bluuebunny/crossref_metadata_2025 huggingface dataset:
X‐ray imaging performance of scintillator‐filled silicon pore arrays
Authors: Simon Matthias , Engel Klaus Jürgen , Menser Bernd , Badel Xavier , Linnros Jan
Published: March 2008

The need for fine detail visibility in various applications such as dental imaging, mammography, but also neurology and cardiology, is the driver for intensive efforts in the development of new x‐ray detectors. The spatial resolution of current scintillator layers is limited by optical diffusion. This limitation can be overcome by a pixelation, which prevents optical photons from crossing the interface between two neighboring pixels. In this work, an array of pores was etched in a silicon wafer with a pixel pitch of . A very high aspect ratio was achieved with wall thicknesses of and pore depths of about . Subsequently, the pores were filled with Tl‐doped cesium iodide (CsI:Tl) as a scintillator in a special process, which includes powder melting and solidification of the CsI. From the sample geometry and x‐ray absorption measurement the pore fill grade was determined to be 75%. The scintillator‐filled samples have a circular active area of 16 mm diameter. They are coupled with an optical sensor binned to the same pixel pitch in order to measure the x‐ray imaging performance. The x‐ray sensitivity, i.e., the light output per absorbed x‐ray dose, is found to be only 2.5%–4.5% of a commercial CsI‐layer of similar thickness, thus very low. The efficiency of the pores to transport the generated light to the photodiode is estimated to be in the best case 6.5%. The modulation transfer function is 40% at 4 lp/mm and 10%–20% at 8 lp/mm. It is limited most likely by the optical gap between scintillator and sensor and by ‐escape quanta. The detective quantum efficiency (DQE) is determined at different beam qualities and dose settings. The maximum DQE(0) is 0.28, while the x‐ray absorption with the given thickness and fill factor is 0.57. High Swank noise is suspected to be the reason, mainly caused by optical scatter inside the CsI‐filled pores. The results are compared to Monte Carlo simulations of the photon transport inside the pore array structure. In addition, some x‐ray images of technical and anatomical phantoms are shown. This work shows that scintillator‐filled pore arrays can provide x‐ray imaging with high spatial resolution, but are not suitable in their current state for most of the applications in medical imaging, where increasing the x‐ray doses cannot be tolerated.
Effect of Ketoconazole on the Pharmacokinetics of Maribavir in Healthy Adults
Authors: Goldwater D. Ronald , Dougherty Carolyn , Schumacher Mary , Villano Stephen A.
Published: March 2008

Maribavir, an oral antiviral drug with activity against cytomegalovirus, is currently undergoing studies to assess its efficacy and safety as cytomegalovirus prophylaxis following stem cell or solid organ transplantation. The main objective of this study was to assess the effects of oral ketoconazole, a potent inhibitor of the cytochrome P450 3A4 (CYP3A4) isoenzyme, on the pharmacokinetics of maribavir. This was an open-label crossover study with 20 healthy adults. Subjects were administered a single dose of maribavir at 400 mg. After a washout period, subjects received a single dose of ketoconazole at 400 mg followed by a single dose of maribavir. Blood samples were collected for each drug sequence, and pharmacokinetic parameters for maribavir and its principal metabolite, VP 44469, were determined. Safety was evaluated by physical examination, clinical laboratory testing, 12-lead electrocardiogram, and monitoring for adverse events. Ketoconazole moderately reduced the clearance of both maribavir and VP 44469; oral clearance values were 35% and 13% lower, respectively, for maribavir-plus-ketoconazole treatment than for maribavir alone. Based on the assumption of complete inhibition of CYP3A4 activity, CYP3A4 is responsible for 35% of the overall clearance of maribavir. Treatment was generally well tolerated. The most-common adverse event was dysgeusia (taste disturbance), reported by nine (47%) and seven (35%) subjects in the maribavir alone and maribavir-plus-ketoconazole groups, respectively. The pharmacokinetic findings, in combination with the acceptable tolerability within the maribavir and maribavir-plus-ketoconazole treatment groups, suggest that no dose adjustment of maribavir is necessary when coadministered with CYP3A4 inhibitors or substrates.
Persistence ofBorrelia burgdorferifollowing Antibiotic Treatment in Mice
Authors: Hodzic Emir , Feng Sunlian , Holden Kevin , Freet Kimberly J. , Barthold Stephen W.
Published: March 2008

The effectiveness of antibiotic treatment was examined in a mouse model of Lyme borreliosis. Mice were treated with ceftriaxone or saline solution for 1 month, commencing during the early (3 weeks) or chronic (4 months) stages of infection withBorrelia burgdorferi. Tissues from mice were tested for infection by culture, PCR, xenodiagnosis, and transplantation of allografts at 1 and 3 months after completion of treatment. In addition, tissues were examined for the presence of spirochetes by immunohistochemistry. In contrast to saline solution-treated mice, mice treated with antibiotic were consistently culture negative, but tissues from some of the mice remained PCR positive, and spirochetes could be visualized in collagen-rich tissues. Furthermore, when some of the antibiotic-treated mice were fed on byIxodes scapularisticks (xenodiagnosis), spirochetes were acquired by the ticks, as determined based upon PCR results, and ticks from those cohorts transmitted spirochetes to naïve SCID mice, which became PCR positive but culture negative. Results indicated that following antibiotic treatment, mice remained infected with nondividing but infectious spirochetes, particularly when antibiotic treatment was commenced during the chronic stage of infection.
Iminosugars in Combination with Interferon and Ribavirin Permanently Eradicate Noncytopathic Bovine Viral Diarrhea Virus from Persistently Infected Cells
Authors: Woodhouse Stephen D. , Smith Caroline , Michelet Maud , Branza-Nichita Norica , Hussey Mark , Dwek Raymond A. , Zitzmann Nicole
Published: March 2008

We evaluated interferon (IFN) and ribavirin (RBV) as dual therapy and as part of triple-combination therapies with the iminosugarsN-butyl-deoxynojirimycin (NB-DNJ),N-nonyl-deoxynojirimycin, andN-7-oxanonyl-6-deoxymethyl-galactonojirimycin. The ability of these compounds to clear bovine viral diarrhea virus (BVDV), a surrogate model for hepatitis C virus (HCV), from a persistently infected Madin-Darby bovine kidney cells cell line was determined by monitoring the secretion of viral RNA and the infectivity of secreted virions. In the BVDV system, after treatment with IFN-RBV alone, viral rebound was observed immediately after removal of the drugs. In contrast, we demonstrate that a triple drug combination of IFN, RBV, and an iminosugar eradicated the BVDV infection in a time- and a dose-dependent manner, leading to sustained viral clearance. Importantly, in the case ofNB-DNJ, the sustained viral clearance was achieved by using physiologically relevant and tolerated drug concentrations. Therefore, the use of a triple-combination therapy that includes an iminosugar may prove to be of greater therapeutic value for the treatment of HCV infection than the use of IFN-RBV alone.
Single-Dose Safety and Pharmacokinetics of ST-246, a Novel Orthopoxvirus Egress Inhibitor
Authors: Jordan Robert , Tien Deborah , Bolken Tove' C. , Jones Kevin F. , Tyavanagimatt Shanthakumar R. , Strasser Josef , Frimm Annie , Corrado Michael L. , Strome Phoebe G. , Hruby Dennis E.
Published: March 2008

ST-246 is a novel, potent orthopoxvirus egress inhibitor that is being developed to treat pathogenic orthopoxvirus infections of humans. This phase I, double-blind, randomized, placebo-controlled single ascending dose study (first time with humans) was conducted to determine the safety, tolerability, and pharmacokinetics of ST-246 in healthy human volunteers. ST-246 was administered in single oral doses of 500, 1,000, and 2,000 mg to fasting healthy volunteers and 1,000 mg to nonfasting healthy volunteers. ST-246 was generally well tolerated with no serious adverse events, and no subject was withdrawn from the study due to ST-246. The most commonly reported drug-related adverse event was neutropenia, which was found, upon further analysis, not to be treatment related. ST-246 was readily absorbed following oral administration with mean times to maximum concentration from 2 h to 3 h. Absorption was greater in nonfasting volunteers than in fasting volunteers. Administration of ST-246 resulted in exposure levels predicted to be sufficient for inhibiting orthopoxvirus replication compared to exposure levels in nonhuman primates in which ST-246 protected animals from lethal orthopoxvirus infection.
In Vitro Activities of the Rx-01 Oxazolidinones against Hospital and Community Pathogens
Authors: Lawrence Laura , Danese Paul , DeVito Joe , Franceschi Francois , Sutcliffe Joyce
Published: March 2008

Rx-01_423 and Rx-01_667 are two members of the family of oxazolidinones that were designed using a combination of computational and medicinal chemistry and conventional biological techniques. The compounds have a two- to eightfold-improved potency over linezolid against serious gram-positive pathogens, including methicillin-resistant
Staphylococcus aureus
(MRSA), multidrug-resistant streptococci, and vancomycin-resistant enterococci. This enhanced potency extends to the coverage of linezolid-resistant gram-positive microbes, especially multidrug-resistant enterococci and pneumococci. Compounds from this series expand the spectrum compared with linezolid to include fastidious gram-negative organisms like
Haemophilus influenzae
and
Moraxella catarrhalis
. Like linezolid, the Rx-01 compounds are bacteriostatic against MRSA and enterococci but are generally bactericidal against
S. pneumoniae
and
H. influenzae
.
Differential Effects of Quinoline Antimalarials on Endocytosis inPlasmodium falciparum
Authors: Roberts Lindi , Egan Timothy J. , Joiner Keith A. , Hoppe Heinrich C.
Published: March 2008

The effects of quinoline antimalarials on endocytosis byPlasmodium falciparumwas investigated by measuring parasite hemoglobin levels, peroxidase uptake, and transport vesicle content. Mefloquine, quinine, and halofantrine inhibited endocytosis, and chloroquine inhibited vesicle trafficking, while amodiaquine shared both effects. Protease inhibitors moderated hemoglobin perturbations, suggesting a common role for heme binding.
Enhanced Resistance to Bacterial Infection in Protegrin-1 Transgenic Mice
Authors: Cheung Queenie C. K. , Turner Patricia V. , Song Cheng , Wu De , Cai Hugh Y. , MacInnes Janet I. , Li Julang
Published: March 2008

Antibiotic-resistant bacteria have become a public health concern. It was suggested that one source of resistant pathogens may be food-producing animals. Alternative approaches are therefore needed to enhance the resistance of farm animals to bacterial infection. Protegrin-1 (PG-1) is a neutrophil-derived antimicrobial peptide that possesses activity against a wide range of bacteria and enveloped viruses. Here we report on the production of transgenic mice that ectopically expressed PG-1 and compare their susceptibilities toActinobacillus suisinfection with those of their wild-type (WT) littermates. Of the 126 mice that were challenged withA. suis, 87% of the transgenic mice survived, whereas 31% of their WT littermates survived. The PG-1 transgenic mice had significantly lower bacterial loads in their lungs and reduced numbers of pulmonary pathological lesions. The antimicrobial function of PG-1 was confirmed in vitro by using fibroblast cells isolated from the transgenic mice but not the WT mice. Moreover, differential blood cell counts in bronchoalveolar lavage fluid indicated greater number of neutrophils in PG-1 transgenic mice than in their WT littermates after bacterial challenge. Our data suggest that the ectopic expression of PG-1 in mice confers enhanced resistance to bacterial infection, laying the foundation for the development of livestock with improved resistance to infection.
Composition of the Surface Proteome ofAnaplasma marginaleand Its Role in Protective Immunity Induced by Outer Membrane Immunization
Authors: Noh Susan M. , Brayton Kelly A. , Brown Wendy C. , Norimine Junzo , Munske Gerhard R. , Davitt Christine M. , Palmer Guy H.
Published: March 2008

Surface proteins of tick-borne, intracellular bacterial pathogens mediate functions essential for invasion and colonization. Consequently, the surface proteome of these organisms is specifically relevant from two biological perspectives, induction of protective immunity in the mammalian host and understanding the transition from the mammalian host to the tick vector. In this study, the surface proteome ofAnaplasma marginale, a tick-transmitted bacterial pathogen, was targeted by using surface-specific cross-linking to form intermolecular bonds between adjacent proteins. Liquid chromatography and tandem mass spectroscopy were then employed to characterize the specific protein composition of the resulting complexes. The surface complexes ofA. marginaleisolated from erythrocytes of the mammalian host were composed of multiple membrane proteins, most of which belong to a protein family, pfam01617, which is conserved among bacteria in the genusAnaplasmaand the closely related genusEhrlichia. In contrast, the surface proteome ofA. marginaleisolated from tick cells was much less complex and contained a novel protein, AM778, not identified within the surface proteome of organisms from the mammalian host. Immunization using the cross-linked surface complex induced protection against high-level bacteremia and anemia uponA. marginalechallenge of cattle and effectively recapitulated the protection induced by immunization with whole outer membranes. These results indicate that a surface protein subset of the outer membrane is capable of inducing protective immunity and serves to direct vaccine development. Furthermore, the data support that remodeling of the surface proteome accompanies the transition between mammalian and arthropod hosts and identify novel targets for blocking transmission.
Pseudomonas aeruginosa
Induces Membrane Blebs in Epithelial Cells, Which Are Utilized as a Niche for Intracellular Replication and Motility
Authors: Angus Annette A. , Lee Amanda Ackerman , Augustin Danielle K. , Lee Ellen J. , Evans David J. , Fleiszig Suzanne M. J.
Published: March 2008

Pseudomonas aeruginosa
is known to invade epithelial cells during infection and in vitro. However, little is known of bacterial or epithelial factors modulating
P. aeruginosa
intracellular survival or replication after invasion, except that it requires a complete lipopolysaccharide core. In this study, real-time video microscopy revealed that invasive
P. aeruginosa
isolates induced the formation of membrane blebs in multiple epithelial cell types and that these were then exploited for intracellular replication and rapid real-time motility. Further studies revealed that the type three secretion system (T3SS) of
P. aeruginosa
was required for blebbing. Mutants lacking either the entire T3SS or specific T3SS components were instead localized to intracellular perinuclear vacuoles. Most T3SS mutants that trafficked to perinuclear vacuoles gradually lost intracellular viability, and vacuoles containing those bacteria were labeled by the late endosomal marker lysosome-associated marker protein 3 (LAMP-3). Interestingly, mutants deficient only in the T3SS translocon structure survived and replicated within the vacuoles that did not label with LAMP-3. Taken together, these data suggest two novel roles of the
P. aeruginosa
T3SS in enabling bacterial intracellular survival: translocon-dependent formation of membrane blebs, which form a host cell niche for bacterial growth and motility, and effector-dependent bacterial survival and replication within intracellular perinuclear vacuoles.
Leishmania majorInfection Activates NF-κB and Interferon Regulatory Factors 1 and 8 in Human Dendritic Cells
Authors: Jayakumar Asha , Donovan Michael J. , Tripathi Vinita , Ramalho-Ortigao Marcelo , McDowell Mary Ann
Published: March 2008

The salient feature of dendritic cells (DC) is the initiation of appropriate adaptive immune responses by discriminating between pathogens. Using a prototypic model of intracellular infection, we previously showed thatLeishmania majorparasites prime human DC for efficient interleukin-12 (IL-12) secretion.L. majorinfection is associated with self-limiting cutaneous disease and powerful immunity. In stark contrast, the causative agent of visceral leishmaniasis,Leishmania donovani, does not prime human DC for IL-12 production. Here, we report that DC priming byL. majorinfection results in the early activation of NF-κB transcription factors and the up-regulation and nuclear translocation of interferon regulatory factor 1 (IRF-1) and IRF-8. The inhibition of NF-κB activation by the pretreatment of DC with caffeic acid phenethyl ester blocksL. major-induced IRF-1 and IRF-8 activation and IL-12 expression. We further demonstrate that IRF-1 and IRF-8 obtained fromL. major-infected human DC specifically bind to their consensus binding sites on theIL-12p35promoter, indicating thatL. majorinfection either directly stimulates a signaling cascade or induces an autocrine pathway that activates IRF-1 and IRF-8, ultimately resulting inIL-12transcription.
A Novel Sensor Kinase-Response Regulator Hybrid Controls Biofilm Formation and Type VI Secretion System Activity in
Burkholderia cenocepacia
Authors: Aubert Daniel F. , Flannagan Ronald S. , Valvano Miguel A.
Published: March 2008

Burkholderia cenocepacia
is an important opportunistic pathogen causing serious chronic infections in patients with cystic fibrosis (CF). Adaptation of
B. cenocepacia
to the CF airways may play an important role in the persistence of the infection. We have identified a sensor kinase-response regulator (BCAM0379) named AtsR in
B. cenocepacia
K56-2 that shares 19% amino acid identity with RetS from
Pseudomonas aeruginosa
.
atsR
inactivation led to increased biofilm production and a hyperadherent phenotype in both abiotic surfaces and lung epithelial cells. Also, the
atsR
mutant overexpressed and hypersecreted an Hcp-like protein known to be specifically secreted by the type VI secretion system (T6SS) in other gram-negative bacteria. Amoeba plaque assays demonstrated that the
atsR
mutant was more resistant to
Dictyostelium
predation than the wild-type strain and that this phenomenon was T6SS dependent. Macrophage infection assays also demonstrated that the
atsR
mutant induces the formation of actin-mediated protrusions from macrophages that require a functional Hcp-like protein, suggesting that the T6SS is involved in actin rearrangements. Three
B. cenocepacia
transposon mutants that were found in a previous study to be impaired for survival in chronic lung infection model were mapped to the T6SS gene cluster, indicating that the T6SS is required for infection in vivo. Together, our data show that AtsR is involved in the regulation of genes required for virulence in
B. cenocepacia
K56-2, including genes encoding a T6SS.
Population Diversity and Dynamics of
Streptococcus mitis
,
Streptococcus oralis
, and
Streptococcus infantis
in the Upper Respiratory Tracts of Adults, Determined by a Nonculture Strategy
Authors: Bek-Thomsen Malene , Tettelin Hervé , Hance Ioana , Nelson Karen E. , Kilian Mogens
Published: March 2008

We reinvestigated the clonal diversity and dynamics of
Streptococcus mitis
and two other abundant members of the commensal microbiota of the upper respiratory tract,
Streptococcus oralis
and
Streptococcus infantis
, to obtain information about the origin of frequently emerging clones in this habitat. A culture-independent method was used, based on cloning and sequencing of PCR amplicons of the housekeeping gene
gdh
, which shows remarkable, yet species-specific, genetic polymorphism. Samples were collected from all potential ecological niches in the oral cavity and pharynx of two adults on two occasions separated by 2 years. Based on analysis of close to 10,000 sequences, significant diversity was observed in populations of all three species. Fluctuations in the relative proportions of individual clones and species were observed over time. While a few clones dominated, the proportions of most clones were very small. The results show that the frequent turnover of
S. mitis
,
S. oralis
, and
S. infantis
clones observed by cultivation can be explained by fluctuations in the relative proportions of clones, most of which are below the level of detection by the traditional culture technique, possibly combined with loss and acquisition from contacts. These findings provide a platform for understanding the mechanisms that govern the balance within the complex microbiota at mucosal sites and between the microbiota and the mucosal immune system of the host.
Modulation of the Bovine Trophoblastic Innate Immune Response byBrucella abortus
Authors: Carvalho Neta Alcina V. , Stynen Ana P. R. , Paixão Tatiane A. , Miranda Karina L. , Silva Fabiana L. , Roux Christelle M. , Tsolis Renée M. , Everts Robin E. , Lewin Harris A. , Adams L. Garry , Carvalho Alex F. , Lage Andrey P. , Santos Renato L.
Published: March 2008

Brucellosis is still a widespread zoonotic disease. Very little is known about the interaction betweenBrucella abortusand trophoblastic cells, which is essential for better understanding the pathogenesis of theBrucella-induced placentitis and abortion, a key event for transmission of the disease. The goal of this study was to evaluate the profile of gene expression by bovine trophoblastic cells during infection withB. abortus. Explants of chorioallantoic membranes were inoculated withB. abortusstrain 2308. Microarray analysis was performed at 4 h after infection, and expression of cytokines and chemokines by trophoblastic cells was assessed by real-time reverse transcription-PCR at 6 and 12 h after inoculation. In addition, cytokine and chemokine expression in placentomes from experimentally infected cows was evaluated. Expression of proinflammatory genes by trophoblastic cells was suppressed at 4 h after inoculation, whereas a significant upregulation of CXC chemokines, namely, CXCL6 (GCP-2) and CXCL8 (interleukin 8), was observed at 12 but not at 6 h after inoculation. Placentomes of experimentally infected cows had a similar profile of chemokine expression, with upregulation of CXCL6 and CXCL8. Our data indicate thatB. abortusmodulates the innate immune response by trophoblastic cells, suppressing the expression of proinflammatory mediators during the early stages of infection that is followed by a delayed and mild expression of proinflammatory chemokines, which is similar to the profile of chemokine expression in the placentomes of experimentally infected cows. This trophoblastic response is likely to contribute to the pathogenesis ofB. abortus-induced placentitis.
Role of RppA in the Regulation of Polymyxin B Susceptibility, Swarming, and Virulence Factor Expression in
Proteus mirabilis
Authors: Wang Won-Bo , Chen I-Chun , Jiang Sin-Sien , Chen Hui-Ru , Hsu Chia-Yu , Hsueh Po-Ren , Hsu Wei-Bin , Liaw Shwu-Jen
Published: March 2008

Proteus mirabilis
, a human pathogen that frequently causes urinary tract infections, is intrinsically highly resistant to cationic antimicrobial peptides, such as polymyxin B (PB). To explore the mechanisms underlying
P. mirabilis
resistance to PB, a mutant which displayed increased (>160-fold) sensitivity to PB was identified by transposon mutagenesis. This mutant was found to have Tn
5
inserted into a novel gene,
rppA
. Sequence analysis indicated that
rppA
may encode a response regulator of the two-component system and is located upstream of the
rppB
gene, which may encode a membrane sensor kinase. An
rppA
knockout mutant of
P. mirabilis
had an altered lipopolysaccharide (LPS) profile. The LPS purified from the
rppA
knockout mutant could bind more PB than the LPS purified from the wild type. These properties of the
rppA
knockout mutant may contribute to its PB-sensitive phenotype. The
rppA
knockout mutant exhibited greater swarming motility and cytotoxic activity and expressed higher levels of flagellin and hemolysin than the wild type, suggesting that RppA negatively regulates swarming, hemolysin expression, and cytotoxic activity in
P. mirabilis
. PB could modulate LPS synthesis and modification, swarming, hemolysin expression, and cytotoxic activity in
P. mirabilis
through an RppA-dependent pathway, suggesting that PB could serve as a signal to regulate RppA activity. Finally, we demonstrated that the expression of
rppA
was up-regulated by a low concentration of PB and down-regulated by a high concentration of Mg
2+
. Together, these data highlight the essential role of RppA in regulating PB susceptibility and virulence functions in
P. mirabilis
.
Limited Role for Iron Regulation in
Coxiella burnetii
Pathogenesis
Authors: Briggs Heather L. , Pul Nicolein , Seshadri Rekha , Wilson Mary J. , Tersteeg Claudia , Russell-Lodrigue Kasi E. , Andoh Masako , Bäumler Andreas J. , Samuel James E.
Published: March 2008

In gram-negative bacteria, iron acquisition proteins are commonly regulated by Fur (
f
erric
u
ptake
r
egulator), which binds iron-regulated promoters (the Fur box). We hypothesized that
Coxiella burnetii
requires iron and employs an iron-regulatory system and used various approaches to define a Fur regulon. Cloned
C. burnetii fur
complemented an
Escherichia coli fur
deletion mutant. A ferrous iron transporter gene (CBU1766), a putative iron binding protein-encoding gene (CBU0970), and a cation efflux pump gene (CBU1362) were identified by genome annotation and using a Fur titration assay. Bioinformatically predicted Fur box-containing promoters were tested for transcriptional control by iron. Five genes demonstrated at least a twofold induction with minimal iron. Putatively regulated genes were evaluated in a two-plasmid regulator/promoter heterologous expression system. These data suggested a very limited Fur-regulated system in
C. burnetii
. In an in vitro tissue culture model, a significant increase in bacterial growth was observed with infected cells treated with deferoxamine in comparison to growth under iron-replete conditions. In an iron-overloaded animal model in vivo, the level of bacterial growth detected in the iron-injected animals was significantly decreased in comparison to growth in control animals. In a low-iron-diet animal model, a significant increase in splenomegaly was observed, but no significant change in bacterial growth was identified. The small number of predicted iron acquisition systems, few Fur-regulated genes, and enhanced replication under a decreased iron level predict a requirement of a low level of iron for survival, perhaps to avoid creation of additional reactive oxygen radicals.
Documenting ancient plant management in the northwest of North AmericaThis paper was submitted for the Special Issue on Ethnobotany, inspired by the Ethnobotany Symposium organized by Alain Cuerrier, Montréal Botanical Garden, and held in Montréal at the 2006 annual meeting of the Canadian Botanical Association.
Authors: Lepofsky Dana , Lertzman Ken
Published: March 2008

Ethnographic literature documents the pervasiveness of plant-management strategies, such as prescribed burning and other kinds of cultivation, among Northwest Peoples after European contact. In contrast, definitive evidence of precontact plant management has been elusive. Documenting the nature and extent of precontact plant-management strategies has relevance to historians, archaeologists, managers, conservationists, forest ecologists, and First Nations. In this paper, we summarize the various lines of evidence that have been, or could be, used to document ancient cultivation in the northwest of North America. We organize this discussion by the ecological consequences of ancient plant-management practices and their documented or potential visibility in the paleo-, neo-ecological, and archaeological records. Our review demonstrates that while finding evidence of ancient plant management can be difficult, such evidence can be found when innovative research methods are applied. Further, when various independent lines of evidence are compiled, reconstructions of past plant-management strategies are strengthened considerably.
From complex to simple: balsamroot, inulin, and the chemistry of traditional Interior Salish pit-cooking technologyThis paper was submitted for the Special Issue on Ethnobotany, inspired by the Ethnobotany Symposium organized by Alain Cuerrier, Montréal Botanical Garden, and held in Montréal at the 2006 annual meeting of the Canadian Botanical Association/l’Association Botanique du Canada.
Authors: Peacock Sandra L.
Published: March 2008

This paper presents the results of an experiment replicating traditional Interior Salish pit-cooking methods to process balsamroot ( Balsamorhiza sagittata (Pursh) Nutt.), a former food staple that contains the complex carbohydrate inulin. Analysis of fresh and cooked balsamroot samples reveals that with sufficient heat, moisture, and the release of volatile organic acids, inulin is hydrolyzed during pit cooking. This process converts complex carbohydrates into simple ones, resulting in an increase of 250% in the energy provided by simple sugars. When the average energy contributions of protein, simple and complex carbohydrates are tallied, the net result is an energy gain of approximately 65% between fresh and pit-cooked balsamroot. This research demonstrates the effectiveness of ancient pit-cooking practices in transforming unpalatable and inedible root resources into sweet-tasting, highly digestible sources of carbohydrate energy and supports my assertion that this processing technology was a key component of the wild plant food production systems of Interior Salish Peoples.
Influences of climate on the radial growth of lodgepole pine in Alberta
Authors: Chhin Sophan , Hogg E.H. (Ted) , Lieffers Victor J. , Huang Shongming
Published: March 2008

We examined a network of 17 lodgepole pine ( Pinus contorta Dougl. ex Loud. var. latifolia Engelm.) sites in Alberta in the cordilleran forests along the eastern slopes of the Rocky Mountains and in western Cypress Hills, using a dendrochronological approach to identify the principal climatic factors that have influenced the historical, regional-scale pattern of radial growth of lodgepole pine. Correlation and regression analysis of the regional growth–climate relationships showed that radial growth was negatively associated with late-summer temperatures, and positively related to the late-summer precipitation totals from the previous growth season. Radial growth also responded positively to winter and spring temperatures, and was negatively related to late winter–early spring precipitation. The results suggested that the lag in response to heat and moisture stress, cold and snowy winters, and the length of the current growing season are important determinants of the radial growth of lodgepole pine in Alberta.
Patterns of post-glacial colonization by western redcedar (Thuja plicata, Cupressaceae) as revealed by microsatellite markers
Authors: O’Connell Lisa M. , Ritland Kermit , Thompson Stacey Lee
Published: March 2008

As knowledge of historical migration in response to climatic change allows insight into the dynamic nature of range shifts, patterns of post-glacial colonization were evaluated for the western redcedar ( Thuja plicata Donn ex D. Don). We sampled and genotyped 620 trees from 23 populations across its range, including disjunct coastal and interior mesic sites. Genetic variation at eight microsatellite loci (mean alleles/locus = 10.30, mean expected heterozygosity = 0.755) was much higher than previous studies involving other markers, and inbreeding coefficients were predominantly positive (mean = 0.110). The two southernmost populations showed greatest genetic distances, while remaining populations clustered into three distinct geographic groups, comprising northern–coastal, central, and southern–interior populations, respectively. Genetic diversity decreased with latitude, while genetic and geographic distances were strongly correlated (r = 0.788). Our findings are consistent with independent routes of relatively recent colonization from one major refugium, located south of the glacial maximum, rather than ancient vicariant events. Regional bottlenecks, detected in the south of the range, may have resulted from local extinctions as the range of western redcedar advanced northward. Combined with inbreeding and the evolution of inbreeding tolerance, this may have promoted homozygosity for most classes of genetic markers as observed in other studies of this species.
Plants and habitats — a consideration of Dene ethnoecology in northwestern CanadaThis paper was submitted for the Special Issue on Ethnobotany, inspired by the Ethnobotany symposium organized by Alain Cuerrier, Montréal Botanical garden, and held in Montréal at the 2006 annual meeting of the Canadian Botanical Association/l’Association botanique du Canada.
Authors: Johnson Leslie Main
Published: March 2008

This paper discusses local understanding of plants and habitats, based on the linguistic evidence [terms for plants and (or) habitats] gathered from ethnobotanical and ethnoecological field work conducted with several Dene Nations of the Canadian northwestern boreal forest and adjacent regions. Nations involved in the study include Gwich’in (Mackenzie Delta Region), Sahtú’otine’ (Great Bear Lake), Kaska Dena (southern Yukon), and Witsuwit’en (northwest British Columbia). Key plant-related habitats include meadow, “swamp”, forest, “willows”, and “brush”. The ethnobotanical classification of willows is explored in conjunction with the explanation of the Dene habitat concept. In local classifications, ‘willow’ is not co-extensive with the genus Salix , but includes a variety of medium to tall woody shrubs that lack either conspicuous flowers, ‘berries’, or thorns; these may include shrubby species of Salix, Alnus , Cornus , and Betula . Shoreline and alpine environments are also discussed as plant habitats. Dene use of alpine environments and resources is ancient, according to the results of recent alpine ice patch research in the Yukon region. The Human dimensions of habitat knowledge are presented. Indigenous concepts of plant taxa and of landscape associations or habitats may differ substantially from those of scientific botany and ecology, and are based in a holistic and interactive ethnoecology.
Sex ratio, flowering and fruit set in dioecious Rubus chamaemorus (Rosaceae) in Labrador
Authors: Karst Amanda L. , Antos Joseph A. , Allen Geraldine A.
Published: March 2008

Rubus chamaemorus L. is a dioecious clonal herb with highly variable fruit production. Our overall objective was to determine how fruit production (and the reproductive stages leading to fruit) for R. chamaemorus varied with habitat and population (especially sex ratio) characteristics at scales from 1 m2 quadrats to whole populations in southeastern Labrador, Canada. During the climatically favourable year studied, reproductive variables were only weakly correlated with habitat characteristics. Strongly biased sex ratios were found at scales of 1–10 m. Male-dominated quadrats exhibited a significantly higher proportion of flowering ramets than did female-dominated quadrats. Female-biased sex ratios of flowering ramets and large distances between male and female flowers were correlated with decreased seed set. We found no differences in microhabitats of males and females. Although the biased local sex ratios could limit sexual reproduction, the high fruit set we measured clearly indicates that populations are able to produce abundant fruit during favourable years in this unpredictable environment.
Analysis of rock–support interaction using numerical and multiple regression modeling
Authors: Basarir Hakan
Published: March 2008

This paper presents the results of performance analysis on the support systems recommended by the RMR (rock mass rating) rock mass classification system. Rock–support interaction is analyzed by means of both numerical and multiple regression modeling. Five different rock mass conditions were assumed from very poor to very good, each representing varied RMR. Extensive computer simulations were conducted to investigate the stresses, displacements, and yielded zones around a circular opening excavated at different depths, and under different rock conditions. The performances of the RMR recommended support systems were analyzed and the stability of excavation was evaluated. Multiple regression modeling was conducted to assess the relationship between support pressure, depth, and tunnel deformation for different rock conditions. Regression models were derived and the response surfaces were constructed, showing the interaction between tunnel depth, support pressure, and tunnel displacement. Using the derived models and the constructed response surfaces, engineers are able to describe the support performance and assess the practical range of expected deformation for their specific site conditions. Also, the approach presented can be used for any special case.
Development of the K-stiffness method for geosynthetic reinforced soil walls constructed with c-ϕ soils
Authors: Miyata Yoshihisa , Bathurst Richard J.
Published: March 2008

In this paper the K-stiffness method is extended to the case of c-ϕ soils using data obtained from a total of nine new case studies – six from Japan and three from the USA. A common feature in this new data set is that the walls were all constructed with a vertical face using backfill soils with a range of fines content. The walls varied widely with respect to facing type. This new data set together with previously published data for vertical walls is now used to isolate the effect of soil cohesion on reinforcement loads within the framework of the original K-stiffness method. The new data set is used to calibrate a modified K-stiffness method equation that includes a cohesion influence factor. The modified K-stiffness method is demonstrated to quantitatively improve the estimate of the magnitude and distribution of reinforcement loads for internal stability design of vertical-faced geosynthetic reinforced soil walls with c-ϕ soil backfills when compared to the current American Association of State Highway and Transportation Officials simplified method.
A new genetic programming model for predicting settlement of shallow foundations
Authors: Rezania Mohammad , Javadi Akbar A.
Published: March 2008

In this paper, a new genetic programming (GP) approach for predicting settlement of shallow foundations is presented. The GP model is developed and verified using a large database of standard penetration test (SPT) based case histories that involve measured settlements of shallow foundations. The results of the developed GP model are compared with those of a number of commonly used traditional methods and artificial neural network (ANN) based models. It is shown that the GP model is able to learn, with a very high accuracy, the complex relationship between foundation settlement and its contributing factors, and render this knowledge in the form of a function. The attained function can be used to generalize the learning and apply it to predict settlement of foundations for new cases not used in the development of the model. The advantages of the proposed GP model over the conventional and ANN based models are highlighted.
A capillary-tube model for two-phase transient flow through bentonite materials
Authors: Siemens Greg , Blatz James A. , Ruth Douglas
Published: March 2008

Swelling mechanisms occurring on the pore scale or at the molecular level of high plasticity, unsaturated soils often control macroscopic behaviour. In this paper, a new capillary tube model is proposed. The model is used to represent laboratory-scale infiltration tests on a bentonite-rich soil. The goal is to develop a greater understanding of bulk behaviour by closely examining microscopic behaviour. A decrease in hydraulic conductivity with increasing water content has been observed in laboratory studies on flow through shrink–swell materials. The proposed mechanism causing a decrease in conductivity is a change in pore-size distribution. The unique feature of the new capillary-tube model is that, as water flows down the tube, the tube’s cross-sectional area contracts to restrict flow, thus representing the change in pore-size distribution observed in the physical tests. Flow data from the capillary tube are used to model the laboratory results, and new insight is gained into bulk flow behaviour. Finally, a comparison with a three-dimensional network model for bentonite-coated sand mixtures is presented.
Application of a multilaminate model to simulate the undrained response of structured clay to shield tunnelling
Authors: Dang H. Kien , Meguid Mohamed A.
Published: March 2008

A constitutive model based on the multilaminate framework has been implemented into a finite element program to investigate the effect of soil structure on the ground response to tunnelling. The model takes into account the elastic unloading–reloading, inherent and induced anisotropy, destructuration, and bonding effects. The model is successfully calibrated and used to investigate the undrained response of structured sensitive clay in the construction of the Gatineau tunnel in Gatineau, Quebec. Numerical results were compared to the field measurements taken during tunnel construction. To improve the performance of the numerical model, an implicit integration algorithm is implemented and proven to be very effective when coupled with the multilaminate framework as compared to the conventional explicit integration methods. The effect of different soil parameters including bonding and anisotropy on the tunnelling induced displacements and lining stresses is also examined using a comprehensive parametric study. The results indicated that soil bonding and anisotropy have significant effects on the shape of the settlement trough as well as the magnitudes of surface displacements and lining stresses induced by tunnelling.
Modelling evaporation of paste tailings from the Bulyanhulu mine
Authors: Simms Paul , Grabinsky Murray , Zhan Guosheng
Published: March 2008

Accurate predictions of drying rates are desirable to optimize surface deposition of thickened or paste tailings. A series of laboratory and field trials were implemented to study evaporation from tailings at the Bulyanhulu gold mine and were compared with numerical simulations using the unsaturated flow model SoilCover. The laboratory tests included two “large-scale” experiments on 10 cm thick layers of tailings 2 m by 1 m in plan, and a smaller column test on a 20 cm thick and 20 cm diameter sample. Data monitored during these tests included albedo, volume change, degree of cracking, matric suction, water content, and drying rate. Field data included gravimetric water contents and albedo values. The model could reasonably simulate the laboratory experiments when adjustments were made to account for self-weight consolidation and the effect of volume change on the relative permeability function. The model could simulate drying in the field for up to 3 weeks after deposition before the accumulation of gypsum and magnesium sulphate salts began to affect evaporation. Cracking and salt accumulation were observed both in the laboratory and in the field. A general model for simulating drying from paste tailings should incorporate the effects of cracking and salts.
Tunneling effects on jointed pipelines
Authors: Klar Assaf , Marshall Alec M. , Soga Kenichi , Mair Robert J.
Published: March 2008

The problem of tunneling effects on existing jointed pipelines is studied using the boundary integral method. Normalized solutions to evaluate the maximum bending moments and rotations are presented. They depend on tunnel-induced ground settlements at pipeline level, relative soil–pipe stiffness, relative pipe-joint stiffness, and the location of the joints in relation to the tunnel centerline. A jointed pipeline generally experiences smaller bending moments than a continuous one owing to the joint rotation. The solutions indicate that there are certain cases where hinged systems result in greater bending moments than continuous ones. However, these cases rarely occur in reality.
A particulate-scale investigation of cemented sand behavior
Authors: Wang Y.-H. , Leung S.-C.
Published: March 2008

In this paper, triaxial tests and numerical simulations using the discrete element method (DEM) are combined to explore the underlying mechanisms of the unique behavior of artificially cemented sands. The experimental results show that strength enhancement, volumetric dilation, and the shear banding associated failure mode are observed in Portland cement sand; these features become more pronounced with increasing cement content. Different responses are found in gypsum-cemented sand even though both types of cemented sand specimens were prepared under very similar void ratios before shearing. The DEM simulations on the Portland cement sand were carried out under two particular arrangements (i.e., the use of small cementing particles and flexible membrane boundaries). The simulation results reveal that particles in the bonding network jointly share the loading and many micro force-chains associated with cementation are created. Compared with uncemented sand, a more stable and stronger force–chain complex subjected to smaller force concentration is formed in cemented sand, which gives rise to higher strength. Intensive bond breakage, concentrated relative particle movement, column-like force chains, great particle rotation, and high local porosity are found inside the shear band. The bonded clusters remain at large strains to help stabilize the particle arch and therefore to maintain the volumetric dilation.
Seismic active earth pressure behind a nonvertical retaining wall using pseudo-dynamic analysis
Authors: Ghosh Priyanka
Published: March 2008

This note describes a study on the seismic active earth pressure behind a nonvertical cantilever retaining wall using pseudo-dynamic analysis. A planar failure surface has been considered behind the retaining wall. The effects of soil friction angle, wall inclination, wall friction angle, amplification of vibration, and horizontal and vertical earthquake acceleration on the active earth pressure have been explored in this study. Unlike the Mononobe–Okabe method, which incorporates pseudo-static analysis, the present analysis predicts a nonlinear variation of active earth pressure along the wall. The results have been compared with the existing values in the literature.
Driven high capacity H-piles in Hong Kong saprolites: A reliability evaluation of two methods
Authors: Lo S. R. , Li K. S. , Lam J.
Published: March 2008

A database for high capacity driven H-piles in Hong Kong saprolites was established so that predicted pile capacities could be compared to values measured by maintained load tests. This gave the statistical attributes that were needed for reliability analyses. Two prediction methods based on set value and dynamic measurements were examined. The uncertainty of a prediction method is characterized by a bias factor. The coefficients of variation of bias factors for both prediction methods are small in the context of geotechnical engineering. A simplified reliability analysis was conducted using the statistical attributes of the database. This enabled an objective assessment of the two prediction methods. Both prediction methods perform equally well relative to the current Hong Kong practice of targetting an overall safety factor of two on geotechnical capacity. The reliability index achieved by current Hong Kong practice for high capacity driven H-piles is in excess of three.