gebhart/patrepeval huggingface dataset:
Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. (2007)

Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, "PD", has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, "cryptic", taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based "species" designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.
Selective concentration of human cancer cells using contactless dielectrophoresis (2011)

This work is the first to demonstrate the ability of contactless dielectrophoresis (cDEP) to isolate target cell species from a heterogeneous sample of live cells. Since all cell types have a unique molecular composition, it is expected that their dielectrophoretic (DEP) properties are also unique. cDEP is a technique developed to improve upon traditional and insulator-based DEP devices by replacing embedded metal electrodes with fluid electrode channels positioned alongside desired trapping locations. Through the placement of the fluid electrode channels and the removal of contact between the electrodes and the sample fluid, cDEP mitigates issues associated with sample/electrode contact. MCF10A, MCF7, and MDA-MB-231 human breast cells were used to represent early, intermediate, and late-staged breast cancer, respectively. Trapping frequency responses of each cell type were distinct, with the largest difference between the cells found at 20 and 30 V. MDA-MB-231 cells were successfully isolated from a population containing MCF10A and MCF7 cells at 30 V and 164 kHz. The ability to selectively concentrate cells is the key to development of biological applications using DEP. The isolation of these cells could provide a workbench for clinicians to detect transformed cells at their earliest stage, screen drug therapies prior to patient treatment, increasing the probability of success, and eliminate unsuccessful treatment options.
A classification strategy for mapping trochus shell habitat in Torres Strait, Australia (1994)

Abstract Trochus niloticus is a large, marine gastropod that is harvested from the coral reefs of Torres Strait, to the north of Australia. Prime habitat for the large, commercial sized trochus is restricted to narrow zones of coral rubble and pavement on the windward edges of reefs. These areas are difficult to map and survey for trochus shell. Initial research demonstrated that Landsat TM imagery could be used to produce an accurate map of trochus habitat for a single reef. A methodology was then developed to transfer a classification mask, generated from this intensively surveyed reef to others in Bourke Group of islands. The procedure returned results that were within 2% to 12% (underestimates) of areal estimates based on fieldwork and air photo interpretation This methodology offers potential as an accurate and cost effective way of monitoring habitat across the remote environments occupied by trochus.
Inhibition of Retinal Pigment Epithelial Cell Attachment by a Synthetic Peptide Derived From the Cell-Binding Domain of Fibronectin (1986)

Retinal pigment epithelial (RPE) cells are dispersed into the vitreous cavity during retinal reattachment surgery and attach to the vitreous gel and internal limiting membrane. Subsequent migration and cell-mediated contraction can result in traction retinal detachment. Fibronectin (FN) can enhance the attachment of various cell types. We now report that FN enhances the attachment of human and porcine RPE cells. A synthetic tetrapeptide, arg-gly-asp-ser (RGDS), derived from the FN cell-binding domain, has been shown to interfere with attachment of some cell types. We now report that RGDS inhibits RPE cell attachment to FN in a dose-dependent manner with 70% inhibition at 1 mg/mL. Also, RGDS inhibits attachment to types I and II collagen, as well as to lens capsule basement membrane by 40%, 50%, and 25%, respectively. Therefore, RGDS or its derivatives may have some eventual role in the management of proliferative vitreoretinopathy.
Sacrificial Agent for Reducing Adsorption of Anionic Surfactants (2013)

Abstract An important economical factor affecting Enhanced Oil Recovery (EOR) is the adsorption of surfactants on the rocks. Sacrificial agents may be used to reduce the adsorption of surfactants. An alkali (traditionally, sodium carbonate or sodium hydroxide) is often used as sacrificial adsorption agent; however, sodium carbonate is not an effective sacrificial agent in the presence of anhydrite in the rocks due to the reaction between sodium carbonate and sparingly-soluble anhydrite. Therefore, it is essential to develop a sacrificial adsorption agent that can act effectively in the presence of anhydrite. In this work, sodium polyacrylate is evaluated as a sacrificial agent, and is compared to many other conventional or recently- recommended sacrificial agents, and has shown advantage over all of them for the case of presence of anhydrite. Some experiments have been conducted to demonstrate the ineffectiveness of sodium carbonate as sacrificial agent in the presence of anhydrite. Effect of molecular weight of sodium polyacrylate is tested, and it is found that increase in molecular weight results in decrease in adsorption of surfactant until a certain molecular weight of polyacrylate is reached after which molecular weight has no further effect on reducing adsorption of surfactant. Addition of polyacrylate was shown to reduce adsorption of a selected anionic surfactant on different outcrop minerals, including Carlpool dolomite, industrial calcite, kaolinite, Berea sandstone, and Indiana limestone. To prove the point further, application of polyacrylate was tested with two different anionic surfactants. Adsorption of polyacrylate itself is measured in the presence and absence of surfactant and showed to be independent of the presence of surfactant. The effect of concentration of divalent ions and salinity in the brine on effectiveness of sodium polyacrylate as sacrificial agent has been evaluated on different minerals/rocks. Finally, dynamic adsorption data has been presented in different concentrations of sodium polyacrylate. All these experiments demonstrate the advantage of using sodium polyacrylate as sacrificial adsorption agent for anionic surfactants even in the presence of anhydrite in the rock.
Tri‐Layered Nanocomposite Hydrogel Scaffold for the Concurrent Regeneration of Cementum, Periodontal Ligament, and Alveolar Bone (2017)

A tri-layered scaffolding approach is adopted for the complete and concurrent regeneration of hard tissues-cementum and alveolar bone-and soft tissue-the periodontal ligament (PDL)-at a periodontal defect site. The porous tri-layered nanocomposite hydrogel scaffold is composed of chitin-poly(lactic-co-glycolic acid) (PLGA)/nanobioactive glass ceramic (nBGC)/cementum protein 1 as the cementum layer, chitin-PLGA/fibroblast growth factor 2 as the PDL layer, and chitin-PLGA/nBGC/platelet-rich plasma derived growth factors as the alveolar bone layer. The tri-layered nanocomposite hydrogel scaffold is cytocompatible and favored cementogenic, fibrogenic, and osteogenic differentiation of human dental follicle stem cells. In vivo, tri-layered nanocomposite hydrogel scaffold with/without growth factors is implanted into rabbit maxillary periodontal defects and compared with the controls at 1 and 3 months postoperatively. The tri-layered nanocomposite hydrogel scaffold with growth factors demonstrates complete defect closure and healing with new cancellous-like tissue formation on microcomputed tomography analysis. Histological and immunohistochemical analyses further confirm the formation of new cementum, fibrous PDL, and alveolar bone with well-defined bony trabeculae in comparison to the other three groups. In conclusion, the tri-layered nanocomposite hydrogel scaffold with growth factors can serve as an alternative regenerative approach to achieve simultaneous and complete periodontal regeneration.
STEREOSPECIFIC POLYMERIZATION OF DIOLEFIN IN THE PRESENCE OF A NEW TYPE OF CATALYTIC-SYSTEM BASED ON CYCLOPENTADIENYL DICHLORIDES OF THE LANTHANIDES (1984)

The preparation of the compounds C,H, LnCl2·nTHF（C,H, =cyclopentadienyl; Ln=Ce, Pr, Nd, Gd and Y;n= 0, 1, 2, 3） or C,H,LnCl2·HCl·2THF （Ln=Pr and Nd） was describ.ed in another article by the present authors. These compounds are combined with an alkylalu-
Immunocytochemical localization of galactosyltransferase in HeLa cells: codistribution with thiamine pyrophosphatase in trans-Golgi cisternae. (1982)

An affinity-purified, monospecific rabbit antibody against soluble human milk galactosyltransferase was used to localize the enzyme in HeLa cells by immunofluorescence and by the protein A-gold technique at the electron microscope level. Specific immunofluorescence was observed in a juxtanuclear cytoplasmic region which was identified, on immunostained thin sections of low-temperature Lowicryl K4M-embedded HeLa cells, as Golgi apparatus. Label by gold particles was limited to two to three trans cisternae of the Golgi apparatus, indicating a compartmentalization of galactosyltransferase in the cisternal stack. Combination of preembedding thiamine pyrophosphatase cytochemistry, with postembedding immunostaining for galactosyltransferase proved codistribution of the two enzymes. However, the acid phosphatase-positive, trans-most cisterna was negative for galactosyltransferase. The close topological association of both galactosyltransferase and thiamine pyrophosphatase (or nucleoside diphosphatase) suggests a concerted action of both enzymes in glycosylation.
Diffusion Processes for Retrieval Revisited (2013)

In this paper we revisit diffusion processes on affinity graphs for capturing the intrinsic manifold structure defined by pair wise affinity matrices. Such diffusion processes have already proved the ability to significantly improve subsequent applications like retrieval. We give a thorough overview of the state-of-the-art in this field and discuss obvious similarities and differences. Based on our observations, we are then able to derive a generic framework for diffusion processes in the scope of retrieval applications, where the related work represents specific instances of our generic formulation. We evaluate our framework on several retrieval tasks and are able to derive algorithms that e.\, g.~achieve a 100\% bulls eye score on the popular MPEG7 shape retrieval data set.
Supercritical Fluid Fabrication of Metal Nanowires and Nanorods Templated by Multiwalled Carbon Nanotubes (2003)

Metal nanorods and nanowires (see Figure) have been synthesized using multiwalled carbon nanotubes (MWCNTs) as templates and supercritical CO 2 as the reaction medium. This rapid, direct, and clean approach can also be used to fabricate other metal/CNT composites and to coat the CNTs with metal films or nanoparticles.
Influence of Calcined Temperature on the Piezoelectric Properties of (Na<sub>0.48</sub>K<sub>0.47</sub>Li<sub>0.05</sub>)NbO<sub>3</sub> Lead-Free Piezoelectric Ceramics Doped with CuO (2013)

Na 0.48 K 0.47 Li 0.05 )NbO 3 (NKLN)Lead-free piezoelectric ceramics doped with CuO were prepared by traditional solid-state reaction method. Influence of calcined temperature on the material phase of NKLN lead-free piezoelectric ceramics doped with CuO by X-ray diffraction (XRD) and the influence of calcined temperature and sintered temperature on the properties of NKLN lead-free piezoelectric ceramics doped with CuO by others analysis method. The results show that the best calcined temperature is got, when calcined temperature is up to 850 °C, the mixed phase disappeares, a single phase perovskites structure is formed. With the increase of calcined temperature, piezoelectric strain constant (d 33 ) planar electromechanical coupling factor (K p ) of NKLN lead-free piezoelectric ceramics increase first and then decrease, while only dielectric loss (tanδ) decreases first and then increases.The best calcined temperature is 850 °C, the best sintered temperature is 1080 °C, the NKLN lead-free piezoelectric ceramics doped with CuO with good comprehensive properties are obtained, whose d 33 , K p , tanδ are 85 pC/N, 0.3, 0.038, respectively.
Magnetic Interaction Between Recording Layer and Soft Underlayer in Granular-Type Perpendicular Magnetic Recording Media With Thin Intermediate Layer (2008)

CoPt-TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> granular-type media with extremely thin Ru intermediate layer were prepared on a highly oriented high-B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">s</sub> FeCo soft underlayer (SUL). The minimum Ru layer thickness for obtaining the squareness ratio (SQ) more than 0.99 was 1.6 nm. The H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> of the recording layer and the H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ch</sub> (H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> in the hard axis direction) of the SUL oscillated as a function of Ru intermediate layer thickness. The oscillation period was 0.5-0.8 nm. A medium with Ru intermediate layers of larger H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> (peak position) showed smaller H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ch</sub> of the SUL than that of valley position. Strong magnetic interlayer interaction deteriorates the magnetic properties of the recording layer and the SUL. The recording performance was measured for the media with different magnetic interlayer interaction by using a single-pole-type (SPT) head. The S/N for the medium with the strong interlayer interaction largely decreased compared with that for the medium with weak interlayer interaction. This indicates that magnetic interaction between the recording layer and the SUL can be controlled by choosing an appropriate film thickness of Ru intermediate layer.
Reduction in body weight and cholesterol in spontaneously obese dogs by dehydroepiandrosterone. (1990)

We studied the effect(s) of exogenous dehydroepiandrosterone (DHEA) in spontaneously obese dogs. Nineteen euthyroid obese and six non-obese normal dogs were evaluated. Dogs received DHEA for three months at an escalating dose of 30-75 mg/kg p.o. daily. We found a 3 percent reduction in total body weight/month in 68 percent of the obese dogs, without reduction in food intake. The normal dogs did not lose weight or reduce food intake. Serum cholesterol in obese dogs went from 226 to 173 mg/dl post-treatment and in normal dogs from 128 to 89 mg/dl. Analysis of lipoproteins in four normal dogs revealed that the marked reduction in cholesterol most significantly affected the LDL-HDL1 fraction.
Synthesis, Characterization, and Luminescence of β-Cyclodextrin Inclusion Compounds Containing Europium(III) and Gadolinium(III) Tris(β-diketonates) (2002)

β-Cyclodextrin (β-CD) inclusion compounds containing the lanthanide complexes Eu(NTA)3·xH2O and Gd(NTA)3·xH2O [NTA = 1-(2-naphthoyl)-3,3,3-trifluoroacetone)] were prepared by treating a saturated aqueous solution of β-CD with a solution of the complex in ethanol. The molar ratio of host to guest in the reaction was either 3:1 or 1:1, leading to products designated as M(NTA)3·3β-CD and M(NTA)3·β-CD (M = Eu, Gd), respectively. The products were characterized in the solid state by elemental analysis, powder X-ray diffraction, thermogravimetric analysis, FTIR, and 13C CP MAS NMR spectroscopy, indicating the formation of true inclusion compounds in which the naphthoyl moieties of the guest species are encapsulated within the β-CD cavities. The photoluminescence results, in particular the determination of the experimental intensity parameters Ω2 and Ω4, show that this encapsulation seems to modify essentially the second Eu3+ coordination shell, namely, the energy and the lifetime of the lowest triplet state of the naphthalene groups. The encapsulation induces emission from the singlet excited state of the ligands with the corresponding presence of an inefficient ligand-to-metal ion energy transfer step.
Frequency stability of high overtone bulk acoustic resonators (2002)

The authors report the results of phase noise measurements for high overtone bulk acoustic resonators (HBARs) operating at 640 MHz with insertion losses of 10-15 dB and unmatched Qs greater than 110 K. Noise measurements made on these resonators with input drive levels of 16 dBm have shown self-noise levels of S/sub y/(f=100 Hz)=8.0*10/sup -26/ for 1/f noise, which represents the state-of-the-art for a UHF resonator. It is concluded that HBAR technology provides the means for generating UHF and microwave signals exhibiting short-term frequency stability superior to that obtainable using quartz resonator based sources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Optical emission spectroscopy during sputtering of Y-Ba-CU-oxide targets (1990)

The sputter deposition of high-temperature superconducting thin films was studied using optical emission spectroscopy. Argon or oxygen ions generated by a Kaufman ion gun were used to sputter material from a composite target containing yttrium, barium, and copper which had been oxygen annealed. The impact of ions onto the target generates a plume of sputtered material which includes various excited-state atoms and molecules. In these studies, optical emission is detected for all the metallic components of the film as well as for metallic oxides ejected from the target. No emission due to atomic or molecular oxygen was detected, however. Variations in sputter conditions such as changes in sputter ion energy, oxygen content of the beam, and target temperature are shown to greatly affect the emission intensity, which may correlate to the characteristics of the sputtering and the quality of the films deposited. The results suggest that optical emission from the sputtered material may be useful for real-time monitoring and control of the sputter deposition process.
Influence of major structural features of tocopherols and tocotrienols on their ω-oxidation by tocopherol-ω-hydroxylase (2007)

Human cytochrome P450 4F2 (CYP4F2) catalyzes the initial omega-hydroxylation reaction in the metabolism of tocopherols and tocotrienols to carboxychromanols and is, to date, the only enzyme shown to metabolize vitamin E. The objective of this study was to characterize this activity, particularly the influence of key features of tocochromanol substrate structure. The influence of the number and positions of methyl groups on the chromanol ring, and of stereochemistry and saturation of the side chain, were explored using HepG2 cultures and microsomal reaction systems. Human liver microsomes and microsomes selectively expressing recombinant human CYP4F2 exhibited substrate activity patterns similar to those of HepG2 cells. Although activity was strongly associated with substrate accumulation by cells or microsomes, substantial differences in specific activities between substrates remained under conditions of similar microsomal membrane substrate concentration. Methylation at C5 of the chromanol ring was associated with markedly low activity. Tocotrienols exhibited much higher Vmax values than their tocopherol counterparts. Side chain stereochemistry had no effect on omega-hydroxylation of alpha-tocopherol (alpha-TOH) by any system. Kinetic analysis of microsomal CYP4F2 activity revealed Michaelis-Menten kinetics for alpha-TOH but allosteric cooperativity for other vitamers, especially tocotrienols. Additionally, alpha-TOH was a positive effector of omega-hydroxylation of other vitamers. These results indicate that CYP4F2-mediated tocopherol-omega-hydroxylation is a central feature underlying the different biological half-lives, and therefore biopotencies, of the tocopherols and tocotrienols.
Proposal of roll angle control method using positive and negative anti-dive force for electric vehicle with four in-wheel motors (2013)

Electric vehicles (EVs) have been gaining a lot of attention due to its environmental friendliness. EVs can be controlled precisely with the quick response of the motor. Moreover, using in-wheel motors, several types of motion controls can be performed. Therefore, such motion control of EVs have been intensely researched. This paper focuses on the control of roll angle which occurs during cornering. If this roll angle becomes large, steering response will be deteriorated, and also stability will decrease. Therefore, it is necessary to appropriately control the roll angle. In this paper, roll angle control method using positive and negative anti-dive force for EVs with four in-wheel motors has been proposed. Using positive and negative anti-dive force, the number of necessary actuators such as active suspensions can be reduced. The proposed method is also considering workload control of each wheel based on least square method. By estimating the roll moment disturbance using the roll moment observer, roll angle control has become a robust control system against disturbances. Thus, the proposed method allows improvement of vehicle's stability, safety and riding comfort during cornering. The effectiveness of the proposed method is verified by simulation and experimental results. Results of the roll angle control system without workload consideration and results of the case with workload consideration are also compared.
Determination of Ultrasonic Velocities by Measurement of Angles of Total Reflection (1960)

A simple method, based on the total reflection of a sound beam from a liquid-solid boundary at the critical angles, is described. With this method, it is possible to measure the velocity of longitudinal and shear waves in the solid by locating the angles of maximum reflection in the liquid.
Quantitative review of operative management of hallux rigidus (2011)

There is a need to perform appropriately powered randomized clinical trials of using standard diagnostic assessment, common and validated scoring system comparing reported outcomes and duration of follow-up >2 years.