gebhart/patrepeval huggingface dataset:
In vivo evidence for a dependence on interleukin 15 for survival of natural killer cells (2002)

Cellular homeostasis requires a balance between cell production, cell survival, and cell death. Production of natural killer (NK) cells from bone marrow precursor cells requires interleukin 15 (IL-15); however, very little is known about the factors controlling survival of mature NK cells in vivo. Because mice deficient in IL-15 (IL-15(-/-) mice) fail to develop NK cells, it is not known whether mature NK cells can survive in an environment lacking IL-15. We hypothesized that IL-15 might indeed be required for survival of mature NK cells in vivo. Freshly isolated NK cells labeled with 5-(and-6)-carboxyfluorescein diacetate, succinimidyl ester (CFSE) were adoptively transferred into IL-15(-/-) mice and littermate control (IL-15(+/-)) mice. Within 36 hours after transfer, NK cells were detected in both IL-15(-/-) and IL-15(+/-) mice; however, significantly more (P <.003) CFSE-positive (CFSE(+)) NK cells were found in control mice than in IL-15(-/-) mice. By 5 days, similar numbers of CFSE(+) NK cells were still easily detected in IL-15(+/-) mice, whereas no CFSE(+) NK cells survived in IL-15(-/-) mice. Furthermore, mice with severe combined immunodeficiency treated with the Fab fragment of a blocking antibody recognizing a signaling subunit of the IL-15 receptor, IL-2/15Rbeta, had a significant ( approximately 90%) loss of NK cells compared with control mice. Finally, NK cells from Bcl-2 transgenic mice that were adoptively transferred into IL-15(-/-) mice did survive. These results show conclusively that IL-15 is required for mature NK cell survival in vivo and suggest that IL-15 mediates its effect on NK cell survival by means of Bcl-2.
Kits and Their Unique Role in Molecular Biology: a Brief Retrospective (2008)

Since their initial development nearly 20 years ago, molecular biology kits have evolved from simple protocols and reagents for cloning of DNA to the more recent complex reagent sets that enable whole genomic sequencing. Initially met with resistance by some who felt that using them deprived researchers of the basic knowledge of how to create reagents, molecular biology kits have taken on an important role in the biological sciences. In this article we describe kit development, why kits have succeeded in molecular biology, and how they have paved the way for the more recent widespread use of core facilities.
Role of Nitric Oxide in Surgical Flap Survival (2005)

Topp, Shelby G. BS; Zhang, Feng MD, PhD; Chatterjee, Tanya; Lineaweaver, William C. MD* Author Information
Band Reject Filter in BAW Technology (2008)

This document shows the feasibility of a band reject filter in Bulk Acoustic Wave (BAW) technology. This type of filter is usually composed of series and shunt resonators. We present two setups centred at 2.5 GHz which measurement is agreed with simulation for rejection band. Filters give a -20 dB rejection on a bandwidth greater than 60 MHz for each topology. The best measured filter achieves a -1.4 dB insertion loss in the passband with a 200 MHz bandwidth.
Influence of heat and humidity on the airway obstruction induced by exercise in asthma. (1978)

A C T We examined the degree of airway obstruction that developed in eight asthmatics who exercised while breathing air under four conditions: (a) ambient room temperature and water content; (b) body temperature and ambient water content; (c) ambient room temperature fully saturated; and (d) body temper- ature fully saturated. These test conditions were performed in random order. Multiple aspects of pulmonary mechanics were measured before and 5 min after exercise. When air at ambient conditions was inhaled, the expected airway obstruction developed after exercise, and all variables changed significantly from their pre-challenge values. Heating the air to body temperature did not influence this response. Increasing the humidity at ambient temperatures significantly blunted the response, and by inhaling body temperature, fully saturated air completely prevented it from occurring. Thus, the water content of inspired air is an important variable in the development of exercise- induced asthma.
Studying software evolution information by visualizing the change history (2004)

Before re-engineering a large and complex software system, it is wise to study its change history in order to identify the most valuable and problematic parts. Unfortunately, typical change histories contain thousands of entries, therefore the challenge is to discover those changes which are relevant for both the current and future situations of our product and process. We demonstrate how a simple visualization allows us to recognize relevant changes. Applying the technique on the change history of Tomcat, we have been able to identify (a) unstable components, (b) coherent entities, (c) design and architectural evolution, and (d) fluctuations in team productivity.
Isolation of a GB virus-related genome from a chimpanzee (1998)

Recently, two new flaviviruses, GB virus A (GBV-A) and GB virus B (GBV-B), were identified in the plasma of a tamarin infected with the hepatitis GB agent. A third virus, GB virus C (GBV-C), was subsequently identified in humans. In the current study, representational difference analysis (RDA) was used to search for a new virus in the serum of a chimpanzee that developed acute resolving hepatitis following inoculation with a pool of chimpanzee plasma. The plasma pool originated from serial passages of a human sample containing virus-like particles. Numerous cDNA clones were obtained that exhibited 62-80% identity with GBV-C. With the exception of the extreme 5' and 3' ends, the complete viral genome was sequenced, revealing a single large open reading frame encoding a 2833 amino acid polyprotein that contains two envelope proteins, two proteases, a helicase, and an RNA-dependent RNA polymerase. Phylogenetic analysis of the new virus indicates that it is closely related to GBV-C, yet still sufficiently divergent as to be placed in a separate group, tentatively labeled GB virus Ctroglodytes (GBV-Ctro). Numerous human samples were screened by reverse transcriptase-polymerase chain reaction (RT-PCR), but GBV-Ctro sequence was not detected. However, a second chimpanzee inoculated with the same plasma pool was shown to develop a GBV-Ctro infection. Although isolated from an Old World primate with hepatitis, the primary host of GBV-Ctro and any association with disease remains to be determined.
Retroviral Transfer of the Glucocerebrosidase Gene into CD34 + Cells from Patients with Gaucher Disease: In Vivo Detection of Transduced Cells without Myeloablation (1998)

Retroviral gene transfer of the glucocerebrosidase gene to hematopoietic progenitor and stem cells has shown promising results in animal models and corrected the enzyme deficiency in cells from Gaucher patients in vitro. Therefore, a clinical protocol was initiated to explore the safety and feasibility of retroviral transduction of peripheral blood (PB) or bone marrow (BM) CD34+ cells with the G1Gc vector. This vector uses the viral LTR promoter to express the human glucocerebrosidase cDNA. Three adult patients have been entered with follow-up of 6-15 months. Target cells were G-CSF-mobilized and CD34-enriched PB cells or CD34-enriched steady state BM cells, and were transduced ex vivo for 72 hr. Patient 1 had PB cells transduced in the presence of autologous stromal marrow cells. Patient 2 had PB cells transduced in the presence of autologous stroma, IL-3, IL-6, and SCF. Patient 3 had BM cells transduced in the presence of autologous stroma, IL-3, IL-6, and SCF. At the end of transduction, the cells were collected and infused immediately without any preparative treatment of the patients. The transduction efficiency of the CD34+ cells at the end of transduction was approximately 1, 10, and 1 for patients 1, 2, and 3, respectively, as estimated by semiquantitative PCR on bulk samples and PCR analysis of individual hematopoietic colonies. Gene marking in vivo was demonstrated in patients 2 and 3. Patient 2 had vector-positive PB granulocytes and mononuclear bone marrow cells at 1 month postinfusion and positive PB mononuclear cells at 2 and 3 months postinfusion. Patient 3 had a positive BM sample at 1 month postinfusion but was negative thereafter. These results indicate that gene-marked cells can engraft and persist for at least 3 months postinfusion, even without myeloablation. However, the level of corrected cells (<0.02%) is too low to result in any clinical benefit, and glucocerebrosidase enzyme activity did not increase in any patient following infusion of transduced cells. Modifications of vector systems and transduction conditions, along with partial myeloablation to allow higher levels of engraftment, may be necessary to achieve beneficial levels of correction in patients with Gaucher disease.
Property and Structure of YBa2Cu3O7-x-Nb2O5 Composite (1992)

Nb 2 O 5 -doped YBa 2 Cu 3 O 7- x superconductors were prepared by heating at 950°C for 24 h in air and cooling to room temperature at a rate of 5°C/min in air. The bulk density and critical current density ( J c , 77 K and H =0 T) increased with increasing amount of Nb 2 O 5 ≦0.5 wt%; up to 5.80 g/cm 3 and 437 A/cm 2 (sample thickness 1 mm), respectively. The critical temperature ( T c (zero)) was about 92 K. Experimentally we have succeeded in improving the superconducting properties, microstructure and degradation in moisture with addition of Nb 2 O 5 ≦0.5 wt%.
Signal transduction of interleukin-6 involves tyrosine phosphorylation of multiple cytosolic proteins and activation of Src-family kinases Fyn, Hck, and Lyn in multiple myeloma cell lines. (1997)

Binding of interleukin-6 to its receptor (IL-6R) induces the association of the IL-6R alpha chain (IL-6Ralpha) with a 130-kDa transmembrane glycoprotein, gp130. This event activates tyrosine kinases of the Janus kinase (JAK) family and transduces signals to the cytosol or nucleus. To further characterize the biochemical mechanisms by which IL-6 promotes cell proliferation, we investigated the effects of IL-6 on the growth and transmembrane signaling of several lymphoid cell lines. In the IL-6-dependent cell line B-9, IL-6 induced a rapid, transient, and concentration-dependent tyrosine phosphorylation of several cytosolic proteins as detected by antiphosphotyrosine immunoblots. The molecular weight of major bands on sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 44, 65, 70, 80, 137, 148, 184, and 190 kDa, respectively. Similar effects of IL-6 on tyrosine phosphorylation were observed in the human multiple myeloma cell line LP-1. Because JAKs were unlikely to mediate all the biological effects of IL-6, we investigated whether members of the Src family of tyrosine kinases were also activated in B-9 or LP-1 cells. IL-6 induced the activation and tyrosine phosphorylation of p59Fyn, p56/59Hck, and p56Lyn. Coprecipitation experiments with anti-Hck, anti-Lyn, anti-Fyn, and anti-gp130 antibodies revealed a physical association with gp130 of p56/59Hck and p56Lyn, but not p59Fyn, in LP-1 cells. Together, these results show for the first time that several Src kinases may become activated by IL-6 (p59Fyn, p56/59Hck, and p56Lyn) and associate with gp130 (p56/59Hck and p56Lyn).
Continuous Fermentation and Stripping of Ethanol (1995)

Recycling the contents of a continuous fermentor through a stripping column is proposed as a means of reducing product inhibition and lowering the cost of fuel ethanol production. A 2-L fermentor and 10-cm packed column were continuously operated for 150 days without contamination. Some fouling of the packing with attached yeast cells was observed which partially blocked the column. Cell yield was lower than in a simple continuous fermentor. Complete conversion of 200 g/L glucose feed and 90% conversion of 600 g/L glucose feed were achieved. Data were analyzed by computerized process simulation. Cost analysis indicated that, with heat recovery to reduce heating and cooling costs, the continuous fermentor/stripper is possibly a lower-cost alternative to conventional fermentation and distillation.
The Early Humoral Response in Human Granulocytic Ehrlichiosis (1997)

The early antibody response in patients with human granulocytic ehrlichiosis (HGE) and in mice infected with the HGE agent was characterized by using sera to probe lysates of HL-60 cells infected with HGE organisms. Sera were obtained from 18 patients with HGE, mostly within the first 6 weeks of clinical infection, and from mice infected with the HGE agent for up to 3 weeks. A 44-kDa antigen was reactive with IgG in all 18 patients, and IgG to 40-, 65-, and 80-kDa antigens was present in 6, 8, and 7 patients, respectively. In addition, IgM to 40-, 44-, 65-, and 80-kDa antigens was found in 9, 5, 4, and 4 subjects. Immunoglobulins to antigens ranging between 95 and 125 kDa were detected less frequently. HGE agent-infected C3H/HeJ mice had an antibody response similar to that in humans. Thus, the 40- and 44-kDa proteins of the HGE agent elicit early strong antibody responses during infection. Characterization of the antigens recognized by antibodies during HGE should aid in diagnosis and understanding of the disease.
UV written Bragg gratings in tapered waveguides, a response shaping approach (2002)

Bragg gratings in tapered waveguides are investigated numerically and experimentally. A 1 cm long 40 dB grating with 1 nm 3 dB bandwidth is demonstrated. Numerical modelling shows that a bandwidth of 2 nm is achievable, maintaining single mode operation.
Development of a High-Speed Real-Time Polymerase Chain Reaction System Using a Circulating Water-Based Rapid Heat-Exchange (2010)

Polymerase chain reaction (PCR) is a powerful technique to detect microorganisms, viruses, or cells by amplifying a single copy or a few copies of a fragment of a particular DNA sequence. To reduce acquisition time, it is necessary to decrease the temperature transition time between denaturation and extension. We have developed a simple rapid real-time microlitter-sample droplet PCR system accomplished by the rapid liquid-based heat-exchange of sample droplets by quick switching of two circulating hot waters of denaturation and extension, a microlitter-sized droplet and a thin-film aluminum chip. Using this system, rapid PCR amplification of a set of droplets lined up on an aluminum chip was conducted successfully as shown by the increase in fluorescence intensity, and was accomplished within 3.5 min in 40 cycles of 1 s denaturation and 3 s extension reaction, which is one magnitude faster than conventional fast PCR systems. This method allows the rapid detection of DNA fragments and has a possibility for measuring multiple samples simultaneously in a miniaturized microfluidic chip.
Interactions of Heteroaromatic Compounds with Nucleic Acids (1975)

In the present paper we report the results of a study on the base specificity and affinity of eight dyes potentially able to interact with DNA. These compounds include four triphenylmethane dyes used in histochemistry, auramine, "Hoechst 33258" and two acridines substituted with t-butyl groups. They were selected with regard to their inability to intercalate between the base pairs of helical polynucleotides due to structural limitations. Hydrodynamic studies performed with the DNA complexes of crystal violet and Hoechst 33258 confirmed our assumptions that compounds of this type bind to the outside of DNA. The main results from DNA binding studies indicate that the triphenylmethane dyes except p-fuchsin are bound with high preference to two adjacent A - T pairs while Hoechst 33258 seems to need three A - T pairs as the binding site. Model studies with synthetic polynucleotides revealed that not only a sequence of A - T pairs, but also their structural arrangement in a helix, is crucial for the high affinities observed for most of the ligands when interacting with natural DNA. Methyl green and Hoechst 33258 can be used for increasing the resolution power of cesium chloride density gradients for DNAs with different (A + T) content.
Use of fluorogenic histocompatibility leukocyte antigen-A*0201/HPV 16 E7 peptide complexes to isolate rare human cytotoxic T-lymphocyte-recognizing endogenous human papillomavirus antigens. (2000)

Cervical cancer (CaCx) is the second most common female malignancy worldwide and remains a clinical problem despite improvements in early detection and therapy. CaCx and preinvasive cervical intraepithelial neoplasia (CIN3) are strongly associated with infection by human papillomavirus (HPV), particularly types 16 and 18. Two nonstructural viral proteins, E6 and E7, are constitutively expressed in cervical tumors and are crucial for the maintenance of the transformed phenotype. These proteins thus provide attractive targets for immunotherapy of CaCx mediated by CD8+ CTLs. However, reliable detection and generation of HPV-specific CTLs in humans has been difficult. Recently, soluble fluorogenic MHC-peptide complexes (tetramers) have greatly increased the sensitivity of antiviral and antitumor CTL detection. To examine the feasibility of this approach for detecting HPV-specific CTLs, we constructed a tetramer consisting of HLA-A*0201 and the best studied HPV CTL peptide epitope, HPV 16 E711-20. Between 2 and 12% of short-term HPV 16 E711-2 CTL lines derived from CaCx patients stained highly with the tetramer. Direct ex vivo staining of peripheral blood mononuclear cells revealed CD8+ tetramer+ high cells at low frequencies in both CIN3 patients (1 of 1,260 to 1 of 19,073) and normal controls (1 of 1,855 to 1 of 42,004). However, short-term in vitro stimulation with the HPV 16 E711-20 peptide expanded CD8+tetramer+ cells to a greater extent in the peripheral blood mononuclear cells from CIN3 patients. Furthermore, the tetramer provided a powerful tool to isolate polyclonal and clonal peptide-specific CTLs from an established HPV 16 E7,11-20-specific CTL line. These purified CTLs were able to lyse both peptide-pulsed targets and targets expressing endogenously processed HPV antigens. This tetramer may therefore be useful for selecting rare high-affinity HPV-specific CTLs for the immunotherapy of CaCx.
Surface-marker cluster design criteria for 3-D bone movement reconstruction (1997)

When three-dimensional (3-D) human or animal movement is recorded using a photogrammetric system, bone-embedded frame positions and orientations are estimated from reconstructed surface marker trajectories using either nonoptimal or optimal algorithms. The effectiveness of these mathematical procedures in accommodating for both photogrammetric errors and skin movement artifacts depends on the number of markers associated with a given bone as well as on the size and shape characteristics of the relevant cluster. One objective of this paper deals with the identification of marker-cluster design criteria aimed at the minimization of error propagation from marker coordinates to bone-embedded frame position and orientation. Findings allow for the quantitative estimation of these errors for any given cluster configuration and suggest the following main design criteria. A cluster made up of four markers represents a good practical compromise. Planar clusters are acceptable, provided in quasi-isotropic distribution. The root mean square distance of the markers from their centroid should be greater than ten times the standard deviation of the marker position error. The second objective of this paper deals with the identification of the optimal cluster position and orientation on the limb aimed at the minimization of error propagation to anatomical landmark laboratory coordinates. Cluster position should be selected to minimize skin movement artifacts. The longest principal axis of the marker distribution should be oriented toward the relevant anatomical landmark position.
Central nervous system mechanisms of analgesia (1976)

Department of Physiology, Medical College of Virginia, Virginia Commonwealth University, Richmond, Va. 23298 and National Institute of Dental Research, Bethesda, Md. 20014 U.S.A. Accepted June 22, 1976.
Biological Costs and Mechanisms of Fosfomycin Resistance in Escherichia coli (2003)

Fosfomycin is a cell wall inhibitor used mainly for the treatment of uncomplicated lower urinary tract infections. As shown here, resistance to fosfomycin develops rapidly in Escherichia coli under experimental conditions, but in spite of the relatively high mutation rate in vitro, resistance in clinical isolates is rare. To examine this apparent contradiction, we mathematically modeled the probability of resistance development in the bladder during treatment. The modeling showed that during a typical episode of urinary tract infection, the probability of resistance development was high (>10(-2)). However, if resistance was associated with a reduction in growth rate, the probability of resistance development rapidly decreased. To examine if fosfomycin resistance causes a reduced growth rate, we isolated in vitro and in vivo a set of resistant strains. We determined their resistance mechanisms and examined the effect of the different resistance mutations on bacterial growth in the absence and presence of fosfomycin. The types of mutations found in vitro and in vivo were partly different. Resistance in the mutants isolated in vitro was caused by ptsI, cyaA, glpT, uhpA/T, and unknown mutations, whereas no cyaA or ptsI mutants could be found in vivo. All mutations caused a decreased growth rate both in laboratory medium and in urine, irrespective of the absence or presence of fosfomycin. According to the mathematical model, the reduced growth rate of the resistant strains will prevent them from establishing in the bladder, which could explain why fosfomycin resistance remains rare in clinical isolates.
Laser welding of lightweight structural steel panels (1993)

The Applied Research Laboratory, The Pennsylvania University (ARL Penn State) has developed a relatively low heat input high power carbon dioxide (CO2) robotic laser beam welding (LBW) technique for fabrication of lightweight corrugated core steel sandwich structures. Both HSLA 80 and type 316L stainless steel structures have been produced. Over 276 test panels ranging in size from 3″ × 5″ to 8′ × 8′ have been produced. Specimens have been rigorously tested by the Carderock Division of the Naval Surface Warfare Center (NSWC) private industry and foreign Governments and have been evaluated in terms of static and dynamic strengths, fatigue, fire, acoustics, thermal and insulation performance, and corrosion resistance. Lightweight corrugated core steel panels (LASCOR) fabricated by ARL Penn State have been shown to have exceeded or met the performance requirements established by NSWC in the areas of weight, fire, weld fatigue, static strength, thermal and insulation performance. Additional work has been conducted by NSWC in the area of blast analysis. Development of fabrication procedures, testing and evaluation procedures, and results to-date will be reviewed.
Clinicopathologic Studies in Cognitively Healthy Aging and Alzheimer Disease (1998)

(1) The order of the strength of relationships between densities of histologic markers and dementia severity in AD is neurofibrillary tangles greater than cored senile plaques greater than total senile plaques. (2) Advanced age at death is associated with somewhat less severe dementia and fewer senile plaques and neurofibrillary tangles. (3) Plaque-predominant AD may represent a developmental stage in AD. (4) Despite a substantial effect of apolipoprotein E epsilon4 as a risk factor for AD, on decreasing the age at AD onset, and increasing the amount of cerebral amyloid angiopathy, its effect on senile plaque densities is variable and complex, being confounded with age, dementia severity, and methodologic differences. (5) Stringent clinical diagnostic criteria for DAT, even in the very mild stage, and senile plaque-based neuropathologic criteria for AD are highly accurate.