gebhart/patrepeval huggingface dataset:
The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries (2017)

Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and sound surfaces were associated with a reduction in bacterial diversity. PCoA plots displayed differences in bacterial community profiles between sound and diseased surfaces. Our study showed that, in addition to mutans streptococci, other species may be associated with the initiation of dental caries on occlusal surfaces, and that biofilm diversity of tooth surfaces is influenced by carbohydrate consumption and a surface's health status.
The Lichen Vegetation of Chalk and Limestone Streams in Britain (1996)

Abstract The results of a nationwide survey of lichens associated with streams on chalk and limestone are reported. The lichen communities are present as a series of overlapping bands related to length of submergence. These have been named the submerged, fluvial mesic, fluvial xeric and fluvial terrestrial zones. The flora involves around 50 lichens, many of which are rarely recorded specialists restricted to this habitat. The richest sites for submerged species are headwaters, especially around springs. Active tufa deposition and disturbance of the stream bed by farm stock are detrimental to aquatic lichens. Diversity further downstream is related to the amount of exposed limestone available for colonization, with topographical complexity also important. An investigation of the influence of water quality suggests that suspended solids (silting) is a significant determinant of lichen distribution together with eutrophication.
Mutational Analysis of the Epimerization Domain in the Initiation Module PheATE of Gramicidin S Synthetase (2000)

The epimerase (E) domain of the three-domain (ATE) initiation module of Bacillus brevis gramicidin S synthetase equilibrates the Calpha configuration of the phenylalanyl moiety presented as Phe-S-4'-phosphopantetheine-modified (Ppant) acyl enzyme. Mutants at 22 residues of this E domain that are conserved across the approximately 450 residue E domains of nonribosomal peptide synthetases were constructed, and the PheATE derivatives expressed in Escherichia coli as C-terminal His tag fusions and then purified and assayed for three activities: (1) the L-Phe Calpha-[(3)H] exchange to solvent, (2) the rate of approach to D-Phe/L-Phe-S-Ppant acyl enzyme equilibrium from either L- or D-Phe, and (3) the rate of Phe-Pro dipeptidyl-S-Ppant enzyme formation with the downstream ProCAT module. We found that for wild-type PheATE epimerization is much faster than subsequent condensation, leading to a 1.9:1 ratio of D-Phe-S-Ppant/L-Phe-S-Ppant acyl enzyme. Only D-Phe is then transferred to yield D-Phe-L-Pro-S-Ppant ProCAT acyl enzyme. Among the mutants generated, three PheATE constructs, H753A, D757S, and Y976A, showed no detectable Calpha-(3)H washout, while E892A and R896A were among a larger set partially impaired. All these mutants were dramatically impaired in approach to D-Phe/L-Phe-S-Ppant equilibrium from either D- or L-Phe, while another construct, D767S, was asymmetrically impaired only for D-to-L-Phe direction. In the D-Phe-L-Pro dipeptidyl-S-Ppant condensation assay, the H753A and E892A forms of PheATE were only slightly active from L-Phe but unimpaired from D-Phe; N975A epimerizes faster than Y976A from L-Phe. When the chirality of the Phe-Pro-diketopiperazine released product was analyzed the D,L/L,L ratio from wild-type PheATE and ProCAT was 98:2. From E892A and N975A it was comparably 95:5 and 92:8, but H753A and Y976A yielded 56% of the L,L-product, reflecting a gain of function to transfer L-Phe. The 98:2 preference of wild-type PheATE for D-Phe transfer reflects the kinetically controlled stereopreference of the condensation (C) domain of ProCAT for the D-Phe-S-Ppant donor substrate. It may be that other NRPS C domains immediately downstream of E domains will likewise be D-selective.
Local phonon density of states in an elastic substrate (2004)

The local, eigenfunction-weighted acoustic phonon density of states (DOS) tensor is calculated for a model substrate consisting of a semi-infinite isotropic elastic continuum with a stress-free surface. On the surface, the local DOS is proportional to the square of the frequency $\ensuremath{\omega}$, as for the three-dimensional Debye model, but with a constant of proportionality that is considerably enhanced compared to the Debye value, a consequence of the Rayleigh surface modes. The local DOS tensor at the surface is also anisotropic, as expected. Inside the substrate the local DOS is both spatially anisotropic and nonquadratic in frequency. However, at depths that are large compared with ${v}_{l}∕\ensuremath{\omega}$, where ${v}_{l}$ is the bulk longitudinal sound velocity, the local DOS approaches the isotropic Debye value. The results are applied to a Si substrate.
cDNA cloning and chromosomal assignment of the human O6-methylguanine-DNA methyltransferase. cDNA expression in Escherichia coli and gene expression in human cells. (1990)

The O6-methylguanine-DNA methyltransferases are the most common form of cellular defense against the biological effects of O6-methylguanine in DNA. By screening a cDNA library with oligonucleotide probes derived from the active site amino acid sequence of the bovine methyltransferase, we have isolated a cDNA clone for the human enzyme. The cDNA contains a single open reading frame encoding a protein of Mr 21,700 which exhibits considerable homology to three bacterial methyltransferases. When provided with an Escherichia coli lac promoter, the encoded polypeptide can be expressed in E. coli to produce an active methyltransferase which is indistinguishable in size from the protein from human cells. The enzyme expressed in this way is functional in vivo and protects an E. coli methyltransferase deletion mutant against the mutational and cytotoxic properties of the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine. The methyltransferase gene spans at least 15 kilobases and is located on human chromosome 10. Alkylating agent-resistant Mex+ cells which express the methyltransferase protein contain a methyltransferase mRNA of about 1 kilobase. However, this mRNA is absent from three alkylation sensitive Mex- human cell lines indicating that the regulation of methyltransferase gene expression in these cell lines may be transcriptional.
Development of an enzyme‐linked immunosorbent assay (ELISA) for detecting IgA antibodies to the epstein‐barr virus (1988)

A 3-step enzyme-linked immunosorbent assay (ELISA) was developed for detecting IgA antibodies to purified Epstein-Barr virus (EBV) polypeptides. The 3-step procedure included the use of a mouse anti-human IgA monoclonal antibody (MAb) to amplify the IgA reaction. The 2 major EBV proteins used in this assay were the 125-kDa component (gp125) associated with the viral capsid antigen (VCA) complex and a major glycoprotein (gp250/200) associated with the membrane antigen (MA) complex. Eighty-two sera were tested on ELISA plates containing either both of the glycoproteins or each one separately. These included 45 IgA antibody-positive sera from patients with nasopharyngeal carcinoma (NPC). With these sera, there was a good correlation, both qualitatively and quantitatively, between results with the immunofluorescence (IF) and ELISA procedures. Although most IgA antibody-positive sera contained antibodies reactive with both gp125 and gp250/200, a number of sera contained antibodies reactive with one of the glycoproteins but not with both. The data indicated that both of these glycoproteins should be used in assays for detecting IgA antibodies to EBV, to avoid false-negative results. This assay should be useful for screening large populations for IgA antibodies to EBV and also possibly for monitoring disease course in patients with NPC.
DC–DC Converter With Digital Adaptive Slope Control in Auxiliary Phase for Optimal Transient Response and Improved Efficiency (2011)

In this paper, a digital adaptive slope control technique is presented to improve the dynamic response of a current-programmed mode (CPM) buck converter employing a low-cost auxiliary phase. The advantages and drawbacks of the existing analog and digital nonlinear control techniques are discussed in detail. The benefits of the proposed control scheme include superior voltage drop and settling time, adaptive slope control to accommodate a range of auxiliary phase inductor values, and on-line calibration to compensate for tolerance in the main phase and auxiliary phase inductance. The proposed technique is experimentally verified on a 500-kHz, 10-2.5 V CPM buck converter prototype. Charge balancing and optimal transient response are achieved for a range of positive and negative load steps. Operating the auxiliary phase under light-load condition is also demonstrated to further justify the use of the auxiliary phase. Compared to a representative single-phase converter, the proposed system not only has over two times improvement on the voltage drop and three times lower steady-state voltage ripple but also achieves approximately 2% heavy-load and 10% light-load efficiency improvement. The impact of the auxiliary phase operation on the converter's dynamic efficiency is also evaluated at different load step amplitudes and frequencies.
Dose-Response Analysis Using R (2015)

Dose-response analysis can be carried out using multi-purpose commercial statistical software, but except for a few special cases the analysis easily becomes cumbersome as relevant, non-standard output requires manual programming. The extension package drc for the statistical environment R provides a flexible and versatile infrastructure for dose-response analyses in general. The present version of the package, reflecting extensions and modifications over the last decade, provides a user-friendly interface to specify the model assumptions about the dose-response relationship and comes with a number of extractors for summarizing fitted models and carrying out inference on derived parameters. The aim of the present paper is to provide an overview of state-of-the-art dose-response analysis, both in terms of general concepts that have evolved and matured over the years and by means of concrete examples.
Losses and phase constant changes caused by bends in the general class of hollow waveguides for the infrared (1981)

It is shown that losses and phase constants in the general class of 2-D bent hollow waveguides are expressed by only one normalized parameter including the core width and the bending radius. Numerical analysis is made to obtain losses and phase constants, and simple approximate formulas are presented for several lower-order modes with reasonable accuracy.
‘The Great Educators’ (1979)

MOST people concerned in education will tell you that there is no such creature as a 'Great Educator' nowadays; some will contend there never was. The concept is seen as part of the hero myth, now widely and enthusiastically discredited, the fantasy that an individual with a message is capable of changing the course of human affairs. In a world of 'superpowers' and international combines, it has become increasingly difficult to imagine an individual exercising any significant influence at all. The hero has been converted into an abstraction, an image required by ordinary men and women to see them through the confused, messy business of daily living. In war he is Douglas Haig, Foch, 'Monty', Rommel; in politics Churchill, Stalin, Fidel Castro, Che Guevara; in education the 'Great Educators'. The image exists because we want it to exist. We live in chaos, but continue to believe that somewhere someone holds the key to order. We are all educational alchemists, in quest of the Educator's Stone.
The acoustic noise characteristics of HDD due to the structural excitation of spindle motor (2002)

HDD structure is excited by the dynamic motion of disk-spindle motor components. Those excitations which are generated from stator, magnet rotor, bearings and disks, are transmitted through motor spindle and flange to HDD cover and base. The operational deflection shape measurement can show the structural elicitation patterns at the most influential frequency of the acoustic noise level. One of those components is the axial excitation along spindle, and the other is the local orbital excitation at the contact area of motor flange and base. In order to make a reduction of those structural transmission excitations, the structure of spindle motor should be modified to the direction of reinforcement at transmission path. Some excitation of spindle motor component carrying out essential function is unavoidable. So it is the efficient may of HDD noise improvement to control the structural transmission of excitation.
Removing dissolved phosphorus from drainage ditch water with phosphorus sorbing materials (2007)

Abstract: The loss of nutrients, particularly phosphorus (P), in agricultural drainage waters is a priority conservation concern. Open drainage ditches concentrate runoff and therefore offer opportunities for capturing P in runoff from large areas of land. This paper provides an overview of the potential to use P sorbing materials in drainage ditches to sequester dissolved P from ditch water. We describe factors affecting the selection of P sorbing materials for use in treating ditch water and review several approaches to their application in ditches. In addition, experiential insight is provided with regard to developing and installing a P removal structure within a ditch that has high concentrations of dissolved P in flow. Preliminary data indicate that such structures have great promise in treating not only dissolved P in ditch flow, but also trace metals (arsenic, copper, nickel, zinc).
Electron paramagnetic resonance spectroscopy in radiation research: Current status and perspectives (2010)

Exposure to radiation leads to a number of health-related malfunctions. Ionizing radiation is more harmful than non-ionizing radiation, as it causes both direct and indirect effects. Irradiation with ionizing radiation results in free radical-induced oxidative stress. Free radical-mediated oxidative stress has been implicated in a plethora of diseased states, including cancer, arthritis, aging, Parkinson's disease, and so on. Electron Paramagnetic Resonance (EPR) spectroscopy has various applications to measure free radicals, in radiation research. Free radicals disintegrate immediately in aqueous environment. Free radicals can be detected indirectly by the EPR spin trapping technique in which these forms stabilize the radical adduct and produce characteristic EPR spectra for specific radicals. Ionizing radiation-induced free radicals in calcified tissues, for example, teeth, bone, and fingernail, can be detected directly by EPR spectroscopy, due to their extended stability. Various applications of EPR in radiation research studies are discussed in this review.
Towards dynamic generation of knowledge-based environments for software process assistance (1992)

To provide support for the development of reliable software in a cost-effective way, software engineering environments should be based on a software process model containing explicit representations of the knowledge needed to perform a software process, being able to offer an active assistance to that process. Moreover, process models can vary to reflect specific characteristics of projects and can change dynamically, as the process occurs. To support this changing nature of software process models, the environment should have mechanisms that allow generation of process models according to project needs and dynamic modification of the models during the software process. This paper describes a software engineering environment that combines knowledge-based assistant with dynamic meta-system concepts to offer active and flexible support for software processes. The main concern is to discuss the knowledge representation issues related to this environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mixing Crowded Biological Solutions in Milliseconds (2005)

In vitro studies of biological reactions are rarely performed in conditions that reflect their native intracellular environments where macromolecular crowding can drastically change reaction rates. Kinetics experiments require reactants to be mixed on a time scale faster than that of the reaction. Unfortunately, highly concentrated solutions of crowding agents such as bovine serum albumin and hemoglobin that are viscous and sticky are extremely difficult to mix rapidly. We demonstrate a new droplet-based microfluidic mixer that induces chaotic mixing of crowded solutions in milliseconds due to protrusions of the microchannel walls that generate oscillating interfacial shear within the droplets. Mixing in the microfluidic mixer is characterized, mechanisms underlying mixing are discussed, and evidence of biocompatibility is presented. This microfluidic platform will allow for the first kinetic studies of biological reactions with millisecond time resolution under conditions of macromolecular crowding similar to those within cells.
Estimation of Load and Torque in the Hot Rolling Process (1962)

A shear plane theory of hot rolling is proposed, based on the well-known observation of localized deformation during the rolling process. Equations of simple form in terms of yield stress and geometric functions enable roll load and torque to be readily evaluated with or without tensions. Comparison with the experimental results of Wallquist suggests that the theory gives a more satisfactory indication of the influence of the R/h ratio on load and torque than does the Sims analysis. Equations are presented in four forms: the general case with tensions; the more common case without tensions; simplified equations which are valid for most practical conditions; and graphical functions for use with the Cook and McCrum yield stress data.
Performance Evaluation and Planning for Patient-Based Quality Control Procedures (2000)

In a recent publication, the effect of the length of time between the routine testing of quality-control (QC) samples on QC performance was studied using a newly proposed performance measure: the average number of patient samples that contain unacceptable analytic error due to an out-of-control error condition (ANPTE). We show that ANPTE also perfectly suits the evaluation of patient-based QC procedures. We used ANPTE to study the effect of the number of patient results averaged and the width of the truncation limits on an average of normals QC procedure. Estimates of ANPTE were obtained by using computer simulations that use actual patient result distributions. Based on ANPTE, the conclusions about the effects of truncation limits and number of patient results averaged on the performance of an average of normals QC procedure are substantially different from those described by others using the probability of error detection to characterize QC performance.
Attention-Deficit Hyperactivity Disorders in Adolescence (1995)

Child Health Services, Westchester County Department of Health, Hawthorne, New York and Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
A fast adaptive heuristic for FPGA placement (2004)

The time to compile current field programmable gate arrays (FPGAs) can easily take hours or even days to complete for large (8-million gate) chips, which may nullify the time-to-market advantage of FPGAs. This paper presents a novel adaptive placement heuristic that significantly reduces the amount of computation time required to achieve high-quality placements, compared with the state-of-the-art placement and routing tool, VPR. Like VPR, our algorithm is based on simulated annealing (SA). However, we include a special type of short-term memory that dramatically improves the convergence rate of the traditionally slow SA algorithm. Our experimental results show (on average) a 70% reduction in runtime while still achieving very high-quality placements.
Modeling Hard-Disk Power Consumption (2003)

Excessive power consumption is a major barrier to the market acceptance of hard disks in mobile electronic devices. Studying and reducing power consumption, however, often involves running timeintensive disk traces on real hardware with specialized power-monitoring equipment. This paper presents Dempsey, a disk simulation environment that includes accurate modeling of disk power consumption. It includes tools to automatically extract performance and power consumption parameters from a given disk drive, without needing detailed specifications from the manufacturer. The tools use stimulus-based measurements to extract these parameters. Dempsey is experimentally validated for two mobile hard disks, namely, the 1 GB IBM Microdrive and the 5 GB Toshiba Type II PC Card HDD. In the worst observed case, Dempsey&apos;s estimate of power consumption di#ers from the measured consumption by 7.5%. This demonstrates that disk power consumption can be simulated both e#ciently and accurately.
<i>Bacillus</i>probiotics: an alternative to antibiotics for livestock production (2018)

The use of probiotics as feed supplements in animal production has increased considerably over the last decade, particularly since the ban on antibiotic growth promoters in the livestock sector. Several Bacillus sp. are attractive for use as probiotic supplements in animal feed due to their ability to produce spores. Their heat stability and ability to survive the low pH of the gastric barrier represent an advantage over other probiotic micro-organisms. This review discusses important characteristics required for selection of Bacillus probiotic strains and summarizes the beneficial effect of Bacillus-based feed additives on animal production. Although the mechanism of action of Bacillus probiotics has not been fully elucidated, they are effective in improving the growth, survival and health status of terrestrial and aquatic livestock. Bacillus strains also have utility in bioremediation and can reduce nitrogenous waste, thereby improving environmental conditions and water quality. Finally, recent innovative approaches for using Bacillus spores in various applications are discussed.