gebhart/patrepeval huggingface dataset:
Pathway of Detergent‐Mediated and Peptide Ligand‐Mediated Refolding of Heterodimeric Class II Major Histocompatibility Complex (MHC) Molecules (1997)

We investigated the mechanism of refolding and reassembly of recombinant alpha and beta chains of the class II major histocompatibility molecules (MHC-II) HLA-DRB5*0101. Both chains were expressed in the cytosol of Escherichia coli, purified in urea and SDS, and reassembled to functional heterodimers by replacement of SDS by mild detergents, incubation in a redox-shuffling buffer and finally by oxidation and removal of detergent. Refolding was mediated by mild detergents and by peptide ligands. Early stages of structure formation were characterized by circular dichroism, fluorescence, and time-resolved fluorescence anisotropy decay (FAD) spectroscopies. We found that formation of secondary structure was detectable after replacement of SDS by mild detergents. At that stage the alpha and beta chains were still monomeric, the buffer was strongly reducing, and the folding intermediates did not yet interact with peptide ligands. Formation of folding intermediates capable of interacting with peptide ligands was detected after adjusting the redox potential with oxidized glutathione and incubation in mild detergents. We conclude that at that stage a tertiary structure close to the native structure is formed at least locally. The nature and concentration of detergent critically determined the refolding efficiency. We compared detergents with different carbohydrate headgroups, and with aliphatic chains ranging from C6 to C14 in length. For each of the detergents we observed a narrow concentration range for mediating refolding. Surprisingly, detergents with long aliphatic chains had to be used at higher concentrations than short-chain detergents, indicating that increasing the solubility of folding intermediates is not the only function of detergents during a refolding reaction. We discuss structure formation and interactions of detergents with stable folding intermediates. Understanding such interactions will help to develop rational strategies for refolding hydrophobic or oligomeric proteins.
Experimental Antitumor Activity of Pyrazomycin (1973)

Summary Pyrazomycin (PM) completely inhibited the growth of Walker carcinosarcoma 256. Mammary carcinoma 755, Gardner lymphosarcoma, and X5563 plasma cell myeloma were inhibited more than 50% by PM. Tumors that showed more than a minimum response of 30% were the C3H and 115 mammary carcinomas, Mecca lymphosarcoma, Taper liver tumor, and Ridgeway osteogenic sarcoma. The S91 melanoma, Sarcoma 180 ascites tumors, and Ehrlich ascites solid tumor showed no significant biological responses. PM also caused several well-established dimethyl-benzanthracene-induced mammary carcinomas to regress completely. The majority of the dimethylbenzanthracene-induced tumors in the treated rats regressed to some degree while most of the control tumors increased in size. The murine leukemias L1210, C1498, P1534, AKR, P388, or B82 showed no response to PM. Although PM did not inhibit the Ehrlich or Sarcoma 180 ascites tumors in mice, PM did cause up to 90% prolongation of life in rats with the Walker carcinosarcoma 256 ascites, and 9 of the 30 rats survived more than 45 days. PM showed comparable activity against either Walker carcinosarcoma 256 or Gardner lymphosarcoma when given p.o., i.p., i.v., or i.m. It also showed comparable activity against Walker carcinosarcoma 256 when given once every 2, 3, 4, or 5 days. Plasma levels of PM-like activity were detected 3 days after a single p.o. dose of PM at 10 mg/kg in rats.
Thermally Activated Delayed Fluorescence from Sn4+–Porphyrin Complexes and Their Application to Organic Light Emitting Diodes — A Novel Mechanism for Electroluminescence (2009)

Electroluminescence based on TADF, that is, thermally activated delayed fluorescence, is demonstrated in Sn4+–porphyrin complexes. On excitation by a short electrical pulse, prompt and delayed electroluminescence components were clearly observed. The delayed component was composed of both TADF and phosphorescence (see figure), and the TADF component significantly increased with increasing temperature.
Melodic matching techniques for large music databases (1999)

With the growth in digital representations of music, and of music stored in these representations, it is increasingly attractive to search collections of music. One mode of search is by similarity, but, for music, similarity search presents several difficulties: in particular, for melodic query support, deciding what part of the music is likely to be perceived as the theme by a listener, and deciding whether two pieces of music with different sequences of notes represent the same theme. In this paper we propose a three-stage framework for matching pieces of music. We use the framework to compare a range of techniques for determining whether two pieces of music are similar, by experimentally testing their ability to retrieve different transcriptions of the same piece of music from a large collection of MIDI files. These experiments show that different comparison techniques differ widely in their effectiveness; and that, by instantiating the framework with appropriate music manipulation and comparison techniques, pieces of music that match a query can be identified in a large collection.
Optical activity of single‐stranded polydeoxyadenylic and polyriboadenylic acids; dependence of adenine chromophore cotton effects on polymer conformation (1969)

Abstract Circular dichroism (CD) curves are reported for poly dA, (pdA) 6 , (pdA) 2 , poly A, ApAp, ApA, AMP, dApA, pdApA, A‐2′‐ O ‐methyl pA, and A‐2′‐ O ‐methyl pAp. Analysis of these curves indicated the presence of single CD bands at 228–230 mμ and at 278–280 mμ in oligomers longer than dinucleotides. In the case of dinucleotides and mononucleotides (from the literature, in addition to those studied here), the 230 mμ CD of band appears but the 280 mμ CD band does not. We assign the 230 mμ band to a very weak π–π* transition at this wavelength. From theoretical considerations, we show that the 280 mμ band is not an exciton component of the strong π–π* transition at 260 mμ in adenine. We conclude that the 280 mμ CD band must be assigned to a distinct absorption, not previously reported, which we suggest arises from an n –π* transition. The fact that the n –π* CD band at 280 mμ is not seen in mononucleotides or dinucleotides is ascribed to solvation of the adenine ring by water, which shifts the band to shorter wavelengths. Therefore, only interior residues of oligomers have the 280 mμ band, and the optical activity of a polymer cannot be computed from that of a dinucleotide, by using a nearest‐neighbor approximation. The existence of this end effect hag been tested, by taking it into account in computing the rotational strengths of the 278 mμ n –π* transition for several oligomers; it is pointed out that a more sensitive test of this end effect would require CD data for the oligo dA series of 3 to 5 residues. We speculate about the structural and optical differences between poly dA and poly A, and point out the need for a theoretical treatment of n –π* Cotton effects in polynucleotides.
Effect of resist components on image spreading during postexposure bake of chemically amplified resists (2000)

The ultimate feature size achievable using a chemically amplified resist is determined by chemical and physical processes occurring during the post-exposure bake process. Using a combined experimental-modelling procedure we previously have developed a physically accurate, predictive description of coupled deprotection and diffusion in poly(p- tert-butyloxycar-bonyloxystyrene) (PTBOCST) resist containing a diaryliodonium perfluorobutanesulfonate salt as photoacid generator (PAG). In the present work we extend that study to quantify the impact of anion size and of added base on resist reaction diffusion kinetics. Our results show that both short and long range mobility of the PAG anion influence image spreading; the small triflate counterion leads to acid diffusion larger by a factor of 9 - 70 than that observed with the larger perfluoro-butanesulfonate counterion. The addition of tetra-n-butylammonium hydroxide leads to an overall suppression of image spreading in the exposed resist. This effect can be analyzed quantitatively using a proportional neutralization model, which reveals that base addition can lead to an overall sharpening of the developable latent image of deprotection even in the absence of acid diffusion.
Preliminary characterization of four bacteriocins from Streptococcus mutans (1990)

The various properties of the inhibitory substances produced by Streptococcus mutans strains C67-1, Ny257-S, Ny266, and T8, and the fact that inhibitory zones produced could not be associated with lactic acid (or other organic acids), bacteriophages, or hydrogen peroxide indicate that these substances can be classified as mutacins. The substances produced by strains C67-1, Ny266, and T8 possessed similar properties. They were shown to be thermoresistant (100 degrees C, 30 min), low molecular weight (less than 3500) substances sensitive to proteolytic enzymes (chymotrypsin, papain, pronase E, proteinase K, and trypsin) and they were active against most of the Gram-positive bacteria tested but not against most of the Gram-negative bacteria. The substance produced by strain Ny257-S differs from the other three by its narrower activity spectrum, its lower thermoresistance (80 degrees C, 30 min), and its higher molecular weight (8,000-14,000). The gene or the genes coding for the mutacins are probably located on the chromosome since no plasmid DNA could be detected in these four producing strains. Restriction-fragment patterns of C67-1 and T8 suggest that these strains are closely related, as supported by the strong similarity observed between the properties of their mutacins.
Global spliceosome activity regulates entry into cellular senescence (2020)

Cellular senescence is a state of permanent growth arrest that can ultimately contribute to aging. Senescence can be induced by various stressors and is associated with a myriad of cellular functions and phenotypic markers. Alternative splicing is emerging as a critical contributor to senescence and aging. However, it is unclear how the composition and function of the spliceosome are involved in senescence. Here, using replicative and oxidative stress-induced senescence models in primary human fibroblasts, we report a common shift in the expression of 58 spliceosomal genes at the pre-senescence stage, prior to the detection of senescence-associated β-galactosidase (SA-β-gal) activity. Spliceosomal perturbation, induced by pharmacologic and genetic inhibition of splicesomal genes, triggered cells to enter senescence, suggesting a key role as a gatekeeper. Association analysis of transcription factors based on the 58 splicesomal genes revealed Sp1 as a key regulator of senescence entry. Indeed, Sp1 depletion suppressed the expression of downstream spliceosomal genes (HNRNPA3, SRSF7, and SRSF4) and effectively induced senescence. These results indicate that spliceosomal gene sets, rather than a single spliceosomal gene, regulate the early transition into senescence prior to SA-β-gal expression. Furthermore, our study provides a spliceosome signature that may be used as an early senescence marker.
Arbitrarily Primed PCR To Type Vibrio spp. Pathogenic for Shrimp (1999)

A molecular typing study on Vibrio strains implicated in shrimp disease outbreaks in New Caledonia and Japan was conducted by using AP-PCR (arbitrarily primed PCR). It allowed rapid identification of isolates at the genospecies level and studies of infraspecific population structures of epidemiological interest. Clusters identified within the species Vibrio penaeicida were related to their area of origin, allowing discrimination between Japanese and New Caledonian isolates, as well as between those from two different bays in New Caledonia separated by only 50 km. Other subclusters of New Caledonian V. penaeicida isolates could be identified, but it was not possible to link those differences to accurate epidemiological features. This contribution of AP-PCR to the study of vibriosis in penaeid shrimps demonstrates its high discriminating power and the relevance of the epidemiological information provided. This approach would contribute to better knowledge of the ecology of Vibrio spp. and their implication in shrimp disease in aquaculture.
Hypoxia Promotes Osteogenesis but Suppresses Adipogenesis of Human Mesenchymal Stromal Cells in a Hypoxia-Inducible Factor-1 Dependent Manner (2012)

Hypoxia promotes osteogenesis but suppresses adipogenesis of human MSCs in a competitive and HIF-1-dependent manner. We therefore conclude that the effects of hypoxia are crucial for effective bone healing, which may potentially lead to the development of novel therapeutic approaches.
Hsp27 inhibits release of mitochondrial protein Smac in multiple myeloma cells and confers dexamethasone resistance (2003)

Smac, second mitochondria-derived activator of caspases, promotes apoptosis via activation of caspases. Heat shock protein 27 (Hsp27) negatively regulates another mitochondrial protein, cytochrome c, during apoptosis; however, the role of Hsp27 in modulating Smac release is unknown. Here we show that Hsp27 is overexpressed in both dexamethasone (Dex)-resistant multiple myeloma (MM) cell lines (MM.1R, U266, RPMI-8226) and primary patient cells. Blocking Hsp27 by an antisense (AS) strategy restores the apoptotic response to Dex in Dex-resistant MM cells by triggering the release of mitochondrial protein Smac, followed by activation of caspase-9 and caspase-3. Moreover, AS-Hsp27 overcomes interleukin-6 (IL-6)-mediated protection against Dex-induced apoptosis. These data demonstrate that Hsp27 inhibits the release of Smac, and thereby confers Dex resistance in MM cells.
Histones and basic polypeptides activate Ca2+/cation influx in various cell types (1998)

Histone H2A (1-10 microg/ml) added to Ehrlich ascite cell suspensions promoted: (i) Ca2+ influx, but no apparent intracellular Ca2+ mobilization; (ii) plasma-membrane depolarization and Na+ influx in Ca2+-free medium, which were recovered by Ca2+ readmission; (iii) influx of other cations such as Ba2+, Mn2+, choline+ and N-methyl-d-glucamine+, but not of propidium+, ethidium bromide and Trypan Blue. H2A-induced Ca2+ influx and cell depolarization were: (i) blocked by La3+ and Gd3+, but not by various inhibitors of receptor-activated Ca2+-influx pathways/channels; (ii) mimicked by various basic polypeptides, with Mr>4000; (iii) prevented or reversed by polyanions such as polyglutamate or heparin; (iv) present in other cell types, such as Jurkat, PC12 and Friend erythroleukaemia cells, but virtually absent from rat hepatocytes and thymocytes. We conclude that cationic proteins/polypeptides, by interacting in a cell-specific manner with the cell surface, can activate in those cells putative non-selective Ca2+ channels and membrane depolarization.
ET-743: a novel agent with activity in soft-tissue sarcomas (2006)

ET-743 is a novel active drug for sarcoma which yields prolonged disease-free survival in subsets of patients.
High-Resolution Analysis of DNA Copy Number Using Oligonucleotide Microarrays (2004)

Genomic copy number alterations are a feature of many human diseases including cancer. We have evaluated the effectiveness of an oligonucleotide array, originally designed to detect single-nucleotide polymorphisms, to assess DNA copy number. We first showed that fluorescent signal from the oligonucleotide array varies in proportion to both decreases and increases in copy number. Subsequently we applied the system to a series of 20 cancer cell lines. All of the putative homozygous deletions (10) and high-level amplifications (12; putative copy number >4) tested were confirmed by PCR (either qPCR or normal PCR) analysis. Low-level copy number changes for two of the lines under analysis were compared with BAC array CGH; 77% (n = 44) of the autosomal chromosomes used in the comparison showed consistent patterns of LOH (loss of heterozygosity) and low-level amplification. Of the remaining 10 comparisons that were discordant, eight were caused by low SNP densities and failed in both lines. The studies demonstrate that combining the genotype and copy number analyses gives greater insight into the underlying genetic alterations in cancer cells with identification of complex events including loss and reduplication of loci.
Abnormalities of p53 and p110RB tumor suppressor gene expression in human soft tissue tumors: correlations with cell proliferation and tumor grade. (1995)

The authors tested the hypothesis that alterations in tumor suppressor gene expression play a role in tumorigenesis of human soft tissue tumors through alterations in control of cell proliferation. Using a set of 66 soft tissue tumors, including benign tumors and all three grades of sarcomas, expression of the p53 and p110RB tumor suppressor gene products were localized using sensitive immunocytochemistry techniques. The hypothesis that alterations in tumor suppressor gene expression was related to cell proliferation was tested by simultaneously demonstrating the expression of the proliferating cell nuclear antigen in methacarn-fixed, paraffin-embedded tissue sections of the same tumors. Twenty-two of 66 (33%) and 35 of 68 (53%) tumors demonstrated any degree of p53 overexpression or loss of p110RB, respectively. A strong correlation between increasing tumor grade and both p53 overexpression (P = 0.006) and loss of p110RB (P = 0.003) was found. Although there was a correlation between increasing proliferating cell nuclear antigen index and overexpression of p53 (P = 0.04), no correlations were found between cell proliferation indices and loss of p110RB (P = 0.19). Finally, there was a significant correlation between the presence of immunocytochemically detectable p53 overexpression and detectable p110RB loss (P = 0.02). These studies suggest that although alterations in p110RB may play a role in soft tissue sarcoma tumorigenesis and be related to p53 dysfunction, p110RB may act through mechanisms other than direct loss of cell proliferation control.
Matchmaker (2003)

Texture mapping enhances the visual realism of 3D models by adding fine details. To achieve the best results, it is often necessary to force a correspondence between some of the details of the texture and the features of the model.The most common method for mapping texture onto 3D meshes is to use a planar parameterization of the mesh. This, however, does not reflect any special correspondence between the mesh geometry and the texture. The Matchmaker algorithm presented here forces user-defined feature correspondence for planar parameterization of meshes. This is achieved by adding positional constraints to the planar parameterization. Matchmaker allows users to introduce scores of constraints while maintaining a valid one-to-one mapping between the embedding and the 3D surface. Matchmaker's constraint mechanism can be used for other applications requiring parameterization besides texture mapping, such as morphing and remeshing.Matchmaker begins with an unconstrained planar embedding of the 3D mesh generated by conventional methods. It moves the constrained vertices to the required positions by matching a triangulation of these positions to a triangulation of the planar mesh formed by paths between constrained vertices. The matching triangulations are used to generate a new parameterization that satisfies the constraints while minimizing the deviation from the original 3D geometry.
Introduction: The Poetics of the Eruv (2011)

Abstract The eruv is a talmudic provision that permits orthodox Jews to carry small objects outside of their homes on the Sabbath, a practice that would otherwise be forbidden on that day. Often intended to be visible, it is marked in a variety of ways with a range of materials, and frequently serves as a metaphor for relations within a community, as suggested in the articles and works of art included in the symposium and portfolio to which this essay serves as an introduction.
Finding the most significant common sequence and structure motifs in a set of RNA sequences (1997)

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.
Toxoplasmic Encephalitis in AIDS (1992)

Involvement of the central nervous system (CNS) is common in patients with advanced disease due to human immunodeficiency virus (HIV). Symptoms range from lethargy and apathy to coma, incoordination and ataxia to hemiparesis, loss of memory to severe dementia, and focal to major motor seizures. Involvement may be closely associated with HIV infection per se, as in the AIDS dementia complex, but is frequently caused by opportunistic pathogens such as Toxoplasma gondii and Cryptococcus neoformans or malignancies such as primary lymphoma of the CNS. The clinical presentations of attendant and direct CNS involvement are remarkably non-specific and overlapping, yet a correct diagnosis is critical to successful intervention. Toxoplasmic encephalitis is one of the most common and most treatable causes of AIDS-associated pathology of the CNS. A great deal has been learned in the last 10 years about its unique presentation in the HIV-infected patient with advanced disease. Drs. Benjamin J. Luft of the State University of New York at Stony Brook and Jack S. Remington of the Stanford University School of Medicine and Palo Alto Medical Foundation's Research Institute have studied T. gondii for many years and are two of the leading experts in the field. This commentary comprises an update of their initial review (J Infect Dis 1988;157:1-6) and a presentation of the current approaches to diagnosing and managing toxoplasmic encephalitis in HIV-infected patients.
Automatically generating malicious disks using symbolic execution (2006)

Many current systems allow data produced by potentially malicious sources to be mounted as a file system. File system code must check this data for dangerous values or invariant violations before using it. Because file system code typically runs inside the operating system kernel, even a single unchecked value can crash the machine or lead to an exploit. Unfortunately, validating file system images is complex: they form DAGs with complex dependency relationships across massive amounts of data bound together with intricate, undocumented assumptions. This paper shows how to automatically find bugs in such code using symbolic execution. Rather than running the code on manually-constructed concrete input, we instead run it on symbolic input that is initially allowed to be "anything." As the code runs, it observes (tests) this input and thus constrains its possible values. We generate test cases by solving these constraints for concrete values. The approach works well in practice: we checked the disk mounting code of three widely-used Linux file systems: ext2, ext3, and JFS and found bugs in all of them where malicious data could either cause a kernel panic or form the basis of a buffer overflow attack.