gebhart/patrepeval huggingface dataset:
Main features of DNA-based immunization vectors (1999)

DNA-based immunization has initiated a new era of vaccine research. One of the main goals of gene vaccine development is the control of the levels of expression in vivo for efficient immunization. Modifying the vector to modulate expression or immunogenicity is of critical importance for the improvement of DNA vaccines. The most frequently used vectors for genetic immunization are plasmids. In this article, we review some of the main elements relevant to their design such as strong promoter/enhancer region, introns, genes encoding antigens of interest from the pathogen (how to choose and modify them), polyadenylation termination sequence, origin of replication for plasmid production in Escherichia coli, antibiotic resistance gene as selectable marker, convenient cloning sites, and the presence of immunostimulatory sequences (ISS) that can be added to the plasmid to enhance adjuvanticity and to activate the immune system. In this review, the specific modifications that can increase overall expression as well as the potential of DNA-based vaccination are also discussed.
Phosphorylation of Ser-129 Is the Dominant Pathological Modification of α-Synuclein in Familial and Sporadic Lewy Body Disease (2006)

A comprehensive, unbiased inventory of synuclein forms present in Lewy bodies from patients with dementia with Lewy bodies was carried out using two-dimensional immunoblot analysis, novel sandwich enzyme-linked immunosorbent assays with modification-specific synuclein antibodies, and mass spectroscopy. The predominant modification of alpha-synuclein in Lewy bodies is a single phosphorylation at Ser-129. In addition, there is a set of characteristic modifications that are present to a lesser extent, including ubiquitination at Lys residues 12, 21, and 23 and specific truncations at Asp-115, Asp-119, Asn-122, Tyr-133, and Asp-135. No other modifications are detectable by tandem mass spectrometry mapping, except for a ubiquitous N-terminal acetylation. Small amounts of Ser-129 phosphorylated and Asp-119-truncated alpha-synuclein are present in the soluble fraction of both normal and disease brains, suggesting that these Lewy body-associated forms are produced during normal metabolism of alpha-synuclein. In contrast, ubiquitination is only detected in Lewy bodies and is primarily present on phosphorylated synuclein; it therefore likely occurs after phosphorylated synuclein has deposited into Lewy bodies. This invariant pattern of specific phosphorylation, truncation, and ubiquitination is also present in the detergent-insoluble fraction of brain from patients with familial Parkinson's disease (synuclein A53T mutation) as well as multiple system atrophy, suggesting a common pathogenic pathway for both genetic and sporadic Lewy body diseases. These observations are most consistent with a model in which preferential accumulation of normally produced Ser-129 phosphorylated alpha-synuclein is the key event responsible for the formation of Lewy bodies in various Lewy body diseases.
The human immunodeficiency virus type 1 long terminal repeat specifies two different transcription complexes, only one of which is regulated by Tat (1993)

The human immunodeficiency virus type 1 long terminal repeat sets up two different transcription complexes, which have been called processive and nonprocessive complexes. By mutating and substituting cis-acting sequences, we mapped elements of the human immunodeficiency virus long terminal repeat that are responsible for creating each transcription complex. Whereas processive complexes are efficiently assembled by upstream promoter elements in the absence of the TATA box, nonprocessive complexes absolutely require the TATA box. Moreover, the TATA box alone can set up these nonprocessive complexes, and nonprocessive but not processive complexes are trans activated by Tat. Finally, a strong DNA-binding site between the TATA box and trans-activation-responsive region interferes with either the assembly or movement of these nonprocessive complexes and diminishes the effects of Tat. Thus, Tat affects a critical step in the formation of elongation-competent transcription complexes.
The First Direct Characterization of a High-Valent Iron Intermediate in the Reaction of an α-Ketoglutarate-Dependent Dioxygenase:  A High-Spin Fe(IV) Complex in Taurine/α-Ketoglutarate Dioxygenase (TauD) from Escherichia coli (2003)

The Fe(II)- and alpha-ketoglutarate(alphaKG)-dependent dioxygenases have roles in synthesis of collagen and sensing of oxygen in mammals, in acquisition of nutrients and synthesis of antibiotics in microbes, and in repair of alkylated DNA in both. A consensus mechanism for these enzymes, involving (i) addition of O(2) to a five-coordinate, (His)(2)(Asp)-facially coordinated Fe(II) center to which alphaKG is also bound via its C-1 carboxylate and ketone oxygen; (ii) attack of the uncoordinated oxygen of the bound O(2) on the ketone carbonyl of alphaKG to form a bicyclic Fe(IV)-peroxyhemiketal complex; (iii) decarboxylation of this complex concomitantly with formation of an oxo-ferryl (Fe(IV)=O(2)(-)) intermediate; and (iv) hydroxylation of the substrate by the Fe(IV)=O(2)(-) complex via a substrate radical intermediate, has repeatedly been proposed, but none of the postulated intermediates occurring after addition of O(2) has ever been detected. In this work, an oxidized Fe intermediate in the reaction of one of these enzymes, taurine/alpha-ketoglutarate dioxygenase (TauD) from Escherichia coli, has been directly demonstrated by rapid kinetic and spectroscopic methods. Characterization of the intermediate and its one-electron-reduced form (obtained by low-temperature gamma-radiolysis of the trapped intermediate) by Mössbauer and electron paramagnetic resonance spectroscopies establishes that it is a high-spin, formally Fe(IV) complex. Its Mössbauer isomer shift is, however, significantly greater than those of other known Fe(IV) complexes, suggesting that the iron ligands in the TauD intermediate confer significant Fe(III) character to the high-valent site by strong electron donation. The properties of the complex and previous results on related alphaKG-dependent dioxygenases and other non-heme-Fe(II)-dependent, O(2)-activating enzymes suggest that the TauD intermediate is most probably either the Fe(IV)-peroxyhemiketal complex or the taurine-hydroxylating Fe(IV)=O(2)(-) species. The detection of this intermediate sets the stage for a more detailed dissection of the TauD reaction mechanism than has previously been reported for any other member of this important enzyme family.
导电碳黑填充的乙丙橡胶—氯磺化聚乙烯共混物：用作可剥离型半导电层 (1992)

用不同数量的高导电性炉法碳黑和ERR-CSP共混物制备复合材料,并测试其电气和固态物理性能,以估价导电破黑对共混物的影响。根据所得结果,采用含60％碳黑的复合材料来探测它对EPR绝缘和XLPE绝缘的粘接性能。测试结果发现,复合材料由粘接型转向剥离型。转变发生在EPR中CSP占60～70％之间,并制作了一只模型来加以验证。
Human Brain Metabolic Response to Caffeine and the Effects of Tolerance (1999)

These results provide direct evidence for the loss of caffeine tolerance in the human brain subsequent to caffeine discontinuation and suggest mechanisms for the phenomenon of caffeine intolerance other than its metabolic effects on elevating brain lactate.
The biological lifetime of nitric oxide: Implications for the perivascular dynamics of NO and O 2 (2000)

Endothelial nitric oxide (nitrogen monoxide) is synthesized at the intravascular/extravascular interface. We previously have reported the intravascular half-life of NO, as a result of consumption by erythrocytes, as approximately 2 ms. We report here studies designed to estimate the lifetime of NO in the parenchymal (extravascular) tissue and describe the implications of these results for the distribution of NO and oxygen concentration gradients away from the blood vessel. The rate of consumption of NO by parenchymal cells (hepatocytes) linearly depends on both NO and O(2) concentration. We estimate that the extravascular half-life of NO will range from 0.09 to > 2 s, depending on O2 concentration and thus distance from the vessel. Computer modeling reveals that this phenomenon, coupled with reversible NO inhibition of cellular mitochondrial oxygen consumption, substantially extends the zone of adequate tissue cellular oxygenation away from the blood vessel, with an especially dramatic effect during conditions of increased tissue work (oxygen consumption). This represents a second action of NO, in addition to vasodilation, in enhancing tissue cellular respiration and provides a possible physiological function for the known reversible inhibition of mitochondrial respiration by low concentrations of NO.
Theory of fault-tolerant quantum computation (1998)

In order to use quantum error-correcting codes to improve the performance of a quantum computer, it is necessary to be able to perform operations fault-tolerantly on encoded states. I present a theory of fault-tolerant operations on stabilizer codes based on symmetries of the code stabilizer. This allows a straightforward determination of which operations can be performed fault-tolerantly on a given code. I demonstrate that fault-tolerant universal computation is possible for any stabilizer code. I discuss a number of examples in more detail, including the five-quantum-bit code.
Testing of new agents in childhood cancer preclinical models: meeting summary. (2002)

A workshop on pediatric preclinical testing, sponsored by the National Cancer Institute and the Children's Oncology Group Phase 1 Consortium, was held on June 26-27, 2001 in Bethesda, Maryland. Drs. Peter Adamson, Peter Houghton, and Malcolm Smith organized and hosted the meeting. There were 20 participants from 12 institutions. The primary objectives of the workshop included: (a) development of a working inventory of available preclinical models (including human tumor xenografts in immunodeficient mice, transgenic and syngeneic tumors, and selected in vitro models), with a basic understanding of the strengths and weaknesses of each as possible components of a preclinical testing program; (b) identification of the key scientific issues related to establishment of a program for preclinical testing of new agents for their applicability to childhood cancers; and (c) identification of the key infrastructure requirements for a program for preclinical testing of new agents for their applicability to childhood cancers. This report is a synthesis of the workshop's presentations and discussions.
Comparison of antiproliferative effects of metformine and progesterone on estrogen-induced endometrial hyperplasia in rats (2013)

Metformin has been shown to inhibit the growth of endometriotic implants, and reverse endometrial hyperplasia when combined with oral contraceptive in a case report. The aim of this study is to compare the antiproliferative effects of medroxyprogesterone acetate (MPA), and metformin in oopherectomized rat endometrium. Forty oopherectomized Wistar-Albino rats were used, and assigned to receive saline, 17 β Estradiol hemihydrate (4 mg/kg), 17 β Estradiol hemihydrate (4 mg/kg) and metformin (50 mg/kg), 17 β Estradiol hemihydrate (4 mg/kg) and MPA (1 mg/day) for 14 days. Histological markers of uterotrophy, including endometrial height, luminal ephitelial cell height and density of endometrial glands on hysterectomy speciments were quantified for each specimen. Rats treated with estradiol had significantly increased in endometrial height, endomerial luminal epithelial height and endometrial gland densitiy than the other groups. Metformin and MPA acetate significantly reduced all parameters indicating endometrial hyperplasia, and uterotrophy with respect to the control group. Antiproliferative effects of metformin, and MPA was found to be comparable for all three parameters. In conclusion, metformin attenuates estrogen-induced endometrial hyperplasia in ooferectomized rats to the same degree as progesterone.
Insulin-like growth factor II activates mitogenic signaling in pancreatic cancer cells via IRS-1 (1996)

Insulin-like growth factor-II (IGF-II) action and expression were examined in 3 human pancreatic cancer cell lines. IGF-II expression was also studied in 17 normal and 12 malignant pancreatic tissues. IGF-II enhanced the growth of all 3 cell lines. In COLO-357 and PANC-1 cells, one-half maximal stimulation occurred at 0.3 and 0.4 nM IGF-II, respectively. In ASPC-1 cells, one-half maximal stimulation occurred at 0.9 nM IGF-II. A monoclonal antibody (alpha IR3) that blocks ligand binding to the insulin-like growth factor I (IGF-I) receptor (IGF-IR) inhibited IGF-II-mediated growth stimulation, and IGF-II enhanced insulin-receptor substrate 1 (IRS-1) phosphorylation. IGF-II mRNA transcripts were present in COLO-357 cells, in 4 of 17 normal human pancreatic tissues, and in 8 of the 12 cancer samples. By immunohistochemistry, IGF-II was present in the islets of both normal and malignant pancreatic tissues, and occasionally in the cancer cells within the tumor mass. These findings indicate that IGF-II acts via IGF-IR to enhance mitogenic signaling in pancreatic cancer cells and suggest that islet-derived IGF-II may contribute to pancreatic cancer cell growth in vivo.
In situ hybridization on May-Grunwald Giemsa-stained bone marrow and blood smears of patients with hematologic disorders allows detection of cell-lineage-specific cytogenetic abnormalities (1993)

Bone marrow and blood from patients with acute myeloid leukemia and myelodysplastic syndrome were studied by simultaneous analysis of cell morphology and karyotype. A combined technique of May-Grunwald Giemsa (MGG) for cell morphology and fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes for detection of cytogenetic aberrations allowed us to investigate cell-lineage-specific chromosomal abnormalities. We introduced video recordings to examine large numbers of cells. Briefly, evaluation was first performed on MGG slides, during which cell position and morphology were recorded on an S-VHS recorder. Subsequently, the same slides were used for FISH. This resulted in the identification of MGG-stained cells on the video screen and, at the same time, the interpretation of FISH signals in the fluorescence microscope. Specimens of bone marrow or blood samples from four patients with different hematologic malignancies were studied. One of these patients was studied before and after cytotoxic treatment. The gain or loss of chromosomes could be detected easily and morphologically assigned to the blasts in all patients and to a variable proportion of the myelomonocytic lineage in two patients, but not to the lymphocytes. Thus, this method provides new possibilities for investigating the clonality of hematologic malignancies.
Immunoprecipitation and Western Blotting of Phosphotyrosine-Containing Proteins (2003)

Changes in the tyrosine phosphorylation state of a protein in response to external stimuli can have profound effects on cellular signal transduction. The addition of a phosphate group to a tyrosine residue can change a protein' activation state or create a high affinity binding site for other proteins. Conversely, removal of a phosphate group can also change the catalytic activity of an enzyme. Tyrosine phosphorylation of cellular proteins is a rare event that can be increased growth factor addition or cellular attachment to extracellular matrix. Therefore, it is important to be able to observe changes in tyrosine phosphorylation of particular proteins under the influence of different stimuli. Tyrosine phosphorylation of proteins is difficult to detect unless external stimuli are present; even then, many proteins are phosphorylated only in response to one stimulus. Therefore, it is necessary to concentrate the protein of interest in order to observe the phosphorylation state changes between stimulated and unstimulated cells. 32P-labeling of cellular proteins can be used; however, phosphoserine and phosphothreonine are also detected along with phosphotyrosine. Phosphoamino acid analysis can be helpful, but it is not quantitative because acid hydrolysis, which breaks down the proteins into individual amino acids, can remove the phosphate group from the tyrosine. Therefore, other methods of detecting changes in tyrosine phosphorylation states have been developed.
Selective mutation testing for concurrent code (2013)

Concurrent code is becoming increasingly important with the advent of multi-cores, but testing concurrent code is challenging. Researchers are developing new testing techniques and test suites for concurrent code, but evaluating these techniques and test suites often uses a small number of real or manually seeded bugs.
Anaplastic lymphoma kinase proteins in growth control and cancer (2004)

The normal functions of full-length anaplastic lymphoma kinase (ALK) remain to be completely elucidated. Although considered to be important in neural development, recent studies in Drosophila also highlight a role for ALK in gut muscle differentiation. Indeed, the Drosophila model offers a future arena for the study of ALK, its ligands and signalling cascades. The discovery of activated fusion forms of the ALK tyrosine kinase in anaplastic large cell lymphoma (ALCL) has dramatically improved our understanding of the pathogenesis of these lymphomas and enhanced the pathological diagnosis of this subtype of non-Hodgkin's lymphoma (NHL). Likewise, the realisation that a high percentage of inflammatory myofibroblastic tumours express activated-ALK fusion proteins has clarified the causation of these mesenchymal neoplasms and provided for their easier discrimination from other mesenchymal-derived inflammatory myofibroblastic tumour (IMT) mimics. Recent reports of ALK expression in a range of carcinoma-derived cell lines together with its apparent role as a receptor for PTN and MK, both of which have been implicated in tumourigenesis, raise the possibility that ALK-mediated signalling could play a role in the development and/or progression of a number of common solid tumours. The therapeutic targeting of ALK may prove to have efficacy in the treatment of many of these neoplasms.
Flow cytometric and immunohistochemical characterization of the gamma/delta T-lymphocyte population in normal human lymphoid tissue and peripheral blood. (1990)

We determined the quantitative and topographic distribution of gamma/delta lymphocytes in normal human lymphoid tissue and peripheral blood using a monoclonal antibody that detects a framework determinant on delta molecules and delineated the immunophenotypic characteristics of the gamma/delta lymphocyte population by one- and/or two-color immunohistochemical and two- and/or three-color flow cytometric analysis. Variable, but generally small, numbers of gamma/delta lymphocytes are present in peripheral blood and in all lymphoid tissues. The vast majority, greater than or equal to 90%, of lymphoid tissue delta lymphocytes reside in interfollicular (T-cell) zones. Approximately 90% of delta thymocytes are present in the thymic medulla. The percentage of CD3-positive T cells that express delta are: spleen 12.5 +/- 8.1%, peripheral blood 4.0 +/- 3.1%, appendix 2.9 +/- 1%, lymph node 2.2 +/- 1%, thymus 1.4 +/- 0.5%, and tonsil 0.7 +/- 0.5%. We further demonstrated that 1) gamma/delta-thymocytes and gamma/delta peripheral lymphocytes express T-cell lineage restricted antigens CD3 and CD2 but only a variable subset, 30% to 90%, express T-cell lineage associated antigens CD5 and/or CD8; (2) approximately 60% of gamma/delta thymocytes express low-density CD4 while all gamma/delta peripheral lymphocytes lack detectable CD4; 3) gamma/delta lymphocytes lack natural killer (NK), macrophage, and B-cell associated antigens CD16, CD14, and CD20, respectively, but greater than or equal to 70% of gamma/delta T lymphocytes express CD11b, Leu7, and NKH-1, antigens, which are also expressed by suppressor/cytotoxic and NK cells; and 4) a large subpopulation, approximately 25%, of gamma/delta thymocytes are in S1-G2 phase, while greater than or equal to 98% of gamma/delta peripheral lymphocytes are small lymphocytes in G0-G1 phase and lack activation/proliferation markers. Together these results indicate that gamma/delta lymphocytes are resting, mature T cells that probably play a primary role in suppressor/cytotoxic phenomena. They also indicate that gamma/delta lymphocytes variably express multiple-cell surface antigens associated with various cell lineages, suggesting that gamma/delta lymphocytes represent a considerably more heterogeneous cell population than previously appreciated and that they may actually subserve multiple functions.
Quality Control During Endovascular Aneurysm Repair: Monitoring Aneurysmal Sac Pressure and Superficial Femoral Artery Flow Velocity (1999)

Measuring aneurysm pressure in combination with SFA Doppler flow monitoring can detect complications of endovascular aneurysm repair.
Evaluation of a live attenuated bovine parainfluenza type 3 vaccine in two- to six-month-old infants (1996)

This study demonstrated that the BPIV-3 vaccine was safe and infectious in infants younger than 6 months of age and was also immunogenic in the majority of these young infants. Additional studies are needed to determine whether two or more doses will enhance the immunogenicity of the BPIV-3 vaccine in young infants and to assess its safety and immunogenicity when given simultaneously with routine childhood immunizations.
Exploration and Exploitation of Synthetic Use of Oxoammonium Ions in Alcohol Oxidation (2008)

Novel synthetic uses of oxoammonium ions enabling facile and efficient oxidation of several classes of alcohols to their related carbonyl compounds have been exploited on the basis of two strategies: (i) modifying the molecular framework of the oxoammonium ion, and (ii) enhancing its reactive nature by altering the counter ion. The reaction systems developed allow: (1) efficient oxidation of sterically crowded secondary alcohols to ketones; (2) facile, one-pot oxidation of primary alcohols to carboxylic acids; (3) oxidative rearrangement of tertiary allylic alcohols to β-substituted α, β-unsaturated carbonyl compounds under transition-metal-free conditions.
[Treatment of advanced renal cell carcinoma with interferon alpha and OK-432 (streptococcal preparation)]. (1992)

A total of 12 patients with advanced renal cell carcinoma received interferon alpha (3 million units intramuscularly 6 times weekly) and OK-432 (5 KE (Klinische Einheit) intramuscularly twice weekly). Metastatic lesions appeared before operation in six patients and after operation in six patients. Among them 5 patients had received interferon therapy and this combination therapy was started after the judgment of progressive disease for interferon therapy. Eleven pulmonary and 5 bone metastases were evaluable. The median duration of the combination therapy was 89.3 weeks. There were 4 partial responses and no complete responses among the 12 patients, giving a response rate of 33.3%. The median duration of response was 25 months, with a range of 6 to 54 months. Responses were seen predominantly in patients in whom metastases appeared after operation (3 of 4 responders). However, regarding the individual organs, two complete and 2 partial responses were observed among 11 pulmonary metastases and 2 partial responses among 5 bone metastases. The survival period after discovery of the metastasis was 10 to 67 months and the 5-year survival rate was 70.5%. Almost all patients had fever and induration at the injection site. Other side effects included leukopenia, anorexia, and depression. This combination therapy is thought to be effective against bone or other organs metastasis resistant to interferon alone.