gebhart/patrepeval huggingface dataset:
Mutant androgen receptors in prostatic tumors distinguish between amino‐acid‐sequence requirements for transactivation and ligand binding (1995)

Mutant androgen receptors are thought to contribute to hormone resistance in prostate carcinoma. The part they play in this process, however, is ill-defined. Here we report on transactivation by 2 mutant androgen receptors from prostatic tumors with single amino-acid exchanges in their hormone-binding domains. These exchanges enhance the transactivation property of the receptors, particularly to androsterone and androstanediol, 2 metabolized derivatives of testosterone present in the prostate. Additionally, they enhance the transactivation potential of the mutant receptors to hydroxyflutamide, an anti-androgen frequently used in hormone ablation therapy. The increased transactivation by the mutant receptors did not result from altered affinity of the receptors to the inducing ligands nor from measurable changes in conformation of the liganded receptors. Thus the single amino-acid exchanges identify differences in amino-acid-sequence requirements for transactivation and ligand binding in the hormone-binding domain of the androgen receptor. These results provide new insights into ligand-dependent transactivation, and form a framework for the search for effective antagonists to be used in prostate-cancer therapy.
Design and in vitro studies of a needle-type glucose sensor for subcutaneous monitoring (1991)

A new miniaturized glucose oxidase based needle-type glucose microsensor has been developed for subcutaneous glucose monitoring. The sensor is equivalent in shape and size to a 26-guage needle (0.45-mm o.d.) and can be implanted with ease without any incision. The novel configuration greatly facilitates the deposition of enzyme and polymer films so that sensors with characteristics suitable for in vivo use (upper limit of linear range greater than 15 mM, response time less than 5 min, and sensitivity yielding a 5:1 signal-to-background ratio at normal basal glucose levels) can be prepared in high yield (greater than 60%). The sensor response is largely independent of oxygen tension in the normal physiological range. It also exhibits good selectivity against common interferences except for the exogenous drug acetaminophen.
Push and rotate: cooperative multi-agent path planning (2013)

In cooperative multi-agent path planning, agents must move between start and destination locations and avoid collisions with each other. Many recent algorithms require some sort of restriction in order to be complete, except for the Push and Swap algorithm [Luna and Bekris, 2011], which claims only to require two unoccupied locations in a connected graph. Our analysis shows, however, that for certain types of instances Push and Swap may fail to find a solution.We present the Push and Rotate algorithm, an adaptation of the Push and Swap algorithm, and prove that by fixing the latter's shortcomings, we obtain an algorithm that is complete for the class of instances with two unoccupied locations in a connected graph. In addition, we provide experimental results that show our algorithm to perform competitively on a set of benchmark problems from the video game industry.
The Clinical Usefulness of Prostate Specific Antigen: Update 1994 (1994)

In conclusion, PSA is the first prostate specific serum marker of clinical usefulness in urology. It represents a valuable clinical tool that has improved our ability to detect early prostate cancer and to monitor response to therapy. While large PSA screening studies have demonstrated an appreciable increase in the detection of organ confined, potentially curable prostate cancers, no study to date has yet demonstrated that the increased detection rate will decrease the prostate cancer-specific mortality rate. Yet more importantly, no study to date has demonstrated that early diagnosis using PSA will not decrease the prostate cancer specific mortality rate and until such data exist, PSA should be used to aid in early diagnosis and treatment planning for men with prostate cancer. PSA, when combined with other variables such as Gleason score and clinical stage, improves the prediction of pathological stage for prostate cancer. The introduction of PSA velocity and age specific reference ranges should further enhance the clinical usefulness of PSA. New advances in PSA research hold great promise for further improvements in PSA, and truly make it the most important and useful tumor marker for adenocarcinoma of the prostate.
Involvement of Two Distinct N‐Acetylglucosaminyltransferases and a Dual‐Function Deacetylase in Neomycin Biosynthesis (2008)

A new enzyme family: The glycosylation steps in the biosynthesis of neomycin were clarified through recombinant enzyme assays. NeoD catalyzes the first transglucosaminylation, and NeoK catalyzes the second, while NeoL catalyzes both deacetylations. We found that NeoK and its homologous proteins constitute a novel glycosyltransferase family. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2008/z700717_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Content-Based Video Preprocessing for Remote Monitoring of Neurosurgery (2006)

Transmitting high-quality video via the Internet is a challenging problem in distributed diagnosis system. We propose a content-based video data preprocessing scheme, which is adaptive to the video data acquired during intraoperative monitoring and can cascade with essentially any video codec. IOM video is first decomposed into temporal wavelet subband frames and motion compensation is incorporated into these transforms to exploit inter-frame redundancy efficiently. Highpass subband frames are then adaptively weighted according to an importance map, which specifies the importance of the video contents for clinical observation. This map has higher value near the surgical site and lower value at the surrounding area. The surgical site can be located automatically by a surgical tool tracking system
Efficacy of the Entomogenous Nematode Steinernema feltiae Against a Subterranean Termite, Reticulitermes tibialis (Isoptera: Rhinotermitidae) (1988)

Journal Article Efficacy of the Entomogenous Nematode Steinernema feltiae Against a Subterranean Termite, Reticulitermes tibialis (Isoptera: Rhinotermitidae) Get access Nancy D. Epsky, Nancy D. Epsky 1 Department of Entomology, Colorado State University, Fort Collins, Colorado 80523 1Current address: Department of Entomology & Nematology, University of Florida, Gainesville, Fla. 32611. Search for other works by this author on: Oxford Academic PubMed Google Scholar John L. Capinera John L. Capinera 1 Department of Entomology, Colorado State University, Fort Collins, Colorado 80523 1Current address: Department of Entomology & Nematology, University of Florida, Gainesville, Fla. 32611. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 81, Issue 5, 1 October 1988, Pages 1313–1317, https://doi.org/10.1093/jee/81.5.1313 Published: 01 October 1988 Article history Received: 01 July 1987 Accepted: 04 May 1988 Published: 01 October 1988
Multivalent DR5 Peptides Activate the TRAIL Death Pathway and Exert Tumoricidal Activity (2010)

Abstract Ongoing clinical trials are exploring anticancer approaches based on signaling by TRAIL, a ligand for the cell death receptors DR4 and DR5. In this study, we report on the selective apoptotic effects of multivalent DR5 binding peptides (TRAILmim/DR5) on cancer cells in vitro and in vivo. Surface plasmon resonance revealed up to several thousand-fold increased affinities of TRAILmim/DR5-receptor complexes on generation of divalent and trivalent molecules, the latter of which was achieved with a conformationally restricted adamantane core. Notably, only multivalent molecules triggered a substantial DR5-dependent apoptotic response in vitro. In tumor models derived from human embryonic kidney cells or primary foreskin fibroblasts, TRAILmim/DR5 peptides exerted a cancer cell–selective action that could synergize with resveratrol in a manner independent of p53. In a xenograft model of human colon cancer, a divalent TRAILmim/DR5 peptide inhibited tumor growth. Our results offer a proof-of-principle for the development of synthetic small molecules to trigger the TRAIL apoptosis pathway for cancer therapy. Cancer Res; 70(3); 1101–10
Molecular characterization of Bip 1, a monoclonal antibody that modulates IgE binding to birch pollen allergen, Bet v 1 (1996)

Bet v 1 and homologous proteins represent major cross-reactive allergens for more than 95% of tree pollen-, fruit-, and vegetable-allergic individuals. To study the interaction of Bet v 1 and the immune system, we characterized a Bet v 1-specific mAb, Bip 1. Soluble rBip 1 Fabs were expressed in Escherichia coli and purified by affinity chromatography using immobilized Bet v 1. Bip 1 Fabs displayed a cross-reactivity to homologous allergens comparable with that of IgE Abs from allergic patients. Preincubation of Bet v 1 with Bip 1 led to an up to fivefold increase of allergic patients' IgE binding to Bet v 1. This enhancement in IgE binding may be interpreted as stabilization of a Bet v 1 state, in which certain IgE epitopes are better applicable. It also shows that allergic patients possess IgE Abs directed against different Bet v 1 conformations. The modulation of Ab binding to a given Ag by other Abs was observed also for human Bet v 1-specific IgG Abs, and may represent a novel mechanism for the regulation of specific humoral immune responses in a complex network.
Guide wire reconstruction and visualization in 3DRA using monoplane fluoroscopic imaging (2005)

A method has been developed that, based on the guide wire position in monoplane fluoroscopic images, visualizes the approximate guide wire position in the three-dimensional (3-D) vasculature, that is obtained prior to the intervention with 3-D rotational X-ray angiography (3DRA). The method assumes the position of the guide wire in the fluoroscopic images is known. A two-dimensional feature image is determined from the 3DRA data. In this feature image, the guide wire position is determined in a two-step approach: a mincost algorithm is used to determine a suitable position for the guide wire, and subsequently a snake optimization technique is applied to move the guide wire to a better position. The resulting guide wire can then be visualized in 3-D in combination with the 3DRA dataset. The reconstruction accuracy of the method has been evaluated using a 3DRA image of a vascular phantom filled with contrast, and monoplane fluoroscopic images of the same phantom without contrast and with a guide wire inserted. The evaluation has been performed for different projection angles, and with different parameters for the method. The final result does not appear to be very sensitive to the parameters of the method. The average mean error of the estimated 3-D guide wire position is 1.5 mm, and the average tip distance is 2.3 mm. The effect of inaccurate C-arm geometry information is also investigated. Small errors in geometry information (up to 1 degrees) will slightly decrease the 3-D reconstruction accuracies, with an error of at most 1 mm. The feasibility of this approach on clinical data is demonstrated.
Selective etching of metallic single-wall carbon nanotubes with hydrogen plasma (2005)

We present Raman scattering and scanning tunnelling microscopy (STM) measurements on hydrogen plasma etched single-wall carbon nanotubes (SWNTs). Interestingly, both the STM and Raman spectroscopy show that the metallic SWNTs are dramatically altered and highly defected by the plasma treatment. In addition, structural characterizations show that metal catalysts are detached from the ends of the SWNT bundles. For semiconducting SWNTs we observe no feature of defects or etching along the nanotubes. Raman spectra in the radial breathing mode region of plasma-treated SWNT material show that most of the tubes are semiconducting. These results show that hydrogen plasma treatment favours etching of metallic nanotubes over semiconducting ones and therefore could be used to tailor the electronic properties of SWNT raw materials.
Inhibition of the activation of hageman factor (factor XII) by eosinophils and eosinophilic constituents (1993)

Several syndromes characterized by striking eosinophilia may be complicated by thrombosis. The experiments described indicate that, paradoxically, eosinophils and certain of their constituents inhibit the activation of Hageman factor (HF, factor XII). In earlier studies, suspensions of mixed types of granulocytes, other nucleated peripheral blood cells, and platelets inhibited activation of Hageman factor by ellagic acid, glass, and sulfatides. After these cells were sedimented by centrifugation, the supernatant fluids were also inhibitory. No attempt had been made earlier to distinguish among different granulocytic species. In the present study, suspensions of eosinophils and the supernatant fluid after eosinophils had been separated by centrifugation inhibited activation of Hageman factor by ellagic acid. The protein concentration of that amount of supernatant fluid that inhibited activation by about half was 16 micrograms/ml, approximately the same as had been described for suspensions of peripheral blood mononuclear cells. Activation of Hageman factor by ellagic acid was also inhibited by certain constituents of eosinophils, including eosinophil peroxidase, eosinophil major basic protein and eosinophil cationic protein. Inhibition was not specific for ellagic acid-induced activation of Hageman factor, as inhibition was also observed with sulfatide-induced activation. Inhibition was presumably related to neutralization of the negative charge of activators of Hageman factor. Thus, bismuth subgallate, a particulate activator of Hageman factor, was no longer effective after it had been exposed to eosinophil cationic protein. The observations reported here raise the question of whether in vivo eosinophils modulate certain of the defense reactions ascribed to Hageman factor.
Stability and characterization of protein and peptide drugs : case histories (1993)

Stability and Characterization of Human Growth Hormone R. Pearlman, T.A. Bewley. Characterization and Formulation Considerations for Recombinantly-Derived Bovine Somatotropin S.R. Davis, M.J. Hageman. Stability Characterization and Formulation Development of Altepase, a Recombinant Tissue Plasminogen Activator T.H. Nguyen, C. Ward. Orthoclone OKT3 P.E. Rao, D.J. Kroon. Leuprolide and Other LHRH Analogues A.L. Adjei, L. Hsu. Stability of Adrenocorticotropic Hormone and Pathways of Deamidation of Asparaginyl Residue in Hexapeptide Segments K. Patel. Stability and Characterization of Human Interleikin1b L. Gu, J. Fausnaugh. Development and ShelfLife Determination of Recombinant Interleukin2 J. Geigert, et al. Formulation and Stability of Recomibinant a1Antitrypsin S. Vemuri, et al. Fibrolase D. Pretzer, et al. Insulin Structure and Stability J. Brange, L. Langkjoer. Index.
Pentostatin (2′-Deoxycoformycin, dCF) in Patients with Low-Grade (B-T-Cell) and Intermediate- and High-Grade (T-Cell) Malignant Lymphomas: Phase II Study of the EORTC Early Clinical Trials Group (1996)

Thirty-seven eligible patients with advanced non-Hodgkin's lymphoma of low-grade, T-cell intermediate- and high-grade histology were treated with pentostatin (2'-deoxycoformycin, dCF) 4mg/m2 i.v. weekly for 3 weeks and then every 14 days to be followed after 3 doses by the same dosage every 4 weeks until maximum response or progression. Only patients with no more than two chemotherapy regimens were entered in this trial. All patients had measurable disease, performance status of 1,0 and 2 and adequate bone marrow, renal and liver function. Five of 37 eligible patients experienced a partial response of 8 months' median duration (range 7-12). The response rate was 17% in low-grade, 8% in T-cell intermediate- and high-grade and 14% in cutaneous T cell lymphoma. The only eligible patient with Hodgkin's disease underwent progression while on treatment. One case presented with grade 3 leukopenia and another one died of septicaemia, possibly treatment-related. Elevated but reversible creatinine levels were observed in 13% of patients and conjunctivitis in 7%. The toxicity of dCF at this low-dose schedule was acceptable, but the therapeutic activity in pretreated patients with low-grade, T-cell intermediate- and high-grade and cutaneous T-cell lymphomas was limited.
Observation of a small oligonucleotide duplex by electrospray ionization mass spectrometry (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTObservation of a small oligonucleotide duplex by electrospray ionization mass spectrometryK. J. Light-Wahl, D. L. Springer, B. E. Winger, C. G. Edmonds, D. G. Camp II, B. D. Thrall, and R. D. SmithCite this: J. Am. Chem. Soc. 1993, 115, 2, 803–804Publication Date (Print):January 1, 1993Publication History Published online1 May 2002Published inissue 1 January 1993https://pubs.acs.org/doi/10.1021/ja00055a070https://doi.org/10.1021/ja00055a070research-articleACS PublicationsRequest reuse permissionsArticle Views329Altmetric-Citations139LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Detection and relevance of epigenetic markers on ctDNA: recent advances and future outlook (2021)

Liquid biopsy, a minimally invasive approach, is a highly powerful clinical tool for the real-time follow-up of cancer and overcomes many limitations of tissue biopsies. Epigenetic alterations have a high potential to provide a valuable source of innovative biomarkers for cancer, owing to their stability, frequency, and noninvasive accessibility in bodily fluids. Numerous DNA methylation markers are now tested in circulating tumor DNA (ctDNA) as potential biomarkers, in various types of cancer. DNA methylation in combination with liquid biopsy is very powerful in identifying circulating epigenetic biomarkers of clinical importance. Blood-based epigenetic biomarkers have a high potential for early detection of cancer since DNA methylation in plasma can be detected early during cancer pathogenesis. In this review, we summarize the latest findings on DNA methylation markers in ctDNA for early detection, prognosis, minimal residual disease, risk of relapse, treatment selection, and resistance, for breast, prostate, lung, and colorectal cancer.
A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 Å resolution (1996)

Stellacyanins are blue (type I) copper glycoproteins that differ from other members of the cupredoxin family in their spectroscopic and electron transfer properties. Until now, stellacyanins have eluded structure determination. Here we report the three-dimensional crystal structure of the 109 amino acid, non-glycosylated copper binding domain of recombinant cucumber stellacyanin refined to 1.6 A resolution. The crystallographic R-value for all 18,488 reflections (sigma > 0) between 50-1.6 A is 0.195. The overall fold is organized in two beta-sheets, both with four beta-stands. Two alpha-helices are found in loop regions between beta-strands. The beta-sheets form a beta-sandwich similar to those found in other cupredoxins, but some features differ from proteins such as plastocyanin and azurin in that the beta-barrel is more flattened, there is an extra N-terminal alpha-helix, and the copper binding site is much more solvent accessible. The presence of a disulfide bond at the copper binding end of the protein confirms that cucumber stellacyanin has a phytocyanin-like fold. The ligands to copper are two histidines, one cysteine, and one glutamine, the latter replacing the methionine typically found in mononuclear blue copper proteins. The Cu-Gln bond is one of the shortest axial ligand bond distances observed to date in structurally characterized type I copper proteins. The characteristic spectroscopic properties and electron transfer reactivity of stellacyanin, which differ significantly from those of other well-characterized cupredoxins, can be explained by its more exposed copper site, its distinctive amino acid ligand composition, and its nearly tetrahedral ligand geometry. Surface features on the cucumber stellacyanin molecule that could be involved in interactions with putative redox partners are discussed.
Rapid and nonisotopic SSCP-based analysis of the BAT-26 mononucleotide repeat for identification of the replication error phenotype in human cancers (1998)

Microsatellite instability is an important new form of genetic alteration that characterizes tumors of the replication error phenotype (RER+). The RER status of tumors has been determined until now by analyzing several microsatellite loci for size variations compared with matching normal DNA. This has been done by separating isotopically labeled PCR products on denaturing gels. We recently showed that deletions within BAT-26, a polyadenine tract within the hMSH2 gene, could be used to establish the RER status of tumors without the need for matching normal DNA. We now propose a rapid and nonisotopic method of determining RER status based on PCR-SSCP analysis of the BAT-26 poly(A) tract. Compared with conventional means of examining RER+, this method reduces the PCR and gel manipulations involved by 10-fold. Size variations of as little as 2 bp in the BAT-26 sequence were readily detected using mini-sized, silver-stained SSCP gels run for 2.5 h. The incidence of RER+ detected in 183 right-sided colonic, 121 gastric, and 123 endometrial carcinomas was 20%, 10%, and 5% respectively, using this method. Frameshift mutations in the mononucleotide repeat of the TGF-beta RII gene were found in 86% (42/49) of RER+ but less than 1% (1/237) of RER- colon and gastric tumors identified by BAT-26 analysis. Our results demonstrate that nonisotopic PCR-SSCP of the poly(A) BAT-26 tract is a specific, sensitive and rapid method for determining the RER status of human tumors.