gebhart/patrepeval huggingface dataset:
Comparative Analysis of Antisense RNA, Double-Stranded RNA, and Delta Ribozyme-Mediated Gene Regulation in Toxoplasma gondii (2002)

RNA tools, namely, antisense RNA, double-stranded RNA (dsRNA), and delta ribozyme, were comparatively analyzed for the development of effective RNA-based gene modulators. The gene encoding uracil phosphoribosyltransferase (UPRT) of Toxoplasma gondii was used as a target and a negative selectable marker. Using plasmid transformation and drug selection assays, we obtained T. gondii transformants resistant to 5-fluoro-2'-deoxyuridine (FDUR), the cytotoxic prodrug and substrate of UPRT, when the plasmids expressing dsRNA and active delta ribozyme were used. No resistant transformants were detected when the plasmids carrying the antisense RNA, the inactive delta ribozyme, or the chloramphenicol acetyltransferase (CAT) genes were used. Parasites generated using the plasmids expressing dsRNA and the delta ribozyme become resistant to FDUR with an LD50 of 50 +/- 5 microM and 25 +/- 8 microM, respectively. These values are approximately 25-fold and 12-fold higher than that of the RH parental parasite strain, indicating that UPRT activity of the transformed parasites was drastically inhibited. Using Northern and Southern blot analysis, we demonstrated that dsRNA and the delta ribozyme interrupt the expression of UPRT. These two RNA tools should, thus, be very useful for the study of gene expression.
THEORETICAL APPROACH FOR THE CALCULATION OF RADIATION D10‐VALUE (2010)

ABSTRACT In the design of the food irradiation process, the knowledge of the radiation resistance of the target organism in the specific food commodity is required. The D 10 ‐value, the radiation dose needed to inactivate 90% of the microbial load in the food medium, is used to relate the amount of absorbed energy to the fractional population of the viable cells. Numerous experimental studies have been performed to determine the D 10 values of several food borne microorganisms irradiated under various conditions. Nevertheless, accurate prediction of D 10 value for a radiation treatment of a food product that has not been empirically examined can not be made due to insufficient understanding of the biological response to radiation exposure. A theoretical model for the derivation of the D 10 ‐value has been proposed in this study to mechanistically assess the DNA damage by energetic electrons. The step‐by‐step Monte‐Carlo simulation technique which employed the detailed histories of the ionizing particles and the radiolytic species was utilized. The impacts of the genomic sequence, the number of the genome equivalents, and the method of DNA double strand break determination were hypothetically investigated. The developed computational methodology as well as the results presented can be used as an analytical tool to evaluate the effect of ionizing radiation on the cell survival. PRACTICAL APPLICATIONS The presented methodology can be employed as an investigative technique complementary to other approaches to understand the physical, chemical and biological changes in food‐born pathogens exposed to e‐beam.
A Complexity-Effective Approach to ALU Bandwidth Enhancement for Instruction-Level Temporal Redundancy (2004)

Previous proposals for implementing instruction-level temporalredundancy in out-of-order cores have reported a performancedegradation of upto 45% in certain applications compared to anexecution which does not have any temporal redundancy. An importantcontributor to this problem is the insufficient number ofALUs for handling the amplified load injected into the core. At thesame time, increasing the number of ALUs can increase the complexityof the issue logic, which has been pointed out to be oneof the most timing critical components of the processor. This paperproposes a novel extension of a prior idea on instruction reuseto ease ALU bandwidth requirements in a complexity-effective wayby exploiting certain interesting properties of a dual (temporallyredundant) instruction stream. We present microarchitectural extensionsnecessary for implementing an instruction reuse buffer(IRB) and integrating this with the issue logic of a dual instructionstream superscalar core, and conduct extensive evaluationsto demonstrate how well it can alleviate the ALU bandwidth problem.We show that on the average we can gain back nearly 50%of the IPC loss that occurred due to ALU bandwidth limitationsfor an instruction-level temporally redundant superscalar execution,and 23% of the overall IPC loss.
Application performance in the QLinux multimedia operating system (2000)

In this paper, we argue that conventional operating systems need to be enhanced with predictable resource management mechanisms to meet the diverse performance requirements of emerging multimedia and web applications. We present QLinux—a multimedia operating system based on the Linux kernel that meets this requirement. QLinux employs hierarchical schedulers for fair, predictable allocation of processor, disk and network bandwidth, and accounting mechanisms for appropriate charging of resource usage. We experimentally evaluate the efficacy of these mechanisms using benchmarks and real-world applications. Our experimental results show that (i) emerging applications can indeed benefit from predictable allocation of resources, and (ii) the overheads imposed by the resource allocation mechanisms in QLinux are small. For instance, we show that the QLinux CPU scheduler can provide predictable performance guarantees to applications such as web servers and MPEG players, albeit at the expense of increasing the scheduling overhead. We conclude from our experiments that the benefits due to the resource management mechanisms in QLinux outweigh their increased overheads, making them a practical choice for conventional operating systems.
Image Transmission Over Voice Grade Telephone Lines (1988)

There are various systems available commercially designed to transmit images over voice grade telephone lines. This project was undertaken to compare moderate cost systems. The application of these systems used for the current study was to send radiographic images. The various sytems have different degrees of resolution and transmission speed.
The effect of three-dimensional culture on the ameloblastic differentiation of dental epithelial cells (2016)

We have developed three-dimensional (3D) cell culture devices. The present study investigated that the effect of 3D culture of rat incisor-derived dental epithelial cells on their differentiation into ameloblast-like cells.
Production of functionally active Penicillium chrysogenum isopenicillin N synthase in the yeast Hansenula polymorpha (2008)

In P. chrysogenum, the enzymes involved in penicillin production are compartmentalized in the cytosol and in microbodies. In this study, we focus on the cytosolic enzyme IPNS. Our data show that high amounts of functionally active IPNS enzyme can be produced in the heterologous host during cultivation at 25 degrees C, the optimal growth temperature for P. chrysogenum. This is a new step forward in the metabolic reprogramming of H. polymorpha to produce penicillin.
Infection control practices across Canada: do dentists follow the recommendations? (1999)

This study investigated provincial and territorial differences in dentists' compliance with recommended infection control practices in Canada (1995). Questionnaires were mailed to a stratified random sample of 6,444 dentists, of whom 66.4% responded. Weighted analyses included Pearson's chi-square test and multiple logistic regression. Significant provincial and territorial differences included testing for immune response after hepatitis B virus (HBV) vaccination, HBV vaccination for all clinical staff, use of infection control manuals and post-exposure protocols, biological monitoring of heat sterilizers, handwashing before treating patients, using gloves and changing them after each patient, heat-sterilizing handpieces between patients, and using masks and uniforms to protect against splatter of blood and saliva. Excellent compliance (compliance with a combination of 18 recommended infection control procedures) ranged from 0% to 10%; the best predictors were more hours of continuing education on infection control in the last two years, practice location in larger cities (> 500,000) and sex (female). Clearly, improvements in infection control are desirable for dentists in all provinces and territories. Extending mandatory continuing education initiatives to include infection control may promote better compliance with current recommendations.
β-catenin/LEF1/IGF-IIR Signaling Axis Galvanizes the Angiotensin-II- induced Cardiac Hypertrophy (2019)

Cardiovascular diseases have a high prevalence worldwide and constitute the leading causes of mortality. Recently, malfunctioning of β-catenin signaling has been addressed in hypertensive heart condition. Ang-II is an important mediator of cardiovascular remodeling processes which not only regulates blood pressure but also leads to pathological cardiac changes. However, the contribution of Ang-II/β-catenin axis in hypertrophied hearts is ill-defined. Employing in vitro H9c2 cells and in vivo spontaneously hypertensive rats (SHR) cardiac tissue samples, western blot analysis, luciferase assays, nuclear-cytosolic protein extracts, and immunoprecipitation assays, we found that under hypertensive condition β-catenin gets abnormally induced that co-activated LEF1 and lead to cardiac hypertrophy changes by up-regulating the IGF-IIR signaling pathway. We identified putative LEF1 consensus binding site on IGF-IIR promoter that could be regulated by β-catenin/LEF1 which in turn modulate the expression of cardiac hypertrophy agents. This study suggested that suppression of β-catenin expression under hypertensive condition could be exploited as a clinical strategy for cardiac pathological remodeling processes.
Intragastric balloon treatment of obesity must be combined with bariatric surgery: A pilot study in Turkey (2010)

BioEnterics intragastric balloon is a safe and effective but temporary therapeutic modality for obesity treatment. After BioEnterics intragastric balloon removal, almost all patients had returned to their initial weights. Therefore, BioEnterics intragastric balloon must only be offered for patients who accept to undergo bariatric surgery after BioEnterics intragastric balloon removal. Losing weight by BioEnterics intragastric balloon before bariatric surgery will improve the morbidity and mortality rates of this modality.
Effects of lovastatin on progression of non-dilated and dilated coronary segments and on restenosis in patients after PTCA. The Cholesterol Lowering Atherosclerosis PTCA Trial (CLAPT) (1999)

Lovastatin reduced the progression of dilated lesions in men with elective PTCA. Independent of treatment allocation, the dilated lesions regressed and the non-dilated segments progressed during the study follow-up. Four weeks of pre-treatment with lovastatin did not influence the rate of restenosis. Lovastatin had no statistically significant effect on non-dilated segments.
Partial deletion of p75 NTR in large‐diameter DRG neurons exerts no influence upon the survival of peripheral sensory neurons in vivo (2020)

The p75 neurotrophin receptor (p75<sup>NTR</sup> ) is required for maintaining peripheral sensory neuron survival and function; however, the underlying cellular mechanism remains unclear. The general view is that expression of p75<sup>NTR</sup> by the neuron itself is required for maintaining sensory neuron survival and myelination in the peripheral nervous system (PNS). Adopting a neuronal-specific conditional knockout strategy, we demonstrate the partial depletion of p75<sup>NTR</sup> in neurons exerts little influence upon maintaining sensory neuron survival and peripheral nerve myelination in health and after demyelinating neuropathy. Our data show that the density and total number of dorsal root ganglion (DRG) neurons in 2-month-old mice is not affected following the deletion of p75<sup>NTR</sup> in large-diameter myelinating neurons, as assessed by stereology. Adopting experimental autoimmune neuritis induced in adult male mice, an animal model of demyelinating peripheral neuropathy, we identify that deleting p75<sup>NTR</sup> in myelinating neurons exerts no influence upon the disease progression, the total number of DRG neurons, and the extent of myelin damage in the sciatic nerve, indicating that the expression of neuronal p75<sup>NTR</sup> is not essential for maintaining peripheral neuron survival and myelination after a demyelinating insult in vivo. Together, results of this study suggest that the survival and myelination of peripheral sensory neurons is independent of p75<sup>NTR</sup> expressed by a subtype of neurons in vivo. Thus, our findings provide new insights into the mechanism underpinning p75<sup>NTR</sup> -mediated neuronal survival in the PNS.
Imaging myocardial fiber architecture in vivo with magnetic resonance (1995)

Methods are presented to image the fiber architecture of the human myocardium in vitro and in vivo. NMR images are obtained of the diffusion anisotropy tensor, indicative of local myofiber orientation. Studies of cardiac necropsy specimens demonstrate classic features of ventricular myoarchitecture including the continuous endocardial to epicardial variation of fiber helix angles (angles to the ventricular circumferential direction) of approximately +1.3 to -1.3 radians. Cross-fiber anisotropy is also observed. In the beating heart, NMR diffusion data must be corrected for the effects of myocardial deformation during the cardiac cycle. This correction can be performed using an independent MRI method to map the strain-rate tensor field of the myocardium through time. Combining fiber orientation with local myocardial strain rate, local rates of myocardial fiber shortening may be computed.
Dispersion and loss properties of generalized shielded asymmetrical coupled microstrip lines (1994)

This paper presents computed data on the dispersion and loss properties of asymmetrical coupled microstrip lines with asymmetrically placed side walls. The computing method is based on mode matching technique. The computed data is found to agree very well with those obtained via the finite difference time domain method for the odd mode; and the difference is within six percent for the even mode. The results and the method of analysis will be useful in MIC and MMIC design and in transient analysis of generalized coupled microstrip lines.
Exercise-induced changes in branched chain amino acid/aromatic amino acid ratio in the rat brain and plasma. (1987)

Central fatigue was induced by running rats on a treadmill. Amino acid and ammonia metabolism in the brain and blood were followed with time to correlate its changes with physical exhaustion. The blood ammonia level did not change during running, but was prominently increased at exhaustion. The brain level of ammonia was also prominently high at the end of exercise with a time course of change similar to that of the blood level. Plasma concentrations of branched chain amino acids (BCAA) and aromatic amino acids (AAA) increased as the animals continued to run; however, the plasma BCAA/AAA ratio was definitely depressed at exhaustion. This was also true with the brain BCAA/AAA ratio. A positive correlation was demonstrated between the plasma and brain BCAA/AAA ratios at r=0.5040 and P less than 0.05. These exercise-related changes suggest that physical exercise-induced central fatigue involves not only an increase in brain ammonia, but also a disturbance in brain amine metabolism accompanying plasma and brain BCAA/AAA ratio depression. Furthermore, the ammonia level and BCAA/AAA ratio in the brain correlated with those in the blood. It is reasonable to consider that the blood ammonia concentration and plasma BCAA/AAA ratio may serve as important indices of the clinical condition of exercise-induced central fatigue.
Resilience in Incident Hemodialysis: Characterization and Outcome Prediction (2020)

Abstract The Resiliency in Dialysis Initiation (ReDI) Study aims to develop physical resilience signatures in older adults initiating hemodialysis. Study design—comprising a pilot, confirmatory study, and secondary data analyses—will be presented. So also will a method for characterizing resilience phenotypes—using mixed-model analysis of SF-36 subscale trajectories—among participants of age 55 and older who had undergone hemodialysis in the Choices for Healthy Outcomes in Caring for ESRD study (n=485). Analyses revealed stable, improving, and declining phenotypes. In Cox models, both baseline phenotypic status and trajectory type predicted mortality after adjusting for age, CVD status, and CHF (global Wald test for trajectory type P-value=0.020 for vitality; 0.030 for general health). These analyses evidence usefulness of resilience phenotypes as markers of adverse outcome risk and foreshadow application to novel ReDI data.
Stereochemie der Ringöffnung von Aziridinonen (α‐Lactamen) (1991)

Stereochemistry of Ring Opening of Aziridinones (α‐Lactams) The chiral, non‐racemic aziridinone ( R )‐ 4 (e.e. 92%) reacts with magnesium halides to afford the α‐halo amides ( S )‐ 3a (e.e. 88.8%), ( S )‐ 3b (e.e. 89.0%), and ( S )‐ 3c (e.e. 88.2%) in high yields. Acid‐catalysed hydrolysis of ( R )‐4 in aqueous acetone yields 74% of the α‐hydroxy amide ( S )‐3d (e.e. 88.0%). Methanolysis of ( R )‐ 4 in [D 4 ]methanol at 60°C followed the first‐order rate law with k = 1.53 ṁ 10 –5 s –1 yielding quantitatively a 82:18 mixture of the α‐methoxy amide ( S )‐ 3e (e.e. 89%) and the α‐amino ester ( R )‐ 14 (e.e. 87%). The latter is obtained exclusively (e.e. 87%) when ( R )‐ 4 reacts with sodium methoxide and methanol in ether while only the former is formed (e.e. 88.2%) by slow methanolysis in the presence of a catalytic amount of 4 ‐toluenesulfonic acid. The absolute configurations of the major enantiomers derived from ( R )‐ 4 are based on the retention on a Chirasil‐L‐Val capillary gas chromatography column, CD spectra, and the comparison with authentic samples of ( S )‐ 3a , obtained from ( S )‐ tert ‐leucine [( S )‐ 1 ] and ( S )‐ 3d . The results demonstrate that the N – C(3) bond of the aziridinone ( R )‐ 4 is cleaved by nucleophiles with a high degree of stereospecificity and inversion of configuration. This stereochemical course is at variance with that inferred from the methanolysis of the similar aziridinone ( R )‐ 7 . – Treatment of ( R )‐ 4 in [D 4 ]methanol with one equivalent of 3‐chloroperbenzoic acid ( 15 ) containing 5% of 3‐chlorobenzoic acid ( 16 ) affords carbon monoxide and the racemic oxaziridine 18 in quantitative yield, which is also obtained from the imine 19 in a very fast reaction. The acid 16 effects slow decomposition of ( R,S )‐ 4 into carbon monoxide and imine 19 , probably by general acid catalysis. The stereochemical result obtained from ( R )‐ 4 as well as the reaction conditions and differences in rate for formation and epoxidation of 19 suggest that in the peracid oxidation of an aziridinone the sequence of events consists of a rate‐limiting, acid‐catalysed decomposition into carbon monoxide and an imine, followed by very fast epoxidation of the latter. The previous mechanism, invoking as intermediates alleged aziridinone N ‐oxides, e.g. 17 , is not supported by the present study.
Fine Mapping and Functional Analysis of the Multiple Sclerosis Risk Gene CD6 (2013)

CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2(nd) SRCR domain with susceptibility to MS (P max(T) permutation = 1×10(-4)). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. - CD4(+) naïve cells, P = 0.0001; CD8(+) naïve cells, P<0.0001; CD4(+) and CD8(+) central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4(+) and CD8(+) T cells.
Selective Optical Switching of Interface-Coupled Relaxation Dynamics in Carbon Nanotube–Si Heterojunctions (2014)

By properly tuning the photon energy of a femtosecond laser pump, we disentangle, in carbon nanotube–Si (CNT/Si) heterojunctions, the fast relaxation dynamics occurring in CNT from the slow repopulation dynamics due to hole charge transfer at the junction. In this way we are able to track the transfer of the photogenerated holes from the Si depletion layer to the CNT layer, under the action of the built-in heterojunction potential. This also clarifies that CNT play an active role in the junction and do not act only as channels for charge collection and transport.
Improving the Cooperation of Fuzzing and Symbolic Execution by Test-cases Prioritizing (2017)

Nowadays much attention is paid to the threat of vulnerabilities on the software security. Fuzzing and symbolic execution, complementary to each other, are two effective techniques in software testing. In this paper, we develop the prototype called FAS(Fuzzing and Symbolic) for software testing under both fuzzing and symbolic execution. In our method, the test cases are prioritized through deep-oriented strategy and large-distance-first strategy, in order to get a higher path-coverage with the condition of limited resource.
Nonlinear Phase Noise Compensation Using a Modified Nonlinear Optical Loop Mirror (2010)

Nonlinear phase noise compensation with possibility of simultaneous amplitude noise suppression has been experimentally demonstrated in a DPSK transmission system using a modified NOLM. As main application quadrature and higher PSK modulation formats are expected.
Study on bio-filtration system for livestock wastewater and the water quality testing technique (2006)

This paper introduced the processing of the domestic and international livestock wastewater. The actuality of environmental problems caused by livestock husbandry was discussed and the relationship between husbandry and sustainable development was remarked on. From the point of ecosystem, dealing with livestock wastewater harmlessly with bio-filtration system is advised. A bio-filtration system is set up based on the analysis of a typical and simple water treatment system. The system mainly consists of a solid removal basin and a planting filter. We elect ryegrass as the planting-filter, because it gets best sod, mechanic filtration and bio-filtration. Effects of static bio-filtration were studied in ryegrass. Under this system, to achieve preferable purification efficiency, the wastewater concentration and the area of planting which suited for pasture growth will be provided. Near infrared spectra was used to analyze the water quality, about chemical oxygen demand (CODcr). A set of 20 samples of livestock wastewater with different concentrations was taken from the Animal Institution of Zhejiang Agricultural Science Organization, and the partial least square (PLS) was used to develop predictive models. To validate these models, some samples were used. SEP were 22, 32 and r<sup>2</sup> values using the validation set of data were 0.9895, 0.9985 for COD of wastewater.