gebhart/patrepeval huggingface dataset:
The X as Model for RNA's Niche in Epigenomic Regulation (2010)

The X-linked region now known as the "X-inactivation center" (Xic) was once dominated by protein-coding genes but, with the rise of Eutherian mammals some 150-200 million years ago, became infiltrated by genes that produce long noncoding RNA (ncRNA). Some of the noncoding genes have been shown to play crucial roles during X-chromosome inactivation (XCI), including the targeting of chromatin modifiers to the X. The rapid establishment of ncRNA hints at a possible preference for long transcripts in some aspects of epigenetic regulation. This article discusses the role of RNA in XCI and considers the advantages RNA offers in delivering allelic, cis-limited, and locus-specific control. Unlike proteins and small RNAs, long ncRNAs are tethered to the site of transcription and effectively tag the allele of origin. Furthermore, long ncRNAs are drawn from larger sequence space than proteins and can mark a unique region in a complex genome. Thus, like their small RNA cousins, long ncRNAs may emerge as versatile and powerful regulators of the epigenome.
Models of DNA structure achieve almost perfect discrimination between normal prostate, benign prostatic hyperplasia (BPH), and adenocarcinoma and have a high potential for predicting BPH and prostate cancer (1997)

In our previous studies of DNA, wavenumber-absorbance relationships of infrared spectra analyzed by principal components analysis (PCA) were expressed as points in space. Each point represented a highly discriminating measure of structural modifications that altered vibrational and rotational motion, thus changing the spatial orientation of the points. PCA/Fourier transform-infrared technology has now provided a virtually perfect separation of clusters of points representing DNA from normal prostate tissue, BPH, and adenocarcinoma. The findings suggest that the progression of normal prostate tissue to BPH and to prostate cancer involves structural alterations in DNA that are distinctly different. The hydroxyl radical is likely a major contributor to these structural alterations, which is consistent with previous studies of breast cancer. Models based on logistic regression of infrared spectral data were used to calculate the probability of a tissue being BPH or adenocarcinoma. The models had a sensitivity and specificity of 100% for classifying normal vs. cancer and normal vs. BPH, and close to 100% for BPH vs. cancer. Thus, the PCA/Fourier transform-infrared technology was shown to be a powerful means for discriminating between normal prostate tissue, BPH and prostate cancer and has considerable promise for risk prediction and clinical application.
Large-scale wireless LAN design (2001)

The design of a large-scale wireless LAN poses a number of interesting questions. Building the Wireless Andrew network at Carnegie Mellon University has given us the opportunity to deal with these questions. This article describes the approaches we have developed for the design of similar networks. A large-scale wireless LAN must be designed so that all of the target space has radio coverage (i.e., there are no coverage gaps). It must also be designed so that its capacity is adequate to carry the expected load. These requirements generally can be met by using the proper combination of access point locations, frequency assignments, and receiver threshold settings.
A Five-Year Experience With the Bovine Heterograft for Vascular Access (1986)

We retrospectively analyzed 385 bovine heterografts inserted in 331 patients receiving dialysis to determine patency and complication rates. Eighty-two grafts were inserted in diabetics, 303 in nondiabetics; 129 were primary grafts, 256 secondary. There were 251 "distal" grafts using the distal radial artery and 134 "proximal" grafts using the distal brachial artery (127 grafts) or the superficial femoral artery (seven grafts). During this five-year interval, 209 complications were identified with the most prevalent being thrombosis (160), aneurysms (18), and puncture site (18) or wound (eight) infections. An aggressive surgical approach to these complications prolonged graft patency, as evidenced by only 82 irreversible graft failures. The overall patency rate at one through four years was 79%, 69%, 63%, and 51% respectively. One- and two-year patency for diabetics (81%, 74%) vs nondiabetics (78%, 70%), primary (85%, 77%) vs secondary grafts (73%, 64%), and proximal (80%, 66%) vs distal grafts (75%, 64%) were not significantly different. Long-term patency was unaffected by diabetes, previous access procedures, or graft location.
Overexpression of IGF-I in skeletal muscle of transgenic mice does not prevent unloading-induced atrophy (1998)

This study examined the association between local insulin-like growth factor I (IGF-I) overexpression and atrophy in skeletal muscle. We hypothesized that endogenous skeletal muscle IGF-I mRNA expression would decrease with hindlimb unloading (HU) in mice, and that transgenic mice overexpressing human IGF-I (hIGF-I) specifically in skeletal muscle would exhibit less atrophy after HU. Male transgenic mice and nontransgenic mice from the parent strain (FVB) were divided into four groups (n = 10/group): 1) transgenic, weight-bearing (IGF-I/WB); 2) transgenic, hindlimb unloaded (IGF-I/HU); 3) nontransgenic, weight-bearing (FVB/WB); and 4) nontransgenic, hindlimb unloaded (FVB/HU). HU groups were hindlimb unloaded for 14 days. Body mass was reduced (P < 0.05) after HU in both IGF-I (-9%) and FVB mice (-13%). Contrary to our hypothesis, we found that the relative abundance of mRNA for the endogenous rodent IGF-I (rIGF-I) was unaltered by HU in the gastrocnemius (GAST) muscle of wild-type FVB mice. High-level expression of hIGF-I peptide and mRNA was confirmed in the GAST and tibialis anterior (TA) muscles of the transgenic mice. Nevertheless, masses of the GAST and TA muscles were reduced (P < 0.05) in both FVB/HU and IGF-I/HU groups compared with FVB/WB and IGF-I/WB groups, respectively, and the percent atrophy in mass of these muscles did not differ between FVB and IGF-I mice. Therefore, skeletal muscle atrophy may not be associated with a reduction of endogenous rIGF-I mRNA level in 14-day HU mice. We conclude that high local expression of hIGF-I mRNA and peptide in skeletal muscle alone cannot attenuate unloading-induced atrophy of fast-twitch muscle in mice.
The primary structures of two yeast enolase genes. Homology between the 5' noncoding flanking regions of yeast enolase and glyceraldehyde-3-phosphate dehydrogenase genes. (1981)

Segments of yeast genomic DNA containing two enolase structural genes have been isolated by subculture cloning procedures using a cDNA hybridization probe synthesized from purified yeast enolase mRNA. Based on restriction endonuclease and transcriptional maps of these two segments of yeast DNA, each hybrid plasmid contains a region of extensive nucleotide sequence homology which forms hybrids with the cDNA probe. The DNA sequences which flank this homologous region in the two hybrid plasmids are nonhomologous indicating that these sequences are nontandemly repeated in the yeast genome. The complete nucleotide sequence of the coding as well as the flanking noncoding regions of these genes has been determined. The amino acid sequence predicted from one reading frame of both structural genes is extremely similar to that determined for yeast enolase (Chin, C. C. Q., Brewer, J. M., Eckard, E., and Wold, F. (1981) J. Biol. Chem. 256, 1370-1376), confirming that these isolated structural genes encode yeast enolase. The nucleotide sequences of the coding regions of the genes are approximately 95% homologous, and neither gene contains an intervening sequence. Codon utilization in the enolase genes follows the same biased pattern previously described for two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes (Holland, J. P., and Holland, M. J. (1980) J. Biol. Chem. 255, 2596-2605). DNA blotting analysis confirmed that the isolated segments of yeast DNA are colinear with yeast genomic DNA and that there are two nontandemly repeated enolase genes per haploid yeast genome. The noncoding portions of the two enolase genes adjacent to the initiation and termination codons are approximately 70% homologous and contain sequences thought to be involved in the synthesis and processing messenger RNA. Finally there are regions of extensive homology between the two enolase structural genes and two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes within the 5- noncoding portions of these glycolytic genes.
A high performance epitaxial SiGe-base ECL BiCMOS technology (1992)

In this work we present a high speed, self-aligned SiGe epitaxial-base ECL BiCMOS technology in which we achieved a record 18.9 ps ECL gate delay at 7.7 mW, 59 GHz peak f/sub max/, 50 GHz peak f/sub T/, and 0.25 mu m-channel CMOS devices with transconductances of 240 mS/mm for the nFET and 140 mS/mm for the pFET. Key technology features include a dielectric-filled deep and shallow trench isolation, a polysilicon-emitter SiGe-epitaxial-base NPN, a low-thermal-cycle 0.25 mu m-channel CMOS, a self-aligned silicide on extrinsic base and Source/Drain/Gate, a thin Ti/W local interconnect combined with two metal levels of AlCu, a nitride/oxide decoupling capacitor, and polysilicon resistors. This BiCMOS process is the highest level of integration and performance yet achieved in a SiGe-base technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Antitumor activity of NKG2D CAR-T cells against human colorectal cancer cells in vitro and in vivo. (2019)

Colorectal cancer is one of the most common malignancies worldwide, as it is often diagnosed at an advanced stage. Chimeric antigen receptor (CAR) T cell therapy has demonstrated remarkable success and emerged as one of the most promising therapeutic strategies in multiple malignancies. The purpose of this study was to investigate the anti-tumor activity of NKG2D CAR-T cells against human colorectal cancer cells. A non-viral third-generation NKG2D CAR was constructed, and subsequently transduced into T cells to obtain the NKG2D CAR-T cells. In vitro, NKG2D CAR-T cells showed cytotoxicity against human colorectal cancer cells in a dose-dependent manner compared with untransduced T cells. In addition, IL-2 and IFN-γ secreted by these cells were significantly higher than those by untransduced T cells. In vivo, NKG2D CAR-T cells significantly suppressed tumor growth, reduced tumor sizes and extended overall survival of mice in a xenograft model of HCT-116 cells. Furthermore, human NKG2D-positive lymphocytes infiltration could be found in the tumor sections of NKG2D CAR-T cells-treated mice. There were no severe pathological changes found in vital organs in any of the treatment groups. NKG2D CAR-T cells showed excellent killing effect and represented a promising immunotherapeutic strategy against human colorectal cancer.
The KryptoKnight family of light-weight protocols for authentication and key distribution (1995)

An essential function for achieving security in computer networks is reliable authentication of communicating parties and network components. Such authentication typically relies on exchanges of cryptographic messages between the involved parties, which in turn implies that these parties be able to acquire shared secret keys or certified public keys. Provision of authentication and key distribution functions in the primitive and resource-constrained environments of low-function networking mechanisms, portable, or wireless devices presents challenges in terms of resource usage, system management, ease of use, efficiency, and flexibility that are beyond the capabilities of previous designs such as Kerberos or X.509. This paper presents a family of light-weight authentication and key distribution protocols suitable for use in the low layers of network architectures. All the protocols are built around a common two-way authentication protocol. The paper argues that key distribution may require substantially different approaches in different network environments and shows that the proposed family of protocols offers a flexible palette of compatible solutions addressing many different networking scenarios. The mechanisms are minimal in cryptographic processing and message size, yet they are strong enough to meet the needs of secure key distribution for network entity authentication. The protocols presented have been implemented as part of comprehensive security subsystem prototype called KryptoKnight.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Interstitial delivery of dexamethasone in the brain for the reduction of peritumoral edema (1991)

Controlled-release polymers have facilitated the interstitial delivery of drugs within the central nervous system. In the present study, dexamethasone was incorporated into ethylene-vinyl acetate polymers, which were then implanted adjacent to a 9L gliosarcoma in the brain of Fischer 344 rats. The effect of interstitial delivery of dexamethasone on peritumoral edema was assessed and compared to the effect of dexamethasone delivered systemically. Eighty-five rats underwent intracranial implantation of the 9L gliosarcoma. Five days later, the animals were randomly assigned to one of four treatment groups: Group 1 received intracranial implantation of controlled-release polymers containing dexamethasone; Group 2 received intraperitoneal implantation of controlled-release polymers containing dexamethasone; Group 3 received serial intraperitoneal injections of dexamethasone; and Group 4 received sham treatment. The animals were sacrificed 3 days after initiation of therapy and their brains were removed for measurement of the water content (edema) in the tumor-bearing and contralateral hemispheres. Brain and plasma samples were analyzed by reverse-phase high-performance liquid chromatography to determine the tissue and plasma concentrations of dexamethasone. Measurement of the release kinetics of dexamethasone from the ethylene-vinyl acetate polymers in an in vitro system showed that the drug was released in a controlled, tapering fashion. During the first 3 days of controlled release in vitro, 330 micrograms of a total content of 7.5 mg of dexamethasone was released into the medium. Analysis of tissue for drug levels demonstrated, however, that the interstitial delivery of this fractional amount of dexamethasone within the brain resulted in levels 19 times higher than those achieved by administering the full dose of 7.5 mg systemically over a 3-day period. Conversely, the systemic administration of dexamethasone resulted in plasma levels 16 times higher than those measured in the interstitial delivery of dexamethasone in the brain. Brain-water content determinations showed that the interstitial controlled release of the fractional amount of dexamethasone within the brain was as effective in controlling peritumoral edema as systemic administration of the full dose by serial intraperitoneal injections. The study demonstrates the following: 1) controlled-release polymeric carriers deliver biologically active dexamethasone in a sustained fashion; 2) very high concentrations of dexamethasone in brain tissue can be achieved using interstitial polymer-mediated drug delivery while minimizing plasma concentrations of this drug which are sometimes associated with serious systemic side effects; and 3) peritumoral brain edema can be effectively treated by the interstitial delivery of dexamethasone directly within the tumor bed.
Low molecular weight bioactive peptides derived from the enzymatic hydrolysis of collagen after isoelectric solubilization/precipitation process of turkey by-products (2014)

A process based on the isoelectric solubilization/precipitation (ISP) method was developed to recover collagen from low value poultry by-products. The application of the ISP process to turkey heads generated protein isolates and an insoluble biomass that was used to extract collagen. Isolated turkey head collagen was then enzymatically hydrolyzed for different time periods using alcalase, flavorzyme, and trypsin. The enzymatic hydrolysis approaches consisted of digesting collagen with each one of the 3 enzymes alone (alcalase, flavorzyme, or trypsin), or one of the 3 combinations of 2 enzymes (alcalase/flavorzyme, alcalase/trypsin, or flavorzyme/trypsin), or a cocktail of all 3 enzymes together (alcalase/flavorzyme/trypsin). The molecular weight distribution of turkey head collagen hydrolysates was determined using size exclusion chromatography and matrix-assisted laser desorption ionization-time of flight-mass spectrometry. The enzyme cocktail produced collagen hydrolysates with the greatest amount of low molecular weight peptides ranging from 555.26 to 2,093.74 Da. These collagen peptides showed excellent solubility over a wide pH range (2 -: 8) and were able to bind cholic and deoxycholic acids and significantly (P < 0.05) inhibited plasma amine oxidase in a dose- and time-dependent manner. The ISP process combined with enzyme cocktail hydrolysis represents a potential new way to produce low molecular weight bioactive collagen peptides from low value poultry by-products.
1α,25-Dihydroxycholecalciferol Receptors in Intestine (1974)

Abstract Vitamin D3 (cholecalciferol) is known to be metabolized to 1α,25-dihydroxycholecalciferol, and this sterol is thought to be the active form of the vitamin. The present report shows that administration of increasing amounts of radioactive vitamin D3 to vitamin D-deficient chicks results in a saturable binding of 1α,25-dihydroxycholecalciferol to the intestinal chromatin that parallels saturation of the calcium absorption response. The appearance of 1α,25-dihydroxycholecalciferol in the chromatin precedes the calcium absorption response by 2 to 8 hours after a physiologic dose of 1α,25-dihydroxycholecalciferol. This sterol also specifically associates with the chromatin fraction after incubation with intestinal mucosa homogenates in vitro. The chromatin fraction contains a finite number of binding sites for 1α,25-dihydroxycholecalciferol, and closely related sterols such as 25-hydroxycholecalciferol in equal concentration do not bind to this fraction; however, displacement of the hormone from the receptor can be achieved by concentrations of cholecalciferol = dihydrotachysterol2 >> 1α-hydroxycholecalciferol g 25-hydroxycholecalciferol >> 1α,25-dihydroxycholecalciferol. Pretreatment of rachitic chicks with unlabeled vitamin D3 or 1α,25-dihydroxycholecalciferol reduced the subsequent binding of radioactive 1α,25-dihydroxycholecalciferol to the intestinal chromatin in vitro. It is concluded that localization of the apparent hormonal form of vitamin D3, 1α,25-dihydroxycholecalciferol, in the nucleus of the target tissue is probably involved in the physiologic response of calcium transport.
Simple method for the quantification of milk fat content in foods by LC-APCI-MS/MS using 1,2-dipalmitoyl-3-butyroyl-glycerol as an indicator (2013)

We have developed a simple method for the quantification of milk fat in foods using 1,2-dipalmitoyl-3-butyroyl-glycerol (PPBu) as an indicator of milk fat content by high-performance liquid chromatography coupled with atmospheric pressure chemical ionization tandem mass spectrometry. The separation of the triacylglycerol positional isomer, 1,3-dipalmitoyl-2-butyroyl-glycerol (PBuP) and PPBu, was achieved using an octacocyl silylation (C28) column, and multiple reaction monitoring was employed. The milk fat contents in butter, butter-blended margarine, and butter cookies were quantified using two different sample preparation methods. In the first method (Method A), the lipid in the food was extracted with organic solvents and used for the preparation of a sample solution. In the other method (Method B), the sample solution was prepared by dissolving the food in organic solvents; the PPBu content in the fat and oil was corrected by the lipid content in the food obtained by the rapid NMR method. The calibration curve of standard PPBu was a first-order equation over the range of 1-250 µg/mL. The recovery rates of PPBu spiked into butter evaluated by Methods A and B were 99.9-105.0% and 106.5-110.1%, respectively. PBuP was not detected in milk fat. The milk fat contents in blends of butter and margarine determined by the method developed in this study were equivalent to the contents calculated with the butyric acid (Bu) method using GC-FID. The milk fat contents in butter-blended margarine analyzed by Methods A and B were almost the same. The PPBu content in blends of butter and margarine was correlated with the butter content. Thus, we succeeded in developing an efficient method for the rapid quantification of milk fat content and the detection of milk fat adulteration.
Emulsion‐Based Pressure‐Sensitive Adhesives: A Review (2004)

Abstract Pressure sensitive adhesives (PSAs) adhere instantaneously to a variety of surfaces upon application of slight pressure and can be obtained using different technologies. Increasing environmental concerns and regulations are the major driving forces for the development of emulsion‐based PSAs. Given the number of factors affecting the emulsion polymerization process and versatility of emulsion‐based polymers, there is a need to identify and model those factors that significantly influence particular PSA applications. In this review, factors such as emulsion polymerization components, latex rheology, and film formation are examined in light of their relevance to adhesion. In addition, the body of knowledge related to measurement methods, design factors, and modeling of each of the three major PSA performance characteristics (i.e., tack, peel strength, and shear strength) is reviewed with a particular emphasis on emulsion‐based PSAs. Keywords: Pressure sensitive adhesivesEmulsion polymerizationPeel strengthTackShear strength
Fibrosis and hypertensive heart disease (2000)

The normal myocardium is composed of a variety of cells: cardiac myocytes and noncardiomyocytes, which include endothelial and vascular smooth muscle cells and fibroblasts. Hypertensive heart disease involves a structural remodeling of muscular and nonmuscular compartments. It is not the quantity but rather the quality of myocardium that accounts for pathologic hypertrophy and predisposes to ventricular dysfunction and arrhythmias, which, in turn, confer increased risk of adverse cardiovascular events. Herein, factors regulating growth of these compartments are reviewed and in particular signals involved in promoting adverse remodeling of intramyocardial coronary arteries and arterioles by fibrous tissue.
Three-dimensional imaging of living neurons and glia with the atomic force microscope (1993)

The atomic force microscope (AFM) was used to directly image hippocampal neurons and glia. Using chemically fixed and living cells it was possible to reconstruct three-dimensional cell structure and detect sub-cellular features such as the nucleus, mitochondria and filaments. By repeatedly scanning a single living cell we observed the movement of filaments beneath the cell membrane. Furthermore, by controlling the force applied to the scanning tip, nanosurgery was performed to selectively remove cells from the culture substratum. Thus, the atomic force microscope offers the opportunity to gain three-dimensional information about living cells and to observe the behavior of cellular components by imaging through the intact cell membrane.