gebhart/patrepeval huggingface dataset:
Transcriptional Program of Early Sporulation and Stationary-Phase Events in Clostridium acetobutylicum (2005)

DNA microarray analysis of Clostridium acetobutylicum was used to examine the genomic-scale gene expression changes during the shift from exponential-phase growth and acidogenesis to stationary phase and solventogenesis. Self-organizing maps were used to identify novel expression patterns of functional gene classes, including aromatic and branched-chain amino acid synthesis, ribosomal proteins, cobalt and iron transporters, cobalamin biosynthesis, and lipid biosynthesis. The majority of pSOL1 megaplasmid genes (in addition to the solventogenic genes aad-ctfA-ctfB and adc) had increased expression at the onset of solventogenesis, suggesting that other megaplasmid genes may play a role in stationary-phase phenomena. Analysis of sporulation genes and comparison with published Bacillus subtilis results indicated conserved expression patterns of early sporulation genes, including spo0A, the sigF operon, and putative canonical genes of the sigma(H) and sigma(F) regulons. However, sigE expression could not be detected within 7.5 h of initial spo0A expression, consistent with the observed extended time between the appearance of clostridial forms and endospore formation. The results were compared with microarray comparisons of the wild-type strain and the nonsolventogenic, asporogenous M5 strain, which lacks the pSOL1 megaplasmid. While some results were similar, the expression of primary metabolism genes and heat shock proteins was higher in M5, suggesting a difference in metabolic regulation or a butyrate stress response in M5. The results of this microarray platform and analysis were further validated by comparing gene expression patterns to previously published Northern analyses, reporter assays, and two-dimensional protein electrophoresis data of metabolic genes (including all major solventogenesis genes), sporulation genes, heat shock proteins, and other solventogenesis-induced gene expression.
Real-time control of ultrafast laser micromachining by laser-induced breakdown spectroscopy (2004)

Ultrafast laser micromachining provides many advantages for precision micromachining. One challenging problem, however, particularly for multilayer and heterogeneous materials, is how to prevent a given material from being ablated, as ultrafast laser micromachining is generally material insensitive. We present a real-time feedback control system for an ultrafast laser micromachining system based on laser-induced breakdown spectroscopy (LIBS). The characteristics of ultrafast LIBS are reviewed and discussed so as to demonstrate the feasibility of the technique. Comparison methods to identify the material emission patterns are developed, and several of the resulting algorithms were implemented into a real-time computer control system. LIBS-controlled micromachining is demonstrated for the fabrication of microheater structures on thermal sprayed materials. Compared with a strictly passive machining process without any such feedback control, the LIBS-based system provides several advantages including less damage to the substrate layer, reduced machining time, and more-uniform machining features.
Architecture recovery of dynamically linked applications: a case study (2003)

Most previously published case studies in architecture recovery have been performed on statically linked software systems. Due to the increase in use of middleware technologies, such as CORBA, and object-oriented programming concepts, such as polymorphism, there is an opportunity and a need to analyze architectures of these dynamically linked systems. This paper presents the results of software architecture extraction of the Nautilus file manager, which employs CORBA in its implementation. A combination of existing static analysis and use-case modeling architecture recovery techniques was used, with the expectation of complex but complete architecture extraction of a system such as Nautilus. We have found that this combined approach, named Dynamo-1, presented in this paper provided successful focused architecture recovery and guidance for future work in the complete architecture recovery of dynamically linked applications.
A Host Cell Reactivation Assay for DNA Repair System Analysis in Primary Hematopoietic Cells. (2004)

Abstract Therapy related acute myelogenous leukemia (t-AML) is frequently observed among patients who undergo a high dose chemotherapy and its incidence varies between 5 to 15% in non-myeloablative and myeloablative treatment protocols. Deficiencies in individual DNA-repair systems seem to be involved in t-AML leukemogenesis since indirect genetic markers of impaired DNA repair, e.g. microsatellite instability (mismatch repair) and polymorphisms of XRCC genes (base/nucleotide excision repair), are frequent in these patients. To directly determine the activity of different DNA repair systems we developed a modified host cell reactivation (HCR) assay which is applicable for the analysis of primary hematopoietic cells of clinical samples. This assay determines the ability of transfected host cells to repair damaged plasmid DNA as reflected in the recovery of luciferase activity. Depending on the type of DNA damage introduced to the plasmid prior to transfection, different DNA repair systems can be analysed, e.g. nucleotide excision repair (NER) or double strand break repair. We performed the HCR assay using 75 to 250 ng luciferase reporter gene plasmid (pCMV-Luc). Lymphocytes and cord blood CD34+-progenitor cells from healthy donors were collected according to the convention of Helsinki. 200,000 to 2,000,000 cells were cryopreserved, thawed and transfected using DEAE-dextran at a concentration of 0,1 mg/ml in a transfection volume of 250 μl. We obtained luciferase activities of 350-fold above background in CD34+ progenitor cells (1000-fold in lymphocytes) rendering these cells applicable for DNA repair analysis. In addition, we evaluated the normalized NER capacity (1000 J/m2 UVC irradiated plasmid vs. unirradiated control) of lymphocytes and two AML cell lineages, Kasumi-1 and HL60. Kasumi-1 and HL60 cells exhibited a significantly reduced NER capacity compared to lymphocytes (6.15% +/− 1.57% and 6.5% +/− 1.59% vs. 12.3% +/− 3.2%). Clinical AML samples are currently been investigated. Our modified HCR can be used for functional DNA repair analysis in fresh and cryopreserved patient samples of pre- and post-leukemic conditions as well as in leukemic blasts to elucidate the role of defective DNA repair during t-AML leukemogenesis. Furthermore, the modified HCR may also be used to determine the individual susceptibility for therapy related myeloid leukemia prior to chemotherapy.
T‐cell receptor proximal signaling via the Src‐family kinases, Lck and Fyn, influences T‐cell activation, differentiation, and tolerance (2009)

T-cell development in the thymus and activation of mature T cells in secondary lymphoid organs requires the ability of cells to respond appropriately to environmental signals at multiple stages of their development. The process of thymocyte selection insures a functional T-cell repertoire, while activation of naive peripheral T cells induces proliferation, gain of effector function, and, ultimately, long-lived T-cell memory. The T-cell immune response is initiated upon engagement of the T-cell receptor (TCR) and coreceptor, CD4 or CD8, by cognate antigen/major histocompatibility complexes presented by antigen-presenting cells. TCR/coreceptor engagement induces the activation of biochemical signaling pathways that, in combination with signals from costimulator molecules and cytokine receptors, direct the outcome of the response. Activation of the src-family kinases p56(lck) (Lck) and p59(fyn) (Fyn) is central to the initiation of TCR signaling pathways. This review focuses on our current understanding of the mechanisms by which these two proteins orchestrate T-cell function.
The mechanisms of antiviral immunity induced by a vaccinia virus recombinant expressing herpes simplex virus type 1 glycoprotein D: clearance of local infection. (1987)

We have shown that immunization of mice with a vaccinia virus recombinant expressing glycoprotein D of Herpes simplex virus (HSV)-1 will induce a variety of L3T4+ T cell responses. These included a HSV-specific delayed-type hypersensitivity response, T cell help for the induction of antiviral antibodies, and the ability to eliminate a challenge dose of HSV from the pinna. This protection against a subcutaneous virus challenge was not mediated by the delayed-type hypersensitivity response because intravenous inoculation of the vaccinia virus recombinant expressing HSV-1-gD induced a state of split tolerance. Thus, mice could still clear a HSV challenge inoculum from the pinna yet were unable to mount a HSV-specific delayed-type hypersensitivity response. Evidence is presented that suggests the protective response was, at least, in part mediated by a T cell-dependent induction of virus-neutralizing antibodies. Evidence is also presented that may suggest the failure of a vaccinia virus recombinant expressing HSV-1-gD to induce HSV-specific cytotoxic T cell responses appears to minimize the protective response to only efficiently clearing low 10(4) 50% tissue culture infective dose) challenge populations of virus. These findings are discussed with relevance to the immune control of HSV infections and to the future development of anti-HSV vaccines.
Signal Transduction by the Ras–MAP Kinase Pathway in Prostate Cancer Progression (2008)

Prostate cancer (PC) initially appears as an androgen-dependent disease but progresses to one that is refractory to hormone ablation therapy. Substantial evidence suggests that autocrine and paracrine growth factor loops fuel PC progression to hormone independence: (1) overexpression of numerous growth factors and their cognate receptors correlates with PC progression; (2) ectopic overexpression of some receptors can drive hormone-independent growth; and (3) neuroendocrine (NE)-like cells that produce growth-regulatory
Copper‐catalyzed thermal aggregation of human gamma‐globulin inhibition by histidine, gold thiomalate, and penicillamine (1974)

Abstract Gold thiomalate (40 μM), penicillamine (40 μM), and histidine (20 μM) inhibit the copper‐catalyzed (20 μM) thermal aggregation of human gamma globulin (0.8 mg/ml). At these concentrations, inhibition of gamma globulin aggregation was 87%, 96%, and 99% complete. This effect may be related to the reported suppressive effect of these agents in rheumatoid arthritis and adds support to the hypothesis that the hypohistidinemia of rheumatoid arthritis participates in the pathogenesis of the disease.
Targeted knockouts of Physcomitrella lacking plant‐specific immunogenic N‐glycans (2004)

Using plants as production factories for therapeutic proteins requires modification of their N-glycosylation pattern because of the immunogenicity of plant-specific sugar residues. In an attempt towards such humanization, we disrupted the genes for alpha1,3-fucosyltransferase and beta1,2-xylosyltransferase in Physcomitrella patens by homologous recombination. The single Deltafuc-t and Deltaxyl-t plants, as well as the double knockout, lacked transcripts of the corresponding genes, but did not differ from the wild-type moss in morphology, growth, development, and ability to secrete a recombinant protein, the human vascular endothelial growth factor VEGF(121), into the culture medium. N-Glycan analysis, however, revealed the absence of 1,3-fucosyl and/or 1,2-xylosyl residues, respectively. Therefore, the modifications described here represent the key step towards the generation of moss lines suitable for the production of plant-made glycosylated biopharmaceuticals with nonallergenic N-glycans.
Crystal Structure of Formate Dehydrogenase H: Catalysis Involving Mo, Molybdopterin, Selenocysteine, and an Fe 4 S 4 Cluster (1997)

Formate dehydrogenase H from Escherichia coli contains selenocysteine (SeCys), molybdenum, two molybdopterin guanine dinucleotide (MGD) cofactors, and an Fe4S4 cluster at the active site and catalyzes the two-electron oxidation of formate to carbon dioxide. The crystal structures of the oxidized [Mo(VI), Fe4S4(ox)] form of formate dehydrogenase H (with and without bound inhibitor) and the reduced [Mo(IV), Fe4S4(red)] form have been determined, revealing a four-domain alphabeta structure with the molybdenum directly coordinated to selenium and both MGD cofactors. These structures suggest a reaction mechanism that directly involves SeCys140 and His141 in proton abstraction and the molybdenum, molybdopterin, Lys44, and the Fe4S4 cluster in electron transfer.
Content based video indexing and retrieval (1994)

Video management tools and techniques are based on pixels rather than perceived content. Thus, state-of-the-art video editing systems can easily manipulate such things as time codes and image frames, but they cannot "know," for example, what a basketball is. Our research addresses four areas of content-based video management.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oligodendrocyte progenitors are generated throughout the embryonic mouse brain, but differentiate in restricted foci (1996)

Recent evidence from studies mapping the expression of putative oligodendrocyte progenitor specific mRNAs has suggested that oligodendrocyte progenitors arise during embryogenesis, in specific foci of the neuroectoderm. In order to test this hypothesis, we have assayed different regions of the embryonic central nervous system for their ability to generate oligodendrocytes following transplantation into neonatal cerebrum. To allow identification of donor-derived oligodendrocytes in wild-type host brain, we used the MbetaP transgenic mouse, which expresses lacZ in oligodendrocytes, as donor tissue. We found that tissue fragments derived from several levels of the anterior-posterior axis of the neural tube at E14.5 and E12.5, chosen to include (hindbrain, cervical and lumbar spinal cord), or exclude (dorsal telencephalon) putative foci of oligodendrocyte progenitors, all produced oligodendrocytes following transplantation. In addition, these same regions taken from E10.5, prior to the appearance of putative oligodendrocyte progenitor markers, also all yielded oligodendrocytes on transplantation. This indicates that precursor cells that can generate oligodendrocytes are widespread throughout the neuroectoderm as early as E10.5. We have also used the oligodendrocyte lineage-specific glycolipid antibodies O4, R-mAb and O1 to identify those regions of the developing brain that first support the differentiation of oligodendrocytes from their progenitor cells. We found that the first oligodendrocytes arise in prenatal brain at E14.5, in a restricted zone adjacent to the midline of the medulla. These cells are mitotically inactive, differentiated oligodendrocytes and, using light and electron microscopy, we show that they become functional, myelin-bearing oligodendrocytes. We have mapped the subsequent appearance of differentiated oligodendrocytes in the prenatal brain and show that they appear in a restricted, tract-specific manner. Our results suggest that oligodendrocytes are generated from neuroectodermal cells positioned throughout the rostrocaudal axis of the neural tube, rather than at restricted locations of the neuroectoderm. By contrast, the differentiation of such cells into oligodendrocytes does occur in a restricted manner, consistent with local regulation of oligodendrocyte progenitor differentiation.
Embedding 3D models of biological specimens in PDF publications (2008)

By providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations are discussed, including better explanation capabilities for spatial arrangements, higher information contents, and limiting options for disguising results by authors. Possibilities for additional applications reaching far beyond the examples presented are suggested. Problems such as long-term compatibility of file format and hardware plus software, editing and embedding of files, file size and differences in information contents between printed and electronic version will likely be overcome by technical development and increasing tendency toward electronic at the cost of printed publications. Since 3D visualization plays an increasing role in manifold disciplines of science and appropriate tools for the popular PDF format are readily available, we propose routine application of this way of illustration in electronic life science papers.
Genomics of secondary metabolite production by Pseudomonas spp. (2009)

Covering: up to June 2009
Defect-Free Nanoporous Thin Films from ABC Triblock Copolymers (2006)

The self-assembly of triblock copolymers of poly(ethylene oxide-b-methyl methacrylate-b-styrene) (PEO-b-PMMA-b-PS), where PS is the major component and PMMA and PEO are minor components, provides a robust route to highly ordered, nanoporous arrays with cylindrical pores of 10-15 nm that show promise in block copolymer lithography. These ABC triblock copolymers were synthesized by controlled living radical polymerization, and after solvent annealing, thin films showing defect-free cylindrical microdomains were obtained. The key to the successful generation of highly regular, porous thin films is the use of PMMA as a photodegradable mid-block which leads to nanoporous structures with an unprecedented degree of lateral order. The power of using a triblock copolymer when compared to a traditional diblock copolymer is evidenced by the ability to exploit and combine the advantages of two separate diblock copolymer systems, the high degree of lateral ordering inherent in PS-b-PEO diblocks plus the facile degradability of PS-b-PMMA diblock copolymer systems, while negating the corresponding disadvantages, poor degradability in PS-b-PEO systems and no long-range order for PS-b-PMMA diblocks.
Hydrothermal decomposition of potassium feldspar under alkaline conditions (2015)

For the first time, a transitional compound [Ca<sup>2+</sup> ≡ 2AlSi<sub>3</sub>O<sub>8</sub><sup>−</sup> ≡ <italic>x</italic>OH<sup>−</sup>] was observed for K-feldspar hydrothermal alkaline decomposition, and a model was presented.
Dimension of Strange Attractors (1980)

A relationship between the Lyapunov numbers of a map with a strange attractor and the dimension of the strange attractor has recently been conjectured. Here, the conjecture is numerically tested with use of several different maps, one of which results from a system of ordinary differential equations occurring in plasma physics. For the cases tested, the conjecture is verified to within the obtained accuracy.
Exogenous Valine Reduces Conversion of Leucine to 3-Methyl-1-Butanol in Saccharomyces cerevisiae (1983)

Mutant strains of the yeast Saccharomyces cerevisiae that require branched-chain amino acids must be supplemented with large concentrations (up to 10 mM) of these amino acids to satisfy their nutritional requirement. The utilization of one branched-chain amino acid, leucine, was examined in several leul strains of yeast grown aerobically in a glucose-ammonium salts minimal medium containing a limiting concentration (0.2 mM) of leucine. In this medium, the leucine requirement of the auxotrophic strains could be reduced by valine, another branched-chain amino acid. Increasing the valine concentration increased the cell yields of cultures and also reduced the levels of 3-methyl-1-butanol detected in the medium by gas chromatography. The concentration of 3-methyl-1-butanol was reduced from 122.0 to 48.9 muM when 5.0 mM valine was supplemented to limiting-leucine cultures. The amino acids isoleucine, threonine, norleucine, norvaline, alpha-amino-butyrate, alanine, and glycine also spared the leucine requirement of leucine auxotrophs, most likely because they resembled leucine and competed for its uptake. We propose that leucine analogs restrict the entry and degradation of leucine and thus reduce its conversion to 3-methyl-1-butanol, a major component of fusel oil.
Online Large-Margin Training for Statistical Machine Translation (2007)

We achieved a state of the art performance in statistical machine translation by using a large number of features with an online large-margin training algorithm. The millions of parameters were tuned only on a small development set consisting of less than 1K sentences. Experiments on Arabic-to-English translation indicated that a model trained with sparse binary features outperformed a conventional SMT system with a small number of features. 1
Altered Mitochondrial Sensitivity for ADP and Maintenance of Creatine-stimulated Respiration in Oxidative Striated Muscles from VDAC1-deficient Mice (2001)

Voltage-dependent anion channels (VDACs) form the main pathway for metabolites across the mitochondrial outer membrane. The mouse vdac1 gene has been disrupted by gene targeting, and the resulting mutant mice have been examined for defects in muscle physiology. To test the hypothesis that VDAC1 constitutes a pathway for ADP translocation into mitochondria, the apparent mitochondrial sensitivity for ADP (Km(ADP)) and the calculated rate of respiration in the presence of the maximal ADP concentration (Vmax) have been assessed using skinned fibers prepared from two oxidative muscles (ventricle and soleus) and a glycolytic muscle (gastrocnemius) in control and vdac1(-/-) mice. We observed a significant increase in the apparent Km((ADP)) in heart and gastrocnemius, whereas the V(max) remained unchanged in both muscles. In contrast, a significant decrease in both the apparent Km((ADP)) and V(max) was observed in soleus. To test whether VDAC1 is required for creatine stimulation of mitochondrial respiration in oxidative muscles, the apparent Km((ADP)) and Vmax were determined in the presence of 25 mm creatine. The creatine effect on mitochondrial respiration was unchanged in both heart and soleus. These data, together with the significant increase in citrate synthase activity in heart, but not in soleus and gastrocnemius, suggest that distinct metabolic responses to altered mitochondrial outer membrane permeability occur in these different striated muscle types.