bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computing in Finite Time
Authors: De Vos Alexis 
Published: May 2006

If a message can have n different values and all values are equally probable, then the entropy of the message is log (n). In the present paper, we discuss the expectation value of the entropy, for an arbitrary probability distribution. We introduce a mixture of all possible probability distributions. We assume that the mixing function is uniform. • either in flat probability space, i.e. the unitary n-dimensional hypertriangle, • or in Bhattacharyya's spherical statistical space, i.e. the unitary n-dimensional hyperoctant. A computation is a manipulation of an incoming message, i.e. a mapping in probability space: • either a reversible mapping, i.e. a symmetry operation (rotation or reflection) in n-dimensional space, • or an irreversible mapping, i.e. a projection operation from n-dimensional to lower-dimensional space. During a reversible computation, no isentropic path in the probability space can be found. Therefore we have to conclude that a computation cannot be represented by a message which merely follows a path in n-dimensional probability space. Rather, the point representing the mixing function travels along a path in an infinite-dimensional Hilbert space.
Zn uptake by maize under the influence of AM‐fungi and Collembola Folsomia candida
Authors: Seres A. , Bakonyi G. , Posta K. 
Published: May 2006

AbstractZn uptake by maize plants may be affected by the presence of arbuscular mycorrhizal fungi (AMF). Collembola often play an important controlling role in the inter‐relationship between AMF and host plants. The objective of this experiment was to examine whether the presence of Collembola at different densities (0.4 and 1 individuals g−1 dry soil) and their activity have any effect on Zn uptake by maize through the plant–AMF system. The presence of the AMF (Glomus intraradices) and of the Collembola species Folsomia candida was studied in a laboratory microcosm experiment, applying a Zn exposure level of 250 mg kg−1 dry soil. Biomass and water content of the plants were no different when only AMF or when both AMF and Collembola were present. In the presence of AMF the Zn content of the plant shoots and roots was significantly higher than without AMF. This effect was reduced by Collembola at both low and high density. High densities of Collembola reduced the extent of AMF colonization of the plant roots and hyphal length in the soil, but low densities had no effect on either. The results of this experiment reveal that the F. candida–G. intraradices interaction affects Zn uptake by maize, but the mechanisms are still unknown.
Acute effect of β amyloid on synchronized spontaneous Ca2+ oscillations in cultured hippocampal networks
Authors: Rui Yanfang , Li Ruxin , Liu Yifu , Zhu Shaoqing , Yu Xinzhu , Sheng Zhonghua , Xie Zuoping 
Published: May 2006

AbstractThe effects of β amyloid (Aβ) on cytoplasmic Ca2+ ([Ca2+]c) have been studied extensively, but the current literature on this aspect is confusing. We reported that 20 μM Aβ25–35 significantly inhibited the synchronized spontaneous cytoplasmic Ca2+ transients immediately after application, whereas it had little effect on the baseline [Ca2+]c concentration in neurons. Aβ1–42 had a similar effect on the Ca2+ transients as Aβ25–35, while it increased baseline [Ca2+]c concentration gradually. However, Aβ1–40 had little effect on either Ca2+ transients or baseline [Ca2+]c. Such differential effects of Aβ on Ca2+ signals might explain, at least partially, the confusing observations from the previous studies and provide important therapeutic implications for preventing or reversing early neuron damage in Alzheimer's disease.
Behavior ontogeny in the elevated plus‐maze: prenatal stress effects
Authors: Estanislau Celio , Morato Silvio 
Published: May 2006

AbstractPrenatal stress is a putative model for studying some psychopathological disorders. Indeed, submitting pregnant animals to stress leads to enhanced anxiety in the adult offspring. However, little is known about how prenatal stress effects interacts with anxiety throughout development. To study this issue, prenatally stressed rats were tested in the elevated plus‐maze at different ages. During pregnancy female rats were submitted to uncontrollable electric foot shock sessions every other day or kept undisturbed (controls). After delivery, litters from control and stressed dams were left undisturbed from the 3rd to the 14th postnatal days. Male and female rats were tested in the elevated plus‐maze at the ages of 30, 45 or 60 days. The following measures were taken in the elevated plus‐maze: number of entries and time spent in the arms (or their extremities) and frequency and time spent in naturalistic behaviors (stretching, rearing, end exploring, grooming and head dipping). Decreases in the percentage of entries into and in the time spent (only females) in the open arms were shown by 60‐day‐old prenatally stressed rats, but not by 30‐ and 45‐day old. Increased open arm ends exploration was shown by 45‐day‐old prenatally stressed males. Rearing behavior was found to increase with age, a phenomenon more pronounced in females. Additionally, at the younger ages prenatally stressed rats were heavier than controls, an effect which disappeared at young adulthood. In conclusion, anxiogenic prenatal stress effects in the elevated plus‐maze could only be detected at early adulthood, not before. Nonetheless, at late adolescence (45 days of age) prenatal stress leaded to an anxiolytic‐like effect which can be interpreted as increased risk‐taking behavior.
Morphine exposure prevents up‐regulation of MR and GR binding sites in the brain of adult male and female rats due to prenatal stress
Authors: Rimanóczy Ágnes , Šlamberová Romana , Bar Noffar , Vathy Ilona 
Published: May 2006

AbstractOur previous work demonstrated that the hormone response to stress and the negative feedback inhibition to these hormones are sex‐dependently altered by prenatal morphine exposure in adult rats. An alteration in the glucocorticoid negative feedback inhibition is mediated by glucocorticoid receptors (GR) that are distributed throughout the brain, and mineralocorticoid receptors (MR) localized mainly in the hippocampus and involved in a tonic influence of brain functions. Therefore, the present study examined the binding characteristics of MR and GR in young adult male and female rats exposed prenatally (E11–E18) to morphine (10 mg/kg/2×/day), saline or no treatment at all (controls). At 60–90 days of age, animals were adrenalectomized (ADX) 24 h prior to decapitation. The hippocampus and hypothalamus were dissected for saturation binding assays. The data demonstrate that prenatal stress due to maternal saline injections up‐regulates MR and GR binding in the hippocampus of adult male rats and this effect is prevented by prenatal morphine exposure. There is no effect of prenatal morphine exposure on GR binding in the hypothalamus of males. In female rats, prenatal morphine exposure does not affect the binding of MR and GR in the hippocampus or GR in the hypothalamus relative to controls; however, they are affected by ovarian hormone fluctuation. Moreover, prenatal stress decreases MR binding in the hippocampus of diestrous females and GR binding in the hypothalamus of estrous females. Both decreases are prevented by prenatal morphine exposure. Thus, the present study demonstrates that: (1) prenatal stress due to maternal saline injections alters MR and GR binding of adult male and female rats and is prevented by prenatal morphine exposure; (2) the MR and GR binding in adult female rats are affected by ovarian hormone fluctuations.
Improved pharmacological properties for superoxide dismutase modified with mannan
Authors: Valdivia Aymara , Pérez Yunel , Dominguez Amalia , Caballero Julio , Hernández Yunior , Villalonga Reynaldo 
Published: May 2006

Mannan from Sacharomyces cerevisiae was activated by oxidation with NaIO4 (sodium m‐periodate) and further linked to SOD (superoxide dismutase) via reductive alkylation with NaBH4 (sodium borohydride). The gly‐cosidated enzyme contained an average of 1.2 mol of polysaccharide per mol of protein and retained 52% of its initial activity. The modified enzyme was 560‐fold more resistant to inactivation with H2O2 and acquired a lectin‐recognition capacity in respect of concanavalin A. The anti‐inflammatory activity of SOD was increased 2‐fold and its plasma half‐life time was prolonged from 4.8 min to 1.7 h after glycosylation with the polymer.
Effect of Ku proteins on IRES‐mediated translation
Authors: Silvera Deborah , Koloteva‐Levine Nadejda , Burma Sandeep , Elroy‐Stein Orna 
Published: May 2006

Background information. Ku is an abundant nuclear heterodimeric protein composed of 70 and 86 kDa subunits. As an activator of the catalytic subunit of DNA‐PK (DNA‐dependent protein kinase), Ku plays an important role in DNA repair and recombination. Ku is also involved in actions independent of DNA‐PK, such as transcription regulation and telomere maintenance. Although Ku is localized in the cytoplasm under specific cellular conditions, no functions for Ku outside of the nucleus have as yet been reported. In addition to DNA binding, Ku binds specific RNA sequences with high affinity. However, no specific cellular mRNA targets for Ku have been identified.Results. In a yeast three‐hybrid system, Ku70 bound to an RNA bait that contained an IRES (internal ribosomal entry site) element. A single band with migration properties similar to those of Ku70 was immunoprecipitated with anti‐Ku antibody, using UV cross‐linked complexes formed by HeLa cell nuclear extracts and an IRES‐containing RNA probe. IRES activity was reduced in Ku80−/− cells. Overexpression of Ku proteins stimulated IRES‐dependent translation.Conclusions. The present study suggests that Ku binds IRES elements within RNA molecules, and that Ku plays a role in the modulation of IRES‐mediated mRNA translation.
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
Authors: Nakano Yoshio , Takeshita Toru , Yamashita Yoshihisa 
Published: May 2006

Abstract
Summary: TRFMA provides a Web environment for analyzing T-RFLP results based on molecular weights of the fragments, rather than the numbers of nucleotides, to increase accuracy. The 16S rRNA data are saved as an XML file containing around 650 sequences (light version) and a MySQL database containing around 50 000 sequences (full version), which are connected to Web server via PHP5 and manipulated on an Internet browser.
Availability: TRFMA is freely available at and can be downloaded from the same site.
Contact: yosh@dent.kyushu-u.ac.jp
Combo: a whole genome comparative browser
Authors: Engels Reinhard , Yu Tamara , Burge Chris , Mesirov Jill P. , DeCaprio David , Galagan James E. 
Published: May 2006

Abstract
Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization perspectives. The perpendicular (dot plot) view provides a dot plot of genome alignments synchronized with a display of genome annotations along each axis. The parallel view displays two genome annotations horizontally, synchronized through a panel displaying local alignments as trapezoids. Users can zoom to any resolution, from whole chromosomes to individual bases. They can select, highlight and view detailed information from specific alignments and annotations. Combo is an organism agnostic and can import data from a variety of file formats.
Availability: Combo is integrated as part of the Argo Genome Browser which also provides single-genome browsing and editing capabilities. Argo is written in Java, runs on multiple platforms and is freely available for download at .
Contact: reinhard@broad.mit.edu
INFO-RNA—a fast approach to inverse RNA folding
Authors: Busch Anke , Backofen Rolf 
Published: May 2006

Abstract
Motivation: The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure.
Results: We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programming method for good initial sequences and a following improved stochastic local search that uses an effective neighbor selection method. During the initialization, we design a sequence that among all sequences adopts the given structure with the lowest possible energy. For the selection of neighbors during the search, we use a kind of look-ahead of one selection step applying an additional energy-based criterion. Afterwards, the pre-ordered neighbors are tested using the actual optimization criterion of minimizing the structure distance between the target structure and the mfe structure of the considered neighbor.
We compared our algorithm to RNAinverse and RNA-SSD for artificial and biological test sets. Using INFO-RNA, we performed better than RNAinverse and in most cases, we gained better results than RNA-SSD, the probably best inverse RNA folding tool on the market.
Availability:
Contact: backofen@informatik.uni-freiburg.de
Supplementary information: Supplementary data are available on Bioinformatics online.
Comparative gene marker selection suite
Authors: Gould Joshua , Getz Gad , Monti Stefano , Reich Michael , Mesirov Jill P. 
Published: May 2006

AbstractMotivation: An important step in analyzing expression profiles from microarray data is to identify genes that can discriminate between distinct classes of samples. Many statistical approaches for assigning significance values to genes have been developed. The Comparative Marker Selection suite consists of three modules that allow users to apply and compare different methods of computing significance for each marker gene, a viewer to assess the results, and a tool to create derivative datasets and marker lists based on user-defined significance criteria.Availability: The Comparative Marker Selection application suite is freely available as a GenePattern module. The GenePattern analysis environment is freely available atContact: jgould@broad.mit.edu
Group process in Jungian analytic training and institute life
Authors: Kirsch Jean , Spradlin Suzy 
Published: May 2006

Abstract:  Group process experience for analytic candidates is a neglected dimension of training, and receives little attention in the analytic literature. Jung observed group dynamics, but he never studied them closely, attending instead to the psychology of the individual. Unconscious currents in small groups have been studied by others, most notably by Wilfred Bion, and there are similarities between his theories of the group unconscious and Jung's theories of complexes.Experiential and didactic seminars in group process were added to the analytic curriculum at the C.G. Jung Institute of San Francisco in the early 1990s, leading to changes in the group dynamic of trainees and analysts alike. A discussion of the theories of Bion and Jung are followed by a report on our experiences of facilitating group process for analytic candidates. We give quotes from candidates and analyst members to illustrate the group process and its effects. The need for further study to develop a uniquely Jungian perspective on the unconscious structure and dynamics of the group is suggested.
A word about words
Authors: Proner Barry D. 
Published: May 2006

Abstract:  The title of my paper comes from an essay by Václav Havel. In his essay, Havel addressed most evocatively the question of the unique power of words for thinking and to influence, for good or for harm, as well as to inform and to educate.As analysts our medium is the word. I suggest that it is of inestimable importance that we are able to listen deeply to our patients’ words and to be aware of our own. The quality of our ability to think deeply and consistently about the unconscious experience of our patient is intimately related to our ability to hear what is being said. The effect of our own words upon the patient likewise cannot be overstated. I offer my reflections on words in the analytic relationship and I give some clinical examples that I hope will illustrate my thoughts as to the power and the importance of what and how we hear and of what we say.
Postmodern consciousness in psychotherapy
Authors: Kawai Toshio 
Published: May 2006

Abstract:  Modern consciousness is a cultural and historical achievement in the West and a developmental task for each person now. Modern consciousness consists in the emancipation from the power of community, animistic nature and the unconscious. It is connected with neurosis and psychotherapy because it has to do with inner conflicts. But today there is an increasing number of cases which are characterized by dissociation and acting out, without the feeling of conflicts. Consciousness seems to be changing toward a new conception which might be called ‘postmodern consciousness’.The essence of postmodern consciousness is shown by interpreting two dreams internally. The first dream from a case of depersonalization indicates that it is not necessary to be entangled with the object. There is a different kind of coniunctio in the mode of seeing. The second dream from a case of dissociative disorder shows a world which has neither traces of pre‐modern cosmology—high and low, here and the beyond—nor modern interiority. There is only surface and self‐reflection without content. The discussion of dreams suggests that postmodern consciousness is not to be understood as premature and pathological. It is therapeutically important to refine and deepen postmodern consciousness.
Effects of Nile perch, Lates niloticus, on functional and specific fish diversity in Uganda's Lake Kyoga system
Authors: Schwartz Jesse D. M. , Pallin Marla J. , Michener Robert H. , Mbabazi Dismiss , Kaufman Les 
Published: May 2006

AbstractThe introduction of Nile perch, Lates niloticus, to Lake Victoria, East Africa, interacted with eutrophication to cause a reorganization of the lake's food web and the extirpation of many endemic fishes. The Lake Kyoga satellite system lies downstream from Lake Victoria. It encompasses species‐rich lakes where Nile perch are absent or very rare, and low diversity lakes where L. niloticus is abundant. In 1999 we surveyed seven lakes in the Kyoga system using experimental monofilament gill nets (1/4–1 inches variable mesh). At Boston University we assessed δ15N signatures of epaxial muscle from subsamples of the catch (n = 361). These signatures are often highly correlated with the near‐term mean realized trophic position of an individual organism. A neural network analysis of fish length, species name, trophic level, and lake of origin fish explained 94% of the sample variance in δ15N. We analysed statistical patterns in these signatures at a number of spatial scales. The relationship between trophic level and δ15N varied greatly among lakes. Higher diversity perch‐free lakes had greater variance in δ15N values and fish lengths than lower diversity Nile perch lakes, suggesting an important relationship between species diversity and functional diversity. Against expectations, lake size was negatively correlated with δ15N. Patterns in stable isotope signatures indicated that Nile perch lakes have shorter food chains than perch‐free lakes. The results throw up two management problems for the Kyoga system. Impacted lakes need to be studied to understand and ameliorate the community‐level effects of Nile perch introduction, whereas the species‐rich nonperch lakes, which harbour a large proportion of the remaining diversity of regionally endemic taxa, are in need of conservation planning.
Research Review: The role of grandparents in intergenerational support for families with disabled children: a review of the literature
Authors: Mitchell Wendy 
Published: May 2006

ABSTRACTThe family in late modernity faces demographic change. However, it is still apparent that intergenerational relationships and exchanges of resources are valued. There is a growing literature on the important role that grandparents play in their children’s families. In contrast, there is limited research exploring the support grandparents provide to families with disabled children. This is an important gap in our knowledge, as families with disabled children frequently face additional caring responsibilities and emotional demands. From the studies that do exist, it is clear that grandparents’ support to families with disabled children is generally valued. However, the literature remains partial: past studies are small‐scale, focused upon parents’ perceptions of support (especially mother’s), and frequently based upon North American data. Recognizing these limitations and the fact that grandparents themselves have support needs which require consideration, this paper identifies key areas where important issues remain unanswered and further research is required. It argues that research is needed to begin untangling the different support needs of parents, grandparents and other family members, and the different effects of grandparent support that different family members’ experience. Exploration of grandparents’ own support needs also indicates the need for wider policy and service consideration.
Models of ‘ordinary’ and ‘special’ daily living: matching residential care to the mental‐health needs of looked after children
Authors: Ward Adrian 
Published: May 2006

ABSTRACTThis paper proposes a set of distinctions between ‘ordinary’ and ‘special’ modes of everyday living in residential settings for young people in the ‘looked after’ system. The paper begins by reviewing both quantitative and qualitative evidence on the mental‐health needs of the young people, arguing that there is evidence of very high levels of mental distress and disturbance within this group, and that this distress is often undiagnosed and untreated both by psychiatric professionals and within the residential care system itself. There follows a commentary on the tacit assumptions underpinning much residential practice, especially the emphasis in some policy and legal documentation on the young people’s need for ‘ordinary’ everyday experience. The concept of the ‘ordinary’ is problematized, and it is argued that while young people do need to be supported towards mainstream ‘ordinary’ everyday living, they also need specialized everyday care in which their emotional and psychological needs can be recognized and responded to. Four models of ‘special everyday living’ are proposed, based upon existing literature on residential practice, and it is argued that residential care programmes should be based upon a mix of these special and ordinary provisions if the young people’s emotional needs are to be met.