gebhart/patrepeval huggingface dataset:
Lack of End-Product Inhibition and Repression of Leucine Synthesis in a Strain of <i>Salmonella typhimurium</i> (1967)

Mutants of Salmonella have been isolated which luck either end product inhibition or repression of leucine biosynthesis. In a minimal saltsglucose medium, growth is not impaired by the lack of either control mechanism alone. The loss of both control mechanisms, however, leads to a 43 percent reduction in cell yield and a 1.5-fold reduction in the growth rate.
View-based query processing and constraint satisfaction (2002)

View-based query processing requires answering a query posed to a database only on the basis of the information on a set of views, which are again queries over the same database. This problem is relevant in many aspects of database management, and has been addressed by means of two basic approaches: query rewriting and query answering. In the former approach, one tries to compute a rewriting of the query in terms of the views, whereas in the latter, one aims at directly answering the query based on the view extensions. We study view based query processing for the case of regular-path queries, which are the basic querying mechanisms for the emergent field of semistructured data. Based on recent results, we first show that a rewriting is in general a co-NP function wrt to the size of view extensions. Hence, the problem arises of characterizing which instances of the problem admit a rewriting that is PTIME. A second contribution of the work is to establish a tight connection between view based query answering and constraint satisfaction problems, which allows us to show that the above characterization is going to be difficult. As a third contribution, we present two methods for computing PTIME rewritings of specific forms. The first method, which is based on the established connection with constraint satisfaction problems, gives us rewritings expressed in Datalog with a fixed number of variables. The second method, based on automata-theoretic techniques, gives us rewritings that are formulated as unions of conjunctive regular-path queries with a fixed number of variables.
RTRACS: A Modularized RNA-Dependent RNA Transcription System with High Programmability (2011)

Creating artificial biological systems is an important research endeavor. Each success contributes to synthetic biology and adds to our understanding of the functioning of the biomachinery of life. In the construction of large, complex systems, a modular approach simplifies the design process: a multilayered system can be prepared by integrating simple modules. With the concept of modularity, a variety of synthetic biological systems have been constructed, both in vivo and in vitro. But to properly develop systems with desired functions that integrate multiple modules, researchers need accurate mathematical models. In this Account, we review the development of a modularized artificial biological system known as RTRACS (reverse transcription and transcription-based autonomous computing system). In addition to modularity, model-guided predictability is an important feature of RTRACS. RTRACS has been developed as an in vitro artificial biological system through the assembly of RNA, DNA, and enzymes. A fundamental module of RTRACS receives an input RNA with a specific sequence and returns an output RNA with another specific sequence programmed in the main body, which is composed of DNA and enzymes. The conversion of the input RNA to the output RNA is achieved through a series of programmed reactions performed by the components assembled in the module. Through the substitution of a subset of components, a module that performs the AND operation was constructed. Other logical operations could be constructed with RTRACS modules. An integration of RTRACS modules has allowed the theoretical design of more complex functions, such as oscillation. The operations of these RTRACS modules were readily predicted with a numerical simulation based on a mathematical model using realistic parameters. RTRACS has the potential to model highly complex systems that function like a living cell. RTRACS was designed to be integrated with other molecules or molecular devices, for example, aptazymes, cell-free expression systems, and liposomes. For the integration of these new modules, the quantitative controls of each module based on the numerical simulation will be instructive. The capabilities of RTRACS promise to provide models of complex biomolecular systems that are able to detect the environment, assess the situation, and react to overcome the situation. Such a smart biomolecular system could be useful in many applications, such as drug delivery systems.
Quasi-cubes (1997)

A data cube is a popular organization for summary data. A cube is simply a multidimensional structure that contains at each point an aggregate value, i.e., the result of applying an aggregate function to an underlying relation. In practical situations, cubes can require a large amount of storage. The typical approach to reducing storage cost is to materialize parts of the cube on demand. Unfortunately, this lazy evaluation can be a time-consuming operation. In this paper, we describe an approximation technique that reduces the storage cost of the cube without incurring the run time cost of lazy evaluation. The idea is to provide an incomplete description of the cube and a method of estimating the missing entries with a certain level of accuracy. The description, of course, should take a fraction of the space of the full cube and the estimation procedure should be faster than computing the data from the underlying relations. Since cubes are used to support data analysis and analysts are rarely interested in the precise values of the aggregates (but rather in trends), providing approximate answers is, in most cases, a satisfactory compromise. Alternatively, the technique can be used to implement a multiresolution system in which a tradeoff is established between the execution time of queries and the errors the user is willing to tolerate. By only going to the disk when it is necessary (to reduce the errors), the query can be executed faster. This idea can be extended to produce a system that incrementally increases the accuracy of the answer while the user is looking at it, supporting on-line aggregation.
Morbilidad respiratoria en la zona industrial de tarragona (1988)

Se realiza un estudio descriptivo de las urgencias respiratorias (Asma, EPOC), correspondientes al municipio de Tarragona y que fueron atendidas en el servicio de urgencias del Hospital «Joan XXIII» de Tarragona durante 1985. Los resultados indican una mayor tasa de casos de asma, sobre todo en la infancia. Analizando su distribución geográfica, Ilama la atención que las zonas con una mayor tasa, se encuentran más cercanas a los complejos industriales (química y petroquímica) que las zonas con menor tasa. Sería interesante el poder realizar un estudio más exhaustivo para determinar la influencia que las industrias de esta zona pueden tener sobre la salud de la población. A retrospective study has been made of respiratory emergencies (asthma and COLD) in the city of Tarragona who received treatment in the accident and emergency department of Joan XXIII during 1985. The results show a higher rate of asthma, particularly in childhood. Analysing the geographical distribution, it is noticeable that the zones with the highest rates are those nearer to industrial complexes (chemical and petrochemical) than zones with lower rates. It would de interesting to undertake a more exhaustive study to determine the influence of the industries in this zone on the health of the population.
Study of magnetic helicity injection via plasma imaging using a high-speed digital camera (2002)

The evolution of a plasma generated by a novel planar coaxial gun is photographed using a state-of-the-art digital camera, which captures eight time-resolved images per discharge. This experiment is designed to study the fundamental physics of magnetic helicity injection, which is an important issue in fusion plasma confinement, as well as solar and astrophysical phenomena such as coronal mass ejections and accretion disk dynamics. The images presented in this paper are not only beautiful but provide a powerful way to understand the global dynamics of the plasma.
Purification and characterization of a bacteriocin-like compound (Lichenin) produced anaerobically by Bacillus licheniformis isolated from water buffalo (2001)

Lichenin could be a potential candidate for manipulating the rumen function at molecular level intended for improving the productivity of the ruminant.
A high-throughput screen identifies miRNA inhibitors regulating lung cancer cell survival and response to paclitaxel (2013)

microRNAs (miRNAs) are small RNAs endogenously expressed in multiple organisms that regulate gene expression largely by decreasing levels of target messenger RNAs (mRNAs). Over the past few years, numerous studies have demonstrated critical roles for miRNAs in the pathogenesis of many cancers, including lung cancer. Cellular miRNA levels can be easily manipulated, showing the promise of developing miRNA-targeted oligos as next-generation therapeutic agents. In a comprehensive effort to identify novel miRNA-based therapeutic agents for lung cancer treatment, we combined a high-throughput screening platform with a library of chemically synthesized miRNA inhibitors to systematically identify miRNA inhibitors that reduce lung cancer cell survival and those that sensitize cells to paclitaxel. By screening three lung cancer cell lines with different genetic backgrounds, we identified miRNA inhibitors that potentially have a universal cytotoxic effect on lung cancer cells and miRNA inhibitors that sensitize cells to paclitaxel treatment, suggesting the potential of developing these miRNA inhibitors as therapeutic agents for lung cancer. We then focused on characterizing the inhibitors of three miRNAs (miR-133a/b, miR-361-3p, and miR-346) that have the most potent effect on cell survival. We demonstrated that two of the miRNA inhibitors (miR-133a/b and miR-361-3p) decrease cell survival by activating caspase-3/7-dependent apoptotic pathways and inducing cell cycle arrest in S phase. Future studies are certainly needed to define the mechanisms by which the identified miRNA inhibitors regulate cell survival and drug response, and to explore the potential of translating the current findings into clinical applications.
NON‐NUCLEAR DAMAGE AND CELL LYSIS ARE INDUCED BY UVA, BUT NOT UVB OR UVC, RADIATION IN THREE STRAINS OF L5178Y CELLS (1993)

The potential to induce non-nuclear changes in mammalian cells has been examined for (1) UVA1 radiation (340-400 nm, UVASUN 2000 lamp), (2) UVA+UVB (peak at 313 nm) radiation (FS20 lamp), and (3) UVC (254 nm) radiation (G15T8 lamp). The effects of irradiation were monitored in vitro using three strains of L5178Y (LY) mouse lymphoma cells that markedly differ in sensitivity to UV radiation. Comparisons were made for the effects of approximately equitoxic fluences that reduced cell survival to 1-15%. Depending on the cell strain, the fluences ranged from 830 to 1600 kJ/m2 for the UVASUN lamp, 75 to 390 J/m2 for the FS20 lamp and 3.8 to 17.2 J/m2 for the G15T8 lamp. At the exposure level used in this study, irradiation with the UVASUN, but not the FS20 or G15T8, lamp induced a variety of non-nuclear changes including damage to cytoplasmic organelles and increased plasma membrane permeability and cell lysis. Cell lysis and membrane permeabilization were induced by the UVA1 emission of the UVASUN lamp, but not by its visible+IR components (> 400 nm). The results show that the plasma membrane and other organelles of LY cells are highly sensitive to UVA1 but not to UVB or UVC radiation. Also UVA1, but not UVB or UVC radiation, causes rapid and extensive lysis of LY cells. In conclusion, non-nuclear damage contributes substantially to UVA cytotoxicity in all three strains of LY cells.
Analysis and design of wide-angle foveated optical systems (2009)

The development of compact imaging systems capable of transmitting high-resolution images in real-time while covering a wide field-of-view (FOV) is critical in a variety of military and civilian applications: surveillance, threat detection, target acquisition, tracking, remote operation of unmanned vehicles, etc. Recently, optical foveated imaging using liquid crystal (LC) spatial light modulators (SLM) has received considerable attention as a potential approach to reducing size and complexity in fast wide-angle lenses. The fundamental concept behind optical foveated imaging is reducing the number of elements in a fast wide-angle lens by placing a phase SLM at the pupil stop to dynamically compensate aberrations left uncorrected by the optical design. In the recent years, considerable research and development has been conducted in the field of optical foveated imaging based on the LC SLM technology, and several foveated optical systems (FOS) prototypes have been built. However, most research has been focused so far on the experimental demonstration of the basic concept using off the shelf components, without much concern for the practicality or the optical performance of the systems. Published results quantify only the aberration correction capabilities of the FOS, often claiming diffraction limited performance at the region of interest (ROI). However, these results have continually overlooked diffraction effects on the zero-order efficiency and the image quality. The research work presented in this dissertation covers the methods and results of a detailed theoretical research study on the diffraction analysis, image quality, design, and optimization of fast wide-angle FOSs based on the current transmissive LC SLM technology. The amplitude and phase diffraction effects caused by the pixelated aperture of the SLM are explained and quantified, revealing fundamental limitations imposed by the current transmissive LC SLM technology. As a part of this study, five different fast wide-angle lens designs that can be used to build practical FOSs were developed, revealing additional challenges specific to the optical design of fast wide-angle systems, such as controlling the relative illumination, distortion, and distribution of aberrations across a wide FOV. One of the lens design examples was chosen as a study case to demonstrate the design, analysis, and optimization of a practical wide-angle FOS based on the current state-of-the-art transmissive LC SLM technology. The effects of fabrication and assembly tolerances on the image quality of fast wide-angle FOSs were also investigated, revealing the sensitivity of these fast well-corrected optical systems to manufacturing errors. The theoretical study presented in this dissertation sets fundamental analysis, design, and optimization guidelines for future developments in fast wide-angle FOSs based on transmissive SLM devices.
Microbiological Predictors of Caries Risk (1993)

The prediction of caries risk has been of long-standing interest. Generally, few of the tests involving oral bacteria or their products have become accepted. Presently, the main focus is on counts of lactobacilli (L) and mutans streptococci (MS). Due to their positive numerical association with human caries and the linkage of this association to carbohydrate consumption, counts of L and MS may, potentially, serve not only as a caries risk predictor but also as an indicator of carbohydrate consumption, another caries-risk factor. The value of counts of L and MS as caries-risk predictors has been evaluated by means of studies providing data on test sensitivity, specificity, and predictive values. These and other studies indicate that their use for the prediction of caries risk of individuals is not possible but is more promising for that of the caries risk of groups (e.g., identification of high-caries-risk subjects); further, the prediction of low caries risk may be more reliable than that of high caries risk. The influence of test variables on the test results has been discussed. These include the level of caries increment, subject age, methods of caries evaluation, use of saliva or dental plaque as test sample, sampling frequency, type of bacterial growth medium, and the use of simplified methods rather than conventional laboratory procedures for microbial enumeration. An approach to optimize the use of microbiological caries-risk predictors in different populations as well as their use in conjunction with other caries-risk predictors has been discussed. The latter include the incipient caries lesion or past caries experience and salivary buffering capacity and flow rate. Due to the multifactorial nature of caries etiology, it is expected that multivariate approaches rather than the use of single parameters may improve caries risk prediction for individuals as well as groups of subjects.
X-ray Spectrographic Analysis of Liquids and Solutions (1964)

The unique features of X-ray spectrographic analysis of solutions with specific advantages and limitations which they impose are enumerated. Pretreatment of samples, types of media or substrates in which the element is sought, and cells for containing the sample are briefly considered. Several methods of standardizing by using different types of intensity reference are illustrated. Matrix effects are discussed and methods to cope with them are presented. Typical applications involving both aqueous and nonaqueous substrates are cited from the literature to illustrate the progress made in recent years using the liquid sample approach.
Biocrude Production from Switchgrass Using Subcritical Water (2009)

Subcritical water is an environmentally attractive solvent for organic matters and can be used to liquefy biomass to biocrude, which is a mixture of oxygenated hydrocarbons of varying molecular weights. Liquefaction of switchgrass in subcritical water is studied using a semicontinuous reactor in the temperature range of 235−260 °C. Subcritical water is pumped through a tubular reactor packed with switchgrass particles of 40−60 mesh size. The effects of reaction temperature and catalysis by K2CO3 are examined. Potassium carbonate significantly enhances the hydrolysis of macromoleculer components of switchgrass into water-soluble products. More than 50 wt % of the organic carbon available in switchgrass was converted to biocrude after 20 min of steady operation at 235 °C in the presence of 0.15 wt % of K2CO3. At the high temperature (260 °C), dehydration of biomass was favored over hydrolysis reactions. On the basis of chromatography and mass spectrometry analyses, biocrude contains lignin derived products, sugars, and its decomposition products. On the basis of the infrared spectroscopy and electron microscopy of residue solid, the subcritical water treatment causes complete breakdown of lignocellulosic structure of switchgrass. In fact, the residue solid mainly contained lignin fractions.
Degradation and solubilization of pectin by β‐galactosidases purified from avocado mesocarp (1993)

Three β‐galactosidase (EC 3. 2. 1. 23) isozymes were purified from the mesocarp of ripe fruit of Persea americana Mill. cv. Lula. and their effects on pectin derived from mature‐green tomato fruit were investigated. The β‐galactosidases had pl values of 5. 0,5. 1 and 5. 2. and molecular weights of 41. 49 and 54 KDa. respectively. There was a partial degradation of pectin resulting in the release of monomeric galactose upon treatment with avocado β‐galactosidase. This degradation resulted in increased pectin solubility and decreased apparent average molecular size as determined by microfiltration and gel permeation by high‐performance liquid chromatography. The increase in solubility was due. in part. to an apparent decrease in the ability of pectin molecules to aggregate together.
Low Dark Count Rate and High Single-Photon Detection Efficiency Avalanche Photodiode in Geiger-Mode Operation (2007)

An In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As-InP avalanche photodiode with very low dark current (0.15 pA at 95% breakdown voltage, 200 K) has been characterized in gated mode for single-photon detection. The temperature dependence of dark current and dark count yields activation energy of ~0.4 eV from 240 K to 297 K. High single-photon detection efficiency (SPDE) at telecom wavelengths with very low dark count rate (DCR) (e.g., DCR =12 kHz at SPDE =45% at 1.31 mum and 200 K) was achieved
Highly polarised He(2<sup>3</sup>S) thermal metastable atom source (1983)

A source of polarised He(23S) metastable atoms is described providing a thermal energy beam of the order of approximately 1013 N s-1 at a polarisation Pz approximately 95%. The polarisation can be simply reversed using an adiabatic transition, without changing the beam trajectory or its intensity.
Whole genome sequencing of phage resistant Bacillus anthracismutants reveals an essential role for cell surface anchoring protein CsaB in phage AP50c adsorption (2012)

Taken together, these data suggest an essential role for csaB in AP50c phage infection, most likely in phage adsorption. (The whole genome sequences generated from this study have been submitted to GenBank under SRA project ID: SRA023659.1 and sample IDs: AP50 R1: SRS113675.1, AP50 R2: SRS113676.1, AP50 R3: SRS113728.1, AP50 R4: SRS113733.1, AP50 R6: SRS113734.1, JB220 Parent: SRS150209.1, JB220 Mutant: SRS150211.1).
The Combination of the Proteasome Inhibitor Bortezomib and the Bcl-2 Antisense Molecule Oblimersen Sensitizes Human B-Cell Lymphomas to Cyclophosphamide (2006)

The use of Bcl-2-directed therapy and a proteasome inhibitor sensitizes human lymphoma cells to cytotoxic drugs like cyclophosphamide. This combination may offer new opportunities for integrating novel targeted therapies with conventional chemotherapy.