gebhart/patrepeval huggingface dataset:
Apolipoprotein (apo) A-I production and mRNA abundance explain plasma apoA-I and high density lipoprotein differences between two nonhuman primate species with high and low susceptibilities to diet-induced hypercholesterolemia. (1988)

Earlier studies have shown that African green monkeys develop a more modest hypercholesterolemia, higher high density lipoprotein (HDL) concentrations, and less atherosclerosis than cynomolgus monkeys fed diets with the same cholesterol content. In the present study, cynomolgus monkeys were fed less cholesterol than was fed to African green monkeys to induce equivalent hypercholesterolemia in both species. African green monkeys still had 2-fold higher plasma HDL cholesterol concentrations and 2.7-fold higher plasma apolipoprotein (apo) A-I concentrations. Therefore, the higher HDL concentration in African green monkeys appears to result from factors that act independently of dietary cholesterol intake or total plasma cholesterol concentration. Two aspects of HDL production were examined to determine the metabolic basis of the species difference in HDL concentration. The rate of hepatic apoA-I secretion, as estimated by the accumulation of apoA-I in the medium during recirculating liver perfusion, was 5-fold higher in livers of African green monkeys. In addition, the concentration of apoA-I mRNA was 2-fold higher in the liver and 3.7-fold higher in the intestine of African green monkeys. Taken together, these findings indicate that differences in apoA-I production in the liver and small intestine are large enough to be responsible for the differences in the plasma concentrations of HDL and apoA-I between these species. Factors which regulate apoA-I secretion, including modulation of tissue apoA-I mRNA concentrations, are important determinants of plasma HDL concentrations and may contribute to the relative resistance of African green monkeys to dietary cholesterol-induced hypercholesterolemia and atherosclerosis. ApoA-I mRNA was also detected at low levels in the kidney and testis of African green and cynomolgus monkeys but not in the adrenal or brain. The tissue distribution and abundance of apoA-I mRNA in peripheral tissues was very different than that seen for apoE mRNA. Kidney and testis apoA-I mRNAs were the same size as liver apoA-I mRNA when examined by Northern blot analysis. Testis apoA-I mRNA appeared to be functionally active as judged by its presence in cytoplasmic polyribosomes. The low levels of apoA-I expression in kidney and testis are unlikely to contribute significantly to the plasma apoA-I pool but might function in some aspect of local lipid metabolism within these tissues.
High-yield anaerobic succinate production by strategically regulating multiple metabolic pathways based on stoichiometric maximum in Escherichia coli (2016)

It's the first time to rationally regulate pentose phosphate pathway to improve NADH supply for succinate synthesis in E. coli. 90 % of stoichiometric maximum succinate yield was achieved by combining further flux increase towards succinate and engineering its export. Regulation of NADH supply via PP pathway is therefore recommended for the production of products that are NADH-demanding in E. coli.
Functionally distinct human marrow stromal cell lines immortalized by transduction with the human papilloma virus E6/E7 genes (1995)

A replication-defective recombinant retrovirus containing the human papilloma virus E6/E7 genes (LXSN-16 E6E7) was used to immortalize stromal cells from human marrow. The E6/E7 gene products interfere with the function of tumor-suppressor proteins p53 and Rb, respectively, thereby preventing cell cycle arrest without causing significant transformation. Twenty-seven immortalized clones designated HS-1 to HS-27 were isolated, four of which are characterized in this report. Two cell lines, HS-5 and HS-21, appear to be fibroblastoid and secrete significant levels of granulocyte colony-stimulating factor (G-CSF), granulocyte-macrophage-CSF (GM-CSF), macrophage-CSF (M-CSF), Kit ligand (KL), macrophage-inhibitory protein-1 alpha, interleukin-6 (IL-6), IL-8, and IL-11. However, only HS-5 supports proliferation of hematopoietic progenitor cells when cocultured in serum-deprived media with no exogenous factors. Conditioned media (CM) from HS-5 promotes growth of myeloid colonies to significantly greater extent than a cocktail of recombinant factors containing 10 ng/mL of IL-1, IL-3, IL-6, G-CSF, GM-CSF, and KL and 3 U of erythropoietin (Epo). Two additional clones, HS-23 and HS-27, resemble "blanket" cells, with an epithelioid morphology, and are much larger, broader, and flatter when compared with HS-5 and HS-21. These lines secrete low levels of growth factors and do not support proliferation of isolated progenitor cells in cocultures. CM from HS-23 and HS-27 also fail to support growth of myeloid colonies. Both HS-23 and HS-27 express relatively high levels of VCAM-1, yet HS-27 is the only line that supports the formation of "cobblestone" areas by isolated CD34+38lo cells. We hypothesize that HS-5, HS-21, HS-23, and HS-27 represent functionally distinct components of the marrow microenvironment.
Staphylococcal Enterotoxin B as a Biological Weapon: Recognition, Management, and Surveillance of Staphylococcal Enterotoxin (2006)

One of the most important toxin threats in warfare or bioterrorism is Staphylococcal enterotoxin B (SEB), an incapacitating toxin. SEB had been considered and produced as an offensive biologic warfare agent. Staphylococcal enterotoxin B is a toxin associated with incidences of massive food poisoning. The bacteria that produce this toxin (SEB) are universally associated with man and other warm blooded mammals and their spheres of environmental influence include sewage and plumes. Staphylococcus aureus can readily be isolated from nose, armpits or anal swabs and about 50% of clinical isolates produce this toxin. Staphylococcal enterotoxin B is one of the superantigens capable of massive nonspecific activation of the immune system including a massive release of cytokines, such as interferon-gamma, interleukin-6 and tumor necrosis factor-alpha. Staphylococcal enterotoxin B is a potential agent of bioterrorism because of the ease of its production and dispersion, a delayed onset of symptoms, an ability to cause high morbidity and the difficulty in discerning between intentional intoxication and natural intoxication when a viable organism is the etiologic agent. This article presents a brief discussion on the recognition, management and surveillance of SEB, as well as the pathogenesis, clinical manifestation, diagnosis, and treatment of patients exposed to this toxin.
The Tyrosine Kinase Inhibitors Imatinib and Dasatinib Reduce Myeloid Suppressor Cells and Release Effector Lymphocyte Responses (2015)

Immune escape mechanisms promote tumor progression and are hurdles of cancer immunotherapy. Removing immunosuppressive cells before treatment can enhance efficacy. Tyrosine kinase inhibitors (TKI) may be of interest to combine with immunotherapy, as it has been shown that the inhibitor sunitinib reduces myeloid suppressor cells in patients with renal cell carcinoma and dasatinib promotes expansion of natural killer-like lymphocytes in chronic myeloid leukemia (CML). In this study, the capacity of dasatinib and imatinib to reduce myeloid suppressor cells and to induce immunomodulation in vivo was investigated ex vivo. Samples from CML patients treated with imatinib (n = 18) or dasatinib (n = 14) within a Nordic clinical trial (clinicalTrials.gov identifier: NCT00852566) were investigated for the presence of CD11b(+)CD14(-)CD33(+) myeloid cells and inhibitory molecules (arginase I, myeloperoxidase, IL10) as well as the presence of natural killer cells, T cells (naïve/memory), and stimulatory cytokines (IL12, IFNγ, MIG, IP10). Both imatinib and dasatinib decreased the presence of CD11b(+)CD14(-)CD33(+) myeloid cells as well as the inhibitory molecules and the remaining myeloid suppressor cells had an increased CD40 expression. Monocytes also increased CD40 after therapy. Moreover, increased levels of CD40, IL12, natural killer cells, and experienced T cells were noted after TKI initiation. The presence of experienced T cells was correlated to a higher IFNγ and MIG plasma concentration. Taken together, the results demonstrate that both imatinib and dasatinib tilted the immunosuppressive CML tumor milieu towards promoting immune stimulation. Hence, imatinib and dasatinib may be of interest to combine with cancer immunotherapy.
Suggestive Evidence for Receptors for Morphine and Methionine-Enkephalin on Normal Human Blood T Lymphocytes (1979)

This study reports the in vitro influence of morphine, dextromoramide, levomoramide, and methionine-enkephalin upon normal human T blood lymphocytes by using the active and total rosette tests. Morphine and dextromoramide inhibited the percentage of active T rosettes. This effect was completely reversed in the presence of naloxone, their specific antagonist. The specificity was further demonstrated by the absence of the effect of levomoramide, the inactive enantiomere, upon the rosette system. Methionine-enkephalin increased the percentage of active T rosettes. This effect was specifically inhibited by naloxone. These observations suggest that normal human blood T lymphocytes bear surface receptor-like structures for morphine, dextromoramide, and methionine-enkephalin. Such findings may provide a link between the central nervous system and the immune system.
Cooling three-dimensional integrated circuits using power delivery networks (2012)

Our comprehensive analysis, over a range of 3D integration methods and application power density characteristics, quantifies major benefits of PDNs on the temperature distribution of 3D ICs. For example, PDNs can reduce the maximum steady-state temperature by over 35 °C for a 2-layer monolithic 3D IC. Our OpenSPARC T2 case study also demonstrates that the cooling benefits of PDNs are essential to achieve monolithic 3D integration. Our analysis framework can be adopted for exploring technology-circuit-application interactions for a wide variety of 3D technologies, cooling options, PDN designs, or even software-level task scheduling approaches. Of course, it is essential to experimentally validate the simulation results presented in this paper.
A review of polyvinyl alcohol and its uses in cartilage and orthopedic applications (2012)

Polyvinyl alcohol (PVA) is a synthetic polymer derived from polyvinyl acetate through partial or full hydroxylation. PVA is commonly used in medical devices due to its low protein adsorption characteristics, biocompatibility, high water solubility, and chemical resistance. Some of the most common medical uses of PVA are in soft contact lenses, eye drops, embolization particles, tissue adhesion barriers, and as artificial cartilage and meniscus. The purpose of this review is to evaluate the available published information on PVA with respect to its safety as a medical device implant material for cartilage replacement. The review includes historical clinical use of PVA in orthopedics, and in vitro and in vivo biocompatibility studies. Finally, the safety recommendation involving the further development of PVA cryogels for cartilage replacement is addressed.
Better library design: data‐driven protein engineering (2006)

Data-driven protein engineering is increasingly used as an alternative to rational design and combinatorial engineering because it uses available knowledge to limit library size, while still allowing for the identification of unpredictable substitutions that lead to large effects. Recent advances in computational modeling and bioinformatics, as well as an increasing databank of experiments on functional variants, have led to new strategies to choose particular amino acid residues to vary in order to increase the chances of obtaining a variant protein with the desired property. Strategies for limiting diversity at each position, design of small sub-libraries, and the performance of scouting experiments, have also been developed or even automated, further reducing the library size.
Thermal stabilization of a single‐chain Fv antibody fragment by introduction of a disulphide bond (1995)

A disulphide bond was introduced into a single-chain Fv form of the anticarbohydrate antibody, Se155-4 by replacing Ala-L57 of the light chain and Asp-H106 of the heavy chain with cysteines, by site-directed mutagenesis. To maintain the salt-bridge from the latter residue to Arg-H98, Tyr-107 was also altered to Asp. The resulting ds-scFv was shown to retain full antigen-binding activity, by enzyme immunoassay and surface plasmon resonance analysis of binding kinetics. Compared with the parent scFv, the disulphide bonded form was shown to have enhanced thermal stability, by Fourier transform IR spectroscopy. The Tm was raised from 60 degrees C to 69 degrees C. The ds-scFv form thus combines the stable monomeric form of the disulphide form with the expression advantages of the scFv.
Coupling of light from an LED into a thin light guide by diffractive gratings (2004)

Ring-shaped and radial diffractive gratings are designed with rigorous diffraction theory to couple light of a nearly monochromatic LED into a thin planar light guide on the bottom side. The theoretical coupling efficiencies for ring-shaped and radial gratings are 41% and 66%, respectively. Optimized diffractive elements are manufactured with direct electron-beam lithography and reactive-ion-etching into SiO2 substrates. Good agreement between experimental and theoretical results for selected radial gratings is reached. Furthermore, the mass production tests using injection molding are carried out with good replicability.
Effect of Carrier Concentration on the Raman Frequencies of Si and Ge (1972)

The first-order Raman spectrum of Ge and Si has been investigated as a function of carrier concentration. In $p$-type materials we observed large broadenings of the Raman line and large shifts to higher frequencies of the Stokes line. We attribute these effects to the splitting of the valence band produced by the $\stackrel{\ensuremath{\rightarrow}}{\mathrm{k}}\ensuremath{\simeq}0$ optical phonon in a manner similar to the effects of doping on the ${C}_{44}$ elastic constant discussed by Keyes. From these results it is possible to estimate the coupling constant ${d}_{0}$ between optical phonons and holes. The $\stackrel{\ensuremath{\rightarrow}}{\mathrm{k}}\ensuremath{\simeq}0$ phonon should also produce a splitting of the conduction band of Ge (but not of Si). However, for a given impurity concentration, the shifts observed in $n$-type materials are much smaller than those for $p$-type materials. The absence of large effects is probably due to the low rate of intervalley scattering. An effect on $n$-type Si related to the splitting of the ${X}_{1}$ conduction-band degeneracy by the phonon is also discussed and compared with the analogous effect on the elastic constants. It is shown that the internal stress parameter $\ensuremath{\zeta}$ is also affected by doping.
Heterogeneity amongst fibroblasts in the production of migration stimulating factor (MSF): Implications for cancer pathogenesis (1991)

Fetal skin fibroblasts migrate into 3D collagen gels to a significantly greater extent than do adult cells. This enhanced motility of fetal fibroblasts appears to result from the production of a "migration stimulating factor" (MSF) which is not made by their normal adult counterparts. Adult skin fibroblasts retain responsiveness to MSF and cells exposed to this factor achieve the elevated levels of migration characteristic of fetal cells. MSF has been purified to homogeneity, has an apparent molecular mass of 70 kD and has been further characterized in terms of a number of biochemical parameters. Studies concerned with the mechanism of action of MSF indicate that it stimulates the production of a high molecular weight class of hyaluronic acid (HA). Concurrent exposure of cells to Streptomyces hyaluronidase blocks the stimulation of adult fibroblast migration by MSF. In a related series of experiments, we have shown that TGF-beta inhibits the effects of MSF on both cell migration and HA production. Taken together, these data suggest that the stimulation of fibroblast migration by MSF is dependent upon (and may directly result from) a primary induction of HA synthesis. We have previously reported that skin fibroblasts obtained from patients with sporadic and familial breast cancer, as well as the unaffected first-degree relatives of familial breast cancer patients, commonly display a fetal-like migratory phenotype. Subsequent work has indicated that (a) these fetal-like cells also produce MSF, and (b) detectable levels of MSF are present in the serum of sporadic breast cancer patients both prior to and following surgical resection of the primary tumor mass. On the basis of these and related observations, we have put forward an hypothesis suggesting that the disruption in normal epithelial-mesenchymal interactions caused by the persistent production of MSF by fibroblasts in the adult may contribute directly to the pathogenesis of an epithelial cancer. The demonstration of aberrant fibroblasts in sporadic cancer patients (both in our own and independent studies) is not consistent with the "germ-line genetic lesion" model commonly invoked to account for the presence of such cells in patients with hereditary cancer syndromes.(ABSTRACT TRUNCATED AT 400 WORDS)
Association of childhood trauma with cognitive function in healthy adults: a pilot study (2010)

Our results suggest that physical neglect and emotional abuse might be associated with memory deficits in adulthood, which in turn might pose a risk factor for the development of psychopathology.
Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity (2015)

The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms.
Bacillus subtilis Metabolism and Energetics in Carbon-Limited and Excess-Carbon Chemostat Culture (2001)

The energetic efficiency of microbial growth is significantly reduced in cultures growing under glucose excess compared to cultures growing under glucose limitation, but the magnitude to which different energy-dissipating processes contribute to the reduced efficiency is currently not well understood. We introduce here a new concept for balancing the total cellular energy flux that is based on the conversion of energy and carbon fluxes into energy equivalents, and we apply this concept to glucose-, ammonia-, and phosphate-limited chemostat cultures of riboflavin-producing Bacillus subtilis. Based on [U-(13)C(6)]glucose-labeling experiments and metabolic flux analysis, the total energy flux in slow-growing, glucose-limited B. subtilis is almost exclusively partitioned in maintenance metabolism and biomass formation. In excess-glucose cultures, in contrast, uncoupling of anabolism and catabolism is primarily achieved by overflow metabolism, while two quantified futile enzyme cycles and metabolic shifts to energetically less efficient pathways are negligible. In most cultures, about 20% of the total energy flux could not be assigned to a particular energy-consuming process and thus are probably dissipated by processes such as ion leakage that are not being considered at present. In contrast to glucose- or ammonia-limited cultures, metabolic flux analysis revealed low tricarboxylic acid (TCA) cycle fluxes in phosphate-limited B. subtilis, which is consistent with CcpA-dependent catabolite repression of the cycle and/or transcriptional activation of genes involved in overflow metabolism in the presence of excess glucose. ATP-dependent control of in vivo enzyme activity appears to be irrelevant for the observed differences in TCA cycle fluxes.
Recent advances in X-ray microtomography applied to materials (2008)

This review highlights recent advances in X-ray microcomputed tomography (microCT) as applied to materials, specifically advances made since the first materials microCT review appeared in International Materials Reviews . Improvements in instrumentation are covered, and one focus is microCT using phase (as opposed to absorption) contrast. Instead of grouping studies by disciplines, the reviewed reports are organised by type of application, specifically the study of the spatial distribution of phases, of cellular solids (including static and temporally evolving structures, fibrous network solids, mineralised tissues and biomedical applications), of channel structures, of deformation, fatigue and fracture, of processing and of corrosion and environmental interactions. Metrology applications are covered briefly, and several applications where microCT is combined with position resolved X-ray scattering are described in more detail. The accuracy of microCT reconstructions is discussed before data handling challenges are outlined. The review closes with speculations on the future directions of materials microCT.
Interferences in Immunoassay—Still a Threat (2000)

Few things in life are perfect, and unfortunately this also applies to medical diagnostic procedures such as clinical laboratory testing. In spite of the careful efforts of the developers and manufacturers of clinical laboratory tests and the vigilance of the laboratory staffs that perform the testing, most if not all tests are, on occasion, subject to interferences that lead to false-positive or false-negative results (1)(2). Immunoassay tests are no exception. Recent literature has documented false-positive or false-negative results in immunoassays or reports investigations of specific interferences (3)(4). Sources of interferences include plasma (5), serum proteins (e.g., rheumatoid factor, binding proteins) (6)(7), heterophile and anti-animal antibodies (2)(8)(9), drugs and drug metabolites (10)(11), hemolysis (12), agar (13), and cross-reacting substances (14).

In most cases, a significant interference is recognized and flagged, but sometimes the interference is unsuspected and undetected. There now is adequate evidence that bad …