gebhart/patrepeval huggingface dataset:
RiboTRIBE: Monitoring Translation with ADAR-meditated RNA Editing (2021)

Abstract RNA translation is tightly regulated to ensure proper protein expression in cells and tissues. Translation is often assayed with biochemical assays such as ribosome profiling and TRAP, which are effective in many contexts. These assays are however not ideal with limiting amounts of biological material when it can be difficult or even impossible to make an extract with sufficient signal or sufficient signal:noise. Because of our interest in translational regulation within the few Drosophila adult circadian neurons, we fused the ADAR catalytic domain (ADARcd) to several small subunit ribosomal proteins and assayed mRNA editing in Drosophila S2 cells. The strategy is named RiboTRIBE and is analogous to a recently published APOBEC-based method. The list of RiboTRIBE-edited transcripts overlaps well with ribosome profiling targets, especially with more highly ranked targets. There is also an enriched number of editing sites in ribosome-associated mRNA comparing to total mRNA, indicating that editing occurs preferentially on polyribosome-associated transcripts. The use of cycloheximide to freeze translating ribosomes causes a substantial increase in the number of RiboTRIBE targets, which is decreased by pretreating cells with the chain terminating drug puromycin. NOTE: Additional experiments performed after first submitting this manuscript to BioRxiv estimate that less than 5% of Rps28b-ADAR is ribosome-associated. This is because the vast majority of the fusion protein sediments at the top of a polyribosome gradient. We therefore suggest that most editing reported in the manuscript is not catalyzed by ribosome-associated ADAR (10/2/2021).
Organogel formation rationalized by Hansen solubility parameters: improved methodology (2018)

An organogel is obtained when a low molar mass compound forms a network of anisotropic fibres in a liquid that is therefore transformed into a macroscopic solid. Various approaches have been proposed to correlate organogel formation and Hansen solubility parameters. These approaches are well adapted to specific experimental datasets but lack universality. A general method to determine the gelation domain from the solubility data of low molecular weight gelators is here reported.
Stent thrombosis following bare-metal stent implantation: success of emergency percutaneous coronary intervention and predictors of adverse outcome (2005)

Emergency PCI for treatment of stent thrombosis effectively restores vessel patency and flow. Patients presenting with stent thrombosis are at risk for recurrent myocardial infarction and recurrent stent thrombosis.
The Teaching and Learning Cycle: Integrating Curriculum, Instruction, and Assessment (2008)

The philosophies of educators and government entities guide the teaching and learning cycle of curriculum, instruction, and assessment. The educator’s worldview plays an important part in developing these concepts which is demonstrated throughout history. Studying the history of the educational philosophers reveals their beliefs about curriculum, instruction, and assessments and the effects on education today. It shows the importance of integrating all three concepts in the educational process creating the teaching and learning cycle.
IDENTIFICATION AND ENUMERATION OF CULTURED AND WILD PSEUDO‐NITZSCHIA (BACILLARIOPHYCEAE) USING SPECIES‐SPECIFIC LSU rRNA‐TARGETED FLUORESCENT PROBES AND FILTER‐BASED WHOLE CELL HYBRIDIZATION (1998)

Efforts to understand the ecologic and environmental parameters that govern harmful algal blooms (HABs) require rapid and specific identification of causative species. Traditional methods of species identification using light and electron microscopy are useful in this regard but are also time consuming, making routine analysis of a large number of samples difficult. Techniques that speed and ease the detection of HAB species as they occur in natural populations are therefore desirable. In this paper, we continue efforts to develop species‐specific large subunit ribosomal RNA (LSU rRNA)‐targeted fluorescent DNA probes for a variety of Pseudo‐nitzschia H. Peragallo species, a group of marine pennate diatoms that includes representatives linked to production of domoic acid and amnesic shellfish poisoning (ASP). A custom filter tube and filtration manifold that has utility for both whole cell ( in situ ) hybridization as well as preparing samples for scanning electron microscopy (SEM) is described. Filter‐based whole cell hybridization was used to identify a variety of newly isolated Pseudo‐nitzschia clones, and probe results were confirmed using SEM. Some isolates of P. pungens (Grunow) Hasle exhibited variable (intraclonal) reactivity toward the P. pungens ‐specific probe. Three isolates of P. subpacifica (Hasle) Hasle were found to cross‐react with probes designed for P. fraudulenta (Cleve) Hasle and P. heimii Manguin. Four isolates did not react with any species‐specific probes; this group comprised three distinct morphotypes whose fine‐scale morphologic features did not agree with published descriptions of Pseudo‐nitzschia species. Evaluation of the filter method using cultured cells added to natural (whole water) samples indicated quantitative recovery of target species. Confirming results of probe assays using SEM was difficult when the target species was less than 10 4 cells·L −1 in the presence of greater than 10 6 cells·L −1 of other nontarget diatom species. A variety of Pseudo‐nitzschia, including P. australis Frenguelli, P. fraudulenta, P. heimii, P. pseudodelicatissima (Hasle) Hasle, P. pungens, P. multiseries (Hasle) Hasle, and Nitzschia americana Hasle, were identified using whole cell hybridization in a variety of field samples containing mixed assemblages of plankton, and these results were confirmed using SEM. The filter tube method of applying probes was used onboard ship for near real‐time identification and enumeration of a variety of Pseudo‐nitzschia species.
Architecture for IP Flow Information Export (2009)

This memo defines the IP Flow Information eXport (IPFIX) architecture for the selective monitoring of IP Flows, and for the export of measured IP Flow information from an IPFIX Device to a Collector.
SAG12, a Major Cysteine Protease Involved in Nitrogen Allocation during Senescence for Seed Production in Arabidopsis thaliana (2018)

SAG12 is the most widely used senescence-associated reference gene for characterizing leaf senescence, and the increase in SAG12 protein during leaf senescence is remarkable. However, the role of this cysteine protease in N remobilization and the leaf senescence process remains unclear. The role of SAG12 has been poorly investigated and the few reports dealing with this are somewhat controversial. Indeed, sag12 Arabidopsis mutants have not shown any phenotype, while OsSAG12-1 and OsSAG12-2 overexpression in rice moderates senescence progression. Therefore, this study aims at clarifying the role of the SAG12 cysteine protease during the entire plant life span and during leaf senescence. Arabidopsis thaliana plants knocked-out for the SAG12 gene (sag12) did not exhibit any special phenotypic traits when grown under optimal nitrogen supply (HN), suggesting that other cysteine proteases could provide compensatory effects. Moreover, for the first time, this study shows that aspartate protease activity is significantly increased in sag12. Among the putative aspartate proteases involved, a CND41-like aspartate protease has been identified. Under low nitrogen (LN) availability, when inducible proteolytic systems are not sufficient to cope with SAG12 depletion, a decrease in yield is observed. Altogether, these results show that SAG12 (and perhaps also aspartate proteases) could be involved in RuBisCO degradation during the leaf senescence associated with seed filling.
The method for improving TCP performance in bandwidth-guaranteed network (2009)

This paper discusses the efficiency of TCP transmission over a bandwidth-guaranteed network, where the bandwidth for each flow is guaranteed by traffic policing at edge nodes. In particular, it explores a method for improving TCP performance focusing on the size of the buffer to absorb jitter and promote a faster increase in the congestion window size. We propose a rate control method at an edge node based on controlling the advertised window for improving TCP performance in a bandwidth-guaranteed network. We also evaluate the effectiveness of the proposed method using a prototype.
Optimal phase function for gradient-index optical filters (1993)

Fourier transform techniques for design of gradient-index optics have previously used arbitrary forms for the complex part of the reflectance profile.
Crossatron-based modulator for high repetition rate operation with arbitrary pulse widths (1994)

This article describes a Crossatron-based modulator for driving 10–1000 μs duration plasma discharges. The modulator has demonstrated burst mode operation at pulse repetition rates of 50 kHz. Insulated gate bipolar transistors (IGBTs) are used to trigger the Crossatron. The pulse width of each individual pulse in a burst can be varied over a large range. A Jorway 221 timing and sequencing module command triggers the modulator, and a Labview-based program is used to control the timing module via a GPIB bus. The modulator can output 25 kV pulses at 100 A. It can also operate at 10% duty cycle with peak currents of 10–20 A.
THE INVESTIGATING ON THE RELATIONSHIP BETWEEN HIGH MYOPIA AND FINGERPRINT (2008)

[Objective]To study the relationship between high myopia and fingerprint.[Methods]7 462 students in East China Institute of Technology were mass surveyed,206 students were detected to be high myopia including(including 104 males and 102 females,and identification of fingerprint were performed to them.[Results]When compared with people with health vision,the number of ridge among students with high myopia was significantly fewer,and the incidence of radial loop was also higher. The radial loop was concentrated on index finger. Our study showed that the incidence of congenital myopia was higher among people with the radial loop on the fingers except index finger.[Conclusion]High myopia is associated with fingerprint. We could detect the high myopia and protect ourselves as soon as possible on the basis of the permanence of our fingerprint.
Radical Reaction Mechanisms in Infrared Multiphoton Dissociation of UF6with Scavenger Gases (1989)

Abstract The radical reaction mechanisms in the presence of F-atom scavenger gases were investigated in the p-H2 Raman laser-induced infrared multiphoton dissociation (IRMPD) of gaseous 236UF6/238UF6 cooled to —35°C in a static gas cell. When CH4 was added as a scavenger of F-atoms produced via IRMPD of UFC, the dissociation rate of UF6 became several tens of times larger than when no scavenger gas was added. Gas-chromatographic analysis revealed that as low as 7% of the nascent CH3 radicals were involved in the radical reaction with UF6. On the other hand, H2 and C2H6 were found to increase both the dissociation rate of UF6 and the contribution of this non-selective reaction. These results agreed with those obtained in the UV photolysis of UF6 with scavengers.
Topologically disordered systems at the glass transition (2006)

The thermodynamic approach to the viscosity and fragility of amorphous oxides was used to determine the topological characteristics of the disordered network-forming systems. Instead of the disordered system of atoms we considered the congruent disordered system of interconnecting bonds. The Gibbs free energy of network-breaking defects (configurons) was found based on available viscosity data. Amorphous silica and germania were used as reference disordered systems for which we found an excellent agreement of calculated and measured glass transition temperatures. We reveal that the Hausdorff dimension of the system of bonds changes from Euclidian three-dimensional below to fractal 2.55 ± 0.05-dimensional geometry above the glass transition temperature.
Short-term low-dose triple therapy for the eradication of Helicobacter pylori (1994)

Background: Helicobacter pylori infection causes antral gastritis and is strongly associated with duodenal ulcer relapse. Eradication of H. pylori infection may be difficult to achieve due to antimicrobial resistance, side effects and poor patient compliance. Objective: To evaluate the efficacy, tolerability and patient compliance of short-term triple therapy with clarithromycin, omeprazole and tinidazole. Methods: Triple therapy, comprising clarithromycin 250 mg twice daily, omeprazole 20 mg once daily and tinidazole 500 mg twice daily, was administered to 65 patients with H. pylori gastritis for 1 week. H. pylori infection before and after treatment was determined by histology, the urease test and the 13C-urea breath test. Upper gastrointestinal endoscopy, during which four antral biopsy specimens were taken, and the 13C-urea breath test were performed in all patients before treatment and at 1 and 6 months after treatment. Drug tolerance was evaluated by patient interviews and compliance by counting returned pills at the end of treatment. Results: Sixty-three patients with H. pylori infection were studied. One month after treatment, on intent-to-treat analysis, H. pylori infection had been eradicated in 62 out of 65 patients (95.4%), confirmed by a negative urease test, 13C-urea breath test and histological examination of antral biopsy specimens. All patients were free of infection 6 months after treatment ended. All but one patient completed treatment and took more than 90% of the prescribed medication. There were no side effects except for one case of mild nausea (not severe enough to stop treatment) and one case of urticaria, following which treatment was withdrawn. Conclusions: Short-term, low-dose triple therapy with clarithromycin, omeprazole and tinidazole is highly effective for the eradication of H. pylori infection. The lack of side effects and good compliance are important for successful eradication.
Posebits for Monocular Human Pose Estimation (2014)

We advocate the inference of qualitative information about 3D human pose, called posebits, from images. Posebits represent Boolean geometric relationships between body parts (e.g., left-leg in front of right-leg or hands close to each other). The advantages of posebits as a mid-level representation are 1) for many tasks of interest, such qualitative pose information may be sufficient (e.g., semantic image retrieval), 2) it is relatively easy to annotate large image corpora with posebits, as it simply requires answers to yes/no questions, and 3) they help resolve challenging pose ambiguities and therefore facilitate the difficult talk of image-based 3D pose estimation. We introduce posebits, a posebit database, a method for selecting useful posebits for pose estimation and a structural SVM model for posebit inference. Experiments show the use of posebits for semantic image retrieval and for improving 3D pose estimation.
Age Estimation in Short Speech Utterances Based on LSTM Recurrent Neural Networks (2018)

Age estimation from speech has recently received increased interest as it is useful for many applications such as user-profiling, targeted marketing, or personalized call-routing. This kind of applications need to quickly estimate the age of the speaker and might greatly benefit from real-time capabilities. Long short-term memory (LSTM) recurrent neural networks (RNN) have shown to outperform state-of-the-art approaches in related speech-based tasks, such as language identification or voice activity detection, especially when an accurate real-time response is required. In this paper, we propose a novel age estimation system based on LSTM-RNNs. This system is able to deal with short utterances (from 3 to 10 s) and it can be easily deployed in a real-time architecture. The proposed system has been tested and compared with a state-of-the-art i-vector approach using data from NIST speaker recognition evaluation 2008 and 2010 data sets. Experiments on short duration utterances show a relative improvement up to 28% in terms of mean absolute error of this new approach over the baseline system.
Bibliography of the Megapodiidae (1999)

The Proceedings of the First International Megapode Symposium (Zoologische Verhandelingen Leiden, vol. 278) published in December 1992 included the paper Bibliography of the Megapodiidae with references to literature on megapodes upto 1992 (Dekker &amp; Jones, 1992: 57-78). The bibliography presented here is supplementary as it continues where the previous list ended.
[Transcorneal and transscleral iontophoresis of the dexamethasone phosphate into the rabbit eye]. (2007)

A short, low-current, non-invasive iontophoretic treatment using the dexamethasone-loaded hydrogels has a potential clinical value in increasing the drug's penetration into the anterior and posterior segment of the eye.
Crystallization and compatibilization of polypropylene-liquid crystalline polyester blends (2000)

A liquid crystalline polyester, LC3000, has been blended with polypropylene. These polymers form an incompatible and immiscible blend. Polypropylene grafted with epoxy via glycidyl methacrylate forms an effective compatibilizer. The dispersed liquid crystalline polyester particle size was decreased when the compatibilizer was used. The polyester influenced the morphology of the polypropylene continuous phase by increasing the nucleation, and the effect was enhanced when the compatibilizer was present. This was demonstrated using continuous cooling DSC where the crystallization temperatures were increased. Isothermal crystallization showed decreased crystallization half-times with the polyester present, and these were further reduced with compatibilizer. Avrami analysis showed that the exponent values increased by an average of 0.1–0.2, so nucleation was assisted by the LC3000, and the rate coefficients were increased. The continuous cooling and isothermal DSC measurements provided complementary results. Optical microscopy showed that the spherulite size of the polypropylene was reduced. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 2229–2236, 2000
Posttranslational association of immunoglobulin heavy chain binding protein with nascent heavy chains in nonsecreting and secreting hybridomas. (1986)

A rat monoclonal antibody specific for immunoglobulin (Ig) heavy chain binding protein (BiP) has allowed the examination of the association of BiP with assembling Ig precursors in mouse B lymphocyte-derived cell lines. The anti-BiP monoclonal antibody immunoprecipitates BiP along with noncovalently associated Ig heavy chains. BiP is a component of the endoplasmic reticulum and binds free intracellular heavy chains in nonsecreting pre-B (mu+, L-) cell lines or incompletely assembled Ig precursors in (H+, L+) secreting hybridomas and myelomas. In the absence of light chain synthesis, heavy chains remain associated with BiP and are not secreted. The association of BiP with assembling Ig molecules in secreting hybridomas is transient and is restricted to the incompletely assembled molecules which are found in the endoplasmic reticulum. BiP loses affinity and disassociates with Ig molecules when polymerization with light chain is complete. We propose that the association of BiP with Ig heavy chain precursors is a novel posttranslational processing event occurring in the endoplasmic reticulum. The Ig heavy chains associated with BiP are not efficiently transported from the endoplasmic reticulum to the Golgi apparatus. Therefore, BiP may prevent the premature escape and eventual secretion of incompletely assembled Ig molecules.
The mind switch environmental control system: Remote hands free control for the severely disabled (2002)

Recent research by the authors has resulted in the development of an environmental control system (ECS) that enables severely disabled persons to activate devices using their brain signals. This ECS has been called the Mind Switch and its effectivene
Atypical Pestivirus and Severe Respiratory Disease in Calves, Europe (2011)

In 2010, a HoBi-like pestivirus was isolated from clinically affected calves in Italy. This European virus reproduced a milder form of disease under experimental conditions and was genetically related to previously reported HoBi-like strains. Isolation of this novel virus from a clinical outbreak may have implications for cattle health and prophylactic programs.
Cohesive energy densities of polymers. Part 1.—Cohesive energy densities of rubbers by swelling measurements (1958)

The first page of this article is displayed as the abstract.
New Route for the Preparation of 2H-3-Aryl-3,4- dihydro-1,3-benzoxazines and 2H-3-Aryl-3,4- dihydro-4-methyl- 1 ,3-benzoxazines (1988)

Organic Chemistry Laboratory, University Department of Chemical Technology, Matunga, Bombay-400 019 <em>Manuscript recoiled 27 November 1986, revised 10 September 1987, accepted 11 December 1987</em> 2-Hydroxybenzaldehyde (1) and 1-(2-hydroxyphenyl)ethanone (2) on reaction with different primary aromatic amines gave 2-(arylimino)methylphenols (3) and 2-[1 -aryl­imino)ethyl]phenols (4), respectively. 3 and 4 on reduction with sodium borohydride gave 2-(arylamino)methylphenols (5) and 2-[1 (arylamino)ethyliphenols (6), which underwent cyclisation with formaldehyde to form 2<em>H</em>-3-aryl-3,4-dihydro-1,3-benzoxa­zines (7) and 2<em>H</em>-3-aryl-3,4-dihydro-4-methyl-1,3-benzoxszines (8), respectively.
An International Standard for whole blood folate: evaluation of a lyophilised haemolysate in an international collaborative study (2004)

Folate measurements, particularly for whole blood, show wide inter-laboratory and inter-methodology variability. This variability appears to be due in part to the lack of internationally accepted reference materials. A whole blood haemolysate, lyophilised in ampoules and designated 95/528, was therefore evaluated by 15 laboratories in five countries for its suitability as an International Standard (IS) for whole blood folate. The preparation was assayed using a variety of microbiological and protein-binding methodologies against local standards and calibrators. A consensus folate content was assigned to 95/528. The inclusion of three whole blood samples in the study with widely differing folate levels demonstrated a considerable reduction in inter-laboratory variability when the folate content of the samples was determined relative to the proposed IS 95/528 rather than to laboratories' local standards and calibrators. Accelerated degradation studies indicated that the folate content of 95/528 is stable when stored at -20 degrees C. On the basis of the results presented here, the World Health Organization Expert Committee on Biological Standardization established 95/528 as an IS for whole blood folate.