gebhart/patrepeval huggingface dataset:
Acute multi-sgRNA knockdown of KEOPS complex genes reproduces the microcephaly phenotype of the stable knockout zebrafish model (2018)

Until recently, morpholino oligonucleotides have been widely employed in zebrafish as an acute and efficient loss-of-function assay. However, off-target effects and reproducibility issues when compared to stable knockout lines have compromised their further use. Here we employed an acute CRISPR/Cas approach using multiple single guide RNAs targeting simultaneously different positions in two exemplar genes (osgep or tprkb) to increase the likelihood of generating mutations on both alleles in the injected F0 generation and to achieve a similar effect as morpholinos but with the reproducibility of stable lines. This multi single guide RNA approach resulted in median likelihoods for at least one mutation on each allele of >99% and sgRNA specific insertion/deletion profiles as revealed by deep-sequencing. Immunoblot showed a significant reduction for Osgep and Tprkb proteins. For both genes, the acute multi-sgRNA knockout recapitulated the microcephaly phenotype and reduction in survival that we observed previously in stable knockout lines, though milder in the acute multi-sgRNA knockout. Finally, we quantify the degree of mutagenesis by deep sequencing, and provide a mathematical model to quantitate the chance for a biallelic loss-of-function mutation. Our findings can be generalized to acute and stable CRISPR/Cas targeting for any zebrafish gene of interest.
Dominant genetic screen for cofactors that enhance antisense RNA-mediated gene silencing in fission yeast (2002)

Specific gene silencing has been demonstrated in a number of organisms by the introduction of antisense RNA. Mutagenesis of host-encoded factors has begun to unravel the mechanism of several forms of RNA-mediated gene silencing and has suggested that it may have been conserved through evolution. This has led to the identification of certain host genes, which, when mutated, abrogate this phenomenon. Conversely, the identification of other factors that, when co-expressed or overexpressed, can enhance gene inhibition is equally important for both elucidating the mechanism of this process and enhancing gene silencing in recalcitrant systems. We have taken such a dominant genetic approach to identify several host-encoded factors that dramatically enhance target gene silencing when co-expressed with antisense RNA in fission yeast. The transcription factor thi1 and, surprisingly, the ATP-dependent RNA helicase ded1 were initially shown to enhance gene silencing in this system. Additionally, screening of a Schizosaccharomyces pombe cDNA library identified four novel antisense-enhancing sequences (aes factors) all of which are homologous to genes encoding proteins with natural affinities for nucleic acids. These findings demonstrate the utility of this strategy in identifying host-encoded factors that can modulate gene silencing when co-expressed with antisense RNA and possibly other forms of gene-silencing activators.
The human endometrium as a fertility-determining factor (2006)

Intensive research work has been performed to better understand the regulation of the endometrium and its clinical implications to improve implantation. Although many proteins and molecules may influence endometrial development, their co-ordinated contribution to the implantation process is still poorly understood and a translation into clinical use has not sufficiently been performed. Clinical evaluation of the endometrium by ultrasound and other techniques, like endometrial biopsy and analysis of uterine secretions, has been intensively studied and therapeutic options to improve endometrial function have been suggested and tested. Systemic treatment with heparin, aspirin or corticosteroids did not result in improved implantation rates. Gene therapy and cervical treatment, e.g. with seminal plasma, are still in the phase of clinical research. Therefore, this review focuses on different aspects of endometrial research, which all contribute to the diagnosis, evaluation and therapy of endometrial function and dysfunction. First, the endometrial development towards a receptive milieu is described. Second, the actual clinical evaluation of endometrial receptivity, possible therapeutic strategies and in particular, the evaluation of endometrial function in the non-natural situation of hormonal stimulation is critically evaluated. In conclusion, the endometrium shall be considered as an important fertility-determining factor and therapeutic options should be developed in near future.
The effect of post‐sintering heat treatments on the fatigue properties of porous coated Ti‐6Al‐4V Alloy (1988)

Porous coated Ti-6Al-4V alloy implant systems provide a biocompatible interface between implant and bone, resulting in firm fixation and potential long-term retention via bony ingrowth. In order to achieve an acceptable porous coating structure, the sintering protocol for Ti-6Al-4V alloy systems often requires that the material be heat treated above the beta transus. This transforms the as-received equiaxed microstructure, recommended for surgical implants, to a lamellar alpha-beta distribution, which has been shown to have the worst fatigue properties of the most common structures attainable in Ti-6Al-4V alloy. However, post-sintering heat treatments may be used to improve these properties by producing microstructures more resistant to crack initiation and propagation. This study investigated the influence of microstructural variations on the fatigue properties of porous coated Ti-6Al-4V alloy material. Nonporous coated and porous coated Ti-6Al-4V alloy fatigue specimens were subjected to a standard sintering heat treatment to produce a lamellar microstructure. In addition, two post-sintering heat treatments were used to produce coarse and fine acicular microstructures. Rotating beam (reversed bending) fatigue testing was performed and the endurance limits determined for the noncoated and porous coated microstructures. The values determined were 668 MPa (noncoated as-received equiaxed), 394 MPa (noncoated lamellar), 488 MPa (non-coated coarse acicular), 494 MPa (noncoated fine acicular), 140 MPa (porous coated lamellar), 161 MPa (porous coated coarse acicular), and 162 MPa (porous coated fine acicular). The noncoated coarse and fine acicular specimens displayed an approximate 25% increase over the noncoated lamellar specimens. The porous coated coarse and fine acicular specimens showed an approximate 15% improvement over the porous coated lamellar specimens.
Replicative intermediate of hepatitis B virus in transfected murine fibroblasts (1987)

The NIH 3T3-derived cell line psi AM22b, which carries a defective Moloney murine leukemia virus, was transfected with a plasmid carrying the neo gene and two head-to-tail copies of the hepatitis B virus (HBV) genome positioned with opposing polarities. Both the two HBV dimers and the neo gene were located between two Moloney murine leukemia virus long terminal repeats. Poly(A)+ RNAs isolated from one clone that grew in the presence of G418 contained the two major classes of HBV-specific transcripts (3.5-kilobase pregenome and 2.1-kilobase mRNAs) in approximately equivalent amounts, which was reminiscent of the profiles of viral mRNAs from the livers of infected humans and chimpanzees.
A method for nested PCR with single closed reaction tubes. (1992)

Toward the goal of reducing diagnostic false positives while retaining high sensitivity, a closed-tube nested PCR procedure has been developed for detecting low-copy-number human immunodeficiency virus (HIV) gag target DNA sequences. Master mix for amplification 2, in a hanging gel matrix at the reaction tube top, remains sequestered from the reaction space of the tube during amplification 1. A severalfold excess of inner over outer primers is built into the procedure to assure the high sensitivity of nested PCR. The master mix for amplification 2 is then introduced into the reaction space by centrifugation, and the second amplification is performed as usual. The closed-tube nested procedure shows sensitivity approaching that of the open-tube control procedure, which detects a single copy of HIV gag target DNA at near-theoretical frequency, typically with microgram yields of specific amplification product.
Nanopore sensor for copper ion detection using a polyamine decorated β-cyclodextrin as the recognition element (2017)

A novel and simple nanopore sensing method has been developed for the detection of Cu<sup>II</sup> ions using polyamine decorated cyclodextrin as the recognition element.
Automatic word assignment to images based on image division and vector quantization (2000)

We propose a method that relates images and words. This method is based on statistical learning from image databases with words. The method uses two processes. The first uniformly divides each image into sub-images. With this division, all words assigned to images are inherited by each sub-image. The second process clusters sub-images by vector quantization. These processes produce results which show that each sub-image can be correlated to a set of words, each of which is selected from words assigned to original images. After clustering, the voting probability of each word for a set of divided images is estimated. This is done for each cluster of the feature vector of sub-images. Experiments show that this method is effective.
Correlations of three-dimensional motion of chromosomal loci in yeast revealed by the double-helix point spread function microscope (2014)

Single-particle tracking has been applied to study chromatin motion in live cells, revealing a wealth of dynamical behavior of the genomic material once believed to be relatively static throughout most of the cell cycle. Here we used the dual-color three-dimensional (3D) double-helix point spread function microscope to study the correlations of movement between two fluorescently labeled gene loci on either the same or different budding yeast chromosomes. We performed fast (10 Hz) 3D tracking of the two copies of the GAL locus in diploid cells in both activating and repressive conditions. As controls, we tracked pairs of loci along the same chromosome at various separations, as well as transcriptionally orthogonal genes on different chromosomes. We found that under repressive conditions, the GAL loci exhibited significantly higher velocity cross-correlations than they did under activating conditions. This relative increase has potentially important biological implications, as it might suggest coupling via shared silencing factors or association with decoupled machinery upon activation. We also found that on the time scale studied (∼0.1-30 s), the loci moved with significantly higher subdiffusive mean square displacement exponents than previously reported, which has implications for the application of polymer theory to chromatin motion in eukaryotes.
DNA Binding of an Ethidium Intercalator Attached to a Monolayer-Protected Gold Cluster (2002)

Ethidium intercalation has been investigated as a means of inducing binding of Au nanoparticles to DNA. The ethidium sites are attached to the nanoparticles as thiolate ligands, using 3,8-diamino-5-mercaptododecyl-6-phenylphenanthridinium (ethidium thiolate). Each nanoparticle bears only one or two ethidium thiolate ligands. The rest of the thiolate monolayer ligands on the monolayer-protected Au clusters (MPCs) were either N-(2-mercaptopropionyl)glycine (tiopronin/ethidium MPC) or trimethyl(mercaptoundecyl)ammonium (TMA/ethidium MPC). In solution mixtures of DNA and MPCs, the energy-transfer quenching of the ethidium ligands by the metal-like MPC core is partially released by ethidium binding to DNA, as observed by an increase in the intensity of ethidium fluorescence. Binding of the cationic TMA/ethidium MPC to DNA was efficient and rapid. The negatively charged tiopronin/ethidium MPC, in contrast, exhibits slow intercalation kinetics, relative to ethidium cation not attached to an MPC. The slow kinetics were analyzed as two competing binding interactions. The tiopronin/ethidium MPC binding to DNA was imaged by AFM.
Calcitonin Down-regulates E-cadherin Expression in Rodent Uterine Epithelium during Implantation (2002)

Previous studies indicated that calcitonin (CT), a peptide hormone involved in calcium homeostasis, is transiently expressed in the receptive rat and human endometrial epithelia within the window of implantation. Attenuation of uterine CT expression using antisense methods severely impaired implantation in the rat. The molecular pathway of CT in the pregnant uterus, however, remains unknown. In the present study, we investigated the cellular events following the binding of CT to its membrane receptors in human endometrial epithelial cell line Ishikawa. We observed that CT treatment triggers a transient rise in intracellular calcium in these cells. Most interestingly, CT treatment also led to the disappearance of E-cadherin, a critical cell adhesion molecule, from cell-cell contact sites. Blockade of intracellular calcium release by BAPTA-AM (1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid-acetoxymethyl) prevented the CT-induced disappearance of E-cadherin. Our studies further revealed that CT treatment markedly down-regulates the level of E-cadherin mRNA in Ishikawa cells. We also examined whether CT influences the expression of E-cadherin mRNA in intact rat uterine tissue during implantation. In pregnant rats, high levels of E-cadherin mRNA were expressed during the first 3 days of gestation when the CT mRNA in uterine epithelial cells is undetectable. Concomitant with a transient burst of CT expression during days 4-5 of pregnancy, the level of E-cadherin mRNA declined sharply. Furthermore, administration of exogenous CT to animals on day 2 of pregnancy led to a premature suppression of E-cadherin mRNA level on day 3, indicating a direct link between elevated levels of uterine CT and the down-regulation of E-cadherin expression in the surface epithelium. Collectively, our results are consistent with the hypothesis that CT-induced reduction in E-cadherin expression may remodel the adherens junctions between epithelial cells, and this change in epithelial cell phenotype might be a critical event during the implantation of the blastocyst.
Inactivation of hepatitis B virus and non-A, non-B hepatitis by chloroform (1983)

To determine whether a non-A, non-B hepatitis agent contained essential lipids, we extracted with chloroform a dilution of human plasma that contained approximately 10(4) chimpanzee infectious doses of non-A, non-B hepatitis virus and then tested for infectivity in chimpanzees. In addition, we treated a serum containing hepatitis B virus in the same way. Both of these samples were also sham extracted as controls. Known chloroform-sensitive and chloroform-resistant viruses were added directly to the hepatitis-containing serum or plasma as internal controls or to fetal calf serum as external controls and were assayed for infectivity in vitro after chloroform extraction or sham extraction. All infectivity of the diluted plasma that contained at least 10(4) chimpanzee infective doses of non-A, non-B hepatitis agent and all infectivity of the serum that contained 10(3.5) chimpanzee infective doses of hepatitis B virus were destroyed by chloroform. The chloroform-sensitive control viruses were completely inactivated, but the chloroform-resistant control viruses lost less than 0.5 log10 of infectivity. Sham-extracted non-A, non-B hepatitis agent-containing plasma was shown to maintain its infectivity in chimpanzees that had initially been inoculated with the chloroform-extracted plasma. Thus, both hepatitis type B and non-A, non-B hepatitis appear to be caused by viruses that can be inactivated by a lipid solvent.
Analysis of gene expression data using BRB-ArrayTools. (2007)

BRB-ArrayTools is an integrated software system for the comprehensive analysis of DNA microarray experiments. It was developed by professional biostatisticians experienced in the design and analysis of DNA microarray studies and incorporates methods developed by leading statistical laboratories. The software is designed for use by biomedical scientists who wish to have access to state-of-the-art statistical methods for the analysis of gene expression data and to receive training in the statistical analysis of high dimensional data. The software provides the most extensive set of tools available for predictive classifier development and complete cross-validation. It offers extensive links to genomic websites for gene annotation and analysis tools for pathway analysis. An archive of over 100 datasets of published microarray data with associated clinical data is provided and BRB-ArrayTools automatically imports data from the Gene Expression Omnibus public archive at the National Center for Biotechnology Information.
Antisense strategies in the treatment of leukemias. (1996)

Oligodeoxynucleotides are short nucleotide sequences of DNA synthesized as reverse complements of the desired mRNA target's nucleotide sequence. On formation of the RNA-DNA duplex, gene expression is prevented. Delivery of oligodeoxynucleotides targeting oncogene-encoded mRNAs to human cells in culture is associated with inhibition of cell proliferation and, in some circumstances, cell death. Oligodeoxynucleotides chemically modified to survive nuclease attack have been used systemically in murine models of human hematologic malignancies. In some studies, a measurable antileukemia effect has been observed. On the basis of these preclinical investigations, phase 1 clinical trials involving ex vivo and systemic administration of such compounds are now in progress at different institutions. Despite the remarkable progress of the past few years, much remains to be addressed on uptake, cellular distribution, mechanism(s) of action, and metabolism of such compounds. Furthermore, the "antisense effects" of the oligodeoxynucleotides might also be associated with nonspecific effects. In conclusion, time, a great deal of effort, and patience will tell whether such compounds will have a role as novel antileukemia therapeutic agents.
PI3Kβ Plays a Critical Role in Neutrophil Activation by Immune Complexes (2011)

Neutrophils are activated by immunoglobulin G (IgG)-containing immune complexes through receptors that recognize the Fc portion of IgG (FcγRs). Here, we used genetic and pharmacological approaches to define a selective role for the β isoform of phosphoinositide 3-kinase (PI3Kβ) in FcγR-dependent activation of mouse neutrophils by immune complexes of IgG and antigen immobilized on a plate surface. At low concentrations of immune complexes, loss of PI3Kβ alone substantially inhibited the production of reactive oxygen species (ROS) by neutrophils, whereas at higher doses, similar suppression of ROS production was achieved only by targeting both PI3Kβ and PI3Kδ, suggesting that this pathway displays stimulus strength-dependent redundancy. Activation of PI3Kβ by immune complexes involved cooperation between FcγRs and BLT1, the receptor for the endogenous proinflammatory lipid leukotriene B₄. Coincident activation by a tyrosine kinase-coupled receptor (FcγR) and a heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor (BLT1) may provide a rationale for the preferential activation of the β isoform of PI3K. PI3Kβ-deficient mice were highly protected in an FcγR-dependent model of autoantibody-induced skin blistering and were partially protected in an FcγR-dependent model of inflammatory arthritis, whereas combined deficiency of PI3Kβ and PI3Kδ resulted in near-complete protection in the latter case. These results define PI3Kβ as a potential therapeutic target in inflammatory disease.
Differential Interactions of Camptothecin Lactone and Carboxylate Forms with Human Blood Components (1994)

The intrinsic fluorescent emissions from the lactone and carboxylate forms of camptothecin have been exploited in order to elucidate their markedly different interactions with the various components of human blood. In phosphate-buffered saline (PBS) at pH 7.4, human serum albumin (HSA) preferentially binds the carboxylate form with a 150-fold higher affinity than the lactone form; these interactions result in camptothecin opening more rapidly and completely in the presence of HSA than in the protein's absence [Burke, T.G., & Mi, Z. (1993) Anal. Biochem. 212, 285-287]. In human plasma, at pH 7.4 and 37 degrees C, we have observed camptothecin lactone to open rapidly and fully to the carboxylate form (t1/2 = 11 min; % lactone at equilibrium, 0.2%). Substitution of a 10-hydroxy moiety into the camptothecin fluorophore makes the agent's emission spectrum highly sensitive to microenvironment polarity; we have observed pronounced blue shifting (from 530 to 430 nm) in the emission spectra of the hydroxy-substituted carboxylate both upon HSA association as well as upon drug dissolution in organic solvents of low dielectric strength. Hence, it appears that camptothecin carboxylate's fluorophore locates in a hydrophobic binding pocket in native HSA. Ionic interactions also appear to strongly affect binding between camptothecin carboxylate and the HSA binding pocket, since a 6-fold increase in solution salt concentration diminished camptothecin carboxylate binding by 10-fold. Our findings that HSA denaturation abolishes high-affinity binding indicate that interactions of the carboxylate drug form are specific for the native HSA conformation. Interestingly, high-affinity binding of the carboxylate appeared not to occur in the presence of other blood proteins, such as gamma-globulin, alpha 1-acid glycoprotein, fibrinogen, and the oxy and deoxy forms of hemoglobin. In whole blood versus plasma, camptothecin was found to display enhanced stability (t1/2 value of 22 min and a lactone concentration at equilibrium value of 5.3%). The enhanced stability of camptothecin in human blood was found to be due to drug associations with the lipid bilayers of red blood cells. Camptothecin lactone partitions into the lipid bilayers of erythrocytes, with the drug locating in a hydrophobic environment protected from hydrolysis.
Cucurbit[8]uril‐Mediated Redox‐Controlled Self‐Assembly of Viologen‐Containing Dendrimers (2004)

The dimerization of dendrimers that contain a single 4,4′-bipyridinium (viologen) unit, upon one-electron reduction, is strongly enhanced by the presence of the host cucurbit[8]uril. This behavior is attributed to the formation of a stable inclusion complex between the host and two π-stacked viologen radical-cation guests—the one-electron-reduced form of viologen (see scheme).
Increased pulsed amplifier efficiency by manipulating the fiber dopant distribution (2006)

In the pulse application, a significantly increased efficiency of high power largemode area fiber amplifiers is demonstrated by improving the overlap of the doped region with the fundamental mode of the fiber.