gebhart/patrepeval huggingface dataset:
Plasmid ColE1 incompatibility determined by interaction of RNA I with primer transcript. (1981)

Mutants of plasmid pNT7 that can coexist with plasmid pMB9 in growing bacteria have been isolated. These mutants show altered incompatibility properties and increased copy numbers. Each mutant has a single base change at or near the center of one of the three palindromes in the region that specifies two RNA species: a larger one (primer transcripts) that provides a primer for DNA replication and a smaller one (RNA I) that is the incompatibility-specific inhibitor of primer formation. In vitro transcription studies show that the single base changes affect both the ability of RNA I to inhibit primer formation and the sensitivity of primer formation to inhibition by RNA I. RNA I hybridizes to the primer transcript, and the rate of hybridization is reduced by the single base changes. Based on analyses of inhibition of in vitro primer formation by RNA I and of in vivo properties of the mutant plasmids, we conclude that incompatibility between two plasmids can be attributed to inhibition of primer formation on one of the plasmids by the RNA I of the other. Inhibition of primer formation by RNA I appears to be the mechanism that determines the copy number of pNT7 and its derivatives.
Association of prior infection with Chlamydia pneumoniae and angiographically demonstrated coronary artery disease (1992)

<h3>Objective.</h3> —To evaluate the association between prior infection with<i>Chlamydia pneumoniae</i>, as measured by IgG antibody, and coronary artery disease. <h3>Design.</h3> —A population-based, case-control study. <h3>Setting.</h3> —Group Health Cooperative of Puget Sound, a Seattle-based health maintenance organization. <h3>Participants.</h3> —Men 55 years of age and younger and women 65 years of age and younger. Cases (n=171) were members of Group Health Cooperative undergoing diagnostic coronary angiography who had at least one coronary artery lesion occupying 50% or more of the luminal diameter. The population controls (n=120) were Group Health Cooperative members without known coronary heart disease. <h3>Main Outcome Measure.</h3> —The adjusted odds ratio (OR) for coronary artery disease associated with prior<i>Cpneumoniae</i>infection as measured by the presence of IgG antibody. <h3>Results.</h3> —After adjusting for age, gender, and calendar quarter of blood drawing, the OR for coronary artery disease associated with the presence of antibody was 2.6 (95% confidence interval, 1.4 to 4.8). The association was limited to cigarette smokers, in whom the OR was 3.5 (95% confidence interval, 1.7 to 7.0). Among never-smokers, the OR was 0.8 (95% confidence interval, 0.3 to 1.9). When cases and controls were restricted to those assayed concurrently, the adjusted OR (smokers and nonsmokers combined) was 4.2 (95% confidence interval, 1.8 to 10.0). Adjustment for serum cholesterol, hypertension, alcohol use, diabetes, and socioeconomic status did not change these results. Only a weak association was found when cases were compared with 63 subjects whose angiographic results were normal (OR, 1.2; 95% confidence interval, 0.6 to 2.2). <h3>Conclusions.</h3> —These results generally support the previously reported association between<i>Cpneumoniae</i>infection and coronary heart disease. However, caution should be used in interpreting the basis for this association. (<i>JAMA</i>. 1992;268:68-72)
<i>Techniques of Vacuum Ultraviolet Spectroscopy</i> (1968)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation James A. R. Samson, Stanley S. Ballard; Techniques of Vacuum Ultraviolet Spectroscopy. Physics Today 1 December 1968; 21 (12): 79–81. https://doi.org/10.1063/1.3034674 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
Non-invasive assessment of atrial electrophysiology in AF-influence of posture change (2002)

The authors sought to non-invasively defect changes in atrial fibrillation rhythm during autonomic provocative maneuvers. Digital Holter from 23 patients with chronic AF before and after active postural change were subjected to routine editing, and then underwent QRS and T wave subtraction, leaving pure atrial fibrillatory records. Spectral analysis by autoregressive method was performed on this record. The total spectral power, and that in the 4-10 Hz range was calculated and compared before and after posture change. Analysable data was acquired front 17 patients. Postural change caused a fall in spectral power (total power: from 19442 to 8154, 4-10 Hz power: 4031 to 1764), and a concentration of the power in the 4-10 Hz range. Increased sympathetic tone due to active postural change causes a fall in total spectral power and a concentration of that power in the AF frequency band. Atrial electrophysiology during AF can be studied noninvasively.
Delivery of Antigen to CD40 Induces Protective Immune Responses against Tumors (2007)

Ligation of CD40 induces maturation of dendritic cells (DC) and could be a useful target for vaccines. In this study, we have constructed two types of Ab-based vaccine constructs that target mouse CD40. One type is a recombinant Ab with V regions specific for CD40 and has defined T cell epitopes inserted into its C region. The other type is a homodimer, each chain of which is composed of a targeting unit (single-chain fragment variable targeting CD40), a dimerization motif, and an antigenic unit. Such proteins bound CD40, stimulated maturation of DC, and enhanced primary and memory T cell responses. When delivered i.m. as naked DNA followed by electroporation, the vaccines induced T cell responses against MHC class II-restricted epitopes, Ab responses, and protection in two tumor models (myeloma and lymphoma). Two factors apparently contributed to these results: 1) agonistic ligation of CD40 and induction of DC maturation, and 2) delivery of Ag to APC and presentation on MHC class II molecules. These results highlight the importance of agonistic targeting of Ag to CD40 for induction of long-lasting and protective immune responses.
Effects of glyphosate on <i>Fusarium</i> spp.: its influence on root colonization of weeds, propagule density in the soil, and crop emergence (1987)

Glyphosate is a broad spectrum herbicide that can lead to root rot like damage on crops. This study was undertaken to investigate the effect of glyphosate on the root-colonizing Fusarium spp. The research was conducted at two sites. Site one was densely covered with perennial weeds, and site two with annuals. At site one, spraying the weed cover with glyphosate increased (p &lt; 0.05) the level of colonization by Fusarium spp. in Ranunculus repens and Holcus lanatus, but not in Stellaria media and Plantago lanceolata. At site two, glyphosate enhanced colonization in Spergula arvensis, Stellaria media, Echinochloa crusgalli, and Chenopodium album, but not in Capsella bursa-pastoris and Polygonum persicaria. At both sites, the number of colony-forming units of Fusarium spp. per gram of dried soil was increased by the application of glyphosate. Nevertheless, crops subsequently sown in the field containing the annual weeds were not detrimentally affected by glyphosate treatment of these weeds.
Effect of Vaccination with Selective Bacterins on Conventional Pigs Infected with Type 2 Porcine Circovirus (2003)

The objective of this study was to determine whether vaccination with bacterins commonly used in the USA, when administered at a time typical of US protocol, enhances porcine circovirus type 2 (PCV2) replication and the incidence and severity of clinical signs and lesions characteristic of postweaning multisystemic wasting syndrome (PMWS) in conventional pigs. Sixty-one pigs free of PCV2 were randomly assigned to four groups. Groups 1 (n = 15) and 2 (n = 15) pigs served as sham-inoculated negative controls. Groups 3 (n = 14) and 4 (n = 17) pigs were inoculated intralymphoid with PCV2 field isolate ISU-40895. Pigs in groups 2 and 4 were vaccinated with Actinobacillus pleuropneumoniae (APP) and Mycoplasma hyopneumoniae (M. hyopneumoniae) bacterins 21 days before and again 1 day before inoculation with PCV2. Mild transient respiratory disease and diarrhea were observed from 13 to 34 days postinoculation (DPI) in pigs in groups 3 and 4. Half the pigs from each group were necropsied at 22 and 34 DPI, respectively. Moderately enlarged, tan-colored lymph nodes were observed in the majority of pigs in groups 3 and 4. There was a significantly (P < 0.05) longer length of viremia (2.14 +/- 0.26 versus 4.44 +/- 0.23 weeks), a higher copy number of the PCV2 genome in serum, a wider range of tissue distribution of PCV2 antigen, and an increased severity of lymphoid depletion in pigs vaccinated with commercial APP and M. hyopneumoniae vaccines and inoculated with PCV2 compared with PCV2-inoculated unvaccinated pigs. Swine producers and veterinarians may need to consider changes in vaccination protocols in herds with recurrent PCV2-associated PMWS.
Lymph node metastases (2000)

Promising results obtained in the human setting with the use of dendritic cells as novel immunotherapeutic tools have recently renewed interest in active immunotherapy for the treatment of solid tumors. However, for accomplishing this goal, the maintenance of the integrity of the immune system remains a crucial issue. Studies showing that radical tumor-draining RLN dissections exert a markedly negative influence on the efficacy of postoperative immunotherapy protocols in mice as well as in humans seem to support adoption of a more conservative approach regarding uninvolved RLNs in the treatment of cancer patients.
Prolyl Hydroxylation of Collagen Type I Is Required for Efficient Binding to Integrin α1β1 and Platelet Glycoprotein VI but Not to α2β1 (2003)

Collagen is a potent adhesive substrate for cells, an event essentially mediated by the integrins alpha 1 beta 1 and alpha 2 beta 1. Collagen fibrils also bind to the integrin alpha 2 beta 1 and the platelet receptor glycoprotein VI to activate and aggregate platelets. The distinct triple helical recognition motifs for these receptors, GXOGER and (GPO)n, respectively, all contain hydroxyproline. Using unhydroxylated collagen I produced in transgenic plants, we investigated the role of hydroxyproline in the receptor-binding properties of collagen. We show that alpha 2 beta 1 but not alpha 1 beta 1 mediates cell adhesion to unhydroxylated collagen. Soluble recombinant alpha 1 beta 1 binding to unhydroxylated collagen is considerably reduced compared with bovine collagens, but binding can be restored by prolyl hydroxylation of recombinant collagen. We also show that platelets use alpha 2 beta 1 to adhere to the unhydroxylated recombinant molecules, but the adhesion is weaker than on fully hydroxylated collagen, and the unhydroxylated collagen fibrils fail to aggregate platelets. Prolyl hydroxylation is thus required for binding of collagen to platelet glycoprotein VI and to cells by alpha 1 beta 1. These observations give new insights into the molecular basis of collagen-receptor interactions and offer new selective applications for the recombinant unhydroxylated collagen I.
Differential gene expression in healing rat corneal epithelium. (1995)

mRNA differential display provides a unique and powerful experimental system to study differential gene expression in wound healing and cell migration. Using this system, differential expression of nine genes was observed. Detection of genes differentially expressed in healing epithelium may prompt studies that will define the specific role of each of the proteins in wound healing.
Direct evidence for ATP modulation of sugar transport in human erythrocyte ghosts. (1986)

Sugar transport in human erythrocyte ghosts is modulated by low molecular weight factors present in red cell cytosol that induce an asymmetry in Michaelis and velocity constants for sugar entry and exit (Carruthers, A., and Melchior, D. L. (1983) Biochim. Biophys. Acta 728, 254-266). This study examines the possibility that ATP is the transport-modulating factor. The intracellular factor must satisfy at least three criteria. It must reduce Km and Vmax for sugar efflux from inside-out red cell membrane vesicles. It should increase Km for efflux from red cell ghosts. It should have a molecular weight of less than 10 kDa. These criteria are satisfied by ATP. AMP, ADP, GTP, UTP, and ITP are without effect on sugar transport. The following results support the view that the cytosolic factor is ATP. Red cell lysate (obtained by hypotonic lysis of red cells) is unable to modify transport following dialysis against ATP-free medium. The ability of lysate to modify transport is retained following acid extraction. ATP depletion of acid-extracted lysate by treatment with apyrase results in the loss of transport-modulating potency. Myokinase partly restores both the ATP content and the ability of ATP-depleted (apyrase-treated) lysate to modify transport. Addition of ATP to ATP-depleted lysate mimics the ability to myokinase to restore the transport-modulating potency of lysate. ATP is without effect on the number and molecular size of D-glucose-sensitive cytochalasin B-binding proteins in the red cell membrane. These findings demonstrate that the transport-modulating potency of red cell cytosol is quantitatively accounted for by intracellular ATP which acts to modify the catalytic activity of plasmalemmal transporters.
A new peace in Africa (2008)

Following the end of the Cold War, the number of armed conflicts being waged around the world declined sharply. By 2005, there were 40% fewer conflicts of all types than in 1991, while high-intensity conflicts declined by some 80%. The one region in the world in which there was no sustained decline was sub-Saharan Africa, where there were 25% more conflicts in the 1990s than in the 1980s. Towards the end of the 1990s, while most of the rest of the world was becoming less violent, Africa's conflict numbers and associated death tolls increased considerably.
A Survey of Surface Reconstruction from Point Clouds (2016)

Abstract The area of surface reconstruction has seen substantial progress in the past two decades. The traditional problem addressed by surface reconstruction is to recover the digital representation of a physical shape that has been scanned, where the scanned data contain a wide variety of defects. While much of the earlier work has been focused on reconstructing a piece‐wise smooth representation of the original shape, recent work has taken on more specialized priors to address significantly challenging data imperfections, where the reconstruction can take on different representations—not necessarily the explicit geometry. We survey the field of surface reconstruction, and provide a categorization with respect to priors, data imperfections and reconstruction output. By considering a holistic view of surface reconstruction, we show a detailed characterization of the field, highlight similarities between diverse reconstruction techniques and provide directions for future work in surface reconstruction.
Topoisomerase IIα Gene Amplification Predicts Favorable Treatment Response to Tailored and Dose-Escalated Anthracycline-Based Adjuvant Chemotherapy in <i>HER-2/neu</i>–Amplified Breast Cancer: Scandinavian Breast Group Trial 9401 (2006)

Coamplification of HER-2/neu and TOP2A may define a subgroup of high-risk breast cancer patients who benefit from individually tailored and dose-escalated adjuvant anthracyclines.
Agent-based simulation of disease spread aboard ship (2005)

Extreme examples like the Spanish Flu pandemic of 1918 make clear the devastating impact that communicable diseases can have on military readiness. It is highly desirable to have models and tools that can be used to evaluate the course of a disease over time. These tools can help assess the effectiveness of strategies employed to contain the outbreak such as constraining movement, wearing protective gloves or masks, closing high traffic areas, etc. Armed with these tools, a medical practitioner can better assess the right course of action in a time critical situation. The primary difficulty with creating models and simulations for this purpose is that disease spread depends upon the details of human behavior and environmental variables which are not accounted for in current mathematical models. The likelihood that a particular individual will catch a given disease depends upon such specifics as where he works, whom he interacts with, where he sleeps, what he eats, his habits of personal hygiene, etc. It is hypothesized that a software disease simulation can combine agents that mimic human behavior, a ship specific environment, and disease specific attributes to more accurately model the spread of disease aboard ship than a mathematical model.
A Compendium of Directional Calculations Based on the Minimum Curvature Method (2005)

Summary The minimum curvature method has emerged as the accepted industry standard for the calculation of 3D directional surveys. Using this model, the well' strajectory is represented by a series of circular arcs and straight lines. Collections of other points, lines, and planes can be used to represent features such as adjacent wells, lease lines, geological targets, and faults. The relationships between these objects have simple geometrical interpretations, making them am enable to mathematical treatment. The calculations are now used extensively in 3D imaging and directional collision scans, making them critical for both business and safety. However, references for the calculations are incomplete, scattered in the literature, and have no systematic mathematical treatment. These features make programming a consistent and reliable set of algorithms more difficult. Increased standardization is needed. Investigation shows that iterative schemes have been used in situations in which explicit solutions are possible. Explicit calculations are preferred because they confer numerical predictability and stability. Though vector methods were frequently adopted in the early stages of the published derivations, opportunities for simplification were missed because of premature translation to Cartesian coordinates. This paper contains a compendium of algorithms based on the minimum curvature method (includes coordinate reference frames, toolface, interpolation, intersection with a target plane, minimum and maximum true vertical depth (TVD) in a horizontal section, point closest to a circular arc, survey station to a target position with and without the direction defined, nudges, and steering runs). Consistent vector methods have been used throughout with improvements in mathematical efficiency, stability, and predictability of behavior. The resulting algorithms are also simpler and more cost effective to code and test. This paper describes the practical context in which each of the algorithms is applied and enumerates some key tests that need to be performed.
Use of the Case Western Reserve/Veterans Administration neuroprosthesis for exercise, standing and transfers by a paraplegic subject (2011)

Functional electric stimulation (FES) is a technology that may allow patients with spinal cord injury (SCI) to transfer stand and walk. This paper reports upon the use of the Case Western Reserve Neuroprosthesis by a T6 ASIA B paraplegic subject. The subject was able to stand for two minutes and 50 seconds. He could walk 35 feet with a swing to gait. Measurement of energy consumption showed that metabolic demand was only 2.1 metabolic equivalent units. The factors that limited the use of the device that need to be improved to make the technology practical for household or community ambulation are speed (5.8 m/min) of ambulation and fatigue of the stimulated muscles.
Rabbits with elevated serum C-reactive protein exhibit diminished neutrophil infiltration and vascular permeability in C5a-induced alveolitis. (1993)

In previous studies, we have shown that C-reactive protein (CRP) inhibits chemotaxis of neutrophils to complement fragments in vitro. To evaluate the effect of CRP on C5a-induced inflammation in vivo, a rabbit model of alveolitis was used. Rabbits pretreated with subcutaneous injections of croton oil had serum CRP increase from undetectable levels to 270 +/- 70 micrograms/ml 48 hours later. Rabbits were intubated and C5a des arg (10 micrograms/ml) instilled directly into the lungs via an endotracheal tube. Four to six hours later, the animals were killed and bronchoalveolar lavage performed. Rabbits pretreated with croton oil had significantly (P < 0.01) reduced C5a des arg-stimulated neutrophil infiltration (30 +/- 5%) into alveolar air spaces compared to untreated rabbits (64 +/- 9%). Increased numbers of total leukocytes in the alveolar washes coincided with increased neutrophil numbers whereas alveolar macrophages remained unchanged in all groups. Rabbits pretreated with croton oil also had a significant decrease (P < 0.05) in total protein (320 +/- 50 micrograms/ml) in lavage fluid after C5a instillation compared with untreated animals (850 +/- 140 micrograms/ml). In vitro, rabbit CRP (50 micrograms/ml) added to normal rabbit serum significantly (P < 0.05) inhibited chemotaxis of human neutrophils by 41%. Finally, direct intravenous pretreatment of rabbits with purified CRP also significantly reduced C5a-induced alveolitis. The CRP-C5a group had 33 +/- 10% neutrophil infiltration, a significant (P < 0.01) reduction from the C5a group (71 +/- 6%). The total protein content of the CRP-C5a rabbits was 986 +/- 165 micrograms/ml in the lavage fluid, which was significantly (P < 0.05) lower than the C5a group (1645 +/- 363 micrograms/ml). Therefore, CRP inhibits the development of neutrophil alveolitis and protein leakage in vivo and inhibits neutrophil chemotaxis in vitro. These data indicate that CRP offers a protective effect in neutrophil-mediated lung injury by reducing neutrophil influx and protein leak.
Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins (2015)

The 3'-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 2'-O-methyltransferase (2'-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 5' cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 5' cap although no candidate MTases have been identified thus far. To address this knowledge gap, we analysed the uncharacterized nsp12 of arteriviruses, which occupies the ORF1b position equivalent to that of the nidovirus 2'-O-MTase (coronavirus nsp16). In our in-depth bioinformatics analysis of nsp12, the protein was confirmed to be family specific whilst having diverged much further than other nidovirus ORF1b-encoded proteins, including those of the family Coronaviridae. Only one invariant and several partially conserved, predominantly aromatic residues were identified in nsp12, which may adopt a structure with alternating α-helices and β-strands, an organization also found in known MTases. However, no statistically significant similarity was found between nsp12 and the twofold larger coronavirus nsp16, nor could we detect MTase activity in biochemical assays using recombinant equine arteritis virus (EAV) nsp12. Our further analysis established that this subunit is essential for replication of this prototypic arterivirus. Using reverse genetics, we assessed the impact of 25 substitutions at 14 positions, yielding virus phenotypes ranging from WT-like to non-viable. Notably, replacement of the invariant phenylalanine 109 with tyrosine was lethal. We concluded that nsp12 plays an essential role during EAV replication, possibly by acting as a co-factor for another enzyme.