gebhart/patrepeval huggingface dataset:
Accurate and objective preoperative diagnosis of thyroid papillary carcinomas by reverse transcription-PCR detection of oncofetal fibronectin messenger RNA in fine-needle aspiration biopsies. (1998)

Recently, the restricted expression of oncofetal fibronectin mRNA was reported in thyroid papillary and anaplastic carcinomas. In this study, by extracting RNA from the leftover cells inside the needles used for fine-needle aspiration biopsy, we establish a new method for gene diagnosis of these carcinomas without further invasiveness to the patient (aspiration biopsy-reverse transcription-PCR, ABRP). RNA was extracted from 177 fine-needle aspiration biopsies of thyroid nodules that were suspicious for malignancy, and then the gene diagnoses made by reverse transciption-PCR detection of oncofetal fibronectin mRNA were compared with cytological diagnoses. Thirty-five (94.6%) of 37 samples that were diagnosed as papillary or anaplastic carcinomas by cytological examination showed a positive result by gene diagnosis, whereas only 4 (3.7%) of 109 samples that were cytologically diagnosed negative for both carcinomas showed a positive result. Among all of the cases, 50 patients underwent surgery, and a histological diagnosis was consequently made. The sensitivity and specificity of this method were 96.9 and 100%, respectively. A combined examination using both genetic and cytological approaches may contribute to a more precise preoperative diagnosis of papillary and anaplastic carcinomas.
Superparamagnetic Iron Oxide–enhanced MR Imaging of Head and Neck Lymph Nodes (2002)

SPIO-enhanced MR imaging has an important effect on planning the extent of surgery. On a patient basis, SPIO-enhanced MR images compared well with resected specimens.
Botulinum toxin type B: a new injectable treatment for cervical dystonia (2001)

Cervical dystonia (CD) causes involuntary muscle spasms and is often associated with pain. Recently, botulinum toxin type B (BTX-B) (Myobloc, Elan South San Francisco, CA, USA) was approved for general use in the treatment of CD in the USA. In two large pivotal trials, BTX-B was found to be safe and effective in decreasing the movements, pain and disability associated with CD. Benefits were noted both in patients who no longer respond and in those who continue to respond to botulinum toxin type A (BTX-A). BTX-B offers an additional therapeutic option for patients with CD.
Neutrophils Are Required for Endotoxin-Induced Myocardial Cross-Tolerance to Ischemia-Reperfusion Injury (1996)

(1) Sublethal endotoxin induces myocardial cross-tolerance to I/R; (2) PMN induction is required for endotoxin-mediated myocardial resistance to I/R; and (3) while myocardial I/R injury is equally severe after antibody-mediated PMN depletion, endotoxin-induced tolerance to I/R does not occur in the neutropenic host.
Selective RNA amplification: a novel method using dUMP-containing primers and uracil DNA glycosylase. (1993)

The application of PCR to a wide variety of biological problems and molecular techniques has gained wide acceptance. RNA-PCR, a technique in which first-strand cDNA synthesis is followed by PCR amplification, has enabled detection and characterization of rare transcripts. One problem confronting the researcher involves specific amplification of transcribed sequences in the presence of small amounts of genomic DNA of identical sequence. We describe a novel technique, selective RNA amplification, which will specifically amplify RNA sequences in a background of homologous DNA. The method involves first-strand cDNA synthesis from a specific dUMP-containing oligonucleotide that contains unique user-defined 5' sequence (adapter sequence) not found in the message of interest. RNA template is degraded using RNase H, which is specific for RNA/DNA hybrids. This is followed by second-strand synthesis using a gene-specific primer (GSP). The original adapter primer is digested with uracil DNA glycosylase (UDG) to prevent its participation in subsequent amplification. PCR is then performed using the GSP and a second primer corresponding to the unique adapter sequence. In this paper, we apply this method to the amplification of RNA derived from human papilloma virus sequences. Using Southern analysis, we demonstrate specific amplification of 10(5) molecules of an in vitro-transcribed RNA. Denatured DNA of identical sequence and concentration was not amplified using the RNA-specific method. The method could eliminate the need for stringent purification of RNA and enables amplification of rare messages from RNA preparations containing homologous DNA of identical sequence and size.
Epothilones, a new class of microtubule-stabilizing agents with a taxol-like mechanism of action. (1995)

Tubulin polymerization into microtubules is a dynamic process, with the equilibrium between growth and shrinkage being essential for many cellular processes. The antineoplastic agent taxol hyperstabilizes polymerized microtubules, leading to mitotic arrest and cytotoxicity in proliferating cells. Using a sensitive filtration-calorimetric assay to detect microtubule nucleating activity, we have identified epothilones A and B as compounds that possess all the biological effects of taxol both in vitro and in cultured cells. The epothilones are equipotent and exhibit kinetics similar to taxol in inducing tubulin polymerization into microtubules in vitro (filtration, light scattering, sedimentation, and electron microscopy) and in producing enhanced microtubule stability and bundling in cultured cells. Furthermore, these 16-membered macrolides are competitive inhibitors of [3H]taxol binding, exhibiting a 50% inhibitory concentration almost identical to that of taxol in displacement competition assays. Epothilones also cause cell cycle arrest at the G2-M transition leading to cytotoxicity, similar to taxol. In contrast to taxol, epothilones retain a much greater toxicity against P-glycoprotein-expressing multiple drug resistant cells. Epothilones, therefore, represent a novel structural class of compounds, the first to be described since the original discovery of taxol, which not only mimic the biological effects of taxol but also appear to bind to the same microtubule-binding site as taxol.
Label-free probing of the binding state of DNA by time-domain terahertz sensing (2000)

We present a promising approach for the label-free characterization of genetic material. Time-resolved terahertz (THz) transmission analysis of polynucleotides demonstrate a strong dependence of the complex refractive index on the binding state (hybridized/denatured) of deoxyribonucleic acid (DNA) molecules. By monitoring THz transients, one can thus infer the binding state of oligo- and polynucleotides, and hence identify polynucleotides by detecting the binding of unknown polynucleotide DNA sequences to known probe molecules. A broadband experimental demonstration in a free-space configuration, as well as a discussion of the potential application for next generation gene chips is presented.
Semantic texton forests for image categorization and segmentation (2008)

We propose semantic texton forests, efficient and powerful new low-level features. These are ensembles of decision trees that act directly on image pixels, and therefore do not need the expensive computation of filter-bank responses or local descriptors. They are extremely fast to both train and test, especially compared with k-means clustering and nearest-neighbor assignment of feature descriptors. The nodes in the trees provide (i) an implicit hierarchical clustering into semantic textons, and (ii) an explicit local classification estimate. Our second contribution, the bag of semantic textons, combines a histogram of semantic textons over an image region with a region prior category distribution. The bag of semantic textons is computed over the whole image for categorization, and over local rectangular regions for segmentation. Including both histogram and region prior allows our segmentation algorithm to exploit both textural and semantic context. Our third contribution is an image-level prior for segmentation that emphasizes those categories that the automatic categorization believes to be present. We evaluate on two datasets including the very challenging VOC 2007 segmentation dataset. Our results significantly advance the state-of-the-art in segmentation accuracy, and furthermore, our use of efficient decision forests gives at least a five-fold increase in execution speed.
Discovery, Synthesis, and Biological Evaluation of Thiazoloquin(az)olin(on)es as Potent CD38 Inhibitors (2015)

A series of thiazoloquin(az)olinones were synthesized and found to have potent inhibitory activity against CD38. Several of these compounds were also shown to have good pharmacokinetic properties and demonstrated the ability to elevate NAD levels in plasma, liver, and muscle tissue. In particular, compound 78c was given to diet induced obese (DIO) C57Bl6 mice, elevating NAD > 5-fold in liver and >1.2-fold in muscle versus control animals at a 2 h time point. The compounds described herein possess the most potent CD38 inhibitory activity of any small molecules described in the literature to date. The inhibitors should allow for a more detailed assessment of how NAD elevation via CD38 inhibition affects physiology in NAD deficient states.
Monitoring and control of ATM networks using special cells (1996)

This article describes a framework for monitoring and controlling ATM networks based on the use of management cells. By management cells we refer to a broad class of special cells that circulate around the network to perform a variety of useful functions for monitoring and optimizing the operation of the network. The proposed framework includes current ATM-layer OAM (operations and maintenance) methods as well as new mechanisms for more sophisticated long-term network management. This article explores various existing and new uses of management cells for performance monitoring, traffic control, fault management, and network administration.
Variation of 25-hydroxyvitamin D3 and 25-hydroxyvitamin D2 levels in human plasma obtained from 758 Japanese healthy subjects. (1983)

Plasma levels of 25-hydroxyvitamin D3 (25-OH-D3) and 25-hydroxyvitamin D2 (25-OH-D2) in 758 Japanese healthy subjects (most of them adults) were determined by a high-performance liquid chromatographic method previously reported (6) and the following results were obtained: The mean and standard deviation (M +/- SD) of the assayed values of 25-OH-D (sum of 25-OH-D3 and 25-OH-D2) was 23.8 +/- 10.1 ng/ml. 25-OH-D3 was detected in all the samples and the M +/- SD was 23.0 +/- 10.1 ng/ml. The plasma levels clearly showed the seasonal variation that the levels in summer were significantly higher than those in winter. Moreover, the plasma levels were significantly correlated with the amounts of UV light in solar radiation. These results strongly suggested that 25-OH-D3 in plasma mainly originated from endogenous vitamin D3 formed by photo-conversion of 7-dehydrocholesterol in skin. 25-OH-D2 was detected only in 18.3% of the plasma samples and the M +/- SD in the detected samples was 4.4 +/- 2.9 ng/ml which was much lower than those of 25-OH-D3. The results suggested that few healthy Japanese are taking daily exogenous vitamin D2 from multivitamin preparations or others. The M +/- SD values of 25-OH-D3 plasma levels in men and women were 26.2 +/- 10.4 and 19.3 +/- 8.0 ng/ml, respectively. The formers were significantly higher than the latters. The results were thought to be due to the reason that men might be outdoors for longer periods than women. When age variation of plasma 25-OH-D3 levels was examined, the levels in the twenties were significantly lower than the other generations. This was confirmed to be due to the low values observed in the female twenties group, but the detailed reason is unclear at the present time. When 4 healthy volunteers were orally administered 400 I.U./day of vitamin D2 every day for 8 weeks, maximum levels (average: 11.5 ng/ml) were observed at the 8 weeks and the levels gradually decreased after stopping the administration. The results suggested that the half life of 25-OH-D2 in plasma might be 4-5 weeks.
Measurement and imaging of birefringent properties of the human cornea with phase-resolved, polarization-sensitive optical coherence tomography (2004)

Optical coherence tomography (OCT) is an emerging technology for high-resolution, noncontact imaging of transparent and scattering media. Polarization-sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that can image birefringent properties of a biological sample. PS-OCT was used to measure and image retardation and birefringent axis orientation of in vitro human cornea. We used a two-channel PS-OCT system employing a phase-sensitive recording of the interferometric signals in two orthogonal polarization channels. Using an algorithm based on a Hilbert transform, it is possible to calculate the retardation and the slow axis orientation of the sample with only a single A-scan per transversal measurement location. While the retardation information is encoded in the amplitude ratio of the two interferometric signals, the axis orientation is encoded entirely in their phase difference. We present maps of retardation and the distribution of slow axis orientation of the human cornea in longitudinal cross-sections and en face images obtained at the back surface of the cornea. The retardation increases in a radial direction and with depth; the slow axis varies in the transversal direction. Knowledge of the retardation and the slow axis distribution of the cornea might improve nerve fiber polarimetry for glaucoma diagnostics and could be useful for diagnosing different types of pathologies of the cornea.
Novel Experimental and Clinical Therapeutic Uses of Low-Molecular-Weight Heparin/Protamine Microparticles (2012)

Low-molecular-weight heparin/protamine microparticles (LMW-H/P MPs) were produced as a carrier for heparin-binding growth factors (GFs) and for various adhesive cells. A mixture of low-molecular-weight heparin (MW: approximately 5000 Da, 6.4 mg/mL) and protamine (MW: approximately 3000 Da, 10 mg/mL) at a ratio of 7:3 (vol:vol) yields a dispersion of microparticles (0.5-3 µm in diameter). LMW-H/P MPs immobilize, control the release and protect the activity of GFs. LMW-H/P MPs can also bind to cell surfaces, causing these cells to interact with the LMW-H/P MPs, inducing cells/MPs-aggregate formation and substantially promoting cellular viability. Furthermore, LMW-H/P MPs can efficiently bind to tissue culture plates and retain the binding of important GFs, such as fibroblast growth factor (FGF)-2. The LMW-H/P MPs-coated matrix with various GFs or cytokines may provide novel biomaterials that can control cellular activity such as growth and differentiation. Thus, LMW-H/P MPs are an excellent carrier for GFs and various cells and are an efficient coating matrix for cell cultures.
Role of Gastrointestinal Hormones in the Proliferation of Normal and Neoplastic Tissues (2003)

Gastrointestinal (GI) hormones are chemical messengers that regulate the physiological functions of the intestine and pancreas, including secretion, motility, absorption, and digestion. In addition to these well-defined physiological effects, GI hormones can stimulate proliferation of the nonneoplastic intestinal mucosa and pancreas. Furthermore, in an analogous fashion to breast and prostate cancer, certain GI cancers possess receptors for GI hormones; growth can be altered by administration of these hormones or by blocking their respective receptors. The GI hormones that affect proliferation, either stimulatory or inhibitory, include gastrin, cholecystokinin, gastrin-releasing peptide, neurotensin, peptide YY, glucagon-like peptide-2, and somatostatin. The effects of these peptides on normal and neoplastic GI tissues will be described. Also, future perspectives and potential therapeutic implications will be discussed.
An initial demonstration of underwater acoustic communication using time reversal (2002)

In July 1999, an at-sea experiment to measure the focus of a 3.5-kHz centered time-reversal mirror (TRM) was conducted in three different environments: an absorptive bottom, a reflective bottom, and a sloping bottom. The experiment included a preliminary exploration of using a TRM to generate binary-phase shift keying communication sequences in each of these environments. Broadside communication transmissions were also made, and single-source communications were simulated using the measured-channel response. A comparison of the results is made and time reversal is shown to be an effective approach for mitigating inter-symbol interference caused by channel multipath.
Gas-phase production of carbon single-walled nanotubes from carbon monoxide via the HiPco process: A parametric study (2001)

We have demonstrated large-scale production (10 g/day) of high-purity carbon single-walled nanotubes (SWNTs) using a gas-phase chemical-vapor-deposition process we call the HiPco process. SWNTs grow in high-pressure (30–50 atm), high-temperature (900–1100 °C) flowing CO on catalytic clusters of iron. The clusters are formed in situ: Fe is added to the gas flow in the form of Fe(CO)5. Upon heating, the Fe(CO)5 decomposes and the iron atoms condense into clusters. These clusters serve as catalytic particles upon which SWNT nucleate and grow (in the gas phase) via CO disproportionation: CO+CO⇒CO2+C(SWNT). SWNT material of up to 97 mol % purity has been produced at rates of up to 450 mg/h. The HiPco process has been studied and optimized with respect to a number of process parameters including temperature, pressure, and catalyst concentration. The behavior of the SWNT yield with respect to various parameters sheds light on the processes that currently limit SWNT production, and suggests ways that the production rate can be increased still further.
Sequence Analysis on Microcomputers (1987)

Overall, each of the program packages performed their tasks satisfactorily. For analyses where there was a well-defined answer, such as a search for a restriction site, there were few significant differences between the program sets. However, for tasks in which a degree of flexibility is desirable, such as homology or similarity determinations and database searches, DNASTAR consistently afforded the user more options in conducting the required analysis than did the other two packages. However, for laboratories where sequence analysis is not a major effort and the expense of a full sequence analysis workstation cannot be justified, MicroGenie and IBI-Pustell offer a satisfactory alternative. MicroGenie is a polished program system. Many may find that its user interface is more "user friendly" than the standard menu-driven interfaces. Its system of filing sequences under individual passwords facilitates use by more than one person. MicroGenie uses a hardware device for software protection that occupies a card slot in the computer on which it is used. Although I am sympathetic to the problem of software piracy, I feel that a less drastic solution is in order for a program likely to be sharing limited computer space with other software packages. The IBI-Pustell package performs the required analysis functions as accurately and quickly as MicroGenie but it lacks the clearness and ease of use. The menu system seems disjointed, and new or infrequent users often find themselves at apparent "dead-end menus" where the only clear alternative is to restart the entire program package. It is suggested from published accounts that the user interface is going to be upgraded and perhaps when that version is available, use of the system will be improved. The documentation accompanying each package was relatively clear as to how to run the programs, but all three packages assumed that the user was familiar with the computational techniques employed. MicroGenie and IBI-Pustell further complicated their documentation by mixing instructions for the version based on floppy disk operation with that for the hard disk version.(ABSTRACT TRUNCATED AT 400 WORDS)
alpha Subunit of rat pituitary glycoprotein hormones. Primary structure of the precursor determined from the nucleotide sequence of cloned cDNAs. (1982)

Double-stranded complementary DNAs were constructed enzymatically from polyadenylated RNA extracted from pituitary glands of ovariectomized rats, were inserted into the Pst I site of plasmid pBR322 and were cloned in Escherichia coli chi 1776. Cloned cDNAs encoding the precursor to the alpha subunit (pre-alpha) of the glycoprotein hormones were identified by hybridization with a restriction fragment of a previously cloned and sequenced cDNA encoding the precursor to the alpha subunit of mouse thyrotropin (Chin, W. W., Kronenberg, H. M., Dee, P. C., Maloof, F., and Habener, J. F. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 5329-5333). The DNA sequences of the two largest rat cDNA inserts (591 and 554 base pairs) were determined and the amino acid sequence of the rat pre-alpha subunit was deduced from these sequences. The composite sequence determined from these cDNAs spans 610 base pairs, or almost the entire length of the messenger RNA (mRNA) of 800 bases, when account is taken of the 3' poly(A) tract. The rat alpha precursor consists of a 24 amino acid leader sequence and a 96 amino acid alpha subunit apoprotein. The amino acid homologies between the rat and mouse, and between the rat and human sequences are 95% and 74%, respectively. Nucleotide homologies between the rat and mouse cDNAs in the coding and untranslated regions are 94% and 80%, respectively. This cloned cDNA will be applied to analysis of the structure of the rat alpha subunit gene(s) and of the regulation of alpha subunit gene expression.
Structural relationships and the classification of aminoacyl-tRNA synthetases. (1991)

The aminoacyl-tRNA synthetases are a family of 20 enzymes that catalyze the same two-step chemical reaction,
The kinematics of the swing phase obtained from accelerometer and gyroscope measurements (2002)

The kinematics needed to calculate the knee moment during the initial swing phase were obtained from a set of eight leg-mounted uni-axial accelerometers and two gyroscopes. The angular and linear accelerations of shank and thigh were calculated from the signals of two accelerometers mounted on each of the leg segments directed tangentially and radially to the movement. The angular velocities of shank and thigh were measured by the gyroscopes. The absolute angles of shank and thigh were obtained by integration of the gyroscope signal plus an added offset angle, estimated from radial and tangential accelerometer signals registered while standing. Movement was assumed to be in the saggital plane. The accuracy of the quantities found from the leg mounted sensors was calculated in terms of correlation and the RMS error by comparing against measurements obtained by a VICON/sup TM/ system. The results were indistinguishable. The system was later applied in research measurements.
A new allele of the sparse fur gene in the mouse (1974)

Journal Article A new allele of the sparse fur gene in the mouse Get access D. P. DOOLITTLE, D. P. DOOLITTLE Associate professor of animal sciences Animal sciences, Purdue UniversityLafayette, Indiana 47907 Search for other works by this author on: Oxford Academic PubMed Google Scholar LINDA L. HULBERT, LINDA L. HULBERT Former graduate assistant Search for other works by this author on: Oxford Academic PubMed Google Scholar COLLEEN CORDY COLLEEN CORDY Former student NSF Life Science Summer Training ProgramPurdue Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 65, Issue 3, May 1974, Pages 194–195, https://doi.org/10.1093/oxfordjournals.jhered.a108500 Published: 01 May 1974