gebhart/patrepeval huggingface dataset:
Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader. (1986)

The leucine operon of Salmonella typhimurium is controlled by a transcription attenuation mechanism. Four adjacent leucine codons within a 160-nucleotide leu leader RNA are thought to play a central role in this mechanism. Three of the four codons are CUA, a rarely used leucine codon within enteric bacteria. To determine whether the nature of the leucine codon affects the regulation of the leucine operon, we used oligonucleotide-directed mutagenesis to first convert one CUA of the leader to CUG and then convert all three CUA codons to CUG. CUG is the most frequently used leucine codon in enteric bacteria. A mutant having (CUA)2CUGCUC in place of (CUA)3CUC has an altered response to leucine limitation, requiring a slightly higher degree of limitation to effect derepression. Changing (CUA)3CUC to (CUG)3CUC has more dramatic effects upon operon expression. First, the basal level of expression is lowered to the point that the mutant grows more slowly than the parent in a minimal medium lacking leucine. Second, the response of the mutant to a leucine limitation is dramatically altered such that even a strong limitation elicits only a modest degree of derepression. If the mutant is grown under conditions of leucyl-tRNA limitation rather than leucine limitation, complete derepression can be achieved, but only at a much higher degree of limitation than for the wild-type operon. These results provide a clear-cut example of codon usage having a dramatic effect upon gene expression.
Biomaterial Coatings by Stepwise Deposition of Silk Fibroin (2005)

A completely aqueous, stepwise deposition process with Bombyx mori silk fibroin for the assembly of nanoscale thin film coatings is reported the first time. The focus of this work was to develop an understanding of the control of this deposition process and to characterize the films formed from a physicochemical perspective. The deposition process was monitored by UV spectrophotometry and research quartz crystal microbalance. Both absorbance and film thickness correlated linearly with the number of silk fibroin layers deposited, analogous to multilayered materials fabricated from conventional polyelectrolytes. The polymer adsorption process was stable and reproducible, with control of a single layer thickness ranging from a few to tens of nanometers, determined by the concentrations of silk fibroin, salt concentration in the dipping solution, and method of rinsing. The driving force for the assembly of silk fibroin onto the substrate was primarily hydrophobic interactions, while some electrostatic interactions were also involved. The difference with this approach from traditional polyelectrolyte layer-by-layer techniques is that an intervening drying step is used to control the structure and stability of the self-assembled silk fibroin. The assembled films were stable under physiological conditions and supported human bone marrow stem cell adhesion, growth, and differentiation. This approach offers new options to engineer biomaterial coatings as well as bulk materials with control of both interfacial properties conducive to specific cellular or tissue responses and the potential to entrap and deliver labile molecules or other components due to the all-aqueous process described.
The microtubule binding domain of microtubule-associated protein MAP1B contains a repeated sequence motif unrelated to that of MAP2 and tau. (1989)

We report the complete sequence of the microtubule-associated protein MAP1B, deduced from a series of overlapping genomic and cDNA clones. The encoded protein has a predicted molecular mass of 255,534 D and contains two unusual sequences. The first is a highly basic region that includes multiple copies of a short motif of the form KKEE or KKEVI that are repeated, but not at exact intervals. The second is a set of 12 imperfect repeats, each of 15 amino acids and each spaced by two amino acids. Subcloned fragments spanning these two distinctive regions were expressed as labeled polypeptides by translation in a cell-free system in vitro. These polypeptides were tested for their ability to copurify with unlabeled brain microtubules through successive cycles of polymerization and depolymerization. The peptide corresponding to the region containing the KKEE and KKEVI motifs cycled with brain microtubules, whereas the peptide corresponding to the set of 12 imperfect repeats did not. To define the microtubule binding domain in vivo, full-length and deletion constructs encoding MAP1B were assembled and introduced into cultured cells by transfection. The expression of transfected polypeptides was monitored by indirect immunofluorescence using anti-MAP1B-specific antisera. These experiments showed that the basic region containing the KKEE and KKEVI motifs is responsible for the interaction between MAP1B and microtubules in vivo. This region bears no sequence relationship to the microtubule binding domains of kinesin, MAP2, or tau.
The Biology of Plasmids (1996)

The Anatomy Of Bacterial Plasmids. The Unity Of Plasmid Biology. Plasmid Replication And Its Control. Plasmid Inheritance. Plasmid Dissemination. The Clinical And Veterinary Importance Of Plasmids. References.
Critical role of the disintegrin metalloprotease ADAM17 for intestinal inflammation and regeneration in mice (2010)

The protease a disintegrin and metalloprotease (ADAM) 17 cleaves tumor necrosis factor (TNF), L-selectin, and epidermal growth factor receptor (EGF-R) ligands from the plasma membrane. ADAM17 is expressed in most tissues and is up-regulated during inflammation and cancer. ADAM17-deficient mice are not viable. Conditional ADAM17 knockout models demonstrated proinflammatory activities of ADAM17 in septic shock via shedding of TNF. We used a novel gene targeting strategy to generate mice with dramatically reduced ADAM17 levels in all tissues. The resulting mice called ADAM17(ex/ex) were viable, showed compromised shedding of ADAM17 substrates from the cell surface, and developed eye, heart, and skin defects as a consequence of impaired EGF-R signaling caused by failure of shedding of EGF-R ligands. Unexpectedly, although the intestine of unchallenged homozygous ADAM17(ex/ex) mice was normal, ADAM17(ex/ex) mice showed substantially increased susceptibility to inflammation in dextran sulfate sodium colitis. This was a result of impaired shedding of EGF-R ligands resulting in failure to phosphorylate STAT3 via the EGF-R and, consequently, in defective regeneration of epithelial cells and breakdown of the intestinal barrier. Besides regulating the systemic availability of the proinflammatory cytokine TNF, our results demonstrate that ADAM17 is needed for vital regenerative activities during the immune response. Thus, our mouse model will help investigate ADAM17 as a potential drug target.
RBP-L, a Transcription Factor Related to RBP-Jκ (1997)

RBP-Jkappa is a sequence-specific DNA binding protein which plays a central role in signalling downstream of the Notch receptor by physically interacting with its intracellular region. Although at least four Notch genes exist in mammals, it is unknown whether each Notch requires a specific downstream signalling molecule. Here we report isolation and characterization of a mouse RBP-Jkappa-related gene named RBP-L that is expressed almost exclusively in lung, in contrast to the ubiquitous expression of RBP-Jkappa. For simplicity, we propose to call RBP-Jkappa RBP-J. The RBP-L protein bound to a DNA sequence almost identical to that of RBP-J. Surprisingly, RBP-L did not interact with any of the known four mouse Notch proteins. Although we found that RBP-L and EBNA-2 cooperated in transcriptional activation, they did not show significantly strong protein-protein interaction that can be detected by several in vivo and in vitro assays. This is again in contrast to physical association of RBP-J with EBNA-2. Several models to explain functional interaction between RBP-L and EBNA-2 are discussed.
Acceptable levels of digital image compression in chest radiology (2000)

The introduction of picture archival and communications systems (PACS) and teleradiology has prompted an examination of techniques that optimize the storage capacity and speed of digital storage and distribution networks. The general acceptance of the move to replace conventional screen-film capture with computed radiography (CR) is an indication that clinicians within the radiology community are willing to accept images that have been 'compressed'. The question to be answered, therefore, is what level of compression is acceptable. The purpose of the present study is to provide an assessment of the ability of a group of imaging professionals to determine whether an image has been compressed. To undertake this study a single mobile chest image, selected for the presence of some subtle pathology in the form of a number of septal lines in both costphrenic angles, was compressed to levels of 10:1, 20:1 and 30:1. These images were randomly ordered and shown to the observers for interpretation. Analysis of the responses indicates that in general it was not possible to distinguish the original image from its compressed counterparts. Furthermore, a preference appeared to be shown for images that have undergone low levels of compression. This preference can most likely be attributed to the 'de-noising' effect of the compression algorithm at low levels.
Preparation and crystal structure of a stable and persistent twisted tetraketene (1996)

A. D. Allen, A. J. Lough and T. T. Tidwell, Chem. Commun., 1996, 2171 DOI: 10.1039/CC9960002171
Species identification of Chlamydia isolates by analyzing restriction fragment length polymorphism of the 16S-23S rRNA spacer region (1997)

The genetic diversity of the 16S-23S rRNA spacer region of 12 Chlamydia pneumoniae isolates, 7 Chlamydia trachomatis isolates (human biovars: the trachoma serovars B and C, the urogenital serovars D, E, and F, and the lymphogranuloma venereum serovar L2; and a mouse biovar), 6 Chlamydia psittaci isolates (5 avian isolates and 1 feline isolate), and one Chlamydia pecorum isolate was studied. The 16S-23S rRNA spacer region was amplified by PCR and digested with the restriction enzymes MseI, PstI, AluI, BglII, NlaIV, and BclI. All 26 isolates could be amplified by using one genus-specific primer pair, yielding an amplicon with a size of 803 bp. The analytical sensitivity of the PCR assay was < or = 100 inclusion-forming units per reaction. Digestion with MseI or AluI made it possible to differentiate the four species from each other, the C. trachomatis human biovars from the mouse biovar, and the C. psittaci avian isolates from the feline isolate. The MseI profiles were more distinct than the AluI profiles. Phylogenetic analysis of the results for all enzymes combined supported the current classification of four Chlamydia species: C. pneumoniae, C. trachomatis, C. psittaci, and C. pecorum. Phylogenetic analysis also suggested subdivision of isolates of C. trachomatis and C. psittaci into subgroups that coincide with their host range. In conclusion, we have developed an easy and rapid method for species and subspecies identification of Chlamydia based on restriction fragment length polymorphism analysis of the 16S-23S rRNA spacer region.
Pestivirus NS3 (p80) protein possesses RNA helicase activity (1995)

The pestivirus bovine viral diarrhea virus (BVDV) p80 protein (referred to here as the NS3 protein) contains amino acid sequence motifs predictive of three enzymatic activities: serine proteinase, nucleoside triphosphatase, and RNA helicase. We have previously demonstrated that the former two enzymatic activities are associated with this protein. Here, we show that a purified recombinant BVDV NS3 protein derived from baculovirus-infected insect cells possesses RNA helicase activity. BVDV NS3 RNA helicase activity was specifically inhibited by monoclonal antibodies to the p80 protein. The activity was dependent on the presence of nucleoside triphosphate and divalent cation, with a preference for ATP and Mn2+. Hydrolysis of the nucleoside triphosphate was necessary for strand displacement. The helicase activity required substrates with an un-base-paired region on the template strand 3' of the duplex region. As few as three un-base-paired nucleotides were sufficient for efficient oligonucleotide displacement. However, the enzyme did not act on substrates having a single-stranded region only to the 5' end of the duplex or on substrates lacking single-stranded regions altogether (blunt-ended duplex substrates), suggesting that the directionality of the BVDV RNA helicase was 3' to 5' with respect to the template strand. The BVDV helicase activity was able to displace both RNA and DNA oligonucleotides from RNA template strands but was unable to release oligonucleotides from DNA templates. The possible role of this activity in pestivirus replication is discussed.
Use of Complete Eluted Peptide Sequence Data from HLA-DR and -DQ Molecules to Predict T Cell Epitopes, and the Influence of the Nonbinding Terminal Regions of Ligands in Epitope Selection (1998)

In diseases with a strong association with an HLA haplotype, identification of relevant T cell epitopes may allow alteration of the pathologic process. In this report we use a reverse immunogenetic approach to predict possible HLA class II-restricted T cell epitopes by using complete pool sequencing data. Data from HLA-DR2(B1*1501), -DR3(B1*0301), -DQ2(A1*0501, B1*0201), and -DQ8(A1*0301, B1*0302) alleles were used by a computer program that searches a candidate protein to predict ligands with a relatively high probability of being processed and presented. This approach successfully identified both known T cell epitopes and eluted single peptides from the parent protein. Furthermore, the program identified ligands from proteins in which the binding motif of the HLA molecule was unable to do so. When the information from the nonbinding N- and C-terminal regions in the pool sequence was removed, the ability to predict several ligands was markedly reduced, particularly for the HLA-DQ alleles. This suggests a possible role for these regions in determining ligands for HLA class II molecules. Thus, the use of complete eluted peptide sequence data offers a powerful approach to the prediction of HLA-DQ and -DR peptide ligands and T cell epitopes.
Current Trends in Dental Composites (1995)

The clinical performance of dental composites has been significantly improved over the past decade through modifications in formulation that include: using more stable polymerization promoters for greater color stability; incorporating high concentrations of finely ground fillers to produce adequate strength and excellent wear resistance while retaining translucency; adding radiopacifying agents for improved diagnostics; and utilizing dentin adhesives. However, there are problems which limit the use of composites, especially in posterior teeth. The materials remain very technique-sensitive, due to the extensive contraction which accompanies polymerization and negatively influences marginal sealing. In addition, the materials are generally considered to have inadequate mechanical properties and wear resistance in contact areas to serve as total replacements for amalgams. Current efforts are focusing on several areas, including the development of non- or minimally-shrinking dental composites containing spiro-orthocarbonates as additives to dimethacrylates or epoxy-base resins, and the production of alternative filler materials for ideal wear resistance and esthetics. This paper reviews the composition and characteristics of current dental composites, as well as recent areas of study.
Optical investigation of a new type of valence-band configuration inInxGa1−xAs-GaAs strained superlattices (1985)

We present optical absorption experiments in strained ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As-GaAs superlattices grown by molecular-beam epitaxy. From our data, we show that ground heavy- and light-hole states are confined in the ${\mathrm{In}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As and in the GaAs layers, respectively. We also use a new method to observe the optical selection rules in such two-dimensional structures.
Identification of immunoglobulin superfamily 11 (IGSF11) as a novel target for cancer immunotherapy of gastrointestinal and hepatocellular carcinomas (2005)

We previously performed gene expression profile analyses of 20 intestinal-type gastric cancers, and identified a set of genes whose expression levels were elevated in cancer tissues compared to their corresponding non-cancerous tissues. In the present study we focused on the immunoglobulin superfamily 11 gene (IGSF11). Its expression was also elevated in colorectal cancers and hepatocellular carcinomas as well as intestinal-type gastric cancers. Northern blot analysis showed that it was expressed abundantly in testis and ovary. These data suggest that IGSF11 is a good candidate of cancer-testis antigen. Furthermore, suppression of IGSF11 by siRNA retarded the growth of gastric cancer cells. To investigate the possibility of clinical application of peptide vaccine to IGSF11, we synthesized candidate epitope peptides for IGSF11 and tested whether the peptides elicit IGSF11-specific CTL. As a result, we successfully established oligo-clonal CTL by stimulation with IGSF11-9-207 (ALSSGLYQC). In addition, we also established additional CTL using IGSF11-9V (ALSSGLYQV), anchor-modified peptides of IGSF11-9-207. These peptides showed IGSF11-specific cytotoxic activity in an HLA-A*0201-restricted fashion, suggesting that these peptides may be applicable for cancer immunotherapy. These findings have provided a novel insight into carcinogenesis of the stomach, colon and liver, and will be helpful for the development of novel therapeutic strategies to a wide range of human cancers.
Targeting Endogenous Transforming Growth Factor β Receptor Signaling in SMAD4-Deficient Human Pancreatic Carcinoma Cells Inhibits Their Invasive Phenotype (2004)

Transforming growth factor-beta (TGF-beta) suppresses tumor formation by blocking cell cycle progression and maintaining tissue homeostasis. In pancreatic carcinomas, this tumor suppressive activity is often lost by inactivation of the TGF-beta-signaling mediator, Smad4. We found that human pancreatic carcinoma cell lines that have undergone deletion of MADH4 constitutively expressed high endogenous levels of phosphorylated receptor-associated Smad proteins (pR-Smad2 and pR-Smad3), whereas Smad4-positive lines did not. These elevated pR-Smad levels could not be attributed to a decreased dephosphorylation rate nor to increased expression of TGF-beta type I (TbetaR-I) or type II (TbetaR-II) receptors. Although minimal amounts of free bioactive TGF-beta1 and TGF-beta2 were detected in conditioned medium, treatment with a pan-specific (but not a TGF-beta3 specific) TGF-beta-neutralizing antibody and with anti-alpha(V)beta(6) integrin antibody decreased steady-state pSmad2 levels and activation of a TGF-beta-inducible reporter gene in neighboring cells, respectively. Thus, activation of TGF-beta at the cell surface was responsible for the increased autocrine endogenous and paracrine signaling. Blocking TbetaR-I activity using a selective kinase inhibitor (SD-093) strongly decreased the in vitro motility and invasiveness of the pancreatic carcinoma cells without affecting their growth characteristics, morphology, or the subcellular distribution of E-cadherin and F-actin. Moreover, exogenous TGF-beta strongly stimulated in vitro invasiveness of BxPC-3 cells, an effect that could also be blocked by SD-093. Thus, the motile and invasive properties of Smad4-deficient pancreatic cancer cells are at least partly driven by activation of endogenous TGF-beta signaling. Therefore, targeting the TbetaR-I kinase represents a potentially powerful novel therapeutic approach for the treatment of this disease.
Low convergence path to fusion ignition (2016)

Slide 4Consider the Revolver multi-shell class targets 1. Predominantly metal -order 99% by mass 2. Upstream ignition with minimal deceleration to maximize burn fraction and minimize Rayleigh-Taylor disruption of the fuel-pusher interface 3. Mass ratio per stage of order 6 for velocity multiplication > 1.5 4. Fuel convergence C10 and implosion velocity u I < 20 cm/s 5. Reciprocal relationship convergence & implosion velocity: u I C (incompatible with existing, optically thin ignition targets -a defining property of Revolver class capsules) Spherical form of Multi-shell* targets for "Equilibrium Ignition"** --Nested, concentric, spherical, thick, heavy-metal shells; buffer gas between the shells and a central volume filled with DT fuel (probably as a cryogenic liquid) --The shells provide pressure and velocity amplification, radiation trapping (and shielding), and symmetry preservation
Comparison of captive and pulsating bubble surfactometers with use of lung surfactants (1994)

We compared surface tension measures of surfactants with various surface activities by using a pulsating bubble surfactometer (PBS) and a captive bubble surfactometer (CBS). Rabbit lung lavage surfactant (60,000 x average g for 60 min), bovine surfactant extract (Survanta), and a synthetic lipid surfactant mixture (dipalmitoylphosphatidylcholine-egg phosphatidylglycerol-palmitic acid) were studied at 1.25 mg phospholipid/ml. The PBS was used either unmodified according to manufacturer's instructions or with the sample chamber capillary kept dry and the sample adsorbing at maximum bubble size (5 min). The CBS was used in a manner that imitated the unmodified PBS. We found that all three techniques indicated low surface tension on the first cycle for 60K. For Survanta, the CBS and the modified PBS reported low surface tension on the first cycle, whereas the unmodified PBS did not achieve this within 10 cycles. For the synthetic lipid surfactant mixture, only the CBS measured low surface tension within 10 cycles. Video observations indicate that the modified PBS performs better than the unmodified PBS because keeping the capillary dry prevents surface film from occupying this large surface during cycling, thereby allowing larger area compressions.
Well Structure by High-Energy Boron Implantation for Soft-Error Reduction in Dynamic Randam Access Memories (DRAMs) (1995)

The susceptibility against soft-errors in dynamic random access memories (DRAMs) has been evaluated using nuclear microprobes by monitoring various addresses of a memory cell array to determine the influence of upper wiring layers such as word lines, bit lines and other patterns. The correlations between irradiated positions of microprobes and monitored cell positions were discussed. The effect of buried implanted layers against carrier collection has also been investigated using ion-beam-induced-current (IBIC) measurement. IBIC measurement revealed that the retrograde well structure was more effective in suppressing soft errors than conventional well structures in bulk or epitaxial substrates.
EPIZOOTIC VENEZUELAN EQUINE ENCEPHALOMYELITIS IN CENTRAL AMERICA. DISEASE PATTERN AND VACCINE EVALUATION IN NICARAGUA, 1969–19701 (1972)

During an epizootic of Venezuelan equine encephalomyelitis (VEE) in Nicaragua, 1969–1970, serologic studies on horses and cows and an evaluation of the TC-83 attenuated vaccine were initiated. Most Equidae in the Pacific littoral lacked neutralizing antibody to VEE virus. Vaccination stimulated the production of antibody detectable with the plaque neutralization test in 93% of the horses studied. As a result, it appears that the course and direction of a major epizootic were significantly altered. Cattle failed to develop neutralizing antibody suggesting that transmission of vaccine virus did not occur. VEE antigenic subtype I-B, identical to strains isolated elsewhere in Central America, was recovered from two horses.