gebhart/patrepeval huggingface dataset:
Robust optimization of radiation therapy accounting for geometric uncertainty (2013)

Geometric errors may compromise the quality of radiation therapy treatments. Optimization methods that account for errors can reduce their effects. The first paper of this thesis introduces minimax optimization to account for systematic range and setup errors in intensity-modulated proton therapy. The minimax method optimizes the worst case outcome of the errors within a given set. It is applied to three patient cases and shown to yield improved target coverage robustness and healthy structure sparing compared to conventional methods using margins, uniform beam doses, and density override. Information about the uncertainties enables the optimization to counterbalance the effects of errors. In the second paper, random setup errors of uncertain distribution---in addition to the systematic range and setup errors---are considered in a framework that enables scaling between expected value and minimax optimization. Experiments on a phantom show that the best and mean case tradeoffs between target coverage and critical structure sparing are similar between the methods of the framework, but that the worst case tradeoff improves with conservativeness. Minimax optimization only considers the worst case errors. When the planning criteria cannot be fulfilled for all errors, this may have an adverse effect on the plan quality. The third paper introduces a method for such cases that modifies the set of considered errors to maximize the probability of satisfying the planning criteria. For two cases treated with intensity-modulated photon and proton therapy, the method increased the number of satisfied criteria substantially. Grasping for a little less sometimes yields better plans. In the fourth paper, the theory for multicriteria optimization is extended to incorporate minimax optimization. Minimax optimization is shown to better exploit spatial information than objective-wise worst case optimization, which has previously been used for robust multicriteria optimization. The fifth and sixth papers introduce methods for improving treatment plans: one for deliverable Pareto surface navigation, which improves upon the Pareto set representations of previous methods; and one that minimizes healthy structure doses while constraining the doses of all structures not to deteriorate compared to a reference plan, thereby improving upon plans that have been reached with too weak planning goals.
Design and Synthesis of Biomimetic Hydrogel Scaffolds with Controlled Organization of Cyclic RGD Peptides (2009)

We report on the rational design and synthesis of a new type of bioactive poly(ethylene glycol) diacrylate (PEGDA) macromers, cyclic Arg-Gly-Asp (cRGD)-PEGDA, to mimic the cell-adhesive properties of extracellular matrix (ECM), aiming to create biomimetic scaffolds with controlled spatial organization of ligands and enhanced cell binding affinity for tissue engineering. To attach the cRGD peptide in the middle of PEGDA chain, a tailed cRGD peptide, c[RGDfE(SSSKK-NH2)] (1), was synthesized with c(RGDfE) linked to a tail of SSSKK. The tail consists of a spacer with three serine residues and a linker with two lysine residues for conjugating with acryloyl-PEG-NHS (5) to create cRGD-PEGDA (6). cRGD-PEGDA possesses good photopolymerization ability to fabricate hydrogel scaffolds under UV radiation. Surface morphology and composition analysis demonstrates that cRGD-PEGDA hydrogels were well-constructed with porous three-dimensional (3D) structures and uniform distribution of cRGD ligands. Our results show that cRGD-PEGDA hydrogels facilitate endothelial cell (EC) adhesion and spreading on the hydrogel surfaces and exhibit significantly higher EC population in comparison with linear RGD-modified hydrogels at low peptide incorporation. Since ligand presentation in biomimetic scaffolds plays an important role in controlling cell behavior, cRGD-PEGDA has great advantages of controlling hydrogel properties and ligand spatial organization in the resulting scaffolds. Furthermore, cRGD-PEGDA is an attractive candidate for the future development of tissue engineering scaffolds with optimum cell adhesive strength and ligand density.
Model of Vapor-Induced Resistivity Changes in Gold−Thiolate Monolayer-Protected Nanoparticle Sensor Films (2007)

An investigation of the modulation of charge transport through thin films of n-octanethiolate monolayer-protected gold nanoparticles (MPN) induced by the sorption of organic vapors is presented. A model is derived that allows predictions of MPN-coated chemiresistor (CR) responses from vapor-film partition coefficients, and analyte densities and dielectric constants. Calibrations with vapors of 28 compounds collected from an array of CRs and a parallel thickness-shear-mode resonator are used to verify assumptions inherent in the model and to assess its performance. Results afford insights into the nature of the vapor-MPN interactions, including systematic variations in apparent film swelling efficiencies, and show that the model can predict CR responses typically to within 24%. Using CRs of different dimensions, vapor sensitivities are found to be virtually independent of the MPN film volume over a range of 104 (device-area x MPN layer thickness). Sensitivities vary inversely with analyte vapor pressure similarly for the two sensor types, but the CR sensor affords significantly greater signal-to-noise ratios, yielding calculated detection limits in the low-part-per-billion concentration range for several of the analytes tested. The implications of these results for implementing MPN-coated CR arrays as detectors in microanalytical systems are considered.
CD52 antigen--a review. (2001)

Human CD52 is a glycosylphosphatidylinositol (GPI)--anchored antigen expressed on the all lymphocytes as well as within the male genital tract, where it can be produced by epithelial cells of the distal epididymis and duct deferens. CD52 can be shed into seminal plasma and then acquired by sperm cells during their passage through the genital tract, thus it is detectable on the surface of epididymal sperm and in the ejaculate but not on either spermatogenetic cells or testicular spermatozoa. Protein core of the sperm and lymphocyte CD52 is identical and it is a product of a single copy gene located on chromosome 1. However, N-linked carbohydrate side chains (attached to Asn-3) and GPI-anchor structure are different. Physiological role of CD52 on lymphocytes is unclear, although antibody directed to CD52, CAMPATH-1, is capable of complement activation and it can be clinically useful to treat lympho-proliferative disorders and to deplete lymphocytes in bone marrow transplants. Monoclonal antibodies directed against sperm CD52 may cause sperm immobilisation and agglutination and affect hamster oocyte penetration suggesting an association of this molecule with fertilisation.
Molecular characterization of a 40‐kDa outer membrane protein, FomA, of Fusobacterium periodonticum and comparison with Fusobacterium nucleatum (1995)

The 40 kDa-outer membrane protein FomA of Fusobacterium periodonticum ATCC 33693 was found to exhibit heat modifiable properties, typical for a porin, and N-terminal sequencing indicated a close relationship to the porin FomA of Fusobacterium nucleatum. A polymerase chain reaction approach was therefore applied for sequencing the fomA gene of F. periodonticum, and nucleotide and deduced amino acid sequences were aligned and compared with the corresponding sequences of different strains of F. nucleatum. In all strains we found a common protein upstream of the fomA gene. The noncoding area upstream of the putative -35 region of the F. periodonticum fomA gene exhibited little sequence similarity with the F. nucleatum gene. The transcriptional unit of FomA, on the other hand, was very similar, with the similarities concentrated in domains that were interspersed with hypervariable regions. A topology model was made and compared with those made for F. nucleatum. This indicated that the great similarities reside in the membrane-spanning segments of the protein, while most cell surface exposed loops were hypervariable. The results strongly support the proposed model for FomA and also indicate that these taxa are related but on a lower level than the subspecies level. The codon usage of F. periodonticum is comparable to that of F. nucleatum, and the triplet AGA is the only codon used for arginine.
Synergies between Bio‐ and Oil Refineries for the Production of Fuels from Biomass (2007)

As petroleum prices continue to increase, it is likely that biofuels will play an ever-increasing role in our energy future. The processing of biomass-derived feedstocks (including cellulosic, starch- and sugar-derived biomass, and vegetable fats) by catalytic cracking and hydrotreating is a promising alternative for the future to produce biofuels, and the existing infrastructure of petroleum refineries is well-suited for the production of biofuels, allowing us to rapidly transition to a more sustainable economy without large capital investments for new reaction equipment. This Review discusses the chemistry, catalysts, and challenges involved in the production of biofuels.
Domain II of Pseudomonas Exotoxin A Arrests the Transfer of Translocating Nascent Chains into Mammalian Microsomes (1994)

The translocation of PE from the extracytosolic compartment to the cytosol during the intoxication of mammalian cells is mediated by domain II of the toxin. We have shown previously that within domain II amino acids 280-313 of PE promote their own export from mammalian microsomes following signal sequence-directed membrane insertion. In this study, we attempted to target full-length PE into mammalian microsomes using the preprocecropin signal sequence, but found that translocation was arrested to generate a transmembrane protein. "Stop transfer" required the presence of amino acids 280-313 of PE, and the first 313 amino acids of PE were sufficient to generate a transmembrane protein (N-terminus-in/C-terminus-out). The mechanism of stop transfer appears to be different from that described previously because amino acids 280-313 of PE are not highly hydrophobic and do contain many charged residues. In addition, the transmembrane segment appeared to be influenced by the cytoplasmic domain of the transmembrane proteins.
Antibody Raised to AKAAAKAAAKA Sequence on Tropoelastin Recognizes Tropoelastin but not Mature Crosslinked Elastin: A New Tool in Metabolic and Structural Studies of Elastogenesis (1999)

Tropoelastin, which is secreted from the cell in a soluble form, contains specific alanine rich repeat domains that are destined to form covalent desmosine and isodesmosine crosslinks in mature insoluble elastin. We raised a monospecific polyclonal antibody to a AKAAAKAAAKA synthetic peptide (AKA) which represents this alanine rich region of tropoelastin. The antibody was reactive with the original peptide antigen and purified tropoelastin, but not with mature crosslinked elastin isolated from several animal species. Conditioned media from chick aorta smooth muscle cells in culture reacted in an ELISA with the AKA antibody, but only in the presence of BAPN to block the conversion of the epsilon-amino groups to aldehydes. Immunofluorescence demonstrated that the AKA antibody decorated newly deposited tropoelastin assembled in fine fibrils in matrix produced by cultured human skin fibroblasts. EM-immunogold specifically localized this antibody to the immature elastic fibers present in fetal sheep ductus arteriosus. Moreover, immunohistochemistry demonstrated that the antibody recognized nonpolymerized tropoelastin assembled on the periphery of elastic fibers in the aorta of chicks raised on copper deficient and BAPN containing diets. These studies demonstrate that this new anti-tropoelastin antibody can be used as a useful tool to investigate elastin metabolism where it is important to distinguish between tropoelastin and mature crosslinked elastin.
Cellular pH gradient in tumor versus normal tissue: potential exploitation for the treatment of cancer. (1996)

Although limited data exist, electrode-measured pH values of human tumors and adjacent normal tissues, which are concurrently obtained by the same investigator in the same patient, consistently show that the electrode pH (believed to primarily represent tissue extracellular pH) is substantially and consistently lower in the tumor than in normal tissue. In contrast, the 31P-magnetic resonance spectroscopy estimated that intracellular pH is essentially identical or slightly more basic in tumor compared to normal tissue. As a consequence, the cellular pH gradient is substantially reduced or reversed in tumor compared to normal tissue: in normal tissue the extracellular pH is relatively basic, and in tumor tissue the magnitude of the pH gradient is reduced or reversed. The difference provides an exploitable avenue for the treatment of cancer. The extent to which drugs exhibiting weakly acid or basic properties are ionized is strongly dependent on the pH of their milieu. Weakly acidic drugs which are relatively lipid soluble in their nonionized state may diffuse freely across the cell membrane and, upon entering a relatively basic intracellular compartment, become trapped and accumulate within a cell, leading to substantial differences in the intracellular/extracellular drug distribution between tumor and normal tissue for drugs exhibiting appropriate pKas.
Size and genomic location of the pMGA multigene family of Mycoplasma gallisepticum (1996)

The pMGA multigene family encodes variant copies of the cell surface haemagglutinin of Mycoplasma gallisepticum. Quantitative Southern blotting, using an oligonucleotide probe complementary to a region conserved in the leader sequence of all known pMGA genes, was used to estimate the number of members of the family in the genome of seven strains of M. gallisepticum. The number of copies estimated to be present in the genome varied from 32 in strain F to 70 in strain R, indicating that the pMGA gene family may be second in size only to the tRNA family among prokaryotes. If all members of the pMGA family are of similar length to those which have been characterized, a minimum of 79 kb (7.7%) of the genome of strain S6, 82 kb (8.2%) of PG31 and 168 kb (16%) of the genome of strain R is dedicated to encoding variants of the same haemagglutinin. The GAA repeat motif identified in the intergenic region between all characterized pMGA genes appeared to be a feature common to most, if not all, pMGA genes, and furthermore probably exclusive to them. The genomic locations of members of the pMGA family were determined by PFGE and Southern blot hybridization of M. gallisepticum strain S6. The hybridizing regions were localized to four separate regions on the chromosome. The pMGA genes are likely to be predominantly arranged as tandem repeats within these regions, similar to the restricted regions for which the genomic sequence has been determined.
Impact of Protein Folding on Biotechnology (1993)

Protein folding has played a major role in both academic and industrial research and development in biotechnology. The biotechnology industry has relied on both in vivo and in vitro protein folding to successfully produce the currently approved therapeutic proteins. In this article, the methods used to produce therapeutic proteins are discussed along with the rationale for choosing an expression system. An industrial perspective of the protein folding problem and potential solutions is provided with an emphasis on the practical aspects of improving in vivo or in vitro folding based on current research. In addition, the future directions of research in protein folding are projected focusing on the potential for improving in vivo folding, predicting protein structure, and ultimately developing new therapeutics.
Determination of the orientation of aromatic molecules adsorbed on platinum electrodes. The effect of solute concentration (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the orientation of aromatic molecules adsorbed on platinum electrodes. The effect of solute concentrationManuel P. Soriaga and Arthur T. HubbardCite this: J. Am. Chem. Soc. 1982, 104, 14, 3937–3945Publication Date (Print):July 1, 1982Publication History Published online1 May 2002Published inissue 1 July 1982https://pubs.acs.org/doi/10.1021/ja00378a026https://doi.org/10.1021/ja00378a026research-articleACS PublicationsRequest reuse permissionsArticle Views478Altmetric-Citations127LEARN 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
Targeting key angiogenic pathways with a bispecific Cross MA b optimized for neovascular eye diseases (2017)

This editorial expression of concern is to alert our readership that the data presented in Figures 4 and 5 require further analysis and verification. The scientific record will be updated once this process has been completed. J.T.R., P.L.v.L., R.F., D.I., E.N., G.W., P.S., C.K., D.T.S., and G.H. agree. The other authors could either not be reached or did not provide a response.
Multiplex genotype determination at a large number of gene loci. (1996)

To facilitate large-scale genotype analysis, an efficient PCR-based multiplex approach has been developed. For simultaneously amplifying the target sequences at a large number of genetic loci, locus-specific primers containing 5' universal tails are used. Attaching the universal tails to the target sequences in the initial PCR steps allows replacement of all specific primers with a pair of primers identical to the universal tails and converts the multiplex amplification into "uniplex." Simultaneous amplification of 26 genetic loci with this approach is described. The multiplex amplification can be coupled with genotype determination. By incorporating a single-base mismatch between a primer and the template into the target sequences, a polymorphic site can be converted into a desirable restriction fragment length polymorphism when it is necessary. In this way, the allelic PCR products for the polymorphic loci can be discriminated by gel electrophoresis after restriction enzyme digestion. In this study, 32 loci were typed in such a multiplex way.
[Genealogic study of women suffering from alcoholism and drug addiction]. (1992)

The similarity of hereditary load in the women, suffering from alcoholism and drug addiction has been determined. The degree of parents exogamy has no influence on daughters resistance to alcoholism and drug addiction. The sick women with loaded pedigree have higher probability to form concordant couple than unloaded ones.
An investigation of circuit partitioning for parallel test generation (2003)

Explores the feasibility of using circuit partitioning approach to reduce the run-time complexity of test generation via parallel processing. Characterization of the major phases of test generation is used to show how the inherent parallelism existing in test generation can be exploited during forward implication and backward justification. Upper bounds on the concurrency available in specific are empirically determined by simulating the behavior of a 'perfect' conflict-free test generation algorithm that operates without backtracking. Results presented for a number of benchmark circuits indicate that the average available parallelism is fairly low, limiting the potential speedup of a circuit partitioning approach to test generation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mechanisms of Action of Adjuvants (2013)

Adjuvants are used in many vaccines, but their mechanisms of action are not fully understood. Studies from the past decade on adjuvant mechanisms are slowly revealing the secrets of adjuvant activity. In this review, we have summarized the recent progress in our understanding of the mechanisms of action of adjuvants. Adjuvants may act by a combination of various mechanisms including formation of depot, induction of cytokines and chemokines, recruitment of immune cells, enhancement of antigen uptake and presentation, and promoting antigen transport to draining lymph nodes. It appears that adjuvants activate innate immune responses to create a local immuno-competent environment at the injection site. Depending on the type of innate responses activated, adjuvants can alter the quality and quantity of adaptive immune responses. Understanding the mechanisms of action of adjuvants will provide critical information on how innate immunity influences the development of adaptive immunity, help in rational design of vaccines against various diseases, and can inform on adjuvant safety.
Bcl-2 Antisense Oligonucleotide Overcomes Resistance toE1AGene Therapy in a Low HER2-Expressing Ovarian Cancer Xenograft Model (2005)

We are currently conducting clinical trials of E1A gene therapy for patients with ovarian cancer. The adenovirus type 5 E1A gene suppresses growth of ovarian cancer cells that overexpress HER-2/neu (HER2) and growth of some--but not all--that express low HER2. In HER2-overexpressing cells, suppression by E1A is predominantly by down-regulation of HER2, but the mechanism in low HER2-expressing cells is not fully understood. The adenoviral E1B protein has sequential and functional homology to Bcl-2 and prolongs the viability of adenovirus host cells by inhibiting E1A-induced apoptosis. Bcl-2 is overexpressed in ovarian cancer and participates in chemoresistance; we hypothesized that Bcl-2 inhibits E1A-induced apoptosis leading to resistance to E1A gene therapy. E1A suppressed colony formation of ovarian cancer cells that express low levels of Bcl-2 and HER2 (OVCAR-3 and OVCA 433), but enhanced colony formation in low HER2-, high Bcl-2-expressing ovarian cancer cells (2774 and HEY). Treating 2774 or HEY cells with antisense oligonucleotide Bcl-2 (Bcl-2-ASO) did not reduce cell viability. E1A combined with Bcl-2-ASO led to significant decreases in cell viability resulting from increased apoptosis relative to cells treated with E1A alone (P < 0.05). The increase in apoptosis was partly due to cytochrome c release and subsequently caspase-9 activation by Bcl-2-ASO. Finally, in an ovarian cancer xenograft model, treatment with Bcl-2-ASO did not prolong survival, but E1A plus Bcl-2-ASO did (P < 0.001). In conclusion, ovarian tumors overexpressing Bcl-2 may not respond well to E1A gene therapy, but treatment with a combination of E1A and Bcl-2-ASO may overcome this resistance.