gebhart/patrepeval huggingface dataset:
Detection of stable pre-rRNA in toxigenic Pseudo-nitzschia species (1997)

Nucleotide sequence analysis of ribosomal DNA (rDNA) spacer regions is useful for taxonomic comparisons of closely related microorganisms. These regions have been less useful for routine microbial identification and detection, partly because rRNA precursors (pre-rRNAs) in microbial cells are assumed to be too labile to be detectable by high-throughput probe hybridization methods. We characterized the sequence diversity and physiological stability of pre-rRNA in the toxigenic marine diatoms Pseudo-nitzschia australis, P. multiseries, and P. pungens. As with nucleotide sequences of the first internal transcribed spacer (ITS1) reported previously, sequences of ITS2 and the 5' external transcribed spacer (ETS1) exhibited considerable divergence among these species, including large insertions-deletions detectable by PCR-based spacer length analysis. In slot blot hybridization assays on RNA extracted from lysates of Pseudo-nitzschia cells, oligonucleotide probes directed to pre-rRNA spacers generated much stronger signals than did complementary probes directed to the coding strands of the rDNAs, indicating that the pre-rRNA-targeted probes detected multicopy transcripts. A group of probes directed to a discrete 90-base region within the ITS1 pre-rRNA gave no detectable signal, suggesting that this region is degraded early in the rRNA maturation pathway. Other pre-rRNA regions were always detectable and, in marked contrast to prokaryotic systems analyzed in this manner, were stable and abundant in both actively dividing and nondividing cells. Long, multilabeled RNA probes, which would exhibit considerable cross-reactivity if directed to mature rRNA sequences, detected species-specific pre-rRNA sequences from as few as 1,000 cells. Pre-rRNA is a potentially useful molecular target for detecting and identifying Pseudo-nitzschia species and possibly other unicellular eukaryotes as well.
U1 snRNP regulates cancer cell migration and invasion in vitro (2020)

Stimulated cells and cancer cells have widespread shortening of mRNA 3'-untranslated regions (3'UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in introns and last exons. U1 snRNP (U1), vertebrates' most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread premature transcription termination and mRNA shortening. Here we show that low U1 AMO doses increase cancer cells' migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3'UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected role for U1 homeostasis (available U1 relative to transcription) in oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.
Femtosecond Two‐photon Excited Fluorescence of Melanin* (1999)

Fluorescence of synthetic melanin in dimethyl sulfoxide has been excited by two-photon absorption at 800 nm, using 120 fs pulses with photon flux densities > or = 10(27) cm-2 s-1. The shortest main component of the three-exponential decay of fluorescence is 200 +/- 2 ps. The overall spectral shape is red-shifted with respect to the 400 nm excited fluorescence. Two-photon excited melanin fluorescence also has been measured from excised samples of healthy human skin tissue. Because of the selectivity of melanin excitation via resonant two-photon absorption, it is hypothesized that fluorescence excited in this way may yield information on malignant transformation.
Predictive Sea State Estimation for Automated Ride Control and Handling - PSSEARCH (2012)

PSSEARCH provides predictive sea state estimation, coupled with closed-loop feedback control for automated ride control. It enables a manned or unmanned watercraft to determine the 3D map and sea state conditions in its vicinity in real time. Adaptive path-planning/ replanning software and a control surface management system will then use this information to choose the best settings and heading relative to the seas for the watercraft. PSSEARCH looks ahead and anticipates potential impact of waves on the boat and is used in a tight control loop to adjust trim tabs, course, and throttle settings. The software uses sensory inputs including IMU (Inertial Measurement Unit), stereo, radar, etc. to determine the sea state and wave conditions (wave height, frequency, wave direction) in the vicinity of a rapidly moving boat. This information can then be used to plot a safe path through the oncoming waves. The main issues in determining a safe path for sea surface navigation are: (1) deriving a 3D map of the surrounding environment, (2) extracting hazards and sea state surface state from the imaging sensors/map, and (3) planning a path and control surface settings that avoid the hazards, accomplish the mission navigation goals, and mitigate crew injuries from excessive heave, pitch, and roll accelerations while taking into account the dynamics of the sea surface state. The first part is solved using a wide baseline stereo system, where 3D structure is determined from two calibrated pairs of visual imagers. Once the 3D map is derived, anything above the sea surface is classified as a potential hazard and a surface analysis gives a static snapshot of the waves. Dynamics of the wave features are obtained from a frequency analysis of motion vectors derived from the orientation of the waves during a sequence of inputs. Fusion of the dynamic wave patterns with the 3D maps and the IMU outputs is used for efficient safe path planning.
Amberlite IRA 900 versus calcium alginate in immobilization of a novel, engineered β‐fructofuranosidase for short‐chain fructooligosaccharide synthesis from sucrose (2019)

The immobilization of β-fructofuranosidase for short-chain fructooligosaccharide (scFOS) synthesis holds the potential for a more efficient use of the biocatalyst. However, the choice of carrier and immobilization technique is a key to achieving that efficiency. In this study, calcium alginate (CA), Amberlite IRA 900 (AI900) and Dowex Marathon MSA (DMM) were tested as supports for immobilizing a novel engineered β-fructofuranosidase from Aspergillus japonicus for scFOS synthesis. Several immobilization parameters were estimated to ascertain the effectiveness of the carriers in immobilizing the enzyme. The performance of the immobilized biocatalysts are compared in terms of the yield of scFOS produced and reusability. The selection of carriers and reagents was motivated by the need to ensure safety of application in the production of food-grade products. The CA and AI900 both recorded impressive immobilization yields of 82 and 62%, respectively, while the DMM recorded 47%. Enzyme immobilizations on CA, AI900 and DMM showed activity recoveries of 23, 27, and 17%, respectively. The CA, AI900 immobilized and the free enzymes recorded their highest scFOS yields of 59, 53, and 61%, respectively. The AI900 immobilized enzyme produced a consistent scFOS yield and composition for 12 batch cycles but for the CA immobilized enzyme, only 6 batch cycles gave a consistent scFOS yield. In its first record of application in scFOS production, the AI900 anion exchange resin exhibited potential as an adequate carrier for industrial application with possible savings on cost of immobilization and reduced technical difficulty.
Inferring Quality in Point Cloud-based 3D Printed Objects using Topological Data Analysis (2018)

Assessing the quality of 3D printed models before they are printed remains a challeng- ing problem, particularly when considering point cloud-based models. This paper introduces an approach to quality assessment, which uses techniques from the field of Topological Data Analy- sis (TDA) to compute a topological abstraction of the eventual printed model. Two main tools of TDA, Mapper and persistent homology, are used to analyze both the printed space and empty space created by the model. This abstraction enables investigating certain qualities of the model, with respect to print quality, and identifies potential anomalies that may appear in the final product.
Grassmannian Predictive Coding for Limited Feedback in Multiple Antenna Wireless Systems (2011)

Limited feedback is a paradigm for the feedback of channel state information in wireless systems. In multiple antenna wireless systems, limited feedback usually entails quantizing a source that lives on the Grassmann manifold. Most work on limited feedback beamforming considered single-shot quantization. In wireless systems, however, the channel is temporally correlated, which can be used to reduce feedback requirements. Unfortunately, conventional predictive quantization does not incorporate the non-Euclidean structure of the Grassmann manifold. In this paper, we propose a Grassmannian predictive coding algorithm where the differential geometric structure of the Grassmann manifold is used to formulate a predictive vector quantization encoder and decoder. We analyze the quantization error and derive bounds on the distortion attained by the proposed algorithm. We apply the algorithm to a multiuser multiple-input multiple-output wireless system and show that it improves the achievable sum rate as the temporal correlation of the channel increases.
Terahertz pulse measurement with an optical streak camera (1999)

Incorporating an electro-optic modulator with a conventional optical streak camera extends the spectral range of the streak camera from the optical region (UV, visible, and near-IR) to the terahertz region (far-IR and millimeter-wave) with a minimum modification. We demonstrate the temporal measurement of freely propagating terahertz pulses with single-shot capability.
Hierarchical Aggregation of Consumer Ratings for Service Ecosystem (2015)

With the wide availability of products and services through popular e-commerce platforms and dozens of similar offerings to choose from, there is a need to accurately assess and evaluate the quality of offerings. Several studies have shown that consumer feedback is an important source of information. This paper presents: (a) consumer Rating as a Service (RaaS) -- a building block service that can be used to add the consumer feedback lifecycle feature in the development of e-commerce platforms, (b) an approach to evaluate the quality of composite offerings based on the aggregation of consumer ratings using the composition structure and component relationships. Benefits of the proposed service include reduced development effort, shorter delivery time and a fine-grained aggregation of consumer ratings for composite offerings even with limited ratings.
Electron field emission for ultrananocrystalline diamond films (2001)

Ultrananocrystalline diamond (UNCD) films 0.1–2.4 μm thick were conformally deposited on sharp single Si microtip emitters, using microwave CH4–Ar plasma-enhanced chemical vapor deposition in combination with a dielectrophoretic seeding process. Field-emission studies exhibited stable, extremely high (60–100 μA/tip) emission current, with little variation in threshold fields as a function of film thickness or Si tip radius. The electron emission properties of high aspect ratio Si microtips, coated with diamond using the hot filament chemical vapor deposition (HFCVD) process were found to be very different from those of the UNCD-coated tips. For the HFCVD process, there is a strong dependence of the emission threshold on both the diamond coating thickness and Si tip radius. Quantum photoyield measurements of the UNCD films revealed that these films have an enhanced density of states within the bulk diamond band gap that is correlated with a reduction in the threshold field for electron emission. In addition, scanning tunneling microscopy studies indicate that the emission sites from UNCD films are related to minima or inflection points in the surface topography, and not to surface asperities. These data, in conjunction with tight binding pseudopotential calculations, indicate that grain boundaries play a critical role in the electron emission properties of UNCD films, such that these boundaries: (a) provide a conducting path from the substrate to the diamond–vacuum interface, (b) produce a geometric enhancement in the local electric field via internal structures, rather than surface topography, and (c) produce an enhancement in the local density of states within the bulk diamond band gap.
SCR device for ESD protection in sub-micron triple well silicided CMOS processes (2005)

A high-holding-low-trigger-voltage-silicon-controlled-rectifier (HHLVTSCR) is fabricated in a sub-micron triple well CMOS technology in complementary nand p-types. The HHLVTSCRs occupy less area than typical electrostatic discharge (ESD) protection devices and the corresponding I-V characteristics are adjustable to different protection requirements. The characteristics of these devices are tuned by the appropriate choice of the internal dimensions and device interconnections. Both n- and p-type devices are characterized using the transmission line pulse (TLP) technique. Comparisons between n- and p-type devices show that n-type devices perform better than p-type devices for low holding voltages (V/sub H/), but for relatively high holding voltages the p-type devices show better characteristics. Results demonstrate that ESD protection capabilities in n- and p-type devices are adequate for the design of multiple IC's ESD protection schemes with very low leakage current and without latchup concerns.
Wideband antenna array for step-frequency ground penetrating radar (2012)

This work investigates the properties of a novel wideband air-launched antenna array for high speed 3-dimensional GPR surveys. It consists of boomerang-shaped monopole antenna elements mounted on a layer of microwave absorbing material, backed by a ground plane. The antenna element provides a very flat frequency response ranging from 200 MHz to 3 GHz. This allows us to take full advantage of the step-frequency radar's property of covering a wide frequency range without switching between different frequency band antennas. The transmitting and receiving elements are arranged on a V-shaped structure where the tip of the V is pointing towards the ground. This structure gives high isolation between the transmitter and receiver and suppresses the multiple reflections between antenna and ground surface. The antenna was studied both numerically and experimentally to characterize the electromagnetic behavior. The main design objective was to maximize the radiation in the downward direction while minimizing the coupling between the transmitter and receiver. Based on these studies, more than 40 dB of isolation between transmitting and receiving antenna has been obtained. Furthermore, the flat frequency response ensures a clean impulse response with low ringing which is very important when measuring thin pavement layers. The paper also presents field measurement results from a high-speed road survey.
”Parallelized variable selection and modeling based on prediction” algorithm on GPU for feature selection and ADMET model generation (2017)

Lack of safety and efficacy are the two major reasons for the failures of drug candidates in drug discovery and development. Reliable prediction of blood-brain barrier permeation even before chemical synthesis still remains as one of the major challenges in drug discovery. New approaches and models that are reliable and can reduce experimental evaluations of pre-clinical candidates are in urgent need. We describe herein Parallelized Variable Selection and Modeling based on the Prediction, an exhaustive search algorithm for feature selection and robust model ADMET model generation using publically available blood-brain barrier permeation data.
Extended cavity laser enhanced two-photon flow cytometry (2008)

We demonstrate enhanced sensitivity in two-photon flow cytometry with an extended cavity laser excitation source. At low power, the home-built 20-MHz oscillator was able to detect a significantly larger fraction, in either phosphate buffered saline (PBS) or whole blood, of green fluorescent protein (GFP)-expressing MCA-207 cells cross-labeled with the membrane-binding lipophilic dye DiD. A geometrical model is used to explain unique features of the signals resulting from the different spatial distribution of DiD and GFP. These unique features include sub-square law scaling of unsaturated two-photon signal, a sigmoidal sensitivity curve for detection under varying powers for cell detection thresholds as low as a single photon, and uncorrelated signal strengths in two detection channels.
GENETIC CHARACTERIZATION OF SUNFLOWER MUTANTS WITH HIGH CONTENT OF SATURATED FATTY ACIDS IN SEED OIL / CARACTERIZACION GENETICA DE MUTANTES DE GIRASOL CON ALTO CONTENIDO EN ACIDOS GRASOS SATURADOS / CARACTÉRISATION GÉNÉTIQUE DES MUTANTS DE TOURNESOL À HAUT CONTENU D’ACIDES GRAS SATURÉS DANS L’HUILE (2000)

SUMMARY The genetic control of the high saturated fatty acid content in sunflower seed oil has been studied in the high palmitic acid (C16:0) mutant line CAS-5, and in the high stearic acid (C18:0) mutant line CAS-3. This review summarizes the pertinent results. The high saturated fatty acid content in sunflower seed oil is controlled by partially recessive alleles at two loci ( Es1 , Es2 ) for the high C18:0 content and at three loci ( P1 , P2 , P3 ) for the high C16:0 content. The high C16:0 and the high C18:0 traits are not inherited independently. When their combined segregation was studied, the expected phenotypic expression of both high C16:0 and high C18:0 levels was not observed. This fact was attributed to the existence of an epistatic effect of the loci controlling the high C16:0 trait on the loci controlling the high C18:0 trait. The results obtained indicate that sunflower hybrids with a high saturated fatty acid content in their seed oil can be developed and will be in cultivation in a few years.
Failure-Aware Application Placement Modeling and Optimization in High Turnover DevOps Environment (2019)

DevOps (software DEVelopment and information technology OPerationS) has established a culture and environment, in which building, testing, and releasing software happen more rapidly, frequently, and reliably through automated pipelines. To support this high turnover application cycle, the cluster orchestration frameworks such as Kubernetes or Docker Swarm have evolved to provide high flexibility and reliability. However, while cluster orchestrators run on the cloud infrastructure, any failure incurred from the infrastructure can directly impact the nodes of a cluster, so infrastructure failures can disrupt applications running on the cluster. In this paper, we propose proactive application placement algorithms with prediction of infrastructure failures. The proposed algorithms utilize failure-risk measurements, Failure-Index, determined from turnover rate of applications and prediction of infrastructure failures. We build stochastic models for application turnover and infrastructure failure processes, and provide various types of Failure-Index. Our placement algorithms are implemented in an orchestration framework, Kubernetes, and in the simulation model. Experimental results show that our methods reduce the amount of application disruption by 20% than the state-of-the-art algorithms in Kubernetes.
A stereoselective total synthesis of prostaglandin E1 (1970)

D. Taub, R. D. Hoffsommer, C. H. Kuo, H. L. Slates, Z. S. Zelawski and N. L. Wendler, J. Chem. Soc. D, 1970, 1258 DOI: 10.1039/C29700001258
Vasodilating Procyanidins Derived from Grape Seeds (2002)

We have shown in previous work that extracts of grape seeds (GSE) and skins, grape juice, and many red wines exhibit endothelium-dependent relaxing (EDR) activity in vitro. This EDR activity involves endothelial nitric oxide (NO) release and subsequent increase in cyclic GMP levels in the vascular smooth muscle cells. The NO/cyclic GMP pathway is known to be involved in many cardiovascular-protective roles. The current study focuses on the isolation and identification of EDR-active compounds (procyanidins) from GSE. Crushed Concord grape seeds were extracted with methanol and the extract was separated into seven fractions (A-G) on a Toyopearl TSK-HW-40 column. EDR-active fractions (D-G) were further separated into 25 individual compound peaks by HPLC, 16 of which were EDR active (threshold for relaxation ranged between less than 0.5 microg/mL and greater than 4 microg/mL). Procyanidin identification was accomplished by electrospray-ion trap mass spectrometry (ES-ITMS), MS/MS, and by tannase treatment and acid thiolysis, followed by HPLC and ES-ITMS of the products. Activity of isolated procyanidins tended to increase with degree of polymerization, epicatechin content, and with galloylation. These EDR-active compounds (many of which also possess antioxidant activity), individually or in the form of wines, juices, or nutritional supplements, may be useful in preventing or treating cardiovascular diseases.
CRISPR-Mediated Reorganization of Chromatin Loop Structure (2018)

Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown. Until recently, how chromatin looping affects the regulation of gene activity and cellular function has been relatively ambiguous, and limitations in existing methods to manipulate these structures prevented in-depth exploration of these interactions. To resolve this uncertainty, we engineered a method for selective and reversible chromatin loop re-organization using CRISPR-dCas9 (CLOuD9). The dynamism of the CLOuD9 system has been demonstrated by successful localization of CLOuD9 constructs to target genomic loci to modulate local chromatin conformation. Importantly, the ability to reverse the induced contact and restore the endogenous chromatin conformation has also been confirmed. Modulation of gene expression with this method establishes the capacity to regulate cellular gene expression and underscores the great potential for applications of this technology in creating stable de novo chromatin loops that markedly affect gene expression in the contexts of cancer and development.
Failure of Over-Reinforced Hybrid Fiber Reinforced Polymer Concrete Beam Columns (1999)

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Post-Learning Optimization of Tree Ensembles for Efficient Ranking (2016)

Learning to Rank (LtR) is the machine learning method of choice for producing high quality document ranking functions from a ground-truth of training examples. In practice, efficiency and effectiveness are intertwined concepts and trading off effectiveness for meeting efficiency constraints typically existing in large-scale systems is one of the most urgent issues. In this paper we propose a new framework, named CLEaVER, for optimizing machine-learned ranking models based on ensembles of regression trees. The goal is to improve efficiency at document scoring time without affecting quality. Since the cost of an ensemble is linear in its size, CLEaVER first removes a subset of the trees in the ensemble, and then fine-tunes the weights of the remaining trees according to any given quality measure. Experiments conducted on two publicly available LtR datasets show that CLEaVER is able to prune up to 80% of the trees and provides an efficiency speed-up up to 2.6x without affecting the effectiveness of the model.