gebhart/patrepeval huggingface dataset:
Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts (2014)

The outcome of respiratory virus infection is determined by a complex interplay of viral and host factors. Some potentially important host factors for the antiviral response, whose functions remain largely unexplored, are long non-coding RNAs (lncRNAs). Here we systematically inferred the regulatory functions of host lncRNAs in response to influenza A virus and severe acute respiratory syndrome coronavirus (SARS-CoV) based on their similarity in expression with genes of known function. We performed total RNA-Seq on viral-infected lungs from eight mouse strains, yielding a large data set of transcriptional responses. Overall 5,329 lncRNAs were differentially expressed after infection. Most of the lncRNAs were co-expressed with coding genes in modules enriched in genes associated with lung homeostasis pathways or immune response processes. Each lncRNA was further individually annotated using a rank-based method, enabling us to associate 5,295 lncRNAs to at least one gene set and to predict their potential cis effects. We validated the lncRNAs predicted to be interferon-stimulated by profiling mouse responses after interferon-α treatment. Altogether, these results provide a broad categorization of potential lncRNA functions and identify subsets of lncRNAs with likely key roles in respiratory virus pathogenesis. These data are fully accessible through the MOuse NOn-Code Lung interactive database (MONOCLdb).
Head and neck squamous cell carcinoma (2020)

Most head and neck cancers are derived from the mucosal epithelium in the oral cavity, pharynx and larynx and are known collectively as head and neck squamous cell carcinoma (HNSCC). Oral cavity and larynx cancers are generally associated with tobacco consumption, alcohol abuse or both, whereas pharynx cancers are increasingly attributed to infection with human papillomavirus (HPV), primarily HPV-16. Thus, HNSCC can be separated into HPV-negative and HPV-positive HNSCC. Despite evidence of histological progression from cellular atypia through various degrees of dysplasia, ultimately leading to invasive HNSCC, most patients are diagnosed with late-stage HNSCC without a clinically evident antecedent pre-malignant lesion. Traditional staging of HNSCC using the tumour-node-metastasis system has been supplemented by the 2017 AJCC/UICC staging system, which incorporates additional information relevant to HPV-positive disease. Treatment is generally multimodal, consisting of surgery followed by chemoradiotherapy (CRT) for oral cavity cancers and primary CRT for pharynx and larynx cancers. The EGFR monoclonal antibody cetuximab is generally used in combination with radiation in HPV-negative HNSCC where comorbidities prevent the use of cytotoxic chemotherapy. The FDA approved the immune checkpoint inhibitors pembrolizumab and nivolumab for treatment of recurrent or metastatic HNSCC and pembrolizumab as primary treatment for unresectable disease. Elucidation of the molecular genetic landscape of HNSCC over the past decade has revealed new opportunities for therapeutic intervention. Ongoing efforts aim to integrate our understanding of HNSCC biology and immunobiology to identify predictive biomarkers that will enable delivery of the most effective, least-toxic therapies.
YAV-8B reaction control system bleed and control power usage in hover and transition (1993)

Using a calibrated Rolls-Royce Pegasus engine and existing aircraft instrumentation and pressure taps, total and individual nozzle reaction control system (RCS) bleed flow rates have been measured on a YAV-8B Harrier during typical short takeoff, transition, hover, and vertical landing maneuvers. RCS thrust forces were calculated from RCS nozzle total pressure measurements, and control power was determined from the moments produced by these thrusts and the aircraft's moments of inertia. These data document the characteristics of the YAV-8B RCS with its basic stability augmentation system (SAS) engaged. Advanced control system designs for the YAV-8B can be compared to the original SAS based on the total bleed use and the percentage of available bleed used. In addition, the peak and mean values of the bleed and control power data can be used for sizing the reaction controls for a future short takeoff and vertical landing (STOVL) aircraft.
Could Skype be more satisfying? a QoE-centric study of the FEC mechanism in an internet-scale VoIP system (2010)

The phenomenal growth of Skype in recent years has surpassed all expectations. Much of the application's success is attributed to its FEC mechanism, which adds redundancy to voice streams to sustain audio quality under network impairments. Adopting the quality of experience approach (i.e., measuring the mean opinion scores), we examine how much redundancy Skype adds to its voice streams and systematically explore the optimal level of redundancy for different network and codec settings. This study reveals that Skype's FEC mechanism, not so surprisingly, falls in the ballpark, but there is surprisingly a significant margin for improvement to ensure consistent user satisfaction.
Role and regulation of bacterial LuxR-like regulators (2011)

LuxR transcriptional regulator is a key player in Quorum Sensing (QS), coordinates the expression of a variety of genes, including those encoding virulence factors and antibiotics biosynthesis, motility, nodulation, plasmid transfer, bioluminescence, and biofilm formation. The characteristics and roles of this family, especially those of Mycobacterium, are summarized in this paper to give clues for drug target discovery.
A unified framework for simulating Markovian models of highly dependable systems (1992)

The authors present a unified framework for simulating Markovian models of highly dependable systems. It is shown that a variance reduction technique called importance sampling can be used to speed up the simulation by many orders of magnitude over standard simulation. This technique can be combined very effectively with regenerative simulation to estimate measures such as steady-state availability and mean time to failure. Moveover, it can be combined with conditional Monte Carlo methods to quickly estimate transient measures such as reliability, expected interval availability, and the distribution of interval availability. The authors show the effectiveness of these methods by using them to simulate large dependability models. They discuss how these methods can be implemented in a software package to compute both transient and steady-state measures simultaneously from the same sample run.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The antioxidant butylated hydroxytoluene protects against atherosclerosis. (1991)

Rabbits fed a 1% cholesterol diet with or without the antioxidant butylated hydroxytoluene (BHT) developed typical atherosclerotic lesions. The addition of BHT gave higher levels of total cholesterol (+40%), triglycerides (+250%), low density lipoprotein (LDL), and very low density lipoprotein (VLDL) in plasma. Despite the lower plasma lipid levels, the degree of atherosclerosis of the aortic surface was considerably higher in rabbits fed cholesterol than in the group treated with cholesterol and BHT. The mean atherosclerotic involvement was 18.6 +/- 4.4% in the former group and 5.9 +/- 1.7% in the latter group (p = 0.02). In all animals, there was a high correlation between the area of the arterial lesion and cholesterol content (r = 0.96). Serum levels of cholesterol autooxidation products (7-ketocholesterol and cholesterol 5 alpha,6 alpha-epoxide) were lower in the group of rabbits treated with BHT (p less than 0.005). Serum levels of vitamin E were slightly higher in the BHT group. There was no significant difference in the clearance of beta-VLDL between the two treatment groups after using either beta-VLDL from cholesterol-fed animals or beta-VLDL from BHT-fed animals. The results are in accord with the contention that oxidative modification of lipoproteins is important for the development of atherosclerosis and that antioxidants may have a protective effect. At present, however, other explanations cannot be completely excluded, for example, effects of antioxidants on immunologic factors or monocyte adhesion.
Population Structure, Fungicide Resistance Profile, and <i>sdhB</i> Mutation Frequency of <i>Botrytis cinerea</i> from Strawberry and Greenhouse-Grown Tomato in Greece (2014)

Botrytis cinerea is a pathogen with high genetic variability that has also shown high risk for fungicide resistance development. In total, 1,169 isolates obtained from strawberry (n = 297) and tomato (n = 872) in five geographic regions of Greece were tested for their sensitivity to several botryticides. A high frequency of isolates with multiple resistance to carbendazim, cyprodinil, pyraclostrobin, and boscalid was found in isolates from strawberry. In the isolates from tomato, the predominant phenotype was that of dual resistance to carbendazim and cyprodinil in the Crete island, of single resistance to carbendazim in the region of Preveza, and of sensitive isolates in the region of Kyparissia. None of the tested isolates was found to be fludioxonil resistant. High frequencies of boscalid-resistant phenotypes were observed in the strawberry isolates, while boscalid-resistance frequency in the tomato isolates was lower. H272R was the predominant sdhB mutation, associated with resistance to boscalid, in all the sampled isolates, while other sdhB mutations were found at low frequencies. B. cinerea group S, identified by the presence of a 21-bp insertion in the transcription factor mrr1 gene, was predominant within the tomato isolates obtained from all three sampled regions, with frequencies ranging from 62 to 75% of the isolates; whereas, within strawberry isolates, B. cinerea was predominant, with frequencies of 75 to 95%. Correlations of isolate genotype and fungicide resistance profile showed that B. cinerea sensu stricto isolates were more prone to the development of resistance to boscalid compared with the Botrytis group S isolates, which may explain the observed predominance of B. cinerea sensu stricto in strawberry fields.
O-Glycosylation of Serum IgD in IgA Nephropathy (2006)

In IgA nephropathy (IgAN), serum IgA1 with abnormal O-glycosylation preferentially deposits in the glomerular mesangium. The control of O-glycosylation is poorly understood. Among Ig isotypes, only IgD, produced early in B cell development, and IgA1, produced by mature B cells, are O-glycosylated. For investigation of the stage of B cell maturation at which the defect seen in IgAN arises, the O-glycosylation of serum IgA1 and IgD was studied in IgAN and controls. Serum was obtained from 20 patients with IgAN and 20 control subjects. The O-glycosylation profiles of native and desialylated IgA1 and IgD were measured in an ELISA-type system using the lectins Helix aspersa and peanut agglutinin, which bind to alternative forms of O-glycan moieties. The lectin-binding patterns of the two immunoglobulins differed in all participants, with that of IgD suggesting that it is more heavily galactosylated than IgA1. Defective O-glycosylation of IgA1, probably taking the form of reduced galactosylation, was confirmed in IgAN in this study. This undergalactosylation was not shared by IgD; in contrast, IgD carried more galactosylated O-glycans in IgAN than controls. The contrasting lectin-binding patterns of IgA1 and IgD shows that Ig O-glycosylation is differentially controlled during B cell maturation. Compared with controls, O-glycosylation in IgAN is incomplete in IgA1 but more complete in IgD. These observations show that abnormal IgA1 O-glycosylation in IgAN is not due to an inherent defect in glycosylation mechanisms but arises only at a later stage in B cell development and may be secondary to aberrant immunoregulation.
Order-Chaos Transition of Two Trapped Ions (1988)

Phase transitions of trapped particles and ions, observed initially in 1959 by collisional cooling and recently by laser cooling, are explained as order-chaos transitions. Here, two trapped ${\mathrm{Ba}}^{+}$ ions are examined experimentally and by computer solution of the equations of motion. The ordered state, quasiperiodic with two frequencies, becomes chaotic when a bifurcation introduces a third frequency at a critical value of a control parameter. This route evolves from the nonlinear Coulomb coupling of the ion pair's axial and radial motions, displaying frequency locking and hysteresis, which is observed.
Harmonic phase based low coherence interferometry : a method for studying the dynamics and structures of cells (2001)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2002.
Algorithms for a Broadcast Protocol Multiprocessor. (1982)

Multi-electrode extracellular recordings in area 17 of awake behaving ferrets were conducted to characterize the pattern of spontaneous activity in the developing visual cortex before eye opening. A linear array of 16 microwire electrodes was used to record extracellular neuronal activity across a 3.2 mm strip of visual cortex between postnatal days 22 and 28. Whereas synchronous bursts of activity were observed at all recording sites, cross-correlation analysis revealed that the timing of spike activity at all electrodes was not precisely correlated. Correlated activity between cortical sites exhibited a patchy organization having long-range components. Long-range correlated activity was observed between cortical patches that were separated by a mean distance of 1 mm. The spatial pattern of correlated activity persisted during transient lateral geniculate nucleus (LGN) activity block, indicating that long-range correlated activity is generated by intrinsic circuits within the cortex, independent of LGN input activity. These results demonstrate an innate patchy organization of correlated spontaneous activity within the cortex during the early development of cortical functional and anatomical organization.
Development of Smart Remote Terminal Unit for Water Treatment SCADA System (2014)

In this paper, a new remote terminal unit(hereafter RTU) is proposed to manage a wide range of applications and a variety of sensors (eg, , pressure, water quality, temperature and humidity sensors, the amount of pollutants, CO₂ , etc.) to monitor and control the facility such as water treatment plant, intake and effluent pumping station, water tank and distribution network. Fault status of local sensor devices and network are alerted by using the embedded fault handling capabilities of the RTU in the system and also sent to the fault handling server, by which fault can be easily monitored to users. The developed system was applied to one of K-water branch offices in Geoje city and improved its reliability and stability for controlling and monitoring water facility.
A new reverse engineering process, the combination between the knowledge extraction and the geometrical recognition techniques (2009)

Reverse engineering (RE) is a research field where physical models are measured or digitised in order to be reconstructed to obtain a clever CAD model with the opened geometry. The rebuilt geometric models using currently geometrical approaches are generally frozen or not re-usable. This paper deals with a new reverse engineering process which combines ldquoknowledge extractionrdquo of a part and classical techniques of 3D building. This combination of both approaches defines a methodology which assists the user in the reverse engineering process. The issued CAD model consists of topologic features structured in a tree of designing. This structure opens the geometry of the model and allows an underlying reverse engineering.
Iridium-Mediated Asymmetric Hydrogenation of 2,3-Diphenylbutadiene:  A Revealing Kinetic Study (2003)

Hydrogenation of 2,3-diphenylbutadiene mediated by a chiral iridium carbene oxazoline complex was studied. The kinetics of the reaction showed that it occurred in two distinct stages. The first corresponded to slow consumption of the diene to form half-hydrogenated products, i.e., monoenes. After all the diene was consumed, however, the reaction was much faster and more stereoselective. These data were interpreted in terms of possible catalytic intermediates.
Limits on Pauli principle violation by nucleons (1999)

We consider nuclei produced in core collapse supernovas and subjected to a high neutron flux. We show that an accelerator mass spectrometry experiment that searches for traces of anomalous iron isotopes could set limits of the order of ${10}^{\ensuremath{-}20}--{10}^{\ensuremath{-}25}$ on (or perhaps discover) Pauli principle violation by neutrons. A similar search for anomalous Co isotopes could set limits in the range ${10}^{\ensuremath{-}13}--{10}^{\ensuremath{-}18}$ on Pauli principle violation by protons. We show that existing data on oxygen can be used to set a limit of about ${10}^{\ensuremath{-}17}$ in one proposed model of such violation.
Study on the Voltage Traveling Wave wavefront Detection for CVT (2005)

Voltage traveling wave wavefronts are essential for the traveling-wave based relays. capacitive voltage transformers (CVTs) are the predominant source of the voltage signals for the relays in HV/EHV/UHV power systems. To study the influence of the CVT on the detection of the voltage traveling wavefronts, this paper firstly analyzes the frequency response, especially the high frequency response of the CVT with the transfer function. The contributing factors to the high frequency response of the CVT are deeply studied. Then the companion model of the CVT is modeled and the wavelet transform is utilized to simulate and analyze the influence of the CVT on the voltage traveling wavefronts The study results show that the CVT causes severe attenuation and phase shift for the high frequency components, consequently it seriously suppresses and disturbs the voltage traveling wavefronts. Adjusting the parameters of the CVT can improve the wavefronts in the CVT's output, but serious errors are still inevitable. Further study is needed to recover and detect the wavefronts precisely from the CVT's output
Multi‐frequency planar monopole antenna for GSM/DCS/PCS/WLAN operation (2003)

Abstract A novel planar monopole antenna capable of multi‐frequency operation at about 900, 1800, and 2450 MHz is presented. The monopole antenna occupies a small area of 6.5 × 50 mm 2 , and is easy to construct with low cost by printing on an FR4 substrate. The monopole antenna can be mounted perpendicularly to the system circuit board of a communication device so that a low profile to the system ground plane will result. In addition, the obtained impedance bandwidths of the proposed antenna at about 900, 1800, and 2450 MHz can cover the GSM (890–960 MHz), DCS (1710–1880 MHz), PCS (1850–1990 MHz), and WLAN (2400–2484 MHz) bands. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 36: 350–352, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10761
A quasi-3D simulation for high-voltage level-shifting circuit by divided RESURF structure (2009)

A new quasi-3D simulation technique to verify the high-voltage level-shifting circuit by divided RESURF structure is proposed. It simulates the 3D performances of the structure by combining the devices paralleled to plane x-y and plane y-z with the circuit analysis advanced application module of Medici. The punch-through effect and parasitic n-MOST effect in the structure are analyzed and simulated. The results prove that only the parasitic n-MOST has been developed in this structure. The optimized parameters of the divided RESURF structure can be proposed to suppress the parasitic n-MOST effect. The quasi-3D simulation technique has many merits, such as computing quickly, no demand on the high-end computer terminals and operating easily.
Improvement in Reduction Performance of LNT-Catalyst System with Micro-Reformer in Diesel Engine (2010)

디젤엔진은 높은 열효율과 우수한 연비 성능 등의 장점을 가지고 있으나, 기화된 연료와 주변 공기가 혼합된 후 착화되는 과정을 거치기 때문에 이론 공연비 영역에서는 질소산화물(NOx) 배출이 증가되는 문제점을 가지고 있다. 최근 활발히 연구되고 있는 높은 정화 효율을 가진 LNT촉매는 희박 분위기 조건에서는 NOx를 흡장하게 되고 과농한 분위기에서는 환원 분위기 형성을 통하여 를 NOx저감시키게 된다. 희박 공연비에서 동작하는 디젤 엔진에서는 이러한 환원 과정을 이루기 위해 주기적으로 과농한 분위기를 형성해주어야만 하는데, 이러한 연구는 NOx저감을 위해 HC를 포함한 환원제의 농도를 제어하는 기술로서 본 연구에서는 디젤을 연료로 하는 수소농후가스 발생장치를 이용하여 LNT 촉매에 환원제로서 수소농후가스를 직접 공급하는 방식으로 LNT촉매의 NOx저감 특성을 파악하였다.
The Maize <i>Floury1</i> Gene Encodes a Novel Endoplasmic Reticulum Protein Involved in Zein Protein Body Formation (2007)

The maize (Zea mays) floury1 (fl1) mutant was first reported almost 100 years ago, but its molecular identity has remained unknown. We report the cloning of Fl1, which encodes a novel zein protein body membrane protein with three predicted transmembrane domains and a C-terminal plant-specific domain of unknown function (DUF593). In wild-type endosperm, the FL1 protein accumulates at a high level during the period of zein synthesis and protein body development and declines to a low level at kernel maturity. Immunogold labeling showed that FL1 resides in the endoplasmic reticulum surrounding the protein body. Zein protein bodies in fl1 mutants are of normal size, shape, and abundance. However, mutant protein bodies ectopically accumulate 22-kD alpha-zeins in the gamma-zein-rich periphery and center of the core, rather than their normal discrete location in a ring at outer edge of the core. The 19-kD alpha-zein is uniformly distributed throughout the core in wild-type protein bodies, and this distribution is unaffected in fl1 mutants. Pairwise yeast two-hybrid experiments showed that FL1 DUF593 interacts with the 22-kD alpha-zein. Results of these studies suggest that FL1 participates in protein body formation by facilitating the localization of 22-kD alpha-zein and that this is essential for the formation of vitreous endosperm.
Control of Coccidiosis in Calves by Vaccination (2014)

The immunizing effect of inactivated sporulated oocyst and inactivated sonicated vaccines against bovine coccidiosis was observed in calves. Indirect haemagglutination (IHA) test was developed for detecting antibodies to coccidian. Serum antibody levels in calves were measured against soluble oocyst (sporulated) antigen. IHA antibody titer was significantly higher (P<0.05) in calves vaccinated with inactivated sonicated vaccines as compared to the calves vaccinated with inactivated sporulated vaccines. Results of the challenge experiments indicated that the inactivated sonicated vaccine gave protection to the challenge calves as immune calves contained high level of antibodies that resisted heavy dose of challenge. Disease was observed in control group (non-vaccinated) calves post challenge whereas vaccinated remained healthy. Then the oocyst count per gram of faeces was significantly higher (P<0.05) in control group (unvaccinated) as compared with the vaccinated groups.
Identification of a cloned cytokinin biosynthetic gene (1984)

A small region of the Ti plasmid (the tmr locus), thought to be involved in phytohormone metabolism in Agrobacterium tumefaciens-transformed plant tissue, was cloned and expressed in Escherichia coli. By enzyme assay, the tmr locus was shown to encode isopentenyltransferase, an enzyme that catalyzes the first step in cytokinin biosynthesis.