gebhart/patrepeval huggingface dataset:
Correlation of Corneal and Scleral Topography in Cases with Ectasias and Normal Corneas (2019)

Background and Objective To determine the relationships between corneal and scleral elevation topography in subjects with corneal ectasias and normal corneas. Material and Methods This is a multi-site retrospective study. Ocular surface topography (sMap3D, Precision Ocular Metrology, US) was collected on 115 eyes with prolate cornea profile (Group A) and 227 eyes showing corneal ectasia (Group B). Sagittal height (SAG 1) was measured in the axis of the highest elevated point of the cornea (apex), defined by the meridian joining this apex to the geometrical center of the cornea at an 16 mm chord diameter (8-mm radius). Another sag value was evaluated 180° away (SAG 2) at the same diameter/radius. The difference in height between SAG 1 and SAG 2 represents a quadrant specific effect (QSE). Conjunctival toricity is estimated by comparing the best fit of the conjunctival/scleral shape data to a toric (Sin2) curve; the root- mean-squared error (RMSE) of this curve, a measure of irregularity, was also calculated. Results The ectasia subjects demonstrated greater QSE, (p<0.001), standard toricity (p<0.001) and RMSE (p<0.001) on the sclera compared to normal cornea cases. If the apex of the ectasia was ≥1.25mm from the corneal center, the asymmetry was greater. Within the Group A, standard toricity was significantly higher than QSE (p<0.001) suggesting a more regular conjunctival pattern. As a proof, a significantly greater proportion of cases in Group B vs. Group A (57% vs. 26%, p<0.001) were found with conjunctival irregular shape, as previously defined. In both groups, subjects graded as having spherical/toric scleral shape had significantly lower RMSE values than those graded as having irregular shapes (p<0.001). Conclusion Subjects with corneal ectasia have a different scleral shape compared to those with normal corneal profiles, largely presenting as a quadrant specific effect along the same axis. This difference is higher if the apex of the ectasia is ≥1.25 mm from the corneal center. RMSE seems to correlate with scleral shape classification in both groups.
Effects of Alternative Dietary Substrates on Competition between Human Colonic Bacteria in an Anaerobic Fermentor System (2003)

Duplicate anaerobic fermentor systems were used to examine changes in a community of human fecal bacteria supplied with different carbohydrate energy sources. A panel of group-specific fluorescent in situ hybridization probes targeting 16S rRNA sequences revealed that the fermentors supported growth of a greater proportion of Bacteroides and a lower proportion of gram-positive anaerobes related to Faecalibacterium prausnitzii, Ruminococcus flavefaciens-Ruminococcus bromii, Eubacterium rectale-Clostridium coccoides, and Eubacterium cylindroides than the proportions in the starting fecal inoculum. Nevertheless, certain substrates, such as dahlia inulin, caused a pronounced increase in the number of bacteria related to R. flavefaciens-R. bromii and E. cylindroides. The ability of three strictly anaerobic, gram-positive bacteria to compete with the complete human fecal flora was tested in the same experiment by using selective plating to enumerate the introduced strains. The Roseburia-related strain A2-183(F) was able to grow on all substrates despite the fact that it was unable to utilize complex carbohydrates in pure culture, and it was assumed that this organism survived by cross-feeding. In contrast, Roseburia intestinalis L1-82(R) and Eubacterium sp. strain A2-194(R) survived less well despite the fact that they were able to utilize polysaccharides in pure culture, except that A2-194(R) was stimulated 100-fold by inulin. These results suggest that many low-G+C-content gram-positive obligate anaerobes may be selected against during in vitro incubation, although several groups were stimulated by inulin. Thus, considerable caution is necessary when workers attempt to predict the in vivo effects of probiotics and prebiotics from their effects in vitro.
Machine Learning Algorithms Outperform Conventional Regression Models in Predicting Development of Hepatocellular Carcinoma (2013)

Machine-learning algorithms improve the accuracy of risk stratifying patients with cirrhosis and can be used to accurately identify patients at high-risk for developing HCC.
Identification of<i>Mycobacterium tuberculosis</i>RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS) (1999)

A widely applicable, positive cDNA selection method was developed to identify RNAs synthesized by Mycobacterium tuberculosis in response to phagocytosis by cultured human primary macrophages. cDNAs for sigE and sigH (alternative sigma factors), aceA (isocitrate lyase), ponA (class I penicillin-binding protein), pks2 (polyketide synthase), uvrA (UvrABC endonuclease), and ctpV (putative cation transporter) were obtained from macrophage-grown bacteria. cDNAs for ORFs Rv3070, Rv3483c, Rv0903c (encoding a putative bacterial two-component transcriptional activator), and Rv0170 of the mce1 virulence operon also were obtained from phagocytized bacilli. cDNAs for these genomic regions were not obtained from approximately 1, 000-fold more bacteria grown in laboratory broth. Methods described here, which have identified M. tuberculosis genes expressed in response to host interaction, will allow the study of gene expression in a variety of microorganisms, including expression resulting from interaction with human tissues in natural disease states.
Object Pose Estimation using Patch-Duplet/SIFT Hybrids (2009)

Recent years have seen a lot of work on local descriptors. In all published comparisons or evaluations, the now quite well-known SIFT-descriptor has been one of the top performers. For the application of object pose estimation, one comparison showed a local descriptor, called the Patch-Duplet, of equal or better performance than SIFT. This paper examines different properties of those two descriptors by forming hybrids between them and extending the object pose tests of the original Patch-Duplet paper. All tests use real images. 1
Polarisation diversity cavity back reconfigurable array antenna for C‐band application (2016)

A new circularly polarised broadband multiple‐input–multiple‐output antenna array designed for wireless communication in C‐band is presented. Some reconfigurable circularly polarised antenna designs based on the polarisation diversity technique have been previously reported. However, most of such designs have the disadvantages of an increased antenna size, reduced gain and decreased axial ratio (AR) bandwidth (BW). The proposed antenna in this work combines a low profile cylindrical cavity back, a parasitic patch and a reconfigurable antenna in a novel structure in order to increase the impedance, 3 dB ARBWs and the gain. Another important feature of the antenna is its polarisation diversity capability by employing PIN diodes in a broadband feed network composed of 90° and 180° couplers, a crossover and delay lines.
Polarized microwave and RF radiation effects on the structure and stability of liquid water (2010)

It is now established that liquid water has many structures with distinctive properties. We have established that ultradilute (≈ 1 ppm) aquasols are different both in structure and properties. We present here, the effects of electromagnetic radiation on water, including our own work from Penn State established in the past decade on the effects of polarized microwave (2.45 GHz) on solids and liquids and radiofrequency (RF) (13.56 MHz) radiation on water. Detailed Raman spectroscopy provides the data on major changes in the water structure including striking reduction in the main stretching modes. The time required for relaxation of the structure at room temperature is in hours.
Proadrenomedullin-derived peptides as autocrine-paracrine regulators of cell growth. (2001)

Proadrenomedullin (pADM)-derived peptides, adrenomedullin (ADM) and pADM N-terminal 20 peptide (PAMP), are hypotensive peptides, which are expressed, along with their receptors, in several tissues and organs, the function of which they regulate by acting in an autocrine-paracrine manner. Apart from their involvement in the regulation of blood pressure and fluid and electrolyte homeostasis, pADM-derived peptides appear to play a role in the modulation of cell and tissue growth. Evidence has been provided that ADM: 1) favors the remodeling of cardiovascular system under pathological conditions, by exerting an antiapoptotic effect on endothelial cells and an antiproliferogenic and antimigratory action on vascular smooth-muscle cells during neointimal hyperplasia, and by decreasing proliferation and protein synthesis of cardiac myocytes and fibroblasts. These last two effects are mediated by calcitonin gene-related peptide type 1 (CGRP1) receptors coupled to the adenylate cyclase (AC)/protein kinase (PK) A-dependent cascade; 2) inhibits proliferation and enhances apoptosis of kidney mesangial cells, through the modulation of mitogen-activated PK (MAPK) cascades; 3) stimulates proliferation of adrenal zona glomerulosa cells, acting via CGRP1 receptor coupled to the tyrosine kinase-dependent MAPK cascade, thereby possibly being involved in the maintenance and stimulation of adrenal growth; 4) enhances proliferation of skin and mucosa epithelial cells and fibroblasts, by activating CGRP1 receptor coupled to the AC/PKA signaling pathway; and 5) enhances proliferation of several tumor-cell lines through the activation of the AC/PKA cascade, which suggests a potential role for ADM as promoter of neoplastic growth. The growth effects of PAMP have been far less investigated: findings indicate that this peptide, like ADM, enhances adrenal zona glomerulosa-cell proliferation, and, in contrast with ADM, depresses DNA synthesis in some cancer-cell lines. Both pADM-derived peptides are thought to be involved in embryogenesis, such a contention being based on the demonstration of high pADM-gene expression during the crucial phases of organ growth and differentiation.
Vines avoid coiling around neighbouring plants infested by polyphagous mites (2019)

Vines that coil around plants heavily infested with ambulate polyphagous mites can be heavily damaged by the mites. To explore whether vines avoid mite-infested plants, we observed the coiling responses of morning glory (Ipomoea nil var. Heavenly Blue) vines and bush killer (Cayratia japonica (Thunb) Gagnep) tendrils around nearby kidney bean (Phaseolus vulgaris L.) plants that were either uninfested or heavily infested with the two-spotted spider mite (Tetranychus urticae Koch). The proportions of I. nil vines that coiled around spider mite-infested and uninfested bean plants did not differ significantly; however, no C. japonica tendril coiled around spider mite-infested plants. The proportion of such tendrils was thus significantly lower than that around uninfested plants. The ability of C. japonica tendrils to avoid spider mite-infested plants would prevent serious "contact infections" by mites. We further found that tendril avoidance seemed to be attributable to the mite webs that covered infested plants; neither spider mite-induced bean volatiles nor spider mite intrusion onto tendrils seemed to explain the avoidance.
The biosynthesis of ectoine (1990)

The biosynthetic pathway of the novel compatible solute ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) was studied in the two extremely halophilic eubacteria Ectothiorhodospira halochloris and Halomonas elongata. The pathway starts with the phosphorylation of l-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase and l-aspartate-β-semialdehyde dehydrogenase. Evidence is presented for the presence of the enzymes l-diaminobutyric acid transaminase and l-diaminobutyric acid acetyl transferase and for the new enzyme the ring-forming ectoine synthase.
Characterization of [<sup>3</sup>H]‐(2S,2′R,3′R)‐2‐(2′,3′‐dicarboxy‐ cyclopropyl)glycine ([<sup>3</sup>H]‐DCG IV) binding to metabotropic mGlu<sub>2</sub> receptor‐transfected cell membranes (1998)

1. The binding of the new selective group II metabotropic glutamate receptor radioligand, [3H]-(2S,2'R,3'R)-2-(2',3'-dicarboxycyclopropyl)glycine ([3H]-DCG IV), was characterized in rat mGlu2 receptor-transfected CHO cell membranes. 2. [3H]-DCG IV binding was pH-dependent, but was not sensitive to temperature. Saturation analysis showed the presence of a single binding site, with a Kd value of 160 nM and a Bmax value of 10 pmol mg(-1) protein. Binding was not sensitive to Na+-dependent glutamate uptake blockers or Cl-dependent glutamate binding inhibitors. Furthermore, up to concentrations of 1 mM, the glutamate ionotropic receptor agonists, N-methyl-D-aspartic acid (NMDA), (S)-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and kainate, did not affect [3H]-DCG IV binding. 3. Of the compounds observed to inhibit [3H]-DCG IV binding, the most potent were the recently described selective group II agonist, (+)-2-aminobicyclo-[3.1.0]hexane-2,6-dicarboxylate (LY 354740; Ki value 16 nM) and antagonist, 2-amino-2-(2-carboxycyclopropan-1-yl)-3-(dibenzopyran-4-yl) propanoic acid (LY 341495; Ki value 19 nM). As expected, for a G-protein-coupled receptor, guanosine-5'-O-(3-thiotriphosphate) (GTPgammaS) inhibited [3H]-DCG IV binding in a concentration-dependent manner, with an IC50 value of 12 nNM. 4. A highly significant correlation was observed between the potencies of compounds able to inhibit [3H]-DCG IV binding and potencies obtained for agonist activity in a GTPgamma35S binding functional assay. In addition, these studies identified a number of compounds with previously unknown activity at mGlu2 receptors, including L(+)-2-amino-3-phosphonopropionic acid (L-AP3), L(+)-2-amino-5-phosphonopentanoic acid (L-AP5), 3-((RS)-2-carboxypiperazin-4-yl)-propyl-1-phosphonic acid (R-CPP), N-acetyl-L-aspartyl-L-glutamic acid (NAAG) and (RS)-alpha-methylserine-O-phosphate (MSOP).
Characteristics of hydroxyapatite film formed on human enamel with the powder jet deposition technique (2011)

This study aimed to create hydroxyapatite (HAp) film by powder jet deposition with manipulating the blasting nozzle above human enamel and to examine the microstructural and mechanical properties of the HAp film and the bonding strength at the interface between the HAp film and the enamel substrate. HAp particles calcinated at 1200°C with an average size of 4.7 μm were used. The HAp particles were mixed with carrier gas (N₂) to form an aerosol flow and was accelerated and blasted from the nozzle onto the enamel substrate at room temperature and atmospheric pressure. To evaluate the microstructure, scanning electron microscope (SEM) images of the surface and cross section of the HAp films and a three-dimensional profile of the HAp films were observed. To evaluate the mechanical properties, the micro-Vickers hardness and the bonding strength of the HAp films to the enamel substrate were measured. The deposition area of the HAp film was over 3 × 4 mm. The average and maximum thickness were about 30 and 40 μm, respectively. No significant difference was observed between the hardness of the HAp film and the enamel (p > 0.05). The bonding strength of the HAp film was the same as the bonding strength between composite resin and enamel. Compared with previous reports, wider and thicker HAp film was created on the enamel substrate successfully. The HAp film, which has same hardness with enamel and same bonding strength to the enamel with composite resin, would be a candidate as dental restorative materials.
Generation of slowly rotating microwave plasma by amplitude-modulated resonant cavity (2017)

Slow rotation of microwave plasma at a rotational frequency of Ω/2π = 0.1–1000 Hz is realized to improve plasma uniformity by using a resonant cylindrical cavity and a solid-state microwave generator at a frequency of ω/2π = 2.4–2.5 GHz. The microwave at ω/2π is modulated in amplitude at Ω/2π and injected into the cavity from two orthogonal positions, exciting the TE111 mode. The cavity fields rotate either clockwise or anticlockwise at a frequency of Ω/2π when the phase differences, Δϕ at ω and ΔΦ at Ω, between the input microwaves are properly set as calculated by a theoretical analysis and finite-difference time-domain simulation. Rotating plasmas are experimentally measured in the microwave discharges of argon at 0.1–20 Torr. When the rotational frequency is low (Ω/2π < 30 Hz), a plasma rotation is visible in the optical emission image; the azimuthal rotation of a local ion density is also confirmed by a rotatable Langmuir probe array. Conversely, when Ω/2π > 1000 Hz, the electron density measurement by a curling probe reveals that the plasma rotation disappears in the downstream region. This observation is supported by a simplified analysis based on the diffusion equation, proving a characteristic distance of plasma rotation disappearance to be (Da: ambipolar diffusion coefficient).
Creep characteristics and constitutive model of coal under triaxial stress and gas pressure (2019)

Abstract Creep behavior is one of the most important mechanical behaviors of coal. In the present study, we systematically carried out a series of creep experiments of briquette samples under triaxial compression and gas pressure. The experimental results showed that the creep deformation characteristics of coal were related to deviatoric stress and gas pressure. The accelerating creep stage initiated when the deviatoric stress reached or exceeded the yield stress until failure took place. In contrast, when the deviatoric stress was less than the yield strength, only transient and steady creep stage occurred. Besides, gas pressure played a positive role in the creep process of coal. The axial strain of coal slightly increased with gas pressure (range from 0.13 to 0.40 MPa) when the effective triaxial stress remained constant. For example, in the steady creep stage ( σ 1 = 9 MPa, p = 0.13 MPa), the axial strain of sample S 1 is 2.710% and that of sample S 2 is 3.361%, that is, coal samples with high gas pressure have higher axial strain. Moreover, gas pressure has two main effects on the mechanical behavior of coal. One is that the coal adsorbs gas molecules resulting in swelling strain and swelling stress, and the other is that the gas pressure may compress the coal particles. Considering the swelling stress and gas pressure, we intensively studied the effective stress formula of coal containing gas. Then, the effective stress was taken into consideration in the nonlinear Nishihara creep model. Furthermore, the tertiary creep factor n was introduced in the nonlinear model to control the creep deformation evolution with time so that the nonlinear model could accurately describe the full creep stage of coal. In contrast, due to the lack of such a controlling parameter, the Nishihara model failed to reproduce the accelerating creep stage.
Methods to Evaluate Skin Penetration In Vitro (2019)

Dermal and transdermal drug therapy is increasing in importance nowadays in drug development. To completely utilize the potential of this administration route, it is necessary to optimize the drug release and skin penetration measurements. This review covers the most well-known and up-to-date methods for evaluating the cutaneous penetration of drugs in vitro as a supporting tool for pharmaceutical research scientists in the early stage of drug development. The aim of this article is to present various experimental models used in dermal/transdermal research and summarize the novel knowledge about the main in vitro methods available to study skin penetration. These techniques are: Diffusion cell, skin-PAMPA, tape stripping, two-photon microscopy, confocal laser scanning microscopy, and confocal Raman microscopic method.
Simple Method for Identification of Metallothionein Isoforms in Cultured Human Prostate Cells by MALDI-TOF/TOF Mass Spectrometry (2007)

The present paper describes a rapid method for identification and characterization of human metallothionein (MT) isoforms in complex cell cultures using high-resolution matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF). In the proposed method, the sample preparation of MTs from cultured cells is both simple and fast. It is accomplished by trypsin cleavage of cell proteins into small peptide species, the majority of which are subsequently removed by gel filtration using beads with an exclusion limit of 4000 Da. In contrast to most cell proteins, MTs remain intact (undigested) upon being treated with trypsin, being excluded by the gel beads and thus recovered by low-speed centrifugation. To identify the protein constitutes of the MT preparation, the MT sample is divided into two parts, one for intact protein accurate mass measurement, the other for tryptic digestion followed by MS and MS/MS analyses. In the latter case, the MT proteins are denatured by the addition of EDTA which strips heavy metals from MTs and renders them susceptible to tryptic digestion. The obtained accurate mass with the unique peptide sequences of each MT isoform allows for unambiguous identification of MT isoforms in the prepared mixture. The method has been applied to RWPE-1 cells derived from normal human prostate epithelium. Four MT isoforms, 1E, 1G, 1X, and 2A, have been confidently identified, being primarily acetylated at N-termini. These results are in agreement with the expression of MT mRNAs in RWPE-1 cells determined by real-time reverse-transcription polymerase chain reaction (RT-PCR).
Detecting Performance Anomalies in Cloud Platform Applications (2018)

We present Roots, a full-stack monitoring and analysis system for performance anomaly detection and bottleneck identification in cloud platform-as-a-service (PaaS) systems. Roots facilitates application performance monitoring as a core capability of PaaS clouds, and relieves the developers from having to instrument application code. Roots tracks HTTP/S requests to hosted cloud applications and their use of PaaS services. To do so it employs lightweight monitoring of PaaS service interfaces. Roots processes this data in the background using multiple statistical techniques that in combination detect performance anomalies (i.e. violations of service-level objectives). For each anomaly, Roots determines whether the event was caused by a change in the request workload or by a performance bottleneck in a PaaS service. By correlating data collected across different layers of the PaaS, Roots is able to trace high-level performance anomalies to bottlenecks in specific components in the cloud platform. We implement Roots using the AppScale PaaS and evaluate its overhead and accuracy.