gebhart/patrepeval huggingface dataset:
Stromal fibroblast heparan sulfate is required for cytokine-mediated ex vivo maintenance of human long-term culture-initiating cells (1996)

We have recently demonstrated that 50% of primitive human long-term culture-initiating cells (LTC-IC) are maintained for up to 8 weeks in stroma-dependent cultures in which progenitor-stroma contact is prevented (stroma noncontact), or when progenitors are cultured in medium conditioned by stromal feeders. This indicates that factors responsible for LTC-IC maintenance are present in soluble form in stromal supernatant (SN). Although the picogram concentrations of cytokines present in stromal SN can induce the differentiation of CD34+/HLA-DR- (DR-) cells to clonogenic cells (colony forming cells; CFC), they maintain only 10% of LTC-IC for 5 weeks, suggesting that factors other than these cytokines are required for LTC-IC maintenance. To characterize the factor(s) in stromal SN responsible for LTC-IC maintenance, we purified glycoproteins and proteoglycans (PG) from the SN of the LTC-IC supportive murine marrow stromal fibroblast cell line M2-10B4 by ion exchange high performance liquid chromatography (HPLC). Culture of DR- cells in a combination of M2-10B4-derived PG, but not glycoproteins and picogram concentrations of recombinant human interleukin-6 (IL-6), granulocyte colony-stimulating factor (G-CSF), stem cell factor (SCF), leukemia inhibitory factor (LIF), granulocyte-macrophage colony-stimulating factor (GM-CSF), and macrophage inflammatory protein-1alpha (MIP-1alpha) resulted in the recovery of 96% +/- 8% of LTC-IC maintained in cultures supplemented with unfractionated stromal SN. LTC-IC maintenance was largely retained after digestion of the PG-rich fraction with proteinase K and after dissociative gel filtration chromatography, but was completely abolished following treatment with nitrous acid, which digests heparan sulfate glycosaminoglycans (HS GAG). As for M2-10B4-derived HS GAG, high concentrations of bovine kidney HS GAG, but not bovine tracheal chondroitin sulfate, significantly improved cytokine-mediated LTC-IC maintenance. Maintenance of LTC-IC by these nonmarrow-derived HS GAG was, however, significantly lower than that seen with M2-10B4-derived HS. These studies demonstrate a role for marrow stroma-derived HS GAG in the long-term in vitro maintenance of human LTC-IC. Further structure-function analysis of these HS GAG may have important implications for ex vivo stem cell expansion and gene transfer into hematopoietic progenitors.
Induction of germ-line and mature C epsilon transcripts in human B cells stimulated with rIL-4 and EBV. (1990)

EBV and rIL-4 induce T cell-independent IgE production by normal human B cells. We demonstrate here that EBV and IL-4 induced the synthesis of IgE by surface IgE-negative B cell precursors isolated by cell sorting. This result suggests that the induction of IgE by EBV and IL-4 results not merely from the expansion of a precommitted surface IgE-positive B cell population but more likely from IL-4-directed switching to IgE. At the molecular level, IL-4 and EBV induced the appearance of 2.0- and of 1.8-kilobase (kb) RNA bands, both of which hybridized with an 0.88-kb HinfI fragment spanning part of the C epsilon 1 exon and the entire C epsilon 2 exon. The 1.8-kb band but not the 2.0-kb band also hybridized with a cloned genomic 0.7-kb SmaI fragment located approximately 2 kb upstream of C epsilon. Thus, EBV and IL-4 induced germline (1.8-kb) as well as mature (2.0-kb) C epsilon transcripts. IL-4 by itself induced germ-line C epsilon transcripts but not mature C epsilon transcripts in purified normal B cells. IL-4 failed to induce IgE synthesis in established EBV B cell lines and failed to induce 2.0-kb mature C epsilon transcripts but induced 1.8-kb germ-line C epsilon transcripts. These data show that IL-4 is sufficient for the induction of C epsilon germ-line transcription. In contrast, the transcription of mature epsilon mRNA requires an additional activating signal, provided by infection with EBV. Established EBV transformation results in a dissociation between germ-line C epsilon transcription and the ability to undergo IgE switching in response to IL-4.
Nucleotide sequence of the Staphylococcus aureus gyrB-gyrA locus encoding the DNA gyrase A and B proteins (1992)

We have determined the nucleotide sequence of a 5.3-kb segment of the Staphylococcus aureus chromosome that includes the gyrA and gyrB genes coding for both subunits of DNA gyrase, the enzyme that catalyzes ATP-dependent DNA supercoiling. The gene order at this locus, dnaA-dnaN-recF-gyrB-gyrA, is similar to that found in the Bacillus subtilis replication origin region. S. aureus recF, gyrB, and gyrA genes are closely spaced, occupy the same reading frame, and may be coordinately expressed. The S. aureus gyrB and gyrA genes encode 640- and 889-residue proteins, respectively, that share strong homology with other bacterial gyrase subunits, notably those from B. subtilis. These results are discussed in regard to the mechanism of DNA gyrase and its role as a target for the 4-quinolones and other antistaphylococcal agents.
Isolation of intact detergent‐free phycobilisomes by trypsin (1983)

Phycobilisomes have been detached from red algal thylakoids by means of trypsin and purified by sucrosegradient centrifugation in the absence of detergents. These phycobilisomes have identical absorbance and fluorescence properties to phycobilisomes prepared with detergent. Their peptide composition determined by SDS‐PAGE suggests that a lamellar peptide is cleaved by trypsin to release the intact phycobilisome. Subsequently trypsin attacks the 94 kDa peptide implicated [Redlinger, T. and Gantt, E. (1982) Proc. Natl. Acad. Sci. USA 79, 5542‐5546] in the phycobilisome attachment.
MR angiography with two-dimensional acquisition and three-dimensional display. Work in progress. (1989)

Magnetic resonance arteriograms of healthy volunteers and selected patients were produced with a new spoiled gradient-echo pulse sequence based on time-of-flight phenomena. The procedure involves sequential acquisition of many contiguous, thin (1.5-mm) axial two-dimensional sections. These volume data are then submitted to a raytracing projection program, which retrospectively yields multiple arbitrary projection angles rotating through any plane. Venous structures are suppressed with a presaturation slab superior to the current section. The slab location is advanced in concert with advancement of each new section location. The acquisition time varies from 6 to 13 minutes, depending on the number of sections acquired for three-dimensional display. This method obviates the subtraction of image data sets to suppress signals from stationary spins, is more sensitive to slow blood flow than three-dimensional methods of acquisition, and shows special promise for the study of extracranial vascular disease.
The immune recognition of gluten in coeliac disease (2005)

Coeliac disease, the most common intestinal disorder of western populations, is an autoimmune enteropathy caused by an abnormal immune response to dietary gluten peptides that occurs in genetically susceptible individuals carrying the HLA-DQ2 or -DQ8 haplotype. Despite the recent progresses in understanding the molecular mechanisms of mucosal lesions, it remains unknown how increased amounts of gluten peptides can enter the intestinal mucosa to initiate the inflammatory cascade. Current knowledge indicates that different gluten peptides are involved in the disease process in a different manner, some fragments being 'toxic' and others 'immunogenic'. Those defined as 'toxic' are able to induce mucosal damage either when added in culture to duodenal endoscopic biopsy or when administered in vivo, while those defined as 'immunogenic' are able to specifically stimulate HLA-DQ2- or DQ8-restricted T cell clones isolated from jejunal mucosa or peripheral blood of coeliac patients. These peptides are able to trigger two immunological pathways: one is thought to be a rapid effect on the epithelium that involves the innate immune response and the other represents the adaptive immune response involving CD4+ T cells in the lamina propria that recognize gluten epitopes processed and presented by antigen presenting cells. These findings are the subject of the present review.
Enhanced external radiative efficiency for 20.8% efficient single-junction GaInP solar cells (2013)

We demonstrate 1.81 eV GaInP solar cells approaching the Shockley-Queisser limit with 20.8% solar conversion efficiency, 8% external radiative efficiency, and 80–90% internal radiative efficiency at one-sun AM1.5 global conditions. Optically enhanced voltage through photon recycling that improves light extraction was achieved using a back metal reflector. This optical enhancement was realized at one-sun currents when the non-radiative Sah-Noyce-Shockley junction recombination current was reduced by placing the junction at the back of the cell in a higher band gap AlGaInP layer. Electroluminescence and dark current-voltage measurements show the separate effects of optical management and non-radiative dark current reduction.
WalkType (2012)

The lack of tactile feedback on touch screens makes typing difficult, a challenge exacerbated when situational impairments like walking vibration and divided attention arise in mobile settings. We introduce WalkType, an adaptive text entry system that leverages the mobile device's built-in tri-axis accelerometer to compensate for extraneous movement while walking. WalkType's classification model uses the displacement and acceleration of the device, and inference about the user's footsteps. Additionally, WalkType models finger-touch location and finger distance traveled on the screen, features that increase overall accuracy regardless of movement. The final model was built on typing data collected from 16 participants. In a study comparing WalkType to a control condition, WalkType reduced uncorrected errors by 45.2% and increased typing speed by 12.9% for walking participants.
Intestinal epithelial exosomes carry MHC class II/peptides able to inform the immune system in mice (2003)

Epithelial exosomes are antigen presenting vesicles bearing MHC class II/peptide complexes that prime for an immunogenic rather than tolerogenic response in the context of a systemic challenge. In the intestine, both the mucosal microenvironment and local effector cells are probably key players in determining the outcome of the immune response to exosome derived epitopes.
Epidermal Growth Factor and a New Derivative (1972)

A new procedure has been devised for the preparation of pure epidermal growth factor in high yield. The method involves a two-step column fractionation of crude extracts of the submaxillary gland obtained from adult male mice. Biologically active epidermal growth factor lacking the COOH-terminal Leu-Arg residues was also isolated.
A preliminary performance comparison of five machine learning algorithms for practical IP traffic flow classification (2006)

The identification of network applications through observation of associated packet traffic flows is vital to the areas of network management and surveillance. Currently popular methods such as port number and payload-based identification exhibit a number of shortfalls. An alternative is to use machine learning (ML) techniques and identify network applications based on per-flow statistics, derived from payload-independent features such as packet length and inter-arrival time distributions. The performance impact of feature set reduction, using Consistency-based and Correlation-based feature selection, is demonstrated on Naïve Bayes, C4.5, Bayesian Network and Naïve Bayes Tree algorithms. We then show that it is useful to differentiate algorithms based on computational performance rather than classification accuracy alone, as although classification accuracy between the algorithms is similar, computational performance can differ significantly.
A Randomized, Clinical Trial of Frozen Versus Standard Nasogastric Tube Placement (2009)

A simple method of freezing an NGT with distilled water increased the success rate of insertion for intubated patients.
Automated Docking Screens: A Feasibility Study (2009)

Molecular docking is the most practical approach to leverage protein structure for ligand discovery, but the technique retains important liabilities that make it challenging to deploy on a large scale. We have therefore created an expert system, DOCK Blaster, to investigate the feasibility of full automation. The method requires a PDB code, sometimes with a ligand structure, and from that alone can launch a full screen of large libraries. A critical feature is self-assessment, which estimates the anticipated reliability of the automated screening results using pose fidelity and enrichment. Against common benchmarks, DOCK Blaster recapitulates the crystal ligand pose within 2 A rmsd 50-60% of the time; inferior to an expert, but respectrable. Half the time the ligand also ranked among the top 5% of 100 physically matched decoys chosen on the fly. Further tests were undertaken culminating in a study of 7755 eligible PDB structures. In 1398 cases, the redocked ligand ranked in the top 5% of 100 property-matched decoys while also posing within 2 A rmsd, suggesting that unsupervised prospective docking is viable. DOCK Blaster is available at http://blaster.docking.org .
Palmitoylation: a post-translational modification that regulates signalling from G-protein coupled receptors (1996)

Protein acylation is a post-translational modification that has seized much attention in the last few years. Depending on the nature of the fatty acid added, protein acylation can take the form of palmitoylation, myristoylation, or prenylation. Palmitoylation has been implicated in the modification of several different proteins and is particularly prevalent in G-protein coupled receptors and their cognate G-proteins, where it is thought to have an important regulatory function. Given that palmitoylation of these proteins is a dynamic phenomenon in which turnover rate is modulated by agonist activation, it is thought to be implicated in processes such as receptor phosphorylation and desensitization as well as in G-protein membrane translocation. A better understanding of the regulation of signal transduction mediated by G-protein coupled receptors will require the identification and characterization of those enzymes implicated in the palmitoylation and depalmitoylation process of this large class of receptors and their signalling allies.
Dominant Negative ATM Mutations in Breast Cancer Families (2002)

At least two ATM mutations are associated with a sufficiently high risk of breast cancer to be found in multiple-case breast cancer families. Full mutation analysis of the ATM gene in such families could help clarify the role of ATM in breast cancer susceptibility.
The context-tree weighting method: basic properties (1995)

Describes a sequential universal data compression procedure for binary tree sources that performs the "double mixture." Using a context tree, this method weights in an efficient recursive way the coding distributions corresponding to all bounded memory tree sources, and achieves a desirable coding distribution for tree sources with an unknown model and unknown parameters. Computational and storage complexity of the proposed procedure are both linear in the source sequence length. The authors derive a natural upper bound on the cumulative redundancy of the method for individual sequences. The three terms in this bound can be identified as coding, parameter, and model redundancy, The bound holds for all source sequence lengths, not only for asymptotically large lengths. The analysis that leads to this bound is based on standard techniques and turns out to be extremely simple. The upper bound on the redundancy shows that the proposed context-tree weighting procedure is optimal in the sense that it achieves the Rissanen (1984) lower bound.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Isolation and characterization of a heat-inducible simian virus 40 mutant (1976)

We have isolated a new type of temperature-sensitive mutant of simian virus 40 (SV40) that is capable of productive infection in permissive cells but not of maintenance of viral DNA integration in transformed cells at the conditional temperature. Virus development is induced when cells transformed by this mutant are shifted to temperatures above 39 degrees C, but is not induced below this temperature. The plaque-purified, temperature-sensitive mutant virus confers heat inducibility to new host cells, indicating that the conditional function is a property of the viral genome. Unlike previously described temperature-sensitive SV40 mutants, in (ts)-1501 is capable of productive infection in permissive cells at the conditional temperature. The morphology, growth, and oncogenicity of in (ts)-1501-transformed cells at 37 degrees C are similar to those of cell lines transformed by wild-type SV40. HK10-c2(in(ts)-1501), a cloned cell line, transformed at 37 degrees C by the mutant virus, exhibits a transient increase in DNA synthesis before cell death at the conditional temperature. Many properties of in(ts)-1501 are analogous to those of the heat-inducible mutants of bacteriophages in which a heat-inactivated protein is responsible for the stable integration of the prophage in the bacterial chromosome.
PRSS3/Mesotrypsin Is a Therapeutic Target for Metastatic Prostate Cancer (2012)

PRSS3/mesotrypsin is an atypical isoform of trypsin that has been associated with breast, lung, and pancreatic cancer cell malignancy. In analyses of open source transcriptional microarray data, we find that PRSS3 expression is upregulated in metastatic prostate cancer tissue, and that expression of PRSS3 in primary prostate tumors is prognostic of systemic progression following prostatectomy. Using a mouse orthotopic model with bioluminescent imaging, we show that PRSS3/mesotrypsin is critical for prostate cancer metastasis. Silencing of PRSS3 inhibits anchorage-independent growth of prostate cancer cells in soft agar assays, and suppresses invasiveness in Matrigel transwell assays and three-dimensional (3D) cell culture models. We further show that treatment with recombinant mesotrypsin directly promotes an invasive cellular phenotype in prostate cancer cells and find that these effects are specific and require the proteolytic activity of mesotrypsin, because neither cationic trypsin nor a mesotrypsin mutant lacking activity can drive the invasive phenotype. Finally, we show that a newly developed, potent inhibitor of mesotrypsin activity can suppress prostate cancer cell invasion to a similar extent as PRSS3 gene silencing. This study defines mesotrypsin as an important mediator of prostate cancer progression and metastasis, and suggests that inhibition of mesotrypsin activity may provide a novel modality for prostate cancer treatment.
Blocking of CD4 cell receptors for the human immunodeficiency virus type 1 (HIV‐1) by chemically modified bovine milk proteins: Potential for AIDS prophylaxis (1995)

The chemical transformation of synthetic combinatorial libraries to increase the diversity of compounds of medicinal interest was reported recently. Chemical modification of natural products represents a complementary approach to accomplish this aim. Modification of lysines by aromatic acid anhydrides, preferentially by 3-hydroxyphthalic and trimellitic anhydrides and trimellitic anhydride chloride, converted commonly available proteins (human and bovine serum albumin and casein) into potent inhibitors of (i) binding between the HIV-1 gp 120 envelope glycoprotein and the CD4 cell receptor, probably owing to their binding to CD4, and (ii) infection by HIV-1. Modified bovine milk proteins are also potent HIV-1 inhibitors and may have potential for anti-HIV-1 prophylaxis.
Hypoxia-inducible factor-1alpha is a positive factor in solid tumor growth. (2000)

Deficiencies in oxygenation are widespread in solid tumors. The transcription factor hypoxia-inducible factor (HIF)-1alpha is an important mediator of the hypoxic response of tumor cells and controls the up-regulation of a number of factors important for solid tumor expansion, including the angiogenic factor vascular endothelial growth factor (VEGF). We have isolated two cell lines nullizygous for HIF-1alpha, one from embryos genetically null for HIF-1alpha, and the other from embryos carrying loxP-flanked alleles of the gene, which allows for cre-mediated excision. The loss of HIF-1alpha negatively affects tumor growth in these two sets of H-ras-transformed cell lines, and this negative effect is not due to deficient vascularization. Despite differences in VEGF expression, vascular density is similar in wild-type and HIF-1alpha-null tumors. The evidence from these experiments indicates that hypoxic response via HIF-1alpha is an important positive factor in solid tumor growth and that HIF-1alpha affects tumor expansion in ways unrelated to its regulation of VEGF expression.
The eosinophilic variant of acute myelomonocytic leukemia developing as a secondary leukemia in a patient with mycosis fungoides. (1987)

The eosinophilic variant of acute myelomonocytic leukemia (AMML) is highly associated with characteristic abnormalities of chromosome 16. Leukemias developing secondary to chemotherapy frequently show abnormalities of chromosomes 5 and 7. This report describes a secondary AMML, eosinophilic variant (M4Eo), developing in a patient with coexistent mycosis fungoides who had received chemotherapy, including an alkylating agent, and showing characteristic abnormalities of both chromosomes 7 and 16. This is the first reported case of the M4Eo arising secondarily in a patient treated for another hematopoietic malignancy, and the second case of treatment-induced M4Eo to show coexistent abnormalities of chromosomes 7 and 16. Additional cytochemical, ultrastructural, and cell surface marker findings are described supporting malignant transformation of the eosinophilic cell line.
New developments in the understanding of cerebral vasoregulation and vasospasm: the endothelin-nitric oxide network (1995)

Endothelins, which are powerful vasoconstrictors, and nitric oxide, which is a powerful vasodilator, together form a balanced system that regulates blood flow in the brain and in other organs. Ongoing research may yield new drugs that act on this system to prevent or reverse cerebral vasospasm in subarachnoid hemorrhage and other conditions. Many compounds are involved in cerebral vasoregulation under physiologic and pathologic conditions; of these, endothelins and nitric oxide have attracted considerable attention over the last several years. Endothelins and nitric oxide differ in chemical structure and pharmacological properties: endothelins are potent vasoconstrictor peptides consisting of 21 amino acids; nitric oxide is a free radical with a half-life of only a few seconds and exerts powerful vasodilatory effects. Both are produced by a number of cell types in the brain and interact at various levels to profoundly influence cerebral vessel function.
Cysteine-Reactive Polymers Synthesized by Atom Transfer Radical Polymerization for Conjugation to Proteins (2004)

In this communication we report a strategy for the synthesis of semitelechelic polymers reactive to cysteines. An initiator modified with a pyridyl disulfide was prepared and used for the CuBr/2,2'-bipyridine-mediated atom transfer radical polymerization (ATRP) of 2-hydroxyethyl methacrylate. Polydispersity indices (M(w)/M(n)) of the polymers with different molecular weights were 1.25 or less. The pyridyl disulfide end group was preserved during the polymerization and allowed direct conjugation of the polymer to cysteine residues of bovine serum albumin. The described method provides a general way for the preparation of protein-polymer conjugates through a reversible disulfide bond without the need for postsynthesis modification of the polymers.