gebhart/patrepeval huggingface dataset:
Defined transversion mutations at a specific position in DNA using synthetic oligodeoxyribonucleotides as mutagens (1979)

The oligodeoxyribonucleotides, pCCCAGCCTCAA, which is complementary to nucleotides 5274--4284 of bacteriophage phi X174 viral DNA , and pCCCAGCCTAAA, which corresponds to the same sequence with a C leads to A change at the ninth nucleotide, were synthesized enzymatically. The second of these oligonucleotides was used as a primer for E. coli DNA polymerase I, from which the 5'-exonculease has been removed by proteolysis (Klenow enzyme), on wild-type phi X174 viral DNA template. After ligation, this yielded closed circular heteroduplex DNA with a G, A mismatch at nucleotide 5276. Transfection of E. coli spheroplasts with the heteroduplex DNA produced phage mutated at this nucleotide (G leads to T in the viral DNA) with high efficiency (13%). The mutant DNA, which corresponds to the gene B mutant am16, was reverted (T leads to G) by the wild type oligonucleotide with an efficiency of 19%. The nucleotide changes were established by sequence determination of the mutated viral DNA using the enzymatic terminator method. The production of specific transversion mutations, together with a previous demonstration of specific transition mutations (1), established that short enzymatically synthesized oligodeoxyribonucleotides can be used to induce any class of single nucleotide replacement with high efficiency and thus provide a powerful tool for specific genetic manipulations in circular genomes like that of phi X174.
Method for efficient fast spin echo Dixon imaging (2002)

In order to satisfy the Carr-Purcell-Meiboom-Gill (CPMG) condition, echo shift as dictated in fast-spin-echo (FSE)-based Dixon imaging was previously achieved by applying a time shift to the readout gradient and the data acquisition window. Accordingly, interecho spacing is increased, which entails increased image blurring and, in multislice imaging, a significant reduction in the slice coverage for a given imaging time. In this work, a new method is developed by which the echo shift is induced by "sandwiching" in time the readout gradient with a pair of small gradients of equal area and of opposite polarity. While data with non-zero phase shifts between water and fat signals are collected as fractional echoes, no increase in echo spacing is necessary with the modified acquisition strategy, and increased time efficiency is therefore achieved. In order to generate separate water-only and fat-only images in data processing, a set of low-resolution images are first reconstructed from the central symmetric portion (either 128 x 128 or 64 x 64) of the acquired multipoint Dixon data. High-resolution images using all the acquired data, including some partial Fourier-reconstructed images, are then phase demodulated using the phase errors determined from the low-resolution images. The feasibility of the technique is demonstrated using a water and fat phantom as well as in clinical patient imaging.
Genetic interactions between Hoxa1 and Hoxb1 reveal new roles in regulation of early hindbrain patterning (1998)

In the developing vertebrate hindbrain Hoxa1 and Hoxb1 play important roles in patterning segmental units (rhombomeres). In this study, genetic analysis of double mutants demonstrates that both Hoxa1 and Hoxb1 participate in the establishment and maintenance of Hoxb1 expression in rhombomere 4 through auto- and para-regulatory interactions. The generation of a targeted mutation in a Hoxb1 3' retinoic acid response element (RARE) shows that it is required for establishing early high levels of Hoxb1 expression in neural ectoderm. Double mutant analysis with this Hoxb1(3'RARE) allele and other targeted loss-of-function alleles from both Hoxa1 and Hoxb1 reveals synergy between these genes. In the absence of both genes, a territory appears in the region of r4, but the earliest r4 marker, the Eph tyrosine kinase receptor EphA2, fails to be activated. This suggests a failure to initiate rather than maintain the specification of r4 identity and defines new roles for both Hoxb1 and Hoxa1 in early patterning events in r4. Our genetic analysis shows that individual members of the vertebrate labial-related genes have multiple roles in different steps governing segmental processes in the developing hindbrain.
SerratiaProtease (1971)

Journal Article Serratia Protease: Part III. Characteristics of the Enzyme as Metalloenzyme Get access Kouichi Miyata, Kouichi Miyata Microbiological Research Laboratories, Research and Development Division, Takeda Chemical Industries, Ltd., Osaka Search for other works by this author on: Oxford Academic Google Scholar Katsumi Tomoda, Katsumi Tomoda Microbiological Research Laboratories, Research and Development Division, Takeda Chemical Industries, Ltd., Osaka Search for other works by this author on: Oxford Academic Google Scholar Masao Isono Masao Isono Microbiological Research Laboratories, Research and Development Division, Takeda Chemical Industries, Ltd., Osaka Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 35, Issue 4, 1 April 1971, Pages 460–467, https://doi.org/10.1080/00021369.1971.10859949 Published: 01 April 1971 Article history Received: 22 July 1970 Published: 01 April 1971
Autistic children exhibit distinct plasma amino acid profile. (2013)

In order to ascertain whether autistic children display characteristic metabolic signatures that are of diagnostic value, plasma amino acid analyses were carried out on a cohort of 138 autistic children and 138 normal controls using reverse-phase HPLC. Pre-column derivatization of amino acids with phenyl isothiocyanate forms phenyl thio-carbamate derivates that have a lamba(max) of 254 nm, enabling their detection using photodiode array. Autistic children showed elevated levels of glutamic acid (120 +/- 89 vs. 83 +/- 35 micromol/L) and asparagine (85 +/- 37 vs. 47 +/- 19 micromol/L); lower levels of phenylalanine (45 +/- 20 vs. 59 +/- 18 micromol/L), tryptophan (24 +/- 11 vs. 41 +/- 16 micromol/L), methionine (22 +/- 9 vs. 28 +/- 9 micromol/L) and histidine (45 +/- 21 vs. 58 +/- 15 micromol/L). A low molar ratio of (tryptophan/large neutral amino acids) x 100 was observed in autism (5.4 vs 9.2), indicating lesser availability of tryptophan for neurotransmitter serotonin synthesis. To conclude, elevated levels of excitatory amino acids (glutamate and asparagine), decreased essential amino acids (phenylalanine, tryptophan and methionine) and decreased precursors of neurotransmitters (tyrosine and tryptophan) are the distinct characteristics of plasma amino acid profile of autistic children. Thus, such metabolic signatures might be useful tools for early diagnosis of autism.
High affinity human antibodies by phage display (1997)

The development of phage display has now made it possible to consider the isolation of human antibodies directly without immunization. Recent advances in the field of human immunogenetics and in phage technology have led to the assembly of 'naive' human repertoires in vitro whose complexity approach that of the natural immune system. Screening of these libraries has allowed the isolation in one step of antibodies with affinities in the nanomolar range.
Microbial Biodiversity: Approaches to Experimental Design and Hypothesis Testing in Primary Scientific Literature from 1975 to 1999 (2002)

Research interest in microbial biodiversity over the past 25 years has increased markedly as microbiologists have become interested in the significance of biodiversity for ecological processes and as the industrial, medical, and agricultural applications of this diversity have evolved. One major challenge for studies of microbial habitats is how to account for the diversity of extremely large and heterogeneous populations with samples that represent only a very small fraction of these populations. This review presents an analysis of the way in which the field of microbial biodiversity has exploited sampling, experimental design, and the process of hypothesis testing to meet this challenge. This review is based on a systematic analysis of 753 publications randomly sampled from the primary scientific literature from 1975 to 1999 concerning the microbial biodiversity of eight habitats related to water, soil, plants, and food. These publications illustrate a dominant and growing interest in questions concerning the effect of specific environmental factors on microbial biodiversity, the spatial and temporal heterogeneity of this biodiversity, and quantitative measures of population structure for most of the habitats covered here. Nevertheless, our analysis reveals that descriptions of sampling strategies or other information concerning the representativeness of the sample are often missing from publications, that there is very limited use of statistical tests of hypotheses, and that only a very few publications report the results of multiple independent tests of hypotheses. Examples are cited of different approaches and constraints to experimental design and hypothesis testing in studies of microbial biodiversity. To prompt a more rigorous approach to unambiguous evaluation of the impact of microbial biodiversity on ecological processes, we present guidelines for reporting information about experimental design, sampling strategies, and analyses of results in publications concerning microbial biodiversity.
Cytokine blocking agents in dermatology (2002)

Cytokines are intercellular messengers that have an important role in the development and maintenance of cutaneous inflammation. The primacy of cytokines in eliciting cutaneous immune responses makes them a highly attractive target for new biological response modifiers. Targeting of cytokines is still in its infancy for therapy of skin disease. However, blocking tumour necrosis factor alpha by infliximab or etanercept has shown particular promise, especially in the management of psoriasis. Anecdotally, this approach is also effective for a variety of dermatological conditions including pyoderma gangrenosum and Behçet's syndrome. We review the current and prospective roles of cytokine blocking agents in the treatment of skin disease.
Glucocorticoid Regulation of Alkaline Phosphatase in the Osteoblastic Osteosarcoma Cell Line ROS 17/2.8* (1985)

Dexamethasone increased alkaline phosphatase levels up to 7-fold in the osteoblast-like rat osteosarcoma cell line ROS 17/2.8. This effect was associated with reduced cell growth and took place over several days in culture. The increase in enzyme activity was dose dependent, (half-maximum near 1 nM, with a hormone specificity suggesting glucocorticoid receptor mediation). Dexamethasone also increased enzyme activity in ROS 2/3 cells, but not in two nonosteoblastic osteosarcoma cell lines, indicating that among these cell lines, the effect is specific for osteoblast-like cells. Moreover, enzyme activity in both control and dexamethasone-treated cells correlated directly with levels of radioimmunoassayable bone-type isoenzyme. Increases in alkaline phosphatase activity in response to dexamethasone were detectable after about 5 h and were inhibited by both actinomycin D and cycloheximide. Thus glucocorticoids appear to increase de novo enzyme synthesis in ROS 17/2.8 cells. Finally, the cAMP-elevating agents PTH, isoproterenol, and 8-bromo-cAMP, which were previously shown to reduce alkaline phosphatase activity in osteoblast-like cells, antagonized the effects of dexamethasone. Moreover, in the presence of dexamethasone, lower concentrations of these agents were required for inhibitory effects on alkaline phosphatase.
Histocompatible Miniature Pig (d/d Haplotype): Generation of Hybridomas Secreting A or M Monoclonal Antibody (1991)

Two Hypoxanthine/Aminopterin/Thymidine-sensitive cell sublines (L142 and L231) have been derived from independent lymphoblastoid cell lines of B lineage. After propagation for more than 100 population doublings (1 year) in culture, these cells still retained a doubling time between 19 to 20 hours, near diploïdy and relatively low (L142) and high (L231) secretion rate of M immunoglobulins. Near diploid hybrid cells were easily generated with leukocytes from the spleen, the gut lamina propria or the mesenteric lymph nodes of pigs immunized against the transmissible gastroenteritis virus. Both the tumor sublines and the B cells were derived from histocompatible miniature pigs (d/d haplotype). Demonstration of fusion between the tumor sublines and B-cells was supported by the selection of hybridomas making the antigen-specific heavy (alpha isotype) and light chains from the B cell parent as well as the heavy and light chains of the lymphoblastoid parent. Moreover, some hybridomas were found to secrete only class A (dimeric) or class M immunoglobulins (0.2-10 micrograms/ml). Forty hybridomas secreted antibodies reactive in a virus-enzyme-linked cell immunoassay against cell-bound antigens and two were found to produce an antibody active only against the infected cell monolayer. Construction of intraspecies hybridoma can be used to perpetuate lymphocyte subsets useful for the study of the porcine immune system.
A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome (2017)

Vibrio cholerae-specific bacteriophages are common features of the microbial community during cholera infection in humans. Phages impose strong selective pressure that favors the expansion of phage-resistant strains over their vulnerable counterparts. The mechanisms allowing virulent V. cholerae strains to defend against the ubiquitous threat of predatory phages have not been established. Here, we show that V. cholerae PLEs (phage-inducible chromosomal island-like elements) are widespread genomic islands dedicated to phage defense. Analysis of V. cholerae isolates spanning a 60-year collection period identified five unique PLEs. Remarkably, we found that all PLEs (regardless of geographic or temporal origin) respond to infection by a myovirus called ICP1, the most prominent V. cholerae phage found in cholera patient stool samples from Bangladesh. We found that PLE activity reduces phage genome replication and accelerates cell lysis following ICP1 infection, killing infected host cells and preventing the production of progeny phage. PLEs are mobilized by ICP1 infection and can spread to neighboring cells such that protection from phage predation can be horizontally acquired. Our results reveal that PLEs are a persistent feature of the V. cholerae mobilome that are adapted to providing protection from a single predatory phage and advance our understanding of how phages influence pathogen evolution.
Formation and Size Control of Silver Nanoparticles by Laser Ablation in Aqueous Solution (2000)

Silver nanoparticles were produced by laser ablation of a metal silver plate in an aqueous solution of sodium dodecyl sulfate, C12H25OSO3Na. The absorption spectrum of the silver nanoparticles is found to be essentially the same as that of silver nanoparticles chemically prepared in a solution. The size distribution of the nanoparticles measured by an electron microscope shifts to a smaller size with increase in the concentration of sodium dodecyl sulfate and with a decrease in the irradiation laser power. These findings are explained by a scheme that the nanoparticles are formed via rapid formation of an embryonic silver particle and a consecutive slow particle growth in competition with termination of the growth due to SDS coating on the particle.
Synthesis and Evaluation of New Thiodigalactoside‐Based Chemical Probes to Label Galectin‐3 (2009)

New chemical probes were synthesized to label galectin-3. They are based on the high affinity thiodigalactoside ligand. The probes were synthesized with benzophenone or acetophenone moieties as the photolabel for covalent attachment to the protein. Besides labeling the protein, these aromatic photolabels also greatly enhance the affinity of the probes towards galectin-3, due to the interaction of the photolabel with two arginine guanidinium groups of the protein. The linkage between the sugar and the photolabel was varied as an ester, an amide, and a triazole. For the amide and triazole derivatives, a versatile synthetic route towards a symmetrical 3-azido-3-deoxy-thiodigalactoside was developed. The new probes were evaluated for their binding affinity of human galectin-3. They were subsequently tested for their labeling efficiency, as well as specificity in the presence of a protein mixture and a human cancer cell lysate.
Bridged Polysilsesquioxanes. Molecular-Engineered Hybrid Organic−Inorganic Materials (2001)

The class of hybrid organic−inorganic materials called bridged polysilsesquioxanes are used for everything from surface modifiers and coatings to catalysts and membrane materials. This paper examines how bridged polysilsesquioxanes are prepared, processed, characterized, and used. In particular, it describes how attaching several “inorganic” cross-linking trialkoxysilanes on organic bridging groups permits facile formation of network polymers and gels with high levels of chemical functionality. There are a number of synthetic entries into bridged polysilsesquioxane monomers that have allowed a multitude of different bridging groups to be integrated into xerogels (dry gels) or aerogels (supercritically dried “air gels”). Much of the research to date has been successfully focused on engineering of the size of pores through the choice of the bridging groups. For example, materials with some of the highest known surface areas in porous materials have been prepared, and parameters allowing control of the pore size distributions are well understood. More recently, however, the focus has shifted to building functionality into the bridging groups to make materials with controlled porosity that are capable of selective adsorption or catalysis or electronic and optic effects. This is the area where the full potential of bridged polysilsesquioxanes as molecular-engineered materials is being explored.
Automated Quantitative Plaque Burden from Coronary CT Angiography Noninvasively Predicts Hemodynamic Significance by using Fractional Flow Reserve in Intermediate Coronary Lesions (2015)

Compared with stenosis grading, automatic quantification of total, noncalcified, and low-attenuation noncalcified plaque burden substantially improves determination of lesion-specific hemodynamic significance by FFR in patients with intermediate coronary lesions.
Interactions between polyomavirus medium T antigen and three cellular proteins of 88, 61, and 37 kilodaltons (1987)

Affinity-purified medium T antigen of wild-type polyomavirus and dl8, a transforming mutant with a deletion in the medium T gene, is associated with three cellular proteins with apparent molecular weights of 88,000 (88K protein), 61,000 (61K protein), and 37,000 (37K protein). Medium T antigen encoded by the nontransforming hrt mutants fails to associate with these proteins, whereas medium T antigen of the nontransforming mutant dl1015 is able to do so. Medium T antigen of the nontransforming mutant dl23 binds to the 61K and 37K proteins; however, binding to the 88K protein is uncertain. The pattern of complex formation between these proteins and medium T antigen resembles that of pp60c-src and medium T antigen. The binding of medium T antigen to the 88K, 61K, and 37K proteins, as well as to pp60c-src, might represent a necessary but insufficient step in transformation. By mixing extracts from infected and uninfected cells, complex formation between medium T antigen and the 88K, 61K, and 37K proteins can be demonstrated in vitro. Pulse-chase experiments indicated that in vivo the association between medium T antigen and the 61K and 37K proteins is a slow process. The latter two proteins are probably bound to each other in uninfected cells. On two-dimensional gels of whole-cell extract, the 61K protein comigrated with a minor protein with an isoelectric point of 5.2. The 61K protein was neither phosphorylated nor glycosylated. Polyomavirus tumor serum precipitated the 61K and 37K proteins independently of medium T antigen. Therefore, the 61K protein or the 37K protein or both have the properties of a cellular tumor antigen.
Excluding Pulmonary Embolism at the Bedside without Diagnostic Imaging: Management of Patients with Suspected Pulmonary Embolism Presenting to the Emergency Department by Using a Simple Clinical Model and d-dimer (2001)

Managing patients for suspected pulmonary embolism on the basis of pretest probability and D -dimer result is safe and decreases the need for diagnostic imaging.
High-Resolution Genotyping by Amplicon Melting Analysis Using LCGreen (2003)

High-resolution melting analysis of PCR products amplified in the presence of LCGreen can identify both heterozygous and homozygous sequence variants. The technique requires only the usual unlabeled primers and a generic double-stranded DNA dye added before PCR for amplicon genotyping, and is a promising method for mutation screening.
Cellular Localization of Gene Expression for Progranulin (2000)

Granulins, also called epithelins, are 6-kD peptides with growth modulatory effects on a variety of cells. The granulin/epithelin precursor supports tumorigenesis in appropriate cell models and is the only growth factor able to overcome the cell cycle block that occurs in murine fibroblasts after deletion of a functional IGF-1 receptor. However, little is known of the role of granulin/epithelin gene products in vivo. To understand the physiological role of granulins it is essential to know the cell types and conditions in which it is expressed. We examined granulin/epithelin gene expression in adult rodents by in situ hybridization. The granulin/epithelin precursor is constitutively expressed in a number of epithelia, particularly in the skin, GI tract, and reproductive system. Other epithelia express the gene less strongly. Progranulin is expressed in immune cells in vivo and in specific neurons in the brain, including Purkinje cells, pyramidal cells of the hippocampus, and some cerebral cortical neurons. Little expression was detected in muscle cell, connective tissue, or endothelium. Cumulatively, these results define the basal gene expression of a new growth factor system and suggest that the progranulin/epithelin gene is multifunctional, with important constitutive roles in epithelial homeostasis, reproductive, immunological, and neuronal function.
Seroepidemiology of water-borne hepatitis in India and evidence for a third enterically-transmitted hepatitis agent. (1994)

Many epidemics of water-borne hepatitis have occurred throughout India. These were thought to be epidemics of hepatitis A until 1980, when evidence for an enterically transmitted non-A, non-B hepatitis was first reported. Subsequently, hepatitis E virus was discovered and most recent epidemics of enterically transmitted non-A, non-B hepatitis have been attributed to hepatitis E virus infection. However, only a limited number of cases have been confirmed by immuno electron microscopy, polymerase chain reaction, or seroconversion. In the present study we have performed a retrospective seroepidemiologic study of 17 epidemics of water-borne hepatitis in India. We have confirmed that 16 of the 17 epidemics were caused at least in part by serologically closely related hepatitis E viruses. However, one epidemic, in the Andaman Islands, and possibly a significant minority of cases in other epidemics, appears to have been caused by a previously unrecognized hepatitis agent.