gebhart/patrepeval huggingface dataset:
Ethylene-mediated phenotypic plasticity in root nodule development on <i>Sesbania rostrata</i> (1998)

Leguminous plants in symbiosis with rhizobia form either indeterminate nodules with a persistent meristem or determinate nodules with a transient meristematic region. Sesbania rostrata was thought to possess determinate stem and root nodules. However, the nature of nodule development is hybrid, and the early stages resemble those of indeterminate nodules. Here we show that, depending on the environmental conditions, mature root nodules can be of the indeterminate type. In situ hybridizations with molecular markers for plant cell division, as well as the patterns of bacterial nod and nif gene expression, confirmed the indeterminate nature of 30-day-old functional root nodules. Experimental data provide evidence that the switch in nodule type is mediated by the plant hormone ethylene.
Interactions and penetration at metal/self-assembled organic monolayer interfaces (1996)

The purpose of research on metals (M) deposited onto self-assembled monolayers (SAMs) is to understand the interactions between the metal and eventually metal oxide overlayers on well-ordered organic surfaces. Applications of M/SAM and inorganic/SAM research results to the understanding of real inorganic/organic interfaces in vacuum and under environmental conditions can potentially play a key role in the development of advanced devices with stable interfacial properties. The results of M/SAM studies to date are reviewed, M/SAM combinations ranked according to reactivity and penetration, and specific examples of reactive interfaces (Cu/COOH, and Cr/COOH) and nonreactive interfaces with penetration (Ag/COOH) are used to illustrate the extremes.
MicroRNA-125a Reduces Proliferation and Invasion of Oral Squamous Cell Carcinoma Cells by Targeting Estrogen-related Receptor α (2014)

Estrogen-related receptor α (ESRRA) functions as a transcription factor and regulates the expression of several genes, such as WNT11 and OPN. Up-regulation of ESRRA has been reported in several cancers. However, the mechanism underlying its up-regulation is unclear. Furthermore, the reports regarding the role and regulation of ESRRA in oral squamous cell carcinoma (OSCC) are completely lacking. Here, we show that tumor suppressor miR-125a directly binds to the 3'UTR of ESRRA and represses its expression. Overexpression of miR-125a in OSCC cells drastically reduced the level of ESRRA, decreased cell proliferation, and increased apoptosis. Conversely, the delivery of an miR-125a inhibitor to these cells drastically increased the level of ESRRA, increased cell proliferation, and decreased apoptosis. miR-125a-mediated down-regulation of ESRRA impaired anchorage-independent colony formation and invasion of OSCC cells. Reduced cell proliferation and increased apoptosis of OSCC cells were dependent on the presence of the 3'UTR in ESRRA. The delivery of an miR-125a mimic to OSCC cells resulted in marked regression of xenografts in nude mice, whereas the delivery of an miR-125a inhibitor to OSCC cells resulted in a significant increase of xenografts and abrogated the tumor suppressor function of miR-125a. We observed an inverse correlation between the expression levels of miR-125a and ESRRA in OSCC samples. In summary, up-regulation of ESRRA due to down-regulation of miR-125a is not only a novel mechanism for its up-regulation in OSCC, but decreasing the level of ESRRA by using a synthetic miR-125a mimic may have an important role in therapeutic intervention of OSCC and other cancers.
Rapid Detection and Identification of Hepatitis C Virus (HCV) Sequences using Mismatch-Tolerant Hybridization Probes: A General Method for Analysis of Sequence Variation (2013)

Detection and identification of highly variable viral sequences is important for tracking infectious outbreaks and determining treatment regimens using targeted drug therapy. This report describes a single tube assay that is able to distinguish extensive sequence variation in hepatitis C virus (HCV) by using mismatch tolerant probes to analyze single-stranded amplicons generated with reverse transcription linear-after-the-exponential PCR (RT-LATE-PCR). Detection and identification of sequences from the 5' non-coding region (NCR) of 31 different HCV strains was first evaluated via hybridization of two fluorescently labeled, mismatch-tolerant probes to synthetic DNA strands. The resulting data were used to calculate the ratio of fluorescent signals for the two probes over a wide temperature range as well as the melting temperature (Tm) of each probe with the targets. Although the Tm measurements alone distinguished only 5 sequences from the others, fluorescent signal ratio analysis provided a unique set of values for 27 of the 31 strains. RT-LATE-PCR was then used to amplify Armored RNA (AR) containing the 5' NCR of five different strains of HCV. Melting analysis of the resulting single-stranded DNA with the two probes distinguished all five AR sequences. This assay can be expanded to include additional gene segments, and it points the way to construction of highly informative single-tube assays for HCV and other RNA viruses.
The increased level of β1,4-galactosyltransferase required for lactose biosynthesis is achieved in part by translational control (1998)

beta1,4-Galactosyltransferase (beta4GalT-I) participates in both glycoconjugate biosynthesis (ubiquitous activity) and lactose biosynthesis (mammary gland-specific activity). In somatic tissues, transcription of the mammalian beta4GalT-I gene results in a 4.1-kb mRNA and a 3.9-kb mRNA as a consequence of initiation at two start sites separated by approximately 200 bp. In the mammary gland, coincident with the increased beta4GalT-I enzyme level ( approximately 50-fold) required for lactose biosynthesis, there is a switch from the 4.1-kb start site to the preferential use of the 3.9-kb start site, which is governed by a stronger tissue-restricted promoter. The use of the 3.9-kb start site results in a beta4GalT-I transcript in which the 5'- untranslated region (UTR) has been truncated from approximately 175 nt to approximately 28 nt. The 5'-UTR of the 4.1-kb transcript [UTR(4.1)] is predicted to contain extensive secondary structure, a feature previously shown to reduce translational efficiency of an mRNA. In contrast, the 5'-UTR of the 3.9-kb mRNA [UTR(3.9)] lacks extensive secondary structure; thus, this transcript is predicted to be more efficiently translated relative to the 4.1-kb mRNA. To test this prediction, constructs were assembled in which the respective 5'-UTRs were fused to the luciferase-coding sequence and enzyme levels were determined after translation in vitro and in vivo. The luciferase mRNA containing the truncated UTR(3.9) was translated more efficiently both in vitro (approximately 14-fold) and in vivo (3- to 5-fold) relative to the luciferase mRNA containing the UTR(4.1). Consequently, in addition to control at the transcriptional level, beta4GalT-I enzyme levels are further augmented in the lactating mammary gland as a result of translational control.
Robust detection of skew in document images (1997)

We describe a robust yet fast algorithm for skew detection in binary document images. The method is based on interline cross-correlation in the scanned image. Instead of finding the correlation for the entire image, it is calculated over small regions selected randomly. The proposed method does not require prior segmentation of the document into text and graphics regions. The maximum median of cross-correlation is used as the criterion to obtain the skew, and a Monte Carlo sampling technique is chosen to determine the number of regions over which the correlations have to be calculated. Experimental results on detecting skews in various types of documents containing different linguistic scripts are presented here.
Nitric oxide and its role in orthopaedic disease. (1995)

Nitric oxide (.NO) is synthesized by the enzyme nitric oxide synthase (NOS). There are 2 constitutive forms of NOS (cNOS) and 1 inducible form (iNOS). Cells containing cNOS rapidly and transiently produce small amounts of NO in response to agonists that raise cytosolic levels of free Ca2+, whereas cells expressing inducible iNOS produce large amounts of .NO for extended periods after a lag of several hours during which time the enzyme is induced. Until recently, the 2 constitutive isoforms of NOS were thought to be confined to endothelial cells (eNOS) and brain (bNOS or nNOS). However, eNOS and bNOS have been identified in an increasing variety of additional cells. Many, if not most, types of cells are capable of expressing iNOS in response to cytokines, endotoxin, and phagocytosis. Regulation of iNOS occurs at transcriptional, translational, and posttranslational levels. Because .NO is rapidly diffusible and soluble in hydrophobic and aqueous environments, it is well suited to its role as an intercellular messenger with the unique ability to penetrate solid tissue. However, it is rapidly inactivated by hemoglobin. The biochemistry of .NO is dominated by its rapid reaction with oxygen and transitional metals, notably iron. The former reaction may be protective, as when neutralizing superoxide (.O2-), or harmful in forming additional highly damaging radicals such as peroxynitrite. Interaction of .NO with iron-containing proteins has a number of sequelae, including the activation of guanylate cyclase, inhibition of mitochondrial respiration, and inhibition of cell division. Nitric oxide has been implicated in a number of conditions of orthopaedic interest, including inflammation, arthritis, osteoporosis, sepsis, ligament healing, and aseptic loosening of joint prostheses.
A Critical Review of Experimental Research on Hydrogen Fueled SI Engines (2006)

<div class="htmlview paragraph">The literature on hydrogen fueled internal combustion engines is surprisingly extensive and papers have been published continuously from the 1930's up to the present day. Ghent University has been working on hydrogen engines for more than a decade. A summary of the most important findings, resulting from a literature study and the experimental work at Ghent University, is given in the present paper, to clarify some contradictory claims and ultimately to provide a comprehensive overview of the design features in which a dedicated hydrogen engine differs from traditionally fueled engines.</div> <div class="htmlview paragraph">Topics that are discussed include abnormal combustion (backfire, pre-ignition and knock), mixture formation techniques (carbureted, port injected, direct injection) and load control strategies (power output versus NOx trade-off). Attention is given to the most recent research by car manufacturers BMW and Ford, reporting hybrid control strategies (PFI+DI, lean burn + stoichiometric operation using EGR) to obtain power outputs equivalent to gasoline engines with extremely low emission levels. Recent results from experiments with EGR on a hydrogen engine at Ghent University are also given. Finally, a synthesis of hydrogen engine design features is given, that make the most of hydrogen's advantages and counter its disadvantages. Areas requiring further research are highlighted.</div>
Amino Acid Requirements and Proteolytic Activity of <i>Streptococcus sanguis</i> (1975)

The growth response of Streptococcus sanguis groups 1:A and 1:B in a complete chemically defined medium was not influenced by the oxygen concentration of the growth atmosphere. All of the cultures required cysteine and arginine; tyrosine and branched-chain amino acids were frequently required. Proteolysis of casein, mucin, and the anionic proteins of germfree rat saliva by S. sanguis was demonstrated. Hydrolytic activity toward casein was found in the soluble contents of the cells and in the cellular debris after disruption of the cells, with the soluble fractions exhibiting greater proteolytic activity toward casein. The soluble fractions from S. sanguis did not hydrolyze mucin, but this substrate was hydrolyzed by the cell debris fraction. When the amino acid requirements and proteolytic activity of S. sanguis and S. mutans were compared, these two oral streptococcal species exhibited distinct and characteristic differences.
Comparison of Fibronectin and Collagen in Supporting the Isolation and Expansion of Endothelial Progenitor Cells from Human Adult Peripheral Blood (2013)

Overall, the results of this study indicate that, although both fibronectin and collagen efficiently sustain ECFC cultures, each of them brings some advantages within individual steps of the entire process. We suggest that colony isolation performed on fibronectin followed by cell expansion performed on collagen may represent a novel and the most efficient strategy to obtain ECFCs from adult peripheral blood samples.
Decay of high-frequency phonons in amorphous silicon (1996)

We present measurements concerning the dynamics of high-frequency phonons (\ensuremath{\Elzxh}\ensuremath{\omega}\ensuremath{\ge}150 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$) in amorphous silicon at 2 K. From pulsed anti-Stokes Raman experiments, estimates of the population decay time are obtained for high-frequency phonons, generated by fast carrier relaxation. The fracton model explains the counterintuitive sense of the decay-time dependence on frequency in terms of the decrease of the localization length of the vibrational states towards higher frequencies, and the concomitant suppression of the anharmonic decay rate. This model fits our data with a very realistic third-order elastic constant. \textcopyright{} 1996 The American Physical Society.
An LDAP-based User Modeling Server and its Evaluation (2006)

Representation components of user modeling servers have been traditionally based on simple file structures and database systems. We propose directory systems as an alternative, which offer numerous advantages over the more traditional approaches: international vendor-independent standardization, demonstrated performance and scalability, dynamic and transparent management of distributed information, built-in replication and synchronization, a rich number of pre-defined types of user information, and extensibility of the core representation language for new information types and for data types with associated semantics. Directories also allow for the virtual centralization of distributed user models and their selective centralized replication if better performance is needed. We present UMS, a user modeling server that is based on the Lightweight Directory Access Protocol (LDAP). UMS allows for the representation of different models (such as user and usage profiles, and system and service models), and for the attachment of arbitrary components that perform user modeling tasks upon these models. External clients such as user-adaptive applications can submit and retrieve information about users. We describe a simulation experiment to test the runtime performance of this server, and present a theory of how the parameters of such an experiment can be derived from empirical web usage research. The results show that the performance of UMS meets the requirements of current small and medium websites already on very modest hardware platforms, and those of very large websites in an entry-level business server configuration.
Low-Temperature Growth of Carbon Nanotube by Plasma-Enhanced Chemical Vapor Deposition using Nickel Catalyst (2003)

Carbon nanotubes (CNTs) were grown on silicon (Si) substrates with a native oxide layer using a nickel (Ni) catalyst by the plasma-enhanced chemical vapor deposition method at 550 and 650°C. Multiwall CNTs with a large inside hollow core were observed with samples deposited on Si substrates with a native oxide layer. However, no CNT growth was observed with samples deposited on Si substrates without a native oxide layer due to the formation of Ni-silicide. The native oxide layer was believed to act as the diffusion barrier and to suppress the formation of Ni-silicide. The typical diameter and length of CNTs ranged from about 30 to 100 nm and 2 to 3 µm, respectively. The size of CNTs was more strongly dependent on the thickness of the Ni layer than on the growth temperature. The surface roughness and amount of surface defects decreased with increasing process temperature. We performed a post hydrogen plasma treatment for the purification of raw CNTs. The post hydrogen plasma treatment successfully removed residual graphite particles and/or metallic impurities without significant damage to the CNTs.
The electromigration of liquid metal inclusions in Si (1980)

The electromigration velocities of liquid metal inclusions in single-crystal Si were found to follow an Arrhenius relationship with temperature. The activation energies and preexponential factors of liquid metal inclusions of Pd, Au, Cu, Al, Ag, Ga, In, and Sn were measured. Liquid Sb inclusions did not electromigrate. Electromigration velocities were linearly proportional to the applied electric current. Inclusions of Pd, Au, and Cu which have relatively high work functions electromigrate towards the anode while inclusions of Al, Ag, Ga, In, and Sn which have relatively low work functions electromigrate toward the cathode. The relative order of electromigration velocities within the anode-directed group and within the cathode-directed group can be accounted for by setting the electromigration force proportional to the difference between the work function of the metal of the inclusions and an experimentally determined null-point work function and by considering the solubility of silicon in the inclusion.
Regulatory T Cells as Immunotherapy (2014)

Regulatory T cells (Tregs) suppress exuberant immune system activation and promote immunologic tolerance. Because Tregs modulate both innate and adaptive immunity, the biomedical community has developed an intense interest in using Tregs for immunotherapy. Conditions that require clinical tolerance to improve outcomes - autoimmune disease, solid organ transplantation, and hematopoietic stem cell transplantation - may benefit from Treg immunotherapy. Investigators have designed ex vivo strategies to isolate, preserve, expand, and infuse Tregs. Protocols to manipulate Treg populations in vivo have also been considered. Barriers to clinically feasible Treg immunotherapy include Treg stability, off-cell effects, and demonstration of cell preparation purity and potency. Clinical trials involving Treg adoptive transfer to treat graft versus host disease preliminarily demonstrated the safety and efficacy of Treg immunotherapy in humans. Future work will need to confirm the safety of Treg immunotherapy and establish the efficacy of specific Treg subsets for the treatment of immune-mediated disease.
PET Designated Flouride-18 Production and Chemistry (2010)

Positron emission tomography (PET) is a nuclear medicine imaging technology which allows for four-dimensional, quantitative determination of the distribution of labeled biological compounds within the human body. PET is becoming an increasingly important tool for the measurement of physiological, biochemical and pharmacological functions at the molecular level in healthy and pathological conditions. This review will focus on Flouride-18, one of the common isotopes used for PET imaging, which has a half life of 109.8 minutes. This isotope can be produced with an efficient yield in a cyclotron as a nucleophile or as an electrophile. Flouride-18 can be thereafter introduced into small molecules or biomolecules using various chemical synthetic routes, to give the desired imaging agent.
RESISTANCE TO GRAIN PROTECTANTS AND PHOSPHINE IN COLEOPTEROUS PESTS OF GRAIN STORED ON FARMS IN NEW SOUTH WALES (1990)

Tribolium castaneum (Herbst), T. confusum Jacquelin du Val, Sitophilus oryzae (L.), S. granarius (L.), Oryzaephilus surinamensis (L.) and Rhyzopertha dominica (F.) were collected from farms in grain‐growing areas in southern and northern N.S.W. and bioassayed for resistance to the grain protectants malathion, fenitrothion, bioresmethrin, carbaryl, pirimiphos‐methyl, chlorpyrifos‐methyl and the fumigant phosphine. Results showed that resistance on farms in N.S.W. is similar to resistance reported elsewhere in Australia's grain handling system during the past decade. The only new resistance of practical significance was detected in O. surinamensis where 50% of populations were resistant to fenitrothion (maximum R.F. 68.4x). Fenitrothion resistance was uncommon or not detected in other species. Pirimiphos‐methyl resistance was detected in 70% of O. surinamensis populations (maximum RF 44.2x) and in 1 population of T. castaneum (maximum RF 3.1x). Resistance to chlorpyrifos‐methyl was detected in 39% of the O. surinamensis populations (maximum RF 8.4x), the only species tested. Low level phosphine resistance was detected in all species (maximum RF 2.2x). Malathion resistance was detected in all species except S. granarius . Resistance to bioresmethrin and carbaryl was not detected in R. dominica , the only species tested.
Reciprocity Calibration for Massive MIMO: Proposal, Modeling, and Validation (2017)

This paper presents a mutual coupling-based calibration method for time-division-duplex massive MIMO systems, which enables downlink precoding based on uplink channel estimates. The entire calibration procedure is carried out solely at the base station (BS) side by sounding all BS antenna pairs. An expectation-maximization (EM) algorithm is derived, which processes the measured channels in order to estimate calibration coefficients. The EM algorithm outperforms the current state-of-the-art narrow-band calibration schemes in a mean squared error and sum-rate capacity sense. Like its predecessors, the EM algorithm is general in the sense that it is not only suitable to calibrate a co-located massive MIMO BS, but also very suitable for calibrating multiple BSs in distributed MIMO systems. The proposed method is validated with experimental evidence obtained from a massive MIMO testbed. In addition, we address the estimated narrow-band calibration coefficients as a stochastic process across frequency, and study the subspace of this process based on measurement data. With the insights of this study, we propose an estimator which exploits the structure of the process in order to reduce the calibration error across frequency. A model for the calibration error is also proposed based on the asymptotic properties of the estimator, and is validated with measurement results.
Segmentation of liver tumors in ultrasound images based on scale-space analysis of the continuous wavelet transform (2002)

We have developed a simple, yet robust method for segmentation of low-contrast objects embedded in noisy images. Our technique has been applied to segmenting of liver tumors in B-scan ultrasound images with hypoechoic rims. In our method, first a B-scan image is processed by a median filter for removal of speckle noise. Then several one-dimensional profiles are obtained along multiple radial directions which pass through the manually identified center of the region of a tumor. After smoothing by a Gaussian kernel smoother, these profiles are processed by Sombrero's continuous wavelets to yield scalograms over a range of scales. The modulus maxima lines, which represent the degree of regularity at individual points on the profiles, are then utilized for identifying candidate points on the boundary of the tumor. These detected boundary points are fitted by an ellipse and are used as an initial configuration of a wavelet snake. The wavelet snake is then deformed so that the accurate boundary of the tumor is found. A preliminary result for several metastases with various sizes of hypoechoic rims showed that our method could extract boundaries of the tumors which were close to the contours drawn by expert radiologists. Therefore, our new method can segment the regions of focal liver disease in sonograms with accuracy, and it can be useful as a preprocessing step in our scheme for automated classification of focal liver disease in sonography.