gebhart/patrepeval huggingface dataset:
Generating CRISPR/Cas9-Derived Mutant Mice by Zygote Cytoplasmic Injection Using an Automatic Microinjector (2018)

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) assisted generation of mutant animals has become the method of choice for the elucidation of gene function in development and disease due to the shortened timelines for generation of a desired mutant, the ease of producing materials in comparison to other methodologies (such as embryonic stem cells, ESCs) and the ability to simultaneously target multiple genes in one injection session. Here we describe a step by step protocol, from preparation of materials through to injection and validation of a cytoplasmic injection, which can be used to generate CRISPR mutants. This can be accomplished from start of injection to completion within 2-4 h with high survival and developmental rates of injected zygotes and offers significant advantages over pronuclear and other previously described methodologies for microinjection.
Role of the 3′ untranslated region of baculovirus p10 mRNA in high-level expression of foreign genes (1999)

The p10 gene of Autographa californica nucleopolyhedrovirus has two putative AATAAA polyadenylation signals. The downstream signal is used predominantly, as was determined by analysing 3' cDNA ends. This downstream motif is followed by a GT-rich sequence, known to be important for efficient polyadenylation in mammalian systems. To analyse the importance of polyadenylation for p10 gene expression, recombinant viruses with altered 3' untranslated regions (UTRs) were tested using chloramphenicol acetyltransferase (CAT) as a reporter. Surprisingly, after inactivation of the downstream AATAAA motif, CAT expression remained at the same high level as observed with a wild-type 3' UTR. Polyadenylation occurred 24-28 nucleotides further downstream, probably due to an ATTAAA sequence motif. Replacing the p 10 3' UTR with the SV40 early terminator sequence as part of an hsp70-lacZ-SV40 gene cassette, which is commonly used in baculovirus expression vectors, resulted in a reduction in reporter gene expression. Polyadenylation occurred far more efficiently in the original p10 3' UTR than in the SV40 terminator sequence, as was shown by testing the SV40 terminator separately. These results indicate that in order to obtain high levels of foreign gene expression, vectors that provide a wild-type p10 3' UTR are to be preferred over those containing the hsp70-lacZ-SV40 gene cassette. Comparison of the p10 genes of various baculoviruses showed the presence of at least one AATAAA or ATTAAA motif in combination with a GT-rich sequence in the 3' UTR, suggesting an evolutionary conservation of these two elements, thereby maintaining the high level of p10 gene expression.
Unifying analysis of full reference image quality assessment (2008)

This paper studies two increasingly popular paradigms for image quality assessment - Structural SIMilarity (SSIM) metrics and Information Fidelity metrics. The relation of the SSIM metric to Mean Squared Error and Human Visual System (HVS) based models of quality assessment are studied. The SSIM model is shown to be equivalent to models of contrast gain control of the HVS. We study the information theoretic metrics and show that the Information Fidelity Criterion (IFC) is a monotonic function of the structure term of the SSIM index applied in the sub-band filtered domain. Our analysis of the Visual Information Fidelity (VIF) criterion shows that improvements in VIF include incorporation of a contrast comparison, in addition to the structure comparison in IFC. Our analysis attempts to unify quality metrics derived from different first principles and characterize the relative performance of different QA systems.
Idle Computing Resources as Micro-Currencies -Bartering CPU Time for Online Content (1999)

In this paper we present a brokerage system for using idle computing resources as a micro-currency for Web services hardly quantifyable with real currencies as downloading stock charts or accessing a search engine. The Locust (LOw cost Computing Utilizing Skimmed idle Time) system acts as a Broker for micro-payable services by demanding a part of the user&apos;s idle computing resources in exchange for accessing the service. We introduce the price/market model of Locust enabling the collection, aggregation and trade of resource surpluses or lacks between coupled sub-markets and eventually leading to an electronic resource market focused on the mainstream Internet user as supplier of idle computing time. We further describe Locust&apos;s inter-operable, secure and ubiquitious Web and Java based infrastructure to make micro-paying with CPU cycles for online content literally as easy as surfing a Web page with embedded banner advertisements.
<scp>PRMT</scp>5 promotes cell proliferation by inhibiting <scp>BTG</scp>2 expression via the <scp>ERK</scp> signaling pathway in hepatocellular carcinoma (2018)

Increasing evidence suggests that PRMT5, a protein arginine methyltransferase, has roles in cell growth regulation and cancer development. However, the role of PRMT5 in hepatocellular carcinoma (HCC) progression remains unclear. Here, we showed that PRMT5 expression was frequently upregulated in HCC tissues, and its expression was inversely correlated with overall survival in HCC patients. PRMT5 knockdown markedly inhibited in vitro HCC proliferation and in vivo tumorigenesis. We revealed that the mechanism of PRMT5-induced proliferation was partially mediated by BTG downregulation, leading to cell cycle arrest during the G1 phase in HCC cells. Ectopic BTG2 overexpression decreased HCC growth, caused cell cycle arrest at the G1 phase, and downregulated Cyclin D1 and Cyclin E1 protein expression. Furthermore, we found that PRMT5-induced ERK phosphorylation regulated BTG2 expression in HCC cells, whereas pretreatment with a selective ERK1/2 inhibitor (PD184352) significantly reversed the effect of PRMT5 on BTG2 expression. Our results indicated that PRMT5 promotes HCC proliferation by downregulating BTG2 expression via the ERK pathway.
Performance comparison of middleware threading strategies (2004)

The spectacular growth of E-business applications on the Internet has boosted the development of middleware technology. Middleware is software that manages interactions between applications distributed across a heterogeneous computing environment. In the competitive E-business market the ability to deliver a high and predictable performance of E-business applications is crucial to avoid customer churn, and thus loss of revenue. This raises the need for service providers to be able to predict and control performance. The performance of middleware-based applications depends strongly on the choice of the so-called threading strategy, describing how the middleware layer handles competing method invocation requests.The goal of this paper is to provide an understanding of the impact of threading strategies on the performance of middleware-based applications. To this end, we (1) develop new quantitative models for the performance of middleware under different threading strategies, (2) perform extensive test lab experiments to compare the performance under different threading strategies, and(3) explain the experimental results by relating them to the quantitative models. As such, this paper provides new and fundamental insight in the impact of threading strategies on the performance of E-business applications.
A la Anna: Ploughmans with cider (2015)

In these days of the paleo and Atkins diets, loving carbs the way I do is perhaps not something I should advertise. But, sadly 'tis true - there is nothing I love more than a crusty loaf of bread with cheese.
Variation in Physical Activity as an Indication of Estrus in Dairy Cows (1977)

Pedometers were used to measure daily physical activity of cows to determine if variation related to estrus was great enough to be useful in estrus detection. Forty cows in free stalls and 28 cows in comfort stalls were studied during the breeding period after calving. Pedometers were enclosed in specially designed cases and attached to a cow's lower rear leg with a plastic ankle strap. Readings were taken twice daily when the cows were milked in a milking parlor. Data from free stalls were available for 5163 intervals between milkings, 87 of which were periods of estrus. Activity definitely increased at the time of estrus; cows were about four times as active during estrus as they were when not in estrus. Data from comfort stalls were available for 2433 intervals between milkings, 39 of which were periods of estrus. Cows in comfort stalls were about 2.75 times as active during estrus as when not in estrus. There was relatively little variation within cow in activity from day to day among cows not in estrus. Activity monitoring appears to have potential as an aid in estrus detection.
Auxin and kinetin interaction during xylem differentiation. (1970)

Interfascicular xylem differentiation was experimentally induced in cultured explants from the first internode of Phaseoltts vttlgaris L. (var.Oregon Giant pole bean) seedlings by an indole-3-acetic acid (IAA) treatment (O.2 ppm, 30 hr).Control first internode slices indicated no interfascicular xylem differentiation at the time of explant excision.The minirnum time for IAA stimulation of intet-fascicular xylogenesis, in the presence of O.Ol-0o! colchicine as a tracheary element marker, was 18 hr.Treatrr)ent of explants with kinetin (O.1 ppm, 30 hr) in the absence of exogenous IAA induced the formatlon of large numbers of lignified pitted fiber-tracheids and tracheary elements in the interfascicular cambial region.The combined application of kinetin (O. 1 ppm) and IAA (O. 2 ppm) for 30 hr had a marked synergistic effect on intevfascicular scalariform-reticulate vessel member differentiation.The morphology of the differentiated cells from the combined treatment resembled the cells produced by the IAA-alone treatment and not the kinetin-alone treatrnent.Explants apparently synthesized endogenous auxin during prolonged culture (48-72 hr) on sucrose-agar as indicated by the differentiation of cambial initials and wound vessel member formation.Sequential treatments involving IAA and kinetin indicated that kinetin required a rninimum of 24-30 hr of uninterrupted treatment either concomitant with or followed by a minimum of 18 hr IAA treatment.Differentiation of cambial initials demonstrated a strict polarity since stimulation of xylogenesis by a combined treatment of auxin and kinetin was always produced in the morphological basal end of ehe explant regardless of the application site of the growth substances.Auxin-cytokinin synergism was also given by substituting benzylamino purine (O.1 ppm), or zeatin (O.1 ppm), or kinetin riboside (O.2 ppm) for kinetin.However, treatment of explants with L-proline was ineffective in stimulating xylogenesis under experimental conditions that produced xylogenic responses in Coletts explants.Increasing the concentration of IAA frorn O.2 ppm to O.5 ppm and lengtheni'ng the incubation period from 30 to 48-72 hr led to extremely large numbers of small isodiametric wound vessel members.ti'ansverse cuts at each end to 12 min lengths, and were positioned vertically with
Analysis of Android Applications' Permissions (2012)

We developed an architecture that automatically searches for and downloads Android applications from the Android Market. Furthermore, we created a detailed mapping of Android application programming interface (API) calls to the required permission(s), if any, for each call. We then performed an analysis of 141,372 Android applications to determine if they have the appropriate set of permissions based on the static analysis of the APK bytecode of each application. Our findings indicate that the majority of mobile software developers are not using the correct permission set and that they either over-specify or under-specify their security requirements.
Directed microspore‐specific recombination of transgenic alleles to prevent pollen‐mediated transmission of transgenes (2006)

A major challenge for future genetically modified (GM) crops is to prevent undesired gene flow of transgenes to plant material intended for another use. Recombinase-mediated auto excision of transgenes directed by a tightly controlled microspore-specific promoter allows efficient removal of either the selectable marker gene or of all introduced transgenes during microsporogenesis. This way, transgene removal becomes an integral part of the biology of pollen maturation, not requiring any external stimulus such as chemical induction by spraying. We here show the feasibility of engineering transgenic plants to produce pollen devoid of any transgene. Highly efficient excision of transgenes from tobacco pollen was achieved with a potential failure rate of at most two out of 16,800 seeds (0.024%). No evidence for either premature activation or absence of activation of the recombinase system was observed under stress conditions in the laboratory. This approach can prevent adventitious presence of transgenes in non-GM crops or related wild species by gene flow. Such biological containment may help the deployment and management of coexistence practices to support consumer choice and will promote clean molecular farming for the production of high-value compounds in plants.
<title>Full polarimetric display of NASA/JPL AIRSAR P-band data from Gilmore Creek, AK (1993), Half Moon Bay, CA (1994), and Bishop, CA (1995)</title> (1997)

Full polarization data gathered by the NASA/JPL AIRSAR P-band radar in Gilmore Creek, Alaska (1993), Half Moon Bay, California (1994), and Bishop, California (1995) are imaged using full polarization displays. Full polarization symbol displays of reflector signatures and of simulated small aircraft crash sites are presented. In addition, ideal polarimetric reflector responses are compared to measured reflector signatures extracted from ADTS MMW SAR scenes and AIRSAR scenes. It is demonstrated that full polarization displays can be used to quickly identify polarization calibration errors based on clutter responses alone.
Transmission line balanced inductive plasma sources (2000)

A new class of transmission line balanced inductive plasma sources having discrete inductive zones is reviewed. The problems of undesirable capacitive currents, azimuthal non-uniformity and the energy efficiency of inductive plasma sources are considered and basically solved. The main principles of operation, discharge performance and the most interesting experimental observations are discussed.
Efficient RFID Tag Identification Exploiting Hybrid UHF-UWB Tags and Compressive Sensing (2016)

In this paper, we propose a novel tags identification protocol based on compressive sensing (CS) and ultra-wideband (UWB) for radio frequency identification (RFID) systems. In a hybrid RFID system, ultra-high-frequency (UHF) reader-to-tag communications are combined with the UWB transceivers for localization and ranging purposes. Here, the UWB information of such a hybrid UHF-UWB architecture is exploited to reduce the ID search space of a UHF-CS decoding scheme. Simulation results prove that our solution significantly decreases the amount of bits required for successful tags identification, compared with the state-of-the-art protocols.
Dimethyl sulfoxide induces microtubule formation in cultured arterial smooth muscle cells (1987)

Prolonged exposure of cultured arterial smooth muscle cells to 1% dimethyl sulfoxide (DMSO) resulted in a remarkable increase in cytoplasmic microtubules and an appearance of bundle-like aggregates of microtubules associated with ribosomes (microtubule-ribosome-complex). In this complex, fine filaments of 8 to 16 nm diameter were interspersed, some of which displayed continuity with the microtubules and were studded with a single array of ribosomes. The microtubule-ribosome-complex may represent an unusual aggregate of microtubules containing incompletely polymerized forms of newly synthesized tubulin induced by prolonged effect of DMSO.
On the synthesis and reactivity of 4,10‐dihydrobenzo‐[<i>b</i>]thieno[2,3‐<i>e</i>]thiepin‐10‐acetic acid and 5,10‐dihydrobenzo[<i>e</i>]thieno[3,2‐<i>b</i>]thiepin‐10‐acetic acid (1992)

Abstract A simple method to synthesize 4,10‐dihydrobenzo[ b ]thieno[2,3‐ e ]thiepin‐10‐acetic acid (8a) and 5,10‐dihydrobenzo[ e ]thieno[3,2‐ b ]thiepin‐10‐acetic acid (8b) starting from ketones la,b is described. The reactivity of the acid 8a has been investigated and some derivatives are reported.
Forward error correction control on AAL 5: FEC-SSCS (2002)

ATM networks is realized as the future communication platform that accommodate a variety of communication services. A novel cell-level FEC (forward error correction) scheme at SSCS of AAL type 5 for error-free data transmission services is proposed and evaluated. In the proposed cell-level FEC scheme, both the length of user data (e.g. IP packet) and appended redundant data can be modified based on the sender's local decision without any end-to-end parameter re-negotiation. The writing and reading order regarding an interleave matrix for the cell-level FEC algorithm are the same, in order to perform pipelining data transmission. The end-to-end data transmission latency and the amount of retransmission packets due to packet error at the receiver entity are evaluated by computer simulation with a correlated cell dropping process. Simulation results show that the benefits of cell-level FEC scheme for the error-free data transmission services, i.e., by use of a cell-level FEC scheme, the amount of retransmitted packets can be reduced, even if the average latency for end-to-end data transmission increases slightly.
Morphology and optical responses of SERS active π-conjugated poly(N-ethyl-2-ethynylpyridinium iodide)/Ag nanocomposite systems (2009)

The influence of the poly(N-ethyl-2-ethynylpyridinium iodide) (PEEP-I) concentration on the morphology and optical properties of nanocomposite systems prepared by mixing the polymer solution with a hydrosol of ca. 9 nm Ag nanoparticles (NPs) was investigated by a combination of surface plasmon extinction (SPE) measurements, transmission electron microscope (TEM) imaging and surface-enhanced Raman spectroscopy (SERS). The PEEP-I concentration was found to have a strong impact on the assembly of Ag NPs and, consequently, on the optical responses of the composite systems. At low polymer concentrations in the composite (corresponding to ca. 50-1800 monomer units/NP), the formation of fractal aggregates was observed. In particular, the average fractal dimension D = 1.9 +/- 0.1 was determined for aggregates in the system with 5 x 10(-6) M polymer concentration. By contrast, in systems with polymer concentrations higher than about 1 x 10(-5) M, relatively small aggregates of Ag NPs with large interparticle distances were formed. The differences in the morphology of the composite systems with various polymer concentrations manifested themselves clearly in their SPE spectra. Furthermore, upon optical excitation with appropriate wavelengths (488.0 and 514.5 nm), the fractal aggregates acted as carriers of "hot spots", i.e. strong, localized, nanoscale optical fields, from which intense and well resolved SERS spectra of the polymer were obtained.
Insight into the Chemistry of Surfactant-Based Enhanced Oil Recovery Processes (2009)

During the past several decades, significant and considerable research has been carried out on secondary and tertiary recovery of trapped residual oil remaining within the producing formations underground despite the efficient, current primary production strategies and methods. Methods have been sought of increasing oil recovery, while revamping and improving the economic viability and efficiency of operations. One method that has received much attention and intensive study over these past decades is the use of surfactant-based chemical flooding. Initial patents and laboratory tests have shown conclusively that chemical solutions and slugs including surfactants, remove considerable oil from the porous medium normally trapped after initial waterflooding. Oil recovery processes by means of surfactant micellar solutions or microemulsions have included the injection of slugs of varied compositions. Patents on surfactant-based enhanced oil recovery processes (such as dilute surfactant flooding, surfactant/polymer flooding, and alkaline/surfactant/polymer flooding) have been issued, starting from the 1920s and particularly after the 1960s, when the technology was put on a scientific basis. These patents were generally concerned with the chemistry of surfactant-based enhanced oil recovery processes including envisioning the use of chemical solutions (slugs) to decrease the surface tension between oil and the flooding medium, screening of surfactants for oil recovery efficiency, chemical (surfactant) slug designs and formulation to mobilize residual oil, documenting petroleum sulfonates useful in surfactant flooding, and other important factors in the chemistry of surfactant-based chemical flooding processes. Moreover, evaluation and determination of optimum chemical systems (slugs) for the best economics for a specific field application have been disclosed and documented in several large oil companies patents in the surfactant-polymer area. In this article, a full-fledged review of the patents on different aspects of the chemistry of surfactant-based enhanced oil recovery processes is presented. Keywords: Surfactant, enhanced oil recovery, chemistry, chemical slug, patent
Autofluorescence of Human Skin Fibroblasts during Growth Inhibition and in vitro Ageing (1985)

The increase in autofluorescence (AF) of human skin fibroblasts during their in vitro ageing and growth inhibition was investigated by means of flow cytophotometry. The cellular AF of in vitro ageing cultures increased while the relative number of (3H)-thymidine incorporating cells decreased. Therefore, the rate of accumulation of cellular AF during in vitro ageing of the cultures is inversely related to the proliferation rate of the culture. The rates of increase of AF varied widely among the cell strains, being the highest in cells from patients with Werner's syndrome. Upon growth inhibition in a confluent culture the net rates of increase of cellular AF were found to vary widely among the cell strains. The respective net rates of increase of AF of the cells from patients with Werner's syndrome and the Spielmeyer-Vogt syndrome were within the range covered by the normal cell strains. The ultrastructure of the bright AF cells from patients with Werner's syndrome and the Spielmeyer-Vogt syndrome differed from the ultrastructure of AF cells from control persons with regard to the morphology of their residual bodies, those from the patients contained more multilamellar and multivesicular structures. In sorted non-AF cells vitamin E was found to completely inhibit the accumulation of AF without affecting the formation of 'residual bodies'. We infer that cellular AF is caused by lipid peroxidative reactions and that the accumulation of AF is due to a decrease in cellular proliferation rate.