protein production and synthetic biology (2008)

Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements.
Spasm of the sternocleidomastoid muscle induced by vagal nerve stimulation (2001)

Vagal nerve stimulation (VNS) is a recently introduced treatment for drug-resistant epilepsies.1 Both partial and generalized seizures, especially atonic, may improve with this device, although the mechanism of action is not clearly understood. Approximately one third of patients treated with VNS have had a 50% reduction in the frequency of their seizures, thus making a significant impact on their quality of life.1 Efficacy has been related to the intensity of the stimulation. Side effects are generally infrequent and mild. They may be produced by the stimulation or the implant procedure. Voice alteration, hoarseness, dysphonia, cough, pain, dyspnea, vomiting, nausea, hiccups, paresthesia, fever, local infection, accidental injury, aspiration, and bradycardia have been quoted as side effects.1-3⇓⇓ Bradycardia is avoided by placing the stimulator by the left vagal nerve; however, even with this precaution, asystolia has been reported.4,5⇓ These complications usually did not lead to termination of the therapy. The occurrence of sudden death in these patients was not greater than in other epileptic patients.6 Overall, VNS treatment has proved to be safe, efficient, and cost-beneficial.

A patient had a spasm of the sternocleidomastoid (SCM) when the stimulation intensity reached 2 mA. Clinically it was similar to an episodic torticollis. …
Remodeling of sperm chromatin induced in egg extracts of amphibians (1994)

Sperm nuclear basic proteins of Bufo japonicus consist of 2 distinct protamines, whereas those of Xenopus laevis consist of 6 sperm-specific basic proteins (SP1-6) in addition to H3, H4 and smaller amounts of H2A and H2B. Cloning of pertinent cDNAs and partial amino acid sequence studies suggested that these 6 sperm-specific proteins of Xenopus are encoded by 3 distinct genes. Despite differences in their initial compositions of chromatin, sperm nuclei exposed to amphibian egg extracts rapidly decondense, lose sperm-specific basic proteins, and concomitantly form an ordinary nucleosome core consisting of H2A, H2B, H3, H4, and cleavage-stage specific subtype H1X. In this remodeling process, nucleoplasmin plays dual roles as a molecular chaperone, selectively removing sperm-specific basic proteins from, and bringing H2A and H2B to, sperm DNA. Thus remodeling of chromatin is induced even in mammalian (human) sperm nuclei under defined conditions including nucleoplasmin and exogenous histones.
Generalized transduction in Streptomyces coelicolor (2001)

We report the isolation of generalized transducing phages for Streptomyces species able to transduce chromosomal markers or plasmids between derivatives of Streptomyces coelicolor, the principal genetic model system for this important bacterial genus. We describe four apparently distinct phages (DAH2, DAH4, DAH5, and DAH6) that are capable of transducing multiple chromosomal markers at frequencies ranging from 10(-5) to 10(-9) per plaque-forming unit. The phages contain DNA ranging in size from 93 to 121 kb and mediate linked transfer of genetic loci at neighboring chromosomal sites sufficiently close to be packaged within the same phage particle. The key to our ability to demonstrate transduction by these phages was the establishment of conditions expected to severely reduce superinfection killing during the selection of transductants. The host range of these phages, as measured by the ability to form plaques, extends to species as distantly related as Streptomyces avermitilis and Streptomyces verticillus, which are among the most commercially important species of this genus. Transduction of plasmid DNA between S. coelicolor and S. verticillus was observed at frequencies of approximately 10(-4) transductants per colony-forming unit.
Anti-interleukin 2 receptor antibody suppresses murine diabetic insulitis and lupus nephritis. (1988)

In order to assess the importance of interleukin 2 receptor (IL-2R)-positive activated lymphocytes and macrophages in the pathogenesis of autoimmunity, we tested the prophylactic therapeutic efficacy of an anti-IL-2R (M7/20) monoclonal antibody, which recognizes the 55-kDa subunit of the heterodimeric IL-2R in two distinct models: the nonobese diabetic mouse and the NZB x NZW F1 hybrid with lupus. Treatment with anti-IL-2R monoclonal antibody suppressed autoimmune insulitis in nonobese diabetic mice and lupus nephritis in the NZB x NZW F1 hybrid. These studies indicate that highly selective targeting to activated lymphocytes and macrophages expressing the IL-2R provides a discrete method of dampening autoimmunity.
Illustrating the Beats Phenomenon with Excel: the construction of meaning through experimentation (2003)

The work of students on a specific mathematical topic is described in terms of their initial lack of confidence to take the concept on board through to their final understanding of the topic; a change that was greatly supported by their use of spreadsheets. The outcome for the students parallels the findings of the study by Sutherland and Rojano which showed that, for Year 10-11 students âpupils initially had difficulty accepting the idea of working with a general unknownâ but that the âspreadsheet environment supported pupils to move from thinking with the specific to the generalâ. In the mathematics education literature, the use of spreadsheets as a tool has an established level of acceptance both through research studies and policy documents, but there remains the need for further studies of its practical application both as a program that can enhance learning and as a tool with which students can express their understanding. This article is but one step in this direction, and adopts the pedagogical approach of Cobb where the students are given opportunities through social interaction in the classroom to develop their own understanding and representations of a concept.
Endocytosis and lysosomal delivery of tissue plasminogen activator- inhibitor 1 complexes in Hep G2 cells (1992)

Receptor-mediated endocytosis of tissue-type plasminogen activator (t- PA)-plasminogen activator inhibitor type 1 (PAI-1) complexes results in their clearance by Hep G2 cells. After complexes are internalized, the t-PA component is degraded. However, neither the locus of intracellular catabolism nor the fate of PAI-1 has been elucidated. To characterize these aspects of t-PA-PAI-1 catabolism, the subcellular distribution of a prebound cohort of ligand molecules was delineated after internalization at 37 degrees C. 125I-t-PA.PAI-1 and t-PA.125I-PAI-1 were compared in separate experiments. After ligand uptake, intracellular vesicles were separated on density gradients. Internalized 125I-t-PA.PAI-1 concentrated initially in endosomes. After 20 minutes of uptake, the complex began to appear in lysosomes. Subsequently, low molecular weight labeled ligand fragments were detected in culture media. A panel of lysosomotropic agents, including primaquine, chloroquine, ammonium chloride, and a combination of leupeptin and pepstatin A, inhibited degradation. When t-PA.125I-PAI-1 rather than 125I-t-PA.PAI-1 was internalized, strikingly different results were observed. Although the kinetics of internalization and the intracellular itinerary were indistinguishable for the differently labeled complexes, the 125I-PAI-1 component of t-PA.125I-PAI-1 resisted rapid degradation. After a rapid loss of t-PA, the 125I-PAI-1 moiety persisted in lysosomes for up to 180 minutes. Thus, internalized t- PA.PAI-1 is targeted to lysosomes in which PAI-1 is relatively more stable than t-PA.
Inhibition of melanoma tumor growth in vivo by survivin targeting (2001)

A role of apoptosis (programmed cell death) in tumor formation and growth was investigated by targeting the apoptosis inhibitor survivin in vivo. Expression of a phosphorylation-defective survivin mutant (Thr(34)-->Ala) triggered apoptosis in several human melanoma cell lines and enhanced cell death induced by the chemotherapeutic drug cisplatin in vitro. Conditional expression of survivin Thr(34)-->Ala in YUSAC2 melanoma cells prevented tumor formation upon s.c. injection into CB.17 severe combined immunodeficient-beige mice. When induced in established melanoma tumors, survivin Thr(34)-->Ala inhibited tumor growth by 60-70% and caused increased apoptosis and reduced proliferation of melanoma cells in vivo. Manipulation of the antiapoptotic pathway maintained by survivin may be beneficial for cancer therapy.
Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers (2018)

Huntingtin N-terminal fragments (Htt-NTFs) with expanded polyglutamine tracts form a range of neurotoxic aggregates that are associated with Huntington's disease. Here, we show that aggregation of Htt-NTFs, irrespective of polyglutamine length, yields at least three phases (designated M, S, and F) that are delineated by sharp concentration thresholds and distinct aggregate sizes and morphologies. We found that monomers and oligomers make up the soluble M phase, ∼25-nm spheres dominate in the soluble S phase, and long, linear fibrils make up the insoluble F phase. Previous studies showed that profilin, an abundant cellular protein, reduces Htt-NTF aggregation and toxicity in cells. We confirm that profilin achieves its cellular effects through direct binding to the C-terminal proline-rich region of Htt-NTFs. We show that profilin preferentially binds to Htt-NTF M-phase species and destabilizes aggregation and phase separation by shifting the concentration boundaries for phase separation to higher values through a process known as polyphasic linkage. Our experiments, aided by coarse-grained computer simulations and theoretical analysis, suggest that preferential binding of profilin to the M-phase species of Htt-NTFs is enhanced through a combination of specific interactions between profilin and polyproline segments and auxiliary interactions between profilin and polyglutamine tracts. Polyphasic linkage may be a general strategy that cells utilize to regulate phase behavior of aggregation-prone proteins. Accordingly, detailed knowledge of phase behavior and an understanding of how ligands modulate phase boundaries may pave the way for developing new therapeutics against a variety of aggregation-prone proteins.
Serum antibodies to HIV-1 in recombinant vaccinia virus recipients boosted with purified recombinant gp160 (1992)

Serum antibody responses were studied in detail in four vaccinia-naive volunteers in a phase I trial evaluating primary vaccination with a recombinant vaccinia virus expressing the HIV-1 gp160 envelope glycoprotein (HIVAC-1e, Oncogen/Bristol-Myers Squibb), followed by booster immunization with baculovirus-derived rgp160 (VaxSyn, MicroGeneSys). Prior to boosting, low-titer Fc receptor (FcR)-mediated, antibody-dependent enhancing (ADE) activity was detected in two of four volunteers but no IgM, IgG, IgA, neutralizing activity, or complement-mediated ADE activity was detected. Two weeks after boosting, all four volunteers developed HIV-1-specific IgG with titers of 1:160 to 1:640 by immunofluorescence assay. IgG1 was present in sera from each individual, while IgG2 and IgG3 were present in sera from two individuals, and IgG4 was present in serum from one individual. IgM and IgA were undetectable in all sera. Only one volunteer had IgG to the heterologous HIV-1 isolates, RF, MN, and SF2, after boosting. Serum from this volunteer neutralized the vaccine strain, LAV/IIIB, but not the heterologous strains, RF, MN, and SF2. Antibodies from the remaining volunteers had no neutralizing activity. The neutralizing serum had a positive reaction in a peptide-based ELISA utilizing a peptide corresponding to the principal neutralizing domain of the third hypervariable region (i.e., V3 loop) of the envelope glycoprotein. Neutralizing activity was partially removed by adsorption to this peptide, suggesting that it contained a type-specific neutralizing vaccine epitope. A low titer (1:40 to 1:80) of complement-mediated ADE activity to HIV-1 IIIB was present in sera from three vaccinees after boosting. FcR-ADE activity for HIV-1 SF2 and SF-128A were present in sera from two of these three vaccinees. None of the volunteers developed antisyncytial antibodies. These results indicate that inoculation with recombinant vaccinia followed by rgp160 boosting is the most effective strategy to date for inducing serum antibodies to the envelope glycoproteins of HIV-1, but further study is needed to optimize the functionality and cross-reactivity of these responses.
Genetic Analysis of Susceptibility to Induced Pulmonary Tumors in Mice (1942)

Genetic Analysis of Susceptibility to Induced Pulmonary Tumors in Mice Get access W. E. Heston W. E. Heston geneticist National Cancer Institute, National Institute of Health, United States Public Health Service Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 3, Issue 1, August 1942, Pages 69–78, https://doi.org/10.1093/jnci/3.1.69 Published: 01 August 1942
Terahertz radiation from InAs induced by carrier diffusion and drift (2006)

Terahertz (THz) radiation from a (100) oriented InAs surfaces is dominated by the photo-Dember effect. The strength of the radiation is influenced by screening the radiation with doped carriers. When irradiated by femtosecond pulses, the wafer with the lowest doping concentration radiates THz power nearly two orders higher than the wafer with highest doping concentration. With identical optical excitation and same doping concentration, a $p$-type InAs generates stronger THz waves than an $n$-type InAs due to the weaker screening effect. The low doping $p$-type InAs ($1\ifmmode\times\else\texttimes\fi{}{10}^{16}\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}3}$) sample is the strongest THz wave emitter among all the unbiased semiconductors we have ever tested with a Ti:sapphire laser oscillator. The drift-diffusion equation (DDE) is used in the study of carrier drift and diffusion as well as subsequent THz radiation from InAs wafers. The calculation explains well the experimental observation of the relationship between a THz electric field and the doping properties of InAs. The physical pictures of the carrier drift and diffusion characteristics in InAs surfaces are also clearly provided in this report.
Uses of 1-(3-Cyano-4,5,6,7-tetrahydrobenzo[<i>b</i>]-thiophen-2-yl)-3-dodecanoylthiourea as a Building Block in the Synthesis of Fused Pyrimidine and Thiazine Systems (2015)

The reaction of lauroyl isothiocyanate and 2-amino-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carbonitrile was used to synthesize the title compound 2. Compound 2 could serve as the main building block in the synthesis of many target heterocyclic systems. Various fused pyrimidines were synthesized in the reactions of compound 2 with sodium ethoxide, hydrazine hydrate, phenyl hydrazine, ethyl carbazate, thiourea, and/or 2-aminothiophenol. The structures of the synthesized compounds were confirmed by microanalytical and spectral data.
The Complete Nucleotide Sequence of Tobacco Rattle Virus RNA-1 (1987)

The complete nucleotide sequence of tobacco rattle virus (TRV) strain SYM RNA-1 was determined from a series of overlapping cDNA clones. cDNA prepared by primer extension was used to determine the exact 5' terminus. The RNA sequence was 6791 nucleotides in length and contained four open reading frames (ORFs). The ORF nearest the 5' terminus coded for a polypeptide of predicted mol. wt. 134,000 (134K) and terminated at an opal (UGA) stop codon. Readthrough of this stop codon would result in the production of a protein of 194K. The gene for a 29K polypeptide started one base beyond the 194K stop codon and, in turn, was followed by the gene for a 16K protein at the 3' end of RNA-1. Amino acid comparisons of the 194K protein with the putative replicase of tobacco mosaic virus showed three regions of strong homology, suggesting that the 134K and 194K proteins were similarly involved in virus replication. The 5' terminal sequences of both genome RNA species of TRV strains ORY, N5 and PRN together with that of SYM RNA-2 were also determined. Alignments of these sequences showed that there was a 22 base repeated sequence close to the 5' terminus in all these RNA species. It was also shown that the 5' terminus of RNA-1 was homologous with the same region in RNA-2.
A thermal dissociation–chemical ionization mass spectrometry (TD‐CIMS) technique for the simultaneous measurement of peroxyacyl nitrates and dinitrogen pentoxide (2004)

We have developed a thermal dissociation–chemical ionization mass spectrometry (TD‐CIMS) technique for fast measurements of a series of peroxyacyl nitrates and dinitrogen pentoxide. Thermally generated acylperoxy radicals react with I − to produce a carboxylate ion that is unique for each parent species. NO 3 resulting from the decomposition of N 2 O 5 reacts with I − to form NO 3 − . The measurement technique was verified for PAN and PPN during an informal comparison with a gas chromatograph (GC) equipped with an electron capture detector (ECD) in Boulder, Colorado, during October 2002. Good agreement was obtained between the two instruments with R 2 = 0.91 for PAN (n = 657) and R 2 = 0.89 for PPN (n = 655). Detection limits of 7 pptv and 4 pptv were determined for PAN and PPN, respectively, for a 1 s integration period and a signal‐to‐noise ratio of 3. The TD‐CIMS simultaneously detected ambient PiBN and N 2 O 5 + NO 3 in addition to PAN and PPN during the intercomparison period. We estimate a detection limit of 3 pptv in 1 s for PiBN. PnBN would be detected at the same mass, so we cannot rule out a contribution from PnBN to our PiBN estimate. Sensitivity to MPAN was found to be lower than to PAN in laboratory experiments, but a detection limit of 10 pptv can still be achieved by integrating for 15 s. Assuming the same sensitivity as for PAN, the detection limit for the sum of N 2 O 5 and NO 3 was estimated to be 12 pptv in 1 s. The fast time response of the TD‐CIMS combined with a sensitivity and limit of detection comparable to the GC/ECD make this a promising technique for PAN flux measurements by eddy covariance. PAN uptake by different types of vegetation could be important input for global and regional ozone models, and PAN deposition to snow is of interest in polar regions.
PH effects on experimental wound healing of human fibroblasts in vitro (1995)

The aim of the present study was to examine to what extent pH affects human fibroblast repopulation of an experimental wound in vitro laying special emphasis on cell migration, DNA synthesis, and alterations in cell morphology. Wounds were simulated in vitro by partially scraping off monolayers of human embryonic diploid lung fibroblast and human periodontal ligament fibroblast-like cells respectively. The wounded monolayers were cultured at pHs ranging from 7.2 to 8.4. The experiments were evaluated by autoradiography as well as light and scanning electron microscopic techniques. A significant, approximately linear, decrease was noted both in cell migration into and DNA synthesis in the experimental wounds as a result of pH increase. The surviving cells in the wounds showed cytoplasmatic vacuoles and blebbing at pH levels above 7.8. Clinical implications of these results for endodontic calcium hydroxide treatment are that hydroxyl ions, diffusing through root dentin, may interfere with vital cell functions necessary for healing on the root surface.
Effector differentiation is not prerequisite for generation of memory cytotoxic T lymphocytes (2001)

The lineage relationship between short-lived effector T cells and long-lived memory cells is not fully understood. We have described T-GFP mice previously, in which naive and early activated T cells express GFP uniformly, whereas cells that have differentiated into effector cytotoxic T cells selectively lose GFP expression. Here we studied antigen-specific CD8 T cell differentiation using T-GFP mice crossed to the TCR transgenic (Tg) mice P14 (specific for the lymphocytic choriomeningitis virus glycoprotein peptide, gp33-41). After activation with antigenic peptide, P14XT-GFP CD8(+) T cells cultured in high-dose IL-2 developed into cells with effector phenotype and function: they were blastoid, lost GFP expression, expressed high levels of activation and effector markers, and were capable of immediate cytotoxic function. In contrast, cells cultured in IL-15 or low-dose IL-2 never developed into full-fledged effector cells. Rather, they resembled memory cells: they were smaller, were GFP(+), did not express effector markers, and were incapable of immediate cytotoxicity. However, they mediated rapid-recall responses in vitro. After adoptive transfer, they survived in vivo for at least 10 weeks and mounted a secondary immune response after antigen rechallenge that was as potent as endogenously generated memory cells. In addition to providing a simple means to generate memory cells in virtually unlimited numbers, our results suggest that effector differentiation is not a prerequisite for memory cell generation.
Behavioral Testing in Mouse Models of Stroke (2010)

For decades, histological assessments were the only end-point in stroke research, typically using lesion size determination to evaluate the potential therapeutic effectiveness of an agent in in vivo stroke models. While this approach is indeed valid, failures in developing effective drugs point out the fact that histological means are simply not enough to evaluate the potential of a drug or intervention and that an evaluation at the functional level is necessary. Animals subjected to stroke models develop sensory-motor, learning and memory problems and “psychological symptoms.” Evaluating these symptoms via behavior is not only important in helping us to understand the pathological mechanisms, but it also gives us a powerful tool to test the therapeutic potential of interventions. This chapter will introduce some of the widely used and reliable behavior tests in stroke research. Basic tests of motor function, memory, anxiety, and depression-like behavior will be covered. Each test will be discussed in detail and widely used protocols will be introduced.