bluuebunny/crossref_metadata_2025_split huggingface dataset:
EDGE: extraction and analysis of differential gene expression
Authors: Leek Jeffrey T. , Monsen Eva , Dabney Alan R. , Storey John D. 
Published: December 2005

Abstract
Summary: EDGE (Extraction of Differential Gene Expression) is an open source, point-and-click software program for the significance analysis of DNA microarray experiments. EDGE can perform both standard and time course differential expression analysis. The functions are based on newly developed statistical theory and methods. This document introduces the EDGE software package.
Availability: EDGE is freely available for non-commercial users. EDGE can be downloaded for Windows, Macintosh and Linux/UNIX from
Contact: jtleek@u.washington.edu
RNAshapes: an integrated RNA analysis package based on abstract shapes
Authors: Steffen Peter , Voß Björn , Rehmsmeier Marc , Reeder Jens , Giegerich Robert 
Published: December 2005

Abstract
Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach.
Availability: RNAshapes is freely available at as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package.
Contact: psteffen@techfak.uni-bielefeld.de
Impulsivity in abstinent early‐ and late‐onset alcoholics: differences in self‐report measures and a discounting task
Authors: Dom G. , D’haene P. , Hulstijn W. , Sabbe B. 
Published: December 2005

ABSTRACTAims  To test the hypothesis that early‐onset alcoholics (EOAs) can be differentiated from late‐onset alcoholics (LOAs) by more severe substance‐related problems and higher levels of impulsivity and aggression.Design and measurements  A cross‐sectional patient survey with a community comparison group. The European Addiction Severity Index was used to assess substance‐related problems and the Barratt Impulsiveness Scale, the Dutch version of the Zuckermann Sensation Seeking Scale and the Buss–Durkee Hostility Inventory were used to assess impulsive and aggressive traits. Impulsive decision making was assessed using a delay discounting task (DDT) with hypothetical monetary rewards.Participants and setting  Participants were EOAs (n = 42) and LOAs (n = 46) recruited from an addiction treatment centre and an unmatched, non‐substance‐abusing comparison group (n = 54).Findings  The EOAs had higher levels of impulsive decision making than both the LOAs and the comparison group. The EOAs had higher scores than the LOAs on measures of impulsiveness, aggressiveness and the severity of substance‐related problems.Conclusions  This study provides evidence that EOAs are more impulsive and aggressive than LOAs. Further identification of alcoholism subtypes based on dimensions of impulsivity should be considered in the light of their relationship with pharmacological and behavioural treatment interventions.
The relationship between patterns of alcohol use and mental and physical health disorders in two American Indian populations
Authors: O'Connell Joan , Novins Douglas K. , Beals Janette , Croy Calvin , Barón Anna E. , Spicer Paul , Buchwald Dedra ,   the American Indian Service Utilization, Psychiatric Epidemiology, Risk and Protective Factors Project Team
Published: December 2005

ABSTRACTAims First, define alcohol use categories among two reservation‐based American Indian (AI) populations based on the relationship between alcohol consumption and dependence. Secondly, examine associations between the alcohol use categories and other indicators of health status.Design, participants and measurements Epidemiological data on 1287 AIs aged 18–57 years who consumed alcohol during the past year. CHAID tree analysis, a hierarchical partitioning method, was used to analyze alcohol quantity (highest number of drinks consumed during 1 day) and frequency (number of days drank during the past month) data to define quantity–frequency categories distinguished by differing rates of alcohol dependence. Multivariate analyses assessed relationships between the alcohol use categories thus identified and a number of health outcomes.Findings People who reported drinking 12 or more drinks during 1 day and more than 4 days a month had the highest prevalence of alcohol dependence. Among the males who drank > 18 drinks the prevalence was 42.12% and among females who drank 12 or more drinks, 44.58%. The prevalence among males who drank > 18 drinks yet drank less frequently was also high (24.06%). Although findings differed by gender, drinkers in the highest risk category for alcohol dependence were most likely to report drug use disorders, mood/anxiety disorders, alcohol‐related physical disorders and lower quality of life.Conclusions The quantity thresholds defined to identify AIs at highest risk for alcohol dependence in this study differed by gender and were higher than typically reported for non‐AIs. They are consistent with previous findings regarding the pattern of high‐quantity, low‐frequency alcohol consumption among AIs residing on reservations.
High‐resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL
Authors: Sato S. , Hasebe H. , Sato S. , Asahi Y. , Hayashi T. , Kobayashi E. , Sugimoto Y. 
Published: December 2005

SummaryWe previously mapped a locus for porcine intramuscular fat content (IMF) by linkage analysis to a 17.1‐cM chromosome interval on Sus scrofa chromosome 7 (SSC7) flanked by microsatellite markers SW1083 and SW581. In this study, we identified 34 microsatellite markers and 14 STSs from the 17.1‐cM IMF quantitative trait loci (QTL) region corresponding to HSA14q and aligned those loci using the INRA‐University of Minnesota porcine radiation hybrid (IMpRH) panel. We then constructed a 5.2‐Mb porcine bacterial artificial chromosome (BAC) contig of this region that was aligned using the RH panel. Finally, the IMF QTL was fine‐mapped to 12.6 cM between SJ169 and MM70 at the 0.1% chromosome‐wise significance level by genotyping the previously studied F2 resource family with 17 additional microsatellites. We also demonstrated that the SJ169–MM70 interval spans approximately 3.0 Mb and contains at least 12 genes: GALC, GPR65, KCNK10, SPATA7, PTPN21, FLJ11806, EML5, TTC8, CHES1, CAP2P1, CHORDC2P and C14orf143.
Mesoscale physical processes and the distribution and composition of ichthyoplankton on the southern Brazilian shelf break
Authors: FRANCO BÁRBARA CRISTIE , MUELBERT JOSÉ HENRIQUE , MATA MAURICIO MAGALHÃES 
Published: December 2005

AbstractThe southern Brazilian shelf supports the largest fish stocks in the country, and studies on physical–biological processes in the ecology of ichthyoplankton have been recommended to provide a better understanding of the variability of the recruitment of fishing resources. This study is the first to examine the influence of mesoscale physical processes on the distribution of early life stages of fish in this shelf‐break region. Collections of fish eggs and larvae and measurements of temperature and salinity were made at 13 stations along cross‐shelf transects in December 1997. Myctophidae, Bregmacerotidae, Clupeidae, Synodontidae and Engraulidae were the most abundant larvae in the northern region, while Engraulidae and Bregmacerotidae prevailed further south. In situ hydrographic data, NOAA/AVHRR images and merged TOPEX/POSEIDON + ERS‐1/2 satellite altimetry taken during the cruise revealed an anticyclonic eddy dominating the shelf around 31°S. Larval fish abundance was lower at the centre of this feature, suggesting that the eddy advected poorer offshore waters of tropical origin towards the inner shelf‐concentrating the larvae around the eddy.
Indirect ant‐protection against crab herbivory: damage‐induced susceptibility to crab grazing may lead to its reduction on ant‐colonized trees
Authors: OFFENBERG J. , MACINTOSH D. J. , NIELSEN M. G. 
Published: December 2005

Summary

Mangrove trees colonized by weaver ants (Oecophylla smaragdina) experience less insect and crab herbivory compared with trees without ants. However, it is unlikely that ants prey on and deter crabs as they do insects. Protection could be indirect if leaves damaged by insects are more susceptible to crab herbivory.
In the field and in laboratory tests, leaves with artificial holes simulating leaf beetle‐feeding marks were more susceptible than intact leaves to damage by the crab Episesarma versicolor.
The study further revealed that damaged leaves showed increased susceptibility only to male crab feeding whereas females were indiscriminate, probably because of differences in claw morphology between the sexes.
Combined with previous findings at the same field site, these results suggest that ants can indirectly protect trees against crab herbivory by directly removing insect herbivores and thus decreasing the leaf damage they inflict. The system illustrates a complex trophic cascade involving density and trait‐mediated indirect interactions.
Positive effect of parathyroidectomy on bone mineral density in mild asymptomatic primary hyperparathyroidism*
Authors: HAGSTRÖM E. , LUNDGREN E. , MALLMIN H. , RASTAD J. , HELLMAN P. 
Published: December 2005

Abstract.Objectives.  Patients with mild primary hyperparathyroidism (pHPT) often appear asymptomatic, and have previously been regarded as not requiring treatment. However, increased cardiovascular morbidity and dyslipidaemia have also been recognized in mild pHPT, which also seem to be normalized after parathyroidectomy. The present study explores whether postmenopausal women with mild pHPT have decreased bone mineral density (BMD) compared with age‐matched healthy controls, and the effects on BMD of parathyroidectomy.Design, Subjects and Intervention.  A population‐based health screening of 5202 postmenopausal women identified 87 overtly asymptomatic patients with mild pHPT as well as age‐matched healthy controls. A 5‐year follow‐up included 49 cases who had undergone parathyroidectomy. BMD was measured with DXA at the femoral neck, the lumbar spine and the total body.Results.  At study entry, BMD was 5–6% lower in the lumbar spine (L2‐L4) and femoral neck in cases compared with matched controls. After the 5‐year follow‐up, BMD increased in L2‐L4 by 2.9% (P = 0.002) in the parathyroidectomized cases and remained stable in the femoral neck. However, femoral neck BMD increased 4.1% (P = 0.013) for cases <67 years old (50% of the cohort).Conclusion.  In accordance with recent NIH guidelines for pHPT treatment, the level of BMD per se in the investigated group of patients justifies parathyroidectomy in almost half of the cases with mild pHPT. Surgery could be expected to increase BMD in L2‐L4 to the level of the controls, to increase femoral neck BMD in patients <67 years of age and to preserve femoral neck BMD in the elderly population.
Dissecting Ascaris glycosphingolipids for immunomodulatory moieties – the use of synthetic structural glycosphingolipid analogues
Authors: KEAN D. E. , OHTSUKA I. , SATO K. , HADA N. , TAKEDA T. , LOCHNIT G. , GEYER R. , HARNETT M. M. , HARNETT W. 
Published: December 2005

SUMMARY We have previously shown glycosphingolipids of Ascaris suum to have phosphorylcholine (PC) and non‐PC immunomodulatory moieties. In the present study we further investigated the nature of the immunomodulatory moieties by employing three synthetic glycosphingolipids each possessing features of the original molecule to examine effects on macrophage and dendritic cell (DC) cytokine production and surface co‐stimulatory molecule expression. Compound 2, which lacked PC but contained ceramide, had no effect on either macrophages or DCs. Surprisingly however, Compound 1, which contained PC and hence arguably most resembled the native material, had, with the exception of a small increase in surface antigen expression, no immunomodulatory properties. Conversely, Compound 3, which contained PC but was otherwise least like the native molecule, demonstrated a number of effects on both macrophages and DCs, including induction of Th‐1/pro‐inflammatory cytokines, inhibition of such cytokines induced by IFN‐γ/LPS and increased expression of co‐stimulatory molecules. Taken together these results indicate: (i) that although PC is an immunomodulatory component of the native molecule other structural feature are necessary to allow it to act; (ii) that carbohydrate rather than ceramide is likely to represent a non‐PC immunomodulatory moiety; and (iii) that synthetic PC‐containing molecules have the potential to act as immunomodulatory drugs.
Genetic variation in resistance to repeated infections with Heligmosomoides polygyrus bakeri, in inbred mouse strains selected for the mouse genome project
Authors: BEHNKE J. M. , MUGAMBI J. M. , CLIFFORD S. , IRAQI F. A. , BAKER R. L. , GIBSON J. P. , WAKELIN D. 
Published: December 2005

SUMMARY Since the publication of the mouse genome, attention has focused on the strains that were selected for sequencing. In this paper we report the results of experiments that characterized the response to infection with the murine gastrointestinal nematode Heligmosomoides polygyrus of eight new strains (A/J, C57BL/6, C3H, DBA/2, BALB/c, NIH, SJL and 129/J), in addition to the well‐characterized CBA (poor responder) and SWR (strong responder) as our controls. We employed the repeated infection protocol (consisting of 7 superimposed doses of 125L3 each administered at weekly intervals, faecal egg counts in weeks 2, 4 and 6 and assessment of worm burdens in week 6) that was used successfully to identify quantitative trait loci for genes involved in resistance to H. polygyrus. SWR, SJL and NIH mice performed indistinguishably and are confirmed as strong responder strains to H. polygyrus. CBA, C3H and A/J mice all tolerated heavy infections and are assessed as poor responders. In contrast, DBA/2, 129/J and BALB/c mice performed variably between experiments, some tolerating heavy worm burdens comparable to those in poor responders, and some showing evidence of resistance, although only in one experiment with female 129/J females and one with female BALB/c was the pattern and extent of worm loss much like that in SWR mice. Because the genetic relationships between six of the strains exploited in this study are now well‐understood, our results should enable analysis through single nucleotide polymorphisms and thereby provide more insight into the role of the genes that control resistance to H. polygyrus.
Antibodies enhance the protective effect of CD4+ T lymphocytes in SCID mice perorally infected with Encephalitozoon cuniculi
Authors: SAK B. , SALÁT J. , HORKÁ H. , SAKOVÁ K. , DITRICH O. 
Published: December 2005

SUMMARY The role of antibodies in the immune response to microsporidiosis was studied using a novel anti‐exospore monoclonal antibody (MAb) P5/H1, which recognizes surface antigens of Encephalitozoon cuniculi. The effect of the MAb on microsporidial infection in vivo was to prolong the survival of previously CD4+ reconstituted, perorally infected and intraperitoneally MAb‐treated SCID mice. The MAb decreased the numbers of E. cuniculi spores in peritoneal smears obtained post mortem. These results suggest a possible role for antibodies in protection against perorally acquired E. cuniculi infection.
The maize viviparous15 locus encodes the molybdopterin synthase small subunit
Authors: Suzuki Masaharu , Mark Settles A. , Tseung Chi‐Wah , Li Qin‐Bao , Latshaw Susan , Wu Shan , Porch Timothy G. , Schmelz Eric A. , James Martha G. , McCarty Donald R. 
Published: December 2005

SummaryA new Zea mays viviparous seed mutant, viviparous15 (vp15), was isolated from the UniformMu transposon‐tagging population. In addition to precocious germination, vp15 has an early seedling lethal phenotype. Biochemical analysis showed reduced activities of several enzymes that require molybdenum cofactor (MoCo) in vp15 mutant seedlings. Because MoCo is required for abscisic acid (ABA) biosynthesis, the viviparous phenotype is probably caused by ABA deficiency. We cloned the vp15 mutant using a novel high‐throughput strategy for analysis of high‐copy Mu lines: We used MuTAIL PCR to extract genomic sequences flanking the Mu transposons in the vp15 line. The Mu insertions specific to the vp15 line were identified by in silico subtraction using a database of MuTAIL sequences from 90 UniformMu lines. Annotation of the vp15‐specific sequences revealed a Mu insertion in a gene homologous to human MOCS2A, the small subunit of molybdopterin (MPT) synthase. Molecular analysis of two allelic mutations confirmed that Vp15 encodes a plant MPT synthase small subunit (ZmCNX7). Our results, and a related paper reporting the cloning of maize viviparous10, demonstrate robust cloning strategies based on MuTAIL‐PCR. The Vp15/CNX7, together with other CNX genes, is expressed in both embryo and endosperm during seed maturation. Expression of Vp15 appears to be regulated independently of MoCo biosynthesis. Comparisons of Vp15 loci in genomes of three cereals and Arabidopsis thaliana identified a conserved sequence element in the 5′ untranslated region as well as a micro‐synteny among the cereals.
The maize Viviparous10/Viviparous13 locus encodes the Cnx1 gene required for molybdenum cofactor biosynthesis
Authors: Porch Timothy G. , Tseung Chi‐Wah , Schmelz Eric A. , Mark Settles A. 
Published: December 2005

SummaryAbscisic acid (ABA), auxin and nitrate are important signaling molecules that affect plant growth responses to the environment. The synthesis or metabolism of these compounds depends on the molybdenum cofactor (MoCo). We show that maize (Zea mays) viviparous10 (vp10) mutants have strong precocious germination and seedling lethal phenotypes that cannot be rescued with tissue culture. We devised a novel PCR‐based method to clone a transposon‐tagged allele of vp10, and show that Vp10 encodes the ortholog of Cnx1, which catalyzes the final common step of MoCo synthesis. The seedling phenotype of vp10 mutants is consistent with disruptions in ABA and auxin biosynthesis, as well as a disruption in nitrate metabolism. Levels of ABA and auxin are reduced in vp10 mutants, and vp10 seedlings lack MoCo‐dependent enzyme activities that are repairable with exogenous molybdenum. vp10 and an Arabidopsis cnx1 mutant, chlorate6 (chl6), have similar defects in aldehyde oxidase (AO) enzyme activity, which is required for ABA synthesis. Surprisingly, chl6 mutants do not show defects in abiotic stress responses. These observations confirm an orthologous function for Cnx1 and Vp10, as well as defining a characteristic viviparous phenotype to identify other maize cnx mutants. Finally, the vp10 mutant phenotype suggests that cnx mutants can have auxin‐ as well as ABA‐biosynthesis defects, while the chl6 mutant phenotype suggests that low levels of AO activity are sufficient for normal abiotic stress responses.
Using ‘mute’ plants to translate volatile signals
Authors: Paschold Anja , Halitschke Rayko , Baldwin Ian T. 
Published: December 2005

SummaryWhen attacked by herbivores, plants release volatile organic compounds (VOCs) that attract natural enemies of the herbivores and function as indirect defenses. Whether or not neighboring plants ‘eavesdrop’ on these VOCs remains controversial because most studies use unrealistic experimental conditions and VOC exposures. In order to manipulate exposures of wild‐type (WT) Nicotiana attenuata‘receiver’ plants, we elicited transformed ‘emitter’ plants, whose production of herbivore‐induced C6 green leaf volatiles (GLVs) or terpenoid volatiles was genetically silenced, and placed them up‐wind of WT ‘receiver’ plants in open‐flow experimental chambers. We compared the transcriptional and secondary metabolite defense responses of WT receiver plants exposed to VOCs from these transgenic emitter plants with those of plants exposed to VOCs from WT emitter plants. No differences in the constitutive accumulation of defense metabolites and the signal molecule jasmonic acid (JA) were found. Additional elicitation of receiver plants revealed that exposure to WT, GLV‐deficient and terpenoid‐deficient volatile blends did not prime induced defenses, JA accumulation, or the expression of lipoxygenase 3 (NaLOX3), a gene involved in JA biosynthesis. However, exposure to wound‐ and herbivore‐induced VOCs significantly altered the transcriptional patterns in receiver plants. We identified GLV‐dependent genes by complementing the GLV‐deficient volatile blend with a mixture of synthetic GLVs. Blends deficient in GLVs or cis‐α‐bergamotene regulated numerous genes in receiver plants that did not respond to the complete VOC blends of WT emitters, indicating a suppressive effect of GLVs and terpenoids. Whether these transcriptional responses translate into changes in plant fitness in nature remains to be determined.
Atypical Cyclopia in a Brown Swiss Cross Calf: A Case Report
Authors: ÖZcan K. , Gürbulak K. , Takçi̇ İ. , ÖZen H. , Kaçar C. , Pancarci̇ M. Ş. 
Published: December 2005

SummaryIn this report, an atypical form of cyclopia is described in a stillborn Brown Swiss cross male calf. The changes were confined to the head. The most significant malformation was the presence of a median orbita‐like opening that did not contain an eyeball. Other defects included prosencephalic aplasia, brachygnathia superior and arrhinia. The possible cause of this congenital defect could not be ascertained.
Contribution of baroreflex sensitivity and vascular reactivity to variable haemodynamic responses to cocaine in conscious rats
Authors: Traub Michael , Aochi Tamiko , Kawada Toru , Shishido Toshiaki , Sunagawa Kenji , Knuepfer Mark M 
Published: December 2005

SUMMARY1. Baroreflex function is critical for short‐term arterial pressure regulation and decreased baroreflex responsivity may predict a predisposition to hypertension and sudden cardiac death. In the present study, we assessed whether baroreflex sensitivity (BRS) and/or vascular reactivity covary with haemodynamic responsiveness to cocaine in vascular and mixed responders.2. We assessed the heart rate index of BRS in resting animals. We examined dose–response relationships to pressor and depressor agents to determine cardiovascular reactivity. Subsequently, rats were given cocaine (5 mg/kg, i.v.) to classify them as vascular or mixed responders. Vascular responders (n = 16) were defined as those rats with a substantial (> 8%) decrease in cardiac output in response to cocaine owing to a larger increase in systemic vascular resistance. The remaining rats (n = 8) were mixed responders because they had smaller increases in vascular resistance and little change or an increase in cardiac output.3. The BRS determined with angiotensin (Ang) II, but not with phenylephrine, was impaired in mixed responders compared with vascular responders. At equipressor doses, there were significantly greater reductions in cardiac output in vascular responders compared with mixed responders in response to phenylephrine or AngII. Methacholine produced greater decreases in heart rate in vascular responders, suggesting greater muscarinic responsivity.4. We conclude that differences in vascular reactivity to AngII may contribute to differences in haemodynamic response profiles to cocaine in individual rats. More importantly, the differences in vascular responsivity and BRS do not appear to be primary determinants of haemodynamic response variability.