gebhart/patrepeval huggingface dataset:
The B-cell tumor–associated antigen ROR1 can be targeted with T cells modified to express a ROR1-specific chimeric antigen receptor (2010)

Monoclonal antibodies and T cells modified to express chimeric antigen receptors specific for B-cell lineage surface molecules such as CD20 exert antitumor activity in B-cell malignancies, but deplete normal B cells. The receptor tyrosine kinase-like orphan receptor 1 (ROR1) was identified as a highly expressed gene in B-cell chronic lymphocytic leukemia (B-CLL), but not normal B cells, suggesting it may serve as a tumor-specific target for therapy. We analyzed ROR1-expression in normal nonhematopoietic and hematopoietic cells including B-cell precursors, and in hematopoietic malignancies. ROR1 has characteristics of an oncofetal gene and is expressed in undifferentiated embryonic stem cells, B-CLL and mantle cell lymphoma, but not in major adult tissues apart from low levels in adipose tissue and at an early stage of B-cell development. We constructed a ROR1-specific chimeric antigen receptor that when expressed in T cells from healthy donors or CLL patients conferred specific recognition of primary B-CLL and mantle cell lymphoma, including rare drug effluxing chemotherapy resistant tumor cells that have been implicated in maintaining the malignancy, but not mature normal B cells. T-cell therapies targeting ROR1 may be effective in B-CLL and other ROR1-positive tumors. However, the expression of ROR1 on some normal tissues suggests the potential for toxi-city to subsets of normal cells.
Development and validation of a liquid chromatography-tandem mass spectrometry assay for serum 25-hydroxyvitamin D2/D3 using a turbulent flow online extraction technology (2009)

The LC-MSMS method coupled with turbulent flow technology for serum 25OHD quantitation is rapid, efficient, and suitable for clinical testing.
Characterization of Poly(ethylene glycol) and PEGylated Products by LC/MS with Postcolumn Addition of Amines (2008)

PEGylation of peptides and proteins presents significant challenges for structural characterization due to the heterogeneity of the poly(ethylene glycol) (PEG), the number of PEG moieties attached, and the site(s) of PEGylation. In this work, a novel and powerful methodology using a postcolumn addition combined with LC/MS was developed and applied to examine high molecular weight (>/=20 kDa) PEG as well as PEGylated peptide and protein products. The PEG and PEGylated compounds were eluted from RP-HPLC, and the HPLC stream was mixed with diethylmethylamine (DEMA) or triethylamine (TEA) through a T mixer coupled to a time-of-flight mass spectrometer. With these conditions, PEG is diethylmethyl- or triethyl-ammoniated instead of protonated while the protein or peptide remains protonated. The charges for PEG and the PEGylated compounds were greatly reduced, and there was no convolution among differently charged ions, even for 40 kDa PEG or tri-20 kDa PEGylated IgG4 heavy chain. Mass accuracies (<0.01%) obtained are similar to large molecular weight proteins. By selecting specific amines, such as DEMA, commercially available software was used to deconvolute the spectra composed of the diethylmethylammoniated PEG or the diethylmethylammoniated and protonated PEGylated peptide or protein to obtain accurate masses. The examples presented in this report demonstrate that the methodology can be used to elucidate different PEG structures and modifications, such as oxidation and maleimide ring opening of PEGylated peptides or proteins.
c-Myc controls the balance between hematopoietic stem cell self-renewal and differentiation (2004)

The activity of adult stem cells is essential to replenish mature cells constantly lost due to normal tissue turnover. By a poorly understood mechanism, stem cells are maintained through self-renewal while concomitantly producing differentiated progeny. Here, we provide genetic evidence for an unexpected function of the c-Myc protein in the homeostasis of hematopoietic stem cells (HSCs). Conditional elimination of c-Myc activity in the bone marrow (BM) results in severe cytopenia and accumulation of HSCs in situ. Mutant HSCs self-renew and accumulate due to their failure to initiate normal stem cell differentiation. Impaired differentiation of c-Myc-deficient HSCs is linked to their localization in the differentiation preventative BM niche environment, and correlates with up-regulation of N-cadherin and a number of adhesion receptors, suggesting that release of HSCs from the stem cell niche requires c-Myc activity. Accordingly, enforced c-Myc expression in HSCs represses N-cadherin and integrins leading to loss of self-renewal activity at the expense of differentiation. Endogenous c-Myc is differentially expressed and induced upon differentiation of long-term HSCs. Collectively, our data indicate that c-Myc controls the balance between stem cell self-renewal and differentiation, presumably by regulating the interaction between HSCs and their niche.
Conjugated linoleic acid inhibits osteoclast differentiation of RAW264.7 cells by modulating RANKL signaling (2006)

Bone destruction is a pathological hallmark of several chronic inflammatory diseases, including rheumatoid arthritis, periodontitis, and osteoporosis. Inflammation-induced bone loss of this sort results from increased numbers of bone-resorbing osteoclasts. Numerous studies have indicated that conjugated linoleic acid (CLA) positively influences calcium and bone metabolism. Gene-deletion studies have shown that receptor activator of nuclear factor-kappaB ligand (RANKL) is one of the critical mediators of osteoclastogenesis. In this report, we examine the ability of CLA to suppress RANKL signaling and osteoclastogenesis in RAW264.7 cells, a murine monocytic cell line. Treatment of these cells with RANKL activated nuclear factor-kappaB (NF-kappaB), and preexposure of the cells to CLA significantly suppressed RANKL-induced NF-kappaB activation, including phosphorylation of I-kappaBalpha, degradation of I-kappaBalpha, and nuclear translocation of p65. RANKL induced osteoclastogenesis in these monocytic cells, and CLA inhibited RANKL-induced tumor necrosis factor-alpha production and osteoclast differentiation, including osteoclast-specific genes such as tartrate-resistant acid phosphatase, cathepsin K, calcitonin receptor, and matrix metalloproteinase-9 expression and osteoclast-specific transcription factors such as c-Fos, nuclear factor of activated T-cells expression, and bone resorption pit formation. CLA also inhibited RANKL-induced activation of mitogen-activated protein kinase p38 but had little effect on c-Jun N-terminal kinase activation. Collectively, these data demonstrate for the first time that CLA inhibits osteoclastogenesis by modulating RANKL signaling. Thus, CLA may have important therapeutic implications for the treatment of bone diseases associated with enhanced bone resorption by excessive osteoclastogenesis.
Supramolecular Aggregates of Dendritic Multishell Architectures as Universal Nanocarriers (2007)

Chemical chameleons: Highly stable supramolecular aggregates built from dendritic multishell architectures show a universal transport ability for both polar and nonpolar guest molecules and can adapt to various solvent environments, ranging from toluene to water.
Advances in molecular diagnostics for avian influenza. (2006)

Recent outbreaks of avian influenza (AI) have highlighted the necessity to improve existing tests and to develop new methods, in order to detect spread or new outbreaks more quickly, which is vital for the early and successful implementation of control strategies. Conventionally, the time between clinical suspicion and laboratory confirmation of AI can be relatively long because of the logistics of sending samples to laboratories and their capacity for providing high throughput of sensitive and specific assays. Increasingly, new-generation assays based on molecular diagnostics have become available and applied successfully to disease investigation or active surveillance programmes. There has been widespread application of techniques based on the amplification of specific nucleic acid sequences by polymerase chain reaction (PCR), ligase chain reaction and nucleic acid sequence-based amplification (NASBA). The approaches generally offer high specificity and sensitivity. One of the most promising technologies is real-time PCR, which enables amplification of nucleic acids and detection of the amplified products through specific probes at the same time. A rapid diagnosis can be achieved, together with potential for high throughput resulting from process automation. Currently, microarray technology is developing rapidly and has been applied to diagnosis of influenza A virus but generally lacks the necessary sensitivity for direct application to clinical specimens. In addition, these new technologies have been increasingly applied to rapid and reliable subtyping of AI viruses. The application of molecular technologies to the "field" is now potentially an option, through the availability of portable machines for conducting such tests, with prospects for radically changing diagnostic approaches for AI in the future.
Lentiviral vectors for cutaneous RNA managing (2011)

Post-transcriptional managing of RNA plays a key role in the intricate network of cellular pathways that regulate our genes. Numerous small RNA species have emerged as crucial regulators of RNA processing and translation. Among these, microRNAs (miRNAs) regulate protein synthesis through specific interactions with target RNAs and are believed to play a role in almost any cellular process and tissue. Skin is no exception, and miRNAs are intensively studied for their role in skin homoeostasis and as potential triggers of disease. For use in skin and many other tissues, therapeutic RNA managing by small RNA technologies is now widely explored. Despite the easy accessibility of skin, the natural barrier properties of skin have challenged genetic intervention studies, and unique tools for studying gene expression and the regulatory role of small RNAs, including miRNAs, in human skin are urgently needed. Human immunodeficiency virus (HIV)-derived lentiviral vectors (LVs) have been established as prominent carriers of foreign genetic cargo. In this review, we describe the use of HIV-derived LVs for efficient gene transfer to skin and establishment of long-term transgene expression in xenotransplanted skin. We outline the status of engineered LVs for delivery of small RNAs and their in vivo applicability for expression of genes and small RNA effectors including small hairpin RNAs, miRNAs and miRNA inhibitors. Current findings suggest that LVs may become key tools in experimental dermatology with particular significance for cutaneous RNA managing and in vivo genetic intervention.
Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli. (1984)

The five enzymes responsible for the conversion of L-aspartate to L-threonine in Escherichia coli were purified to homogeneity and subsequently reconstituted in vitro in ratios approximating those found in vivo. 31P NMR was used to conveniently monitor the rates of consumption of the substrates ATP and NADPH, the accumulation of the intermediates beta-aspartyl phosphate and homoserine phosphate, and the formation of the products ADP, NADP+, and Pi in a single experiment. By this method, the flux of aspartic acid through the enzymes of the pathway was monitored in the absence and in the presence of several alternative substrates and inhibitors. Several known antimetabolites were found to be alternative substrates that ultimately became inhibitors of pathway flux. L-threo-3-Hydroxyaspartic acid was converted to 3-hydroxyhomoserine phosphate by the first four enzymes of the pathway. The antimetabolite L-threo-3-hydroxyhomoserine was found to bind to and inhibit aspartokinase-homoserine dehydrogenase I in a cooperative fashion (I 0.5 = 3 mM, nH = 2.5), similar to the action of the allosteric end product inhibitor L-threonine (I 0.5 = 0.36 mM, nH = 2.4). In the presence of the remaining enzymes of the pathway, however, L-threo-3-hydroxyhomoserine was phosphorylated to the apparent ultimate antimetabolite L-threo-3-hydroxyhomoserine phosphate that was a potent inhibitor of threonine synthase and consequently of L-threonine biosynthesis. When aspartic acid alone was examined as a substrate of the enzymes of the pathway, no accumulation of the beta-aspartyl phosphate and homoserine phosphate intermediates was observed. However, in the presence of either 5 mM L-threo-3-hydroxyhomoserine or 5 mM L-threo-3-hydroxyhomoserine phosphate, homoserine phosphate was found to accumulate. In contrast to the homoserine phosphate and 3-hydroxyhomoserine phosphate intermediates, both of which were very stable, the acylphosphate intermediates beta-aspartyl phosphate and beta-3-hydroxyaspartyl phosphate were highly susceptible to hydrolysis, with first-order rate constants of 4.6 X 10(-3) min-1 and 4.5 X 10(-2) min-1 (pH 7.8, 25 degrees C), respectively.
In vitro antioxidant properties of calcium dobesilate (1998)

Calcium dobesilate, a vascular protective agent, was tested in vitro for its scavenging action against oxygen free radicals. Calcium dobesilate was as potent as rutin to scavenge hydroxyl radicals (IC50 = 1.1 vs 0.7 microM, respectively). It was also able to scavenge superoxide radicals, but with 23 times less potency than rutin (IC50 = 682 vs 30 microM, respectively). Calcium dobesilate significantly reduced platelet activating factor (PAF)-induced chemiluminescence in human PMN cells and lipid peroxidation by oxygen free radicals in human erythrocyte membranes, although these actions required calcium dobesilate concentrations > or = 50 microM. Finally, in cultured bovine aortic endothelial cells, magnesium dobesilate reduced the increase in cytosolic free calcium induced by hydrogen peroxide and inhibited phenazine methosulfate-induced cell potassium loss. In conclusion, calcium dobesilate was effective in scavenging hydroxyl radicals in vitro, at therapeutically relevant concentrations. Conversely, higher concentrations of the compound were required to scavenge superoxide radicals or to protect the cells against the deleterious effects of intracellular reactive oxygen species. Further studies in vivo are required to determine if these antioxidant properties of calcium dobesilate can play a role in its vascular protective mechanisms.
Microwave fixation versus formalin fixation of surgical and autopsy tissue. (1978)

Microwave irradiation of surgical and autopsy tissue penetrates, fixes, and hardens the tissue almost immediately (the fluid media used in the microwave consisted of saline, ten percent phosphate buffered formalin, and distilled water). Tissue sections from a representative sample of organs were tested. Comparable sections were simultaneously fixed in a phosphate buffered ten percent formalin bath in a vaccum oven as a control. Hematoxylin and eosin were used to stain the sections. Results equal to and superior to the control method were obtained. Saline microwave fixation was superior to formalin microwave fixation. Tissues placed in Zenker's solution and fixed in standard microwave oven (for approximately one minute) yielded results at least equal to conventional Zenker fixation (approximately two hours). No tissue hardening resulted from Zenker microwave fixation. A unique time versus temperature graph (microwave heating curve) reduces individual variation with this technique.
Recovery and purification process development for monoclonal antibody production (2010)

Hundreds of therapeutic monoclonal antibodies (mAbs) are currently in development, and many companies have multiple antibodies in their pipelines. Current methodology used in recovery processes for these molecules are reviewed here. Basic unit operations such as harvest, Protein A affinity chromatography, and additional polishing steps are surveyed. Alternative processes such as flocculation, precipitation, and membrane chromatography are discussed. We also cover platform approaches to purification methods development, use of high throughput screening methods, and offer a view on future developments in purification methodology as applied to mAbs.
Relationships Amongst the Fast‐growing Rhizobia of Lablab purpureus, Leucaena leucocephala, Mimosa spp., Acacia farnesiana and Sesbania grandiflora and their Affinities with Other Rhizobial Groups (1980)

Colony characteristics, growth in litmus milk, precipitation in calcium glycerophosphate medium and utilization of carbon sources of the root‐nodule bacteria isolated from the tropical legumes Leucaena, Mimosa, Acacia, Sesbania and Lablab were similar to fast‐growing rhizobia of temperate legumes, particularly Rhizobium meliloti. In agglutination tests, isolates from each host shared antigens with one or more of five Rhizobium strains from Leucaena. Infective characteristics of the fast‐growing rhizobia were studied in modified Leonard jars and in agar culture. Cross‐infections by rhizobia between these plants were common and the association often effective. Lablab was effectively nodulated by its own fast‐growing isolate but only formed root swellings, possibly ineffective pseudonodules, with the other isolates. Slow‐growing rhizobia which were able to nodulate Macroptilium atropurpureus were unable to form nodules on these legumes except Lablab which was considered more akin to the cowpea group. All fast‐growing isolates nodulated, often effectively, Vigna unguiculata and V. unguiculata ssp. sesquipedalis. The isolate from Lablab also effectively nodulated a number of other tropical legumes which have previously only been reported to nodulate with slow‐growing nodule bacteria and it also produced ineffective nodulation on Medicago sativa. This is the first record of an effective fast‐growing isolate from Lablab.
Disruption of tonB in Bordetella bronchiseptica and Bordetella pertussis prevents utilization of ferric siderophores, haemin and haemoglobin as iron sources The GenBank accession number for the sequence reported in this paper is AF087669. (1999)

The Bordetella bronchiseptica tonB gene was cloned by detection of a chromosomal restriction fragment hybridizing with each of two degenerate oligonucleotides that corresponded to Pro-Glu and Pro-Lys repeats characteristic of known TonB proteins. The tonB(Bb) gene was situated upstream of exbB and exbD homologues and downstream of a putative Fur-regulated promoter. Hybridization results indicated that the tonB operon and flanking regions were highly conserved between B. bronchiseptica, Bordetella pertussis and Bordetella parapertussis. Disruption of tonB in B. bronchiseptica resulted in inability to grow in iron-limiting media, and inability to utilize alcaligin, enterobactin, ferrichrome, desferroxamine B, haemin and haemoglobin. Although it was not possible to inactivate tonB in a clinical B. pertussis isolate, tonB was disrupted in a laboratory B. pertussis strain previously selected for the ability to grow on Luria-Bertani medium. This B. pertussis tonB mutant shared a similar iron complex utilization deficient phenotype with the B. bronchiseptica tonB mutant. The B. bronchiseptica tonB operon present on a plasmid did not complement an Escherichia coli tonB mutant, but inefficient reconstitution of enterobactin utilization was observed in one fepA mutant harbouring plasmid copies of the B. pertussis fepA homologue and tonB(Bb) operon.
Evaluation of Eluents from Separations of CD34+ Cells from Human Cord Blood Using a Commerical, Immunomagnetic Cell Separation System (2001)

Human CD34+ cells from cord blood were separated in a two-step process using a commercial, immunomagnetic cell retention system. The performance of the system was evaluated by analyzing a number of eluents from the separations with a number of analytical techniques. In addition to cell counts and flow cytometry analysis, a new experimental technique that is undergoing development, cell tracking velocimetry (CTV), was used. CTV measures the degree to which a cell is immunomagnetically labeled, known as the magnetophoretic mobility, of a population of cells on a cell-by-cell basis and presents the results in the form of a histogram similar to flow cytometry data. The average recovery and purity of CD34+ cells from 10 separations was 52% and 60%, respectively. CTV analysis indicated that the mean magnetophoretic mobility of the positively enriched CD34 cells was 9.64 x 10(-5) mm3/T-A-s, while the mean mobility from negative eluents was -2.02 x 10(-6) mm3/T-A-s, very similar to the mobility of unlabeled cells. Within the positive eluents, the range of magnetophoretic mobility was approximately 50-fold, representing a plausible 50-fold range in surface CD34 antigen expression. CTV analysis also indicated that in some separations, positive cells were not retained by the immunomagnetic cell retention system. Finally, preliminary studies indicate that monocytes might be a primary cause in the lower purities and recoveries seen in this study. It is suggested that the monocytes phagocytose the magnetic nanobeads and become sufficiently magnetized to be retained within the Miltenyi column, reducing the purity of the positive eluent.
Further experience with interfascicular grafting of the median, ulnar, and radial nerves (1976)

The results of interfascicular nerve-grafting, a procedure developed in 1964, were reported in The Journal in 1972 9. Between 1964 and 1972, defects in forty-three median, fourty-four ulnar, and sixteen radial nerves were grafted using this technique. Final functional results after a minimum follow-up of two years are known for thirty-eight patients with median, thirty-nine patients with ulnar, and thirteen patients with radial-nerve lesions. In the median-nerve cases useful motor recovery (M 3 or higher) was achieved in 82% and protective sensibility was restored in all but one. In all of the patients with ulnar-nerve lesions useful motor recovery (M 2+ or higher) occurred, while in 77% of the patients with radial-nerve lesions an M 4 or M 5 level of function was achieved. The majority of the patients with poor results had some unfavorable circumstance such as advanced age, severity of the original trauma, or long time interval before repair. Comparison of our results with those in other series indicates that interfascicular nerve-grafting gives results which are at least as good as those after epineural nerve suture under ideal conditions and better than those after neurorrhaphy under tension.
ASSAY OF POLY-β-HYDROXYBUTYRIC ACID (1961)

Law, John H. (Harvard University, Cambridge, Mass.) and Ralph A. Splepecky. Assay of poly-beta-hydroxybutyric acid. J. Bacteriol. 82:33-36. 1961-A convenient spectrophotometric assay of bacterial poly-beta-hydroxybutyric acid has been devised. Quantitative conversion of poly-beta-hydroxybutyric acid to crotonic acid by heating in concentrated sulfuric acid and determination of the ultraviolet absorption of the produce permits an accurate determination of this material in quantities down to 5 mug. This method has been used to follow the production of poly-beta-hydroxybutyric acid by Bacillus megaterium strain KM.