bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical/otologic score before and during treatment of acute otitis media
Authors: Satran R , Leibovitz E , Raiz S , Piglansky L , Press J , Leiberman A , Dagan R
Published: October 2007

Objectives: To determine clinical characteristics of AOM at presentation and during therapy according to specific etiologies.

Patients and Methods: 1003 patients studied during 1996–2001 in antibiotic efficacy studies underwent tympanocentesis and middle ear fluid culture at enrollment and on Day 4–6 (in initially culture‐positive patients only). We used a clinical/otologic (CO) score for evaluating severity of fever, irritability and tympanic membrane redness and bulging (0–3 each parameter, maximal score = 12).

Results: Seven hundred sixty‐three patients had positive cultures with 392 (39%) Haemophilus influenzae, 198 (20%) Streptococcus pneumoniae and 173 (17%) mixed H. influenzae and S. pneumoniae infection. Mean CO score was higher in culture‐positive versus culture‐negative patients (8.21 ± 2.17 vs. 7.73 ± 2.32, p = 0.003) regardless of isolated organism. A marked improvement in CO score was observed on Day 4–6 in all patients: 1.83 ± 2.18 in children initially culture‐positive and 0.9 ± 1.67 in those initially culture‐negative (p < 0.001). The improvement was greater in patients with eradication versus those with bacteriological failure (CO score 1.52 ± 1.82 vs. 2.77 ± 2.85, p < 0.001).

Conclusions: CO score before treatment, after bacterial eradication or in bacteriologic failures are similar in bacterial AOM and are not predictive of the etiology of the disease.
SKELETAL LESIONS OF HISTIOCYTIC SARCOMA IN NINETEEN DOGS
Authors: SCHULTZ RYAN M. , PUCHALSKI SARAH M. , KENT MICHAEL , MOORE PETER F.
Published: October 2007

The purpose of this study was to describe the clinical and radiographic findings in dogs with bone lesions secondary to histiocytic sarcoma. Nineteen dogs with radiographically identified bone lesions that were histologically diagnosed as histiocytic sarcoma were assessed. The medical records, all available radiographs and histologic sections were reviewed retrospectively. Dogs were subcategorized into localized or disseminated histiocytic sarcoma groups. Golden Retrievers or Rottweilers greater than 5 years of age, with a history of lameness or neurologic deficits localized to the spinal cord was the most common presentation. Fifteen of 19 dogs had a radiographically detectable soft tissue mass associated with bone destruction. The bone lesions had aggressive characteristics and the sites of involvement included periarticular bones (n=11), vertebrae (n=6), proximal humerus (n=5), and rib (n=2). Fifteen of 19 dogs had disseminated histiocytic sarcoma, and four had localized histiocytic sarcoma. All Rottweilers had disseminated histiocytic sarcoma. Histiocytic sarcoma should be considered as a differential diagnosis for aggressive periarticular, vertebral, or proximal humeral bone lesions identified on radiographs. The index of suspicion should be increased in greater than 5‐year‐old Golden Retrievers and Rottweilers when a soft tissue mass is associated with the bone lesion on radiographs or myelography. Bone involvement with histiocytic sarcoma, and the Rottweiler breed, was associated with the disseminated form of the disease.
ULTRASONOGRAPHIC DESCRIPTION OF CANINE MASTITIS
Authors: TRASCH KATJA , WEHREND AXEL , BOSTEDT HARTWIG
Published: October 2007

Ultrasonographic images were acquired of the mammary glands of 40 bitches with physiologically lactating (n=20) or inflamed glands (n=20). Echogenicity, structure, homogeneity, thickness, and distinguishability of each tissue layer were assessed. Additionally, overall echogenicity was noted. In the normal lactating gland, different tissues could be differentiated easily. The parenchyma was, without exception, separated from adjacent tissues and was visible as medium echogenic tissue with a coarse‐grained structure. The tissue always had some echogenic lines and anechoic areas and was slightly heterogeneous. The loss of distinct layering of the tissue was characteristic of an inflamed mammary gland and inflamed regions had reduced echogenicity. Additionally in five bitches with mastitis, the ultrasound examination was repeated five times for documentation of the progress of the illness and associated changes, supplemented with a color Doppler sonogram to assess changes in blood vessel density. Information from the examinations carried out via B‐mode did not allow treatment success to be predicted. Two bitches with reduced blood vessel density centrally had a poor outcome whereas three bitches with increased blood vessel density had a good outcome. Thus, Doppler sonography might be a useful tool to obtain information of the prognosis in acute canine mastitis.
Intralesional injections of Citoprot‐P® (recombinant human epidermal growth factor) in advanced diabetic foot ulcers with risk of amputation
Authors: Fernández‐Montequín José I , Infante‐Cristiá Ena , Valenzuela‐Silva Carmen , Franco‐Pérez Neobalis , Savigne‐Gutierrez William , Artaza‐Sanz Heriberto , Morejón‐Vega Lourdes , González‐Benavides Cecilio , Eliseo‐Musenden Osvaldo , García‐Iglesias Elizeth , Berlanga‐Acosta Jorge , Silva‐Rodríguez Ricardo , Betancourt Blas Y , López‐Saura Pedro A ,   Cuban Citoprot‐P Study Group
Published: October 2007

To investigate the efficacy and safety of recombinant human epidermal growth factor (rhEGF) in advanced diabetic foot ulcers (DFU) A double‐blind trial was carried out to test two rhEGF dose levels in type 1 or 2 diabetes patients with Wagner’s grade 3 or 4 ulcers, with high risk of amputation. Subjects were randomised to receive 75 (group I) or 25 μg (group II) rhEGF through intralesional injections, three times per week for 5–8 weeks together with standardised good wound care. Endpoints were granulation tissue formation, complete healing and need of amputation. Safety was assessed by clinical adverse events (AEs) and laboratory evaluations. Forty‐one patients were included. After 5–8 weeks of treatment, 83% patients in the higher dose group and 61% in group II achieved useful granulation tissue covering more than 98% of the wound area. At long‐term assessment, 13 (56·5%) patients healed in group I and 9 (50%) in group II. The mean time to complete healing in group I was 20·6 weeks (95% CI: 17·0–24·2) and 19·5 weeks (16·3–22·7) in group II. After 1‐year follow‐up, only one patient relapsed. Amputation was not necessary in 65% and 66·7% of groups I and II, respectively. The AEs rates were similar. The most frequent were sepsis (33%), burning sensation (29%), tremors, chills and local pain (25% each). rhEGF local injection enhances advanced DFU healing and reduces the risk of major amputation. No dose dependency was observed.
Adolescents’ Pain Experiences Following Acute Blunt Traumatic Injury: Struggle for Internal Control
Authors: Crandall Margie , Kools Susan , Miaskowski Christine , Savedra Marilyn
Published: October 2007

ISSUES AND PURPOSE. Although blunt trauma injury is a common cause for adolescent pain, little is known about the experience of pain as perceived by adolescents.

DESIGN AND METHOD. Semistructured interviews were conducted with 13 adolescents following blunt trauma injury. Two age‐appropriate valid measures (i.e., Adolescent Pediatric Pain Tool and Temporal Dot Matrix) were incorporated into the interviews to elaborate their pain experiences. Grounded theory method was used to analyze data and build substantive theory.

RESULTS. Adolescents’ behavioral and cognitive actions (i.e., “internal control”) to manage and endure pain were influenced by their pain perceptions, physical losses, and clinicians’ actions.

PRACTICE IMPLICATIONS. Nurses, family members, and peers have a crucial role in alleviating adolescents’ distress and pain.
Pacifiers: An Update on Use and Misuse
Authors: Marter Abigail , Agruss Janyce Cagan
Published: October 2007

PURPOSE.  The use of pacifiers is a controversial topic; this article looks at the subject from both a historical and cultural perspective, with a review of current research.

CONCLUSIONS.  The use of pacifiers in infants older than 1 month is currently recommended by multiple researchers to prevent sudden infant death syndrome, and is associated with other benefits for premature infants. However, pacifier use has also been associated with higher risk of otitis media.

PRACTICE IMPLICATIONS.  Knowledge of the most recent evidence will enable providers to communicate appropriate guidelines on pacifier use to families.
The Department of Agriculture and pasture improvement, 1892–1914
Authors: Star Paul , Brooking Tom
Published: October 2007

Abstract:  Even before 1900, the emphasis in New Zealand agriculture shifted from extensive agriculture to more intensive use of existing farmland through pasture improvement. Examination of the contribution of the Department of Agriculture, which together with the Department of Scientific and Industrial Research activated the later ‘grasslands revolution’, shows both the extent and the limits of its role in pasture improvement before 1914. It is suggested that until then, the prime agents in this transformation were not Department of Agriculture staff but rather enlightened farmers, with co‐operation between them on an equal footing towards the end of the period.
Two New Alkamides from Spilanthes callimorpha
Authors: Li Gan‐Peng , Shen Bao‐Chun , Zhao Jing‐Feng , Yang Xiao‐Dong , Li Liang
Published: October 2007

Two new alkamides, 8,11‐dihydroxy‐dodeca‐2E,4E,9E‐triensaureisobutylamid (Compound 1) and 7‐hydroxy‐trideca‐2E,8E‐dien‐10,12‐diynoic acid isobutylamide (Compound 2), as well as eight known compounds were isolated from the whole plants of Spilanthes callimorpha. The structures of the alkamides were characterized on the basis of their spectral data.
Triterpenoids from the Roots of Craibiodendron henryi W. W. Smith
Authors: Huang Xiang‐Zhong , Liu Yue , Yu Shi‐Shan , Hu You‐Cai , Qu Jing
Published: October 2007

A new triterpenoid, 11α‐O‐trans‐p‐coumaroyltaraxerol (1), along with 11 known triterpenoids, taraxerone (2), taraxerol (3), 2α,3β,23,24‐tetrahydroxyolean‐12‐en‐28‐oic acid (4), oleanolic acid (5), β‐amyrin (6), 3β,23‐dihydroxylursan‐12‐en‐28‐oic acid (7), 2α,3β‐dihydroxyursan‐12‐en‐28‐oic acid (8), 2α,3β,23‐trihydroxyursan‐12‐en‐28‐oic acid (9), 2α,3β,24‐trihydroxyursan‐12‐en‐28‐oic acid (10), ursolic acid (11), and 3‐O‐acetylursolic acid (12), was isolated from Craibiodendron henryi W. W. Smith (Ericaceae). The structures of these compounds were elucidated on the basis of spectral evidence. Antioxidant activity and vasodilator effect of compound 1 were assessed.
Identification of Soybean Genes Involved in Circadian Clock Mechanism and Photoperiodic Control of Flowering Time by In Silico Analyses
Authors: Quecini Vera , Zucchi Maria I. , Baldin José , Vello Natal A.
Published: October 2007

Glycine max is a photoperiodic short‐day plant and the practical consequence of the response is latitude and sowing period limitations to commercial crops. Genetic and physiological studies using the model plants Arabidopsis thaliana and rice (Oryza sativa) have uncovered several genes and genetic pathways controlling the process, however information about the corresponding pathways in legumes is scarce. Data mining prediction methodologies, including multiple sequence alignment, phylogenetic analysis, bioinformatics expression and sequence motif pattern identification, were used to identify soybean genes involved in day length perception and photoperiodic flowering induction. We have investigated approximately 330 000 sequences from open‐access databases and have identified all bona fide central oscillator genes and circadian photoreceptors from A. thaliana in soybean sequence databases. We propose a working model for the photoperiodic control of flowering time in G. max, based on the identified key components. These results demonstrate the power of comparative genomics between model systems and crop species to elucidate the several aspects of plant physiology and metabolism.
Mapping of Defense Response Gene Homologs and Their Association with Resistance Loci in Maize
Authors: Wang Gui‐Xiang , Chen Yu , Zhao Jiu‐Ran , Li Lin , Korban Schuyler S. , Wang Feng‐Ge , Li Jian‐Sheng , Dai Jin‐Rui , Xu Ming‐Liang
Published: October 2007

Defense response genes in higher plant species are involved in a variety of signal transduction pathways and biochemical reactions to counterattack invading pathogens. In this study, a total of 366 non‐redundant defense response gene homologs (DRHs), including 124 unigenes/expressed sequence tags, 226 tentative consensuses, and 16 DRH contigs have been identified by mining the Maize Genetics and Genomics and The Institute for Genomic Research maize databases using 35 essential defense response genes. Of 366 DRHs, 202 are mapped to 152 loci across ten maize chromosomes via both the genetic and in silico mapping approaches. The mapped DRHs seem to cluster together rather than be evenly distributed along the maize genome. Approximately half of these DHRs are located in regions harboring either major resistance genes or quantitative trait loci (QTL). Therefore, this comprehensive DRH linkage map will provide reference sequences to identify either positional candidate genes for resistance genes and/or QTLs or to develop makers for fine‐mapping and marker‐assisted selection of resistance genes and/or QTLs.
Seed Dynamics in Relation to Gaps in a Tropical Montane Rainforest of Hainan Island, South China: (I) Seed Rain
Authors: Zang Run‐Guo , Zhang Wei‐Yin , Ding Yi
Published: October 2007

Seed dynamics is an important part of stand dynamics in forest ecosystems. In this paper, 26 gaps were randomly selected to study the influence of gaps on the spatial and temporal patterns of seed rains in a tropical montane rainforest of Hainan Island, South China. Three zones for each gap, including outside gap zone (Non‐gap), transitional gap zone (EG‐CG), and central gap zone (CG), were designed, and four seed traps (each 1m × 1m in size) were placed in each zone. Seed rains were collected by these traps every 10 days from June 2001 to May 2002. Seed rain varied greatly with season and generally exhibited a pattern of unimodal change during the study period: seed abundance and species richness were both greater in the wet season than in the dry season. Gaps significantly influenced the temporal patterns of both species richness and density of seed rains. Gaps had no significant influences on the spatial distribution patterns of seed rain species richness, but significantly affected the spatial distribution pattern of seed rain densities. Among the three different zones of gaps, the outside gap zone generally received more seeds inputs than the two other gap zones.
Shoot Apex Demand Determines Assimilate and Nutrients Partitioning and Nutrient‐uptake Rate in Tobacco Plants
Authors: Yang Huai‐Yu , Li Chun‐Jian , Zhang Fu‐Suo
Published: October 2007

Our previous experiment revealed that apex‐removed plants have larger root systems but a lower K+‐uptake rates than intact tobacco plants. Since the apex is not only a center of growth and metabolism, but also an important place of auxin synthesis and export, the aims of this study were to distinguish whether the apex demand or auxin synthesized in the apex regulates assimilate and nutrients partitioning within plant, and to explain the reason for the lower K+‐uptake rate of the apex‐removed plant. In comparison with the control plant, covering the shoot apex with a black transparent plastic bag reduced net increases in dry matter and nutrients; however, the distribution of the dry matter and nutrients between shoot and roots and nutrient‐uptake rates were not changed. Removal of the shoot apex shifted the dry mass and nutrients distributions to roots, and reduced the rate of nutrient uptake. Application of 1‐naphthylacetic acid (NAA) could partly replace the role of the removed apex, stimulated assimilate and nutrient deposition into the treated tissue, and enhanced the reduced plasma membrane ATPase activity of roots to the control level. However, treatment of the apex‐removed plants with NAA could not rescue the reduced nutrient uptake rate and the shifted assimilates and nutrients partitioning caused by excision of the apex. Higher nutrient uptake rate of the intact plants could not be explained by root growth parameters, such as total root surface area and number of root tips. The results from the present study indicate that strong apex demand determined assimilates and nutrients partitioning and nutrient‐uptake rate in tobacco (Nicotiana tabacum) plants.
Genetic Diversity of
Actinobacillus pleuropneumoniae
Assessed by Amplified Fragment Length Polymorphism Analysis
Authors: Kokotovic Branko , Angen Øystein
Published: October 2007

Amplified fragment length polymorphism (AFLP) was evaluated as a method for genotypic characterization and subtyping within the bacterial species
Actinobacillus pleuropneumoniae
. A total of 155 isolates of
A. pleuropneumoniae
, representing the serotypic variation described to occur within this species, were analyzed. In order to elucidate the species boundaries, six strains of the phylogenetically closely related species
Actinobacillus lignieresii
were also included. Furthermore, the ability of AFLP to subtype was studied using 42 isolates of serovar 2 and the performance compared to that obtained by pulsed-field gel electrophoresis (PFGE). AFLP analysis provided a clear separation of
A. lignieresii
and
A. pleuropneumoniae
and divided the isolates of
A. pleuropneumoniae
into 20 clusters. Most of the serovars of
A. pleuropneumoniae
were represented by single and quite homogeneous clusters. The exceptions were serovars 10, K2:O7, and K1:O7, which were represented by two clusters each. In the cases where the serovars were represented by more than one cluster, the existence of these clusters was supported by additional phenotypic or genotypic properties. Furthermore, AFLP typing was able to allocate serologically nontypeable isolates to appropriate genetic groups within the species. Further investigations are needed to determine whether some of the clusters revealed through AFLP analysis represent additional serovars. When evaluated as a method for subtyping within serovar 2 of
A. pleuropneumoniae
, AFLP was found to achieve a degree of separation among isolates superior to that obtained by PFGE. However, a higher degree of separation between serovar 2 isolates was obtained by a combination of the two methods.
Detection of High-Risk Papillomavirus DNA with Commercial Invader-Technology-Based Analyte-Specific Reagents following Automated Extraction of DNA from Cervical Brushings in ThinPrep Media
Authors: Schutzbank Ted E. , Jarvis Charlene , Kahmann Nicole , Lopez Katherine , Weimer Marlea , Yount Aleta
Published: October 2007

We compared the performances of the Third Wave Technology Invader method and the Digene Hybrid Capture 2 assay to detect high-risk human papillomaviruses in 87 cervical brushing specimens submitted in Cytyc ThinPrep media. Two different methods for the extraction of DNA from squamous epithelial cells were also evaluated.
Recognition of Escape Variants in ELISPOT Does Not Always Predict CD8
+
T-Cell Recognition of Simian Immunodeficiency Virus-Infected Cells Expressing the Same Variant Sequences
Authors: Valentine Laura E. , Piaskowski Shari M. , Rakasz Eva G. , Henry Nathan L. , Wilson Nancy A. , Watkins David I.
Published: October 2007

Human immunodeficiency virus (HIV)'s tremendous sequence variability is a major obstacle for the development of cytotoxic-T-lymphocyte-based vaccines, especially since much of this variability is selected for by CD8
+
T cells. We investigated to what extent reactivity to escape variant peptides in standard enzyme-linked immunospot (ELISPOT) assays predicts the recognition of cells infected with corresponding escape variant viruses. Most of the variant peptides tested were recognized in standard ELISPOT and intracellular cytokine stain (ICS) assays. Functional avidity of epitope-specific T cells for some of the variants was, however, markedly reduced. These mutations which reduced avidity also abrogated recognition by epitope-specific CD8
+
T cells in a viral suppression assay. Our results indicate that “cross-reactive” CD8
+
T-cell responses identified in ELISPOT and ICS assays using a single high concentration of variant peptide often fail to predict the recognition of cells infected with variant viruses.
Adaptation of the Human Immunodeficiency Virus Type 1 Envelope Glycoproteins to New World Monkey Receptors
Authors: Pacheco Beatriz , Basmaciogullari Stephane , LaBonte Jason A. , Xiang Shi-Hua , Sodroski Joseph
Published: October 2007

Human immunodeficiency virus type 1 (HIV-1) infection encounters an early block in the cells of New World monkeys because the CD4 receptor does not efficiently support HIV-1 entry. We adapted HIV-1(NL4-3) and HIV-1(KB9), two HIV-1 variants with different envelope glycoproteins, to replicate efficiently in cells expressing the CD4 and CXCR4 proteins of the common marmoset, a New World monkey. The HIV-1(NL4-3) adaptation involves three gp120 changes that result in a specific increase in affinity for the marmoset CD4 glycoprotein. The already high affinity of the HIV-1(KB9) envelope glycoproteins for marmoset CD4 did not significantly change as a result of the adaptation. Instead, changes in the gp120 variable loops and gp41 ectodomain resulted in improved replication in cells expressing the marmoset receptors. HIV-1(KB9) became relatively sensitive to neutralization by soluble CD4 and antibodies as a result of the adaptation. These results demonstrate the distinct mechanistic pathways by which the HIV-1 envelope glycoproteins can adapt to less-than-optimal CD4 molecules and provide HIV-1 variants that can overcome some of the early blocks in New World monkey cells.
Human Immunodeficiency Virus Type 1 Vpu Protein Interacts with CD74 and Modulates Major Histocompatibility Complex Class II Presentation
Authors: Hussain Amjad , Wesley Clement , Khalid Mohammad , Chaudhry Ashutosh , Jameel Shahid
Published: October 2007

The human immunodeficiency virus type 1 (HIV-1) Vpu accessory protein is a transmembrane protein that down regulates CD4 expression and promotes the release of new virions. We screened a human leukocyte-specific yeast two-hybrid expression library to discover novel Vpu-interacting cellular proteins. The major histocompatibility complex class II (MHC II) invariant chain, also called Ii or CD74, was found to be one such protein. We show direct binding of Vpu and CD74 by using a yeast two-hybrid assay and coimmunoprecipitation from HIV-1-infected cells. The cytoplasmic region of Vpu was found to interact with the 30-amino-acid cytoplasmic tail of CD74. Human monocytic U937 cells infected with wild-type or Vpu-defective HIV-1 and transfected cells showed that Vpu down modulated the surface expression of mature MHC II molecules. The reduction in cell surface mature MHC II molecules correlated with decreased antigen presentation to T cells in culture. Thus, the Vpu protein also contributes to viral persistence by attenuating immune responses during HIV infection. This report further exemplifies the rich diversity and redundancy shown by HIV in immune evasion.
Expression of the E3L Gene of Vaccinia Virus in Transgenic Mice Decreases Host Resistance to Vaccinia Virus and
Leishmania major
Infections
Authors: Domingo-Gil Elena , Pérez-Jiménez Eva , Ventoso Iván , Nájera José L. , Esteban Mariano
Published: October 2007

The E3L gene of vaccinia virus (VACV) encodes the E3 protein that in cultured cells inhibits the activation of interferon (IFN)-induced proteins, double-stranded RNA-dependent protein kinase (PKR), 2′-5′-oligoadenylate synthetase/RNase L (2-5A system) and adenosine deaminase (ADAR-1), thus helping the virus to evade host responses. Here, we have characterized the in vivo E3 functions in a murine inducible cell culture system (E3L-TetOFF) and in transgenic mice (TgE3L). Inducible E3 expression in cultured cells conferred on cells resistance to the antiviral action of IFN against different viruses, while expression of the E3L gene in TgE3L mice triggered enhanced sensitivity of the animals to pathogens. Virus infection monitored in TgE3L mice by different inoculation routes (intraperitoneal and tail scarification) showed that transgenic mice became more susceptible to VACV infection than control mice. TgE3L mice were also more susceptible to
Leishmania major
infection, leading to an increase in parasitemia compared to control mice. The enhanced sensitivity of TgE3L mice to VACV and
L
.
major
infections occurred together with alterations in the host immune system, as revealed by decreased T-cell responses to viral antigens in the spleen and lymph nodes and by differences in the levels of specific innate cell populations. These results demonstrate that expression of the E3L gene in transgenic mice partly reverses the resistance of the host to viral and parasitic infections and that these effects are associated with immune alterations.
Suppression of Acute Anti-Friend Virus CD8+T-Cell Responses by Coinfection with Lactate Dehydrogenase-Elevating Virus
Authors: Robertson Shelly J. , Ammann Christoph G. , Messer Ronald J. , Carmody Aaron B. , Myers Lara , Dittmer Ulf , Nair Savita , Gerlach Nicole , Evans Leonard H. , Cafruny William A. , Hasenkrug Kim J.
Published: October 2007

Friend virus (FV) and lactate dehydrogenase-elevating virus (LDV) are endemic mouse viruses that can cause long-term chronic infections in mice. We found that numerous mouse-passaged FV isolates also contained LDV and that coinfection with LDV delayed FV-specific CD8+T-cell responses during acute infection. While LDV did not alter the type of acute pathology induced by FV, which was severe splenomegaly caused by erythroproliferation, the immunosuppression mediated by LDV increased both the severity and the duration of FV infection. Compared to mice infected with FV alone, those coinfected with both FV and LDV had delayed CD8+T-cell responses, as measured by FV-specific tetramers. This delayed response accounted for the prolonged and exacerbated acute phase of FV infection. Suppression of FV-specific CD8+T-cell responses occurred not only in mice infected concomitantly with LDV but also in mice chronically infected with LDV 8 weeks prior to infection with FV. The LDV-induced suppression was not mediated by T regulatory cells, and no inhibition of the CD4+T-cell or antibody responses was observed. Considering that most human adults are carriers of chronically infectious viruses at the time of new virus insults and that coinfections with viruses such as human immunodeficiency virus and hepatitis C virus are currently epidemic, it is of great interest to determine how infection with one virus may impact host responses to a second infection. Coinfection of mice with LDV and FV provides a well-defined, natural host model for such studies.
Identification and Classification of Endogenous Retroviruses in Cattle
Authors: Xiao Rui , Park Kwangha , Lee Hoontaek , Kim Jinhoi , Park Chankyu
Published: October 2007

The aim of this study was to identify the endogenous retrovirus (ERV) sequences in a bovine genome. We subjected bovine genomic DNA to PCR with degenerate or ovine ERV (OERV) family-specific primers that aimed to amplify the retroviral
pro/pol
region. Sequence analysis of 113 clones obtained by PCR revealed that 69 were of retroviral origin. On the basis of the OERV classification system, these clones from degenerate PCR could be divided into the β3, γ4, and γ9 families. PCR with OERV family-specific primers revealed an additional ERV that was classified into the bovine endogenous retrovirus (BERV) γ7 family. In conclusion, here we report the results of a genome scale study of the BERV. Our study shows that the ERV family expansion in cattle may be somewhat limited, while more diverse family members of ERVs have been reported from other artiodactyls, such as pigs and sheep.
Different Abilities of Escape Mutant-Specific Cytotoxic T Cells To Suppress Replication of Escape Mutant and Wild-Type Human Immunodeficiency Virus Type 1 in New Hosts
Authors: Fujiwara Mamoru , Tanuma Junko , Koizumi Hirokazu , Kawashima Yuka , Honda Kazutaka , Mastuoka-Aizawa Saori , Dohki Sachi , Oka Shinichi , Takiguchi Masafumi
Published: October 2007

There is much evidence that in human immunodeficiency virus type 1 (HIV-1)-infected individuals, strong cytotoxic T lymphocyte (CTL)-mediated immune pressure results in the selection of HIV-1 mutants that have escaped from wild-type-specific CTLs. If escape mutant-specific CTLs are not elicited in new hosts sharing donor HLA molecules, the transmission of these mutants results in the accumulation of escape mutants in the population. However, whether escape mutant-specific CTLs are definitively not elicited in new hosts sharing donor HLA molecules still remains unclear. A previous study showed that a Y-to-F substitution at the second position (2F) of the Nef138-10 epitope is significantly detected in HLA-A*2402+hemophilic donors. Presently, we confirmed that this 2F mutant was an escape mutant by demonstrating strong and weak abilities of Nef138-10-specific CTL clones to suppress replication of the wild-type and 2F mutant viruses, respectively. We demonstrated the existence of the 2F-specific CTLs in three new hosts who had been primarily infected with the 2F mutant. The 2F-specific CTL clones suppressed the replication of both wild-type and mutant viruses. However, the abilities of these clones to suppress replication of the 2F virus were much weaker than those of wild-type-specific and the 2F-specific ones to suppress replication of the wild-type virus. These findings indicate that the 2F mutant is conserved in HIV-1-infected donors having HLA-A*2402, because the 2F-specific CTLs failed to completely suppress the 2F mutant replication and effectively prevented viral reversion in new hosts carrying HLA-A*2402.
Identification of Human Cytomegalovirus UL84 Virus- and Cell-Encoded Binding Partners by Using Proteomics Analysis
Authors: Gao Yang , Colletti Kelly , Pari Gregory S.
Published: October 2007

Human cytomegalovirus (HCMV) UL84 is a phosphoprotein that shuttles from the nucleus to the cytoplasm and is required for
ori
Lyt-dependent DNA replication and viral growth. UL84 was previously shown to interact with IE2 (IE86) in infected cells, and this interaction down-regulates IE2-mediated transcriptional activation in transient assays. UL84 and IE2 were also shown to cooperatively activate a promoter within HCMV
ori
Lyt. UL84 alone can interact with an RNA stem-loop within
ori
Lyt and is bound to this structure within the virion. In an effort to investigate the binding partners for UL84 in infected cells, we pulled down UL84 from protein lysates prepared from HCMV-infected human fibroblasts by using a UL84-specific antibody and resolved the immunoprecipitated protein complexes by two-dimensional gel electrophoresis. We subsequently identified individual proteins by matrix-assisted laser desorption ionization-tandem time of flight analysis. This analysis revealed that UL84 interacts with viral proteins UL44, pp65, and IE2. In addition, a number of cell-encoded proteins were identified, including ubiquitin-conjugating enzyme E2, casein kinase II (CKII), and the multifunctional protein p32. We also confirmed the interaction between UL84 and IE2 as well as the interaction of UL84 with importin α. UL44, pp65, and CKII interactions were confirmed to occur in infected and cotransfected cells by coimmunoprecipitation assays followed by Western blotting. Ubiquitination of UL84 occurred in the presence and absence of the proteasome activity inhibitor MG132 in infected cells. The identification of UL84 binding partners is a significant step toward the understanding of the function of this significant replication protein.
Reovirus Apoptosis and Virulence Are Regulated by Host Cell Membrane Penetration Efficiency
Authors: Danthi Pranav , Kobayashi Takeshi , Holm Geoffrey H. , Hansberger Mark W. , Abel Ty W. , Dermody Terence S.
Published: October 2007

Apoptosis plays an important role in the pathogenesis of reovirus encephalitis and myocarditis in infected animals. Differences in apoptosis efficiency displayed by reovirus strains are linked to the viral μ1-encoding M2 gene segment. Studies using pharmacologic inhibitors of reovirus replication demonstrate that apoptosis induction by reovirus requires viral disassembly in cellular endosomes but not RNA synthesis. Since the μ1 protein functions to pierce endosomal membranes during this temporal window, these findings point to an important role for μ1 in activating signaling pathways that lead to apoptosis. To understand mechanisms used by μ1 to induce apoptosis, a panel of μ1 mutant viruses generated by reverse genetics was analyzed for the capacities to penetrate host cell membranes, activate proapoptotic signaling pathways, evoke cell death, and produce encephalitis in newborn mice. We found that single amino acid changes within the δ region of μ1 reduce the efficiency of membrane penetration. These mutations also diminish the capacities of reovirus to activate proapoptotic transcription factors NF-κB and IRF-3 and elicit apoptosis. Additionally, we observed that following intracranial inoculation, an apoptosis-deficient μ1 mutant is less virulent in newborn mice in comparison to the wild-type virus. These results indicate a critical function for the membrane penetration activity of μ1 in evoking prodeath signaling pathways that regulate reovirus pathogenesis.
Root-rotting fungi associated with mortality of conifer saplings in northern Ontario
Authors: Whitney Roy D. , Myren Donald T.
Published: October 2007

The roots of 435 dead or dying saplings, averaging 10 years of age, of seven conifer species from the Boreal Forest of northern Ontario were examined for root rot. Only trees with no obvious cause of death or decline, other than root rot, were selected. Eighty-three percent of the trees had root rot. Cultures revealed that Armillariamellea (Vahl ex Fr.) Kummer was associated with root rot in 68% of all trees examined, including more than 45% of the trees in each species. Ten other root-rotting fungi were isolated from 1% or fewer of the trees, 7 of them from balsam fir (Abiesbalsamea [L.] Mill.) and 3 from black spruce (Piceamariana [Mill.] B.S.P.). Scytinostromagalactinum (Fr.) Donk was isolated from sapwood of roots and lower stems of red pine (Pinusresinosa Ait.), balsam fir, white pine (P. strobes L.), and black spruce and appeared to be parasitic on these species. Coniophoraputeana (Schum. ex Fr.) Karst. was apparently associated with the death of one balsam fir.
Biomass distribution and crown characteristics in two Alaskan Piceamariana ecosystems
Authors: Barney Richard J. , VanCleve Keith , Schlentner Robert
Published: October 2007

Allometric relations for tree phytomass distribution on two black spruce (Piceamariana Mill. B.S.P.) sites in interior Alaska were developed and compared with entire unit area samples. Tree component mass equations provided R2 values ranging from a low of 0.24 to a high of 0.97, with the majority of values above 0.75. Equations were developed for foliage; live and dead cones; dead branch total, dead branch bark, dead branchwood; live branch total, live branch bark, live branchwood; bole total, bole bark, bole wood; and tree total. Regression equations were developed to predict tree height, distance from crown bottom to ground, crown width, and crown length using basal diameters. R2 values for these equations ranged from 0.89 to 0.20. Foliage comprised from 37% to 17% of the total mass for the lowland stand and 50% to 17% of the total tree mass in the upland stand for trees with a diameter class ranging from 0.32 to 7.94 cm. For these same diameter classes, the total bole mass ranged from 11% to 58% and 21% to 61% of the total mass in the lowland and upland stands, respectively. Comparisons of predicted total aboveground tree biomass, measured biomass, and an average-tree-per-diameter-class procedure showed the lowland site predictions were about 6% low and the upland site predictions were approximately 3% high. Using a second, all-tree component method of prediction, results were about 3% low for lowland sites and 4% low for upland sites. A method of prediction using an average stand diameter yielded differences ranging from 31% low for the lowland site to 45% low for the upland site.
Weight loss of litter and cellulose bags in a thinned white spruce forest in interior Alaska
Authors: Piene Harald , Cleve Keith Van
Published: October 2007

Thinning in a white spruce, Piceaglanca (Moench) Voss, forest in interior Alaska stimulated organic matter decomposition in the forest floor as indicated by weight loss of litter and cellulose bags. The general higher weight loss in the most heavily thinned plot is attributed to observed higher average seasonal temperatures. Cellulose bags placed in the boundary between the fermentation–humus and the humus–mineral soil layers of the forest floor showed a significantly higher weight loss than those placed on top of the litter layer. This was attributed to more favorable moisture conditions and a more direct contact with the decomposing microbial populations in the fermentation–humus and humus–mineral soil layers.Regardless of thinning treatment, elements were grouped according to their rate of release from decomposing organic matter as follows: K > Mg > C ≈ P ≈ N ≈ Ca, where potassium is lease resistant. Since relatively small differences in weight loss of litter bags were observed between the treatments, similar studies should extend over a longer period in order to obtain a better understanding of the decomposition processes.
Community stability and forest policy in British Columbia
Authors: Byron R. N.
Published: October 2007

Many jurisdictions including British Columbia have adopted sustained-yield forest management as the cornerstone of their forest policies. It has been argued that one consequence is 'community stability.' This paper examines the origins of the argument and its validity in the current context. It is concluded that the permanence or survival of forest industry centres is neither assured by nor solely dependent upon the perpetual maintenance of nearby forests at or near sustained-yield levels. Rather the size and distribution of wood-processing centres seems to be determined by technological economies of scale and location with respect to means of transportation. Secondly, even-flow regulations perse cannot achieve short-term stability of employment or incomes when the forest industry of a region produces primarily for volatile export markets.Evidence is presented to show that the logging, processing, and associated occupations are unstable, relative to other occupational groups, in each of the forest industry centres examined. The instability of total employment seems much greater in a single-industry town than in a diversified city. Much of the short-term employment instability is correlated with changes in the price of lumber destined for export markets. Some means of reducing the instability are discussed.
Effects of late-season defoliation and dark periods on initial growth of planted northern red oak seedlings
Authors: Larson M. M.
Published: October 2007

Northern red oak (Quercusrubra L.) seedlings were defoliated to various degrees in the seedbed on September 23, lifted the following April, and planted. Spring shoot growth of completely defoliated trees was about half that of control plants. Partial fall defoliation treatments included removal of upper leaves, lower leaves, terminal halves of leaves, and lateral halves of leaves. Spring shoot growth was related more closely to amount rather than type of leaves removed in the fall. When seedlings were lifted in the spring, total weight and root carbohydrate content were similar between treatments.In a second study, some seedlings were completely defoliated on September 4th, and others were subjected to total darkness for monthly or longer periods beginning in August. Nearly all leaves abscised during dark treatments. Defoliated trees and trees kept dark during August or September remained small and had low root carbohydrate contents when planted. Also, root regeneration was poor and shoot growth averaged one-third or less than that of control trees. Spring growth of seedlings increased as dark treatments were applied later in the fall, although shoot growth of October and November dark trees remained lower than that of control trees.It is suggested that some factor, possibly cytokinin, is translocated from late-season foliage and promotes seedling growth in the spring.
Spatial arrangement of lateral buds at the time that they form on leaders of Picea and Larix
Authors: Cannell M. G. R. , Bowler K. C.
Published: October 2007

Lateral buds were formed on Piceasitchensis (Bong.) Carr. leaders in April–May before the leaders emerged from the winter buds. At that time, the lateral buds seemed to be evenly (not randomly) dispersed over the cone-shaped surfaces of the parent leader buds. This observation was confirmed and extended by defining the positions of lateral buds on fully extended leaders of P. sitchensis, P. abies (L.) Karst., P. omorika (Pancic) Purkyne, and Larixdecidua Mill. and 'theoretically' telescoping the leaders to their probable shapes in April–May by using computer simulations. It was concluded that the centres of cell division which preceded lateral bud formation were positioned by inhibition–competition mechanisms. This explained why (a) the numbers of lateral buds were related to the sizes of the parent shoots, (b) lateral branches were dispersed with equal expectation in all compass directions, with minimal mutual shading, and (c) a variety of staggered and whorled branch arrangements could occur on leaders of different trees, as long as each whorl was associated with a branchless zone.
OPINION FORMATION MODELS BASED ON GAME THEORY
Authors: DI MARE ALESSANDRO , LATORA VITO
Published: October 2007

A way to simulate the basic interactions between two individuals with different opinions, in the context of strategic game theory, is proposed. Various games are considered, which produce different kinds of opinion formation dynamics. First, by assuming that all individuals (players) are equals, we obtain the bounded confidence model of continuous opinion dynamics proposed by Deffuant et al. In such a model a tolerance threshold is defined, such that individuals with difference in opinion larger than the threshold can not interact. Then, we consider that the individuals have different inclinations to change opinion and different abilities in convincing the others. In this way, we obtain the so-called "Stubborn individuals and Orators" (SO) model, a generalization of the Deffuant et al. model, in which the threshold tolerance is different for every couple of individuals. We explore, by numerical simulations, the dynamics of the SO model, and we propose further generalizations that can be implemented.
ROLE OF SELECTIVE MATING IN POPULATION SPLITTING
Authors: PȨKALSKI ANDRZEJ
Published: October 2007

We present a simple model of pseudo-speciation driven only by selective mating. Using Monte Carlo simulation on a lattice we show that even without considering the genetic structure of the individuals a population living in a homogeneous habitat will divide into two, spatially separated, groups having different values of their trait. After some time one group (species) will change their trait and will be absorbed into the winning species.
A GENERALIZED CELL METHOD FOR HARD DISK MOLECULAR DYNAMICS SIMULATION OF POLYDISPERSE SYSTEMS
Authors: BULUT MEVLUT , CAMATA RENATO P.
Published: October 2007

Hard Disk Molecular Dynamics (HDMD) techniques often exhibit significant loss in calculation speed when applied to the simulation of highly polydisperse particle systems. The collision rate of the reported algorithms may be lower by as much as two orders of magnitude if compared to the collision rate of a monodisperse system of the same number of particles. This is mainly due to the fact that the rectangular cells in the simulation domain used in HDMD methods must meet a certain size criterion. In this paper, we introduce a cell technique that removes the requirement on the cell size enabling simulation of particles with sizes much larger than the cell size. This approach improves the collision rates in the simulation of tested polydisperse systems by factors ranging from 5.5 to 57 depending on the size distribution of the particle population simulated. This may enable the simulation of grand canonical systems in which the size and the number of particles can change throughout the simulation. The technique is compatible with the simulation of disk-like as well as irregularly shaped particles and can be extended to three dimensions.
WEIGHTED EVOLVING NETWORKS WITH INTRINSIC STRENGTH
Authors: GENG XIANMIN , WEN GUANGHUI
Published: October 2007

In this paper, we introduce the concept of intrinsic strength which is used to describe the node's intrinsic property. Furthermore, we present a single preferential attachment model for the evolution of weighted networks in which the network growth is coupled with dynamical evolution of weights and intrinsic strength. The model yields a nontrivial time evolution of nodes' properties and generalized power law distributions for the weight, strength and degree, as confirmed in many real networks. The numerical simulation results are in good agreement with the analytical expressions.
CHAOTIC MEAN FIELD DYNAMICS OF A BOOLEAN NETWORK WITH RANDOM CONNECTIVITY
Authors: JOY MALIACKAL POULO , INGBER DONALD E. , HUANG SUI
Published: October 2007

Random Boolean networks have been used as simple models of gene regulatory networks, enabling the study of the dynamic behavior of complex biological systems. However, analytical treatment has been difficult because of the structural heterogeneity and the vast state space of these networks. Here we used mean field approximations to analyze the dynamics of a class of Boolean networks in which nodes have random degree (connectivity) distributions, characterized by the mean degree k and variance D. To achieve this we generalized the simple cellular automata rule 126 and used it as the Boolean function for all nodes. The equation for the evolution of the density of the network state is presented as a one-dimensional map for various input degree distributions, with k and D as the control parameters. The mean field dynamics is compared with the data obtained from the simulations of the Boolean network. Bifurcation diagrams and Lyapunov exponents for different parameter values were computed for the map, showing period doubling route to chaos with increasing k. Onset of chaos was delayed (occurred at higher k) with the increase in variance D of the connectivity. Thus, the network tends to be less chaotic when the heterogeneity, as measured by the variance of connectivity, was higher.
SPIN CHAIN SIMULATIONS WITH A MERON CLUSTER ALGORITHM
Authors: BOYER THOMAS , BIETENHOLZ WOLFGANG , WUILLOUD JAIR
Published: October 2007

We apply a meron cluster algorithm to the XY spin chain, which describes a quantum rotor. This is a multi-cluster simulation supplemented by an improved estimator, which deals with objects of half-integer topological charge. This method is powerful enough to provide precise results for the model with a θ-term — it is therefore one of the rare examples, where a system with a complex action can be solved numerically. In particular we measure the correlation length, as well as the topological and magnetic susceptibility. We discuss the algorithmic efficiency in view of the critical slowing down. Due to the excellent performance that we observe, it is strongly motivated to work on new applications of meron cluster algorithms in higher dimensions.