bluuebunny/crossref_metadata_2025 huggingface dataset:
Hormonal induction of undescribed males resolves cryptic species of cladocerans
Authors: Kim Keonho , Kotov Alexey A , Taylor Derek J
Published: November 2005

Cyclic parthenogens have a mixed breeding system with both meiotic and ameiotic eggs. Although investment in sexual stages is often synchronized with seasonal cycles, the degree of investment is a quantitative trait associated with habitat instability. Populations of cyclic parthenogens from stable environments, such as large lakes and oceans, generally show reduced or undetectable investment in males. Indeed, males of many species of lacustrine cyclic parthenogens are unknown to science. Methyl farnesoate (MF), a crustacean juvenile hormone, has been implicated as an inducer of male formation in
Daphnia magna
(Crustacea: Cladocera), a denizen of unstable habitats with marked sexual recruitment. Here, we show experimentally that MF induces male production in four distantly related lacustrine species of cladocerans under growth conditions unfavourable for male production. The males of three species are new to science. Unlike females, the anatomy of the previously unknown males of
Bosmina
(
Lunobosmina
)
oriens
permitted ready morphological diagnosis of sibling species and subfossils. The results suggest that the role for MF in the sex determination of cladocerans is general.
Accepting loss: the temporal limits of reciprocity in brown capuchin monkeys
Authors: Ramseyer A , Pelé M , Dufour V , Chauvin C , Thierry B
Published: November 2005

Delayed reciprocity is a potentially important mechanism for cooperation to occur. It is however rarely reported among animals, possibly because it requires special skills like the ability to plan a loss. We tested six brown capuchin monkeys (Cebus apella) in such skills. Subjects were studied in exchange tasks in which they had to retain a food item for a given time lag before returning it to an experimenter and obtaining a more desirable reward. Experiments showed that the subjects could wait for several minutes when allowed to return only part of the initial item. When required to return the full item intact, however, most subjects could not sustain a time lag longer than 10 s. Although the duration of waiting increased with the amount of return expected by subjects, in most cases it did not extend beyond 20 s even when the eperimenter offered a food amount 40 fold the initial item. The failure of capuchin monkeys to sustain long-lasting waiting periods may be explained by limited self-control abilities. This would prevent them achieving reciprocal altruism.
Experimental evolution of resistance to an antimicrobial peptide
Authors: Perron Gabriel G , Zasloff Michael , Bell Graham
Published: November 2005

A novel class of antibiotics based on the antimicrobial properties of immune peptides of multicellular organisms is attracting increasing interest as a major weapon against resistant microbes. It has been claimed that cationic antimicrobial peptides exploit fundamental features of the bacterial cell so that resistance is much less likely to evolve than in the case of conventional antibiotics. Population models of the evolutionary genetics of resistance have cast doubt on this claim. We document the experimental evolution of resistance to a cationic antimicrobial peptide through continued selection in the laboratory. In this selection experiment, 22/24 lineages of
Escherichia coli
and
Pseudomonas fluorescens
independently evolved heritable mechanisms of resistance to pexiganan, an analogue of magainin, when propagated in medium supplemented with this antimicrobial peptide for 600–700 generations.
Apparent seasonality of parasite dynamics: analysis of cyclic prevalence patterns
Authors: Lass Sandra , Ebert Dieter
Published: November 2005

Seasonal disease dynamics are common in nature, but their causes are often unknown. Our case study provides insight into the cyclic prevalence pattern of the horizontally and vertically transmitted microsporidiumOctosporea bayeriin itsDaphnia magnahost. Data from several populations over a four year period revealed a regular prevalence increase during summer and a decrease over winter when hosts underwent diapause. Prevalence also decreased after summer diapause indicating that the decline is causally linked to diapause rather than to winter conditions. Experiments showed that host diapause itself can explain a certain proportion of the decline. The decline further depends on the environmental conditions during diapause: infected resting eggs suffered from higher mortality under experimental winter than under experimental summer diapause conditions. Investigating the mechanisms of prevalence increase after diapause, the parasite was found to survive winter outside its host, enabling horizontal infection of susceptible hosts in the following growing season. Allowing for horizontal transmission in experimental host populations resulted in a steep prevalence increase, while excluding it led to a pronounced decline. Thus, the apparent seasonality inO. bayeriprevalence is characterized by a decline during host diapause followed by horizontal spread of the parasite during the host's asexual growth phase.
A newly recognized fossil coelacanth highlights the early morphological diversification of the clade
Authors: Friedman Matt , Coates Michael I
Published: November 2005

Previously considered an actinopterygian or an osteichthyanincertae sedis, the Devonian (Givetian–Frasnian)Holopterygius nudusis reinterpreted as a coelacanth. This genus is among the oldest coelacanths known from articulated remains, but its eel-like morphology marks a considerable departure from the conventional coelacanth body plan. A cladistic analysis placesHolopterygiusas the sister taxon of the Carboniferous (Serpukhovian) genusAllenypterus. Despite the specialized morphology of these genera, they occupy a surprisingly basal position in coelacanth phylogeny; onlyDiplocercidesandMiguashaiaare further removed from the crown. A morphometric analysis reveals that coelacanths were anatomically disparate early in their history. Conflicts between this result and those of previous studies challenge the adequacy of systematic character sets for describing historical patterns of morphological variety. Coelacanths have long had an iconic place in the study of vertebrate evolution for their apparent anatomical conservatism over geological time, butHolopterygiusprovides clear evidence for rapid morphological evolution early in the history of this clade.
Shifts in phenology due to global climate change: the need for a yardstick
Authors: Visser Marcel E , Both Christiaan
Published: November 2005

Climate change has led to shifts in phenology in many species distributed widely across taxonomic groups. It is, however, unclear how we should interpret these shifts without some sort of a yardstick: a measure that will reflect how much a species should be shifting to match the change in its environment caused by climate change. Here, we assume that the shift in the phenology of a species' food abundance is, by a first approximation, an appropriate yardstick. We review the few examples that are available, ranging from birds to marine plankton. In almost all of these examples, the phenology of the focal species shifts either too little (five out of 11) or too much (three out of 11) compared to the yardstick. Thus, many species are becoming mistimed due to climate change. We urge researchers with long-term datasets on phenology to link their data with those that may serve as a yardstick, because documentation of the incidence of climate change-induced mistiming is crucial in assessing the impact of global climate change on the natural world.
The physical and chemical composition of the lower mantle
Authors: Bovolo C. Isabella
Published: November 2005

This article reviews some of the recent advances made within the field of mineral physics. In order to link the observed seismic and density structures of the lower mantle with a particular mineral composition, knowledge of the thermodynamic properties of the candidate materials is required. Determining which compositional model best matches the observed data is difficult because of the wide variety of possible mineral structures and compositions. State-of-the-art experimental and analytical techniques have pushed forward our knowledge of mineral physics, yet certain properties, such as the elastic properties of lower mantle minerals at high pressures and temperatures, are difficult to determine experimentally and remain elusive. Fortunately, computational techniques are now sufficiently advanced to enable the prediction of these properties in a self-consistent manner, but more results are required.

A fundamental question is whether or not the upper and lower mantles are mixing. Traditional models that involve chemically separate upper and lower mantles cannot yet be ruled out despite recent conflicting seismological evidence showing that subducting slabs penetrate deep into the lower mantle and that chemically distinct layers are, therefore, unlikely.

Recent seismic tomography studies giving three-dimensional models of the seismic wave velocities in the Earth also base their interpretations on the thermodynamic properties of minerals. These studies reveal heterogeneous velocity and density anomalies in the lower mantle, which are difficult to reconcile with mineral physics data.
The oxygen sensing signal cascade under the influence of reactive oxygen species
Authors: Acker Helmut
Published: November 2005

Structural and functional integrity of organ function profoundly depends on a regular oxygen and glucose supply. Any disturbance of this supply becomes life threatening and may result in severe loss of organ function. Particular reductions in oxygen availability (hypoxia) caused by respiratory or blood circulation irregularities cannot be tolerated for longer periods due to an insufficient energy supply by anaerobic glycolysis. Complex cellular oxygen sensing systems have evolved to tightly regulate oxygen homeostasis. In response to variations in oxygen partial pressure (PO
2
), these systems induce adaptive and protective mechanisms to avoid or at least minimize tissue damage. These various responses might be based on a range of oxygen sensing signal cascades including an isoform of the neutrophil NADPH oxidase, different electron carrier units of the mitochondrial chain such as a specialized mitochondrial, low PO
2
affinity cytochrome
c
oxidase (aa
3
) and a subfamily of 2-oxoglutarate dependent dioxygenases termed HIF (hypoxia inducible factor) prolyl-hydroxylase and HIF asparaginyl hydroxylase called factor-inhibiting HIF (FIH-1). Thus, specific oxygen sensing cascades involving reactive oxygen species as second messengers may by means of their different oxygen sensitivities, cell-specific and subcellular localization help to tailor various adaptive responses according to differences in tissue oxygen availability.
A central role for ROS in the functional remodelling of L-type Ca
2+
channels by hypoxia
Authors: Peers Chris , Scragg Jason L , Boyle John P , Fearon Ian M , Taylor Shafeena C , Green Kim N , Webster Nicola J , Ramsden Martin , Pearson Hugh A
Published: November 2005

Periods of prolonged hypoxia are associated clinically with an increased incidence of dementia, the most common form of which is Alzheimer's disease. Here, we review recent studies aimed at providing a cellular basis for this association. Hypoxia promoted an enhanced secretory response of excitable cells via formation of a novel Ca
2+
influx pathway associated with the formation of amyloid peptides of Alzheimer's disease. More strikingly, hypoxia potentiated Ca
2+
influx specifically through L-type Ca
2+
channels in three distinct cellular systems. This effect was post-transcriptional, and evidence suggests it occurred via increased formation of amyloid peptides which alter Ca
2+
channel trafficking via a mechanism involving increased production of reactive oxygen species by mitochondria. This action of hypoxia is likely to contribute to dysregulation of Ca
2+
homeostasis, which has been proposed as a mechanism of cell death in Alzheimer's disease. We suggest, therefore, that our data provide a cellular basis to account for the known increased incidence of Alzheimer's disease in patients who have suffered prolonged hypoxic episodes.
Ca
2+
signals and death programmes in neurons
Authors: Berliocchi Laura , Bano Daniele , Nicotera Pierluigi
Published: November 2005

Cell death programmes are generally defined by biochemical/genetic routines that are linked to their execution and by the appearance of more or less typical morphological features. However, in pathological settings death signals may engage complex and interacting lethal pathways, some of which are common to different cells, whereas others are linked to a specific tissue and differentiation pattern. In neurons, death programmes can be spatially and temporally segregated. Most importantly physiological Ca
2+
signals are essential for cell function and survival. On the other hand, Ca
2+
overload or perturbations of intracellular Ca
2+
compartmentalization can activate or enhance mechanisms leading to cell death. An imbalance between Ca
2+
influx and efflux from cells is the initial signal leading to Ca
2+
overload and death of ischaemic neurons or cardiomyocytes. Alterations of intracellular Ca
2+
storage can integrate with death signals that do not initially require Ca
2+
, to promote processing of cellular components and death by apoptosis or necrosis. Finally, Ca
2+
can directly activate catabolic enzymes such as proteases, phospholipases and nucleases that directly cause cell demise and tissue damage.
Oxidative stress and ageing: is ageing a cysteine deficiency syndrome?
Authors: Dröge Wulf
Published: November 2005

Reactive oxygen species (ROS) are constantly produced in biological tissues and play a role in various signalling pathways. Abnormally high ROS concentrations cause oxidative stress associated with tissue damage and dysregulation of physiological signals. There is growing evidence that oxidative stress increases with age. It has also been shown that the life span of worms, flies and mice can be significantly increased by mutations which impede the insulin receptor signalling cascade. Molecular studies revealed that the insulin-independentbasalactivity of the insulin receptor is increased by ROS and downregulated by certain antioxidants. Complementary clinical studies confirmed that supplementation of the glutathione precursor cysteine decreases insulin responsiveness in the fasted state. In several clinical trials, cysteine supplementation improved skeletal muscle functions, decreased the body fat/lean body mass ratio, decreased plasma levels of the inflammatory cytokine tumour necrosis factor α (TNF-α), improved immune functions, and increased plasma albumin levels. As all these parameters degenerate with age, these findings suggest: (i) that loss of youth, health and quality of life may be partly explained by a deficit in cysteine and (ii) that the dietary consumption of cysteine is generally suboptimal andeverybodyis likely to have a cysteine deficiency sooner or later.
Normal brain ageing: models and mechanisms
Authors: Toescu Emil C
Published: November 2005

Normal ageing is associated with a degree of decline in a number of cognitive functions. Apart from the issues raised by the current attempts to expand the lifespan, understanding the mechanisms and the detailed metabolic interactions involved in the process of normal neuronal ageing continues to be a challenge. One model, supported by a significant amount of experimental evidence, views the cellular ageing as a metabolic state characterized by an altered function of the metabolic triad: mitochondria–reactive oxygen species (ROS)–intracellular Ca
2+
. The perturbation in the relationship between the members of this metabolic triad generate a state of decreased homeostatic reserve, in which the aged neurons could maintain adequate function during normal activity, as demonstrated by the fact that normal ageing is not associated with widespread neuronal loss, but become increasingly vulnerable to the effects of excessive metabolic loads, usually associated with trauma, ischaemia or neurodegenerative processes. This review will concentrate on some of the evidence showing altered mitochondrial function with ageing and also discuss some of the functional consequences that would result from such events, such as alterations in mitochondrial Ca
2+
homeostasis, ATP production and generation of ROS.
Diet choice of large carnivores in northern Cameroon
Authors: Breuer Thomas
Published: November 2005

The diet of African wild dogs, lions and spotted hyenas was studied in the woodland savannah of Faro National Park and surrounding hunting zones in northern Cameroon during the dry season. Faecal analysis revealed that the diet of the three large carnivores overlaps considerably. Frequencies of prey remains of large and medium‐sized antelopes were highest, with Buffon's kob being by far the most common prey species. Carnivores seem to consume the most abundant prey species. No prey item of domestic livestock was found in the faeces. Faecal analysis has proved to be a useful method to reveal diet choice for large carnivores in northern Cameroon. Detailed information on the distribution and density of large carnivores and their prey is needed to give a better picture of the status of carnivores in northern Cameroon and to help resolve conflicts with livestock. Further investigations into the seasonal variation of predation and other factors structuring the large carnivore community in northern Cameroon are recommended.
Determining the rate of varicella vaccine rash in children with moderate–severe eczema
Authors: Frydenberg AR , Buttery JP , Royle J
Published: November 2005

Objectives: To determine the rate and severity of vesicular reactions following varicella vaccine in children with moderate–severe eczema. Secondary endpoints included the rates and severity of local reactions and eczema severity change within 42 days of vaccination.

Methods: Prospective open intervention pilot study of varicella vaccine in children aged 12 months to 13 years with moderate–severe eczema. Children were given varicella vaccine alone and followed for 42 days after vaccination.

Results: Fifty children, aged 12 months to 10.5 years were recruited, with complete follow‐up for 48. A vesicular rash with a single lesion occurred in one child (2.1% (95% CI: 0, 11.1%)), 10 days following vaccination. Local reactions, including erythema, swelling and tenderness, were reported in eight children (16.7%). A flare‐up of moderate–severe generalized eczema was reported in one child (2.1%) during the first week following varicella vaccine.

Conclusions: Vesicular rash and local reactions following varicella vaccination were no more common or severe in children with moderate–severe eczema than that reported in the published literature in children without eczema. Eczema in the 42 days following vaccination did not appear to increase in severity.
Changing face of paediatric and adolescent thyroid cancer
Authors: Hameed R , Zacharin MR
Published: November 2005

Objectives: The aims of our study were to review the Royal Children's Hospital cohort of children having thyroidectomy for thyroid nodules over the last 8 years and to report the changing pattern of thyroid cancer seen in our institution over that time.

Methods: We undertook a retrospective case‐note review of all patients who underwent thyroid surgery between 1997 and 2004.

Results: Of 69 patients identified, the pathological diagnoses were 51 benign tumours, 14 thyroid cancers and four cases of multiple endocrine neoplasia type 2, who were treated with prophylactic thyroidectomy. Sixteen of the 69 patients had a history of childhood cancer and 10/16 had cancer treatment which included direct or scatter radiation. Of the 10 patients who received irradiation, four had follicular adenomas and six developed thyroid cancer. All six patients were euthyroid: one patient was presented with a palpable nodule and the other five were detected on surveillance ultrasound.

Conclusions: Our results confirm a high detection of malignancy in thyroid nodules in childhood. Compared to an earlier study at this institution, the number of thyroid malignancies appears to be increasing. Surveillance at the Royal Children's Hospital has changed, with increased long‐term cancer survival. Prospective 2‐yearly evaluation of those with a past history of radiation exposure has resulted in earlier detection of benign and malignant thyroid lesions. Nodular changes are usually not clinically apparent for many years and lifelong surveillance is necessary for cancer detection in this group.
Economic evaluation of neonatal screening for phenylketonuria and congenital hypothyroidism
Authors: Geelhoed EA , Lewis B , Hounsome D , O'Leary P
Published: November 2005

Objective: To evaluate the costs and benefits of neonatal screening for phenylketonuria (PKU) and congenital hypothyroidism (CH). Neonatal screening for PKU and CH is common throughout the developed world. It represents a model of preventive care in that the screening procedure is simple and intellectual disability is otherwise irreversible. Changes in treatment and care, and in particular the advent of maternal PKU, require regular evaluation of a programme that also impacts on a large healthy population.

Method: Costs of screening were based on the programme provided within Western Australia. Costs averted were derived using patterns of care currently adopted in Western Australia and applied according to historical patterns of intellectual disability for each condition.

Results: A net saving of $A2.9 million is attributable to the programme annually. The economic benefits derive from the prevention of intellectual disability which otherwise incurs costs throughout the life of the affected individual. Maternal PKU represented a minor proportion of overall costs. Sensitivity analysis showed that the cost savings were robust, given changes in the levels of intellectual disability, but varied according to the discount rate. The result of a net saving was evident under all assumptions.

Conclusion: Neonatal screening for PKU and CH is a cost saving use of resources and the emergence of maternal PKU has not had a significant effect on the economic outcomes.
Kidney stone disease and risk factors for coronary heart disease
Authors: HAMANO SATOSHI , NAKATSU HIROOMI , SUZUKI NORIYUKI , TOMIOKA SUSUMU , TANAKA MASASHI , MURAKAMI SHINO
Published: November 2005

Abstract  Background:  We conducted a case‐control study to examine the impact of coronal heart disease (CHD) risk factors on calcium oxalate (CaOX) stone formation.

Methods:  Variables included body mass index (BMI), current alcohol use, smoking habit, hypertension, hypercholesterolemia, diabetes mellitus, and hyperuricemia. Data sufﬁcient for analysis were obtained for 181 CaOX stone formers and 187 controls.

Results:  Seven of 181 stone formers (3.9%) had a history of CHD compared with none of 187 control subjects (P = 0.007). In univariate logistic regression analysis, smoking habit (OR 4.41, 95% CI 2.85–6.84, P < 0.0001), hypertension (OR 4.24, 95% CI 2.61–6.91, P < 0.0001), hypercholesterolemia (OR 3.03, 95% CI 1.77–5.20, P < 0.0001) and BMI (OR 1.10, 95% CI 1.04–1.17, P = 0.007) reached statistical signiﬁcance. In a multivariate logistic regression analysis, smoking habit (OR 4.29, 95% CI 2.68–6.86, P < 0.0001), hypertension (OR 3.57, 95% CI 2.11–6.07, P < 0.0001), and hypercholesterolemia (OR 2.74, 95% CI 1.51–5.00, P = 0.001) reached statistical signiﬁcance, while BMI (OR 1.06, 95% CI 0.99–1.12, P = 0.09) did not.

Conclusions:  CaOX stone formers are signiﬁcantly associated with several CHD risk factors, including smoking habit, hypertension, hypercholesterolemia, and obesity.
Value of prostate volume measurement using transabdominal ultrasonography for the improvement of prostate‐speciﬁc antigen‐based cancer detection
Authors: KOBAYASHI TAKASHI , KAWAHARA TAKASHI , NISHIZAWA KOJI , OGURA KEIJI , MITSUMORI KENJI , IDE YOSHIHIRO
Published: November 2005

Abstract  Purpose:  To examine value of prostate‐speciﬁc antigen (PSA) adjusted by prostate volume measured using transabdominal ultrasonography in prostate cancer detection among men with elevated PSA.

Methods:  238 men aged 79 years or younger with serum PSA levels of 2.0–20.0 ng/mL and normal digital rectal examination ﬁndings were studied in terms of total and free PSA, prostate volumes with transrectal (TRUS) and transabdominal (TAUS) ultrasonography and transition zone volumes with TRUS prior to transrectal 10‐core biopsy. In addition to sole PSA values and the free‐to‐total PSA ratio, volume‐adjusted PSA values, PSA densities determined by TRUS (PSADTRUS), and TAUS (PSADTAUS), and PSA transition zone densities (PSATzD) were compared using receiver operating characteristic (ROC) analysis.

Results:  Prostate cancer was diagnosed in 58 (24.4%) of the 238 men who underwent prostate biopsies. Of the areas under ROC curves (AUC) of studied parameters, PSATzD (AUC 0.751) was the best and signiﬁcantly superior to PSADTAUS (AUC 0.664, P = 0.007). However, PSADTAUS exceeded PSA (AUC 0.559, P = 0.004) and showed potential capability of a one‐fourth reduction in unnecessary biopsies without spoiling sensitivity (90%). Cancer detection rate was only 4.2% in the 48 patients whose prostate volume in TAUS was > 50 mL and PSADTAUS was < 0.075.

Conclusions:  Since PSADTRUS and PSATzD were signiﬁcantly superior to PSADTAUS, TRUS is feasible as the standard fashion to determine prostate volume in the diagnosis of prostate cancers. However, TAUS is also worthwhile as it can improve the prostate cancer detection using sole PSA, and primary use of TAUS has the potential to reduce the substantial number of unnecessary biopsy safely.
Testicular tumor in Down syndrome
Authors: SUZUKI KURI , NISHIMI DAISUKE , YAGISHITA TSUGUO , TAKANAMI MASAHARU , HIRUTA NOBUYUKI
Published: November 2005

Abstract  A 33‐year‐old male patient with Down syndrome, who stayed in a welfare institution, visited our hospital due to left testicular enlargement. He was diagnosed as having a left testicular tumor and underwent radical inguinal orchiectomy.

 Preoperatively, serum level of beta‐human chorionic gonadotrophin (β‐HCG) increased to 0.9 ng/mL (normal range <0.2 ng/mL). For the last 2 years after orchiectomy, the serum level of β‐HCG remained normal.

 Histopathological examination of specimen revealed a typical seminoma. It is currently thought that risk of developing leukemia in patients with Down syndrome is 20‐ to 30‐fold higher than that in normal subjects. Furthermore, the incidence of testicular cancer as a complication other than leukemia is expected to increase because of the increasing postpubertal population with Down syndrome.
Fibroblast growth factor 2 applied to the optic nerve after axotomy up‐regulates BDNF and TrkB in ganglion cells by activating the ERK and PKA signaling pathways
Authors: Soto Ileana , Rosenthal Joshua J. C. , Blagburn Jonathan M. , Blanco Rosa E.
Published: November 2005

Application of basic fibroblast growth factor (FGF‐2) to the optic nerve after axotomy promotes the survival of retinal ganglion cells (RGCs) in the frog,Rana pipiens. Here we investigate the effects of FGF‐2 treatment upon the synthesis of brain‐derived neurotrophic factor (BDNF) and its receptor, tyrosine receptor kinase B (TrkB). Axotomy alone increased the amounts ofBDNFandTrkBmRNA in RGCs after 1 week and 48 h, respectively; FGF‐2 treatment to the nerve accelerated and increased this up‐regulation of both. FGF‐2 also increased the amounts of phosphorylated cAMP response element binding protein (pCREB) in the retina. Blocking extracellular‐regulated kinase (ERK) activation with PD98059 or U0126 prevented the FGF‐2‐induced up‐regulation ofBDNFtranscription but had no effect onTrkB. However, blocking protein kinase A (PKA) with H89 or Rp‐8‐Cl‐cAMPS reduced the up‐regulation of bothBDNFandTrkB, and reduced pCREB. In addition, H89 inhibited ERK activation, indicating cross‐talk between the pathways. Finally, axonal application of blocking antibody against the FGF receptor 1 (FGFR1) prevented the FGF‐2‐induced up‐regulation of BDNF and TrkB. Our results suggest that FGF‐2 acts on RGCs via FGFR1, activating the ERK pathway and CREB to increase BDNF synthesis, and PKA and CREB to increase TrkB synthesis.
Group‐specific primers for amplifying DNA sequences that identify Amphipoda, Cephalopoda, Echinodermata, Gastropoda, Isopoda, Ostracoda and Thoracica
Authors: JARMAN S. N. , REDD K. S. , GALES N. J.
Published: November 2005

We describe seven group‐specific primer pairs that amplify small sections of ribosomal RNA genes suitable for identification of animal groups of major importance as prey items in marine ecosystems. These primer sets allow the isolation of DNA from the target animal groups from mixed pools of DNA, where DNA‐based identification using universal primers is unlikely to succeed. The primers are designed for identifying prey in animal diets, but could be used in any situation where these animal groups are to be identified by their DNA.
Development of 10 polymorphic microsatellite markers from herbicide‐bleached tissues of the brooding pocilloporid coral Seriatopora hystrix
Authors: UNDERWOOD J. N. , SOUTER P. B. , BALLMENT E. R. , LUTZ A. H. , VAN OPPEN M. J. H.
Published: November 2005

Here we report the isolation of 44 microsatellites from the brooding, pocilloporid coral, Seriatopora hystrix, developed from a partial genomic DNA library using a repeat enrichment protocol. A further eight previously published microsatellites were also tested; five of these were developed for S. hystrix, whereas three were isolated from corals of the closely related genus Pocillopora. Out of these, we incorporated nine and 10 primer pairs into two multiplex reactions that reliably amplified polymorphic microsatellites in populations from the west and the east coast of Australia, respectively. Number of alleles ranged from three to 22 per locus.
Polymorphic microsatellite markers in the painted dragon lizard, Ctenophorus pictus
Authors: AUSTIN JEREMY J. , ROSE REBECCA J. , MELVILLE JANE
Published: November 2005

We isolated eight polymorphic microsatellite markers from the painted dragon, Ctenophorus pictus, from a genomic library simultaneously enriched for a suite of di‐, tri‐ and tetranucleotide repeat units. Genetic variation was assessed in 40 individuals from populations in Victoria and South Australia. The number of alleles per locus ranged from four to 45 with observed heterozygosity ranging from 0.23 to 0.95. These markers will be useful for studies of natural and sexual selection and the effects of habitat fragmentation in semiarid Australia.
HLA class II haplotype DRB1*04–DQB1*0301 contributes to risk of familial generalized vitiligo and early disease onset
Authors: Fain Pamela R. , Babu Sunanda R. , Bennett Dorothy C. , Spritz Richard A.
Published: November 2005

Generalized vitiligo is a common autoimmune disorder characterized by white patches of skin and overlying hair caused by loss of pigment‐forming melanocytes from involved areas. Familial clustering of vitiligo is not uncommon, and patients and their relatives are at increased risk for a specific complex of other autoimmune diseases. Compared with sporadic vitiligo, familial vitiligo is characterized by earlier disease onset and greater risk and broader repertoire of autoimmunity, suggesting a stronger genetic component, and perhaps stronger associations with specific alleles. To determine whether the major histocompatibility complex (MHC) contributes to the familial clustering of vitiligo and vitiligo‐associated autoimmune/autoinflammatory diseases, we performed case–control and family‐based association analyses of HLA class II‐DRB1 and ‐DQB1 alleles and haplotypes in affected probands and their parents from 76 European‐American Caucasian families with familial vitiligo. Affected probands showed a significantly increased frequency of DRB1*04–DQB1*0301 and a significantly decreased frequency of DRB1*15–DQB1*0602 compared with a large sample of reference chromosomes. Family‐based association analyses confirmed these results. Probands with DRB1*04–DQB1*0301 developed vitiligo an average of 13.32 yr earlier than probands with DRB1*15–DQB1*0602. Overall, our results indicate that specific MHC‐linked genetic variation contributes to risk of familial vitiligo, although HLA does not completely explain familial clustering of vitiligo‐associated autoimmune/autoinflammatory diseases.
Prediction of ultraviolet-induced damage during plasma processes in dielectric films using on-wafer monitoring techniques
Authors: Ishikawa Yasushi , Katoh Yuji , Okigawa Mitsuru , Samukawa Seiji
Published: November 2005

We measured electron-hole pairs generated in dielectric film using our developed on-wafer monitoring technique to detect electrical currents in the film during the plasma etching processes. The electron-hole pairs were generated by plasma induced ultraviolet (UV) photons, and the number of electron-hole pairs depends on the UV wavelength. In SiO2 film, UV light, which has a wavelength of less than 140nm, generates electron-hole pairs, because the band gap energy of the film is 8.8eV. On the other hand, in Si3N4 film, which has a band gap energy level of 5.0eV, UV light below 250nm induces the electron-hole pairs. Additionally, we evaluated the fluorocarbon gas plasma process that induces UV radiation damage using multilayer sensors that consisted of both SiO2 and Si3N4 stacked films. In these cases, electron-hole pair generation depended on the dielectric film structure. There were more electron-hole pairs generated in the SiO2 deposited on the Si3N4 film than in the Si3N4 deposited on the SiO2 film. As a result, our developed on-wafer monitoring sensor was able to predict electron-hole pair generation and the device characteristics.
Etching of high aspect ratio features in Si using SF6∕O2∕HBr and SF6∕O2∕Cl2 plasma
Authors: Gomez Sergi , Belen Rodolfo Jun , Kiehlbauch Mark , Aydil Eray S.
Published: November 2005

We have investigated the etching of high aspect ratio holes (∼4μm deep, ∼0.2μm diameter) in silicon using plasmas maintained in mixtures of SF6, O2, and HBr or Cl2 gases. The etching experiments were conducted in a low pressure (25mTorr), high density, inductively coupled plasma etching reactor with a planar coil. Visualization of the profiles with scanning electron microscopy is used in conjunction with plasma diagnostics such as optical emission and mass spectroscopies to understand the key factors that control the feature profile shape and etch rate. HBr addition to SF6∕O2 mixture reduces the F-to-O ratio, increases sidewall passivation and reduces mask undercut. Addition of Cl2 to SF6∕O2 discharge also decreases the F-to-O ratio, but Cl-enhanced F chemical etching of silicon significantly increases the mask undercut and lateral etching. In both SF6∕O2∕HBr and SF6∕O2∕Cl2 mixtures, reduction of O2 flow rate and subsequent increase of the halogen-to-O ratio eventually results in significant lateral etching because of the lack of oxygen required to form a siliconoxyhalide passivating film on the sidewalls.
Electron conditioning of technical aluminium surfaces: Effect on the secondary electron yield
Authors: Le Pimpec F. , Kirby R. E. , King F. K. , Pivi M.
Published: November 2005

The effect of electron conditioning on commercially available aluminium alloys 1100 and 6063 was investigated. Contrary to the assumption that electron conditioning, if performed long enough, can reduce and stabilize the secondary electron yield (SEY) to low values (⩽1.3, the value for many pure elements), the SEY of aluminium did not go lower than 1.8. In fact, it reincreased with continued electron exposure dose. The SEY was monitored as a function of electron dose and the surface chemistry was measured with x-ray photoelectron spectroscopy (XPS). The XPS carbon and aluminium core levels showed that the late increase in SEY is due to electron desorption of adsorbed gas, thereby exposing high-SEY Al2O3.
Effect of surface temperature on plasma-surface interactions in an inductively coupled modified gaseous electronics conference reactor
Authors: Zhou Baosuo , Joseph Eric A. , Sant Sanket P. , Liu Yonghua , Radhakrishnan Arun , Overzet Lawrence J. , Goeckner Matthew J.
Published: November 2005

The effect of wall temperature, from 50to200°C, on gas phase chemistry and substrate etching rates has been studied in inductively coupled CF4 plasma under two distinctive initial wall conditions, namely “clean” and “seasoned.” During plasma etching, we found that the gas phase chemistry exhibits a weak dependence on the initial wall cleanliness when the wall is either cold (50°C) or hot (200°C). In the mid-temperature range, the wall cleanliness can strongly affect gas phase chemistry. The study of temperature dependence of the fluorocarbon film deposition on the substrate indicates that ion-assisted incorporation, direct ion incorporation and ion-assisted desorption are the major factors determining film growth and removal. Ion-assisted incorporation and desorption are surface-temperature-dependent, while direct ion incorporation is independent of the surface temperature.
Physical properties of high pressure reactively sputtered TiO2
Authors: Andrés E. San , Toledano-Luque M. , Prado A. del , Navacerrada M. A. , Mártil I. , González-Díaz G. , Bohne W. , Röhrich J. , Strub E.
Published: November 2005

We present a study of the physical properties of TiO2 thin films deposited at 200°C on Si by high pressure reactive sputtering, a nonconventional deposition method. Just after deposition, the TiO2 films were in situ annealed in the deposition chamber at temperatures between 600 and 900°C in O2 atmosphere. Morphological, compositional, structural and electrical characterization of the samples was performed by means of several techniques, including transmission electron microscopy, heavy-ion elastic recoil detection analysis, infrared spectroscopy, x-ray and electron diffraction and capacitance-voltage measurements. Microscopy images show that the TiO2 films are polycrystalline, and that a SiO2 film spontaneously grows at the TiO2∕Si interface. The unannealed TiO2 films are oxygen rich, as shown by compositional measurements. By annealing this oxygen excess is released. For temperatures above 600°C the TiO2 films are stoichiometric. Infrared spectroscopy and diffraction measurements show that as-deposited films are a mixture of anatase and rutile grains. During annealing there is a phase transformation, and at 900°C the anatase phase disappears and only the rutile phase is found. The relative dielectric permittivity of the TiO2 film is calculated from capacitance-voltage measurements, and very high values in the 88–102 range are obtained.
Crystallization and segregation in vitreous rutile films annealed at high temperature
Authors: Omari M. A. , Sorbello R. S. , Aita C. R.
Published: November 2005

Vitreous titania films with rutile short-range order were sputter deposited on unheated fused silica substrates, sequentially annealed at 973 and 1273 K, and examined by Raman microscopy, scanning electron microscopy, and x-ray diffraction. A segregated microstructure developed after the 1273 K anneal. This microstructure consists of supermicron-size craters dispersed in a matrix of submicron rutile crystals. Ti–O short-range order in the craters is characteristic of a mixture of two high pressure phases, m-TiO2 (monoclinic P21∕c space group) and α-TiO2 (tetragonal Pbcn space group). We calculated that a high average compressive stress parallel to the substrate must be accommodated in the films at 1273 K, caused by the difference in the thermal expansion coefficients of titania and fused silica. The formation of the segregated microstructure is modeled by considering two processes at work at 1273 K to lower a film’s internal energy: crystallization and nonuniform stress relief. The Gibbs–Thomson relation shows that small m-TiO2 crystallites are able to form directly from vitreous TiO2 at 1273 K. However, the preferred mechanism for forming α-TiO2 is likely to be by epitaxial growth at crystalline rutile twin boundaries (secondary crystallization). Both phases are denser than crystalline rutile and reduce the average thermal stress in the films.
Optical band gaps and composition dependence of hafnium–aluminate thin films grown by atomic layer chemical vapor deposition
Authors: Nguyen N. V. , Sayan S. , Levin I. , Ehrstein J. R. , Baumvol I. J. R. , Driemeier C. , Krug C. , Wielunski L. , Hung P. Y. , Diebold Alain
Published: November 2005

We report the optical properties of unannealed hafnium–aluminate (HfAlO) films grown by atomic layer chemical vapor deposition (ALCVD) and correlate them with the aluminum contents in the films. Vacuum ultraviolet spectroscopic ellipsometry (VUV-SE), high-resolution transmission electron microscopy (HRTEM), channeling Rutherford backscattering spectrometry (RBS), and resonant nuclear reaction analysis (NRA) were employed to characterize these films. In the analyses of ellipsometry data, a double Tauc–Lorentz dispersion produces a best fit to the experimental VUV-SE data. As a result, the determined complex pseudodielectric ⟨ε⟩ functions of the films clearly exhibit a dependency on the aluminum densities measured by RBS and NRA. We show that the optical fundamental band gap Eg shifts from 5.56±0.05eV for HfO2 to 5.92±0.05eV for HfAlO. The latter was grown by using an equal number of pulses of H2O∕HfCl4 and H2O∕TMA (trimethylaluminum) precursors in each deposition cycle for HfO2 and Al2O3, respectively. The shift of Eg to higher photon energies with increasing aluminum content indicates that intermixing of HfO2 and Al2O3 occurred during the ALCVD growth process. We found that Eg varies linearly with the mole fraction x of Al2O3 in the alloy (HfO2)x(Al2O3)1−x, but has a parabolic dependency with the aluminum density. We also observed a consistent decrease in the magnitudes of the real ⟨ε1⟩ and imaginary ⟨ε2⟩ part of ⟨ε⟩ of HfAlO films with respect to those of HfO2 as the Al density increased. The absence of the ≈5.7eV peak in the ⟨ε⟩ spectrum, which was previously reported for polycrystalline HfO2 films, indicates that these films are amorphous as confirmed by their HRTEM images.
Patterning and Plasticity of the Cerebral Cortex
Authors: Sur Mriganka , Rubenstein John L. R.
Published: November 2005

The cerebral cortex of the human brain is a sheet of about 10 billion neurons divided into discrete subdivisions or areas that process particular aspects of sensation, movement, and cognition. Recent evidence has begun to transform our understanding of how cortical areas form, make specific connections with other brain regions, develop unique processing networks, and adapt to changes in inputs.
Neuronal Activity Regulates Diffusion Across the Neck of Dendritic Spines
Authors: Bloodgood Brenda L. , Sabatini Bernardo L.
Published: November 2005

In mammalian excitatory neurons, dendritic spines are separated from dendrites by thin necks. Diffusion across the neck limits the chemical and electrical isolation of each spine. We found that spine/dendrite diffusional coupling is heterogeneous and uncovered a class of diffusionally isolated spines. The barrier to diffusion posed by the neck and the number of diffusionally isolated spines is bidirectionally regulated by neuronal activity. Furthermore, coincident synaptic activation and postsynaptic action potentials rapidly restrict diffusion across the neck. The regulation of diffusional coupling provides a possible mechanism for determining the amplitude of postsynaptic potentials and the accumulation of plasticity-inducing molecules within the spine head.
Fast Readout of Object Identity from Macaque Inferior Temporal Cortex
Authors: Hung Chou P. , Kreiman Gabriel , Poggio Tomaso , DiCarlo James J.
Published: November 2005

Understanding the brain computations leading to object recognition requires quantitative characterization of the information represented in inferior temporal (IT) cortex. We used a biologically plausible, classifier-based readout technique to investigate the neural coding of selectivity and invariance at the IT population level. The activity of small neuronal populations (∼100 randomly selected cells) over very short time intervals (as small as 12.5 milliseconds) contained unexpectedly accurate and robust information about both object “identity” and “category.” This information generalized over a range of object positions and scales, even for novel objects. Coarse information about position and scale could also be read out from the same population.
Meteorite Phosphates Show Constant
176
Lu Decay Rate Since 4557 Million Years Ago
Authors: Amelin Yuri
Published: November 2005

The use of radioactive decay of
176
Lu to
176
Hf to study the evolution of the Earth requires a precise and accurate value for the
176
Lu decay constant. Recent determinations of this decay constant by age comparison to the more precisely calibrated U-Pb isotopic system produced internally consistent but discrepant values between terrestrial minerals and meteorites. New highly radiogenic Lu-Hf data for phosphate minerals from Richardton (ordinary chondrite) and Acapulco (primitive achondrite) yield decay constant values of 1.864 × 10
–11
± 0.016 × 10
–11
and 1.832 × 10
–11
± 0.029 × 10
–11
year
–1
, respectively, identical to the value determined from terrestrial minerals.
Culture-Independent Techniques for Rapid Detection of Bacteria Associated with Loss of Chloramine Residual in a Drinking Water System
Authors: Hoefel Daniel , Monis Paul T. , Grooby Warwick L. , Andrews Stuart , Saint Christopher P.
Published: November 2005

Chloramination is often the disinfection regimen of choice for extended drinking water systems. However, this process is prone to instability due to the growth of nitrifying bacteria. This is the first study to use alternative approaches for rapid investigation of chloraminated drinking water system instability in which flow cytometric cell sorting of bacteria with intact membranes (membrane-intact fraction) (BacLight kit) or with active esterases (esterase-active fraction) (carboxyfluorescein diacetate) was combined with 16S rRNA gene-directed PCR and denaturing gradient gel electrophoresis (DGGE). No active bacteria were detected when water left the water treatment plant (WTP), but 12 km downstream the chloramine residual had diminished and the level of active bacteria in the bulk water had increased to more than 1 × 105bacteria ml−1. The bacterial diversity in the system was represented by six major DGGE bands for the membrane-intact fraction and 10 major DGGE bands for the esterase-active fraction. PCR targeting of the 16S rRNA gene of chemolithotrophic ammonia-oxidizing bacteria (AOB) and subsequent DGGE and DNA sequence analysis revealed the presence of an activeNitrosospira-related species andNitrosomonas cryotoleransin the system, but no AOB were detected in the associated WTP. The abundance of active AOB was then determined by quantitative real-time PCR (qPCR) targeting theamoAgene; 3.43 × 103active AOB ml−1were detected in the membrane-intact fraction, and 1.40 × 104active AOB ml−1were detected in the esterase-active fraction. These values were several orders of magnitude greater than the 2.5 AOB ml−1detected using a routine liquid most-probable-number assay. Culture-independent techniques described here, in combination with existing chemical indicators, should allow the water industry to obtain more comprehensive data with which to make informed decisions regarding remedial action that may be required either prior to or during an instability event.