gebhart/patrepeval huggingface dataset:
Quantifying the accessibility of the metagenome by random expression cloning techniques (2004)

The exploitation of the metagenome for novel biocatalysts by functional screening is determined by the ability to express the respective genes in a surrogate host. The probability of recovering a certain gene thereby depends on its abundance in the environmental DNA used for library construction, the chosen insert size, the length of the target gene, and the presence of expression signals that are functional in the host organism. In this paper, we present a set of formulas that describe the chance of isolating a gene by random expression cloning, taking into account the three different modes of heterologous gene expression: independent expression, expression as a transcriptional fusion and expression as a translational fusion. Genes of the last category are shown to be virtually inaccessible by shotgun cloning because of the low frequency of functional constructs. To evaluate which part of the metagenome might in this way evade exploitation, 32 complete genome sequences of prokaryotic organisms were analysed for the presence of expression signals functional in E. coli hosts, using bioinformatics tools. Our study reveals significant differences in the predicted expression modes between distinct taxonomic groups of organisms and suggests that about 40% of the enzymatic activities may be readily recovered by random cloning in E. coli.
Unrolled Optimization with Deep Priors (2017)

A broad class of problems at the core of computational imaging, sensing, and low-level computer vision reduces to the inverse problem of extracting latent images that follow a prior distribution, from measurements taken under a known physical image formation model. Traditionally, hand-crafted priors along with iterative optimization methods have been used to solve such problems. In this paper we present unrolled optimization with deep priors, a principled framework for infusing knowledge of the image formation into deep networks that solve inverse problems in imaging, inspired by classical iterative methods. We show that instances of the framework outperform the state-of-the-art by a substantial margin for a wide variety of imaging problems, such as denoising, deblurring, and compressed sensing magnetic resonance imaging (MRI). Moreover, we conduct experiments that explain how the framework is best used and why it outperforms previous methods.
Pepperdine Student Out-group Impressions, Interactions, and Anxiety (2017)

Uncertainty reduction theory and intergroup bias suggest that remaining in homogenous environments could lead to negative impression of outgroups.The undergraduate campus at Pepperdine University has recently seen discrimination against LGBTQ+ and the African American communities.Regarding the current charged political climate at Seaver College, the researchers hypothesized that young adult outgroup impressions were directly affected by exposure to White-Anglo-Saxon-Protestant (WASP) communities, social anxiety, and self-disclosure.Research questions also asked if there was an effect of exposure to Christian culture on anxiety levels when in contact with outgroups and what other personal factors influence outgroup impression.This study tested these propositions by having 132 university students respond to a survey sent out on Facebook.The researchers ran correlational and mean differences tests to check the hypotheses and research questions.While social anxiety and self-disclosure did not prove to be significant influencers, there was a strong correlation between time spent in WASP communities and negative outgroup impression.
Biotreatment of persistent substances using effective microorganisms (2000)

To efficiently biotreat the persistent substances contained in wastewater, it is necessary to fully elucidate the degradation mechanisms of the substances by specific degrading microorganisms. Especially clarifying the enzymatic reactions responsible for the degradation of persistent substances is very important. Here three different kinds of aerobic or oxidative degradation reactions of persistent substances are introduced. Polyvinyl alcohol (PVA) degradation by Pseudomonas vesicularis var. povalolyticus strain PH, co-oxidative degradation of trichloroethylene (TCE) by a variety of phenol degrading bacteria, and decolorization of melanoidin by a white rot fungus Coriolus hirsutus were shown.
Characterization of the β-Carotene Hydroxylase Gene <i>DSM2</i> Conferring Drought and Oxidative Stress Resistance by Increasing Xanthophylls and Abscisic Acid Synthesis in Rice    (2010)

Drought is a major limiting factor for crop production. To identify critical genes for drought resistance in rice (Oryza sativa), we screened T-DNA mutants and identified a drought-hypersensitive mutant, dsm2. The mutant phenotype was caused by a T-DNA insertion in a gene encoding a putative β-carotene hydroxylase (BCH). BCH is predicted for the biosynthesis of zeaxanthin, a carotenoid precursor of abscisic acid (ABA). The amounts of zeaxanthin and ABA were significantly reduced in two allelic dsm2 mutants after drought stress compared with the wild type. Under drought stress conditions, the mutant leaves lost water faster than the wild type and the photosynthesis rate, biomass, and grain yield were significantly reduced, whereas malondialdehyde level and stomata aperture were increased in the mutant. The mutant is also hypersensitive to oxidative stresses. The mutant had significantly lower maximal efficiency of photosystem II photochemistry and nonphotochemical quenching capacity than the wild type, indicating photoinhibition in photosystem II and decreased capacity for eliminating excess energy by thermal dissipation. Overexpression of DSM2 in rice resulted in significantly increased resistance to drought and oxidative stresses and increases of the xanthophylls and nonphotochemical quenching. Some stress-related ABA-responsive genes were up-regulated in the overexpression line. DSM2 is a chloroplast protein, and the response of DSM2 to environmental stimuli is distinctive from the other two BCH members in rice. We conclude that the DSM2 gene significantly contributes to control of the xanthophyll cycle and ABA synthesis, both of which play critical roles in the establishment of drought resistance in rice.
Production of semi-biosynthetic nepetalactone in yeast (2019)

Microbial-based production of natural products provides a promising alternative to synthetic production and isolation from the native producer. The recently discovered NEPS1 cyclase/oxidase completes the biosynthetic pathway to nepetalactone, a biologically relevant iridoid known as both an insect repellent and cat attractant. In this work, we employ yeast-based whole-cell biocatalysis to produce semi-biosynthetic nepetalactone from a low-cost precursor via a four-step enzymatic process. The dependence of product yield on bioprocess parameters ranging from induction of gene expression to substrate loading was investigated. Subsequent factorial design and response surface methodology optimization approach enabled a 5.8-fold increase in nepetalactone titer to 153 mg/L. Our study provides insights into strategies for operating plasmid-based bioconversion of a fed substrate and sets the stage for scalable, microbial synthesis of nepetalactone.
History Matching Using the Ensemble Kalman Filter on a North Sea Field Case (2008)

Summary This paper applies the ensemble Kalman filter (EnKF) to history match a North Sea field model. This is, as far as we know, one of the first published studies in which the EnKF is applied in a realistic setting using real production data. The reservoir-simulation model has approximately 45,000 active grid cells, and 5 years of production data are assimilated. The estimated parameters consist of the permeability and porosity fields, and the results are compared with a model previously established using a manual history-matching procedure. It was found that the EnKF estimate improved the match to the production data. This study, therefore, supported previous findings when using synthetic models that the EnKF may provide a useful tool for history matching reservoir parameters such as the permeability and porosity fields.
A polynomial quantum algorithm for approximating the Jones polynomial (2006)

The Jones polynomial, discovered in 1984 [18], is an important knot invariant in topology. Among its many connections to various mathematical and physical areas, it is known (due to Witten [32]) to be intimately connected to Topological Quantum Field Theory (TQFT). The works of Freedman, Kitaev, Larsen and Wang [13, 14] provide an efficient simulation of TQFT by a quantum computer, and vice versa. These results implicitly imply the existence of an efficient quantum algorithm that provides a certain additive approximation of the Jones polynomial at the fifth root of unity, e2π i/5, and moreover, that this problem is BQP-complete. Unfortunately, this important algorithm was never explicitly formulated. Moreover, the results in [13, 14] are heavily based on TQFT, which makes the algorithm essentially inaccessible to computer scientists.We provide an explicit and simple polynomial quantum algorithm to approximate the Jones polynomial of an n strands braid with m crossings at any primitive root of unity e2π i/k, where the running time of the algorithm is polynomial in m,n and k. Our algorithm is based, rather than on TQFT, on well known mathematical results (specifically, the path model representation of the braid group and the uniqueness of the Markov trace for the Temperly Lieb algebra). By the results of [14], our algorithm solves a BQP complete problem.The algorithm we provide exhibits a structure which we hope is generalizable to other quantum algorithmic problems. Candidates of particular interest are the approximations of other downwards self-reducible P-hard problems, most notably, the Potts model.
Simulation and Optimal Control of Diesel Engine Propulsion System (2009)

Based on the modeling method of the co-operation between the characteristic maps and the mathematical equations, a propulsion system simulation model which includes model for large low speed two-stroke diesel engine (MAN B&W 10L90MC) and model for shaft, propeller and ship hull dynamics is proposed. To calculate propeller's characteristic, the regression functions are adopted. The simulation experiments demonstrate the model can be used for engine performance prediction as well as investigating control schedules of marine propulsion system. The increased use of digital electronic technology for marine diesel propulsion control leads to more reliable and efficient propulsion power plants. Neural networks have been used for the implementation of continuous propeller torque demand prediction that can be exploited by engine control preventively in order to avoid excessive overspeed at near-MCR engine running under rough sea conditions. The neural predictor has been validated through simulation, using data recorded during scheduled operation of a large containership, as well as, from simulation.
Exposure to Low pH Is Not Required for Penetration of Mosquito Cells by Sindbis Virus (2001)

It is widely held that the penetration of cells by alphaviruses is dependent on exposure to the acid environment of an endosome. The alphavirus Sindbis virus replicates in both vertebrate and invertebrate cell cultures. We have found that exposure to an acid environment may not be required for infection of cells of the insect host. In this work, we investigated the effects of two agents (NH(4)Cl and chloroquine), which raise the pH of intracellular compartments (lysosomotropic weak bases) on the infection and replication of Sindbis virus in cells of the insect host Aedes albopictus. The results show that both of these agents increase the pH of endosomes, as indicated by protection against diphtheria toxin intoxication. NH(4)Cl blocked the production of infectious virus and blocked virus RNA synthesis when added prior to infection. Chloroquine, in contrast to its effect on vertebrate cells, had no inhibitory effect on infectious virus production in mosquito cells even when added prior to infection. Treatment with NH(4)Cl did not prevent the penetration of virus RNA into the cell cytoplasm or translation of the RNA to produce a precursor to virus nonstructural proteins. These data suggest that while these two drugs raise the pH of endosomes, they do not block insect cell penetration. These data support previous results published by our laboratory suggesting that exposure to an acid environment within the cell may not be an obligatory step in the process of infection of cells by alphaviruses.
Terahertz Thermometry: Combining Hyperspectral Imaging and Temperature Mapping at Terahertz Frequencies (2017)

Abstract The accurate and non‐invasive determination of multiple physical parameters, with well‐defined spatial resolution, is crucial for applications in manufacturing, chemistry, medicine and biology. Specifically, the ability to simultaneously measure both temperature and spectral signatures is still experimentally unavailable. To this end, we propose a mapping technique for biological systems, which exploits a linear correlation between terahertz wave reflectivity and temperature, and allows to spatially and spectrally resolve thermal distributions. This method is applied to a model biological system in two relevant cases where in one example, nanoplasmonic‐induced photothermal effects are imaged gaining new insights into collective heating phenomena. In the second example, we demonstrate a joint thermal‐hyperspectral imaging approach to chemically map the presence of a model drug formulation and simultaneously investigate its thermal stability in our biological system. This concept can be easily extended and widely applied to all materials that demonstrate a measurable change in their dielectric properties.
Preliminary Phytochemical Studies and Evaluation of Antibacterial Activity of Psoralea corylifolia Seed Extract (2014)

Present study aims to evaluate antibacterial efficacy of Bakuchi (Psoralea corylifolia ) seed extracts prepared in two different solvents. Antibacterial assay was performed by agar well diffusion method against Gram positive skin pathogens, like Staphylococcus aureus , Staphylococcus epidermidis Pseudomonas aeruginosa and Gram negative skin pathogens, which included Klebsiella pneumoniae , Proteus mirabilis, Proteus vulgaris and Escherichia coli . Bakuchi seed extract in methanol and diethyl ether exhibited broad spectrum antibacterial activity against skin pathogens, however comparatively bakuchi seed extract in methanol was found to be more promising with maximum zone of inhibition against K. pneumoniae with zone of inhibition 21mm in diameter and the minimum inhibitory concentration (MIC) 2.5mg/ml. These results confirmed the potential of the Bakuchi seed extract in the development of ayurvedic topical skin formulations.
The Cardiac Glycosides Digitoxin, Digoxin and Ouabain Induce a Potent Inhibition of Glycolysis in Lung Cancer Cells (2013)

Cardiac glycosides are promising anticancer drugs. We have recently shown that the cardiac glycosides digitoxin, digoxin and ouabain induce selective killing of lung cancer cells, and that the cytotoxicity of digitoxin against these cells occurs at concentrations below those observed in the plasma of cardiac patients treated with this drug (Oncogene, 2013. doi: 10.1038/onc.2013.229). Here we report that digitoxin, digoxin and ouabain induce a potent inhibition of glycolysis (glucose consumption and lactate production) in A549 cells at nanomolar concentrations. This inhibition was comparable to that observed with millimolar concentrations of the glycolysis inhibitor dichloroacetate, which is currently undergoing clinical trials for the treatment of cancer. Because platinum compounds are commonly used in the treatment of lung cancer, we tested the cytotoxicity of several combinations of cisplatin with each cardiac glycoside; these combinations induced synergistic, antagonistic or additive effects mainly depending on the order at which the drugs were added to the cells.
Measurement of Cellular Adhesion Under Static Conditions (2000)

This unit describes procedures for measuring the adhesion of lymphoid cells to immobilized ligands or adherent cell monolayers. The basic protocol, which is optimized for human T cells, can be easily modified to study almost any cell type in suspension if the corresponding adhesive ligand is available. Alternate protocols describe modifications to the basic protocol that allow analysis of cell adhesion in the presence of stimulators of lymphocyte activation or monoclonal antibodies (MAbs) that react with adhesion molecules or their ligands, or analysis of cell adhesion to adherent cell monolayers. A support protocol is provided for determining the optimal concentration of adhesion ligands and choosing the appropriate type of microtiter plate for static adhesion assays.
A high precision reference data set for pedestrian navigation using foot-mounted inertial sensors (2010)

In this paper we present a reference data set that we are making publicly available to the indoor navigation community. This reference data is intended for the analysis and verification of algorithms based on foot mounted inertial sensors. Furthermore, we describe our data collection methodology that is applicable to the analysis of a broad range of indoor navigation approaches. We employ a high precision optical reference system that is traditionally being used in the film industry for human motion capturing and in applications such as analysis of human motion in sports and medical rehabilitation. The data set provides measurements from a six degrees of freedom foot mounted inertial MEMS sensor array, as well as synchronous high resolution data from the optical tracking system providing ground truth for location and orientation. We show the use of this reference data set by comparing the performance of algorithms for an essential part of pedestrian dead reckoning systems for positioning, namely identification of the rest phase during the human gait cycle.
Towards Collaborative Editing of Structured Data on Mobile Devices (2011)

The age of collaborative editing applications on mobile devices is upon us. However, such applications traditionally rely on centralized servers and thus do not operate in fully decentralized environments. This is a problem on mobile devices where network partitions are the norm due to mobility. Furthermore, such systems typically use either a fixed schema for the data, which makes them inflexible to change and leads to abuse of structured data fields for purposes other than the original intent, or else are based on XML, which limits data to document oriented data stores or else makes querying much more cumbersome for developers and users. In contrast, our Interdroid Versioned Database system provides distributed, fully decentralized, compact, relational, versioned databases for Android powered mobile phones. It offers application designers a unique set of tools for easily building decentralized collaborative applications on Android powered mobile devices using familiar Content Provider and SQL like interfaces. Unfortunately, this system requires that the structure of the database and the user interface (UI) used to edit records in the database to be written at compile time. What users would like is to beable to define and adapt the structure of the data at runtime. What developers would like is a system which makes building structured applications, including editing UI even easier than it is with our prior work. In this paper we present an extension to our Interdroid Versioned Database system which adds the ability to define a Content Provider using an Avro schema, as well as a generic editing interface for instances of that schema. We demonstrate how this system allows us to create powerful data oriented applications at either compile or runtime using an example "ToDo" application, and detail how this work will serve as a basis for our future work on merging shared structured data.
PVF <sub>2</sub> tranducers for Rayleigh waves (1980)

PVF2 thin-film transducers have been incorporated in a 8 MHz s.a.w. delay line. The flexibility of the transducer material will allow its use on curved as well as plane surfaces. Losses at frequencies typical in n.d.t. applications are in principle relatively low; it is for such tasks that the use of PVF2 s.a.w. transducers is seen as particularly appropriate.
Non-rigid MR/US registration for tracking brain deformations (2002)

During a neuro-surgical intervention, the brain tissues shift and warp. In order to keep an accurate positioning of the surgical instruments, one has to estimate this deformation from intra-operative images. 3D ultrasound (US) imaging is an innovative and low-cost modality which appears to be suited for such computer-assisted surgery tools. We present a new image-based technique to register intra-operative 3D US with pre-operative magnetic resonance (MR) data. A first automatic rigid registration is achieved by the maximisation of a similarity measure that generalises the correlation ratio. Then, brain deformations are tracked in the 3D US time-sequence using a "demon's" like algorithm. Experiments show that a registration accuracy of the MR voxel size is achieved for the rigid part, and a qualitative accuracy of a few millimetres could be obtained for the complete tracking system.
Sequential pattern based multi document summarization &#x2014; An exploratory approach (2013)

Sequential Pattern Mining which aims to discover all frequent sequences of itemsets (patterns) from a large data collection has been applied in the Text Mining domain such as Text Categorization and Pattern Identification. However, in the area of Document Summarization the effort is still considered as green and exploratory. In the real world, a sentence is more than just a collection of un-ordered sequence of words, where each sentence carries their own meaning. By discovering these textual patterns is essential since the patterns can describe the text, by preserving the sequential order of the words in the document. Thus, the motivation here is to investigate the feasibility to develop a Sequential Pattern-based Summarizer model near future in order to reduce redundancy information from multiple text resources; at same time preserving the meaning of the original text document using the Semantic similarity approach. This paper reviewed some of the existing techniques in the area of multiple document summarizations to better understand the gap and issues underlying this area. By incorporating the semantic knowledge of sentences in the multiple documents is hoped to assist and alleviate the long-winding process for non-subject expert researches in trying to find the similarities and correlation between text resources.