gebhart/patrepeval huggingface dataset:
Nucleotide sequence of the triose phosphate isomerase gene of Saccharomyces cerevisiae. (1982)

The gene coding for the glycolytic enzyme triose phosphate isomerase (TPI1) was isolated from a yeast library in the shuttle vector pYE13. Selecting for a deletion mutant of the plasmid which enhances expression of the otherwise dormant yeast gene in E. coli facilitated the identification of the coding region. The DNA sequences of the wild type and mutant genes were determined by chemical methods. The 5' flanking region of the wild-type TPI1 resembles the analogous regions of the yeast genes coding for two other glycolytic enzymes. The sequence of the deletion mutant indicates that, upstream from -65 in the 5' flanking region, 3.3 kilobases have been lost from entirely within the yeast insert. The mutation reduces enzyme activity by tenfold in yeast, and its implications for the expression of the gene in yeast and E. coli are discussed. The amino acid sequence deduced from the nucleotide order is consistent with the electron density map of the protein as well as the sequence of its N-terminal 16 amino acids and amino acid composition. The amino acid sequence is approximately 50% homologous with the triose phosphate isomerases from rabbit, chicken, and coelacanth and 37% homologous with the Bacillus stearothermophilus enzyme. Residues which are thought to be catalytically important are conserved.
Identification of Salmonella typhimurium Genes Required for Colonization of the Chicken Alimentary Tract and for Virulence in Newly Hatched Chicks (1998)

From a collection of 2,800 Tn5-TC1 transposon mutants of Salmonella typhimurium F98, 18 that showed reduced intestinal colonization of 3-week-old chicks were identified. The sites of transposon insertion were determined for most of the mutants and included insertions in the lipopolysaccharide biosynthesis genes rfaK, rfaY, rfbK, and rfbB and the genes dksA, clpB, hupA, and sipC. In addition, identification was made of an insertion into a novel gene that encodes a protein showing similarity to the IIC component of the mannose class of phosphoenolpyruvate-carbohydrate phosphotransferase systems, which we putatively called ptsC. Transduction of most of the transposon mutations to a fresh S. typhimurium F98 genetic background and construction of defined mutations in the rfbK, dksA, hupA, sipC, and ptsC genes of S. typhimurium F98 supported the role in colonization of all but the pts locus. The virulence of the rfbK, dksA, hupA, sipC, and ptsC defined mutants and clpB and rfaY transductants in 1-day-old chicks was tested. All but the ptsC and rfaY mutants were attenuated for virulence. A number of other phenotypes associated with some of the mutations are described.
Accell particle-mediated DNA immunization elicits humoral, cytotoxic, and protective immune responses. (1994)

Accell particle-mediated gene delivery technology was employed for the intracellular delivery of antigen-encoding expression vectors in epidermal tissues in laboratory animals. Delivery of plasmid DNA-coated gold microparticles using the Accell gene delivery system resulted in de novo antigen expression in epidermal cells that stimulated the induction of antigen-specific humoral and cytotoxic cellular immune responses. Optimal DNA delivery conditions favoring maximal humoral responses required the delivery of 5 x 10(7) micron-sized gold particles containing 300 plasmid copies per particle (80 ng of vector total) into a 4-cm2 area of abdominal skin. Comparison of immune responses between animals that received intramuscular injections of relatively large quantities of vector DNA (100 micrograms) and those that received intracellular deliveries of submicrogram quantities of the same DNA to the epidermis demonstrated that the latter approach was considerably more effective at eliciting strong humoral responses. In addition, cytotoxic cellular immune responses were elicited to HIV-1 gp120 following epidermal delivery of HIV-1 gp160 or gp120 expression constructs. A qualitative shift from predominantly cytotoxic cellular to predominantly humoral immune responses with continued immunization indicated the potential for optimizing delivery conditions to favor specifically one type of response over the other.
What do color changes reveal about an outdoor scene? (2008)

In an extended image sequence of an outdoor scene, one observes changes in color induced by variations in the spectral composition of daylight. This paper proposes a model for these temporal color changes and explores its use for the analysis of outdoor scenes from time-lapse video data. We show that the time-varying changes in direct sunlight and ambient skylight can be recovered with this model, and that an image sequence can be decomposed into two corresponding components. The decomposition provides access to both radiometric and geometric information about a scene, and we demonstrate how this can be exploited for a variety of visual tasks, including color-constancy, background subtraction, shadow detection, scene reconstruction, and camera geo-location.
An Autonomous Wearable System for Predicting and Detecting Localised Muscle Fatigue (2011)

Muscle fatigue is an established area of research and various types of muscle fatigue have been clinically investigated in order to fully understand the condition. This paper demonstrates a non-invasive technique used to automate the fatigue detection and prediction process. The system utilises the clinical aspects such as kinematics and surface electromyography (sEMG) of an athlete during isometric contractions. Various signal analysis methods are used illustrating their applicability in real-time settings. This demonstrated system can be used in sports scenarios to promote muscle growth/performance or prevent injury. To date, research on localised muscle fatigue focuses on the clinical side and lacks the implementation for detecting/predicting localised muscle fatigue using an autonomous system. Results show that automating the process of localised muscle fatigue detection/prediction is promising. The autonomous fatigue system was tested on five individuals showing 90.37% accuracy on average of correct classification and an error of 4.35% in predicting the time to when fatigue will onset.
Increased PSGL-1 expression on granulocytes from allergic-asthmatic subjects results in enhanced leukocyte recruitment under flow conditions (2002)

Allergic asthma is increasing in incidence and severity in many industrial countries. Leukocyte recruitment into the airways of affected individuals contributes to the severity of the disease. In this study, whole blood from normal, allergic, asthmatic, or allergic-asthmatic subjects was perfused over immobilized adhesion molecules using an in vitro flow chamber system to determine if there were differences in leukocyte recruitment in these patient populations. Leukocytes from allergic-asthmatic subjects showed a threefold increase in recruitment on P-selectin as compared with normal controls. In both patient populations, the accumulated cells were exclusively neutrophils and eosinophils. Increased granulocyte recruitment was specific for P-selectin, as neither purified E-selectin nor vascular cell adhesion molecule-1 (VCAM-1) supported enhanced leukocyte recruitment from allergic-asthmatics. Leukocyte accumulation on P-selectin was completely blocked by an anti-P-selectin or anti-P-selectin glycoprotein ligand-1 (PSGL-1) monoclonal antibody. Flow cytometry revealed that neutrophils and eosinophils from allergic-asthmatic subjects had increased expression of PSGL-1, whereas expression of another adhesion molecule, L-selectin, was unchanged. PSGL-1 expression on peripheral blood mononuclear cells of allergic-asthmatic patients was unaffected. The increased PSGL-1 expression on granulocytes from allergic-asthmatic patients also led to enhanced leukocyte recruitment on interleukin-4-stimulated human umbilical vein endothelial cells, which express P-selectin and VCAM-1. Thus, increased PSGL-1 expression on granulocytes from allergic-asthmatic subjects resulted in increased leukocyte recruitment on P-selectin under flow conditions.
Phase II trial of interferon gamma and monoclonal antibody 17-1A in pancreatic cancer: biologic and clinical effects. (1990)

Thirty patients with advanced measurable pancreatic adenocarcinoma were entered onto a phase II trial with recombinant interferon gamma (Biogen, Cambridge, MA; 10(6) U/m2 daily for 4 days) and monoclonal antibody (Mab) 17-1A (Centocor, Malvern, PA; 150 mg in autologous leukocytes on days 2, 3, and 4 following interferon infusion). The effect of a single interferon gamma treatment on natural and antibody-dependent cellular cytotoxicity (ADCC), Fc receptor occupancy by antibody, and human leukocyte antigen-DR (HLA-DR) expression on monocytes and lymphocytes was also studied. Toxicity was modest and generally limited to grade I to II fever, nausea and vomiting, and hepatotoxicity. Five patients were considered to be nonassessable for response. Of the 25 assessable patients, one objective response (complete remission for a duration of 4 months) was observed. Stable disease for 2 months or greater was noted in nine patients. The median survival for the group was 5 months. Analysis of cytotoxicity data obtained prior to treatment showed reduced natural cytotoxic activity in these patients compared with normal volunteers. A significant improvement in natural cytotoxic activity to normal levels occurred within 24 hours following the interferon gamma infusion. This was also associated with augmented antibody-dependent cellular cytotoxicity. Although HLA-DR expression was not increased on either monocytes or lymphocytes, an increased capacity of both lymphocytes and monocytes to bind Mab 17-1A was observed. In all in vitro assays of ADCC, the presence of antibody excess was associated with improved cytolytic activity. In spite of the favorable modulation of cytolytic activity and improved ability of effector cells to bind Mab, we failed to demonstrated adequate clinical efficacy in the treatment of patients with pancreatic adenocarcinoma using this dose and schedule of interferon gamma and Mab 17-1A. Future trials will focus on alternate schedules of Mab 17-1A with the hope of improving tumor antigen saturation and circulating levels of infused antibody.
Laser-assisted optoporation of single cells (2002)

The plasma membrane of Chinese hamster ovary cells was made permeable using the focused beam of an argon ion laser (488 nm) and phenol red as a light absorbing dye. Small circular dark spots on the cell surface appeared immediately after laser irradiation and disappeared within about 5 min. They were related to transient changes in membrane properties, which could be visualized using the fluorescent marker laurdan, and were probably due to a local increase in temperature. According to a colony forming assay, cell viability was maintained by using light doses up to 2.5 MJ/cm(2) applied for 1 s. In addition to measurements of the efflux of the cytoplasmic marker calcein, cell transfection using a green fluorescent protein (GFP) coding plasmid was studied: brightly fluorescent GFP with an emission maximum around 510 nm was observed within part of the cells after 24 h. The transfection rates after laser irradiation were around 30% for younger subcultures and less than 10% for aging cells. This may be due to age dependent changes in the phase transition of membrane lipids from gel phase to liquid crystalline phase. High transfection rates, visual control and universality towards various cell lines are possibly the main advantages of laser-assisted optoporation in comparison with presently existing methods of cell transfection.
A multilevel banded graph cuts method for fast image segmentation (2005)

In the short time since publication of Boykov and Jolly's seminal paper [2001], graph cuts have become well established as a leading method in 2D and 3D semi-automated image segmentation. Although this approach is computationally feasible for many tasks, the memory overhead and supralinear time complexity of leading algorithms results in an excessive computational burden for high-resolution data. In this paper, we introduce a multilevel banded heuristic for computation of graph cuts that is motivated by the well-known narrow band algorithm in level set computation. We perform a number of numerical experiments to show that this heuristic drastically reduces both the running time and the memory consumption of graph cuts while producing nearly the same segmentation result as the conventional graph cuts. Additionally, we are able to characterize the type of segmentation target for which our multilevel banded heuristic yields different results from the conventional graph cuts. The proposed method has been applied to both 2D and 3D images with promising results.
SLK: A Capability System Based on Safe Language Technology (1997)

Safe language technology allows multiple protection domains to coexist within a single address space. The protection is enforced by the language system, in particular the type system, which provides unforgeable object references. This paper develops a new capability model (called the type-capability model) which relates the protection offered by safe languages to that of traditional capability systems. This model is used to show that the power of capabilities can be obtained in a safe language at low cost through a combination of link-time and run-time protection checks. The Safe Language Kernel (SLK) leverages the type-capability model to implement multiple protection domains with low-overhead fine-grain sharing in a single address space. A Java-based prototype implementation of SLK is used to describe the mechanisms available for sharing data and code. A set of micro-benchmarks demonstrates the low overhead of crossing protection domain boundaries and three server-based application studies (an extensible web server, a shared annotation system, and Active Networks) illustrate the use of SLK.
Imaging of apoptosis (programmed cell death) with 99mTc annexin V. (1999)

These data suggest that 99mTc-HYNIC annexin V can be used to image apoptotic and necrotic cell death in vivo.
High-power multimodeX-band rf pulse compression system for future linear colliders (2005)

We present a multimode $X$-band rf pulse compression system suitable for a TeV-scale electron-positron linear collider such as the Next Linear Collider (NLC). The NLC main linac operating frequency is 11.424 GHz. A single NLC rf unit is required to produce 400 ns pulses with 475 MW of peak power. Each rf unit should power approximately 5 m of accelerator structures. The rf unit design consists of two 75 MW klystrons and a dual-moded resonant-delay-line pulse compression system that produces a flat output pulse. The pulse compression system components are all overmoded, and most components are designed to operate with two modes. This approach allows high-power-handling capability while maintaining a compact, inexpensive system. We detail the design of this system and present experimental cold test results. We describe the design and performance of various components. The high-power testing of the system is verified using four 50 MW solenoid-focused klystrons run off a common 400 kV solid-state modulator. The system has produced 400 ns rf pulses of greater than 500 MW. We present the layout of our system, which includes a dual-moded transmission waveguide system and a dual-moded resonant line (SLED-II) pulse compression system. We also present data on the processing and operation of this system, which has set high-power records in coherent and phase controlled pulsed rf.
Film evaporation of a spherical droplet over a hot surface: fluid mechanics and heat/mass transfer analysis (1991)

Film evaporation of a spherical droplet over a hot surface is investigated in this paper. In view of the radial evaporation-induced velocity at the liquid-gas interface, an improvement over the classical flow field solution of Stimson &amp; Jeffery (1926) needs to be employed. In addition to the flow, the energy equation internally and externally to the droplet and the species equation in the gas phase are also solved. The boundary conditions at the droplet surface couple the temperature, species and flow field. Analytical expressions for the hydrodynamic force and its components (viscous and pressure) that the droplet experiences are obtained. It is shown that, depending on the droplet separation distance from the hot surface and the type of liquid, there may be a substantial temperature variation along the droplet surface. Furthermore, considering a quasi-steady approximation for the droplet regression rate and balancing at each time step the weight of the droplet with the hydrodynamic force it experiences, time histories are obtained numerically for various quantities of interest. Thus, it is predicted that the droplet moves away from the hot surface while evaporating and that the initially substantial temperature variation along the droplet surface decreases with time and diminishes towards the end of the droplet lifetime. It is also shown that the droplet surface temperature is more uniform at higher hot-surface temperature.
Prediction of chemosensitivity for patients with acute myeloid leukemia, according to expression levels of 28 genes selected by genome-wide complementary DNA microarray analysis. (2002)

To identify genes involved in the sensitivity of acute myeloid leukemia (AML) cells to chemotherapy, we monitored gene-expression profiles of cancer cells from 76 AML patients using a cDNA microarray consisting of 23,040 genes. We identified 63 genes that were commonly overexpressed and 372 genes suppressed in AML. Because these genes represent key molecules for disclosing the molecular mechanisms of AML, they may be potential targets for drug development. We also found 28 that revealed different expression levels between good and poor responders to chemotherapy and appeared to be associated with chemosensitivity. On that basis, we developed a "Drug Response Scoring" system that was correlated well with individual sensitivity to an anticancer drug regimen. Among the 44 cases with positive drug-response scores by our definition, 40 achieved complete remission after treatment, whereas the only 3 of the 20 cases with negative scores responded well to the treatment. An ability to predict chemosensitivity should eventually lead to achievement of our goal of "personalized therapy."
NOTES: Ehrlichia ewingii sp. nov., the Etiologic Agent of Canine Granulocytic Ehrlichiosis (1992)

The 16S rRNA gene was amplified, cloned, and sequenced from the blood of two dogs that were experimentally infected with the etiologic agent of canine granulocytic ehrlichiosis. The 16S rRNA sequence was found to be unique when it was compared with the sequences of other members of the genus Ehrlichia. The most closely related species were Ehrlichia canis (98.0% related) and the human ehrlichiosis agent (Ehrlichia chaffeensis) (98.1% related); all other species in the genus were found to be phylogenetically much more distant. Our results, coupled with previous serologic data, provide conclusive evidence that the canine granulocytic ehrlichiosis agent is a new species of the genus Ehrlichia that is related to, but is distinct from, E. canis and all other members of the genus. We propose the name Ehrlichia ewingii sp. nov.; the Stillwater strain is the type strain.
Molecular cytogenetic characterization of the 11q13 amplicon in head and neck squamous cell carcinoma (2006)

Amplification of 11q13 DNA sequences and overexpression of CCND1 are common findings in head and neck squamous cell carcinoma (HNSCC), identified in about 30% of the cases. However, little is known about initiation of the amplification and the organization of the amplicon. In order to study the structure of the amplicon in more detail and to learn more about the mechanisms involved in its initiation, prometaphase, metaphase, and anaphase fluorescence in situ hybridization (FISH) with 40 BAC clones spanning a 16-Mb region in chromosome bands 11q12.2 to 11q13.5 was performed in nine HNSCC cell lines with homogeneously staining regions. FISH analysis showed that the size of the amplicon varied among the nine cell lines, the smallest being 2.12 Mb and the largest 8.97 Mb. The smallest overlapping region of amplification was approximately 1.61 Mb, covering the region from BAC 729E14 to BAC 102B19. This region contained several genes previously shown to be amplified and overexpressed in HNSCC, including CCDN1, CTTN, SHANK2, and ORAOV1. The cell lines were also used to study the internal structure of the amplicon. Various patterns of amplified DNA sequences within the amplicon were found among the nine cell lines. Even within the same cell line, different amplicon structures could be found in different cell populations, indicating that the mechanisms involved in the development of the amplicons in HNSCC were more complex than previously assumed. The frequent finding of inverted repeats within the amplicons, however, suggests that breakage-fusion-bridge cycles are important in the initiation, but the fact that such repeats constituted only small parts of the amplicons indicate that they are further rearranged during tumor progression.
Cyclic GMP Phosphodiesterases and Regulation of Smooth Muscle Function (2003)

Cyclic GMP (cGMP) made in response to atrial natriuretic peptide (ANP) or nitric oxide (NO) is an important regulator of short-term changes in smooth muscle tone and longer-term responses to chronic drug treatment or proliferative signals. The ability of smooth muscle cells (SMCs) to utilize different combinations of phosphodiesterase (PDE) isozymes allows cGMP to mediate these multiple processes. For example, PDE5 as a major cGMP-hydrolyzing PDE effectively controls the development of smooth muscle relaxation. In order for contraction to occur, PDE5 is activated and cGMP falls. Conversely, blockade of PDE5 activity allows the relaxation cycle to be prolonged and enhanced. A recently shown direct activation of PDE5 by cGMP binding to the GAF A domain suggests that this regulatory site might be a target for new drug development. The calcium surge associated with vasoconstrictor initiated contraction also activates a calcium/calmodulin-dependent PDE (PDE1A). Together, PDE5 and PDE1A lower cGMP sufficiently to allow contraction. Longer term, both PDE5 and PDE1A mRNA are induced by chronic stimulation of guanylyl cyclase. This induction is a major cause of the tolerance that develops to NO-releasing drugs. Finally, high levels of cGMP or cAMP also act as a brake to attenuate the proliferative response of SMCs to many mitogens. After vessel damage, in order for SMC proliferation to occur, the levels of cGMP and cAMP must be decreased. In humans, this decrease is caused in large part by induction of another Ca2+/calmodulin-dependent PDE (PDE1C) that allows the brake to be released and proliferation to start.