gebhart/patrepeval huggingface dataset:
High Mobility Group 1 Protein (Hmg-1) Stimulates Proinflammatory Cytokine Synthesis in Human Monocytes (2000)

Lipopolysaccharide (LPS) is lethal to animals because it activates cytokine release, causing septic shock and tissue injury. Early proinflammatory cytokines (e.g., tumor necrosis factor [TNF] and interleukin [IL]-1) released within the first few hours of endotoxemia stimulate mediator cascades that persist for days and can lead to death. High mobility group 1 protein (HMG-1), a ubiquitous DNA-binding protein, was recently identified as a "late" mediator of endotoxin lethality. Anti-HMG-1 antibodies neutralized the delayed increase in serum HMG-1, and protected against endotoxin lethality, even when passive immunization was delayed until after the early cytokine response. Here we examined whether HMG-1 might stimulate cytokine synthesis in human peripheral blood mononuclear cell cultures. Addition of purified recombinant HMG-1 to human monocyte cultures significantly stimulated the release of TNF, IL-1alpha, IL-1beta, IL-1RA, IL-6, IL-8, macrophage inflammatory protein (MIP)-1alpha, and MIP-1beta; but not IL-10 or IL-12. HMG-1 concentrations that activated monocytes were within the pathological range previously observed in endotoxemic animals, and in serum obtained from septic patients. HMG-1 failed to stimulate cytokine release in lymphocytes, indicating that cellular stimulation was specific. Cytokine release after HMG-1 stimulation was delayed and biphasic compared with LPS stimulation. Computer-assisted image analysis demonstrated that peak intensity of HMG-1-induced cellular TNF staining was comparable to that observed after maximal stimulation with LPS. Administration of HMG-1 to Balb/c mice significantly increased serum TNF levels in vivo. Together, these results indicate that, like other cytokine mediators of endotoxin lethality (e.g., TNF and IL-1), extracellular HMG-1 is a regulator of monocyte proinflammatory cytokine synthesis.
Soluble Tumor Necrosis Factor Receptors are Elevated in Relation to Severity of Congestive Heart Failure (1997)

The level of tumor necrosis factor alpha (TNF-alpha) is increased in patients with congestive heart failure and may play an important role in the development and progression of heart failure. Two types of TNF receptor (TNF-RI and TNF-RII) are expressed in virtually every cell and have different biologic roles. Soluble forms of the two receptors (sTNF-RI and sTNF-RII) have been identified as extracellular domain fragments. Serum levels of TNF-alpha, sTNF-RI and sTNF-RII were measured in 66 patients with heart failure and 27 control subjects using an enzyme-linked immunosorbent assay (ELISA). Hemodynamic variables, norepinephrine, atrial natriuretic peptide (ANP), and brain natriuretic peptide (BNP) were evaluated. TNF-alpha was significantly higher in patients with heart failure than in controls subjects (9.4 +/- 1.4 vs 4.8 +/- 0.8 pg/ml; p < 0.05). sTNF-RI and -RII were significantly increased in relation to the severity of heart failure (control subjects, 0.66 +/- 0.04 and 1.97 +/- 0.15 ng/ml; NYHA class II, 1.10 +/- 0.08 and 2.28 +/- 0.12 ng/ml; NYHA class III, 1.63 +/- 0.22 and 3.00 +/- 0.24 ng/ml; NYHA class IV, 2.78 +/- 0.46 and 4.52 +/- 0.62 ng/ml, respectively). In 9 patients whose clinical symptoms improved after treatment, the levels of sTNF-RI and -RII decreased by 17.3 +/- 5.7% (p < 0.05) and 22.1 +/- 6.9% (p < 0.05), respectively. There were significant positive correlations between sTNF-RI and -RII and mean pulmonary pressure (r = 0.69 and r = 0.61; p < 0.001) and mean capillary wedge pressure (r = 0.65 and r = 0.54; p < 0.001 and p < 0.01, respectively), but not with left ventricular end-diastolic volume or ejection fraction (NS). sTNF-RI and -RII were also significantly positively correlated with plasma levels of norepinephrine (r = 0.75 and r = 0.50; p < 0.001 and p < 0.05), ANP (r = 0.72 and r = 0.70; p < 0.001), and BNP (r = 0.60 and r = 0.60; p < 0.001). In conclusion, soluble TNF receptors are increased in proportion to the severity of congestive heart failure and may reflect the current status of congestive heart failure rather than the level of left ventricular dysfunction.
Morphine Use after Combat Injury in Iraq and Post-Traumatic Stress Disorder (2010)

Our findings suggest that the use of morphine during trauma care may reduce the risk of subsequent development of PTSD after serious injury.
Tumor Vascularity in the Prognostic Assessment of Primary Cutaneous Melanoma (2002)

Tumor vascularity is an important prognostic factor in melanoma, rivaling tumor thickness. Increasing tumor vascularity is highly correlated with ulceration, possibly helping to explain the biologic basis of this known prognostic factor.
Parameters tell the design story: ideation and abstraction in design optimization (2014)

We report qualitative findings from interviews and observations detailing how professionals generate and evaluate design ideas using design optimization tools. We interviewed 18 architects and manufacturing design professionals. We frame our findings using the Geneplore model of creative cognition and classify examples of ideation and abstract design thinking arising from optimization workflows. Contrary to our expectations, we found that the computed optimum was often used as the starting point for design exploration, not the end product. We also found that parametric models, plus their associated parameters and simulations serve as an alternate, highly valued form of design documentation distinct from engineering schematics.
Human constant regions influence the antibody binding characteristics of mouse‐human chimeric IgG subclasses (1996)

Although antibody affinity is primarily determined by immunoglobulin variable region structure human IgG antibodies of the four subclasses specific for the same antigen have been shown to differ in their affinity. To explore the influence of the immunoglobulin constant region on functional antibody affinity, a set of V region identical mouse-human chimeric IgG subclasses specific for TAG72 (tumour-associated glycoprotein) were studied. Biomolecular interaction analysis (BIA) was used to determine the binding kinetics of whole IgG subclasses and F(ab')2 fragments. Despite identical V regions, binding kinetics differed for the four subclasses. The apparent dissociation rate constants of the intact immunoglobulins ranked IgG4 < IgG3 < IgG2 < IgG1. In contrast, analysis of the binding characteriztics of the F(ab')2 fragments derived from IgG1, IgG2 and IgG4 revealed identical binding kinetics. The structure of the constant regions of the humanized IgG subclass antibodies clearly influenced functional antibody affinity, as has been described for the murine IgG subclasses. The exact mechanism for this phenomenon remains obscure but such differences should be taken into account when designing or choosing antibodies for therapeutic use.
AAV-Mediated gene delivery of BDNF or GDNF is neuroprotective in a model of huntington disease (2004)

Huntington disease (HD) is a neurodegenerative disorder that results in the progressive loss of GABAergic medium spiny projection neurons in the striatum. Neurotrophic factors have demonstrated neuroprotective actions on striatal neurons, suggesting that increased neurotrophic factor expression may prevent or reduce neuronal loss in the HD brain. We investigated whether enhanced expression of brain-derived neurotrophic factor (BDNF) or glial cell line-derived neurotrophic factor (GDNF), achieved by adeno-associated viral (AAV) vector-mediated gene delivery, could protect striatal neurons in the quinolinic acid (QA) rodent model of HD. Adult Wistar rats received unilateral intrastriatal injections of AAV-BDNF, AAV-GDNF, AAV-GFP, or PBS. Three weeks later, the rats were lesioned with QA, a toxin that induces striatal neuron death by an excitotoxic process. Both AAV-BDNF and AAV-GDNF significantly reduced the loss of both NeuN- and calbindin-immunopositive striatal neurons 2 weeks after lesion compared to controls. AAV-BDNF also provided significant neurotrophic support to NOS-immunopositive striatal interneurons, while AAV-GDNF-treated rats demonstrated significant protection of parvalbumin-immunopositive striatal interneurons compared to controls. These results indicate that AAV-mediated gene transfer of BDNF or GDNF into the striatum provides neuronal protection in a rodent model of HD.
Unintentional Weight Loss in Long-term Care: Predictor of Mortality in the Elderly (1995)

We retrospectively reviewed the medical records of 153 long-term care residents. Of these, 24 had lost at least 5% of their body weight during a 1-month interval. An unmatched control group of 51 patients was randomly selected from the remaining patients. Subjects who lost at least 5% body weight in 1 month were 4.6 times more likely to die within 1 year. Using multiple logistic regression, the odds ratio for weight loss and mortality was 5.1 (95% confidence interval 1.5 to 17.1) after adjustment for potential confounding by age and sex. The relatively simple anthropometric measure of body weight could be used by a multidisciplinary team in long-term care settings to identify patients at increased risk of dying. Further work is needed to clarify the role that nutrition could play in decreasing mortality in long-term care facilities.
Collection efficiencies of a point-to-plane electrostatic precipitator (1981)

Collection efficiencies of a point-to-plane electrostatic precipitator were evaluated as functions of particle size, aerosol flow and ion current. Monodisperse aerosols ranging from 0.03 to 2.0 μm were used. Collection efficiencies decrease with 1) an increase of aerosol flow rate, 2) a decrease of particle size and 3) an increase of ion current. At the lowest tested flow, 100 cm3min, the effects of ion current and particle size seem to be minimal. Average efficiencies were found to be 90, 85 and 85% over the entire particle size range used in this study, for ion currents of 1.0, 3.5 and 5.0 microamperes respectively.
Development of an Aggregation-Based Immunoassay for Anti-Protein A Using Gold Nanoparticles (2002)

A unique, sensitive, and highly specific immunoassay system for antibodies using gold nanoparticles has been developed. The assay is based on the aggregation of gold nanoparticles that are coated with protein antigens in the presence of their corresponding antibodies. The aggregation of the gold nanoparticles results in an absorption change at 620 nm that is monitored using an absorption plate reader. To demonstrate the analytical capabilities of the new technique, monodispersed protein A-coated gold particles, averaging 10 nm in diameter, were used to determine the level of anti-protein A in serum samples. The effects of the pH, the temperature, and the concentration of protein A-coated gold nanoparticles on the sensitivity of the assay were investigated using transmission electron microscopy (TEM) and UV/vis absorption spectroscopy. A dynamic range of 2 orders of magnitude and a limit of detection of 1 microg/mL of anti-protein A were observed. The new technique could be used for fast, high-throughput screening of antibodies in clinical diagnostic applications.
RNA aptamers that functionally interact with green fluorescent protein and its derivatives (2011)

Green Fluorescent Protein (GFP) and related fluorescent proteins (FPs) have been widely used to tag proteins, allowing their expression and subcellular localization to be examined in real time in living cells and animals. Similar fluorescent methods are highly desirable to detect and track RNA and other biological molecules in living cells. For this purpose, we have developed a group of RNA aptamers that bind GFP and related proteins, which we term Fluorescent Protein-Binding Aptamers (FPBA). These aptamers bind GFP, YFP and CFP with low nanomolar affinity and binding decreases GFP fluorescence, whereas slightly augmenting YFP and CFP brightness. Aptamer binding results in an increase in the pKa of EGFP, decreasing the 475 nm excited green fluorescence at a given pH. We report the secondary structure of FPBA and the ability to synthesize functional multivalent dendrimers. FPBA expressed in live cells decreased GFP fluorescence in a valency-dependent manner, indicating that the RNA aptamers function within cells. The development of aptamers that bind fluorescent proteins with high affinity and alter their function, markedly expands their use in the study of biological pathways.
Partial strain relaxation via misfit dislocation generation at heterointerfaces in (Al,In)GaN epitaxial layers grown on semipolar (112¯2) GaN free standing substrates (2009)

Misfit strain relaxation via misfit dislocation (MD) generation was observed in heteroepitaxially grown (Al,In)GaN layers on free-standing semipolar (112¯2) GaN substrates. Cross-section transmission electron microscope images revealed MD arrays at alloy heterointerfaces, with the MD line direction and Burgers vector parallel to [11¯00] and [112¯0], respectively. The MD structure is consistent with plastic relaxation by dislocation glide on the (0001) plane. Since (0001) is the only slip plane, the plastic relaxation is associated with tilt of the epitaxial (Al,In)GaN layers. The tilt, measured via high-resolution x-ray diffraction, can be used to quantify the relaxation.
Multimedia support over bluetooth Piconets (2001)

In this paper we explore the ability to support multimedia traffic in indoor, wireless ad hoc PANs (Personal Area Networks) using the Bluetooth technology. We first define the representative ad hoc networking applications such as wireless access to the Internet, document distribution, videoconferencing, webcasting, interaction with sensors and actuators, etc. For such applications, we define the performance requirements placed on the PAN. There are two technologies now competing for the PAN market: the IEEE802.11 “legacy” technology, and the newly introduced Bluetooth technology. By IEEE802.11, we refer to the operation of 802.11 in the DCF mode, which is the mode implemented in the commercial WaveLAN cards. In the rest of the paper, we will use WaveLAN to refer to 802.11 in its DCF mode. We will attempt to answer the questions: how effective is the Bluetooth technology in supporting collaborative, “virtual ad hoc networking” applications and how does it compare with WaveLAN? To answer these questions, we have developed an NS-2 model of Bluetooth. We have also developed models of adaptive applications such as voice and video. For WaveLAN, we have used the existing NS-2 models. The results show that Bluetooth provides better support for real-time applications as compared to WaveLAN. It does not exhibit the “capture” behavior observed, for example, in WaveLAN. Also, with the addition of nodes to the “indoor” space, it adds to the total “system” capacity and gives a better overall throughput.
Depth of penetration of negative pressure wound therapy into underlying tissues (2009)

Negative pressure wound therapy has become ubiquitous in orthopedic surgery and it is therefore important to understand the physiologic conditions of this therapy. The purpose of this study was to determine the magnitude and depth of negative pressure transmission into underlying muscle tissue in a wound model. We hypothesized that the negative pressure is not transmitted beyond 2 mm into underlying muscle tissue. Using both an isolated muscle and a live animal wound model, we applied open cell foam dressing to the tissue. Using a series of vacuum-assisted closure negative pressure settings (0, -75, -125, -200 mmHg) interstitial fluid pressure was measured in the underlying tissue with a solid-state pressure transducer catheter at 1/10 mm depth intervals. In the ex vivo isolated-muscle model, the effect of negative pressure wound therapy on interstitial fluid pressure was extinguished and not significantly different than controls at a depth <2 mm. In the live animal wound model, the magnitude of interstitial fluid pressures corresponded directly with negative pressure settings (p<0.01) and inversely with depth into muscle (p<0.01). Interstitial fluid pressures were significantly (p<0.05) less than control interstitial fluid pressures (0 mmHg setting) at depths of 0.5, 0.4, and 0.9 mm below the foam/muscle interface when the applied pressures were -75, -125, and -200 mmHg, respectively. Negative pressure wound therapy penetrates no more than 1 mm into rabbit wound tissue at the highest negative pressure setting (-200 mmHg) when using open-cell foam dressing.
VHS domain – a longshoreman of vesicle lines (2001)

The VHS (Vps-27, Hrs and STAM) domain is a 140 residue long domain present in the very NH2-terminus of at least 60 proteins. Based on their functional characteristics and on recent data on the involvement of VHS in cargo recognition in trans-Golgi, VHS domains are considered to have a general membrane targeting/cargo recognition role in vesicular trafficking. Structurally, VHS is a right-handed superhelix of eight helices with charged surface patches probably serving as sites of protein-protein recognition and docking.
Phased amplitude-shift signaling (PASS) codes: increasing the spectral efficiency of DWDM transmission (2002)

We propose and analyze a new class of transmission line codes, called PASS codes, capable of dramatically increasing the spectral efficiency of DWDM transmission. PASS codes generalize the spectral shaping characteristics of duobinary signaling to multi-bit data representations.
Expression of a functional human type I interferon receptor in hamster cells: application of functional yeast artificial chromosome (YAC) screening. (1994)

The previously cloned human interferon alpha/beta (Hu-IFN-alpha/beta; Type I interferon) receptor cDNA appears to be only one component of a receptor complex since expression of the cDNA in mouse cells confers sensitivity only to Hu-IFN-alpha B2, but a monoclonal antibody against this cloned receptor subunit inhibits biological activities of Hu-IFN-alpha A, Hu-IFN-alpha B2, Hu-IFN-omega, and Hu-IFN-beta. Here we report that a yeast artificial chromosome (YAC) containing a segment of human chromosome 21 introduced into Chinese hamster ovary (CHO) cells confers upon these cells a greatly enhanced response to Hu-IFN-alpha A and Hu-IFN-alpha B2 as well as an increased response to Hu-IFN-omega, Hu-IFN-alpha A/D(Bgl), andd Hu-IFN-beta. These responses were measured by induction of class I MHC antigens and by protection against encephalomyocarditis virus and vesicular stomatitis virus. Furthermore, these cells exhibit specific high affinity binding of Hu-IFN-alpha A and Hu-IFN-alpha B2, Hu-IFN-beta, and Hu-IFN-omega. The results indicate that all the genes necessary to reconstitute a biologically active Type I human IFN receptor complex are located within the human DNA insert of this YAC clone.
SCA8 CAG/CTG Expansions, a Tale of Two TOXICities: A Unique or Common Case? (2009)

International audience
Initiation of Tumor Necrosis Factor-α Antagonists and the Risk of Hospitalization for Infection in Patients With Autoimmune Diseases (2011)

Among patients with autoimmune diseases, compared with treatment with nonbiologic regimens, initiation of TNF-α antagonists was not associated with an increased risk of hospitalizations for serious infections.
Macrophages and fibroblasts express embryonic fibronectins during cutaneous wound healing. (1993)

Fibronectins (FN) comprise a family of adhesive glycoproteins that are prominent components of wound healing. These proteins arise by alternative splicing of a single gene transcript at three sites, termed EIIIA, EIIIB, and V. Extravasated plasma FN, which lacks the EIIIA and EIIIB domains, along with fibrin, comprise the "provisional" matrix that forms within minutes of tissue injury. By 2 days after cutaneous excisional wounding in rats, total FN messenger RNA (mRNA) expression is increased locally and dramatically within the surrounding dermis, in the subjacent muscle (panniculus carnosus) and, notably, at the wound margins. Moreover, in contrast to normal skin, 2-day wounds express EIIIA- and EIIIB-containing "embryonic" FN mRNAs. To identify the cells responsible for synthesizing the various FN isoforms, we performed in situ hybridization with probes for the various FN mRNAs. Collagen and lysozyme probes were employed to distinguish fibroblasts from macrophages. At early intervals (2 days) after wounding, macrophages were the principal cells that expressed FN mRNA. Moreover, many of these cells expressed embryonic FN mRNAs. At 7 to 10 days, when the wound defect was maturing, fibroblasts were the major cells synthesizing these embryonic FNs. It is widely accepted that wound macrophages phagocytose debris and provide degradative enzymes and cytokines essential for early stages of tissue repair. Our findings suggest an additional function for wound macrophages--synthesis of embryonic FNs providing an extracellular matrix that facilitates wound repair, perhaps by promoting cell migration.
Effect of Surfactants on the Interfacial Tension between Supercritical Carbon Dioxide and Polyethylene Glycol (1996)

The effects of various surfactants on the interfacial tension between supercritical CO2 and 600 MW polyethylene glycol (PEG) are reported at 45 °C on the basis of measurements with a novel tandem variable-volume pendant drop tensiometer. The interfacial tension of the CO2−polyethylene glycol binary system decreases from 9.0 dyn/cm at 85 bar to 3.1 dyn/cm at 300 bar, primarily because of the increase in the density and likewise the free energy density of the CO2 phase. This result is predicted quantitatively with a gradient model using the lattice fluid equation of state. The experimental results for the effects of three surfactants on the interfacial tension are described by a modified Winsor R theory in terms of the molecular interactions on each side of the interface and the surfactant solubility in each phase. At 276 bar, the addition of 1 wt % ammonium carboxylate perfluoropolyether (PFPE) surfactant reduces the interfacial tension from 3.2 to 2.1 dyn/cm and the interfacial area of the surfactant is 437 Å2/molecule. In contrast, surface activity is not observed for a hydrocarbon polyether (Brij30), since it favors the organic phase, or for a high molecular weight fluoropolymer (PolyFOA), since it favors the CO2 phase. Because PFPE is interfacially active, it stabilizes PEG-in-CO2 microemulsions.
Miniature Protein Ligands for EVH1 Domains:  Interplay between Affinity, Specificity, and Cell Motility (2007)

Dynamic rearrangements of the actin cytoskeleton power cell motility in contexts ranging from intracellular microbial pathogenesis to axon guidance. The Ena/VASP family proteins-Mena, VASP, and Evl-are believed to control cell motility by serving as a direct link between signaling events and the actin cytoskeleton. It has previously been reported that a novel miniature protein, pGolemi, binds with high affinity to the EVH1 domain of Mena (Mena1-112) but not to those of VASP (VASP1-115) or Evl (Evl1-115) and also causes an unusual defect in actin-driven Listeria monocytogenes motility. Here, scanning mutagenesis was used to examine the effects of single amino acid changes within pGolemi on EVH1 domain affinity and specificity, miniature protein secondary structure, and L. monocytogenes motility. The data suggest that pGolemi contains the expected aPP-like fold and binds Mena1-112 in a manner highly analogous to the proline-rich repeat region of L. monocytogenes ActA protein. Residues throughout pGolemi contribute to both EVH1 domain affinity and paralog specificity. Moreover, the affinities of pGolemi variants for Mena1-112 correlate with selectivity against the EVH1 domains of VASP and Evl. In L. monocytogenes motility assays, speed and speed variability correlate strongly with EVH1 paralog specificity, suggesting that the Ena/VASP paralogs do not play equivalent roles in the process of L. monocytogenes actin tail maturation.