gebhart/patrepeval huggingface dataset:
Sniffing out the Truth: Clinical Diagnosis Using the Electronic Nose (2000)

Recently the use of smell in clinical diagnosis has been rediscovered due to major advances in odour sensing technology and artificial intelligence (AI). It was well known in the past that a number of infectious or metabolic diseases could liberate specific odours characteristic of the disease stage. Later chromatographic techniques identified an enormous number of volatiles in human clinical specimens that might serve as potential disease markers. "Artificial nose" technology has been employed in several areas of medical diagnosis, including rapid detection of tuberculosis (TB), Helicobacter pylori (HP) and urinary tract infections (UTI). Preliminary results have demonstrated the possibility of identifying and characterising microbial pathogens in clinical specimens. A hybrid intelligent model of four interdependent "tools", odour generation "kits", rapid volatile delivery and recovery systems, consistent low drift sensor performance and a hybrid intelligent system of parallel neural networks (NN) and expert systems, have been applied in gastric, pulmonary and urine diagnosis. Initial clinical tests have shown that it may be possible in the near future to use electronic nose technology not only for the rapid detection of diseases such as peptic ulceration, UTI, and TB but also for the continuous dynamic monitoring of disease stages. Major advances in information and gas sensor technology could enhance the diagnostic power of future bio-electronic noses and facilitate global surveillance models of disease control and management.
Culture of human nasal epithelial cells on collagen matrix supports. A comparison of bioelectric properties of normal and cystic fibrosis epithelia. (1985)

The feasibility of culturing human nasal epithelial cells was tested by plating on permeable collagen matrices primary isolates of epithelial cells from normal (n = 21) and atopic (n = 5) subjects and from subjects with cystic fibrosis (CF) (n = 13). The cells were cultured in serum-free, hormone-supplemented medium for 5 days followed by maintenance in conditioned medium with 1% serum. A transepithelial electric potential difference (PD) exceeding 1.0 mV developed in most preparations (71%). The PD reached a peak by Day 10 and declined slowly thereafter. The maximal PD of CF epithelia (-32.4 +/- 5.8 mV, n = 9) on collagen matrices exceeded that of normal (-11.3 +/- 1.8 mV, n = 15) and atopic (-13.5 +/- 2.5, n = 5) epithelia. The maximal PD for both CF and normal cultures exceeded that of freshly excised preparations. This difference reflected higher transepithelial resistance of cultures as compared with intact preparations. The efficacy of amiloride (10(-4) M) to reduce the PD was greater in cultures of CF epithelia (-85 +/- 4.6%, n = 7) than it was in cultures of normal (-45.5 +/- 5.0%, n = 11) and atopic (-50.5 +/- 2.9%, n = 5) epithelia, whereas the hyperpolarization induced by replacement of Cl- in the apical bath was smaller for CF cultures (5.9 +/- 1.5 mV) than it was for normal (9.3 +/- 0.9 mV) and atopic (8.8 +/- 0.5 mV) cultures. We conclude that nasal epithelial cells will form high resistance barriers when cultured on collagen matrices.(ABSTRACT TRUNCATED AT 250 WORDS)
Laryngopharyngeal Dysfunction From the Implant Vagal Nerve Stimulator (2003)

Patients in whom a vagal nerve stimulator is placed can have adverse side effects. These can be related to the surgical manipulation of the vagus nerve, resulting in a temporary paresis of the vocal folds. A second set of side effects is related to the actual electrical stimulation of the device, and these side effects can directly affect the laryngeal musculature.
Neutralization of Biological Activity and Inhibition of Receptor Binding by Antibodies Against Human Thrombopoietin (1998)

Thrombopoietin (TPO) is a recently isolated cytokine that primarily regulates megakaryocytopoiesis and thrombopoiesis. We recently reported the development of a variety of antibodies (Abs) to synthetic peptides of human (h)TPO and to recombinant human TPO (rhTPO). In this study, we characterized the Abs and mapped immunologically distinct areas of the molecule. Among the five different antipeptide polyclonal Abs, only one, raised against synthetic peptide D8 to Q28, neutralized the TPO-dependent growth of FDCP-2 cells expressing human Mpl (FDCP-hMpl5 cells). One out of seven anti-rhTPO monoclonal Abs, designated as TN1, also showed neutralizing activity. TN1 was found to be specifically reactive with two proteolytic fragments, residues S1 to R117 and A60 to K122 of hTPO, indicating that the epitope(s) of TN1 is localized in residues A60 to R117 of the molecule. These two neutralizing Abs inhibited the binding of biotinylated rhTPO to FDCP-hMpl5 cells. On the other hand, the other Abs, which reacted with five polypeptides of S47 to D62, L108 to A126, N172 to A190, S262 to T284, and P306 to G332 of hTPO, did not show either the neutralizing activity or the ability to inhibit the binding of biotinylated rhTPO to the cell surface hMpl. These findings indicate that two regions, residues D8 to Q28 and A60 to R117 of hTPO, may contain the domains associated with its receptor, C-Mpl. These Abs characterized here are valuable for studying the structural analysis and the biological function of hTPO mediated by its receptor.
Correlation of spectral luminescence with threading dislocations in green-light-emitting InGaN quantum wells (2007)

A direct correlation has been established between the spatial variation of spectral luminescence and the distribution of threading dislocations in a green-light-emitting InGaN quantum well structure grown on a sapphire substrate. Transmission electron microscopy and monochromatic cathodoluminescence images, taken from the same region, indicate that the nature of the quantum well emission is influenced by the microstructure of the underlying GaN. The microstructure is defined by threading dislocations that reflect a columnar structure with low-angle grain boundaries. A strong correlation is observed between this microstructure and the peak and low-energy portion of the quantum well luminescence, with threading dislocations as boundaries between bright and darker regions. The high-energy portion of the luminescence is localized and is generally complementary to the rest of the spectrum.
The Chemoattractant Receptor-like Protein C5L2 Binds the C3a des-Arg77/Acylation-stimulating Protein (2003)

The orphan receptor C5L2 has recently been described as a high affinity binding protein for complement fragments C5a and C3a that, unlike the previously described C5a receptor (CD88), couples only weakly to G(i)-like G proteins (Cain, S. A., and Monk, P. N. (2002) J. Biol. Chem. 277, 7165-7169). Here we demonstrate that C5L2 binds the metabolites of C4a and C3a, C4a des-Arg(77), and C3a des-Arg(77) (also known as the acylation-stimulating protein or ASP) at a site distinct from the C5a binding site. The binding of these metabolites to C5L2 does not stimulate the degranulation of transfected rat basophilic leukemia cells either through endogenous rat G proteins or when co-transfected with human G(alpha 16). C3a des-Arg(77)/ASP and C3a can potently stimulate triglyceride synthesis in human skin fibroblasts and 3T3-L1 preadipocytes. Here we show that both cell types and human adipose tissue express C5L2 mRNA and that the human fibroblasts express C5L2 protein at the cell surface. This is the first demonstration of the expression of C5L2 in cells that bind and respond to C3a des-Arg(77)/ASP and C3a. Thus C5L2, a promiscuous complement fragment-binding protein with a high affinity site that binds C3a des-Arg(77)/ASP, may mediate the acylation-stimulating properties of this peptide.
NTRK1 fusions for the therapeutic intervention of Korean patients with colon cancer (2015)

The identification and clinical validation of cancer driver genes are essential to accelerate the translational transition of cancer genomics, as well as to find clinically confident targets for the therapeutic intervention of cancers. Here we identified recurrent LMNA-NTRK1 and TPM3-NTRK1 fusions in Korean patients with colon cancer (3 out of 147, 2%) through next-generation RNA sequencing (RNA-seq). NTRK1 fusions were mutually exclusive oncogenic drivers of colon cancer that were accompanied with in vitro potential of colony formation and in vivo tumorigenicity comparable to KM12, a human colon cancer cell line harboring TPM3-NTRK1 fusion. NTRK1-encoded TrkA protein was prevalent in 11 out of 216 Korean (5.1%) and 28 out of 472 Chinese patients (5.9%) from independent cohorts, respectively. The expression level of TrkA was significantly correlated with NTRK1 fusion (p = 0.0192), which was verified by a fluorescence in situ hybridization (FISH). Korean patients with TrkA-positive colon cancer had a marginal but significant shorter overall survival time than TrkA-negative colon cancer [hazard ratio (HR) = 0.5346, 95% confidential interval (CI) = 0.2548-0.9722, p = 0.0411]. In addition, KM12 cell line was sensitive to selective TrkA inhibitors. These results demonstrate that NTRK1 fusion is granted as a clinically relevant target for therapeutic intervention of colon cancer.
Human lymphocytes with either the OKT4 or OKT8 phenotype produce interleukin 2 in culture. (1982)

In this study, we demonstrate that both highly purified T4+ and T8+ lymphocytes can produce substantial amounts of Interleukin 2(IL 2) when stimulated with the combination of concanavalin A (Con A) and phorbol myristate acetate. Furthermore, addition of IL 1 to macrophage-depleted T lymphocytes significantly increased IL 2 production by lymphocytes of either the T4+ or T8+ phenotype. These findings provide a basis for further studies of the molecular mechanisms involved in human immune cell interactions.
Cell Damage in the Brain: A Speculative Synthesis (1981)

All cells in living organisms have a limited life span, and when the time set by their biological clocks has run out, they will die , their highly orga­ nized macromolec ular structure will disintegrate, and the low-molec ul ar degrad ation products be­ come part of the disorder of the surroundings . In thermodynamic terms, this series of events consti­ tutes what has been c alled the entropic doom. We know little about those molec ul ar mechanisms that limit the life span of cells in the absence of dise ase. For the clinician, therefore, the important task is to prevent or tre at dise ases that jeopardize the proper functioning and viability of cells whose biologic al clocks have not yet run out . Measures instituted to prevent brain cell death have a special importance . This i s partly due t o the fact that w e equate human life with the functioning of the brain. However, this importance also resides in the v ulnerability of brain cells to conditions that allow cells of most other tissue to survive , and to continue or res ume their activitie s . The clinically most important conditions leading to brain cell death are those associated with cere­ brovascul ar dise ase, particularly stroke, and with head trauma. We will begin, though, by rec alling the traditional view of the occ urrence and loc alization of neuronal damage in four conditions that lead to more disseminated alterations, e specially since they have been considered to c ause nerve cell injury of a
Reshaping Human Antibodies: Grafting an Antilysozyme Activity (1988)

The production of therapeutic human monoclonal antibodies by hybridoma technology has proved difficult, and this has prompted the "humanizing" of mouse monoclonal antibodies by recombinant DNA techniques. It was shown previously that the binding site for a small hapten could be grafted from the heavy-chain variable domain of a mouse antibody to that of a human myeloma protein by transplanting the hypervariable loops. It is now shown that a large binding site for a protein antigen (lysozyme) can also be transplanted from mouse to human heavy chain. The success of such constructions may be facilitated by an induced-fit mechanism.
A Tutorial on Graph-Based SLAM (2010)

Being able to build a map of the environment and to simultaneously localize within this map is an essential skill for mobile robots navigating in unknown environments in absence of external referencing systems such as GPS. This so-called simultaneous localization and mapping (SLAM) problem has been one of the most popular research topics in mobile robotics for the last two decades and efficient approaches for solving this task have been proposed. One intuitive way of formulating SLAM is to use a graph whose nodes correspond to the poses of the robot at different points in time and whose edges represent constraints between the poses. The latter are obtained from observations of the environment or from movement actions carried out by the robot. Once such a graph is constructed, the map can be computed by finding the spatial configuration of the nodes that is mostly consistent with the measurements modeled by the edges. In this paper, we provide an introductory description to the graph-based SLAM problem. Furthermore, we discuss a state-of-the-art solution that is based on least-squares error minimization and exploits the structure of the SLAM problems during optimization. The goal of this tutorial is to enable the reader to implement the proposed methods from scratch.
Electric Double Layer Capacitance Performance of Porous Carbons Prepared by Defluorination of Polytetrafluoroethylene with Potassium (2002)

Porous carbons (Brunauer-Emmett-Teller surface area prepared by defluorination of polytetrafluoroethylene (PTFE) powder with potassium metal showed a very high capacitance of the electrical double layer (229 F/g). Such a high value is considered to be due not only to the contribution of microporosity, but also to the development of mesoporosity. When the original PTFE was subjected to γ-ray irradiation to reduce the polymerization degree, the carbon obtained in the same procedure showed only a slightly higher value (237 F/g). The relationship between the capacitance and pore size was discussed by taking into consideration the results for conventional activated carbon fibers. © 2002 The Electrochemical Society. All rights reserved.
Polysilicon films of high photoresponse, obtained by vacuum annealing of aluminum capped hydrogenated amorphous silicon (1995)

Hydrogenated amorphous silicon (a-Si:H) films having a thickness of 7 μm were deposited on molybdenum by dc glow discharge and then capped with a 0.1-μm-thick aluminum (Al) layer by thermal evaporation. Subsequent vacuum annealing at 500–725 °C resulted in the formation of crystalline Si, as observed by Raman scattering and x-ray diffraction. This was in contrast to the uncapped a-Si:H films which were still amorphous at the same annealing temperatures, except at ≳700 °C. That the Al capped films were crystalline caused a ten-fold increase in the dark conductivity in comparison to the uncapped film annealed at the same temperature. The capped films annealed at 500 °C showed a photoresponse (the ratio of the photoconductivity to dark conductivity) of 30, a photoconductivity of 2×10−4 (Ω cm)−1, and a carrier diffusion length of 5.3 μm—values much higher than those of the uncapped films (heated or not). This was due to a large grain size combined with the retention of hydrogen, which passivated the grain boundaries. On the other hand, a significant loss of hydrogen from the capped film at 580 °C, as observed by in situ evolved gas analysis, resulted in the diffusion length reducing to 1.8 μm and ten-fold decreases of the photoconductivity and photoresponse. All three parameters increased slightly with a further increase in the annealing temperature from 600 to 680 °C, due to the increase in the grain size. At 695 °C, further hydrogen evolution caused a sharp decrease in the values of these parameters.
DNA vaccines : methods and protocols (2006)

In the early 1990s, almost 200 yr after Edward Jenner demonstrated the effectiveness of the smallpox vaccine, a new paradigm for vaccination emerged. The conventional method of vaccination required delivery of whole pathogens or structural subunits, but in this new approach, DNA or genetic information was administered to elicit an immunological response. Once it was observed that plasmid DNA delivered in vivo led to production of an encoded transgene (1), two ground-breaking studies demonstrated that immunological responses could be generated against antigenic transgenes via plasmid DNA delivered by DNA vaccination (as this approach is called) (2,3). The appe- ance of this new vaccination strategy coincided with advances in molecular biology, which provided new tools to study and manipulate the basic elements of an organism’s genome and also could also be applied to the design and production of DNA vaccines. DNA Vaccines is a major updated and enhancement of the first edition. It reviews state-of-the-art methods in DNA vaccine technology, with chapters describing DNA vaccine design, delivery systems, adjuvants, current appli- tions, methods of production, and quality control. Consistent with the approach of the Methods in Molecular Medicine series, these chapters contain detailed practical procedures on the latest DNA vaccine technology. The enthusiasm for DNA vaccine technology is made clear by the number of research studies published on this topic since the mid-1990s
Distilling Free-Form Natural Laws from Experimental Data (2009)

For centuries, scientists have attempted to identify and document analytical laws that underlie physical phenomena in nature. Despite the prevalence of computing power, the process of finding natural laws and their corresponding equations has resisted automation. A key challenge to finding analytic relations automatically is defining algorithmically what makes a correlation in observed data important and insightful. We propose a principle for the identification of nontriviality. We demonstrated this approach by automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula. Without any prior knowledge about physics, kinematics, or geometry, the algorithm discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation. The discovery rate accelerated as laws found for simpler systems were used to bootstrap explanations for more complex systems, gradually uncovering the "alphabet" used to describe those systems.
Comparison of expression systems in the yeasts Saccharomyces cerevisiae, Hansenula polymorpha, Klyveromyces lactis, Schizosaccharomyces pombe and Yarrowia lipolytica. cloning of two novel promoters from Yarrowia lipolytica (1998)

We have compared expression systems based on autonomously replicating vectors in the yeasts Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Hansenula polymorpha and Yarrowia lipolytica in order to identify a more suitable host organism for use in the expression cloning method (Dalbøge and Heldt-Hansen, 1994) in which S. cerevisiae has traditionally been used. The capacity of the expression systems to secrete active forms of six fungal genes encoding the enzymes galactanase, lipase, polygalacturonase, xylanase and two cellulases was examined, as well as glycosylation pattern, plasmid stability and transformation frequency. All of the examined alternative hosts were able to secrete more active enzyme than S. cerevisiae but the relative expression capacity of the individual hosts varied significantly in a gene-dependent manner. One of the most attractive of the alternative host organisms, Y. lipolytica, yielded an increase which ranged from 4·5 times to more than two orders of magnitude. As the initially employed Y. lipolytica XPR2 promoter is unfit in the context of expression cloning, two novel promoter sequences for highly expressed genes present in only one copy on the genome were isolated. Based on sequence homology, the genes were identified as TEF, encoding translation elongation factor-1α and RPS7, encoding ribosomal protein S7. Using the heterologous cellulase II (celII) and xylanase I (xylI) as reporter genes, the effect of the new promoters was measured in qualitative and quantitative assays. Based on the present tests of the new promoters, Y. lipolytica appears as a highly attractive alternative to S. cerevisiae as a host organism for expression cloning. GenBank Accession Numbers: TEF gene promoter sequence: AF054508; RPS7 gene promoter sequence: AF054509. © 1998 John Wiley & Sons, Ltd.
Molecular Methods for the Identification of Apoptosis in Tissues (1994)

There has been an upsurge in the interest paid to the process of apoptosis in recent years as a consequence of the realization that apoptosis is important in the regulation of cell number in normal tissues and in a wide variety of diseases. However, the methods used to identify apoptosis in tissues have not progressed. In this review, the development of novel methods for the identification of apoptosis in histological material is discussed. These methods rely on the degradation of DNA that is seen in apoptotic cells and that can be labeled by the incorporation of a biotinylated nucleotide, followed by an enzyme histochemical demonstration method. The problems inherent in the use of these techniques are discussed, particularly relating to situations other than apoptosis where degraded DNA will occur. These methods will prove to be a useful adjunct to morphological examination for the identification and quantification of apoptosis. (The J Histotechnol 17:261, 1994)
P4‐214: IDENTIFICATION OF NOVEL SMALL‐MOLECULE TAU AGGREGATION INHIBITORS FOR TREATMENT OF TAUOPATHIES (2014)

Accumulation of intraneuronal neurofibrillary tangles composed of pathological tau fibrils is the hallmark pathology of Alzheimer's disease (AD) and related tauopathies. Targeting abnormally aggregated tau has emerged as one of the promising therapeutic strategies for treatment of AD and other tauopathies. ProteoTech Inc. (ProteoTech) has designed, and synthesized a unique small molecule library that specifically targets misfolded proteins and amyloid diseases. From this library, we initially screened more than 150 compounds for tau aggregation inhibitors using various in vitro techniques. These studies led to the discovery of at least five potent inhibitors that effectively inhibit formation of beta-sheet-containing tau aggregates and disrupt preformed tau fibrils. To select potent tau aggregation inhibitors that are effective for various tau isoforms, and also possess good drugability, we compared the top compounds for their in vitro inhibitory potencies on different tau proteins using Thioflavin S fluorometry and circular dichroism spectroscopy. We also evaluated the top compounds for CYP450 inhibition using fluorescence-based screenings, and pharmacokinetic (PK) profiles and brain penetration after peripheral administration of each compound at 50 mg/kg, followed by HPLC/MS bio-analysis. Preliminary results demonstrate that our top compounds have robust inhibitory activity on both four-repeat (4R), and three-repeat tau proteins (both isoforms are present in the AD brain at mixed ratios). In addition, the top compounds also potently inhibit aggregation of a mutant Cys-free 4R tau, suggesting that the compounds target the tau protein through a Cys-independent mechanism. Preliminary results from PK and brain penetration studies demonstrate that select top compounds also have good drugability characteristics, including reasonable bioavailability and brain exposure. ProteoTech has identified at least five top lead compounds that possess robust potency against aggregation of various tau proteins in vitro. The results of drugability profiles will help us to select the best compounds for testing in tau transgenic mouse models for their in vivo efficacy as tau aggregation inhibitors for treatment of AD and other tauopathies.