gebhart/patrepeval huggingface dataset:
Circular RNAs from transcripts of the rat cytochrome P450 2C24 gene: correlation with exon skipping. (1996)

The cytochrome P450 2C24 gene is characterized by the capability to generate, in rat kidney, a transcript containing exons 2 and 4 spliced at correct sites but having the donor site of exon 4 directly joined to the acceptor site of exon 2 (exon scrambling). By reverse transcriptase-PCR analysis, it is now shown that the only exons present in the scrambled transcript are exons 2, 3, and 4 and that this molecule lacks a poly(A)+ tail. Furthermore, the use of PCR primers in both orientations of either exon 2 or exon 4 revealed that the orders of the exons in the scrambled transcript are 2-3-4-2 and 4-2-3-4, respectively. These results, combined with the observation that P450 2C24 is a single-copy gene, with no duplication of the exon 2 to exon 4 segment, suggest that the scrambled transcript has properties consistent with that of a circular molecule. In line with this is the observation of an increased resistance of the transcript to phosphodiesterase I, a 3'-exonuclease. Moreover, an alternatively processed cytochrome P450 2C24 mRNA, lacking the three scrambled exons and having exon 1 directly joined to exon 5, has been identified in kidney and liver, tissues that express the scrambled transcript. This complete identity of the exons that are absent in the alternatively processed mRNA but present in the scrambled transcript is interpreted as indicative of the possibility that exon scrambling and exon skipping might be interrelated phenomena. It is therefore proposed that alternative pre-mRNA processing has the potential to generate not only mRNAs lacking one or more exons but also circular RNA molecules.
Innate immune responses and neuroepithelial degeneration and regeneration in the mouse olfactory mucosa induced by intranasal administration of Poly(I:C) (2014)

The pathogenesis of postviral olfactory disorder (PVOD) has not been fully elucidated. We investigated morphological changes and innate immune responses in the mouse olfactory mucosa induced by intranasal administration of polyinosinic-polycytidylic acid [Poly(I:C)], a synthetic analog of viral double-stranded RNA. Mice received three administrations of saline with or without Poly(I:C), once every 24 h. The olfactory mucosa was harvested at various intervals after the first administration (8 h, 3, 9 and 24 days). In the Poly(I:C) group, the number of apoptotic cells in the olfactory neuroepithelium had increased at 8 h. At 9 days, the olfactory neuroepithelium had severely degenerated and behavioral tests demonstrated that the mice showed signs of olfactory deterioration. At 24 days, the structure of the neuroepithelium had regenerated almost completely. Regarding the innate immune responses, many neutrophils had infiltrated the olfactory neuroepithelium at 8 h and had exuded into the nasal cavity by 3 days. Macrophages had also infiltrated the olfactory neuroepithelium at 8 h although to a lesser extent, but they still remained in the neuroepithelium at 24 days. Poly(I:C)-induced neuroepithelial damage was significantly inhibited by a neutrophil elastase inhibitor and was suppressed in neutropenic model mice. These findings suggest that the secondary damage caused by the neutrophil-mediated innate immune response plays an important role in the pathogenesis of PVOD.
Inflammatory bowel disease: The genetic background and beyond (2014)

Inflammatoire darm ziekten (IBD) zoals de ziekte van Crohn (CD) en colitis ulcerosa (CU) zijn deels erfelijk en deels omgevingsbepaalde ziekten en worden gekenmerkt door een chronisch recidiverende ontsteking van de darm. Waarschijnlijk zijn een verstoorde immuunreactie op normale darmflora samen met een verminderde darmwand integriteit onderliggend aan deze soms zeer ernstige en hardnekkige ziekte. Meer inzicht in de pathogenese is derhalve essentieel. Door het DNA te screenen op risico gebieden, zijn er tot op heden 163 gebieden gevonden geassocieerd met een verhoogd ziekte risico. Hiermee kan 15-25% van de totale erfelijkheid verklaard worden. In dit proefschrift worden een aantal potentiële bronnen van de ontbrekende erfelijkheid onderzocht. Er zouden meer risico gebieden kunnen zijn voor IBD. Wij analyseerden een aantal strategisch gekozen gebieden en vonden twee nieuwe risico gebieden voor IBD, en we vonden een omgekeerde associatie voor een specifiek gen voor CD en CU. Verder kan er mogelijk meer van de erfelijkheid verklaard worden met bekende risico gebieden. Mogelijk heeft dezelfde genetisch code een ander effect op ziekte risico als deze van vader of moeder wordt geërfd. Wij testten de overlappende IBD risico gebieden en vonden hier weinig aanwijzingen voor. Daarnaast werd onderzocht wat de effecten van de hoeveelheid risico gebieden is op cel niveau in afweer cellen. Deze relatie hebben wij niet kunnen vinden, wel vonden we een verschil tussen gezonde mensen en patiënten. Wij hebben bijgedragen aan de identificatie van nieuwe risico gebieden op het DNA voor inflammatoire darmziekten en potentiële bronnen voor de ontbrekende erfelijkheid onderzocht.
Evaluation of nitrogen incorporation into bulk 4H-SiC grown on seeds of different orientation from optical absorption spectra (2016)

The effectiveness of n-type nitrogen doping of bulk 4H-SiC grown on seeds of different orientation is studied by optical absorption measurements. The 4H-SiC ingots have been grown by physical vapour transport (PVT), with nitrogen doping from the SiC source. The nitrogen concentration was determined at room temperature from the absorption peak intensity at 464 nm, with account for the degree of donor ionization. It has been shown that 4H-SiC ingots grown on Si (11-22) faces are significantly less doped by nitrogen than the ones grown on C (11-2-2).
Micro-payment systems and their application to mobile networks (2006)

This Paper summarizes the first phase of an ongoing investigation into the application of mobile-enabled commerce (m-Commerce) in developing markets. The Paper was commissioned by infoDev, in partnership with the International Finance Corporation (IFC) and the GSM Association (GSMA). The investigation is aimed at identifying the opportunities provided to mobile networks in offering an m-Commerce service, as well as establishing the drivers of a successful implementation.
Electrodeposit Formation in Solid Electrolytes (2006)

Devices based on polarity-dependent switching in solid electrolytes show great promise as next generation memory and perhaps even logic devices. These elements operate by the formation of robust but reversible electrodeposited conducting pathways which can be grown and dissolved at low voltage and current. Although such devices have been well characterized, little has been presented on the exact growth mechanism and nature of the conducting links themselves. In this paper we will show and discuss examples of electrodeposition within ternary silver-chalcogenide electrolyte device structures. The electrolyte was sectioned using focused ion beam milling and imaged with an in-situ scanning electron microscope to reveal the profile of the structure. A variety of Ag electrodeposits were imaged in overwritten devices and it was clear that programming times in the order of a few seconds will create multiple deposits on the inert cathode, some of which appear to extend through to the anode. The electron beam itself was also used to reduce silver ions within the electrolyte to reveal how the electrodeposits might nucleate on the Ag-rich phases within the film.
Glycoprotein 130 Regulates Cardiac Myocyte Survival in Doxorubicin-Induced Apoptosis Through Phosphatidylinositol 3-Kinase/Akt Phosphorylation and Bcl-xL/Caspase-3 Interaction (2001)

Activation of gp130 inhibits DOX-induced cell death in cardiac myocytes, resulting in the restoration of PI 3-kinase/Akt activities and in the inactivation of caspase-3, leading to facilitation of the protective function of Bcl-xL.
On the Calculation and Interpretation of NMR Relaxation Time Distributions (1994)

ABSTRACT We analyzed NMR relaxation time data using a multi-exponential model. The inversion of NMR data using such a model is an ill-posed problem. The answer is often not unique and requires subjective judgement We studied two methods of regularization. One uses norm smoothing based on an article by Butler et al. We found that optimal norm smoothing depends on the input of measurement errors. The second method uses curvature smoothing which minimizes variations in the second derivative. The latter is more effective for suppressing fluctuations in the relaxation time distribution, but doesn’t directly account for data quality. We studied NMR T1 data at full and partial saturations with desaturation pressures ranging from 15 to 400 psi (air/brine). As a general guideline, we found that the relaxation time cutoff which corresponds to irreducible water saturation is about 33 ms. For a limited number of samples, we found that the T1 relaxation time distribution has very little dependence on the frequency from 200 down to 1 MHz. We also found that T2 could be correlated to permeability.
Controlling anatase coating of diatom frustules by varying the binding layer (2012)

Diatoms have ordered three dimensional porous exoskeletons (frustules) comprised primarily of amorphous silica which can be used as templates for materials applications. Hydrolysis of titanium(IV) isopropoxide (TIP) in the presence of surface bound poly(4-vinyl pyridine) or citric acid results in the formation of anatase on the surface after calcining at 450 °C, however as shown with atomic force microscopy (AFM), different morphologies are formed. Citric acid preferentially resulted in a thin film of anatase over the surface of the frustule whereas poly(4-vinyl pyridine) resulted in the formation of nano-particles of anatase (90–100 nm) on the surface.
On the design of ultrafast shutters for time-resolved synchrotron experiments (2006)

A comprehensive treatment of the limitations and possibilities for single-pulse selection in synchrotron operating modes with approximately 150 ns bunch separation, as occurs in the standard operating mode at the Advanced Photon Source, is presented. It is shown that the strength of available materials and allowable kinetic energy build-up limit single-bunch selection for this separation to sample sizes of approximately 100 microm, and that for minimization of kinetic energy build-up it is preferable to increase the r.p.m. within physically acceptable limits rather than increase the disc radius to obtain a desirable peripheral speed. A slight modification of the equal-bunch spacing standard fill patterns is proposed that allows use of samples as large as 500 microm. The corresponding peripheral speed of the chopper wheel is approximately 600 m s(-1), which is within the limits of high-strength titanium alloys. For smaller samples, peripheral speeds are proportionally lower. Versatility can be achieved with interchangeable chopper wheels and the use of different orientations of the rotation axis relative to the X-ray beam, which opens the possibility of larger, rather than one-of-a-kind, production runs.
Reputation Guided Genetic Scheduling Algorithm for Independent Tasks in Inter-clouds Environments (2013)

Evolutionary computing offers different methods to solve NP-hard problems, finding a near-optimal solution. Task scheduling is a complex problem for large environments like Clouds. Genetic algorithms are a good method to find a solution for this problem considering multi-criteria constrains. This is also a method used for optimization. In these type of environments service providers want to increase the profit and the customers (end-users) want to minimize the costs. So, its all about money and we have minimum two optimization constrains. On the other hand, a good technique to ensure the QoS is to use the reputation of resources offered. This aspect is very important for service providers because represents a ranking method for them. We present in this paper a reputation guided genetic scheduling algorithm for independent tasks in inter-Clouds environments. The reputation is considered in the selection phase of genetic algorithm as an evolutionary criteria for the algorithm. We evaluate the proposed solution considering load-balancing as a way to measure the optimization impact for providers and maxspan as a metric for user performance.
Cronobacter gen. nov., a new genus to accommodate the biogroups of Enterobacter sakazakii, and proposal of Cronobacter sakazakii gen. nov., comb. nov., Cronobacter malonaticus sp. nov., Cronobacter turicensis sp. nov., Cronobacter muytjensii sp. nov., Cronobacter dublinensis sp. nov., Cronobacter genomospecies 1, and of three subspecies, Cronobacter dublinensis subsp. dublinensis subsp. nov., Cronobacter dublinensis subsp. lausannensis subsp. nov. and Cronobacter dublinensis subsp. lactaridi subsp. nov. (2008)

[Enterobacter] sakazakii is an opportunistic pathogen that can cause infections in neonates. This study further clarifies the taxonomy of isolates described as [E.] sakazakii and completes the formal description of the proposed reclassification of these organisms as novel species and subspecies within a proposed novel genus, Cronobacter gen. nov. [E.] sakazakii was first defined in 1980, however recent polyphasic taxonomic analysis has determined that this group of organisms consists of several genomospecies. In this study, the phenotypic descriptions of the proposed novel species are expanded using Biotype 100 and Biolog Phenotype MicroArray data. Further DNA-DNA hybridization experiments showed that malonate-positive strains within the [E.] sakazakii genomospecies represent a distinct species, not a subspecies. DNA-DNA hybridizations also determined that phenotypically different strains within the proposed species, Cronobacter dublinensis sp. nov., belong to the same species and can be considered as novel subspecies. Based on these analyses, the following alternative classifications are proposed: Cronobacter sakazakii gen. nov., comb. nov. [type strain ATCC 29544(T) (=NCTC 11467(T))]; Cronobacter malonaticus sp. nov. [type strain CDC 1058-77(T) (=LMG 23826(T)=DSM 18702(T))]; Cronobacter turicensis sp. nov. [type strain z3032(T) (=LMG 23827(T)=DSM 18703(T))]; Cronobacter muytjensii sp. nov. [type strain ATCC 51329(T) (=CIP 103581(T))]; Cronobacter dublinensis sp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. dublinensis subsp. nov. [type strain DES187(T) (=LMG 23823(T)=DSM 18705(T))]; Cronobacter dublinensis subsp. lausannensis subsp. nov. [type strain E515(T) (=LMG 23824=DSM 18706(T))], and Cronobacter dublinensis subsp. lactaridi subsp. nov. [type strain E464(T) (=LMG 23825(T)=DSM 18707(T))].
<title>Update with out-of-sequence measurements in tracking: exact solution</title> (2000)

In target tracking systems measurements are typically collected in scans or frames and then they are transmitted to a processing center. In multisensor tracking systems that operate in a centralized manner there are usually different time delays in transmitting the scans or frames from the various sensors to the center. This can lead to situations where measurements from the same target arrive out of sequence. Such out-of-sequence measurement (OOSM) arrivals can occur even in the absence of scan/frame communication time delays. The resulting negative- time measurement update problem, which is quite common in real multisensor systems, was solved approximately in [2] by neglecting the process nosie in the backward prediction or retrodiction. In the standard case, the (forward) state prediction can be easily carried out, since the process noise, because of its whiteness, is independent of the current state. However, in retrodiction this independence does not hold anymore. The standard smoothing algorithms cannot be used because the time stamp of the measurement is, in general, arbitrary. The results of [4,3] accounted only partially for the process noise. In view of this, the exact state update equation for such a problem is presented. The three algorithms are compared on a number of realistic examples, including a GMTI (ground moving target indicator) radar case.
특집 : 물정책과 법 ; 물관리기본법의 제정 필요성과 그 방향 및 내용 (2003)

Water is essential not only for lifes including human being but also for economic development as water resources. Its efficient and environmental friendly use are critical to Korea, one of water shortage countries. Environmentally sound and sustainable development is required to management of water resources. Even though more than 15 acts regarding water exist, no umbrella act which controls and harmonizes those acts. Therefore, it is said that a kind of basic water act is necessary for handle water resources problems which is from v however, for some reason, it have not played successful role as expected in coordinating different water policy. This article makes a recommendation that it is reasonable to make up currents problem of the Commission rather than to provide a third alternative with recommendations to strengthen the Commission such as upgrading its legal status from temporary organization without legal established basis to permanent legal organization, providing strong authority to control different policy with enforcement measures, and supporting from civil society through public participation such as citizen suits system. This article enumerates components of a basic water management act. First, basic value of the law is provided as sustainable development which is including principle of responsibility for future generation (inter-generational equity), the principle of social and economic equity: intra-generational equity), and the principle of ecological equity or ecological sustainable principle. Next, basic principles also must be established in the law, and they are a main subject of management, management ways including master plan which encompasses or coordinates many plans, and management costs including polluter pay principle, manager pay principle and beneficiary pay principle. finally, it is also important to improve fact information system including to collect, to make database, and to manage for efficient sharing.
Diagnosis and Management of Acute Compartment Syndrome (2020)

The Major Extremity Trauma and Rehabilitation Consortium and the American Academy of Orthopaedic Surgeons have developed the Appropriate Use Criteria (AUC) for the Diagnosis and Management of Acute Compartment Syndrome (ACS). Evidence-based information, in conjunction with the clinical expertise of physicians, was used to develop the criteria to improve patient care, aid decision-making, and obtain the best possible outcomes while considering the subtleties and distinctions necessary in making clinical decisions. The AUC for the Diagnosis and Management of ACS were derived by identifying clinical indications typical of patients suspected of an ACS in clinical practice. These indications were most often parameters observable by the clinician, including symptoms or results of diagnostic tests. The 135 patient scenarios and five treatments were developed by the writing panel, a group of clinicians who are specialists in this AUC topic. Next, a separate, multidisciplinary, voting panel (made up of specialists and nonspecialists) rated the appropriateness of treatment of each patient scenario using a nine-point scale to designate a treatment as "appropriate" (median rating, seven to nine), "may be appropriate" (median rating, four to six), or "rarely appropriate" (median rating, one to three).
On using the CAM concept for parametric curve extraction (2000)

In this correspondence, a parallel algorithm, in order to extract parametric curves from a two-dimensional (2-D) image space, is proposed. It is based on the Hough transform (HT) and uses the content addressable memory (CAM) as the main processor. A set of simulated results for circular shape extraction are presented in order to demonstrate its merit. Hence, voting, thresholding, and three-dimensional (3-D) peak extraction are efficiently performed within the CAM. In addition, and in order to reduce the quantization errors, a weighted AT algorithm (WHT), which uses a weighted voting is proposed. Experimental results indicate that a real-time shape extraction for an image 256/spl times/256 can be achieved within a small amount of hardware. Therefore, CAM-based HT can be considered as a promising attraction for next generation pattern recognition platforms.
Correlating measurements across samples improves accuracy of large-scale expression profile experiments (2009)

Gene expression profiling technologies suffer from poor reproducibility across replicate experiments. However, when analyzing large datasets, probe-level expression profile correlation can help identify flawed probes and lead to the construction of truer probe sets with improved reproducibility. We describe methods to eliminate uninformative and flawed probes, account for dependence between probes, and address variability due to transcript-isoform mixtures. We test and validate our approach on Affymetrix microarrays and outline their future adaptation to other technologies.
Nanostructure fabrication by direct electron-beam writing of nanoparticles (2002)

Direct additive-layer fabrication of nanostructures is a widely sought goal, which is not possible using traditional layered resist optical and electron-beam lithographic techniques. However, recently, it has been shown that certain metallic and semiconducting nanoparticles capped with protective organic groups are promising “inklike” resist materials for patterning a variety of electronic and mechanical structures [C. A. Bulthaup et al., Appl. Phys. Lett. 79, 1525 (2001)]. Several groups have successfully patterned single-layer gold nanoparticle films by means of direct electron-beam writing [X. M. Lin, R. Parthasarathy, and H. M. Jaeger, Appl. Phys. Lett. 78, 1915 (2001); T. R. Bedson, R. E. Palmer, T. E. Jenkins, D. J. Hayton, and J. P. Wilcoxon, Appl. Phys. Lett. 78, 1921 (2001); L. Clarke et al., Appl. Phys. Lett. 71, 617 (1997)]. In this work, we apply these materials in a new lithographic mode, using an electron beam to cause direct sintering of these 2–10 nm nanoparticles, building structures of multiple layers and multiple materials with linewidth resolutions of 80–100 nm.
A field evaluation of Nobi<sup>®</sup>‐Vac Atrophic Rhinitis vaccine (1987)

A field trial was carried out with Nobi-Vac AR vaccine in 11 swine breeding herds. One herd suffered from severe B. bronchiseptica (BB+) rhinitis in piglets, while no clinical Atrophic Rhinitis (AR) was observed. Ten herds were described as AR problem herds, because clinical AR was observed for at least 1 year in spite of the fact that medication of sows and piglets was carried out and adequate housing and management systems were available in most herds. BB+ was isolated in 9 of these 10 farms and the AR pathogenic P. multocida (PM+) in all these farms. The trial started when piglets were born of sows which had been vaccinated 3 times. All piglets between 7 and 10 weeks old were examined clinically for AR. Nasal swabs from 20 pigs on each farm were screened bacteriologically for BB+ and PM+ every other month. A severe reoccurrence of AR was found in 2 of the 10 AR problem farms. In these 2 herds the 'all in-all out' system was not applied in farrowing and weaning houses. In the 8 other AR problem herds the percentage of pigs with AR decreased significantly below the average level of 1% per year. The percentage of pigs infected with BB+ and PM+ also decreased significantly. PM+ was significantly related to the percentage of clinical AR piglets. Seasonal effects contributed to a minor extent to the percentage of AR piglets. After 2.5 years of this trial PM+ could not be isolated during the last 12 months in six of the remaining AR problems herds. The conclusion is that Nobi-Vac AR vaccination of the sow gave protection against clinical AR in piglets on those farms (80%) which provided adequate housing and management systems.