gebhart/patrepeval huggingface dataset:
Targeting of aluminum (III) phthalocyanine tetrasulfonate by use of internalizing monoclonal antibodies: improved efficacy in photodynamic therapy. (2001)

The use of monoclonal antibodies (MAbs) directed against tumor-associated antigens for targeting of photosensitizers is an interesting option to improve the selectivity of photodynamic therapy (PDT). Hydrophilic photosensitizers are most suitable for conjugation to MAbs because of their water solubility. The photosensitizer aluminum (III) phthalocyanine tetrasulfonate [AlPc(SO3H)4] has many ideal photochemical properties; however, because of its hydrophilicity, the free form of this sensitizer does not readily reach the critical intracellular target and, therefore, is ineffective in PDT. On the basis of our previous studies, we hypothesized that AlPc(SO3H)4 might be suitable for PDT when coupled to internalizing tumor-selective MAbs. In this study, a reproducible procedure is presented for coupling of AlPc(SO3H)4 to MAbs via the tetra-glycine derivative AlPc(SO2Ngly)4. Conjugation was performed to chimeric MAb (cMAb) U36 and murine MAbs (mMAb) E48 and 425 using a labile ester. Conjugates showed preservation of integrity and immunoreactivity and full stability in serum in vitro. At molar ratios >4, the solubility of the conjugates decreased. Data on the in vitro efficacy of PDT showed that in the chosen experimental setup the internalizing AlPc(SO2Ngly)4-mMAb 425 conjugate was about 7500 times more toxic to A431 cells than the free sensitizer (IC50s, 0.12 nM versus 900 nM). The AlPc(SO2Ngly)4-mMAb 425 conjugate was also more toxic than meta-tetrahydroxyphenylchlorin-mMAb 425 conjugates and free meta-tetrahydroxyphenylchlorin that had been tested previously (M. B. Vrouenraets et al., Cancer Res., 59: 1505-1513, 1999) in the same system (IC50s, 7.3 nm and 2.0 nM, respectively). Biodistribution analysis of AlPc(SO2Ngly)4-125I-labeled cMAb U36 conjugates with different sensitizer:MAb ratios in squamous cell carcinoma-bearing nude mice revealed selective accumulation in the tumor, although to a lesser extent than for the unconjugated 125I-labeled cMAb U36, whereas tumor:blood ratios were similar. These findings indicate that AlPc(SO3H)4 has high potential for use in PDT when coupled to internalizing tumor-selective MAbs.
Grain consolidation and electrical conductivity in porous media (1985)

A simple geometrical model is proposed for diagenesis. Diagenesis is the process by which granular systems evolve geologically from unconsolidated, high-porosity packings toward more consolidated, less porous, materials. We find that the relation between the electrical conductivity \ensuremath{\sigma} and the porosity \ensuremath{\varphi} can be approximated by a nontrivial power law over a wide range of porosity for both ordered and disordered lattice configurations. The most realistic model is generated from a dense disordered packing. This leads to a problem involving both short-range structural disorder and correlated percolation. In comparison with experiment, our calculations (on both ordered and disordered systems) are shown to reproduce the qualitative trends found in recent data on the conductivity of systems comprised of fused glass beads.
Solid‐Phase Synthesis of Oligodeoxynucleotides containing phosphoramidate internucleotide linkages and their specific chemical cleavage (1988)

Abstract Oligonuclecotides bearing phosphoramidate internucleotide linkages can be prepared chemically by standard solid‐phase DNA synthesis. Thus, phosphoramidate internucleotide bonds can be placed at will into specific positions within a given DNA fragment. The backbone‐modified DNA fragments prepared in this way are susceptible to a specific chemical cleavage.
Chimeric (mouse/human) anti-colon cancer antibody c30.6 inhibits the growth of human colorectal cancer xenografts in scid/scid mice. (1994)

The mouse monoclonal antibody, m30.6 (IgG2b), detects an antigenic determinant expressed predominantly on the surface of colorectal adenocarcinoma cells and has been shown previously to be a potentially useful therapeutic and diagnostic reagent for human colon cancer. We report the production and characterization of a mouse/human chimeric antibody, c30.6, with potent in vitro and in vivo antitumor activity. The genes encoding the variable domains for heavy and light chains were amplified by thermal cycling using degenerate oligonucleotide primers complementary to conserved immunoglobulin framework sequences. The gene segments were sequenced, subcloned into eukaryotic expression vectors containing human constant region genes (IgG1 and kappa), and cotransfected into nonsecreting Sp2/0 mouse myeloma cells. There were significant differences in the biological activities of the murine and chimeric antibodies. The i.p. administration of c30.6 but not of m30.6 produced a marked growth inhibition of s.c. 30.6+ COLO 205 tumors in scid/scid mice (approximately 40% reduction in tumor size, measured 21 days after tumor inoculation). Reduced tumor growth was not due to altered binding characteristics of c30.6 because: (a) the chimeric antibody was shown by flow cytometry to bind exclusively to cell lines that expressed the 30.6 determinant; (b) c30.6 was able to completely inhibit the binding of m30.6 on 30.6+ cells; and (c) the affinity of binding of the two antibodies was the same (Ka, approximately 1.50 x 10(8)). Up to 15% of the total injected antibody dose/g tissue was localized in 30.6+ tumors at 24 h, approximately 13% was present in the tumors at 48 h, and approximately 10% was present at 72 h. Furthermore, c30.6 demonstrated a shorter circulating half-life (53 h; m30.6, 72 h) when given i.p. to C57BL6 x BALB/cF1 mice. Unlike m30.6, c30.6 was also strongly active in antibody-dependent cell-mediated cytotoxicity against a range of 30.6+ tumor target cells in vitro. Up to 80% specific 51Cr release was achieved using either freshly isolated human peripheral blood mononuclear cells or 2-day-old interleukin 2-stimulated human peripheral blood mononuclear cells as effectors. The enhanced antitumor activity of c30.6 suggests that it might be a useful immunotherapeutic reagent for colorectal carcinoma.
Pain Tolerance Threshold: A Pilot Study of an Objective Measurement of Spinal Cord Stimulator Trial Results (2000)

PTT may possibly serve as an objective measurement of the SCS trial outcome.
Mitigation of Narrowband Interference in Filter Bank Based Multicarrier Systems (2006)

In this paper we present a method to mitigate the effects of a narrowband interference present in an adjacent subchannel of a filter bank based multicarrier (FBMC) system. For this purpose, we use the spectral shaping capabilities of a low-complexity subchannel equalizer for filter banks. With this method, over 20 dB stronger narrowband interference (NBI) power can be tolerated as compared to a system without interference mitigation. These findings are relevant when improving the throughput / spectral efficiency of an FBMC system in environments with narrowband interference.
Synthese und Reaktionen von 1‐(1‐Cyanoalkyl)‐1‐hydroxyharnstoffen (1978)

Abstract Die Hydroxyharnstoffe 5 cyclisieren entweder zu Imidazolidinen 8 oder bei gleichzeitiger Carbamoylierung des Hydroxylsauerstoffs zu Oxazolidin‐Derivaten 1 , deren Äthanolyse die Oxazolidine 2 liefert. Aus den Hydroxylaminen 3 entstehen mit Phenylsenföl die Imidazolidine 12 .
Reading Comprehension Strategies (2007)

Contents: D.S. McNamara, Preface. Part I: Theories of Text Comprehension: The Importance of Reading Strategies to Theoretical Foundations of Reading Comprehension. A.C. Graesser, An Introduction to Strategic Reading Comprehension. P. Kendeou, P. van den Broek, M.J. White, J. Lynch, Comprehension in Preschool and Early Elementary Children: Skill Development and Strategy Interventions. J. Oakhill, K. Cain, Issues of Causality in Children's Reading Comprehension. M.R. Vitale, N.R. Romance, A Knowledge-Based Framework for Unifying Content-Area Reading Comprehension and Reading Comprehension Strategies. Part II: Using Assessment to Guide Reading Interventions. J.P. Magliano, K. Millis, Y. Ozuru, D.S. McNamara, A Multidimensional Framework to Evaluate Reading Assessment Tools. A. VanderVeen, K. Huff, M. Gierl, D.S. McNamara, M. Louwerse, A. Graesser, Developing and Validating Instructionally Relevant Reading Competency Profiles Measured by the Critical Reading Section of the SAT. Part III: Reading Comprehension Strategy Interventions. D. Fuchs, L.S. Fuchs, Increasing Strategic Reading Comprehension With Peer-Assisted Learning Activities. J.P. Williams, Literacy in the Curriculum: Integrating Text Structure and Content Area Instruction. A.M. Glenberg, B. Jaworski, M. Rischal, J. Levin, What Brains Are For: Action, Meaning, and Reading Comprehension. J.T. Guthrie, A. Taboada, C.S. Coddington, Engagement Practices for Strategy Learning in Concept-Oriented Reading Instruction. A. King, Beyond Literal Comprehension: A Strategy to Promote Deep Understanding of Text. Part IV: Automated Interventions to Improve Reading Comprehension Strategies. M.C. Johnson-Glenberg, Web-Based Reading Comprehension Instruction: Three Studies of 3D-Readers. N. Yuill, Visiting Joke City: How Can Talking About Jokes Foster Metalinguistic Awareness in Poor Comprehenders? B.J.F. Meyer, K. Wijekumar, A Web-Based Tutoring System for the Structure Strategy: Theoretical Background, Design, and Findings. D. Caccamise, M. Franzke, A. Eckhoff, E. Kintsch, W. Kintsch, Guided Practice in Technology-Based Summary Writing. D.S. McNamara, T. O'Reilly, M. Rowe, C. Boonthum, I. Levinstein, iSTART: A Web-Based Tutor That Teaches Self-Explanation and Metacognitive Reading Strategies. B. Dalton, C.P. Proctor, Reading as Thinking: Integrating Strategy Instruction in a Universally Designed Digital Literacy Environment. A.S. Palincsar, R.J. Spiro, L. Kucan, S.J. Magnusson, B. Collins, S. Hapgood, A. Ramchandran, N. DeFrance, A. Gelpi-Lomangino, Research to Practice: Designing a Hypermedia Environment to Support Elementary Teachers' Learning of Robust Comprehension Instruction. Part V: Conclusion. D.S. McNamara, Y. Ozuru, R. Best, T. O'Reilly, The 4-Pronged Comprehension Strategy Framework.
Analysis of pol Integrase Sequences in Diverse HIV Type 1 Strains Using a Prototype Genotyping Assay (2009)

A prototype assay was used to genotype integrase (IN) from 120 HIV-1- infected IN inhibitor-naive adults from Argentina, Brazil, Cameroon, South Africa, Thailand, and Uganda. Subtype designations based on analysis of pol IN sequences were A (14), B (15), C (12), D (11), F (12), G (7), H (1), CRF01_AE (9), CRF02_AG (34), CRF22_01A1 (4), and CRF37_cpx (1). Ten (8.3%) of 120 samples had mutations associated with reduced susceptibility to the IN inhibitors, raltegravir and elvitegravir. Two samples had E92Q (both subtype B) and eight had E157Q (2A, 1C, 1D, 1F, 3 CRF02_AG). Some samples had other mutations selected by these drugs including T97A, and some had amino acid polymorphisms at positions associated with raltegravir and elvitegravir resistance. Mutations associated with other investigational HIV IN inhibitors were also identified. This suggests that HIV strains may vary in their natural susceptibility to HIV IN inhibitors.
Specificity of chicken liver carbohydrate binding protein (1984)

Chicken hepatic lectin was isolated with affinity chromatography by using neoglycoproteins of bovine serum albumin (BSA) to which n moles of glycosides has been attached by amidination (Glycn-AI-BSA) [Lee, Y. C., Stowell, C. P., & Krantz, M. J. (1976) Biochemistry 15, 3956-3963] attached to Sepharose 4B. The same protein could be isolated from Man-, GlcNAc-, and Glc-AI-BSA-Sepharose columns and was identical with the protein previously reported [Kawasaki, T., & Ashwell, G. (1977) J. Biol. Chem. 252, 6536-6543]. The sugar specificity for binding to the isolated chicken hepatic lectin examined with Glycn-AI-BSA showed the order of potency for binding Glycn-AI-BSA to be D-GlcNAc greater than D-Glc, D-Man, L-Fuc greater than D-Gal, and the estimated Ki's for binding GlcNAc36-AI-BSA, Glc37-AI-BSA, Man33-AI-BSA, and L-Fuc28-AI-BSA were (6-20) X 10(-11), (2-3) X 10(-8), (3-9) X 10(-8), and 5 X 10(-8) M, respectively. The binding requirements of the binding protein were studied with a wide variety of Glycn-BSA's with different sugars and aglyconic linkages, as well as simple sugars and glycosides. It was concluded that (1) GlcNAc is the most potent sugar for binding, (2) the requirement for C-2 substituents is flexible, (3) an equatorial OH group at C-3 and C-4 must be present, (4) the 5-CH2OH group is not required for binding, (5) the lectin cannot accommodate a negative charge at C-6, and (6) D-Man and L-Fuc bind equally well.(ABSTRACT TRUNCATED AT 250 WORDS)
Isolation and Identification of Cancer Stem-Like Cells in Esophageal Carcinoma Cell Lines (2008)

Side population (SP) cells may play an important role in tumorigenesis and cancer therapy. We isolate and identify the cancer stem-like cells in human esophageal carcinoma (EC) cell lines, EC9706 and EC109 cells labeled with Hoechst 33342. Both the cell lines contained SP cells, and the cells that had the strongest dye efflux activity ("Tip"-SP cell) in EC9706 had higher clone formation efficiency than non-SP cells. When transplanted into nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice, "Tip"-SP cells showed at least 50 times higher tumorigenicity than non-SP cells. Microarray analysis discriminated a differential gene expression profile between "Tip"-SP and non-SP cells, which is further tested using quantitative real-time RT-PCR. It is ascertained that several important stem cell-related genes (including OCT-4, SOX-2, BMI-1, and ZFX), two ATP-binding cassette (ABC) transporter genes (ABCG2 and ABCA5), and three Wnt and two Notch signal pathway-related genes (such as FZD10, PTGS2, KLF5, TTK, and RBM15) were upregulated in "Tip"-SP cells. Western blot showed a higher expression of beta-catenin protein in "Tip"-SP cells. All these indicated that the minority population described as "Tip"-SP cells possessed cancer stem cell character. Further understanding of tumor stem cell-specific traits will offer insights on the early stages of tumorigenesis for prevention and enhanced selectivity of antitumor therapeutics.
NONDESTRUCTIVE MEASUREMENT OF LONGITUDINAL RAIL STRESSES (1975)

A study of the effect of applied stress on the wave velocity (acoustoelasticity) of railroad rail steel has shown that a potentially useful technique exists for the nondestructive measurement of longitudinal stresses. The detection of extreme stress levels would contribute toward increased rail safety by decreasing accidents due to track buckling and weld pull aparts in continuously welded rail. Velocity variations between various new rails and between new and used rails were found to be significant. The overall effect of this is expected to be minimized by either establishing a base line velocity profile for rail or by comparing the velocity change of two waves, each experiencing a different change with applied stress.
Total Synthesis of the Bacteroides fragilis Zwitterionic Polysaccharide A1 Repeating Unit (2010)

Nearly all bacteria capsular polysaccharides are T-cell-independent antigens that do not promote immunoglobulin class switching from IgM to IgG nor memory responses. In contrast, zwitterionic polysaccharides activate T-cell-dependent immune responses by major histocompatability complex class II presentation, a mechanism previously believed to be reserved for peptidic antigens. The best studied zwitterionic polysaccharide, polysaccharide A1 (PS A1) is found on the capsule of the commensal bacteria Bacteroides fragilis . Its potent immunomodulatory properties have been linked to postoperative intra-abdominal abscess formation. Here, we report the synthesis of the PS A1 tetrasaccharide repeating unit (2) as a tool to investigate the biological role of this polysaccharide. A modular synthetic strategy originating from the reducing end of the PS A1 repeating unit was unsuccessful and illustrated the limitations of glycosylation reactions between highly armed glycosylating agents and poor nucleophiles. Thus, a [3 + 1] glycosylation relying on trisaccharide 5 and pyruvalated galactose 6 was used to complete the first total synthesis of the PS A1 repeating unit (2).
Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data (2003)

We have developed a computer based method to identify candidate single nucleotide polymorphisms (SNPs) and small insertions/deletions from expressed sequence tag data. Using a redundancy-based approach, valid SNPs are distinguished from erroneous sequence by their representation multiple times in an alignment of sequence reads. A second measure of validity was also calculated based on the cosegregation of the SNP pattern between multiple SNP loci in an alignment. The utility of this method was demonstrated by applying it to 102,551 maize (Zea mays) expressed sequence tag sequences. A total of 14,832 candidate polymorphisms were identified with an SNP redundancy score of two or greater. Segregation of these SNPs with haplotype indicates that candidate SNPs with high redundancy and cosegregation confidence scores are likely to represent true SNPs. This was confirmed by validation of 264 candidate SNPs from 27 loci, with a range of redundancy and cosegregation scores, in four inbred maize lines. The SNP transition/transversion ratio and insertion/deletion size frequencies correspond to those observed by direct sequencing methods of SNP discovery and suggest that the majority of predicted SNPs and insertion/deletions identified using this approach represent true genetic variation in maize.
Irreversible Electroporation in the Liver: Contrast-enhanced Inversion-Recovery MR Imaging Approaches to Differentiate Reversibly Electroporated Penumbra from Irreversibly Electroporated Ablation Zones (2010)

http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.10100645/-/DC1.
Azabenzomorphane and Related Compounds. IV (1965)

In order to synthesize 1, 2, 3, 4, 6-pentahydro-5H-2, 6-methanobenzo [d] [1, 3] diazocine (I), a compound related to 1-azabenzomorphane, 2-substituted 4-quinolineacetic acid derivatives were synthesized for use as its starting material. Diethyl 3-oxoglutarate was prepared from citric acid, reaction of the glutarate with aniline furnished the dianilide which was cyclized and esterified to ethyl 2-oxo-1, 2-dihydroquinoline-4-acetate (II). II was derived to the chloro compound (III) and then through the acetamide (VII) tothe objective amino acid (VIII) by treatment with 48% hydrobromic acid. The compound (VIII) was identified as its ester (IX) and acetylated compound (XI). Reduction of IX was not effected.
Stability of Thiol-Passivated Gold Particles at Elevated Temperatures Studied by X-ray Photoelectron Spectroscopy (2005)

The thermal stability of thiol-passivated gold colloids has been studied by means of X-ray photoelectron spectroscopy. Different colloids were chemically synthesized with thiol lengths from 3 to 8, and 16 carbon atoms. Depending on the synthesis parameters, the mean gold particle size varied from 1.6 to 4.9 nm for the particular colloid. Temperature-dependent measurements revealed a general tendency of shells with longer thiol chains (>5 carbon atoms) to be more stable in terms of desorption but to show a X-ray radiation-induced damage, which was absent with shorter thiols. Additionally, the self-assembling properties of the colloids were characterized by TEM, showing differences as a function of the chain lengths.
Allometric respiration/body mass data for animals to be used for estimates of inhalation toxicity to young adult humans (2000)

The relationship between body weight (BW) and respiratory minute volume (V(m)) was reviewed by collecting a database from the literature. The data were separated into anaesthetized and non-anaesthetized groups. Only young adult terrestrial mammals were included in the final data set. This database is the largest to be reported to date, is the first to separate the anaesthetized and non-anaesthetized groups and is matched to the target population of young, fit adult humans. The data set of non-anaesthetized animals contained 142 studies representing 2616 animals and 18 species from mice at 12 g body weight to horses and a giraffe at ca. 500 kg body weight. Analysis of the data indicated a power law (allometric) relationship between the minute volume and body weight. The resulting allometric equations for the empirical relationship between minute volume and body weight are: log(10)V()(m)= -0.302 + 0.809 log(10)BW and V(m) = 0.499 BW(0.809)where V(m) is the minute volume (l min(-1)) and BW is the body weight (kg). From these equations, a minute volume of 15.5 lmin(-1)was obtained for a 70 kg human in the same physiological and/or emotional state as the animals. The results of the analyses were compared to other empirical studies in the literature, the more recent of which also indicated a scaling factor of 0.8. The relationship between minute volume and body weight is recommended for use in estimating the inhalation toxicity to young adult humans (military personnel), because this is the first study to use a large database focused exclusively upon non-anaesthetized young adult terrestrial mammals.
Crystal Structure and Binding Properties of the Serratia marcescens Chitin-binding Protein CBP21 (2004)

Chitin proteins are commonly found in bacteria that utilize chitin as a source of energy. CBP21 is a chitin-binding protein from Serratia marcescens, a Gram-negative soil bacterium capable of efficient chitin degradation. When grown on chitin, S. marcescens secretes large amounts of CBP21, along with chitin-degrading enzymes. In an attempt to understand the molecular mechanism of CBP21 action, we have determined its crystal structure at 1.55 angstroms resolution. This is the first structure to be solved of a family 33 carbohydrate-binding module. The structure reveals a "budded" fibronectin type III fold consisting of two beta-sheets, arranged as a beta-sheet sandwich, with a 65-residue "bud" consisting of three short helices, located between beta-strands 1 and 2. Remarkably, conserved aromatic residues that have been suggested previously to play a role in chitin binding were mainly found in the interior of the protein, seemingly incapable of interacting with chitin, whereas the structure revealed a surface patch of highly conserved, mainly hydrophilic residues. The roles of six of these conserved surface-exposed residues (Tyr-54, Glu-55, Glu-60, His-114, Asp-182, and Asn-185) were probed by site-directed mutagenesis and subsequent binding studies. All single point mutations lowered the affinity of CBP21 for beta-chitin, as shown by 3-8-fold increases in the apparent binding constant. Thus, binding of CBP21 to chitin seems to be mediated primarily by conserved, solvent-exposed, polar side chains.