gebhart/patrepeval huggingface dataset:
An rpsL Cassette, Janus, for Gene Replacement through Negative Selection in Streptococcus pneumoniae (2001)

Natural genetic transformation offers a direct route by which synthetic gene constructs can be placed into the single circular chromosome of Streptococcus pneumoniae. However, the lack of a general negative-selection marker has hampered the introduction of constructs that do not confer a selectable phenotype. A 1.3-kb cassette was constructed comprising a kanamycin (Kn) resistance marker (kan) and a counterselectable rpsL(+) marker. The cassette conferred dominant streptomycin (Sm) sensitivity in an Sm-resistant background in S. pneumoniae. It was demonstrated that it could be used in a two-step transformation procedure to place DNA of arbitrary sequence at a chosen target site. The first transformation into an Sm-resistant strain used the cassette to tag a target gene on the chromosome by homologous recombination while conferring Kn resistance but Sm sensitivity on the recombinant. Replacement of the cassette by an arbitrary segment of DNA during a second transformation restored Sm resistance (and Kn sensitivity), allowing construction of silent mutations and deletions or other gene replacements which lack a selectable phenotype. It was also shown that gene conversion occurred between the two rpsL alleles in a process that depended on recA and that was susceptible to correction by mismatch repair.
Ig V Gene Mutation Status and CD38 Expression As Novel Prognostic Indicators in Chronic Lymphocytic Leukemia (1999)

Cellular immunophenotypic studies were performed on a cohort of randomly selected IgM(+) B-chronic lymphocytic leukemia (B-CLL) cases for which Ig V(H) and V(L) gene sequences were available. The cases were categorized based on V gene mutation status and CD38 expression and analyzed for treatment history and survival. The B-CLL cases could be divided into 2 groups. Those patients with unmutated V genes displayed higher percentages of CD38(+) B-CLL cells (>/=30%) than those with mutated V genes that had lower percentages of CD38(+) cells (<30%). Patients in both the unmutated and the >/=30% CD38(+) groups responded poorly to continuous multiregimen chemotherapy (including fludarabine) and had shorter survival. In contrast, the mutated and the <30% CD38(+) groups required minimal or no chemotherapy and had prolonged survival. These observations were true also for those patients who stratified to the Rai intermediate risk category. In the mutated and the <30% CD38(+) groups, males and females were virtually equally distributed, whereas in the unmutated and the >/=30% CD38(+) groups, a marked male predominance was found. Thus, Ig V gene mutation status and the percentages of CD38(+) B-CLL cells appear to be accurate predictors of clinical outcome in B-CLL patients. These parameters, especially CD38 expression that can be analyzed conveniently in most clinical laboratories, should be valuable adjuncts to the present staging systems for predicting the clinical course in individual B-CLL cases. Future evaluations of new therapeutic strategies and drugs should take into account the different natural histories of patients categorized in these manners.
Minireview: Thioredoxin-Interacting Protein: Regulation and Function in the Pancreatic β-Cell (2014)

Pancreatic β-cells are responsible for insulin production, and loss of functional β-cell mass is now recognized as a critical step in the pathogenesis of both type 1 and type 2 diabetes. However, the factors controlling the life and death of the pancreatic β-cell have only started to be elucidated. Discovered as the top glucose-induced gene in a human islet microarray study 12 years ago, thioredoxin-interacting protein (TXNIP) has now emerged as such a key player in pancreatic β-cell biology. Since then, β-cell expression of TXNIP has been found to be tightly regulated by multiple factors and to be dramatically increased in diabetic islets. Elevated TXNIP levels induce β-cell apoptosis, whereas TXNIP deficiency protects against type 1 and type 2 diabetes by promoting β-cell survival. TXNIP interacts with and inhibits thioredoxin and thereby controls the cellular redox state, but it also belongs to the α-arrestin family of proteins and regulates a variety of metabolic processes. Most recently, TXNIP has been discovered to control β-cell microRNA expression, β-cell function, and insulin production. In this review, the current state of knowledge regarding regulation and function of TXNIP in the pancreatic β-cell and the implications for drug development are discussed.
COMPLEXES (1989)

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Free‐Standing Ultrathin Ceramic Foils (2010)

Ceramic thin films are used in various applications for their structural or functional properties. Below a thickness of approximately 25 μm, ceramic films are typically deposited, sintered, and used on a supporting substrate due to their fragility. Here, we present a set of easy and versatile green film deposition and sintering techniques that allow the fabrication of free‐standing micrometer‐thin alumina and yttria‐stabilized zirconia foils. Because of their extremely low thickness, the foils were transparent and flexible but still strong enough that they were self‐supporting and could be handled manually. The presented concepts are not limited to the materials used here and can potentially be extended to most ceramic materials and glasses. So prepared free‐standing ultrathin ceramic foils allow new assembly and fabrication methods of devices and novel materials that contain thin ceramic membranes.
Macrophages and inflammatory damage in spinal cord injury. (1992)

Disruption of myelinated nerve fibers usually constitutes the most significant damage contributing to chronic neurologic deficits in severe spinal cord injuries. Inflammatory responses form one facet of a wide array of pathologic phenomena that combined to produce this damage. The therapeutic importance of inflammation is amplified by its delayed time-course and the number of different approaches that may be taken to its modulation. The response to trauma involves two significant waves of cellular infiltration: the first, dominated by polymorphonuclear leukocytes, peaks within a few hours; the second, by macrophages, begins after 1-2 days and reaches a peak at 5-7 days. Secondary demyelination of surviving nerve fibers and delayed loss of axons coincide with the macrophage response, and may be an example of "bystander damage" caused by the cytotoxic products of activated phagocytes. We know relatively few details of this delayed pathologic change, even in animal models. In particular, it is difficult to separate potential beneficial effects of macrophages in removing cellular debris, stimulating tissue revascularization and repair of the central nervous system environment, from the potential destructive effects associated with their phagocytic activity and their stimulation of scar formation through the release of factors that induce proliferation of peripheral cellular components within the injured spinal cord.
<title>Multispectral edge detection by relaxation algorithm</title> (1996)

In this paper, we propose an algorithm which detects boundaries of objects from a color image. The result of this method is a binary image where the boundary points are only represented. A lot of methods of edge detection from color images have been developed before. One of the most efficient ones is based on vectorial computations of the tristimuli R, G, B. But, in the case of complex color images, it is difficult to automatically determine a global threshold, in order to find the boundary pixels. For this reason, we suggest a local thresholding algorithm, using co-operating relaxation process to enhance edge probabilities. The labeling relaxation algorithm processes probabilities which are the result of a gradient application to the different features of the color images. So, this algorithm is able to detect edges from a slope of intensity, saturation or hue. The relaxation algorithm analyzes four classes of pixels. Three classes represent a gradient filter output of the three color image features, R, G, B. At each pixel, the higher the response of a feature value, the higher the probability of the pixel to belong to the class corresponding to this feature. The last label represents the no edge pixel, whose probability to belong to it is computed with the probabilities of the three other ones. For each pixel, the sum of the four probabilities must be equal to 1. The process is iterated as many times as the probability of each pixel to belong to the no edge class is near 0 or 1. We consider that a pixel with a low probability to belong to no edge class represents an edge pixel. The efficacy of the relaxation algorithm depends on the choice of the compatibility coefficients. We propose to compute these coefficients with the initial probabilities of the pixels to belong to the four classes, by the evaluation of the neighboring mutual information between two classes. The compatibility coefficients definition is based on the mutual information of the classes at neighboring points. The presented method has been successfully tested on complex color images and compared with the classic edge detection methods. We show that this local segmentation method is better than a global one.
Structure-Function Relationships in an Antifreeze Polypeptide (1993)

We have proposed that the antifreeze activity of an alanine-rich a-helical antifreeze polypeptide (AFP) is due in part to side-by-side hydrophobic interactions of AFP molecules bound on the ice surface (Wen, D., and Laursen, R. A. (1992b) Biophye. J. 63, 1669-1662). To test this hypothesis and to assess the importance of a hydrophobic surface on the outward facing (non-icebinding) portions of the helix, we synthesized several AFP analogs with up to four Ala + Gln or Ala - Leu replacements and determined the effect of these changes on antifreeze activity and helix stability. Although Gln replacements caused some helix destabilization and resultant reduction of antifreeze activity, they were in general well tolerated, suggesting that the bulk hydrophobicity of the non-ice-binding faces of the AFP, per se, is probably not a major factor determining AFP activity. However, placement of either Gln or Leu in position 17 on one side of the helix completely abolished activity, demonstrating that the specific location of bulky groups can dramatically alter activity. We conclude from molecular modeling studies that the effect seen by placing bulky groups in position 17 is due to steric hindrance that prevents effective association or packing of AFP molecules on the ice surface, in support of our hypothesis.
Insulin restores neuronal nitric oxide synthase expression and function that is lost in diabetic gastropathy (2000)

Gastrointestinal dysfunction is common in diabetic patients. In genetic (nonobese diabetic) and toxin-elicited (streptozotocin) models of diabetes in mice, we demonstrate defects in gastric emptying and nonadrenergic, noncholinergic relaxation of pyloric muscle, which resemble defects in mice harboring a deletion of the neuronal nitric oxide synthase gene (nNOS). The diabetic mice manifest pronounced reduction in pyloric nNOS protein and mRNA. The decline of nNOS in diabetic mice does not result from loss of myenteric neurons. nNOS expression and pyloric function are restored to normal levels by insulin treatment. Thus diabetic gastropathy in mice reflects an insulin-sensitive reversible loss of nNOS. In diabetic animals, delayed gastric emptying can be reversed with a phosphodiesterase inhibitor, sildenafil. These findings have implications for novel therapeutic approaches and may clarify the etiology of diabetic gastropathy.
Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. (1988)

We have constructed a restriction fragment length polymorphism linkage map for the nuclear genome of the flowering plant Arabidopsis thaliana. The map, containing 90 randomly distributed molecular markers, is physically very dense; greater than 50% of the genome is within 1.9 centimorgans, or approximately 270 kilobase pairs, of the mapped DNA fragments. The map was based on the meiotic segregation of markers in two different crosses. The restriction fragment length polymorphism linkage groups were integrated with the five classically mapped linkage groups by virtue of mapped mutations included in these crosses. Markers consist of both cloned Arabidopsis genes and random low-copy-number genomic DNA clones that are able to detect polymorphisms with the restriction enzymes EcoRI, Bgl II, and/or Xba I. These cloned markers can serve as starting points for chromosome walking, allowing for the isolation of Arabidopsis genes of known map location. The restriction fragment length polymorphism map also can associate clones of unknown gene function with mutant phenotypes, and vice versa.
Survey of n- 3 and n-6 polyunsaturated fatty acids in fish and fish products (2012)

Since fish species vary with respect to their n-3 LC PUFA contents, eating a variety of fish is advisable. High n-6 PUFA containing pre-fried fish support the imbalance of n-3/n-6 ratio in the Western diet. Thus, consumption of pure fish fillets is to be favoured. The lower n-3 PUFA portion in farmed fish can be offset by the higher fat content, however, with an unfavourable FA distribution compared to wild fellows.
Studies on the opening of dioxanone and acetal templates and application to the synthesis of 1.alpha.,25-dihydroxyvitamin D2 (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on the opening of dioxanone and acetal templates and application to the synthesis of 1.alpha.,25-dihydroxyvitamin D2Juan R. Granja, Luis Castedo, and Antonio MourinoCite this: J. Org. Chem. 1993, 58, 1, 124–131Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/jo00053a024https://doi.org/10.1021/jo00053a024research-articleACS PublicationsRequest reuse permissionsArticle Views310Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The Bacillus stearothermophilus Mannitol Regulator, MtlR, of the Phosphotransferase System (1999)

D-Mannitol is taken up by Bacillus stearothermophilus and phosphorylated via a phosphoenolpyruvate-dependent phosphotransferase system (PTS). The genes involved in the mannitol uptake were recently cloned and sequenced. One of the genes codes for a putative transcriptional regulator, MtlR. The presence of a DNA binding helix-turn-helix motif and two antiterminator-like PTS regulation domains, suggest that MtlR is a DNA-binding protein, the activity of which can be regulated by phosphorylation by components of the PTS. To demonstrate DNA binding of MtlR to a region upstream of the mannitol promoter, by DNA footprinting, MtlR was overproduced and purified. EI, HPr, IIAmtl, and IICBmtl of B. stearothermophilus were purified and used to demonstrate that MtlR can be phosphorylated and regulated by HPr and IICBmtl, in vitro. Phosphorylation of MtlR by HPr increases the affinity of MtlR for its binding site, whereas phosphorylation by IICBmtl results in a reduction of this affinity. The differential effect of phosphorylation, by two different proteins, on the DNA binding properties of a bacterial transcriptional regulator has not, to our knowledge, been described before. Regulation of MtlR by two components of the PTS is an example of an elegant control system sensing both the presence of mannitol and the need to utilize this substrate.
Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase (2005)

Double-stranded RNA (dsRNA) has been shown to be a useful tool for silencing genes in zebrafish (Danio rerio), while the blocking specificity of dsRNA is still of major concern for application. It was reported that siRNA (small interfering RNA) prepared by endoribonuclease digestion (esiRNA) could efficiently silence endogenous gene expression in mammalian embryos. To test whether esiRNA could work in zebrafish, we utilized Escherichia coli RNaseIII to digest dsRNA of zebrafish no tail (ntl), a mesoderm determinant in zebrafish and found that esi-ntl could lead to developmental defects, however, the effective dose was so close to the toxic dose that esi-ntl often led to non-specific developmental defects. Consequently, we utilized SP6 RNA polymerase to produce si-ntl, siRNA designed against ntl, by in vitro transcription. By injecting in vitro synthesized si-ntl into zebrafish zygotes, we obtained specific phenocopies of reported mutants of ntl. We achieved up to a 59%no tail phenotype when the injection concentration was as high as 4 microg/microL. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) and whole-mount in situ hybridization analysis showed that si-ntl could largely and specifically reduce mRNA levels of the ntl gene. As a result, our data indicate that esiRNA is unable to cause specific developmental defects in zebrafish, while siRNA should be an alternative for downregulation of specific gene expression in zebrafish in cases where RNAi techniques are applied to zebrafish reverse genetics.
Categorical Data Analysis (1991)

categorical data analysis , categorical data analysis , کتابخانه مرکزی دانشگاه علوم پزشکی تهران
Resistance to respiratory syncytial virus (RSV) challenge induced by infection with a vaccinia virus recombinant expressing the RSV M2 protein (Vac-M2) is mediated by CD8+ T cells, while that induced by Vac-F or Vac-G recombinants is mediated by antibodies (1992)

It was previously demonstrated that the vaccinia virus recombinants expressing the respiratory syncytial virus (RSV) F, G, or M2 (also designated as 22K) protein (Vac-F, Vac-G, or Vac-M2, respectively) induced almost complete resistance to RSV challenge in BALB/c mice. In the present study, we sought to identify the humoral and/or cellular mediators of this resistance. Mice were immunized by infection with a single recombinant vaccinia virus and were subsequently given a monoclonal antibody directed against CD4+ or CD8+ T cells or gamma interferon (IFN-gamma) to cause depletion of effector T cells or IFN-gamma, respectively, at the time of RSV challenge (10 days after immunization). Mice immunized with Vac-F or Vac-G were completely or almost completely resistant to RSV challenge after depletion of both CD4+ and CD8+ T cells prior to challenge, indicating that these cells were not required at the time of virus challenge for expression of resistance to RSV infection induced by the recombinants. In contrast, the high level of protection of mice immunized with Vac-M2 was completely abrogated by depletion of CD8+ T cells, whereas depletion of CD4+ T cells or IFN-gamma resulted in intermediate levels of resistance. These results demonstrate that antibodies are sufficient to mediate the resistance to RSV induced by the F and G proteins, whereas the resistance induced by the M2 protein is mediated primarily by CD8+ T cells, with CD4+ T cells and IFN-gamma also contributing to resistance.
Nucleosides of 2-Fluoroadenine (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleosides of 2-FluoroadenineJohn Montgomery and Kathleen HewsonCite this: J. Med. Chem. 1969, 12, 3, 498–504Publication Date (Print):May 1, 1969Publication History Published online23 September 2003Published inissue 1 May 1969https://pubs.acs.org/doi/10.1021/jm00303a605https://doi.org/10.1021/jm00303a605research-articleACS PublicationsRequest reuse permissionsArticle Views564Altmetric-Citations122LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A Cholesky Decomposition of the Inverse of Covariance Matrix (2003)

A recursive procedure for finding the Cholesky root of the inverse of sample covariance matrix, leading to a direct solution for the inverse of a positive definite matrix, is developed using the likelihood equation for the maximum likelihood estimation of the Cholesky root under normality assumptions. An example of the Hilbert matrix is considered for an illustration of the procedure.
Twists and turns in the development and maintenance of the mammalian small intestine epithelium (2005)

Experimental studies during the last decade have revealed a number of signaling pathways that are critical for the development and maintenance of the intestinal epithelium and that demonstrate the molecular basis for a variety of diseases. The Notch-Delta, Wnt, Hedge Hog, TGF-beta, and other signaling pathways have been shown to form and steadily maintain the crypt-villus system, generating the proper quantities of highly-specialized cells, and ultimately defining the architectural shape of the system. Based on the characterized phenotypes and functional defects of mice resulting from various targeted knockouts, and overexpression and misexpressions of genes, a picture is emerging of the sequence of gene expression events from within the epithelium, and in the underlying mesenchyme that contribute to the regulation of cell differentiation and proliferation. This review focuses on the contributions of multiple signaling pathways to intestinal epithelial proliferation, differentiation, and structural organization, as well as the possible opportunities for cross-talk between pathways. The Notch pathway's potential ability to maintain and regulate the intestinal epithelial stem cell is discussed, in addition to its role as the primary mediator of lineage specification. Recent research that has shed light on the function of Wnt signaling and epithelial-mesenchymal cross-talk during embryonic and postnatal development is examined, along with data on the interplay of heparan sulfate proteoglycans in the signaling process.