gebhart/patrepeval huggingface dataset:
Deaminocolchinyl Methyl Ether: Synthesis from 2,3,4,4′‐Tetramethoxybiphenyl‐2‐carbaldehyde. Comparison of antitubulin effects of deaminocolchinyl methyl ether and dehydro analogs (1989)

Abstract Synthesis of deaminocolchinyl methyl ether 9 was achieved from tetramethoxy‐substituted biphenyl‐2‐carb‐aldehyde 12 via tricyclic ketone 20 and 5,6‐didehydro congener 11 . Compound 9 was identical in every respect with material prepared from colchicine via 6,7‐didehydro congener 10 . Measuring inhibition of tubulin polymerization in vitro showed compounds 4 , 5 , and 9 – 11 of the alloseries of colchicinoids to be particularly potent inhibitors.
Precise online camera calibration in a robot navigating vision system (2006)

This paper proposes a camera calibration method with the aid of a robot, which is navigated by a vision system after all cameras in the system are calibrated. It can be carried out easily not only in the laboratory, but also in the working area. All that is needed in the calibration procedure is a stick with a ball on one end, with the other end of the stick mounted on the robot hand. The calibration program guides the robot to move to appropriate positions, while at the same time the ball is accurately recognized in camera images. Without knowing any initial specifics about the camera, all intrinsic and extrinsic parameters are well calibrated in the robot base coordinate frame. In order to obtain high accuracy, the lens radial distortion is also modelled.
Xylose isomerase from Escherichia coli. Characterization of the protein and the structural gene. (1984)

The gene that codes for xylose isomerase in Escherichia coli has been cloned by complementation of a xylose isomerase-negative E. coli mutant. The structural gene is 1320 nucleotides in length and codes for a protein of 440 amino acids. An additional 209 nucleotides 5' and 82 nucleotides 3' to the structural gene were also sequenced. To verify that the cloned gene encodes E. coli xylose isomerase, the enzyme was purified to homogeneity and the sequence of the first 25 amino acid residues was determined by a semimicromanual Edman procedure. These results establish that the NH2-terminal methionine of xylose isomerase is specified by an ATG which is 7 nucleotides downstream from a Shine-Dalgarno sequence.
Platelet lysate stimulates wound repair of HaCaT keratinocytes (2008)

Data indicate that PL increases wound healing rate by stimulating keratinocyte migration through a calcium- and p38-dependent mechanism. ERK1/2 and phosphoinositide-3 kinase seem to play minor roles.
Structural gene and complete amino acid sequence of Vibrio alginolyticus collagenase (1992)

The DNA encoding the collagenase of Vibrio alginolyticus was cloned, and its complete nucleotide sequence was determined. When the cloned gene was ligated to pUC18, the Escherichia coli expression vector, bacteria carrying the gene exhibited both collagenase antigen and collagenase activity. The open reading frame from the ATG initiation codon was 2442 bp in length for the collagenase structural gene. The amino acid sequence, deduced from the nucleotide sequence, revealed that the mature collagenase consists of 739 amino acids with an Mr of 81875. The amino acid sequences of 20 polypeptide fragments were completely identical with the deduced amino acid sequences of the collagenase gene. The amino acid composition predicted from the DNA sequence was similar to the chemically determined composition of purified collagenase reported previously. The analyses of both the DNA and amino acid sequences of the collagenase gene were rigorously performed, but we could not detect any significant sequence similarity to other collagenases.
Human milk oligosaccharides: a novel method provides insight into human genetics. (2001)

Human milk is a unique reservoir of oligosaccharides. The presence of many of these oligosaccharides is determined genetically and is related to the Lewis blood group and secretor antigen status of each donor. A method to quantitate neutral human milk oligosaccharides was developed. Sample preparation was based on a single centrifugation-filtration step that yields oligosaccharide extracts. These extracts first were fractionated to remove a significant portion of their lactose content and were analyzed using high-pH anion-exchange chromatography. Oligosaccharide profiles from 386 milk samples obtained in this fashion generated quantitative information on lactose, the neutral cores lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNneoT), and the key fucosylated oligosaccharides. Additionally, the profiles provided genetic footprints of the Lewis and secretor status of the donors. Furthermore, unusual profiles that could not have been predicted from known genotypes were found. For this reason, milk glycoproteins were studied using carbohydrate-binding probes. Results confirm that oligosaccharides are an accurate predictor of the Lewis blood group status of the donor, and that glycosyltransferases have exquisite specificities. The data obtained in this study corroborate that Lewis-related antigens are tissue specific. This attribute of immunodominant carbohydrate sequences has significant implications for epidemiological studies of breast-fed infants.
Antibody Targeting to a Class I MHC-Peptide Epitope Promotes Tumor Cell Death (2006)

Therapeutic mAbs that target tumor-associated Ags on the surface of malignant cells have proven to be an effective and specific option for the treatment of certain cancers. However, many of these protein markers of carcinogenesis are not expressed on the cells' surface. Instead these tumor-associated Ags are processed into peptides that are presented at the cell surface, in the context of MHC class I molecules, where they become targets for T cells. To tap this vast source of tumor Ags, we generated a murine IgG2a mAb, 3.2G1, endowed with TCR-like binding specificity for peptide-HLA-A*0201 (HLA-A2) complex and designated this class of Ab as TCR mimics (TCRm). The 3.2G1 TCRm recognizes the GVL peptide (GVLPALPQV) from human chorionic gonadotropin beta presented by the peptide-HLA-A*0201 complex. When used in immunofluorescent staining reactions using GVL peptide-loaded T2 cells, the 3.2G1 TCRm specifically stained the cells in a peptide and Ab concentration-dependent manner. Staining intensity correlated with the extent of cell lysis by complement-dependent cytotoxicity (CDC), and a peptide concentration-dependent threshold level existed for the CDC reaction. Staining of human tumor lines demonstrated that 3.2G1 TCRm was able to recognize endogenously processed peptide and that the breast cancer cell line MDA-MB-231 highly expressed the target epitope. The 3.2G1 TCRm-mediated CDC and Ab-dependent cellular cytotoxicity of a human breast carcinoma line in vitro and inhibited in vivo tumor implantation and growth in nude mice. These results provide validation for the development of novel TCRm therapeutic reagents that specifically target and kill tumors via recognition and binding to MHC-peptide epitopes.
High performance thin-film flip-chip InGaN–GaN light-emitting diodes (2006)

Data are presented on the operation of thin-film flip-chip InGaN∕GaN multiple-quantum-well light-emitting diodes (LEDs). The combination of thin-film LED concept with flip-chip technology is shown to provide surface brightness and flux output advantages over conventional flip-chip and vertical-injection thin-film LEDs. Performance characteristics of blue, white, and green thin-film flip-chip 1×1mm2 LEDs are described. Blue (∼441nm) thin-film flip-chip LEDs are demonstrated with radiance of 191mW∕mm2sr at 1A drive, more than two times brighter than conventional flip-chip LEDs. An encapsulated thin-film flip-chip blue LED lamp is shown to have external quantum efficiency of 38% at forward current of 350mA. A white lamp based on a YAG:Ce phosphor coated device exhibits luminous efficacy of 60lm∕W at 350mA with peak efficiency of 96lm∕W at 20mA and luminance of 38Mcd∕m2 at 1A drive current. Green (∼517nm) devices exhibit luminance of 37Mcd∕m2 at 1A.
Differences in the effects of pH on the hydrolytic and transgalactosylic reactions of β-galactosidase (Escherichia coli) (1983)

Steady-state kinetic studies with beta-galactosidase and various substrates were carried out to determine why the ratio of transgalactosylis to hydrolysis increased as a function of pH from 7.0 to 10.0. The rate constant (k'3) for the formation of galactose (hydrolytic reaction) decreased whereas the rate constant (k4) for the transgalactosylic reaction (i.e., the formation of allolactose) remained constant. The equilibrium constant for acceptor dissociation from the galactosyl form of the enzyme was also unaffected by pH in the range studied; this was true whether the acceptor was glucose, sucrose, or glycerol. These results suggest that there is a group of high pKa at, or of influence at, the enzyme's active site which affects hydrolysis but not transgalactosylis. A further finding was that the rate constant for the breakage of the glycosidic bond decreased with pH in a manner different from the change observed for the hydrolytic rate constant (pKa 9.4 for glycosidic breakage as compared with 8.6 for hydrolysis). This could explain why the pH optimum for beta-galactosidase activity varies with substrate; different steps are rate limiting for different substrates.
Sol−Gel-Encapsulated Heme Proteins. Evidence for CO2 Adducts (1998)

Heme proteins have been the subjects of numerous studies of photoinduced ligand dissociation and recombination (e.g., O2, CO, and NO). Much of this work1 is aimed at unraveling the dynamical behavior of myoglobin (Mb), which lacks a crystallographic channel connecting the iron center with the solvent. Despite its importance as a conspicuous metabolic breakdown product, CO2 interactions with metalloproteins are not well understood. CO2 is required for the assembly of the active sites of some multinuclear metalloproteins (e.g., the Ni2 center of urease2). In carbonic anhydrase, zinc-coordinated hydroxide is believed3 to attack CO2, forming a bicarbonate product complex. Deoxyhemoglobin forms carbaminohemoglobin4 in red blood cells upon reaction of CO2 with the amino termini more readily than oxyhemoglobin does; oxygenation in the lungs causes CO2 release. More importantly, there is no direct evidence for the existence of a metal-ligated CO2 adduct of any metalloprotein. In addition to transporting gases, hemoglobin and myoglobin possess enzymatic activity: reactions of the met forms with peroxides generate intermediates5,6 containing ferryl (FeIVdO) and protein radical species that are capable of oxidizing small substrates. In the case of linoleic acid, it has been established7 that substrate oxidation by Mb occurs by direct ferryl oxygen atom transfer. In this paper, we demonstrate that ferrylMb oxidizes carbon monoxide to produce CO2. In addition, we present the first spectroscopic evidence for Fe-CO2 coordination in heme proteins. The reaction7 of metMb with excess hydrogen peroxide generates a metastable intermediate, containing ferryl iron, that decays within minutes to produce degraded forms of myoglobin. However, in a saturated CO solution, Mb is observed8 to produce a gaseous product. Table 1 presents the results of mass spectrometric analyses9 of the gases in sealed pear flasks containing combinations of metMb, H2O2, and CO in phosphate buffer (50 mM, pH 7.0). The m/e ) 44 signal clearly indicates that the product of the catalyzed reaction is CO2. However, the low solubility of CO2 precluded attempts to obtain the electronic spectrum of the product complex under these conditions. Following the suggestion of Ibers10 that liquid CO2 be used in searching for new CO2 complexes, we reasoned that supercritical CO2 would be an even better choice, owing to its gaslike viscosity. Furthermore, supercritical fluids constitute reaction media that are of emerging biotechnological interest.11
Template directed incorporation of nucleotide mixtures using azole- nucleobase analogs (1997)

DNA that encodes elements for degenerate replication events by use of artificial nucleobases offers a versatile approach to manipulating sequences for applications in biotechnology. We have designed a family of artificial nucleobases that are capable of assuming multiple hydrogen bonding orientations through internal bond rotations to provide a means for degenerate molecular recognition. Incorporation of these analogs into a single position of a PCR primer allowed for analysis of their template effects on DNA amplification catalyzed by Thermus aquaticus (Taq) DNA polymerase. All of the nucleobase surrogates have similar shapes but differ by structural alterations that influence their electronic character. These subtle distinctions were able to influence the Taq DNA polymerase dependent incorporation of the four natural deoxyribonucleotides and thus, significantly expand the molecular design possibilities for biochemically functional nucleic acid analogs.
A practical dynamic buffer overflow detector (2004)

Despite previous efforts in auditing software manually and automatically, buffer overruns are still being discovered in programs in use. A dynamic bounds checker detects buffer overruns in erroneous software before it occurs and thereby prevents attacks from corrupting the integrity of the system. Dynamic buffer overrun detectors have not been adopted widely because they either (1) cannot guard against all buffer overrun attacks, (2) break existing code, or (3) incur too high an overhead. This paper presents a practical detector called CRED (C Range Error Detector) that avoids each of these deficiencies. CRED finds all buffer overrun attacks as it directly checks for the bounds of memory accesses. Unlike the original referent-object based bounds-checking technique, CRED does not break existing code because it uses a novel solution to support program manipulation of out-of-bounds addresses. Finally, by restricting the bounds checks to strings in a program, CRED’s overhead is greatly reduced without sacrificing protection in the experiments we performed. CRED is implemented as an extension of the GNU C compiler version 3.3.1. The simplicity of our design makes possible a robust implementation that has been tested on over 20 open-source programs, comprising over 1.2 million lines of C code. CRED proved effective in detecting buffer overrun attacks on programs with known vulnerabilities, and is the only tool found to guard against a testbed of 20 different buffer overflow attacks[34]. Finding overruns only on strings impose an overhead of less
Pretargeting of prostate cancer with an internalizing anti-EGP-1 x anti-HSG bispecific antibody (2011)

1680 Objectives The monoclonal antibody RS7 (anti-EGP-1) effectively targets prostate cancer (PC), and because it internalizes, 111In-RS7 provides good tumor uptake. This study examined the prospects for using an anti-EGP-1 x anti-HSG bispecific antibody (bsMAb), TF12, for pretargeting. Methods Internalization of the anti-EGP1 antibody, RS7, and the bsMAb, TF12, by PC3 cells was determined in vitro in the presence or absence of di-HSG peptide (IMP288). Mice with s.c. human PC3 tumors were given 111In-TF12 and 125I-TF12 and necropsied 16 h later, while other mice were given 111In-IMP288 after the TF12 injection and then necropsied at 1, 2, 4, 24, 48, and 72 h p.i. Results RS7 and TF12 internalized at a comparable rate over 24 h, with evidence of early enhanced internalization in the presence of IMP288 (Table 1). 111In-TF12 uptake in PC3 cells was 7-fold higher than 125I-TF12 (4.9±0.6% ID/g vs. 0.7±0.2 %ID/g, respectively), indicating internalization also occurs in vivo. Nevertheless, TF12-pretargeted 111In-IMP288 uptake in the tumor was still high at 48 h after injection (50% of the %ID/g at 1 h). Conclusions Even though TF12 internalizes, it was highly effective for pretargeting prostate cancer. Due to the internalizing properties of the antibody, the radiolabel shows excellent retention in the tumor
The nature of adhesion in composites of modified cellulose fibers and polypropylene (1991)

Abstract Cellulose fibers were surface modified with polypropylene–maleic anhydride copolymer. The physical properties of such fibers were characterized by contact angle measurements, and the chemical structure was identified with ESCA and FTIR. ESCA showed that the modifying agent was localized at the surface of the fibers. The modified fibers were compounded with polypropylene, and composites with various amount of fibers were manufactured by injection molding. All mechanical properties were improved when treated fibers were used. SEM showed improved dispersion, wetting of fibers, and adhesion. The nature of adhesion was studied using FTIR. It was found that the surface modifying agent is covalently bonded to the fibers through esterification. The degree of esterification is enhanced by activating the modifying agent before fiber treatment. This study has shown the effects of treatment conditions on activation of reactive species and chemical reaction between fiber and modifying agent. Moreover, a better understanding has been achieved of the nature of adhesion for the system.
The BMP Coreceptor RGMb Promotes While the Endogenous BMP Antagonist Noggin Reduces Neurite Outgrowth and Peripheral Nerve Regeneration by Modulating BMP Signaling (2011)

Repulsive guidance molecule b (RGMb) is a bone morphogenetic protein (BMP) coreceptor and sensitizer of BMP signaling, highly expressed in adult dorsal root ganglion (DRG) sensory neurons. We used a murine RGMb knock-out to gain insight into the physiological role of RGMb in the DRG, and address whether RGMb-mediated modulation of BMP signaling influences sensory axon regeneration. No evidence for altered development of the PNS and CNS was detected in RGMb(-/-) mice. However, both cultured neonatal whole DRG explants and dissociated DRG neurons from RGMb(-/-) mice exhibited significantly fewer and shorter neurites than those from wild-type littermates, a phenomenon that could be fully rescued by BMP-2. Moreover, Noggin, an endogenous BMP signaling antagonist, inhibited neurite outgrowth in wild-type DRG explants from naive as well as nerve injury-preconditioned mice. Noggin is downregulated in the DRG after nerve injury, and its expression is highly correlated and inversely associated with the known regeneration-associated genes, which are induced in the DRG by peripheral axonal injury. We show that diminished BMP signaling in vivo, achieved either through RGMb deletion or BMP inhibition with Noggin, retarded early axonal regeneration after sciatic nerve crush injury. Our data suggest a positive modulatory contribution of RGMb and BMP signaling to neurite extension in vitro and early axonal regrowth after nerve injury in vivo and a negative effect of Noggin.
High precision realtime RF-measurement system for imaging of stroke (2017)

Statistics show, that stroke is one of the main causes of death worldwide, and reliable and fast diagnosis is key to recovery. Modern medical imaging devices provide intricate detail, but lack portability and are in some cases invasive. This paper presents a multiport vector network analyzer (MPVNA) measurement system for electromagnetic tomography (EMT) - an alternative medical imaging technique that complements more established methods. The portability of the system allows stroke to be detected very soon after occurrence. The architecture of the MPVNA enables parallelization of hundreds of measurements, which supports realtime operation without compromising measurement performance. Given the high attenuation caused by the human head and the limited signal power allowed in medical applications, the system is designed to measure signals at power levels as low as -150 dBm.
STEAP: A prostate-specific cell-surface antigen highly expressed in human prostate tumors (1999)

In search of novel genes expressed in metastatic prostate cancer, we subtracted cDNA isolated from benign prostatic hypertrophic tissue from cDNA isolated from a prostate cancer xenograft model that mimics advanced disease. One novel gene that is highly expressed in advanced prostate cancer encodes a 339-amino acid protein with six potential membrane-spanning regions flanked by hydrophilic amino- and carboxyl-terminal domains. This structure suggests a potential function as a channel or transporter protein. This gene, named STEAP for six-transmembrane epithelial antigen of the prostate, is expressed predominantly in human prostate tissue and is up-regulated in multiple cancer cell lines, including prostate, bladder, colon, ovarian, and Ewing sarcoma. Immunohistochemical analysis of clinical specimens demonstrates significant STEAP expression at the cell-cell junctions of the secretory epithelium of prostate and prostate cancer cells. Little to no staining was detected at the plasma membranes of normal, nonprostate human tissues, except for bladder tissue, which expressed low levels of STEAP at the cell membrane. Protein analysis located STEAP at the cell surface of prostate-cancer cell lines. Our results support STEAP as a cell-surface tumor-antigen target for prostate cancer therapy and diagnostic imaging.
Iodotrimethylsilane-mediated 2-monohalogenation of 4-aza-5.alpha.-androstan-3-one steroids (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIodotrimethylsilane-mediated 2-monohalogenation of 4-aza-5.alpha.-androstan-3-one steroidsAnthony O. King, R. Kevin Anderson, Richard F. Shuman, Sandor Karady, N. Lee Abramson, and Alan W. DouglasCite this: J. Org. Chem. 1993, 58, 12, 3384–3386Publication Date (Print):June 1, 1993Publication History Published online1 May 2002Published inissue 1 June 1993https://pubs.acs.org/doi/10.1021/jo00064a028https://doi.org/10.1021/jo00064a028research-articleACS PublicationsRequest reuse permissionsArticle Views577Altmetric-Citations24LEARN 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
The anti‐interleukin‐6 antibody siltuximab down‐regulates genes implicated in tumorigenesis in prostate cancer patients from a phase I study (2011)

Preliminary safety of siltuximab is favorable. Future studies in which siltuximab could be combined with androgen-deprivation therapy and experimental therapies in advanced prostate cancer are justified.