gebhart/patrepeval huggingface dataset:
Metabolic and clinical response to recombinant human insulin-like growth factor I in myotonic dystrophy--a clinical research center study. (1995)

Muscle weakness and wasting in myotonic dystrophy (MyD) are believed to be due to a decrease in muscle protein synthesis, secondary to insulin resistance. A 4-month, randomized, double blind, placebo-controlled trial was undertaken to assess whether recombinant human insulin-like growth factor I (rhIGF-I) may overcome the insulin resistance. Patients received either 5 mg rhIGF-I (n = 7) or placebo (n = 9), sc, twice daily. Glucose metabolism was assessed by stable label iv glucose tolerance test, amino acid metabolism by L-[13C] leucine turnover, body composition by dual energy x-ray absorptiometry and N excretion, and muscle response by manual muscle strength and neuromuscular function. In the treated group, the insulin sensitivity index, insulin action, and glucose disposal all increased (P < 0.05). Leucine flux and leucine incorporation into protein increased (P < 0.05), and the rate of leucine oxidation to leucine turnover decreased (P < 0.05), findings indicative of increased protein synthesis. Body weight and lean body mass increased, whereas percent body fat decreased (P < 0.05). An increase in manual muscle strength of 0.42 +/- 0.30 (P < 0.02) and in neuromuscular function of 17.5 +/- 11.7 (P < 0.02) occurred in the four patients who received a rhIGF-I dose greater than 70 micrograms/kg, whereas a more modest response occurred in the three patients who received a dose less than 70 micrograms/kg. Two patients showed dramatic improvement. Long term rhIGF-I therapy appears to cause metabolic and muscle improvement in optimally treated MyD patients.
Human recombinant macrophage colony stimulating factor activates murine Kupffer cells to a cytotoxic state. (1990)

Activated macrophages mediate cytotoxicity against tumor targets and thus may modulate development and growth of metastatic tumor cells. Macrophage colony stimulating factor (M-CSF) has a potential role in activating mature macrophages to a cytotoxic state. We employed a murine Kupffer cell (KC) model of cytotoxicity against a tumor necrosis factor (TNF) - sensitive murine colon adenocarcinoma cell line (MCA26) to evaluate the ability of recombinant human M-CSF (rhM-CSF) 1) to act alone as a KC-activating agent and 2) to enhance KC cytotoxicity against MCA26 cells in association with known macrophage activating compounds. rhM-CSF produced a dose-dependent increase in TNF release by KC in vitro with a parallel increase in MCA26 killing. KC activated by rhM-CSF produced less TNF and concomitantly demonstrated a lower cytotoxicity against MCA26 cells when compared with KC activated by gamma interferon (gamma IFN) with or without lipopolysaccharide (LPS). M-CSF did not act in a synergistic fashion with gamma IFN and LPS to increase TNF secretion or cytotoxicity against MCA26 cells. rhM-CSF thus acts as a single agent capable of activating murine KC to a cytotoxic state but does not cooperate with classical priming/triggering signals to achieve KC activation.
Efficacy of Modified Hive Entrances and a Bottom Screen Device for Controlling Aethina tumida (Coleoptera: Nitidulidae) Infestations in Apis mellifera (Hymenoptera: Apidae) Colonies (2003)

This study was designed to test whether hive entrances reduced with polyvinyl chloride pipe reduce the ingress of Aethina tumida Murray into Apis mellifera L. colonies and whether screen-mesh bottom boards alleviate side effects associated with restricted entrances. Forty-eight colonies distributed equally between two locations each received one of six experimental treatments: 1) conventional solid bottom board and open entrance, 2) ventilated bottom board and open entrance, 3) conventional bottom and 1.9-cm-i.d. pipe entrance, 4) conventional bottom and 3.8-cm pipe entrance, 5) screen bottom and 1.9-cm pipe entrance, and 6) screen bottom and 3.8-cm pipe entrance. Results were inconsistent between apiaries. In apiary 1, colonies with 3.8-cm pipe entrances had fewer A. tumida than colonies with open entrances, but this benefit was not apparent in apiary 2. Pipe entrances tended to reduce colony and brood production in both apiaries, and these losses were only partly mitigated with the addition of screened bottom boards. Pipe entrances had no measurable liability concerning colony thermoregulation. There were significantly fewer frames of adult A. mellifera in colonies with 3.8- or 1.9-cm pipe entrances compared with open entrances but more in colonies with screens. There were more frames of pollen in colonies with open or 3.8-cm pipe entrances than 1.9-cm entrances. We conclude that the efficacy of reduced hive entrances in reducing ingress of A. tumida remains uncertain due to observed differences between apiaries. Furthermore, there were side effects associated with restricted entrances that could be only partly mitigated with screened bottom boards.
Involvement of IQGAP3, a regulator of Ras/ERK‐related cascade, in hepatocyte proliferation in mouse liver regeneration and development (2009)

The spatio-temporal regulation of hepatocyte proliferation is a critical issue in liver regeneration. Here, in normal and regenerating liver as well as in developing liver, we examined its expression/localization of IQGAP3, which was most recently reported as a Ras/Rac/Cdc42-binding proliferation factor associated with cell-cell contacts in epithelial-type cells. In parallel, the expression/localization of Rac/Cdc42-binding IQGAP1/2 was examined. IQGAP3 showed a specific expression in proliferating hepatocytes positive for the proliferating marker Ki-67, the levels of expressions of mRNAs and proteins were significantly increased in hepatocytes in liver regeneration and development. In immunofluorescence, IQGAP3 was highly enriched at cell-cell contacts of hepatocytes. IQGAP1 and IQGAP2 were exclusively expressed in Kupffer and sinusoidal endothelial cells, respectively, in normal, regenerating, and developing liver. The expression of IQGAP1, but not of IQGAP2, was increased in CCl4-induced (but not in partial hepatectomy-induced) liver regeneration. Exclusive expression/localization of IQGAP3 to hepatocytes in the liver likely reflects the specific involvement of the IQGAP3/Ras/ERK signaling cascade in hepatocyte proliferation in addition to the previously identified signaling pathways, possibly by integrating cell-cell contact-related proliferating signaling events. On the other hand, the Rac/Cdc42-binding properties of IQGAP1/2/3 may be related to the distinct modes of remodeling due to the different strategies which induced proliferation of liver cells; partial hepatectomy, CCl4 injury, or embryonic development. Thus, the functional orchestration of Ras and the Ras homologous (Rho) family proteins Rac/Cdc42 likely plays a critical role in liver regeneration and development.
The Disease Resistance Signaling Components EDS1 and PAD4 Are Essential Regulators of the Cell Death Pathway Controlled by LSD1 in Arabidopsis (2001)

Specific recognition of pathogens is mediated by plant disease resistance (R) genes and translated into a successful defense response. The extent of associated hypersensitive cell death varies from none to an area encompassing cells surrounding an infection site, depending on the R gene activated. We constructed double mutants in Arabidopsis between positive regulators of R function and a negative regulator of cell death, LSD1, to address whether genes required for normal R function also regulate the runaway cell death observed in lsd1 mutants. We report here that EDS1 and PAD4, two signaling genes that mediate some but not all R responses, also are required for runaway cell death in the lsd1 mutant. Importantly, this novel function of EDS1 and PAD4 is operative when runaway cell death in lsd1 is initiated through an R gene that does not require EDS1 or PAD4 for disease resistance. NDR1, another component of R signaling, also contributes to the control of plant cell death. The roles of EDS1 and PAD4 in regulating lsd1 runaway cell death are related to the interpretation of reactive oxygen intermediate-derived signals at infection sites. We further demonstrate that the fate of superoxide at infection sites is different from that observed at the leading margins of runaway cell death lesions in lsd1 mutants.
Computational Design of an α-Gliadin Peptidase (2012)

The ability to rationally modify enzymes to perform novel chemical transformations is essential for the rapid production of next-generation protein therapeutics. Here we describe the use of chemical principles to identify a naturally occurring acid-active peptidase, and the subsequent use of computational protein design tools to reengineer its specificity toward immunogenic elements found in gluten that are the proposed cause of celiac disease. The engineered enzyme exhibits a k(cat)/K(M) of 568 M(-1) s(-1), representing a 116-fold greater proteolytic activity for a model gluten tetrapeptide than the native template enzyme, as well as an over 800-fold switch in substrate specificity toward immunogenic portions of gluten peptides. The computationally engineered enzyme is resistant to proteolysis by digestive proteases and degrades over 95% of an immunogenic peptide implicated in celiac disease in under an hour. Thus, through identification of a natural enzyme with the pre-existing qualities relevant to an ultimate goal and redefinition of its substrate specificity using computational modeling, we were able to generate an enzyme with potential as a therapeutic for celiac disease.
Genotype Dependent Interspecific Hybridization of Sorghum bicolor (2006)

Wild Australian Sorghum species are a tertiary gene pool to grain sorghum [ Sorghum bicolor (L.) Moench], and they are of interest to breeders because of their resistance to important insects and pathogens. However, strong reproductive barriers have prevented hybridization between S. bicolor and these wild species. The purpose of this study was to determine if the recessive iap allele (dominant allele Iap = inhibition of alien pollen ) would reduce or eliminate the pollen–pistil incompatibilities that prevent hybridization between S. bicolor and divergent Sorghum species. Cytoplasmic male‐sterile S. bicolor plants, homozygous for the iap allele, were pollinated with three divergent Sorghum species, S. angustum Blake, S. nitidum (Vahl) Pers., and S. macrospermum Garber. The pollen of these three wild species readily germinated and the pollen tubes grew to the base of the S. bicolor ovary within 2 h after pollination. Hybrid embryos were detected in the S. bicolor florets 13 to 20 d post‐pollination. Sorghum bicolor × S. angustum and S. bicolor × S. nitidum hybrids were obtained using embryo rescue followed by in vitro culture techniques and hybrids between S. bicolor and S. macrospermum were obtained by simply germinating the hybrid seed. These hybrids were confirmed by their morphological and cytological traits. These findings clearly demonstrate that the recessive iap allele circumvents pollen–pistil incompatibilities in the genus Sorghum and permits hybrids to be made between S. bicolor and species of the tertiary gene pool.
Real-time monitoring of in vitro transcriptional RNA synthesis using fluorescence resonance energy transfer (2000)

We have developed a novel method for real-time monitoring of RNA synthesis in in vitro transcription reactions using fluorescence resonance energy transfer (FRET). Two 15mer DNAs, either of which was labeled with Bodipy493/503 as a donor or Cy5 as an acceptor, were prepared. When the two fluorescent DNAs hybridized to adjacent locations on Xenopus: elongation factor 1-alpha (xelf1-alpha) RNA, the distance between the two fluorophores became very close, causing FRET to occur and resulting in changes in fluorescence spectra. A high accessibility 30mer site of xelf1-alpha RNA was found and excess amounts of a pair of donor and acceptor DNA probes that were complementary to the site were added to the in vitro transcription reaction solution. Changes in fluorescence spectra were observed in response to progression of xelf1-alpha RNA synthesis that showed that the fluorescent probes hybridized to the synthesized RNA. Furthermore, when probes hybridizing to the synthesized xelf1-alpha RNA with less efficiency were used to monitor the reaction, spectral changes in response to RNA synthesis were also observed. This result suggests that the probes hybridized to synthesizing RNA molecules before they folded to form secondary structure and that there is no need to select sites on the RNA for the probes, which is required for probes hybridizing to folded RNA molecules.
FOXP3 expression accurately defines the population of intratumoral regulatory T cells that selectively accumulate in metastatic melanoma lesions (2008)

Regulatory T (T(reg)) cells are often found in human tumors; however, their functional characteristics have been difficult to evaluate due to low cell numbers and the inability to adequately distinguish between activated and T(reg) cell populations. Using a novel approach, we examined the intracellular cytokine production capacity of tumor-infiltrating T cells in the single-cell suspensions of enzymatically digested tumors to differentiate T(reg) cells from effector T cells. Similar to T(reg) cells in the peripheral blood of healthy individuals, tumor-infiltrating FOXP3(+)CD4 T cells, unlike FOXP3(-) T cells, were unable to produce IL-2 and IFN-gamma upon ex vivo stimulation, indicating that FOXP3 expression is a valid biological marker for human T(reg) cells even in the tumor microenvironment. Accordingly, we enumerated FOXP3(+)CD4 T(reg) cells in intratumoral and peritumoral sections of metastatic melanoma tumors and found a significant increase in proportion of FOXP3(+)CD4 T(reg) cells in the intratumoral compared with peritumoral areas. Moreover, their frequencies were 3- to 5-fold higher in tumors than in peripheral blood from the same patients or healthy donors, respectively. These findings demonstrate that the tumor-infiltrating CD4 T(reg) cell population is accurately depicted by FOXP3 expression, they selectively accumulate in tumors, and their frequency in peripheral blood does not properly reflect tumor microenvironment.
Thrombospondin interactions with fibronectin and fibrinogen. Mutual inhibition in binding (1984)

Thrombospondin synthesized and secreted by human endothelial cells in culture binds specifically to fibronectin immobilized on Sepharose beads. It can also bind to immobilized platelet-derived thrombospondin but not to immobilized gelatin or albumin. These interactions are not dependent on the presence of divalent cations or of other secreted materials. Purified platelet thrombospondin binds to fibronectin and fibrinogen immobilized on plastic surfaces with dissociation constants of 1.12 +/- 0.37 X 10(-7) M and 1.27 +/- 0.41 X 10(-7) M respectively, and to thrombospondin immobilized on plastic with dissociation constant of 4.82 +/- 1.01 X 10(-7) M. The affinities of interaction are not significantly affected by removal of divalent cations. Soluble fibrinogen inhibits binding of thrombospondin to fibronectin regardless of which of the latter two is surface-bound. Thrombospondin-fibronectin interaction is also inhibited by soluble thrombospondin. The binding of soluble thrombospondin to surface-bound fibrinogen is inhibited both by soluble fibronectin and soluble fibrinogen. These results suggest that thrombospondin plays a role both in platelet-platelet aggregation and in platelet-substratum adhesion, and that it may also take part in the construction of the extracellular matrix.
A new general global array calibration method (2002)

A new method is proposed for calibrating a planar array of general geometry with respect to errors in location, phase and gain, even when all errors are present simultaneously (global calibration). The method requires the use of three pilot sources, which operate one at a time and from at least two different azimuth angles. Since the sources need not operate simultaneously, one only pilot source may be used from three different directions. The method assumes that the electrical errors (phase and gain errors) are not direction dependent. Simulation results that support the performance of the proposed method are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DISPARITY BETWEEN FUNDUS CAMERA AND SCANNING LASER OPHTHALMOSCOPE INDOCYANINE GREEN IMAGING OF RETINAL PIGMENT EPITHELIUM DETACHMENTS (1998)

The apparent fluorescence of serous fluid beneath RPE detachments in fundus camera early-phase ICG angiogram images is not attributable to the presence of dye; rather, it appears to be attributable to serous fluid light scatter of fluorescent light arising from adjacent fluorescent structures. This light scatter is a consequence of the fundus camera illumination and recording optics and is not present in SLO-generated images. The necessity of understanding such phenomena as absorption, diffraction, polarization, and scatter of light and routinely applying them to ICG angiogram interpretation is underscored when it is shown that they offer simple explanations for unusual or unexpected angiographic results, as in the case of the patients with RPE detachment discussed here.
Manganese, superoxide dismutase, and oxygen tolerance in some lactic acid bacteria (1981)

A previous study of the aerotolerant bacterium Lactobacillus plantarum, which lacks superoxide dismutase (SOD), demonstrated that it possesses a novel substitute for this defensive enzyme. Thus, L. plantarum contains 20 to 25 mM Mn(II),m in a dialyzable form, which is able to scavenge O2- apparently as effectively as do the micromolar levels of SOD present in most other organisms. This report describes a survey of the lactic acid bacteria. The substitution of millimolar levels of Mn(II) for micromolar levels of SOD is a common occurrence in this group of microorganisms, which contained either SOD or high levels of Mn(II), but not both. Two strains were found which had neither high levels of Mn(II) nor SOD, and they were, as was expected, very oxygen intolerant. Lactic acid bacteria containing SOD grew better aerobically than anaerobically, whereas the organisms containing Mn(II) in place of SOD showed aerobic growth which was best, at best, equal to anaerobic growth. Plumbagin (5-hydroxy-2-methyl-1,4-naphthoquinone) increases the rate of O2- production in these organisms. Lactobacillus strains containing high intracellular Mn(II) were more resistant to the oxygen-dependent toxicity of plumbagin than were strains containing lower levels of Mn(II). The results support the conclusion that a high internal level of Mn(II) provides these organisms with an important defence against endogenous O2-.
Application-specific workload shaping in multimedia-enabled personal mobile devices (2006)

Today, most personal mobile devices (e.g. cell phones and PDAs) are multimedia-enabled and support a variety of concurrently running applications such as audio/video players, word processors and web browsers. Media-processing applications are often computationally expensive and most of these devices typically have 100 - 400 MHz processors. As a result, the user-perceived application response times are often poor when multiple applications are concurrently fired. In this paper we show that by using application-specific dynamic buffering techniques, the workload of these applications can be suitably "shaped" to fit the available processor bandwidth. Our techniques are analogous to traffic shaping which is widely used in communication networks to optimally utilize network bandwidth. Such shaping techniques have recently attracted a lot of attention in the context of embedded systems design (e.g. for dynamic voltage scaling). However, they have not been exploited for enhanced schedulability of multiple applications, as we do in this paper.
GDNF – a stranger in the TGF‐β superfamily? (2000)

Glial cell line-derived neurotrophic factor (GDNF) family, consisting of GDNF, neurturin, artemin and persephin are distant members of the transforming growth factor-beta (TGF-beta) superfamily. Unlike other members of the TGF-beta superfamily, which signal through the receptor serine-threonine kinases, GDNF family ligands activate intracellular signalling cascades via the receptor tyrosine kinase Ret. GDNF family ligands first bind to the glycosylphosphatidylinositol (GPI)-anchored GDNF family receptor alpha (GFRalpha) and then the GDNF family ligand-GFRalpha complex binds to and stimulates autophosphorylation of Ret. Alternatively, a preassociated complex between GFRalpha and Ret could form the binding site for the GDNF family ligand. GFRalpha1, GFRalpha2, GFRalpha3 and GFRalpha4 are the physiological coreceptors for GDNF, neurturin, artemin and persephin, respectively. Although all GDNF family ligands signal via activated Ret, GDNF can signal also via GFRalpha1 in the absence of Ret. GPI-anchored GFRalpha receptors are localized in plasma membrane to lipid rafts. GDNF binding to GFRalpha1 also recruits Ret to the lipid rafts and triggers association with Src, which is required for effective downstream signalling, leading to differentiation and neuronal survival. GDNF family ligands are potent survival factors for midbrain dopamine neurons, motoneurons, noradrenergic neurons, as well as for sympathetic, parasympathetic and sensory neurons. However, for most neuronal populations, except for motoneurons, TGF-beta is required as a cofactor for GDNF family ligand signalling. Because GDNF and neurturin can rescue dopamine neurons in the animal models of Parkinson disease, as well as motoneurons in vivo, hopes have been raised that GDNF family ligands may be new drugs for the treatment of neurodegenerative diseases. GDNF also has distinct functions outside the nervous system, promoting ureteric branching in kidney development and regulating spermatogenesis.