gebhart/patrepeval huggingface dataset:
Mechanisms of Neutropenia Involving Myeloid Maturation Arrest in Burn Sepsis (1998)

In thermal injury with superimposed sepsis, neutropenia and myeloid maturation arrest, despite the elevated levels of G-CSF, correlate with the reduction in bone marrow G-CSF receptor expression. These observations may provide a potential mechanism for neutropenia in sepsis.
Multi-Stage Fracturing Stimulations Improve Well Performance in Tight Oil Reservoirs of the Changqing Oilfield (2008)

Abstract The oil reservoirs in the Changqing Oilfield consist of stacked sand/shale deposits, and the majority of the target zones have a permeability of 0.05–0.3mD. All oil wells completed in tight reservoirs from the Changqing Oilfield require fracture stimulation to achieve commercial production and to improve well productivity. Fracture stimulation is also very common for water injection wells to enhance injectivity. Multiple payzones in the region were either stimulated with standalone treatments that were isolated and pumped separately or with single-stage treatments to simultaneously treat several intervals using a kind of limited-entry technique. However, with the continuing development in these fields, larger pay intervals (gross pay thickness up to 75 meters) with poorer reservoir quality were encountered. Post-fracture production results indicated that the above stimulation techniques were not always effective in these tight reservoirs. As a result, a new staging technique was evolved and employed to stimulate these tighter reservoirs with better economic effectiveness. With this technique, two or three pay intervals were first perforated and dual-stage fracture treatments were then performed: one stage at a time without using any mechanical isolation. The idea was two-fold:using the stress increase around the fracture created by the first injection to divert the subsequent treatment to un-stimulated interval(s), andusing the proppant banks created from the first propped treatment to minimize the proppant settling to the bottom portion of the fracture created by the second propped treatment. Three-month average post-treatment production data indicated that the dual-stage treatments outperformed conventional single-stage treatments in some reservoir environments. Candidate selection was a key to the success of this technique, and reservoir conditions that favor these types of treatments are as follows: multiple pays, lower permeability, lower net pressure, and less stress contrast between different payzones. Radioactive tracer logging and microseismic fracture mapping were conducted to evaluate fracture height growth. This paper presents a case history of fracture performance evaluations. Reservoir data, fracture modeling and post-fracture production data were compiled and employed to demonstrate the benefits of this fracture treatment technique in some tight oil reservoirs.
Programmable chirp compensation for 6-fs pulse generation with a prism-pair-formed pulse shaper (2000)

We describe a TF5 prism-pair-formed pulse shaper for programmable pulse chirp compensation. The advantages of this kind of pulse shaper are: (1) very broad bandwidth of transmission; (2) smaller losses; and (3) no requirement for a large-size spatial light modulator (SLM) if the input spectrum is very broad. In our experiment, an ultrabroad spectral (500-1000 nm) pulse is produced by launching 1-kHz, 30-fs, 400-/spl mu/J pulses at 780 nm into an argon filled glass capillary fiber at the gas pressure of 2.0 bar. The fiber has an inner diameter of 140 /spl mu/m and a length of 60 cm. The chirped pulse is first precompressed by a pair of BK7 prisms with a separation length of 65 cm and then directed into the prism-pair-formed pulse-shaping apparatus with a 128-pixel SLM, which provides quadratic and cubic phase compensation. When the quadratic and cubic phases are -330 fs/sup 2/ and +2000 fs/sup 3/, respectively, at the wavelength of 760 nm, an ultrashort optical pulse of 6 fs (FWHM) is generated. This is, to the best of our knowledge, the shortest optical pulse ever compressed using the SLM pulse-shaping technique.
Production in yeast of -galactosidase A, a lysosomal enzyme applicable to enzyme replacement therapy for Fabry disease (2002)

A mammalian-like sugar moiety was created in glycoprotein by Saccharomyces cerevisiae in combination with bacterial alpha-mannosidase to produce a more economic enzyme replacement therapy for patients with Fabry disease. We introduced the human alpha-galactosidase A (alpha-GalA) gene into an S. cerevisiae mutant that was deficient in the outer chains of N-linked mannan. The recombinant alpha-GalA contained both neutral (Man(8)GlcNAc(2)) and acidic ([Man-P](1-2)Man(8)GlcNAc(2)) sugar chains. Because an efficient incorporation of alpha-GalA into lysosomes of human cells requires mannose-6-phosphate (Man-6-P) residues that should be recognized by the specific receptor, we trimmed down the sugar chains of the alpha-GalA by a newly isolated bacterial alpha-mannosidase. Treatment of the alpha-GalA with the alpha-mannosidase resulted in the exposure of a Man-6-P residue on a nonreduced end of oligosaccharide chains after the removal of phosphodiester-linked nonreduced-end mannose. The treated alpha-GalA was efficiently incorporated into fibroblasts derived from patients with Fabry disease. The uptake was three to four times higher than that of the nontreated alpha-GalA and was inhibited by the addition of 5 mM Man-6-P. Incorporated alpha-GalA was targeted to the lysosome, and hydrolyzed ceramide trihexoside accumulated in the Fabry fibroblasts after 5 days. This method provides an effective and economic therapy for many lysosomal disorders, including Fabry disease.
Development of Disease and Virus Recovery in Transgenic Mice Containing HIV Proviral DNA (1988)

Transgenic mice containing intact copies of the human immunodeficiency virus (HIV) proviral DNA were constructed. Founder animals were not viremic for HIV and remained healthy during a 9-month observation period. After being mated with nontransgenic animals, one founder mouse (No. 13) gave rise to F1 progeny that developed a disease syndrome characterized by marked epidermal hyperplasia, lymphadenopathy, splenomegaly, pulmonary lymphoid infiltrates, growth retardation, and death by day 25 of life. Infectious HIV, indistinguishable from parental virus by immunoblot analysis, was recovered from the spleen, lymph nodes, and skin of five of five affected animals.
General vector basis function solution of Maxwell’s equations (1997)

A general method for solving Maxwell's equations exactly, based on expansion of the solution in a complete set of vector basis functions, is developed. These vector eigenfunctions are derived from the complete set of separable solutions to the scalar Helmholtz equation and are shown to form a complete set. The method is applicable to a variety of problems, including the study of near and far field electromagnetic scattering from particles with arbitrary shapes, for particles whose characteristic length scale $d$ $\ensuremath{\approx}\ensuremath{\lambda}$, the wavelength of the incident electromagnetic wave.
Photonic Band Structure of fcc Colloidal Crystals (1996)

Polystyrene colloidal crystals form three dimensional periodic dielectric structures which can be used for photonic band structure measurements in the visible regime. From transmission measurements the photonic band structure of an fcc crystal has been obtained along the directions between the $L$ point and the $W$ point. Kossel line patterns were used for locating the symmetry points of the lattice for exact positioning and orientation of the crystals. In addition, these patterns reveal the underlying photonic band structure of the crystals in a qualitative way.
Oxidation Resistance of the Sulfur Amino Acids: Methionine and Cysteine (2017)

Sulfur amino acids are a kind of amino acids which contain sulfhydryl, and they play a crucial role in protein structure, metabolism, immunity, and oxidation. Our review demonstrates the oxidation resistance effect of methionine and cysteine, two of the most representative sulfur amino acids, and their metabolites. Methionine and cysteine are extremely sensitive to almost all forms of reactive oxygen species, which makes them antioxidative. Moreover, methionine and cysteine are precursors of S-adenosylmethionine, hydrogen sulfide, taurine, and glutathione. These products are reported to alleviate oxidant stress induced by various oxidants and protect the tissue from the damage. However, the deficiency and excess of methionine and cysteine in diet affect the normal growth of animals; thereby a new study about defining adequate levels of methionine and cysteine intake is important.
A method of correcting DNA ploidy measurements in tissue sections. (1994)

A new method of performing DNA ploidy measurements in tissue sections using image cytometry is described. The method involves an image processing "object" filtering operation to remove cut and overlapping nuclei, and DNA correction of larger nuclei for the part of the DNA cut away. The methodology of the technique is developed in detail, and the results of testing using sections of rat liver are presented. The results indicated reliable correction of DNA ploidy histograms to reconstruct the polyploid nature of this material. The sensitivity of the material to sectioning thickness errors and methods to overcome this were shown, along with an example of its use on prostate bioptic gun tissue sections.
Preclinical and clinical gene therapy for haemophilia (2004)

The goal of all haemophilia therapy is to prevent bleeding and its associated complications. Replacement by factor concentrates can only ever be suboptimum, and efforts are being made to correct the genetic cause of the disorder. Haemophilia is an ideal candidate for gene therapy, as it is caused by mutations in a single gene. A number of vectors have been used in an attempt to obtain therapeutic levels of factor VIII and factor IX in animal models, with some success. A number of phase 1 clinical trials have been conducted, and, although connection of the bleeding disorder was neither complete nor long-lasting, they do offer hope for a permanent gene-therapy cure for the disease.
Downregulation of Selective microRNAs in Trigeminal Ganglion Neurons Following Inflammatory Muscle Pain (2007)

Active regulation of gene expression in the nervous system plays an important role in the development and/or maintenance of inflammatory pain. MicroRNA (miRNA) negatively regulates gene expression via posttranscriptional or transcriptional inhibition of specific genes. To explore the possible involvement of miRNA in gene regulation during inflammatory pain, we injected complete Freund's adjuvant (CFA) unilaterally into the rat masseter muscle and quantified changes in neuron-specific mature miRNAs in the trigeminal ganglion (TG). Real-time reverse-transcription polymerase chain reaction revealed significant, but differential, downregulation of mature miR-10a, -29a, -98, -99a, -124a, -134, and -183 in the ipsilateral mandibular division (V3) of the TG within 4 hr after CFA. In contrast, levels of tested miRNAs did not change significantly in the contralateral V3 or the ipsilateral ophthalmic and maxillary divisions of the TG from inflamed rats, nor in the ipsilateral V3 of saline-injected animals. The downregulated miRNAs recovered differentially to a level equal to or higher than that in naive animals. Full recovery time varied with miRNA species but was at least 4 days. Expression and downregulation of some miRNAs were further confirmed by in situ hybridization of TG neurons that innervate the inflamed muscle. Although neurons of all sizes expressed these miRNAs, their signals varied between neurons. Our results indicate that miRNA species specific to neurons are quickly regulated following inflammatory muscle pain.
Analysis of intact bacteria using rapid evaporative ionisation mass spectrometry (2013)

An identification system for microorganisms based on recently developed rapid evaporative ionisation mass spectrometry (REIMS) is presented. Nine bacterial species cultured on various growth media were correctly identified to family-, genus-, and species-level based on their different mass spectral fingerprints using a cross-validated maximum margin criterion model.
Local injection of TGF-β increases the strength of tibial fractures in the rat (1994)

The effect of Transforming Growth Factor beta (TGF-beta) administered locally around the fracture line of healing rat tibial fractures was investigated after 40 days of healing. TGF-beta in a dose of 4 ng or 40 ng was injected every second day during the healing period. The strength, stiffness, energy absorption and deflection of the fractures were measured in a materials-testing machine. Compared with placebo-treated animals, the ultimate load of the fractures increased in the group injected with 40 ng of TGF-beta, but not in those injected with 4 ng. TGF-beta induced a dose-dependent increase in the cross-sectional area of the callus and bone at the fracture line. Consequently, local treatment of fractures with TGF-beta increases the callus formation and strength. The energy absorption and deflection capacities of the healing fractures are preserved.
Results of the Phase I Trial of RG7112, a Small-Molecule MDM2 Antagonist in Leukemia (2015)

RG7112 demonstrated clinical activity against relapsed/refractory AML and CLL/sCLL. MDM2 inhibition resulted in p53 stabilization and transcriptional activation of p53-target genes. We provide proof-of-concept that MDM2 inhibition restores p53 function and generates clinical responses in hematologic malignancies.
Genetics and Child Psychiatry: II Empirical Research Findings (1999)

Key substantive findings from quantitative and molecular genetic research are reviewed in relation to affective disorder, schizophrenia, autism, hyperkinetic/attention deficit disorder, oppositional and conduct disorders, drug/alcohol problems, and Tourette's syndrome/chronic tics.
Derepression of Mineral Phosphate Solubilization Phenotype by Insertional Inactivation of iclR in Klebsiella pneumoniae (2015)

The mode of succinate mediated repression of mineral phosphate solubilization and the role of repressor in suppressing phosphate solubilization phenotype of two free-living nitrogen fixing Klebsiella pneumoniae strains was studied. Organic acid mediated mineral phosphate solubilization phenotype of oxalic acid producing Klebsiella pneumoniae SM6 and SM11 were transcriptionally repressed by IclR in presence of succinate as carbon source. Oxalic acid production and expression of genes of the glyoxylate shunt (aceBAK) was found only in glucose but not in succinate- and glucose+succinate-grown cells. IclR, repressor of aceBAK operon, was inactivated using an allelic exchange system resulting in derepressed mineral phosphate solubilization phenotype through constitutive expression of the glyoxylate shunt. Insertional inactivation of iclR resulted in increased activity of the glyoxylate shunt enzymes even in succinate-grown cells. An augmented phosphate solubilization up to 54 and 59% soluble phosphate release was attained in glucose+succinate-grown SM6Δ and SM11Δ strains respectively, compared to glucose-grown cells, whereas phosphate solubilization was absent or negligible in wildtype cells grown in glucose+succinate. Both wildtype and iclR deletion strains showed similar indole-3-acetic acid production. Wheat seeds inoculated with wildtype SM6 and SM11 improved both root and shoot length by 1.2 fold. However, iclR deletion SM6Δ and SM11Δ strains increased root and shoot length by 1.5 and 1.4 folds, respectively, compared to uninoculated controls. The repressor inactivated phosphate solubilizers better served the purpose of constitutive phosphate solubilization in pot experiments, where presence of other carbon sources (e.g., succinate) might repress mineral phosphate solubilization phenotype of wildtype strains.
Lymphocyte proliferative responses to soluble and liposome-conjugated envelope peptides of HIV-1. (1990)

The proliferation of lymphocytes from HIV-seronegative (HIV Ab-) and seropositive (HIV Ab+) individuals in response to two synthetic peptide epitopes of HIV envelope glycoproteins (ENVgp) was evaluated as an index of cell-mediated immunity in infected individuals. All HIV Ab- and most HIV Ab+ individuals' lymphocytes failed to proliferate in primary cultures in response to the two soluble HIV ENVgp peptides, ENVP346 and ENVP466 even in the presence of rIL-2. After stimulation with liposome-conjugates of ENVP346 or ENVP466 and soluble rIL-2, however, CD4 lymphocytes from some HIV Ab+ individuals were able to proliferate. Significantly higher frequencies of rIL-2-augmented proliferative responses to liposome-conjugated ENVP346 or ENVP466 were observed in HIV Ab+ asymptomatic individuals as compared to patients with AIDS-related conditions or AIDS. These studies indicate that the conjugation of HIV peptides or proteins to liposomes and stimulation with rIL-2 may enhance cell-mediated responses to these peptides.
Structure and expression of the murine retinoblastoma gene and characterization of its encoded protein. (1989)

We have isolated a cDNA clone of the murine homologue of the human retinoblastoma (Rb) susceptibility gene. DNA sequence analysis reveals a high degree of conservation with the human Rb sequence, both in the coding and in the noncoding regions. The predicted amino acid sequence of the mouse Rb protein shows 91% identity to that of the human protein. Both proteins were found to contain a peptide sequence reminiscent of a leucine-repeat motif ("leucine-zipper") that is also found in the myc, fos, and jun oncogenes. Synthetic peptide antiserum directed against a portion of the mouse Rb protein detects three proteins of 104-110 kDa in cells that were transiently transfected with a mouse Rb gene expression construct. In the mouse embryo the expression of Rb mRNA was ubiquitous, with maximal expression being observed around 13 days of gestation. In the embryo, the highest level of expression was observed in liver and brain. In contrast, the Rb gene was found to be expressed at a very low level in adult mouse liver with high levels being found in lung, thymus, and spleen. A shorter Rb transcript was detected in mouse testes.
Alterations of Ceramide/Sphingosine 1-Phosphate Rheostat Involved in the Regulation of Resistance to Imatinib-induced Apoptosis in K562 Human Chronic Myeloid Leukemia Cells (2007)

In this study, mechanisms of resistance to imatinib-induced apoptosis in human K562 cells were examined. Continuous exposure to stepwise increasing concentrations of imatinib resulted in the selection of K562/IMA-0.2 and -1 cells, which expressed approximately 2.3- and 19-fold resistance, respectively. Measurement of endogenous ceramides by high performance liquid chromatography/mass spectroscopy showed that treatment with imatinib increased the generation of ceramide, mainly C18-ceramide, which is generated by the human longevity assurance gene 1 (hLASS1), in sensitive, but not in resistant cells. Inhibition of hLASS1 by small interfering RNA partially prevented imatinib-induced cell death in sensitive cells. In reciprocal experiments, overexpression of hLASS1, and not hLASS6, in drug-resistant cells caused a marked increase in imatinib-induced C18-ceramide generation, and enhanced apoptosis. Interestingly, there were no defects in the levels of mRNA and enzyme activity levels of hLASS1 for ceramide generation in K562/IMA-1 cells. However, expression levels of sphingosine kinase-1 (SK1) and generation of sphingosine 1-phosphate (S1P) were increased significantly in K562/IMA-1 cells, channeling sphingoid bases to the sphingosine kinase pathway. The partial inhibition of SK1 expression by small interference RNA modulated S1P levels and increased sensitivity to imatinib-induced apoptosis in resistant cells. On the other hand, forced expression of SK1 in K562 cells increased the ratio between total S1P/C18-ceramide levels approximately 6-fold and prevented apoptosis significantly in response to imatinib. Additional data indicated a role for SK1/S1P signaling in the up-regulation of the Bcr-Abl expression at the post-transcriptional level, which suggested a possible mechanism for resistance to imatinib-mediated apoptosis. In conclusion, these data suggest a role for endogenous C18-ceramide synthesis mainly via hLASS1 in imatinib-induced apoptosis in sensitive cells, whereas in resistant cells, alterations of the balance between the levels of ceramide and S1P by overexpression of SK1 result in resistance to imatinib-induced apoptosis.
Electronic brokerage and electronic auction: the impact of IT on market structures (1996)

Great progress has been made over the past few years in the study of the impact of IT on inter-firm trade relationships and markets. Most works in this area focus on firm boundaries (purchasing or outsourcing) or buyer-seller relations in general. Although these works are based on reasonable theoretical grounding and many of them have been tested empirically, they do not provide a complete explanation for why different forms of electronic markets have emerged. This article identifies two types of electronic markets-electronic brokerage and electronic auction-by investigating the impact of IT on transaction costs (search, coordination and trade settlement costs) under four different market structures. The economic forces behind the introduction of electronic marketplaces, which either change or support existing market structures, are analyzed along these two market dimensions. Social and organizational barriers to successful implementation of electronic market systems are also discussed.
How will bioinformatics influence metabolic engineering? (1998)

Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development.