gebhart/patrepeval huggingface dataset:
Cas13d: A New Molecular Scissor for Transcriptome Engineering (2022)

The discovery of Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and its associated Cas endonucleases in bacterial and archaeal species allowed scientists to modify, utilized, and revolutionize this tool for genetic alterations in any species. Especially the type II CRISPR-Cas9 system has been extensively studied and utilized for precise and efficient DNA manipulation in plant and mammalian systems over the past few decades. Further, the discovery of the type V CRISPR-Cas12 (Cpf1) system provides more flexibility and precision in DNA manipulation in prokaryotes, plants, and animals. However, much effort has been made to employ and utilize the above CRISPR tools for RNA manipulation but the ability of Cas9 and Cas12 to cut DNA involves the nuisance of off-target effects on genes and thus may not be employed in all RNA-targeting applications. Therefore, the search for new and diverse Cas effectors which can precisely detect and manipulate the targeted RNA begins and this led to the discovery of a novel RNA targeting class 2, type VI CRISPR-Cas13 system. The CRISPR-Cas13 system consists of single RNA-guided Cas13 effector nucleases that solely target single-stranded RNA (ssRNA) in a programmable way without altering the DNA. The Cas13 effectors family comprises four subtypes (a-d) and each subtype has distinctive primary sequence divergence except the two consensuses Higher eukaryotes and prokaryotes nucleotide-binding domain (HEPN) that includes RNase motifs i.e. R-X4-6-H. These two HEPN domains are solely responsible for executing targetable RNA cleavage activity with high efficiency. Further, recent studies have shown that Cas13d exhibits higher efficiency and specificity in cleaving targeted RNA in the mammalian system compared to other Cas13 endonucleases of the Cas13 enzyme family. In addition to that, Cas13d has shown additional advantages over other Cas13 variants, structurally as well as functionally which makes it a prominent and superlative tool for RNA engineering and editing. Therefore considering the advantages of Cas13d over previously characterized Cas13 subtypes, in this review, we encompass the structural and mechanistic properties of type VI CRISPR-Cas13d systems, an overview of the current reported various applications of Cas13d, and the prospects to improve Cas13d based tools for diagnostic and therapeutic purposes.
Differences in optical trapping prompt investigations of Agrobacterium surface characteristics (1998)

Comparison of the optical trapping efficiency of Agrobacterium rhizogenes and A. tumefaciens strains indicates the A. rhizogenes strain, ATCC 11325, is significantly less efficiently trapped than A. rhizogenes A4, ATCC 15834, and the A. tumefaciens strain LBA4404. Differences were also found in capsule generation, growth media viscosity, and transmission electron microscopy negative staining. These observations imply a difference in surface structure exists. Calcofluor fluorescence suggests the difference involves an exopolysaccharide.
Mitochondrial acyl carrier protein is involved in lipoic acid synthesis in <i>Saccharomyces cerevisiae</i> (1997)

The yeast gene, ACP1, encoding the mitochondrial acyl carrier protein, was deleted by gene replacement. The resulting acp1-deficient mutants had only 5-10% of the wild-type lipoic acid content remaining, and exhibited a respiratory-deficient phenotype. Upon meiosis, the lipoate deficiency co-segregated with the acp1 deletion. The role of ACP1 in long-chain fatty acid synthesis was studied in fast and fas2 null mutants completely lacking cytoplasmic fatty acid synthase. When grown on odd-chain (13:0 and 15:0) fatty acids, these cells showed less than 1% of C-16 and C-18 acids in their total lipids. Mitochondrial ACP is therefore suggested to be involved with the biosynthesis of octanoate, a precursor to lipoic acid.
Prp43 Is an Essential RNA-dependent ATPase Required for Release of Lariat-Intron from the Spliceosome (2002)

The essential Saccharomyces cerevisiae PRP43 gene encodes a 767-amino acid protein of the DEXH-box family. Prp43 has been implicated in spliceosome disassembly (Arenas, J. E., and Abelson, J. N. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 11798-11802). Here we show that purified recombinant Prp43 is an RNA-dependent ATPase. Alanine mutations at conserved residues within motifs I ((119)GSGKT(123)), II ((215)DEAH(218)) and VI ((423)QRAGRAGR(430)) that diminished ATPase activity in vitro were lethal in vivo, indicating that ATP hydrolysis is necessary for the biological function of Prp43. Overexpression of lethal, ATPase-defective mutants in a wild-type strain resulted in dominant-negative growth inhibition. The ATPase-defective mutant T123A interfered in trans with the in vitro splicing function of wild-type Prp43. T123A did not affect the chemical steps of splicing or the release of mature mRNA from the spliceosome, but it blocked the release of the excised lariat-intron from the spliceosome. We show that the lariat-intron is not accessible to debranching by purified Dbr1 when it is held in the T123A-arrested splicing complex. Our results define a new ATP-dependent step of splicing that is catalyzed by Prp43.
Colistin‐Tobramycin Combinations Are Superior to Monotherapy Concerning the Killing of Biofilm<i>Pseudomonas aeruginosa</i> (2010)

Colistin-tobramycin combinations are more efficient than respective single antibiotics for killing P. aeruginosa in biofilms in vitro, and they significantly reduced P. aeruginosa cell counts in a rat lung infection model and in patients with cystic fibrosis.
Reseña de Libro Becerra, M. y Mastrini, G. (2009) Los dueños de la palabra. Acceso, estructura y concentración de los medios en la América latina del Siglo XXI. Buenos Aires: Prometeo Libros. (2011)

Becerra y Mastrini presentan un trabajo de investigacion hecho a traves del Instituto Prensa y Sociedad (IPYS) de Argentina, el cual complementa la informacion ya publicada en su anterior libro Periodistas y Magnates (2006). Los autores, reconocidos ya en el estudio de los conglomerados y concentraciones mediaticas en America Latina, exponen en esta obra los mas recientes resultados en el tema, cuyo estudio inicia desde el ano 2003.
Correction of Bone Marrow Nucleated Cell Counts for the Presence of Fat Particles (1995)

Although the use of bone marrow transplantation has increased greatly in recent years, the quality control procedures used in bone marrow processing laboratories remain less than ideal. Accurate marrow total nucleated cell (TNC) counts are essential for effective monitoring of bone marrow collection and processing. Aspirated marrow is variably contaminated by fat particles, resulting in overestimation of marrow TNC by automated analyzers. A recently-marketed hematological analyzer (Cobas-Helios; Roche Diagnostic Systems, Branchburg, NJ) offers the potential to correct marrow TNC counts for fat particles using available software. The authors investigated the accuracy of corrected TNC counts on 21 marrow samples, using a visual chamber count as the reference method. The correction methods studied were software correction, using the Cobas-Helios differential system, and replacement of the sample plasma with saline. Uncorrected automated marrow TNC counts (mean, 28.4 x 10(9)/L) were significantly higher than the visual reference counts (mean, 23.1 x 10(9)/L). Neither the mean corrected automated count (24.3 x 10(9)/L) nor the mean saline replaced count (24.6 x 10(9)/L) differed significantly from the mean visual reference count. For both the corrected automated and saline replaced counts, 20 of the 21 data points (95%) fell within a 95% confidence interval computed for the reference method. The authors conclude that both the corrected automated method, using the Cobas-Helios, and the saline replacement method are acceptable alternatives to the visual chamber count.
An expert system for transmission substation event analysis (1993)

Digital fault recorders (DFRs) are used in substations to capture recordings of various disturbances and fault events. Protection engineers use these recordings to identify reasons for particular operation of protection relays and circuit breakers. In performing this task protection engineers use their expertise related to specific power system conditions, equipment and operations. This paper describes implementation of an expert system which performs fault detection and diagnosis automatically and can aid operators in their task of analyzing disturbances and fault events.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
MANAGEMENT OPTIONS FOR PRODUCERS WHO TRADITIONALLY PLANT BARLEY FOR GRAIN OR FORAGE (2007)

<p>The objective of the experiment was to evaluate barley management options by varying seed band width, seeding rates, and harvest endpoint under dryland production conditions in Northern Montana. The experimental design was a randomized complete block with a factorial arrangement and was conducted for three years. Treatments consisted of two cultivars ('Harrington' and 'Haybet'), two band widths (125 mm and 193 mm), and three seeding rates (140, 184 and 226 seeds m<sup>-2</sup>). Year effects were significant. All established plant populations were lower than planned. Band width was confounded with seeding rate. Established plant populations increased from the narrow to the wide band width, any effect attributed to band width appears to be more what would be expected for increasing the seeding rate. Malt quality was never achieved and no treatment combination aided in moving the quality towards an acceptable malt grade of barley. Feed barley production was greatest in 2001 for the lowest seeding rate where as in 2002 and 2003 no difference existed between seeding rates. No beneficial water use patterns were established for any management endpoint or management option. Whole plant DM forage yield favored the highest seeding rate increasing 368 kg over the lowest seeding rate for the early harvest (soft dough) and when the crop matured 7 d longer, DM yield increased by 408 kg over both the lower rates. Nitrate-N was reduced 16 and 19% in the highest seeding rate for the early and late harvest, respectively. Reductions in Nitrate-N exhibited a linear and quadratic response for the early and a linear response for late harvest. With no quadratic affect observed for DM yield and substantially lower established plantsm<sup>-2</sup> than predicted, additional research of seeding rate and band width interactions may be warranted to optimize both forage and grain production. Optimal management strategies for grain production and forage production were different, especially for seeding rate. A producer should decide on how the crop is to be utilized prior to planting of the crop. </p>
Estudio del contenido de huevo y colesterol en pastas alimenticias (1996)

The aim of this work is to analyze the cholesterol content of the egg nourishing pasta. Samples of dry and fresh pasta were bought and analyzed. Food shops were chosen randomly. The egg content was analyzed by Hadorn method and cholesterol by gas chromatography. A simple transformation of the results gave a second value of the egg content. Both results were not different statiscally. Although the cholesterol content of the groups of pasta analysed showed a big scattering (20-135 mg cholesterol/100 g pasta), the mean value was very close to those of the other common foods.
Development of a Cutting Tool with a Textured Surface for Dry Cutting of Aluminum Alloys (2009)

The demand for dry/near-dry cutting has been rapidly increasing to reduce the environmental impact. However, cutting technologies for aluminum alloys have not actually gained widespread use because the aluminum chips adhere strongly to the cutting edge of the tool, leading to tool breakage. To solve this problem, a cutting tool with a banded textured surface was developed, and a series of face-milling experiments for aluminum alloys showed that the textured surface significantly improves the anti-adhesive and anti-frictional properties at the tool-chip interface under dry cutting conditions.
Simultaneous sulfation of endogenous chondroitin sulfate and chondroitin-derived oligosaccharides. Studies with separate 4-sulfating and 6-sulfating microsomal systems. (1986)

Microsomal preparations from chondroitin 6-sulfate-producing chick embryo epiphyseal cartilage and from chondroitin 4-sulfate-producing mouse mastocytoma cells were incubated with varying concentrations of 3'-phosphoadenylylphospho[35S]sulfate and chondroitin hexasaccharide in the presence or absence of Triton X-100. [35S]Sulfate incorporation into hexasaccharide and into endogenous microsomal chondroitin 6-sulfate or endogenous microsomal chondroitin 4-sulfate was measured. With both microsomal systems, Triton X-100 increased the incorporation of [35S]sulfate into hexasaccharide but had much less effect on the incorporation into endogenous chondroitin sulfate. Higher concentrations of hexasaccharide inhibited the incorporation of [35S]sulfate into endogenous chondroitin sulfate. The apparent Km for 3'-phosphoadenylylphosphosulfate for both the 6-sulfotransferase and 4-sulfotransferase with hexasaccharide and with endogenous chondroitin sulfate in the presence or absence of Triton X-100 were all similar. However, the apparent Km for hexasaccharide was lower in the presence of Triton X-100 for both the microsomal sulfotransferases. This is consistent with solubilization of sulfotransferases, and indicates that hexasaccharide access to these enzymes had been limited in the particulate system. Examination of 35S-oligosaccharide products formed with each system demonstrated good 6-sulfation or 4-sulfation of penultimate GalNAc at the non-reducing end of the chondroitin hexasaccharide. However, no 6-sulfation of terminal GalNAc at the non-reducing end of a chondroitin pentasaccharide derived from hexasaccharide was observed, and there was only minimal 4-sulfation of this terminal GalNAc. Concurrent addition of GalNAc to hexasaccharide resulting in heptasaccharide did not appear to promote significant 6-sulfation or 4-sulfation of newly added non-reducing terminal GalNAc.
Racket Control for a Table Tennis Robot to Return a Ball (2013)

This paper mainly proposes a racket control method for returning a table tennis ball to a desired position with a desired rotational velocity. The method determines the racket's state, i.e., the racket's striking posture and translational velocity by using two physical models: the racket rebound model and the aerodynamics model. The algorithm of determining the racket's state is derived by solving nonlinear equations and solving a two-point boundary value problem of a differential equation. But this is not suitable for a real-time process because of large computing time. The paper proposed a modified algorithm which could be used for a real-time process by introducing a simple aerodynamics model. Numerical simulations and experimental results show effectiveness of the proposed methods.
Reactive latex studies, 2. Kinetics and retention of enzymatic activity in the covalent protein bonding to a polymer latex (1985)

Abstract Bovine serum albumin (BSA) was coupled to the reactive chloromethyl groups of poly(vinylbenzyl chloride) latex following the process both by the amount of BSA covalently bound and the chloride ion released. The primary bond formation is very insensitive to temperature with protein adsorption probably rate determining. Subsequent bond formation has an unusually high temperature coefficient and may depend on the deformability of the BSA molecule. On covalent bonding of ribonuclease 10% of the enzyme activity is retained.
DELVING INTO DENDRIMERS (1997)

RETURN TO ISSUEPREVNewsNEXTDELVING INTO DENDRIMERSInsight into treelike macromolecules' unique properties opens possibilities for use as coatings and catalystsSTEPHEN C. STINSONView Author Information C&EN Northeast News BureauCite this: Chem. Eng. News 1997, 75, 38, 28–30Publication Date (Print):September 22, 1997Publication History Published online12 November 2010Published inissue 22 September 1997https://doi.org/10.1021/cen-v075n038.p028Copyright © 1997 AMERICAN CHEMICAL SOCIETYArticle Views6Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) SUBJECTS:Dendrons Get e-Alerts
Size-controlled oriented crystallization in SiO_2-based glasses by femtosecond laser irradiation (2014)

3D nano-crystallization has been investigated with a femtosecond laser beam in 33Li2O-33Nb2O5-34SiO2 glass by changing the pulse energy and polarization direction. Electron backscattered diffraction was used to characterize the size and the orientation of crystals in cross sections of laser tracks, while second harmonic generation was employed to investigate the nonlinear optical properties of laser lines macroscopically. We are the first, to the best of our knowledge, to reveal that crystals of nano-size were precipitated both at low pulse energy with laser polarization parallel to the laser motion direction and at high pulse energy in the perpendicular case, but they preferred to orientate perpendicularly to the written lines in the former case.
Mechanism of formation of diatremes (1979)

(1979). Mechanism of formation of diatremes. International Geology Review: Vol. 21, No. 10, pp. 1131-1139.
Redundant Color Coding on Airborne CRT Displays (1984)

An experiment is described that compares the use of redundant color coding for search and identification tasks under dual-task conditions; subjects made judgments about the state of components of a systems-management display while performing a compensatory tracking task. The availability of redundant color coding on the secondary task resulted in a global improvement in tracking performance (primary task) that applied at all times, even when subjects were not attending to the systems-managment display. With regard to the response-time data for the color-coded display, redundant color coding improved search performance, but there was no benefit for performance on the identification task. The implications of the results for hypotheses relating to the serial or parallel processing of shape and color, and for cockpit applications generally, are discussed.
The Java factor (1998)

The "write once, run anywhere" slogan is synonymous with the Java programming language. The Java run-time library provides application developers with the ability to write code in one single language and the confidence that the code will execute without modification on virtually any hardware, any operating system, and any application environment. Developers are freed from the costs of porting their applications to a myriad of target platforms and worse, of maintaining those multiple-code bases. Of course, powerful cross-platform run-time systems have existed for many years, dating back to Lisp, Smalltalk, and many other interpreted languages. However, Java is the first to achieve widespread popularity among commercial developers.
Interleukin-6 Affects Insulin Secretion and Glucose Metabolism of Rat Pancreatic Islets<i>in Vitro</i>* (1990)

Recently it has been postulated that interleukin-1 (IL-1) locally released by infiltrating mononuclear cells may destroy the pancreatic B cells during the development of insulin-dependent diabetes mellitus. Since IL-1 is a potent inducer of interleukin-6 (IL-6) in various cells, it is conceivable that IL-6 is a second mediator of the IL-1 action. In the present study the effects of IL-6 alone or in combination with IL-1 were studied on pancreatic islet function in vitro after tissue culture and compared with the effects observed after exposure to IL-1 only. Rat pancreatic islets were cultured in medium RPMI 1640 + 10% calf serum with or without the addition of human recombinant IL-6 (500-5000 pg/ml) for 48 h. The medium insulin accumulation was increased by 40-50% after culture with 500-2000 pg/ml IL-6, but was similar to the controls at 5000 pg/ml. When islets were cultured for 18 h only, also 5000 pg/ml IL-6 stimulated the medium insulin accumulation. IL-6 did not affect the islet insulin content and the rates of islet (pro)insulin and total protein biosynthesis. It inconsistently decreased the islet DNA content. In short-term experiments after 48-h culture with IL-6, there was a dose-dependent inhibition of the glucose-stimulated insulin release. On the other hand, islets cultured with IL-6 (5000 pg/ml) exhibited an elevated glucose oxidation and oxygen uptake, but a lower ATP content at 16.7 mM glucose and an unaffected glucose utilization and glutamine oxidation compared to the controls. This raises the possibility that IL-6 had induced a condition with an increased energy expenditure, resulting in an enhanced mitochondrial metabolism of glucose. Islets cultured with human recombinant IL-1 beta (25 units/ml) showed a strong inhibition of the insulin accumulation in the culture medium and of glucose-stimulated insulin release and a marked decrease in the islet DNA and insulin content. A combination of IL-1 (25 U/ml) + IL-6 (1000 pg/ml) did not alter the inhibitory action of IL-1 alone. The present findings thus show that IL-6 induces a dissociation between insulin secretion and glucose oxidation in islets in vitro. This has not been observed in islets exposed to IL-1, which suggests that IL-6 does not solely mediate the inhibitory effects of IL-1 on islet function.(ABSTRACT TRUNCATED AT 250 WORDS)
Observations on Molecular Weight Determinations on Polyacrylamide Gel (1969)

Abstract 1. A simple internal calibration technique was used to construct accurate molecular weight-mobility profiles on polyacrylamide gels with well characterized proteins, and the existence of a critical point was observed for small polypeptides. The useful size range limits were determined for several gel concentrations. Apparent molecular weights generally fell within 5 to 6% of literature values, although a few anomalous proteins, notably ribonuclease, considerably exceeded this margin of error. 2. The effects of intrinsic molecular charge and conformation on electrophoretic behavior in the presence of sodium dodecyl sulfate, evaluated by studies on a set of model proteins, were found to be small. 3. The results are in accord with a model in which the protein somehow organizes the sodium dodecyl sulfate anions into a micellar complex of definite size. Although the stoichiometry of the complex is apparently governed not only by the size of the molecule, but also by its state of foldedness, the interplay of anion binding and frictional resistance to passage through the gel is such as to produce a relatively constant log size to mobility ratio. 4. The apparent molecular weights of the five polypeptide chains of Mouse-Elberfeld virus were determined.
PEARSON'S SYSTEM OF FREQUENCY CURVES (1969)

1. When it becomes necessary in practical work to decide on a system of curves for describing frequency distributions, we have to bear in mind that