bluuebunny/crossref_metadata_2025 huggingface dataset:
Puella's shadow
Authors: Schwartz Susan E.
Published: September 2009

Puella is the eternal girl, an aspect of the psyche that has been virtually ignored in the Jungian literature. She appears in the Western attitudes to be ever younger and thinner, devalued and stuck in the shadow of the patriarchy. Living ‘as if’, she is bolstered by persona adaptation, masking the emptiness within, experiencing but not facing the narcissistic wounds. The attachment problems result in a distorted and split self-image, divorced from her body, and difficulty with intimacy and commitment. The dreams and writings from the American poetess Sylvia Plath illustrate parallels with the Puella figure.
The Book of Job revisited
Authors: Woolfson Tony
Published: September 2009

A vicious trick is played on Biblical Job by Satan and the half-conscious God-image. He loses almost everything, but his conscious suffering places him on the archetypal and ultimately life-affirming journey of spiritual seekers – from ego to Self. In hisAnswer to Job, Jung takes momentous issue with the Old Testament God-image, a ‘monster’ in Jung's view. Archetypally, Job is not patient but heroic in his ability to hold the opposites simultaneously, the light and dark sides of the God-image. He experiences the everlasting truth of Jung's dictum: ‘one can love God, but must fear Him.’
What case reports omit: the sense of smell as a root of intuitive interpretations
Authors: Plaut Fred
Published: September 2009

In this article, I explore the importance of smell in defining the interplay of context with the analyst's activity of working up a case study following sessions with a patient. Audio and visual sense reports are more easily measurable and so they have taken precedence but the immediate and unconscious combination of smell with intuition underscores my contention that there are no ‘spontaneous’ insights – the build up of sensual clues plays into the analyst's and the patient's memories to portray a more valid and complete (albeit subjective) reporting of the ‘dynamic unconscious’ – in fact, analytic theory comes after the sensual clues are in place.
A multi-cavity approach for enhanced efficiency in TOPICA RF antenna code
Authors: Milanesio D. , Meneghini O. , Lancellotti V. , Maggiora R. , Vecchi G.
Published: September 2009

This paper describes recent upgrades of TOPICA (Torino Politecnico Ion Cyclotron Antennas) formulation and implementation. TOPICA is a code capable of handling both the actual geometry of ion cyclotron (IC) antennas and an accurate plasma description; it can predict the performances of IC launchers with an unprecedented accuracy and numerical efficiency, validated against data measured in plasma operation conditions. In the reported upgrade, a new multi-cavity approach is introduced, producing significant savings in terms of CPU and memory requirements and allowing the analysis of large antennas even with limited computational resources. In fact, by formally separating the structure's cavities with a number of mathematical surfaces called ‘apertures’, the method of moments interaction matrix is block-wise sparse and, as a consequence, can be manipulated with a far higher numerical efficiency; this also allows an out-of-core solution.
Paxillin-Kinase-Linker Tyrosine Phosphorylation Regulates Directional Cell Migration
Authors: Yu Jianxin A. , Deakin Nicholas O. , Turner Christopher E.
Published: September 2009

Directed cell migration requires the coordination of growth factor and cell adhesion signaling and is of fundamental importance during embryonic development, wound repair, and pathological conditions such as tumor metastasis. Herein, we demonstrate that the ArfGAP, paxillin-kinase-linker (PKL/GIT2), is tyrosine phosphorylated in response to platelet-derived growth factor (PDGF) stimulation, in an adhesion dependent manner and is necessary for directed cell migration. Using a combination of pharmacological inhibitors, knockout cells and kinase mutants, FAK, and Src family kinases were shown to mediate PDGF-dependent PKL tyrosine phosphorylation. In fibroblasts, expression of a PKL mutant lacking the principal tyrosine phosphorylation sites resulted in loss of wound-induced cell polarization as well as directional migration. PKL phosphorylation was necessary for PDGF-stimulated PKL binding to the focal adhesion protein paxillin and expression of paxillin or PKL mutants defective in their respective binding motifs recapitulated the polarization defects. RNA interference or expression of phosphorylation mutants of PKL resulted in disregulation of PDGF-stimulated Rac1 and PAK activities, reduction of Cdc42 and Erk signaling, as well as mislocalization of βPIX. Together these studies position PKL as an integral component of growth factor and cell adhesion cross-talk signaling, controlling the development of front–rear cell polarity and directional cell migration.
MOODS: fast search for position weight matrix matches in DNA sequences
Authors: Korhonen Janne , Martinmäki Petri , Pizzi Cinzia , Rastas Pasi , Ukkonen Esko
Published: September 2009

Summary: MOODS (MOtif Occurrence Detection Suite) is a software package for matching position weight matrices against DNA sequences. MOODS implements state-of-the-art online matching algorithms, achieving considerably faster scanning speed than with a simple brute-force search. MOODS is written in C++, with bindings for the popular BioPerl and Biopython toolkits. It can easily be adapted for different purposes and integrated into existing workflows. It can also be used as a C++ library.

Availability: The package with documentation and examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind. The source code is also available under the terms of a GNU General Public License (GPL).

Contact:  janne.h.korhonen@helsinki.fi
Feasibility of Video Capsule Endoscopy in the Management of Children With Peutz‐Jeghers Syndrome: A Blinded Comparison With Barium Enterography for the Detection of Small Bowel Polyps
Authors: Postgate Aymer , Hyer Warren , Phillips Robin , Gupta Arun , Burling David , Bartram Clive , Marshall Michelle , Taylor Stuart , Brown Gregor , Schofield Gill , Bassett Paul , Spray Christine , Fitzpatrick Aine , Fraser Chris , Latchford A
Published: September 2009

Objectives:

Peutz‐Jeghers syndrome (PJS) in children may present with anaemia, intussusception, or obstruction from an early age and surgery is common. Prophylactic polypectomy may reduce subsequent complications. Traditional barium enterography (BE) has poor sensitivity and requires significant radiation. We compared the performance of capsule endoscopy (CE) with BE in children with PJS.

Materials and Methods:

Children with PJS (ages 6.0–16.5 years) were prospectively recruited and underwent BE followed by CE, each reported by expert reviewers blinded to the alternate modality. Number of “significant” (>10 mm) and total number of polyps were recorded. Child preference was assessed using a visual analogue questionnaire. Definitive findings were assessed at laparotomy or enteroscopy, when performed.

Results:

There was no significant difference for >10 mm polyp detection. Six polyps were found in 3 children by both modalities: 3 polyps in 2 children at CE, 3 polyps in 1 child at BE (P = 0.50). Re‐review of 1 CE identified 3 polyps that were missed in 1 child at initial reading. Significantly more <10 mm polyps were identified by CE than BE: 61 vs 6 (P = 0.02). CE was significantly more comfortable than BE (median score CE 76 [interquartile range 69–87] vs BE 37 [interquartile range 31–68], P = 0.03) and was the preferred investigation in 90% (P = 0.02).

Conclusions:

CE is a feasible, safe, and sensitive test for small bowel polyp surveillance in children with PJS. It is significantly more comfortable than BE and is the preferred test of most children for future surveillance. There is a learning curve for reporting CE studies in PJS and appropriate training is essential.
Water‐immersion Technique During Standard Upper Endoscopy May Be Useful to Drive the Biopsy Sampling of Duodenal Mucosa in Children With Celiac Disease
Authors: Cammarota Giovanni , Cazzato Alessia , Genovese Orazio , Pantanella Adriano , Ianiro Gianluca , Giorgio Valentina , Montalto Massimo , Vecchio Fabio M , Larocca Luigi M , Gasbarrini Giovanni , Fundarò Carlo
Published: September 2009

Objective:

To evaluate the accuracy of the water‐immersion technique during upper endoscopy in recognizing the duodenal villous pattern in a series of children who were undergoing endoscopy to obtain duodenal biopsy for histological analysis.

Materials and Methods:

The water‐immersion technique was performed in 19 children. Endoscopic findings were compared with histology. Results were assessed on per biopsy analysis and per patient analysis, taking into account the worst endoscopic finding in each patient and correlating it with the worst histological diagnosis.

Results:

Per biopsy analysis: A total of 57 biopsy specimens were obtained and assessed. The endoscopic duodenal investigation correctly identified 53 areas (93%), which corresponded to histology, giving it an accuracy rate of 93%. Per patient analysis: The worst histology of the duodenal bulb was predicted by endoscopy in 18 of the 19 enrolled patients (95%), whereas the worst histopathological lesion of the second portion of the duodenum was recognized in 100% of cases. On the whole, therefore, the endoscopist suggested a diagnosis of celiac disease in 11 patients, with both positive and negative predictive values of 100%.

Conclusions:

The water‐immersion technique during upper endoscopy is highly accurate in recognizing the duodenal villous pattern in subjects who need a duodenal investigation. Our findings encourage a cost‐saving and patient‐retaining approach to the diagnosis of celiac disease by driving biopsy and reducing the number of duodenal samplings.
Infant Feeding Practices and Associated Factors Through the First 9 Months of Life in Bavaria, Germany
Authors: Rebhan Barbara , Kohlhuber Martina , Schwegler Ursula , Koletzko Berthold V , Fromme Hermann
Published: September 2009

Objectives:

To investigate infant feeding and breast‐feeding practices during the first 9 months of life in Bavaria, Germany, in relation to recommendations and to identify factors associated with early feeding of semisolid food.

Materials and Methods:

Data from 3103 infants throughout Bavaria, Germany, were collected in a prospective cohort study. Questionnaires were administered at the age of 6 days, and 2, 4, 6, and 9 months.

Results:

There was a considerable variety concerning the time when complementary feeding was introduced. Only 16.4% of the infants ate solid/semisolid food before the age of 5 months. Most of the infants received as their first solid food a mash of vegetable, meat, and potato. Compared to national guidelines fluids were introduced early. More than 37% of the breast‐fed infants received additional fluids/formula. The strongest risk factor associated with complementary feeding before the fifth month was breast‐feeding duration of less than 4 months (any breast‐feeding) with an odds ratio of 8.57 (95% confidence interval 6.16–11.94). Other factors were low level of education, young age of the mother, smoking habit of the mother, and mother not being born in Germany.

Conclusions:

Further improvements in nutrition of infants may be achieved in 2 ways: promotion of breast‐feeding according to current recommendations and better counselling on the correct timing of introduction of semisolid food—especially for parents of not‐ or short‐time breast‐fed babies and focused on young mothers with low levels of education.
Maternal HLA Class I Compatibility in Patients With Biliary Atresia
Authors: Irie Naoki , Muraji Toshihiro , Hosaka Naoki , Takada Yasutsugu , Sakamoto Seisuke , Tanaka Kohichi
Published: September 2009

Biliary atresia (BA) is an inflammatory cholangiopathy of unknown etiology. Maternal microchimerism has been identified in the livers of patients with BA. We analyzed the human leukocyte antigen (HLA) compatibility between 57 BA patient‐mother pairs and 50 control‐mother pairs. The HLA class I matching was significantly more frequent in BA pairs (odds ratio [OR] = 2.46) than controls. Similar results were also found in child‐to‐mother HLA compatibility (OR = 2.16). Our results indicate that patients with BA have an immunogenetic histocompatible relationship with their mothers, which may result in an increase in maternal microchimerism found in BA.
Rapid adaptive evolution of northeastern coyotes via hybridization with wolves
Authors: Kays Roland , Curtis Abigail , Kirchman Jeremy J.
Published: September 2009

The dramatic expansion of the geographical range of coyotes over the last 90 years is partly explained by changes to the landscape and local extinctions of wolves, but hybridization may also have facilitated their movement. We present mtDNA sequence data from 686 eastern coyotes and measurements of 196 skulls related to their two-front colonization pattern. We find evidence for hybridization with Great Lakes wolves only along the northern front, which is correlated with larger skull size, increased sexual dimorphism and a five times faster colonization rate than the southern front. Northeastern haplotype diversity is low, suggesting that this population was founded by very few females moving across the Saint Lawrence River. This northern front then spread south and west, eventually coming in contact with an expanding front of non-hybrid coyotes in western New York and Pennsylvania. We suggest that hybridization with wolves in Canada introduced adaptive variation that contributed to larger size, which in turn allowed eastern coyotes to better hunt deer, allowing a more rapid colonization of new areas than coyotes without introgressed wolf genes. Thus, hybridization is a conduit by which genetic variation from an extirpated species has been reintroduced into northeastern USA, enabling northeastern coyotes to occupy a portion of the niche left vacant by wolves.
A Poetics of Teaching
Authors: Hansen David T.
Published: September 2009

In this article, I elucidate the idea of a poetics of teaching and outline its value to scholars and teachers who seek a deeper understanding of the practice. A poetics of teaching draws together aesthetic, intellectual, and moral dimensions of the work that are often treated separately, if treated at all, in both research and in the classroom. In so doing, a poetics clarifies our picture of what the work offers to the men and women who take up the role. A poetics of teaching calls attention to how teaching can enrich the life of the teacher, even as he or she seeks to deepen and to broaden students' knowledge, understandings, and outlooks. I draw upon aspects of art, of inquiry, and of metaphor to help illuminate these educational values.
What's the Use of Philosophy? Democratic Citizenship and the Direction of Higher Education
Authors: Altman Matthew C.
Published: September 2009

In order to justify the discipline to administrators and prospective majors, many philosophy departments have begun to emphasize the "transferable skills" that students can develop in their courses — problem‐solving and communication skills, the ability to argue and write well, and the capacity to engage in systematic analysis. However, designing the study of philosophy around job preparation reinforces a particular conception of the good life and undermines philosophy's primary goal: to invite us to question the values we already hold and to ask whether those values should govern our lives. Philosophers should encourage students' capacity to question conventional norms and to engage in the rational pursuit of the good life. Education then becomes a social activity of holding ourselves to certain values. This shift in subject matter and teaching methods will serve the larger political purpose of better preparing students to be democratic citizens who are able to participate in public dialogue about questions of justice and morality.
Beyond Foundations — Signs of a New Normativity in Philosophy of Education
Authors: Goor Roel van , Heyting Frieda , Vreeke Gert‐Jan
Published: September 2009

We analyzed how philosophers of education received the ‘antifoundationalist’ turn in epistemology, particularly with respect to its practical relevance. Our main conclusion is, that antifoundationalist philosophers of education discharge the primacy of epistemology, replacing it by a primacy of commitment. Consequently, they no longer understand practical relevance in terms of contributing to ‘improved’ foundations for educational judgement. Stressing the contextual embedding of any justification, they rather concentrate on demonstrating the restrictive, excluding, implications of any educational judgement. We check the tenability of this position against some critical objections. Finally, we contrast the ‘new normativity’ that emerges from this contextualist approach with traditional, prescriptive normativity as well as with the non‐prescriptive normativity of the Frankfurt School from the nineteen‐seventies.
Agonistic sounds in the skunk clownfish Amphiprion akallopisos: size‐related variation in acoustic features
Authors: Colleye O. , Frederich B. , Vandewalle P. , Casadevall M. , Parmentier E.
Published: September 2009

Fourteen individuals of the skunk clownfish Amphiprion akallopisos of different sizes and of different sexual status (non‐breeder, male or female) were analysed for four acoustic features. Dominant frequency and pulse duration were highly correlated with standard length (r = 0·97), and were not related to sex. Both the dominant frequency and pulse duration were signals conveying information related to the size of the emitter, which implies that these sound characteristics could be useful in assessing size of conspecifics.
The role of free amino acids in semen of rainbow trout Oncorhynchus mykiss and carp Cyprinus carpio
Authors: Lahnsteiner F.
Published: September 2009

The present study investigated (1) the free amino acid (FAA) composition in semen of rainbow trout Oncorhynchus mykiss and carp Cyprinus carpio, (2) enzyme systems involved in amino acid metabolism and (3) the effect of amino acids on sperm viability under in vitro storage conditions. In the seminal plasma of O. mykiss, the main FAAs were arginine, glutamic acid, isoleucine, leucine, methionine and proline, in spermatozoa cysteine, arginine and methionine. In the seminal plasma of C. carpio, the main FAAs were alanine, arginine, cysteine, glutamic acid, histidine, leucine, lysine, methionine and proline, in spermatozoa arginine, glutamic acid, histidine, leucine and lysine. When spermatozoa were incubated for 48 h together with the seminal plasma, the quantitative amino acid pattern changed in both species indicating their metabolism. In spermatozoa and seminal plasma of O. mykiss and C. carpio, the following enzymes were found to be related to amino acid metabolism: transaminases (specific for alanine, aspartate, isoleucine and leucine), decarboxylases (specific for valine and lysine), glutamate dehydrogenase and α‐keto acid dehydrogenases (substrates: 3‐methyl‐2‐oxovaleric acid and 4‐methyl‐2‐oxovalerate). These data demonstrate that amino acid catabolism by transamination, decarboxylation and oxidative deamination can occur in semen of the two species. Also activity of methionine sulphoxide reductase was detected, an enzyme which reduces methionine sulphoxide to methionine. This reaction plays an important role in antioxidant defence. To determine the effect of FAAs on the sperm viability, C. carpio and O. mykiss spermatozoa were incubated in sperm motility inhibiting saline solution containing different amino acids. Methionine had a positive effect on the sperm viability in both species. Taken together this result with the in vivo occurrence of methionine and of methionine reductase in semen, it can be assumed that this amino acid plays an important role in antioxidant defence. Also isoleucine in O. mykiss and leucine in C. carpio had a positive effect on sperm viability. As seminal plasma and spermatozoa of the two species exhibit enzyme activities to catabolize leucine and isoleucine, they might serve as additional energy resources especially during prolonged incubation and storage periods.
Rare occurrence of a bigeye tuna Thunnus obesus in British waters, with notes on other occurrences of sub‐tropical tunas
Authors: Powell A. , Parry G. S. , Houghton J. D. R. , Herdson D. M.
Published: September 2009

A freshly dead bigeye tuna Thunnus obesus was washed ashore near Burry Port, Wales (51°40′ N; 4°15′ W) in August, 2006. This is only the third occasion that the species has been observed in British waters, and is the largest and most northerly recorded specimen.
Ionoregulatory physiology of two species of African lungfishes Protopterus dolloi and Protopterus annectens
Authors: Patel M. , Iftikar F.I. , Leonard E.M. , Ip Y.K. , Wood C.M.
Published: September 2009

Basic ionoregulatory physiology was characterized in two species of African lungfish, slender African lungfish Protopterus dolloi and West African lungfish Protopterus annectens, largely under aquatic conditions. There were no substantive differences between the two species. Plasma [Na], [Cl] and [Ca] were only 60–80% of those typical of freshwater teleosts, and plasma Ca activity was particularly low. Unidirectional Na and Cl influx rates from water were also very low, only c. 10% of teleost values, whereas unidirectional Ca influx rates were comparable with teleost rates. Protopterus spp. were fed a 3% ration of bloodworms every 48 h. The bloodworm diet provided similar amounts of Na and Ca as uptake from water, but almost no Cl. Efflux rates of Na and Cl through the urine were greater than via the faeces, whereas the opposite was true for Ca. Net ion flux measurements and ionic balance sheet calculations indicated that (1) both water and dietary uptake routes are important for Na and Ca acquisition; (2) the waterborne route predominates for Cl uptake; (3) unidirectional ion effluxes across the body surface (gills and skin) rather than urine and faeces are the major routes of loss for Na, Cl and Ca. Tissues (muscle, liver, lung, kidney, intestine and heart) and plasma ions were also examined in P. dolloi‘terrestrialized’ in air for up to 5 months, during which plasma ion concentrations (Na, Cl, Ca and Mg) did not change and there were only a few alterations in tissue ions, that is, increased [Na] in intestine, decreased [Cl] in kidney and increased [Ca] in liver and kidney.
Sperm design and function in the redside dace Clinostomus elongatus
Authors: Pitcher T. E. , Beausoleil J. J. , Abbott J. A. , Vandereerden J. L.
Published: September 2009

A study was undertaken to examine sperm morphometry in relation to sperm velocity and sperm longevity in the redside dace Clinostomus elongatus. There was significant between‐male variance in sperm size and shape metrics (total sperm length, sperm head length, flagellum length and sperm head length to width ratio) and positive relationships were found between these morphometrics and sperm velocity. There were no significant relationships found between sperm morphometry and sperm longevity, nor was there a trade‐off between sperm velocity and sperm longevity.
Assessment of digestive enzymes activity during the fry development of the endangered Caspian brown trout Salmo caspius
Authors: Zamani A. , Hajimoradloo A. , Madani R. , Farhangi M.
Published: September 2009

The study of digestive enzymes activity at Salmo caspius fry showed that enzymes were available at the moment of mouth opening on the first day post hatching (dph) and the activity of enzymes showed no significant difference from the hatching day 28 dph. An increased activity was seen between 32 and 43 dph and this activity was significantly higher than the activity during the first 28 days. In the primary stages after yolk sac resorption (43–58 dph), enzymes activity showed an increased profile, however none of them showed a significant difference between 43 and 58 dph.
Support and Control among ‘Friends’ and ‘Special Friends’: Peer Groups' Social Resources as Emotional and Moral Performances amidst Teenagers
Authors: Korkiamäki Riikka
Published: September 2009

Children are often regarded as being supported and controlled by adults, rather than their peer groups. In contrast, drawing on research carried out in Finland, this article considers peers as a resource. Using mainly a 14‐year‐old’s oral narratives, it is shown how the spatial and social context enables and inhibits children’s mutual support and control, reflecting and producing social and moral positions, and inclusion and exclusion. The analysis exploits the performance approach, which stresses children’s active role in the formation of social resources and reconstructs support and control from a child’s point of view.
Potential for therapeutic targeting of tumor stem cells
Authors: Saini Vaibhav , Shoemaker Robert H.
Published: September 2009

Recent developments in isolation and characterization of tumor stem cells (TSCs) have opened new possibilities for developing TSC‐targeted therapies. Extensive efforts have been made to ascertain markers of TSCs, including cell surface, enzymatic, gene expression profile, and functional markers. These markers and the technologies used to identify and isolate TSCs are discussed in this review. TSC characteristics, such as quiescence, multidrug resistance, enhanced DNA repair ability, and anti‐apoptotic mechanisms, and various features of the in vivo niche, which may make them resistant to conventional therapy, are also discussed here. The increasing understanding of aberrantly expressed molecules and signaling pathways in TSCs may provide the foundation for design of therapeutic strategies for TSC ablation. (Cancer Sci 2009)
FLT3‐ITD expression levels and their effect on STAT5 in AML with and without NPM mutations
Authors: Seedhouse Claire H. , Pallis Monica , Grundy Martin , Shang Shili , Russell Nigel H.
Published: September 2009

FLT3‐internal tandem duplication (ITD) mutations are heterogeneous with regards to length and proportion of DNA harbouring the mutation and the expression level of FLT3 also varies widely, however very little is known about the biological effects of these variables. We studied FLT3‐associated biological parameters in 322 acute myeloid leukaemia samples to establish their importance. Expression of total FLT3 transcripts was shown to be significantly higher in the FLT3‐ITD cohort (n = 121) compared to the wild‐type cohort (P = 0·004). Whilst phosphorylated signal transducer and activator of transcription 5 (phospho‐STAT5) was not confined to FLT3‐ITD samples, within the FLT3‐ITD group phosphorylation correlated with adjusted FLT3‐ITD levels assessed by determining the total transcripts and proportion of FLT3‐ITD within a sample. Expression of the STAT5 downstream target Bcl‐xl (an isoform of BCL2L1) was strongly correlated with FLT3 total and adjusted FLT3‐ITD levels in FLT3‐ITD samples (P < 0·001), however there was no association between Bcl‐xl and phospho‐STAT5 levels suggesting that STAT5 is not the sole regulator of Bcl‐xl in FLT3‐ITD cells. We further stratified our cohort by the presence/absence of a cytoplasmic nucleophosmin NPMc+ mutation. Samples co‐expressing NPMc+ had longer FLT3‐ITD mutations (P = 0·01) and there was a high occurrence of NPMc+ in samples that had >1 FLT3‐ITD mutation. Phospho‐STAT5 levels were reduced in the FLT3‐ITD/NPMc+ group (P = 0·04) suggesting that NPMc+ may oppose the FLT3‐ITD‐dependent activation of STAT5.
Where the rare species are
Authors: MOOERS ARNE O. , REDDING DAVID W.
Published: September 2009

Prioritizing geographic areas for conservation attention is important – time and money are in short supply but endangered species are not – and difficult. One popular perspective highlights areas with many species found nowhere else (Myers et al. 2000). Another identifies areas that contain species with fewer close relatives elsewhere (Faith 1992). One might characterize the first as focusing on geographic, and the second on phylogenetic, rarity. To the extent that geographically rare species are at greater risk of extinction (Gaston & Fuller 2009), and that phylogenetically rare species contribute disproportionally to overall biodiversity (Crozier 1997), it would seem reasonable to formally integrate the two approaches. In this issue, Rosauer et al. (2009) do just that; their elegant combined metric pinpoints areas missed out when the two types of rarity are looked at in isolation.
Analysis of the Yersinia enterocolitica PspBC proteins defines functional domains, essential amino acids and new roles within the phage‐shock‐protein response
Authors: Gueguen Erwan , Savitzky Diana C. , Darwin Andrew J.
Published: September 2009

The Yersinia enterocolitica phage‐shock‐protein (Psp) stress response system is activated by mislocalized outer‐membrane secretin components of protein export systems and is essential for virulence. The cytoplasmic membrane proteins PspB and PspC were proposed to be dual function components of the system, acting both as positive regulators of psp gene expression and to support survival during secretin‐induced stress. In this study we have uncoupled the regulatory and physiological functions of PspBC and discovered unexpected new roles, functional domains and essential amino acids. First, we showed that PspB controls PspC concentration by both pre‐ and post‐transcriptional mechanisms. We then screened for PspBC mutants with altered transcriptional regulatory function. Unexpectedly, we identified PspB and PspC mutants that activated psp gene expression in the absence of secretin‐induced stress. Together with a subsequent truncation analysis, this revealed that the PspC cytoplasmic domain plays an unforeseen role in negatively regulating psp gene expression. Conversely, mutations within the PspC periplasmic domain abolished its ability to activate psp gene expression. Significantly, PspC mutants unable to activate psp gene expression retained their ability to support survival during secretin‐induced stress. These data provide compelling support for the proposal that these two functions are independent.
Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367
Authors: Tolonen Andrew C. , Chilaka Amanda C. , Church George M.
Published: September 2009

Microbial cellulose degradation is a central part of the global carbon cycle and has great potential for the development of inexpensive, carbon‐neutral biofuels from non‐food crops. Clostridium phytofermentans has a repertoire of 108 putative glycoside hydrolases to break down cellulose and hemicellulose into sugars, which this organism then ferments primarily to ethanol. An understanding of cellulose degradation at the molecular level requires learning the different roles of these hydrolases. In this study, we show that interspecific conjugation with Escherichia coli can be used to transfer a plasmid into C. phytofermentans that has a resistance marker, an origin of replication that can be selectively lost, and a designed group II intron for efficient, targeted chromosomal insertions without selection. We applied these methods to disrupt the cphy3367 gene, which encodes the sole family 9 glycoside hydrolase (GH9) in the C. phytofermentans genome. The GH9‐deficient strain grew normally on some carbon sources such as glucose, but had lost the ability to degrade cellulose. Although C. phytofermentans upregulates the expression of numerous enzymes to break down cellulose, this process thus relies upon a single, key hydrolase, Cphy3367.
Needle traits of an evergreen, coniferous shrub growing at wind‐exposed and protected sites in a mountain region: does Pinus pumila produce needles with greater mass per area under wind‐stress conditions?
Authors: Nagano S. , Nakano T. , Hikosaka K. , Maruta E.
Published: September 2009

Snow depth is one of the most important determinants of vegetation, especially in mountainous regions. In such regions, snow depth tends to be low at wind‐exposed sites such as ridges, where stand height and productivity are limited by stressful environmental conditions during winter. Siberian dwarf pine (Pinus pumila Regel) is a dominant species in mountainous regions of Japan. We hypothesized that P. pumila produces needles with greater mass per area at wind‐exposed sites than at wind‐protected sites because it invests more nitrogen (N) in cell walls at the expense of N investment in the photosynthetic apparatus, resulting in increased photosynthetic N use efficiency (PNUE). Contrary to our hypothesis, plants at wind‐exposed site invested less resources in needles, as exhibited by lower biomass, N, Rubisco and cell wall mass per unit area, and had higher photosynthetic capacity, higher PNUE and shorter needle life‐span than plants at a wind‐protected site. N partitioning was not significantly different between sites. These results suggest that P. pumila at wind‐exposed sites produces needles at low cost with high productivity to compensate for a short leaf life‐span, which may be imposed by wind stress when needles appear above the snow surface in winter.
Assessment of transpiration efficiency in peanut (Arachis hypogaea L.) under drought using a lysimetric system
Authors: Ratnakumar P. , Vadez V. , Nigam S. N. , Krishnamurthy L.
Published: September 2009

Transpiration efficiency (TE) is an important trait for drought tolerance in peanut (Arachis hypogaea L.). The variation in TE was assessed gravimetrically using a long time interval in nine peanut genotypes (Chico, ICGS 44, ICGV 00350, ICGV 86015, ICGV 86031, ICGV 91114, JL 24, TAG 24 and TMV 2) grown in lysimeters under well‐watered or drought conditions. Transpiration was measured by regularly weighing the lysimeters, in which the soil surface was mulched with a 2‐cm layer of polythene beads. TE in the nine genotypes used varied from 1.4 to 2.9 g kg−1 under well‐watered and 1.7 to 2.9 g kg−1 under drought conditions, showing consistent variation in TE among genotypes. A higher TE was found in ICGV 86031 in both well‐watered and drought conditions and lower TE was found in TAG‐24 under both water regimes. Although total water extraction differed little across genotypes, the pattern of water extraction from the soil profile varied among genotypes. High water extraction within 24 days following stress imposition was negatively related to pod yield (r2 = 0.36), and negatively related to water extraction during a subsequent period of 32 days (r2 = 0.73). By contrast, the latter, i.e. water extraction during a period corresponding to grain filling (24 to 56 days after flowering) was positively related to pod yield (r2 = 0.36). TE was positively correlated with pod weight (r2 = 0.30) under drought condition. Our data show that under an intermittent drought regime, TE and water extraction from the soil profile during a period corresponding to pod filling were the most important components.
Rapid reversal of hyperpigmentation in pityriasis versicolor upon short‐term topical cycloserine application
Authors: Mayser Peter , Rieche Inga
Published: September 2009

The clinical phenomena of pityriasis versicolor (PV), a common Malassezia‐associated skin disease, such as hyperpigmentation, depigmentation and fluorescence of the lesions may at least partly be explained by the generation of Trp‐derived indole pigments through the action of transaminase 1 (TAM 1). Cycloserine, a TAM inhibitor, was able to completely inhibit pigment production in M. furfur in vitro in a dose‐dependent manner. Application of a 0.2‐mol l−1 aqueous cycloserine solution b.i.d. for 5 days in three patients with hyperpigmented PV resulted in complete healing within 3–5 days without side‐effects. Topically applied TAM inhibitors may therefore represent a new therapeutic principle for prophylaxis and therapy of PV, thus underlining the importance of the TAM pathway for the pathogenesis of the disease.
Inverse determination of the elastoplastic and damage parameters on small punch tests
Authors: PEÑUELAS I. , CUESTA I. I. , BETEGÓN C. , RODRIGUEZ C. , BELZUNCE F. J.
Published: September 2009

The small punch test (SPT) is very useful in those situations where it is necessary to use small volumes of material. The aim of this paper is to create and validate a methodology for the determination of the mechanical and damage properties of steels from the load‐displacement curve obtained by means of SPTs. This methodology is based on the inverse method, the design of experiments, the polynomial curve adjustment and the evolutionary multi‐objective optimization, and also allows simulating the SPTs. In order to validate the proposed methodology, the numerical results have been compared with experimental results obtained by means of normalized tests. Two dimensional axisymmetric and three‐dimensional simulations have been performed in order to allow the analysis of isotropic and anisotropic materials, respectively.
Experimental warming transforms multiple predator effects in a grassland food web
Authors: Barton Brandon T. , Schmitz Oswald J.
Published: September 2009

Ecology Letters (2009) 12: 1317–1325

This experimental study tests new theory for multiple predator effects on communities by using warming to alter predator habitat use and hence direct and indirect interactions in a grassland food web containing two dominant spider predator species, a dominant grasshopper herbivore and grass and herb plants. Experimental warming further offers insight into how climate change might alter direct and indirect effects. Under ambient environmental conditions, spiders used habitat in spatially complementary locations. Consistent with predictions, the multiple predator effect on grasshoppers and on plants was the average of the individual predator effects. Warming strengthened the single predator effects. It also caused the spider species to overlap lower in the vegetation canopy. Consistent with predictions, the system was transformed into an intraguild predation system with the consequent extinction of one spider species. The results portend climate caused loss of predator diversity with important consequences for food web structure and function.
A Shape Grammar for Developing Glyph‐based Visualizations
Authors: Karnick P. , Jeschke S. , Cline D. , Razdan A. , Wentz E. , Wonka P.
Published: September 2009

In this paper we address the question of how to quickly model glyph‐based Geographic Information System visualizations. Our solution is based on using shape grammars to set up the different aspects of a visualization, including the geometric content of the visualization, methods for resolving layout conflicts and interaction methods. Our approach significantly increases modelling efficiency over similarly flexible systems currently in use.
Fast Inverse Reflector Design (FIRD)
Authors: Mas A. , Martín I. , Patow G.
Published: September 2009

This paper presents a new inverse reflector design method using a GPU‐based computation of outgoing light distribution from reflectors. We propose a fast method to obtain the outgoing light distribution of a parametrized reflector, and then compare it with the desired illumination. The new method works completely in the GPU. We trace millions of rays using a hierarchical height‐field representation of the reflector. Multiple reflections are taken into account. The parameters that define the reflector shape are optimized in an iterative procedure in order for the resulting light distribution to be as close as possible to the desired, user‐provided one. We show that our method can calculate reflector lighting at least one order of magnitude faster than previous methods, even with millions of rays, complex geometries and light sources.
GIzMOs: Genuine Image Mosaics with Adaptive Tiling
Authors: Pavić D. , Ceumern U. , Kobbelt L.
Published: September 2009

We present a method that splits an input image into a set of tiles. Each tile is then replaced by another image from a large database such that, when viewed from a distance, the original image is reproduced as well as possible. While the general concept of image mosaics is not new, we consider our results as ‘genuine image mosaics’ (or short GIzMOs) in the sense that the images from the database are not modified in any way. This is different from previous work, where the image tiles are usually colour shifted or overlaid with the high‐frequency content of the input image. Besides the regular alignment of the tiles we propose a greedy approach for adaptive tiling where larger tiles are placed in homogenous image regions. By this we avoid the visual periodicity, which is induced by the equal spacing of the image tiles in the completely regular setting. Our overall system addresses also the cleaning of the image database by removing all unwanted images with no meaningful content. We apply differently sophisticated image descriptors to find the best matching image for each tile. For aesthetic and artistic reasons we classify each tile as ‘feature’ or ‘non‐feature’ and then apply a suitable image descriptor. In a user study we have verified that our descriptors lead to mosaics that are significantly better recognizable than just taking, e.g. average colour values.
Geographical Proximity and Immigrant Labour in Agriculture: Albanian Immigrants in the Greek Countryside
Authors: Labrianidis Lois , Sykas Theodosis
Published: September 2009

We investigate the importance of geographical proximity between Greece and Albania for the migrating experience of Albanian immigrants who work in the Greek countryside. From the fieldwork research we conducted in the countryside of northern Greece we find that the geographical proximity between Greece and Albania (the fact that they are bordering countries) and the inherent seasonality of agricultural employment allow immigrants to make rapid and repeated moves between the two countries and also work on a seasonal basis on their family agricultural holdings for the few months when they return home. Hence, these features embody a range of employment options that give these immigrants the opportunity to work on both sides of the border, transferring resources and skills acquired in Greece to Albania. As a result, a considerable proportion of immigrants working in agriculture actually work in both countries, and their annual employment and attempts at upward economic mobility are geographically dispersed in the two countries.
Education for Sustainable Development as Peace Education
Authors: Bajaj Monisha , Chiu Belinda
Published: September 2009

This article examines the intersections among peace education and environmental education to understand how these commonalities frame education for sustainable development. The authors trace the intersection of the two disciplines and explore the role of the United Nations in promoting and empowering individuals with the values to advance the twin goals of peace and ecological sustainability. The paper profiles the United Nation’s Decade of Education for Sustainable Development, particularly as formal education, nonformal learning channels, and popular culture have embraced the holistic notion of ecological responsibility, peace, and social justice.
Reflections on Peace and Solidarity in the Classroom
Authors: Hostetter David
Published: September 2009

Incorporating a peace perspective into teaching history requires hands‐on activities that expose students to the craft of the historian. Research into the legacy of the Nobel Peace Prize, debates on issues of war and peace, and oral history interviews have proven to be productive methods for engaging students. Remaining open to the experiences of students themselves is essential to creating a classroom where students and teachers can learn about making peace.
Imagining a Peace Curriculum: What Second‐Language Education Brings to the Table
Authors: Morgan Brian , Vandrick Stephanie
Published: September 2009

Just as peace and justice studies contributes much to Teaching English to Speakers of Other Languages, the reverse is also true: second‐language classes are particularly rich sites to explore diverse notions of the common good and implications for peace and war. Because of the intercultural interactions in such classrooms, and because such classes focus on language and communication, these settings offer unique opportunities to develop pedagogies addressing interethnic conflict and the dehumanizing language and images that promote it. English as a Second Language classrooms are productive settings for the telling of stories that counter official ones. Here we focus on critical pedagogies and curricula in two classroom settings. In the first, a class including Muslim students employs a critical media literacy perspective to investigate post‐September 11th biases against Muslims. In the second, students read literature related to war and peace, examine its language, and make connections with their own stories and identities.
The Promise of Hope: Creating a Classroom Peace Summit
Authors: Franklin Catherine
Published: September 2009

This article examines an innovative way to engage young adolescents in developing deep understandings of peace. Using an approach called curriculum drama, the class works together to construct a “World Peace Summit” within the classroom. This extended project creates a pedagogical bridge that links student interests and energies to curricular content and academic skills. It emboldens students to use the power of imagination and inquiry in their learning and creates situations for student leadership and peer collaboration. Challenged by the task of portraying a notable figure of peace and interacting with others within this context, students take ownership in researching a particular biography of an individual who participated in a social reform movement. Through this process, students get involved in conversations within the topic of peace and, through their character portrayal, they begin to walk in the shoes of another.
The Transparency President? The Obama Administration and Open Government
Authors: COGLIANESE CARY
Published: September 2009

President Obama has trumpeted transparency as a major part of his agenda, promising “unprecedented” openness throughout the federal government. Although Obama benefits politically from the contrast with his predecessor's reputation for secrecy, in the long run an excessive emphasis on fishbowl governance can raise unrealistic expectations and ultimately backfire. After all, at some point transparency has its costs, such as when disclosure dampens internal deliberation or undermines privacy. The real issue, then, is how much transparency and what type. Despite its rhetoric, the Obama Administration has placed limits on transparency and will likely continue to do so. Yet members of the public and open government activists are unlikely to appreciate the need for such limits, leading to disappointment and charges of hypocrisy. It remains unclear whether Barack Obama will earn the mantle of the “transparency president”—or whether the hopes he has raised will, when unfulfilled, only reinforce public cynicism.