gebhart/patrepeval huggingface dataset:
Versatility of chemically synthesized guide RNAs for CRISPR-Cas9 genome editing (2016)

The CRISPR-Cas9 system has become the most popular and efficient method for genome engineering in mammalian cells. The Streptococcus pyogenes Cas9 nuclease can function with two types of guide RNAs: the native dual crRNA and tracrRNA (crRNA:tracrRNA) or a chimeric single guide RNA (sgRNA). Although sgRNAs expressed from a DNA vector are predominant in the literature, guide RNAs can be rapidly generated by chemical synthesis and provide equivalent functionality in gene editing experiments. This review highlights the attributes and advantages of chemically synthesized guide RNAs including the incorporation of chemical modifications to enhance gene editing efficiencies in certain applications. The use of synthetic guide RNAs is also uniquely suited to genome-scale high throughput arrayed screening, particularly when using complex phenotypic assays for functional genomics studies. Finally, the use of synthetic guide RNAs along with DNA-free sources of Cas9 (mRNA or protein) allows for transient CRISPR-Cas9 presence in the cell, thereby resulting in a decreased probability of off-target events.
Thermal Stability of Fibroblast Growth Factor Protein Is a Determinant Factor in Regulating Self-Renewal, Differentiation, and Reprogramming in Human Pluripotent Stem Cells (2011)

Fibroblast growth factor (FGF), transforming growth factor (TGF)/Nodal, and Insulin/insulin-like growth factor (IGF) signaling pathways are sufficient to maintain human embryonic stem cells (ESCs) and induced pluripotent stem cells in a proliferative, undifferentiated state. Here, we show that only a few FGF family members (FGF2, FGF4, FGF6, and FGF9) are able to sustain strong extracellular-signal-regulated kinase (ERK) phosphorylation and NANOG expression levels in human ESCs. Surprisingly, FGF1, which is reported to target the same set of receptors as FGF2, fails to sustain ERK phosphorylation and NANOG expression under standard culture conditions. We find that the failure of FGF1 to sustain ES is due to thermal instability of the wild-type protein, not receptor specificity, and that a mutated thermal-stable FGF1 sustains human ESCs and supports both differentiation and reprogramming protocols.
A trans -Golgi network golgin is required for the regulated secretion of TNF in activated macrophages in vivo (2008)

The transmembrane precursor of tumor necrosis factor-α (TNF) exits the trans -Golgi network (TGN) in tubular carriers for subsequent trafficking and delivery to the cell surface; however, the molecular machinery responsible for Golgi export is unknown. We previously reported that members of the TGN golgin family are associated with subdomains and tubules of the TGN. Here, we show that the TGN golgin, p230/golgin-245 (p230), is essential for intracellular trafficking and cell surface delivery of TNF in transfected HeLa cells and activated macrophages. Live-cell imaging revealed that TNF transport from the TGN is mediated selectively by tubules and carriers marked by p230. Significantly, LPS activation of macrophages resulted in a dramatic increase of p230-labeled tubules and carriers emerging from the TGN, indicating that macrophages up-regulate the transport pathway for TNF export. Depletion of p230 in LPS-stimulated macrophages reduced cell surface delivery of TNF by &gt;10-fold compared with control cells. To determine whether p230 depletion blocked TNF secretion in vivo , we generated retrogenic mice expressing a microRNA-vector to silence p230. Bone-marrow stem cells were transduced with recombinant retrovirus containing microRNA constructs and transplanted into irradiated recipients. LPS-activated peritoneal macrophages from p230 miRNA retrogenic mice were depleted of p230 and had dramatically reduced levels of cell surface TNF. Overall, these studies have identified p230 as a key regulator of TNF secretion and have shown that LPS activation of macrophages results in increased Golgi carriers for export. Also, we have demonstrated a previously undescribed approach to control cytokine secretion by the specific silencing of trafficking machinery.
Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron (1990)

We have completed a comprehensive deletion analysis of the Tetrahymena ribozyme in order to define the minimum secondary structure requirements for phosphoester transfer activity of a self-splicing group I intron. A total of 299 nucleotides were removed in a piecewise fashion, leaving a catalytic core of 114 nucleotides that form 7 base-paired structural elements. Among the various deletion mutants are a 300-nucleotide single-deletion mutant and a 281-nucleotide double-deletion mutant whose activity exceeds that of the wild type when tested under physiologic conditions. Consideration of those structural elements that are essential for catalytic activity leads to a simplified secondary structure model of the catalytic core of a group I intron.
<title>Cadmium selenide quantum dot doping of organic-inorganic hybrid materials derived by sol-gel processing</title> (1997)

Nano-sized, phenyl-capped CdSe quantum dots were isolated, after preparation inside reversed micelles present in AOT/H<SUB>2</SUB>O/heptane, and then successfully redispersed in the amino- silicate ormosil (i.e. organically modified silicate) derived from 3-aminopropyl-(trimethoxy)silane. Doped ormosils were formed into films of a few micrometer thickness or small bulk samples. The ormosils were structurally characterized by means of absorption spectroscopy in the visible and near-infrared ranges, and by <SUP>29</SUP>Si solid state nuclear magnetic resonance spectroscopy. The siloxane matrix of the amino-silicate ormosil was found to be 84% condensed and polymeric water molecules are hydrogen bonded into the matrix, presumably at silanol and amine sites. CdSe dots of apparently good monodispersity and radius 1.5 to 2.4 nm (going from yellow to red in visual appearance) were redispersed in the amino- silicate ormosil. Attempts to prepare larger dots resulted in flocculation of the CdSe. The maximum loading of CdSe dots in the amino-silicate matrix was measured to be 2.05 weight% CdSe<SUB>0.72</SUB>, where the density of the amino-silicate host was around 0.5 to 0.7 of the density of a typical, melt-derived silicate glass.
Crowdroid (2011)

The sharp increase in the number of smartphones on the market, with the Android platform posed to becoming a market leader makes the need for malware analysis on this platform an urgent issue.
Optimization of retroviral vector-mediated gene transfer into endothelial cells in vitro. (1992)

Retroviral vector-mediated gene transfer into endothelial cells is relatively inefficient with transduction rates as low as 1-2% in vitro and even lower in vivo. To increase the efficiency of gene transfer into endothelial cells, we used retroviral vectors expressing beta-galactosidase and urokinase and measured endothelial cell transduction efficiencies with quantitative assays for beta-galactosidase and urokinase protein. We evaluated several techniques reported to improve the efficiency of retroviral transduction in vitro, including 1) extended periods of exposure to vector, 2) repeated exposures to vector, 3) maximization of the ratio of vector particles to endothelial cells by increasing the volume and concentration of vector particles or by decreasing the number of endothelial cells exposed, 4) cocultivation of endothelial cells with vector-producing cells, and 5) variation of the type and concentration of polycation used with the retroviral vector. Only the use of more concentrated (higher titer) vector-containing supernatant and the use of the polycation DEAE-dextran improved the efficiency of gene transfer into endothelial cells in vitro. In an optimized transduction protocol, a 60-second exposure to 1 mg/ml DEAE-dextran followed by a single 6-hour exposure to supernatant of a titer of 10(5)-10(6) colony-forming units/ml resulted in transduction efficiencies of 50-90% with both vectors. Decreasing the time of the supernatant exposure to 15 minutes permitted transduction efficiencies of 15-20% while significantly minimizing the duration of the transduction. Therefore, the optimized protocol allows high efficiency in vitro gene transfer into endothelial cells within several hours. The briefer protocol may prove useful for in vivo gene transfer in which the time of exposure to the supernatant is limited.
Motion Artifacts in fMRI: Comparison of 2DFT with PR and Spiral Scan Methods (1995)

Activation signals based on BOLD contrast changes consequent to neuronal stimulation typically produce cortical intensity differences of < 10% at 1.5T. Hemodynamically driven pulsation of the brain can cause highly pulsatile phase shifts, which in turn result in motion artifacts whose intensity is larger than the activation signals in 2DFT scan methods. This paper presents a theoretical and experimental comparison of the magnitude of such artifacts for 2DFT and two other methods using non-Cartesian k-space trajectories. It is shown that artifacts increase with TR for 2DFT methods, and that projection reconstruction (PR) and spiral methods have significantly reduced artifact intensities, because these trajectories collect low spatial frequencies with every view. The spiral technique is found to be superior in terms of efficiency and motion insensitivity.
Self Antigen Prognostic for Human Immunodeficiency Virus Disease Progression (2001)

We have recently found that an extracellular protein, alpha(1) proteinase inhibitor (alpha(1)PI; alpha(1) antitrypsin), is required for in vitro human immunodeficiency virus (HIV) infectivity outcome. We show here in a study of HIV-seropositive patients that decreased viral load is significantly correlated with decreased circulating alpha(1)PI. In the asymptomatic category of HIV disease, 100% of patients manifest deficient levels of active alpha(1)PI, a condition known to lead to degenerative lung diseases and a dramatically reduced life span. Further, HIV-associated alpha(1)PI deficiency is correlated with circulating anti-alpha(1)PI immunoglobulin G. These results suggest that preventing HIV-associated alpha(1)PI deficiency may provide a strategic target for preventing HIV-associated pathophysiology.
RNA virus vectors: Where are we and where do we need to go? (1998)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Nutritionally Improved Agricultural Crops (2008)

Agricultural innovation has always involved new, science-based products and processes that have contributed reliable methods for increasing productivity and sustainability. Biotechnology has introduced a new dimension to such innovation, offering efficient and cost-effective means to produce a
Ru(ii)-Catalyzed C–H activation and annulation of salicylaldehydes with monosubstituted and disubstituted alkynes (2016)

The Ru(ii)-catalyzed C-H activation and annulation reaction of salicylaldehydes and disubstituted alkynes affords chromones in high yields. This reaction also works with terminal alkynes and tolerates a wide range of sensitive functional groups. The selectivity pattern of this Ru(ii)-catalyzed annulation reaction is different from the known Au(i), Rh(iii)-catalyzed annulation reactions of salicylaldehydes and terminal alkynes.
Considering individual cognitive ability in the provision of usable navigation assistance (2003)

It is noted that the design of vehicle navigation aids has tended to emphasize hardware innovations and software optimized to this hardware. User interfaces generally adopt a single paradigm for the presentation of navigation information. It is argued that this assumes a homogeneous user community and ignores individual driver ability in spatial cognition, attention, and other problem-solving issues. It is suggested that the next generation of aids should be designed with more attention to the manner in which people structure, recall, and utilize spatial information naturally. Literature on spatial knowledge, individual differences, and human subject categorization is reviewed. Recommendations are made for the design of future user interfaces in order to provide more usable navigation assistance to individual drivers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low Levels of the Omega‐3 Index are Associated with Sudden Cardiac Arrest and Remain Stable in Survivors in the Subacute Phase (2011)

In previous studies, low blood levels of n-3 fatty acids (FA) have been associated with increased risk of cardiac death, and the omega-3 index (red blood cell (RBC) eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) expressed as weight percentage of total FA) has recently been proposed as a new risk factor for death from coronary artery disease, especially following sudden cardiac arrest (SCA). As blood samples often haven been harvested after the event, the aim of our study was to evaluate the stability of RBC fatty acids following SCA. The total FA profile, including the omega-3 index, was measured three times during the first 48 h in 25 survivors of out-of-hospital cardiac arrest (OHCA), in 15 patients with a myocardial infarction (MI) without SCA and in 5 healthy subjects. We could not demonstrate significant changes in the FA measurements in any of the groups, this also applied to the omega-6/omega-3 ratio and the arachidonic acid (AA)/EPA ratio. Furthermore, we compared the omega-3 index in 14 OHCA-patients suffering their first MI with that of 185 first-time MI-patients without SCA; mean values being 4.59% and 6.48%, respectively (p = 0.002). In a multivariate logistic regression analysis, a 1% increase of the omega-3 index was associated with a 58% (95% CI: 0.25-0.76%) reduction in risk of ventricular fibrillation (VF). In conclusion, the omega-3 index remained stable after an event of SCA and predicted the risk of VF.
A new family of carbon‐nitrogen hydrolases (1994)

Using computer methods for database search and multiple alignment, statistically significant sequence similarities were identified between several nitrilases with distinct substrate specificity, cyanide hydratases, aliphatic amidases, beta-alanine synthase, and a few other proteins with unknown molecular function. All these proteins appear to be involved in the reduction of organic nitrogen compounds and ammonia production. Sequence conservation over the entire length, as well as the similarity in the reactions catalyzed by the known enzymes in this family, points to a common catalytic mechanism. The new family of enzymes is characterized by several conserved motifs, one of which contains an invariant cysteine that is part of the catalytic site in nitrilases. Another highly conserved motif includes an invariant glutamic acid that might also be involved in catalysis.
Rapid Phase Retrieval Using The Fast Fourier Transform (1995)

Phase retrieval from intensity data based purely on the Fourier transform is demonstrated experimentally and theoretically. Our method does not require boundary conditions.
Measuring single-cell density (2011)

We have used a microfluidic mass sensor to measure the density of single living cells. By weighing each cell in two fluids of different densities, our technique measures the single-cell mass, volume, and density of approximately 500 cells per hour with a density precision of 0.001 g mL(-1). We observe that the intrinsic cell-to-cell variation in density is nearly 100-fold smaller than the mass or volume variation. As a result, we can measure changes in cell density indicative of cellular processes that would be otherwise undetectable by mass or volume measurements. Here, we demonstrate this with four examples: identifying Plasmodium falciparum malaria-infected erythrocytes in a culture, distinguishing transfused blood cells from a patient's own blood, identifying irreversibly sickled cells in a sickle cell patient, and identifying leukemia cells in the early stages of responding to a drug treatment. These demonstrations suggest that the ability to measure single-cell density will provide valuable insights into cell state for a wide range of biological processes.
Apoptosis is induced by the active metabolite of vitamin D3 and its analogue EB1089 in colorectal adenoma and carcinoma cells: possible implications for prevention and therapy. (2000)

Vitamin D3 is believed to reduce the risk of colon cancer, and serum levels inversely correlate with colorectal cancer incidence. The active metabolite, 1alpha,25-dihydroxyvitamin D3, has previously been shown to inhibit growth and promote differentiation of colon cancer cells. The vitamin D analogue, EB1089, is currently under clinical trial in a variety of cancers because of its growth-inhibitory effects in vitro and reduced hypercalcemic effects in vivo. The mechanism of growth inhibition by EB1089, however, remained to be determined. In this study we examined the effects of alpha,25-dihydroxyvitamin D3 and EB1089 on five colorectal tumor cell lines (two adenoma and three carcinoma) to determine the mechanism of growth inhibition and to ascertain whether premalignant adenoma cells were responsive to these agents. 1alpha,25-Dihydroxyvitamin D3 and EB1089 induced p53-independent apoptosis in adenoma and carcinoma cell lines in a dose-dependent manner between 10(-10) and 10(-6) M. EB1089, as well as inducing apoptosis, increased the proportion of cells in the G1 phase, particularly in the adenoma cell lines. In two of the three carcinoma cell lines (SW620 and PC/JW), levels of apoptosis induced by EB1089 were similar or greater than those induced by 1alpha,25-dihydroxyvitamin D3. Although the carcinoma cell line HT29 was relatively resistant to apoptosis induced by EB1089 compared with 1alpha,25-dihydroxyvitamin D3, EB1089 markedly inhibited cell yields. These observations offer promise for the clinical use of EB1089. To determine whether the induction of apoptosis by 1alpha,25-dihydroxyvitamin D3 and EB1089 was potentially via a differentiation pathway, alkaline phosphatase activity was measured as a marker of differentiation. Induction of alkaline phosphatase was observed in the floating apoptotic cells as well as in the adherent population. A link between the induction of differentiation and apoptosis by 1alpha,25-dihydroxyvitamin D3 and EB1089 is suggested by the occurrence of apoptosis subsequent to the induction of differentiation. To investigate the molecular pathway to apoptosis induction, members of the Bcl-2 family of proteins were examined (Bcl-2, Bcl-x, Bax, and Bak). Decreased Bcl-2 was observed in some cell lines, particularly in response to EB1089, but was not essential for apoptosis. Levels of the proapoptotic protein Bak, however, were consistently increased in all of the five cell lines in association with apoptosis induced by either agent. The results implicate Bak protein in the induction of apoptosis by 1alpha,25-dihydroxyvitamin D3 or its analogue EB1089. The ability of EB1089 to induce apoptosis in colorectal carcinoma cells suggests that this or other vitamin D analogues may prove clinically effective for the treatment of colorectal cancer. Furthermore, the fact that it induces cell cycle arrest and apoptosis in the premalignant adenoma cells may suggest an application in colorectal cancer chemoprevention.
Statins Reduce Interleukin-6–Induced C-Reactive Protein in Human Hepatocytes (2005)

These results demonstrate that statins reduce IL-6-induced CRP production directly in hepatocytes via inhibition of protein geranylgeranylation. We further show that statins act via inhibition of STAT3 phosphorylation. These findings furnish new evidence for direct antiinflammatory properties of statins and provide new mechanistic insight into their clinical benefits.
Two- and Three-body Ion-Electron Recombination Rate Coefficients in Neon (1995)

The rates of recombination of electrons with Net ions over a wide range of pressure (1001000 Torr) and at temperatures of 133, 233 and 295 K were measured. Two- and three-body recombination processes were resolved. The observed two-body rate coefficient is lower than earlier reports. The three-body rate measured agrees well with predictions from Flarinery's modified theory by Bates for termolecular ion-electron recombination in a monatomic gas.
Data compression for communication networks: The delay-distortion function (1976)

The problem of data compression for communication networks is considered. The system performance criterion is the signal distortion resulting both from data compression and from average message delay through the network. The delay-distortion function is defined as the smallest message delay among all data-compression schemes that yield the given distortion value. The distortion-delay region is similarly defined. The capacity region is defined to include all incoming message rates for which there exists a set of data-compression schemes yielding a prescribed network distortion-delay value. The basic characteristics of these functions and regions are derived. In particular, it is shown that their evaluations can be performed by solving separately the source coding problem and the network's queuing problem. The distortion-delay functions and regions are explicitly derived for single channel systems.
Conformational Changes in the Fibronectin Binding MSCRAMMs Are Induced by Ligand Binding (1996)

Bacterial adherence to host tissue involves specific microbial surface adhesins of which a subfamily termed microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) specifically recognize extracellular matrix components. We now report on the biophysical characterization of recombinant fibronectin binding MSCRAMMs originating from several different species of Gram-positive bacteria. The far-UV CD spectra (190-250 nm) of recombinant forms of the ligand binding domain of the MSCRAMMs, in a phosphate-buffered saline solution at neutral pH, were characteristic of a protein containing little or no regular secondary structure. The intrinsic viscosity of this domain was found to be the same in the presence or absence of 6 M guanidine hydrochloride, indicating that the native and denatured conformations are indistinguishable. On addition of fibronectin NH2 terminus as ligand to the recombinant adhesin there is a large change in the resulting far-UV CD difference spectra. At a 4.9 M excess of the NH2 terminus the difference spectra shifted to what was predominately a beta-sheet conformation, as judged by comparison with model far-UV CD spectra. The fibronectin NH2-terminal domain undergoes a minute but reproducible blue-shift of its intrinsic tryptophan fluorescence on addition of rFNBD-A, which contains no tryptophan residues. Since this result indicates that there is no large change in the environment of the tryptophan residues of the NH2 terminus on binding, the large shift in secondary structure observed by CD analysis is attributed to induction of a predominately beta-sheet secondary structure in the adhesin on binding to fibronectin NH2 terminus.