gebhart/patrepeval huggingface dataset:
Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles (2019)

Inherited retinal dystrophies (IRDs) are characterized by progressive photoreceptor degeneration and vision loss. Usher syndrome (USH) is a syndromic IRD characterized by retinitis pigmentosa (RP) and hearing loss. USH is clinically and genetically heterogeneous, and the most prevalent causative gene is <i>USH2A</i>. <i>USH2A</i> mutations also account for a large number of isolated autosomal recessive RP (arRP) cases. This high prevalence is due to two recurrent <i>USH2A</i> mutations, c.2276G>T and c.2299delG. Due to the large size of the <i>USH2A</i> cDNA, gene augmentation therapy is inaccessible. However, CRISPR/Cas9-mediated genome editing is a viable alternative. We used enhanced specificity Cas9 of <i>Streptococcus pyogenes</i> (eSpCas9) to successfully achieve seamless correction of the two most prevalent <i>USH2A</i> mutations in induced pluripotent stem cells (iPSCs) of patients with USH or arRP. Our results highlight features that promote high target efficacy and specificity of eSpCas9. Consistently, we did not identify any off-target mutagenesis in the corrected iPSCs, which also retained pluripotency and genetic stability. Furthermore, analysis of <i>USH2A</i> expression unexpectedly identified aberrant mRNA levels associated with the c.2276G>T and c.2299delG mutations that were reverted following correction. Taken together, our efficient CRISPR/Cas9-mediated strategy for <i>USH2A</i> mutation correction brings hope for a potential treatment for USH and arRP patients.
The organization of the human GSTP1-1 gene promoter and its response to retinoic acid and cellular redox status (1996)

High levels of expression of GSTP1-1 are associated with cell proliferation, embryogenesis and malignancy. Given the role of glutathione S-transferase (GST) in detoxication, it is possible that GSTP1-1 evolved specifically to protect proliferating cells and share regulatory mechanisms with other cellular genes which are involved in cell division and tumorigenesis. We have previously shown that the expression of GSTP1 is suppressed by retinoic acid (RA) in the presence of the retinoic acid receptor (RAR) as a result of decreased transcription from its promoter. Through deletion analysis, we show here that the RA-RAR-dependent repression is mediated by the region -73 to +8. Further mutation analysis of this region indicates that the DNA sequence required for RA-RAR-dependent repression co-localizes with a consensus activator protein-1 (AP1) site essential for the promoter activity. The degree of repression correlates with the residual activity of the AP1 site. There are two adjacent G/C boxes. The one immediately downstream from the AP1 site is not essential for the promoter activity, but mutation of the second, further downstream, impairs the promoter. On the other hand, mutation of either of these two G/C boxes has little effect on RA-RAR suppression. We also show that the expression of GSTP1 is regulated by the redox status of the cell. Using the chloramphenicol acetyltransferase assay system, we have demonstrated that treatment with H2O2 induced transcription from the promoter and that this effect can be blocked by pre-incubation with N-acetylcysteine (NAC). It was shown that the induction by H2O2 is mediated by trans-acting factor NF-kappa B (nuclear factor kappa B), via a putative NF-kappa B site, 'GGGACCCTCC', located from -96 to -86. Co-transfection with an NF-kappa B (p65) expression construct increased the promoter activity, an effect which could be blocked by co-transfection with an I kappa B (MAD-3) expression construct. Deletion of the NF-kappa B site abolished the effect of both H2O2 and co-transfection of NF-kappa B. Interestingly, NAC is also an inducer for GSTP1. The effect of NAC was shown to be mediated largely by the AP1 site, since mutation of this site abolished the induction by NAC.
Characterization of 69- and 100-kDa forms of 2-5A-synthetase from interferon-treated human cells. (1988)

The existence of distinct 69- and 100-kDa forms of 2-5A-synthetase in addition to the smaller (40 and 46 kDa) forms has recently been established. Using specific monoclonal antibodies we investigated the induction, synthesis, and activity of 69- and 100-kDa 2',5'-oligoadenylate (2-5A) synthetases in interferon-treated human Daudi cells. Although induction of these synthetases is detectable in cells treated with as little as 1-5 units/ml of human alpha-interferon, higher concentrations are required for maximum synthesis of the 100 kDa than the 69-kDa protein. At 5 units/ml of interferon, enhanced synthesis of both proteins is detectable at 4 h with maximum synthesis occurring between 8 to 12 and 12 to 16 h for 69- and 100-kDa 2-5A-synthetases, respectively. At 24 h after addition of interferon, synthesis of these synthetases declines due to a decrease of active interferon in the culture medium. The synthesis of both synthetases is blocked by actinomycin D, and the half-life of these proteins is estimated to be 8 h. The activities of immunoaffinity purified 69- and 100-kDa synthetases are dependent on double-stranded (ds)RNA but show different requirements for optimum concentration of dsRNA and pH of the reaction. The apparent Km of 69- and 100-kDa synthetases for ATP is 1.7 X 10(-3) M and 3.6 X 10(-3) M, respectively. At optimum conditions for the activity of these enzymes, the pattern of 2',5'-linked oligoadenylates synthesized are different, the 69-kDa protein synthesizing higher oligomers than the 100-kDa species. Taken together, these results indicate that the 69- and 100-kDa 2-5A-synthetases are distinct proteins each with specific characteristics of induction and enzymatic activity.
Translation of Drosophila melanogaster sequences in Escherichia coli (1977)

Thirty-seven independently cloned segments of Drosophila melanogaster DNA (Dm segments) were individually tested for their ability to promote the synthesis of new polypeptides in Escherichia coli K-12. The cloning vector was the pSC101 plasmid and the test system consisted of E. coli K-12 minicells that contained the hybrid pDm plasmids. Each of four pDm plasmids produced a new polypeptide, and one, pDm107, was selected for detailed mapping of the sequences required for the translation of its 38,000-dalton polypeptide, the Dm107 protein. Mapping was accomplished by constructing (i) deletion derivatives of pDm107 and (ii) new plasmids consisting of fragments of the Dm107 segment inserted into other vectors, and then testing these hybrids for their ability to promote the synthesis of the Dm107 protein, or truncated versions of this protein, in minicells. The 1000 base pairs of sequences that are translated to yield the Dm107 protein were thereby mapped at the center of the 18,000-base pair Dm107 segment, which consists of nonrepetitive sequences located at the base of the right arm of chromosome 2. The four polypeptides produced by the four pDm plasmids require sequences of 4000 base pairs for their translation, and the total amount of DNA in the 37 cloned Dm segments that were tested is approximately 400,000 base pairs. Because no new polypeptides were detected with the remaining 33 pDm plasmids, the fraction of D. melanogaster sequences that can be efficiently translated in E. coli K-12 is estimated to be 1 x 10(-2).
Everolimus and Reduced-Exposure Cyclosporine in de novo Renal-Transplant Recipients: A Three-Year Phase II, Randomized, Multicenter, Open-Label Study (2004)

In de novo renal-transplant recipients, the regimen of everolimus plus RDN was well tolerated, with low efficacy failure and better renal function in comparison with everolimus plus FDN.
Increased lipid peroxidation in type 2 poorly controlled diabetic patients. (1993)

An increased lipid peroxidation, due to the altered intracellular ratio between free radicals and antioxidant systems, has been recently related to diabetes. To study the possible relationship between lipid peroxidation and metabolic control, we measured the plasma concentrations of malondialdehyde (MDA), end product of the oxidation of polyunsaturated fatty acids, in poorly and well controlled Type 2 diabetic patients. A significant increase in plasma malondialdehyde concentrations was found in poorly controlled diabetics when compared to well controlled patients (p < 0.001) and to healthy normoglycaemic subjects (p < 0.001), whereas no significant difference was observed between the two latter groups. Plasma MDA/Cholesterol and MDA/triglyceride ratios were both higher in poorly controlled diabetics than in well controlled (p < 0.005) and in normal subjects (p < 0.01 and p < 0.02 for MDA/CHOL and MDA/TG respectively). In diabetic patients a positive correlation was found between plasma MDA levels and mean daily blood glucose (p < 0.01), plasma fructosamines (p < 0.001), HbA1 (p < 0.05) and plasma triglycerides (p < 0.05), while no significant correlation was shown between plasma malondialdehyde and total cholesterol. Malondialdehyde levels were followed-up for 7 days running (T1-T7) in five poorly controlled diabetics, treated with conventional insulin therapy. This group showed normalized plasma lipid peroxide values (0.486 +/- 0.13 mumol/l, T5, M +/- SEM) 72 h after the restoration of glycaemic control (145 +/- 25 mg/dl, T2, M +/- SEM). These results confirm the increase of lipid peroxidation during Type 2 diabetes. The correlation with the degree of metabolic imbalance suggests a possible role for lipid peroxidation in the occurrence of glucose-induced macromolecular changes.
Peritonitis and Septic Shock &ndash; An Evaluation of Two Experimental Models in the Rat (1985)

Two different experimental models for inducing septic shock have been characterized. In one, septic shock was induced by intraperitoneal injection of live Escherichia coli bacteria. This resulted in a dose-dependent mortality. Those animals surviving the first 24 h are considered as permanent survivors. In the other models, septic shock and peritonitis was induced by ligation and needle punctures of the cecum. This resulted in a slower development of shock which was almost invariably lethal within 96 h. Arterial blood pressure remained within the normal range in both models for up to 3 h after inducing peritonitis. Then a rapid deterioration was noticed in animals injected with live E. coli. White blood cells and platelets in arterial blood were reduced compared to controls in both groups. This reduction was more pronounced in animals injected with live E. coli. Both models are considered as useful tools in further studies of the pathophysiology of peritonitis and septic shock.
Efficient tumor cell lysis mediated by a bispecific single chain antibody expressed in Escherichia coli. (1994)

Recent advances in the expression of Abs in Escherichia coli have raised the possibility that virtually any specificity can be obtained by either cloning Ab genes from characterized hybridomas or by de novo selection using Ab gene libraries. Bispecific Abs have been more difficult to engineer because of problems inherent in the proper folding and association of VH and VL domains. In this report, a model system for expressing and testing the activity of a single chain bispecific Ab was used. The Ab contained the VH and VL genes from the anti-TCR Ab 1B2 joined by a 25 amino acid residue linker to the VH and VL genes from the anti-fluorescein Ab 4420. The 57-kDa single chain bispecific Ab (scFv2) was purified in a single step by affinity chromatography through a fluorescein column at a yield of 1 mg/L of bacterial culture. Despite the presence of 1B2 V regions at the NH2-terminus and a 10-residue c-myc peptide at the COOH-terminus, the refolded protein had an affinity for fluorescein that was nearly identical with the monospecific single chain Ab. The scFv2 also bound the TCR of the mouse CTL clone 2C and redirected the lysis of human tumor cells that had fluorescein covalently linked to their surface. Lysis was mediated at scFv2 concentrations that were 100-fold lower than the concentrations of Ab that inhibited normal recognition by CTL 2C. These results show that single chain bispecific Abs can mediate CTL lysis of target cells without the immunosuppressive side effects associated with the use of anti-TCR Abs.
Human Hand1 basic helix-loop-helix (bHLH) protein: extra-embryonic expression pattern, interaction partners and identification of its transcriptional repressor domains (2002)

The basic helix-loop-helix (bHLH) transcription factor, Hand1, plays an important role in the development of the murine extra-embryonic trophoblast cell lineage. In the present study, we have analysed the expression of Hand1 in human extra-embryonic cell types and determined its binding specificity and transcriptional activity upon interaction with different class A bHLH factors. Northern blotting and in situ hybridization showed that Hand1 mRNA is specifically expressed in amnion cells at different stages of gestation. Accordingly, we demonstrate that the protein is exclusively produced in the amniotic epithelium in vivo and in purified amnion cells in vitro using a novel polyclonal Hand1 antiserum. Reverse transcriptase-PCR and immunohistochemical staining of blastocysts revealed the production of Hand1 mRNA and polypeptide in the trophectodermal cell layer. In the presence of E12/E47, Hand1 stimulated the transcription of luciferase reporters harbouring degenerate E-boxes, suggesting that E-proteins are potential dimerization partners in trophoblastic tumour and amnion cells. In contrast, Hand1 diminished E12/E47-dependent transcription of reporters containing perfect E-boxes by inhibiting the interaction of Hand1/E-protein heterodimers with the palindromic cognate sequence. Furthermore, we show that Hand1 down-regulated GAL—E12-dependent reporter expression, indicating that the protein can also act directly as a transcriptional repressor. Mutational analyses of GAL-Hand1 suggested that two protein regions located within its N-terminal portion mainly confer the repressing activity. In conclusion, human Hand1 may play an important role in the differentiation of the amniotic membrane and the pre-implanting trophoblast. Furthermore, the data suggest that Hand1 can act as a repressor by two independent mechanisms; sequestration of class A bHLH factors from E-boxes and inhibition of their transcriptional activity.
Interaction of laser-produced cavitation bubbles with an elastic tissue model (2001)

We investigated the interaction of a laser-induced cavitation bubble with an elastic tissue model by high-speed photography with up to 5 Mill. frames/sec. The elastic material consisted of a transparent polyacrylamide (PAA) gel whose elastic properties can be controlled by modifying the water content to mimic various biological tissues. The elastic modulus E of the PAA sample was varied between 0.017 and 2 MPa. The dimensionless bubble-boundary distance &gamma;(distance between laser focus and sample boundary, scaled by the maximum bubble radius) was for each value of E varied between &gamma; = 0 and &gamma; = 2.2. In this parameter space, we determined the jetting behavior, jet velocity, jet penetration into the PAA sample and bubble- induced removal of PAA material. The jetting behavior varies between unidirectional jets towards or away from the boundary, and formation of an annular jet which results in bubble splitting and subsequent formation of two very fast axial jets flowing simultaneously towards the boundary and away from it. General principles of the formation of annular and axial jets are discussed which allow to interpret the complex dynamics. The liquid jet directed away form the boundary reaches a maximum velocity between 300 m/s and 600 m/s (depending on E) while the peak velocity of the jet directed towards the boundary ranges between 400 m/s and 960 m/s. The peak velocities near an elastic material are 10 times higher than close to a rigid boundary. The liquid jet penetrates PAA samples with an elastic modulus in the intermediate range 0.12 &lt; E &lt; 0.4 MPa. In this same range of elastic moduli and for small &gamma;-values, PAA material is ejected into the surrounding liquid due to the elastic rebound of the sample surface that was deformed during bubble expansion. The surface of the PAA sample is, furthermore, lifted during bubble collapse when a region of low pressure develops between bubble and sample. For stiffer boundaries, only an axial liquid jet towards the boundary is formed, similar to the bubble dynamics next to a rigid wall. For softer sample, the liquid jet is directed away from the boundary, and material is torn off the PAA sample during bubble collapse, if the bubble is produced close to the boundary. These processes play an important role for the efficiency and side effects of pulsed laser surgery inside the human body.
Large-Scale Computational Modeling of [Rh(DuPHOS)]+-Catalyzed Hydrogenation of Prochiral Enamides:  Reaction Pathways and the Origin of Enantioselection (2000)

The potential energy surface for the [Rh((R,R)-Me-DuPHOS)]+-catalyzed asymmetric hydrogenation of a prochiral enamide, α-formamidoacrylonitrile, has been computed using a three-layer hybrid quantum mechanics/molecular mechanics method (ONIOM). The bond-breaking and bond-forming region is modeled using a nonlocal density functional method (B3LYP), whereas HF theory and molecular mechanics (UFF) are used to describe the electronic and steric impact of the outer coordination sphere of the catalyst. Intermediates and transition states were calculated along four isomeric pathways of two diastereomeric manifolds. The starting point for each manifold is a square planar catalyst−enamide complex. Binding of the re enantioface of the enamide to the catalyst generates the more stable, major diastereomer, favored by 3.6 kcal/mol over the minor diastereomer, which has the si face bound. However, the net free energy barrier for the reaction is 4.4 kcal/mol lower for the minor diastereomer than for the major diastereomer, making the minor diastereomer considerably more reactive and reproducing the “anti-lock-and-key” behavior observed experimentally in rhodium-catalyzed asymmetric hydrogenations. The difference in transition-state energies corresponds to an enantiomeric excess of 99.9% (R), within the range of experimental enantioselectivities of [Rh((R,R)-Me-DuPHOS)]+ hydrogenations. The stability and reactivity differences of the two diastereomers are explained using simple steric and electronic arguments. The sequence of elementary steps, as well as the relative orderings of intermediates and transition states, is very similar to that found in our previous work on the achiral model system [Rh(PH3)2(α-formamidoacrylonitrile)]+. We find oxidative addition to be the turnover-limiting step of the catalytic cycle. Our results are consistent with available empirical data for rhodium-catalyzed asymmetric hydrogenations, although more detailed experimental studies are needed on the specific model system studied herein.
5′-Tailed Octanucleotide Primers for Cycle Sequencing (1999)

Abstract Recently we reported the use of octamer primers tailed with 5-nitroindole for use as primers in cycle sequencing reactions. Here we report the successful use of some other universal base analogues to improve the effectiveness of an octamer sequencing primer. These analogues are 5-nitroindazole, 3-nitropyrrole and benzimidazole.
Comparison of Caspofungin and Amphotericin B for Invasive Candidiasis (2002)

Caspofungin is at least as effective as amphotericin B for the treatment of invasive candidiasis and, more specifically, candidemia.
High-definition video coding with super-macroblocks (2007)

A high definition video coding technique using super-macroblocks is investigated in this work. Our research is motivated by the observation that the macroblock-based partition in H.264/AVC may not be efficient for high definition video since the maximum macroblock size of 16 x 16 is relatively small against the whole image size. In the proposed super-macboblock based video coding scheme, the original block size MxN in H.264 is scaled to 2Mx2N. Along with the super-macroblock prediction framework, a low-complexity 16 x 16 discrete cosine transform (DCT) is proposed. As compared with the 1D 8 x 8 DCT, only 16 additions are added for a 1D 16 points 16 x 16 DCT. Furthermore, an adaptive scheme is proposed for the selection the best coding mode and best transform size. It is shown by experimental results that the super-macroblock coding scheme can achieve a higher coding gain.
Surfactant protein B: lipid interactions of synthetic peptides representing the amino-terminal amphipathic domain. (1991)

The mechanisms by which pulmonary surfactant protein B (SP-B) affects the surface activity of surfactant lipids are unclear. We have studied the peptide/lipid interactions of the amino-terminal amphipathic domain of SP-B by comparing the secondary conformations and surface activities of a family of synthetic peptides based on the native human SP-B sequence, modified by site-specific amino acid substitutions. Circular dichroism measurements show an alpha-helical structure correlating with the ability of the peptides to interact with lipids and with the surface activity of peptide/lipid dispersions. Amino acid substitutions altering either the charge or the hydrophobicity of the residues lowered the helical content and reduced the association of the aminoterminal segment with lipid dispersions. Surface activity of peptide/lipid mixtures was maximally altered by reversal of charge in synthetic peptides. These observations indicate that electrostatic interactions and hydrophobicity are important factors in determining optimal structure and function of surfactant peptides in lipid dispersions.
Identification of nuclear matrix proteins in the cancer and normal rat prostate. (1991)

The nuclear matrix is the structural component of the nucleus that determines nuclear morphology and organizes the DNA in a three-dimensional fashion that is tissue specific. Previously, some of the nuclear matrix proteins have been reported to be both tissue and cell type specific and are altered with the state of differentiation and transformation. This study demonstrates that the nuclear matrix is specific for the individual lobes of the normal rat prostate and that the nuclear matrix undergoes changes in protein composition in the Dunning prostate cancer tissue. Additionally, in the Dunning rat prostate adenocarcinoma cell lines, there is a range of tumor phenotypes and the nuclear matrix varies in composition in each tumor cell type. These differences in the nuclear matrix proteins are associated with quantitative changes in nuclear morphology that form the pleiomorphic state of the cancer nucleus.
Three-dimensional Structural Interactions of Insulin and Its Receptor (2003)

Electron microscopic imaging of the large insulin receptor protein in complex with insulin and in its free form, coupled with three-dimensional reconstruction and fitting of atomic subdomains, has yielded a structural model that permits an understanding of insulin binding at the atomic level. The model corroborates and explains the biological activity and binding behavior of virtually all naturally occurring insulins and insulin analogues, as well as the effects of receptor mutations on insulin binding. The model also provides a basis to address the fundamental question on the mechanism of transmembrane activation of receptors by ligand binding.
Comparison of tilidine/naloxone, tramadol and bromfenac in experimental pain: a double-blind randomized crossover study in healthy human volunteers. (1999)

The results support previous conclusions about the analgesic efficacy of tilidine/naloxone and tramadol in experimental pain. Moreover, the findings suggest that 75 mg bromfenac might be suitable for fast but short relief of pain of non-inflammatory genesis.