gebhart/patrepeval huggingface dataset:
Role of Interleukin-1β Converting Enzyme (ICE) in Acute Myelogenous Leukemia Cell Proliferation and Programmed Cell Death (1997)

The proinflammatory cytokine interleukin (IL)-1 has been shown to play a pivotal role in stimulating acute myelogenous leukemia (AML) cell proliferation. The gene for its prominent IL-1 beta form produces a 31-kDa precursor protein (pro-IL-1 beta) that is biologically inactive unless cleaved to its mature form by a cytoplasmic cysteine protease termed Il- 1 beta converting enzyme (ICE). Although ICE was first thought to be a unique enzyme with a single biologic activity, several investigators have demonstrated that ICE shares sequence homology with the protein product of ced-3, the gene for cell death of the nematode Caenorhabditis elegans, and induces apoptosis in different experimental models. It was therefore hypothesized that ICE may either augment the production of mature IL-1 beta and stimulate the proliferation of cells, in which IL-1 beta acts as an autocrine growth factor, or induce apoptosis. Recent data indicate that ICE is a member of an increasingly recognized family of cysteine proteases. Unlike ICE, the other members of this family do not cleave pro-IL-1 beta but are effective inducers of apoptotic cell death, whereas ICE acts primarily as an IL-1 beta converting enzyme. Because IL-1 beta serves as either an autocrine or paracrine growth factor in AML, we recently investigated the effect of ICE inhibition on AML colony growth and found that ICE inhibition reduced the production of mature IL-1 beta and suppressed AML progenitor proliferation. Our data suggest that ICE does not function as an apoptosis gene in AML but rather increases mature Il-1 beta production and AML cell proliferation. It is possible, therefore, that ICE inhibitors may be beneficial in AML therapy.
Synthesis of 1H-Indazoles and 1H-Pyrazoles via FeBr3/O2 Mediated Intramolecular C–H Amination (2013)

A new synthesis of substituted 1H-indazoles and 1H-pyrazoles from arylhydrazones via FeBr(3)/O(2) mediated C-H activation/C-N bond formation reactions is reported. The corresponding 1,3-diaryl-substituted indazoles and trisubstituted pyrazoles were obtained in moderate to excellent yields under mild conditions.
Poly(ADP-ribose) polymerase inhibitors suppress UV-induced human immunodeficiency virus type 1 gene expression at the posttranscriptional level. (1991)

Gene expression of human immunodeficiency virus type 1 (HIV-1) is induced not only by trans activation mediated through a gene product (tat) encoded by the virus but also by treatment of virus-carrying cells with DNA-damaging agents such as UV light. Employing an artificially constructed DNA in which the chloramphenicol acetyltransferase gene was placed under the control of the HIV-1 long terminal repeat, we analyzed the induction process in HeLa cells and found that inhibitors of poly(ADP-ribose) polymerase suppressed UV-induced HIV-1 gene expression but not tat-mediated expression. We also found that suppression occurs at the posttranscriptional level. These results indicate that HIV-1 gene expression is activated by at least two different mechanisms, one of which involves poly-ADP ribosylation. A possible new role of poly-ADP ribosylation in the regulation of specific gene expression is also discussed.
Review of "The Ombudsman: Factors Influencing Academic Research Productivity: A Survey of Management Scientists." (1992)

Terence Hancock, Julia Lane, Russ Ray, and Dennis Glennon (1992), “The Ombudsman: Factors Influencing Academic Research Productivity: A Survey of Management Scientists,” Interfaces, 22(5), 26-38. Reviewed by: J. Scott Armstrong, The Wharton School, University of Pennsylvania, Interfaces, 22(5), 26- 27.\nSome researchers are more prolific than others. What do you think explains the differences between those who publish a great deal and those who publish less?
Analysis of the delay and jitter of voice traffic over the Internet (2002)

In the future, voice communication is expected to migrate from the public switched telephone network (PSTN) to the Internet. Because of the particular characteristics (low volume and burstiness) and stringent delay and loss requirements of voice traffic, it is important to separate voice traffic from other traffic in the network by providing it with a separate queue. In this study, we conduct a thorough assessment of voice delay in this context. We conclude that priority queuing is the most appropriate scheduling scheme for the handling of voice traffic, while preemption of non-voice packets is strongly recommended for sub-10 Mbit/s links. We also find that per-connection custom packetization is in most cases futile, i.e. one packet size allows a good compromise between an adequate end-to-end delay and an efficient bandwidth utilization for voice traffic.
Non-repetitive single-chain Fv linkers selected by selectively infective phage (SIP) technology (1998)

By using the selectively infective phage (SIP) technology, we selected non-repetitive linkers for a single-chain Fv fragment to have genes more robust against deletions in PCR-based gene assembly and directed evolution experiments than is the case for the classical (Gly4Ser)3 linker. We designed linkers encoding turns at both ends and random positions in the middle where glycines and polar and charged residues were allowed to occur. After only a single round of SIP, all clones obtained were fully functional. Properties such as antigen binding constants, urea denaturation curves and expression of soluble scFv fragments were identical with those of the parental fragment with the (Gly4Ser)3 linker. This demonstrates that SIP is a very fast and powerful technique to remove rapidly sequences of poor functionality, exclusively yielding sequences of the desired overall property in a single round.
Improved Expression in Hematopoietic and Lymphoid Cells in Mice After Transplantation of Bone Marrow Transduced With a Modified Retroviral Vector (1999)

Retroviral vectors based on the Moloney murine leukemia virus (MoMuLV) are currently the most commonly used vehicles for stable gene transfer into mammalian hematopoietic cells. But, even with reasonable transduction efficiency, expression only occurs in a low percentage of transduced cells and decreases to undetectable levels over time. We have previously reported the modified MND LTR (myeloproliferative sarcoma virus enhancer,negative control region deleted, dl587rev primer-binding site substituted) to show increased expression frequency and decreased methylation in transduced murine embryonic stem cells and hematopoietic stem cells. We have now compared expression of the enhanced green fluorescent protein (eGFP) from a vector using the MoMuLV LTR (LeGFPSN) with that from the modified vector (MNDeGFPSN) in mature hematopoietic and lymphoid cells in the mouse bone marrow transplant (BMT) model. In primary BMT recipients, we observed a higher frequency of expression from the MND LTR (20% to 80%) in hematopoietic cells of all lineages in spleen, bone marrow, thymus, and blood compared with expression from the MoMuLV LTR (5% to 10%). Expression from the MND LTR reached 88% in thymic T lymphocytes and 54% in splenic B lymphocytes for up to 8 months after BMT. The mean fluorescence intensity of the individual cells, indicating the amount of protein synthesized, was 6- to 10-fold higher in cells expressing MNDeGFPSN compared with cells expressing LeGFPSN. Transduction efficiencies determined by DNA polymerase chain reaction of vector copy number were comparable for the 2 vectors. Therefore, the MND vector offers an improved vehicle for reliable gene expression in hematopoietic cells.
Differentiation‐specific expression of a novel G protein‐coupled receptor from Burkitt's lymphoma (1992)

Deregulation of the proto-oncogene MYC by specific chromosomal translocations has been shown to be essential but not sufficient for the development of Burkitt's lymphoma (BL). To identify other genes which either mark important steps in tumorigenesis or which reflect the cellular differentiation state of BL cells we have compared tumor cells to immortalized lymphoblastoid B cells by subtractive hybridization. We have identified a complementary DNA clone which encodes a novel member of the superfamily of GTP-binding (G) protein-coupled receptors, designated BLR1. The corresponding mRNA is expressed in BL and lymphatic tissues but not in other cell lines either of the B cell lineage or of other hematopoietic or non-hematopoietic origin. This exclusive expression of BLR1 and the oncogenic potential of this receptor class supports the hypothesis that BLR1 exerts a regulatory function in BL lymphomagenesis and/or B cell differentiation. Moreover, the protein sequence is highly related to that of receptors for the cytokine interleukin (IL)-8 and other neutrophil chemoattractants. We conclude that BLR1 may represent a potential candidate involved in the process of physiologic trafficking, cell-cell interactions, and activation of mature B lymphocytes in lymphatic tissues.
Evaluation of Electrochemical Interface Area and Lithium Diffusion Coefficient for a Composite Graphite Anode (2004)

A structural model to calculate the electrochemical interface area for a composite graphite electrode is described. A new equation using the model predicted area to calculated chemical diffusion coefficient eliminates the effects from fabrication such as active mass and geometric area The chemical diffusion coefficient values calculated for graphite electrodes of different thicknesses and porosities using the new equation are almost the same as expected. The values of in the graphite vary between and over the course of the lithium deintercalation in the graphite samples. © 2004 The Electrochemical Society. All rights reserved.
Age Changes in the Lipid Composition of Whole Homogenates and Isolated Myelin Fractions of Mouse Brain (1972)

Journal Article Age Changes in the Lipid Composition of Whole Homogenates and Isolated Myelin Fractions of Mouse Brain Get access Grace Y. Sun, PhD, Grace Y. Sun, PhD Search for other works by this author on: Oxford Academic PubMed Google Scholar Thaddeus Samorajski, PhD Thaddeus Samorajski, PhD 2Laboratory Of Neurochemistry, Cleveland Psychiatric InstituteCleveland 44109. Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Gerontology, Volume 27, Issue 1, January 1972, Pages 10–17, https://doi.org/10.1093/geronj/27.1.10 Published: 01 January 1972
Amplitude Phase Shift Keying Constellation Design and its Applications to Satellite Digital Video Broadcasting (2010)

Amplitude Phase Shift Keying Constellation Design and its Applications to Satellite Digital Video Broadcasting
Exogenous human OKSM factors maintain pluripotency gene expression of bovine and porcine iPS-like cells obtained with STEMCCA delivery system (2018)

Protocols based on the integrative lentiviral vector STEMCCA produced porcine iPS-like cells more efficiently than in bovine cells. The iPS-like cells generated displayed stem cell features; however, expression of exogenous factors was maintained along at least 12 passages. Since inactivation of the exogenous factors is still a major bottleneck for establishing fully reprogrammed iPS cells, defining culture conditions that support endogenous OKSM expression is critical for the efficient generation of farm animals' iPS cells.
Structural organization and splice variants of the POLE1 gene encoding the catalytic subunit of human DNA polymerase ε (1999)

The catalytic subunit of human DNA polymerase epsilon, an enzyme involved in nuclear DNA replication and repair, is encoded by the POLE1 gene. This gene is composed of 51 exons spanning at least 97 kb of genomic DNA. It was found to encode three alternative mRNA splice variants that differ in their 5'-terminal sequences and in the N-termini of the predicted proteins. A CpG island covers the promoter region for the major transcript in HeLa cells. This promoter is TATA-less and contains several putative binding sites for transcription factors typical of S-phase-up-regulated and serum-responsive promoters. Potential promoter regions were also identified for the two other alternative transcripts. Interestingly, no nuclear polyadenylation signal sequence was detected in the 3'-untranslated region, although a poly(A) tail was present. These results suggest a complicated regulatory machinery for the expression of the human POLE1 gene, including three alternative transcripts expressed from three promoters.
Selective inhibition of catalytic activity of smooth muscle myosin light chain kinase. (1987)

Systematically synthesized derivatives of ML-9, 1-(5-chloronaphthalenesulfonyl)-1H-hexahydro-1,4-diazepine, were found to inhibit both Ca2+-calmodulin-dependent and -independent smooth muscle myosin light chain kinases with a similar concentration dependence, and their inhibitions were of the competitive type with respect to ATP. Moreover, ML-9 as well as ATP or ADP exhibited an effective protection to inactivation of smooth muscle myosin light chain kinase by the nucleotide affinity label 5'-p-fluorosulfonylbenzoyladenosine, suggesting that ML-9 binds at or near the ATP-binding site on the kinase molecule. These derivatives, which were structurally unrelated to ATP and exhibited more hydrophobic properties detected by reverse-phase high-performance liquid chromatography, exhibited more potent inhibition toward smooth muscle myosin light chain kinase, indicating that the hydrophobic properties of these derivatives positively correlated well with their potencies of inhibiting the catalytic activity for the enzyme. These findings suggest that the ATP-binding site at the active center of smooth muscle myosin light chain kinase is located in a hydrophobic environment. The potent vaso-relaxing effect of ML-9 on rabbit vascular strips and on saponin-treated skinned smooth muscle cells was discussed in relation to the in vivo inhibition by this drug of smooth muscle myosin light chain kinase.
Structure of the effector-binding domain of the arabinose repressor AraR fromBacillus subtilis (2012)

In Bacillus subtilis, the arabinose repressor AraR negatively controls the expression of genes in the metabolic pathway of arabinose-containing polysaccharides. The protein is composed of two domains of different phylogenetic origin and function: an N-terminal DNA-binding domain belonging to the GntR family and a C-terminal effector-binding domain that shows similarity to members of the GalR/LacI family. The crystal structure of the C-terminal effector-binding domain of AraR in complex with the effector L-arabinose has been determined at 2.2 Å resolution. The L-arabinose binding affinity was characterized by isothermal titration calorimetry and differential scanning fluorimetry; the K(d) value was 8.4 ± 0.4 µM. The effect of L-arabinose on the protein oligomeric state was investigated in solution and detailed analysis of the crystal identified a dimer organization which is distinctive from that of other members of the GalR/LacI family.
The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy (2009)

Neuroblastoma is one of the most common solid tumors of childhood, arising from immature sympathetic nervous system cells. The clinical course of patients with neuroblastoma is highly variable, ranging from spontaneous regression to widespread metastatic disease. Although the outcome for children with cancer has improved considerably during the past decades, the prognosis of children with aggressive neuroblastoma remains dismal. The clinical heterogeneity of neuroblastoma mirrors the biological and genetic heterogeneity of these tumors. Ploidy and MYCN amplification have been used as genetic markers for risk stratification and therapeutic decision making, and, more recently, gene expression profiling and genome-wide DNA copy number analysis have come into the picture as sensitive and specific tools for assessing prognosis. The applica tion of new genetic tools also led to the discovery of an important familial neuroblastoma cancer gene, ALK, which is mutated in approximately 8% of sporadic tumors, and genome-wide association studies have unveiled loci with risk alleles for neuroblastoma development. For some of the genomic regions that are deleted in some neuroblastomas, on 1p, 3p and 11q, candidate tumor suppressor genes have been identified. In addition, evidence has emerged for the contribution of epigenetic disturbances in neuroblastoma oncogenesis. As in other cancer entities, altered microRNA expression is also being recognized as an important player in neuroblastoma. The recent successes in unraveling the genetic basis of neuroblastoma are now opening opportunities for development of targeted therapies.
Highly Efficient Generation of Human Hepatocyte–Like Cells From Induced Pluripotent Stem Cells (2009)

We demonstrate that mouse iPS cells retain full potential for fetal liver development and describe a procedure that facilitates the efficient generation of highly differentiated human hepatocyte-like cells from iPS cells that display key liver functions and can integrate into the hepatic parenchyma in vivo.
Vascular Endothelial Growth Factor Is More Important Than Basic Fibroblastic Growth Factor During Ischemic Wound Healing (1999)

Vascular endothelial growth factor seems to be more important than basic fibroblastic growth factor during ischemic wound healing. Treatment of ischemic wounds with VEGF improves the deficit in wound healing produced by ischemia.
Reevaluation of the Definition of Legionnaires' Disease: Use of the Urinary Antigen Assay (1995)

Cases of Legionnaires' disease have been categorized as definitive and presumptive. The sensitivity and specificity of antibody titers of > or = 256 and of urinary antigen ratios of > or = 3 were evaluated in 68 patients with "definitive" Legionnaires' disease and in 636 patients with pneumonia who had negative cultures and did not have fourfold rises in titers of antibody to Legionella pneumophila. An acute-phase antibody titer of > or = 256 did not discriminate between cases and noncases (10% vs. 6%; P = .29). The urinary antigen assay gave a positive result in fewer than 1% of noncases but was positive in 55.9% of all cases. This assay was most sensitive (80%) in cases in which L. pneumophila serogroup 1 was isolated. We propose that the case definition for definitive Legionnaires' disease be expanded to include positive urinary antigen assays and that the category of presumptive Legionnaires' disease--based on acute-phase or standing antibody titers of > or = 256 in the nonoutbreak setting--be discarded. The urinary antigen assay will be a valuable tool in the prompt diagnosis of Legionnaires' disease.
Murine leukemia virus mutant with a frameshift in the reverse transcriptase coding region: implications for pol gene structure (1984)

The molecular defect in the nonconditional B-tropic MuLV pol mutant, clone 23 (Gerwin et al., J. Virol. 31:741-751, 1979), has been characterized by recombinant DNA technology. The entire mutant genome was cloned from an EcoRI digest of integrated cellular DNA into bacteriophage lambda Charon 4A and then subcloned at the EcoRI site of pBR322. NIH-3T3 cells transfected with the plasmid clone, termed pRTM (RTM, reverse transcriptase mutant), reproduced the properties of clone 23 virus-infected cells. In vivo ligation experiments involving cotransfection of subclones of pRTM and wild-type murine leukemia virus localized the defect in the clone 23 genome to an approximately 400-base-pair region in the pol gene between the SalI and XhoI sites. Sequence analysis of this region in the wild-type and mutant genomes revealed that the mutant has one additional C residue located 231 bases downstream of the last base of the SalI recognition site. This 1-base insertion brings three TGA termination codons into phase. Thus, the mutation in clone 23 leads to premature termination of translation, explaining the presence in clone 23 virions of a truncated polymerase with low levels of enzymatic activity. It was previously shown that the gag precursor is cleaved normally in clone 23-infected cells; therefore, if a virus-coded protease is involved in this cleavage, it must be encoded by sequences upstream of the reverse transcriptase region of the pol gene. This consideration, coupled with the observed molecular weight of the mutant polymerase and our precise determination of its C terminus, have led to a proposal for the genetic organization of the murine leukemia virus pol gene.
Identification of a Fungal 1,8-Cineole Synthase from Hypoxylon sp. with Specificity Determinants in Common with the Plant Synthases (2015)

Terpenes are an important and diverse class of secondary metabolites widely produced by fungi. Volatile compound screening of a fungal endophyte collection revealed a number of isolates in the family Xylariaceae, producing a series of terpene molecules, including 1,8-cineole. This compound is a commercially important component of eucalyptus oil used in pharmaceutical applications and has been explored as a potential biofuel additive. The genes that produce terpene molecules, such as 1,8-cineole, have been little explored in fungi, providing an opportunity to explore the biosynthetic origin of these compounds. Through genome sequencing of cineole-producing isolate E7406B, we were able to identify 11 new terpene synthase genes. Expressing a subset of these genes in Escherichia coli allowed identification of the hyp3 gene, responsible for 1,8-cineole biosynthesis, the first monoterpene synthase discovered in fungi. In a striking example of convergent evolution, mutational analysis of this terpene synthase revealed an active site asparagine critical for water capture and specificity during cineole synthesis, the same mechanism used in an unrelated plant homologue. These studies have provided insight into the evolutionary relationship of fungal terpene synthases to those in plants and bacteria and further established fungi as a relatively untapped source of this important and diverse class of compounds.
More knocks to the oxidation hypothesis for vascular disease? (2008)

The oxidation hypothesis for CHD (coronary heart disease) is attractive; however, the almost universal failure of antioxidant vitamin supplementation as a CVD (cardiovascular disease) risk modifier challenges the oxidation hypothesis, at least as a concept that easily 'translates' into clinical benefit for the population. At the same time, quality prospective data on lipid or protein oxidation markers as predictors of vascular events are sparse. In the present issue of Clinical Science, Woodward and co-workers provide much needed prospective data examining the relationship between markers of oxidative damage and CHD outcome in a general population. Despite noting the expected associations between several established CHD risk factors and CHD events, no significant link was observed between measured oxidation markers and CHD risk, a finding which further challenges the oxidation hypothesis for CHD.