gebhart/patrepeval huggingface dataset:
Site-specific recombination for the modification of transgenic strains of the Mediterranean fruit fly Ceratitis capitata (2009)

Insect transgenesis is mainly based on the random genomic integration of DNA fragments embedded into non-autonomous transposable elements. Once a random insertion into a specific location of the genome has been identified as particularly useful with respect to transgene expression, the ability to make the insertion homozygous, and lack of fitness costs, it may be advantageous to use that location for further modification. Here we describe an efficient method for the modification of previously inserted transgenes by the use of the site-specific integration system from phage phiC31 in a tephritid pest species, the Mediterranean fruit fly Ceratitis capitata. First, suitable transgenic strains with randomly integrated attP landing sites within transposon-based vectors were identified by molecular and functional characterization. Second, donor plasmids containing an attB site, with additional markers, and transposon ends were integrated into attP sites by phiC31 integrase-mediated recombination. Third, transposase-encoding 'jumpstarter' strains were created and mated to transgenic strains resulting in the postintegrational excision of transposon ends, which left stably integrated transgene insertions that could not be remobilized. This three-step integration and stabilization system will allow the combination of several transgene-encoded advantageous traits at evaluated genomic positions to generate optimized strains for pest control that minimize environmental concerns.
Glucansucrases: mechanism of action and structure–function relationships (1999)

Glucansucrases are produced principally by Leuconostoc mesenteroides and oral Streptococcus species, but also by the lactic acid bacteria (Lactococci, Lactobacilli). They catalyse the synthesis of high molecular weight D-glucose polymers, named glucans, from sucrose. In the presence of efficient acceptors, they catalyse the synthesis of low molecular weight oligosaccharides. Glucosidic bond synthesis occurs without the mediation of nucleotide activated sugars and cofactors are not necessary. Glucansucrases have an industrial value because of the production of dextrans and oligosaccharides and a biological importance by their key role in the cariogenic process. They were identified more than 50 years ago. The first glucansucrase encoding gene was cloned more than 10 years ago. But the mechanism of their action remains incompletely understood. However, in order to synthesise oligosaccharides of biological interest or to develop vaccines against dental caries, elucidation of the factors determining the regiospecificity and the regioselectivity of glucansucrases is necessary. The cloning of glucansucrase encoding genes in addition to structure-function relationship studies have allowed the identification of important amino acid residues and have shown that glucansucrases are composed of two functional domains: a core region (ca. 1000 amino acids) involved in sucrose binding and splitting and a C-terminal domain (ca. 500 amino acids) composed of a series of tandem repeats involved in glucan binding. Enzymology studies have enabled different models for their action mechanism to be proposed. The use of secondary structure prediction has led to a clearer knowledge of structure-function relationships of glucansucrases. However, mainly due to the large size of these enzymes, data on the three-dimensional structure of glucansucrases (given by crystallography and modelling) remain necessary to clearly identify those features which determine function.
Reactivity of a 10-I-3 Hypervalent Iodine Trifluoromethylation Reagent With Phenols (2008)

The reaction of the 10-I-3 hypervalent iodine electrophilic trifluoromethylation reagent 1-trifluoromethyl-1,2-benziodoxol-3-(1H)-one (2) with 2,4,6-trimethylphenol, after deprotonation with NaH and in the presence of 18-crown-6 in a polar, nonprotic solvent, affords 1,3,5-trimethyl-2-(trifluoromethoxy)benzene (4) only as a byproduct. Trifluoromethylation occurs preferentially at the ortho- and para-positions of the aromatic core, giving the corresponding trifluoromethylcyclohexadienones 5 and 6. In case the ortho- and/or para-positions are not substituted, the corresponding products of an aromatic, electrophilic substitution are obtained in moderate yield, for example, 2-trifluoromethyl-4-tert-butylphenol (10a) from 4-tert-butylphenol (10).
Fibroblast growth factors are required for efficient tumor angiogenesis. (2000)

Although the function of vascular endothelial growth factor in the induction of tumor angiogenesis is well understood, the role of a second group of angiogenic factors, the fibroblast growth factors (FGFs), remains elusive. We used a recombinant adenovirus expressing soluble FGF receptor (AdsFGFR) to interfere with FGF function in tumor angiogenesis. AdsFGFR repressed endothelial cell proliferation in vitro and inhibited tumor angiogenesis in an ex vivo bioassay, in which endothelial cells were cocultured with angiogenic tumor biopsies in a collagen gel. Moreover, AdsFGFR repressed tumor angiogenesis and hence tumor growth in vivo in allograft transplantation experiments. Whereas adenoviral expression of a soluble form of VEGF receptor 1 (AdsFlt) predominantly affected the initiation of tumor angiogenesis, soluble FGF receptor (sFGFR) appeared to impair the maintenance of tumor angiogenesis. The combination of sFGFR and soluble Flt exhibited a synergistic effect in the repression of tumor growth. Finally, i.v. injection of AdsFGFR resulted in a dramatic repression of tumor growth in a transgenic mouse model of pancreatic beta cell carcinogenesis. Similar to control infections with AdsFlt, tumor-associated vessel density was decreased, indicating that the expression of sFGFR impaired tumor angiogenesis. These data indicate that FGFs play a critical role in tumor angiogenesis.
Charge- and Flux-Insensitive Tunable Superconducting Qubit (2017)

A central challenge in building a scalable quantum computer with superconducting qubits is simultaneously achieving long coherence times and fast two-qubit gates. Currently, fast (tunable) gates are obtained at the expense of coherence time. The authors propose a ``flatsonium'' qubit, based on the highly nonlinear fluxonium qubit, that yields both coherence and tunability---jackpot. Dephasing due to global flux noise is reduced by engineering flux-insensitive sweet spots in the qubit spectrum at the frequencies of interest, while leakage errors are eliminated by the typically large anharmonicity of its energy spectrum.
Probing Chemical and Conformational Differences in the Resting and Active Conformers of Platelet Integrin αIIbβ3 (2000)

Integrin alpha(IIb)beta(3) is the fibrinogen receptor that mediates platelet adhesion and aggregation. The ligand binding function of alpha(IIb)beta(3) is "activated" on the platelet surface by physiologic stimuli. Two forms of alpha(IIb)beta(3) can be purified from platelet lysates. These forms are facsimiles of the resting (Activation State-1 or AS-1) and the active (Activation State-2 or AS-2) conformations of the integrin found on the platelet surface. Here, the differences between purified AS-1 and AS-2 were examined to gain insight into the mechanism of activation. Four major findings are put forth. 1) The association rate (k(1)) between fibrinogen and the integrin is a key difference between AS-1 and AS-2. 2) Although the divalent ion Mn(2+) enhances the ligand binding function of AS-1, this ion is unable to convert AS-1 to AS-2. Therefore, its effect on integrin is unrelated to activation. 3) Peptide mass fingerprints indicate that the chemical structure of AS-1 and AS-2 are virtually identical, calling into question the idea that post-translational modifications are necessary for activation. 4) The two forms of alpha(IIb)beta(3) have significant conformational differences at three positions. These include the junction of the heavy and light chain of alpha(IIb), the divalent ion binding sites on alpha(IIb), and at a disulfide-bonded knot linking the amino terminus of beta(3) to the cysteine-rich domain. These observations indicate that integrin is activated by a series of specific conformational rearrangements in the ectodomain that increase the rate of ligand association.
Replication-competent retrovirus vectors for cancer gene therapy (2007)

Oncolytic virotherapy represents an emerging field with tremendous promise for harnessing the replicative capabilities of viruses against rapidly proliferating cancer cells. Among the different replicating virus technologies being tested, replication-competent retrovirus (RCR) vectors based on murine leukemia virus (MLV) exhibit unique characteristics. MLV exhibits intrinsic tumor selectivity due to its inability to infect quiescent cells, and can achieve highly selective and stable gene transfer throughout entire solid tumors in vivo at efficiencies of up to >99%, even after initial inoculation at MOIs as low as 0.01. RCR vectors with suicide genes mediate synchronized cell killing after prodrug administration, and due to their ability to undergo stable integration, residual cancer cells serve as a reservoir for long-term viral persistence even as they migrate to new sites, enabling multiple cycles of prodrug to achieve prolonged survival benefit. Further testing in various tumor models, new vector targeting and delivery strategies, and development of GMP manufacturing, are being pursued through a multi-national consortium, and preparations are now being undertaken for clinical trials using RCR vectors in glioblastoma.
The role of the thalamus in the flow of information to the cortex (2002)

The lateral geniculate nucleus is the best understood thalamic relay and serves as a model for all thalamic relays. Only 5-10% of the input to geniculate relay cells derives from the retina, which is the driving input. The rest is modulatory and derives from local inhibitory inputs, descending inputs from layer 6 of the visual cortex, and ascending inputs from the brainstem. These modulatory inputs control many features of retinogeniculate transmission. One such feature is the response mode, burst or tonic, of relay cells, which relates to the attentional demands at the moment. This response mode depends on membrane potential, which is controlled effectively by the modulator inputs. The lateral geniculate nucleus is a first-order relay, because it relays subcortical (i.e. retinal) information to the cortex for the first time. By contrast, the other main thalamic relay of visual information, the pulvinar region, is largely a higher-order relay, since much of it relays information from layer 5 of one cortical area to another. All thalamic relays receive a layer-6 modulatory input from cortex, but higher-order relays in addition receive a layer-5 driver input. Corticocortical processing may involve these corticothalamocortical 're-entry' routes to a far greater extent than previously appreciated. If so, the thalamus sits at an indispensable position for the modulation of messages involved in corticocortical processing.
Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas (2011)

The novel epigenetic marker panel shows very high sensitivity and specificity for both colorectal cancers and adenomas. Our findings suggest this biomarker panel to be highly suitable for early tumor detection.
Comparison of external and internal approaches for transplantation of autologous retinal pigment epithelium. (1992)

The feasibility of autologous transplantation of retinal pigment epithelial (RPE) cells from just posterior to the ora serrata to the posterior pole was demonstrated in the rabbit model. Two techniques for introducing the transplanted cells were compared: an internal (anterior transvitreal) and an external (posterior transscleral) penetration to the subretinal space. In both approaches, RPE cells were obtained by biopsy from the peripheral retina of a rabbit eye, cultured, labeled with a fluorescent dye and 3H-thymidine, and transplanted to the posterior pole of the same or contralateral eye. The external approach consistently resulted in a greater number of transplanted cells on Bruch's membrane. The internal technique was more precise because it permitted direct visualization of the placement of the transplanted RPE. Transplantation of autologous RPE is a possibility that should be further pursued.
Contribution of Domain Interface Residues to the Stability of Antibody CH3 Domain Homodimers (1998)

Dimers of CH3 domains from human IgG1 were used to study the effect of mutations constructed at a domain-domain interface upon domain dissociation and unfolding, "complex stability". Alanine replacement mutants were constructed on one side of the interface for each of the sixteen interdomain contact residues by using a single-chain CH3 dimer in which the carboxyl terminus of one domain was joined to the amino terminus of the second domain via a (G4S)4 linker. Single-chain variants were expressed in Escherichia coli grown in a fermentor and recovered in yields of 6-90 mg L-1 by immobilized metal affinity chromatography. Guanidine hydrochloride-induced denaturation was used to follow domain dissociation and unfolding. Surprisingly, the linker did not perturb the complex stability for either the wild type or two destabilizing mutants. The CH3 domain dissociation and unfolding energetics are dominated by six contact residues where corresponding alanine mutations each destabilize the complex by >2.0 kcal mol-1. Five of these residues (T366, L368, F405, Y407, and K409) form a patch at the center of the interface and are located on the two internal antiparallel beta-strands. These energetically key residues are surrounded by 10 residues on the two external beta-strands whose contribution to complex stability is small (three have a Delta DeltaG of 1.1-1.3 kcal mol-1) or very small (seven have a Delta DeltaG of </=0.7 kcal mol-1). Thus, at the center of the CH3 structural interface there is a small "functional interface" of residues that make significant contributions to complex stability.
Ability of iron(III)‐loaded carboxylated polyacrylamide‐grafted sawdust to remove phosphate ions from aqueous solution and fertilizer industry wastewater: Adsorption kinetics and isotherm studies (2002)

Abstract Iron(III)‐loaded carboxylated polyacrylamide‐grafted sawdust was investigated as an adsorbent for the removal of phosphate from water and wastewater. The carboxylated polyacrylamide‐grafted sawdust was prepared by graft copolymerization of acrylamide and N,N ′‐methylenebisacrylamide onto sawdust in the presence of an initiator, potassium peroxydisulfate. Iron(III) was strongly attached to the carboxylic acid moiety of the adsorbent. The adsorbent material exhibits a very high adsorption potential for phosphate ions. The coordinated unsaturated sites of the iron(III) complex of polymerized sawdust were considered to be the adsorption sites for phosphate ions, the predominating species being H 2 PO ions. Maximum removal of 97.6 and 90.3% with 2 g L −1 of the adsorbent was observed at pH 2.5 for an initial phosphate concentration of 100 and 250 μmol L −1 , respectively. The adsorption process follows second‐order kinetics. Adsorption rate constants as a function of concentration and temperature and kinetic parameters, such as Δ G ± , Δ H ± , and Δ S ± , were calculated to predict the nature of adsorption. The L‐type adsorption isotherm obtained in the sorbent indicated a favorable process and fitted the Langmuir equation model well. The adsorption capacity calculated by the Langmuir adsorption isotherm gave 3.03 × 10 −4 mol g −1 of phosphate removal at 30°C and pH 2.5. The isosteric heat of adsorption was also determined at various surface loadings of the adsorbent. The adsorption efficiency toward phosphate removal was tested using industrial wastewater. Different reagents were tested for extracting phosphate ions from the spent adsorbent. About 98.2% of phosphate can be recovered from the adsorbent using 0.1 M NaOH. Alkali regeneration was tried for several cycles with a view to recover the adsorbed phosphate and also to restore the adsorbent to its original state. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 2541–2553, 2002
Dual‐Syringe Reactive Electrospinning of Cross‐Linked Hyaluronic Acid Hydrogel Nanofibers for Tissue Engineering Applications (2006)

A facile fabrication of a cross-linked hyaluronic acid (HA) hydrogel nanofibers by a reactive electrospinning method is described. A thiolated HA derivative, 3,3'-dithiobis(propanoic dihydrazide)-modified HA (HA-DTPH), and poly(ethylene glycol) diacrylate (PEGDA) are selected as the cross-linking system. The cross-linking reaction occurs simultaneously during the electrospinning process using a dual-syringe mixing technique. Poly(ethylene oxide) (PEO) is added into the spinning solution as a viscosity modifier to facilitate the fiber formation and is selectively removed with water after the electrospinning process. The nanofibrous structure of the electrospun HA scaffold is well preserved after hydration with an average fiber diameter of 110 nm. A cell morphology study on fibronectin (FN)-adsorbed HA nanofibrous scaffolds shows that the NIH 3T3 fibroblasts migrate into the scaffold through the nanofibrous network, and demonstrate an elaborate three-dimensional dendritic morphology within the scaffold, which reflects the dimensions of the electrospun HA nanofibers. These results suggest the application of electrospun HA nanofibrous scaffolds as a potential material for wound healing and tissue regeneration. [image: see text] Laser scanning confocal microscopy demonstrates that the NIH3T3 fibroblast develops an extended 3D dendritic morphology within the fibronectin-adsorbed electrospun HA nanofibrous scaffold.
Comparison of three Yarrowia lipolytica strains for lipase production: NBRC 1658, IFO 1195, and a local strain (2012)

Lipase production was examined with 3 strains of Yarrowia lipolytica: NBRC 1658, IFO 1195, and a local strain. All strains were obtained from Hacettepe University's Department of Food Engineering. The addition of nitrogen and carbon sources and the effects of initial pH and temperature parameters were studied. For all 3 strains, the growth temperature range was 20-40 °C, and maximum growth was determined at 30 °C. The initial pH range was 6-9 for growth and 3-6 for lipase production. Maximum growth results were detected as follows: Y. lipolytica NBRC 1658 at 30 °C and pH 8, Y. lipolytica IFO 1195 at 30 °C and pH 8-9, and Y. lipolytica local strain at 30 °C and pH 7. However, maximum lipase production was detected at 30 °C and pH 4.4 for Y. lipolytica NBRC 1658, at 30 °C and pH 4.8 for Y. lipolytica IFO 1195, and at 30 °C and pH 4.6 for Y. lipolytica local strain. The effects of various nitrogen sources on lipase production showed that ammonium sulfate increased the lipase production, whereas urea, peptone, and casein did not show a distinct effect on lipase production. The addition of various sugars also did not increase lipase production efficiently. However, some oils showed a distinct effect on lipase production. The highest lipase activity determined was 16 U/mL, with the addition of 1% ammonium sulfate and 1% olive oil into the production medium of Y. lipolytica NBRC 1658.
Specific real-time PCR vs. fluorescent dyes for serum free DNA quantification (2007)

Aside from the disadvantage that the QPCR assays can only be used in clinical biochemistry laboratories that possess QPCR apparatus, the use of direct PicoGreen quantification displays major advantages in a routine context: it is less time-consuming and is quite inexpensive, but is still correlated with QPCR.
Experimental Colitis Models (2012)

Inflammatory Bowel Diseases (IBD) are life-threatening chronic and relapsing disorders of the immune system affecting the lower gastrointestinal tract. Despite the considerable efforts of many researchers, much remains to be learnt of their causes and appropriate treatment options. Crohn’s disease and ulcerative colitis comprise the majority of clinical IBD cases but differ considerably in terms of clinical representation and likely underlying mechanisms. As such, different animal models have been developed over the last 20 years to best characterize these diseases. It is widely accepted that DSS-induced colitis models ulcerative colitis, while TNBS induced colitis models Crohn’s disease. More recently, these models have been extended to investigate the mechanisms underlying the reciprocal regulation of the neuro-immune axis, both in times of acute inflammation and post-inflammation, with the latter modeling aspects of Irritable Bowel Syndrome. We describe the methodology involved in setting up, maintenance and evaluation of these two models of colitis, both of which are simply and economically achieved in a standard laboratory environment.
A common haplotype in the complement regulatory gene factor H ( HF1/CFH ) predisposes individuals to age-related macular degeneration (2005)

Age-related macular degeneration (AMD) is the most frequent cause of irreversible blindness in the elderly in developed countries. Our previous studies implicated activation of complement in the formation of drusen, the hallmark lesion of AMD. Here, we show that factor H (HF1), the major inhibitor of the alternative complement pathway, accumulates within drusen and is synthesized by the retinal pigmented epithelium. Because previous linkage analyses identified chromosome 1q25-32, which harbors the factor H gene (HF1/CFH), as an AMD susceptibility locus, we analyzed HF1 for genetic variation in two independent cohorts comprised of approximately 900 AMD cases and 400 matched controls. We found association of eight common HF1 SNPs with AMD; two common missense variants exhibit highly significant associations (I62V, chi2 = 26.1 and P = 3.2 x 10(-7) and Y402H, chi2 = 54.4 and P = 1.6 x 10(-13)). Haplotype analysis reveals that multiple HF1 variants confer elevated or reduced risk of AMD. One common at-risk haplotype is present at a frequency of 50% in AMD cases and 29% in controls [odds ratio (OR) = 2.46, 95% confidence interval (1.95-3.11)]. Homozygotes for this haplotype account for 24% of cases and 8% of controls [OR = 3.51, 95% confidence interval (2.13-5.78)]. Several protective haplotypes are also identified (OR = 0.44-0.55), further implicating HF1 function in the pathogenetic mechanisms underlying AMD. We propose that genetic variation in a regulator of the alternative complement pathway, when combined with a triggering event, such as infection, underlie a major proportion of AMD in the human population.
Efficient and heritable functional knock-out of an adult phenotype in Drosophila using a GAL4-driven hairpin RNA incorporating a heterologous spacer (2001)

We have developed a modified RNA interference (RNAi) method for generating gene knock-outs in Drosophila melanogaster. We used the sequence of the yellow (y) locus to construct an inverted repeat that will form a double-stranded hairpin structure (y-IR) that is under the control of the upstream activating sequence (UAS) of the yeast transcriptional activator GAL4. Hairpins are extremely difficult to manipulate in Escherichia coli, so our method makes use of a heterologous 330 bp spacer encoding sequences from green fluorescent protein to facilitate the cloning steps. When the UAS-y-IR hairpin is expressed under the control of different promoter-GAL4 fusions, a high frequency of y pigment phenocopies is obtained in adults. Consequently this method for producing gene knock-outs has several advantages over previous methods in that it is applicable to any gene within the fly genome, greatly facilitates cloning of the hairpin, can be used if required with GAL4 drivers to avoid lethality or to induce RNAi in a specific developmental stage and/or tissue, is useful for generating knock-outs of adult phenotypes as reported here and, finally, the system can be manipulated to investigate the trans-acting factors that are involved in the RNAi mechanism.