gebhart/patrepeval huggingface dataset:
Foamed hydrocarbons: an effective and economical alternative to conventional stimulation methods (1979)

Foamed hydrocarbons have been applied with great success in paraffin and heavy hydrocarbon penetration, foamed fracturing treatments, and fluid cleanout in wells in which hydrostatic pressure interferes with or completely stops gas production. Results of laboratory and field tests show this system to be effective as well as economical as an alternative in well treatment. The paraffin and heavy hydrocarbons removed in foamed aromatic hydrocarbons constituted up to 41% of the total volume of solids removed after a one hour shutin period. A nonproductive well in the San Miguel Formation which had been shutin for a year was fractured with foamed gel condensate resulting in 70 MCFD of gas. Gas wells in the Sonora area have periodical condensate buildups which restrict the gas flow. With the addition of a hydrocarbon foamer, the hydrostatic head was removed in the form of foamed condensate, allowing production of the natural gas. Procedures and results of lab and field tests are discussed along with comparative results of more conventional treatments. 10 references.
Anti-Endothelial Cell Antibodies in Systemic Sclerosis (1999)

Systemic sclerosis (SSc), or scleroderma, is characterized by early vascular endothelial cell (EC) damage, followed by cutaneous and visceral fibrosis. There is substantial interest in the role of anti-EC antibodies (AECA) in SSc as recent findings have brought new insights into the understanding of
The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell (2010)

thomas.junier@unige.ch
Skin-homing, CLA+ memory T cells are activated in atopic dermatitis and regulate IgE by an IL-13-dominated cytokine pattern: IgG4 counter-regulation by CLA- memory T cells (1997)

Cutaneous lymphocyte-associated Ag (CLA) is a skin-homing receptor displayed by memory/effector T cells recognizing skin-related allergens. Here we demonstrate that peripheral blood CLA+ CD45RO+ T cells in patients with atopic dermatitis (AD) are in vivo activated. They spontaneously proliferate and release an IL-13-dominated Th2 cytokine profile and are capable of inducing IgE in autologous B cells without further activation. The spontaneous cytokine release occurred within the first hour of culture and was not inhibited by cycloheximide or by other immunosuppressive drugs, indicating that cytokine transcription and translation had been completed in vivo. In contrast, the CLA- CD45RO+ T cells from the same patients and from nonatopic controls represented a resting memory T cell subset, secreted borderline quantities of cytokines, and induced IgG4. Polyclonal activation by the anti-CD2/anti-CD3/anti-CD28 mAb mixture generated distinct cytokine patterns in the two memory/effector T cell subsets. CLA+ T cells secreted Th2 cytokines with high IL-13 levels, and the CLA- subset mainly produced IFN-gamma. There was no difference in in vitro activated cytokine pattern between AD patients and nonatopic subjects. These results indicate that the CLA+ memory/effector T cells of AD patients are activated in vivo and play a pivotal role in allergic inflammation by production of IL-13 and induction of IgE Abs. In contrast, the CLA- resting memory T cell population may exert immunoprotective properties toward allergen by high IFN-gamma secretion and induction of IgG4.
A comparative study of allometric scaling with plasma concentrations predicted by species-invariant time methods (1999)

The objective of this study is to compare the empirical allometric approaches with species invariant time methods using equivalent time, kallynochron, apolysichron, and dienetichrons. Pharmacokinetic parameters (clearance, volume of distribution, and elimination half-life) of ethosuximide, cyclosporine and ciprofloxacin were scaled-up from animal data obtained from the literature. Two methods were utilized to generate plots for the prediction of clearance in humans: (i) clearance versus body weight (simple allometric equation); and (ii) the product of clearance and maximum life-span potential (MLP) versus body weight. Plasma concentrations of each of the drugs were predicted using elementary and complex Dedrick plots, equivalent time with an exponent of 0.25 and equivalent time with the exponent obtained from the plot of body weight and half-life. Plasma concentrations of cyclosporine and ciprofloxacin were also predicted by MLP normalization (dienetichrons). Almost similar results in the pharmacokinetic parameters of the tested drugs were obtained by the allometric approach and by the species invariant time methods.
Mutant superoxide dismutase 1 (SOD1), a cause of amyotrophic lateral sclerosis, disrupts the recruitment of SMN, the spinal muscular atrophy protein to nuclear Cajal bodies (2012)

Spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS) are among the most common motor neuron diseases to afflict the human population. A deficiency of the survival of motor neuron (SMN) protein causes SMA and is also reported to be an exacerbating factor in the development of ALS. However, pathways linking the two diseases have yet to be defined and it is not clear precisely how the pathology of ALS is aggravated by reduced SMN or whether mutant proteins underlying familial forms of ALS interfere with SMN-related biochemical pathways to exacerbate the neurodegenerative process. In this study, we show that mutant superoxide dismutase-1 (SOD1), a cause of familial ALS, profoundly alters the sub-cellular localization of the SMN protein, preventing the formation of nuclear 'gems' by disrupting the recruitment of the protein to Cajal bodies. Overexpressing the SMN protein in mutant SOD1 mice, a model of familial ALS, alleviates this phenomenon, most likely in a cell-autonomous manner, and significantly mitigates the loss of motor neurons in the spinal cord and in culture dishes. In the mice, the onset of the neuromuscular phenotype is delayed and motor function enhanced, suggestive of a therapeutic benefit for ALS patients treated with agents that augment the SMN protein. Nevertheless, this finding is tempered by an inability to prolong survival, a limitation most likely imposed by the inexorable denervation that characterizes ALS and eventually disrupts the neuromuscular synapses even in the presence of increased SMN.
Translating 2A Research into Practice (2012)

Viruses have evolved a number of unconventional translation strategies to amplify the coding potential of their condensed genetic information. Leaky stop codons may be readthrough to produce either the predicted translation product, or at a very low level an extended “read-through” protein. Overlapping (e.g. –UAAUG-; -UGAUG-; AUGA-), or highly proximal stop/start codons may give rise to termination accompanied by a low level of re-initiation. There are a number of cases where a single mRNA is translated into more than one protein by recoding, where the rules for decoding are altered through specific sites and signals in the mRNA such as frameshifting and readthrough. Ribosomal “skipping”, first identified in the foot-and-mouth disease virus (FMDV), represents yet another translational trick to deliver multiple gene products from limited primary sequence. Briefly, when a ribosome encounters 2A within an open reading frame (ORF), the synthesis of a specific peptide bond is “skipped”. The process gives rise to two alternative outcomes: either (i) translation terminates at the end of 2A, or (ii) translation of the downstream sequence occurs. In this manner discrete translation products can be synthesized from a single ORF (for in-depth reviews of recoding see Atkins & Gesteland, 2010).
A monoclonal anti-mouse LFA-1 alpha antibody mimics the biological effects of B cell stimulatory factor-1 (BSF-1). (1986)

This study describes the generation of a monoclonal mouse x rat antibody (G-48) that recognizes a determinant on the serologically defined LFA-1 alpha-chain. It immunoprecipitates two noncovalently associated polypeptides of 176,000 and 95,000 Mr respectively from lysates of radioiodinated BCL1 cells, T cells, and B cells. G-48 mimics the biological actions of BSF-1 by inducing increased levels of Ia antigen expression on resting B cells, augmenting the proliferation of anti-delta-stimulated B cells, and in insolubilized form, inducing IgG1 secretion by LPS-activated B cells. G-48 does not have BCDF mu, BCGF II, nor IL 2 activity. These results demonstrate that LFA-1 plays an important role in B cell activation, proliferation, and differentiation.
The Cognitive Neuroscience of Music (2003)

Music offers a unique opportunity to understand better the organization of the human brain. Like language, music exists in all human societies. Like language, music is a complex, rule-governed activity that seems specific to humans, and associated with a specific brain architecture. Yet unlike most other high-level functions of the human brain — and unlike language — music is a skill at which only a minority of people become proficient. The study of music as a major brain function has for some time been relatively neglected. Just recently, however, we have witnessed an explosion in research activities on music perception and performance and their correlates in the human brain. This volume brings together a collection of authorities — from the fields of music, neuroscience, psychology, and neurology — to describe the advances being made in understanding the complex relationship between music and the brain. It is a book that will lay the foundations for a cognitive neuroscience of music.
Online Raman spectroscopy for bioprocess monitoring (2005)

Online monitoring of bioprocesses is essential to expanding the potential of biotechnology. In this thesis, a system to estimate concentrations of chemical components of an Escherichia Coli fermentation growth medium via a remote fiber-optic Raman spectroscopy probe was studied in depth. The system was characterized to determine sources of instability and systematic error. A complete first-order error analysis was conducted to determine the theoretical sensitivity of the instrument. A suite of improvements and new features, including an online estimation of optical density and biomass, a method to correct for wavelength shifts, and a setup to increase repeatability and throughput for offline and calibration methods was developed accordingly. The theoretical and experimental ground work for developing a correction for spectrum distortions caused by elastic scattering, a fundamental problem for many spectroscopic applications, was laid out. In addition, offline Raman spectroscopy was used to estimate concentrations of fructose, glucose, sucrose, and nitrate in an oil palm (Elais guineensis) bioreaction. Finally, an expansion
Leukoaraiosis (2003)

Leukoaraiosis shares with stroke common pathophysiological mechanisms and, because it is likely an expression of the same disease, must be regarded as an intermediate surrogate of stroke rather than a true stroke risk factor.
Real-time tracking of non-rigid objects using mean shift (2002)

A new method for real time tracking of non-rigid objects seen from a moving camera is proposed. The central computational module is based on the mean shift iterations and finds the most probable target position in the current frame. The dissimilarity between the target model (its color distribution) and the target candidates is expressed by a metric derived from the Bhattacharyya coefficient. The theoretical analysis of the approach shows that it relates to the Bayesian framework while providing a practical, fast and efficient solution. The capability of the tracker to handle in real time partial occlusions, significant clutter, and target scale variations, is demonstrated for several image sequences.
Polymer Alloys of Nodax Copolymers and Poly(lactic acid) (2004)

Properties of polymer alloys comprising poly(lactic acid) and Nodax copolymers are investigated. Nodax is a family of bacterially produced polyhydroxyalkanoate (PHA) copolymers comprising 3-hydroxybutyrate (3HB) and other 3-hydroxyalkanoate (3HA) units with side groups greater than or equal to three carbon units. The incorporation of 3HA units with medium-chain-length (mcl) side groups effectively lowers the crystallinity and the melt temperature, Tm, of this class of PHA copolymers, in a manner similar to that of alpha olefins controlling the properties of linear low density polyethylene. The lower Tm makes the material easier to process, as the thermal decomposition temperature of PHAs is then relatively low. The reduced crystallinity provides the ductility and toughness required for many plastics applications. When a small amount of ductile PHA is blended with poly(lactic acid) (PLA), a new type of polymer alloy with much improved properties is created. The toughness of PLA is substantially increased without a reduction in the optical clarity of the blend. The synergy between the two materials, both produced from renewable resources, is attributed to the retardation of crystallization of PHA copolymers finely dispersed in a PLA matrix as discrete domains.
Advances in Radiation Therapy: Conventional to 3D, to IMRT, to 4D, and Beyond (2005)

Modern advances in computers have fueled parallel advances in imaging technologies. The improvements in imaging have in turn allowed a higher level of complexity to be incorporated into radiotherapy treatment planning systems. As a result of these changes, the delivery of radiotherapy evolved from therapy designed based primarily on plain (two dimensional) x-ray images and hand calculations to three-dimensional x-ray based images incorporating increasingly complex computer algorithms. More recently, biologic variables based on differences between tumor metabolism, tumor antigens, and normal tissues have been incorporated into the treatment process. In addition, greater awareness of the challenges to the accuracy of the treatment planning process, such as problems with set-error and organ movement, have begun to be systematically addressed, ushering in an era of so-called Four-Dimensional Radiotherapy. This review article discusses how these advances have changed the way the most common neoplasms are treated now and will be treated in the near future.
Stabilin-1 expression defines a subset of macrophages that mediate tissue homeostasis and prevent fibrosis in chronic liver injury (2016)

Macrophages are key regulators of fibrosis development and resolution. Elucidating the mechanisms by which they mediate this process is crucial for establishing their therapeutic potential. Here, we use experimental models of liver fibrosis to show that deficiency of the scavenger receptor, stabilin-1, exacerbates fibrosis and delays resolution during the recovery phase. We detected a subset of stabilin-1(+) macrophages that were induced at sites of cellular injury close to the hepatic scar in mouse models of liver fibrosis and in human liver disease. Stabilin-1 deficiency abrogated malondialdehyde-LDL (MDA-LDL) uptake by hepatic macrophages and was associated with excess collagen III deposition. Mechanistically, the lack of stabilin-1 led to elevated intrahepatic levels of the profibrogenic chemokine CCL3 and an increase in GFAP(+) fibrogenic cells. Stabilin-1(-/-) macrophages demonstrated a proinflammatory phenotype during liver injury and the normal induction of Ly6C(lo) monocytes during resolution was absent in stabilin-1 knockouts leading to persistence of fibrosis. Human stabilin-1(+) monocytes efficiently internalized MDA-LDL and this suppressed their ability to secrete CCL3, suggesting that loss of stabilin-1 removes a brake to CCL3 secretion. Experiments with cell-lineage-specific knockouts revealed that stabilin-1 expression in myeloid cells is required for the induction of this subset of macrophages and that increased fibrosis occurs in their absence. This study demonstrates a previously unidentified regulatory pathway in fibrogenesis in which a macrophage scavenger receptor protects against organ fibrosis by removing fibrogenic products of lipid peroxidation. Thus, stabilin-1(+) macrophages shape the tissue microenvironment during liver injury and healing.
Akt activity in Alzheimer’s disease and other neurodegenerative disorders (2004)

Enzyme activities of the serine/threonine kinase Akt were compared in mid-temporal and mid-frontal cortices from Alzheimer's disease cases and matched controls. Activities (GSK-3alpha/beta fusion protein phosphorylation by immunoprecipitated Akt) were significantly increased in temporal cortex soluble fractions from Alzheimer's disease compared with non-disease controls and positive disease controls with another neurodegenerative disease. Temporal cortex soluble fraction Akt activities positively correlated with Braak staging for neurofibrillary changes. Frontal cortex soluble fraction activities were significantly reduced in positive disease compared with Alzheimer's disease cases and non-disease controls. Strong Ser Akt immunoreactivity was seen in Alzheimer's disease pyramidal neurons likely undergoing degeneration and in reactive astroglia. Non-disease and positive disease controls showed moderate Ser Akt immunostaining of occasional pyramidal neurons.
Binding and endocytosis of cluster glycosides by rabbit hepatocytes. Evidence for a short-circuit pathway that does not lead to degradation. (1982)

Synthetic cluster glycosides containing either one, two, or three galactosyl or lactosyl residues per ligand were used to test the effect of carbohydrate clustering on binding by the rabbit hepatic Gal/GalNAc-binding lectin using either isolated rabbit hepatocytes or the solubilized, affinity-purified lectin. The tris- and bis-glycosides were superior to the mono-glycosides for inhibition of 125I-asialoorosomucoid binding to rabbit hepatocytes at 0 degrees C. The concentrations of the tris-glycosides required for 50% inhibition of 125I-asialoorosomucoid binding (4-8 microM) to hepatocytes were 50-100 times lower than the concentrations of the corresponding mono-glycosides required for 50% inhibition (400-500 microM). The isolated lectin, however, did not effectively discriminate between the mono-, bis-, and tris-glycosides, possibly indicating an organizational difference between the lectin in the cell membrane and the isolated lectin. When the cluster glycosides were labeled with 125I-tyrosine, it was shown that the tris- and bis-galactosides were bound to the hepatocytes at 37 degrees C, and that binding was followed by a step that led to ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid resistance, probably internalization. The process could be specifically inhibited by the neoglycoprotein Gal44-AI-bovine serum albumin, or by IgG specific for the hepatic lectin, but not by preimmune IgG. Internalization of the cluster glycosides did not lead to accumulation of ligand inside the cell, nor to degradation. Instead, the ligands were quickly released from the cells.
14-3-3 Proteins Mediate an Essential Anti-apoptotic Signal (2001)

The 14-3-3 proteins are a family of highly conserved eukaryotic regulatory molecules that play important roles in many biological processes including cell cycle control and regulation of cell death. They are able to carry out these effects through binding and modulating the activity of a host of signaling proteins. The ability of 14-3-3 to inhibit Bad and other proapoptotic proteins argues that 14-3-3 can support cell survival. To examine this issue in a global sense, a specific inhibitor of 14-3-3/ligand interactions, difopein, was used. Difopein expression led to induction of apoptosis. Studies using various components of survival and death signaling pathways were consistent with a vital role for 14-3-3/ligand interactions in signal transduction from upstream pro-survival kinases to the core apoptotic machinery. Because these kinases often become activated during oncogenesis, the effect of difopein on cell death induced by antineoplastic drugs was examined. It was found that difopein enhances the ability of cisplatin to kill cells. These data support the model that 14-3-3, through binding to Bad and other ligands, is critical for cell survival signaling. Inhibition of 14-3-3 may represent a useful therapeutic target for treatment of cancer and other diseases involving inappropriate cell survival.
Isolation of a New Polysaccharide-Digesting Bacterium from a Salt Marsh (1988)

A new marine bacterium that digested a variety of storage and structural polysaccharides, including agar, was isolated. Strain 2-40 is a nonfermentative gram-negative, polarly flagellated rod that sometimes grew as a filamentous helix and secreted a melaninlike pigment. Its characteristics conform to those of no previously described species.
Inhibition of activation-induced programmed cell death and restoration of defective immune responses of HIV+ donors by cysteine protease inhibitors. (1994)

In vitro activation of PBLs from HIV+ individuals resulted in programmed cell death (PCD) within 2 days in 58 of 95 HIV+ blood donors, in contrast to only two of 30 control HIV- donors. CD4+ and CD8+ T cells from HIV+ donors died under these conditions, and these cells showed apoptotic nuclear morphology and DNA fragmentation. To test the hypothesis that this cell death shares a common biochemical pathway with that induced by TCR cross-linking in normal dividing T cells, inhibitors of the calcium-activated cysteine protease calpain were tested for their ability to block the activation-induced PCD of HIV+ donors. The E-64 (epoxysuccinyl) class of cysteine protease inhibitors gave 40% to 60% inhibition of HIV+ PCD responses, while the aldehyde inhibitors, leupeptin and calpain inhibitor II, gave 60% to 67% inhibition. The involvement of this calpain-dependent death pathway in HIV-induced functional T helper cell deficiency was tested by examining the effect of calpain inhibitors on the defective Ag- and mitogen-dependent proliferative responses of HIV+ donors. Twenty to fifty percent of such defective responses were significantly restored toward normal levels by calpain inhibitors, whereas control responses by normal donors were largely unaffected. These data suggest that a calpain-dependent PCD pathway contributes to HIV-associated immunodeficiency and suggest the use of calpain inhibitors as a possible route to therapy of HIV infection.
Atomic force microscopy using single-wall C nanotube probes (2002)

We examine the factors that govern the stability and resolution of atomic force microscopy (AFM) using single-wall C nanotubes as imaging probes. Nonvertical alignment of the nanotubes with respect to the sample surface causes such probes to bend in response to the surface–nanotube interaction forces during imaging. For long nanotubes this bending response causes the nanotube tip to jump into contact with the surface and renders it unsuitable for imaging. For short nanotubes, stable noncontact-mode imaging can be achieved using a small cantilever vibration amplitude. In such cases it is possible to achieve lateral resolution that is comparable to the diameter of the nanotube.