gebhart/patrepeval huggingface dataset:
Fiber diffraction of synthetic α-synuclein filaments shows amyloid-like cross-β conformation (2000)

Filamentous inclusions made of alpha-synuclein constitute the defining neuropathological characteristic of Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Rare familial cases of Parkinson's disease are associated with mutations A53T and A30P in alpha-synuclein. We report here the assembly properties and secondary structure characteristics of recombinant alpha-synuclein. Carboxy-terminally truncated human alpha-synuclein (1-87) and (1-120) showed the fastest rates of assembly, followed by human A53T alpha-synuclein, and rat and zebra finch alpha-synuclein. Wild-type human alpha-synuclein and the A30P mutant showed slower rates of assembly. Upon shaking, filaments formed within 48 h at 37 degrees C. The related proteins beta- and gamma-synuclein only assembled after several weeks of incubation. Synthetic human alpha-synuclein filaments were decorated by an antibody directed against the carboxy-terminal 10 amino acids of alpha-synuclein, as were filaments extracted from dementia with Lewy bodies and multiple system atrophy brains. Circular dichroism spectroscopy indicated that alpha-synuclein undergoes a conformational change from random coil to beta-sheet structure during assembly. X-ray diffraction and electron diffraction of the alpha-synuclein assemblies showed a cross-beta conformation characteristic of amyloid.
The Length of the Cervix and the Risk of Spontaneous Premature Delivery (1996)

The risk of spontaneous preterm delivery is increased in women who are found to have a short cervix by vaginal ultrasonography during pregnancy.
The Nonconcept of Species Diversity: A Critique and Alternative Parameters (1971)

The recent literature on species diversity contains many semantic, conceptual, and technical problems. It is suggested that, as a result of these problems, species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species-number relations and rely less on information theoretic and other analogies. As multispecific collections of organisms possess numerous statistical properties which conform to the conventional criteria for diversity indices, such collections are not intrinsically arrangeable in linear order along some diversity scale. Several such properties or "species composition parameters" having straightforward biological interpretations are presented as alternatives to the diversity approach. The two most basic of these are simply ▵<sub>1</sub> =[n/n-1][<sup>1</sup><sup>-</sup><sup>Σ</sup><sub>i</sub> (<sup>N</sup> _i/_N)<sup>2</sup> ] =the proportion of potential interindividual encounters which is interspecific (as opposed to intraspecific), assuming every individual in the collection can encounter all other individuals, E(S<sub>n</sub> ) = <sup>Σ</sup><sub>i</sub> [1-(<sup>N</sup><sup>-</sup><sup>N</sup><sub>i</sub><sub>n</sub> )/(<sup>N</sup><sub>n</sub> )] =the expected number of species in a sample of n individuals selected at random from a collection containing N individuals, S species, and N<sub>i</sub> individuals in the ith species.
Ambiguity function as a design tool for high focal depth (1988)

The optical transfer functions for variable focus error are contained as a single picture representation in the ambiguity function that is associated with the pupil function. This picture representation is shown to be useful for designing pupil functions that increase the depth of focus. We specify a criterion for an optical transfer function with low sensitivity defocus in terms of a nonlinear differential equation for the point spread function. Based on this approach, we design and compare five new spatial filters for achieving high focal depth.
Identification of a Streptolysin S-Associated Gene Cluster and Its Role in the Pathogenesis ofStreptococcus iniaeDisease (2002)

Streptococcus iniae causes meningoencephalitis and death in cultured fish species and soft-tissue infection in humans. We recently reported that S. iniae is responsible for local tissue necrosis and bacteremia in a murine subcutaneous infection model. The ability to cause bacteremia in this model is associated with a genetic profile unique to strains responsible for disease in fish and humans (J. D. Fuller, D. J. Bast, V. Nizet, D. E. Low, and J. C. S. de Azavedo, Infect. Immun. 69:1994-2000, 2001). S. iniae produces a cytolysin that confers a hemolytic phenotype on blood agar media. In this study, we characterized the genomic region responsible for S. iniae cytolysin production and assessed its contribution to virulence. Transposon (Tn917) mutant libraries of commensal and disease-associated S. iniae strains were generated and screened for loss of hemolytic activity. Analysis of two nonhemolytic mutants identified a chromosomal locus comprising 9 genes with 73% homology to the group A streptococcus (GAS) sag operon for streptolysin S (SLS) biosynthesis. Confirmation that the S. iniae cytolysin is a functional homologue of SLS was achieved by PCR ligation mutagenesis, complementation of an SLS-negative GAS mutant, and use of the SLS inhibitor trypan blue. SLS-negative sagB mutants were compared to their wild-type S. iniae parent strains in the murine model and in human whole-blood killing assays. These studies demonstrated that S. iniae SLS expression is required for local tissue necrosis but does not contribute to the establishment of bacteremia or to resistance to phagocytic clearance.
Differential toxicities of anticancer agents among DNA repair and checkpoint mutants of Saccharomyces cerevisiae. (2000)

Most cytotoxic anticancer agents damage DNA directly, interfere with DNA metabolism or chromosome segregation, and are particularly toxic in dividing cells. Although a considerable amount of information on the mechanisms of action of these agents is available, the molecular bases for selective tumor cell killing by chemotherapy are largely unknown. Many genetic alterations found in sporadic and hereditary cancers affect functions in DNA repair and cell cycle control and result in sensitivity to DNA damaging agents. We have therefore set out to determine the effects of these cancer mutations on sensitivity or resistance to various chemotherapeutic agents. Because most of the affected genes are well conserved among eukaryotes, we have carried out a comprehensive analysis of a panel of isogenic yeast strains, each defective in a particular DNA repair or cell cycle checkpoint function, for sensitivity to the Food and Drug Administration-approved cytotoxic anticancer agents. Widely different toxicity profiles were observed for 23 agents and X-rays, indicating that the type of DNA repair and cell cycle checkpoint mutations in individual tumors could strongly influence the outcome of a particular chemotherapeutic regimen.
Characterization of the steric defense of the HIV‐1 gp41 N‐trimer region (2008)

During viral entry, HIV gp41 adopts a transient conformation called the "prehairpin intermediate" in which a highly conserved therapeutic target, the N-trimer, is exposed. Despite extensive discovery efforts, potent and broadly neutralizing antibodies that target the N-trimer are elusive. We previously demonstrated the N-trimer is protected by a steric block that prevents large proteins, such as antibodies, from accessing it. Here we further characterize the steric block and identify its source. To study the N-trimer steric accessibility, we produced two sets of C-peptide inhibitors (a potent inhibitor targeting the N-trimer) fused to cargo proteins of increasing size facing either the virus or cell side of the prehairpin intermediate. Both bulky inhibitor sets show a steric block, but the effect is more pronounced with virus-side cargo. Additionally, both sets maintain their potencies in a modified entry assay that removes possible sources of target cell steric hindrance. These results implicate a viral source, likely gp120, as the primary component of the steric block. In addition, we studied the steric accessibility of the "pocket" region of the N-trimer, a highly attractive drug and vaccine target. We demonstrated a pocket-specific antibody, D5, is more potent as an scFv than as a full-length IgG, suggesting the N-trimer steric restriction extends to the pocket. This characterization will facilitate the design of sterically restricted antigens that mimic the steric environment of the N-trimer in the prehairpin intermediate and are capable of inducing potent and broadly neutralizing antibodies that circumvent the N-trimer steric block.
Modeling acoustics in virtual environments using the uniform theory of diffraction (2001)

Realistic modeling of reverberant sound in 3D virtual worlds provides users with important cues for localizing sound sources and understanding spatial properties of the environment. Unfortunately, current geometric acoustic modeling systems do not accurately simulate reverberant sound. Instead, they model only direct transmission and specular reflection, while diffraction is either ignored or modeled through statistical approximation. However, diffraction is important for correct interpretation of acoustic environments, especially when the direct path between sound source and receiver is occluded.
Single cell origin of multilineage colonies in culture. Evidence that differentiation of multipotent progenitors and restriction of proliferative potential of monopotent progenitors are stochastic processes. (1984)

In this paper, we report analysis of differentiation in human hemopoietic colonies derived from a single cell. Cord blood mononulear cells and panned My-10 antigen-positive bone marrow and cord blood cells were plated in methylcellulose medium containing erythropoietin and conditioned medium. Initially, we performed mapping studies to identify candidate colony-forming cells. Subsequently, using a micromanipulator, we transferred single cells individually to 35-mm dishes for analysis of colony formation. Cellular composition of the colony was determined by identifying all of the cells in the May-Grunwald-Giemsa stained preparation. Of 150 single candidate cells replated, 63 produced colonies. The incidences of single lineage colonies included 19 erythroid, 17 monocyte-macrophage, and 9 eosinophil colonies. There were 18 mixed hemopoietic colonies consisting of cells in two, three, four, and five lineages in varying combinations. In some instances, we noted the predominance of one lineage and the presence of very small populations of cells in a second or third lineage. These results provide evidence for the single-cell origin of human multilineage hemopoietic colonies, and are consistent with the stochastic model of stem cell differentiation in man. They also indicate that restriction of the proliferative potential of committed progenitors is a stochastic process.
Synthetic Gene Networks That Count (2009)

Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.
Lentiviral Vectors Bearing the Cardiac Promoter of the Na+-Ca2+ Exchanger Report Cardiogenic Differentiation in Stem Cells (2008)

Cardiosphere-derived resident cardiac stem cells (CDCs) are readily isolated from adult hearts and confer functional benefit in animal models of heart failure. To study cardiogenic differentiation in CDCs, we developed a method to genetically label and selectively enrich for cells that have acquired a cardiac phenotype. Lentiviral vectors achieved significantly higher transduction efficiencies in CDCs than any of the nine adeno-associated viral (AAV) serotypes tested. To define the most suitable vector system for reporting cardiogenic differentiation, we compared the cell specificity of five commonly-used cardiac-specific promoters in the context of lentiviral vectors. The promoter of the cardiac sodium-calcium exchanger (NCX1) conveyed the highest degree of cardiac specificity, as assessed by transducing seven cell types with each vector and measuring fluorescence intensity by flow cytometry. NCX1-GFP-positive CDC subpopulations, demonstrating prolonged expression of a variety of cardiac markers, could be isolated and expanded in vitro. Finally, we used chemical biology to validate that lentiviral vectors bearing the cardiac NCX1-promoter can serve as a highly accurate biosensor of cardiogenic small molecules in stem cells. The ability to accurately report cardiac fate and selectively enrich for cardiomyocytes and their precursors has important implications for drug discovery and the development of cell-based therapies.
Variable‐Focus Liquid Microlenses and Microlens Arrays Actuated by Thermoresponsive Hydrogels (2007)

Variable-focus cylindrical liquid/liquid microlenses and spherical liquid microlens arrays formed using liquid/liquid interfaces are actuated by thermoresponsive hydrogels (see figure). The shapes of the microlenses are realized by patterning apertures with corresponding shapes. Hydrogels located within microfluidic channels regulate the focal lengths of the microlenses by expanding and contracting, in response to changes in the environmental temperature. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c1561_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
1,4-Addition of the methylenecarbonyl unit (-CH2CO-) to dienes (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1,4-Addition of the methylenecarbonyl unit (-CH2CO-) to dienesE. J. Corey, T. Ravindranathan, and Shiro TerashimaCite this: J. Am. Chem. Soc. 1971, 93, 17, 4326–4327Publication Date (Print):August 1, 1971Publication History Published online1 May 2002Published inissue 1 August 1971https://pubs.acs.org/doi/10.1021/ja00746a058https://doi.org/10.1021/ja00746a058research-articleACS PublicationsRequest reuse permissionsArticle Views556Altmetric-Citations49LEARN 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
Phase II Study of Donepezil in Irradiated Brain Tumor Patients: Effect on Cognitive Function, Mood, and Quality of Life (2006)

Cognitive functioning, mood, and health-related QOL were significantly improved following a 24-week course of the acetylcholinesterase inhibitor donepezil. Toxicities were minimal. We are planning a double blinded, placebo-controlled, phase III trial of donepezil to confirm these favorable results.
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats (1995)

The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles.
Native Type II Collagen‐Induced Arthritis in the Rat (1981)

Antibodies to native bovine type II collagen may be important in initiating arthritis in rats immunized with this antigen. The cross-reactivity of these antibodies with native rat type II collagen was higher in rats that developed arthritis than in those that did not. Depletion of serum C3 levels by cobra venom factor delayed the onset of arthritis until C3 levels were returning to normal; therefore, complement may be involved in initiation of the arthritis, and this arthritis may be an example of an immune complex--mediated disease.
Autogeneic bone marrow and porous biphasic calcium phosphate ceramic for segmental bone defects in the canine ulna. (1991)

The purpose of this study was to evaluate a porous biphasic hydroxyapatite-calcium phosphate ceramic as a modifier and extender of an autogeneic marrow graft for filling a 2.5-cm segmental bony defect. Twenty adult mongrel dogs were surgically treated to create diaphyseal defects in the left ulnae. The defects were (1) filled with autogeneic bone marrow mixed with granular hydroxyapatite-tricalcium phosphate ceramic (granular ceramic); (2) grafted with a solid block of ceramic soaked in autogeneic bone marrow (block ceramic); (3) received no graft (no implant); or (4) were grafted with autogeneic bone marrow alone (bone marrow). All animals were followed clinically and roentgenographically for 24 weeks and then killed. Repair of diaphyseal defects with the block ceramic led to three solid unions and three fibrous unions; with the granular ceramic implants and marrow, the defects of five dogs formed solid unions, and one progressed to a fibrous union. Defects in all five dogs grafted with autogeneic bone marrow united. The three dogs with no implant formed nonunions. Histology showed normal marrow and only a light immune reaction. Complete bridging of the defect in the dogs treated with the granular ceramic occurred significantly earlier than bridging in the dogs grafted with bone marrow alone. Histomorphometry, performed on the block ceramic implants indicated active resorption of ceramic. Clinically, addition of ceramic to a marrow graft improved the handling characteristics of the graft material and accelerated healing according to roentgenographic evaluation.
Monoclonal antibody specific for T cell-derived human IgE binding factors. (1987)

A B cell hybridoma secreting monoclonal antibody against human IgE binding factors was obtained by immunization of BALB/c mice with partially purified IgE binding factors, and fusion of their spleen cells with SP-2/0-AG14 cells. The monoclonal antibody bound all of the 60,000, 30,000, and 15,000 dalton IgE binding factors from two T cell hybridomas and those from activated T cells of a normal individual. The antibody bound both IgE-potentiating factors, which had affinity for lentil lectin, and IgE-suppressive factors, which had affinity for peanut agglutinin. However, the monoclonal anti-IgE-binding factor bound neither Fc epsilon R on RPMI 8866 cells nor IgE binding factors from the B lymphoblastoid cells. A monoclonal antibody against Fc epsilon R on B cells (H107) bound the 60,000 and 30,000 dalton IgE binding factors from both T cell hybridomas and RPMI 8866 cells but did not bind the 15,000 dalton IgE binding factors from either T cells or B cells. The results indicate that T cell-derived IgE binding factors have a unique antigenic determinant that is lacking in both Fc epsilon R on B cells and B cell-derived IgE binding factors. The anti-IgE binding factor and anti-Fc epsilon R monoclonal antibodies both failed to stain cell surface components of IgE binding factor-producing T cell hybridomas. However, both antibodies induced the T cell hybridoma to form IgE binding factors. The results suggest that the T cell hybridomas bear low numbers of Fc epsilon R that share antigenic determinants with IgE binding factors secreted from the cells.
Mode localization phenomena in large space structures (1987)

The possibility of localization or confinement of vibratory modes in large space structures is investigated theoretically and numerically. These structures belong to a class of periodic structures that have recently been shown to be sensitive to periodicity-b reaking disorder or imperfections . When localization occurs, the modal amplitude of a global mode becomes confined to a local region of the structure, with serious implications for the control problem. The results of this study indicate that mode localization is most likely to occur in structures consisting of a large number of weakly coupled substructures. Certain large space structures with high modal densities fall in this category, and it is therefore important to include the effect of structural imperfections and disorder when designing control systems for shape or directional control of such structures. [ / ] K, Kh , Kw,Ku [K] [k] [M] [ m ] m n N p qi qt t u, v, w uf 8fj e 6
Zoeal Development of Novorostrum indicum (Crustacea : Decapoda : Porcellanidae) Reared under Laboratory Conditions (2000)

The zoeal development of the porcellanid crab Novorostrum indicum is described and illustrated from laboratory-reared material. Zoeal characters of this species appear to support the establishment of Novorostrum. Furthermore, a closer affinity of this genus with Petrolisthes ornatus, P. japonicus, and P. elongatus than with other species of Petrolisthes for which the larval morphology is known, and also the exclusion of P. ornatus from Novorostrum, are supported.