gebhart/patrepeval huggingface dataset:
Membrane Association of Conjugally Transferred Deoxyribonucleic Acid in Escherichia coli Minicells (1971)

The conjugally acquired deoxyribonucleic acid (DNA) of small, anucleate cells ("minicells") of a mutant strain of Escherichia coli K-12 was found to be predominantly associated with the bacterial membrane. Evidence from X-irradiation studies in vivo shows that there is no decrease in DNA-membrane association under conditions which reduce the DNA to one-sixth its original size and suggests the possibility of multiple DNA-membrane association sites. Preliminary enzymatic studies indicate the involvement of protein, DNA, and lipids in the membrane association of the DNA.
Microwave and wireless synthesizers: theory and design (1998)

Loop Fundamentals. Noise and Spurious Response of Loops. Special Loops. Loop Components. Digital PLL Synthesizers. High-Performance Hybrid Synthesizer. Appendices. Index.
Archaebacterial DNA Polymerases Tightly Bind Uracil-containing DNA (1996)

We show that archaebacterial DNA polymerases are strongly inhibited by the presence of small amounts of uracil-containing DNA. Inhibition appears to be competitive, with the DNA polymerase exhibiting approximately 6500-fold greater affinity for binding the inhibitor than a DNase I-activated DNA substrate. All six archaebacterial DNA polymerases tested were inhibited, while no eubacterial, eukaryotic, or bacteriophage enzymes showed this effect. Only a small inhibition resulted when uracil was present as the deoxynucleoside triphosphate, dUTP. The rate of DNA synthesis was reduced by approximately 40% when dUTP was used in place of dTTP for archaebacterial DNA polymerases. Furthermore, an incorporated dUMP served as a productive 3'-primer terminus for subsequent elongation. In contrast, the presence of an oligonucleotide containing as little as a single dUrd residue was extremely inhibitory to DNA polymerase activity on other primer-template DNA.
Rapid assessment of antibiotic effects on Escherichia coli by bis-(1,3-dibutylbarbituric acid) trimethine oxonol and flow cytometry (1997)

The effects of selected antibiotics on Escherichia coli were studied by flow cytometry with the fluorescent anionic membrane potential probe bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)]. The actions of azithromycin, cefuroxime, and ciprofloxacin at five times the MIC on E. coli were compared by the traditional CFU assay and flow cytometry. Changes in viable counts of bacteria determined with DiBAC4(3) and by flow cytometry following treatment with the antibiotics showed trends similar to those found by the CFU assays. However, viable counts determined by flow cytometry following antibiotic treatment were 1 to 2 logs higher than those determined by the corresponding CFU assays. All the results obtained by flow cytometry were provided within 10 min after sampling, whereas the conventional CFU assay results took at least 18 h. The results indicated that flow cytometry is a sensitive analytical technique that can rapidly monitor the physiological changes of individual microorganisms following antibiotic action and can provide information on the mode of action of a drug. The membrane potential probe DiBAC4(3) provides a robust flow cytometric indicator for bacterial cell viability.
The NCI preclinical screen of biological response modifiers. (1984)

The development of successful approaches to immunotherapy is dependent upon proper consideration of the pathobiology of metastasis and the establishment of a better scientific understanding of the principles of biological response modification. The studies we have undertaken are aimed at the rational development of a preclinical data base to help provide this understanding. Ultimately, these studies will be correlated with clinical trials to assess the predictive value of the preclinical screen. We anticipate that the testing of biological response modifiers (BRMs) in a controlled but evolving system will help eliminate arbitrary decisions on the preparations and use of a given BRM and ultimately will contribute to the development of novel approaches for the treatment of disseminated cancer. Immunotherapy alone or in combination with other therapeutic modalities is an area of rapid evolution with tremendous potential as an adjuvant therapy of disseminated cancer.
Effects of Noise Correlations on Information Encoding and Decoding (2006)

Response variability is often correlated across populations of neurons, and these noise correlations may play a role in information coding. In previous studies, this possibility has been examined from the encoding and decoding perspectives. Here we used d prime and related information measures to examine how studies of noise correlations from these two perspectives are related. We found that for a pair of neurons, the effect of noise correlations on information decoding can be zero when the effect of noise correlations on the information encoded obtains its largest positive or negative values. Furthermore, there can be no effect of noise correlations on the information encoded when it has an effect on information decoding. We also measured the effect of noise correlations on information encoding and decoding in simultaneously recorded neurons in the supplementary motor area to see how well d prime accounted for the information actually present in the neural responses and to see how noise correlations affected encoding and decoding in real data. These analyses showed that d prime provides an accurate measure of information encoding and decoding in our population of neurons. We also found that the effect of noise correlations on information encoding was somewhat larger than the effect of noise correlations on information decoding, but both were relatively small. Finally, as predicted theoretically, the effects of correlations were slightly greater for larger ensembles (3-8 neurons) than for pairs of neurons.
Coherence and Cohesion for the Assessment of Text Readability (2013)

Text readability depends on a variety of variables. While lexico-semantic and syntactic factors have been widely used in the literature, more high-level discursive and cognitive properties such as cohesion and coherence have received little attention. This paper assesses the efficiency of 41 measures of text cohesion and text coherence as predictors of text readability. We compare results manually obtained on two corpora including texts with different difficulty levels and show that some cohesive features are indeed useful predictors.
A prototype table-top inverse-geometry volumetric CT system (2006)

A table-top volumetric CT system has been implemented that is able to image a 5-cm-thick volume in one circular scan with no cone-beam artifacts. The prototype inverse-geometry CT (IGCT) scanner consists of a large-area, scanned x-ray source and a detector array that is smaller in the transverse direction. The IGCT geometry provides sufficient volumetric sampling because the source and detector have the same axial, or slice direction, extent. This paper describes the implementation of the table-top IGCT scanner, which is based on the NexRay Scanning-Beam Digital X-ray system (NexRay, Inc., Los Gatos, CA) and an investigation of the system performance. The alignment and flat-field calibration procedures are described, along with a summary of the reconstruction algorithm. The resolution and noise performance of the prototype IGCT system are studied through experiments and further supported by analytical predictions and simulations. To study the presence of cone-beam artifacts, a "Defrise" phantom was scanned on both the prototype IGCT scanner and a micro CT system with a +/-5 cone angle for a 4.5-cm volume thickness. Images of inner ear specimens are presented and compared to those from clinical CT systems. Results showed that the prototype IGCT system has a 0.25-mm isotropic resolution and that noise comparable to that from a clinical scanner with equivalent spatial resolution is achievable. The measured MTF and noise values agreed reasonably well with theoretical predictions and computer simulations. The IGCT system was able to faithfully reconstruct the laminated pattern of the Defrise phantom while the micro CT system suffered severe cone-beam artifacts for the same object. The inner ear acquisition verified that the IGCT system can image a complex anatomical object, and the resulting images exhibited more high-resolution details than the clinical CT acquisition. Overall, the successful implementation of the prototype system supports the IGCT concept for single-rotation volumetric scanning free from cone-beam artifacts.
A PPxY motif within the VP40 protein of Ebola virus interacts physically and functionally with a ubiquitin ligase: Implications for filovirus budding (2000)

VP40, the putative matrix protein of both Ebola and Marburg viruses, possesses a conserved proline-rich motif (PY motif) at its N terminus. We demonstrate that the VP40 protein can mediate its own release from mammalian cells, and that the PY motif is important for this self-exocytosis (budding) function. In addition, we used Western-ligand blotting to demonstrate that the PY motif of VP40 can mediate interactions with specific cellular proteins that have type I WW-domains, including the mammalian ubiquitin ligase, Nedd4. Single point mutations that disrupted the PY motif of VP40 abolished the PY/WW-domain interactions. Significantly, the full-length VP40 protein was shown to interact both physically and functionally with full-length Rsp5, a ubiquitin ligase of yeast and homolog of Nedd4. The VP40 protein was multiubiquitinated by Rsp5 in a PY-dependent manner in an in vitro ubiquitination assay. These data demonstrate that the VP40 protein of Ebola virus possesses a PY motif that is functionally similar to those described previously for Gag and M proteins of specific retroviruses and rhabdoviruses, respectively. Last, these studies imply that VP40 likely plays an important role in filovirus budding, and that budding of retroviruses, rhabdoviruses, and filoviruses may proceed via analogous mechanisms.
3-bromo-2-pyrone: an easily prepared chameleon diene and a synthetic equivalent of 2-pyrone in thermal diels-alder cycloadditions (1991)

3-Bromo-2-pyrone, a stable solid prepared by a new route (eq. 1), has been found to undergo smooth and regiospecific 2+4-cycloadditions between 78-90°C with both electron-rich and electron-deficient dienophiles; subsequent high-yield reductive debrominations produced halogen-free cycloadducts thus showing 3-bromo-2-pyrone to be a practical and effective synthetic equivalent of 2-pyrone in thermal Diels-Alder cycloadditions.
Novel immunoregulatory functions of phenotypically distinct subpopulations of CD4+ cells in the human neonate. (1990)

Although normal numbers of CD4+ T cells are present in the human neonate, cord blood CD4+ cells are deficient in their ability to provide help for antibody production. In the present studies, we have examined the cellular basis for this functional deficit by analyzing the phenotypic properties and immunoregulatory functions of the subsets of cord blood CD4+ cells defined by anti-CD45RA mAb. In contrast to CD4+ cells from adults, greater than 90% of cord blood CD4+ cells expressed the CD45RA, CD38, and Leu-8 membrane Ag. When neonatal CD4+ cells were cultured with adult B cells and PWM or anti-CD4+ mAb, no helper function was apparent. However, when the small number of CD4+CD45RA- cells in cord blood were purified and similarly analyzed, helper activity comparable to that of adult CD4+CD45RA- cells was found. This helper function was profoundly suppressed by the presence of even small numbers of cord blood (but not adult) CD4+CD45RA+ cells. Irradiation of mitomycin C treatment of neonatal CD4+CD45RA+ cells abrogated their suppressor activity, but did not induce helper capability. However, after activation with PHA and culture in IL-2, cord blood CD4+CD45RA+ cells lost their suppressor activity and acquired the ability to provide help for B cell differentiation. This functional maturation was accompanied by their conversion to the CD4+CD45RA- phenotype. Thus, whereas cord blood CD4+CD45RA+ and CD4+CD45RA- cells share certain properties with the analogous subsets in adults, our data show that the dominant immunoregulatory function of cord blood CD4+ cells is suppression mediated by CD4+CD45RA+ (and CD38+) cells. In view of these phenotypic and functional differences between neonatal and adult CD4+CD45RA+ cells, we propose that "naive" CD4+CD45RA+ cells undergo age-related maturational changes that are unrelated to their postulated activation-dependent post-thymic differentiation into CD4+CD45RA- "memory" cells capable of helper functions.
Potential of mid IR spectroscopy in the rapid label free identification of skin malignancies (2016)

The rapid inspection of suspicious skin lesions for pathological cell types is the objective of optical point of care diagnostics technologies. A marker free fast diagnosis of skin malignancies would overcome the limitations of the current gold standard surgical biopsy. The time consuming and costly biopsy procedure requires the inspection of each sample by a trained pathologist, which limits the analysis of potentially malignant lesions. Optical technologies like RAMAN or infrared spectroscopy, which provide both, localization and chemical information, can be used to differentiate malignant from healthy tissue by the analysis of multi cell structures and cell type specific spectra. We here report the application of midIR spectroscopy towards fast and reliable skin diagnostics. Within the European research project MINERVA we developed standardized in vitro skin systems with increasing complexity, from single skin cell types as fibroblasts, keratinocytes and melanoma cells, to mixtures of these and finally three dimensional human skin equivalents. The standards were characterized in the established midIR range and also with newly developed systems for fast imaging up to 12 &mu;m. The analysis of the spectra by novel data processing algorithms demonstrated the clear separation of all cell types, especially the tumor cells. The signals from single cell layers were sufficient for cell type differentiation. We have compared different midIR systems and found all of them suitable for specific cell type identification. Our data demonstrate the potential of midIR spectroscopy for fast image acquisition and an improved data processing as sensitive and specific optical biopsy technology.
Base calling error rates in next-generation DNA sequencing (2012)

We study the problem of base calling in next-generation DNA sequencing platforms that rely on reversible terminator chemistry. After reviewing a statistical model of the generated signal and the Viterbi algorithm for finding the maximum-likelihood solution to the base calling problem, we present a closed form expression for the upper bound on the probability of base calling error. Simulation results demonstrate that the derived upper bound provides a useful characterization of the error rate performance of the considered sequencing platform.
Ribosome substructure investigated by scanning force microscopy and image processing (1998)

Scanning force microscopy was used to study the ultrastructure of eukaryotic ribosomes from Chironomus pallidivittatus in the polysomal complex. Positively stained polysomes were imaged, and the resulting three‐dimensional ribosomal structures were further processed by statistical analyses of virtual cross‐sections parallel to the substrate plane. Structural investigations were based on parameters which are minimally influenced by the tip geometry, like section plane centre or axis ratio. In the lower part of the structure a shift of the section centres was observed, suggesting an attached structure. The geometry of the sections revealed an elliptical shape in the upper part (axis ratio 1.52 ± 0.22), with a less elongated shape in the lower region (axis ratio 1.41 ± 0.18). A model for the surface topography of a positively stained ribosome exhibiting a small subunit attached along the long side of an elliptical large structure is proposed.
Role of Ras/ERK-dependent pathway in the erythroid differentiation of K562 cells (1999)

The chronic myelogenous leukemic K562 cell line carrying Bcr-Abl tyrosine kinase is considered as pluripotent hematopoietic progenitor cells expressing markers for erythroid, granulocytic, monocytic, and megakaryocytic lineages. Here we investigated the signaling modulations required for induction of erythroid differentiation of K562 cells. When the K562 cells were treated with herbimycin A (an inhibitor of protein tyrosine kinase), ras antisense oligonucleotide, and PD98059 (a specific inhibitor of MEK), inhibition of ERK/MAPK activity and cell growth, and induction of erythroid differentiation were observed. The ras mutant, pZIPRas61leu-transfected cells, K562-Ras61leu, have shown a markedly decreased cell proliferation rate with approximately 2-fold doubling time, compared with the parental K562 cells, and about 60% of these cells have shown the phenotype of erythroid differentiation. In addition, herbimycin A inhibited the growth rate and increased the erythroid differentiation, but did not affect the elevated activity of ERK/MAPK in the K562-Ras61leu cells. On the other hand, effects of PD98059 on the growth and differentiation of K562-Ras61leu cells were biphasic. At low concentration of PD98059, which inhibited the elevated activity of ERK/MAPK to the level of parental cells, the growth rate increased and the erythroid differentiation decreased slightly, and at high concentration of PD98059, which inhibited the elevated activity of ERK/MAPK below that of the parental cells, the growth rate turned down and the erythroid differentiation was restored to the untreated control level. Taken together, these results suggest that an appropriate activity of ERK/MAPK is required to maintain the rapid growth and transformed phenotype of K562 cells.
A human alpha-fetoprotein enhancer-binding protein, ATBF1, contains four homeodomains and seventeen zinc fingers. (1991)

We have isolated a full-length cDNA encoding a protein (ATBF1) that binds to an AT-rich motif in the human alpha-fetoprotein gene enhancer. The amino acid sequence deduced from the cDNA revealed that this is the largest DNA-binding protein (306 kDa) known to date, containing four homeodomains, 17 zinc finger motifs, and a number of segments potentially involved in transcriptional regulation. Although the exact function of this protein has not been determined, these structural features suggest that ATBF1 plays a transcriptional regulatory role.
Non-phenotypic selection of N-methyl-N-nitrosourea-induced mutations in human cells (1992)

The distribution of mutations in a particular gene as detected by a selective mutation assay could be affected by the structural properties of the target protein. To investigate this, we have analysed N-methyl-N-nitrosourea (MNU)-induced mutations in two restriction recognition sequences of a target gene for mutation analysis and compared these data with what previously observed in a phenotypic mutation assay. DNA base changes in the Ncil and EcoRV sites of the gpt gene maintained in human cells by a shuttle vector system were measured by restriction fragment length polymorphism/polymerase chain reaction (RFLP/PCR) technique. After MNU-treatment of human cells, mutations were detected in the Ncil recognition sequence but not in the EcoRV site. DNA sequencing analysis revealed that all Ncil-resistant mutations were GC to AT transitions located over four bases of the Ncil recognition sequence. Only one of these mutations drastically affected the functionality of the GPT protein. The Ncil-resistant mutations were randomly distributed in both DNA strands of the gpt gene and were preferentially targeted at guanine residues flanked 5' by a guanine. Our results indicate that the structure of the GPT protein is the main contributor to the strand-specificity of MNU-induced mutations previously reported by using a phenotypic mutation assay. The potential use of the RFLP/PCR technique as a general tool for mutation detection is also discussed.
Sequential Functionalization of Pyrazole 1-Oxides via Regioselective Metalation:  Synthesis of 3,4,5-Trisubstituted 1-Hydroxypyrazoles (2002)

A range of 3,5-diarylated and 3,4,5-triarylated 2-(4-methoxybenzyl)pyrazole 1-oxides have been prepared by regioselective deprotonation at C-5 or bromine-magnesium exchange at C-3 or C-4 followed by transmetalation with ZnCl(2) and palladium(0)-catalyzed cross-coupling. Furthermore, the metalated pyrazole 1-oxides could be trapped with electrophiles. The sequential metalation/functionalization of the pyrazole 1-oxides may follow the order C-5, C-3, C-4, or alternatively the order C-3, C-5, C-4. The 4-methoxybenzyl group of the functionalized 2-(4-methoxybenzyl)pyrazole 1-oxides could be removed by treatment with TFA and i-Pr(3)SiH in CH(2)Cl(2), providing the corresponding functionalized 1-hydroxypyrazoles.
Complete coding sequence of a human B-raf cDNA and detection of B-raf protein kinase with isozyme specific antibodies. (1990)

A 2.2 kb cDNA clone which presumably includes the complete human B-raf coding sequence was isolated from a human testes cDNA library. Sequence analysis showed the presence of all three conserved regions CR1, CR2 and CR3 previously identified in raf protein kinases. The cDNA was expressed in E. coli yielding a B-raf fusion protein which reacts with antibodies specific for B-raf raised against the C-terminal peptide as well as with monoclonal antibodies which map into the kinase domain.
Pollen-specific gene expression in transgenic plants: coordinate regulation of two different tomato gene promoters during microsporogenesis (1990)

To investigate the regulation of gene expression during male gametophyte development, we analyzed the promoter activity of two different genes (LAT52 and LAT59) from tomato, isolated on the basis of their anther-specific expression. In transgenic tomato, tobacco and Arabidopsis plants containing the LAT52 promoter region fused to the beta-glucuronidase (GUS) gene, GUS activity was restricted to pollen. Transgenic tomato, tobacco and Arabidopsis plants containing the LAT59 promoter region fused to GUS also showed very high levels of GUS activity in pollen. However, low levels of expression of the LAT59 promoter construct were also detected in seeds and roots. With both constructs, the appearance of GUS activity in developing anthers was correlated with the onset of microspore mitosis and increased progressively until anthesis (pollen shed). Our results demonstrate co-ordinate regulation of the LAT52 and LAT59 promoters in developing microspores and suggest that the mechanisms that regulate pollen-specific gene expression are evolutionarily conserved.