gebhart/patrepeval huggingface dataset:
Post-transcriptional modifications of mRNA. Purification and characterization of cap I and cap II RNA (nucleoside-2'-)-methyltransferases from HeLa cells. (1981)

The existence in HeLa cell extracts of two separate RNA (nucleoside-2')-methyltransferases involved in the modification of mRNA was established using assays that specifically measure the conversion of cap O [m7G(5')pppNpN-] to cap I [m7G(5')pppNmpN-] and cap I to cap II [m7G(5')pppNmpNm-]. Cap II methyltransferase activity was found almost exclusively in cytoplasmic fractions while cap I methyltransferase activity was also found in the nucleus, its apparent biological site of action. The two enzymes were purified by DEAE-cellulose and phosphocellulose chromatography and their optimal reaction conditions were determined. The substrate specificity of cap I methyltransferase was examined with particular regard to information that would help elucidate the natural order of capping and methylation was drawn from data presented here. Both purine and pyrimidine nucleosides in the N position of M7G(5')pppN- were methylated by purified cap I methyltransferase.
A hyperplane based approach for optimizing spatial locality in loop nests (1998)

This paper presents a data layout optimization technique based on the theory of hyperplanes from linear algebra. Given a program, our framework automatically determines the optimal layouts that can be expressed by hyperplanes for each array that is referenced. We discuss the cases where data transformations are preferable to loop transformations and show that under specific conditions a loop nest can be optimized for perfect spatial locality by using data transformations. We divide the problem of optimizing data layout into two independent subproblems: (1) determining optimal layouts, and (2) determining data transformation matrices to implement optimal layouts. By postponing the determination of the transformation matrix to the last stage, our method can be adapted to compilers with different default layouts. Our results on eight programs on SGI Origin 2000 distributed-shared-memory multiprocessor show that the layout optimizations are effective in optimizing spatial locality.
Cloning, expression, purification, and characterization of LC-1 ScFv with GFP tag (2005)

Total RNA was isolated from the hybridoma cell line (LC-1), which secretes anti-lung adenocarcinoma monoclonal antibody, and was transferred into cDNA. Based on the FR1 (framework region 1) and FR4 conserved regions of LC-1 gene, the variable regions of heavy chain (Vh) and light chain (Vl) were amplified, and the Vh and modified Vl were connected to single chain Fv (ScFv) by SOE-PCR (splice overlap extension PCR). The modified ScFv was fused with green fluorescent protein (GFP) and introduced into E. coli JM109. The fusion protein induced by IPTG (Isopropylthiogalactoside) was about 57000 on a 10% SDS-PAGE gel (10% Sds Polyacrylamide Gel Electrophoresis), and primarily manifested as inclusion bodies. The renatured protein purified by Ni-NTA Superflow resins showed ability to bind to antigen on SPC-A-1 lung adenocarcinoma. In addition, the induced host cells fluoresced bright green under 395 nm wavelength, which indicated that the expected protein with dual activity was expressed in the prokaryotic system. The ScFv with GFP tag used in this research can be applied as a new reagent to detect immunological dye, and provide a feasible way to detect adenocarcinoma in a clinical setting.
Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data (2012)

OPINION article Front. Genet., 31 October 2012 | https://doi.org/10.3389/fgene.2012.00230
Distinct mechanisms of epithelial adhesion for Candida albicans and Candida tropicalis. Identification of the participating ligands and development of inhibitory peptides. (1993)

The yeast Candida albicans is the leading cause of disseminated fungal infection in neonates, immunocompromised hosts, diabetics, and postoperative patients; Candida tropicalis is the second most frequent isolate. Because the integrin analogue in C. albicans shares antigenic, structural, and functional homologies with the beta 2-integrin subunits alpha M and alpha X, we investigated the role of integrin analogues in epithelial adhesion of C. albicans and C. tropicalis. On flow cytometry with the monoclonal antibody (mAb) OKM1, surface fluorescence was highest for C. albicans and significantly reduced for C. tropicalis (P < 0.001). However, adhesion to the human epithelial cell line HeLa S3 did not differ for these two candidal species: specific adhesion was highest for C. albicans at 44.0 +/- 1.8%, and only slightly lower for C. tropicalis at 38.8 +/- 3.6% (P = NS). The disparity between expression of the integrin analogue and epithelial adhesion suggested distinct mechanisms for this process in C. albicans versus C. tropicalis. Preincubation of C. albicans with anti-alpha M mAbs, with purified iC3b (the RGD ligand for the integrin analogue), or with 9-15-mer RGD peptides from iC3b all inhibited epithelial adhesion significantly (P < 0.001-0.04). Purified fibronectin or fibronectin-RGD peptides failed to block C. albicans adhesion. In contrast, epithelial adhesion of C. tropicalis was significantly inhibited by purified fibronectin and its RGD peptides (P < or = 0.021), but not by iC3b nor the iC3b-RGD peptides. Both iC3b and fibronectin were identified on the surface of epithelial cells after growth in serum-free medium. A polyclonal antibody to C3 inhibited C. albicans adhesion while a control antibody to fibronectin was ineffective; the converse was true for C. tropicalis. These results indicate that the pathogenic yeasts C. albicans and C. tropicalis recognize distinct RGD ligands present at the surface of the epithelial cell and that these interactions can be differentially inhibited by defined RGD peptides containing appropriate flanking sequences.
Antibodies for Therapeutic Uses and the Evolution of Biotechniques (2009)

Protein therapeutics are playing an expanding role in modern medicinal chemistry. Among them, native or engineered molecules exploiting the binding and catalytic potential of the immune repertoire form an extremely exciting and emerging business area. They represent by far the single largest category of biopharmaceutical substances under investigation. The fast increase of this pharmaceutical category paralleled the scientific and technical progress from murine to chimeric, humanized and, finally, human engineered antibodies. Indeed, the development of the phage display technology, allowing libraries of shuffled murine or human antibody binding domains to be screened for affinity against a selected target antigen or activity against a specific reaction substrate, open new perspectives, disclosing the opportunity to circumvent restrictions inherent to the in vivo immunisation. Transgenic technology represents another powerful method for generating fully human monoclonal antibodies against a wide variety of drug targets, while recombinant technology continues to evolve, improving the pharmacodynamic and pharmacokinetic properties of antibody therapeutics, with the production of different antibody constructs or formats, such as bispecific antibodies, diabodies and others, and different functional activities, such as catalysis, cellular internalisation and antigen-mimicking. The aim of the present review is to overview native or recombinant antibodies while discussing the underlying antibody technology, with the aim to favour understanding of the antibody therapeutics that are in use or will enter market in the near future.
Differences in genetic diversity of nonecapsulated Haemophilus influenzae from various diseases (1997)

Genetic relationships among 80 isolates of nonencapsulated Haemophilus influenzae recovered from different disease types were determined by multilocus enzyme electrophoresis (MEE) at 13 enzyme loci in an attempt to assess the association between multilocus genotype and disease. The isolates were obtained from 15 patients with meningitis, 10 with otitis media, 19 with chronic bronchitis, 20 with cystic fibrosis, and 16 were obtained from healthy carriers. The 80 isolates were assigned to 69 electrophoretic types (ETs) falling into 5 groups. Isolates from each disease entity were represented by a variety of genotypes; however, cluster analysis from a matrix of genetic distances between ETs revealed that the ETs of the otitis media and meningitis isolates were all clustered within a genetic distance of 0.55 (group I). In addition, no genotypes were shared between H. influenzae carrier isolates and isolates from cases of disease, H. influenzae isolates from healthy individuals were distributed significantly differently from those from chronic bronchitis meningitis and otitis media patients. The genetic diversity (H) of carrier strains was greatest, although not statistically different from that of isolates from patients with disease. It was concluded that the genetic distribution of acute disease isolates is not random over the five ET groups, although the genetic diversity within the groups is not different. The effect of bacterial persistence in the host on the genetic diversity of H. influenzae is discussed.
Targeting NS5B RNA-Dependent RNA Polymerase for Anti-HCV Chemotherapy (2003)

The global prevalence of persistent hepatitis C virus (HCV) infection and the lack of a highly effective and well-tolerated antiviral therapy have spurred intensive efforts to discover and develop novel anti-HCV therapy in the pharmaceutical industry. HCV NS5B RNA-dependent RNA polymerase (RdRp), the centerpiece for viral replication, constitutes a valid target for drug discovery. Compared to the host RNA and DNA polymerases, NS5B RdRp has distinct subcellular localization at the interface of the endoplasmic reticulum (ER) membrane and cytoplasm, a novel catalytic mechanism and many unique structural features, all of which make it an attractive target for developing effective anti-HCV therapeutics. High genetic variation among the major HCV genotypes commands that any efficacious NS5B inhibitors have to be broadly active against NS5Bs from various genotypes. Rapid viral replication and its inherent genetic diversity will certainly culminate drug resistance to any NS5B inhibitors. Therefore, iterative drug design and combination therapies of drugs that intervene with different steps in the HCV replicative cycle are needed to combat the viral infection. Many classes of nucleoside and non-nucleoside inhibitors of NS5B RdRp have been identified and appeared in literatures and patent applications. These progresses hold a considerable promise to the development of novel, specific and highly effective therapeutics to achieve sustained response and ultimately the eradication of HCV infection.
MicroRNAs as Therapeutic Targets and Biomarkers of Cardiovascular Disease (2014)

MicroRNAs play central roles in cardiovascular disease, and their therapeutic manipulation raises exciting opportunities as well as challenges in the path toward clinical development.
Aminoguanidine treatment increases elasticity and decreases fluid filtration of large arteries from diabetic rats. (1993)

The accumulation of advanced glycosylation end-products (AGEs) on collagen and the subsequent stiffening of this matrix protein in diabetes has been described many years ago. Structural modification of collagen in the arterial wall might have important effects on arterial elasticity. Aminoguanidine is known to decrease the formation of AGEs. In this study we evaluated the effects of aminoguanidine treatment on different parameters reflecting arterial wall elasticity in diabetic rats. We demonstrated that treatment of diabetic rats with aminoguanidine resulted in a significant increase in carotid static compliance (+39%, P < 0.01 under control conditions, and +27%, P < 0.01 after abolition of vascular tone by KCN), and a decrease in characteristic aortic input impedance (-40%, P < 0.01). The arterial pulse pressure in aminoguanidine-treated rats was decreased (-15%, P < 0.05) and the pulsatile component of left ventricular power output was relatively diminished (-35%, P < 0.05). In addition, we observed a lower fluid filtration across the carotid wall. These results indicate an increased vascular elasticity, an improved left ventricular-arterial coupling, and a decreased vascular permeability in diabetic rats after aminoguanidine treatment, suggesting that AGE-accumulation on collagen negatively affects arterial wall properties in experimental diabetes.
PROTECTION AGAINST CYTOSINE ARABINOSIDE‐INDUCED ALOPECIA BY MINOXIDIL IN A RAT ANIMAL MODEL (1995)

The mechanism of action of minoxidil in its prevention against Ara-C-induced alopecia is currently unknown. This observation may shed some light on the in vivo mechanism of action of minoxidil and may prove to be important in our efforts to search for agents to prevent alopecia among patients receiving chemotherapy.
VEGF Gene Transfer Reduces Intimal Thickening via Increased Production of Nitric Oxide in Carotid Arteries (1997)

Thickening of the arterial intima and smooth muscle cell (SMC) proliferation remain major problems after vascular surgery and other types of vascular manipulations. We studied the effect of endothelial cell (EC)-specific vascular endothelial growth factor (VEGF) gene transfer on the thickening of the intima using a silicone collar inserted around carotid arteries that acted both as the agent that caused intimal SMC growth and as a reservoir for the transfected gene. The model preserved EC integrity and permitted direct extravascular gene transfer without any intravascular manipulation. Compared to beta-galactosidase (lacZ)-transfected control arteries, plasmid/liposome-mediated VEGF gene transfer significantly reduced intimal thickening 1 week after the gene transfer. Administration to the experimental animals of the nitric oxide (NO) synthase inhibitor L-NAME abolished the difference in intimal thickening between VEGF and lacZ-transfected arteries. Furthermore, VEGF caused NO release from cultured human umbilical vein EC. It is concluded that extravascular VEGF gene transfer attenuates intimal growth and could be useful for the prevention of intimal thickening during vascular surgery. Our results further suggest that VEGF may reduce SMC proliferation via a mechanism that involves VEGF-induced NO production from the endothelium.
Advances in Scalable Video Coding (2004)

Scalable video coding is attractive due to the capability of reconstructing lower resolution or lower quality signals from partial bit streams. This allows for simple solutions in adaptation to network and terminal capabilities. Different modalities of scalability are specified by video coding standards like MPEG-2 and MPEG-4. This paper gives a short overview over these techniques and analyzes in more detail the encoder/decoder drift problem, which is the major reason why scalable coding has been significantly less efficient than single-layer coding in most of these implementations. Only recently, new scalable video coding technology has evolved, which seems to close the gap of compression performance compared to state of the art single-layer video coding. New methods of efficient enhancement layer prediction were developed to improve traditional (motion-compensated hybrid) scalable coders, providing more flexible compromises on the drift problem. As a new technology trend, motion-compensated spatiotemporal wavelet coding has matured which entirely discards the drift and allows most flexible combinations of spatial, temporal, and signal-to-noise ratio (SNR) scalability with fine granularity over a broad range of data rates.
Co-regulation and Physical Association of the 67-kDa Monomeric Laminin Receptor and the α6β4 Integrin (1997)

The interactions between tumor cells and laminin or other components of the extracellular matrix have been shown to play an important role in tumor invasion and metastasis. However, the role of the monomeric 67-kDa laminin receptor (67LR) remains unclear. We analyzed the regulation of 67LR expression under different culture conditions with respect to the expression of other well characterized laminin receptors. In A431 cells treated with laminin for different time periods, the regulation of 67LR expression correlated with expression of the alpha6 integrin subunit but not with the expression of other laminin receptors. Moreover, cytokine treatment resulted in down-modulated expression of the alpha6 integrin subunit and the 67LR. Co-regulation of the expression of the two receptors was further suggested by the observation that specific down-modulation of the alpha6-chain by antisense oligonucleotides was accompanied by a proportional decrease in the cell surface expression of 67LR. Biochemical analyses indicated co-immunoprecipitation of 67LR and the alpha6 subunit with an anti-alpha6 but not an anti-beta1 monoclonal antibody. Co-regulation of 67LR and alpha6 subunit expression, together with the physical association between the two receptors, supports the hypothesis that 67LR is an auxiliary molecule involved in regulating or stabilizing the interaction of laminin with the alpha6beta4 integrin.
An effective data structure for VLSI layout systems (1991)

An effective data structure is presented which is called a B-2 tree (bucket tree with 2-D binary trees) suitable for VLSI layout systems. The B-2 tree consists of a main binary tree which forms a directory for buckets, and bisector lists with 2-D binary trees. Experimental results have shown that the B-2 tree is superior to other data structures in region search performance even for huge size data. It has also been shown that its region search performance is not influenced by the distribution of objects on a chip.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Correlation between EGFR gene mutation pattern and Akt phosphorylation in pulmonary adenocarcinomas (2007)

The detection of gene mutation of epithelial growth factor receptor (EGFR) is important to predict the therapeutic effect of gefitinib. Recently, it was reported that examination of the activation of the downstream protein of EGFR is useful in the same way as the EGFR mutation. Therefore the purpose of the present paper was to determine whether activation of Akt and Erk, which are downstream proteins, and the EGFR gene mutation pattern was correlated. A total of 130 pulmonary adenocarcinomas were studied for the gene mutations of EGFR in exon 19 and 21, and the phosphorylation of Akt and Erk was investigated by immunostaining. The EGFR mutation was detected in 32%, the positivity of p-Akt was 51%, and the rate of p-Erk was 27%. The EGFR mutation-positive cases were the minority in p-Akt-negative cases, and the p-Akt expression was significantly associated with the mutation of EGFR (P=0.0014). In addition, there was a significant correlation between the L858R mutation and the expression of p-Akt (P=0.040). It is suggested that the activation of Akt is dependent on EGFR mutation pattern.
Making choices: The power of information (1997)

David Benton suggests that a system developed in the US for measuring the quality and outcome of health care can help in the implementation of the Government’s new White Paper, A Service with Ambitions, to give patients an opportunity for making informed choice
Role of Protein Kinase CK2 in the Regulation of Tumor Necrosis Factor–Related Apoptosis Inducing Ligand–Induced Apoptosis in Prostate Cancer Cells (2006)

Protein kinase CK2 (formerly casein kinase 2 or II) is a ubiquitous and highly conserved protein Ser/Thr kinase that plays diverse roles such as in cell proliferation and apoptosis. With respect to the latter, we originally showed that elevated CK2 could suppress various types of apoptosis in prostate cancer cells; however, the downstream pathways that respond to CK2 for mediating the suppression of apoptosis have not been fully elucidated. Here, we report studies on the role of CK2 in influencing activities associated with tumor necrosis factor-related ligand (TRAIL/Apo2-L)-mediated apoptosis in prostate carcinoma cells. To that end, we show that both androgen-insensitive (PC-3) and androgen-sensitive (ALVA-41) prostate cancer cells are sensitized to TRAIL by chemical inhibition of CK2 using its specific inhibitor 4,5,6,7-tetrabromobenzotriazole (TBB). Furthermore, we have shown that overexpression of CK2alpha using pcDNA6-CK2alpha protected prostatic cancer cells from TRAIL-mediated apoptosis by affecting various activities associated with this process. Thus, overexpression of CK2 resulted in the suppression of TRAIL-induced apoptosis via its effects on the activation of caspases, DNA fragmentation, and downstream cleavage of lamin A. In addition, the overexpression of CK2 blocked the mitochondrial apoptosis machinery engaged by TRAIL. These findings define the important role of CK2 in TRAIL signaling in androgen-sensitive and -insensitive prostatic carcinoma cells. Our data support the potential usefulness of anticancer strategies that may involve the combination of TRAIL and down-regulation of CK2.
Antiope Teletext Captioning (1980)

There is no need to argue the case for captioning, insofar as TV programs are already being captioned using tried and proven technology. However, it is a well-known fact that there is a demand for much more than classic captioning systems can provide. It would therefore seem that the time has come to extend captioning possibilities through the use of new techniques.
Prevention and treatment of primary intestinal tumors in rats by piroxicam. (1989)

Over 90% of methylazoxymethanol acetate-treated male Lobund Sprague-Dawley rats developed intestinal tumors within 20 weeks; the incidence and numbers of tumors remained basically the same at 40 weeks. However, at week 40 the numbers of large tumors (greater than 0.5 cm in diameter) were increased. At week 40, tumors in methylazoxymethanol acetate-inoculated rats that had been treated with piroxicam (approximately 2.3 mg/day) from week 1 or from week 20 (after tumors had developed) were significantly reduced in numbers, but many large tumors persisted. Rats treated with piroxicam up to 40 weeks carried 0.6 tumor/rat compared with 2.7 tumors/rat among untreated controls (P less than 0.0001). Rats at week 20 had developed 2.8 tumors/rat and rats treated with piroxicam from week 20 to week 40 carried 1.4 tumors/rat (P less than 0.007). Most of the tumors in the piroxicam-treated rats showed evidence of histological differentiation.
The Promise of Microarray Technology in Melanoma Care (2002)

The microarray technique is in its initial development for clinical application in a variety of tumor models. Melanoma is an ideal system to study the genetic changes associated with the stepwise progression of malignancy. It may be possible to efficiently screen the entire human genome to identify the particular aberrations in gene expression responsible for tumorigenesis in melanoma.
Safety, tolerability and pharmacokinetics of single and multiple doses of a novel sigma‐1 receptor antagonist in three randomized phase I studies (2012)

S1RA exhibited an acceptable safety, tolerability, pharmacodynamic and pharmacokinetic profile in healthy subjects over the dose range studied.