gebhart/patrepeval huggingface dataset:
Identification of Bacterial Plant Pathogens Using Multilocus Polymerase Chain Reaction/Electrospray (2008)

Postnikova, E., Baldwin, C., Whitehouse, C. A., Sechler, A., Schaad, N. W., Sampath, R., Harpin, V., Li, F., Melton, R., Blyn, L., Drader, J., Hofstadler, S., and Schneider, W. L. 2008. Identification of bacterial plant pathogens using multilocus polymerase chain reaction/electrospray ionization-mass spectrometry. Phytopathology 98:1156-1164. Polymerase chain reaction/electrospray ionization-mass spectrometry (PCR/ESI-MS, previously known as “TIGER”) utilizes PCR with broadrange primers to amplify products from a wide array of organisms within a taxonomic group, followed by analysis of PCR amplicons using mass spectrometry. Computer analysis of precise masses allows for calculations of base compositions for the broad-range PCR products, which can then be compared to a database for identification. PCR/ESI-MS has the benefits of PCR in sensitivity and high-throughput capacity, but also has the distinct advantage of being able to detect and identify organisms with no prior characterization or sequence data. Existing broad range PCR primers, designed with an emphasis on human pathogens, were tested for their ability to amplify DNA of well characterized phytobacterial strains, as well as to populate the existing PCR/ESI-MS bacterial database with base counts. In a blinded panel study, PCR/ESI-MS successfully identified 93% of unknown bacterial DNAs to the genus level and 73% to the species/subspecies level. Additionally, PCR/ESI-MS was capable of detecting and identifying multiple bacteria within the same sample. The sensitivity of PCR/ESI-MS was consistent with other PCR based assays, and the specificity varied depending on the bacterial species. Preliminary tests with real life samples demonstrate a high potential for using PCR/ ESI-MS systems for agricultural diagnostic applications.
Technology Transfer of HCI Research Innovations (2015)

There has been a longstanding concern within HCI that even though we are accumulating great innovations in the field, we rarely see these innovations develop into products. Our panel brings together HCI researchers from academia and industry who have been directly involved in technology transfer of one or more HCI innovations. They will share their experiences around what it takes to transition an HCI innovation from the lab to the market, including issues around time commitment, funding, resources, and business expertise. More importantly, our panelists will discuss and debate the tensions that we (researchers) face in choosing design and evaluation methods that help us make an HCI research contribution versus what actually matters when we go to market.
Enhanced post‐source decay and cross‐ring fragmentation of oligosaccharides facilitated by conversion to amino derivatives (2004)

Post-source decay (PSD) fragmentation of chemically or enzymatically produced aminoglycans has been evaluated through matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Conversion of native glycans to their respective aminoglycan derivatives improved detection sensitivity of the usual fragments and promoted cross-ring fragmentation of linear oligosaccharides, facilitating linkage recognition. The cross-ring fragmentations for both dextrin and dextran oligosaccharides were not limited to the reducing-end glucose moiety, as they were extended throughout the entire molecule. When the amino group was generated for N-glycans derived from three different glycoproteins, an enhancement of PSD was observed, without a significant extent of cross-ring fragmentation.
Fabrication of an Omnidirectional 2D Photonic Crystal Emitter for Thermophotovoltaics (2016)

In a thermophotovoltaic (TPV) system, a heat source brings an emitter to incandescence and the spectrally confined thermal radiation is converted to electricity by a low-bandgap photovoltaic (PV) cell. Efficiency is dominated by the emitter's ratio of in-band emissivity (convertible by the PV cell) to out-of-band emissivity (inconvertible). Two-dimensional photonic crystals (PhCs) offer high in-band emissivity and low out-of-band emissivity at normal incidence, but have reduced in-band emissivity off-normal. According to Lambert's law, most thermal radiation occurs off-normal. An omnidirectional PhC capable of high in-band emissivity at all angles would increase total in-band power by 55% at 1200°C. In this work, we present the first experimental demonstration an omnidirectional hafnia-filled 2D tantalum PhC emitter suitable for TPV applications such as combustion, radioisotope, and solar TPV. Dielectric filling improved the hemispherical performance without sacrificing stability or ease of fabrication. The numerical simulations, fabrication processes, and optical and thermal characterizations of the PhC are presented in this paper.
Prospective measurements of hearing threshold during military rifle training with in-ear, protected, noise exposure monitoring (2022)

Although a causal relationship exists between military occupational noise exposure and hearing loss, researchers have struggled to identify and/or characterize specific operational noise exposures that produce measurable changes in hearing function shortly following an exposure. Growing evidence suggests that current standards for noise-exposure limits are not good predictors of true hearing damage. In this study, the aim was to capture the dose-response relationship during military rifle training exercises for noise exposure and hearing threshold. To capture exposure, a wearable system capable of measuring impulse noise simultaneously on-body and in-ear, behind hearing protection was used. To characterize hearing threshold changes, portable audiometry was employed within 2 h before and after exposure. The median 8-h time-weighted, protected, free-field equivalent in-ear exposure was 87.5 dBA at one site and 80.7 dBA at a second site. A significant dose-response correlation between in-ear noise exposure and postexposure hearing threshold changes across our population ( R = 0.40 , p = 0.0281) was observed. The results demonstrate an approach for establishing damage risk criteria (DRC) for in-ear, protected measurements based on hearing threshold changes. While an in-ear DRC does not currently exist, it may be critical for predicting the risk of injury for noise environments where protection is mandatory and fit status can vary.
Student Reflections on Needs Finding in Community-Based Design Work (2019)

Abstract Reflection is an important component in design skill development that helps designers better understand their design problem, develop better solutions, and improve their design approaches. This study explored the information that a student design team reflected on as part of a needs finding experience and the outcomes from these reflections. During the needs finding experience, the team exhibited reflection-in- action behavior as they used available data to form and iterate on explanatory hypotheses about potential community needs. After the needs finding experience, the team exhibited reflection-on-action behavior as they drew connections between their interview approaches and stakeholder responses and discussed changes they might make in the future. The team also identified situations where contextual factors of the stakeholder impacted their interviews, but during these reflections did not indicate how they might adapt their approaches to account for such factors in the future. These findings show that student designers can use reflection as a tool to improve their needs finding process but would benefit from pedagogical structures that might help them reflect more effectively.
Nonlinear Regression Analysis of Well-Test Pressure Data with Uncertain Variance (2000)

Abstract The main objective of this study is to explore the use of parameter estimation techniques that handle cases where error variances (weights) in observed well-test data are uncertain. There are two main sources of uncertainty: 1) The gauge resolution and 2) measurement environment. Many gauges are used in well testing are not well characterized in terms of accuracy and resolution. The measurement environment in the wellbore is very noisy because of high frequency events in the wellbore (any producing interval), eg phase segregation. Because of these uncertainties, in this study, we investigated the use of parameter estimation methods based on the maximum likelihood and presented a new efficient method based on this method. The maximum likelihood method enables one to estimate error variances in pressure data along with the unklnown formation parameters. It is shown that the new method is efficient and powerful in estimating formation parameters from well-test data with uncertain variance. A simulated interval test from the multiprobe wireline formation tester in a single layer system as well as a field interval test in a three layer cross-flow system are used to demonstrate the applicability of the proposed methods.
<title>Development of IR-emitting infrared fibers at the Naval Research Laboratory</title> (2001)

Naval Research Laboratory (NRL) has been developing high brightness mid-wave IR emitting fibers for HWIL testing. These fibers, based upon rare-earth doped chalcogenide glass, emit from 3.5 - 5 m and are capable of simulating very high temperatures in this band. To date, temperatures of 2400 K have been simulated. The fiber sources operate at room temperature, are environmentally tolerant, and can be formed into fiber bundles with high fill factors and low pixel to pixel cross- talk for IR scene generation. In this paper, we will present the spectral output, temporal response, temperature simulation and output uniformity of the mid-wave IR emitting fibers. The potential for long-wave IR emitting fiber sources will also be presented.
Silicon-on-insulator microring resonator defect-based photodetector with 3.5-GHz bandwidth (2011)

We have devised and fabricated high-speed silicon-on-insulator resonant microring photodiodes. The detectors comprise a p-i-n junction across a silicon rib waveguide microring resonator. Light absorption at 1550 nm is enhanced by implanting the diode intrinsic region with boron ions at 350 keV with a dosage of 1 × 1013 cm−2. We have measured 3-dB bandwidths of 2.4 and 3.5 GHz at 5 and 15 V reverse bias, respectively, and observed an open-eye diagram at 5 gigabit/s with 5 V bias.
Magnetic ordering in Fe δ-doped Pd (2007)

CircPVT1 acts as an oncogene in BC via promoting the growth, invasion, migration and inhibiting apoptosis through miR-29a-3p-mediated AGR2-HIF-1α axis.
Effects of Organ Culture and Optisol-GS Storage on Structural Integrity, Phenotypes, and Apoptosis in Cultured Corneal Epithelium (2007)

These data indicate that OC storage of cultured HLECs at ambient temperature is superior to OC storage at 31 degrees C and Optisol-GS storage at 5 degrees C and that apoptosis is minimal after eye bank storage of cultured HLECs.
New Hexaketide Inhibitors of Eukaryotic Signal Transduction (1997)

Abstract Three new inhibitors of eukaryotic signal transduction, the hexaketides cycloepoxydon (1), 1-hydroxy-2-hydroxymethyl-3-pent-1-enylbenzene (2) and 1-hydroxy-2-hydroxymethyl-3-pent-1,3-dienylbenzene (3) were isolated from fermentations of a deuteromycete strain. Their structures were determined by spectroscopic techniques.
Resolution of Methyl Nonactate by Rhodococcus erythropolis under Aerobic and Anaerobic Conditions (2006)

[reaction: see text]. An efficient resolution of methyl nonactate is reported by biotransformation in shake flask cultures of Rhodococcus erythropolis. The equilibrium of the reaction redox system can be manipulated by switching from aerobic to anaerobic growth, thereby generating both enantiomers of the target in excellent yield and enantiomeric purity.
Promoters of OrthologousGlycine maxandLotus japonicusNodulation Autoregulation Genes Interchangeably Drive Phloem-Specific Expression in Transgenic Plants (2007)

The nodule autoregulation receptor kinase (GmNARK) of soybean (Glycine max) is essential for the systemic autoregulation of nodulation. Based on quantitative reverse-transcriptase polymerase chain reaction, GmNARK is ex-pressed to varying levels throughout the plant; the transcript was detected at high levels in mature leaves and roots but to a lesser extent in young leaves, shoot tips, and nodules. The transcript level was not significantly affected by Bradyrhizobium japonicum during the first week following inoculation. In addition, the activities of the promoters of GmNARK and Lotus japonicus HARI, driving a beta-glucuronidase (GUSPlus) reporter gene, were examined in stably transformed L. japonicus and transgenic hairy roots of soybean. Histochemical GUS activity in L. japonicus plants carrying either a 1.7-kb GmNARKpr::GUS or 2.0-kb LjHAR1pr::GUS construct was clearly localized to living cells within vascular bundles, especially phloem cells in leaves, stems, roots, and nodules. Phloem-specific expression also was detected in soybean hairy roots carrying these constructs. Our study suggests that regulatory elements required for the transcription of these orthologous genes are conserved. Moreover, rapid amplification of 5' cDNA ends (5' rapid amplification of cDNA ends) revealed two major transcripts of GmNARK potentially originating from two TATA boxes. Further analysis of the GmNARK promoter has confirmed that these two TATA boxes are functional. Deletion analysis also located a region controlling phloem-specific expression to a DNA sequence between 908 bp and 1.7 kb upstream of the translation start site of GmNARK.
05421 Executive Summary – Data Always and Everywhere – Management of Mobile, Ubiquitous, and Pervasive Data (2006)

This report summarizes the important aspects of the workshop on "Management of Mobile, Ubiquitous, and Pervasive Data", which took place from October 16th to October 21st, 2005. Thirty-seven participants from thirteen countries met during that week and discussed a broad range of topics related to the management of data in relation to mobile, ubiquitous, and pervasive applications of information technology. The wealth of the contributions is available at the seminar page at the Dagstuhl server. Here, we provide a short overview.
Induction of Apoptosis by Ethanol Extract of Cnidium officinale in Human Leukemia U937 Cells through Activation of AMPK (2015)

천궁(C. officinale)은 예로부터 민간처방 약재로 사용되었으며, 항염증, 항산화, 항암 및 신생혈관억제 등의 효능을 가지는 것으로 알려져 있다. 하지만 혈구암세포에서 apoptosis 유발과 관련된 분자생물학적 기전에 대해서는 명확히 밝혀져 있지 않다. 본 연구에서는 인체 혈구암세포인 U937 세포에서 천궁의 열수, 에탄올 및 메탄올 추출물(WECO, EECO 및 MECO)이 유발하는 항암효과 및 항암기전을 조사하였다. 먼저 WECO, EECO 및 MECO가 유발하는 증식억제 정도를 조사한 결과 EECO가 가장 뛰어난 효능을 가진다는 것을 알 수 있었으며, 이러한 현상이 apoptosis 유발에 의한 것임을 annexin-V 염색, apoptotic body 형성, DNA 단편화 및 MMP 소실 등을 통하여 확인하였다. EECO 처리에 의한 apoptosis 유발에는 DR4의 발현 증가와 함께 cIAP-1, Bcl-2 및 total Bid의 발현감소가 관여하였으며, caspases-3, -8 및 -9의 활성화와 함께 caspases-3의 기질 단백질인 PARP, &#x3B2;-catenin 및 PLC &#x3B3;1의 단편화도 관찰되었다. 또한 EECO는 AMPK signaling pathway를 활성화시키는 것으로 나타났으며, AMPK 억제제인 compound C를 이용하여 AMPK의 활성을 억제하였을 경우 EECO에 의하여 유발되었던 apoptosis가 현저하게 감소되는 것으로 나타났다. 이상의 결과를 살펴볼 때 인체 혈구암세포인 U937 세포에서 EECO에 의하여 유발되는 apoptosis는 AMPK가 중요한 조절자로서 작용하는 것으로 생각된다. Cnidium officinale, a traditional herb, has diverse beneficial pharmacological activities, such as anti-inflammatory, antioxidant, anticancer, and antiangiogenesis effects. However, the cellular and molecular mechanisms of apoptosis by C. officinale are poorly defined. The present study investigated the proapoptotic effects of water, ethanol, and methanol extract of C. officinale (WECO, EECO, and MECO, respectively) in human leukemia U937 cells. The antiproliferative activity of EECO was higher than that of WECO and MECO. The antiproliferative effect of EECO treatment in U937 cells was associated with the induction of apoptotic cell death, including increased populations of annexin-V positive cells, the formation of apoptotic bodies, DNA fragmentation, and increased numbers of cells with a loss of mitochondrial membrane potential (MMP, &#x394;&#x3C8;m). EECO-induced apoptotic cell death was associated with upregulation of death receptor 4 (DR4) and down-regulation of cellular inhibitor of apoptosis protein-1 (cIAP-1), Bcl-2, and total Bid. The EECO treatment also induced the proteolytic activation of caspases (-3, -8, and -9), and degradation of caspase-3 substrate proteins, such as poly(ADP-ribose) polymerase (PARP), &#x3B2;-catenin, and phospholipase C-&#x3B3;1 (PLC&#x3B3;1). In addition, the EECO treatment effectively activated the adenosine monophosphate-activated protein kinase (AMPK) signaling pathway. However, compound C, a specific inhibitor of AMPK, significantly reduced EECO-induced apoptosis. These results indicate that AMPK is a key regulator of apoptosis in response to EECO in human leukemia U937 cells.
Optical design and characterization of an advanced computational imaging system (2014)

We describe an advanced computational imaging system with an optical architecture that enables simultaneous and dynamic pupil-plane and image-plane coding accommodating several task-specific applications. We assess the optical requirement trades associated with custom and commercial-off-the-shelf (COTS) optics and converge on the development of two low-cost and robust COTS testbeds. The first is a coded-aperture programmable pixel imager employing a digital micromirror device (DMD) for image plane per-pixel oversampling and spatial super-resolution experiments. The second is a simultaneous pupil-encoded and time-encoded imager employing a DMD for pupil apodization or a deformable mirror for wavefront coding experiments. These two testbeds are built to leverage two MIT Lincoln Laboratory focal plane arrays – an orthogonal transfer CCD with non-uniform pixel sampling and on-chip dithering and a digital readout integrated circuit (DROIC) with advanced on-chip per-pixel processing capabilities. This paper discusses the derivation of optical component requirements, optical design metrics, and performance analyses for the two testbeds built.
Chapter 11 Dynamic DVFS Scheduling (2007)

As discussed in the previous chapter, offline analysis can be used to generate a schedule of DVFS state changes to minimize energy consumption, while en- suring sufficient processing cycles are available for all tasks to meet their dead- lines, even under worst-case computation requirements. However, invocations of real-time tasks typically use less than their specified worst-case computation requirements, presenting an opportunity for further energy conservation. This chapter outlines three online, dynamic techniques to more aggressively scale back processing frequency and voltage to conserve energy when task compu- tation cycles vary, yet continue to provide timeliness guarantees for worst-case execution time scenarios.
Bidirectional recurrent neural network language models for automatic speech recognition (2015)

Recurrent neural network language models have enjoyed great success in speech recognition, partially due to their ability to model longer-distance context than word n-gram models. In recurrent neural networks (RNNs), contextual information from past inputs is modeled with the help of recurrent connections at the hidden layer, while Long Short-Term Memory (LSTM) neural networks are RNNs that contain units that can store values for arbitrary amounts of time. While conventional unidirectional networks predict outputs from only past inputs, one can build bidirectional networks that also condition on future inputs. In this paper, we propose applying bidirectional RNNs and LSTM neural networks to language modeling for speech recognition. We discuss issues that arise when utilizing bidirectional models for speech, and compare unidirectional and bidirectional models on an English Broadcast News transcription task. We find that bidirectional RNNs significantly outperform unidirectional RNNs, but bidirectional LSTMs do not provide any further gain over their unidirectional counterparts.
Assessing Transmissible Spongiform Encephalopathy Species Barriers with an <em>In Vitro</em> Prion Protein Conversion Assay (2015)

Studies to understanding interspecies transmission of transmissible spongiform encephalopathies (TSEs, prion diseases) are challenging in that they typically rely upon lengthy and costly in vivo animal challenge studies. A number of in vitro assays have been developed to aid in measuring prion species barriers, thereby reducing animal use and providing quicker results than animal bioassays. Here, we present the protocol for a rapid in vitro prion conversion assay called the conversion efficiency ratio (CER) assay. In this assay cellular prion protein (PrPC) from an uninfected host brain is denatured at both pH 7.4 and 3.5 to produce two substrates. When the pH 7.4 substrate is incubated with TSE agent, the amount of PrPC that converts to a proteinase K (PK)-resistant state is modulated by the original host's species barrier to the TSE agent. In contrast, PrPC in the pH 3.5 substrate is misfolded by any TSE agent. By comparing the amount of PK-resistant prion protein in the two substrates, an assessment of the host's species barrier can be made. We show that the CER assay correctly predicts known prion species barriers of laboratory mice and, as an example, show some preliminary results suggesting that bobcats (Lynx rufus) may be susceptible to white-tailed deer (Odocoileus virginianus) chronic wasting disease agent.
Nanoscale Sensing Assemblies Using Quantum Dot–Protein Bioconjugates (2006)

This chapter contains sections titled: Introduction Quantum Dot–Protein Bioconjugates Förster Formalism and Quantum Dots as Energy Donors Quantum Dots as FRET Donors Quantum-Dot-Based FRET Nanosensors Surface-Attached QD–FRET Nanoassemblies Conclusions Acknowledgments References
Add-On Microchannels for Hotspot Thermal Management of Microelectronic Chips in Compact Applications (2018)

This paper demonstrates an experimental micro- channel solution to cool microelectronic chips with hotspots, using an integrated, yet nonintrusive technique. In microelectronics, approaches such as die thinning induce acute stress on cooling because it increases the hotspot phenomena and reduces chip bulk thickness that could be used for microchannels. In compact devices, heat must be removed using limited pumping power and cooling space. Microchannels etched in the backside of the chip, usually considered as an efficient cooling solution, are impracticable on highly thinned chips. This paper experimentally investigates the cooling performance of a noninvasive and hotspot aware microchannel die that is in direct fluidic contact with the backside of the microelectronic chip. It also proposes a confinement-wise metric. A thermal resistance of 2.8 °C/W is achieved at a heat flux of 812 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> per heat source, for a total dissipated power of 20 W and a maximum allowed temperature rise of 55 °C. Such performance is obtained with only 19.2 kPa of pressure drop and 9.4 ml/min of flow rate, corresponding to a hydraulic power of only 3 mW and a coefficient of performance of 6500. In addition, the complete chip stack, including the thinned chip, measures only <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$660~\mu \text{m}$ </tex-math></inline-formula> high. Therefore, backside cooling appears to be a promising compact and low consumption solution for compact electronic applications having confined hotspots.