gebhart/patrepeval huggingface dataset:
The <i>Escherichia coli</i> Ada Protein Can Interact with Two Distinct Determinants in the ς <sup>70</sup> Subunit of RNA Polymerase According to Promoter Architecture: Identification of the Target of Ada Activation at the <i>alkA</i> Promoter (1999)

The methylated form of the Ada protein (meAda) activates transcription from the Escherichia coli ada, aidB, and alkA promoters with different mechanisms. In this study we identify amino acid substitutions in region 4 of the RNA polymerase subunit sigma70 that affect Ada-activated transcription at alkA. Substitution to alanine of residues K593, K597, and R603 in sigma70 region 4 results in decreased Ada-dependent binding of RNA polymerase to the alkA promoter in vitro and impairs alkA transcription both in vivo and in vitro, suggesting that these residues define a determinant for meAda-sigma70 interaction. In a previous study (P. Landini, J. A. Bown, M. R. Volkert, and S. J. W. Busby, J. Biol. Chem. 273:13307-13312, 1998), we showed that a set of negatively charged amino acids in sigma70 region 4 is involved in meAda-sigma70 interaction at the ada and aidB promoters. However, the alanine substitutions of positively charged residues K593, K597, and R603 do not affect meAda-dependent transcription at ada and aidB. Unlike the sigma70 amino acids involved in the interaction with meAda at the ada and aidB promoters, K593, K597, and R603 are not conserved in sigmaS, an alternative sigma subunit of RNA polymerase mainly expressed during the stationary phase of growth. While meAda is able to promote transcription by the sigmaS form of RNA polymerase (EsigmaS) at ada and aidB, it fails to do so at alkA. We propose that meAda can activate transcription at different promoters by contacting distinct determinants in sigma70 region 4 in a manner dependent on the location of the Ada binding site.
PARTICLE REFLUX IN THE RISER OF A CIRCULATING FLUIDIZED BED (1993)

ABSTRACT Particle reflux has a significant influence on heat and mass transfer and gas back mixing in circulating fluidized beds. An novel heat transfer probe to determine the particle reflux region and details of the experimental procedure are presented and discussed in this paper. Results indicate that the particle velocity is one of the most important factors governing heat transfer between the bed and the surface in a circulating fluidized bed.
Interactive Grounded Language Acquisition and Generalization in a 2D World (2018)

We build a virtual agent for learning language in a 2D maze-like world. The agent sees images of the surrounding environment, listens to a virtual teacher, and takes actions to receive rewards. It interactively learns the teacher's language from scratch based on two language use cases: sentence-directed navigation and question answering. It learns simultaneously the visual representations of the world, the language, and the action control. By disentangling language grounding from other computational routines and sharing a concept detection function between language grounding and prediction, the agent reliably interpolates and extrapolates to interpret sentences that contain new word combinations or new words missing from training sentences. The new words are transferred from the answers of language prediction. Such a language ability is trained and evaluated on a population of over 1.6 million distinct sentences consisting of 119 object words, 8 color words, 9 spatial-relation words, and 50 grammatical words. The proposed model significantly outperforms five comparison methods for interpreting zero-shot sentences. In addition, we demonstrate human-interpretable intermediate outputs of the model in the appendix.
Simultaneous Detection and Differentiation of Pathogenic and Nonpathogenic Leptospira spp. by Multiplex Real-Time PCR (TaqMan) Assay (2010)

Leptospirosis, caused by pathogenic Leptospira, is one of the most important zoonoses in the world. Several molecular techniques have been developed for detection and differentiation between pathogenic and saprophytic Leptospira spp. The aim of this study was to develop a rapid and simple assay for specific detection and differentiation of pathogenic Leptospira spp. by multiplex real-time PCR (TaqMan) assay using primers and probes targeting Leptospira genus specific 16S ribosomal RNA gene, the pathogen specific lig A/B genes and nonpathogen Leptospira biflexa specific 23S ribosomal RNA gene. Sixteen reference strains of Leptospira spp. including pathogenic and nonpathogenic and ten other negative control bacterial strains were used in the study. While the 16S primers amplified target from both pathogenic and non-pathogenic leptospires, the ligA/B and the 23S primers amplified target DNA from pathogenic and non-pathogenic leptospires, respectively. The multiplex real-time PCR (TaqMan) assay detection limit, that is, the sensitivity was found approximately 1 x 10(2) cells/ml for ligA/B gene and 23S ribosomal RNA gene, and 10 cells/ml 16S ribosomal RNA. The reaction efficiencies were 83-105% with decision coefficients of more than 0.99 in all multiplex assays. The multiplex real-time PCR (TaqMan) assay yielded negative results with the ten other control bacteria. In conclusion, the developed multiplex real-time PCR (TaqMan) assay is highly useful for early diagnosis and differentiation between pathogenic and non-pathogenic leptospires in a reaction tube as having high sensitivity and specificity.
A Comparative Passivation Study for InAs/GaSb Pin Superlattice Photodetectors (2013)

In the quest to find ever better passivation techniques for infrared photodetectors, we explore several passivation layers using atomic layer deposition (ALD). We compare the impact of these layers on detectors fabricated under same conditions. We use ALD deposited Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> , HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , ZnO, plasma enhanced chemical vapor deposition deposited SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , Si <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> , and sulfur containing octadecanethiol self assembled monolayer passivation layers on InAs/GaSb p-i-n superlattice diodes with an average cutoff wavelength of 5.1 μm. Passivated and unpassivated photodetectors compared for their electrical performances.
Characterization of hybridoma cell responses to elevated pCO<sub>2</sub> and osmolality: Intracellular pH, cell size, apoptosis, and metabolism (2002)

CO(2) partial pressure (pCO(2)) in industrial cell culture reactors may reach 150-200 mm Hg, which can significantly inhibit cell growth and recombinant protein production. The inhibitory effects of elevated pCO(2) at constant pH are due to a combination of the increases in pCO(2) and [HCO(-) (3)], per se, and the associated increase in osmolality. To decouple the effects of pCO(2) and osmolality, low-salt basal media have been used to compensate for this associated increase in osmolality. Under control conditions (40 mm Hg-320 mOsm/kg), hybridoma cell growth and metabolism was similar in DMEM:F12 with 2% fetal bovine serum and serum-free HB GRO. In both media, pCO(2) and osmolality made dose-dependent contributions to the inhibition of hybridoma cell growth and synergized to more extensively inhibit growth when combined. Elevated osmolality was associated with increased apoptosis. In contrast, elevated pCO(2) did not increase apoptotic cell death. Specific antibody production also increased with osmolality although not with pCO(2). In an effort to understand the mechanisms through which elevated pCO(2) and osmolality affect hybridoma cells, glucose metabolism, glutamine metabolism, intracellular pH (pHi), and cell size were monitored in batch cultures. Elevated pCO(2) (with or without osmolality compensation) inhibited glycolysis in a dose-dependent fashion in both media. Osmolality had little effect on glycolysis. On the other hand, elevated pCO(2) alone had no effect on glutamine metabolism, whereas elevated osmolality increased glutamine uptake. Hybridoma mean pHi was approximately 0.2 pH units lower than control at 140 mm Hg pCO(2) (with or without osmolality compensation) but further increases in pCO(2) did not further decrease pHi. Osmolality had little effect on pHi. Cell size was smaller than control at elevated pCO(2) at 320 mOsm/kg, and greater than control in hyperosmotic conditions at 40 mm Hg.
Ventilator-associated pneumonia in the ICU (2014)

Ventilator-associated pneumonia (VAP) is defined as pneumonia that occurs 48–72 hours or thereafter following endotracheal intubation, characterized by the presence of a new or progressive infiltrate, signs of systemic infection (fever, altered white blood cell count), changes in sputum characteristics, and detection of a causative agent [1]. VAP contributes to approximately half of all cases of hospital-acquired pneumonia [1, 2]. VAP is estimated to occur in 9–27 % of all mechanically ventilated patients, with the highest risk being early in the course of hospitalization [1, 3]. It is the second most common nosocomial infection in the intensive care unit (ICU) and the most common in mechanically ventilated patients [4, 5]. VAP rates range from 1.2 to 8.5 per 1,000 ventilator days and are reliant on the definition used for diagnosis [6]. Risk for VAP is greatest during the first 5 days of mechanical ventilation (3 %) with the mean duration between intubation and development of VAP being 3.3 days [1, 7]. This risk declines to 2 %/day between days 5 to 10 of ventilation, and 1 %/day thereafter [1, 8]. Earlier studies placed the attributable mortality for VAP at between 33–50 %, but this rate is variable and relies heavily on the underlying medical illness [1]. Over the years, the attributable risk of death has decreased and is more recently estimated at 9–13 % [9, 10], largely because of implementation of preventive strategies. Approximately 50 % of all antibiotics administered in ICUs are for treatment of VAP [2, 4]. Early onset VAP is defined as pneumonia that occurs within 4 days and this is usually attributed to antibiotic sensitive pathogens whereas late onset VAP is more likely caused by multidrug resistant (MDR) bacteria and emerges after 4 days of intubation [1, 4]. Thus, VAP poses grave implications in endotracheally intubated adult patients in ICUs worldwide and leads to increased adverse outcomes and healthcare costs. Independent risk factors for development of VAP are male sex, admission for trauma and intermediate underlying disease severity, with odds ratios (OR) of 1.58, 1.75 and 1.47–1.70, respectively [7].
Physiological Characteristics of Youth Synchronized Skaters (2016)

International Journal of Exercise Science 9(3): 270-282, 2016. Figure skating is a lifelong sport with participation rates increasing for skaters of all ages. Development within the five disciplines of figure skating (individual skating, synchronized skating, pairs skating, ice dancing, and theater on ice) has led to increased physical demands placed on skaters’ bodies. As a result, focus on sport performance testing, training, and injury prevention specific to figure skating is increasing. The purpose of this study was to use field tests to describe the physical characteristics of synchronized skaters and to determine the relationships between these physiological characteristics and skating abilities. Anthropometric data were collected and field tests (sit-and-reach, vertical jump, hexagon, one-min sit-ups, one-min modified pushups, timed wall sit, and one-mile walk/run) were performed during off-ice fitness classes as part of synchronized skating camps. Participants were divided into Advanced (ADV) (n = 20; “intermediate and above”) and Beginner (BEG) (n = 21; “juvenile and below”) groups determined by their Moves in the Field (MITF) test levels. Significant differences were found between ADV and BEG groups for age, body weight, height, BMI, sit-and-reach (SR), and vertical jump height (VJ). Results from univariate statistics and paired t-tests (p < 0.05) indicated that the anthropometric variables of age, body weight, height, and BMI were greater for the ADV group as compared to the BEG group and were consistent with their greater physical development. SR (flexibility) and VJ (explosive power) were greater for the ADV group; as such, these may be athletic components to target as skating ability develops. Future research to identify fitness norms for skaters by level of skating ability (MITF) may assist synchronized skating coaches in the design of off-ice training programs to improve on-ice skating performance.
A faster method to reconstruct seismic data using anti-leakage Fourier transform (2016)

Despite the simplicity of the anti-leakage Fourier transform (ALFT), and its ability to regularize pure non-uniform data sets and handle higher dimension seismic data, ALFT still remains less appealing because of its iterative algorithm and so its costly computation. During this study a set of parameters and techniques were studied to reduce needed computation and speed up ALFT. Having a good weighting function and cautiously selecting more Fourier coefficients at each iteration could improve the resolution of each iteration and subsequently enhance the converge speed of ALFT. Here a precomputed matrix by exponential term of Fourier transform is used to compute Fourier components at each iteration of the ALFT. This proposed matrix dramatically reduces the needed complex multiplication and speeds up the ALFT. By merging this process with a proper weighting function, the fast-ALFT will be quicker than the original ALFT, while it will have almost the same output.
A table-lookup scheme for residue-to-binary conversion (2002)

Residue number system (RNS) implementations can provide speedup for addition, subtraction, and multiplication. However, conversion from RNS to binary is a significant bottleneck. We present an efficient scheme to convert residue numbers to binary numbers using table-lookup. The overall goal is to minimize the hardware needed for implementation while maximizing the speed of the conversion. Our design decreases the table size by a factor of 2 and reduces the number of required lookups compared to an existing design.
The Surgical Reduction of Spondylolisthesis (1986)

The Schnöllner operation for reduction of spondylolisthesis was performed through a transversal incision. After removal of the disc, two pedunculus screws with two different threads are inserted. Over these screws the reduction is performed against a slotted sacral plate. The operations were performed at the following levels: 48 at L5-S1, seven at L4-L5, and two at both levels. 70.8% of the patients had preoperative lumboischialgia, 23.3% lumbalgia. Postoperatively, 92.1% were without pain. Twenty-seven patients had preoperative sensory disturbances, while only five had such disorders five years after operation. New sensory disturbances occurred after operation in 11 patients, seven of these persisted. Before operation, 27 patients had pareses of the foot and toe extensors; after operation, ten of them. Paresis occurred in 12 cases, of which three persisted. In 13 cases the reposition was complete, in 17 cases the displacement after operation ranged from 11% to 30%. The lumbosacral angle was markedly diminished.
On Not Meeting Joao Ubaldo Ribeiro: In quest of the indigent (1999)

Hopscotch: A Cultural Review - Volume 2, Number 1, 2000
Physiology of Flowering (1962)

The appearance of the first flower is\nan important event in the life cycle of\na plant. After germination of the seed,\nthe apical meristem initially produces\nonly leaves. And then, abruptly, the\nbud produces, instead of more leaves,\na new organ, a flower or an inflorescence.\nAlthough flowers, from a morphological\npoint of view, are considered\nshoots with metamorphosized leaves,\ntheir structure and function are quite\ndifferent from those of normal shoots\nand leaves. The function of the flowers\nis, of course, sexual reproduction and\nthus maintenance of the species.
A Survey on Mobile Ad Hoc Wireless Network (2004)

This paper presents a coherent survey on ad hoc wireless networks, with the intent of serving as a quick reference to the current research issues in ad hoc networking. It starts with a background on the origin and development stages of ad hoc network, then summaries the characteristics, capabilities, applications and design constraints of ad hoc network fully distinguishing it from traditional networks. The paper discuses a broad range of research issues such as Routing, Medium Access, Multicasting, Quality of service, TCP performance, Energy, Security and Bluetooth, outlining the major challenges which have to be solved before widespread deployment of the technology is possible. Through this survey it would be seen that Ad ho c Networking presence an interesting research area inheriting the problems of wireless and mobile communications in their most difficult form.
Temporal Reasoning in Natural Language Processing: A Survey (2010)

Reasoning with temporal information in natural language text has attracted great attention due to its potential applications in summarization, question answering and other tasks. For example, the chronological ordering of events described in a text is important for presenting the information in the summary. Linking information in a natural language text with temporal relations is essential in question answering system to address time sensitive and dynamic world. A crucial first step towards the computational treatment of the temporal information in these applications is the automatic extraction of events described in the text and identification of temporal relations to link these events. Much of the work done in this direction can be classified as -Annotation schemes for identification of events and time implicit in the text, linking the events using temporal relations and Temporal reasoning for solving practical applications.
Si 1−y C y / Si (001) gas-source molecular beam epitaxy from Si2H6 and CH3SiH3: Surface reaction paths and growth kinetics (2003)

In situ surface probes and postdeposition analyses were used to follow surface reaction paths and growth kinetics of Si1−yCy alloys grown on Si(001) by gas-source molecular-beam epitaxy from Si2H6/CH3SiH3 mixtures as a function of C concentration y (0–2.6 at %) and temperature Ts (500–600 °C). High-resolution x-ray diffraction reciprocal lattice maps show that all layers are in tension and fully coherent with their substrates. Film growth rates R decrease with both y and Ts, and the rate of decrease in R as a function of y increases rapidly with Ts. In situ isotopically tagged D2 temperature-programmed desorption (TPD) measurements reveal that C segregation during steady-state Si1−yCy(001) growth results in charge transfer from Si surface dangling bonds to second-layer C atoms, which have a higher electronegativity than Si. From the TPD results, we obtain the coverage θSi*(y,Ts) of Si* surface sites with C backbonds as well as H2 desorption energies Ed from both Si and Si* surface sites. θSi* increases with increasing y and Ts in the kinetically limited segregation regime while Ed decreases from 2.52 eV for H2 desorption from Si surface sites with Si back bonds to 2.22 eV from Si* surface sites. This leads to an increase in the H2 desorption rate, and hence should yield higher film deposition rates, with increasing y and/or Ts during Si1−yCy(001) growth. The effect, however, is more than offset by the decrease in Si2H6 reactive sticking probabilities at Si* surface sites. Film growth rates R(Ts,JSi2H6,JCH3SiH3) calculated using a simple transition-state kinetic model, together with measured kinetic parameters, were found to be in excellent agreement with the experimental data.
Image-Based Highly Interactive Web Mapping for Geo-Referenced Data Publishing (2002) (2003)

This paper describes an image-based technique that enables highly interactive Web choropleth maps for geo-referenced data publishing and visual exploration. Geographic knowledge is encoded into raster images and delivered to the client, instead of in vector formats. Differing from traditional raster-image-based approaches that are static and allow very little user interaction, it allows varieties of sub-second fine-grained interface controls such as dynamic query, dynamic classification, geographic object data identification, user setting adjusting, as well as turning on/off layers, panning and zooming, with no or minimum server support. Compared to Web GIS approaches that are based on vector geographic data, this technique has the features of short initial download time, near-constant performance scalability for larger numbers of geographic objects, and download-map-segment-only-when-necessary which potentially reduces the overall data transfer over the network. As a result, it accommodates general public users with slow modem network connections and low-end machines, as well as users with fast T-1 connections and fast machines. The client-side (browser) is implemented as light-weight Java applets. YMap, an easy-to-use, user-task-oriented highly interactive mapping tool prototype for visual geo-referenced data exploration is implemented using this technique. (UMIACS-TR-2003-02) (HCIL-TR-2002-26)
Integrating verification testing and logic synthesis (1991)

In this paper, a new design strategy, in which built-in self test (BIST) synthesis tightly interacts with the functional logic design, is described. The authors' method is aimed at VLSI combinational circuits. The BIST design procedure is based on the concept of verification testing. Compared to circuits obtained using conventional design methods, they obtain a reduction in the test signals required and, as a consequence, a substantial reduction in test length and in the complexity of the built-in test pattern generator.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Reservoir uncertainty, Precambrian topography, and carbon sequestration in the Mt. Simon Sandstone, Illinois Basin (2009)

Sequestration sites are evaluated by studying the local geological structure and confirming the presence of both a reservoir facies and an impermeable seal not breached by significant faulting. The Cambrian Mt. Simon Sandstone is a blanket sandstone that underlies large parts of Midwest United States and is this region's most significant carbon sequestration reservoir. An assessment of the geological structure of any Mt. Simon sequestration site must also include knowledge of the paleotopography prior to deposition. Understanding Precambrian paleotopography is critical in estimating reservoir thickness and quality. Regional outcrop and borehole mapping of the Mt. Simon in conjunction with mapping seismic reflection data can facilitate the prediction of basement highs. Any potential site must, at the minimum, have seismic reflection data, calibrated with drill-hole information, to evaluate the presence of Precambrian topography and alleviate some of the uncertainty surrounding the thickness or possible absence of the Mt. Simon at a particular sequestration site. The Mt. Simon is thought to commonly overlie Precambrian basement granitic or rhyolitic rocks. In places, at least about 549 m (1800 ft) of topographic relief on the top of the basement surface prior to Mt. Simon deposition was observed. The Mt. Simon reservoir sandstone is thin or not present where basement is topographically high, whereas the low areas can have thick Mt. Simon. The paleotopography on the basement and its correlation to Mt. Simon thickness have been observed at both outcrops and in the subsurface from the states of Illinois, Ohio, Wisconsin, and Missouri.