bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Characterization of IS
CR8
, IS
CR22
, and IS
CR23
, Subgroups of IS
91
-Like Insertion Elements
Authors: Schleinitz Kathleen M. , Vallaeys Tatiana , Kleinsteuber Sabine 
Published: July 2010

ABSTRACT

Analysis of IS
CR8
(IS
Pps1
) revealed that this group of insertion elements has to be subdivided into three subgroups: IS
CR8
, IS
CR22
, and IS
CR23
. The distinction of three subgroups is supported by phylogenetic analysis of the transposase open reading frames (ORFs). Comparison of over 20 complete and partial IS
CR8
/
22/23
elements identified
ori
IS candidate sequences for all groups and a
ter
IS candidate sequence for IS
CR8
. The
ori
IS sequences, their distance to the transposase ORFs, and the sequence of this intervening region are group specific, further supporting the definition of two new IS
CR
elements. IS
CR8/22/23
have a very broad host range, including Gram-positive and Gram-negative bacteria, among which are several (opportunistic) pathogens. The IS often resides on plasmids or in the vicinity of other mobile elements and is mostly associated with genes for the degradation of halo- or nitro-aromatics. However, in one case IS
CR8
was found in the neighborhood of an antibiotic resistance determinant in
Klebsiella pneumoniae
. IS
CR8
resembles other IS91 family elements in mediating genetic rearrangements by homologous recombination between two copies. In
Delftia acidovorans
this led to the loss of the genes encoding dichlorprop cleavage. In conclusion, this study shows that IS
CR8
could be a fully functional and active member of the IS
91
family of insertion elements.
Phosphorothioate 2′ Deoxyribose Oligomers as Microbicides That Inhibit Human Immunodeficiency Virus Type 1 (HIV-1) Infection and Block Toll-Like Receptor 7 (TLR7) and TLR9 Triggering by HIV-1
Authors: Fraietta Joseph A. , Mueller Yvonne M. , Do Duc H. , Holmes Veronica M. , Howett Mary K. , Lewis Mark G. , Boesteanu Alina C. , Alkan Sefik S. , Katsikis Peter D. 
Published: July 2010

ABSTRACTTopical microbicides may prove to be an important strategy for preventing human immunodeficiency virus type 1 (HIV-1) transmission. We examined the safety and efficacy of sequence-nonspecific phosphorothioate 2′ deoxyribose oligomers as potential novel microbicides. A short, 13-mer poly(T) phosphorothioate oligodeoxynucleotide (OPB-T) significantly inhibited infection of primary peripheral blood mononuclear cells (PBMC) by high-titer HIV-1Ba-Land simian immunodeficiency virus mac251 (SIVmac251). Continuous exposure of human vaginal and foreskin tissue explants to OPB-T showed no toxicity. An abasic 14-mer phosphorothioate 2′ deoxyribose backbone (PDB) demonstrated enhanced anti-HIV-1 activity relative to OPB-T and other homo-oligodeoxynucleotide analogs. When PDB was used to pretreat HIV-1, PDB was effective against R5 and X4 isolates at a half-maximal inhibitory concentration (IC50) of <1 μM in both PBMC and P4-R5 MAGI cell infections. PDB also reduced HIV-1 infectivity following the binding of virus to target cells. This novel topical microbicide candidate exhibited an excellentin vitrosafety profile in human PBMC and endocervical epithelial cells. PDB also retained activity in hydroxyethylcellulose gel at pH 4.4 and after transition to a neutral pH and was stable in this formulation for 30 days at room temperature. Furthermore, the compound displayed potent antiviral activity following incubation with aLactobacillusstrain derived from normal vaginal flora. Most importantly, PDB can inhibit HIV-1-induced alpha interferon production. Phosphorothioate 2′ deoxyribose oligomers may therefore be promising microbicide candidates that inhibit HIV-1 infection and also dampen the inflammation which is critical for the initial spread of the virus.
Efficacy of PTX3 in a Rat Model of Invasive Aspergillosis
Authors: Lo Giudice Pietro , Campo Silvia , Verdoliva Antonio , Rivieccio Vincenzo , Borsini Franco , De Santis Rita , Salvatori Giovanni 
Published: July 2010

ABSTRACT

Pentraxin 3 (PTX3) is an acute-phase glycoprotein with a nonredundant function in the host resistance to
Aspergillus fumigatus
. PTX3 activity was evaluated against pulmonary aspergillosis in rats immunosuppressed with cortisone acetate. PTX3 enhanced the survival rate and reduced the lung fungal burden of infected rats in both therapeutic and prophylactic modalities. Thus, we extended the protective activity of PTX3 in pulmonary aspergillosis to corticosteroid-induced immunodeficiency, which is a relevant clinical condition in graft-versus-host disease and in solid organ transplant.
The changing effects of Alaska’s boreal forests on the climate systemThis article is one of a selection of papers from The Dynamics of Change in Alaska’s Boreal Forests: Resilience and Vulnerability in Response to Climate Warming.
Authors: Euskirchen E.S. , McGuire A.D. , Chapin F.S. , Rupp T.S. 
Published: July 2010

In the boreal forests of Alaska, recent changes in climate have influenced the exchange of trace gases, water, and energy between these forests and the atmosphere. These changes in the structure and function of boreal forests can then feed back to impact regional and global climates. In this manuscript, we examine the type and magnitude of the climate feedbacks from boreal forests in Alaska. Research generally suggests that the net effect of a warming climate is a positive regional feedback to warming. Currently, the primary positive climate feedbacks are likely related to decreases in surface albedo due to decreases in snow cover. Fewer negative feedbacks have been identified, and they may not be large enough to counterbalance the large positive feedbacks. These positive feedbacks are most pronounced at the regional scale and reduce the resilience of the boreal vegetation – climate system by amplifying the rate of regional warming. Given the recent warming in this region, the large variety of associated mechanisms that can alter terrestrial ecosystems and influence the climate system, and a reduction in the boreal forest resilience, there is a strong need to continue to quantify and evaluate the feedback pathways.
The role of mosses in ecosystem succession and function in Alaska’s boreal forestThis article is one of a selection of papers from The Dynamics of Change in Alaska’s Boreal Forests: Resilience and Vulnerability in Response to Climate Warming.
Authors: Turetsky Merritt R. , Mack Michelle C. , Hollingsworth Teresa N. , Harden Jennifer W. 
Published: July 2010

Shifts in moss communities may affect the resilience of boreal ecosystems to a changing climate because of the role of moss species in regulating soil climate and biogeochemical cycling. Here, we use long-term data analysis and literature synthesis to examine the role of moss in ecosystem succession, productivity, and decomposition. In Alaskan forests, moss abundance showed a unimodal distribution with time since fire, peaking 30–70 years post-fire. We found no evidence of mosses compensating for low vascular productivity in low-fertility sites at large scales, although a trade-off between moss and vascular productivity was evident in intermediate-productivity sites. Mosses contributed 48% and 20% of wetland and upland productivity, respectively, but produced tissue that decomposed more slowly than both nonwoody and woody vascular tissues. Increasing fire frequency in Alaska is likely to favor feather moss proliferation and decrease Sphagnum abundance, which will reduce soil moisture retention and decrease peat accumulation, likely leading to deeper burning during wildfire and accelerated permafrost thaw. The roles of moss traits in regulating key aspects of boreal performance (ecosystem N supply, C sequestration, permafrost stability, and fire severity) represent critical areas for understanding the resilience of Alaska’s boreal forest region under changing climate and disturbance regimes.
Resilience of Alaska’s boreal forest to climatic changeThis article is one of a selection of papers from The Dynamics of Change in Alaska’s Boreal Forests: Resilience and Vulnerability in Response to Climate Warming.
Authors: Chapin F.S. , McGuire A.D. , Ruess R.W. , Hollingsworth T.N. , Mack M.C. , Johnstone J.F. , Kasischke E.S. , Euskirchen E.S. , Jones J.B. , Jorgenson M.T. , Kielland K. , Kofinas G.P. , Turetsky M.R. , Yarie J. , Lloyd A.H. , Taylor D.L. 
Published: July 2010

This paper assesses the resilience of Alaska’s boreal forest system to rapid climatic change. Recent warming is associated with reduced growth of dominant tree species, plant disease and insect outbreaks, warming and thawing of permafrost, drying of lakes, increased wildfire extent, increased postfire recruitment of deciduous trees, and reduced safety of hunters traveling on river ice. These changes have modified key structural features, feedbacks, and interactions in the boreal forest, including reduced effects of upland permafrost on regional hydrology, expansion of boreal forest into tundra, and amplification of climate warming because of reduced albedo (shorter winter season) and carbon release from wildfires. Other temperature-sensitive processes for which no trends have been detected include composition of plant and microbial communities, long-term landscape-scale change in carbon stocks, stream discharge, mammalian population dynamics, and river access and subsistence opportunities for rural indigenous communities. Projections of continued warming suggest that Alaska’s boreal forest will undergo significant functional and structural changes within the next few decades that are unprecedented in the last 6000 years. The impact of these social–ecological changes will depend in part on the extent of landscape reorganization between uplands and lowlands and on policies regulating subsistence opportunities for rural communities.
Uncertainty assessment of forest road modeling with the Distributed Hydrology Soil Vegetation Model (DHSVM)
Authors: Surfleet Christopher G. , Skaugset Arne E. , McDonnell Jeffrey J. 
Published: July 2010

We used a generalized likelihood uncertainty estimation procedure with the Distributed Hydrology Soil Vegetation Model (DHSVM) for two streamflow and 11 road ditchflow locations. We observed considerable uncertainty in DHSVM simulations of forest road and stream runoff. The accuracy of simulations decreased as the size of the area modeled decreased. For streamflow, 44% of attempted model structures exceeded a 0.5 Nash–Sutcliffe efficiency threshold for a 630 ha catchment; 12% of attempted model structures exceeded a 0.5 Nash–Sutcliffe efficiency threshold for a 55 ha catchment. DHSVM simulations produced behavioral model structures for only six of the 11 road ditchflow sites (<10 ha). Cumulative distribution functions of parameter values did not indicate specific parameter ranges of parameter values across all locations, indicating that parameter values in DHSVM are influenced by their interaction with other parameters. The sensitivity of parameters and the range of that sensitivity varied across simulations of road ditchflow and streamflow. DHSVM simulations for two streamflow locations varied outside the uncertainty bounds for 10%–22% of storm volumes and 12%–22% of peak flows, respectively. Twenty-eight percent to 52% of storm volumes and 28%–48% of peak flows were outside the uncertainty bounds for the six road ditchflow locations.
Adsorption of the herbicide terbuthylazine across a range of New Zealand forestry soils
Authors: Watt Michael S. , Wang Hailong , Rolando Carol A. , Zaayman Morkel , Martin Katrina 
Published: July 2010

The growing importance of environmental certification in plantation forestry is increasing the pressure to discontinue the use of chemicals including herbicides classified as highly hazardous. One of these herbicides is terbuthylazine, a triazine used widely to control a broad range of weeds in plantation forests in New Zealand. Using soil samples obtained from a national trial series, the key objectives of this study were to (i) determine the variation in soil adsorption of terbuthylazine as measured by distribution constant (Kd) across a range of soil types and (ii) develop a multiple regression model to predict Kd from key soil chemical properties. Across the 34 sampled sites, Kd averaged 21.9 L·kg–1 and ranged 38-fold from 3.9 to 146.7 L·kg–1. There was a highly significant (P < 0.0001) relationship between organic carbon and Kd, which was best described by a power function, that explained 86% of the variance in Kd. Addition of pH to the model using an exponential decay function was significant and increased the R2 for the model to 0.99. Across soil orders, Kd varied significantly by 10-fold. Values of Kd were lowest on Raw and Recent soil orders, which have low soil organic carbon and a relatively high pH.
Quantitative characterization of textures in mantle spinel peridotite xenoliths
Authors: Tabor Felicity A. , Tabor Bryan E. , Downes Hilary 
Published: July 2010

Abstract
A method for quantitative characterization of grain size in thin sections has been established for mantle spinel peridotite xenoliths, using optical scanning of large areas of thin sections, skeletonization of grain-section outlines and computerized measurement of individual grain-section areas. Measurements range from 218 for the coarsest example to more than 3000 in the finest grained. Variability of the samples has been examined in relation to size and number of grain-section areas measured by using multiple and orthogonal sections from several xenoliths. The results show a linear relationship of arithmetic mean against additive standard deviation, including data from coarse-grained protogranular, through porphyroclastic to the finer-grained equigranular examples. This suggests that peridotite textures form a continuous series rather than discrete groups, as suggested by qualitative (subjective) assessment. The observed distributions of grain-section areas have been explored in relation to their description and possible mechanistic origin. By direct measurement and comparison of cumulative number and area distribution curves, we show that qualitatively assessed ‘typical grain sizes’ are influenced by a small number of larger grain sections. Although the arithmetic mean and standard deviation provide a convenient method for comparison, in practice grain-section area distributions show marked positive skewness more consistent with log-normal or power-law functions. Linear log-probability curves also support the existence of a continuous series of peridotite textures, suggesting that the shallow lithospheric mantle has been subject to processes of comminution and/or grain growth dependent on the Law of Proportionate Effect.

Supplementary material:

Details of resolution and boundary recognition can be found at
http://www.geolsoc.org.uk/SUP18398
.
The Lanzo peridotite massif, Italian Western Alps: Jurassic rifting of the Ligurian Tethys
Authors: Piccardo Giovanni B. 
Published: July 2010

Abstract
The Lanzo Massif in the Western Alps consists of three bodies (North, Central and South) of mantle peridotites that were exhumed from the subcontinental mantle lithosphere to the sea floor during lithosphere extension related to the formation of the Jurassic Ligurian Tethys oceanic basin. The North Lanzo protoliths were located at shallower lithospheric levels than the South Lanzo protoliths. During exhumation, early MORB-type fractional melts from the asthenosphere infiltrated and modified the South Lanzo protoliths. Later on, aggregate MORB melts passed through the South Lanzo peridotites, migrating within replacive peridotite channels, and impregnated the North Lanzo peridotites. Ongoing lithosphere extension and stretching caused break-up of the continental crust and sea-floor exposure of the Lanzo peridotites. The North Lanzo peridotites, deriving from shallower lithospheric levels, were exhumed and exposed at more external ocean–continent transition (OCT) zones of the basin, whereas the South Lanzo peridotites, deriving from deeper lithospheric levels, were exhumed and exposed at more internal oceanic (MIO) settings of the basin. Field, petrographical–structural and petrological–geochemical studies on the Lanzo mantle peridotites provide mantle constraints regarding the geodynamic evolution of the Europe–Adria extensional system during the rifting and opening of the Ligurian Tethys basin.
Successful Eradication of Established Peritoneal Ovarian Tumors in SCID-Beige Mice following Adoptive Transfer of T Cells Genetically Targeted to the MUC16 Antigen
Authors: Chekmasova Alena A. , Rao Thapi D. , Nikhamin Yan , Park Kay J. , Levine Douglas A. , Spriggs David R. , Brentjens Renier J. 
Published: July 2010

Abstract
Purpose: Most patients diagnosed with ovarian cancer will ultimately die from their disease. For this reason, novel approaches to the treatment of this malignancy are needed. Adoptive transfer of a patient's own T cells, genetically modified ex vivo through the introduction of a gene encoding a chimeric antigen receptor (CAR) targeted to a tumor-associated antigen, is a novel approach to the treatment of ovarian cancer.
Experimental Design: We have generated several CARs targeted to the retained extracellular domain of MUC16, termed MUC-CD, an antigen expressed on most ovarian carcinomas. We investigate the in vitro biology of human T cells retrovirally transduced to express these CARs by coculture assays on artificial antigen-presenting cells as well as by cytotoxicity and cytokine release assays using the human MUC-CD+ ovarian tumor cell lines and primary patient tumor cells. Further, we assess the in vivo antitumor efficacy of MUC-CD–targeted T cells in SCID-Beige mice bearing peritoneal human MUC-CD+ tumor cell lines.
Results: CAR-modified, MUC-CD–targeted T cells exhibited efficient MUC-CD–specific cytolytic activity against both human ovarian cell and primary ovarian carcinoma cells in vitro. Furthermore, expanded MUC-CD–targeted T cells infused through either i.p. injection or i.v. infusion into SCID-Beige mice bearing orthotopic human MUC-CD+ ovarian carcinoma tumors either delayed progression or fully eradicated disease.
Conclusion: These promising preclinical studies justify further investigation of MUC-CD–targeted T cells as a potential therapeutic approach for patients with high-risk MUC16+ ovarian carcinomas. Clin Cancer Res; 16(14); 3594–606. ©2010 AACR.
International Standards and National Ownership? Judicial Independence in Hybrid Courts: The Extraordinary Chambers in the Courts of Cambodia
Authors: Bertelman Hanna 
Published: July 2010

AbstractThe Extraordinary Chambers in the Courts of Cambodia (ECCC) was established in 2004 through an agreement between the United Nations (UN) and the Cambodian government, as a means to address the crimes committed during the Khmer Rouge regime in Cambodia between 1975 and 1979. The ECCC is one in a row of international judicial institutions set up in response to gross violations of human rights, known as 'hybrid' courts, encompassing both national and international elements in their structure, composition and jurisdiction. Hybrid courts, allowing for a higher degree of participation by national actors, are expected to be better placed to give long-lasting effects in the societies in which mass atrocities have taken place. This article examines that claim with regard to the ECCC, and explores the value added by participation by various national actors in the judicial proceedings. After giving an overview of international standards of judicial independence, it provides an analysis of concerns that may be raised with regard to the judicial independence of the ECCC. This article argues that some aspects of national ownership may be promoted at the cost of lowering international standards of justice, and may cause an overall lack of ownership or accountability of the proceedings.
The Responsibility to Protect: A Legal and Rights-based Perspective
Authors: Gierycz Dorota 
Published: July 2010

AbstractThis article analyses the responsibility to protect from a legal and rights-based perspective. It shows that the responsibility to protect populations from genocide, war crimes, ethnic cleansing and crimes against humanity is rooted in existing International Human Rights Law (IHRL) and International Humanitarian Law (IHL). These crimes fall under the jurisdiction of the International Criminal Court (ICC) and evoke serious international legal consequences under all circumstances, also if tried by national courts. Protection of the individual against atrocities is a primary responsibility of states. However, if a state is unable or unwilling to exercise its protection obligations, these shift to international organisations, including the United Nations or any other authority controlling the territory and its population. The article further analyses various protection tools available within the UN human rights machinery, in particular the Human Rights Council (HRC) and the Office of the High Commissioner for Human Rights (OHCHR) and concludes that they could play a much stronger role in preventing and addressing the atrocities and that the most important obstacle in this respect is the prevailing institutional gap between human rights and security matters within the UN. The article concludes that the responsibility to protect clause adopted by consensus by the 2005 World Summit in its Outcome Document (GA Resolution A/60/1) constitutes an important commitment towards implementing these universal rights and obligations which are lacking enforcement and continue to be violated, especially in armed conflicts. It also identifies research and policy recommendations that may facilitate operationalisation of this important clause.
Acute exacerbation of chronic obstructive pulmonary disease in primary care setting in Spain: the EPOCAP study
Authors: Murio Cristina , Soler Xavier , Pérez Maite , Calero Gabriel , Ruiz-Manzano Juan 
Published: July 2010

Background: The present study was designed to describe the clinical profile of acute exacerbations of chronic obstructive pulmonary disease (COPD) and the treatment prescribed by primary care physicians (PCPs) in Spain. Method: An observational, multicenter and cross-sectional study was performed in patients diagnosed with acute exacerbation of COPD and treated by PCPs. Patients diagnosed with asthma, cystic fibrosis, significant bronchiectasis or pneumonia were not included in the study. Results: A total of 329 general physicians recruited 1088 evaluable patients across the country. Mean age was 66.5±10.2 years; male : female ratio was 3 : 1. Spirometry was performed in 28.3% of the patients. The number of acute exacerbations in the last year was 3.3±2.5; 88.7% had increased expectoration, 87.5% increased dyspnea, 64.4% increased sputum purulence, and 43.5% fever. A total of 6.1% ( n = 59) of patients were hospitalized due to exacerbation. The most frequently prescribed medications were antibiotics (84.5%, n = 919), mucolytic agents (72.5%, n = 789), inhaled corticosteroids (ICs) (71.3%, n = 776), and short-acting beta-adrenergic drugs (67.8%, n = 738). Oral corticosteroids were prescribed to 436 patients (40.1%). Conclusions: The clinical profile of acute exacerbations of COPD treated in a primary care setting in Spain was characterized by shortness of breath and increased sputum production. Patients were managed by PCP mainly in outpatient clinics with antibiotics, mucolytic agents, inhaled corticosteroids, oral corticosteroids and short-acting beta-adrenergic agents. The percentage of patients with confirmed diagnosis of COPD by pulmonary function tests was very low.