gebhart/patrepeval huggingface dataset:
A Rational Approach to Catalytic Enantioselective Enolate Alkylation Using a Structurally Rigidified and Defined Chiral Quaternary Ammonium Salt under Phase Transfer Conditions (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Rational Approach to Catalytic Enantioselective Enolate Alkylation Using a Structurally Rigidified and Defined Chiral Quaternary Ammonium Salt under Phase Transfer ConditionsE. J. Corey, Feng Xu, and Mark C. NoeView Author Information Department of Chemistry and Chemical Biology Harvard University Cambridge, Massachusetts, 02138 Cite this: J. Am. Chem. Soc. 1997, 119, 50, 12414–12415Publication Date (Web):December 17, 1997Publication History Received10 September 1997Published online17 December 1997Published inissue 17 December 1997https://doi.org/10.1021/ja973174yCopyright © 1997 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views10470Altmetric-Citations557LEARN 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 InReddit Read OnlinePDF (84 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Cations,Enolates,Ions,Post-translational modification Get e-Alerts
A Dynamic Model of Resource Allocation in Response to the Presence of a Synthetic Construct (2018)

Introducing synthetic constructs into bacteria often carries a burden that leads to reduced fitness and selective pressure for organisms to mutate their constructs and hence to a reduced functional lifetime. Understanding burden requires suitable methods for accurate measurement and quantification. We develop a dynamic growth model from physiologically relevant first-principles that allows parameters relevant to burden to be extracted from standard growth curves. We test several possibilities for the response of a bacterium to a new environment in terms of resource allocation. We find that burden manifests in the time taken to respond to new conditions as well as the rate of growth in exponential phase. Furthermore, we see that the presence of a synthetic construct hastens the reduction of ribosomes when approaching stationary phase, altering memory effects from previous periods of growth.
Engineering microscale cellular niches for three-dimensional multicellular co-cultures (2009)

Modeling the in vivo microenvironment typically involves placing cells in a three-dimensional (3D) extracellular matrix (ECM) in physiologically relevant context with respect to other cells. The mechanical and chemical features of 3D microenvironments play important roles in tissue engineering, tumor growth and metastasis, and in defining stem cell niches, and it is increasingly recognized that cells behave much differently when surrounded by a 3D ECM than when anchored to a 2D substrate. To create microenvironments that more closely mimic in vivo settings, here we describe a novel microfluidic device that allows multiple discrete constructs of 3D cell-laden hydrogels to be patterned in a sequence of simple steps. The microfluidic platform allows for real-time imaging of the interactions between multiple cell types exposed to both autocrine and paracrine signaling molecules, all within a 3D ECM environment. Detailed modeling determined that surface tension, hydrophobic interactions, and spatial geometry were important factors in containing the gels within distinct separate channels during the filling process. This allowed us to pattern multiple gel types side-by-side and pattern 3D gels spatially with tight dimensional control. Cells embedded in gels could be patterned by culturing MDA-MB-231 metastatic breast cancer cells and RAW 264.1 macrophage cells within distinct collagen type I and Matrigel ECM environments, respectively. Over a 7 day culture experiment, RAW cells invaded into neighboring gels containing MDA-MB-231 cells, but not into gels lacking cells. These studies demonstrate the versatility and potential of this new microfluidic platform to engineer 3D microscale architectures to investigate cell-cell and cell-matrix interactions.
Role of capsid proteins in parvoviruses infection (2015)

The parvoviruses are widely spread in many species and are among the smallest DNA animal viruses. The parvovirus is composed of a single strand molecule of DNA wrapped into an icosahedral capsid. In a viral infection, the massy capsid participates in the entire viral infection process, which is summarized in this review. The capsid protein VP1 is primarily responsible for the infectivity of the virus, and the nuclear localization signal (NLS) of the VP1 serves as a guide to assist the viral genome in locating the nucleus. The dominant protein VP2 provides an "anti-receptor", which interacts with the cellular receptor and leads to the further internalization of virus, and, the N-terminal of VP2 also cooperates with the VP1 to prompt the process of nucleus translocation. Additionally, a cleavage protein VP3 is a part of the capsid, which exists only in several members of the parvovirus family; however, the function of this cleavage protein remains to be fully determined. Parvoviruses can suffer from the extreme environmental conditions such as low pH, or even escape from the recognition of pattern recognition receptors (PRRs), due to the protection of the stable capsid, which is thought to be an immune escape mechanism. The applications of the capsid proteins to the screening and the treatment of diseases are also discussed. The processes of viral infection should be noted, because understanding the virus-host interactions will contribute to the development of therapeutic vaccines.
Cell Death Mechanisms and the Immune System (1991)

The immune system provides good models for cell death, a phenomenon now recognized to be of fundamental importance in many fields of biology. Cell death is strikingly polymorphic: it can proceed via necrosis (as in complement-mediated cell death) or apoptosis, but the latter displays different patterns (in the receptor-mediated death of some thymocytes, in cell death mediated by TNF alpha or by cytotoxic T cells), perhaps reflecting different pathways of control of a common core mechanism. Even though there are differences in the morphological and metabolic changes associated with the different patterns of apoptosis, some recurrent sequences of events are observed in almost all dying cells. The metabolic state of a cell often seems to play a major role in determining if and how this cell will die in given external circumstances. The nature of molecules causally involved in the dying cell can now be approached in some systems.
Stochastic processes in the musification of cellular automata (2012)

This paper discusses Livecell, a system for interactive generative composition through real?.time score generation as well as the triggering and treatment of sound files. The paper outlines the authors’ rationale, discusses the use of cellular automata in this context and provides an insight into the application’s structural design. The authors summarise their approach to CA musification, the representation of data relations in a musical score, and interface design as well as score generation and display. The paper concludes with observations on the musical output and discussion of future developments.
Transfection of human nm23-H1 into the human MDA-MB-435 breast carcinoma cell line: effects on tumor metastatic potential, colonization and enzymatic activity. (1993)

We report the phenotypic effects of transfection of human nm23-H1 cDNA into the human MDA-MB-435 breast carcinoma cell line. Upon mammary fat pad or subcutaneous injection into nude mice, both the nm23-H1 and control transfected lines produced primary tumors; however, the nm23-H1-transfected lines produced metastases in significantly fewer mice than did control transfected lines. Reductions in tumor metastatic potential in vivo were accompanied by decreased colonization in soft agar and an altered colonization response to transforming growth factor beta in vitro. Total nucleoside diphosphate kinase activity, an enzymatic activity possessed by the Nm23 family, was not directly correlated with Nm23-H1 expression levels or suppression of metastatic potential in all cases examined. The data establish that nm23-H1 has functional suppressive effects on the tumor metastatic potential of a human breast carcinoma cell line, and suggest that it may regulate signal responsiveness in the colonization response.
Recognition of HLA‐A1 by murine monoclonal antibodies (1994)

Balb/c mice were immunized with cells from the mouse mastocytoma line P815 transfected with an HLA-A1 gene. The splenocytes of the immunized mice were fused with cells from the murine myeloma NS-1. In an initial screening, supernatants of growing cultures were tested for their binding capacity to the immunizing P815/A1+ cells as well as to P815/A2+ cells. Three out of 756 hybrids produced antibodies which bound to P815/A1+ cells only. They were cloned and further analyzed for their binding reactivity to reference B-lymphoblastoid cells from the Tenth International Histocompatibility Workshop. One monoclonal antibody, designated 6B11, reacted only with HLA-A1+ cells, while the two other antibodies, 3G3 and 7F10, appeared to detect antigenic determinants shared by HLA-A1, A3, A11, A26, and A30 (3G3) and by HLA-A1, A3, A11, A26, A28 and A30 (7F10). Flow cytometric studies on B-lymphoblastoid cell lines as well as on a series of tumor cell lines, including melanoma and colon carcinoma lines, confirmed the specificity of these antibodies. Monoclonal antibodies 7F10 and 6B11 were found to be of the IgM class and 3G3 of the IgG1 class. By complement-dependent 51Cr release experiments it was further shown that the two IgM antibodies 7F10 and 6B11 were able to lyse all cell lines of the HLA-A1 haplotype tested.
Primary structure of sarcotoxin I, an antibacterial protein induced in the hemolymph of Sarcophaga peregrina (flesh fly) larvae. (1985)

The primary structure of sarcotoxin I, a potent bactericidal protein induced in the hemolymph of larvae of Sarcophaga peregrina (flesh fly), was investigated. Sarcotoxin I was a mixture of three proteins (sarcotoxins IA, IB, and IC) with almost identical primary structures. These proteins were found to consist of 39 amino acid residues and to differ in only 2-3 amino acid residues. The amino-terminal half of the molecules was rich in charged amino acids and was hydrophilic, whereas the carboxyl-terminal half was hydrophobic. It is suggested that the carboxyl-terminal half of sarcotoxin I penetrates into the bacterial membrane and that its amino-terminal half rich in basic amino acid residues interacts with acidic phospholipids in the bacterial membrane, resulting in perturbation of the membrane and loss of viability of the bacteria.
Automatic Conversion of Mesh Animations into Skeleton‐based Animations (2008)

Abstract Recently, it has become increasingly popular to represent animations not by means of a classical skeleton‐based model, but in the form of deforming mesh sequences. The reason for this new trend is that novel mesh deformation methods as well as new surface based scene capture techniques offer a great level of flexibility during animation creation. Unfortunately, the resulting scene representation is less compact than skeletal ones and there is not yet a rich toolbox available which enables easy post‐processing and modification of mesh animations. To bridge this gap between the mesh‐based and the skeletal paradigm, we propose a new method that automatically extracts a plausible kinematic skeleton, skeletal motion parameters, as well as surface skinning weights from arbitrary mesh animations. By this means, deforming mesh sequences can be fully‐automatically transformed into fullyrigged virtual subjects. The original input can then be quickly rendered based on the new compact bone and skin representation, and it can be easily modified using the full repertoire of already existing animation tools.
Functional roles of HMGA2 in human embryonic stem cells and human tumor cells (2009)

The state of chromatin in human embryonic stem cells (hESCs) is a key factor determining stem cell identity. The non-histone chromatin-associated factor high-mobility group protein A2 (HMGA2) has been studied mostly in the mouse where its function seems critical for embryonic cell growth and adipocytic cell differentiation, leading to a pygmy phenotype with greatly reduced fat tissue in homozygous knock out mice. We showed that among the major HMG proteins, HMGA2 was highly expressed in two hESC lines. Interestingly, expression was further upregulated during early embryoid body formation before it quickly droped to or below the level found in undifferentiated cells. We also showed that HMGA2 was stably associated with inter- and meta-phase hESC chromatin, and that up to 12 HMGA2 protomers stably associated in vitro with a single nucleosome core particle of known atomic structure. These suggested that HMGA2 might interact with nucleosomes in a way that imposed a global effect on the state of hESC chromatin, which might contribute to the establishment of both hESCs identity and the initiation of specific differentiation programs. We then established HMGA2 as a regulator of human genes linked to mesodermal cell differentiation, adipogenesis, and hESCs growth through siRNA technology in combination with quantitative reverse transcriptase polymerase chain reaction, stem cell-specific microarray analyses, and cell proliferation assays. HMGA proteins are also present in high copy numbers in most neoplasias, and correlations between the degree of malignancy, patient prognostic index, and HMGA levels have been firmly established. Intriguingly, HMGA2 is also found in rare tumor-inducing cells, which are resistant to chemotherapy. Here, we demonstrated that HMGA1a/b and HMGA2 possessed intrinsic dRP and AP lyase activities, which most likely resided in their AT-hook DNA binding domains. We also showed that HMGA2 could be covalently trapped at genomic abasic sites in cancer cells. The associated lyase activities promoted cellular resistance against DNA damage, which was targeted by base excision repair (BER) pathways, and this protective effect directly correlated with the level of HMGA2 expression. Furthermore, we demonstrated an interaction between AP endonuclease 1 and HMGA2 in cancer cells, which strongly supported our conclusion that HMGA2 could be incorporated into the cellular BER machinery.
Support for the involvement of large copy number variants in the pathogenesis of schizophrenia (2009)

We investigated the involvement of rare (<1%) copy number variants (CNVs) in 471 cases of schizophrenia and 2792 controls that had been genotyped using the Affymetrix GeneChip 500K Mapping Array. Large CNVs >1 Mb were 2.26 times more common in cases (P = 0.00027), with the effect coming mostly from deletions (odds ratio, OR = 4.53, P = 0.00013) although duplications were also more common (OR = 1.71, P = 0.04). Two large deletions were found in two cases each, but in no controls: a deletion at 22q11.2 known to be a susceptibility factor for schizophrenia and a deletion on 17p12, at 14.0-15.4 Mb. The latter is known to cause hereditary neuropathy with liability to pressure palsies. The same deletion was found in 6 of 4618 (0.13%) cases and 6 of 36 092 (0.017%) controls in the re-analysed data of two recent large CNV studies of schizophrenia (OR = 7.82, P = 0.001), with the combined significance level for all three studies achieving P = 5 x 10(-5). One large duplication on 16p13.1, which has been previously implicated as a susceptibility factor for autism, was found in three cases and six controls (0.6% versus 0.2%, OR = 2.98, P = 0.13). We also provide the first support for a recently reported association between deletions at 15q11.2 and schizophrenia (P = 0.026). This study confirms the involvement of rare CNVs in the pathogenesis of schizophrenia and contributes to the growing list of specific CNVs that are implicated.
Sialidase‐like Asp‐boxes: Sequence‐similar structures within different protein folds (2001)

Sequence similarity is the most common measure currently used to infer homology between proteins. Typically, homologous protein domains show sequence similarity over their entire lengths. Here we identify Asp box motifs, initially found as repeats in sialidases and neuraminidases, in new structural and sequence contexts. These motifs represent significantly similar sequences, localized to beta hairpins within proteins that are otherwise different in sequence and three-dimensional structure. By performing a combined sequence- and structure-based analysis we detect Asp boxes in more than nine protein families, including bacterial ribonucleases, sulfite oxidases, reelin, netrins, some lipoprotein receptors, and a variety of glycosyl hydrolases. Although the function common to each of these proteins, if any, remains unclear, we discuss possible functions of Asp boxes on the basis of previously determined experimental results and discuss different evolutionary scenarios for the origin of Asp-box containing proteins.
Glycosylation of the T-cell antigen-specific receptor and its potential role in lectin-mediated cytotoxicity. (1986)

Cytotoxic T lymphocytes (CTLs) normally destroy only those cells ("target cells") whose surface antigens they recognize. However, in the presence of lectins such as Con A, CTLs destroy virtually any cell, regardless of its antigens. The oligosaccharides of the T-cell antigen-specific receptor, a dimeric surface glycoprotein composed of disulfide-linked alpha and beta subunits, are of interest because of their potential involvement in this lectin-dependent cytotoxic activity. We report here that three or four asparagine-linked oligosaccharides could be enzymatically removed from each of the receptor subunits expressed by a cloned line of murine CTLs (clone 2C), consistent with the presence of glycosylation sites deduced from cDNA sequences of the alpha and beta genes expressed in this clone. All the N-linked glycans on the alpha subunit were of the complex type (i.e., resistant to endoglycosidase H), but the beta subunit carried two or three endoglycosidase H-sensitive (high-mannose) oligosaccharides. High-mannose glycans can bind tightly to Con A and, indeed, this lectin was found to bind specifically to solubilized 2C T-cell receptor. The Con A-dependent cytotoxic activity of clone 2C, but not of other CTL clones, was inhibited by a monoclonal antibody (1B2) that is specific for the T-cell receptor of clone 2C. Antibody 1B2 also inhibited clone 2C cytotoxicity mediated by phytohemagglutinin, lentil-lectin, and wheat-germ agglutinin. These results suggest that, although lectin-dependent lysis of target cells by CTLs is antigen nonspecific, the cytolytic activity can be triggered by binding of the lectin to the T-cell antigen-specific receptor.
Age‐associated Changes in the Response of Skeletal Muscle Cells to Exercise and Regenerationa (1998)

This paper looks at the effects of aging on the response of skeletal muscle to exercise from the perspective of the behavior of muscle precursor cells (widely termed satellite cells or myoblasts) and regeneration. The paper starts by outlining the ways in which skeletal muscle can respond to damage resulting from exercise or other trauma. The age-related changes within skeletal muscle tissue and the host environment that may affect the proliferation and fusion of myoblasts in response to injury in old animals are explored. Finally, in vivo and in vitro data concerning the wide range of signaling molecules that stimulate satellite cells and other aspects of regeneration are discussed with respect to aging. Emphasis is placed on the important role of the host environment, inflammatory cells, growth factors and their receptors (particularly for FGF-2), and the extracellular matrix.
Rapid Identification of Dihydropyrimidine Dehydrogenase Deficiency by Using a Novel 2-13C-Uracil Breath Test (2004)

We demonstrated statistically significant differences in the 2-(13)C-uracil breath test indices (C(max), T(max), DOB(50), and PDR) among healthy and DPD-deficient individuals. These data suggest that a single time-point determination (50 min) could rapidly identify DPD-deficient individuals with a less costly and time-consuming method that is applicable for most hospitals or physicians' offices.
Electronic tour guide for Android mobile platform with multimedia travel book (2012)

In this paper, a new system for positioning and multimedia reporting, named electronic tour guide, is presented. The mobile device of the system communicates with the server, from which it receives electronic tourist maps, and the GPS satellites. Each location on the map with predetermined irregular shape avoids overlap with other areas and thus it increases the accuracy of the visited location. The device is guiding the tourist using the coordinates received from the GPS signals and the objects that are preloaded as electronic maps. The main functions of the system are: (a) it is displaying the content according to user's movement, position and preferred selections; (b) it generates reports for guiding using existing date stored from the server, the current position, the previous movement and the paid services; (c) it reports and prepares the multimedia travel book based on the paid services; (d) it prepares the daily trip report from images, text and audio files downloaded from server or recorded by user; (e) it submits the recorded data for future individual, group or public usage. This paper presents the main characteristics and advantages of the new system as well as benefits for commercial usage.