gebhart/patrepeval huggingface dataset:
Isolation of transformation-deficient Streptococcus pneumoniae mutants defective in control of competence, using insertion-duplication mutagenesis with the erythromycin resistance determinant of pAM beta 1 (1984)

Several transformation-deficient mutants of Streptococcus pneumoniae were isolated after insertion-duplication mutagenesis. Mutagenesis was accomplished by transformation of competent cells with chimeric DNA formed by the ligation of TaqI fragments of pneumococcal DNA to the erythromycin resistance determinant of the streptococcal plasmid pAM beta 1. The two mutants described were characterized as defective in the control of competence induction, possibly due to a block in the production of the intercellular competence-inducing protein.
Late-onset Stargardt-like macular dystrophy maps to chromosome 1p13 (1994)

Stargardt`s disease (MIM 248200), originally described in 1909, is an autosomal recessive condition of childhood, characterized by a sudden and bilateral loss of central vision. Typically, it has an early onset (7 to 12 years), a rapidly progressive course and a poor final outcome. The central area of the retina (macula) displays pigmentary changes in a ring form with depigmentation and atrophy of the retinal pigmentary epithelium (RPE). Perimacular yellowish spots, termed fundus flavimaculatus, are observed in a high percentage of patients. We have recently reported the genetic mapping of Stargardt`s disease to chromosome 1p13. On the other hand, considering that fundus flavimaculatus (MIM 230100) is another form of fleck fundus disease, with a Stargardt-like retinal aspect but with a late-onset and a more progressive course, we decided to test the hypothesis of allelism between typical Stargardt`s disease and late-onset autosomal recessive fundus flavimaculatus. Significant pairwise lod scores were obtained in each of four multiplex families (11 affected individuals, 12 relatives) with four markers of the 1p13 region (Z = 4.79, 4.64, 3.07, 3.16 at loci D1S435, D1S424, D1S236, and D1S415, respectively at {theta} = 0). Multipoint analysis showed that the best estimate for location of the disease gene ismore » between D1S424 and D1S236 (maximum lod score of 5.20) as also observed in Stargardt`s disease. Our results are consistent with the location of the gene responsible of the late-onset Stargardt-like macular dystrophy in the 1p13 region and raise the hypothesis of either allelic mutational events or contiguous genes in this chromosomal region. The question of possible relationship with some age-related macular dystrophies in now open to debate.« less
An Integrated Genomic Analysis of Human Glioblastoma Multiforme (2008)

Glioblastoma multiforme (GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high-density oligonucleotide arrays, and performed gene expression analyses using next-generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 (IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.
4. In Vitro and In Vivo Analysis of Feline Immunodeficiency Virus-Based Lentiviral Vector Integration (2004)

Retroviral vector-mediated gene transfer holds promise in the treatment of a variety of genetic diseases. A distinguishing feature of retroviral vectors is their ability to integrate into the host genome, resulting in sustained transgene expression. However, with the ability to integrate comes a risk of insertional mutagenesis. Viral integration mapping studies provide an important first step in understanding the biology and fate of the vector DNA in host cells and are directly applicable to gene transfer using retroviral vectors. Using a sensitive nested PCR-based genome walking technique, we analyzed feline immunodeficiency virus (FIV)-based lentiviral vector integration events in vitro in FIV-transduced human HepG2 hepatoma cells and in vivo in the liver of mice receiving systemic injection of FIV vector. For in vitro mapping studies, we analyzed 869 sequences, which represented 211 distinct FIV integration sites. We also compared the FIV integration preferences with published results for HIV and MLV vectors. We found that ~75% of FIV integration occurred in a RefSeq gene and intron regions were preferred over exons. Of the 159 RefSeq genes with FIV integration, 139 were represented on a HepG2 microarray data set (Stanford University). The median expression level for these 139 genes was 138 and was about 3.8-fold higher than that of all the genes on the array (median expression levels for all genes on the array was 36). These data indicate that like HIV and MLV, FIV integration favors actively transcribed genes. Furthermore, similar to HIV but distinct from MLV, FIV integrated throughout the entire length of the transcriptional units, and regions around the transcription start sites were not the favored target for FIV integration. Although no specific sequences in the host genome were identified as FIV integration sites, FIV integration sites appear to be surrounded by A/T rich regions. Interestingly, FIV integrations did not coincide with the hot spots described previously for HIV integration in a human T cell line. For in vivo mapping studies, we analyzed FIV integration events in the liver of FIV-injected mice at day 5 and day 21 post gene transfer. To date, ~30 clones have been sequenced and 8 unique FIV integration sites have been identified. Five of them occurred in a gene (4 in introns and 1 in exon). The remaining 3 FIV integrations were in non-coding regions far away from transcriptional start sites. Similar mapping studies in additional animals are currently ongoing. These data suggest that although FIV integration preference is more similar to HIV than to MLV, certain differences may exist between FIV and HIV vectors. In addition, results may vary depending on the target cell type and the proliferation status of the transduced cells. These findings provide important background for understanding the host-vector interactions and stress the need for developing more site-restricted or insulated lentiviral vectors for gene transfer applications.
Ig domains 1 and 2 of murine CD22 constitute the ligand-binding domain and bind multiple sialylated ligands expressed on B and T cells (1995)

Baby hamster kidney cells transfected with murine CD22 (mCD22) mediate adhesion to B- and T-lineage cells. To further characterize mCD22-mediated cell adhesion, we generated a panel of recombinant globulins (Rg) consisting of different extracellular Ig-like (Ig) domains of mCD22. FACS analysis using these mCD22.Rgs revealed that ligands for mCD22 are expressed on both B and T cell lines and also normal B and T cells. In B-lineage cells, the expression of mCD22 ligands began on sIgM- pre-B cells in bone marrow. The ligand-binding site of mCD22 for ligands was mapped to Ig domains 1 and 2: mCD22.Rgs containing Ig domains 1 and 2 bound target cells and immunoprecipitated sets of glycoproteins similar to Rgs containing Ig domains 1 to 3 or all 7 CD22 Ig domains, whereas Rgs containing Ig domains 2 to 3 or 3 to 7 did not bind either B or T cells. Furthermore, B cells apparently expressed higher levels of mCD22 ligands than that of T cells, suggesting a potential competition for CD22 binding between ligands expressed on the same B cell and those expressed on another B cell or T cells. Immunoprecipitation experiments using the mCD22.Rgs identified mCD22 itself and the B cell-specific isoform of mCD45RA (B220) as two of the mCD22 ligands expressed on B cells. Thus, mCD22 may potentially regulate B cell activation through interactions with itself or mCD45RA/B220.
Met receptor overexpression and oncogenic Ki-ras mutation cooperate to enhance tumorigenicity of colon cancer cells in vivo. (2003)

We have investigated the influence of Ki-ras oncogene on Met/hepatocyte growth factor (HGF) receptor signaling in human carcinoma cells. The model system used in these studies included the DLD-1 colon cancer cell line with a mutated Ki-ras allele, and the DKO-4 cell line generated from DLD-1, with its mutant Ki-ras allele inactivated by targeted disruption. These cell lines were transduced with cDNAs of either active Met receptor or dominant negative Met receptor. As compared to the DLD-1 cells, constitutive overexpression of Met receptor in this cell line (DLD-1-Met) resulted in increased tumorigenicity in SCID mice. In contrast, overexpression of Met in DKO-4 cells (DKO-4-Met) that have lost oncogenic Ras activity demonstrated suppressed tumorigenicity with respect to the parent DKO-4 cell line. Tumors formed by the DLD-1-Met cells showed increased levels of mitogen-activated protein kinase (MAPK) and lower levels of apoptosis compared to the DKO-4-Met tumors. Overexpression of the dominant negative Met receptor cDNA decreased the Met phosphorylation levels in both DLD-1 and DKO-4 cells, but only suppressed tumorigenicity in the DKO-4 cell line. In vitro, HGF stimulation of DLD-1 cells resulted in a prolonged duration of MAPK activation, while DKO-4 cells exhibited a rapid attenuation of MAPK phosphorylation. The results suggest that Ki-ras mutations and HGF signaling cooperate to enhance tumor growth by increased duration of MAPK activation and decreased apoptosis in human carcinoma cells.
Interaction and Comparison of a Class I Hydrophobin from Schizophyllum commune and Class II Hydrophobins from Trichoderma reesei (2006)

Hydrophobins fulfill a wide spectrum of functions in fungal growth and development. These proteins self-assemble at hydrophilic-hydrophobic interfaces into amphipathic membranes. Hydrophobins are divided into two classes based on their hydropathy patterns and solubility. We show here that the properties of the class II hydrophobins HFBI and HFBII of Trichoderma reesei differ from those of the class I hydrophobin SC3 of Schizophyllum commune. In contrast to SC3, self-assembly of HFBI and HFBII at the water-air interface was neither accompanied by a change in secondary structure nor by a change in ultrastructure. Moreover, maximal lowering of the water surface tension was obtained instantly or took several minutes in the case of HFBII and HFBI, respectively. In contrast, it took several hours in the case of SC3. Oil emulsions prepared with HFBI and SC3 were more stable than those of HFBII, and HFBI and SC3 also interacted more strongly with the hydrophobic Teflon surface making it wettable. Yet, the HFBI coating did not resist treatment with hot detergent, while that of SC3 remained unaffected. Interaction of all the hydrophobins with Teflon was accompanied with a change in the circular dichroism spectra, indicating the formation of an alpha-helical structure. HFBI and HFBII did not affect self-assembly of the class I hydrophobin SC3 of S. commune and vice versa. However, precipitation of SC3 was reduced by the class II hydrophobins, indicating interaction between the assemblies of both classes of hydrophobins.
Ribosome-Templated Azide–Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry (2016)

Over half of all antibiotics target the bacterial ribosome-nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semisynthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a 16-component reaction (i.e., azide 2 and 15 alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd values. Computational analysis using the site-identification by ligand competitive saturation (SILCS) approach indicated that the relative affinity of the ligands was associated with the alteration of macrolactone+desosamine-ribosome interactions caused by the different alkynes. Protein synthesis inhibition experiments confirmed the mechanism of action. Evaluation of the minimal inhibitory concentrations (MIC) quantified the potency of the in situ click products and demonstrated the efficacy of this method in the triaging and prioritization of potent antibiotics that target the bacterial ribosome. Cell viability assays in human fibroblasts confirmed 2 and four analogues with therapeutic indices for bactericidal activity over in vitro mammalian cytotoxicity as essentially identical to solithromycin (1).
SpiC Is Required for Translocation of Salmonella Pathogenicity Island 2 Effectors and Secretion of Translocon Proteins SseB and SseC (2002)

The Salmonella pathogenicity island 2 (SPI2) type III secretion system (TTSS) promotes Salmonella enterica serovar Typhimurium virulence for mice and increased survival and replication within eukaryotic cells. After phagocytosis, Salmonella serovar Typhimurium assembles the SPI2 TTSS to translocate over a dozen effector proteins across the phagosome membrane. SpiC has been previously shown to be a translocated effector with a large contribution to virulence (K. Uchiya, M. A. Barbieri, K. Funato, A. H. Shah, P. D. Stahl, and E. A. Groisman, EMBO J. 18:3924-3933, 1999). This report demonstrates by competitive index that the virulence phenotype of a spiC mutant is equivalent to that of a secretion component mutant. In addition, translocation of SPI2 effector proteins was shown to require SpiC. Thus, the severe virulence phenotype resulting from deletion of spiC is likely due to the inability to translocate all SPI2 effectors. SpiC was also required to secrete translocon proteins SseB and SseC but not translocated effector SseJ, indicating that lack of assembly of the translocon explains the spiC mutant phenotype.
WhittleSearch: Image search with relative attribute feedback (2012)

We propose a novel mode of feedback for image search, where a user describes which properties of exemplar images should be adjusted in order to more closely match his/her mental model of the image(s) sought. For example, perusing image results for a query “black shoes”, the user might state, “Show me shoe images like these, but sportier.” Offline, our approach first learns a set of ranking functions, each of which predicts the relative strength of a nameable attribute in an image (`sportiness', `furriness', etc.). At query time, the system presents an initial set of reference images, and the user selects among them to provide relative attribute feedback. Using the resulting constraints in the multi-dimensional attribute space, our method updates its relevance function and re-ranks the pool of images. This procedure iterates using the accumulated constraints until the top ranked images are acceptably close to the user's envisioned target. In this way, our approach allows a user to efficiently “whittle away” irrelevant portions of the visual feature space, using semantic language to precisely communicate her preferences to the system. We demonstrate the technique for refining image search for people, products, and scenes, and show it outperforms traditional binary relevance feedback in terms of search speed and accuracy.
Effects of interferon‐α on cytokine profile, T cell receptor repertoire and peptide reactivity of human allergen‐specific T cells (1996)

A large panel of T cell clones (TCC) specific for the recombinant form of Poa pratensis allergen (rKBG7.2 or Poa p9) were established from the peripheral blood of grass pollen-sensitive donor in the absence or presence of recombinant interferon-alpha (IFN-alpha) in bulk culture and their pattern of cytokine secretion, peptide reactivity and TCR V beta repertoire was examined. The majority of allergen-specific TCC derived in absence of IFN-alpha produced high amounts of interleukin-4 (IL-4) and IL-5 but not IFN-gamma (Th2 cells), while most of TCC derived in presence of IFN-alpha produced IFN-gamma but not, or limited amounts of, IL-4 and IL-5 (Th1 or Th0 cells). Of 24 TCC established in the presence of IFN-alpha, 22 were able to recognize a single allergen peptide, p26, while none of the clones established in the absence of IFN-alpha showed a similar specificity. The majority of both clones expressed the V beta 2 element regardless of whether they were established in the presence of INF-alpha, but the presence of IFN-alpha favored the expansion of V beta 2+, V beta 17+ and V beta 22+ Poa p9-specific T cells, whereas in the absence of IFN-alpha, other TCR V beta-bearing T cells (V beta 5, and V beta 6.7, and V beta 14) were expanded in addition to V beta 2+ T cells. None of V beta 2+ clones established in the absence of IFN-alpha reacted with p26, whereas all the V beta 2+ clones established in its presence in the absence of interferon-alpha reacted with p26, whereas all the V beta 2+ clones established in its presence reacted to this peptide. IFN-alpha also shifted the TCR V beta repertoire of both Poa p9- and Lolium perenne group 1 (Lol p1)-specific T cell lines generated from the same patient and from a different grass-sensitive individual. These data demonstrate that IFN-alpha modulates the development of allergen-specific T cells in vitro, and suggest that IFN-alpha may represent a useful tool for novel immunotherapeutic approaches in allergic disorders.
Local Effect of Serotonin Released during Coronary Angioplasty (1994)

Serotonin is released into the coronary circulation during angioplasty, and this vasoactive substance may contribute to the occurrence of vasoconstriction distal to the dilated site. The vasoconstriction is attenuated by ketanserin, a serotonin2-receptor antagonist.
The Course of Tissue Permeabilization Studied on a Mathematical Model of a Subcutaneous Tumor in Small Animals (2005)

One of the ways to potentiate antitumor effectiveness of chemotherapeutic drugs is by local application of short intense electric pulses. This causes an increase of the cell membrane permeability and is called electropermeabilization. In order to study the course of tissue permeabilization of a subcutaneous tumor in small animals, a mathematical model was built with the commercial program EMAS, which uses the finite element method. The model is based on the tissue specific conductivity values found in literature, experimentally determined electric field threshold values of reversible and irreversible tissue permeabilization, and conductivity changes in the tissues. The results obtained with the model were then compared to experimental results from the treatment of subcutaneous tumors in mice and a good agreement was obtained. Our results and the reversible and irreversible thresholds used coincide well with the effectiveness of the electrochemotherapy in real tumors where experiments show antitumor effectiveness for amplitudes higher than 900 V/cm ratio and pronounced antitumor effects at 1300 V/cm ratio.
REVERSAL OF NATURALLY OCCURRING DIABETES IN PRIMATES BY UNMODIFIED ISLET XENOGRAFTS WITHOUT CHRONIC IMMUNOSUPPRESSION1 (1999)

These results represent the first demonstration in nonhuman primates of stable, long-term acceptance of nonencapsulated xenogeneic islets off all immunosuppression, suggesting operational tolerance. The findings have potential implications for islet transplantation as well as improved and more cost-effective therapy for IDDM.
Effects of Testosterone Replacement and/or Resistance Exercise on the Composition of Megestrol Acetate Stimulated Weight Gain in Elderly Men: A Randomized Controlled Trial (2002)

Megestrol acetate (MA) (Bristol-Myers Squibb Co., Princeton, NJ) increases weight gain in AIDS and cancer patients and in age-related cachexia; however, the weight gain is predominately fat. We determined if adding resistance exercise and/or testosterone (T) replacement to MA administration would result in a more favorable body composition change than MA alone. Thirty older men (aged 67.0 +/- 5.8) completed this 12-wk study. All subjects received MA and were randomly assigned to one of the following groups: placebo (P) injections, resistance training (RT) and P (RT + P), weekly injections of T (100 mg/wk) or, RT and T (RT + T). The mean increase in body weight for all groups combined was 3.8 kg (P < 0.0001), but this increase was not different between groups. There was a significant interaction for the change in thigh muscle cross-sectional area (P = 0.0006). Thigh muscle cross-sectional area was significantly reduced from baseline by 5.20 [1.62] cm(2) (P = 0.05) in P which was not prevented in T [-4.44 (1.66) cm(2) from baseline; P = 0.04]. RT prevented this decline [+0.61 (1.41) cm(2) from baseline]. Muscle cross-sectional area increased 4.51 (1.69) cm(2) from baseline in RT + T (P = 0.002 vs. P and P = 0.002 vs. T). Despite significant weight gain, MA appears to have an antianabolic effect on muscle size even when combined with T replacement. Resistance exercise attenuated this reduction in muscle mass and when combined with T had an anabolic effect on muscle mass.
Truly quantitative XPS characterization of organic monolayers on silicon : study of alkyl and alkoxy monolayers on H-Si(111) (2005)

The quantitative characterization of the chemical composition (bonding at grafted and ungrafted sites, surface coverage) is a key issue for the application of silicon-organic monolayer hybrid interfaces. The primary purpose of this article is to demonstrate that X-ray photoelectron spectroscopy (XPS) requires to be truly quantitative to deal with two main questions. The first one is accounting for X-ray photodiffraction (XPD), a well-known phenomenon that is responsible for azimuthal variations of the XPS signal intensity. A simple procedure is proposed to account for XPD in angle-resolved measurements. The second critical point concerns the choice of photoelectron attenuation lengths (AL). This article demonstrates that n-alkanethiol self-assembled monolayers on Au(111) can be used as a reference system to derive the effective monolayer thickness on silicon substrates and that one may use the empirical relationship established by Laibinis and co-workers to calculate the relevant ALs (Laibinis, P. E.; Bain, C. D.; Whitesides, G. M. J. Phys. Chem. 1991, 95, 7017). A self-consistent approach is presented to justify the above assertions and to give a complete compositional description of alkyl and alkoxy monolayers directly grafted on atomically flat H-Si(111) surfaces. Direct evidences are provided that a Si-C and a Si-O-C linkage is formed, respectively, after reaction with decene and decanol and that the ungrafted sites remain saturated with H atoms. Moreover, the quantitative spectra analysis of satellite peaks at fixed polar angle and three independent angle-resolved Si2p and C1s spectra all give the same surface coverage very close to its theoretical limit.