gebhart/patrepeval huggingface dataset:
Successful Transient Expression of Cas9 and Single Guide RNA Genes in Chlamydomonas reinhardtii (2014)

The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a powerful and precise tool for targeted gene modification (e.g., gene knockout and gene replacement) in numerous eukaryotic organisms. Initial attempts to apply this technology to a model, the single-cell alga, Chlamydomonas reinhardtii, failed to yield cells containing edited genes. To determine if the Cas9 and single guide RNA (sgRNA) genes were functional in C. reinhardtii, we tested the ability of a codon-optimized Cas9 gene along with one of four different sgRNAs to cause targeted gene disruption during a 24-h period immediately following transformation. All three exogenously supplied gene targets as well as the endogenous FKB12 (rapamycin sensitivity) gene of C. reinhardtii displayed distinct Cas9/sgRNA-mediated target site modifications as determined by DNA sequencing of cloned PCR amplicons of the target site region. Success in transient expression of Cas9 and sgRNA genes contrasted with the recovery of only a single rapamycin-resistant colony bearing an appropriately modified FKB12 target site in 16 independent transformation experiments involving >10(9) cells. Failure to recover transformants with intact or expressed Cas9 genes following transformation with the Cas9 gene alone (or even with a gene encoding a Cas9 lacking nuclease activity) provided strong suggestive evidence for Cas9 toxicity when Cas9 is produced constitutively in C. reinhardtii. The present results provide compelling evidence that Cas9 and sgRNA genes function properly in C. reinhardtii to cause targeted gene modifications and point to the need for a focus on development of methods to properly stem Cas9 production and/or activity following gene editing.
Reduction of potassium currents and phosphatidylinositol 3-kinase-dependent AKT phosphorylation by tumor necrosis factor-(alpha) rescues axotomized retinal ganglion cells from retrograde cell death in vivo. (2001)

Tumor-necrosis-factor-alpha (TNF-alpha) prevented secondary death of retinal ganglion cells (RGCs) after axotomy of the optic nerve in vivo. This RGC rescue was confirmed in vitro in a mixed retinal culture model. In accordance with our previous findings, TNF-alpha decreased outward potassium currents in RGCs. Antagonism of the TNF-alpha-induced decrease in outward potassium currents with the potassium channel opener minoxidilsulfate (as verified by electrophysiology) abolished neuroprotection. Western blot analysis revealed an upregulation of phospho-Akt as a consequence of TNF-alpha-induced potassium current reduction. Inhibition of the phosphatidylinositol 3-kinase-Akt pathway with wortmannin decreased TNF-alpha-promoted RGC survival. These data point to a functionally relevant cytokine-dependent neuroprotective signaling cascade in adult CNS neurons.
The “Phantom Effect” of the Rexinoid LG100754: Structural and Functional Insights (2010)

Retinoic acid receptors (RARs) and Retinoid X nuclear receptors (RXRs) are ligand-dependent transcriptional modulators that execute their biological action through the generation of functional heterodimers. RXR acts as an obligate dimer partner in many signalling pathways, gene regulation by rexinoids depending on the liganded state of the specific heterodimeric partner. To address the question of the effect of rexinoid antagonists on RAR/RXR function, we solved the crystal structure of the heterodimer formed by the ligand binding domain (LBD) of the RARα bound to its natural agonist ligand (all-trans retinoic acid, atRA) and RXRα bound to a rexinoid antagonist (LG100754). We observed that RARα exhibits the canonical agonist conformation and RXRα an antagonist one with the C-terminal H12 flipping out to the solvent. Examination of the protein-LG100754 interactions reveals that its propoxy group sterically prevents the H12 associating with the LBD, without affecting the dimerization or the active conformation of RAR. Although LG100754 has been reported to act as a 'phantom ligand' activating RAR in a cellular context, our structural data and biochemical assays demonstrate that LG100754 mediates its effect as a full RXR antagonist. Finally we show that the 'phantom ligand effect' of the LG100754 is due to a direct binding of the ligand to RAR that stabilizes coactivator interactions thus accounting for the observed transcriptional activation of RAR/RXR.
Measurement of local diffusion coefficients in biofilms by microinjection and confocal microscopy (1997)

A new technique for the determination of local diffusion coefficients in biofilms is described. It is based on the microinjection of fluorescent dyes and quantitative analysis of the subsequent plume formation using confocal laser microscopy. The diffusion coefficients of fluorescein (MW 332), TRITC-IgG (MW 150000) and phycoerythrin (MW 240000) were measured in the cell clusters and interstitial voids of a heterogeneous biofilm. The diffusivities measured in the voids were close to the theoretical values in water. Fluorescein had the same diffusivity in cell clusters, voids, and sterile medium. TRITC-IgG did not diffuse in cell clusters, presumably due to binding to the cell cluster matrix. After treatment of the biofilm with bovine serum albumin, binding capacity decreased and the diffusion coefficient could be measured. The diffusivity of phycoerythrin in cell clusters was impeded by 41%, compared to interstitial voids. From the diffusion data of phycoerythrin it was further calculated that the cell cluster matrix had the characteristics of a gel with 0.6 nm thick fibers and pore diameters of 80 nm. (c) 1997 John Wiley & Sons, Inc.
Run by run control of chemical-mechanical polishing (1996)

A prototype hardware/software system has been developed and applied to the control of single wafer chemical-mechanical polishing (CMP) processes. The control methodology consists of experimental design to build response surface and linearized control models of the process, and the use of feedback control to change recipe parameters (machine settings) on a lot by lot basis. Acceptable regression models for a single wafer polishing tool and process were constructed for average removal rate and nonuniformity which are calculated based on film thickness measurement at nine points on 8-in blanket oxide wafers. For control, an exponentially weighted moving average model adaptation strategy was used, coupled to multivariate recipe generation incorporating user weights on the inputs and outputs, bounds on the input ranges, and discrete quantization in the machine settings. We found that this strategy successfully compensated for substantial drift in the uncontrolled tool's removal rate. It was also found that the equipment model generated during the experimental design was surprisingly robust; the same model was effective across more than one CMP tool, and over several months. We believe that the same methodology is applicable to patterned oxide wafers; work is in progress to demonstrate patterned wafer control, to improve the control, communication, and diagnosis components of the system, and to integrate real-time information into the run by run control of the process.
AG-348 enhances pyruvate kinase activity in red blood cells from patients with pyruvate kinase deficiency (2017)

Pyruvate kinase (PK) deficiency is a rare genetic disease that causes chronic hemolytic anemia. There are currently no targeted therapies for PK deficiency. Here, we describe the identification and characterization of AG-348, an allosteric activator of PK that is currently in clinical trials for the treatment of PK deficiency. We demonstrate that AG-348 can increase the activity of wild-type and mutant PK enzymes in biochemical assays and in patient red blood cells treated ex vivo. These data illustrate the potential for AG-348 to restore the glycolytic pathway activity in patients with PK deficiency and ultimately lead to clinical benefit.
Layer-by-Layer Nanoparticles for Systemic Codelivery of an Anticancer Drug and siRNA for Potential Triple-Negative Breast Cancer Treatment (2013)

A single nanoparticle platform has been developed through the modular and controlled layer-by-layer process to codeliver siRNA that knocks down a drug-resistance pathway in tumor cells and a chemotherapy drug to challenge a highly aggressive form of triple-negative breast cancer. Layer-by-layer films were formed on nanoparticles by alternately depositing siRNA and poly-l-arginine; a single bilayer on the nanoparticle surface could effectively load up to 3500 siRNA molecules, and the resulting LbL nanoparticles exhibit an extended serum half-life of 28 h. In animal models, one dose via intravenous administration significantly reduced the target gene expression in the tumors by almost 80%. By generating the siRNA-loaded film atop a doxorubicin-loaded liposome, we identified an effective combination therapy with siRNA targeting multidrug resistance protein 1, which significantly enhanced doxorubicin efficacy by 4 fold in vitro and led to up to an 8-fold decrease in tumor volume compared to the control treatments with no observed toxicity. The results indicate that the use of layer-by-layer films to modify a simple liposomal doxorubicin delivery construct with a synergistic siRNA can lead to significant tumor reduction in the cancers that are otherwise nonresponsive to treatment with Doxil or other common chemotherapy drugs. This approach provides a potential strategy to treat aggressive and resistant cancers, and a modular platform for a broad range of controlled multidrug therapies customizable to the cancer type in a singular nanoparticle delivery system.
SUTURELESS SCLERAL BUCKLE FOR RETINAL DETACHMENT WITH THIN SCLERA (1988)

Retinal detachment surgery can be hazardous in the presence of thin sclera, with increased risk of inadvertent perforation. We designed polymethylmethacrylate belt loops that can be fixed to the sclera with cyanoacrylate tissue adhesive, allowing 360 degrees scleral buckling to be performed without sutures. We report the successful use of this technique in a three-year-old girl with a rhegmatogenous retinal detachment and blue sclerae.
Rapid and sensitive method for evaluating Pseudomonas aeruginosa virulence factors during corneal infections in mice (1995)

A murine corneal scratch model has been used extensively to study various aspects of the pathogenesis of Pseudomonas aeruginosa, a common etiologic agent of corneal infections. This model uses mild inhalation anesthetics which keep the animals immobile for a relatively short time and promote the interaction between the infecting organisms and the corneal wound. Under these circumstances, only a small number of P. aeruginosa isolates delivered at inocula of > 10(7) CFU are infectious. We determined that this model is useful for studying other P. aeruginosa strains given at lower doses if injectable anesthetics are administered prior to infection to keep the animals immobile for 15 to 30 min. Under these conditions, eight clinical isolates of P. aeruginosa tested at doses of 10(8) CFU per eye induced corneal perforation and/or phthisis in C3H/HeN mice. The 50% infective doses of several strains were between 3 x 10(2) and 1 x 10(5) CFU per mouse eye. When this modified anesthetic procedure was used to evaluate the roles of different P. aeruginosa virulence factors in eye infections, pathology was not observed when eyes were inoculated with 10(8) CFU of strains deficient in production of a complete lipopolysaccharide or the RpoN sigma factor. A strain with a point mutation in the fur gene, involved in production of iron-regulated factors, showed decreased virulence, while a mutant deficient in both hemolytic and nonhemolytic phospholipase C was fully virulent. By modifying the anesthesia procedure, the corneal scratch model allows rapid evaluations of the roles of P. aeruginosa virulence factors in corneal infections.
Sensor systems, electronic tongues and electronic noses, for the monitoring of biotechnological processes (2008)

Production of biofuel is based on the conversion by microorganisms of complex organic substrates into the methane or ethanol, which are consequently used as energy sources. Real time monitoring of the fermented media composition is of paramount for the effectiveness of the whole process. However, despite the fact that products worth billions of dollars are produced through fermentation processes annually, analytical instruments used for these processes' monitoring remain relatively primitive. Established laboratory techniques produce exhaustive information about media composition but analysis is often quite time-consuming, expensive, requires skilled personnel and hardly can be automated. Lack of on-line sensors for the fermentation monitoring is commonly stressed in the literature. One of the techniques particularly suitable for this purpose is chemical sensors. Such features as low prices, relatively simple instrumentation, minimal sample preparation and easy automation of measurements make chemical sensors an attractive tool for industrial process control. However, practical use of chemical sensors in complex media is often hindered by their insufficient selectivity. For example, only pH and oxygen probes are routinely used in bio-reactors. One of the emerging approaches permitting to overcome the selectivity problems is the use of systems instead of discrete sensors. Such systems for liquid and gas analysis were named electronic tongues and electronic noses correspondingly. They are capable to perform both quantitative analysis (components' concentrations) and classification or recognition of multicomponent media. This review presents recent achievements in the R&D and applications of electronic tongues and noses to the monitoring of biotechnological processes.
Identification and Characterization of a Novel Secreted Immunoglobulin Binding Protein from Group A Streptococcus (2001)

Immunoglobulin binding proteins are one of several pathogenicity factors which have been associated with invasive disease caused by group A streptococci. The surface-bound M and M-like proteins of Streptococcus pyogenes are the most characterized of these immunoglobulin binding proteins, and in most cases they bind only a single antibody class. Here we report the identification of a novel non-M-type secreted protein, designated SibA (for secreted immunoglobulin binding protein from group A streptococcus), which binds all immunoglobulin G (IgG) subclasses, the Fc and Fab fragments, and also IgA and IgM. SibA has no significant sequence homology to any M-related proteins, is not found in the vir regulon, and contains none of the characteristic M-protein regions, such as the A or C repeats. Like M proteins, however, SibA does have relatively high levels of alanine, lysine, glutamic acid, leucine, and glycine. SibA and M proteins also share an alpha-helical N-terminal secondary structure which has been previously implicated in immunoglobulin binding in M proteins. Evidence presented here indicates that this is also the case for SibA. SibA also has regions of local similarity with other coiled-coil proteins such as Listeria monocytogenes P45 autolysin, human myosin heavy chain, macrogolgin, and Schistoma mansoni paramyosin, some of which are of potential significance since cross-reactive antibodies between myosin proteins and M proteins have been implicated in the development of the autoimmune sequelae of streptococcal disease.
Monolithically Integrated 40-Wavelength Demultiplexer and Photodetector Array on Silicon (2011)

We demonstrated a 40-channel dense-wavelength-division-multiplexed (DWDM) monolithically integrated receiver on silicon, which consists of a silicon nitride <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(\hbox{Si}_{3}\hbox{N}_{4})$</tex> </formula> arrayed waveguide grating (AWG) demultiplexer with integrated germanium-on-silicon waveguide photodetectors. Net responsivities from a cleaved standard single-mode fiber to detectors of <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$0.15\sim 0.22$</tex></formula> A/W are measured, with flattened passbands with 1-dB bandwidth over 60% of the 200-GHz channel spacing. Single-channel operation up to 40 Gb/s is demonstrated with a SiGe transimpedance amplifier.
Electrostrictive polymer artificial muscle actuators (2002)

Many new robotic and teleoperated applications require a high degree of mobility or dexterity that is difficult to achieve with current actuator technology. Natural muscle is an actuator that has many features, including high energy density, fast speed of response, and large stroke, that are desirable for such applications. The electrostriction of polymer dielectrics with compliant electrodes can be used in electrically controllable, muscle-like actuators. These electrostrictive polymer artificial muscle (EPAM) actuators can produce strains of up to 30% and pressures of up to 1.9 MPa. The measured specific energy achieved with polyurethane and silicone polymers exceeds that of electromagnetic, electrostatic, piezoelectric, and magnetostrictive actuators. A simple model using linear elastic theory can predict EPAM actuator performance from mechanical and electrical material properties and load conditions. A spherical joint for a highly articulated (snake-like) manipulator using EPAM actuator elements has been demonstrated. A rotary motor using EPAM actuator elements has been shown to produce a specific torque of 19 mNm/g and a specific power of 0.1 W/g. An improved EPAM motor could produce greater specific power and specific torque than could electric motors.
A fully integrated digital demodulation and forward error correction IC for digital satellite television (2002)

This paper describes a single digital IC that performs the digital demodulation, clock recovery, carrier recovery, Viterbi decoding, de-interleaving, and Reed Solomon decoding for digital satellite delivery of video, audio and data. The chip performs up to 60 Mega-bits per second QPSK decoding, covering both the Digital Video Broadcast Satellite (DVBS) standard in Europe and the Digital Satellite System (DSS) in the US. The 0.5 /spl mu/m CMOS chip contains 504,000 transistors and 56 Kbits of memory in 71 mm/sup 2/. In addition to QPSK, the chip decodes up to 256 QAM with an external equalizer for cable and terrestrial applications.
Isolation and sequence analysis of a novel human tyrosine kinase gene. (1989)

Using v-abl probes, we have identified and cloned a novel fes/fps-homologous human cDNA, which we have designated FER (pronounced "fair"). This apparently full-length cDNA of 3.0 kilobases has an open reading frame of 2,466 base pairs and the capacity to encode a protein of 94,000 molecular weight. The cDNA contains regions homologous to the highly conserved tyrosine protein kinase domain of other oncogenes and growth factor receptors but lacks a clear transmembrane region, indicating that it encodes a tyrosine kinase of the nonreceptor type. The deduced amino acid sequence of FER resembles that of c-fes/fps. Our data indicate that the protein product of FER, p94FER, corresponds to a previously reported cellular phosphoprotein, NCP94, detected with a v-fps-specific antipeptide antiserum.
Enzyme Digests Eliminate Nonfunctional Env from HIV-1 Particle Surfaces, Leaving Native Env Trimers Intact and Viral Infectivity Unaffected (2011)

HIV-1 viruses and virus-like particles (VLPs) bear nonnative "junk" forms of envelope (Env) glycoprotein that may undermine the development of antibody responses against functional gp120/gp41 trimers, thereby blunting the ability of particles to elicit neutralizing antibodies. Here, we sought to better understand the nature of junk Env with a view to devising strategies for its removal. Initial studies revealed that native trimers were surprisingly stable in the face of harsh conditions, suggesting that junk Env is unlikely to arise by trimer dissociation or gp120 shedding. Furthermore, the limited gp120 shedding that occurs immediately after synthesis of primary HIV-1 isolate Envs is not caused by aberrant cleavage at the tandem gp120/gp41 cleavage sites, which were found to cleave in a codependent manner. A major VLP contaminant was found to consist of an early, monomeric form of gp160 that is glycosylated in the endoplasmic reticulum (gp160ER) and then bypasses protein maturation and traffics directly into particles. gp160ER was found to bind two copies of monoclonal antibody (MAb) 2G12, consistent with its exclusively high-mannose glycan profile. These findings prompted us to evaluate enzyme digests as a way to remove aberrant Env. Remarkably, sequential glycosidase-protease digests led to a complete or near-complete removal of junk Env from many viral strains, leaving trimers and viral infectivity largely intact. "Trimer VLPs" may be useful neutralizing antibody immunogens.
Discriminative Feature Selection via Multiclass Variable Memory Markov Model (2003)

We propose a novel feature selection method based on a variable memory Markov (VMM) model. The VMM was originally proposed as a generative model trying to preserve the original source statistics from training data. We extend this technique to simultaneously handle several sources, and further apply a new criterion to prune out nondiscriminative features out of the model. This results in a multiclass discriminative VMM (DVMM), which is highly efficient, scaling linearly with data size. Moreover, we suggest a natural scheme to sort the remaining features based on their discriminative power with respect to the sources at hand. We demonstrate the utility of our method for text and protein classification tasks.
Improved preservation of the ram spermatozoan plasma membrane using betaine in the primary fixative (1997)

Improved preservation of ram spermatozoa was obtained by filtration onto a Millipore filter followed by fixation in a fixative containing 23 mM betaine, which raised fixative osmolality only slightly. In samples fixed in control preparations with betaine omitted the plasma membrane had a ruffled appearance, while the betaine-containing fixative gave the plasma membrane a smooth contour which closely followed underlying structures. Betaine is known to function as an osmoprotectant in other situations, and may protect the cells from osmotic damage during the initial stages of fixation.
Selective gene delivery to head and neck cancer cells via an integrin targeted adenoviral vector. (1999)

In vivo cancer gene therapy approaches for squamous cell carcinoma of the head and neck (SCCHN) based on adenoviral vector-mediated gene delivery have been limited by the suboptimal efficacy of gene transfer to tumor cells. We hypothesized that this issue was due to deficiency of the primary adenoviral receptor, the coxsackie-adenovirus receptor (CAR), on the tumor targets. Studies of CAR levels on SCCHN cell lines confirmed that their relative refractoriness to the adenoviral vector was based on this deficiency. To circumvent this deficiency, we applied an adenoviral vector targeted to a tumor cell marker characteristic of SCCHN. In this regard, integrins of the alpha2beta1 and alpha3beta1 class are frequently overexpressed in SCCHN. Furthermore, these integrins recognize the RGD peptide motif. On this basis, we applied an adenoviral vector genetically modified to contain such a peptide within the HI loop of the fiber protein as a means to alter viral tropism. Studies confirmed that the CAR-independent gene delivery achieved via this strategy allowed enhanced gene transfer efficiencies to SCCHN tumor cells. Importantly, this strategy could achieve preferential augmentation of gene transfer in tumor cells compared with normal cells. The ability to achieve enhanced and specific gene transfer to tumor cells via adenoviral vectors has important implications for gene therapy strategies for SCCHN and for other neoplasms in general.