bluuebunny/crossref_metadata_2025 huggingface dataset:
A data integration methodology for systems biology: Experimental verification
Authors: Hwang Daehee , Smith Jennifer J. , Leslie Deena M. , Weston Andrea D. , Rust Alistair G. , Ramsey Stephen , de Atauri Pedro , Siegel Andrew F. , Bolouri Hamid , Aitchison John D. , Hood Leroy
Published: November 2005

The integration of data from multiple global assays is essential to understanding dynamic spatiotemporal interactions within cells. In a companion paper, we reported a data integration methodology, designated Pointillist, that can handle multiple data types from technologies with different noise characteristics. Here we demonstrate its application to the integration of 18 data sets relating to galactose utilization in yeast. These data include global changes in mRNA and protein abundance, genome-wide protein–DNA interaction data, database information, and computational predictions of protein–DNA and protein–protein interactions. We divided the integration task to determine three network components: key system elements (genes and proteins), protein–protein interactions, and protein–DNA interactions. Results indicate that the reconstructed network efficiently focuses on and recapitulates the known biology of galactose utilization. It also provided new insights, some of which were verified experimentally. The methodology described here, addresses a critical need across all domains of molecular and cell biology, to effectively integrate large and disparate data sets.
Root functioning modifies seasonal climate
Authors: Lee Jung-Eun , Oliveira Rafael S. , Dawson Todd E. , Fung Inez
Published: November 2005

Hydraulic redistribution (HR), the nocturnal vertical transfer of soil water from moister to drier regions in the soil profile by roots, has now been observed in Amazonian trees. We have incorporated HR into an atmospheric general circulation model (the National Center for Atmospheric Research Community Atmospheric Model Version 2) to estimate its impact on climate over the Amazon and other parts of the globe where plants displaying HR occur. Model results show that photosynthesis and evapotranspiration increase significantly in the Amazon during the dry season when plants are allowed to redistribute soil water. Plants draw water up and deposit it into the surface layers, and this water subsidy sustains transpiration at rates that deep roots alone cannot accomplish. The water used for dry season transpiration is from the deep storage layers in the soil, recharged during the previous wet season. We estimate that HR increases dry season (July to November) transpiration by ≈40% over the Amazon. Our model also indicates that such an increase in transpiration over the Amazon and other drought-stressed regions affects the seasonal cycles of temperature through changes in latent heat, thereby establishing a direct link between plant root functioning and climate.
“Clonal” population structure of the malaria agent
Plasmodium falciparum
in high-infection regions
Authors: Razakandrainibe F. G. , Durand P. , Koella J. C. , De Meeüs T. , Rousset F. , Ayala F. J. , Renaud F.
Published: November 2005

The population genetic structure of
Plasmodium falciparum
, the agent of malignant malaria, has been shown to be predominantly “clonal” (i.e., highly inbred) in regions of low infectivity; in high-infectivity regions, it is often thought to be panmictic, or nearly so, although there is little supporting evidence for this. The matter can be settled by investigating the parasite's genetic makeup in the midgut oocysts of the mosquito vector, where the products of meiosis can directly be observed. The developmental stages of
P. falciparum
are haploid, except in the oocysts of infected mosquito vectors, where two gametes fuse, diploidy occurs, and meiosis ensues. We have investigated genetic polymorphisms at seven microsatellite loci located on five chromosomes by assaying 613 oocysts in 145 mosquitoes sampled from 11 localities of Kenya, where malignant malaria is perennial and intense. There is considerable allelic variation, 16.3 ± 2.1 alleles per locus, and considerable inbreeding, ≈50% on the average. The inbreeding is caused by selfing (≈25%) and nonrandom genotype distribution of oocysts among mosquito guts (35%). The observed frequency of heterozygotes is 0.43 ± 0.03; the expected frequency, assuming random mating, is 0.80 ± 0.05. Linkage disequilibrium is statistically significant for all 21 pairwise comparisons between loci, even though 19 comparisons are between loci in different chromosomes, which is consistent with strong deviation from panmixia and the consequent reproduction of genomes as clones, without recombination between gene loci. This is of considerable evolutionary significance and of epidemiological consequence, concerning the spread of multilocus drug and vaccine resistance.
Gemin proteins are required for efficient assembly of Sm-class ribonucleoproteins
Authors: Shpargel Karl B. , Matera A. Gregory
Published: November 2005

Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by loss of spinal motor neurons. The gene encoding the survival of motor neurons (SMN) protein is mutated in >95% of SMA cases. SMN is the central component of a large oligomeric complex, including Gemins2–7, that is necessary and sufficient for the
in vivo
assembly of Sm proteins onto the small nuclear (sn)RNAs that mediate pre-mRNA splicing. After cytoplasmic assembly of the Sm core, both SMN and splicing snRNPs are imported into the nucleus, accumulating in Cajal bodies for additional snRNA maturation steps before targeting to splicing factor compartments known as “speckles.” In this study, we analyzed the function of individual SMN complex members by RNA interference (RNAi). RNAi-mediated knockdown of SMN, Gemin2, Gemin3, and Gemin4 each disrupted Sm core assembly, whereas knockdown of Gemin5 and Snurportin1 had no effect. Assembly activity was rescued by expression of a GFP-SMN construct that is refractive to RNAi but not by similar constructs that contain SMA patient-derived mutations. Our results also demonstrate that Cajal body homeostasis requires SMN and ongoing snRNP biogenesis. Perturbation of SMN function results in disassembly of Cajal bodies and relocalization of the marker protein, coilin, to nucleoli. Moreover, in SMN-deficient cells, newly synthesized SmB proteins fail to associate with U2 snRNA or accumulate in Cajal bodies. Collectively, our results identify a previously uncharacterized function for Gemin3 and Gemin4 in Sm core assembly and correlate the activity of this pathway with SMA.
Long‐chain polyunsaturated fatty acids in Chinese and Swedish mothers: Diet, breast milk and infant growth
Authors: XIANG MINGYAN , HARBIGE LAURENCE S. , ZETTERSTRÖM ROLF
Published: November 2005

Long‐chain polyunsaturated fatty acids (LC‐PUFAs) are essential dietary nutrients required for the optimal growth and development of infants, particularly of the brain and retina. It is important for exclusively breastfed infants to receive milk of a correct balance between ω‐6 and ω‐3 fatty acids. In this study, we compared the composition of LC‐PUFAs in the diet and milk of mothers and their infants' growth between Chinese and Swedish. Twenty‐three and 19 mother‐term infant pairs from a rural area of northern Beijing, China, and Stockholm, Sweden, who were 3 mo old and exclusively breastfed, were studied. The Chinese diet was higher in carbohydrate (17% of energy) but lower in protein (4% of energy) and fat (12% of energy) than the Swedish diet. The intake of Chinese mothers contained more linoleic acid (LA, C18:2 ω‐6) and less arachidonic acid (AA, C20.4 ω‐6), eicosapentaenoic acid (EPA, C20:5 ω‐3) and docosahexaenoic acid (DHA, C22:6 ω‐3) than that of Swedish mothers. The breast milk of the Chinese mothers had significantly higher LA and lower EPA and DHA levels than that of the Swedish mothers. However, in Chinese breast milk the AA level was significantly higher than that in Swedish breast milk. The recommended ranges of the ratios of LA to α‐linolenic acid (LNA, C18:3 ω‐3) and of AA to DHA in human milk are 5–10 and 0.5–1 compared with 23.0 and 3.1 in the Chinese breast milk, and 7.5 and 1.6 in the Swedish breast milk, respectively.

Conclusion: The diet of the studied Chinese mothers is less balanced with regard to the levels of ω‐6 and ω‐3 polyunsaturated fatty acids (PUFAs) than that of the Swedish mothers, which is also mirrored in the breast milk of these mothers. The clinical relevance of the difference between the levels of LC‐PUFAs in the breast milk of Chinese and Swedish mothers may be elucidated by a follow‐up study of the cognitive and visual functions of the infants involved.
Anthropometry at the time of diagnosis in Danish children with inflammatory bowel disease
Authors: PAERREGAARD ANDERS , URNE FREDERIKKE ULDALL
Published: November 2005

All patients below 15 y of age living in the eastern part of Denmark with a diagnosis of inflammatory bowel disease (IBD) during the period 1998–2000 were identified (n = 94) and anthropometrical data at the time of diagnosis were evaluated.

Conclusion: The height‐for‐age and the BMI‐for‐age, as evaluated by z‐scores, of children with ulcerative colitis (UC) did not differ from those of normal Danish children, but Crohn's disease (CD) children had significantly lower height and BMI values, both when compared to normal children and children with UC. In contrast to UC, CD is frequently complicated by malnutrition and growth retardation at the time of diagnosis.
Doxapram and developmental delay at 12 months in children born extremely preterm
Authors: LANDO ANE , KLAMER ANJA , JONSBO FINN , WEISS J ANNE , GREISEN GORM
Published: November 2005

Aim: To examine the relation of doxapram to a developmental score achieved by a structured telephone interview in a group of extremely‐preterm‐born children.

Methods: Parents of 88 children born extremely preterm were contacted by telephone and interviewed by a structured questionnaire (R‐PDQ) when the corrected age of their child was 9–15 mo.

Results: We found that doxapram treatment was associated with a deficit in age‐adjusted R‐PDQ score.

Conclusion: Doxapram may have a negative effect on neurodevelopmental outcome.
The effect of voluntary dehydration on cognitive functions of elementary school children
Authors: BAR‐DAVID YAIR , URKIN JACOB , KOZMINSKY ELY
Published: November 2005

Aims: (1) To describe the occurrence of voluntary dehydration in two classes of elementary school students as expressed by their morning and noon‐time urine osmolality; and (2) to determine the relationship between the children's scores on cognitive tests and their state of hydration.

Methods: Group comparison among fifty‐eight sixth‐grade students (age range 10.1–12.4 y old) during mid‐June at two schools in a desert town. Morning and noon‐time urine samples were collected in school, and five cognitive tests were scored in the morning and at noon‐time. Main outcome measures: (1) morning and noon‐time urine osmolality; (2) scores of five cognitive tests (hidden figures, auditory number span, making groups, verbal analogies, and number addition) that were applied in the morning and at noon‐time.

Results: Thirty‐two students were dehydrated (urine osmolality above 800 mosm/kg H2O) in the morning. An individual's noon‐time urine osmolality was highly related to morning osmolality (r = 0.67, p = 0.000). The morning cognitive scores were similar in the hydrated and dehydrated students (p = 0.443). The adjusted mean scores of the noon‐time tests, with the morning test scores as covariates, demonstrated an overall positive trend in four of the five tests in favor of the hydrated group (p = 0.025). The effect was mainly due to the auditory number span test (p = 0.024).

Conclusion: Voluntary dehydration is a common phenomenon in school‐aged children that adversely affects cognitive functions.
A decreasing rate of neural tube defects following the recommendations for periconceptional folic acid supplementation
Authors: KLUSMANN ANNE , HEINRICH BEATE , STÖPLER HEIKE , GÄRTNER JUTTA , MAYATEPEK ERTAN , VON KRIES RÜDIGER
Published: November 2005

Background/aim: Neural tube defects (NTDs) are the most common birth defects, resulting in severe mortality and morbidity. In 1995, the supplementation of folic acid periconceptionally was officially recommended in Germany. The impact of the recommendations on the rate of NTDs was assessed.

Methods: An active surveillance system was established in the northern Rhine area. From 1996, all departments of obstetrics were asked to report cases of NTDs in all abortions, live births and stillbirths. Compliance with the recommendations was evaluated in a sample of mothers who delivered at the Department of Obstetrics of Düsseldorf University in 2001.

Results: From 1996–2003, 520 NTDs were reported. Compared to the rate of NTDs in 1996 (10.5/10000), the average incidence in the years 1997 to 2003 dropped (6.8/10000). The intake of folic acid, as recommended, was low among the general population (21.1%).

Conclusion: Active surveillance data on the rate of NTDs are compatible with the maximum decrease of about 20% to be expected from data on the implementation of the recommendations. A much greater decrease in NTDs should be the challenge for the future.
Perinatal management of a preterm neonate affected by hyperprostaglandin E2 syndrome (HPS)
Authors: KÖMHOFF MARTIN , TEKESIN ISMAIL , PETERS MELANIE , LEONHARD ANDREAS , SEYBERTH HANNSJÖRG W.
Published: November 2005

Background: Neonates affected by hyperprostaglandin E2 syndrome (HPS) present with severe polyuria. Both urinary losses as well as prostaglandin synthesis inhibitors may precipitate acute renal failure (ARF). Aim: Our goal was to maintain euvolaemia by replacement of urinary losses. Patient: Our patient was born prematurely with a family history typical of HPS. Urinary salt and water losses and PGE2 excretion were determined in 2‐ to 4‐h intervals. Salt and water were replaced accordingly.

Results: Within the first 48 h, urinary losses and PGE2 increased continuously to 50 ml/kg/h and 374 ng/h/1.73 m2, respectively. Following exposure to 0.05–0.5 mg/kg/d indomethacin, urinary output decreased steadily to 10–15/ ml/kg/h.

Conclusion: In euvolaemic preterm neonates with HPS and the need for excessive replacement of salt and water, inhibition of renal PGE2 excretion with indomethacin effectively reduces polyuria and natriuresis without acutely compromising renal function.
Does chronic prenatal Doppler pathology predict feeding difficulties in neonates?
Authors: MÜLLER‐EGLOFF SUSANNE , STRAUSS ALEXANDER , SPRANGER VERONIKA , GENZEL‐BOROVICZÉNY ORSOLYA
Published: November 2005

Aim: To determine whether infants with compromised fetomaternal circulation, but not yet critically threatened by absent end‐diastolic flow velocities in the umbilical arteries, are at a risk for feeding problems.

Methods: In a retrospective case‐control study, enteral feeding and clinical data were compared between infants with decreased prenatal end‐diastolic umbilical flow velocity (DEDFV) or brain‐sparing pathology and controls matched for gestational age (GA). In all infants, enteral feedings were advanced according to a standardized enteral feeding protocol.

Results: 11 (GA > 34 wk) of the 87 infants with DEDFV were fully enterally fed by day 5 and excluded, leaving 76 infants (and matched controls) for final analysis. DEDFV infants were significantly smaller (1230 ± 550 g vs 1600 ± 682 g). Advancement of enteral feedings varied widely, with a significant difference between DEDFV infants and controls. There was no difference in the incidence of NEC (five in both groups). In the most severely affected subgroup of 25 infants with GA<30 wk and prenatal brain sparing, enteral feedings were significantly delayed in comparison to the controls (parenteral amino acid administration for 22 vs 15 d; significantly fewer enteral calories through day 15).

Conclusion: Enteral feeds were introduced more slowly to infants who had shown signs of prenatal distress with brain sparing. However, a predisposition to NEC could not be proven. Our results thus do not support the delay of enteral feedings based on prenatal Doppler pathology.
The changing pattern of A level/AS uptake in England
Authors: Bell John F. , Malacova Eva , Shannon Mark
Published: November 2005

One of the objectives of Curriculum 2000 is to increase the breadth of the curriculum followed by 16–19 year olds. In this paper A level and AS uptake for the years 2001 and 2002 are considered. There was considerable diversity in the uptake of A levels, with nearly 21,000 different combinations of A levels being present in 2002 A level results. Although it is true that biology, chemistry and mathematics is the most common combination of A levels, only 2.2 per cent of candidates took this precise combination. There has been a decline in the percentage of candidates taking three science A levels. In 2002, when only A levels are considered, 35 per cent of candidates could be described as specialists, falling to 21 per cent when AS results are included. AS qualifications appear to have been successful in broadening the curriculum.
PU.1 is not strictly required for B cell development and its absence induces a B-2 to B-1 cell switch
Authors: Ye Min , Ermakova Olga , Graf Thomas
Published: November 2005

In this paper, we describe the unexpected outgrowth of B lineage cells from PU.1−/− fetal liver cultures. The cells express all early B cell genes tested, including the putative PU.1 target genes IL-7R and EBF but not B220, and can produce immunoglobulin M. However, we observed a delay in the PU.1−/− B cell outgrowth and reduced precursor frequencies, indicating that although PU.1 is not strictly required for B cell commitment, it facilitates B cell development. We also ablated PU.1 in CD19-expressing B lineage cells in vivo, using a Cre-lox approach that allows them to be tracked. PU.1 excision resulted in a shift from B-2 cells to B-1–like cells, which dramatically increased with the age of the mice. Our data indicate that this shift is predominantly caused by a B-2 to B-1 cell reprogramming. Furthermore, we found that B-2 cells express substantially more PU.1 than B-1 cells, which is consistent with the idea that maintenance of the B-2 cell phenotype requires relatively high levels of PU.1, but B-1 cells require little.
Yersinia virulence factor YopJ acts as a deubiquitinase to inhibit NF-κB activation
Authors: Zhou Honglin , Monack Denise M. , Kayagaki Nobuhiko , Wertz Ingrid , Yin Jianpin , Wolf Beni , Dixit Vishva M.
Published: November 2005

The bacterial pathogens of the genus Yersinia, the causative agents of plague, septicemia, and gastrointestinal syndromes, use a type III secretion system to inject virulence factors into host target cells. One virulence factor, YopJ, is essential for the death of infected macrophages and can block host proinflammatory responses by inhibiting both the nuclear factor κB (NF-κB) and mitogen-activated protein kinase pathways, which might be important for evasion of the host immune response and aid in establishing a systemic infection. Here, we show that YopJ is a promiscuous deubiquitinating enzyme that negatively regulates signaling by removing ubiquitin moieties from critical proteins, such as TRAF2, TRAF6, and IκBα. In contrast to the cylindromatosis tumor suppressor CYLD, which attenuates NF-κB signaling by selectively removing K63-linked polyubiquitin chains that activate IκB kinase, YopJ also cleaves K48-linked chains and thereby inhibits proteasomal degradation of IκBα. YopJ, but not a catalytically inactive YopJ mutant, promoted deubiquitination of cellular proteins and cleaved both K48- and K63-linked polyubiquitin. Moreover, an in vitro assay was established to demonstrate directly the deubiquitinating activity of purified YopJ.
BAFF regulates B cell survival by downregulating the BH3-only family member Bim via the ERK pathway
Authors: Craxton Andrew , Draves Kevin E. , Gruppi Adriana , Clark Edward A.
Published: November 2005

The B cell activating factor belonging to the tumor necrosis factor family (BAFF) is required for B cell survival and maturation. The mechanisms by which BAFF mediates B cell survival are less understood. We found that BAFF and a proliferation-inducing ligand (APRIL), which are related, block B cell antigen receptor (BCR)–induced apoptosis upstream of mitochondrial damage, which is consistent with a role for Bcl-2 family proteins. BCR ligation strongly increased expression of the proapoptotic Bcl-2 homology 3–only Bcl-2 protein Bim in both WEHI-231 and splenic B cells, and increases in Bim were reversed by BAFF or APRIL. Small interfering RNA vector–mediated suppression of Bim blocked BCR-induced apoptosis. BAFF also induced Bim phosphorylation and inhibited BCR-induced association of Bim with Bcl-2. BAFF induced delayed but sustained stimulation of extracellular signal–regulated kinase (ERK) and its activators, mitogen-activated protein kinase/ERK activating kinase (MEK) and c-Raf, and MEK inhibitors promoted accumulation and dephosphorylation of Bim. These results suggest that BAFF inhibits BCR-induced death by down-regulating Bim via sustained ERK activation, demonstrating that BAFF directly regulates Bim function. Although transitional immature type 1 (T1) B cell numbers are normal in Bim−/− mice, T2 and follicular mature B cells are elevated and marginal zone B cells are reduced. Our results suggest that mature B cell homeostasis is maintained by BAFF-mediated regulation of Bim.
The very 5′ end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions
Authors: Longerich Simonne , Tanaka Atsushi , Bozek Grazyna , Nicolae Dan , Storb Ursula
Published: November 2005

Somatic hypermutation (SHM) is restricted to VDJ regions and their adjacent flanks in immunoglobulin (Ig) genes, whereas constant regions are spared. Mutations occur after about 100 nucleotides downstream of the promoter and extend to 1–2 kb. We have asked why the very 5′ and most of the 3′ region of Ig genes are unmutated. Does the activation-induced cytosine deaminase (AID) that initiates SHM not gain access to these regions, or does AID gain access, but the resulting uracils are repaired error-free because error-prone repair does not gain access? The distribution of mutations was compared between uracil DNA glycosylase (Ung)-deficient and wild-type mice in endogenous Ig genes and in an Ig transgene. If AID gains access to the 5′ and 3′ regions that are unmutated in wild-type mice, one would expect an “AID footprint,” namely transition mutations from C and G in Ung-deficient mice in the regions normally devoid of SHM. We find that the distribution of total mutations and transitions from C and G is indistinguishable in wild-type and Ung-deficient mice. Thus, AID does not gain access to the 5′ and constant regions of Ig genes. The implications for the role of transcription and Ung in SHM are discussed.
The Systemic Theory of Living Systems. Part IV: Systemic Medicine—The Praxis
Authors: Olalde Rangel José A. , Magarici Meyer , Amendola Francis , del Castillo Oswaldo
Published: November 2005

This fourth lecture illustrates the praxis and results of Systemic Medicine (SM) in various therapeutic applications. SM′s success has made it popular throughout Venezuela and Puerto Rico. The treatment of over 300 000 patients by 150 orthodox MD′s, trained and qualified in SM, in 35 medical establishments with above average results corroborate its effectiveness as an eCAM in chronic degenerative diseases. Herein we provide a synopsis of results obtained in four such pathologies—the journal′s necessary space restrictions somewhat limiting content—as well as clinical and photographic evidence. The validity of any medical theory is substantiated by its degree of effectivity and success. The workability of evidence‐based SM corroborates Systemic Theory′s transcendence.
Thomas Addis of Edinburgh (1881–1949) and the coagulation cascade: ‘for the greatest benefit done to practical medicine’
Authors: Doyle Derek
Published: November 2005

Thomas Addis came of evangelical Scots stock; he was brought up to care for others less fortunate than himself, to know what he believed in and to defend it vigorously. Trained at the turn of the 19th and 20th centuries in a Scotland still recovering from wars and ecclesiastical schisms, yet producing record numbers of missionaries and many social improvements, he was a brilliant haematologist and innovative researcher. Moving to Stanford his career continued to blossom as a nephrologist whilst his concern for the less fortunate found expression in his espousal of communist principles. Only in his later years was he finally honoured for his many contributions to medicine, science and social issues.
Cytological study of early cervical adenocarcinoma: special reference to the depth of invasion
Authors: Kaku T. , Kawano Y. , Hirakawa T. , Koga Y. , Kobayashi H. , Amada S. , Ogawa S. , Hagiwara T. , Watanabe S. , Nakano H.
Published: November 2005

Objective:  Early cervical adenocarcinoma (ECA) with a tumour depth of <3 mm has a good prognosis. To clarify the cytological features of ECAs with depth <3 mm, these were compared with those of ECA with 3–5 mm and invasive adenocarcinoma (IA) invading the cervical wall with more than 5 mm in depth.

Methods:  The cervical cytological features of ECAs with depth <3 mm (14 cases) were compared with those of ECA with 3–5 mm (four cases) and IA (13 cases). Cytologically, the presence or absence of tumour diathesis, number of atypical cells, crowded cell groups, groups with glandular structures, feathering, groups with palisading borders, rosettes, clusters, cell shape and size, nuclear shape and size, nucleolar shape and size, chromatin distribution, border and character of cytoplasm, and single cell pattern were evaluated.

Results:  A tumour diathesis was seen in five of 14 ECA <3 mm in depth (36%), all four ECA with 3–5 mm (100%) and 11 of 13 IA with more than 5 mm (85%). Single cells, macronucleoli and coarsely granular chromatin pattern were less frequent in ECA of <3 mm than that in ECA with 3–5 mm and IA. The number of atypical cells and glandular structures in ECA was significantly less than that in IA. Cell crowding, feathering, palisading and rosettes were common in both ECA and IA.

Conclusion:  The characteristic cytological features of ECA with depth <3 mm, having a good prognosis, were clean background, fewer single cells and macronucleoli, and less frequent coarsely granular chromatin pattern compared with those in ECA with 3–5 mm and IA. The number of atypical cells and glandular structures in ECA was significantly less than that in IA. Familiarity with the cytological features of ECA and its mimics is essential.
Atypical glandular cells: criteria to discriminate benign from neoplastic lesions and squamous from glandular neoplasia
Authors: Torres J. C. C. , Derchain S. F. M. , Gontijo R. C. , Do Amaral Westin M. C. , Zeferino L. C. , Angelo‐Andrade L. A. L. , Rabelo‐Santos S. H.
Published: November 2005

Objective:  To evaluate the presence of some criteria in cervical smears with atypical glandular cells and their correlation with histological patterns to identify pre‐neoplastic and neoplastic lesions.

Methods:  Seventy‐three women referred with an atypical glandular cell smear, who had undergone conization or hysterectomy, were included in this study. Referral Pap smears were reviewed using the set of 27 cyto‐morphological criteria that was correlated with the histological diagnosis.

Results:  Histological results showed intraepithelial or invasive neoplasia in 35 (48%) cases and benign lesions in 38 (52%) cases. After logistic regression and decision tree analysis an increased nuclear/cytoplasmic ratio and the presence of dyskeratotic cells were strongly associated with intraepithelial or invasive neoplasia and the differential cyto‐morphological criteria for glandular lesions were decreased cytoplasm, irregular nuclear membranes and the presence of nucleoli.

Conclusion:  The analysis of individual cyto‐morphological criteria can better predict intraepithelial or invasive neoplasia and differentiate glandular from squamous lesions.
Animal and vegetation patterns in natural and man‐made bog pools: implications for restoration
Authors: MAZEROLLE MARC J. , POULIN MONIQUE , LAVOIE CLAUDE , ROCHEFORT LINE , DESROCHERS ANDRÉ , DROLET BRUNO
Published: November 2005

1. Peatlands have suffered great losses following drainage for agriculture, forestry, urbanisation, or peat mining, near inhabited areas. We evaluated the faunal and vegetation patterns after restoration of a peatland formerly mined for peat. We assessed whether bog pools created during restoration are similar to natural bog pools in terms of water chemistry, vegetation structure and composition, as well as amphibian and arthropod occurrence patterns.

2. Both avian species richness and peatland vegetation cover at the site increased following restoration. Within bog pools, however, the vegetation composition differed between natural and man‐made pools. The cover of low shrubs, Sphagnum moss, submerged, emergent and floating vegetation in man‐made pools was lower than in natural pools, whereas pH was higher than in typical bog pools. Dominant plant species also differed between man‐made and natural pools.

3. Amphibian tadpoles, juveniles and adults occurred more often in man‐made pools than natural bog pools. Although some arthropods, including Coleoptera bog specialists, readily colonised the pools, their abundance was two to 26 times lower than in natural bog pools. Plant introduction in bog pools, at the stocking densities we applied, had no effect on the occurrence of most groups.

4. We conclude that our restoration efforts were partially successful. Peatland‐wide vegetation patterns following restoration mimicked those of natural peatlands, but 4 years were not sufficient for man‐made pools to fully emulate the characteristics of natural bog pools.
Developmental expression patterns of testicular olfactory receptor genes during mouse spermatogenesis
Authors: Fukuda Nanaho , Touhara Kazushige
Published: November 2005

A subset of olfactory receptors (ORs) is expressed in mammalian male germ cells. Recent studies on human and mouse sperm have suggested that calcium signaling via a testicular OR regulates sperm flagellar motility. However, it remains to be determined at what stages testicular ORs are expressed during spermatogenesis and whether each germ cell expresses one or multiple ORs. Here we examined the developmental expression profiles of several mouse testicular OR genes using an in situ hybridization technique at the cellular level. We found that OR transcripts in the spermatogenic cells are expressed in three developmental stages: late pachyten spermatocytes, early round spermatids, or late round spermatids. The OR mRNAs were condensed in a single dot‐like structure within the nuclei of a subpopulation of spermatogenic cells. Double‐fluorescent in situ hybridization revealed that some cells contained two dot‐like signals derived from transcripts of two different ORs, suggesting that single spermatogenic cells could express more than one OR. One cell‐multiple OR gene expression combined with variability in expression appears to result in heterogeneity in the repertoire of ORs expressed by individual spermatogenic cells. Although the functional consequence of heterogeneous OR expression awaits development of a methodology for characterizing OR proteins, our observations give insights into OR gene expression as well as OR function(s) in spermatogenic cells.
Ex vivo comparison of two electronic apex locators with different scales and frequencies
Authors: Hör D. , Krusy S. , Attin T.
Published: November 2005

Aim  To compare ex vivo the accuracy of two impedance quotient apex locators with different scales and frequencies of the measuring circuit.

Methodology  In each root of 193 extracted human teeth, electronic working length determination (ELD) was carried out with a newly constructed measuring unit. In all cases, ELD was performed using the apex locators Justy II® (Hager & Werken, Duisburg, Germany) and Raypex 4® (VDW, Munich, Germany) on the scale points (sp) 0/0.5/1 of each device. A Miller Needle reaching working length was fixed with composite. The corresponding sp and the differences to the other sp were recorded. After histological preparation of the apical region, the teeth were examined under a light microscope. The distances of the Miller Needle tips to the target intervals ‘minor foramen–major foramen’ and ‘apical canal constriction’ (apical constriction) were determined for each sp for both devices. The data were statistically analysed by a chi‐square test.

Results  Precise determination of the target interval ‘minor foramen–major foramen’ was successful with Raypex 4 in 94.8% (sp 1), 90.7% (sp 0.5) and 72.5% (sp 0) of cases and with Justy II in 59.6% (sp 1), 92.2% (sp 0.5) and 68% (sp 0) of cases. No measurement carried out by Raypex 4 and by Justy II on sp 1 was beyond the major apical foramen. However, on sp 0.5, there were eight measurements for Raypex 4 and four measurements for Justy II beyond the major apical foramen. Overinstrumentation was also recorded for sp 0 in 49 specimens (Raypex 4) and 59 specimens (JustyII). The major apical constriction was met exactly by Raypex 4 in 50.7% (sp 1), 14% (sp 0.5) and 5.2% (sp 0) of cases and by Justy II in 32.1% (sp 1), 23.8% (sp 0.5) and 4.1% (sp 0) of cases. The differences between the determination made with the sp suggested by the manufacturers for Raypex 4 (sp 1) and Justy II (sp 0.5) were not significant (P > 0.05) for the target interval ‘minor foramen–major foramen’ and significant (P ≤ 0.05) for the apical constriction. The differences between the sp of each device were significant (P ≤ 0.05) for both target intervals.

Conclusions  It is possible to determine the region between the minor and major apical foramen with electronic apex locators ex vivo. The best results were obtained using the sp advised by the manufacturers. Raypex 4 gave the best results on sp one without any measurement beyond the apical foramen. Use of ELD does not result in precise determination of the apical constriction.
Apical extrusion of intracanal bacteria following use of two engine‐driven instrumentation techniques
Authors: Er K. , Sümer Z. , Akpınar K. E.
Published: November 2005

Aim  To evaluate the number of bacteria extruded apically from extracted teeth ex vivo after canal instrumentation using the two engine‐driven techniques utilizing nickel‐titanium instruments (ProTaper and System GT).

Methodology  Forty extracted single‐rooted human mandibular premolar teeth were used. Access cavities were prepared and root canals were then contaminated with a suspension of Enterococcus faecalis and dried. The contaminated roots were divided into two experimental groups of 15 teeth each and one control group of 10 teeth. Group 1, ProTaper group: the root canals were instrumented using ProTaper instruments. Group 2, System GT group: the root canals were instrumented using System GT instruments. Group 3, control group: no instrumentation was attempted. Bacteria extruded from the apical foramen during instrumentation were collected into vials. The microbiological samples from the vials were incubated in culture media for 24 h. Colonies of bacteria were counted and the results were given as number of colony‐forming units. The data obtained were analysed using the Kruskal–Wallis one‐way analysis of variance and Mann–Whitney U‐tests, with α = 0.05 as the level for statistical significance.

Results  There was no significant difference as to the number of extruded bacteria between the ProTaper and System GT engine‐driven systems (P > 0.05).

Conclusions  Both engine‐driven nickel‐titanium systems extruded bacteria through the apical foramen.
Heat shock induces the synthesis of the inflammatory mediator leukotriene B4 in human pulp cells
Authors: Eberhard J. , Zahl A. , Dommisch H. , Winter J. , Acil Y. , Jepsen S.
Published: November 2005

Aim  To measure the synthesis of leukotriene B4 (LTB4) in cultures of human dental pulp cells induced by heat shock.

Methodology  Primary pulp cells (PC) and dental pulp stem cells (DPSC) were cultivated under appropriate conditions. For the characterization of PC the expression of dentine sialophosphoprotein (DSPP) was evaluated by reverse transcription‐polymerase chain reaction. Thermal stimulation of cell cultures was performed at temperatures of 37, 38, 39, 40, 42 and 45 °C for stimulation times of 5 and 30 s. LTB4 was quantified by reversed‐phase high‐performance chromatography and differences between the LTB4 concentrations of controls and heat stimulated cells were analysed with Friedman analysis of variances by ranks and multiple comparisons (P < 0.05).

Results  Both cell cultures expressed DSPP under the conditions of the present experiment. The analysis revealed significantly enhanced LTB4 synthesis following thermal stimulations at 38, 39, 40, 42 and 45 °C compared with unstimulated controls for both PC and DPSC.

Conclusion  The present study demonstrated the capability of pulp cells to synthesize the arachidonic acid mediator LTB4 in response to heat shock. LTB4 has the capacity to induce inflammatory reactions and to sensitise afferent nociceptive nerve endings. LTB4 synthesis is induced by minor temperature changes, which are relevant for various clinical situations.
Loop‐mediated isothermal amplification: an emerging technology for detection of fish and shellfish pathogens
Authors: Savan R , Kono T , Itami T , Sakai M
Published: November 2005

Fish and shellfish diseases are a constant threat to the sustainability and economic viability of aquaculture. Early diagnosis plays a vital role in management of fish and shellfish diseases. Traditionally, various biochemical and serological tests have been used for fish disease diagnosis. However, the time and expertise required for such diagnoses makes it difficult for aquaculturists to easily adopt them under production conditions. Polymerase chain reaction and probe‐based nucleic acid detection have become increasingly popular in fish and shellfish diagnostics. Recently, a novel technique called loop‐mediated isothermal amplification (LAMP) has been developed, which is highly sensitive and rapid. LAMP has been used for the detection of bacterial, viral, fungal and parasitic diseases in both animal and plants. In aquaculture, LAMP‐based detection of pathogens like Edwardsiella tarda, E. ictaluri, Nocardia seriolae, Tetracapsuloides bryosalmonae, white spot syndrome virus and infectious haematopoietic necrosis virus have been reported. In this review, the application of LAMP for the detection of aquaculture‐associated pathogens is discussed.
Influence of dietary lipid composition on cardiac pathology in farmed Atlantic salmon, Salmo salar L.
Authors: Seierstad S L , Poppe T T , Koppang E O , Svindland A , Rosenlund G , Frøyland L , Larsen S
Published: November 2005

The present study investigated the short‐term (5 months) effect of replacing dietary marine oils with vegetable oils on the development of arteriosclerotic changes in the heart of Atlantic salmon, Salmo salar. The experiment was performed as a randomized observer‐blinded and controlled trial. Farmed Atlantic salmon were randomly sampled from a study population containing 900 individuals. The salmon were divided into three groups and given diets with either 100% fish oil (Diet 1), a 50/50% mixture of fish oil and rapeseed oil (Diet 2) or 100% rapeseed oil (Diet 3). Ten sexually immature salmon from each dietary group were sampled in March and August 2002. Additionally, 47 sexually mature wild salmon were randomly collected in mid‐September 2001. Serial histological sections were taken from the bulbus arteriosus and ventricle wall for histopathological evaluation of the coronary arteries and myocardium. No significant differences in mean coronary changes recorded by the main variable ‘mean range lesion’ (MRL) were detected between the groups in March or August. MRL increased significantly between March and August with Diet 2 (P < 0.01), was nearly significant with Diet 3 (P = 0.06) and was unchanged with Diet 1. This pattern coincided with the Diet 2 group having the highest increase in heart weight. MHC class II immunoreactive cells in the coronary changes were detected in sections from one individual in each group. Heart weight was the most dominant variable in the data set and explained linearly 15.5% of the variation in MRL. Body weight, fish length and heart weight were all significantly, positively and linearly correlated to MRL. The Diet 2 group had the highest growth rate and also exhibited a significant increase in MRL. The possible influence of diet composition on weight gain and MRL needs to be further elucidated. Increase in heart weight seems to be the dominating predictor of the appearance of MRL in Atlantic salmon. However, the present results cannot exclude the possibility that differences in fatty acid composition of fish feed can influence the development of arteriosclerotic changes in Atlantic salmon.
Spatio‐temporal variation in serum chemistry of the lobster, Homarus americanus Milne‐Edwards
Authors: Dove A D M , Sokolowski M S , Bartlett S L , Bowser P R
Published: November 2005

Monthly variations in serum chemistry of the American lobster, Homarus americanus Milne‐Edwards, were investigated at one location in Long Island Sound (LIS). Comparisons between three locations within and outside LIS were also made for a single time point. Most serum analytes displayed significant fluctuation over the study period and between locations. Temporal patterns could be classified as: low in cool months/high in warm months, i.e. Na, Cl, Na:K ratio, Ca, albumin:globulin ratio, percentage Fe saturation; high in cool months/low in warm months, i.e. pH, K, urea, total protein, albumin, globulin, alanine aminotransferase (ALT), aspartate aminotransferase (AST), lipaemia; June spike, i.e. glucose, cholesterol, creatine kinase, iron, transferrin iron‐binding capacity; other less obvious fluctuations, i.e. Mg, PO4; and no apparent fluctuation, i.e. HCO3, alkaline phosphatase. The proportion of samples correctly classified into month of collection by a subset of 13 analytes using discriminant analysis improved as the months progressed from May (0.75) to October (>0.95). Discriminant analysis also resolved 96.5% of samples by location. The significant depression of serum calcium at the eastern LIS site correlates with excretory calcinosis, a calcium storage disease described from lobsters at this site, but contrasts with a seasonal elevation in serum calcium recorded in the temporal component of the study. Serum proteins, the electrolytes Ca and K and the enzymes ALT and AST proved to have the strongest spatio‐temporal patterns of variation. Serum chemistry is a useful research tool for lobster populations, but the dearth of information on the homology of analyte functions in this species with those in vertebrate species makes interpretation of the results challenging. Late summer/autumn water conditions appear to cause stress for lobsters in LIS.
GP IIb‐IIIa Receptor Blockers Minimize Vascular and Perivascular Damage in the Hippocampus after Cardiopulmonary Bypass Management
Authors: Arnhold S. , Klein H. , BenMime L. , Südkamp M. , Addicks K.
Published: November 2005

Brain injury remains a significant and potentially devastating outcome of cardiopulmonary bypass (CPB) under circulatory arrest. These outcomes caused by a microvasculature embolization are associated with increased mortality, longer hospital stays and increased use of intermediate or long term care facilities. The administration of heparin in heart surgery during deep hypothermic cardiopulmonary bypass is the basic prophylactic strategy for reducing or even preventing, microvasculature embolization. Unfortunately, an incidence of neuropsychological impairments (NPI) is found in as many as 25 % of the survivors. As it is suspected that these impairments are correlated with morphological alterations, in our study we use the GP IIb‐IIIa receptor blocker Eptifibatide for the inhibition of platelet aggregation, in order to look for a reduction of tissue damage compared to the standard treatment. Two groups of 11 piglets (mean body weight of 15±5 kg) underwent 10‐minute normothermic bypass, 40‐minute cooling on cardiopulmonary bypass, 60‐minutes deep hypothermic circulatory arrest (DHCA) at 15°C, and 40‐minute rewarming to 37°C. Group 1 was treated only with unfractionated heparin (UFH), whereas Group 2 was medicated with Eptifibatide, in addition to the UFH‐treatment group 1. After rewarming, all animals underwent bilateral carotid perfusion with 4% paraformaldehyde. Histological investigations of semi thin sections reveal a marked decrease of hippocampal alterations by using the GP IIb‐IIIa receptor blocker in addition to standard UFH treatment. We detect a reduction of degenerative areas in perivascular (vessels with 10–30 μm in diameter) tissue. These semi‐quantitative data are confirmed by ultrastructural findings.
Expression of the PACAP‐immunoreactivity in the Lymphoid Organs of the Duck
Authors: Squillacioti C. , Mirabella N. , Paesano C. , Varricchio E. , Paino G.
Published: November 2005

Introduction:  The interactions occurring between nervous and immune systems are well documented. These interactions involve several types of chemical messengers including hormones, cytokines, classic neurotransmitters and neuropeptides. It has been observed that the lymphoid organs receive a dense peptidergic innervation and immune cells produce neuropeptides. Neuropeptides, in turn, are involved in the regulation of the inflammatory processes and in the maturation of the lymphoid organs. Several studies have demonstrated that the immunomodulatory neuropeptides and their receptors are expressed in the thymus and bursa of fabricius. PACAP is a glucagon/VIP/secretin family peptide. It was originally isolated from the ovine hypothalamus and then it was found in the autonomic nervous system. PACAP is involved in the regulation of the hypothalamic‐pituitary function, neurotransmission and neuromodulation. In the immune system, PACAP is expressed in lymphoid tissues of the rat and in the lymphocytes of the duck GALT. PACAP, therefore, could be a messenger of the dialogue between nervous and immune system. It may have a role in the regulation of the inflammatory processes by stimulating histamine and serotonin and modulating the production of the cytokines in immune cells.

Methods:  Immunohistochemistry on paraffin‐embedded sections of thymus and bursa of fabricius of the duck of different ages by using an antibody anti‐PACAP38.

Results and Discussion:  In the thymus, PACAP‐immunoreactivity was found in lymphoid cells and, with a lesser extent, in epithelial reticular cells. The immunoreactive lymphocytes were primarily observed in the interlobular septa in close vicinity to the interlobular veins. The number of positive lymphocytes increased with ageing. In the bursa of fabricius, PACAP‐IR was found in nerve fibres and in a few lymphoid cells. These results suggest that PACAP could play a role in the maturation and involution of these organs and in the immune functions.