gebhart/patrepeval huggingface dataset:
Human Phagocytes Employ the Myeloperoxidase-Hydrogen Peroxide System to Synthesize Dityrosine, Trityrosine, Pulcherosine, and Isodityrosine by a Tyrosyl Radical-dependent Pathway (1996)

Myeloperoxidase, a heme protein secreted by activated phagocytes, may be a catalyst for lipoprotein oxidation in vivo. Active myeloperoxidase is a component of human atherosclerotic lesions, and atherosclerotic tissue exhibits selective enrichment of protein dityrosine cross-links, a well characterized product of myeloperoxidase. Tyrosylation of lipoproteins with peroxidase-generated tyrosyl radical generates multiple protein-bound tyrosine oxidation products in addition to dityrosine. The structural characterization of these products would thus serve as an important step in determining the role of myeloperoxidase in lipoprotein oxidation in the artery wall. We now report the identification and characterization of four distinct tyrosyl radical addition products generated by human phagocytes. Activated neutrophils synthesized three major fluorescent products from -tyrosine; on reverse phase HPLC, each compound coeluted with fluorescent oxidation products formed by myeloperoxidase. We purified the oxidation products to apparent homogeneity by cation and anion exchange chromatographies and identified the compounds as dityrosine (3,3'-dityrosine), trityrosine (3,3',5',3"-trityrosine) and pulcherosine (5-[4"-(2-carboxy-2-aminoethyl)phenoxy]3, 3'-dityrosine) by high resolution NMR spectroscopy and mass spectrometry. Additionally, we have found that dityrosine is a precursor to trityrosine, but not pulcherosine. In a search for a precursor to pulcherosine, we identified isodityrosine (3-[4'-(2-carboxy-2-aminoethyl)phenoxy]tyrosine), a non-fluorescent product of L-tyrosine oxidation by human phagocytes. Our results represent the first identification of this family of tyrosyl radical addition products in a mammalian system. Moreover, these compounds may serve as markers specific for tyrosyl radical-mediated oxidative damage in atherosclerosis and other inflammatory conditions.
A Human Minor Histocompatibility Antigen Resulting from Differential Expression due to a Gene Deletion (2003)

Minor histocompatibility antigens (minor H antigens) are targets of graft-versus-host disease and graft-versus-leukemia responses after allogeneic human leukocyte antigen identical hematopoietic stem cell transplantation. Only a few human minor H antigens have been molecularly characterized and in all cases, amino acid differences between homologous donor and recipient proteins due to nucleotide polymorphisms in the respective genes were responsible for immunogenicity. Here, we have used cDNA expression cloning to identify a novel human minor H antigen encoded by UGT2B17, an autosomal gene in the multigene UDP-glycosyltransferase 2 family that is selectively expressed in liver, intestine, and antigen-presenting cells. In contrast to previously defined human minor H antigens, UGT2B17 is immunogenic because of differential expression of the protein in donor and recipient cells as a consequence of a homozygous gene deletion in the donor. Deletion of individual members of large gene families is a common form of genetic variation in the population and our results provide the first evidence that differential protein expression as a consequence of gene deletion is a mechanism for generating minor H antigens in humans.
Evolutionary conservation of possible functional domains of the human and murine XIST genes (1993)

The human XIST gene, a candidate for a role in X chromosome inactivation, has recently been cloned and sequenced, yielding a 17 kb cDNA with no apparent significant, conserved open reading frame. In addition, the XIST transcript has been localized within the nucleus to the Barr body by RNA in situ hybridization. This subnuclear localization and lack of any significant protein-coding potential suggest that XIST may act as a functional RNA within the nucleus. In the absence of a conserved open reading frame, we have turned to evolutionary studies as a first step toward elucidating a function for XIST in the process of X inactivation. While probes for XIST detect homologues in numerous eutherians, sequence comparisons require significant gapping and reveal identity levels intermediate between those seen for coding and non-coding regions in other genes. Further, sequence comparison of the most likely candidate open reading frame among several primate species reveals sequence changes not normally associated with protein-coding regions. Other features of XIST are conserved in different species, however, including the position of a major transcription start site and active X chromosome-specific DNA methylation patterns at the gene's 5' end. Finally, a possible molecular basis for differing propensity toward X inactivation between Xce alleles in mouse is investigated by comparing the sequence of the Xist conserved 5' repeats in mouse strains carrying different Xce alleles.
The History and Future of the Fluorescence Activated Cell Sorter and Flow Cytometry: A View from Stanford (2002)

The Fluorescence Activated Cell Sorter (FACS) was invented in the late 1960s by Bonner, Sweet, Hulett, Herzenberg, and others to do flow cytometry and cell sorting of viable cells. Becton Dickinson Immunocytometry Systems introduced the commercial machines in the early 1970s, using the Stanford patent and expertise supplied by the Herzenberg Laboratory and a Becton Dickinson engineering group under Bernie Shoor. Over the years, we have increased the number of measured FACS dimensions (parameters) and the speed of sorting to where we now simultaneously measure 12 fluorescent colors plus 2 scatter parameters. In this history, I illustrate the great utility of this state-of-the-art instrument, which allows us to simultaneously stain, analyze, and then sort cells from small samples of human blood cells from AIDS patients, infants, stem cell transplant patients, and others. I also illustrate analysis and sorting of multiple subpopulations of lymphocytes by use of 8-12 colors. In addition, I review single cell sorting used to clone and analyze hybridomas and discuss other applications of FACS developed over the past 30 years, as well as give our ideas on the future of FACS. These ideas are currently being implemented in new programs using the internet for data storage and analysis as well as developing new fluorochromes, e.g., green fluorescent protein and tandem dyes, with applications in such areas as apoptosis, gene expression, cytokine expression, cell biochemistry, redox regulation, and AIDS. Finally, I describe new FACS methods for measuring activated kinases and phosphatases and redox active enzymes in individual cells simultaneously with cell surface phenotyping. Thus, key functions can be studied in various subsets of cells without the need for prior sorting.
Reproducibility of HPV DNA Testing by Hybrid Capture 2 in a Screening Setting (2005)

Within a large Italian randomized trial on new technologies for cervical canc+er screening involving 7 laboratories with different levels of experience, an intralaboratory and interlaboratory quality control program for human papillomavirus (HPV) DNA testing by Hybrid Capture 2 (HC2; Digene, Gaithersburg, MD) was implemented. To monitor the hybridization and detection steps, target samples containing purified, concentration-defined, HPV DNA were introduced in each test run. Only 3 of 1,024 showed a mistake in a positive vs negative classification with a 1 relative light unit (RLU)/positive control specimen (PC) ratio cutoff. To monitor the preanalytic steps (particularly denaturation), blinded specimens (33 collected in PreservCyt [Cytyc, Boxborough, MA] and 36 in Specimen Transport Medium [STM, Digene]) were centrally prepared, divided into aliquots, and sent to each laboratory. The multiple-rater κ scores for negative (<1 RLU/PC), low-positive (1 to <11 RLU/PC), and high-positive (≥11 RLU/PC) samples, respectively, were 0.91, 0.60, and 0.69 with PreservCyt and 0.93, 0.87, and 0.90 with STM. Our data showed high reliability and reproducibility with HC2, with κ values higher for STM than ThinPrep (Cytyc) samples.
Design and specificity of long ssDNA donors for CRISPR-based knock-in (2017)

Update: November 12th, 2019. The conclusions of this pre-print are outdated. See Authors note on page 2. CRISPR/Cas technologies have transformed our ability to manipulate genomes for research and gene-based therapy. In particular, homology-directed repair after genomic cleavage allows for precise modification of genes using exogenous donor sequences as templates. While both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) forms of donors have been used as repair templates, a systematic comparison of the performance and specificity of repair using ssDNA versus dsDNA donors is still lacking. Here, we describe an optimized method for the synthesis of long ssDNA templates and demonstrate that ssDNA donors can drive efficient integration of gene-sized reporters in human cell lines. We next define a set of rules to maximize the efficiency of ssDNA-mediated knock-in by optimizing donor design. Finally, by comparing ssDNA donors with equivalent dsDNA sequences (PCR products or plasmids), we demonstrate that ssDNA templates have a unique advantage in terms of repair specificity while dsDNA donors can lead to a high rate of off-target integration. Our results provide a framework for designing high-fidelity CRISPR-based knock-in experiments, in both research and therapeutic settings.
Development of an in vivo model of human multiple myeloma bone disease (1996)

Osteolytic bone destruction and its complications, bone pain, pathologic fractures, and hypercalcemia, are a major source of morbidity and mortality in patients with multiple myeloma. The bone destruction in multiple myeloma is due to increased osteoclast (OCL) activity and decreased bone formation in areas of bone adjacent to myeloma cells. The mechanisms underlying osteolysis in multiple myeloma in vivo are unclear. We used a human plasma cell leukemia cell line, ARH-77, that has disseminated growth in mice with severe combined immunodeficiency (SCID) and expresses IgG kappa, as a model for human multiple myeloma, SCID mice were irradiated with 400 rads and mice were injected either with 10(6) ARH-77 cells intravenously (ARH-77 mice) or vehicle 24 hours after irradiation. Development of bone disease was assessed by blood ionized calcium levels, x-rays, and histology. All ARH-77, but none of control mice that survived irradiation, developed hind limb paralysis 28 to 35 days after injection and developed hypercalcemia (1.35 to 1.46 mmol/L) a mean of 5 days after becoming paraplegic. Lytic bone lesions were detected using x-rays in all the hypercalcemic mice examined. No lytic lesions or hypercalcemia developed in the controls. Controls or ARH-77 mice, after developing hypercalcemia, were then killed and bone marrow plasma from the long bones were obtained, concentrated, and assayed for bone-resorbing activity. Bone marrow plasma from ARH-77 mice induced significant bone resorption in the fetal rat long bone resorption assay when compared with controls (percentage of total 45Ca released = 35% +/- 4% v 11% +/- 1%). Histologic examination of tissues from the ARH-77 mice showed infiltration of myeloma cells in the liver and spleen and marked infiltration in vertebrae and long bones, with loss of bony trabeculae and increased OCL numbers. Interestingly, cultures of ARH-77 mouse bone marrow for early OCL precursors (colony-forming unit-granulocyte-macrophage [CFU-GM]) showed a threefold increase in CFU-GM from ARH-77 marrow versus controls (185 +/- 32 v 40 +/- 3 per 2 x 10(5) cell plated). Bone-resorbing human and murine cytokines such as interleukin-6 (IL-6), IL-1 alpha or beta, TGF-alpha, lymphotoxin, and TNF alpha were not significantly increased in ARH-77 mouse sera or marrow plasma, compared with control mice, although ARH-77 cells produce IL-6 and lymphotoxin in vitro. Conditioned media from ARH-77 cells induced significant bone resorption in the fetal rat long bone resorption assay when compared with untreated media (percentage of total 45Ca released = 22% +/- 2% v 11% +/- 1%). This effect was not blocked by anti-IL-6 or antilymphotoxin (percentage of total 45Ca released = 19% +/- 1% and 22% +/- 1%, respectively). Thus, we have developed a model of human multiple myeloma bone disease that should be very useful to dissect the pathogenesis of the bone destruction in multiple myeloma.
Phosphatidylinositol 4,5‐bisphosphate‐specific AKT1 is oncogenic (2009)

The protein kinase AKT1 (v-akt murine thymoma viral oncogene homolog 1), also referred to as protein kinase B (PKB), is an essential mediator of the phosphatidylinositol 3-kinase signaling pathway. Elevated activity of AKT1 is common in human cancer. Localization at the plasma membrane, leading to enhanced phosphorylation and activation of AKT1, is an important factor determining the oncogenicity of this kinase. Although the phosphatidylinositol 3-kinase signaling pathway is frequently upregulated in cancer, cancer-specific mutations in AKT1 are not common. Recently, such a mutation has been identified in breast, colon and ovarian cancers. The mutation is located in the pleckstrin homology (PH) domain of AKT1 and results in a glutamic acid to lysine substitution at residue 17. The resultant change in the conformation of the PH domain facilitates membrane binding of the mutant protein. Here we show that exchange of the PH domain leading to preferential binding of phosphatidylinositol 4,5-bisphosphate (PIP(2)) over phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) constitutively activates AKT1. AKT1 with this altered PIP affinity induces oncogenic transformation in cultures of chicken embryo fibroblasts and causes neoplastic growth and angiogenesis in the chorioallantoic membrane of the chicken embryo. Gain-of-function mutants of AKT1 may not be affected by PI3K inhibitors that are currently in development. Therefore, AKT1 remains a distinct and important cancer target.
QR Images: Optimized Image Embedding in QR Codes (2014)

This paper introduces the concept of QR images, an automatic method to embed QR codes into color images with bounded probability of detection error. These embeddings are compatible with standard decoding applications and can be applied to any color image with full area coverage. The QR information bits are encoded into the luminance values of the image, taking advantage of the immunity of QR readers against local luminance disturbances. To mitigate the visual distortion of the QR image, the algorithm utilizes halftoning masks for the selection of modified pixels and nonlinear programming techniques to locally optimize luminance levels. A tractable model for the probability of error is developed and models of the human visual system are considered in the quality metric used to optimize the luminance levels of the QR image. To minimize the processing time, the optimization techniques proposed to consider the mechanics of a common binarization method and are designed to be amenable for parallel implementations. Experimental results show the graceful degradation of the decoding rate and the perceptual quality as a function the embedding parameters. A visual comparison between the proposed and existing methods is presented.
A DNA Vaccine Coding for theBrucellaOuter Membrane Protein 31 Confers Protection againstB. melitensisandB. ovisInfection by Eliciting a Specific Cytotoxic Response (2005)

The development of an effective subunit vaccine against brucellosis is a research area of intense interest. The outer membrane proteins (Omps) of Brucella spp. have been extensively characterized as potential immunogenic and protective antigens. This study was conducted to evaluate the immunogenicity and protective efficacy of the B. melitensis Omp31 gene cloned in the pCI plasmid (pCIOmp31). Immunization of BALB/c mice with pCIOmp31 conferred protection against B. ovis and B. melitensis infection. Mice vaccinated with pCIOmp31 developed a very weak humoral response, and in vitro stimulation of their splenocytes with recombinant Omp31 did not induced the secretion of gamma interferon. Splenocytes from Omp31-vaccinated animals induced a specific cytotoxic-T-lymphocyte activity, which leads to the in vitro lysis of Brucella-infected macrophages. pCIOmp31 immunization elicited mainly CD8(+) T cells, which mediate cytotoxicity via perforins, but also CD4(+) T cells, which mediate lysis via the Fas-FasL pathway. In vivo depletion of T-cell subsets showed that the pCIOmp31-induced protection against Brucella infection is mediated predominantly by CD8(+) T cells, although CD4(+)T cells also contribute. Our results demonstrate that the Omp31 DNA vaccine induces cytotoxic responses that have the potential to contribute to protection against Brucella infection. The protective response could be related to the induction of CD8(+) T cells that eliminate Brucella-infected cells via the perforin pathway.
Gemcitabine, vinorelbine and trastuzumab combination (GemVinT) as second-third line therapy for HER-2 overexpressing metastatic breast cancer (MBC) (2004)

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Identification and Characterization of a Novel Protein, Periostin, with Restricted Expression to Periosteum and Periodontal Ligament and Increased Expression by Transforming Growth Factor β (1999)

We had previously identified the cDNA for a novel protein called osteoblast-specific factor 2 (OSF-2) from an MC3T3-E1 cDNA library using subtraction hybridization and differential screening techniques. Here we describe the localization, regulation, and potential function of this protein. Immunohistochemistry using specific antiserum revealed that in adult mice, the protein is preferentially expressed in periosteum and periodontal ligament, indicating its tissue specificity and a potential role in bone and tooth formation and maintenance of structure. Based on this observation and the fact that other proteins have been called OSF-2, the protein was renamed "periostin." Western blot analysis showed that periostin is a disulfide linked 90 kDa protein secreted by osteoblasts and osteoblast-like cell lines. Nucleotide sequence revealed four periostin transcripts that differ in the length of the C-terminal domain, possibly caused by alternative splicing events. Reverse transcription- polymerase chain reaction analysis revealed that these isoforms are not expressed uniformly but are differentially expressed in various cell lines. Both purified periostin protein and the periostin-Fc recombinant protein supported attachment and spreading of MC3T3-E1 cells, and this effect was impaired by antiperiostin antiserum, suggesting that periostin is involved in cell adhesion. The protein is highly homologous to betaig-h3, a molecule induced by transforming growth factor beta (TGF-beta) that promotes the adhesion and spreading of fibroblasts. Because TGF-beta has dramatic effects on periosteal expansion and the recruitment of osteoblast precursors, this factor was tested for its effects on periostin expression. By Western blot analysis, TGF-beta increased periostin expression in primary osteoblast cells. Together, these data suggest that periostin may play a role in the recruitment and attachment of osteoblast precursors in the periosteum.
Selective Optical Generation of Coherent Acoustic Nanocavity Modes (2007)

Femtosecond pump-probe experiments on a Ga0.85In0.15As nanocavity enclosed by two Ga(0.85)In(0.15)As/AlAs phonon Bragg mirrors reveal selective generation of terahertz confined acoustic modes and regular folded phonons. Selective generation of the confined modes alone is achievable for laser excitation at certain energies below the mirror absorption edges, corresponding to electronic transitions within the cavity layer only. Calculations based on the photoelastic effect explain the experimental results. Decay times of cavity and regular modes evidence longer decay times and anharmonic effects for the cavity mode.
Tandem columns and mixed-bed columns in high-performance liquid chromatography of proteins (1986)

By using a cation- and an anion-exchange column in series, mixtures of acidic and basic proteins were separated in a single chromatographic run with increasing salt gradient at pH 7.0. The serial order of the columns was found to affect the chromatographic results, and the effect was attributed to alteration of the salt gradient profile upon traversing the first ion-exchange column. Single columns, packed with a binary mixture of a cation and an anion exchanger gave similar chromatographic results as the tandem columns and thus offered an alternative approach to the separation of both acidic and basic proteins in a single chromatographic run. A ternary mixed phase was obtained by adding a midly hydrophobic stationary phase to the mixture of the two ion exchangers. This column could be used with increasing salt gradient as a cation exchanger for the separation of basic proteins, or as an anion exchanger for the separation of acidic proteins. Furthermore, it could be used as a "bipolar" electrostatic-interaction column with increasing salt gradient and as a hydrophobic-interaction column with decreasing salt gradient for the separation of both types of proteins in a single chromatographic run. The constituent stationary phases used in the mixed-bed columns were prepared from the same silica support, i.e., they had the same particle and pore dimensions, density, and pore volume. Besides their obvious advantages in analytical applications, appropriate mixed stationary phases, all having retentive properties for the components to be separated, are expected to be useful also in preparative chromatography to "tailor" column selectivity for a given separation problem without loss of separating capacity.
Deep Brain Stimulation Does Not Silence Neurons in Subthalamic Nucleus in Parkinson's Patients (2009)

Two broad hypotheses have been advanced to explain the clinical efficacy of deep brain stimulation (DBS) in the subthalamic nucleus (STN) for treatment of Parkinson's disease. One is that stimulation inactivates STN neurons, producing a functional lesion. The other is that electrical stimulation activates the STN output, thus "jamming" pathological activity in basal ganglia-corticothalamic circuits. Evidence consistent with both concepts has been adduced from modeling and animal studies, as well as from recordings in patients. However, the stimulation parameters used in many recording studies have not been well matched to those used clinically. In this study, we recorded STN activity in patients with Parkinson's disease during stimulation delivered through a clinical DBS electrode using standard therapeutic stimulus parameters. A microelectrode was used to record the firing of a single STN neuron during DBS (3-5 V, 80-200 Hz, 90- to 200-micros pulses; 33 neurons/11 patients). Firing rate was unchanged during the stimulus trains, and the recorded neurons did not show prolonged (s) changes in firing rate on termination of the stimulation. However, a brief (approximately 1 ms), short-latency (6 ms) postpulse inhibition was seen in 10 of 14 neurons analyzed. A subset of neurons displayed altered firing patterns, with a predominant shift toward random firing. These data do not support the idea that DBS inactivates the STN and are instead more consistent with the hypothesis that this stimulation provides a null signal to basal ganglia-corticothalamic circuitry that has been altered as part of Parkinson's disease.
Preparation and Use of E. coli S-30 Extracts (2003)

Pioneering work leading to the elucidation of the genetic code and the characterization of the protein synthesis machinery relied heavily on in vitro transcription and translation systems. Such systems allowed the use of defined templates to direct the synthesis of proteins, which could be directly characterized. It is these characteristics of the E. coli-coupled transcription/translation system (S-30) that are still useful for a variety of applications. The in vitro system, first described by Zubay (1), is the basis for the protocol described here.