gebhart/patrepeval huggingface dataset:
Telomere structure in Euplotes crassus: characterization of DNA-protein interactions and isolation of a telomere-binding protein. (1990)

The nucleoprotein structure of telomeres from Euplotes crassus was studied by using nuclease and chemical footprinting. The macronuclear telomeres were found to exist as DNA-protein complexes that are resistant to micrococcal nuclease digestion. Each complex encompassed 85 to 130 base pairs of macronuclear DNA and appeared to consist of two structural domains that are characterized by dissimilar DNA-protein interactions. Dimethyl sulfate footprinting demonstrated that very sequence-specific and salt-stable interactions occur in the most terminal region of each complex. DNase I footprinting indicated that DNA in the region 30 to 120 base-pairs from the 5' end lies on a protein surface; the interactions in this region of the complex are unlikely to be sequence specific. A 50-kilodalton telomere-binding protein was isolated. Binding of this protein protected telomeric DNA from BAL 31 digestion and gave rise to many of the sequence-specific DNA-protein interactions that were observed in vivo. The telomeric complexes from E. crassus were very similar in overall structure to the complexes found at Oxytricha telomeres. However, telomeric complexes from the two ciliates showed significant differences in internal organization. The telomeric DNA, the telomere-binding proteins, and the resultant DNA-protein interactions were all somewhat different. The telomere-binding proteins from the two ciliates were found to be less closely conserved than might have been expected. It appears that the proteins are tailored to match their cognate telomeric DNA.
An anti-inflammatory agent, NS-398, selectively inhibits COX-2 activity (1994)

The renal kallikrein-kinin system has been shown to be important in the development of hypertension, but its precise role remains to be determined. The recent use of mutant rats that are deficient in plasma kininogens and hence incapable of generating kinin in the renal tubules has facilitated elucidation of the involvement of kinin in hypertension. In this article, Masataka Majima and Makoto Katori provide evidence that the renal kallikrein-kinin system plays a crucial role in the development of hypertension and discuss a novel rationale for developing effective new antihypertensive drugs.
A serum factor that activates the phosphatidylinositol phosphate signaling system in Xenopus oocytes. (1990)

Blood sera from many vertebrate species elicit large oscillatory chloride currents in oocytes from the frog Xenopus laevis. Rabbit serum was active at dilutions as great as one part in 10 million. Intracellularly applied serum was ineffective, and externally applied serum failed to trigger oscillatory currents when the intracellular level of ionized calcium was prevented from rising by loading the oocyte with EGTA. The serum also caused an increase of inositol 1,4,5-trisphosphate in the oocyte. We conclude that serum contains a factor which activates a membrane receptor that is coupled to the phosphatidylinositol second messenger system. The active factor is a protein with an apparent molecular mass of 60-70 kDa in gel permeation chromatography. Although the normal function of the serum factor is still unknown, it may have far-reaching implications, because it acts on the multifunctional phosphatidylinositol phosphate signaling system. Also, because of its great potency the serum factor and Xenopus oocytes are very useful for probing the operation of the phosphatidylinositol system.
Ferroportin/IREG-1/MTP-1/SLC40A1 modulates the uptake of iron at the apical membrane of enterocytes (2003)

In addition to release, ferroportin functions in the uptake of iron at the apical membrane, possibly by modulating the activity of DMT1.
Molar incisor hypomineralization: review and recommendations for clinical management. (2006)

Molar incisor hypomineralization (MIH) describes the clinical picture of hypomineralization of systemic origin affecting one or more first permanent molars (FPMs) that are associated frequently with affected incisors. Etiological associations with systemic conditions or environmental insults during the child's first 3 years have been implicated. The complex care involved in treating affected children must address their behavior and anxiety, aiming to provide a durable restoration under pain-free conditions. The challenges include adequate anaesthesia, suitable cavity design, and choice of restorative materials. Restorations in hypomineralized molars appear to fail frequently; there is little evidence-based literature to facilitate clinical decisions on cavity design and material choice. A 6-step approach to management is described: (1) risk identification; (2) early diagnosis; (3) remineralization and desensitization; (4) prevention of caries and posteruption breakdown; (5) restorations and extractions; and (6) maintenance. The high prevalence of MIH indicates the need for research to clarify etiological factors and improve the durability of restorations in affected teeth. The purpose of this paper was to describe the diagnosis, prevalence, putative etiological factors, and features of hypomineralized enamel in molar incisor hypomineralization and to present a sequential approach to management.
A CpG island hypermethylation profile of primary colorectal carcinomas and colon cancer cell lines. (2004)

The present study shows that colon cancer cell lines are in general relevant in vitro models, comparable with the in vivo situation, as the cell lines display many of the same molecular alterations as do the primary carcinomas. The combined pattern of epigenetic and genetic aberrations in the primary carcinomas reveals associations between them as well as to clinicopathological variables, and may aid in the future molecular assisted classification of clinically distinct stages.
Autonomic nervous system response to a solid meal and water loading in healthy children: its relation to gastric myoelectrical activity (2007)

The aim of this study was to investigate the correlation of gastric myoelectrical and autonomic activities in healthy children. Simultaneous recordings of electrogastrography (EGG) and electrocardiogram (ECG) were performed in healthy children before and after a solid meal and water loading respectively. The autonomic activity was assessed by spectral analysis of the heart rate variability (HRV). The solid meal resulted in an increase in EGG-dominant frequency (2.92 cpm vs 3.16 cpm, P < 0.05), dominant power (46.9 dB vs 53.7 dB, P < 0.05) and percentage normal slow waves (81.9%vs 89.0%, P < 0.05), while only dominant power increased following water loading. Power in the low-frequency band of HRV (LF) was significantly increased and power in the high-frequency band of HRV (HF) significantly decreased following the solid meal. Postprandial LF was positively and HF negatively correlated with the postprandial increase in EGG-dominant power. Water loading was not associated with any significant changes in HRV parameters. These results suggest that both vagal and sympathetic pathways are involved in modulation of gastric myoelectrical activity.
Possible involvement of multidrug‐resistance‐associated protein (MRP) gene expression in spontaneous drug resistance to vincristine, etoposide and adriamycin in human glioma cells (1994)

The multidrug-resistance phenotype in human tumors is partly associated with over-expression of the 170 kDa-P-glycoprotein encoded by the multidrug-resistance-1 (MDR1) gene. Another related, but non-P-glycoprotein, multidrug-resistance-associated protein (MRP) gene encodes a 190 kDa-membrane ATP-binding protein. Glioblastoma multiforme is a highly malignant primary neoplasm of the central nervous system which is refractory to anti-cancer chemotherapy, but the mechanism underlying this drug resistance is unknown. Out of glioma cell lines, 2, namely IN500 and T98G, which had elevated MRP mRNA levels, showed the highest resistance to multiple anti-cancer agents such as etoposide, vincristine and adriamycin, and decreased intracellular accumulation of etoposide. In the remaining 5 cell lines, various degrees of sensitivity to adriamycin and etoposide appeared to correlate with their respective MRP mRNA levels. Our study proposes that MRP may be involved in spontaneous multidrug resistance in human gliomas.
PROLONGATION OF RAT PANCREATIC ISLET ALLOGRAFT SURVIVAL BY ANTI-CD2 MONOCLONAL ANTIBODY TREATMENT (1992)

ROARK, JESSICA H.; POSSELT, ANDREW M.; CAMPOS, LUIS; KIM, JAMES; CHAVIN, KENNETH D.; BROMBERG, JONATHAN S.; BARKER, CLYDE F.; NAJI, ALI Author Information
Multi-targeted tyrosine kinase inhibitors in clinical development:Focus on XL-184 (cabozantinib) (2011)

XL-184 (cabozantinib) is a novel, small-molecule, multitargeted receptor tyrosine kinase inhibitor with particular activity against hepatocyte growth factor receptor (tyrosine-protein kinase Met), vascular endothelial growth factor receptor 2 (VEGFR-2) and proto-oncogene tyrosine-protein kinase receptor Ret. There is ample evidence of Met, VEGFR-2 and Ret signaling in several tumor types. Preclinical data suggest that XL-184 has activity in tumors derived from both epithelial and mesenchymal origins. Phase I and II clinical studies support significant antitumor activity, particularly in medullary thyroid cancer and cancers metastatic to the bone. This review will evaluate XL-184's preclinical pharmacology, pharmacokinetics, drug interactions and clinical activity in phase I through phase III studies.
Interleukin 1 induces leukocyte infiltration and cartilage proteoglycan degradation in the synovial joint. (1986)

Interleukin 1 (IL-1) is a polypeptide released by activated macrophages and is thought to be a key mediator of host responses to infection and inflammation. The availability of highly purified and recombinant material has now permitted the evaluation of IL-1 as a mediator of chronic inflammatory processes in vivo. We have demonstrated that intraarticular injection of IL-1 into rabbit knee joints induces the accumulation of polymorphonuclear and mononuclear leukocytes in the joint space and the loss of proteoglycan from the articular cartilage. The effects on cartilage could not be explained solely by the presence of leukocytes, since injections of endotoxin also stimulated leukocyte accumulation in the joint but had no effect on proteoglycan loss. Responses to IL-1 were not associated with increased production of the icosanoids prostaglandin E2 or leukotriene B4 and were not reduced by an inhibitor of their synthesis. The pattern of leukocyte infiltration and cartilage breakdown 24 hr after IL-1 injection was similar to that seen in animals with antigen-induced arthritis of 1 week's duration. These observations support the hypothesis that IL-1 acts directly to mediate the erosive processes of chronic arthritis.
Direct observation of fast protein folding: the initial collapse of apomyoglobin. (1996)

The rapid refolding dynamics of apomyoglobin are followed by a new temperature-jump fluorescence technique on a 15-ns to 0.5-ms time scale in vitro. The apparatus measures the protein-folding history in a single sweep in standard aqueous buffers. The earliest steps during folding to a compact state are observed and are complete in under 20 micros. Experiments on mutants and consideration of steady-state CD and fluorescence spectra indicate that the observed microsecond phase monitors assembly of an A x (H x G) helix subunit. Measurements at different viscosities indicate diffusive behavior even at low viscosities, in agreement with motions of a solvent-exposed protein during the initial collapse.
Random Mutagenesis by Whole-Plasmid PCR Amplification (1998)

Random mutagenesis has become a powerful means of studying the effects of a large number of permutations of a particular DNA sequence. As a prime example, libraries of randomized cDNA clones, when translated into their corresponding proteins, can be useful in investigating the functional contributions of a mutagenized region to the overall properties of a protein. Existing molecular cloning techniques for random mutagenesis are tedious and frequently plagued with high levels of background from wild-type (nonmutagenized) template. We report a PCR-based method involving amplification of an entire plasmid containing a gene sequence of interest with partially complementary degenerate oligonucleotides for randomization of up to 12 consecutive nucleotide residues. Sequential treatment of the PCR product with Dpn/and a second specific restriction endonuclease and T4 DNA ligase followed by high-efficiency electroporation permits the generation of libraries with very low background. This technique should prove useful for studies on enzyme structure-function relationships as well as for other diverse applications.
Preferred orientation and elastic anisotropy of illite-rich shale (2007)

Abstract Shales display significant seismic anisotropy that is attributed in part to preferred orientation of constituent minerals. This orientation pattern has been difficult to quantify because of the poor crystallinity and small grain size of clay minerals. A new method is introduced that uses high-energy synchrotron X-rays to obtain diffraction images in transmission geometry and applies it to an illite-rich shale. The images are analyzed with the crystallographic Rietveld method to obtain quantitative information about phase proportions, crystal structure, grain size, and preferred orientation (texture) that is the focus of the study. Textures for illite are extremely strong, with a maximum of 10 multiples of a random distribution for (001) pole figures. From the three-dimensional orientation distribution of crystallites, and single-crystal elastic properties, the intrinsic anisotropic elastic constants of the illite aggregate (excluding contribution from aligned micropores) can be calculated by appropriate medium averaging. The illitic shale displays roughly transverse isotropy with C11 close to C22 and more than twice as strong as C33. This method will lend itself to investigate complex polymineralic shales and quantify the contribution of preferred orientation to macroscopic anisotropy.
Real-Time Fetal ECG Recording (1986)

We present a real-time abdominal recording method for the FECG based on a minimization procedure for the MECG interference, by weighted addition of four abdominal leads containing FECG with a large amount of MECG. The minimization of the MECG does not influence the FECG recording adversely. FECG complexes coinciding with MECG complexes are also recorded. Use is made of programmable amplifiers that multiply analog abdominal leads by digital coefficients. These coefficients are calculated at the beginning of the recording by a microcomputer system. Experimental results are shown that clarify the advantages of the measurement principle. The real-time recorded FECG is wide-banded, so that all generally known ECG signal processing techniques, such as complex averaging, can be performed.
Mutations and polymorphisms in the bile salt export pump and the multidrug resistance protein 3 associated with drug-induced liver injury (2007)

In summary, our data support a role of ABCB11 and ABCB4 mutations and polymorphisms in drug-induced cholestasis. Genotyping of selected patients with acquired cholestasis might help to identify individuals with a genetic predisposition.
The central role of the propensity score in observational studies for causal effects (1983)

The propensity score is the conditional probability of assignment to a particular treatment given a vector of observed covariates. Both large and small sample theory show that adjustment for the scalar propensity score is sufficient to remove bias due to all observed covariates. Applications include: (i) matched sampling on the univariate propensity score, which is a generalization of discriminant matching, (ii) multivariate adjustment by subclassification on the propensity score where the same subclasses are used to estimate treatment effects for all outcome variables and in all subpopulations, and (iii) visual representation of multivariate covariance adjustment by a two- dimensional plot.
Synthesis of Single-stranded Plasmid pT181 DNA in Vitro (1989)

The origin of replication of plasmid pT181 is nicked by the plasmid-encoded RepC protein. The free 3'-hydroxyl end at the nick is presumably used as primer for leading strand DNA synthesis. In vitro replication of pT181 was found to generate single-stranded DNA in addition to the supercoiled, double-stranded DNA. The single-stranded DNA was circular and corresponded to the pT181 leading strand. Recombinant plasmids were constructed that contain two pT181 origins of replication in either direct or inverted orientation. In vitro replication of the plasmid carrying two origins in direct orientation was shown to generate circular, single-stranded DNA that corresponded to initiation of replication at one origin sequence and termination at the other origin. These results demonstrate that the origin of pT181 leading strand DNA replication also serves as the site for termination of replication. Interestingly, the presence of two origins in inverted orientation resulted in initiation of replication at one origin and stalling of the replisome at the other origin. These results suggest that RepC can reinitiate replication at the second origin by nicking partially replicated, relaxed DNA. These data are consistent with the replication of pT181 by a rolling circle mechanism and indicate that single-stranded DNA is an intermediate in pT181 replication.
Inhibition of tumor cell growth by antibodies induced after vaccination with peptides derived from the extracellular domain of Her‐2/neu (2003)

The anti Her-2/neu monoclonal antibody Trastuzumab has strong inhibiting effects on tumor growth in vitro and in vivo and is therefore used for immunotherapy in breast cancer patients. Due to necessity of frequent applications, however, cost intensiveness of Trastuzumab treatment and its limited duration of affectivity, an active immunization inducing a perhaps preventive and long-term immunity to Her-2/neu remains a desirable goal. We attempted to induce anti Her-2/neu antibodies by peptide vaccination and to test their efficacy in inhibiting tumor cell growth in vitro. By computer aided analyses, 7 putative B cell epitopes of Her-2/neu were defined and synthesized. These peptide epitopes were coupled to tetanus toxoid and used for immunization in BALB/c mice. Among these peptides, immunizations with 2 single peptides or a combination of 2 peptides induced anti-peptide antibody levels, primarily of the IgG1 isotype. These antibodies were also directed against the native Her-2/neu antigen, as shown in precipitation assays and ELISA with cell lysates of the Her-2/neu overexpressing breast cancer cell line SK-BR-3. Isolated IgG fractions from immune sera incubated with SK-BR-3 cells led to a moderate inhibition of the tumor cell growth in vitro, as well as to complement dependent cell lyses comparable to that achieved by incubation with Trastuzumab. Moreover, peptide immunization in rabbits generated anti-Her 2-neu IgG that, in contrast to mouse sera, were able to mediate a 31-46% lysis of SK-BR-3 cells in ADCC experiments. We conclude from our data that immunization with Her-2/neu peptides successfully induced humoral immune response with anti-tumor activity in an animal model.
Synthesis, Surface Activity and Micelle Formation of Novel Cyanine Dyes (1981)

Abstract The synthesis, surface activity and micelle formation of three novel cyanine dyes with amphiphilic character is described. It is illustrated by combined surface tension and absorption measurements that in one case self‐assembly is highly cooperative leading to aggregates with unique absorption properties.
A Packet Radio Network for Library Automation (1987)

The progress of libraries towards establishing online databases and automated search and retrieval tools allows them to share their resources and provide access to remote users. Unfortunately, the steady increase in the cost of leased lines makes them very undesirable as the media for access networks for budget-constrained libraries. An alternative approach-a packet switching radio network-is therefore presented here. Low-cost, commercially available radio transceivers and standard personal computers are the hardware building blocks of the system. The resulting network employs a suite of protocols, including channel access, routing, congestion control, and the higher-level TCP/IP. This network, which is planned to cover a large part of northern California, will provide remote access to University of California's automated library online catalog system. It will also support communication between any two end-points, provide for alternative routes in cases of link or nodal failure, and monitor its own performance. This paper, then, presents the network's topology, its architecture, its basic elements, and the functions it performs.
Packet loss protection of embedded data with fast local search (2003)

Unequal loss protection with systematic Reed-Solomon codes allows reliable transmission of embedded multimedia over packet erasure channels. The design of a fast algorithm with low memory requirements for the computation of an unequal loss protection solution is essential in real-time systems. Because the determination of an optimal solution is time-consuming, fast suboptimal solutions have been used. In this paper, we present a fast iterative improvement algorithm with negligible memory requirements. Experimental results for the JPEG2000, 2D, and 3D set partitioning in hierarchical trees (SPIHT) coders showed that our algorithm provided close to optimal peak signal-to-noise ratio (PSNR) performance, while its time complexity was significantly lower than that of all previously proposed algorithms.