bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphorylated AbsA2 Negatively Regulates Antibiotic Production inStreptomyces coelicolorthrough Interactions with Pathway-Specific Regulatory Gene Promoters
Authors: McKenzie Nancy L. , Nodwell Justin R. 
Published: May 2007

ABSTRACTThe AbsA two-component signal transduction system, comprised of the sensor kinase AbsA1 and the response regulator AbsA2, acts as a negative regulator of antibiotic production inStreptomyces coelicolor, for which the phosphorylated form of AbsA2 (AbsA2∼P) is the agent of repression. In this study, we used chromatin immunoprecipitation to show that AbsA2 binds the promoter regions ofactII-ORF4,cdaR, andredZ, which encode pathway-specific activators for actinorhodin, calcium-dependent antibiotic, and undecylprodigiosin, respectively. We confirm that these interactions also occur in vitro and that the binding of AbsA2 to each gene is enhanced by phosphorylation. Induced expression ofactII-ORF4 andredZin the hyperrepressiveabsA1mutant (C542) brought about pathway-specific restoration of actinorhodin and undecylprodigiosin production, respectively. Our results suggest that AbsA2∼P interacts with as many as four sites in the region that includes theactII-ORF4 promoter. These data suggest that AbsA2∼P inhibits antibiotic production by directly interfering with the expression of pathway-specific regulators of antibiotic biosynthetic gene clusters.
Performance of the HerpeSelect (Focus) and Kalon Enzyme-Linked Immunosorbent Assays for Detection of Antibodies against Herpes Simplex Virus Type 2 by Use of Monoclonal Antibody-Blocking Enzyme Immunoassay and Clinicovirological Reference Standards in Brazil
Authors: Nascimento Maria Claudia , Ferreira Suzete , Sabino Ester , Hamilton Ingrid , Parry John , Pannuti Claudio S. , Mayaud Philippe 
Published: May 2007

ABSTRACT
A total of 586 serum samples were used to evaluate the performance of type-specific herpes simplex virus type 2 (HSV-2) commercial enzyme-linked immunosorbent assays (ELISAs) by using the monoclonal antibody-blocking enzyme immunoassay (MAb-EIA) and a clinicovirological panel as reference standards. The Kalon and HerpeSelect ELISAs had similar sensitivities (93.5% and 93.8% compared with the results obtained by MAb-EIA, respectively, and 100% for both ELISAs compared with the results obtained with a clinicovirological panel). The Kalon ELISA had a higher specificity (96.5% and 96.8% compared with the results obtained by MAb-EIA and with a clinicovirological panel, respectively) than the HerpeSelect ELISA (86.9% and 94% compared with the results obtained by MAb-EIA and with a clinicovirological panel, respectively). A higher cutoff significantly improved the specificity of the HerpeSelect ELISA.
Rare Case of
Nocardia asteroides
Pericarditis in a Human Immunodeficiency Virus-Infected Patient
Authors: Jinno Sadao , Jirakulaporn Tanawat , Bankowski Matthew J. , Kim Wesley , Wong Russell 
Published: May 2007

ABSTRACT

Nocardia asteroides
was isolated after prolonged culture from the pericardial fluid of a human immunodeficiency virus-infected patient. The lengthy duration required for culture growth and identification of this
N. asteroides
isolate affected both initial therapeutic decisions and patient management. A proposed algorithm for the microbiological workup of pericardial fluid for possible
Nocardia
spp. is described in an effort to improve the timeliness of results.
Establishment of a Poliovirus Oral Infection System in Human Poliovirus Receptor-Expressing Transgenic Mice That Are Deficient in Alpha/Beta Interferon Receptor
Authors: Ohka Seii , Igarashi Hiroko , Nagata Noriyo , Sakai Mai , Koike Satoshi , Nochi Tomonori , Kiyono Hiroshi , Nomoto Akio 
Published: May 2007

ABSTRACT

Poliovirus (PV) is easily transferred to humans orally; however, no rodent model for oral infections has been developed because of the alimentary tract's low sensitivity to the virus. Here we showed that PV is inactivated by the low pH of the gastric contents in mice. The addition of 3% NaHCO
3
to the viral inoculum increased the titer of virus reaching the small intestine through the stomach after intragastric inoculation of PV. Transgenic mice (Tg) carrying the human PV receptor (hPVR/CD155) gene and lacking the alpha/beta interferon receptor (IFNAR) gene (hPVR-Tg/
Ifnar
KO) were sensitive to the oral administration of PV with 3% NaHCO
3
, whereas hPVR-Tg expressing IFNAR were much less sensitive. The virus was detected in the epithelia of the small intestine and proliferated in the alimentary tract of hPVR-Tg/
Ifnar
KO. By the ninth day after the administration of a virulent PV, the mice had died. These results suggest that IFNAR plays an important role in determining permissivity in the alimentary tract as well as the generation of virus-specific immune responses to PV via the oral route. Thus, hPVR-Tg/
Ifnar
KO are considered to be the first oral infection model for PV, although levels of anti-PV antibodies were not elevated dramatically in serum and intestinal secretions of surviving mice when hPVR-Tg/
Ifnar
KO were administered an attenuated PV.
Conserved Changes in Envelope Function during Human Immunodeficiency Virus Type 1 Coreceptor Switching
Authors: Pastore Cristina , Nedellec Rebecca , Ramos Alejandra , Hartley Oliver , Miamidian John L. , Reeves Jacqueline D. , Mosier Donald E. 
Published: May 2007

ABSTRACT
We studied the evolution of human immunodeficiency virus type 1 (HIV-1) envelope function during the process of coreceptor switching from CCR5 to CXCR4. Site-directed mutagenesis was used to introduce most of the possible intermediate mutations in the envelope for four distinct coreceptor switch mutants, each with a unique pattern of CCR5 and CXCR4 utilization that extended from highly efficient use of both coreceptors to sole use of CXCR4. Mutated envelopes with some preservation of entry function on either CCR5- or CXCR4-expressing target cells were further characterized for their sensitivity to CCR5 or CXCR4 inhibitors, soluble CD4, and the neutralizing antibodies b12-IgG and 4E10. A subset of mutated envelopes was also studied in direct CD4 or CCR5 binding assays and in envelope-mediated fusion reactions. Coreceptor switch intermediates displayed increased sensitivity to CCR5 inhibitors (except for a few envelopes with mutations in V2 or C2) that correlated with a loss in CCR5 binding. As use of CXCR4 improved, infection mediated by the mutated envelopes became more resistant to soluble CD4 inhibition and direct binding to CD4 increased. These changes were accompanied by increasing resistance to the CXCR4 inhibitor AMD3100. Sensitivity to neutralizing antibody was more variable, although infection of CXCR4-expressing targets was generally more sensitive to neutralization by both b12-IgG and 4E10 than infection of CCR5-expressing target cells. These changes in envelope function were uniform in all four series of envelope mutations and thus were independent of the final use of CCR5 and CXCR4. Decreased CCR5 and increased CD4 binding appear to be common features of coreceptor switch intermediates.
Climatic effects on caterpillar fluctuations in northern hardwood forests
Authors: Reynolds Lindsay V. , Ayres Matthew P. , Siccama Thomas G. , Holmes Richard T. 
Published: May 2007

Fluctuations in the abundance of Lepidoptera are common but inadequately understood. Here we show that caterpillar abundance in the White Mountains of New Hampshire has fluctuated by >20-fold from 1986 to 2005. We report tests of three possible causes: (i) extreme winter cold; (ii) long, warm summers; and (iii) interannual variation in tree growth, which tends to correlate with phytochemistry. Caterpillar fluctuations from summers t to t + 1 were uncorrelated or negatively correlated with minimum air temperature during the intervening winter (does not support the first cause), but were positively correlated with thermal sum during summer t (r = 0.49–0.56) (supports the second cause). There was limited interannual variation in the radial growth of two dominant tree species ( Acer saccharum Marsh. and Betula alleghaniensis Britt.) and no correlation with caterpillar fluctuations (refutes the third cause). Thermal sum might influence caterpillar fluctuations through direct effects on insect development, indirect effects on susceptibility to natural enemies, and (or) indirect effects on plant-insect interactions; the mechanisms are of particular interest because thermal sums have been increasing since local records began in 1957 (r = 0.41–0.45). In hardwoods forests of the northeastern United States, there is some broad-scale driver related to summer temperatures that generates fluctuations in caterpillar abundance, which influences herbivory as well as higher level consumers, such as insectivorous birds.
The role of stand density on growth efficiency, leaf area index, and resin flow in southwestern ponderosa pine forests
Authors: McDowell Nate G. , Adams Henry D. , Bailey John D. , Kolb Thomas E. 
Published: May 2007

We examined the response of growth efficiency (GE), leaf area index (LAI), and resin flow (RF) to stand density manipulations in ponderosa pine ( Pinus ponderosa Dougl. ex Laws.) forests of northern Arizona, USA. The study used a 40 year stand density experiment including seven replicated basal area (BA) treatments ranging from 7 to 45 m2·ha–1. Results were extended to the larger region using published and unpublished datasets on ponderosa pine RF. GE was quantified using basal area increment (BAI), stemwood production (NPPs), or volume increment (VI) per leaf area (Al) or sapwood area (As). GE per Al was positively correlated with BA, regardless of numerator (BAI/Al, NPPs/Al, and VI/Al; r2 = 0.84, 0.95, and 0.96, respectively). GE per As exhibited variable responses to BA. Understory LAI increased with decreasing BA; however, total (understory plus overstory) LAI was not correlated with BA, GE, or RF. Opposite of the original research on this subject, resin flow was negatively related to GE per Al because Al/As ratios decline with increasing BA. BAI, and to a lesser degree BA, predicted RF better than growth efficiency, suggesting that the simplest measurement with the fewest assumptions (BAI) is also the best approach for predicting RF.
Structure of soil microbial communities in sugi plantations and seminatural broad-leaved forests with different land-use historyThis article is one of a selection of papers published in the Special Forum on Towards Sustainable Forestry — The Living Soil: Soil Biodiversity and Ecosystem Function.
Authors: Matsushita Miho , Ito Satoshi , Meguro Sadatoshi , Kawachi Shinsaku 
Published: May 2007

Phospholipid fatty acid profiles were used to evaluate microbial community composition in different soil layers of sugi ( Cryptomeria japonica (L.f.) D. Don) plantations and seminatural secondary forests in southeastern Kyushu, Japan. These forests had previously been utilized as meadows or coppices. Principal components analysis and canonical correspondence analysis of the phospholipid fatty acid data demonstrated differences in microbial community structure between current vegetation (sugi plantations or seminatural forests) in the FH layer. In contrast, differences between the previous land-use types (meadows or coppices) were detected through variation in the soil microbial community structure in the upper part of the A layer (0–5 cm). However, in the deeper part of the A layer (5–10 cm), the influence of the previous land-use history on soil microbial community structure was weak and the influence of the current vegetation could be detected. In the 0–5 cm part of the A layer, the organic matter was correlated with the microbial community structure. However, it cannot be assumed that these soil chemical characteristics were the principal factors responsible for separation of the microbial communities based on previous land-use history because the difference in chemical characteristics between the sites was small.
Fasudil inhibits vascular endothelial growth factor–induced angiogenesisin vitroandin vivo
Authors: Yin Limei , Morishige Ken-ichirou , Takahashi Toshifumi , Hashimoto Kae , Ogata Seiji , Tsutsumi Seiji , Takata Keiko , Ohta Tsuyoshi , Kawagoe Jun , Takahashi Kazuhiro , Kurachi Hirohisa 
Published: May 2007

AbstractVascular endothelial growth factor (VEGF)–induced endothelial cell migration is an important component of tumor angiogenesis. Rho and Rho-associated kinase (ROCK) are key regulators of focal adhesion, stress fiber formation, and thus cell motility. Inhibitors of this pathway have been shown to inhibit endothelial cell motility and angiogenesis. In this study, we investigated the antiangiogenic effect of fasudil, one of the ROCK inhibitors. Fasudil inhibited VEGF-induced endothelial cell migration, viability, and tube formation in vitro in human umbilical vein endothelial cells. VEGF-induced endothelial cell migration was reduced by fasudil associated with loss of stress fiber formation, focal adhesion assembly, and with the suppression of tyrosine phosphorylation of focal adhesion proteins. Furthermore, fasudil inhibited VEGF-induced phosphorylation of myosin light chain, which is one of the main substrates of ROCK. Therefore, the effect of fasudil was suggested to be ROCK dependent. Fasudil not only inhibited VEGF-induced cell proliferation but also reversed the protective effect of VEGF on apoptosis, which resulted in the decrease of cell viability. Moreover, fasudil inhibited VEGF-induced angiogenesis in a directed in vivo angiogenesis assay. These data are the first demonstration that fasudil has antiangiogenic properties. Therefore, fasudil might be useful for the treatment of angiogenesis-related diseases, especially cancer. [Mol Cancer Ther 2007;6(5):1517–25]
5-Aminoimidazole-4-carboxamide riboside sensitizes TRAIL- and TNFα-induced cytotoxicity in colon cancer cells through AMP-activated protein kinase signaling
Authors: Su Rong-Ying , Chao Yee , Chen Tsai-Yu , Huang Duen-Yi , Lin Wan-Wan 
Published: May 2007

Abstract
Death receptor-mediated tumor cell death, either alone or in combination with other anticancer drugs, is considered as a new strategy for anticancer therapy. In this study, we have investigated the effects and molecular mechanisms of 5-aminoimidazole-4-carboxamide riboside [AICAR; a pharmacologic activator of AMP-activated protein kinase (AMPK)] in sensitizing tumor necrosis factor (TNF)–related apoptosis-inducing ligand (TRAIL)– and TNFα-induced apoptosis of human colon cancer HCT116 cells. The cytotoxic action of AICAR requires AMPK activation and may occur at various stages of apoptotic pathways. AICAR cotreatment with either TRAIL or TNFα enhances activities of caspase-8, caspase-9, and caspase-3; down-regulates the antiapoptotic protein Bcl-2; increases the cleavage of Bid and results in the decrease of mitochondrial membrane potential; potentiates activation of p38 and c-Jun NH2-terminal kinase; and inhibits nuclear factor-κB activity. In addition, this sensitized cell apoptosis was neither observed in p53-null HCT116 cells nor affected by the cotreatment with mevalonate. In summary, we have developed a novel strategy of combining AICAR with TRAIL for the treatment of colon cancer cells. The sensitization effect of AICAR in cell apoptosis was mediated through AMPK pathway, requires p53 activity, and involves mitochondria-dependent apoptotic cascades, p38 and c-Jun NH2-terminal kinase. [Mol Cancer Ther 2007;6(5):1562–71]
The Impact of Beam Broadening on the Quality of Radar Polarimetric Data
Authors: Ryzhkov Alexander V. 
Published: May 2007

Abstract
The impact of beam broadening on the quality of radar polarimetric data in the presence of nonuniform beam filling (NBF) is examined both theoretically and experimentally. Cross-beam gradients of radar reflectivity Z, differential reflectivity ZDR, and differential phase ΦDP within the radar resolution volume may produce significant biases of ZDR, ΦDP, and the cross-correlation coefficient ρhv. These biases increase with range as a result of progressive broadening of the radar beam. They are also larger at shorter radar wavelengths and wider antenna beams.
Simple analytical formulas are suggested for estimating the NBF-induced biases from the measured vertical and horizontal gradients of Z, ZDR, and ΦDP. Analysis of polarimetric data collected by the KOUN Weather Surveillance Radar-1988 Doppler (WSR-88D) demonstrates that frequently observed perturbations of the radial ΦDP profiles and radially oriented “valleys” of ρhv depression can be qualitatively and quantitatively explained using the suggested NBF model.
Comparison of target labeling methods for use with Affymetrix GeneChips
Authors: Lonergan William , Whistler Toni , Vernon Suzanne D 
Published: May 2007

Abstract

Background
Several different commercial one-cycle labeling kits are available for preparation of the target for use with the Affymetrix GeneChip platform. However, there have been no evaluations of these different kits to determine if comparable results were generated. We report on the cRNA target synthesis, labeling efficiency and hybridization results using the One-Cycle Target Labeling Assay™ (Affymetrix), the BioArray RNA Amplification and Labeling System™ (Enzo Life Sciences), and the Superscript RNA Amplification System (Invitrogen Life Technologies).

Results
The only notable difference between kits was in the yield of cRNA target synthesized during in vitro transcription, where the BioArray assay had to be repeated several times in order to have sufficient target. However, each kit resulted in comparable signal and detection calls when hybridized to the Affymetrix GeneChip.

Conclusion
These 3 one-cycle labeling kits produce comparable hybridization results. This provides users with several kit options and flexibility when using the Affymetrix system.
Randomized Trial of Adjuvant 13-cis-Retinoic Acid and Interferon Alfa for Patients With Aggressive Skin Squamous Cell Carcinoma
Authors: Brewster Abenaa M. , Lee J. Jack , Clayman Gary L. , Clifford John L. , Reyes Mary Jo T. Necesito , Zhou Xian , Sabichi Anita L. , Strom Sara S. , Collins Robert , Meyers Christina A. , Lippman Scott M. 
Published: May 2007

Purpose To conduct a phase III trial of adjuvant 13-cis-retinoic acid (13cRA) plus interferon alfa (IFN-α) for preventing tumor recurrence and second primary tumors (SPTs) of skin squamous cell carcinoma (SCC) among patients with aggressive skin SCC. Patients and Methods Sixty-six patients with aggressive skin SCC were randomly assigned to receive either 6 months of combined 13cRA (1 mg/kg/d orally) and IFN-α (3 × 106 U subcutaneously three times per week) or no adjuvant therapy (control group) after SCC surgery and/or radiation. Results At 21.5 months median follow-up, treatment did not improve the time to tumor recurrence and SPT versus control (hazard ratio [HR], 1.13; 95% CI, 0.53 to 2.41), time to tumor recurrence (HR, 1.08; 95% CI, 0.43 to 2.72), or time to SPT (HR, 0.89; 95% CI, 0.27 to 2.93). Adjuvant 13cRA and IFN-α was moderately tolerable; 29% of patients in the treatment arm required dose reductions for grade 3 or 4 toxicities. Conclusion Results of this phase III trial do not support 13cRA plus IFN-α for adjuvant therapy of aggressive skin SCC. With high rates of tumor recurrence and SPTs, patients with aggressive skin SCC continue to have an unmet medical need, with devastating mortality, morbidity, and financial consequences. Promising agents with preclinical and early clinical results relevant to aggressive skin SCC deserve a high priority for future clinical drug development.
Proposal for Standardized Definitions for Efficacy End Points in Adjuvant Breast Cancer Trials: The STEEP System
Authors: Hudis Clifford A. , Barlow William E. , Costantino Joseph P. , Gray Robert J. , Pritchard Kathleen I. , Chapman Judith-Anne W. , Sparano Joseph A. , Hunsberger Sally , Enos Rebecca A. , Gelber Richard D. , Zujewski Jo Anne 
Published: May 2007

Purpose Standardized definitions of breast cancer clinical trial end points must be adopted to permit the consistent interpretation and analysis of breast cancer clinical trials and to facilitate cross-trial comparisons and meta-analyses. Standardizing terms will allow for uniformity in data collection across studies, which will optimize clinical trial utility and efficiency. A given end point term (eg, overall survival) used in a breast cancer trial should always encompass the same set of events (eg, death attributable to breast cancer, death attributable to cause other than breast cancer, death from unknown cause), and, in turn, each event within that end point should be commonly defined across end points and studies. Methods A panel of experts in breast cancer clinical trials representing medical oncology, biostatistics, and correlative science convened to formulate standard definitions and address the confusion that nonstandard definitions of widely used end point terms for a breast cancer clinical trial can generate. We propose standard definitions for efficacy end points and events in early-stage adjuvant breast cancer clinical trials. In some cases, it is expected that the standard end points may not address a specific trial question, so that modified or customized end points would need to be prospectively defined and consistently used. Conclusion The use of the proposed common end point definitions will facilitate interpretation of trial outcomes. This approach may be adopted to develop standard outcome definitions for use in trials involving other cancer sites.
Drug addiction from a psychodynamic perspective: Methadone maintenance treatment (MMT) as transitional phenomena
Authors: Potik David , Adelson Miriam , Schreiber Shaul 
Published: May 2007

Purpose. To present a psychodynamic (specifically object‐relations) approach to the understanding of drug addiction and recovery among patients in Methadone Maintenance Treatment (MMT), and to discuss the role of psychodynamic psychotherapy among drug addicts, focusing on the processes which patients undergo during counselling.Methods. We review some psychodynamic explanations of the drug addiction phenomenon, and illustrate the psychodynamic comprehension framework of the issue according to Winnicott's theory, by describing a few psychotherapeutic interventions with our MMT patients.Results. The main premise is that treatment in a MMT program is accompanied by changes in‐patients' life‐styles and behaviour, which are parallel to transitional phenomena. As such, methadone and counselling serve as transitional objects during these processes.Conclusions. Drug addiction is a widespread phenomenon that affects many areas in the addicts' life; therefore, some eclecticism from therapists has a beneficial effect on the outcome.
Quality assurance in thermodynamic databases for performance assessment studies in waste disposal
Authors: Voigt W. , Brendler V. , Marsh K. , Rarey R. , Wanner H. , Gaune-Escard M. , Cloke P. , Vercouter Th. , Bastrakov E. , Hagemann S. 
Published: May 2007

Abstract
Performance assessment studies in underground disposal of radioactive or toxic waste need to consider all reactive interactions between waste and its surroundings. Thermodynamic equilibrium and reaction path calculations represent an important tool for this purpose. The reliability of the results depends first of all on the quality of the thermodynamic database used for the calculations. Several quality criteria of thermodynamic databases are discussed in connection with the characteristics of current database projects [Nuclear Energy Agency Thermochemical Database (NEA-TDB), Yucca Mountain database, Dortmund Databank (DDB), Common Thermodynamic Database (CTD), FreeGS, and Thermodynamic Reference Database (THEREDA)] including the situation for molten salts. The future role of the IUPAC standard for thermophysical and thermochemical data storage is emphasized.