gebhart/patrepeval huggingface dataset:
Lethality of a dut (deoxyuridine triphosphatase) mutation in Escherichia coli (1988)

A chloramphenicol resistance gene was cloned into a plasmid-borne dut gene, producing an insertion mutation that was then transferred to the chromosome by allelic exchange. The mutation could not be acquired by haploid strains through substitutive recombination, even when two flanking markers were simultaneously transduced. The insertion was easily transferred, via generalized transduction, into the chromosomal dut region of strains harboring a lambda dut + transducing phage; however, the resulting dut mutant/lambda dut + merodiploid could not then be cured of the prophage. This apparent lethality of the mutation could not be explained by effects on adjacent genes; the dfp gene retained complementing activity, and a ttk insertion mutant was viable. The dut gene product, deoxyuridine triphosphatase, is known to reduce incorporation of uracil into DNA and to be required in the de novo synthesis of thymidylate. Therefore, an attempt was made to determine whether the dut insertion would be tolerated in strains carrying the following compensatory mutations: dcd (dCTP deaminase) and cdd (deoxycytidine deaminase), which should reduce dUTP formation; ung (uracil-DNA glycosylase), which should reduce fatally excessive excision repair; deoA (thymidine phosphorylase), which should enhance the utilization of exogenous thymidine; and sulA, which should reduce the lethal side effects of SOS regulon induction. These mutations, either alone or in various combinations, did not permit the survival of a haploid dut insertion mutant, suggesting that the dut gene product might have an essential function apart from its deoxyuridine triphosphatase activity.
Weighted regularization in electrical impedance tomography with applications to acute cerebral stroke (2002)

We apply electrical impedance tomography to detect and localize brain impedance changes associated with stroke. Forward solutions are computed using the finite-element method in two dimensions. We assume that baseline conductivity values are known for the major head tissues, and focus on changes in the brain compartment only. We use singular-value decomposition (SVD) to show that different impedance measurement patterns, which are theoretically equivalent by the reciprocity theorem, have different sensitivities to the brain compartment in the presence of measurement noise. The inverse problem is solved in part by standard means, using iterated SVD, and regularizing by truncation. To improve regularization we introduce a weighting scheme which normalizes the sensitivity matrix for voxels at different depths. This increases the number of linearly independent components which contribute to the solution, and forces the different measurement patterns to have similar sensitivity. When applied to stroke, this weighted regularization improves image quality overall.
Interface roughness scattering in semiconducting and semimetallic InAs-Ga1−xInxSb superlattices (1993)

An analysis of magnetotransport results for InAs-Ga1−xInxSb superlattices with a range of layer thicknesses demonstrates that interface roughness scattering dominates the electron mobility under most conditions of interest for infrared detector applications. However, the dependence on well thickness is much weaker than the d16 relation observed in other systems with thicker barriers, which is consistent with predictions based on the sensitivity of the energy levels to roughness fluctuations. Theory also correctly predicts an abrupt mobility decrease at the semiconductor-to-semimetal transition point, as well as the coexistence of two electron species in semimetallic samples.
A Secondary Structure Model of the Integrin a Subunit N-Terminal Domain Based on Analysis of Multiple Alignments (1994)

The integrins are alpha/beta heterodimeric proteins which mediate cell-matrix and cell-cell interactions. Current data indicate that the N-terminal moiety of the alpha subunit is involved in ligand binding. This region of the receptor is made up of a seven-fold repeated sequence of unknown structure which contains EF-hand-like putative divalent cation-binding sites. Recent studies have shown that multiple sequence alignments can be analysed to yield secondary structure predictions. Therefore, to obtain a model structure for the integrin alpha subunit N-terminal domain repeat, a large alignment of the seven repeats from sixteen integrin sequences was generated. Two methods of analysis were used: First, Chou and Fasman and Garnier, Osguthorpe and Robson predictions were carried out for individual sequences and the consensus predictions derived. Consensus hydrophobicity and chain flexibility data were also used to provide additional data. Second, sites of conservation and variation were analysed by a computer program STAMA (STructure After Multiple Alignment) to yield a secondary structure prediction. The two analyses gave essentially the same predicted structure: undefined region, loop, alpha-helix, beta-strand, divalent cation-binding loop, beta-strand, putative turn, loop, beta-strand. This is the first model structure to be presented for an integrin domain. Its implications for integrin function are discussed.
Mutant SOD1G93A microglia are more neurotoxic relative to wild‐type microglia (2007)

Recent studies suggest that microglia over-expressing mutant human superoxide dismutase (mSOD1(G93A)) may contribute to motoneuron death in a transgenic mouse model of familial amyotrophic lateral sclerosis. To further assess the relative neurotoxicity of wild-type microglia, mSOD1(G93A) microglia, and microglia over-expressing wild-type human SOD1, we used primary cultures of microglia and motoneurons in the presence and absence of lipopolysaccharide stimulation. Following activation with lipopolysaccharide, mSOD1(G93A) microglia released more nitric oxide, more superoxide, and less insulin-like growth factor-1 than wild-type microglia. In microglia/motoneuron co-cultures, mSOD1(G93A) microglia induced more motoneuron death and decreased neurite numbers and length compared with wild-type microglia. Mutant SOD1(G93A) microglia also induced more motoneuron injury than microglia over-expressing wild-type human SOD1 in microglia/motoneuron co-cultures. Motoneuron survival was inversely correlated with nitrate + nitrite concentrations in mSOD1(G93A) co-cultures, suggesting the important role of nitric oxide in microglia-induced motoneuron injury. Thus, relative to wild-type microglia, mSOD1(G93A) microglia were more neurotoxic and induced more motoneuron injury than similarly treated wild-type microglia.
A solid‐state amorphous selenium avalanche technology for low photon flux imaging applications (2010)

This is the first experimental demonstration of a solid-state amorphous photoreceptor which provides sufficient internal avalanche gain for photon counting and photon starved imaging applications.
Cold-adapted rhizobia for nitrogen fixation in temperate regions (2003)

Rhizobia from Canadian soils were selected for cold adaptation with the aim of improving productivity of legumes that are subjected to cool temperatures during the growing season. One approach was to use rhizobia associated with legume species indigenous to arctic and subarctic regions: (i) Mesorhizobium sp. isolated from Astragalus and Oxytropis spp. and (ii) Rhizobium leguminosarum from Lathryrus spp. The majority of these rhizobia are considered psychrotrophs because they can grow at 0 °C. The advantages of cold adaptation of arctic Mesorhizobium to improve legume symbiosis were demonstrated with the temperate forage legume sainfoin (Onobrychis viciifolia). In laboratory and field studies, arctic rhizobia were more efficient than temperate (commercial) rhizobia in improving growth of sainfoin and were more competitive in forming nodules. Biochemical studies on cold adaptation showed higher synthesis of cold shock proteins in cold-adapted than in nonadapted arctic rhizobia. Since arctic Mesorhizobium cannot nodulate agronomically important legumes, the nodulation genes and the bacterial signals (Nod factors) were characterized as a first step to modifying the host specificity of nodulation. Another valuable approach was to screen for cold adaptation, that is, rhizobia naturally associated with agronomic legumes cultivated in temperate areas. A superior strain of Sinorhizobium meliloti adapted for nodulation of alfalfa at low temperatures was selected and was the most efficient for improving growth of alfalfa in laboratory and field studies. This strain also performed well in improving regrowth of alfalfa after overwintering under cold and anaerobic (ice encasement) stresses, indicating a possible cross-adaptation of selected rhizobia for various abiotic stresses inherent to temperate climates.Key words: cold adaptation, legumes, symbiotic efficiency, cold shock protein, nodulation genes, anaerobiosis.
Crystal structure of a human aminoacyl-tRNA synthetase cytokine (2002)

The 20 aminoacyl-tRNA synthetases catalyze the first step of protein synthesis and establish the rules of the genetic code through aminoacylation reactions. Biological fragments of two human enzymes, tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase, connect protein synthesis to cell-signaling pathways including angiogenesis. Alternative splicing or proteolysis produces these fragments. The proangiogenic N-terminal fragment mini-TyrRS has IL-8-like cytokine activity that, like other CXC cytokines, depends on a Glu-Leu-Arg motif. Point mutations in this motif abolish cytokine activity. The full-length native TyrRS lacks cytokine activity. No structure has been available for any mammalian tRNA synthetase that, in turn, might give insight into why mini-TyrRS and not TyrRS has cytokine activities. Here, the structure of human mini-TyrRS, which contains both the catalytic and the anticodon recognition domain, is reported to a resolution of 1.18 A. The critical Glu-Leu-Arg motif is located on an internal alpha-helix of the catalytic domain, where the guanidino side chain of R is part of a hydrogen-bonding network tethering the anticodon-recognition domain back to the catalytic site. Whereas the catalytic domains of the human and bacterial enzymes superimpose, the spatial disposition of the anticodon recognition domain relative to the catalytic domain is unique in mini-TyrRS relative to the bacterial orthologs. This unique orientation of the anticodon-recognition domain can explain why the fragment mini-TyrRS, and not full-length native TyrRS, is active in cytokine-signaling pathways.
An in vivo pathway for disulfide bond isomerization in Escherichia coli (1996)

Biochemical studies have shown that the periplasmic protein disulfide oxidoreductase DsbC can isomerize aberrant disulfide bonds. Here we present the first evidence for an in vivo role of DsbC in disulfide bond isomerization. Furthermore, our data suggest that the enzymes DsbA and DsbC play distinct roles in the cell in disulfide bond formation and isomerization, respectively. We have shown that mutants in dsbC display a defect in disulfide bond formation specific for proteins with multiple disulfide bonds. The defect can be complemented by the addition of reduced dithiothreitol to the medium, suggesting that absence of DsbC results in accumulation of misoxidized proteins. Mutations in the dipZ and trxA genes have similar phenotypes. We propose that DipZ, a cytoplasmic membrane protein with a thioredoxin-like domain, and thioredoxin, the product of the trxA gene, are components of a pathway for maintaining DsbC active as a protein disulfide bond isomerase.
Serodiagnosis of Lyme Disease by Kinetic Enzyme‐Linked Immunosorbent Assay Using Recombinant VlsE1 or Peptide Antigens ofBorrelia burgdorferiCompared with 2‐Tiered Testing Using Whole‐Cell Lysates (2003)

In a study of US patients with Lyme disease, immunoglobulin (Ig) G and IgM antibody responses to recombinant Borrelia burgdorferi antigen VlsE1 (rVlsE1), IgG responses to a synthetic peptide homologous to a conserved internal sequence of VlsE (C6), and IgM responses to a synthetic peptide comprising the C-terminal 10 amino acid residues of a B. burgdorferi outer-surface protein C (pepC10) were evaluated by kinetic enzyme-linked immunoassay. At 99% specificity, the overall sensitivities for detecting IgG antibody to rVlsE1 or C6 in samples from patients with diverse manifestations of Lyme disease were equivalent to that of 2-tiered testing. When data were considered in parallel, 2 combinations (IgG responses to either rVlsE1 or C6 in parallel with IgM responses to pepC10) maintained high specificity (98%) and were significantly more sensitive than 2-tiered analysis in detecting antibodies to B. burgdorferi in patients with acute erythema migrans. In later stages of Lyme disease, the sensitivities of the in parallel tests and 2-tiered testing were high and statistically equivalent.
Mechanisms of immunosuppression induced by antithymocyte globulins and OKT3. (1996)

OKT3 monoclonal antibody and polyclonal antithymocyte or antilymphocyte globulins are among the most potent immunosuppressive agents which have been used in organ transplantation for many years. Both induce a rapid and profound lymphocytopenia classically attributed to several mechanisms, such as complement-dependent cytolysis, cell-mediated antibody-dependent cytolysis, as well as opsonization and subsequent phagocytosis by macrophages. However, the relative contribution of these three Fc-dependent mechanisms in vivo is difficult to ascertain and may be less important than previously thought. In addition OKT3 induces T-cell receptor modulation in vivo and modulated T cells no longer interact with antigen-presenting cells. Modulation of the T-cell receptor complex has not been documented for antithymocyte and antilymphocyte globulins as yet. The monoclonal antibody OKT3, which is directed against the epsilon chain of the CD3 molecule on the T-cell surface, but also antithymocyte and antilymphocyte globulins, which contain antibodies directed against CD3 and other functional molecules on the surface of T and B cells, generate various transduction signals to the target cells which can affect their functions in different ways. Recent in vitro studies suggest that these antibodies interfere with activation signals. Indeed, antithymocyte and antilymphocyte globulins, at low concentrations, inhibit T-cell activation induced by alloantigens, whereas they induce polyclonal T-cell activation at higher concentrations. Mitogenic antibodies can trigger an activation-induced cell death phenomenon as documented with anti-CD3 antibodies. Anti-CD3 antibodies can also induce a state of specific unresponsiveness (clonal anergy) which may contribute to their long-lasting immunosuppressive effect. One may hypothesize from in vitro data that in spite of their nonspecific immunosuppressive effects which may result in severe iatrogenic immunodeficiency, antilymphocyte antibodies may also act on stimulated alloreactive T-cell clones and therefore contribute to donor-specific graft adaptation.
Optical methods for sensing and imaging oxygen: materials, spectroscopies and applications (2014)

We review the current state of optical methods for sensing oxygen. These have become powerful alternatives to electrochemical detection and in the process of replacing the Clark electrode in many fields. The article (with 694 references) is divided into main sections on direct spectroscopic sensing of oxygen, on absorptiometric and luminescent probes, on polymeric matrices and supports, on additives and related materials, on spectroscopic schemes for read-out and imaging, and on sensing formats (such as waveguide sensing, sensor arrays, multiple sensors and nanosensors). We finally discuss future trends and applications and summarize the properties of the most often used indicator probes and polymers. The ESI† (with 385 references) gives a selection of specific applications of such sensors in medicine, biology, marine and geosciences, intracellular sensing, aerodynamics, industry and biotechnology, among others.
Single-frequency Er 3+ -doped silica-basedplanar waveguide laser withintegrated photo-imprinted Bragg reflectors (1994)

Single-longitudinal-mode operation of Er3+-P2O5-codoped silica planar waveguide lasers which are equipped with integrated Bragg grating reflectors is demonstrated, with a polarised output of 340 µW at 1546 nm. The gratings are photo-imprinted using 193 nm light exposure through a phase mask in GeO2-free optical waveguides that have been sensitised by H2 loading.
Glycosylation and Processing of High Levels of Active Human Glucocerebrosidase in Invertebrate Cells Using a Baculovirus Expression Vector (1988)

A human cDNA containing the complete coding region for the lysosomal glycoprotein glucocerebrosidase (EC 3.2.1.45) was introduced into the genome of Autographa californica nuclear polyhedrosis virus downstream from the polyhedrin promoter. Infection of Spodoptera frugiperda cells (SF9) with recombinant virus produced high levels of glucocerebrosidase, 40% of which was in the culture medium. The amino-terminal amino acid sequence of the recombinantly produced enzyme was identical to that of mature, human placental glucocerebrosidase, demonstrating that the signal sequence of the human preenzyme was recognized and appropriately removed in the SF9 invertebrate cells. The glucocerebrosidase in both the culture supernatant and SF9 cell pellet was glycosylated and contained, in part, high mannose oligosaccharide. These results demonstrate that insect cells can be used to produce abundant quantities of active mature human glucocerebrosidase that contains high mannose oligosaccharide as a consequence of post-translational processing.
Maturation of somatic embryos as a model for soybean seed development (2009)

Soybean somatic embryos have attracted attention both as a model of zygotic embryos and as explants for the generation of stable transgenic plants. We have now characterized the maturation of soybean somatic embryos in detail by examining both the accumulation of the major seed storage proteins β-conglycinin and glycinin as well as changes in cellular organization. Protein storage vacuoles and oil bodies, which are the main depositories of seed storage reserves, formed within cells during the maturation of somatic embryos. The seed storage proteins were gradually synthesized and accumulated in the protein storage vacuoles in a manner similar to that apparent in seeds. The α and α′ subunits of β-conglycinin were detected earlier than the β subunit of this protein and glycinin. In addition, The α and α′ subunits of β-conglycinin accumulated in both the cotyledons and the hypocotyl of somatic embryos, whereas the β subunit of β-conglycinin and glycinin accumulated only in the cotyledons. These temporal and spatial characteristics of storage protein production in maturating somatic embryos are similar to those in developing seeds, although the maturation of somatic embryos ceases prematurely without attainment of the final stages of development. Our findings suggest that somatic embryos are suitable for verification of seed-specific traits such as the biosynthesis of seed components.
Optimization algorithms for functional deimmunization of therapeutic proteins (2010)

By developing global optimization algorithms leveraging well-established immunogenicity and stability prediction techniques, we provide the protein engineer with a mechanism for exploring the favorable sequence space near a targeted protein therapeutic. Our mechanism not only helps identify designs more likely to be effective, but also provides insights into the interrelated implications of design choices.
Rapid whole-genome mutational profiling using next-generation sequencing technologies (2008)

Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.
Identification of human immunodeficiency virus type 1 Gag protein domains essential to membrane binding and particle assembly (1994)

Assembly of human immunodeficiency virus type 1 (HIV-1) particles occurs at the plasma membrane of infected cells. Myristylation of HIV-1 Gag precursor polyprotein Pr55Gag is required for stable membrane binding and for assembly of viral particles. We expressed a series of proteins representing major regions of the HIV-1 Gag protein both with and without an intact myristyl acceptor glycine and performed subcellular fractionation studies to identify additional regions critical for membrane binding. Myristylation-dependent binding of Pr55Gag was demonstrated by using the vaccinia virus/T7 hybrid system for protein expression. Domains within the matrix protein (MA) region downstream of the initial 15 amino acids were required for membrane binding which was resistant to a high salt concentration (1 M NaCl). A myristylated construct lacking most of the matrix protein did not associate with the plasma membrane but formed intracellular retrovirus-like particles. A nonmyristylated construct lacking most of the MA region also was demonstrated by electron microscopy to form intracellular particles. Retrovirus-like extracellular particles were produced with a Gag protein construct lacking all of p6 and most of the nucleocapsid region. These studies suggest that a domain within the MA region downstream from the myristylation site is required for transport of Gag polyprotein to the plasma membrane and that stable plasma membrane binding requires both myristic acid and a downstream MA domain. The carboxyl-terminal p6 region and most of the nucleocapsid region are not required for retrovirus-like particle formation.
AGPCS - An Automatic GSM-based Positioning and Communication System (1997)

A novel approach to automatic positioning and communication is presented in this paper. The approach is using single GSM (Global System for Mobile Communication) technology to achieve both positioning of the mobile station and communication with the other parties in a system containing a number of mobile stations. The paper deals with the overall system architecture, and briefly describes the aspects of positioning, communication and application of the system, without describing the low-level details applied in system operation. It also describes implementation of two experimental versions of the mobile stations, self-positioning and remote positioning, that integrate positioning information in the platform ready to use for different purposes. The approach is applicable to GSM and its other more recent derivatives.