bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Expression of Commensal
Lactobacillus johnsonii
Strain NCC533 during In Vitro Growth and in the Murine Gut
Authors: Denou Emmanuel , Berger Bernard , Barretto Caroline , Panoff Jean-Michel , Arigoni Fabrizio , Brüssow Harald 
Published: September 2007

ABSTRACT

Work with pathogens like
Vibrio cholerae
has shown major differences between genes expressed in bacteria grown in vitro and in vivo. To explore this subject for commensals, we investigated the transcription of the
Lactobacillus johnsonii
NCC533 genome during in vitro and in vivo growth using the microarray technology. During broth growth, 537, 626, and 277 of the 1,756 tested genes were expressed during exponential phase, “adaptation” (early stationary phase), and stationary phase, respectively. One hundred one, 150, and 33 genes, respectively, were specifically transcribed in these three phases. To explore the in vivo transcription program, we fed
L. johnsonii
containing a resistance plasmid to antibiotic-treated mice. After a 2-day washout phase, we determined the viable-cell counts of lactobacilli that were in the lumina and associated with the mucosae of different gut segments. While the cell counts showed a rather uniform distribution along the gut, we observed marked differences with respect to the expression of the
Lactobacillus
genome. The largest number of transcribed genes was in the stomach (
n
= 786); the next-largest numbers occurred in the cecum (
n
= 391) and the jejunum (
n
= 296), while only 26
Lactobacillus
genes were transcribed in the colon. In vitro and in vivo transcription programs overlapped only partially. One hundred ninety-one of the transcripts from the lactobacilli in the stomach were not detected during in vitro growth; 202 and 213 genes, respectively, were transcribed under all in vitro and in vivo conditions; but the core transcriptome for all growth conditions comprised only 103 genes. Forty-four percent of the NCC533 genes were not detectably transcribed under any of the investigated conditions. Nontranscribed genes were clustered on the genome and enriched in the variable-genome part. Our data revealed not only major differences between in vitro- and in vivo-expressed genes in a
Lactobacillus
gut commensal organism but also marked changes in the expression of genes along the digestive tract.
Molecular alterations ofKITandPDGFRAin GISTs: evaluation of a Portuguese series
Authors: Gomes A L , Gouveia A , Capelinha A F , de la Cruz D , Silva P , Reis R M , Pimenta A , Lopes J M 
Published: September 2007

Aim:To assessKITandPDGFRAmutations frequencies in a Portuguese series of gastrointestinal stromal tumours (GISTs).Methods:78 GISTs were evaluated for CD117 expression and screened for mutations inKIT(exons 9, 11, 13, 14 and 17) andPDGFRA(exons 12, 14 and 18) genes.Results:KITactivating mutations were identified in 44 (56%) of the 78 GISTs. Forty cases (91%) presented a mutation inKITexon 11, and 4 (9%) in exon 9. One case showed a 4 bp deletion in intron 14.PDGFRAmutations were observed in 5 cases (6%): 2 (3%) in exon 12 and 3 (4%) in exon 18. Survival analysis was performed in 63 of the 78 GISTs. The presence of mutatedKITwas significantly correlated with shorter survival of patients (p = 0.0460), and inversely associated with epithelioid histological type of GISTs (p = 0.0064).Conclusions:Overall, the incidence of bothKITandPDGFRAmutations in these Portuguese series was 63%, being in agreement with other studies, mainly of Iberian populations. The great majority of mutations were located inKITexon 11, statistically associated with worse prognosis and indicative of favourable response to imatinib-based therapy in this Portuguese series of GISTs.
Colorectal carcinoma with dome-like phenotype: an under-recognised subset of colorectal carcinoma?
Authors: Asmussen L , Pachler J , Holck S 
Published: September 2007

Background:The term dome carcinoma has been applied to a variant of colorectal carcinoma, thought to derive from M-cells of the gut-associated lymphoid tissue. Its distinguishing morphological features include a non-polypoid plaque-like lesion composed of closely apposed cystically dilated glands lined by a single layer of non-mucinous cells, intensely PAS-positive intraluminal material, and a close spatial relation to lymphoid stroma.Aims and Methods:A search in the literature for such cases and the authors’ experience with carcinomas sharing morphological details with dome carcinoma are presented to direct focus on this unique phenotype of colorectal carcinoma and to expand on its morphology.Results:Four such examples, all stage pT1, pN0 have been previously reported. Here two additional cases, with several features of dome carcinoma, stage pT1 and pT2, respectively, are added. An extensive intramucosal component, unassociated with adenomatous growth, a pink quality of the lesional cells, low grade budding, absence of cytoplasmic pseudofragments, and absence of necrosis characterised the present cases as well as intact MMR-proteins and loss of APC. As opposed to two of the previously reported cases, intraepithelial lymphocytes were unapparent in these cases and the lymphoid stroma was effaced along with tumour progression in one of the present cases. Hence, a range of appearances is encompassed by the dome carcinoma. The uncommon reporting of dome carcinoma may be due to lack of awareness of this particular subset of colorectal carcinoma. Indeed, one of the current cases was signed out as a conventional carcinoma, despite the comment in the pathology report of an unusual morphology.Conclusion:Dome carcinoma may be more under-recognised than rare. The reporting of variants of colorectal carcinoma, displaying histological features suggestive of dome carcinoma, is encouraged in order to obtain more exact knowledge on its putative clinical significance.
Intersexual social behavior of urban white-tailed deer and its evolutionary implications
Authors: Richardson Katherine E. , Weckerly Floyd W. 
Published: September 2007

White-tailed deer ( Odocoileus virginianus (Zimmermann, 1780)) are now common in many urban environments throughout their geographic range. Yet, how male and female deer in the urban environment associate, behave socially, and the evolutionary implications of that behavior remains unstudied. We examined predictions of the predation risk and the social factor hypotheses to explain intersexual grouping patterns and social behavior observed in white-tailed deer inhabiting the small city of San Marcos (population size ~45 000) in central Texas. Two routes were surveyed weekly from a vehicle at dawn and dusk for 1 year. Group size, composition, distance to vehicle, and alarm state of deer to the vehicle were recorded. Focal animal sampling was used to measure the time males and females spent and number of aggressions within one body length of each other when in groups. Female-only groups were most prevalent year round followed by mixed-sex groups, which increased in prevalence in summer and during the mating season. Alarm state was weakly related to group size but not to group composition. Males were farther apart and more aggressive than females in groups. Proportion of males in mixed-sex groups declined with increased group size. Intersexual patterns of grouping and social behavior of urban deer supported the social factor hypothesis but not the predation risk hypothesis.
Copy number variation of the activating FCGR2C gene predisposes to idiopathic thrombocytopenic purpura
Authors: Breunis Willemijn B. , van Mirre Edwin , Bruin Marrie , Geissler Judy , de Boer Martin , Peters Marjolein , Roos Dirk , de Haas Masja , Koene Harry R. , Kuijpers Taco W. 
Published: September 2007

AbstractGene copy number variation (CNV) and single nucleotide polymorphisms (SNPs) count as important sources for interindividual differences, including differential responsiveness to infection or predisposition to autoimmune disease as a result of unbalanced immunity. By developing an FCGR-specific multiplex ligation-dependent probe amplification assay, we were able to study a notoriously complex and highly homologous region in the human genome and demonstrate extensive variation in the FCGR2 and FCGR3 gene clusters, including previously unrecognized CNV. As indicated by the prevalence of an open reading frame of FCGR2C, Fcγ receptor (FcγR) type IIc is expressed in 18% of healthy individuals and is strongly associated with the hematological autoimmune disease idiopathic thrombocytopenic purpura (ITP) (present in 34.4% of ITP patients; OR 2.4 (1.3-4.5), P < .009). FcγRIIc acts as an activating IgG receptor that exerts antibody-mediated cellular cytotoxicity by immune cells. Therefore, we propose that the activating FCGR2C-ORF genotype predisposes to ITP by altering the balance of activating and inhibitory FcγR on immune cells.
Consent for long-term storage of blood samples by Indigenous Australian research participants: the DRUID Study experience
Authors: Cunningham Joan , Dunbar Terry 
Published: September 2007

AbstractBackgroundLittle is known about the characteristics of people who do and do not agree to the long-term storage and use of their biological materials, or about potential biases that may be introduced as a result of differential consent. More specifically, concerns about tissue storage and use are especially relevant among population groups for whom blood and other biological materials are culturally significant, such as Indigenous Australians. Using data from a 2003–2005 study of 1,004 Indigenous Australians, we examined participants' choices regarding long-term storage of excess blood for possible use in future studies.ResultsOverall, 55% of participants agreed to long-term storage. Among 854 participants with a fasting blood sample and completed questionnaire, consent for storage was more likely among those aged 45+ years than those 15–44 (odds ratio (OR) = 1.55, 95% confidence interval (CI): 1.14, 2.11), and was similar for males and females. After adjustment for age and other covariates using logistic regression, consent was more likely for never smokers than current smokers (OR = 1.48, 95% CI: 1.04, 2.10), those reporting any non-Indigenous grandparent(s) (OR = 2.07, 95% CI: 1.50, 2.85), and those whose consent form was administered/witnessed by an Indigenous staff member (OR 1.43, 95% CI: 1.05, 1.94). Consent for long-term storage was associated with only small differences (generally less than ± 5%) in the results of assays performed on all participants' blood samples as part of the baseline health examination.ConclusionThese data show that consent for blood storage among these research participants was neither rare nor universal. It was associated with some socio-demographic/cultural factors but not with blood biochemistry. Decisions about requesting or giving consent for storage and later use of tissue samples must recognize a number of important, and potentially competing, ethical and logistical considerations.
What’s Love Got to Do with It? Sexual Behaviors of Opposite‐Sex Couples Through Emerging Adulthood
Authors: Kaestle Christine Elizabeth , Halpern Carolyn Tucker 
Published: September 2007

CONTEXT:  Sexual relationships in young adulthood may have important ramifications for individuals’ physical and emotional well‐being. Nonetheless, representative information about young adults’ sexual activities in long‐term relationships and the emotional context of such relationships is rare. METHODS:  A subsample of 6,421 participants in Wave 3 of the National Longitudinal Study of Adolescent Health (18–26‐year‐olds) who were in a sexual relationship of at least three months’ duration were selected for analysis. Multiple logistic regression models were used to explore the relationship between love and various sexual activities. RESULTS:  Eighty percent of respondents had engaged in cunnilingus and fellatio as well as vaginal intercourse in their current relationship; this group included 22% who also had engaged in anal sex. Compared with their peers who reported that they and their partner did not love each other a lot, both males and females who reported mutually loving relationships had significantly higher odds of having given oral sex (odds ratios, 3.9 and 2.6, respectively) and having received oral sex (1.8 and 3.3); males in mutually loving relationships also had elevated odds of having had anal sex (3.1). CONCLUSIONS:  Most young adult couples in long‐term relationships engage in a variety of sexual practices with loving partners; the direction of causality in this association and its implications for relationship building require exploration. Furthermore, programs and interventions that address health and well‐being during emerging adulthood should cover issues relevant to a broad range of sexual activities, including oral and anal sex.
Towards a Whole School Approach to Pastoral Care: A Proposed Framework of Principles and Practices
Authors: de Jong Terry , Kerr-Roubicek Helen 
Published: September 2007

AbstractPastoral care in schools has traditionally been associated with notions of help, advice, values development, and children's moral welfare. In the past it has been viewed predominantly as a separate set of extra-curricula activities offered to students by school staff with particular support roles, or ‘pastors’ from affiliated church or religious communities. In some Australian schools and education sectors pastoral care continues to be conceptualised in this way. However, over the past two decades interest has intensified in a ‘whole school approach’ to pastoral care that supports the holistic development of students as they learn. What has influenced this change of direction? What are some of the key challenges encountered when implementing this approach? How might we define ‘a whole school approach’ to pastoral care? What are the core principles and associated school practices of this approach to pastoral care? We attempt to address these questions in this paper. In doing so, we have drawn on the MindMatters Plus Demonstration Project and constructed a ‘whole school’ framework for pastoral care. We emphasise the importance of distributed leadership in our framework, where all staff and students alike are responsible for developing an ethos of care. This is a ‘work-in-progress’. We invite feedback on our proposal.
Adolescent Peer Counselling: Enhancing the Natural Conversational Helping Skills of Young People
Authors: Geldard Kathryn , Patton Wendy 
Published: September 2007

AbstractDuring the developmental stage of adolescence young people face many stressful challenges (Dacey & Kenny, 1997). Some adolescents manage these challenges adaptively but others do not and are therefore at the risk of adopting maladaptive responses to stress (Frydenberg & Lewis, 2002; Patton & Noller, 1990). Because adolescents are generally reluctant to talk in the first instance to parents, or other adults including adult counsellors, programs have been established to train adolescents in peer counselling. The present study examined the conversational skills that young people prefer to use when helping their peers and investigated their response to the use of traditional counselling skills with regard to ease of use and helpfulness. The results suggest that adolescents find some commonly used counselling skills difficult to use and unhelpful. Additionally the study suggests that young people found that some normal adolescent conversational behaviours which have been discouraged in adolescent peer counsellor training programs were helpful. The findings of this study have important implications with regard to training adolescents.
Genetic effects on male sexual coercion
Authors: Johansson Ada , Santtila Pekka , Harlaar Nicole , von der Pahlen Bettina , Witting Katarina , Ålgars Monica , Alanko Katarina , Jern Patrick , Varjonen Markus , Sandnabba N. Kenneth 
Published: September 2007

AbstractThe genetic and environmental influences on sexual coercion, and to what extent its associations with alcohol use and psychopathy depend on shared genetic and environmental effects, were explored in a Finnish population‐based sample of 938 men, aged 33–43 years, using the classical twin study design. All three phenotypes were associated positively and affected by genes (sexual coercion 28%, alcohol use 60%, psychopathy 54%), with 46% of the correlation between sexual coercion and psychopathy, 89% of the correlation between alcohol use and psychopathy and 100% of the correlation between sexual coercion and alcohol use being explained by shared genetic effects. Further, the results showed that a proportion of the variance in sexual coercion was derived from a highly genetic source that was common with alcohol use and psychopathy. This latent factor was hypothesized to reflect a general tendency for antisocial behavior that is pervasive across different situations. Relevant theories on sexual coercion were discussed in light of the results. Aggr. Behav. 34:190–202, 2008. © 2007 Wiley‐Liss, Inc.
Crystal nucleation and growth in poly(ethylene terephthalate)/alumina‐nanoparticle composites
Authors: Bhimaraj Praveen , Yang Hoichang , Siegel Richard W. , Schadler Linda S. 
Published: September 2007

AbstractThe effect of nanoparticles on nonisothermal polymer crystallization was investigated using poly(ethylene terephthalate) (PET) nanocomposites with alumina (Al2O3) nanoparticles of average size 38 nm. The filler content in the nanocomposites was varied from 0 to 10 wt %. The interparticle spacing was observed to decrease (as expected) with an increase in loading of the nanoparticles. Contrary to previous reports in the literature on semicrystalline polymer‐based composites with micron‐size and macroscale particles, our differential scanning calorimetry, transmission electron microscopy, and X‐ray studies showed that the addition of the nanoparticles did not cause heterogeneous nucleation of PET crystals in nanocomposites containing up to 3 wt % Al2O3. This is attributed to the nanoparticle curvature being comparable to the radius of gyration of the polymer. The addition of the nanoparticles was found to disrupt the spherulitic morphology of the PET because of their physical presence and their proximity to one another. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Accelerated ageing versus realistic ageing in aerospace composite materials. IV. Hot/wet ageing effects in a low temperature cure epoxy composite
Authors: Dao B. , Hodgkin J. H. , Krstina J. , Mardel J. , Tian W. 
Published: September 2007

AbstractSamples of an aerospace grade carbon fiber epoxy composite (Hexcel, M20/IM7) were subject to long term (≈1 year) hot/wet ageing and thermal spiking under a variety of humidity levels and temperature conditions related to “in service” conditions seen by military aircraft. Changes to the chemical and physicochemical structure of the composite were analyzed by a range of different techniques including gravimetric analysis, FTIR, and DMA to compare the effects of the various ageing conditions. The results indicated that the chemical effects of hot/wet and spiking conditions on this incompletely cured type of composite are very complex because of the variations in moisture levels and cure chemistry from the composite surface inwards as the resin ages under the different external environments. Physicochemical changes (such as Tg) and structural effects (such as microcracking) are similarly complex and dependent on composite thickness. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007
Spiritual interventions in psychotherapy: Evaluations by highly religious clients
Authors: Martinez Jennifer S. , Smith Timothy B. , Barlow Sally H. 
Published: September 2007

AbstractSpiritual and religious interventions in psychotherapy have increasingly received research attention, particularly with highly religious clients. This study examined client opinions about and experiences with religious interventions in psychotherapy. A sample of 152 clients at a counseling center of a university sponsored by the Church of Jesus Christ of Latter‐Day Saints (LDS) completed a survey with ratings of specific religious interventions concerning appropriateness, helpfulness, and prevalence. Out‐of‐session religious interventions were considered more appropriate by clients than in‐session religious interventions, but in‐session interventions were rated as more helpful. Specific interventions considered both appropriate and helpful by the LDS participants included referencing scriptural passages, teaching spiritual concepts, encouraging forgiveness, involving religious community resources, and conducting assessments of client spirituality. Some religious interventions were perceived as inappropriate or not helpful, and clients provided explanations for why religious interventions can be either effective or ineffective in psychotherapy. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 943–960, 2007.
Urban and rural temperature trends in proximity to large US cities: 1951–2000
Authors: Stone Brian 
Published: September 2007

AbstractThis paper presents a study of urban and rural temperature trends in proximity to the most populous metropolitan areas of the US. As data from urban meteorological stations are typically eliminated or adjusted for use in continental and global analyses of climate change, few studies have addressed how temperatures are changing in the areas most vulnerable to the public health impacts of warming: large cities. In this study, temperature data from urban and proximate rural stations for 50 large US metropolitan areas are analysed to establish the mean decadal rate of change in urban temperatures, rural temperatures, and heat island intensity over five decades. The results of this analysis find the mean decadal rate of change in the heat island intensity of large US cities between 1951 and 2000 to be 0.05 °C and further show a clear division in temperature trends between cities situated in the northeastern and southern regions of the country. Copyright © 2007 Royal Meteorological Society
Well‐posedness and long time behavior of a parabolic‐hyperbolic phase‐field system with singular potentials
Authors: Grasselli Maurizio , Miranville Alain , Pata Vittorino , Zelik Sergey 
Published: September 2007

AbstractIn this article, we study the long time behavior of a parabolic‐hyperbolic system arising from the theory of phase transitions. This system consists of a parabolic equation governing the (relative) temperature which is nonlinearly coupled with a weakly damped semilinear hyperbolic equation ruling the evolution of the order parameter. The latter is a singular perturbation through an inertial term of the parabolic Allen–Cahn equation and it is characterized by the presence of a singular potential, e.g., of logarithmic type, instead of the classical double‐well potential. We first prove the existence and uniqueness of strong solutions when the inertial coefficient ε is small enough. Then, we construct a robust family of exponential attractors (as ε goes to 0). (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Canada's voluntary ARET program: Limited success despite industry cosponsorship
Authors: Antweiler Werner , Harrison Kathryn 
Published: September 2007

AbstractThe Accelerated Reduction/Elimination of Toxins (ARET) Challenge was a voluntary program initiated in 1994 by the Government of Canada. Unlike the U.S. 33/50 Program, ARET involved industry partners in negotiation and cosponsorship of the program, with the intention that early involvement would yield stronger commitment to voluntary reductions. We review the program's self‐reported success in delivering emissions reductions. For 17 ARET substances that were also covered by Canada's National Pollutant Release Inventory, we employ treatment effects regressions to control for self‐selection bias. We find evidence that ARET accelerated emission reductions in five cases, slowed reductions in two cases, and had no discernible effect in ten cases. Industry cosponsorship apparently did not have the intended effect and instead resulted in program features such as data confidentiality that significantly undermined the program's credibility. © 2007 by the Association for Public Policy Analysis and Management