gebhart/patrepeval huggingface dataset:
A 3D model of non-uniform attenuation and detector response for efficient iterative reconstruction in SPECT (1994)

A 3D physical model for iterative reconstruction in SPECT has been developed and applied to experimental data. The model incorporates non-uniform attenuation using reconstructed transmission CT data and distance-dependent detector response based on response function measurements over a range of distances from the detector. The 3D model has been implemented in a computationally efficient manner with practical memory requirements. The features of the model that provide efficiency are described including a new region-dependent reconstruction (RDR) technique. With RDR, filtered backprojection is used to reconstruct areas of the image of minimal clinical importance, and the result is used to supplement the iterative reconstruction of the clinically important areas of the image. The 3D model was incorporated into the maximum likelihood-expectation maximization (ML-EM) reconstruction algorithm and tested in three phantom studies--a point source, a uniform cylinder, and an anthropomorphic thorax--and a patient 9Tc(m) sestamibi study. Reconstructed images with the 3D method exhibited excellent noise and resolution characteristics. With the sestamibi data, the RDR technique produced essentially the conventional ML-EM estimate in the cardiac region with substantial time savings.
A pentapeptide from the laminin B1 chain mediates cell adhesion and binds to 67000 laminin receptor (1987)

Laminin promotes epithelial cell adhesion in part through a site of nine amino acids CDPGYIGSR on the B1 chain. Using smaller synthetic peptides from this sequence as well as various peptides with amino acid substitutions, we find that the minimum sequence necessary for efficient cell adhesion as well as receptor binding is YIGSR. The deletion of tyrosine or the substitution of arginine in the peptides resulted in a significant loss of activity. The presence of an amide group on the terminal arginine of either peptide increases activity significantly. YIGSR is active in promoting the adhesion of a variety of epithelial cells; however, it is inactive with chondrocytes, fibroblasts, and osteoblasts.
Autoinhibition of Casein Kinase I ε (CKIε) Is Relieved by Protein Phosphatases and Limited Proteolysis (1998)

Casein kinase I epsilon (CKI epsilon) is a member of the CKI gene family, members of which are involved in the control of SV40 DNA replication, DNA repair, and cell metabolism. The mechanisms that regulate CKI epsilon activity and substrate specificity are not well understood. We report that CKI epsilon, which contains a highly phosphorylated 123-amino acid carboxyl-terminal extension not present in CKI alpha, is substantially less active than CKI alpha in phosphorylating a number of substrates including SV40 large T antigen and is unable to inhibit the initiation of SV40 DNA replication. Two mechanisms for the activation of CKI epsilon have been identified. First, limited tryptic digestion of CKI epsilon produces a protease-resistant amino-terminal 39-kDa core kinase with several-fold enhanced activity. Second, phosphatase treatment of CKI epsilon activates CKI epsilon 5-20-fold toward T antigen. Similar treatment of a truncated form of CKI epsilon produced only a 2-fold activation. Notably, this activation was transient; reautophosphorylation led to a rapid down-regulation of the kinase within 5 min. Phosphatase treatment also activated CKI epsilon toward the novel substrates I kappa B alpha and Ets-1. These mechanisms may serve to regulate CKI epsilon and related forms of CKI in the cell, perhaps in response to DNA damage.
Toward image based visual servoing for aerial grasping and perching (2014)

This paper addresses the dynamics, control, planning, and visual servoing for micro aerial vehicles to perform high-speed aerial grasping tasks. We draw inspiration from agile, fast-moving birds, such as raptors, that detect, locate, and execute high-speed swoop maneuvers to capture prey. Since these grasping maneuvers are predominantly in the sagittal plane, we consider the planar system and present mathematical models and algorithms for motion planning and control, required to incorporate similar capabilities in quadrotors equipped with a monocular camera. In particular, we develop a dynamical model directly in the image space, show that this is a differentially-flat system with the image features serving as flat outputs, outline a method for generating trajectories directly in the image feature space, develop a geometric visual controller that considers the second order dynamics (in contrast to most visual servoing controllers that assume first order dynamics), and present validation of our methods through both simulations and experiments.
Reversed-Phase-Reversed-Phase Liquid Chromatography Approach with High Orthogonality for Multidimensional Separation of Phosphopeptides (2009)

Protein phosphorylation regulates a series of important biological processes in eukaryotes. However, the phosphorylation sites found up to now are far below than that actually exists in proteins due to the extreme complexity of the proteome sample. Here a new reversed-phase-reversed-phase liquid chromatography (RP-RPLC) approach was developed for multidimensional separation of phosphopeptides. In this approach, a large number of fractions were collected from the first dimensional RPLC separation at high pH. And then these fractions were pooled every two fractions with equal time interval, one from the early eluted section and another one from the later eluted section. The pooled fractions were finally submitted to RPLC-tandem mass spectrometry (MS/MS) analysis at low pH. It was found the resulting 2D separation was highly orthogonal and yielded more than 30% phosphopeptide identifications over the conventional RP-RPLC approach. This study provides a powerful approach for efficient separation of phosphopeptides and global phosphorylation analysis, where the orthogonality of 2D separation is greatly improved and the first dimensional separation is of high resolution.
Characterization of the gene for chromosomal trimethoprim-sensitive dihydrofolate reductase of Staphylococcus aureus ATCC 25923 (1993)

The gene for the trimethoprim-sensitive (Tmps) chromosomal dihydrofolate reductase (DHFR) of Staphylococcus aureus ATCC 25923 was cloned and characterized. The structural gene encodes a polypeptide of 159 amino acid residues and has a calculated molecular weight of 18,251. The amino acid sequences of this Tmps DHFR and those of the trimethoprim-resistant type S1 DHFR encoded by transposon Tn4003 are 80% identical. In contrast to the trimethoprim-resistant enzyme, the Tmps DHFR can be highly overexpressed in Escherichia coli, with most of the recombinant protein occurring in a soluble and an active form.
Sequence-Specific Correction of Genomic Hypoxanthine-Guanine Phosphoribosyl Transferase Mutations in Lymphoblasts by Small Fragment Homologous Replacement (2009)

Oligo/polynucleotide-based gene targeting strategies provide new options for achieving sequence-specific modification of genomic DNA and have implications for the development of new therapies and transgenic animal models. One such gene modification strategy, small fragment homologous replacement (SFHR), was evaluated qualitatively and quantitatively in human lymphoblasts that contain a single base substitution in the hypoxanthine-guanine phosphoribosyl transferase (HPRT1) gene. Because HPRT1 mutant cells are readily discernable from those expressing the wild type (wt) gene through growth in selective media, it was possible to identify and isolate cells that have been corrected by SFHR. Transfection of HPRT1 mutant cells with polynucleotide small DNA fragments (SDFs) comprising wild type HPRT1 (wtHPRT1) sequences resulted in clones of cells that grew in hypoxanthine-aminopterin-thymidine (HAT) medium. Initial studies quantifying the efficiency of correction in 3 separate experiments indicate frequencies ranging from 0.1% to 2%. Sequence analysis of DNA and RNA showed correction of the HPRT1 mutation. Random integration was not indicated after transfection of the mutant cells with an SDF comprised of green fluorescent protein (GFP) sequences that are not found in human genomic DNA. Random integration was also not detected following Southern blot hybridization analysis of an individual corrected cell clone.
JAK2 mutants (e.g., JAK2V617F) and their importance as drug targets in myeloproliferative neoplasms (2013)

The Janus kinase 2 (JAK2) mutant V617F and other JAK mutants are found in patients with myeloproliferative neoplasms and leukemias. Due to their involvement in neoplasia and inflammatory disorders, Janus kinases are promising targets for kinase inhibitor therapy. Several small-molecule compounds are evaluated in clinical trials for myelofibrosis, and ruxolitinib (INCB018424, Jakafi®) was the first Janus kinase inhibitor to receive clinical approval. In this review we provide an overview of JAK2V617F signaling and its inhibition by small-molecule kinase inhibitors. In addition, myeloproliferative neoplasms are discussed regarding the role of JAK2V617F and other mutant proteins of possible relevance. We further give an overview about treatment options with special emphasis on possible combination therapies.
Factor Xa Activates Endothelial Cells by a Receptor Cascade Between EPR-1 and PAR-2 (2000)

In addition to its pivotal role in hemostasis, factor Xa binds to human umbilical vein endothelial cells through the recognition of a protein called effector cell protease receptor (EPR-1). This interaction is associated with signal transduction, generation of intracellular second messengers, and modulation of cytokine gene expression. Inhibitors of factor Xa catalytic activity block these responses, thus indicating that the factor Xa-dependent event of local proteolysis is absolutely required for cell activation. Because EPR-1 does not contain proteolysis-sensitive sites, we investigated the possibility that signal transduction by factor Xa requires proteolytic activation of a member of the protease-activated receptor (PAR) gene family. Catalytic inactivation of factor Xa by DX9065 suppressed factor Xa-induced increase in cytosolic free Ca(2+) in endothelial cells (IC(50)=0.23 micromol/L) but failed to reduce ligand binding to EPR-1. In desensitization experiments, trypsin or the PAR-2-specific activator peptide, SLIGKV, ablated the Ca(2+) signaling response induced by factor Xa. Conversely, pretreatment of endothelial cells with factor Xa blocked the PAR-2-dependent increase in cytosolic Ca(2+) signaling, whereas PAR-1-dependent responses were unaffected. Direct cleavage of PAR-2 by factor Xa on endothelial cells was demonstrated by cleavage of a synthetic peptide duplicating the PAR-2 cleavage site and by immunofluorescence with an antibody to a peptide containing the 40-amino acid PAR-2 extracellular extension. These data suggest that factor Xa induces endothelial cell activation via a novel cascade of receptor activation involving docking to EPR-1 and local proteolytic cleavage of PAR-2.
Altered leukocyte response to CXCL12 in patients with warts hypogammaglobulinemia, infections, myelokathexis (WHIM) syndrome (2004)

The chemokine receptor CXCR4 and its functional ligand, CXCL12, are essential regulators of development and homeostasis of hematopoietic and lymphoid organs. Heterozygous truncating mutations in the CXCR4 intracellular tail cause a rare genetic disease known as WHIM syndrome (warts, hypogammaglobulinemia, infections, myelokathexis), whose pathophysiology remains unclear. We report CXCR4 function in 3 patients with WHIM syndrome carrying heterozygous truncating mutations of CXCR4. We show that CXCR4 gene mutations in WHIM patients do not affect cell surface expression of the chemokine receptor and its internalization upon stimulation with CXCL12. Moreover, no significant differences in calcium mobilization in response to CXCL12 are found. However, the chemotactic response of both polymorphonuclear cells and T lymphocytes in response to CXCL12 is increased. Furthermore, immunophenotypic analysis of circulating T and B lymphocytes reveals a decreased number of memory B cells and of naive T cells and an accumulation of effector memory T cells associated with a restricted T-cell repertoire. Based on our results, we suggest that the altered leukocyte response to CXCL12 may account for the pathologic retention of mature polymorphonuclear cells in the bone marrow (myelokathexis) and for an altered lymphocyte trafficking, which may cause the immunophenotyping abnormalities observed in WHIM patients.
Anxiety, motor activation, and maternal-infant interactions in 5HT-sub(1B ) knockout mice. (1999)

This study describes the development of anxiety and motor activation in mice lacking the serotonin (5HT) 1B receptor and in wild type controls and characterizes their early mother-infant interactions. In the isolation-induced ultrasonic vocalization paradigm, 5HT1B knockout pups vocalized less and were hyperactive, rearing, jumping, and rolling more often than wild type pups. One week postpartum, 5HT1B knockout mothers spent 20% more of their time outside the nest and were also hyperactive, rearing and climbing to the edge of the cage more often than the wild type mothers. There were no genotype effects on pup retrieval. Knockout adults were less anxious in the elevated plus-maze, defecated less, and head-dipped more, although none of the standard measures of anxiety (time and entries in the open arms) were different. 5HT1B knockout mice of both sexes were hyperactive during both the light and the dark phases of the 24-hr cycle. Thus, 5HT1B knockout mice show reduced anxiety and are hyperactive throughout their life.
RNA AND N3′ → P5′ KISSING APTAMERS TARGETED TO THETRANS-ACTIVATION RESPONSIVE (TAR) RNA OF THE HUMAN IMMUNODEFICIENCY VIRUS-1 (2001)

We used in vitro selection to identify RNA aptamers able to selectively bind to the TAR RNA motif of HIV-1, an unperfect RNA hairpin involved in the transcription of the retroviral genome. We selected aptameric RNA hairpins giving rise to kissing complexes with TAR. The N3'-->P5' phosphoramidate variant of the aptamer bind to TAR with a Kd in the low nanomolar range. However, only the RNA-RNA loop-loop complex is recognized by the Rop protein of E. coli which is specific for kissing complexes.
Circulins A and B. Novel human immunodeficiency virus (HIV)-inhibitory macrocyclic peptides from the tropical tree Chassalia parvifolia. (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCirculins A and B. Novel human immunodeficiency virus (HIV)-inhibitory macrocyclic peptides from the tropical tree Chassalia parvifolia.Kirk R. Gustafson, Raymond C. Sowder II, Louis E. Henderson, Ian C. Parsons, Yoel Kashman, John H. Cardellina II, James B. McMahon, Robert W. Buckheit Jr., Lewis K. Pannell, and Michael R. BoydCite this: J. Am. Chem. Soc. 1994, 116, 20, 9337–9338Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/ja00099a064https://doi.org/10.1021/ja00099a064research-articleACS PublicationsRequest reuse permissionsArticle Views591Altmetric-Citations250LEARN 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
Mutations Causing Childhood Ataxia with Central Nervous System Hypomyelination Reduce Eukaryotic Initiation Factor 2B Complex Formation and Activity (2004)

Childhood ataxia with central nervous system hypomyelination (CACH), or vanishing white matter leukoencephalopathy (VWM), is a fatal brain disorder caused by mutations in eukaryotic initiation factor 2B (eIF2B). eIF2B is essential for protein synthesis and regulates translation in response to cellular stresses. We performed mutagenesis to introduce changes equivalent to 12 human CACH/VWM mutations in three subunits of the equivalent factor from yeast (Saccharomyces cerevisiae) and analyzed effects on cell growth, translation, and gene expression in response to stresses. None of the mutations is lethal or temperature sensitive, but almost all confer some defect in eIF2B function significant enough to alter growth or gene expression under normal or stress conditions. Biochemical analyses indicate that mutations analyzed in eIF2Balpha and -epsilon reduce the steady-state level of the affected subunit, while the most severe mutant tested, eIF2Bbeta(V341D) (human eIF2B(betaV316D)), forms complexes with reduced stability and lower eIF2B activity. eIF2Bdelta is excluded from eIF2Bbeta(V341D) complexes. eIF2B(betav341D) function can be rescued by overexpression of eIF2Bdelta alone. Our findings imply CACH/VWM mutations do not specifically impair responses to eIF2 phosphorylation, but instead cause protein structure defects that impair eIF2B activity. Altered protein folding is characteristic of other diseases, including cystic fibrosis and neurodegenerative disorders such as Huntington, Alzheimer's, and prion diseases.
Temporal modulation of spike-timing-dependent plasticity (2010)

Spike-timing-dependent plasticity (STDP) has attracted considerable experimental and theoretical attention over the last decade. In the most basic formulation, STDP provides a fundamental unit - a spike pair - for quantifying the induction of long-term changes in synaptic strength. However, many factors, both pre- and postsynaptic, can affect synaptic transmission and integration, especially when multiple spikes are considered. Here we review the experimental evidence for multiple types of nonlinear temporal interactions in STDP, focusing on the contributions of individual spike pairs, overall spike rate, and precise spike timing for modification of cortical and hippocampal excitatory synapses. We discuss the underlying processes that determine the specific learning rules at different synapses, such as postsynaptic excitability and short-term depression. Finally, we describe the success of efforts toward building predictive, quantitative models of how complex and natural spike trains induce long-term synaptic modifications.
Introduction (2004)

The post—Cold War decade of the 1990s has been labeled the decade of human rights, the decade in which, Michael Ignatieff claims, "human rights has become the dominant moral vocabulary in foreign affairs" (2002, A29).1 Not incidentally, it has also been described as the decade of life narratives, what commentators refer to as the time of memoir. Many of these life narratives tell of human rights violations. Victims of abuse around the world have testified to their experience in an outpouring of oral and written narratives. These stories demand that readers attend to histories, lives, and experiences often vastly different from their own. As people meet together and tell stories, or read stories across cultures, they begin to voice, recognize, and bear witness to a diversity of values, experiences, and ways of imagining a just social world and of responding to injustice, inequality, and human suffering. Indeed, over the last twenty years, life narratives have become one of the most potent vehicles for advancing human rights claims.
Activation of Cancer-Specific Gene Expression by the Survivin Promoter (2002)

Transfection experiments indicate that survivin protein expression in cancer tissue appears to be regulated, at least in part, transcriptionally. Thus, the survivin promoter may be useful in controlling gene expression in cancer cells.
[Endotoxinemia and multiple organ failure after polytrauma]. (1996)

Despite successful management of early complications in polytraumatized patients and obvious reduction of early death, lethality in the late course of the disease--frequently as a result of multiple organ failure (MOF)--remains generally unaffected. Concerning the pathogenesis of sepsis and MOF, there is some evidence that a central role is played by endotoxin. A series of 32 patients with severe polytraumatic injury (Hannover Polytrauma Score > 20 points) comprised the study group. Endotoxin was measured hourly over the first 24 hours. The first measuring point was four hours after injury at the latest. Endotoxin levels were determined by a quantitative turbidimetric limulus assay. The Goris MOF score reached between the 8th and 10th day after injury was used for evaluation of the severity of MOF. Thirty of the 32 patients showed episodes of endotoxemia during the measuring period. There was a strong correlation between observed endotoxin peak concentrations, on the one hand, and outcome as well as positive predictive value (PPV) concerning development of MOF, on the other hand. If the peak concentration was greater than 10 pg/ml, the PPV reached 100%. No patient survived a peak concentration greater than 12 pg/ml. Endotoxemia during the early phase after polytraumatic injury is a frequent phenomenon. It appears to be possible that measurement of endotoxin peak concentration during the early phase gives some indication of the development of MOF and the outcome of these patients.
Spermatogenesis following male germ-cell transplantation. (1994)

In the adult male, a population of diploid stem-cell spermatogonia continuously undergoes self-renewal and produces progeny cells, which initiate the complex process of cellular differentiation that results in mature spermatozoa. We report here that stem cells isolated from testes of donor male mice will repopulate sterile testes when injected into seminiferous tubules. Donor cell spermatogenesis in recipient testes showed normal morpholigical characteristics and produced mature spermatozoa. This methodology, besides opening new avenues of basic research into spermatogenesis and stem-cell self-renewal, may prove useful as a tool for biomedical science and biotechnology.
Efficient modification of a human chromosome by telomere-directed truncation in high homologous recombination-proficient chicken DT40 cells (1998)

Truncation of human chromosomes at desired sites by homologous recombination techniques enables functional and structural analyses of human chromosomes and development of human artificial chromosomes. However, this targeted truncation has been inefficient. We describe here an efficient method for targeted truncation in the chicken DT40 cells with a high homologous recombination rate. The human chromosome 22 was transferred into DT40 cells, where human telomeric repeat (TTAGGG)n was targeted to the LIF locus on the chromosome. Molecular and cytogenetic analyses showed that the predicted truncation at the LIF locus occurred in all of the targeted clones.